[Bioperl-guts-l] [14983] bioperl-live/trunk/t/data/hmmpfam_cs.out: test data for bug 2632

Senduran Balasubramaniam sendu at dev.open-bio.org
Tue Nov 11 13:37:00 EST 2008


Revision: 14983
Author:   sendu
Date:     2008-11-11 13:37:00 -0500 (Tue, 11 Nov 2008)

Log Message:
-----------
test data for bug 2632

Added Paths:
-----------
    bioperl-live/trunk/t/data/hmmpfam_cs.out

Added: bioperl-live/trunk/t/data/hmmpfam_cs.out
===================================================================
--- bioperl-live/trunk/t/data/hmmpfam_cs.out	                        (rev 0)
+++ bioperl-live/trunk/t/data/hmmpfam_cs.out	2008-11-11 18:37:00 UTC (rev 14983)
@@ -0,0 +1,559 @@
+hmmpfam - search one or more sequences against HMM database
+HMMER 2.3.2 (Oct 2003)
+Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
+Freely distributed under the GNU General Public License (GPL)
+- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+HMM file:                 ../Shared/Pfam_fs
+Sequence file:            single_porphyra_AA.fa
+- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+
+Query sequence: gi|90819130|dbj|BAE92499.1|
+Accession:      [none]
+Description:    glutamate synthase [Porphyra yezoensis]
+
+Scores for sequence family classification (score includes all domains):
+Model           Description                             Score    E-value  N 
+--------        -----------                             -----    ------- ---
+Glu_synthase    Conserved region in glutamate synthas   858.6   3.6e-255   2
+GATase_2        Glutamine amidotransferases class-II    731.8   3.9e-226   1
+Glu_syn_central Glutamate synthase central domain       649.1   7.9e-213   1
+GXGXG           GXGXG motif                             367.3   2.7e-107   1
+HdeA            hns-dependent expression protein A (H     9.6      0.015   1
+GDC-P           Glycine cleavage system P-protein         7.1      0.086   1
+Cache_1         Cache domain                              7.0       0.14   1
+IBN_N           Importin-beta N-terminal domain           8.2       0.17   1
+DUF1200         Protein of unknown function (DUF1200)     6.7       0.42   1
+cobW            CobW/HypB/UreG, nucleotide-binding do     5.1       0.45   1
+PUF             Pumilio-family RNA binding repeat         6.5       0.47   1
+Arch_flagellin  Archaebacterial flagellin                 4.1       0.66   1
+FMN_dh          FMN-dependent dehydrogenase               3.2       0.89   1
+RNA_pol_Rpb2_4  RNA polymerase Rpb2, domain 4             4.6        1.4   1
+DUF477          Domain of unknown function (DUF477)       3.8        1.7   1
+FRG1            FRG1-like family                          0.2        1.7   1
+DUF1393         Protein of unknown function (DUF1393)     3.1          2   1
+tRNA_anti       OB-fold nucleic acid binding domain       4.9          2   1
+SelT            Selenoprotein T                           3.1        2.2   1
+RNase_PH_C      3' exoribonuclease family, domain 2       4.2        2.3   1
+Pencillinase_R  Penicillinase repressor                   3.9        2.5   1
+Hormone_4       Neurohypophysial hormones, N-terminal     4.4        2.5   1
+DSRB            Dextransucrase DSRB                       2.7        2.7   1
+FtsK_SpoIIIE    FtsK/SpoIIIE family                       2.6        3.1   1
+UBA             UBA/TS-N domain                           4.2        3.1   1
+DUF1981         Domain of unknown function (DUF1981)      3.6        3.3   1
+Gla             Vitamin K-dependent carboxylation/gam     4.0        3.5   1
