Результат работы orf finder
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- GeneMark.hmm 2.4
Результат работы ORF Finder.
1)ref|ZP_07322565.1| dihydroneopterin aldolase [Prevotella disiens FB035-09AN] длина белка – 125 аминокислот MELKSSYIYIKGARFRACIGVSELEREVGNDYVADLRLRYHIGKAMLSDDVNDTISYADV 60 M+L+SSYIYIKG + A IGVSELER+VGNDYV +LRLRY+I KAMLSDDV DT++YA+V MQLESSYIYIKGIKLHAFIGVSELERKVGNDYVVNLRLRYNIEKAMLSDDVADTLNYAEV 60 YDIVKETMQQPAKLLEYVAHRIAERLEQAFPDIEAIDLCLTKLNPPMGADCNGAGVELHL Y+++K+ M P KLLE+ AH I L + FP IE I L LTKLNPPMGADC GAGVELH+ YEVLKKVMLTPVKLLEHAAHNIEVELGKQFPQIEEIHLQLTKLNPPMGADCYGAGVELHV INDKT 125 IN+K+
INEKS 125 2)ref|ZP_05858616.1| N-acetylmuramoyl-L-alanine amidase [Prevotella veroralis F0319] длина белка – 89 аминокислот MGKRISLFLIMFCLFALASVSAKDKFTVVIDPGHGGKDVGAVGAISNEKSINLNIALALG 74 M K+I+LF++ F LF S +A +FT+VID GHGG D GA+GAIS EK INLN+ALA G MFKKITLFIVFFVLFVGTSWAANGRFTLVIDAGHGGHDAGALGAISKEKDINLNVALAFG 60 NLIERNLSDVRVIYTRKTDVFISLKGRAE 103 +E+NL DV+VIYTRKTDVFI L RA+ RYVEQNLPDVQVIYTRKTDVFIPLHQRAD 89 3)ref|ZP_07322472.1| ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent [Prevotella disiens FB035-09AN] выравнивание произошло только с 794 по 865 аминокислотный остатки
Кассетные интроны, десу. 
http://genome.ucsc.edu/cgi-bin/hgc?hgsid=180410463&g=htcCdnaAli&i=BM563208&c=chr5&l=175819443&r=175843653&o=175819628&aliTable=intronEst&table=intronEst Тут он есть tcctcccatc agagtgcata ctgttattta gcccatttta tgacaaagaa 175825347 agtggctggc acacgctttc ttgagtcttc tgctttgggg gtatcaaaac 175825297 ctataactgg gccagaggca atgatcaggc acagagaggg tgagtaactt 175825247 gcccgcagtc acacaggtgg cggagtgttg ctggcagagg gaacagcaag 175825197 tgcaaagata ggtgtagtca ccagagacag tgggtatgag gttgtttgag 175825147 gctgagttat ccagacatga gtgggtcccc agcaggggca gcagagacag 175825097 cggggcaggt gtgctggctg gatagactgc tgcgtgtttg tgttctagGA 175825047 GGCCAACGGT CCTGCTGATG GCTACGCAGC CATTGCCCAG GCTGACAGGC 175824997 TGACCCAGGA GCCTGAGAGC ATCCGCAAGT GGCGAGAGGA GCAGAGGAAA 175824947 CGGCTGCAAG AGCTGGgtga gggcggggct gaggcggggt tggctgggtg 175824897 ggctgtgtgt ggggtggagt gtggggagtc ctcggagtgc atgggatgct 175824847 gcatgcctta atgtgggact gggccggtgc ggccctgtgg ctgcctggca 175824797 ggggccaggg gaggagcgcg gccgggcctg tgcatcccag ctggaaagca 175824747 gccactcatt ctcttgtggg gtcctagATG CTGCATCTAA GGTCACGGAA 175824697 CAGGAATGGC GGGAGAAGGC CAAGAAGGAC CTGGAGGAGT GGAACCAGCG 175824647 CCAGAGTGAA CAAGTAGAGA AGAACAAGAT CAACAACCGg tgagagggct 175824597 gtagggacat gagggggcca tggggacatg aggggggctg tggggacatg 175824547 agggggccgt ggggacatga gggggccatg gggacatgaa ggggtgggga 175824497 catgagggag