BLASTP 2.2.2 [Dec-14-2001] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= trembl|Q60952|Q60952 Intranuclear protein. (446 letters) Database: /home/mika/Theses/Databases/unique_set/NMP_Database_unique.f asta 43 sequences; 17,163 total letters Searching.done Results from round 1 Score E Sequences producing significant alignments: (bits) Value trembl|Q60952|Q60952 Intranuclear protein. 470 e-135 swiss|Q9M7J4|MFP1_TOBAC MAR binding filament-like protein 1-1. 31 0.003 trembl|Q9FLH0|Q9FLH0 Nuclear matrix constituent protein 1 (NMCP... 26 0.072 trembl|Q9C2H8|Q9C2H8 Related to ser/arg-related nuclear matrix ... 21 2.4 >trembl|Q60952|Q60952 Intranuclear protein. Length = 446 Score = 470 bits (1210), Expect = e-135 Identities = 446/446 (100%), Positives = 446/446 (100%) Query: 1 MRQKQDPAGQLAAGQATLTEQEQELAALRAENQYSRRQEEAAVSQAEALQEALSKAQAAL 60 MRQKQDPAGQLAAGQATLTEQEQELAALRAENQYSRRQEEAAVSQAEALQEALSKAQAAL Sbjct: 1 MRQKQDPAGQLAAGQATLTEQEQELAALRAENQYSRRQEEAAVSQAEALQEALSKAQAAL 60 Query: 61 QEKEQSLLEQAELSHTLEASTAALQATLDTCQARARQLEEALRIREGEIQAQALQHHEVT 120 QEKEQSLLEQAELSHTLEASTAALQATLDTCQARARQLEEALRIREGEIQAQALQHHEVT Sbjct: 61 QEKEQSLLEQAELSHTLEASTAALQATLDTCQARARQLEEALRIREGEIQAQALQHHEVT 120 Query: 121 QHLQQELCQKEEELRQLLEKAGARRSQENGIQEKQSLEQERQEETRRLLESLKELQLTVA 180 QHLQQELCQKEEELRQLLEKAGARRSQENGIQEKQSLEQERQEETRRLLESLKELQLTVA Sbjct: 121 QHLQQELCQKEEELRQLLEKAGARRSQENGIQEKQSLEQERQEETRRLLESLKELQLTVA 180 Query: 181 QREEEILMLREASSPSHRALPAEKPALQPLPAQQELERLQTALRQTEAREIEWREKAQDL 240 QREEEILMLREASSPSHRALPAEKPALQPLPAQQELERLQTALRQTEAREIEWREKAQDL Sbjct: 181 QREEEILMLREASSPSHRALPAEKPALQPLPAQQELERLQTALRQTEAREIEWREKAQDL 240 Query: 241 ALSLAQSKASISSLQEITMFLQASVLERESEQQRLQEELVLSSQALEEQQSGGPHSTSRA 300 ALSLAQSKASISSLQEITMFLQASVLERESEQQRLQEELVLSSQALEEQQSGGPHSTSRA Sbjct: 241 ALSLAQSKASISSLQEITMFLQASVLERESEQQRLQEELVLSSQALEEQQSGGPHSTSRA 300 Query: 301 DQGPKVGQESQPGEVETEPSPGVEEKERLTQRLERLQQAVAELEVDRSKLQCHNAQLRTA 360 DQGPKVGQESQPGEVETEPSPGVEEKERLTQRLERLQQAVAELEVDRSKLQCHNAQLRTA Sbjct: 301 DQGPKVGQESQPGEVETEPSPGVEEKERLTQRLERLQQAVAELEVDRSKLQCHNAQLRTA 360 Query: 361 LEQVERERRKLKRDSVRASRAGSLEARETMTSSPTQQDGRGSQRGSSDSVLVVELQREVA 420 LEQVERERRKLKRDSVRASRAGSLEARETMTSSPTQQDGRGSQRGSSDSVLVVELQREVA Sbjct: 361 LEQVERERRKLKRDSVRASRAGSLEARETMTSSPTQQDGRGSQRGSSDSVLVVELQREVA 420 Query: 421 LLRAQLALERKRGRTTLHGPCRPAVS 446 LLRAQLALERKRGRTTLHGPCRPAVS Sbjct: 421 LLRAQLALERKRGRTTLHGPCRPAVS 446 >swiss|Q9M7J4|MFP1_TOBAC MAR binding filament-like protein 1-1. Length = 722 Score = 30.8 bits (68), Expect = 0.003 Identities = 45/184 (24%), Positives = 83/184 (44%), Gaps = 8/184 (4%) Query: 10 QLAAGQATLTEQEQELAA-LRAENQYSRRQEEAAVSQAEALQEALSKAQAALQEKEQSLL 68 +L +AT E++ + L E Q + A + +AL L+ A++ + Q L Sbjct: 152 KLKEKEATFVSMEKKFQSELLNERDIRNNQLKRAGEERQALVNQLNSAKSTVTNLGQELQ 211 Query: 69 EQAELSHTLEASTAALQATLDTCQARARQLEEALRIREGEIQAQALQHHEVTQHLQQELC 128 ++ ++ L LQ L + ++L+E L+ + IQ E L E+ Sbjct: 212 KEKRIAEELIVQIEGLQNNLMQMKEDKKKLQEELKEKLDLIQVL----QEKITLLTTEIK 267 Query: 129 QKEEELRQLLEKAGARRSQENGIQEKQSLEQERQEETRRLLESLKELQLTVAQREEEILM 188 KE L+ K + S+ + + S+ QE Q++ L +KEL++ V +RE E+ + Sbjct: 268 DKEASLQSTTSKLAEKESE---VDKLSSMYQESQDQLMNLTSEIKELKVEVQKRERELEL 324 Query: 189 LREA 192 RE+ Sbjct: 325 KRES 328 Score = 20.4 bits (41), Expect = 4.4 Identities = 83/395 (21%), Positives = 159/395 (40%), Gaps = 32/395 (8%) Query: 5 QDPAGQLAAGQATLTEQEQELAALRAENQYSRRQEEAAVSQAEALQEALSKAQAALQEKE 64 +D L + + L E+E E+ L + Q S+ Q S+ + L+ + K + L+ K Sbjct: 267 KDKEASLQSTTSKLAEKESEVDKLSSMYQESQDQLMNLTSEIKELKVEVQKRERELELKR 326 Query: 65 QSLLEQAELSHTLEASTAALQATLDTCQARARQLEEALRIREGEIQAQALQHHEVTQHLQ 124 +S + L+ L + + A ++ E I E ++ + A Sbjct: 327 ES---EDNLNVRLNSLLVERDESKKELDAIQKEYSEFKSISEKKVASDA----------- 372 Query: 125 QELCQKEEELRQLLEKAGARRSQENGIQEKQSLEQERQEETRRL----LESLKELQLTVA 180 + L ++E+ L QL E+ G + + + +E RR+ LE++ +L+L V Sbjct: 373 KLLGEQEKRLHQLEEQLGTASDEVRKNNVLIADLTQEKENLRRMLDAELENISKLKLEVQ 432 Query: 181 QREEEILMLREASSPSHRALPAEKPALQPLPA-----QQELERLQTALRQTEAREIEWRE 235 +E + R +S + L + L A Q ELE +T+LR+ E + Sbjct: 433 VTQETLEKSRSDASDIAQQLQQSRHLCSKLEAEVSKLQMELEETRTSLRRNID---ETKR 489 Query: 236 KAQDLALSLAQSKASISSLQEITMFLQASVLERESEQQRLQEELVLSSQALEEQQSGGPH 295 A+ LA L ++ + E + + LQ ELV + E Sbjct: 490 GAELLAAELTTTRELLKKTNEEMHTMSHELAAVTENCDNLQTELVDVYKKAERAA----- 544 Query: 296 STSRADQGPKVGQESQPGEVETEPSPGVEEKERLTQRLERLQQAVAELEVDRSKLQCHNA 355 + ++ V E + +E + + E ++ L + LER +++ E+ + L Sbjct: 545 DELKQEKNIVVTLEKELTFLEAQITREKESRKNLEEELERATESLDEMNRNAFALAKELE 604 Query: 356 QLRTALEQVERERRKLKRDSVRASRAGSLEARETM 390 + + +E ER L++ SV + S E+RE + Sbjct: 605 LANSHISSLEDEREVLQK-SVSEQKQISQESRENL 638 >trembl|Q9FLH0|Q9FLH0 Nuclear matrix constituent protein 1 (NMCP1)-like. Length = 1042 Score = 26.2 bits (56), Expect = 0.072 Identities = 63/301 (20%), Positives = 141/301 (45%), Gaps = 19/301 (6%) Query: 5 QDPAGQLAAGQATLTEQEQELAALRAENQYSRRQEEAAVSQA--------EALQEALSKA 56 Q G L + L+ Q +E+ A E+ + +E++A A E+L++ + A Sbjct: 77 QHNMGLLLLEKNELSSQYEEIKASVDESDLTHMREKSAYVSALAEAKKREESLKKDVGIA 136 Query: 57 QAALQEKEQSLLE-QAELSHTLEASTAALQATLDTCQARARQLEEA-LRIREGE-IQAQA 113 + + E++L E +AE + T ++ + + + ++L +A ++R E +QA+A Sbjct: 137 KECISSLEKTLHEMRAECAETKVSAGSTMSEAHVMIEDALKKLADAEAKMRAAEALQAEA 196 Query: 114 LQHHEVTQHLQQELCQKEEEL-RQLLEKAGARRSQENGIQEKQSLEQERQEETRRLLESL 172 ++H + + +E+ +E++L R+L ++EN + ++ ER++ ++ E L Sbjct: 197 NRYHRIAERKLKEVESREDDLTRRLASFKSECETKENEMVIERQTLNERRKSLQQEHERL 256 Query: 173 KELQLTVAQREEEILMLREASSPSHRALPAEKPALQPLPAQQELER--LQTALRQTEARE 230 + Q+++ QRE+ I + + + L K + E ++ L+ AL RE Sbjct: 257 LDAQVSLNQREDHIFARSQELAELEKGLDTAKTTFEEERKAFEDKKSNLEIALALCAKRE 316 Query: 231 IEWREKAQDLALSLAQSKASISSLQEITMFLQASVLERESEQQRLQEELVLSSQALEEQQ 290 L + ++S L + + +V ERES + ++EL+++ + + ++ Sbjct: 317 EVCFYSHNSLLFLVLHYRSSKKFLGD-----KIAVSERESSLLKKEQELLVAEEKIASKE 371 Query: 291 S 291 S Sbjct: 372 S 372 Score = 22.3 bits (46), Expect = 1.1 Identities = 32/194 (16%), Positives = 90/194 (45%), Gaps = 1/194 (0%) Query: 22 EQELAALRAENQYSRRQEEAAVSQAEALQEALSKAQAALQEKEQSLLEQAEL-SHTLEAS 80 E+E + L+ E + +E+ A ++E +Q L+ + L++++ + + E S ++E Sbjct: 348 ERESSLLKKEQELLVAEEKIASKESELIQNVLANQEVILRKRKSDVEAELECKSKSVEVE 407 Query: 81 TAALQATLDTCQARARQLEEALRIREGEIQAQALQHHEVTQHLQQELCQKEEELRQLLEK 140 + + + + +Q E+ + +E +++ Q+ E + + ++ +E+ + L+ Sbjct: 408 IESKRRAWELREVDIKQREDLVGEKEHDLEVQSRALAEKEKDITEKSFNLDEKEKNLVAT 467 Query: 141 AGARRSQENGIQEKQSLEQERQEETRRLLESLKELQLTVAQREEEILMLREASSPSHRAL 200 + +++++ ++ E ++ L SL++ + V +++ L+ +S Sbjct: 468 EEDINRKTTMLEDEKERLRKLDLELQQSLTSLEDKRKRVDSATQKLEALKSETSELSTLE 527 Query: 201 PAEKPALQPLPAQQ 214 K L L AQ+ Sbjct: 528 MKLKEELDDLRAQK 541 >trembl|Q9C2H8|Q9C2H8 Related to ser/arg-related nuclear matrix protein. Length = 976 Score = 21.2 bits (43), Expect = 2.4 Identities = 24/86 (27%), Positives = 34/86 (38%), Gaps = 13/86 (15%) Query: 238 QDLALSLAQSKASISSLQEITMFLQASVLERESEQQRLQEELVLSSQALEEQQSGGPHST 297 +D A SLA+ S S + S E E + ++L+L LE P Sbjct: 62 EDEADSLAKEYGSPSVI---------SSYEDEPPNRGEIDQLILMEPVLENN----PERR 108 Query: 298 SRADQGPKVGQESQPGEVETEPSPGV 323 GP G+ES+P E +P V Sbjct: 109 FVVVTGPGAGKESEPAPSIVETTPPV 134 Searching.done Results from round 2 Score E Sequences producing significant alignments: (bits) Value Sequences used in model and found again: trembl|Q60952|Q60952 Intranuclear protein. 441 e-127 swiss|Q9M7J4|MFP1_TOBAC MAR binding filament-like protein 1-1. 180 2e-48 Sequences not found previously or not previously below threshold: swiss|Q60611|SAT1_MOUSE DNA-binding protein SATB1 (Special AT-r... 34 3e-04 trembl|Q9FLH0|Q9FLH0 Nuclear matrix constituent protein 1 (NMCP... 29 0.010 trembl|Q9C2H8|Q9C2H8 Related to ser/arg-related nuclear matrix ... 24 0.24 swiss|Q07856|VE6_HPV65 E6 protein. 22 1.8 trembl|Q9CVG5|Q9CVG5 Ser/Arg-related nuclear matrix protein (Fr... 19 9.8 >trembl|Q60952|Q60952 Intranuclear protein. Length = 446 Score = 441 bits (1135), Expect = e-127 Identities = 446/446 (100%), Positives = 446/446 (100%) Query: 1 MRQKQDPAGQLAAGQATLTEQEQELAALRAENQYSRRQEEAAVSQAEALQEALSKAQAAL 60 MRQKQDPAGQLAAGQATLTEQEQELAALRAENQYSRRQEEAAVSQAEALQEALSKAQAAL Sbjct: 1 MRQKQDPAGQLAAGQATLTEQEQELAALRAENQYSRRQEEAAVSQAEALQEALSKAQAAL 60 Query: 61 QEKEQSLLEQAELSHTLEASTAALQATLDTCQARARQLEEALRIREGEIQAQALQHHEVT 120 QEKEQSLLEQAELSHTLEASTAALQATLDTCQARARQLEEALRIREGEIQAQALQHHEVT Sbjct: 61 QEKEQSLLEQAELSHTLEASTAALQATLDTCQARARQLEEALRIREGEIQAQALQHHEVT 120 Query: 121 QHLQQELCQKEEELRQLLEKAGARRSQENGIQEKQSLEQERQEETRRLLESLKELQLTVA 180 QHLQQELCQKEEELRQLLEKAGARRSQENGIQEKQSLEQERQEETRRLLESLKELQLTVA Sbjct: 121 QHLQQELCQKEEELRQLLEKAGARRSQENGIQEKQSLEQERQEETRRLLESLKELQLTVA 180 Query: 181 QREEEILMLREASSPSHRALPAEKPALQPLPAQQELERLQTALRQTEAREIEWREKAQDL 240 QREEEILMLREASSPSHRALPAEKPALQPLPAQQELERLQTALRQTEAREIEWREKAQDL Sbjct: 181 QREEEILMLREASSPSHRALPAEKPALQPLPAQQELERLQTALRQTEAREIEWREKAQDL 240 Query: 241 ALSLAQSKASISSLQEITMFLQASVLERESEQQRLQEELVLSSQALEEQQSGGPHSTSRA 300 ALSLAQSKASISSLQEITMFLQASVLERESEQQRLQEELVLSSQALEEQQSGGPHSTSRA Sbjct: 241 ALSLAQSKASISSLQEITMFLQASVLERESEQQRLQEELVLSSQALEEQQSGGPHSTSRA 300 Query: 301 DQGPKVGQESQPGEVETEPSPGVEEKERLTQRLERLQQAVAELEVDRSKLQCHNAQLRTA 360 DQGPKVGQESQPGEVETEPSPGVEEKERLTQRLERLQQAVAELEVDRSKLQCHNAQLRTA Sbjct: 301 DQGPKVGQESQPGEVETEPSPGVEEKERLTQRLERLQQAVAELEVDRSKLQCHNAQLRTA 360 Query: 361 LEQVERERRKLKRDSVRASRAGSLEARETMTSSPTQQDGRGSQRGSSDSVLVVELQREVA 420 LEQVERERRKLKRDSVRASRAGSLEARETMTSSPTQQDGRGSQRGSSDSVLVVELQREVA Sbjct: 361 LEQVERERRKLKRDSVRASRAGSLEARETMTSSPTQQDGRGSQRGSSDSVLVVELQREVA 420 Query: 421 LLRAQLALERKRGRTTLHGPCRPAVS 446 LLRAQLALERKRGRTTLHGPCRPAVS Sbjct: 421 LLRAQLALERKRGRTTLHGPCRPAVS 446 >swiss|Q9M7J4|MFP1_TOBAC MAR binding filament-like protein 1-1. Length = 722 Score = 180 bits (457), Expect = 2e-48 Identities = 45/184 (24%), Positives = 83/184 (44%), Gaps = 8/184 (4%) Query: 10 QLAAGQATLTEQEQELAA-LRAENQYSRRQEEAAVSQAEALQEALSKAQAALQEKEQSLL 68 +L +AT E++ + L E Q + A + +AL L+ A++ + Q L Sbjct: 152 KLKEKEATFVSMEKKFQSELLNERDIRNNQLKRAGEERQALVNQLNSAKSTVTNLGQELQ 211 Query: 69 EQAELSHTLEASTAALQATLDTCQARARQLEEALRIREGEIQAQALQHHEVTQHLQQELC 128 ++ ++ L LQ L + ++L+E L+ + IQ E L E+ Sbjct: 212 KEKRIAEELIVQIEGLQNNLMQMKEDKKKLQEELKEKLDLIQVL----QEKITLLTTEIK 267 Query: 129 QKEEELRQLLEKAGARRSQENGIQEKQSLEQERQEETRRLLESLKELQLTVAQREEEILM 188 KE L+ K + S+ + + S+ QE Q++ L +KEL++ V +RE E+ + Sbjct: 268 DKEASLQSTTSKLAEKESE---VDKLSSMYQESQDQLMNLTSEIKELKVEVQKRERELEL 324 Query: 189 LREA 192 RE+ Sbjct: 325 KRES 328 Score = 35.5 bits (80), Expect = 1e-04 Identities = 74/390 (18%), Positives = 149/390 (37%), Gaps = 25/390 (6%) Query: 10 QLAAGQATLTEQEQELAALRAENQYSRRQEEAAVSQAEALQEALSKAQAALQEKEQSLLE 69 ++ +A+L +LA +E + + Q L + + + +Q++E+ L Sbjct: 265 EIKDKEASLQSTTSKLAEKESEVDKLSSMYQESQDQLMNLTSEIKELKVEVQKRERELEL 324 Query: 70 QAELSHTLEASTAALQATLDTCQARARQLEEALRIREGEIQAQALQHHEVTQHLQQELCQ 129 + E L +L D + +++ + + L + Sbjct: 325 KRESEDNLNVRLNSLLVERDESKKELDAIQKEYSE-------FKSISEKKVASDAKLLGE 377 Query: 130 KEEELRQLLEKAGARRSQENGIQEKQSLEQERQEETRRL----LESLKELQLTVAQREEE 185 +E+ L QL E+ G + + + +E RR+ LE++ +L+L V +E Sbjct: 378 QEKRLHQLEEQLGTASDEVRKNNVLIADLTQEKENLRRMLDAELENISKLKLEVQVTQET 437 Query: 186 ILMLREASSPSHRALPAEKPALQPLPA-----QQELERLQTALRQTEAREIEWREKAQDL 240 + R +S + L + L A Q ELE +T+LR+ E + A+ L Sbjct: 438 LEKSRSDASDIAQQLQQSRHLCSKLEAEVSKLQMELEETRTSLRRNID---ETKRGAELL 494 Query: 241 ALSLAQSKASISSLQEITMFLQASVLERESEQQRLQEELVLSSQALEEQQSGGPHSTSRA 300 A L ++ + E + + LQ ELV + E + Sbjct: 495 AAELTTTRELLKKTNEEMHTMSHELAAVTENCDNLQTELVDVYKKAERAA-----DELKQ 549 Query: 301 DQGPKVGQESQPGEVETEPSPGVEEKERLTQRLERLQQAVAELEVDRSKLQCHNAQLRTA 360 ++ V E + +E + + E ++ L + LER +++ E+ + L + Sbjct: 550 EKNIVVTLEKELTFLEAQITREKESRKNLEEELERATESLDEMNRNAFALAKELELANSH 609 Query: 361 LEQVERERRKLKRDSVRASRAGSLEARETM 390 + +E ER L++ SV + S E+RE + Sbjct: 610 ISSLEDEREVLQK-SVSEQKQISQESRENL 638 >swiss|Q60611|SAT1_MOUSE DNA-binding protein SATB1 (Special AT-rich sequenc Length = 764 Score = 34.4 bits (77), Expect = 3e-04 Identities = 36/173 (20%), Positives = 64/173 (36%), Gaps = 9/173 (5%) Query: 33 QYSRRQEEAAV-SQAEALQEALSKAQAALQEKEQSLLEQAELSHTLEASTAALQATLDTC 91 Q+ R + + A SQA + A ++ Q L E + + S +L + A+Q L Sbjct: 377 QWVRDELKRAGISQAVFARVAFNRTQGLLSEILRKEEDPKTASQSLLVNLRAMQNFLQLP 436 Query: 92 QARARQLEEALRIREGEIQAQALQHHEVTQHLQQELCQKEEELRQLLEKAGARRSQENGI 151 +A ++ + R R A L + + L + + N + Sbjct: 437 EAERDRIYQDERER----SLNAASAMGPAPLLSTPPSRPPQVKTATLATERNGKPENNTM 492 Query: 152 QEKQSLEQERQEETRRLLESLKELQLTVAQREE----EILMLREASSPSHRAL 200 S+ E Q+E +R S A + + E+L +E SP +R L Sbjct: 493 NINASIYDEIQQEMKRAKVSQAPFAKVAATKSQGWLCELLRWKEDPSPENRTL 545 Score = 20.9 bits (42), Expect = 2.8 Identities = 29/161 (18%), Positives = 59/161 (36%), Gaps = 24/161 (14%) Query: 18 LTEQEQELAALRAENQYSRRQEEAAVSQAEALQEALSKAQAALQEKEQSLLEQAELSHTL 77 L Q+ +A L + R + L +++ + EQ + E+S + Sbjct: 316 LVNQQLVMAQLLNQQYAVNRLLAQQSLNQQYLNHPPPVSRSMNKPLEQQVSTNTEVSSEI 375 Query: 78 EASTAALQATLDTCQARARQLEEALRIREGEIQAQ-ALQHHEVTQHLQQELCQKEEELRQ 136 + + + L+ R G QA A TQ L E+ +KEE+ + Sbjct: 376 Y-----------------QWVRDELK-RAGISQAVFARVAFNRTQGLLSEILRKEEDPKT 417 Query: 137 LLEKAGAR-RSQENGIQ----EKQSLEQERQEETRRLLESL 172 + R+ +N +Q E+ + Q+ +E + ++ Sbjct: 418 ASQSLLVNLRAMQNFLQLPEAERDRIYQDERERSLNAASAM 458 >trembl|Q9FLH0|Q9FLH0 Nuclear matrix constituent protein 1 (NMCP1)-like. Length = 1042 Score = 29.0 bits (63), Expect = 0.010 Identities = 59/301 (19%), Positives = 132/301 (43%), Gaps = 19/301 (6%) Query: 5 QDPAGQLAAGQATLTEQEQELAALRAENQYSRRQEEAAVSQA--------EALQEALSKA 56 Q G L + L+ Q +E+ A E+ + +E++A A E+L++ + A Sbjct: 77 QHNMGLLLLEKNELSSQYEEIKASVDESDLTHMREKSAYVSALAEAKKREESLKKDVGIA 136 Query: 57 QAALQEKEQSLLEQAELSHTLEASTAALQATLDTCQAR--ARQLEEALRIREGE-IQAQA 113 + + E++L E + S + + + + ++R E +QA+A Sbjct: 137 KECISSLEKTLHEMRAECAETKVSAGSTMSEAHVMIEDALKKLADAEAKMRAAEALQAEA 196 Query: 114 LQHHEVTQHLQQELCQKEEEL-RQLLEKAGARRSQENGIQEKQSLEQERQEETRRLLESL 172 ++H + + +E+ +E++L R+L ++EN + ++ ER++ ++ E L Sbjct: 197 