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comparison commons/pyRepetUnit/align/hmmOutputParsing/tests/datas/OutputHmmpfamTest @ 31:0ab839023fe4

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author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
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30:5677346472b5 31:0ab839023fe4
1 hmmpfam - search one or more sequences against HMM database
2 HMMER 2.3.2 (Oct 2003)
3 Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
4 Freely distributed under the GNU General Public License (GPL)
5 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
6 HMM file: /home/choede/hmmer3/Pfam_fs
7 Sequence file: ConsensusTestFile_aaWithoutStop.fsa
8 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
9
10 Query sequence: blumeria_Grouper_590_20:NoCat_1
11 Accession: [none]
12 Description: [none]
13
14 Scores for sequence family classification (score includes all domains):
15 Model Description Score E-value N
16 -------- ----------- ----- ------- ---
17 DUF234 Archaea bacterial proteins of unknown 3.2 1.5 1
18 DUF1414 Protein of unknown function (DUF1414) 2.9 6.3 1
19
20 Parsed for domains:
21 Model Domain seq-f seq-t hmm-f hmm-t score E-value
22 -------- ------- ----- ----- ----- ----- ----- -------
23 DUF234 1/1 91 108 .. 5 22 .. 3.2 1.5
24 DUF1414 1/1 111 119 .. 1 9 [. 2.9 6.3
25
26 Alignments of top-scoring domains:
27 DUF234: domain 1 of 1, from 91 to 108: score 3.2, E = 1.5
28 *->VyPNrseIEsGnikevle<-*
29 VyPN++ IEs ++k++++
30 blumeria_G 91 VYPNIEIIESSTPKPLIN 108
31
32 DUF1414: domain 1 of 1, from 111 to 119: score 2.9, E = 6.3
33 *->HkAPvDLSL<-*
34 H ++DLSL
35 blumeria_G 111 HXSSPDLSL 119
36
37 //
38
39 Query sequence: blumeria_Grouper_590_20:NoCat_2
40 Accession: [none]
41 Description: [none]
42
43 Scores for sequence family classification (score includes all domains):
44 Model Description Score E-value N
45 -------- ----------- ----- ------- ---
46 [no hits above thresholds]
47
48 Parsed for domains:
49 Model Domain seq-f seq-t hmm-f hmm-t score E-value
50 -------- ------- ----- ----- ----- ----- ----- -------
51 [no hits above thresholds]
52
53 Alignments of top-scoring domains:
54 [no hits above thresholds]
55 //
56
57 Query sequence: blumeria_Grouper_590_20:NoCat_3
58 Accession: [none]
59 Description: [none]
60
61 Scores for sequence family classification (score includes all domains):
62 Model Description Score E-value N
63 -------- ----------- ----- ------- ---
64 CPW_WPC Plasmodium falciparum domain of unknown func 1.5 7.7 1
65 HECT HECT-domain (ubiquitin-transferase) 0.0 9.2 1
66
67 Parsed for domains:
68 Model Domain seq-f seq-t hmm-f hmm-t score E-value
69 -------- ------- ----- ----- ----- ----- ----- -------
70 CPW_WPC 1/1 30 37 .. 1 9 [. 1.5 7.7
71 HECT 1/1 55 69 .. 341 355 .] 0.0 9.2
72
73 Alignments of top-scoring domains:
74 CPW_WPC: domain 1 of 1, from 30 to 37: score 1.5, E = 7.7
75 *->CerdYsisk<-*
76 C++dYs sk
77 blumeria_G 30 CQFDYS-SK 37
78
79 HECT: domain 1 of 1, from 55 to 69: score 0.0, E = 9.2
80 *->LllAIneeteGFgle<-*
81 Ll+A+n+ + G+ ++
82 blumeria_G 55 LLTAVNNANTGYTQS 69
83
84 //
85