ctgtggggac atgagggggc cgtggggaca tgagacgggc 175824447 tgtggggaca tgagggagct gtggggacat gagaggggct gtggggacat 175824397 gagagggagc tgtggggaca tgagagggag ctgtggggac atgagagggg 175824347 ctgtggggac atgagagggg ctatggggac atgagagggg ctgtggggac 175824297 atgactgaac actgcccagt gctccctgcc tttgaggctc tgtccttcac 175824247 ggtacaaggt cttccaggaa gggaaaggcc tgttctggga agctaccctt 175824197 http://genome.ucsc.edu/cgi-bin/hgc?hgsid=180410463&g=htcCdnaAli&i=BQ637226&c=chr5&l=175819443&r=175843653&o=175819630&aliTable=intronEst&table=intronEst tgggattaca ggcatgcacc accacgcctg gctaattttt tgtattttta 175825549 gtagagtcgg gatttctcca tgttggtcag gctggtcttg aactcccaac 175825499 ctcaggtgat ttgccgcctc ggcctcccaa agtgttggga ttacaggtgt 175825449 gagccactgc gcccgacatt ctttataatt tttaactcat ttcatcctta 175825399 tgtcctccca tcagagtgca tactgttatt tagcccattt tatgacaaag 175825349 aaagtggctg gcacacgctt tcttgagtct tctgctttgg gggtatcaaa 175825299 acctataact gggccagagg caatgatcag gcacagagag ggtgagtaac 175825249 ttgcccgcag tcacacaggt ggcggagtgt tgctggcaga gggaacagca 175825199 agtgcaaaga taggtgtagt caccagagac agtgggtatg aggttgtttg 175825149 aggctgagtt atccagacat gagtgggtcc ccagcagggg cagcagagac 175825099 agcggggcag gtgtgctggc tggatagact gctgcgtgtt tgtgttctag 175825049 GAGGCCAACG GTCCTGCTGA TGGCTACGCA GCCATTGCCC AGGCTGACAG 175824999 GCTGACCCAG GAGCCTGAGA GCATCCGCAA GTGGCGAGAG GAGCAGAGGA 175824949 AACGGCTGCA AGAGCTGGgt gagggcgggg ctgaggcggg gttggctggg 175824899 tgggctgtgt gtggggtgga gtgtggggag tcctcggagt gcatgggatg 175824849 ctgcatgcct taatgtggga ctgggccggt gcggccctgt ggctgcctgg 175824799 caggggccag gggaggagcg cggccgggcc tgtgcatccc agctggaaag 175824749 cagccactca ttctcttgtg gggtcctagA TGCTGCATCT AAGGTCACGG 175824699 AACAGGAATG GCGGGAGAAG gccaagaagg acctggagga gtggaaccag 175824649 cgccagagtg aacaagtaga gaagaacaag atcaacaacc ggtgagaggg 175824599 ctgtagggac atgagggggc catggggaca tgaggggggc tgtggggaca 175824549 tgagggggcc gtggggacat gagggggcca tggggacatg aaggggtggg 175824499 gacatgaggg agctgtgggg acatgagggg gccgtgggga catgagacgg 175824449 gctgtgggga catgagggag ctgtggggac atgagagggg ctgtggggac 175824399 atgagaggga gctgtgggga catgagaggg agctgtgggg acatgagagg 175824349 ggctgtgggg acatgagagg ggctatgggg acatgagagg ggctgtgggg 175824299 acatgactga acactgccca gtgctccctg cctttgaggc tctgtccttc 175824249 Blastx смог найти два возможных гена, но один из них находится на границе последовательности — выравнивание по первому нуклеотиду начинается с 231 аминокислоты. Если это место действительно является геном данного белка, то его начало просто осталось за пределами выравнивания.
