Отчёт 2го занятия студентки 202 группы Рудневой Василисы.
Мой белок -- KAD_ECOLI, AC=P69441.

1)Запрос на Kodomo-count:
entret sw:P69441 -auto
Запрос в SRS:
((((([embl-AccNumber:X03038*] | [embl-AccNumber:U82664*]) |  [embl-AccNumber:U00096*]) | [embl-AccNumber:AP009048*]) |  [embl-AccNumber:M38777*]) | [embl-AccNumber:D90259*])
Результаты -- в файле wgetz.

2)Запрос на Kodomo-count:
entret embl:X03038 -auto
Результат:
FT   CDS             194..838
FT                   /transl_table=11
FT                   /note="adenylate kinase (adk) (aa 1-214)"
FT                   /db_xref="GOA:P69441"
FT                   /db_xref="InterPro:IPR000850"
FT                   /db_xref="InterPro:IPR006259"
FT                   /db_xref="InterPro:IPR007862"
FT                   /db_xref="InterPro:IPR011769"
FT                   /db_xref="PDB:1AKE"
FT                   /db_xref="PDB:1ANK"
FT                   /db_xref="PDB:1E4V"
FT                   /db_xref="PDB:1E4Y"
FT                   /db_xref="PDB:2ECK"
FT                   /db_xref="PDB:4AKE"
FT                   /db_xref="UniProtKB/Swiss-Prot:P69441"
FT                   /protein_id="CAA26840.1"
FT                   /translation="MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAAVKSGSEL
FT                   GKQAKDIMDAGKLVTDELVIALVKERIAQEDCRNGFLLDGFPRTIPQADAMKEAGINVD
FT                   YVLEFDVPDELIVDRIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTGEELTTRKDDQEET
FT                   VRKRLVEYHQMTAPLIGYYSKEAEAGNTKYAKVDGTKPVAEVRADLEKILG"
FT   misc_feature    complement(158..883)
FT                   /note="open reading frame"

Запрос на Kodomo-count:
entret embl:D90259 -auto
Результат:
1FT   CDS             <1..324
FT                   /codon_start=1
FT                   /transl_table=11
FT                   /gene="adk"
FT                   /product="adenylate kinase"
FT                   /db_xref="GOA:P69441"
FT                   /db_xref="PDB:1AKE"
FT                   /db_xref="PDB:1ANK"
FT                   /db_xref="PDB:1E4V"
FT                   /db_xref="PDB:1E4Y"
FT                   /db_xref="PDB:2ECK"
FT                   /db_xref="PDB:4AKE"
FT                   /db_xref="UniProtKB/Swiss-Prot:P69441"
FT                   /protein_id="BAA14303.1"
FT                   /translation="EFDVPDELIVDRIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTGEE
FT                   LTTRKDDQEETVRKRLVEYHQMTAPLIGYYSKEAEAGNTKYAKVDGTKPVAEVRADLEK
FT                   ILG"

На Kodomo-count:
vasilisa@kodomo-count:Practice2$ seqret x03038.entret -sask
Reads and writes (returns) sequences
     Begin at position [start]: 194
       End at position [end]: 838
        Reverse strand [N]: n
output sequence(s) [x03038.fasta]: X03038_gene1.fasta
vasilisa@kodomo-count:Practice2$ seqret d90259.entret -sask
Reads and writes (returns) sequences
     Begin at position [start]: 1
       End at position [end]: 324
        Reverse strand [N]: n
output sequence(s) [d90259.fasta]: D90259_gene2.fasta
Сравнение последовательностей:
needle со стандартными параметрами:
needle
Needleman-Wunsch global alignment.
Input sequence: X03038.fasta
Second sequence(s): D90259.fasta
Gap opening penalty [10.0]: 10.0
Gap extension penalty [0.5]: 0.5
Output alignment [x03038.needle]: align.needle

Результат:
# Aligned_sequences: 2
# 1: X03038
# 2: D90259
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 214
# Identity:     107/214 (50.0%)
# Similarity:   107/214 (50.0%)
# Gaps:         107/214 (50.0%)
# Score: 555.0
# 
#
#=======================================

X03038             1 MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAAVKSGSELGKQAK     50
                                                                       
D90259             0 --------------------------------------------------      0

X03038            51 DIMDAGKLVTDELVIALVKERIAQEDCRNGFLLDGFPRTIPQADAMKEAG    100
                                                                       
D90259             0 --------------------------------------------------      0

X03038           101 INVDYVLEFDVPDELIVDRIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTG    150
                            |||||||||||||||||||||||||||||||||||||||||||
D90259             1 -------EFDVPDELIVDRIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTG     43

