Mercurial > repos > devteam > ncbi_blast_plus
diff test-data/tblastn_four_human_vs_rhodopsin.html @ 21:7538e2bfcd41 draft
v0.2.00, for NCBI BLAST+ 2.5.0 via bioconda or tool_dependencies.xml
| author | peterjc |
|---|---|
| date | Wed, 19 Apr 2017 05:27:19 -0400 |
| parents | 577d9c12411a |
| children | 31e517610e1f |
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--- a/test-data/tblastn_four_human_vs_rhodopsin.html Mon Nov 07 11:31:37 2016 -0500 +++ b/test-data/tblastn_four_human_vs_rhodopsin.html Wed Apr 19 05:27:19 2017 -0400 @@ -3,31 +3,22 @@ <BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099"> <PRE> -<b>TBLASTN 2.2.31+</b> +<b>TBLASTN 2.5.0+</b> -<b>Query=</b> sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 -OS=Homo sapiens GN=ERP44 PE=1 SV=1 - -Length=406 - -<b>Subject=</b> gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA - -Length=1047 - - -***** No hits found ***** +<b><a +href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=R +etrieve&list_uids=9254694&dopt=Citation">Reference</a>:</b> +Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer, +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. -Lambda K H a alpha - 0.347 0.182 0.684 0.522 1.92 +Database: User specified sequence set (Input: rhodopsin_nucs.fasta). + 6 sequences; 10,296 total letters -Gapped -Lambda K H a alpha sigma - 0.299 0.0710 0.270 1.10 13.8 14.5 - -Effective search space used: 127710 <b>Query=</b> sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 @@ -35,61 +26,6 @@ Length=406 -<b>Subject=</b> gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete -cds - -Length=1574 - - -***** No hits found ***** - - - -Lambda K H a alpha - 0.347 0.182 0.684 0.522 1.92 - -Gapped -Lambda K H a alpha sigma - 0.299 0.0710 0.270 1.10 13.8 14.5 - -Effective search space used: 127710 - - -<b>Query=</b> sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 -OS=Homo sapiens GN=ERP44 PE=1 SV=1 - -Length=406 - -<b>Subject=</b> gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434 -rhodopsin (RHO) gene, exons 1 through 5 and partial cds - -Length=4301 - - -***** No hits found ***** - - - -Lambda K H a alpha - 0.347 0.182 0.684 0.522 1.92 - -Gapped -Lambda K H a alpha sigma - 0.299 0.0710 0.270 1.10 13.8 14.5 - -Effective search space used: 127710 - - -<b>Query=</b> sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 -OS=Homo sapiens GN=ERP44 PE=1 SV=1 - -Length=406 - -<b>Subject=</b> gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin -(RHO) mRNA, partial cds - -Length=983 - ***** No hits found ***** @@ -102,57 +38,7 @@ Lambda K H a alpha sigma 0.299 0.0710 0.270 1.10 13.8 14.5 -Effective search space used: 127710 - - -<b>Query=</b> sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 -OS=Homo sapiens GN=ERP44 PE=1 SV=1 - -Length=406 - -<b>Subject=</b> gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for -rhodopsin, complete cds - -Length=1047 - - -***** No hits found ***** - - - -Lambda K H a alpha - 0.347 0.182 0.684 0.522 1.92 - -Gapped -Lambda K H a alpha sigma - 0.299 0.0710 0.270 1.10 13.8 14.5 - -Effective search space used: 127710 - - -<b>Query=</b> sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 -OS=Homo sapiens GN=ERP44 PE=1 SV=1 - -Length=406 - -<b>Subject=</b> gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh -water form rod opsin, complete cds - -Length=1344 - - -***** No hits found ***** - - - -Lambda K H a alpha - 0.347 0.182 0.684 0.522 1.92 - -Gapped -Lambda K H a alpha sigma - 0.299 0.0710 0.270 1.10 13.8 14.5 - -Effective search space used: 127710 +Effective search space used: 1239330 <b>Query=</b> sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens @@ -160,60 +46,6 @@ Length=1161 -<b>Subject=</b> gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA - -Length=1047 - - -***** No hits found ***** - - - -Lambda K H a alpha - 0.334 0.170 0.615 0.522 1.92 - -Gapped -Lambda K H a alpha sigma - 0.299 0.0710 0.270 1.10 13.8 14.5 - -Effective search space used: 370988 - - -<b>Query=</b> sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens -GN=BMP2K PE=1 SV=2 - -Length=1161 - -<b>Subject=</b> gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete -cds - -Length=1574 - - -***** No hits found ***** - - - -Lambda K H a alpha - 0.334 0.170 0.615 0.522 1.92 - -Gapped -Lambda K H a alpha sigma - 0.299 0.0710 0.270 1.10 13.8 14.5 - -Effective search space used: 370988 - - -<b>Query=</b> sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens -GN=BMP2K PE=1 SV=2 - -Length=1161 - -<b>Subject=</b> gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434 -rhodopsin (RHO) gene, exons 1 through 5 and partial cds - -Length=4301 - ***** No hits found ***** @@ -226,82 +58,7 @@ Lambda K H a alpha sigma 0.299 0.0710 0.270 1.10 13.8 14.5 -Effective search space used: 370988 - - -<b>Query=</b> sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens -GN=BMP2K PE=1 SV=2 - -Length=1161 - -<b>Subject=</b> gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin -(RHO) mRNA, partial cds - -Length=983 - - -***** No hits found ***** - - - -Lambda K H a alpha - 0.334 0.170 0.615 0.522 1.92 - -Gapped -Lambda K H a alpha sigma - 0.299 0.0710 0.270 1.10 13.8 14.5 - -Effective search space used: 370988 - - -<b>Query=</b> sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens -GN=BMP2K PE=1 SV=2 - -Length=1161 - -<b>Subject=</b> gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for -rhodopsin, complete cds - -Length=1047 - - -***** No hits found ***** - - - -Lambda K H a alpha - 0.334 0.170 0.615 0.522 1.92 - -Gapped -Lambda K H a alpha sigma - 0.299 0.0710 0.270 1.10 13.8 14.5 - -Effective search space used: 370988 - - -<b>Query=</b> sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens -GN=BMP2K PE=1 SV=2 - -Length=1161 - -<b>Subject=</b> gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh -water form rod opsin, complete cds - -Length=1344 - - -***** No hits found ***** - - - -Lambda K H a alpha - 0.334 0.170 0.615 0.522 1.92 - -Gapped -Lambda K H a alpha sigma - 0.299 0.0710 0.270 1.10 13.8 14.5 - -Effective search space used: 370988 +Effective search space used: 3667980 <b>Query=</b> sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 @@ -309,10 +66,6 @@ Length=1382 -<b>Subject=</b> gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA - -Length=1047 - ***** No hits found ***** @@ -325,143 +78,27 @@ Lambda K H a alpha sigma 0.299 0.0710 0.270 1.10 13.8 14.5 -Effective search space used: 441350 - - -<b>Query=</b> sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 -SV=4 - -Length=1382 - -<b>Subject=</b> gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete -cds - -Length=1574 - - -***** No hits found ***** - - - -Lambda K H a alpha - 0.346 0.180 0.700 0.522 1.92 - -Gapped -Lambda K H a alpha sigma - 0.299 0.0710 0.270 1.10 13.8 14.5 - -Effective search space used: 441350 - - -<b>Query=</b> sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 -SV=4 - -Length=1382 - -<b>Subject=</b> gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434 -rhodopsin (RHO) gene, exons 1 through 5 and partial cds - -Length=4301 - - -***** No hits found ***** - - - -Lambda K H a alpha - 0.346 0.180 0.700 0.522 1.92 - -Gapped -Lambda K H a alpha sigma - 0.299 0.0710 0.270 1.10 13.8 14.5 - -Effective search space used: 441350 - - -<b>Query=</b> sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 -SV=4 - -Length=1382 - -<b>Subject=</b> gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin -(RHO) mRNA, partial cds - -Length=983 - - -***** No hits found ***** - - - -Lambda K H a alpha - 0.346 0.180 0.700 0.522 1.92 - -Gapped -Lambda K H a alpha sigma - 0.299 0.0710 0.270 1.10 13.8 14.5 - -Effective search space used: 441350 - - -<b>Query=</b> sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 -SV=4 - -Length=1382 - -<b>Subject=</b> gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for -rhodopsin, complete cds - -Length=1047 - - -***** No hits found ***** - - - -Lambda K H a alpha - 0.346 0.180 0.700 0.522 1.92 - -Gapped -Lambda K H a alpha sigma - 0.299 0.0710 0.270 1.10 13.8 14.5 - -Effective search space used: 441350 - - -<b>Query=</b> sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 -SV=4 - -Length=1382 - -<b>Subject=</b> gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh -water form rod opsin, complete cds - -Length=1344 - - -***** No hits found ***** - - - -Lambda K H a alpha - 0.346 0.180 0.700 0.522 1.92 - -Gapped -Lambda K H a alpha sigma - 0.299 0.0710 0.270 1.10 13.8 14.5 - -Effective search space used: 441350 +Effective search space used: 4374000 <b>Query=</b> sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 Length=348 - -<b>Subject=</b> gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA + Score E +Sequences producing significant alignments: (Bits) Value + gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA <a href=#Subject_1>732</a> 0.0 + gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene... <a href=#Subject_5>711</a> 0.0 + gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodo... <a href=#Subject_4>658</a> 0.0 + gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, compl... <a href=#Subject_2>646</a> 0.0 + gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fres... <a href=#Subject_6>626</a> 0.0 + gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020... <a href=#Subject_3>151</a> 1e-71 + + +><a name=Subject_1></a> gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), +mRNA Length=1047 - Score = 732 bits (1689), Expect = 0.0, Method: Compositional matrix adjust. Identities = 336/348 (97%), Positives = 343/348 (99%), Gaps = 0/348 (0%) Frame = +1 @@ -491,27 +128,76 @@ Sbjct 901 YNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA 1044 +><a name=Subject_5></a> gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene +for rhodopsin, complete cds +Length=1047 -Lambda K H a alpha - 0.351 0.182 0.707 0.522 1.92 + Score = 711 bits (1640), Expect = 0.0, Method: Compositional matrix adjust. + Identities = 325/348 (93%), Positives = 337/348 (97%), Gaps = 0/348 (0%) + Frame = +1 + +Query 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY 60 + MNGTEGPNFYVPFSN TGVVRSPFE PQYYLAEPWQFSMLAAYMFLLI+LGFPINFLTLY +Sbjct 1 MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLY 180 + +Query 61 VTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLG 120 + VTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLG +Sbjct 181 VTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLG 360 -Gapped -Lambda K H a alpha sigma - 0.299 0.0710 0.270 1.10 13.8 14.5 +Query 121 GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIP 180 + GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIP +Sbjct 361 GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIP 540 + +Query 181 EGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQES 240 + EG+QCSCGIDYYT E NNESFVIYMFVVHF IP+I+IFFCYGQLVFTVKEAAAQQQES +Sbjct 541 EGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQES 720 -Effective search space used: 109230 +Query 241 ATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAI 300 + ATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGS+FGPIFMTIPAFFAK++A+ +Sbjct 721 ATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAV 900 + +Query 301 YNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA 348 + YNPVIYIMMNKQFRNCM+TT+CCGKNPLGDDEAS TVSKTETSQVAPA +Sbjct 901 YNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA 1044 -<b>Query=</b> sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 +><a name=Subject_4></a> gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin +(RHO) mRNA, partial cds +Length=983 + + Score = 658 bits (1517), Expect = 0.0, Method: Compositional matrix adjust. + Identities = 310/326 (95%), Positives = 322/326 (99%), Gaps = 0/326 (0%) + Frame = +1 -Length=348 +Query 11 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRT 70 + VPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRT +Sbjct 1 VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRT 180 + +Query 71 PLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVV 130 + PLNYILLNLAVA+LFMV GGFT+TLYTS+HGYFVFG TGCNLEGFFATLGGEIALWSLVV +Sbjct 181 PLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVV 360 -<b>Subject=</b> gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete -cds +Query 131 LAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGID 190 + LAIERYVVVCKPMSNFRFGENHAIMG+AFTWVMALACAAPPLAGWSRYIPEG+QCSCGID +Sbjct 361 LAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGID 540 + +Query 191 YYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEV 250 + YYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEV +Sbjct 541 YYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEV 720 +Query 251 TRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMN 310 + TRMVIIMV+AFLICW+PYASVAFYIFTHQGSNFGP+FMTIPAFFAKS++IYNPVIYIMMN +Sbjct 721 TRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMN 900 + +Query 311 KQFRNCMLTTICCGKNPLGDDEASAT 336 + KQFRNCMLTT+CCGKNPLGDDEAS T +Sbjct 901 KQFRNCMLTTLCCGKNPLGDDEASTT 978 + + +><a name=Subject_2></a> gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete +cds Length=1574 - Score = 646 bits (1489), Expect = 0.0, Method: Compositional matrix adjust. Identities = 290/342 (85%), Positives = 320/342 (94%), Gaps = 1/342 (0%) Frame = +3 @@ -541,201 +227,10 @@ Sbjct 942 YNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE 1067 - -Lambda K H a alpha - 0.351 0.182 0.707 0.522 1.92 - -Gapped -Lambda K H a alpha sigma - 0.299 0.0710 0.270 1.10 13.8 14.5 - -Effective search space used: 109230 - - -<b>Query=</b> sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 - -Length=348 - -<b>Subject=</b> gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434 -rhodopsin (RHO) gene, exons 1 through 5 and partial cds - -Length=4301 - - - Score = 151 bits (342), Expect(2) = 1e-72, Method: Compositional matrix adjust. - Identities = 69/74 (93%), Positives = 73/74 (99%), Gaps = 0/74 (0%) - Frame = +3 - -Query 239 ESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSA 298 - ESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGSNFGPIFMT+PAFFAKS+ -Sbjct 3147 ESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSS 3326 - -Query 299 AIYNPVIYIMMNKQ 312 - +IYNPVIYIMMNKQ -Sbjct 3327 SIYNPVIYIMMNKQ 3368 - - - Score = 126 bits (284), Expect(2) = 1e-72, Method: Compositional matrix adjust. - Identities = 54/59 (92%), Positives = 57/59 (97%), Gaps = 0/59 (0%) - Frame = +2 - -Query 177 RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA 235 - RYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKE + -Sbjct 2855 RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS 3031 - - - Score = 229 bits (523), Expect = 9e-67, Method: Compositional matrix adjust. - Identities = 107/111 (96%), Positives = 109/111 (98%), Gaps = 0/111 (0%) - Frame = +1 - -Query 11 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRT 70 - VPFSN TGVVRSPFE+PQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRT -Sbjct 1 VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRT 180 - -Query 71 PLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG 121 - PLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGG -Sbjct 181 PLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG 333 - - - Score = 122 bits (276), Expect = 1e-32, Method: Compositional matrix adjust. - Identities = 55/59 (93%), Positives = 56/59 (95%), Gaps = 0/59 (0%) - Frame = +3 - -Query 119 LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR 177 - L GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+A TWVMALACAAPPL GWSR -Sbjct 1404 LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR 1580 - - - Score = 57.7 bits (125), Expect = 2e-12, Method: Compositional matrix adjust. - Identities = 23/26 (88%), Positives = 24/26 (92%), Gaps = 0/26 (0%) - Frame = +1 - -Query 312 QFRNCMLTTICCGKNPLGDDEASATV 337 - QFRNCMLTT+CCGKNPLGDDEAS T -Sbjct 4222 QFRNCMLTTLCCGKNPLGDDEASTTA 4299 - - - -Lambda K H a alpha - 0.351 0.182 0.707 0.522 1.92 - -Gapped -Lambda K H a alpha sigma - 0.299 0.0710 0.270 1.10 13.8 14.5 - -Effective search space used: 109230 - - -<b>Query=</b> sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 - -Length=348 - -<b>Subject=</b> gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin -(RHO) mRNA, partial cds - -Length=983 - - - Score = 658 bits (1517), Expect = 0.0, Method: Compositional matrix adjust. - Identities = 310/326 (95%), Positives = 322/326 (99%), Gaps = 0/326 (0%) - Frame = +1 - -Query 11 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRT 70 - VPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRT -Sbjct 1 VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRT 180 - -Query 71 PLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVV 130 - PLNYILLNLAVA+LFMV GGFT+TLYTS+HGYFVFG TGCNLEGFFATLGGEIALWSLVV -Sbjct 181 PLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVV 360 - -Query 131 LAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGID 190 - LAIERYVVVCKPMSNFRFGENHAIMG+AFTWVMALACAAPPLAGWSRYIPEG+QCSCGID -Sbjct 361 LAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGID 540 - -Query 191 YYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEV 250 - YYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEV -Sbjct 541 YYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEV 720 - -Query 251 TRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMN 310 - TRMVIIMV+AFLICW+PYASVAFYIFTHQGSNFGP+FMTIPAFFAKS++IYNPVIYIMMN -Sbjct 721 TRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMN 900 - -Query 311 KQFRNCMLTTICCGKNPLGDDEASAT 336 - KQFRNCMLTT+CCGKNPLGDDEAS T -Sbjct 901 KQFRNCMLTTLCCGKNPLGDDEASTT 978 - - - -Lambda K H a alpha - 0.351 0.182 0.707 0.522 1.92 - -Gapped -Lambda K H a alpha sigma - 0.299 0.0710 0.270 1.10 13.8 14.5 - -Effective search space used: 109230 - - -<b>Query=</b> sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 - -Length=348 - -<b>Subject=</b> gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for -rhodopsin, complete cds - -Length=1047 - - - Score = 711 bits (1640), Expect = 0.0, Method: Compositional matrix adjust. - Identities = 325/348 (93%), Positives = 337/348 (97%), Gaps = 0/348 (0%) - Frame = +1 - -Query 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY 60 - MNGTEGPNFYVPFSN TGVVRSPFE PQYYLAEPWQFSMLAAYMFLLI+LGFPINFLTLY -Sbjct 1 MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLY 180 - -Query 61 VTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLG 120 - VTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLG -Sbjct 181 VTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLG 360 - -Query 121 GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIP 180 - GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIP -Sbjct 361 GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIP 540 - -Query 181 EGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQES 240 - EG+QCSCGIDYYT E NNESFVIYMFVVHF IP+I+IFFCYGQLVFTVKEAAAQQQES -Sbjct 541 EGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQES 720 - -Query 241 ATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAI 300 - ATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGS+FGPIFMTIPAFFAK++A+ -Sbjct 721 ATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAV 900 - -Query 301 YNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA 348 - YNPVIYIMMNKQFRNCM+TT+CCGKNPLGDDEAS TVSKTETSQVAPA -Sbjct 901 YNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA 1044 - - - -Lambda K H a alpha - 0.351 0.182 0.707 0.522 1.92 - -Gapped -Lambda K H a alpha sigma - 0.299 0.0710 0.270 1.10 13.8 14.5 - -Effective search space used: 109230 - - -<b>Query=</b> sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 - -Length=348 - -<b>Subject=</b> gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh +><a name=Subject_6></a> gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh water form rod opsin, complete cds - Length=1344 - Score = 626 bits (1444), Expect = 0.0, Method: Compositional matrix adjust. Identities = 281/342 (82%), Positives = 311/342 (91%), Gaps = 1/342 (0%) Frame = +2 @@ -765,6 +260,63 @@ Sbjct 923 YNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE 1048 +><a name=Subject_3></a> gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434 +rhodopsin (RHO) gene, exons 1 through 5 and partial cds +Length=4301 + + Score = 151 bits (342), Expect(2) = 1e-71, Method: Compositional matrix adjust. + Identities = 69/74 (93%), Positives = 73/74 (99%), Gaps = 0/74 (0%) + Frame = +3 + +Query 239 ESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSA 298 + ESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGSNFGPIFMT+PAFFAKS+ +Sbjct 3147 ESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSS 3326 + +Query 299 AIYNPVIYIMMNKQ 312 + +IYNPVIYIMMNKQ +Sbjct 3327 SIYNPVIYIMMNKQ 3368 + + + Score = 126 bits (284), Expect(2) = 1e-71, Method: Compositional matrix adjust. + Identities = 54/59 (92%), Positives = 57/59 (97%), Gaps = 0/59 (0%) + Frame = +2 + +Query 177 RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA 235 + RYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKE + +Sbjct 2855 RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS 3031 + + + Score = 229 bits (523), Expect = 3e-67, Method: Compositional matrix adjust. + Identities = 107/111 (96%), Positives = 109/111 (98%), Gaps = 0/111 (0%) + Frame = +1 + +Query 11 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRT 70 + VPFSN TGVVRSPFE+PQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRT +Sbjct 1 VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRT 180 + +Query 71 PLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG 121 + PLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGG +Sbjct 181 PLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG 333 + + + Score = 122 bits (276), Expect = 2e-32, Method: Compositional matrix adjust. + Identities = 55/59 (93%), Positives = 56/59 (95%), Gaps = 0/59 (0%) + Frame = +3 + +Query 119 LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR 177 + L GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+A TWVMALACAAPPL GWSR +Sbjct 1404 LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR 1580 + + + Score = 57.7 bits (125), Expect = 4e-12, Method: Compositional matrix adjust. + Identities = 23/26 (88%), Positives = 24/26 (92%), Gaps = 0/26 (0%) + Frame = +1 + +Query 312 QFRNCMLTTICCGKNPLGDDEASATV 337 + QFRNCMLTT+CCGKNPLGDDEAS T +Sbjct 4222 QFRNCMLTTLCCGKNPLGDDEASTTA 4299 + + Lambda K H a alpha 0.351 0.182 0.707 0.522 1.92 @@ -773,8 +325,13 @@ Lambda K H a alpha sigma 0.299 0.0710 0.270 1.10 13.8 14.5 -Effective search space used: 109230 +Effective search space used: 1049670 + + Database: User specified sequence set (Input: rhodopsin_nucs.fasta). + Posted date: Unknown + Number of letters in database: 10,296 + Number of sequences in database: 6