monooxygenase/ oxygen binding [Arabidopsis thaliana]
В данном выравнивании blastx предложил для каждого из экзонов по два варианта координат по белку, причем разница в выравниваниях всего 1%. Мною были выбраны те два экзона, у которых больший процент совпадений, хотя, теоретически, оба выравнивания хорошие. Score = 269 bits (688), Expect = 8e-71 Identities = 133/209 (64%), Positives = 170/209 (82%), Gaps = 3/209 (1%) Frame = -1 Query 14204 LILAGSDTTMVTLTWALSLLLNNPRVLKRAQDELDMHVGKDRPLEESDISNLVYLQSIVK 14025 LIL GS+T+ TLTWA+SLLLNN +LK+ QDE+D+HVG+DR +E+SDI NLVYLQ+I+K Sbjct 306 LILGGSETSPSTLTWAISLLLNNKDMLKKVQDEIDIHVGRDRNVEDSDIKNLVYLQAIIK 365 Query 14024 ETLRLYPPSPIIGLRAALEDCTLSTGYHIPSGTRLMVNAWKIQRDERVWPDPHDFQPERF 13845 ETLRLYP +P++G R A+EDCT++ GY++P GTRL+VN WKIQRD +V+ +P++F+PERF Sbjct 366 ETLRLYPAAPLLGHREAMEDCTVA-GYNVPCGTRLIVNVWKIQRDPKVYMEPNEFRPERF 424 Query 13844 LTSH-KDMDFRGQTFELIPFGSGRRSCPGTSLALKMVHFILGRFLHSFDVAKPSKLEDVD 13668 +T KD D RGQ FEL+PFGSGRRSCPG SLA++M+H L RFLHSF+V K VD Sbjct 425 ITGEAKDFDVRGQNFELMPFGSGRRSCPGPSLAMQMLHLGLARFLHSFEV-KTVLDRPVD 483 Query 13667 MTESAGLTNLKATPLEVLVTPRLNSQLYV 13581 M+ES GLT KATPLEVL+ PRL +L+V Sbjct 484 MSESPGLTITKATPLEVLINPRLKRELFV 512 Score = 254 bits (648), Expect = 4e-66 Identities = 128/208 (62%), Positives = 165/208 (80%), Gaps = 4/208 (1%) Frame = -2 Query 18010 LVLAGSDTTMITLTWALSLLLNNPRVLKRAQDELDMHVGKDRLLEESDIRNLVYLHAIVK 17831 L+L GS+T+ TLTWA+SLLLNN +LK+ QDE+D+HVG+DR +E+SDI+NLVYL AI+K Sbjct 306 LILGGSETSPSTLTWAISLLLNNKDMLKKVQDEIDIHVGRDRNVEDSDIKNLVYLQAIIK 365 Query 17830 ETLRLYPPSPII-FRASMEDCTLSTGYHIPAGTRLMVNAWKIQRDERVWPDPHVFKPERF 17654 ETLRLYP +P++ R +MEDCT++ GY++P GTRL+VN WKIQRD +V+ +P+ F+PERF Sbjct 366 ETLRLYPAAPLLGHREAMEDCTVA-GYNVPCGTRLIVNVWKIQRDPKVYMEPNEFRPERF 424 Query 17653 LTSH-KDMEFRGQTFELIPFGSGRRSCPGVSLALQVVHSALASFLQSFEVSKPSKLEDID 17477 +T KD + RGQ FEL+PFGSGRRSCPG SLA+Q++H LA FL SFEV K +D Sbjct 425 ITGEAKDFDVRGQNFELMPFGSGRRSCPGPSLAMQMLHLGLARFLHSFEV-KTVLDRPVD 483 Query 17476 MTESTGLTNLKATPLEVLFTPRLDSKLY 17393 M+ES GLT KATPLEVL PRL +L+ Sbjct 484 MSESPGLTITKATPLEVLINPRLKRELF 511 Score = 265 bits (678), Expect = 1e-69 Identities = 143/318 (45%), Positives = 205/318 (65%), Gaps = 24/318 (7%) Frame = -1 Query 15599 LFTTVCSLVALLSCIYFYQSKKASTHGKRCCTPPQAGGALPVIGHMHLLGG-QQLTHKTL 15423 LF+ S++ + F +SKK + P GA P+IGH+HLLGG +QL ++TL