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  • Committer: Bazaar Package Importer
  • Author(s): Charles Plessy
  • Date: 2009-03-10 07:19:11 UTC
  • mfrom: (1.2.3 upstream)
  • Revision ID: james.westby@ubuntu.com-20090310071911-fukqzw54pyb1f0bd
Tags: 1.6.0-2
https://launchpad.net/bugs/324001
* Removed patch system (not used):
  - removed instuctions in debian/rules;
  - removed quilt from Build-Depends in debian/control.
* Re-enabled tests:
  - uncommented test command in debian/rules;
  - uncommented previously missing build-dependencies in debian/control.
  - Re-enabled tests and uncommented build-dependencies accordingly.
* Removed libmodule-build-perl and libtest-harness-perl from
  Build-Depends-Indep (provided by perl-modules).
* Better cleaning of empty directories using find -type d -empty -delete
  instead of rmdir in debian/rules (LP: #324001).

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Lines of Context:
t/data/blastp2215.blast
 
1
BLASTP 2.2.15 [Oct-15-2006]
 
2
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer, 
 
3
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman 
 
4
(1997), "Gapped BLAST and PSI-BLAST: a new generation of 
 
5
protein database search programs", Nucleic Acids Res. 25:3389-3402.
 
6
 
 
7
Reference: Schäffer, Alejandro A., L. Aravind, Thomas L. Madden, Sergei 
 
8
Shavirin, John L. Spouge, Yuri I. Wolf, Eugene V. Koonin, and 
 
9
Stephen F. Altschul (2001), "Improving the accuracy of PSI-BLAST 
 
10
protein database searches with composition-based statistics 
 
11
and other refinements", Nucleic Acids Res. 29:2994-3005.
 
12
 
 
13
RID: 1169055516-21385-22799250964.BLASTQ4
 
14
 
 
15
 
 
16
Database: All non-redundant GenBank CDS
 
17
translations+PDB+SwissProt+PIR+PRF excluding environmental samples
 
18
           4,460,989 sequences; 1,533,424,333 total letters
 
19
Query= gi|15608519|ref|NP_215895.1| pyrimidine regulatory protein PyrR [Mycobacterium 
 
20
tuberculosis H37Rv]
 
21
Length=193
 
22
 
 
23
 
 
24
                                                                   Score     E
 
25
Sequences producing significant alignments:                       (Bits)  Value
 
26
 
 
27
gi|15608519|ref|NP_215895.1|  pyrimidine regulatory protein Py...   332    8e-90
 
28
gi|55670580|pdb|1W30|A  Chain A, Pyrr Of Mycobacterium Tubercu...   331    1e-89
 
29
gi|41407212|ref|NP_960048.1|  pyrimidine regulatory protein Py...   286    5e-76
 
30
gi|118464931|ref|YP_882576.1|  PyrR bifunctional protein [Myco...   285    1e-75
 
31
gi|118617395|ref|YP_905727.1|  pyrimidine operon regulatory pr...   273    2e-72
 
32
gi|118473305|ref|YP_887358.1|  PyrR bifunctional protein [Myco...   258    1e-67
 
33
gi|89341207|ref|ZP_01193452.1|  Phosphoribosyltransferase [Myc...   254    1e-66
 
34
gi|120403643|ref|YP_953472.1|  Uracil phosphoribosyltransferas...   254    2e-66
 
35
gi|92907430|ref|ZP_01276210.1|  Uracil phosphoribosyltransfera...   244    2e-63
 
36
gi|111024097|ref|YP_707069.1|  probable uracil phosphoribosylt...   238    8e-62
 
37
Query= gi|15595598|ref|NP_249092.1| dihydroorotase [Pseudomonas aeruginosa PAO1]
 
38
Length=423
 
39
 
 
40
 
 
41
                                                                   Score     E
 
42
Sequences producing significant alignments:                       (Bits)  Value
 
43
 
 
44
gi|15595598|ref|NP_249092.1|  dihydroorotase [Pseudomonas aeru...   775    0.0   
 
45
gi|84324488|ref|ZP_00972546.1|  COG0044: Dihydroorotase and re...   771    0.0   
 
46
gi|116054132|ref|YP_788575.1|  noncatalytic dihydroorotase-lik...   770    0.0   
 
47
gi|309886|gb|AAA25977.1|  dihydroorotase-like                       768    0.0   
 
48
gi|94415759|ref|ZP_01295595.1|  hypothetical protein PaerP_010...   744    0.0   
 
49
gi|26991676|ref|NP_747101.1|  dihydroorotase [Pseudomonas puti...   628    4e-179
 
50
gi|82736201|ref|ZP_00899061.1|  Dihydroorotase multifunctional...   627    7e-179
 
51
gi|77461536|ref|YP_351043.1|  dihydroorotase [Pseudomonas fluo...   624    7e-178
 
52
gi|66043748|ref|YP_233589.1|  dihydroorotase [Pseudomonas syri...   622    4e-177
 
53
gi|118056991|ref|ZP_01525457.1|  dihydroorotase, multifunction...   621    5e-177
 
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Query= gi|15595600|ref|NP_249094.1| pyrimidine regulatory protein PyrR [Pseudomonas 
 
55
aeruginosa PAO1]
 
56
Length=170
 
57
 
 
58
 
 
59
                                                                   Score     E
 
60
Sequences producing significant alignments:                       (Bits)  Value
 
61
 
 
62
gi|15595600|ref|NP_249094.1|  pyrimidine regulatory protein Py...   320    2e-86
 