NRYHRIAERKLKEVESREDDLTRRLASFKSECETKENEMVIERQTLNERRKSLQQEHERL 256 Query: 173 KELQLTVAQREEEILMLREASSPSHRALPAEKPALQPLPAQQELER--LQTALRQTEARE 230 + Q+++ QRE+ I + + + L K + E ++ L+ AL RE Sbjct: 257 LDAQVSLNQREDHIFARSQELAELEKGLDTAKTTFEEERKAFEDKKSNLEIALALCAKRE 316 Query: 231 IEWREKAQDLALSLAQSKASISSLQEITMFLQASVLERESEQQRLQEELVLSSQALEEQQ 290 L + ++S L + + +V ERES + ++EL+++ + + ++ Sbjct: 317 EVCFYSHNSLLFLVLHYRSSKKFLGD-----KIAVSERESSLLKKEQELLVAEEKIASKE 371 Query: 291 S 291 S Sbjct: 372 S 372 Score = 27.4 bits (59), Expect = 0.028 Identities = 45/240 (18%), Positives = 108/240 (44%), Gaps = 26/240 (10%) Query: 11 LAAGQATLTEQEQELAALRAENQYSRRQEEAAVSQAEALQEALSKAQAALQEKEQSLLEQ 70 ++ +++L ++EQEL L AE E+ A ++E +Q L+ + L++++ + + Sbjct: 346 VSERESSLLKKEQEL--LVAE-------EKIASKESELIQNVLANQEVILRKRKSDVEAE 396 Query: 71 AEL-SHTLEASTAALQATLDTCQARARQLEEALRIREGEIQAQALQHHEVTQHLQQELCQ 129 E S ++E + + + + +Q E+ + +E +++ Q+ E + + ++ Sbjct: 397 LECKSKSVEVEIESKRRAWELREVDIKQREDLVGEKEHDLEVQSRALAEKEKDITEKSFN 456 Query: 130 KEEELRQLLEKAGARRSQENGIQEKQSLEQERQEETRRLLESLKELQLTVAQREEEILML 189 +E+ + L+ + E I K ++ ++ +E R+ L L + Q + Sbjct: 457 LDEKEKNLV-------ATEEDINRKTTMLEDEKERLRK-------LDLELQQSLTSLEDK 502 Query: 190 REASSPSHRALPAEKPALQPLPAQQELERLQTALRQTEAREIEWREKAQDLALSLAQSKA 249 R+ + + L A K L + +L+ L A+++E +A L + A+ +A Sbjct: 503 RKRVDSATQKLEALKSETSELSTLE--MKLKEELDDLRAQKLEMLAEADRLKVEKAKFEA 560 Score = 23.6 bits (49), Expect = 0.45 Identities = 31/192 (16%), Positives = 72/192 (37%), Gaps = 30/192 (15%) Query: 12 AAGQATLTEQEQELAALRAENQYSRRQEEAAVS----QAEALQEALSKAQAALQEKEQS- 66 +A + E ++ E R Q + V + E + + + K Q Sbjct: 581 RQREAFSMYLKDERDNIKEERDALRNQHKNDVESLNREREEFMNKMVEEHSEWLSKIQRE 640 Query: 67 --------LLEQAELSHTLEASTAALQATLDTCQARARQLEEALRIREGEIQAQALQHHE 118 +++ EL + +E L+ + + R + E+ ++ E IQ+ + Sbjct: 641 RADFLLGIEMQKRELEYCIENKREELENS---SRDREKAFEQEKKLEEERIQSLKEMAEK 697 Query: 119 VTQHLQQELCQKEEE--------------LRQLLEKAGARRSQENGIQEKQSLEQERQEE 164 +H+Q EL + + E +L + + Q ++ ++ + + ++E Sbjct: 698 ELEHVQVELKRLDAERLEIKLDRERREREWAELKDSVEELKVQREKLETQRHMLRAERDE 757 Query: 165 TRRLLESLKELQ 176 R +E LK+L+ Sbjct: 758 IRHEIEELKKLE 769 >trembl|Q9C2H8|Q9C2H8 Related to ser/arg-related nuclear matrix protein. Length = 976 Score = 24.4 bits (51), Expect = 0.24 Identities = 24/86 (27%), Positives = 34/86 (38%), Gaps = 13/86 (15%) Query: 238 QDLALSLAQSKASISSLQEITMFLQASVLERESEQQRLQEELVLSSQALEEQQSGGPHST 297 +D A SLA+ S S + S E E + ++L+L LE P Sbjct: 62 EDEADSLAKEYGSPSVI---------SSYEDEPPNRGEIDQLILMEPVLENN----PERR 108 Query: 298 SRADQGPKVGQESQPGEVETEPSPGV 323 GP G+ES+P E +P V Sbjct: 109 FVVVTGPGAGKESEPAPSIVETTPPV 134 >swiss|Q07856|VE6_HPV65 E6 protein. Length = 140 Score = 21.7 bits (44), Expect = 1.8 Identities = 11/36 (30%), Positives = 14/36 (38%) Query: 74 SHTLEASTAALQATLDTCQARARQLEEALRIREGEI 109 S L S Q C +A LEE + + EI Sbjct: 61 SECLRLSARFEQENYFQCSIKAVNLEEVAQRKIKEI 96 >trembl|Q9CVG5|Q9CVG5 Ser/Arg-related nuclear matrix protein (Fragment). Length = 265 Score = 19.0 bits (37), Expect = 9.8 Identities = 8/37 (21%), Positives = 18/37 (48%) Query: 40 EAAVSQAEALQEALSKAQAALQEKEQSLLEQAELSHT 76 + + Q + QE L+ + ++K++ E+ E S Sbjct: 128 KEEIKQRQIEQEKLASLKKQDEDKDKRDKEEKESSRE 164 Searching.done Results from round 3 Score E Sequences producing significant alignments: (bits) Value Sequences used in model and found again: trembl|Q60952|Q60952 Intranuclear protein. 392 e-112 swiss|Q60611|SAT1_MOUSE DNA-binding protein SATB1 (Special AT-r... 212 7e-58 swiss|Q9M7J4|MFP1_TOBAC MAR binding filament-like protein 1-1. 150 3e-39 Sequences not found previously or not previously below threshold: trembl|Q9FLH0|Q9FLH0 Nuclear matrix constituent protein 1 (NMCP... 28 0.017 swiss|P14733|LAM1_MOUSE Lamin B1. 22 1.8 swiss|P13777|REP1_ZYGBI Trans-acting factor B (REP1). 20 3.5 CONVERGED! >trembl|Q60952|Q60952 Intranuclear protein. Length = 446 Score = 392 bits (1006), Expect = e-112 Identities = 446/446 (100%), Positives = 446/446 (100%) Query: 1 MRQKQDPAGQLAAGQATLTEQEQELAALRAENQYSRRQEEAAVSQAEALQEALSKAQAAL 60 MRQKQDPAGQLAAGQATLTEQEQELAALRAENQYSRRQEEAAVSQAEALQEALSKAQAAL Sbjct: 1 MRQKQDPAGQLAAGQATLTEQEQELAALRAENQYSRRQEEAAVSQAEALQEALSKAQAAL 60 Query: 61 QEKEQSLLEQAELSHTLEASTAALQATLDTCQARARQLEEALRIREGEIQAQALQHHEVT 120 QEKEQSLLEQAELSHTLEASTAALQATLDTCQARARQLEEALRIREGEIQAQALQHHEVT Sbjct: 61 QEKEQSLLEQAELSHTLEASTAALQATLDTCQARARQLEEALRIREGEIQAQALQHHEVT 120 Query: 121 QHLQQELCQKEEELRQLLEKAGARRSQENGIQEKQSLEQERQEETRRLLESLKELQLTVA 180 QHLQQELCQKEEELRQLLEKAGARRSQENGIQEKQSLEQERQEETRRLLESLKELQLTVA Sbjct: 121 QHLQQELCQKEEELRQLLEKAGARRSQENGIQEKQSLEQERQEETRRLLESLKELQLTVA 180 Query: 181 QREEEILMLREASSPSHRALPAEKPALQPLPAQQELERLQTALRQTEAREIEWREKAQDL 240 QREEEILMLREASSPSHRALPAEKPALQPLPAQQELERLQTALRQTEAREIEWREKAQDL Sbjct: 181 QREEEILMLREASSPSHRALPAEKPALQPLPAQQELERLQTALRQTEAREIEWREKAQDL 240 Query: 241 ALSLAQSKASISSLQEITMFLQASVLERESEQQRLQEELVLSSQALEEQQSGGPHSTSRA 300 ALSLAQSKASISSLQEITMFLQASVLERESEQQRLQEELVLSSQALEEQQSGGPHSTSRA Sbjct: 241 ALSLAQSKASISSLQEITMFLQASVLERESEQQRLQEELVLSSQALEEQQSGGPHSTSRA 300 Query: 301 DQGPKVGQESQPGEVETEPSPGVEEKERLTQRLERLQQAVAELEVDRSKLQCHNAQLRTA 360 DQGPKVGQESQPGEVETEPSPGVEEKERLTQRLERLQQAVAELEVDRSKLQCHNAQLRTA Sbjct: 301 DQGPKVGQESQPGEVETEPSPGVEEKERLTQRLERLQQAVAELEVDRSKLQCHNAQLRTA 360 Query: 361 LEQVERERRKLKRDSVRASRAGSLEARETMTSSPTQQDGRGSQRGSSDSVLVVELQREVA 420 LEQVERERRKLKRDSVRASRAGSLEARETMTSSPTQQDGRGSQRGSSDSVLVVELQREVA Sbjct: 361 LEQVERERRKLKRDSVRASRAGSLEARETMTSSPTQQDGRGSQRGSSDSVLVVELQREVA 420 Query: 421 LLRAQLALERKRGRTTLHGPCRPAVS 446 LLRAQLALERKRGRTTLHGPCRPAVS Sbjct: 421 LLRAQLALERKRGRTTLHGPCRPAVS 446 >swiss|Q60611|SAT1_MOUSE DNA-binding protein SATB1 (Special AT-rich sequenc Length = 764 Score = 212 bits (539), Expect = 7e-58 Identities = 36/173 (20%), Positives = 64/173 (36%), Gaps = 9/173 (5%) Query: 33 QYSRRQEEAAV-SQAEALQEALSKAQAALQEKEQSLLEQAELSHTLEASTAALQATLDTC 91 Q+ R + + A SQA + A ++ Q L E + + S +L + A+Q L Sbjct: 377 QWVRDELKRAGISQAVFARVAFNRTQGLLSEILRKEEDPKTASQSLLVNLRAMQNFLQLP 436 Query: 92 QARARQLEEALRIREGEIQAQALQHHEVTQHLQQELCQKEEELRQLLEKAGARRSQENGI 151 +A ++ + R R A L + + L + + N + Sbjct: 437 EAERDRIYQDERER----SLNAASAMGPAPLLSTPPSRPPQVKTATLATERNGKPENNTM 492 Query: 152 QEKQSLEQERQEETRRLLESLKELQLTVAQREE----EILMLREASSPSHRAL 200 S+ E Q+E +R S A + + E+L +E SP +R L Sbjct: 493 NINASIYDEIQQEMKRAKVSQAPFAKVAATKSQGWLCELLRWKEDPSPENRTL 545 Score = 42.8 bits (99), Expect = 8e-07 Identities = 18/90 (20%), Positives = 36/90 (40%), Gaps = 9/90 (10%) Query: 33 QYSRRQEEAA-VSQAEALQEALSKAQAALQEKEQSLLEQAELSHTLEASTAALQATLDTC 91 +++ + A VSQA + A +K+Q L E + + + + TL + + ++ L Sbjct: 500 DEIQQEMKRAKVSQAPFAKVAATKSQGWLCELLRWKEDPSPENRTLWENLSMIRRFLSLP 559 Query: 92 QARARQLEEALRIREGEIQAQALQHHEVTQ 121 Q + E + A+ HH Sbjct: 560 QPERDAIYEQE--------SNAVHHHGDRP 581 Score = 37.0 bits (84), Expect = 4e-05 Identities = 20/101 (19%), Positives = 34/101 (32%), Gaps = 6/101 (5%) Query: 124 QQELCQKEEELRQLLEKAGARRSQENGIQEKQSLEQERQEETRRLLESLKELQLTVAQRE 183 QQ L R + + + S + + Q ++E +R S R Sbjct: 344 QQYLNHPPPVSRSMNKPLEQQVSTNTEVS--SEIYQWVRDELKRAGISQAVFARVAFNRT 401 Query: 184 E----EILMLREASSPSHRALPAEKPALQPLPAQQELERLQ 220 + EIL E + ++L A+Q E ER + Sbjct: 402 QGLLSEILRKEEDPKTASQSLLVNLRAMQNFLQLPEAERDR 442 >swiss|Q9M7J4|MFP1_TOBAC MAR binding filament-like protein 1-1. Length = 722 Score = 150 bits (379), Expect = 3e-39 Identities = 85/430 (19%), Positives = 175/430 (39%), Gaps = 26/430 (6%) Query: 10 QLAAGQATLTEQEQELAA-LRAENQYSRRQEEAAVSQAEALQEALSKAQAALQEKEQSLL 68 +L +AT E++ + L E Q + A + +AL L+ A++ + Q L Sbjct: 152 KLKEKEATFVSMEKKFQSELLNERDIRNNQLKRAGEERQALVNQLNSAKSTVTNLGQELQ 211 Query: 69 EQAELSHTLEASTAALQATLDTCQARARQLEEALRIREGEIQAQALQHHEVTQHLQQELC 128 ++ ++ L LQ L + ++L+E L+ + IQ E L E+ Sbjct: 212 KEKRIAEELIVQIEGLQNNLMQMKEDKKKLQEELKEKLDLIQVL----QEKITLLTTEIK 267 Query: 129 QKEEELRQLLEKAGARRSQENGIQEKQSLEQERQEETRRLLESLKELQLTVAQREEEILM 188 KE L+ K + S+ + + S+ QE Q++ L +KEL++ V +RE E+ + Sbjct: 268 DKEASLQSTTSKLAEKESE---VDKLSSMYQESQDQLMNLTSEIKELKVEVQKRERELEL 324 Query: 189 LREASSPSHRALPAEKPALQPLPAQQELERLQTALRQTEAREIEWREKAQDLAL------ 242 RE+ + L + ++ +++EL+ +Q +E + I ++ A D L Sbjct: 325 KRESEDNLNVRLNSL--LVERDESKKELDAIQKEY--SEFKSISEKKVASDAKLLGEQEK 380 Query: 243 SLAQSKASISSLQEITMFLQASVLERESEQQRLQEEL-----VLSSQALEEQQSGGPHST 297 L Q + + + + + + E++ L+ L +S LE Q + Sbjct: 381 RLHQLEEQLGTASDEVRKNNVLIADLTQEKENLRRMLDAELENISKLKLEVQVTQETLEK 440 Query: 298 SRADQGPKVGQESQPGEVETEPSPGVEE-KERLTQRLERLQQAVAELEVDRSKLQCHNAQ 356 SR+D Q Q + ++ V + + L + L++ + E + L Sbjct: 441 SRSDASDIAQQLQQSRHLCSKLEAEVSKLQMELEETRTSLRRNIDETKRGAELLAAELTT 500 Query: 357 LRTALEQVERERRKLKRDSVRASRAGSLEARETMTSSPTQQDGRGSQRGSSDSVLVVELQ 416 R L++ E + + + + + +T ++ R + + +VV L+ Sbjct: 501 TRELLKKTNEEMHTMSHELAAVTE--NCDNLQTELVDVYKKAERAADELKQEKNIVVTLE 558 Query: 417 REVALLRAQL 426 +E+ L AQ+ Sbjct: 559 KELTFLEAQI 568 >trembl|Q9FLH0|Q9FLH0 Nuclear matrix constituent protein 1 (NMCP1)-like. Length = 1042 Score = 28.2 bits (61), Expect = 0.017 Identities = 64/361 (17%), Positives = 151/361 (41%), Gaps = 14/361 (3%) Query: 22 EQELAALRAENQYSRRQEEAAVSQAEALQEALSKAQAALQEKEQSLLEQAEL-SHTLEAS 80 E+E + L+ E + +E+ A ++E +Q L+ + L++++ + + E S ++E Sbjct: 348 ERESSLLKKEQELLVAEEKIASKESELIQNVLANQEVILRKRKSDVEAELECKSKSVEVE 407 Query: 81 TAALQATLDTCQARARQLEEALRIREGEIQAQALQHHEVTQHLQQELCQKEEELRQLLEK 140 + + + + +Q E+ + +E +++ Q+ E + + ++ +E+ + L+ Sbjct: 408 IESKRRAWELREVDIKQREDLVGEKEHDLEVQSRALAEKEKDITEKSFNLDEKEKNLVAT 467 Query: 141 AGARRSQENGIQEKQSLEQERQEETRRLLESLKELQLTVAQREEEILMLREASSPSHRAL 200 + +++++ ++ E ++ L SL++ + V +++ L+ +S Sbjct: 468 EEDINRKTTMLEDEKERLRKLDLELQQSLTSLEDKRKRVDSATQKLEALKSETSELSTLE 527 Query: 201 PAEKPALQPLPAQQ-----ELERLQTALRQTEAREIEWREKAQDL---ALSLAQSKASIS 252 K L L AQ+ E +RL+ + EA K ++L A + + + + S Sbjct: 528 MKLKEELDDLRAQKLEMLAEADRLKVEKAKFEAEWEHIDVKREELRKEAEYITRQREAFS 587 Query: 253 S-LQEITMFLQASVLERESEQQR----LQEELVLSSQALEEQQSGGPHSTSRADQGPKVG 307 L++ ++ ++ + L E + E+ S R +G Sbjct: 588 MYLKDERDNIKEERDALRNQHKNDVESLNREREEFMNKMVEEHSEWLSKIQRERADFLLG 647 Query: 308 QESQPGEVETEPSPGVEEKERLTQRLERLQQAVAELEVDRSKLQCHNAQLRTALEQVERE 367 E Q E+E EE E ++ E+ + +LE +R + A+ QVE + Sbjct: 648 IEMQKRELEYCIENKREELENSSRDREKAFEQEKKLEEERIQSLKEMAEKELEHVQVELK 707 Query: 368 R 368 R Sbjct: 708 R 708 Score = 22.8 bits (47), Expect = 0.73 Identities = 87/464 (18%), Positives = 179/464 (37%), Gaps = 43/464 (9%) Query: 5 QDPAGQLAAGQATLTEQEQELAALRAENQYSRRQEEAAVSQA--------EALQEALSKA 56 Q G L + L+ Q +E+ A E+ + +E++A A E+L++ + A Sbjct: 77 QHNMGLLLLEKNELSSQYEEIKASVDESDLTHMREKSAYVSALAEAKKREESLKKDVGIA 136 Query: 57 QAALQEKEQSLLEQAELSHTLEASTAAL--QATLDTCQARARQLEEALRIREGE-IQAQA 113 + + E++L E + S + +A + A + + ++R E +QA+A Sbjct: 137 KECISSLEKTLHEMRAECAETKVSAGSTMSEAHVMIEDALKKLADAEAKMRAAEALQAEA 196 Query: 114 LQHHEVTQHLQQELCQKEEELRQLLE--------KAGARRSQENGIQEKQSLEQERQEET 165 ++H + + +E+ +E++L + L K + + E++ Q+ E Sbjct: 197 NRYHRIAERKLKEVESREDDLTRRLASFKSECETKENEMVIERQTLNERRKSLQQEHERL 256 Query: 166 RRLLESLKELQLTVAQREEEILMLREASSPSHRALPAEKPALQPLPAQQELERLQTALRQ 225 SL + + + R +E+ L + + E+ A + + E+ A R+ Sbjct: 257 LDAQVSLNQREDHIFARSQELAELEKGLDTAKTTFEEERKAFEDKKSNLEIALALCAKRE 316 Query: 226 TEA---------REIEWREKAQDLALSLAQSKASISSLQEITMFLQASVLERESEQQRLQ 276 + +R + L +A S+ S L++ L A E + +Q Sbjct: 317 EVCFYSHNSLLFLVLHYRSSKKFLGDKIAVSERESSLLKKEQELLVAEEKIASKESELIQ 376 Query: 277 EELVLSSQALEEQQSGGPHSTSRADQGPKVGQESQPGEVETEPSPGVEEKERL---TQRL 333 L L +++S + +V ES+ E + ++ + L Sbjct: 377 NVLANQEVILRKRKSDVEAELECKSKSVEVEIESKRRAWELREVDIKQREDLVGEKEHDL 436 Query: 334 ERLQQAVAELEVDRSK-----------LQCHNAQLRTALEQVERERRKLKRDSVRASRAG 382 E +A+AE E D ++ L + +E E+ +L++ + ++ Sbjct: 437 EVQSRALAEKEKDITEKSFNLDEKEKNLVATEEDINRKTTMLEDEKERLRKLDLELQQSL 496 Query: 383 -SLEARETMTSSPTQQDGRGSQRGSSDSVLVVELQREVALLRAQ 425 SLE + S TQ+ S S L ++L+ E+ LRAQ Sbjct: 497 TSLEDKRKRVDSATQKLEALKSETSELSTLEMKLKEELDDLRAQ 540 Score = 22.0 bits (45), Expect = 1.3 Identities = 61/378 (16%), Positives = 137/378 (36%), Gaps = 7/378 (1%) Query: 10 QLAAGQATLTEQEQELAALRAENQYSRRQE----EAAVSQAEALQEALSKAQAALQEKEQ 65 +L ++ + + LA+ ++E + + + + ++LQ+ + A Q Sbjct: 206 KLKEVESREDDLTRRLASFKSECETKENEMVIERQTLNERRKSLQQEHERLLDAQVSLNQ 265 Query: 66 SLLEQAELSHTLEASTAALQATLDTCQARARQLEEALRIREGEIQAQALQHHEVTQHLQQ 125 S L A T T R+ E + A + EV + Sbjct: 266 REDHIFARSQEL-AELEKGLDTAKTTFEEERKAFEDKKSNLEIALALCAKREEVCFYSHN 324 Query: 126 ELCQKEEELRQLLEKAGARRSQENGIQEKQSLEQERQEETRRLLESLKELQLTVAQREEE 185 L R + G + + EQE ++ EL V +E Sbjct: 325 SLLFLVLHYRSSKKFLGDKIAVSERESSLLKKEQELLVAEEKIASKESELIQNVLANQEV 384 Query: 186 ILMLREASSPSHRALPAEKPALQPLPAQQELERLQTALRQTEAREIEWREKAQDLALSLA 245 IL R++ + ++ ++ ++ E + ++Q E E + + +LA Sbjct: 385 ILRKRKSDVEAELECKSKSVEVEIESKRRAWELREVDIKQREDLVGEKEHDLEVQSRALA 444 Query: 246 QSKASISSLQEITMFLQASVLERESEQQRLQEELVLSSQALEEQQSGGPHS-TSRADQGP 304 + + I+ + +++ E + R L + L + S TS D+ Sbjct: 445 EKEKDITEKSFNLDEKEKNLVATEEDINRKTTMLEDEKERLRKLDLELQQSLTSLEDKRK 504 Query: 305 KVGQESQPGE-VETEPSPGVEEKERLTQRLERLQQAVAELEVDRSKLQCHNAQLRTALEQ 363 +V +Q E +++E S + +L + L+ L+ E+ + +L+ A+ E Sbjct: 505 RVDSATQKLEALKSETSELSTLEMKLKEELDDLRAQKLEMLAEADRLKVEKAKFEAEWEH 564 Query: 364 VERERRKLKRDSVRASRA 381 ++ +R +L++++ +R Sbjct: 565 IDVKREELRKEAEYITRQ 582 >swiss|P14733|LAM1_MOUSE Lamin B1. Length = 587 Score = 21.6 bits (44), Expect = 1.8 Identities = 34/185 (18%), Positives = 66/185 (35%), Gaps = 5/185 (2%) Query: 211 PAQQELERLQ-----TALRQTEAREIEWREKAQDLALSLAQSKASISSLQEITMFLQASV 265 P QQ+ + T L T ++ +E+ ++L LA + SL+ LQ V Sbjct: 5 PVQQQRAGSRASAPATPLSPTRLSRLQEKEELRELNDRLAVYIDKVRSLETENSALQLQV 64 Query: 266 LERESEQQRLQEELVLSSQALEEQQSGGPHSTSRADQGPKVGQESQPGEVETEPSPGVEE 325 ERE + R L + T+R ++ E + ++ Sbjct: 65 TEREEVRGRELTGLKALYETELADARRALDDTARERAKLQIELGKFKAEHDQLLLNYAKK 124 Query: 326 KERLTQRLERLQQAVAELEVDRSKLQCHNAQLRTALEQVERERRKLKRDSVRASRAGSLE 385 + L+ +L++ A L + L ++ +E + ++ + S A Sbjct: 125 ESDLSGAQIKLREYEAALNSKDAALATALGDKKSLEGDLEDLKDQIAQLEASLSAAKKQL 184 Query: 386 ARETM 390 A ET+ Sbjct: 185 ADETL 189 >swiss|P13777|REP1_ZYGBI Trans-acting factor B (REP1). Length = 322 Score = 20.5 bits (41), Expect = 3.5 Identities = 23/99 (23%), Positives = 31/99 (31%), Gaps = 10/99 (10%) Query: 245 AQSKASISSLQEITMFLQASVLERESEQQRLQEELVLSSQALEEQQSGGPHSTSRADQGP 304 +Q+ SI I A R S++ Q E SS A + + P Q Sbjct: 89 SQTTQSIGRTVSI-----AEATRRASQESPRQTETAGSSSAPDALSTQQPPLEHSTQQNI 143 Query: 305 KVGQESQPGEVE-----TEPSPGVEEKERLTQRLERLQQ 338 S VE S E +ER + E Q Sbjct: 144 PTKLPSTQQAVERVVSSQTTSRAAETRERSPEHTEASTQ 182 Database: /home/mika/Theses/Databases/unique_set/NMP_Database_unique .fasta Posted date: Mar 7, 2003 12:04 PM Number of letters in database: 17,163 Number of sequences in database: 43 Lambda K H 0.294 0.129 0.309 Lambda K H 0.267 0.0395 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 45,508 Number of Sequences: 43 Number of extensions: 2471 Number of successful extensions: 239 Number of sequences better than 10.0: 38 Number of HSP's better than 10.0 without gapping: 38 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 88 length of query: 446 length of database: 17,163 effective HSP length: 58 effective length of query: 388 effective length of database: 14,669 effective search space: 5691572 effective search space used: 5691572 T: 11 A: 40 X1: 16 ( 6.8 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 38 (19.1 bits) S2: 38 (19.3 bits) BLASTP 2.2.2 [Dec-14-2001] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= trembl|Q9EQJ3|Q9EQJ3 Nuclear matrix transcription factor. (563 letters) Database: /home/mika/Theses/Databases/unique_set/NMP_Database_unique.f asta 43 sequences; 17,163 total letters Searching.done Results from round 1 Score E Sequences producing significant alignments: (bits) Value trembl|Q9EQJ3|Q9EQJ3 Nuclear matrix transcription factor. 