Отчёт о 3 занятии студентки 202 группы Рудневой Василисы. 1) Заданный геном -- X. campestris На Kodomo-count: formatdb -i xc_genome.fasta -p F -n xc ls formatdb.log xc.nhr xc.nin xc.nsq xc_genome.fasta 2)Поиск в геноме участков, кодирующих белки, похожие на заданный На kodomo-count: blastall -p tblastn -d xc -i KAD_ECOLI.fasta -o kad_xc.blast -e 0.001 ls KAD_ECOLI.fasta kad_xc.blast xc.nin xc_genome.fasta formatdb.log xc.nhr xc.nsq Лучшая находка: AE012446 AE008922 |AE012446| Xanthomonas campestris pv. campestr... 155 5e-39 >AE012446 AE008922 |AE012446| Xanthomonas campestris pv. campestris str. ATCC 33913, section 354 of 460 of the complete genome. Length = 11287 Score = 155 bits (391), Expect = 5e-39 Identities = 90/218 (41%), Positives = 129/218 (59%), Gaps = 4/218 (1%) Frame = -2 Выравнивание: Query: 1 MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAAVKSGSELGKQAKDIMDAGKLVT 60 MR++LLG PG+GKGTQA + + + IP ISTGD+LRA V +GS LG +AK++M G LV+ Sbjct: 4122 MRLVLLGPPGSGKGTQAARLKDTFQIPHISTGDLLRAEVAAGSPLGLKAKEVMARGDLVS 3943 Query: 61 DELVIALVKERIAQEDCRNGFLLDGFPRTIPQADA----MKEAGINVDYVLEFDVPDELI 116 DE+++ +++ R+ Q D NGF+LDG+PR + QA+A + + G +D V++ DV EL+ Sbjct: 3942 DEILLGMLEARLGQADVANGFILDGYPRNVAQANALDSLLSKIGQPLDAVVQLDVASELL 3763 Query: 117 VDRIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTGEELTTRKDDQEETVRKRLVEYHQMTA 176 V+RI GR K EG R+DD E+VRKRL Y TA Sbjct: 3762 VERIAGR----------------AKAEG-----------REDDNPESVRKRLQVYTDSTA 3664 Query: 177 PLIGYYSKEAEAGNTKYAKVDGTKPVAEVRADLEKILG 214 P+IG+Y + K A+VDG + EV + + LG Sbjct: 3663 PVIGFYEQRG-----KLARVDGVGSLDEVLERIGQALG 3565 3) Аналогичный поиск сразу в нескольких геномах На Kodomo-count: formatdb -i 'xc_genome.fasta st_genome.fasta pm_genome.fasta' -p F -n 3gen blastall -p tblastn -d 3gen -i KAD_ECOLI.fasta -o kad_3gen.blast -e 0.001 Результат: AE008718 AE006468 |AE008718| Salmonella typhimurium LT2, section... 406 e-114 embl|AE006063|AE006063 Pasteurella multocida subsp. multocida st... 315 8e-87 AE012446 AE008922 |AE012446| Xanthomonas campestris pv. campestr... 155 1e-38 Из предыдущего упражнения: >AE008718 AE006468 |AE008718| Salmonella typhimurium LT2, section 26 of 220 of the complete genome. Length = 20938 Score = 406 bits (1043), Expect = e-114 Identities = 206/214 (96%), Positives = 209/214 (97%) Frame = +1 Query: 1 MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAAVKSGSELGKQAKDIMDAGKLVT 60 MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAAVKSGSELGKQAKDIMDAGKLVT Sbjct: 11605 MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAAVKSGSELGKQAKDIMDAGKLVT 11784 Query: 61 DELVIALVKERIAQEDCRNGFLLDGFPRTIPQADAMKEAGINVDYVLEFDVPDELIVDRI 120 DELVIALVKERIAQEDCRNGFLLDGFPRTIPQADAMKEAGI VDYVLEFDVPDELIVDRI Sbjct: 11785 DELVIALVKERIAQEDCRNGFLLDGFPRTIPQADAMKEAGIVVDYVLEFDVPDELIVDRI 11964 Query: 121 VGRRVHAPSGRVYHVKFNPPKVEGKDDVTGEELTTRKDDQEETVRKRLVEYHQMTAPLIG 180 VGRRVHA SGRVYHVKFNPPKVEGKDDVTGE+LTTRKDDQEETVRKRLVEYHQMTAPLIG Sbjct: 11965 VGRRVHAASGRVYHVKFNPPKVEGKDDVTGEDLTTRKDDQEETVRKRLVEYHQMTAPLIG 12144 Query: 181 YYSKEAEAGNTKYAKVDGTKPVAEVRADLEKILG 214 YY KEAEAGNTKYAKVDGT+ VA+VRA LEKILG Sbjct: 12145 YYQKEAEAGNTKYAKVDGTQAVADVRAALEKILG 12246 4) Поиск гомологов с помощью программы BLASTN На Kodomo-count: blastall -p blastn -d 3gen -i X03038_gene1.fasta -o result3.txt Результат: Sequences producing significant alignments: (bits) Value AE008718 AE006468 |AE008718| Salmonella typhimurium LT2, section... 