X03038           151 EELTTRKDDQEETVRKRLVEYHQMTAPLIGYYSKEAEAGNTKYAKVDGTK    200
                     ||||||||||||||||||||||||||||||||||||||||||||||||||
D90259            44 EELTTRKDDQEETVRKRLVEYHQMTAPLIGYYSKEAEAGNTKYAKVDGTK     93

X03038           201 PVAEVRADLEKILG    214
                     ||||||||||||||
D90259            94 PVAEVRADLEKILG    107



needle X03038_gene1.fasta D90259_gene2.fasta gene1-gene2.needle -auto

Результат:
# Aligned_sequences: 2
# 1: X03038
# 2: D90259
# Matrix: EDNAFULL
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 645
# Identity:     324/645 (50.2%)
# Similarity:   324/645 (50.2%)
# Gaps:         321/645 (49.8%)
# Score: 1620.0
# 
#
#=======================================

X03038             1 atgcgtatcattctgcttggcgctccgggcgcggggaaagggactcaggc     50
                                                                       
D90259             0 --------------------------------------------------      0

X03038            51 tcagttcatcatggagaaatatggtattccgcaaatctccactggcgata    100
                                                                       
D90259             0 --------------------------------------------------      0

X03038           101 tgctgcgtgctgcggtcaaatctggctccgagctgggtaaacaagcaaaa    150
                                                                       
D90259             0 --------------------------------------------------      0

X03038           151 gacattatggatgctggcaaactggtcaccgacgaactggtgatcgcgct    200
                                                                       
D90259             0 --------------------------------------------------      0

X03038           201 ggttaaagagcgcattgctcaggaagactgccgtaatggtttcctgttgg    250
                                                                       
D90259             0 --------------------------------------------------      0

X03038           251 acggcttcccgcgtaccattccgcaggcagacgcgatgaaagaagcgggc    300
                                                                       
D90259             0 --------------------------------------------------      0

X03038           301 atcaatgttgattacgttctggaattcgacgtaccggacgaactgatcgt    350
                                          |||||||||||||||||||||||||||||
D90259             1 ---------------------gaattcgacgtaccggacgaactgatcgt     29

X03038           351 tgaccgtatcgtcggtcgccgcgttcatgcgccgtctggtcgtgtttatc    400
                     ||||||||||||||||||||||||||||||||||||||||||||||||||
D90259            30 tgaccgtatcgtcggtcgccgcgttcatgcgccgtctggtcgtgtttatc     79

X03038           401 acgttaaattcaatccgccgaaagtagaaggcaaagacgacgttaccggt    450
                     ||||||||||||||||||||||||||||||||||||||||||||||||||
D90259            80 acgttaaattcaatccgccgaaagtagaaggcaaagacgacgttaccggt    129

X03038           451 gaagaactgactacccgtaaagatgatcaggaagagaccgtacgtaaacg    500
                     ||||||||||||||||||||||||||||||||||||||||||||||||||
D90259           130 gaagaactgactacccgtaaagatgatcaggaagagaccgtacgtaaacg    179

X03038           501 tctggttgaataccatcagatgacagcaccgctgatcggctactactcca    550
                     ||||||||||||||||||||||||||||||||||||||||||||||||||
D90259           180 tctggttgaataccatcagatgacagcaccgctgatcggctactactcca    229

X03038           551 aagaagcagaagcgggtaataccaaatacgcgaaagttgacggcaccaag    600
                     ||||||||||||||||||||||||||||||||||||||||||||||||||
D90259           230 aagaagcagaagcgggtaataccaaatacgcgaaagttgacggcaccaag    279

X03038           601 ccggttgctgaagttcgcgctgatctggaaaaaatcctcggctaa    645
                     |||||||||||||||||||||||||||||||||||||||||||||
D90259           280 ccggttgctgaagttcgcgctgatctggaaaaaatcctcggctaa    324


3)Мой ген: AE006462  	/gene="gs3"
На kodomo-count:
entret embl:AE006462 -auto

FT   CDS             join(12932..13085,13222..13247,14246..14401,16377..16397)
FT                   /codon_start=1
FT                   /gene="gs3"
FT                   /product="unknown"
FT                   /note="GENSCAN prediction; no supporting evidence known at
FT                   this time"
FT                   /db_xref="UniProtKB/TrEMBL:Q96S36"
FT                   /protein_id="AAK61209.1"
FT                   /translation="MRTELPLPRTRMGETAASRHLGTPGDTWGGVRGEDWETLLHLRDT
FT                   TWGRGQVQAKMQVTDDPPRRGHGFETPEDTWGHVRDEDISGTPGAASPGHLGLTLVRGK
FT                   EEEHRDALTRIQLC"

Схема гена: --[12932..13085]--...--[16377..16397]--->
Число экзонов - 4.