842 0.0 swiss|P13779|REP2_KLULA Trans-acting factor C (REP2). 30 0.007 trembl|Q60952|Q60952 Intranuclear protein. 25 0.19 swiss|P25233|NECD_MOUSE Necdin. 22 2.0 swiss|P30735|VE6_MNPV E6 protein. 20 7.9 >trembl|Q9EQJ3|Q9EQJ3 Nuclear matrix transcription factor. Length = 563 Score = 842 bits (2176), Expect = 0.0 Identities = 563/563 (100%), Positives = 563/563 (100%) Query: 1 MEESHFNSNPYFWPSIPTVSGQIENTMFINKMKDQLLPEKGCGLAPPHYPTLLTVPASVS 60 MEESHFNSNPYFWPSIPTVSGQIENTMFINKMKDQLLPEKGCGLAPPHYPTLLTVPASVS Sbjct: 1 MEESHFNSNPYFWPSIPTVSGQIENTMFINKMKDQLLPEKGCGLAPPHYPTLLTVPASVS 60 Query: 61 LSSGISMDTESKSEQLTPHSQASVTQNITVVPVPSTGLMTAGPGLVITSPSGSLVTTASS 120 LSSGISMDTESKSEQLTPHSQASVTQNITVVPVPSTGLMTAGPGLVITSPSGSLVTTASS Sbjct: 61 LSSGISMDTESKSEQLTPHSQASVTQNITVVPVPSTGLMTAGPGLVITSPSGSLVTTASS 120 Query: 121 AQTFPISTPMIVSALPPGSQALQVVPDLSKKVASTLTEEGGGGGGGGGTVAPPKPPRGRK 180 AQTFPISTPMIVSALPPGSQALQVVPDLSKKVASTLTEEGGGGGGGGGTVAPPKPPRGRK Sbjct: 121 AQTFPISTPMIVSALPPGSQALQVVPDLSKKVASTLTEEGGGGGGGGGTVAPPKPPRGRK 180 Query: 181 KKRMLESGLPEMNDPYVLAPGDDDDHQKDGKTYRCRMCSLTFYSKSEMQIHSKSHTETKP 240 KKRMLESGLPEMNDPYVLAPGDDDDHQKDGKTYRCRMCSLTFYSKSEMQIHSKSHTETKP Sbjct: 181 KKRMLESGLPEMNDPYVLAPGDDDDHQKDGKTYRCRMCSLTFYSKSEMQIHSKSHTETKP 240 Query: 241 HKCPHCSKTFANSSYLAQHIRIHSGAKPYSCNFCEKSFRQLSHLQQHTRIHSKMHTETIK 300 HKCPHCSKTFANSSYLAQHIRIHSGAKPYSCNFCEKSFRQLSHLQQHTRIHSKMHTETIK Sbjct: 241 HKCPHCSKTFANSSYLAQHIRIHSGAKPYSCNFCEKSFRQLSHLQQHTRIHSKMHTETIK 300 Query: 301 PHKCPHCSKTFANTSYLAQHLRIHSGAKPYNCSYCQKAFRQLSHLQQHTRIHTGDRPYKC 360 PHKCPHCSKTFANTSYLAQHLRIHSGAKPYNCSYCQKAFRQLSHLQQHTRIHTGDRPYKC Sbjct: 301 PHKCPHCSKTFANTSYLAQHLRIHSGAKPYNCSYCQKAFRQLSHLQQHTRIHTGDRPYKC 360 Query: 361 AHPGCEKAFTQLSNLQSHRRQHNKDKPFKCHNCHRAYTDAASLEAHLSTHTVKHAKVYTC 420 AHPGCEKAFTQLSNLQSHRRQHNKDKPFKCHNCHRAYTDAASLEAHLSTHTVKHAKVYTC Sbjct: 361 AHPGCEKAFTQLSNLQSHRRQHNKDKPFKCHNCHRAYTDAASLEAHLSTHTVKHAKVYTC 420 Query: 421 TICSRAYTSETYLMKHMRKHNPPDLQQQVQAAAAAAAVAQAQAQAQAQAQAQAQAQAQAQ 480 TICSRAYTSETYLMKHMRKHNPPDLQQQVQAAAAAAAVAQAQAQAQAQAQAQAQAQAQAQ Sbjct: 421 TICSRAYTSETYLMKHMRKHNPPDLQQQVQAAAAAAAVAQAQAQAQAQAQAQAQAQAQAQ 480 Query: 481 AQAQAQASQASQQQQQQQPPPPQPPHFQSPGAAPQGGGGGDSNQNPPPQCSFDLTPYKPA 540 AQAQAQASQASQQQQQQQPPPPQPPHFQSPGAAPQGGGGGDSNQNPPPQCSFDLTPYKPA Sbjct: 481 AQAQAQASQASQQQQQQQPPPPQPPHFQSPGAAPQGGGGGDSNQNPPPQCSFDLTPYKPA 540 Query: 541 EHHKDICLTVTTSTIQVEHLASS 563 EHHKDICLTVTTSTIQVEHLASS Sbjct: 541 EHHKDICLTVTTSTIQVEHLASS 563 >swiss|P13779|REP2_KLULA Trans-acting factor C (REP2). Length = 212 Score = 30.0 bits (66), Expect = 0.007 Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 6/65 (9%) Query: 493 QQQQQQPPPPQPPHFQSPGAAPQGGGGGDSNQNPPPQCSFDLTPYKPAEHHKDICLTVTT 552 ++++ P PP PP+ S + G++ P P+ FDLT P + HK C +VT Sbjct: 72 EERENSPSPPIPPYQISEMPLHELLESGNAKLVPNPE--FDLT--DPDDFHK--CFSVTY 125 Query: 553 STIQV 557 S + + Sbjct: 126 SALSL 130 >trembl|Q60952|Q60952 Intranuclear protein. Length = 446 Score = 25.4 bits (54), Expect = 0.19 Identities = 17/53 (32%), Positives = 27/53 (50%) Query: 445 LQQQVQAAAAAAAVAQAQAQAQAQAQAQAQAQAQAQAQAQAQASQASQQQQQQ 497 L +Q Q AA A Q + + A +QA+A +A ++AQA + Q +Q Sbjct: 18 LTEQEQELAALRAENQYSRRQEEAAVSQAEALQEALSKAQAALQEKEQSLLEQ 70 Score = 23.5 bits (49), Expect = 0.59 Identities = 16/52 (30%), Positives = 27/52 (51%) Query: 446 QQQVQAAAAAAAVAQAQAQAQAQAQAQAQAQAQAQAQAQAQASQASQQQQQQ 497 Q+Q AA A + + A +QA+A +A ++AQA Q + S +Q + Sbjct: 21 QEQELAALRAENQYSRRQEEAAVSQAEALQEALSKAQAALQEKEQSLLEQAE 72 Score = 22.7 bits (47), Expect = 0.99 Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 1/55 (1%) Query: 444 DLQQQVQAAAAAAAVAQAQAQAQAQAQAQAQAQAQAQAQAQA-QASQASQQQQQQ 497 +L ++A+ AA QA+A+ +A + + QAQA Q + +Q QQ+ Sbjct: 72 ELSHTLEASTAALQATLDTCQARARQLEEALRIREGEIQAQALQHHEVTQHLQQE 126 Score = 22.3 bits (46), Expect = 1.5 Identities = 15/54 (27%), Positives = 25/54 (45%) Query: 445 LQQQVQAAAAAAAVAQAQAQAQAQAQAQAQAQAQAQAQAQAQASQASQQQQQQQ 498 L+ A A QA+A+ +A + + QAQA + +Q QQ+ Q+ Sbjct: 77 LEASTAALQATLDTCQARARQLEEALRIREGEIQAQALQHHEVTQHLQQELCQK 130 Score = 21.6 bits (44), Expect = 2.6 Identities = 13/47 (27%), Positives = 26/47 (54%) Query: 445 LQQQVQAAAAAAAVAQAQAQAQAQAQAQAQAQAQAQAQAQAQASQAS 491 L+ + Q + A +QA+A +A ++AQA Q + Q+ + ++ S Sbjct: 28 LRAENQYSRRQEEAAVSQAEALQEALSKAQAALQEKEQSLLEQAELS 74 >swiss|P25233|NECD_MOUSE Necdin. Length = 325 Score = 21.9 bits (45), Expect = 2.0 Identities = 10/38 (26%), Positives = 14/38 (36%) Query: 499 PPPPQPPHFQSPGAAPQGGGGGDSNQNPPPQCSFDLTP 536 PP + P AP+G PP + D+ P Sbjct: 34 PPASLAANLAGPPCAPEGPMAAQQASPPPEERIEDVDP 71 >swiss|P30735|VE6_MNPV E6 protein. Length = 207 Score = 20.0 bits (40), Expect = 7.9 Identities = 7/11 (63%), Positives = 7/11 (63%) Query: 420 CTICSRAYTSE 430 CT CSR T E Sbjct: 95 CTFCSRFLTQE 105 Searching.done Results from round 2 Score E Sequences producing significant alignments: (bits) Value Sequences used in model and found again: trembl|Q9EQJ3|Q9EQJ3 Nuclear matrix transcription factor. 928 0.0 Sequences not found previously or not previously below threshold: swiss|P13779|REP2_KLULA Trans-acting factor C (REP2). 33 0.001 trembl|Q60952|Q60952 Intranuclear protein. 27 0.039 swiss|P25233|NECD_MOUSE Necdin. 23 0.72 >trembl|Q9EQJ3|Q9EQJ3 Nuclear matrix transcription factor. Length = 563 Score = 928 bits (2397), Expect = 0.0 Identities = 563/563 (100%), Positives = 563/563 (100%) Query: 1 MEESHFNSNPYFWPSIPTVSGQIENTMFINKMKDQLLPEKGCGLAPPHYPTLLTVPASVS 60 MEESHFNSNPYFWPSIPTVSGQIENTMFINKMKDQLLPEKGCGLAPPHYPTLLTVPASVS Sbjct: 1 MEESHFNSNPYFWPSIPTVSGQIENTMFINKMKDQLLPEKGCGLAPPHYPTLLTVPASVS 60 Query: 61 LSSGISMDTESKSEQLTPHSQASVTQNITVVPVPSTGLMTAGPGLVITSPSGSLVTTASS 120 LSSGISMDTESKSEQLTPHSQASVTQNITVVPVPSTGLMTAGPGLVITSPSGSLVTTASS Sbjct: 61 LSSGISMDTESKSEQLTPHSQASVTQNITVVPVPSTGLMTAGPGLVITSPSGSLVTTASS 120 Query: 121 AQTFPISTPMIVSALPPGSQALQVVPDLSKKVASTLTEEGGGGGGGGGTVAPPKPPRGRK 180 AQTFPISTPMIVSALPPGSQALQVVPDLSKKVASTLTEEGGGGGGGGGTVAPPKPPRGRK Sbjct: 121 AQTFPISTPMIVSALPPGSQALQVVPDLSKKVASTLTEEGGGGGGGGGTVAPPKPPRGRK 180 Query: 181 KKRMLESGLPEMNDPYVLAPGDDDDHQKDGKTYRCRMCSLTFYSKSEMQIHSKSHTETKP 240 KKRMLESGLPEMNDPYVLAPGDDDDHQKDGKTYRCRMCSLTFYSKSEMQIHSKSHTETKP Sbjct: 181 KKRMLESGLPEMNDPYVLAPGDDDDHQKDGKTYRCRMCSLTFYSKSEMQIHSKSHTETKP 240 Query: 241 HKCPHCSKTFANSSYLAQHIRIHSGAKPYSCNFCEKSFRQLSHLQQHTRIHSKMHTETIK 300 HKCPHCSKTFANSSYLAQHIRIHSGAKPYSCNFCEKSFRQLSHLQQHTRIHSKMHTETIK Sbjct: 241 HKCPHCSKTFANSSYLAQHIRIHSGAKPYSCNFCEKSFRQLSHLQQHTRIHSKMHTETIK 300 Query: 301 PHKCPHCSKTFANTSYLAQHLRIHSGAKPYNCSYCQKAFRQLSHLQQHTRIHTGDRPYKC 360 PHKCPHCSKTFANTSYLAQHLRIHSGAKPYNCSYCQKAFRQLSHLQQHTRIHTGDRPYKC Sbjct: 301 PHKCPHCSKTFANTSYLAQHLRIHSGAKPYNCSYCQKAFRQLSHLQQHTRIHTGDRPYKC 360 Query: 361 AHPGCEKAFTQLSNLQSHRRQHNKDKPFKCHNCHRAYTDAASLEAHLSTHTVKHAKVYTC 420 AHPGCEKAFTQLSNLQSHRRQHNKDKPFKCHNCHRAYTDAASLEAHLSTHTVKHAKVYTC Sbjct: 361 AHPGCEKAFTQLSNLQSHRRQHNKDKPFKCHNCHRAYTDAASLEAHLSTHTVKHAKVYTC 420 Query: 421 TICSRAYTSETYLMKHMRKHNPPDLQQQVQAAAAAAAVAQAQAQAQAQAQAQAQAQAQAQ 480 TICSRAYTSETYLMKHMRKHNPPDLQQQVQAAAAAAAVAQAQAQAQAQAQAQAQAQAQAQ Sbjct: 421 TICSRAYTSETYLMKHMRKHNPPDLQQQVQAAAAAAAVAQAQAQAQAQAQAQAQAQAQAQ 480 Query: 481 AQAQAQASQASQQQQQQQPPPPQPPHFQSPGAAPQGGGGGDSNQNPPPQCSFDLTPYKPA 540 AQAQAQASQASQQQQQQQPPPPQPPHFQSPGAAPQGGGGGDSNQNPPPQCSFDLTPYKPA Sbjct: 481 AQAQAQASQASQQQQQQQPPPPQPPHFQSPGAAPQGGGGGDSNQNPPPQCSFDLTPYKPA 540 Query: 541 EHHKDICLTVTTSTIQVEHLASS 563 EHHKDICLTVTTSTIQVEHLASS Sbjct: 541 EHHKDICLTVTTSTIQVEHLASS 563 >swiss|P13779|REP2_KLULA Trans-acting factor C (REP2). Length = 212 Score = 32.8 bits (73), Expect = 0.001 Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 6/65 (9%) Query: 493 QQQQQQPPPPQPPHFQSPGAAPQGGGGGDSNQNPPPQCSFDLTPYKPAEHHKDICLTVTT 552 ++++ P PP PP+ S + G++ P P+ FDLT P + HK C +VT Sbjct: 72 EERENSPSPPIPPYQISEMPLHELLESGNAKLVPNPE--FDLT--DPDDFHK--CFSVTY 125 Query: 553 STIQV 557 S + + Sbjct: 126 SALSL 130 >trembl|Q60952|Q60952 Intranuclear protein. Length = 446 Score = 27.4 bits (59), Expect = 0.039 Identities = 17/53 (32%), Positives = 27/53 (50%) Query: 445 LQQQVQAAAAAAAVAQAQAQAQAQAQAQAQAQAQAQAQAQAQASQASQQQQQQ 497 L +Q Q AA A Q + + A +QA+A +A ++AQA + Q +Q Sbjct: 18 LTEQEQELAALRAENQYSRRQEEAAVSQAEALQEALSKAQAALQEKEQSLLEQ 70 Score = 25.5 bits (54), Expect = 0.14 Identities = 16/52 (30%), Positives = 27/52 (51%) Query: 446 QQQVQAAAAAAAVAQAQAQAQAQAQAQAQAQAQAQAQAQAQASQASQQQQQQ 497 Q+Q AA A + + A +QA+A +A ++AQA Q + S +Q + Sbjct: 21 QEQELAALRAENQYSRRQEEAAVSQAEALQEALSKAQAALQEKEQSLLEQAE 72 Score = 25.5 bits (54), Expect = 0.17 Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 1/55 (1%) Query: 444 DLQQQVQAAAAAAAVAQAQAQAQAQAQAQAQAQAQAQAQAQA-QASQASQQQQQQ 497 +L ++A+ AA QA+A+ +A + + QAQA Q + +Q QQ+ Sbjct: 72 ELSHTLEASTAALQATLDTCQARARQLEEALRIREGEIQAQALQHHEVTQHLQQE 126 Score = 24.3 bits (51), Expect = 0.40 Identities = 15/54 (27%), Positives = 25/54 (45%) Query: 445 LQQQVQAAAAAAAVAQAQAQAQAQAQAQAQAQAQAQAQAQAQASQASQQQQQQQ 498 L+ A A QA+A+ +A + + QAQA + +Q QQ+ Q+ Sbjct: 77 LEASTAALQATLDTCQARARQLEEALRIREGEIQAQALQHHEVTQHLQQELCQK 130 Score = 23.2 bits (48), Expect = 0.73 Identities = 13/47 (27%), Positives = 26/47 (54%) Query: 445 LQQQVQAAAAAAAVAQAQAQAQAQAQAQAQAQAQAQAQAQAQASQAS 491 L+ + Q + A +QA+A +A ++AQA Q + Q+ + ++ S Sbjct: 28 LRAENQYSRRQEEAAVSQAEALQEALSKAQAALQEKEQSLLEQAELS 74 Score = 19.7 bits (39), Expect = 7.6 Identities = 11/39 (28%), Positives = 21/39 (53%) Query: 460 QAQAQAQAQAQAQAQAQAQAQAQAQAQASQASQQQQQQQ 498 +AQ A + AQ++A + + QAS ++ +QQ+ Sbjct: 236 KAQDLALSLAQSKASISSLQEITMFLQASVLERESEQQR 274 >swiss|P25233|NECD_MOUSE Necdin. Length = 325 Score = 23.2 bits (48), Expect = 0.72 Identities = 10/38 (26%), Positives = 14/38 (36%) Query: 499 PPPPQPPHFQSPGAAPQGGGGGDSNQNPPPQCSFDLTP 536 PP + P AP+G PP + D+ P Sbjct: 34 PPASLAANLAGPPCAPEGPMAAQQASPPPEERIEDVDP 71 Searching.done Results from round 3 Score E Sequences producing significant alignments: (bits) Value Sequences used in model and found again: trembl|Q9EQJ3|Q9EQJ3 Nuclear matrix transcription factor. 911 0.0 swiss|P13779|REP2_KLULA Trans-acting factor C (REP2). 106 1e-25 Sequences not found previously or not previously below threshold: trembl|Q60952|Q60952 Intranuclear protein. 27 0.046 trembl|Q9CVG5|Q9CVG5 Ser/Arg-related nuclear matrix protein (Fr... 20 7.2 swiss|P20397|NUCL_XENLA Nucleolin (Protein C23). 