[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. @@
More information about the Bioperl-guts-l
mailing list