86 Query sequence: blumeria_Grouper_590_20:NoCat_4
87 Accession: [none]
88 Description: [none]
89
90 Scores for sequence family classification (score includes all domains):
91 Model Description Score E-value N
92 -------- ----------- ----- ------- ---
93 DUF46 Putative integral membrane protein DUF46 6.4 0.11 1
94
95 Parsed for domains:
96 Model Domain seq-f seq-t hmm-f hmm-t score E-value
97 -------- ------- ----- ----- ----- ----- ----- -------
98 DUF46 1/1 82 91 .. 173 182 .] 6.4 0.11
99
100 Alignments of top-scoring domains:
101 DUF46: domain 1 of 1, from 82 to 91: score 6.4, E = 0.11
102 *->YkLGlKdVpW<-*
103 Y+LGlK V++
104 blumeria_G 82 YLLGLKGVWY 91
105
106 //
107
108 Query sequence: blumeria_Grouper_590_20:NoCat_5
109 Accession: [none]
110 Description: [none]
111
112 Scores for sequence family classification (score includes all domains):
113 Model Description Score E-value N
114 -------- ----------- ----- ------- ---
115 POC4 POC4 chaperone -1.7 6.3 1
116
117 Parsed for domains:
118 Model Domain seq-f seq-t hmm-f hmm-t score E-value
119 -------- ------- ----- ----- ----- ----- ----- -------
120 POC4 1/1 121 125 .. 276 280 .] -1.7 6.3
121
122 Alignments of top-scoring domains:
123 POC4: domain 1 of 1, from 121 to 125: score -1.7, E = 6.3
124 *->SGLYI<-*
125 SGLYI
126 blumeria_G 121 SGLYI 125
127
128 //
129
130 Query sequence: blumeria_Grouper_590_20:NoCat_6
131 Accession: [none]
132 Description: [none]
133
134 Scores for sequence family classification (score includes all domains):
135 Model Description Score E-value N
136 -------- ----------- ----- ------- ---
137 [no hits above thresholds]
138
139 Parsed for domains:
140 Model Domain seq-f seq-t hmm-f hmm-t score E-value
141 -------- ------- ----- ----- ----- ----- ----- -------
142 [no hits above thresholds]
143
144 Alignments of top-scoring domains:
145 [no hits above thresholds]
146 //
147
148 Query sequence: blumeria_Grouper_4152_12:NoCat_1
149 Accession: [none]
150 Description: [none]
151
152 Scores for sequence family classification (score includes all domains):
153 Model Description Score E-value N
154 -------- ----------- ----- ------- ---
155 Peptidase_S29 Hepatitis C virus NS3 protease 4.7 1.1 1
156 DGOK 2-keto-3-deoxy-galactonokinase 0.5 1.3 1
157 TNV_CP Satellite tobacco necrosis virus coat p 0.1 7.9 1
158 TrbL TrbL/VirB6 plasmid conjugal transfer pr 0.8 8 1
159 Amino_oxidase Flavin containing amine oxidoreductase -0.6 9.1 1
160 DUF1301 Protein of unknown function (DUF1301) 0.4 9.9 1
161
162 Parsed for domains:
163 Model Domain seq-f seq-t hmm-f hmm-t score E-value
164 -------- ------- ----- ----- ----- ----- ----- -------
165 Amino_oxidase 1/1 27 38 .. 471 482 .] -0.6 9.1
166 TrbL 1/1 33 67 .. 231 285 .] 0.8 8
167 TNV_CP 1/1 58 80 .. 167 189 .. 0.1 7.9
168 DGOK 1/1 94 109 .. 283 298 .] 0.5 1.3
169 Peptidase_S29 1/1 113 127 .. 1 15 [. 4.7 1.1
170 DUF1301 1/1 148 157 .. 1 10 [. 0.4 9.9
171
172 Alignments of top-scoring domains:
173 Amino_oxidase: domain 1 of 1, from 27 to 38: score -0.6, E = 9.1
174 CS HHHHHHHHHHHH
175 *->veSGlrAAaril<-*
176 veSG rAA +l
177 blumeria_G 27 VESGXRAASTLL 38
178