20 9.6 CONVERGED! >trembl|Q9EQJ3|Q9EQJ3 Nuclear matrix transcription factor. Length = 563 Score = 911 bits (2354), Expect = 0.0 Identities = 563/563 (100%), Positives = 563/563 (100%) Query: 1 MEESHFNSNPYFWPSIPTVSGQIENTMFINKMKDQLLPEKGCGLAPPHYPTLLTVPASVS 60 MEESHFNSNPYFWPSIPTVSGQIENTMFINKMKDQLLPEKGCGLAPPHYPTLLTVPASVS Sbjct: 1 MEESHFNSNPYFWPSIPTVSGQIENTMFINKMKDQLLPEKGCGLAPPHYPTLLTVPASVS 60 Query: 61 LSSGISMDTESKSEQLTPHSQASVTQNITVVPVPSTGLMTAGPGLVITSPSGSLVTTASS 120 LSSGISMDTESKSEQLTPHSQASVTQNITVVPVPSTGLMTAGPGLVITSPSGSLVTTASS Sbjct: 61 LSSGISMDTESKSEQLTPHSQASVTQNITVVPVPSTGLMTAGPGLVITSPSGSLVTTASS 120 Query: 121 AQTFPISTPMIVSALPPGSQALQVVPDLSKKVASTLTEEGGGGGGGGGTVAPPKPPRGRK 180 AQTFPISTPMIVSALPPGSQALQVVPDLSKKVASTLTEEGGGGGGGGGTVAPPKPPRGRK Sbjct: 121 AQTFPISTPMIVSALPPGSQALQVVPDLSKKVASTLTEEGGGGGGGGGTVAPPKPPRGRK 180 Query: 181 KKRMLESGLPEMNDPYVLAPGDDDDHQKDGKTYRCRMCSLTFYSKSEMQIHSKSHTETKP 240 KKRMLESGLPEMNDPYVLAPGDDDDHQKDGKTYRCRMCSLTFYSKSEMQIHSKSHTETKP Sbjct: 181 KKRMLESGLPEMNDPYVLAPGDDDDHQKDGKTYRCRMCSLTFYSKSEMQIHSKSHTETKP 240 Query: 241 HKCPHCSKTFANSSYLAQHIRIHSGAKPYSCNFCEKSFRQLSHLQQHTRIHSKMHTETIK 300 HKCPHCSKTFANSSYLAQHIRIHSGAKPYSCNFCEKSFRQLSHLQQHTRIHSKMHTETIK Sbjct: 241 HKCPHCSKTFANSSYLAQHIRIHSGAKPYSCNFCEKSFRQLSHLQQHTRIHSKMHTETIK 300 Query: 301 PHKCPHCSKTFANTSYLAQHLRIHSGAKPYNCSYCQKAFRQLSHLQQHTRIHTGDRPYKC 360 PHKCPHCSKTFANTSYLAQHLRIHSGAKPYNCSYCQKAFRQLSHLQQHTRIHTGDRPYKC Sbjct: 301 PHKCPHCSKTFANTSYLAQHLRIHSGAKPYNCSYCQKAFRQLSHLQQHTRIHTGDRPYKC 360 Query: 361 AHPGCEKAFTQLSNLQSHRRQHNKDKPFKCHNCHRAYTDAASLEAHLSTHTVKHAKVYTC 420 AHPGCEKAFTQLSNLQSHRRQHNKDKPFKCHNCHRAYTDAASLEAHLSTHTVKHAKVYTC Sbjct: 361 AHPGCEKAFTQLSNLQSHRRQHNKDKPFKCHNCHRAYTDAASLEAHLSTHTVKHAKVYTC 420 Query: 421 TICSRAYTSETYLMKHMRKHNPPDLQQQVQAAAAAAAVAQAQAQAQAQAQAQAQAQAQAQ 480 TICSRAYTSETYLMKHMRKHNPPDLQQQVQAAAAAAAVAQAQAQAQAQAQAQAQAQAQAQ Sbjct: 421 TICSRAYTSETYLMKHMRKHNPPDLQQQVQAAAAAAAVAQAQAQAQAQAQAQAQAQAQAQ 480 Query: 481 AQAQAQASQASQQQQQQQPPPPQPPHFQSPGAAPQGGGGGDSNQNPPPQCSFDLTPYKPA 540 AQAQAQASQASQQQQQQQPPPPQPPHFQSPGAAPQGGGGGDSNQNPPPQCSFDLTPYKPA Sbjct: 481 AQAQAQASQASQQQQQQQPPPPQPPHFQSPGAAPQGGGGGDSNQNPPPQCSFDLTPYKPA 540 Query: 541 EHHKDICLTVTTSTIQVEHLASS 563 EHHKDICLTVTTSTIQVEHLASS Sbjct: 541 EHHKDICLTVTTSTIQVEHLASS 563 >swiss|P13779|REP2_KLULA Trans-acting factor C (REP2). Length = 212 Score = 106 bits (263), Expect = 1e-25 Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 6/65 (9%) Query: 493 QQQQQQPPPPQPPHFQSPGAAPQGGGGGDSNQNPPPQCSFDLTPYKPAEHHKDICLTVTT 552 ++++ P PP PP+ S + G++ P P+ FDLT P + HK C +VT Sbjct: 72 EERENSPSPPIPPYQISEMPLHELLESGNAKLVPNPE--FDLT--DPDDFHK--CFSVTY 125 Query: 553 STIQV 557 S + + Sbjct: 126 SALSL 130 >trembl|Q60952|Q60952 Intranuclear protein. Length = 446 Score = 27.4 bits (59), Expect = 0.046 Identities = 17/53 (32%), Positives = 27/53 (50%) Query: 445 LQQQVQAAAAAAAVAQAQAQAQAQAQAQAQAQAQAQAQAQAQASQASQQQQQQ 497 L +Q Q AA A Q + + A +QA+A +A ++AQA + Q +Q Sbjct: 18 LTEQEQELAALRAENQYSRRQEEAAVSQAEALQEALSKAQAALQEKEQSLLEQ 70 Score = 24.0 bits (50), Expect = 0.49 Identities = 14/50 (28%), Positives = 23/50 (46%) Query: 445 LQQQVQAAAAAAAVAQAQAQAQAQAQAQAQAQAQAQAQAQAQASQASQQQ 494 L+ A A QA+A+ +A + + QAQA + +Q QQ+ Sbjct: 77 LEASTAALQATLDTCQARARQLEEALRIREGEIQAQALQHHEVTQHLQQE 126 Score = 23.2 bits (48), Expect = 0.82 Identities = 13/47 (27%), Positives = 26/47 (54%) Query: 445 LQQQVQAAAAAAAVAQAQAQAQAQAQAQAQAQAQAQAQAQAQASQAS 491 L+ + Q + A +QA+A +A ++AQA Q + Q+ + ++ S Sbjct: 28 LRAENQYSRRQEEAAVSQAEALQEALSKAQAALQEKEQSLLEQAELS 74 Score = 21.6 bits (44), Expect = 2.2 Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 2/49 (4%) Query: 448 QVQAAAAAAAVAQAQAQAQAQAQAQ--AQAQAQAQAQAQAQASQASQQQ 494 + AA A + QA+A+ +A + + QAQA + +Q QQ+ Sbjct: 78 EASTAALQATLDTCQARARQLEEALRIREGEIQAQALQHHEVTQHLQQE 126 >trembl|Q9CVG5|Q9CVG5 Ser/Arg-related nuclear matrix protein (Fragment). Length = 265 Score = 20.1 bits (40), Expect = 7.2 Identities = 4/40 (10%), Positives = 18/40 (45%) Query: 482 QAQAQASQASQQQQQQQPPPPQPPHFQSPGAAPQGGGGGD 521 + ++++ + +++++ P P+P + + D Sbjct: 204 RTKSRSPSPAPEKKEKSPELPEPSVRMKDSSVQEATSTSD 243 >swiss|P20397|NUCL_XENLA Nucleolin (Protein C23). Length = 650 Score = 19.7 bits (39), Expect = 9.6 Identities = 9/30 (30%), Positives = 15/30 (50%) Query: 172 PPKPPRGRKKKRMLESGLPEMNDPYVLAPG 201 P K P G+K++ E ++P +AP Sbjct: 143 PAKKPAGKKQESEEEDDEESEDEPMEVAPA 172 Database: /home/mika/Theses/Databases/unique_set/NMP_Database_unique .fasta Posted date: Mar 7, 2003 12:04 PM Number of letters in database: 17,163 Number of sequences in database: 43 Lambda K H 0.311 0.126 0.380 Lambda K H 0.267 0.0387 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 67,026 Number of Sequences: 43 Number of extensions: 3579 Number of successful extensions: 511 Number of sequences better than 10.0: 28 Number of HSP's better than 10.0 without gapping: 28 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 110 length of query: 563 length of database: 17,163 effective HSP length: 60 effective length of query: 503 effective length of database: 14,583 effective search space: 7335249 effective search space used: 7335249 T: 11 A: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 39 (20.5 bits) S2: 39 (19.7 bits) BLASTP 2.2.2 [Dec-14-2001] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= trembl|Q9UMS4|Q9UMS4 Nuclear matrix protein NMP200. (504 letters) Database: /home/mika/Theses/Databases/unique_set/NMP_Database_unique.f asta 43 sequences; 17,163 total letters Searching.done Results from round 1 Score E Sequences producing significant alignments: (bits) Value trembl|Q9UMS4|Q9UMS4 Nuclear matrix protein NMP200. 1014 0.0 swiss|P13777|REP1_ZYGBI Trans-acting factor B (REP1). 30 0.006 swiss|Q9M7J4|MFP1_TOBAC MAR binding filament-like protein 1-1. 25 0.25 trembl|Q9FLH0|Q9FLH0 Nuclear matrix constituent protein 1 (NMCP... 20 8.9 swiss|P14733|LAM1_MOUSE Lamin B1. 19 9.8 >trembl|Q9UMS4|Q9UMS4 Nuclear matrix protein NMP200. Length = 504 Score = 1014 bits (2623), Expect = 0.0 Identities = 504/504 (100%), Positives = 504/504 (100%) Query: 1 MSLICSISNEVPEHPCVSPVSNHVYERRLIEKYIAENGTDPINNQPLSEEQLIDIKVAHP 60 MSLICSISNEVPEHPCVSPVSNHVYERRLIEKYIAENGTDPINNQPLSEEQLIDIKVAHP Sbjct: 1 MSLICSISNEVPEHPCVSPVSNHVYERRLIEKYIAENGTDPINNQPLSEEQLIDIKVAHP 60 Query: 61 IRPKPPSATSIPAILKALQDEWDAVMLHSFTLRQQLQTTRQELSHALYQHDAACRVIARL 120 IRPKPPSATSIPAILKALQDEWDAVMLHSFTLRQQLQTTRQELSHALYQHDAACRVIARL Sbjct: 61 IRPKPPSATSIPAILKALQDEWDAVMLHSFTLRQQLQTTRQELSHALYQHDAACRVIARL 120 Query: 121 TKEVTAAREALATLKPQAGLIVPQAVPSSQPSVVGAGEPMDLGELVGMTPEIIQKLQDKA 180 TKEVTAAREALATLKPQAGLIVPQAVPSSQPSVVGAGEPMDLGELVGMTPEIIQKLQDKA Sbjct: 121 TKEVTAAREALATLKPQAGLIVPQAVPSSQPSVVGAGEPMDLGELVGMTPEIIQKLQDKA 180 Query: 181 TVLTTERKKRGKTVPEELVKPEELSKYRQVASHVGLHSASIPGILALDLCPSDTNKILTG 240 TVLTTERKKRGKTVPEELVKPEELSKYRQVASHVGLHSASIPGILALDLCPSDTNKILTG Sbjct: 181 TVLTTERKKRGKTVPEELVKPEELSKYRQVASHVGLHSASIPGILALDLCPSDTNKILTG 240 Query: 241 GADKNVVVFDKSSEQILATLKGHTKKVTSVVFHPSQDLVFSASPDATIRIWSVPNASCVQ 300 GADKNVVVFDKSSEQILATLKGHTKKVTSVVFHPSQDLVFSASPDATIRIWSVPNASCVQ Sbjct: 241 GADKNVVVFDKSSEQILATLKGHTKKVTSVVFHPSQDLVFSASPDATIRIWSVPNASCVQ 300 Query: 301 VVRAHESAVTGLSLHATGDYLLSSSDDQYWAFSDIQTGRVLTKVTDETSGCSLTCAQFHP 360 VVRAHESAVTGLSLHATGDYLLSSSDDQYWAFSDIQTGRVLTKVTDETSGCSLTCAQFHP Sbjct: 301 VVRAHESAVTGLSLHATGDYLLSSSDDQYWAFSDIQTGRVLTKVTDETSGCSLTCAQFHP 360 Query: 361 DGLIFGTGTMDSQIKIWDLKERTNVANFPGHSGPITSIAFSENGYYLATAADDSSVKLWD 420 DGLIFGTGTMDSQIKIWDLKERTNVANFPGHSGPITSIAFSENGYYLATAADDSSVKLWD Sbjct: 361 DGLIFGTGTMDSQIKIWDLKERTNVANFPGHSGPITSIAFSENGYYLATAADDSSVKLWD 420 Query: 421 LRKLKNFKTLQLDNNFEVKSLIFDQSGTYLALGGTDVQIYICKQWTEILHFTEHSGLTTG 480 LRKLKNFKTLQLDNNFEVKSLIFDQSGTYLALGGTDVQIYICKQWTEILHFTEHSGLTTG Sbjct: 421 LRKLKNFKTLQLDNNFEVKSLIFDQSGTYLALGGTDVQIYICKQWTEILHFTEHSGLTTG 480 Query: 481 VAFGHHAKFIASTGMDRSLKFYSL 504 VAFGHHAKFIASTGMDRSLKFYSL Sbjct: 481 VAFGHHAKFIASTGMDRSLKFYSL 504 >swiss|P13777|REP1_ZYGBI Trans-acting factor B (REP1). Length = 322 Score = 30.0 bits (66), Expect = 0.006 Identities = 26/106 (24%), Positives = 45/106 (41%), Gaps = 4/106 (3%) Query: 125 TAAREALATLKPQAGLIVPQAVPSSQPSVVGAGEPMDLGELVGMTPEIIQKLQDKATVLT 184 ++A +AL+T +P Q +P+ PS A E + + E ++ + T Sbjct: 122 SSAPDALSTQQPPLEHSTQQNIPTKLPSTQQAVERVVSSQTTSRAAETRERSPEHTEAST 181 Query: 185 TERKKRGKTVPEELVKPEELSKYRQVASHVGLHSASIPGILALDLC 230 E +T E L K E + YR + S + ++P I L +C Sbjct: 182 QE----AETAEEALNKEEFWNLYRSLESKSYISRENVPDIRLLVMC 223 >swiss|Q9M7J4|MFP1_TOBAC MAR binding filament-like protein 1-1. Length = 722 Score = 24.6 bits (52), Expect = 0.25 Identities = 11/20 (55%), Positives = 16/20 (80%) Query: 171 EIIQKLQDKATVLTTERKKR 190 ++IQ LQ+K T+LTTE K + Sbjct: 250 DLIQVLQEKITLLTTEIKDK 269 >trembl|Q9FLH0|Q9FLH0 Nuclear matrix constituent protein 1 (NMCP1)-like. Length = 1042 Score = 19.6 bits (39), Expect = 8.9 Identities = 9/24 (37%), Positives = 12/24 (49%) Query: 183 LTTERKKRGKTVPEELVKPEELSK 206 L RK+RG T +E +P K Sbjct: 901 LEAGRKRRGNTSGDETSEPSNNKK 924 >swiss|P14733|LAM1_MOUSE Lamin B1. Length = 587 Score = 19.2 bits (38), Expect = 9.8 Identities = 8/19 (42%), Positives = 12/19 (63%) Query: 40 DPINNQPLSEEQLIDIKVA 58 D + Q EQL+D+K+A Sbjct: 351 DQMQQQLSDYEQLLDVKLA 369 Searching.done Results from round 2 Score E Sequences producing significant alignments: (bits) Value Sequences used in model and found again: trembl|Q9UMS4|Q9UMS4 Nuclear matrix protein NMP200. 1069 0.0 Sequences not found previously or not previously below threshold: swiss|P13777|REP1_ZYGBI Trans-acting factor B (REP1). 32 0.001 swiss|Q9M7J4|MFP1_TOBAC MAR binding filament-like protein 1-1. 26 0.12 trembl|Q9FLH0|Q9FLH0 Nuclear matrix constituent protein 1 (NMCP... 20 5.6 swiss|P14733|LAM1_MOUSE Lamin B1. 20 6.2 >trembl|Q9UMS4|Q9UMS4 Nuclear matrix protein NMP200. Length = 504 Score = 1069 bits (2764), Expect = 0.0 Identities = 504/504 (100%), Positives = 504/504 (100%) Query: 1 MSLICSISNEVPEHPCVSPVSNHVYERRLIEKYIAENGTDPINNQPLSEEQLIDIKVAHP 60 MSLICSISNEVPEHPCVSPVSNHVYERRLIEKYIAENGTDPINNQPLSEEQLIDIKVAHP Sbjct: 1 MSLICSISNEVPEHPCVSPVSNHVYERRLIEKYIAENGTDPINNQPLSEEQLIDIKVAHP 60 Query: 61 IRPKPPSATSIPAILKALQDEWDAVMLHSFTLRQQLQTTRQELSHALYQHDAACRVIARL 120 IRPKPPSATSIPAILKALQDEWDAVMLHSFTLRQQLQTTRQELSHALYQHDAACRVIARL Sbjct: 61 IRPKPPSATSIPAILKALQDEWDAVMLHSFTLRQQLQTTRQELSHALYQHDAACRVIARL 120 Query: 121 TKEVTAAREALATLKPQAGLIVPQAVPSSQPSVVGAGEPMDLGELVGMTPEIIQKLQDKA 180 TKEVTAAREALATLKPQAGLIVPQAVPSSQPSVVGAGEPMDLGELVGMTPEIIQKLQDKA Sbjct: 121 TKEVTAAREALATLKPQAGLIVPQAVPSSQPSVVGAGEPMDLGELVGMTPEIIQKLQDKA 180 Query: 181 TVLTTERKKRGKTVPEELVKPEELSKYRQVASHVGLHSASIPGILALDLCPSDTNKILTG 240 TVLTTERKKRGKTVPEELVKPEELSKYRQVASHVGLHSASIPGILALDLCPSDTNKILTG Sbjct: 181 TVLTTERKKRGKTVPEELVKPEELSKYRQVASHVGLHSASIPGILALDLCPSDTNKILTG 240 Query: 241 GADKNVVVFDKSSEQILATLKGHTKKVTSVVFHPSQDLVFSASPDATIRIWSVPNASCVQ 300 GADKNVVVFDKSSEQILATLKGHTKKVTSVVFHPSQDLVFSASPDATIRIWSVPNASCVQ Sbjct: 241 GADKNVVVFDKSSEQILATLKGHTKKVTSVVFHPSQDLVFSASPDATIRIWSVPNASCVQ 300 Query: 301 VVRAHESAVTGLSLHATGDYLLSSSDDQYWAFSDIQTGRVLTKVTDETSGCSLTCAQFHP 360 VVRAHESAVTGLSLHATGDYLLSSSDDQYWAFSDIQTGRVLTKVTDETSGCSLTCAQFHP Sbjct: 301 VVRAHESAVTGLSLHATGDYLLSSSDDQYWAFSDIQTGRVLTKVTDETSGCSLTCAQFHP 360 Query: 361 DGLIFGTGTMDSQIKIWDLKERTNVANFPGHSGPITSIAFSENGYYLATAADDSSVKLWD 420 DGLIFGTGTMDSQIKIWDLKERTNVANFPGHSGPITSIAFSENGYYLATAADDSSVKLWD Sbjct: 361 DGLIFGTGTMDSQIKIWDLKERTNVANFPGHSGPITSIAFSENGYYLATAADDSSVKLWD 420 Query: 421 LRKLKNFKTLQLDNNFEVKSLIFDQSGTYLALGGTDVQIYICKQWTEILHFTEHSGLTTG 480 LRKLKNFKTLQLDNNFEVKSLIFDQSGTYLALGGTDVQIYICKQWTEILHFTEHSGLTTG Sbjct: 421 LRKLKNFKTLQLDNNFEVKSLIFDQSGTYLALGGTDVQIYICKQWTEILHFTEHSGLTTG 480 Query: 481 VAFGHHAKFIASTGMDRSLKFYSL 504 VAFGHHAKFIASTGMDRSLKFYSL Sbjct: 481 VAFGHHAKFIASTGMDRSLKFYSL 504 >swiss|P13777|REP1_ZYGBI Trans-acting factor B (REP1). Length = 322 Score = 32.4 bits (72), Expect = 0.001 Identities = 26/106 (24%), Positives = 45/106 (41%), Gaps = 4/106 (3%) Query: 125 TAAREALATLKPQAGLIVPQAVPSSQPSVVGAGEPMDLGELVGMTPEIIQKLQDKATVLT 184 ++A +AL+T +P Q +P+ PS A E + + E ++ + T Sbjct: 122 SSAPDALSTQQPPLEHSTQQNIPTKLPSTQQAVERVVSSQTTSRAAETRERSPEHTEAST 181 Query: 185 TERKKRGKTVPEELVKPEELSKYRQVASHVGLHSASIPGILALDLC 230 E +T E L K E + YR + S + ++P I L +C Sbjct: 182 QE----AETAEEALNKEEFWNLYRSLESKSYISRENVPDIRLLVMC 223 >swiss|Q9M7J4|MFP1_TOBAC MAR binding filament-like protein 1-1. Length = 722 Score = 25.8 bits (55), Expect = 0.12 Identities = 11/20 (55%), Positives = 16/20 (80%) Query: 171 EIIQKLQDKATVLTTERKKR 190 ++IQ LQ+K T+LTTE K + Sbjct: 250 DLIQVLQEKITLLTTEIKDK 269 >trembl|Q9FLH0|Q9FLH0 Nuclear matrix constituent protein 1 (NMCP1)-like. Length = 1042 Score = 20.0 bits (40), Expect = 5.6 Identities = 9/24 (37%), Positives = 12/24 (49%) Query: 183 LTTERKKRGKTVPEELVKPEELSK 206 L RK+RG T +E +P K Sbjct: 901 LEAGRKRRGNTSGDETSEPSNNKK 924 >swiss|P14733|LAM1_MOUSE Lamin B1. Length = 587 Score = 20.0 bits (40), Expect = 6.2 Identities = 8/19 (42%), Positives = 12/19 (63%) Query: 40 DPINNQPLSEEQLIDIKVA 58 D + Q EQL+D+K+A Sbjct: 351 DQMQQQLSDYEQLLDVKLA 369 Searching.done Results from round 3 Score E Sequences producing significant alignments: (bits) Value Sequences used in model and found again: trembl|Q9UMS4|Q9UMS4 Nuclear matrix protein NMP200. 1035 0.0 swiss|P13777|REP1_ZYGBI Trans-acting factor B (REP1). 174 1e-46 Sequences not found previously or not previously below threshold: trembl|O55035|O55035 PEPTIDYLPROLYL ISOMERASE MATRIN CYP (EC 5.... 23 0.68 swiss|P13781|REP2_ZYGBI Trans-acting factor C (REP2). 23 0.77 swiss|Q9M7J4|MFP1_TOBAC MAR binding filament-like protein 1-1. 22 1.4 swiss|P14733|LAM1_MOUSE Lamin B1. 20 6.2 CONVERGED! >trembl|Q9UMS4|Q9UMS4 Nuclear matrix protein NMP200. Length = 504 Score = 1035 bits (2676), Expect = 0.0 Identities = 504/504 (100%), Positives = 504/504 (100%) Query: 1 MSLICSISNEVPEHPCVSPVSNHVYERRLIEKYIAENGTDPINNQPLSEEQLIDIKVAHP 60 MSLICSISNEVPEHPCVSPVSNHVYERRLIEKYIAENGTDPINNQPLSEEQLIDIKVAHP Sbjct: 1 MSLICSISNEVPEHPCVSPVSNHVYERRLIEKYIAENGTDPINNQPLSEEQLIDIKVAHP 60 Query: 61 IRPKPPSATSIPAILKALQDEWDAVMLHSFTLRQQLQTTRQELSHALYQHDAACRVIARL 120 IRPKPPSATSIPAILKALQDEWDAVMLHSFTLRQQLQTTRQELSHALYQHDAACRVIARL Sbjct: 61 IRPKPPSATSIPAILKALQDEWDAVMLHSFTLRQQLQTTRQELSHALYQHDAACRVIARL 120 Query: 121 TKEVTAAREALATLKPQAGLIVPQAVPSSQPSVVGAGEPMDLGELVGMTPEIIQKLQDKA 180 TKEVTAAREALATLKPQAGLIVPQAVPSSQPSVVGAGEPMDLGELVGMTPEIIQKLQDKA Sbjct: 121 TKEVTAAREALATLKPQAGLIVPQAVPSSQPSVVGAGEPMDLGELVGMTPEIIQKLQDKA 180 Query: 181 TVLTTERKKRGKTVPEELVKPEELSKYRQVASHVGLHSASIPGILALDLCPSDTNKILTG 240 TVLTTERKKRGKTVPEELVKPEELSKYRQVASHVGLHSASIPGILALDLCPSDTNKILTG Sbjct: 181 TVLTTERKKRGKTVPEELVKPEELSKYRQVASHVGLHSASIPGILALDLCPSDTNKILTG 240 Query: 241 GADKNVVVFDKSSEQILATLKGHTKKVTSVVFHPSQDLVFSASPDATIRIWSVPNASCVQ 300 GADKNVVVFDKSSEQILATLKGHTKKVTSVVFHPSQDLVFSASPDATIRIWSVPNASCVQ Sbjct: 241 GADKNVVVFDKSSEQILATLKGHTKKVTSVVFHPSQDLVFSASPDATIRIWSVPNASCVQ 300 Query: 301 VVRAHESAVTGLSLHATGDYLLSSSDDQYWAFSDIQTGRVLTKVTDETSGCSLTCAQFHP 360 VVRAHESAVTGLSLHATGDYLLSSSDDQYWAFSDIQTGRVLTKVTDETSGCSLTCAQFHP Sbjct: 301 VVRAHESAVTGLSLHATGDYLLSSSDDQYWAFSDIQTGRVLTKVTDETSGCSLTCAQFHP 360 Query: 361 DGLIFGTGTMDSQIKIWDLKERTNVANFPGHSGPITSIAFSENGYYLATAADDSSVKLWD 420 DGLIFGTGTMDSQIKIWDLKERTNVANFPGHSGPITSIAFSENGYYLATAADDSSVKLWD Sbjct: 361 DGLIFGTGTMDSQIKIWDLKERTNVANFPGHSGPITSIAFSENGYYLATAADDSSVKLWD 420 Query: 421 LRKLKNFKTLQLDNNFEVKSLIFDQSGTYLALGGTDVQIYICKQWTEILHFTEHSGLTTG 480 LRKLKNFKTLQLDNNFEVKSLIFDQSGTYLALGGTDVQIYICKQWTEILHFTEHSGLTTG Sbjct: 421 LRKLKNFKTLQLDNNFEVKSLIFDQSGTYLALGGTDVQIYICKQWTEILHFTEHSGLTTG 480 Query: 481 VAFGHHAKFIASTGMDRSLKFYSL 504 VAFGHHAKFIASTGMDRSLKFYSL Sbjct: 481 VAFGHHAKFIASTGMDRSLKFYSL 504 >swiss|P13777|REP1_ZYGBI Trans-acting factor B (REP1). Length = 322 Score = 174 bits (442), Expect = 1e-46 Identities = 26/106 (24%), Positives = 45/106 (41%), Gaps = 4/106 (3%) Query: 125 TAAREALATLKPQAGLIVPQAVPSSQPSVVGAGEPMDLGELVGMTPEIIQKLQDKATVLT 184 ++A +AL+T +P Q +P+ PS A E + + E ++ + T Sbjct: 122 SSAPDALSTQQPPLEHSTQQNIPTKLPSTQQAVERVVSSQTTSRAAETRERSPEHTEAST 181 Query: 185 TERKKRGKTVPEELVKPEELSKYRQVASHVGLHSASIPGILALDLC 230 E +T E L K E + YR + S + ++P I L +C Sbjct: 182 QE----AETAEEALNKEEFWNLYRSLESKSYISRENVPDIRLLVMC 223 >trembl|O55035|O55035 PEPTIDYLPROLYL ISOMERASE MATRIN CYP (EC 5.2.1.8) (PEPTIDYLPR Length = 752 Score = 23.1 bits (48), Expect = 0.68 Identities = 14/48 (29%), Positives = 20/48 (41%), Gaps = 2/48 (4%) Query: 173 IQKLQDKATVLTTERKKRGKTVPEELVKPEELSKYRQVASHVGLHSAS 220 K +D T E++ K +E + +E SK QV S H S Sbjct: 487 RSKERDHETTKEKEKQLDSKGKDQERSRSKENSK--QVESKSNEHDHS 532 >swiss|P13781|REP2_ZYGBI Trans-acting factor C (REP2). Length = 178 Score = 23.1 bits (48), Expect = 0.77 Identities = 8/30 (26%), Positives = 16/30 (52%) Query: 187 RKKRGKTVPEELVKPEELSKYRQVASHVGL 216 R K+ KT+P+ L+ + + + +H L Sbjct: 5 RTKKLKTIPDTLLIGSIFTIFENLEAHAYL 34 >swiss|Q9M7J4|MFP1_TOBAC MAR binding filament-like protein 1-1. Length = 722 Score = 22.0 bits (45), Expect = 1.4 Identities = 12/30 (40%), Positives = 19/30 (63%) Query: 171 EIIQKLQDKATVLTTERKKRGKTVPEELVK 200 ++IQ LQ+K T+LTTE K + ++ K Sbjct: 250 DLIQVLQEKITLLTTEIKDKEASLQSTTSK 279 Score = 21.6 bits (44), Expect = 2.2 Identities = 19/95 (20%), Positives = 40/95 (42%), Gaps = 2/95 (2%) Query: 93 RQQLQTTRQELSHALYQHDAACRVIARLTKEVTAAREALATLKPQAGLIVPQAVPSSQPS 152 ++ + +EL A D R L KE+ A +++L+ + ++ ++V + Sbjct: 572 KESRKNLEEELERATESLDEMNRNAFALAKELELANSHISSLEDERE-VLQKSVSEQKQI 630 Query: 153 VVGAGEPM-DLGELVGMTPEIIQKLQDKATVLTTE 186 + E + D LV + + L+ +A L E Sbjct: 631 SQESRENLEDAHSLVMKLGKERESLEKRAKKLEDE 665 >swiss|P14733|LAM1_MOUSE Lamin B1. Length = 587 Score = 20.1 bits (40), Expect = 6.2 Identities = 8/19 (42%), Positives = 12/19 (63%) Query: 40 DPINNQPLSEEQLIDIKVA 58 D + Q EQL+D+K+A Sbjct: 351 DQMQQQLSDYEQLLDVKLA 369 Database: /home/mika/Theses/Databases/unique_set/NMP_Database_unique .fasta Posted date: Mar 7, 2003 12:04 PM Number of letters in database: 17,163 Number of sequences in database: 43 Lambda K H 0.311 0.131 0.375 Lambda K H 0.267 0.0400 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 51,812 Number of Sequences: 43 Number of extensions: 2095 Number of successful extensions: 48 Number of sequences better than 10.0: 17 Number of HSP's better than 10.0 without gapping: 17 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 21 length of query: 504 length of database: 17,163 effective HSP length: 59 effective length of query: 445 effective length of database: 14,626 effective search space: 6508570 effective search space used: 6508570 T: 11 A: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 39 (20.5 bits) S2: 39 (19.7 bits) BLASTP 2.2.2 [Dec-14-2001] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= trembl|Q9PSQ1|Q9PSQ1 M57K=57 kDa NUCLEAR MATRIX PROTEIN (FRAGMENTS). (63 letters) Database: /home/mika/Theses/Databases/unique_set/NMP_Database_unique.f asta 43 sequences; 17,163 total letters Searching.done Results from round 1 Score E Sequences producing significant alignments: (bits) Value trembl|Q9PSQ1|Q9PSQ1 M57K=57 kDa NUCLEAR MATRIX PROTEIN (FRAGME... 114 2e-29 swiss|O14682|ENC1_HUMAN Ectoderm-neural cortex-1 protein (ENC-1... 20 0.34 swiss|P12978|EBN2_EBV EBNA-2 nuclear protein. 17 2.6 swiss|P13777|REP1_ZYGBI Trans-acting factor B (REP1). 17 3.4 swiss|P33418|LOS1_YEAST LOS1 protein. 16 4.7 swiss|O08579|EMD_MOUSE Emerin. 16 6.4 >trembl|Q9PSQ1|Q9PSQ1 M57K=57 kDa NUCLEAR MATRIX PROTEIN (FRAGMENTS). Length = 63 Score = 114 bits (285), Expect = 2e-29 Identities = 63/63 (100%), Positives = 63/63 (100%) Query: 1 SDVVELSDADFESGLAERPGLVLEEFFAMIAKTFLDAGHKLMDATANDVPSPYEVKGFPT 60 SDVVELSDADFESGLAERPGLVLEEFFAMIAKTFLDAGHKLMDATANDVPSPYEVKGFPT Sbjct: 1 SDVVELSDADFESGLAERPGLVLEEFFAMIAKTFLDAGHKLMDATANDVPSPYEVKGFPT 60 Query: 61 IYF 63 IYF Sbjct: 61 IYF 63 >swiss|O14682|ENC1_HUMAN Ectoderm-neural cortex-1 protein (ENC-1) (P53-indu Length = 589 Score = 20.0 bits (40), Expect = 0.34 Identities = 13/46 (28%), Positives = 19/46 (41%), Gaps = 6/46 (13%) Query: 13 SGLAERPGLVLEEFFAMIAKTFLDAGHKLMDATAN------DVPSP 52 + L RP F + +TF+ L+D A D+PSP Sbjct: 284 TSLCARPRKTGHALFLLGGQTFMCDKLYLVDQKAKEIIPKADIPSP 329 >swiss|P12978|EBN2_EBV EBNA-2 nuclear protein. Length = 487 Score = 17.3 bits (33), Expect = 2.6 Identities = 6/13 (46%), Positives = 9/13 (69%) Query: 7 SDADFESGLAERP 19 SD D+ G ++RP Sbjct: 470 SDEDYVEGPSKRP 482 >swiss|P13777|REP1_ZYGBI Trans-acting factor B (REP1). Length = 322 Score = 16.5 bits (31), Expect = 3.4 Identities = 6/24 (25%), Positives = 14/24 (58%) Query: 40 KLMDATANDVPSPYEVKGFPTIYF 63 ++ + + N+ S E +G P ++F Sbjct: 48 RVSEGSENESGSGEEYEGAPHVHF 71 >swiss|P33418|LOS1_YEAST LOS1 protein. Length = 1100 Score = 16.2 bits (30), Expect = 4.7 Identities = 6/10 (60%), Positives = 8/10 (80%) Query: 25 EFFAMIAKTF 34 EF ++ AKTF Sbjct: 380 EFDSITAKTF 389 >swiss|O08579|EMD_MOUSE Emerin. Length = 259 Score = 15.8 bits (29), Expect = 6.4 Identities = 6/15 (40%), Positives = 10/15 (66%) Query: 30 IAKTFLDAGHKLMDA 44 ++K+F G L+DA Sbjct: 114 MSKSFRQPGTSLVDA 128 Searching.done Results from round 2 Score E Sequences producing significant alignments: (bits) Value Sequences used in model and found again: trembl|Q9PSQ1|Q9PSQ1 M57K=57 kDa NUCLEAR MATRIX PROTEIN (FRAGME... 123 2e-32 Sequences not found previously or not previously below threshold: swiss|O14682|ENC1_HUMAN Ectoderm-neural cortex-1 protein (ENC-1... 20 0.35 swiss|P12978|EBN2_EBV EBNA-2 nuclear protein. 18 1.3 swiss|P13777|REP1_ZYGBI Trans-acting factor B (REP1). 17 2.2 swiss|O08579|EMD_MOUSE Emerin. 17 3.7 swiss|P33418|LOS1_YEAST LOS1 protein. 16 4.7 CONVERGED! >trembl|Q9PSQ1|Q9PSQ1 M57K=57 kDa NUCLEAR MATRIX PROTEIN (FRAGMENTS). Length = 63 Score = 123 bits (309), Expect = 2e-32 Identities = 63/63 (100%), Positives = 63/63 (100%) Query: 1 SDVVELSDADFESGLAERPGLVLEEFFAMIAKTFLDAGHKLMDATANDVPSPYEVKGFPT 60 SDVVELSDADFESGLAERPGLVLEEFFAMIAKTFLDAGHKLMDATANDVPSPYEVKGFPT Sbjct: 1 SDVVELSDADFESGLAERPGLVLEEFFAMIAKTFLDAGHKLMDATANDVPSPYEVKGFPT 60 Query: 61 IYF 63 IYF Sbjct: 61 IYF 63 >swiss|O14682|ENC1_HUMAN Ectoderm-neural cortex-1 protein (ENC-1) (P53-indu Length = 589 Score = 20.0 bits (40), Expect = 0.35 Identities = 13/46 (28%), Positives = 19/46 (41%), Gaps = 6/46 (13%) Query: 13 SGLAERPGLVLEEFFAMIAKTFLDAGHKLMDATAN------DVPSP 52 + L RP F + +TF+ L+D A D+PSP Sbjct: 284 TSLCARPRKTGHALFLLGGQTFMCDKLYLVDQKAKEIIPKADIPSP 329 >swiss|P12978|EBN2_EBV EBNA-2 nuclear protein. Length = 487 Score = 18.0 bits (35), Expect = 1.3 Identities = 6/13 (46%), Positives = 9/13 (69%) Query: 7 SDADFESGLAERP 19 SD D+ G ++RP Sbjct: 470 SDEDYVEGPSKRP 482 >swiss|P13777|REP1_ZYGBI Trans-acting factor B (REP1). Length = 322 Score = 17.3 bits (33), Expect = 2.2 Identities = 6/24 (25%), Positives = 14/24 (58%) Query: 40 KLMDATANDVPSPYEVKGFPTIYF 63 ++ + + N+ S E +G P ++F Sbjct: 48 RVSEGSENESGSGEEYEGAPHVHF 71 >swiss|O08579|EMD_MOUSE Emerin. Length = 259 Score = 16.5 bits (31), Expect = 3.7 Identities = 6/15 (40%), Positives = 10/15 (66%) Query: 30 IAKTFLDAGHKLMDA 44 ++K+F G L+DA Sbjct: 114 MSKSFRQPGTSLVDA 128 >swiss|P33418|LOS1_YEAST LOS1 protein. Length = 1100 Score = 16.1 bits (30), Expect = 4.7 Identities = 6/10 (60%), Positives = 8/10 (80%) Query: 25 EFFAMIAKTF 34 EF ++ AKTF Sbjct: 380 EFDSITAKTF 389 Database: /home/mika/Theses/Databases/unique_set/NMP_Database_unique .fasta Posted date: Mar 7, 2003 12:04 PM Number of letters in database: 17,163 Number of sequences in database: 43 Lambda K H 0.319 0.139 0.396 Lambda K H 0.267 0.0424 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 4071 Number of Sequences: 43 Number of extensions: 117 Number of successful extensions: 14 Number of sequences better than 10.0: 14 Number of HSP's better than 10.0 without gapping: 14 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 14 length of query: 63 length of database: 17,163 effective HSP length: 39 effective length of query: 24 effective length of database: 15,486 effective search space: 371664 effective search space used: 371664 T: 11 A: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 28 (15.7 bits) S2: 28 (15.3 bits) BLASTP 2.2.2 [Dec-14-2001] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= swiss|P04489|E411_ADE05 Probable early E4 11 kDa protein. (116 letters) Database: /home/mika/Theses/Databases/unique_set/NMP_Database_unique.f asta 43 sequences; 17,163 total letters Searching.done Results from round 1 Score E Sequences producing significant alignments: (bits) Value swiss|P04489|E411_ADE05 Probable early E4 11 kDa protein. 207 4e-57 swiss|P13782|REP2_ZYGRO Trans-acting factor C (REP2). 18 3.4 swiss|Q9M7J4|MFP1_TOBAC MAR binding filament-like protein 1-1. 18 4.2 >swiss|P04489|E411_ADE05 Probable early E4 11 kDa protein. Length = 116 Score = 207 bits (527), Expect = 4e-57 Identities = 116/116 (100%), Positives = 116/116 (100%) Query: 1 MIRCLRLKVEGALEQIFTMAGLNIRDLLRDILRRWRDENYLGMVEGAGMFIEEIHPEGFS 60 MIRCLRLKVEGALEQIFTMAGLNIRDLLRDILRRWRDENYLGMVEGAGMFIEEIHPEGFS Sbjct: 1 MIRCLRLKVEGALEQIFTMAGLNIRDLLRDILRRWRDENYLGMVEGAGMFIEEIHPEGFS 60 Query: 61 LYVHLDVRAVCLLEAIVQHLTNAIICSLAVEFDHATGGERVHLIDLHFEVLDNLLE 116 LYVHLDVRAVCLLEAIVQHLTNAIICSLAVEFDHATGGERVHLIDLHFEVLDNLLE Sbjct: 61 LYVHLDVRAVCLLEAIVQHLTNAIICSLAVEFDHATGGERVHLIDLHFEVLDNLLE 116 >swiss|P13782|REP2_ZYGRO Trans-acting factor C (REP2). Length = 233 Score = 18.1 bits (35), Expect = 3.4 Identities = 5/13 (38%), Positives = 10/13 (76%) Query: 24 IRDLLRDILRRWR 36 + +LL ++LR W+ Sbjct: 23 VANLLENLLRTWK 35 >swiss|Q9M7J4|MFP1_TOBAC MAR binding filament-like protein 1-1. Length = 722 Score = 18.1 bits (35), Expect = 4.2 Identities = 9/27 (33%), Positives = 16/27 (58%) Query: 12 ALEQIFTMAGLNIRDLLRDILRRWRDE 38 ++E+ F LN RD+ + L+R +E Sbjct: 162 SMEKKFQSELLNERDIRNNQLKRAGEE 188 Searching.done Results from round 2 Score E Sequences producing significant alignments: (bits) Value Sequences used in model and found again: swiss|P04489|E411_ADE05 Probable early E4 11 kDa protein. 218 2e-60 Sequences not found previously or not previously below threshold: trembl|Q9Y265|Q9Y265 RUVB-LIKE 1. 19 2.2 swiss|Q9M7J4|MFP1_TOBAC MAR binding filament-like protein 1-1. 18 3.4 swiss|P13782|REP2_ZYGRO Trans-acting factor C (REP2). 18 3.8 CONVERGED! >swiss|P04489|E411_ADE05 Probable early E4 11 kDa protein. Length = 116 Score = 218 bits (555), Expect = 2e-60 Identities = 116/116 (100%), Positives = 116/116 (100%) Query: 1 MIRCLRLKVEGALEQIFTMAGLNIRDLLRDILRRWRDENYLGMVEGAGMFIEEIHPEGFS 60 MIRCLRLKVEGALEQIFTMAGLNIRDLLRDILRRWRDENYLGMVEGAGMFIEEIHPEGFS Sbjct: 1 MIRCLRLKVEGALEQIFTMAGLNIRDLLRDILRRWRDENYLGMVEGAGMFIEEIHPEGFS 60 Query: 61 LYVHLDVRAVCLLEAIVQHLTNAIICSLAVEFDHATGGERVHLIDLHFEVLDNLLE 116 LYVHLDVRAVCLLEAIVQHLTNAIICSLAVEFDHATGGERVHLIDLHFEVLDNLLE Sbjct: 61 LYVHLDVRAVCLLEAIVQHLTNAIICSLAVEFDHATGGERVHLIDLHFEVLDNLLE 116 >trembl|Q9Y265|Q9Y265 RUVB-LIKE 1. Length = 456 Score = 18.7 bits (37), Expect = 2.2 Identities = 8/42 (19%), Positives = 22/42 (52%), Gaps = 1/42 (2%) Query: 24 IRDLLRDILRRWRDENYLGMVEGAGMFIEEIHPEGFSLYVHL 65 +R + ++ ++ D+ +V G +F++E+H + +L Sbjct: 275 LRGEINKVVNKYIDQGIAELVPGV-LFVDEVHMLDIECFTYL 315 >swiss|Q9M7J4|MFP1_TOBAC MAR binding filament-like protein 1-1. Length = 722 Score = 18.3 bits (36), Expect = 3.4 Identities = 9/27 (33%), Positives = 16/27 (58%) Query: 12 ALEQIFTMAGLNIRDLLRDILRRWRDE 38 ++E+ F LN RD+ + L+R +E Sbjct: 162 SMEKKFQSELLNERDIRNNQLKRAGEE 188 >swiss|P13782|REP2_ZYGRO Trans-acting factor C (REP2). Length = 233 Score = 18.0 bits (35), Expect = 3.8 Identities = 5/13 (38%), Positives = 10/13 (76%) Query: 24 IRDLLRDILRRWR 36 + +LL ++LR W+ Sbjct: 23 VANLLENLLRTWK 35 Database: /home/mika/Theses/Databases/unique_set/NMP_Database_unique .fasta Posted date: Mar 7, 2003 12:04 PM Number of letters in database: 17,163 Number of sequences in database: 43 Lambda K H 0.329 0.146 0.438 Lambda K H 0.267 0.0448 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 8382 Number of Sequences: 43 Number of extensions: 313 Number of successful extensions: 7 Number of sequences better than 10.0: 7 Number of HSP's better than 10.0 without gapping: 7 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 7 length of query: 116 length of database: 17,163 effective HSP length: 46 effective length of query: 70 effective length of database: 15,185 effective search space: 1062950 effective search space used: 1062950 T: 11 A: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 32 (18.0 bits) S2: 32 (16.8 bits) BLASTP 2.2.2 [Dec-14-2001] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= swiss|O14682|ENC1_HUMAN Ectoderm-neural cortex-1 protein (ENC-1) (P53-indu (589 letters) Database: /home/mika/Theses/Databases/unique_set/NMP_Database_unique.f asta 43 sequences; 17,163 total letters Searching.done Results from round 1 Score E Sequences producing significant alignments: (bits) Value swiss|O14682|ENC1_HUMAN Ectoderm-neural cortex-1 protein (ENC-1... 1231 0.0 swiss|P13781|REP2_ZYGBI Trans-acting factor C (REP2). 23 0.60 swiss|P33418|LOS1_YEAST LOS1 protein. 21 3.2 swiss|P20397|NUCL_XENLA Nucleolin (Protein C23). 