Sbjct 5 LFSLFVSILVFVFIALFKKSKKP-----KYVKAPAPSGAWPIIGHLHLLGGKEQLLYRTL 59 Query 15422 GAMADKYGPVFSIRLGSHRVLVLNSWEMAKECFTVHDKVFSTRPSIAASKHLGYDFAMFG 15243 G MAD YGP S+RLGS V +S+E+AK+CFTV+DK ++ + AA+KH+GY F Sbjct 60 GKMADHYGPAMSLRLGSSETFVGSSFEVAKDCFTVNDKALASLMT-AAAKHMGYVF---- 114 Query 15242 FAPYGSYWREMRKIATIELLSSHRIDMLKHIRASEVKTAIRELYKSWLSKGSAETEVFVD 15063 W EMRKIA IELLS+ R+ ML ++R SE+ +++LY W+ KG +E V VD Sbjct 115 -------WLEMRKIAMIELLSNRRLQMLNNVRVSEISMGVKDLYSLWVKKGGSEP-VMVD 166 Query 15062 MKQWFGDLTHNIALRMVGGRRYFGPN-ADCEE--ADARRCQKVMRDFVYLFGVFVLSDAI 14892 +K W D+ N+ +RMV G+RYFG A+ E +AR+ +K + F +L G+F +SDA Sbjct 167 LKSWLEDMIANMIMRMVAGKRYFGGGGAESSEHTEEARQWRKGIAKFFHLVGIFTVSDAF 226 Query 14891 PFLGWLDFQGYEKSMKRTAKQLDSLVERWLEEHKQKRLSGGGVIEEQDFMDVMLNILEDG 14712 P LGWLD QG+EK MK+T ++LD ++ERW+E H+Q+R G + DF+DVML++ E G Sbjct 227 PKLGWLDLQGHEKEMKQTRRELDVILERWIENHRQQRKVSGTKHNDSDFVDVMLSLAEQG 286 Query 14711 KIT--GFDADTINKATCL 14664 K++ +DA+T K TCL Sbjct 287 KLSHLQYDANTCIKTTCL 304 Score = 258 bits (658), Expect = 3e-67 Identities = 139/318 (44%), Positives = 203/318 (64%), Gaps = 24/318 (7%) Frame = -3 Query 19752 LFTLVCSLVALLSCIYFYQSKKSSTHRKRVCTAPQAGGALPVIGHMHLLGG-HQLTHKTL 19576 LF+L S++ + F +SKK + AP GA P+IGH+HLLGG QL ++TL Sbjct 5 LFSLFVSILVFVFIALFKKSKKP-----KYVKAPAPSGAWPIIGHLHLLGGKEQLLYRTL 59 Query 19575 GAMADKYGPVFSIRLGSHSALVLNSWEMARECFTVHDKVFSTRPVLTASKVLGYNYAMFG 19396 G MAD YGP S+RLGS V +S+E+A++CFTV+DK ++ + A+K +GY Sbjct 60 GKMADHYGPAMSLRLGSSETFVGSSFEVAKDCFTVNDKALASL-MTAAAKHMGY------ 112 Query 19395 FAPYGSYWREIRRIATIELLSSHRIDMLKHIRASEVKTAVRELYKSWLSKGGGETGVLVD 19216 +W E+R+IA IELLS+ R+ ML ++R SE+ V++LY W+ KGG E V+VD Sbjct 113 -----VFWLEMRKIAMIELLSNRRLQMLNNVRVSEISMGVKDLYSLWVKKGGSEP-VMVD 166 Query 19215 MKQWFGDLTHNIALRMVGGKRFFGPN-ADCEE--AEARRCQKVMRDSAYLFGVFVVSDAL 19045 +K W D+ N+ +RMV GKR+FG A+ E EAR+ +K + +L G+F VSDA Sbjct 167 LKSWLEDMIANMIMRMVAGKRYFGGGGAESSEHTEEARQWRKGIAKFFHLVGIFTVSDAF 226 Query 19044 PFIGWLDFQGYEKAMKRTAKELDILLGGWLEEHKQKKHLGGGLKKEQDFMDVMLNILEDA 18865 P +GWLD QG+EK MK+T +ELD++L W+E H+Q++ + G + DF+DVML++ E Sbjct 227 PKLGWLDLQGHEKEMKQTRRELDVILERWIENHRQQRKVSGTKHNDSDFVDVMLSLAEQG 286 Query 18864 KIT--SFDADTINKATCL 18817 K++ +DA+T K TCL Sbjct 287 KLSHLQYDANTCIKTTCL 304 жүктеу/скачать 115 Kb. Достарыңызбен бөлісу:
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