613 e-175 AE008905 AE006468 |AE008905| Salmonella typhimurium LT2, section... 36 0.099 embl|AE006073|AE006073 Pasteurella multocida subsp. multocida st... 34 0.39 embl|AE006063|AE006063 Pasteurella multocida subsp. multocida st... 34 0.39 AE008861 AE006468 |AE008861| Salmonella typhimurium LT2, section... 34 0.39 AE008915 AE006468 |AE008915| Salmonella typhimurium LT2, section... 32 1.5 AE008808 AE006468 |AE008808| Salmonella typhimurium LT2, section... 32 1.5 AE008746 AE006468 |AE008746| Salmonella typhimurium LT2, section... 32 1.5 AE008735 AE006468 |AE008735| Salmonella typhimurium LT2, section... 32 1.5 AE012375 AE008922 |AE012375| Xanthomonas campestris pv. campestr... 32 1.5 AE012208 AE008922 |AE012208| Xanthomonas campestris pv. campestr... 32 1.5 embl|AE006111|AE006111 Pasteurella multocida subsp. multocida st... 30 6.1 embl|AE006109|AE006109 Pasteurella multocida subsp. multocida st... 30 6.1 embl|AE006104|AE006104 Pasteurella multocida subsp. multocida st... 30 6.1 embl|AE006066|AE006066 Pasteurella multocida subsp. multocida st... 30 6.1 AE008912 AE006468 |AE008912| Salmonella typhimurium LT2, section... 30 6.1 AE008858 AE006468 |AE008858| Salmonella typhimurium LT2, section... 30 6.1 AE008851 AE006468 |AE008851| Salmonella typhimurium LT2, section... 30 6.1 AE008850 AE006468 |AE008850| Salmonella typhimurium LT2, section... 30 6.1 AE008800 AE006468 |AE008800| Salmonella typhimurium LT2, section... 30 6.1 AE008794 AE006468 |AE008794| Salmonella typhimurium LT2, section... 30 6.1 AE008765 AE006468 |AE008765| Salmonella typhimurium LT2, section... 30 6.1 AE008724 AE006468 |AE008724| Salmonella typhimurium LT2, section... 30 6.1 AE012549 AE008922 |AE012549| Xanthomonas campestris pv. campestr... 30 6.1 AE012530 AE008922 |AE012530| Xanthomonas campestris pv. campestr... 30 6.1 AE012523 AE008922 |AE012523| Xanthomonas campestris pv. campestr... 30 6.1 AE012516 AE008922 |AE012516| Xanthomonas campestris pv. campestr... 30 6.1 AE012411 AE008922 |AE012411| Xanthomonas campestris pv. campestr... 30 6.1 AE012388 AE008922 |AE012388| Xanthomonas campestris pv. campestr... 30 6.1 AE012363 AE008922 |AE012363| Xanthomonas campestris pv. campestr... 30 6.1 AE012281 AE008922 |AE012281| Xanthomonas campestris pv. campestr... 30 6.1 AE012119 AE008922 |AE012119| Xanthomonas campestris pv. campestr... 30 6.1 AE012111 AE008922 |AE012111| Xanthomonas campestris pv. campestr... 30 6.1 AE012100 AE008922 |AE012100| Xanthomonas campestris pv. campestr... 30 6.1 AE012099 AE008922 |AE012099| Xanthomonas campestris pv. campestr... 