Документ взят из кэша поисковой машины. Адрес оригинального документа : http://kodomo.cmm.msu.ru/~vasilisa/report.txt Дата изменения: Sun Dec 2 18:15:42 2007 Дата индексирования: Tue Oct 2 00:20:44 2012 Кодировка: Windows-1251

Отчет 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"