21 4.7 >swiss|O14682|ENC1_HUMAN Ectoderm-neural cortex-1 protein (ENC-1) (P53-indu Length = 589 Score = 1231 bits (3185), Expect = 0.0 Identities = 589/589 (100%), Positives = 589/589 (100%) Query: 1 MSVSVHENRKSRASSGSINIYLFHKSSYADSVLTHLNLLRQQRLFTDVLLHAGNRTFPCH 60 MSVSVHENRKSRASSGSINIYLFHKSSYADSVLTHLNLLRQQRLFTDVLLHAGNRTFPCH Sbjct: 1 MSVSVHENRKSRASSGSINIYLFHKSSYADSVLTHLNLLRQQRLFTDVLLHAGNRTFPCH 60 Query: 61 RAVLAACSRYFEAMFSGGLKESQDSEVNFDNSIHPEVLELLLDYAYSSRVIINEENAESL 120 RAVLAACSRYFEAMFSGGLKESQDSEVNFDNSIHPEVLELLLDYAYSSRVIINEENAESL Sbjct: 61 RAVLAACSRYFEAMFSGGLKESQDSEVNFDNSIHPEVLELLLDYAYSSRVIINEENAESL 120 Query: 121 LEAGDMLEFQDIRDACAEFLEKNLHPTNCLGMLLLSDAHQCTKLYELSWRMCLSNFQTIR 180 LEAGDMLEFQDIRDACAEFLEKNLHPTNCLGMLLLSDAHQCTKLYELSWRMCLSNFQTIR Sbjct: 121 LEAGDMLEFQDIRDACAEFLEKNLHPTNCLGMLLLSDAHQCTKLYELSWRMCLSNFQTIR 180 Query: 181 KNEDFLQLPQDMVVQLLSSEELETEDERLVYESAINWISYDLKKRYCYLPELLQTVRLAL 240 KNEDFLQLPQDMVVQLLSSEELETEDERLVYESAINWISYDLKKRYCYLPELLQTVRLAL Sbjct: 181 KNEDFLQLPQDMVVQLLSSEELETEDERLVYESAINWISYDLKKRYCYLPELLQTVRLAL 240 Query: 241 LPAIYLMENVAMEELITKQRKSKEIVEEAIRCKLKILQNDGVVTSLCARPRKTGHALFLL 300 LPAIYLMENVAMEELITKQRKSKEIVEEAIRCKLKILQNDGVVTSLCARPRKTGHALFLL Sbjct: 241 LPAIYLMENVAMEELITKQRKSKEIVEEAIRCKLKILQNDGVVTSLCARPRKTGHALFLL 300 Query: 301 GGQTFMCDKLYLVDQKAKEIIPKADIPSPRKEFSACAIGCKVYITGGRGSENGVSKDVWV 360 GGQTFMCDKLYLVDQKAKEIIPKADIPSPRKEFSACAIGCKVYITGGRGSENGVSKDVWV Sbjct: 301 GGQTFMCDKLYLVDQKAKEIIPKADIPSPRKEFSACAIGCKVYITGGRGSENGVSKDVWV 360 Query: 361 YDTLHEEWSKAAPMLVARFGHGSAELKHCLYVVGGHTAATGCLPASPSVSLKQVEHYDPT 420 YDTLHEEWSKAAPMLVARFGHGSAELKHCLYVVGGHTAATGCLPASPSVSLKQVEHYDPT Sbjct: 361 YDTLHEEWSKAAPMLVARFGHGSAELKHCLYVVGGHTAATGCLPASPSVSLKQVEHYDPT 420 Query: 421 INKWTMVAPLREGVSNAAVVSAKLKLFAFGGTSVSHDKLPKVQCYDQCENRWTVPATCPQ 480 INKWTMVAPLREGVSNAAVVSAKLKLFAFGGTSVSHDKLPKVQCYDQCENRWTVPATCPQ Sbjct: 421 INKWTMVAPLREGVSNAAVVSAKLKLFAFGGTSVSHDKLPKVQCYDQCENRWTVPATCPQ 480 Query: 481 PWRYTAAAVLGNQIFIMGGDTEFSACSAYKFNSETYQWTKVGDVTAKRMSCHAVASGNKL 540 PWRYTAAAVLGNQIFIMGGDTEFSACSAYKFNSETYQWTKVGDVTAKRMSCHAVASGNKL Sbjct: 481 PWRYTAAAVLGNQIFIMGGDTEFSACSAYKFNSETYQWTKVGDVTAKRMSCHAVASGNKL 540 Query: 541 YVVGGYFGIQRCKTLDCYDPTLDVWNSITTVPYSLIPTAFVSTWKHLPS 589 YVVGGYFGIQRCKTLDCYDPTLDVWNSITTVPYSLIPTAFVSTWKHLPS Sbjct: 541 YVVGGYFGIQRCKTLDCYDPTLDVWNSITTVPYSLIPTAFVSTWKHLPS 589 >swiss|P13781|REP2_ZYGBI Trans-acting factor C (REP2). Length = 178 Score = 23.5 bits (49), Expect = 0.60 Identities = 12/40 (30%), Positives = 21/40 (52%) Query: 417 YDPTINKWTMVAPLREGVSNAAVVSAKLKLFAFGGTSVSH 456 Y PT + T+ L EG + +V+ ++++L F V H Sbjct: 55 YLPTRDGETLQEMLSEGAPSTSVLHSEMELSIFDQVQVPH 94 >swiss|P33418|LOS1_YEAST LOS1 protein. Length = 1100 Score = 21.2 bits (43), Expect = 3.2 Identities = 6/13 (46%), Positives = 12/13 (92%) Query: 186 LQLPQDMVVQLLS 198 +QLPQ++ +QL++ Sbjct: 1062 IQLPQELTIQLVN 1074 >swiss|P20397|NUCL_XENLA Nucleolin (Protein C23). Length = 650 Score = 20.8 bits (42), Expect = 4.7 Identities = 7/15 (46%), Positives = 10/15 (66%) Query: 128 EFQDIRDACAEFLEK 142 EF +++DA EF K Sbjct: 244 EFDELKDALREFFSK 258 Searching.done Results from round 2 Score E Sequences producing significant alignments: (bits) Value Sequences used in model and found again: swiss|O14682|ENC1_HUMAN Ectoderm-neural cortex-1 protein (ENC-1... 1264 0.0 Sequences not found previously or not previously below threshold: swiss|P13781|REP2_ZYGBI Trans-acting factor C (REP2). 24 0.58 swiss|P33418|LOS1_YEAST LOS1 protein. 21 3.2 swiss|P20397|NUCL_XENLA Nucleolin (Protein C23). 21 4.7 CONVERGED! >swiss|O14682|ENC1_HUMAN Ectoderm-neural cortex-1 protein (ENC-1) (P53-indu Length = 589 Score = 1264 bits (3270), Expect = 0.0 Identities = 589/589 (100%), Positives = 589/589 (100%) Query: 1 MSVSVHENRKSRASSGSINIYLFHKSSYADSVLTHLNLLRQQRLFTDVLLHAGNRTFPCH 60 MSVSVHENRKSRASSGSINIYLFHKSSYADSVLTHLNLLRQQRLFTDVLLHAGNRTFPCH Sbjct: 1 MSVSVHENRKSRASSGSINIYLFHKSSYADSVLTHLNLLRQQRLFTDVLLHAGNRTFPCH 60 Query: 61 RAVLAACSRYFEAMFSGGLKESQDSEVNFDNSIHPEVLELLLDYAYSSRVIINEENAESL 120 RAVLAACSRYFEAMFSGGLKESQDSEVNFDNSIHPEVLELLLDYAYSSRVIINEENAESL Sbjct: 61 RAVLAACSRYFEAMFSGGLKESQDSEVNFDNSIHPEVLELLLDYAYSSRVIINEENAESL 120 Query: 121 LEAGDMLEFQDIRDACAEFLEKNLHPTNCLGMLLLSDAHQCTKLYELSWRMCLSNFQTIR 180 LEAGDMLEFQDIRDACAEFLEKNLHPTNCLGMLLLSDAHQCTKLYELSWRMCLSNFQTIR Sbjct: 121 LEAGDMLEFQDIRDACAEFLEKNLHPTNCLGMLLLSDAHQCTKLYELSWRMCLSNFQTIR 180 Query: 181 KNEDFLQLPQDMVVQLLSSEELETEDERLVYESAINWISYDLKKRYCYLPELLQTVRLAL 240 KNEDFLQLPQDMVVQLLSSEELETEDERLVYESAINWISYDLKKRYCYLPELLQTVRLAL Sbjct: 181 KNEDFLQLPQDMVVQLLSSEELETEDERLVYESAINWISYDLKKRYCYLPELLQTVRLAL 240 Query: 241 LPAIYLMENVAMEELITKQRKSKEIVEEAIRCKLKILQNDGVVTSLCARPRKTGHALFLL 300 LPAIYLMENVAMEELITKQRKSKEIVEEAIRCKLKILQNDGVVTSLCARPRKTGHALFLL Sbjct: 241 LPAIYLMENVAMEELITKQRKSKEIVEEAIRCKLKILQNDGVVTSLCARPRKTGHALFLL 300 Query: 301 GGQTFMCDKLYLVDQKAKEIIPKADIPSPRKEFSACAIGCKVYITGGRGSENGVSKDVWV 360 GGQTFMCDKLYLVDQKAKEIIPKADIPSPRKEFSACAIGCKVYITGGRGSENGVSKDVWV Sbjct: 301 GGQTFMCDKLYLVDQKAKEIIPKADIPSPRKEFSACAIGCKVYITGGRGSENGVSKDVWV 360 Query: 361 YDTLHEEWSKAAPMLVARFGHGSAELKHCLYVVGGHTAATGCLPASPSVSLKQVEHYDPT 420 YDTLHEEWSKAAPMLVARFGHGSAELKHCLYVVGGHTAATGCLPASPSVSLKQVEHYDPT Sbjct: 361 YDTLHEEWSKAAPMLVARFGHGSAELKHCLYVVGGHTAATGCLPASPSVSLKQVEHYDPT 420 Query: 421 INKWTMVAPLREGVSNAAVVSAKLKLFAFGGTSVSHDKLPKVQCYDQCENRWTVPATCPQ 480 INKWTMVAPLREGVSNAAVVSAKLKLFAFGGTSVSHDKLPKVQCYDQCENRWTVPATCPQ Sbjct: 421 INKWTMVAPLREGVSNAAVVSAKLKLFAFGGTSVSHDKLPKVQCYDQCENRWTVPATCPQ 480 Query: 481 PWRYTAAAVLGNQIFIMGGDTEFSACSAYKFNSETYQWTKVGDVTAKRMSCHAVASGNKL 540 PWRYTAAAVLGNQIFIMGGDTEFSACSAYKFNSETYQWTKVGDVTAKRMSCHAVASGNKL Sbjct: 481 PWRYTAAAVLGNQIFIMGGDTEFSACSAYKFNSETYQWTKVGDVTAKRMSCHAVASGNKL 540 Query: 541 YVVGGYFGIQRCKTLDCYDPTLDVWNSITTVPYSLIPTAFVSTWKHLPS 589 YVVGGYFGIQRCKTLDCYDPTLDVWNSITTVPYSLIPTAFVSTWKHLPS Sbjct: 541 YVVGGYFGIQRCKTLDCYDPTLDVWNSITTVPYSLIPTAFVSTWKHLPS 589 >swiss|P13781|REP2_ZYGBI Trans-acting factor C (REP2). Length = 178 Score = 23.9 bits (50), Expect = 0.58 Identities = 12/40 (30%), Positives = 21/40 (52%) Query: 417 YDPTINKWTMVAPLREGVSNAAVVSAKLKLFAFGGTSVSH 456 Y PT + T+ L EG + +V+ ++++L F V H Sbjct: 55 YLPTRDGETLQEMLSEGAPSTSVLHSEMELSIFDQVQVPH 94 >swiss|P33418|LOS1_YEAST LOS1 protein. Length = 1100 Score = 21.2 bits (43), Expect = 3.2 Identities = 6/13 (46%), Positives = 12/13 (92%) Query: 186 LQLPQDMVVQLLS 198 +QLPQ++ +QL++ Sbjct: 1062 IQLPQELTIQLVN 1074 >swiss|P20397|NUCL_XENLA Nucleolin (Protein C23). Length = 650 Score = 20.8 bits (42), Expect = 4.7 Identities = 7/15 (46%), Positives = 10/15 (66%) Query: 128 EFQDIRDACAEFLEK 142 EF +++DA EF K Sbjct: 244 EFDELKDALREFFSK 258 Database: /home/mika/Theses/Databases/unique_set/NMP_Database_unique .fasta Posted date: Mar 7, 2003 12:04 PM Number of letters in database: 17,163 Number of sequences in database: 43 Lambda K H 0.320 0.134 0.410 Lambda K H 0.267 0.0411 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 42,429 Number of Sequences: 43 Number of extensions: 1877 Number of successful extensions: 33 Number of sequences better than 10.0: 11 Number of HSP's better than 10.0 without gapping: 11 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 11 length of query: 589 length of database: 17,163 effective HSP length: 60 effective length of query: 529 effective length of database: 14,583 effective search space: 7714407 effective search space used: 7714407 T: 11 A: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 39 (20.9 bits) S2: 39 (19.6 bits) BLASTP 2.2.2 [Dec-14-2001] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= swiss|P24836|VE6_HPV56 E6 protein. (155 letters) Database: /home/mika/Theses/Databases/unique_set/NMP_Database_unique.f asta 43 sequences; 17,163 total letters Searching.done Results from round 1 Score E Sequences producing significant alignments: (bits) Value swiss|P24836|VE6_HPV56 E6 protein. 286 6e-81 swiss|Q07856|VE6_HPV65 E6 protein. 59 2e-12 swiss|P30735|VE6_MNPV E6 protein. 46 3e-08 swiss|P06931|VE6_BPV1 E6 protein. 43 2e-07 swiss|P03872|REP2_YEAST Trans-acting factor C (REP2) (Protein c... 20 1.5 trembl|Q9C2H8|Q9C2H8 Related to ser/arg-related nuclear matrix ... 20 2.0 >swiss|P24836|VE6_HPV56 E6 protein. Length = 155 Score = 286 bits (733), Expect = 6e-81 Identities = 155/155 (100%), Positives = 155/155 (100%) Query: 1 MEPQFNNPQERPRSLHHLSEVLEIPLIDLRLSCVYCKKELTRAEVYNFACTELKLVYRDD 60 MEPQFNNPQERPRSLHHLSEVLEIPLIDLRLSCVYCKKELTRAEVYNFACTELKLVYRDD Sbjct: 1 MEPQFNNPQERPRSLHHLSEVLEIPLIDLRLSCVYCKKELTRAEVYNFACTELKLVYRDD 60 Query: 61 FPYAVCRVCLLFYSKVRKYRYYDYSVYGATLESITKKQLCDLLIRCYRCQSPLTPEEKQL 120 FPYAVCRVCLLFYSKVRKYRYYDYSVYGATLESITKKQLCDLLIRCYRCQSPLTPEEKQL Sbjct: 61 FPYAVCRVCLLFYSKVRKYRYYDYSVYGATLESITKKQLCDLLIRCYRCQSPLTPEEKQL 120 Query: 121 HCDRKRRFHLIAHGWTGSCLGCWRQTSREPRESTV 155 HCDRKRRFHLIAHGWTGSCLGCWRQTSREPRESTV Sbjct: 121 HCDRKRRFHLIAHGWTGSCLGCWRQTSREPRESTV 155 >swiss|Q07856|VE6_HPV65 E6 protein. Length = 140 Score = 59.3 bits (142), Expect = 2e-12 Identities = 37/135 (27%), Positives = 63/135 (46%) Query: 11 RPRSLHHLSEVLEIPLIDLRLSCVYCKKELTRAEVYNFACTELKLVYRDDFPYAVCRVCL 70 RP +L +I DL L+C++C + ++ +F +L LV+R YA C CL Sbjct: 5 RPAALDDFCRRFDISFFDLHLTCIFCSHTVDLQDLASFYLKKLSLVFRGGCYYACCSECL 64 Query: 71 LFYSKVRKYRYYDYSVYGATLESITKKQLCDLLIRCYRCQSPLTPEEKQLHCDRKRRFHL 130 ++ + Y+ S+ LE + ++++ ++ IRC C L EK + +L Sbjct: 65 RLSARFEQENYFQCSIKAVNLEEVAQRKIKEICIRCICCLRLLDIVEKLDLLYSDQACYL 124 Query: 131 IAHGWTGSCLGCWRQ 145 I W G C C R+ Sbjct: 125 IRGLWRGYCRNCIRK 139 >swiss|P30735|VE6_MNPV E6 protein. Length = 207 Score = 45.8 bits (107), Expect = 3e-08 Identities = 35/130 (26%), Positives = 54/130 (40%) Query: 13 RSLHHLSEVLEIPLIDLRLSCVYCKKELTRAEVYNFACTELKLVYRDDFPYAVCRVCLLF 72 R++H E L IP DL L C +C + LT+ E+ F + LV+R + +C C Sbjct: 75 RTVHSFVERLGIPREDLLLPCTFCSRFLTQEELTAFDFSAFNLVWRGRCAHGICTACARV 134 Query: 73 YSKVRKYRYYDYSVYGATLESITKKQLCDLLIRCYRCQSPLTPEEKQLHCDRKRRFHLIA 132 + + + ++ S A + L L RC C L+ EK +R F + Sbjct: 135 CASLDLFLHHQNSRPLADVLRDENLTLHGLKARCRVCMKILSVTEKLECAERGESFAKVR 194 Query: 133 HGWTGSCLGC 142 W C C Sbjct: 195 GQWRARCRIC 204 >swiss|P06931|VE6_BPV1 E6 protein. Length = 137 Score = 42.7 bits (99), Expect = 2e-07 Identities = 34/119 (28%), Positives = 48/119 (39%), Gaps = 1/119 (0%) Query: 31 LSCVYCKKELTRAEVYNFACTELKLVYRDDFPYAVCRVCLLFYSKVRKYRYYDYSVYGAT 90 L C++C++ LT + + + +V R+ Y C +CL + + V G Sbjct: 15 LDCLWCREPLTEVDAFRCMVKDFHVVIREGCRYGACTICLENCLATERRLWQGVPVTGEE 74 Query: 91 LESITKKQLCDLLIRCYRCQSPLTPEEKQLHCDRKRRF-HLIAHGWTGSCLGCWRQTSR 148 E + K L L IRC C LT EK H F A+ G C C R SR Sbjct: 75 AELLHGKTLDRLCIRCCYCGGKLTKNEKHRHVLFNEPFCKTRANIIRGRCYDCCRHGSR 133 >swiss|P03872|REP2_YEAST Trans-acting factor C (REP2) (Protein charlie). Length = 296 Score = 20.0 bits (40), Expect = 1.5 Identities = 11/39 (28%), Positives = 17/39 (43%) Query: 77 RKYRYYDYSVYGATLESITKKQLCDLLIRCYRCQSPLTP 115 RK Y ++ L KK+ ++L+R C L P Sbjct: 129 RKQLYKSIAIIIGRLPEKDKKRATEMLMRKMDCTQLLVP 167 >trembl|Q9C2H8|Q9C2H8 Related to ser/arg-related nuclear matrix protein. Length = 976 Score = 19.6 bits (39), Expect = 2.0 Identities = 23/82 (28%), Positives = 34/82 (41%), Gaps = 7/82 (8%) Query: 3 PQFNNPQERPRSLHHLSEVLEIPLIDLRLSCVYCKKELTRAEVYNFACTELKLVYRDDFP 62 P + PQE R + + + + + L CV C K L A + N A T + P Sbjct: 759 PPCSGPQETARKWYGVWDSYKGDFVPLFEVCVGCVKML-EAVLPNLANTLYPIS-----P 812 Query: 63 YAVCRVCLLFYSKVRKYRYYDY 84 C L Y+ RK R+ +Y Sbjct: 813 EPFIAYCQLHYAPGRK-RFIEY 833 Searching.done Results from round 2 Score E Sequences producing significant alignments: (bits) Value Sequences used in model and found again: swiss|P24836|VE6_HPV56 E6 protein. 212 2e-58 swiss|Q07856|VE6_HPV65 E6 protein. 170 8e-46 swiss|P30735|VE6_MNPV E6 protein. 164 4e-44 swiss|P06931|VE6_BPV1 E6 protein. 148 2e-39 Sequences not found previously or not previously below threshold: trembl|Q9FLH0|Q9FLH0 Nuclear matrix constituent protein 1 (NMCP... 19 2.8 swiss|P33418|LOS1_YEAST LOS1 protein. 18 5.7 swiss|P25233|NECD_MOUSE Necdin. 18 6.0 CONVERGED! >swiss|P24836|VE6_HPV56 E6 protein. Length = 155 Score = 212 bits (541), Expect = 2e-58 Identities = 155/155 (100%), Positives = 155/155 (100%) Query: 1 MEPQFNNPQERPRSLHHLSEVLEIPLIDLRLSCVYCKKELTRAEVYNFACTELKLVYRDD 60 MEPQFNNPQERPRSLHHLSEVLEIPLIDLRLSCVYCKKELTRAEVYNFACTELKLVYRDD Sbjct: 1 MEPQFNNPQERPRSLHHLSEVLEIPLIDLRLSCVYCKKELTRAEVYNFACTELKLVYRDD 60 Query: 61 FPYAVCRVCLLFYSKVRKYRYYDYSVYGATLESITKKQLCDLLIRCYRCQSPLTPEEKQL 120 FPYAVCRVCLLFYSKVRKYRYYDYSVYGATLESITKKQLCDLLIRCYRCQSPLTPEEKQL Sbjct: 61 FPYAVCRVCLLFYSKVRKYRYYDYSVYGATLESITKKQLCDLLIRCYRCQSPLTPEEKQL 120 Query: 121 HCDRKRRFHLIAHGWTGSCLGCWRQTSREPRESTV 155 HCDRKRRFHLIAHGWTGSCLGCWRQTSREPRESTV Sbjct: 121 HCDRKRRFHLIAHGWTGSCLGCWRQTSREPRESTV 155 >swiss|Q07856|VE6_HPV65 E6 protein. Length = 140 Score = 170 bits (431), Expect = 8e-46 Identities = 37/135 (27%), Positives = 63/135 (46%) Query: 11 RPRSLHHLSEVLEIPLIDLRLSCVYCKKELTRAEVYNFACTELKLVYRDDFPYAVCRVCL 70 RP +L +I DL L+C++C + ++ +F +L LV+R YA C CL Sbjct: 5 RPAALDDFCRRFDISFFDLHLTCIFCSHTVDLQDLASFYLKKLSLVFRGGCYYACCSECL 64 Query: 71 LFYSKVRKYRYYDYSVYGATLESITKKQLCDLLIRCYRCQSPLTPEEKQLHCDRKRRFHL 130 ++ + Y+ S+ LE + ++++ ++ IRC C L EK + +L Sbjct: 65 RLSARFEQENYFQCSIKAVNLEEVAQRKIKEICIRCICCLRLLDIVEKLDLLYSDQACYL 124 Query: 131 IAHGWTGSCLGCWRQ 145 I W G C C R+ Sbjct: 125 IRGLWRGYCRNCIRK 139 >swiss|P30735|VE6_MNPV E6 protein. Length = 207 Score = 164 bits (417), Expect = 4e-44 Identities = 35/130 (26%), Positives = 54/130 (40%) Query: 13 RSLHHLSEVLEIPLIDLRLSCVYCKKELTRAEVYNFACTELKLVYRDDFPYAVCRVCLLF 72 R++H E L IP DL L C +C + LT+ E+ F + LV+R + +C C Sbjct: 75 RTVHSFVERLGIPREDLLLPCTFCSRFLTQEELTAFDFSAFNLVWRGRCAHGICTACARV 134 Query: 73 YSKVRKYRYYDYSVYGATLESITKKQLCDLLIRCYRCQSPLTPEEKQLHCDRKRRFHLIA 132 + + + ++ S A + L L RC C L+ EK +R F + Sbjct: 135 CASLDLFLHHQNSRPLADVLRDENLTLHGLKARCRVCMKILSVTEKLECAERGESFAKVR 194 Query: 133 HGWTGSCLGC 142 W C C Sbjct: 195 GQWRARCRIC 204 >swiss|P06931|VE6_BPV1 E6 protein. Length = 137 Score = 148 bits (375), Expect = 2e-39 Identities = 34/119 (28%), Positives = 48/119 (39%), Gaps = 1/119 (0%) Query: 31 LSCVYCKKELTRAEVYNFACTELKLVYRDDFPYAVCRVCLLFYSKVRKYRYYDYSVYGAT 90 L C++C++ LT + + + +V R+ Y C +CL + + V G Sbjct: 15 LDCLWCREPLTEVDAFRCMVKDFHVVIREGCRYGACTICLENCLATERRLWQGVPVTGEE 74 Query: 91 LESITKKQLCDLLIRCYRCQSPLTPEEKQLHCDRKRRF-HLIAHGWTGSCLGCWRQTSR 148 E + K L L IRC C LT EK H F A+ G C C R SR Sbjct: 75 AELLHGKTLDRLCIRCCYCGGKLTKNEKHRHVLFNEPFCKTRANIIRGRCYDCCRHGSR 133 >trembl|Q9FLH0|Q9FLH0 Nuclear matrix constituent protein 1 (NMCP1)-like. Length = 1042 Score = 19.0 bits (38), Expect = 2.8 Identities = 8/27 (29%), Positives = 12/27 (43%) Query: 5 FNNPQERPRSLHHLSEVLEIPLIDLRL 31 F E+ +HH E +P L+L Sbjct: 854 FKTSPEKSTLMHHYEEEGGVPSEKLKL 880 >swiss|P33418|LOS1_YEAST LOS1 protein. Length = 1100 Score = 18.2 bits (36), Expect = 5.7 Identities = 7/20 (35%), Positives = 8/20 (40%), Gaps = 2/20 (10%) Query: 99 LCDLLIRCYRCQSPLTPEEK 118 L + I CY C L K Sbjct: 263 LKETKISCYNC--ILAIISK 280 >swiss|P25233|NECD_MOUSE Necdin. Length = 325 Score = 18.2 bits (36), Expect = 6.0 Identities = 6/35 (17%), Positives = 13/35 (37%) Query: 113 LTPEEKQLHCDRKRRFHLIAHGWTGSCLGCWRQTS 147 L ++K++ + + C R+TS Sbjct: 114 LVKDQKRMVLWFPDMVKEVMGSYKKWCRSILRRTS 148 Database: /home/mika/Theses/Databases/unique_set/NMP_Database_unique .fasta Posted date: Mar 7, 2003 12:04 PM Number of letters in database: 17,163 Number of sequences in database: 43 Lambda K H 0.322 0.162 0.503 Lambda K H 0.267 0.0495 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 14,421 Number of Sequences: 43 Number of extensions: 763 Number of successful extensions: 30 Number of sequences better than 10.0: 16 Number of HSP's better than 10.0 without gapping: 16 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 21 length of query: 155 length of database: 17,163 effective HSP length: 49 effective length of query: 106 effective length of database: 15,056 effective search space: 1595936 effective search space used: 1595936 T: 11 A: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 33 (18.0 bits) S2: 34 (17.4 bits) BLASTP 2.2.2 [Dec-14-2001] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= swiss|Q07856|VE6_HPV65 E6 protein. (140 letters) Database: /home/mika/Theses/Databases/unique_set/NMP_Database_unique.f asta 43 sequences; 17,163 total letters Searching.done Results from round 1 Score E Sequences producing significant alignments: (bits) Value swiss|Q07856|VE6_HPV65 E6 protein. 