63
gi|49081516|gb|AAT50158.1|  PA0403 [synthetic construct]            317    2e-85
 
64
gi|94415757|ref|ZP_01295593.1|  hypothetical protein PaerP_010...   310    3e-83
 
65
gi|119856461|ref|ZP_01637894.1|  Uracil phosphoribosyltransfer...   262    8e-69
 
66
gi|67154890|ref|ZP_00416635.1|  Uracil phosphoribosyltransfera...   261    2e-68
 
67
gi|26991674|ref|NP_747099.1|  pyrimidine regulatory protein Py...   260    3e-68
 
68
gi|28872153|ref|NP_794772.1|  pyrimidine regulatory protein Py...   258    9e-68
 
69
gi|104783978|ref|YP_610476.1|  transcriptional regulator PyrR ...   256    3e-67
 
70
gi|71736513|ref|YP_272777.1|  pyrimidine operon regulatory pro...   256    5e-67
 
71
gi|70733117|ref|YP_262890.1|  pyrimidine regulatory protein Py...   256    5e-67
 
72
Query= gi|15598723|ref|NP_252217.1| dihydroorotase [Pseudomonas aeruginosa PAO1]
 
73
Length=348
 
74
 
 
75
 
 
76
                                                                   Score     E
 
77
Sequences producing significant alignments:                       (Bits)  Value
 
78
 
 
79
gi|15598723|ref|NP_252217.1|  dihydroorotase [Pseudomonas aeru...   690    0.0   
 
80
gi|84319753|ref|ZP_00968143.1|  COG0418: Dihydroorotase [Pseud...   687    0.0   
 
81
gi|116051526|ref|YP_789638.1|  dihydroorotase, homodimeric typ...   686    0.0   
 
82
gi|94415333|ref|ZP_01295177.1|  hypothetical protein PaerP_010...   677    0.0   
 
83
gi|104780416|ref|YP_606914.1|  dihydroorotase [Pseudomonas ent...   618    5e-176
 
84
gi|77460740|ref|YP_350247.1|  dihydroorotase [Pseudomonas fluo...   617    1e-175
 
85
gi|26987822|ref|NP_743247.1|  dihydroorotase [Pseudomonas puti...   616    2e-175
 
86
gi|70732180|ref|YP_261936.1|  dihydroorotase [Pseudomonas fluo...   614    8e-175
 
87
gi|118058820|ref|ZP_01527280.1|  dihydroorotase, homodimeric t...   613    1e-174
 
88
gi|82737454|ref|ZP_00900303.1|  Dihydroorotase homodimeric typ...   613    2e-174
 
89
Query= gi|15600734|ref|NP_254228.1| dihydroorotase [Pseudomonas aeruginosa PAO1]
 
90
Length=445
 
91
 
 
92
 
 
93
                                                                   Score     E
 
94
Sequences producing significant alignments:                       (Bits)  Value
 
95
 
 
96
gi|15600734|ref|NP_254228.1|  dihydroorotase [Pseudomonas aeru...   871    0.0   
 
97
gi|116053692|ref|YP_794019.1|  dihydroorotase [Pseudomonas aer...   870    0.0   
 
98
gi|84318214|ref|ZP_00966642.1|  COG0044: Dihydroorotase and re...   869    0.0   
 
99
gi|94417254|ref|ZP_01297073.1|  hypothetical protein PaerP_010...   831    0.0   
 
100
gi|77461883|ref|YP_351390.1|  dihydroorotase [Pseudomonas fluo...   658    0.0   
 
101
gi|104782179|ref|YP_608677.1|  dihydroorotase [Pseudomonas ent...   634    0.0   
 
102
gi|70733466|ref|YP_263241.1|  dihydroorotase [Pseudomonas fluo...   622    2e-177
 
103
gi|118059665|ref|ZP_01528121.1|  amidohydrolase [Pseudomonas m...   606    2e-172
 
104
gi|50084596|ref|YP_046106.1|  dihydroorotase [Acinetobacter sp...   562    3e-159
 
105
gi|117621557|ref|YP_857112.1|  dihydroorotase [Aeromonas hydro...   482    3e-135
 
106
 
 
107
  Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF excluding 
 
108
environmental samples
 
109
    Posted date:  Jan 16, 2007  5:53 PM
 
110
  Number of letters in database: 1,533,424,333
 
111
  Number of sequences in database:  4,460,989
 
112
Lambda     K      H
 
113
   0.319    0.139    0.394 
 
114
Gapped
 
115
Lambda     K      H
 
116
   0.267   0.0410    0.140 
 
117
Matrix: BLOSUM62
 
118
Gap Penalties: Existence: 11, Extension: 1
 
119
Number of Sequences: 4460989
 
120
Number of Hits to DB: 469576580
 
121
Number of extensions: 20639621
 
122
Number of successful extensions: 52293
 
123
Number of sequences better than 10: 358
 
124
Number of HSP's better than 10 without gapping: 0
 
125
Number of HSP's gapped: 52059
 
126
Number of HSP's successfully gapped: 644
 
127
Length of database: 1533424333
 
128
T: 11
 
129
A: 40
 
130
X1: 16 (7.4 bits)
 
131
X2: 38 (14.6 bits)
 
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X3: 64 (24.7 bits)
 
133
S1: 41 (20.4 bits)
 
134
 
 
135