30 6.1 >AE008718 AE006468 |AE008718| Salmonella typhimurium LT2, section 26 of 220 of the complete genome. Length = 20938 Score = 613 bits (309), Expect = e-175 Identities = 558/641 (87%) Strand = Plus / Plus Query: 1 atgcgtatcattctgcttggcgctccgggcgcggggaaagggactcaggctcagttcatc 60 |||||||| |||||||||||||||||||||||||| ||||| |||||||||||||||||| Sbjct: 11605 atgcgtattattctgcttggcgctccgggcgcgggtaaaggaactcaggctcagttcatc 11664 Query: 61 atggagaaatatggtattccgcaaatctccactggcgatatgctgcgtgctgcggtcaaa 120 ||||||||||||||||||||||||||||||||||||||||||||||| || || || ||| Sbjct: 11665 atggagaaatatggtattccgcaaatctccactggcgatatgctgcgcgccgcagtgaaa 11724 Query: 121 tctggctccgagctgggtaaacaagcaaaagacattatggatgctggcaaactggtcacc 180 || ||||||||| |||| ||||| || ||||| || ||||| || || |||||||| ||| Sbjct: 11725 tcaggctccgagttgggcaaacaggcgaaagatatcatggacgccggtaaactggtgacc 11784 Query: 181 gacgaactggtgatcgcgctggttaaagagcgcattgctcaggaagactgccgtaatggt 240 || ||||||||||| ||||||||||||||||| || || ||||||||||||||||| ||| Sbjct: 11785 gatgaactggtgattgcgctggttaaagagcgtatcgcccaggaagactgccgtaacggt 11844 Query: 241 ttcctgttggacggcttcccgcgtaccattccgcaggcagacgcgatgaaagaagcgggc 300 || ||| ||||||| |||||||| || || |||||||| |||||||||||||||||||| Sbjct: 11845 tttctgctggacggtttcccgcgcacgatcccgcaggctgacgcgatgaaagaagcgggt 11904 Query: 301 atcaatgttgattacgttctggaattcgacgtaccggacgaactgatcgttgaccgtatc 360 || || |||||||| ||||||||||||||||||||||||||||||||||||||||| Sbjct: 11905 attgtcgtggattacgtgctggaattcgacgtaccggacgaactgatcgttgaccgtatt 11964 Query: 361 gtcggtcgccgcgttcatgcgccgtctggtcgtgtttatcacgttaaattcaatccgccg 420 || ||||| ||||| || || | ||||| || ||||| |||||||| || ||||||||| Sbjct: 11965 gtgggtcgtcgcgtacacgccgcctctggccgcgtttaccacgttaagtttaatccgccg 12024 Query: 421 aaagtagaaggcaaagacgacgttaccggtgaagaactgactacccgtaaagatgatcag 480 ||||| ||||||||||| ||||| ||||| ||||| ||||| ||||||||||| |||||| Sbjct: 12025 aaagtggaaggcaaagatgacgtcaccggcgaagatctgaccacccgtaaagacgatcag 12084 Query: 481 gaagagaccgtacgtaaacgtctggttgaataccatcagatgacagcaccgctgatcggc 540 ||||||||||| || ||||||||||| ||||| ||||||||||| || |||||||| ||| Sbjct: 12085 gaagagaccgttcgcaaacgtctggtggaatatcatcagatgaccgcgccgctgattggc 12144 Query: 541 tactactccaaagaagcagaagcgggtaataccaaatacgcgaaagttgacggcaccaag 600 |||||| |||||||| |||||||| || ||||||||||| ||||||||||| || || Sbjct: 12145 tactaccagaaagaagcggaagcgggcaacaccaaatacgctaaagttgacggtacgcag 12204 Query: 601 ccggttgctgaagttcgcgctgatctggaaaaaatcctcgg 641 | ||||| || || ||||| | ||||||||||||||||| Sbjct: 12205 gccgttgccgacgtgcgcgcagcgctggaaaaaatcctcgg 12245 ГЕН: FT CDS 11605..12249 FT /codon_start=1 FT /transl_table=11 FT /gene="adk" FT /product="adenylate kinase" FT /EC_number="2.7.4.3" FT /note="adenylate kinase. (SW:KAD_SALTY)" FT /db_xref="GOA:P0A1V4" FT /db_xref="InterPro:IPR000850" FT /db_xref="InterPro:IPR006259" FT /db_xref="InterPro:IPR007862" FT /db_xref="InterPro:IPR011769" FT /db_xref="UniProtKB/Swiss-Prot:P0A1V4" FT /protein_id="AAL19442.1" FT /translation="MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAAVKSGSEL FT GKQAKDIMDAGKLVTDELVIALVKERIAQEDCRNGFLLDGFPRTIPQADAMKEAGIVVD FT YVLEFDVPDELIVDRIVGRRVHAASGRVYHVKFNPPKVEGKDDVTGEDLTTRKDDQEET FT VRKRLVEYHQMTAPLIGYYQKEAEAGNTKYAKVDGTQAVADVRAALEKILG"