229 8e-64 swiss|P30735|VE6_MNPV E6 protein. 59 4e-12 swiss|P24836|VE6_HPV56 E6 protein. 58 5e-12 swiss|P06931|VE6_BPV1 E6 protein. 38 6e-06 trembl|Q9FLH0|Q9FLH0 Nuclear matrix constituent protein 1 (NMCP... 17 8.6 >swiss|Q07856|VE6_HPV65 E6 protein. Length = 140 Score = 229 bits (585), Expect = 8e-64 Identities = 140/140 (100%), Positives = 140/140 (100%) Query: 1 MADGRPAALDDFCRRFDISFFDLHLTCIFCSHTVDLQDLASFYLKKLSLVFRGGCYYACC 60 MADGRPAALDDFCRRFDISFFDLHLTCIFCSHTVDLQDLASFYLKKLSLVFRGGCYYACC Sbjct: 1 MADGRPAALDDFCRRFDISFFDLHLTCIFCSHTVDLQDLASFYLKKLSLVFRGGCYYACC 60 Query: 61 SECLRLSARFEQENYFQCSIKAVNLEEVAQRKIKEICIRCICCLRLLDIVEKLDLLYSDQ 120 SECLRLSARFEQENYFQCSIKAVNLEEVAQRKIKEICIRCICCLRLLDIVEKLDLLYSDQ Sbjct: 61 SECLRLSARFEQENYFQCSIKAVNLEEVAQRKIKEICIRCICCLRLLDIVEKLDLLYSDQ 120 Query: 121 ACYLIRGLWRGYCRNCIRKQ 140 ACYLIRGLWRGYCRNCIRKQ Sbjct: 121 ACYLIRGLWRGYCRNCIRKQ 140 >swiss|P30735|VE6_MNPV E6 protein. Length = 207 Score = 58.5 bits (140), Expect = 4e-12 Identities = 37/125 (29%), Positives = 60/125 (47%) Query: 12 FCRRFDISFFDLHLTCIFCSHTVDLQDLASFYLKKLSLVFRGGCYYACCSECLRLSARFE 71 F R I DL L C FCS + ++L +F +LV+RG C + C+ C R+ A + Sbjct: 80 FVERLGIPREDLLLPCTFCSRFLTQEELTAFDFSAFNLVWRGRCAHGICTACARVCASLD 139 Query: 72 QENYFQCSIKAVNLEEVAQRKIKEICIRCICCLRLLDIVEKLDLLYSDQACYLIRGLWRG 131 + Q S ++ + + RC C+++L + EKL+ ++ +RG WR Sbjct: 140 LFLHHQNSRPLADVLRDENLTLHGLKARCRVCMKILSVTEKLECAERGESFAKVRGQWRA 199 Query: 132 YCRNC 136 CR C Sbjct: 200 RCRIC 204 >swiss|P24836|VE6_HPV56 E6 protein. Length = 155 Score = 57.8 bits (138), Expect = 5e-12 Identities = 37/135 (27%), Positives = 63/135 (46%) Query: 5 RPAALDDFCRRFDISFFDLHLTCIFCSHTVDLQDLASFYLKKLSLVFRGGCYYACCSECL 64 RP +L +I DL L+C++C + ++ +F +L LV+R YA C CL Sbjct: 11 RPRSLHHLSEVLEIPLIDLRLSCVYCKKELTRAEVYNFACTELKLVYRDDFPYAVCRVCL 70 Query: 65 RLSARFEQENYFQCSIKAVNLEEVAQRKIKEICIRCICCLRLLDIVEKLDLLYSDQACYL 124 ++ + Y+ S+ LE + ++++ ++ IRC C L EK + +L Sbjct: 71 LFYSKVRKYRYYDYSVYGATLESITKKQLCDLLIRCYRCQSPLTPEEKQLHCDRKRRFHL 130 Query: 125 IRGLWRGYCRNCIRK 139 I W G C C R+ Sbjct: 131 IAHGWTGSCLGCWRQ 145 >swiss|P06931|VE6_BPV1 E6 protein. Length = 137 Score = 37.7 bits (86), Expect = 6e-06 Identities = 30/115 (26%), Positives = 49/115 (42%), Gaps = 1/115 (0%) Query: 25 LTCIFCSHTVDLQDLASFYLKKLSLVFRGGCYYACCSECLRLSARFEQENYFQCSIKAVN 84 L C++C + D +K +V R GC Y C+ CL E+ + + Sbjct: 15 LDCLWCREPLTEVDAFRCMVKDFHVVIREGCRYGACTICLENCLATERRLWQGVPVTGEE 74 Query: 85 LEEVAQRKIKEICIRCICCLRLLDIVEK-LDLLYSDQACYLIRGLWRGYCRNCIR 138 E + + + +CIRC C L EK +L+++ C + RG C +C R Sbjct: 75 AELLHGKTLDRLCIRCCYCGGKLTKNEKHRHVLFNEPFCKTRANIIRGRCYDCCR 129 >trembl|Q9FLH0|Q9FLH0 Nuclear matrix constituent protein 1 (NMCP1)-like. Length = 1042 Score = 17.3 bits (33), Expect = 8.6 Identities = 6/16 (37%), Positives = 11/16 (68%) Query: 81 KAVNLEEVAQRKIKEI 96 +A +A+RK+KE+ Sbjct: 195 EANRYHRIAERKLKEV 210 Searching.done Results from round 2 Score E Sequences producing significant alignments: (bits) Value Sequences used in model and found again: swiss|P24836|VE6_HPV56 E6 protein. 168 3e-45 swiss|Q07856|VE6_HPV65 E6 protein. 163 9e-44 swiss|P30735|VE6_MNPV E6 protein. 149 1e-39 swiss|P06931|VE6_BPV1 E6 protein. 132 2e-34 Sequences not found previously or not previously below threshold: swiss|P33418|LOS1_YEAST LOS1 protein. 17 8.7 CONVERGED! >swiss|P24836|VE6_HPV56 E6 protein. Length = 155 Score = 168 bits (426), Expect = 3e-45 Identities = 37/135 (27%), Positives = 63/135 (46%) Query: 5 RPAALDDFCRRFDISFFDLHLTCIFCSHTVDLQDLASFYLKKLSLVFRGGCYYACCSECL 64 RP +L +I DL L+C++C + ++ +F +L LV+R YA C CL Sbjct: 11 RPRSLHHLSEVLEIPLIDLRLSCVYCKKELTRAEVYNFACTELKLVYRDDFPYAVCRVCL 70 Query: 65 RLSARFEQENYFQCSIKAVNLEEVAQRKIKEICIRCICCLRLLDIVEKLDLLYSDQACYL 124 ++ + Y+ S+ LE + ++++ ++ IRC C L EK + +L Sbjct: 71 LFYSKVRKYRYYDYSVYGATLESITKKQLCDLLIRCYRCQSPLTPEEKQLHCDRKRRFHL 130 Query: 125 IRGLWRGYCRNCIRK 139 I W G C C R+ Sbjct: 131 IAHGWTGSCLGCWRQ 145 Score = 18.2 bits (36), Expect = 4.9 Identities = 7/36 (19%), Positives = 16/36 (44%) Query: 76 FQCSIKAVNLEEVAQRKIKEICIRCICCLRLLDIVE 111 + +L EV + + ++ + C+ C + L E Sbjct: 9 QERPRSLHHLSEVLEIPLIDLRLSCVYCKKELTRAE 44 >swiss|Q07856|VE6_HPV65 E6 protein. Length = 140 Score = 163 bits (413), Expect = 9e-44 Identities = 140/140 (100%), Positives = 140/140 (100%) Query: 1 MADGRPAALDDFCRRFDISFFDLHLTCIFCSHTVDLQDLASFYLKKLSLVFRGGCYYACC 60 MADGRPAALDDFCRRFDISFFDLHLTCIFCSHTVDLQDLASFYLKKLSLVFRGGCYYACC Sbjct: 1 MADGRPAALDDFCRRFDISFFDLHLTCIFCSHTVDLQDLASFYLKKLSLVFRGGCYYACC 60 Query: 61 SECLRLSARFEQENYFQCSIKAVNLEEVAQRKIKEICIRCICCLRLLDIVEKLDLLYSDQ 120 SECLRLSARFEQENYFQCSIKAVNLEEVAQRKIKEICIRCICCLRLLDIVEKLDLLYSDQ Sbjct: 61 SECLRLSARFEQENYFQCSIKAVNLEEVAQRKIKEICIRCICCLRLLDIVEKLDLLYSDQ 120 Query: 121 ACYLIRGLWRGYCRNCIRKQ 140 ACYLIRGLWRGYCRNCIRKQ Sbjct: 121 ACYLIRGLWRGYCRNCIRKQ 140 >swiss|P30735|VE6_MNPV E6 protein. Length = 207 Score = 149 bits (378), Expect = 1e-39 Identities = 37/130 (28%), Positives = 61/130 (46%) Query: 7 AALDDFCRRFDISFFDLHLTCIFCSHTVDLQDLASFYLKKLSLVFRGGCYYACCSECLRL 66 + F R I DL L C FCS + ++L +F +LV+RG C + C+ C R+ Sbjct: 75 RTVHSFVERLGIPREDLLLPCTFCSRFLTQEELTAFDFSAFNLVWRGRCAHGICTACARV 134 Query: 67 SARFEQENYFQCSIKAVNLEEVAQRKIKEICIRCICCLRLLDIVEKLDLLYSDQACYLIR 126 A + + Q S ++ + + RC C+++L + EKL+ ++ +R Sbjct: 135 CASLDLFLHHQNSRPLADVLRDENLTLHGLKARCRVCMKILSVTEKLECAERGESFAKVR 194 Query: 127 GLWRGYCRNC 136 G WR CR C Sbjct: 195 GQWRARCRIC 204 >swiss|P06931|VE6_BPV1 E6 protein. Length = 137 Score = 132 bits (332), Expect = 2e-34 Identities = 30/115 (26%), Positives = 49/115 (42%), Gaps = 1/115 (0%) Query: 25 LTCIFCSHTVDLQDLASFYLKKLSLVFRGGCYYACCSECLRLSARFEQENYFQCSIKAVN 84 L C++C + D +K +V R GC Y C+ CL E+ + + Sbjct: 15 LDCLWCREPLTEVDAFRCMVKDFHVVIREGCRYGACTICLENCLATERRLWQGVPVTGEE 74 Query: 85 LEEVAQRKIKEICIRCICCLRLLDIVEK-LDLLYSDQACYLIRGLWRGYCRNCIR 138 E + + + +CIRC C L EK +L+++ C + RG C +C R Sbjct: 75 AELLHGKTLDRLCIRCCYCGGKLTKNEKHRHVLFNEPFCKTRANIIRGRCYDCCR 129 >swiss|P33418|LOS1_YEAST LOS1 protein. Length = 1100 Score = 17.4 bits (34), Expect = 8.7 Identities = 8/20 (40%), Positives = 11/20 (55%), Gaps = 2/20 (10%) Query: 93 IKEICIRCICCLRLLDIVEK 112 +KE I C C +L I+ K Sbjct: 263 LKETKISCYNC--ILAIISK 280 Database: /home/mika/Theses/Databases/unique_set/NMP_Database_unique .fasta Posted date: Mar 7, 2003 12:04 PM Number of letters in database: 17,163 Number of sequences in database: 43 Lambda K H 0.324 0.166 0.517 Lambda K H 0.267 0.0507 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 12,851 Number of Sequences: 43 Number of extensions: 652 Number of successful extensions: 30 Number of sequences better than 10.0: 14 Number of HSP's better than 10.0 without gapping: 14 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 17 length of query: 140 length of database: 17,163 effective HSP length: 48 effective length of query: 92 effective length of database: 15,099 effective search space: 1389108 effective search space used: 1389108 T: 11 A: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 33 (18.0 bits) S2: 34 (17.4 bits) BLASTP 2.2.2 [Dec-14-2001] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= swiss|P30735|VE6_MNPV E6 protein. (207 letters) Database: /home/mika/Theses/Databases/unique_set/NMP_Database_unique.f asta 43 sequences; 17,163 total letters Searching.done Results from round 1 Score E Sequences producing significant alignments: (bits) Value swiss|P30735|VE6_MNPV E6 protein. 376 e-108 swiss|Q07856|VE6_HPV65 E6 protein. 59 5e-12 swiss|P24836|VE6_HPV56 E6 protein. 45 6e-08 swiss|P06931|VE6_BPV1 E6 protein. 29 0.005 swiss|Q9M7J4|MFP1_TOBAC MAR binding filament-like protein 1-1. 19 5.0 trembl|Q9EQJ3|Q9EQJ3 Nuclear matrix transcription factor. 18 5.6 >swiss|P30735|VE6_MNPV E6 protein. Length = 207 Score = 376 bits (966), Expect = e-108 Identities = 207/207 (100%), Positives = 207/207 (100%) Query: 1 HPAWHCLRRTCCRDLYRVTVLGSTNTIRFGQDRYGCECWQQSPLHTFFHCTGIVQTYIRR 60 HPAWHCLRRTCCRDLYRVTVLGSTNTIRFGQDRYGCECWQQSPLHTFFHCTGIVQTYIRR Sbjct: 1 HPAWHCLRRTCCRDLYRVTVLGSTNTIRFGQDRYGCECWQQSPLHTFFHCTGIVQTYIRR 60 Query: 61 PHWLWICYCGSRMDRTVHSFVERLGIPREDLLLPCTFCSRFLTQEELTAFDFSAFNLVWR 120 PHWLWICYCGSRMDRTVHSFVERLGIPREDLLLPCTFCSRFLTQEELTAFDFSAFNLVWR Sbjct: 61 PHWLWICYCGSRMDRTVHSFVERLGIPREDLLLPCTFCSRFLTQEELTAFDFSAFNLVWR 120 Query: 121 GRCAHGICTACARVCASLDLFLHHQNSRPLADVLRDENLTLHGLKARCRVCMKILSVTEK 180 GRCAHGICTACARVCASLDLFLHHQNSRPLADVLRDENLTLHGLKARCRVCMKILSVTEK Sbjct: 121 GRCAHGICTACARVCASLDLFLHHQNSRPLADVLRDENLTLHGLKARCRVCMKILSVTEK 180 Query: 181 LECAERGESFAKVRGQWRARCRICKPV 207 LECAERGESFAKVRGQWRARCRICKPV Sbjct: 181 LECAERGESFAKVRGQWRARCRICKPV 207 >swiss|Q07856|VE6_HPV65 E6 protein. Length = 140 Score = 58.9 bits (141), Expect = 5e-12 Identities = 37/125 (29%), Positives = 60/125 (47%) Query: 80 FVERLGIPREDLLLPCTFCSRFLTQEELTAFDFSAFNLVWRGRCAHGICTACARVCASLD 139 F R I DL L C FCS + ++L +F +LV+RG C + C+ C R+ A + Sbjct: 12 FCRRFDISFFDLHLTCIFCSHTVDLQDLASFYLKKLSLVFRGGCYYACCSECLRLSARFE 71 Query: 140 LFLHHQNSRPLADVLRDENLTLHGLKARCRVCMKILSVTEKLECAERGESFAKVRGQWRA 199 + Q S ++ + + RC C+++L + EKL+ ++ +RG WR Sbjct: 72 QENYFQCSIKAVNLEEVAQRKIKEICIRCICCLRLLDIVEKLDLLYSDQACYLIRGLWRG 131 Query: 200 RCRIC 204 CR C Sbjct: 132 YCRNC 136 >swiss|P24836|VE6_HPV56 E6 protein. Length = 155 Score = 45.1 bits (105), Expect = 6e-08 Identities = 35/130 (26%), Positives = 54/130 (40%) Query: 75 RTVHSFVERLGIPREDLLLPCTFCSRFLTQEELTAFDFSAFNLVWRGRCAHGICTACARV 134 R++H E L IP DL L C +C + LT+ E+ F + LV+R + +C C Sbjct: 13 RSLHHLSEVLEIPLIDLRLSCVYCKKELTRAEVYNFACTELKLVYRDDFPYAVCRVCLLF 72 Query: 135 CASLDLFLHHQNSRPLADVLRDENLTLHGLKARCRVCMKILSVTEKLECAERGESFAKVR 194 + + + ++ S A + L L RC C L+ EK +R F + Sbjct: 73 YSKVRKYRYYDYSVYGATLESITKKQLCDLLIRCYRCQSPLTPEEKQLHCDRKRRFHLIA 132 Query: 195 GQWRARCRIC 204 W C C Sbjct: 133 HGWTGSCLGC 142 >swiss|P06931|VE6_BPV1 E6 protein. Length = 137 Score = 28.9 bits (63), Expect = 0.005 Identities = 32/113 (28%), Positives = 42/113 (36%), Gaps = 1/113 (0%) Query: 93 LPCTFCSRFLTQEELTAFDFSAFNLVWRGRCAHGICTACARVCASLDLFLHHQNSRPLAD 152 L C +C LT+ + F++V R C +G CT C C + + L + Sbjct: 15 LDCLWCREPLTEVDAFRCMVKDFHVVIREGCRYGACTICLENCLATERRLWQGVPVTGEE 74 Query: 153 VLRDENLTLHGLKARCRVCMKILSVTEKLECAERGESFAKVRGQ-WRARCRIC 204 TL L RC C L+ EK E F K R R RC C Sbjct: 75 AELLHGKTLDRLCIRCCYCGGKLTKNEKHRHVLFNEPFCKTRANIIRGRCYDC 127 >swiss|Q9M7J4|MFP1_TOBAC MAR binding filament-like protein 1-1. Length = 722 Score = 18.9 bits (37), Expect = 5.0 Identities = 8/14 (57%), Positives = 9/14 (64%) Query: 78 HSFVERLGIPREDL 91 HS V +LG RE L Sbjct: 642 HSLVMKLGKERESL 655 >trembl|Q9EQJ3|Q9EQJ3 Nuclear matrix transcription factor. Length = 563 Score = 18.5 bits (36), Expect = 5.6 Identities = 7/11 (63%), Positives = 7/11 (63%) Query: 95 CTFCSRFLTQE 105 CT CSR T E Sbjct: 420 CTICSRAYTSE 430 Searching.done Results from round 2 Score E Sequences producing significant alignments: (bits) Value Sequences used in model and found again: swiss|P30735|VE6_MNPV E6 protein. 301 4e-85 swiss|P24836|VE6_HPV56 E6 protein. 170 1e-45 swiss|Q07856|VE6_HPV65 E6 protein. 156 2e-41 swiss|P06931|VE6_BPV1 E6 protein. 