[BioRuby-cvs] bioruby/test/data/blast b0002.faa, NONE, 1.1 b0002.faa.m0, NONE, 1.1 b0002.faa.m7, NONE, 1.1 b0002.faa.m8, NONE, 1.1 eco:b0002.faa, 1.1, NONE eco:b0002.faa.m0, 1.1, NONE eco:b0002.faa.m7, 1.1, NONE eco:b0002.faa.m8, 1.1, NONE
Mitsuteru C. Nakao
nakao at pub.open-bio.org
Fri Feb 3 17:21:54 UTC 2006
Update of /home/repository/bioruby/bioruby/test/data/blast
In directory pub.open-bio.org:/tmp/cvs-serv6123/test/data/blast
Added Files:
b0002.faa b0002.faa.m0 b0002.faa.m7 b0002.faa.m8
Removed Files:
eco:b0002.faa eco:b0002.faa.m0 eco:b0002.faa.m7
eco:b0002.faa.m8
Log Message:
* Moved test/data/blast/eco:* to test/data/blast/* to avoid file name problems
in the Windows file sysmtem.
--- eco:b0002.faa.m7 DELETED ---
--- eco:b0002.faa.m0 DELETED ---
--- NEW FILE: b0002.faa.m8 ---
eco:b0002 eco:b0002 100.00 820 0 0 1 820 1 820 0.0 1567
--- NEW FILE: b0002.faa.m7 ---
<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">
<BlastOutput>
<BlastOutput_program>blastp</BlastOutput_program>
<BlastOutput_version>blastp 2.2.10 [Oct-19-2004]</BlastOutput_version>
<BlastOutput_reference>~Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, ~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.</BlastOutput_reference>
<BlastOutput_db>b0002.faa</BlastOutput_db>
<BlastOutput_query-ID>lcl|QUERY</BlastOutput_query-ID>
<BlastOutput_query-def>eco:b0002 thrA, Hs, thrD, thrA2, thrA1; bifunctional: aspartokinase I (N-terminal); homoserine dehydrogenase I (C-terminal) [EC:2.7.2.4 1.1.1.3]; K00003 homoserine dehydrogenase; K00928 aspartate kinase (A)</BlastOutput_query-def>
<BlastOutput_query-len>820</BlastOutput_query-len>
<BlastOutput_param>
<Parameters>
<Parameters_matrix>BLOSUM62</Parameters_matrix>
<Parameters_expect>10</Parameters_expect>
<Parameters_gap-open>11</Parameters_gap-open>
<Parameters_gap-extend>1</Parameters_gap-extend>
<Parameters_filter>S</Parameters_filter>
</Parameters>
</BlastOutput_param>
<BlastOutput_iterations>
<Iteration>
<Iteration_iter-num>1</Iteration_iter-num>
<Iteration_hits>
<Hit>
<Hit_num>1</Hit_num>
<Hit_id>gnl|BL_ORD_ID|0</Hit_id>
<Hit_def>eco:b0002 thrA, Hs, thrD, thrA2, thrA1; bifunctional: aspartokinase I (N-terminal); homoserine dehydrogenase I (C-terminal) [EC:2.7.2.4 1.1.1.3]; K00003 homoserine dehydrogenase; K00928 aspartate kinase (A)</Hit_def>
<Hit_accession>0</Hit_accession>
<Hit_len>820</Hit_len>
<Hit_hsps>
<Hsp>
<Hsp_num>1</Hsp_num>
<Hsp_bit-score>1567.75</Hsp_bit-score>
<Hsp_score>4058</Hsp_score>
<Hsp_evalue>0</Hsp_evalue>
<Hsp_query-from>1</Hsp_query-from>
<Hsp_query-to>820</Hsp_query-to>
<Hsp_hit-from>1</Hsp_hit-from>
<Hsp_hit-to>820</Hsp_hit-to>
<Hsp_query-frame>1</Hsp_query-frame>
<Hsp_hit-frame>1</Hsp_hit-frame>
<Hsp_identity>820</Hsp_identity>
<Hsp_positive>820</Hsp_positive>
<Hsp_align-len>820</Hsp_align-len>
<Hsp_qseq>MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV</Hsp_qseq>
<Hsp_hseq>MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV</Hsp_hseq>
<Hsp_midline>MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV</Hsp_midline>
</Hsp>
</Hit_hsps>
</Hit>
</Iteration_hits>
<Iteration_stat>
<Statistics>
<Statistics_db-num>1</Statistics_db-num>
<Statistics_db-len>820</Statistics_db-len>
<Statistics_hsp-len>42</Statistics_hsp-len>
<Statistics_eff-space>605284</Statistics_eff-space>
<Statistics_kappa>0.041</Statistics_kappa>
<Statistics_lambda>0.267</Statistics_lambda>
<Statistics_entropy>0.14</Statistics_entropy>
</Statistics>
</Iteration_stat>
</Iteration>
</BlastOutput_iterations>
</BlastOutput>
--- eco:b0002.faa DELETED ---
--- NEW FILE: b0002.faa ---
>eco:b0002 thrA, Hs, thrD, thrA2, thrA1; bifunctional: aspartokinase I (N-terminal); homoserine dehydrogenase I (C-terminal) [EC:2.7.2.4 1.1.1.3]; K00003 homoserine dehydrogenase; K00928 aspartate kinase (A)
MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA
LPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINA
ALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIP
ADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQV
PDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRD
EDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISF
CVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAAL
ARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGAL
LEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRL
VKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSR
RKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLA
REMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMA
NLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAF
YSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV
--- eco:b0002.faa.m8 DELETED ---
--- NEW FILE: b0002.faa.m0 ---
BLASTP 2.2.10 [Oct-19-2004]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
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.
Query= eco:b0002 thrA, Hs, thrD, thrA2, thrA1; bifunctional:
aspartokinase I (N-terminal); homoserine dehydrogenase I (C-terminal)
[EC:2.7.2.4 1.1.1.3]; K00003 homoserine dehydrogenase; K00928
aspartate kinase (A)
(820 letters)
Database: b0002.faa
1 sequences; 820 total letters
Searching.done
Score E
Sequences producing significant alignments: (bits) Value
eco:b0002 thrA, Hs, thrD, thrA2, thrA1; bifunctional: aspartokin... 1567 0.0
>eco:b0002 thrA, Hs, thrD, thrA2, thrA1; bifunctional: aspartokinase
I (N-terminal); homoserine dehydrogenase I (C-terminal)
[EC:2.7.2.4 1.1.1.3]; K00003 homoserine dehydrogenase;
K00928 aspartate kinase (A)
Length = 820
Score = 1567 bits (4058), Expect = 0.0
Identities = 806/820 (98%), Positives = 806/820 (98%)
Query: 1 MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA 60
MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA
Sbjct: 1 MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA 60
Query: 61 LPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINA 120
LPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINA
Sbjct: 61 LPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINA 120
Query: 121 ALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIP 180
ALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIP
Sbjct: 121 ALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIP 180
Query: 181 ADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQV 240
ADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQV
Sbjct: 181 ADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQV 240
Query: 241 PDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRD 300
PDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRD
Sbjct: 241 PDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRD 300
Query: 301 EDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISF 360
EDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISF
Sbjct: 301 EDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISF 360
Query: 361 CVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAAL 420
CVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAAL
Sbjct: 361 CVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAAL 420
Query: 421 ARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQXXXXXXXXXXXXXXAL 480
ARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQ AL
Sbjct: 421 ARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGAL 480
Query: 481 LEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRL 540
LEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRL
Sbjct: 481 LEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRL 540
Query: 541 VKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSR 600
VKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSR
Sbjct: 541 VKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSR 600
Query: 601 RKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLA 660
RKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLA
Sbjct: 601 RKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLA 660
Query: 661 REMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMA 720
REMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMA
Sbjct: 661 REMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMA 720
Query: 721 NLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAF 780
NLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAF
Sbjct: 721 NLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAF 780
Query: 781 YSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV 820
YSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV
Sbjct: 781 YSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV 820
Database: b0002.faa
Posted date: Aug 7, 2005 7:29 AM
Number of letters in database: 820
Number of sequences in database: 1
Lambda K H
0.319 0.134 0.383
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1986
Number of Sequences: 1
Number of extensions: 52
Number of successful extensions: 8
Number of sequences better than 10.0: 1
Number of HSP's better than 10.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 1
length of query: 820
length of database: 820
effective HSP length: 42
effective length of query: 778
effective length of database: 778
effective search space: 605284
effective search space used: 605284
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 30 (16.7 bits)
S2: 30 (16.2 bits)
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