+Scm3            Centromere protein Scm3                   2.2        3.5   1
+Ribosomal_S6    Ribosomal protein S6                      3.3        3.7   1
+Cystatin        Cystatin domain                           2.4        3.9   1
+Phage_prot_Gp6  Phage portal protein, SPP1 Gp6-like       1.0          4   1
+DUF1976         Domain of unknown function (DUF1976)     -1.5        4.3   1
+DUF37           Domain of unknown function DUF37          3.0        4.5   1
+Flavodoxin_NdrI NrdI Flavodoxin like                      2.1        4.6   1
+Bac_rhodopsin   Bacteriorhodopsin                         0.9        4.9   1
+Nitro_FeMo-Co   Dinitrogenase iron-molybdenum cofacto     2.1        5.3   1
+MoCF_biosynth   Probable molybdopterin binding domain     1.3        5.6   1
+PaaA_PaaC       Phenylacetic acid catabolic protein       0.4        5.6   1
+Albicidin_res   Albicidin resistance domain               1.7        5.7   1
+DUF1514         Protein of unknown function (DUF1514)     3.5        5.7   1
+T5orf172        T5orf172 domain                           2.0        6.1   1
+Nup133_N        Nup133 N terminal like                   -0.6        6.5   1
+BicD            Microtubule-associated protein Bicaud    -1.6        6.8   1
+Sel1            Sel1 repeat                               2.5          7   1
+CAP_C           DE   Adenylate cyclase associated (CA     1.3        7.4   1
+Colicin         Colicin pore forming domain               1.4        7.5   1
+MADF_DNA_bdg    Alcohol dehydrogenase transcription f     1.8        8.2   1
+DUF258          Protein of unknown function, DUF258       0.3        8.3   1
+PspB            Phage shock protein B                     0.4        8.4   1
+GspM            General secretion pathway, M protein      1.0        8.6   1
+Coq4            Coenzyme Q (ubiquinone) biosynthesis     -0.3        9.1   1
+P22_AR_N        P22_AR N-terminal domain                 -0.2        9.5   1
+C1_2            C1 domain                                 1.1        9.6   1
+Phage_Mu_P      Bacteriophage Mu P protein               -0.4         10   1
+
+Parsed for domains:
+Model           Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
+--------        ------- ----- -----    ----- -----      -----  -------
+GATase_2          1/1      34   404 ..     1   385 []   731.8 3.9e-226
+FRG1              1/1      88   107 ..   151   173 ..     0.2      1.7
+C1_2              1/1     191   210 ..     9    27 ..     1.1      9.6
+MADF_DNA_bdg      1/1     235   261 ..    57    95 .]     1.8      8.2
+PaaA_PaaC         1/1     258   269 ..     1    13 [.     0.4      5.6
+Albicidin_res     1/1     274   289 ..    50    65 ..     1.7      5.7
+UBA               1/1     311   331 ..    18    38 .]     4.2      3.1
+Gla               1/1     342   357 ..    27    42 .]     4.0      3.5
+RNA_pol_Rpb2_4    1/1     369   381 ..     1    13 [.     4.6      1.4
+MoCF_biosynth     1/1     371   396 ..    23    49 ..     1.3      5.6
+DUF1200           1/1     389   401 ..     1    13 [.     6.7     0.42
+Nup133_N          1/1     397   419 ..   475   498 .]    -0.6      6.5
+DUF1976           1/1     428   448 ..  1296  1319 .]    -1.5      4.3
+Bac_rhodopsin     1/1     445   472 ..   219   250 .]     0.9      4.9
+Coq4              1/1     459   481 ..    60    82 ..    -0.3      9.1
+Glu_syn_central   1/1     478   773 ..     1   301 []   649.1 7.9e-213
+Flavodoxin_NdrI   1/1     488   497 ..   122   131 .]     2.1      4.6