139 3e-36 Sequences not found previously or not previously below threshold: trembl|Q9FLH0|Q9FLH0 Nuclear matrix constituent protein 1 (NMCP... 19 5.2 CONVERGED! >swiss|P30735|VE6_MNPV E6 protein. Length = 207 Score = 301 bits (771), Expect = 4e-85 Identities = 207/207 (100%), Positives = 207/207 (100%) Query: 1 HPAWHCLRRTCCRDLYRVTVLGSTNTIRFGQDRYGCECWQQSPLHTFFHCTGIVQTYIRR 60 HPAWHCLRRTCCRDLYRVTVLGSTNTIRFGQDRYGCECWQQSPLHTFFHCTGIVQTYIRR Sbjct: 1 HPAWHCLRRTCCRDLYRVTVLGSTNTIRFGQDRYGCECWQQSPLHTFFHCTGIVQTYIRR 60 Query: 61 PHWLWICYCGSRMDRTVHSFVERLGIPREDLLLPCTFCSRFLTQEELTAFDFSAFNLVWR 120 PHWLWICYCGSRMDRTVHSFVERLGIPREDLLLPCTFCSRFLTQEELTAFDFSAFNLVWR Sbjct: 61 PHWLWICYCGSRMDRTVHSFVERLGIPREDLLLPCTFCSRFLTQEELTAFDFSAFNLVWR 120 Query: 121 GRCAHGICTACARVCASLDLFLHHQNSRPLADVLRDENLTLHGLKARCRVCMKILSVTEK 180 GRCAHGICTACARVCASLDLFLHHQNSRPLADVLRDENLTLHGLKARCRVCMKILSVTEK Sbjct: 121 GRCAHGICTACARVCASLDLFLHHQNSRPLADVLRDENLTLHGLKARCRVCMKILSVTEK 180 Query: 181 LECAERGESFAKVRGQWRARCRICKPV 207 LECAERGESFAKVRGQWRARCRICKPV Sbjct: 181 LECAERGESFAKVRGQWRARCRICKPV 207 >swiss|P24836|VE6_HPV56 E6 protein. Length = 155 Score = 170 bits (431), Expect = 1e-45 Identities = 35/130 (26%), Positives = 54/130 (40%) Query: 75 RTVHSFVERLGIPREDLLLPCTFCSRFLTQEELTAFDFSAFNLVWRGRCAHGICTACARV 134 R++H E L IP DL L C +C + LT+ E+ F + LV+R + +C C Sbjct: 13 RSLHHLSEVLEIPLIDLRLSCVYCKKELTRAEVYNFACTELKLVYRDDFPYAVCRVCLLF 72 Query: 135 CASLDLFLHHQNSRPLADVLRDENLTLHGLKARCRVCMKILSVTEKLECAERGESFAKVR 194 + + + ++ S A + L L RC C L+ EK +R F + Sbjct: 73 YSKVRKYRYYDYSVYGATLESITKKQLCDLLIRCYRCQSPLTPEEKQLHCDRKRRFHLIA 132 Query: 195 GQWRARCRIC 204 W C C Sbjct: 133 HGWTGSCLGC 142 Score = 19.0 bits (38), Expect = 4.3 Identities = 9/36 (25%), Positives = 14/36 (38%) Query: 144 HQNSRPLADVLRDENLTLHGLKARCRVCMKILSVTE 179 + R L + + L L+ C C K L+ E Sbjct: 9 QERPRSLHHLSEVLEIPLIDLRLSCVYCKKELTRAE 44 >swiss|Q07856|VE6_HPV65 E6 protein. Length = 140 Score = 156 bits (396), Expect = 2e-41 Identities = 37/125 (29%), Positives = 60/125 (47%) Query: 80 FVERLGIPREDLLLPCTFCSRFLTQEELTAFDFSAFNLVWRGRCAHGICTACARVCASLD 139 F R I DL L C FCS + ++L +F +LV+RG C + C+ C R+ A + Sbjct: 12 FCRRFDISFFDLHLTCIFCSHTVDLQDLASFYLKKLSLVFRGGCYYACCSECLRLSARFE 71 Query: 140 LFLHHQNSRPLADVLRDENLTLHGLKARCRVCMKILSVTEKLECAERGESFAKVRGQWRA 199 + Q S ++ + + RC C+++L + EKL+ ++ +RG WR Sbjct: 72 QENYFQCSIKAVNLEEVAQRKIKEICIRCICCLRLLDIVEKLDLLYSDQACYLIRGLWRG 131 Query: 200 RCRIC 204 CR C Sbjct: 132 YCRNC 136 >swiss|P06931|VE6_BPV1 E6 protein. Length = 137 Score = 139 bits (350), Expect = 3e-36 Identities = 32/113 (28%), Positives = 42/113 (36%), Gaps = 1/113 (0%) Query: 93 LPCTFCSRFLTQEELTAFDFSAFNLVWRGRCAHGICTACARVCASLDLFLHHQNSRPLAD 152 L C +C LT+ + F++V R C +G CT C C + + L + Sbjct: 15 LDCLWCREPLTEVDAFRCMVKDFHVVIREGCRYGACTICLENCLATERRLWQGVPVTGEE 74 Query: 153 VLRDENLTLHGLKARCRVCMKILSVTEKLECAERGESFAKVRGQ-WRARCRIC 204 TL L RC C L+ EK E F K R R RC C Sbjct: 75 AELLHGKTLDRLCIRCCYCGGKLTKNEKHRHVLFNEPFCKTRANIIRGRCYDC 127 >trembl|Q9FLH0|Q9FLH0 Nuclear matrix constituent protein 1 (NMCP1)-like. Length = 1042 Score = 18.6 bits (37), Expect = 5.2 Identities = 11/36 (30%), Positives = 17/36 (46%), Gaps = 7/36 (19%) Query: 65 WICYCGSRMDRT-------VHSFVERLGIPREDLLL 93 WI C + + +T +H + E G+P E L L Sbjct: 845 WIKRCTNLIFKTSPEKSTLMHHYEEEGGVPSEKLKL 880 Database: /home/mika/Theses/Databases/unique_set/NMP_Database_unique .fasta Posted date: Mar 7, 2003 12:04 PM Number of letters in database: 17,163 Number of sequences in database: 43 Lambda K H 0.329 0.158 0.546 Lambda K H 0.267 0.0485 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 18,255 Number of Sequences: 43 Number of extensions: 966 Number of successful extensions: 33 Number of sequences better than 10.0: 16 Number of HSP's better than 10.0 without gapping: 16 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 21 length of query: 207 length of database: 17,163 effective HSP length: 52 effective length of query: 155 effective length of database: 14,927 effective search space: 2313685 effective search space used: 2313685 T: 11 A: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 35 (19.3 bits) S2: 35 (17.8 bits) BLASTP 2.2.2 [Dec-14-2001] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= swiss|P06931|VE6_BPV1 E6 protein. (137 letters) Database: /home/mika/Theses/Databases/unique_set/NMP_Database_unique.f asta 43 sequences; 17,163 total letters Searching.done Results from round 1 Score E Sequences producing significant alignments: (bits) Value swiss|P06931|VE6_BPV1 E6 protein. 249 9e-70 swiss|P24836|VE6_HPV56 E6 protein. 42 2e-07 swiss|Q07856|VE6_HPV65 E6 protein. 38 4e-06 swiss|P30735|VE6_MNPV E6 protein. 29 0.002 trembl|Q15219|Q15219 Protein p84. 19 2.8 >swiss|P06931|VE6_BPV1 E6 protein. Length = 137 Score = 249 bits (636), Expect = 9e-70 Identities = 137/137 (100%), Positives = 137/137 (100%) Query: 1 MDLKPFARTNPFSGLDCLWCREPLTEVDAFRCMVKDFHVVIREGCRYGACTICLENCLAT 60 MDLKPFARTNPFSGLDCLWCREPLTEVDAFRCMVKDFHVVIREGCRYGACTICLENCLAT Sbjct: 1 MDLKPFARTNPFSGLDCLWCREPLTEVDAFRCMVKDFHVVIREGCRYGACTICLENCLAT 60 Query: 61 ERRLWQGVPVTGEEAELLHGKTLDRLCIRCCYCGGKLTKNEKHRHVLFNEPFCKTRANII 120 ERRLWQGVPVTGEEAELLHGKTLDRLCIRCCYCGGKLTKNEKHRHVLFNEPFCKTRANII Sbjct: 61 ERRLWQGVPVTGEEAELLHGKTLDRLCIRCCYCGGKLTKNEKHRHVLFNEPFCKTRANII 120 Query: 121 RGRCYDCCRHGSRSKYP 137 RGRCYDCCRHGSRSKYP Sbjct: 121 RGRCYDCCRHGSRSKYP 137 >swiss|P24836|VE6_HPV56 E6 protein. Length = 155 Score = 42.4 bits (98), Expect = 2e-07 Identities = 34/119 (28%), Positives = 48/119 (39%), Gaps = 1/119 (0%) Query: 15 LDCLWCREPLTEVDAFRCMVKDFHVVIREGCRYGACTICLENCLATERRLWQGVPVTGEE 74 L C++C++ LT + + + +V R+ Y C +CL + + V G Sbjct: 31 LSCVYCKKELTRAEVYNFACTELKLVYRDDFPYAVCRVCLLFYSKVRKYRYYDYSVYGAT 90 Query: 75 AELLHGKTLDRLCIRCCYCGGKLTKNEKHRHVLFNEPFCKTRANIIRGRCYDCCRHGSR 133 E + K L L IRC C LT EK H F A+ G C C R SR Sbjct: 91 LESITKKQLCDLLIRCYRCQSPLTPEEKQLHCDRKRRF-HLIAHGWTGSCLGCWRQTSR 148 >swiss|Q07856|VE6_HPV65 E6 protein. Length = 140 Score = 38.1 bits (87), Expect = 4e-06 Identities = 30/115 (26%), Positives = 49/115 (42%), Gaps = 1/115 (0%) Query: 15 LDCLWCREPLTEVDAFRCMVKDFHVVIREGCRYGACTICLENCLATERRLWQGVPVTGEE 74 L C++C + D +K +V R GC Y C+ CL E+ + + Sbjct: 25 LTCIFCSHTVDLQDLASFYLKKLSLVFRGGCYYACCSECLRLSARFEQENYFQCSIKAVN 84 Query: 75 AELLHGKTLDRLCIRCCYCGGKLTKNEKHRHVLFNEPFCKTRANIIRGRCYDCCR 129 E + + + +CIRC C L EK +L+++ C + RG C +C R Sbjct: 85 LEEVAQRKIKEICIRCICCLRLLDIVEK-LDLLYSDQACYLIRGLWRGYCRNCIR 138 >swiss|P30735|VE6_MNPV E6 protein. Length = 207 Score = 29.3 bits (64), Expect = 0.002 Identities = 32/113 (28%), Positives = 42/113 (36%), Gaps = 1/113 (0%) Query: 15 LDCLWCREPLTEVDAFRCMVKDFHVVIREGCRYGACTICLENCLATERRLWQGVPVTGEE 74 L C +C LT+ + F++V R C +G CT C C + + L + Sbjct: 93 LPCTFCSRFLTQEELTAFDFSAFNLVWRGRCAHGICTACARVCASLDLFLHHQNSRPLAD 152 Query: 75 AELLHGKTLDRLCIRCCYCGGKLTKNEKHRHVLFNEPFCKTRANIIRGRCYDC 127 TL L RC C L+ EK E F K R R RC C Sbjct: 153 VLRDENLTLHGLKARCRVCMKILSVTEKLECAERGESFAKVRGQ-WRARCRIC 204 >trembl|Q15219|Q15219 Protein p84. Length = 657 Score = 18.9 bits (37), Expect = 2.8 Identities = 7/13 (53%), Positives = 9/13 (68%) Query: 69 PVTGEEAELLHGK 81 PVTGE+ E+ K Sbjct: 568 PVTGEQIEVFANK 580 Searching.done Results from round 2 Score E Sequences producing significant alignments: (bits) Value Sequences used in model and found again: swiss|P06931|VE6_BPV1 E6 protein. 180 8e-49 swiss|P24836|VE6_HPV56 E6 protein. 149 2e-39 swiss|P30735|VE6_MNPV E6 protein. 132 1e-34 swiss|Q07856|VE6_HPV65 E6 protein. 132 1e-34 Sequences not found previously or not previously below threshold: swiss|P33418|LOS1_YEAST LOS1 protein. 18 5.4 swiss|P13742|REP2_ZYGFE Trans-acting factor C (REP2). 17 7.5 CONVERGED! >swiss|P06931|VE6_BPV1 E6 protein. Length = 137 Score = 180 bits (457), Expect = 8e-49 Identities = 137/137 (100%), Positives = 137/137 (100%) Query: 1 MDLKPFARTNPFSGLDCLWCREPLTEVDAFRCMVKDFHVVIREGCRYGACTICLENCLAT 60 MDLKPFARTNPFSGLDCLWCREPLTEVDAFRCMVKDFHVVIREGCRYGACTICLENCLAT Sbjct: 1 MDLKPFARTNPFSGLDCLWCREPLTEVDAFRCMVKDFHVVIREGCRYGACTICLENCLAT 60 Query: 61 ERRLWQGVPVTGEEAELLHGKTLDRLCIRCCYCGGKLTKNEKHRHVLFNEPFCKTRANII 120 ERRLWQGVPVTGEEAELLHGKTLDRLCIRCCYCGGKLTKNEKHRHVLFNEPFCKTRANII Sbjct: 61 ERRLWQGVPVTGEEAELLHGKTLDRLCIRCCYCGGKLTKNEKHRHVLFNEPFCKTRANII 120 Query: 121 RGRCYDCCRHGSRSKYP 137 RGRCYDCCRHGSRSKYP Sbjct: 121 RGRCYDCCRHGSRSKYP 137 >swiss|P24836|VE6_HPV56 E6 protein. Length = 155 Score = 149 bits (376), Expect = 2e-39 Identities = 34/119 (28%), Positives = 48/119 (39%), Gaps = 1/119 (0%) Query: 15 LDCLWCREPLTEVDAFRCMVKDFHVVIREGCRYGACTICLENCLATERRLWQGVPVTGEE 74 L C++C++ LT + + + +V R+ Y C +CL + + V G Sbjct: 31 LSCVYCKKELTRAEVYNFACTELKLVYRDDFPYAVCRVCLLFYSKVRKYRYYDYSVYGAT 90 Query: 75 AELLHGKTLDRLCIRCCYCGGKLTKNEKHRHVLFNEPFCKTRANIIRGRCYDCCRHGSR 133 E + K L L IRC C LT EK H F A+ G C C R SR Sbjct: 91 LESITKKQLCDLLIRCYRCQSPLTPEEKQLHCDRKRRF-HLIAHGWTGSCLGCWRQTSR 148 Score = 18.6 bits (37), Expect = 3.3 Identities = 10/36 (27%), Positives = 15/36 (40%) Query: 66 QGVPVTGEEAELLHGKTLDRLCIRCCYCGGKLTKNE 101 Q P + + L L + C YC +LT+ E Sbjct: 9 QERPRSLHHLSEVLEIPLIDLRLSCVYCKKELTRAE 44 >swiss|P30735|VE6_MNPV E6 protein. Length = 207 Score = 132 bits (334), Expect = 1e-34 Identities = 32/113 (28%), Positives = 42/113 (36%), Gaps = 1/113 (0%) Query: 15 LDCLWCREPLTEVDAFRCMVKDFHVVIREGCRYGACTICLENCLATERRLWQGVPVTGEE 74 L C +C LT+ + F++V R C +G CT C C + + L + Sbjct: 93 LPCTFCSRFLTQEELTAFDFSAFNLVWRGRCAHGICTACARVCASLDLFLHHQNSRPLAD 152 Query: 75 AELLHGKTLDRLCIRCCYCGGKLTKNEKHRHVLFNEPFCKTRANIIRGRCYDC 127 TL L RC C L+ EK E F K R R RC C Sbjct: 153 VLRDENLTLHGLKARCRVCMKILSVTEKLECAERGESFAKVRGQ-WRARCRIC 204 >swiss|Q07856|VE6_HPV65 E6 protein. Length = 140 Score = 132 bits (333), Expect = 1e-34 Identities = 30/115 (26%), Positives = 49/115 (42%), Gaps = 1/115 (0%) Query: 15 LDCLWCREPLTEVDAFRCMVKDFHVVIREGCRYGACTICLENCLATERRLWQGVPVTGEE 74 L C++C + D +K +V R GC Y C+ CL E+ + + Sbjct: 25 LTCIFCSHTVDLQDLASFYLKKLSLVFRGGCYYACCSECLRLSARFEQENYFQCSIKAVN 84 Query: 75 AELLHGKTLDRLCIRCCYCGGKLTKNEKHRHVLFNEPFCKTRANIIRGRCYDCCR 129 E + + + +CIRC C L EK +L+++ C + RG C +C R Sbjct: 85 LEEVAQRKIKEICIRCICCLRLLDIVEK-LDLLYSDQACYLIRGLWRGYCRNCIR 138 >swiss|P33418|LOS1_YEAST LOS1 protein. Length = 1100 Score = 17.8 bits (35), Expect = 5.4 Identities = 6/20 (30%), Positives = 6/20 (30%), Gaps = 2/20 (10%) Query: 83 LDRLCIRCCYCGGKLTKNEK 102 L I C C L K Sbjct: 263 LKETKISCYNC--ILAIISK 280 >swiss|P13742|REP2_ZYGFE Trans-acting factor C (REP2). Length = 200 Score = 17.4 bits (34), Expect = 7.5 Identities = 4/11 (36%), Positives = 4/11 (36%) Query: 110 EPFCKTRANII 120 E F K I Sbjct: 9 ERFGKAIRKIW 19 Database: /home/mika/Theses/Databases/unique_set/NMP_Database_unique .fasta Posted date: Mar 7, 2003 12:04 PM Number of letters in database: 17,163 Number of sequences in database: 43 Lambda K H 0.325 0.162 0.512 Lambda K H 0.267 0.0495 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 12,415 Number of Sequences: 43 Number of extensions: 618 Number of successful extensions: 32 Number of sequences better than 10.0: 15 Number of HSP's better than 10.0 without gapping: 15 Number of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempted gapping in prelim test: 0 Number of HSP's gapped (non-prelim): 22 length of query: 137 length of database: 17,163 effective HSP length: 48 effective length of query: 89 effective length of database: 15,099 effective search space: 1343811 effective search space used: 1343811 T: 11 A: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 33 (18.1 bits) S2: 33 (17.0 bits) BLASTP 2.2.2 [Dec-14-2001] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= swiss|O08579|EMD_MOUSE Emerin. (259 letters) Database: /home/mika/Theses/Databases/unique_set/NMP_Database_unique.f asta 43 sequences; 17,163 total letters Searching.done Results from round 1 Score E Sequences producing significant alignments: (bits) Value swiss|O08579|EMD_MOUSE Emerin. 429 e-123 trembl|Q9FLH0|Q9FLH0 Nuclear matrix constituent protein 1 (NMCP... 21 1.3 swiss|P12978|EBN2_EBV EBNA-2 nuclear protein. 20 4.0 trembl|Q9C2H8|Q9C2H8 Related to ser/arg-related nuclear matrix ... 19 6.6 swiss|P14733|LAM1_MOUSE Lamin B1. 19 6.6 >swiss|O08579|EMD_MOUSE Emerin. Length = 259 Score = 429 bits (1103), Expect = e-123 Identities = 259/259 (100%), Positives = 259/259 (100%) Query: 1 MDDYAVLSDTELAAVLRQYNIPHGPIVGSTRKLYEKKIFEYETQRRRLLPPNSSSSSFSY 60 MDDYAVLSDTELAAVLRQYNIPHGPIVGSTRKLYEKKIFEYETQRRRLLPPNSSSSSFSY Sbjct: 1 MDDYAVLSDTELAAVLRQYNIPHGPIVGSTRKLYEKKIFEYETQRRRLLPPNSSSSSFSY 60 Query: 61 QFSDLDSAAVDSDMYDLPKKEDALLYQSKDYNDDYYEESYLTTKTYGEPESVGMSKSFRQ 120 QFSDLDSAAVDSDMYDLPKKEDALLYQSKDYNDDYYEESYLTTKTYGEPESVGMSKSFRQ Sbjct: 61 QFSDLDSAAVDSDMYDLPKKEDALLYQSKDYNDDYYEESYLTTKTYGEPESVGMSKSFRQ 120 Query: 121 PGTSLVDADTFHHQVRDDIFSSLEEEGKDRERLIYGQDSAYQSIAHYRPISNVSRSSLGL 180 PGTSLVDADTFHHQVRDDIFSSLEEEGKDRERLIYGQDSAYQSIAHYRPISNVSRSSLGL Sbjct: 121 PGTSLVDADTFHHQVRDDIFSSLEEEGKDRERLIYGQDSAYQSIAHYRPISNVSRSSLGL 180 Query: 181 SYYPTSSTSSVSSSSSSPSSWLTRRAIRPEKQAPAAALGQDRQVPLWGQLLLFLVFAAFL 240 SYYPTSSTSSVSSSSSSPSSWLTRRAIRPEKQAPAAALGQDRQVPLWGQLLLFLVFAAFL Sbjct: 181 SYYPTSSTSSVSSSSSSPSSWLTRRAIRPEKQAPAAALGQDRQVPLWGQLLLFLVFAAFL 240 Query: 241 LFVYYSIQAEEGNPFWMDP 259 LFVYYSIQAEEGNPFWMDP Sbjct: 241 LFVYYSIQAEEGNPFWMDP 259 >trembl|Q9FLH0|Q9FLH0 Nuclear matrix constituent protein 1 (NMCP1)-like. Length = 1042 Score = 21.2 bits (43), Expect = 1.3 Identities = 18/66 (27%), Positives = 30/66 (45%), Gaps = 4/66 (6%) Query: 116 KSFRQPGTSLVDADTFHHQVRDDIFSSLEEEGKDRERLIYGQDSAYQSIAHYRPISNVSR 175 KS +Q L+DA +Q D IF+ +E + L G D+A + R + Sbjct: 247 KSLQQEHERLLDAQVSLNQREDHIFARSQELAE----LEKGLDTAKTTFEEERKAFEDKK 302 Query: 176 SSLGLS 181 S+L ++ Sbjct: 303 SNLEIA 308 >swiss|P12978|EBN2_EBV EBNA-2 nuclear protein. Length = 487 Score = 19.6 bits (39), Expect = 4.0 Identities = 6/16 (37%), Positives = 11/16 (68%) Query: 19 YNIPHGPIVGSTRKLY 34 Y++ HGP+ + R L+ Sbjct: 120 YDVGHGPLASAMRMLW 135 Score = 18.5 bits (36), Expect = 7.9 Identities = 9/32 (28%), Positives = 14/32 (43%) Query: 49 LPPNSSSSSFSYQFSDLDSAAVDSDMYDLPKK 80 + P S+ Y F +S + D D + P K Sbjct: 449 IDPADLDESWDYIFETTESPSSDEDYVEGPSK 480 >trembl|Q9C2H8|Q9C2H8 Related to ser/arg-related nuclear matrix protein. Length = 976 Score = 18.9 bits (37), Expect = 6.6 Identities = 7/20 (35%), Positives = 10/20 (50%) Query: 148 KDRERLIYGQDSAYQSIAHY 167 +DR G D YQ + H+ Sbjct: 442 RDRREYPIGDDPRYQQLDHH 461 >swiss|P14733|LAM1_MOUSE Lamin B1. Length = 587 Score = 18.9 bits (37), Expect = 6.6 Identities = 12/52 (23%), Positives = 25/52 (48%) Query: 138 DIFSSLEEEGKDRERLIYGQDSAYQSIAHYRPISNVSRSSLGLSYYPTSSTS 189 +I ++++ D E+L+ + + I+ YR + L LS P+S + Sbjct: 348 EIRDQMQQQLSDYEQLLDVKLALDMEISAYRKLLEGEEERLKLSPSPSSRVT 399 Searching.done Results from round 2 Score E Sequences producing significant alignments: (bits) Value Sequences used in model and found again: swiss|O08579|EMD_MOUSE Emerin. 473 e-137 Sequences not found previously or not previously below threshold: trembl|Q9FLH0|Q9FLH0 Nuclear mat