+P22_AR_N          1/1     524   541 ..   110   126 .]    -0.2      9.5
+Cache_1           1/1     537   557 ..     1    23 [.     7.0     0.14
+Glu_synthase      1/2     650   676 ..   297   323 ..     1.3        3
+HdeA              1/1     727   749 ..    58    79 .]     9.6    0.015
+Sel1              1/1     729   745 ..    32    49 .]     2.5        7
+DUF1981           1/1     765   787 ..    62    88 .]     3.6      3.3
+tRNA_anti         1/1     818   839 ..    54    85 .]     4.9        2
+Cystatin          1/1     826   859 ..     1    38 [.     2.4      3.9
+RNase_PH_C        1/1     827   846 ..    64    84 .]     4.2      2.3
+Glu_synthase      2/2     830  1216 ..     1   412 []   857.3   9e-255
+DUF258            1/1     839   860 ..   282   305 .]     0.3      8.3
+Pencillinase_R    1/1     856   894 ..    84   118 .]     3.9      2.5
+SelT              1/1     872   885 ..    96   111 .]     3.1      2.2
+Nitro_FeMo-Co     1/1     879   897 ..    87   105 .]     2.1      5.3
+DUF37             1/1     927   934 ..    61    68 .]     3.0      4.5
+Scm3              1/1     953   963 ..   103   113 .]     2.2      3.5
+cobW              1/1    1038  1058 ..   202   222 .]     5.1     0.45
+Arch_flagellin    1/1    1050  1072 ..   197   219 .]     4.1     0.66
+DUF1393           1/1    1055  1068 ..     1    14 [.     3.1        2
+FtsK_SpoIIIE      1/1    1107  1143 ..   163   198 ..     2.6      3.1
+FMN_dh            1/1    1109  1148 ..   291   330 ..     3.2     0.89
+DSRB              1/1    1120  1134 ..     1    16 [.     2.7      2.7
+Phage_Mu_P        1/1    1122  1131 ..     1    10 [.    -0.4       10
+Hormone_4         1/1    1168  1176 ..     1     9 []     4.4      2.5
+GDC-P             1/1    1205  1225 ..    10    30 ..     7.1    0.086
+PspB              1/1    1268  1276 ..     1     9 [.     0.4      8.4
+T5orf172          1/1    1271  1293 ..    35    58 ..     2.0      6.1
+CAP_C             1/1    1283  1292 ..   161   170 .]     1.3      7.4
+GXGXG             1/1    1290  1485 ..     1   228 []   367.3 2.7e-107
+DUF1514           1/1    1453  1469 ..    50    66 .]     3.5      5.7
+Colicin           1/1    1456  1467 ..   192   203 .]     1.4      7.5
+Ribosomal_S6      1/1    1461  1481 ..    16    36 ..     3.3      3.7
+BicD              1/1    1465  1481 ..     1    17 [.    -1.6      6.8
+PUF               1/1    1470  1486 ..    19    35 .]     6.5     0.47
+DUF477            1/1    1472  1495 ..     1    24 [.     3.8      1.7
+Phage_prot_Gp6    1/1    1479  1492 ..     1    14 [.     1.0        4
+IBN_N             1/1    1498  1516 ..     1    20 [.     8.2     0.17
+GspM              1/1    1506  1520 ..     1    15 [.     1.0      8.6
+
+Alignments of top-scoring domains:
+GATase_2: domain 1 of 1, from 34 to 404: score 731.8, E = 3.9e-226
+                CS    EEEEEEEEETSSHSBHHHHHHHHHHHHHGGGGSSCSTTSSCECEEEE
+                   *->CGvlGfiAhikgkpshkivedaleaLerLeHRGavgADgktGDGAGI
+                      CGv GfiA+ ++ ++hkiv +aleaL+++eHRGa++AD ++GDGAGI
+  gi|9081913    34    CGV-GFIADVNNVANHKIVVQALEALTCMEHRGACSADRDSGDGAGI 79   
+
+                CS EEECTCCCHHHHHHHCT----S GC-EEEEEEE-SSHHHHHHHHHHHHHH
+                   ltqiPdgFFrevakelGieLpe.gqYAVGmvFLPqdelaraearkifEki
+                    t+iP+++F++  ++++i++ ++   +VGm+FLP   l+    + i+E +
+  gi|9081913    80 TTAIPWNLFQKSLQNQNIKFEQnDSVGVGMLFLPAHKLKES--KLIIETV 127  
+

@@ Diff output truncated at 10000 characters. @@



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