179 TrbL: domain 1 of 1, from 33 to 67: score 0.8, E = 8
180 *->ksstiesfnlfvllaivllslvlilllkqipgiAqglvgavvtlgga
181 ++st+ + +++ ++ +++++l+l++ ++iA
182 blumeria_G 33 AASTLLI-----AVEHIVNCAAFCLALRSSASIA------------- 61
183
184 vaaalaGG<-*
185 a+ +GG
186 blumeria_G 62 --ASNSGG 67
187
188 TNV_CP: domain 1 of 1, from 58 to 80: score 0.1, E = 7.9
189 CS SSSGGGB-TTEEEEEEEES-SS-
190 *->AdvAaSNgpgAvFvLeigdkvag<-*
191 A++AaSN g vF+L +++ g
192 blumeria_G 58 ASIAASNSGGCVFFLPAASSAGG 80
193
194 DGOK: domain 1 of 1, from 94 to 109: score 0.5, E = 1.3
195 *->VdGDeAvrAGLseiAr<-*
196 VdG A AGL ++ r
197 blumeria_G 94 VDGVSALFAGLTSAGR 109
198
199 Peptidase_S29: domain 1 of 1, from 113 to 127: score 4.7, E = 1.1
200 *->GevqvLgTaTqsflG<-*
201 G+v++ + aT+ flG
202 blumeria_G 113 GTVMRFSGATTVFLG 127
203
204 DUF1301: domain 1 of 1, from 148 to 157: score 0.4, E = 9.9
205 *->gVKvFSlSTS<-*
206 ++vFS+STS
207 blumeria_G 148 SARVFSFSTS 157
208
209 //
210
211 Query sequence: blumeria_Grouper_4152_12:NoCat_2
212 Accession: [none]
213 Description: [none]
214
215 Scores for sequence family classification (score includes all domains):
216 Model Description Score E-value N
217 -------- ----------- ----- ------- ---
218 DUF1602 Protein of unknown function (DUF1602) 5.0 0.39 1
219 Toxin_18 Conotoxin O-superfamily 4.2 4.4 1
220 ABC_transp_aux ABC-type uncharacterized transport sys 1.1 5.2 1
221
222 Parsed for domains:
223 Model Domain seq-f seq-t hmm-f hmm-t score E-value
224 -------- ------- ----- ----- ----- ----- ----- -------
225 Toxin_18 1/1 21 26 .. 50 55 .] 4.2 4.4
226 ABC_transp_aux 1/1 126 137 .. 276 287 .] 1.1 5.2
227 DUF1602 1/1 143 159 .. 23 39 .] 5.0 0.39
228
229 Alignments of top-scoring domains:
230 Toxin_18: domain 1 of 1, from 21 to 26: score 4.2, E = 4.4
231 *->gfCLpr<-*
232 +fCL+r
233 blumeria_G 21 NFCLHR 26
234
235 ABC_transp_aux: domain 1 of 1, from 126 to 137: score 1.1, E = 5.2
236 *->wGvrldpdlVlD<-*
237 wG+r+dp+l+l
238 blumeria_G 126 WGIRWDPRLALR 137
239
240 DUF1602: domain 1 of 1, from 143 to 159: score 5.0, E = 0.39
241 *->kPPlSSsGalfanplrP<-*
242 +P l + G+l + +lrP
243 blumeria_G 143 MPKLNRRGFLASRLLRP 159
244
245 //
246
247 Query sequence: blumeria_Grouper_4152_12:NoCat_3
248 Accession: [none]
249 Description: [none]
250
251 Scores for sequence family classification (score includes all domains):
252 Model Description Score E-value N
253 -------- ----------- ----- ------- ---
254 zf-P11 P-11 zinc finger 3.6 1.8 1
255 V-ATPase_G Vacuolar (H+)-ATPase G subunit 2.4 5.3 1
256
257 Parsed for domains:
258 Model Domain seq-f seq-t hmm-f hmm-t score E-value
259 -------- ------- ----- ----- ----- ----- ----- -------
260 zf-P11 1/1 102 122 .. 1 20 [. 3.6 1.8
261 V-ATPase_G 1/1 126 135 .. 1 10 [. 2.4 5.3
262
263 Alignments of top-scoring domains:
264 zf-P11: domain 1 of 1, from 102 to 122: score 3.6, E = 1.8
265 *->GplnCKs..CWfkdknLveCsd<-*
266 Gp +C+s+ CW + + L C d
267 blumeria_G 102 GPHFCRSrxCW-NRDALLGCDD 122
268
269 V-ATPase_G: domain 1 of 1, from 126 to 135: score 2.4, E = 5.3
270 *->sqsqGIQqLL<-*
271 ++s+GIQ LL
272 blumeria_G 126 GGSGGIQDLL 135
273
274 //
275
276 Query sequence: blumeria_Grouper_4152_12:NoCat_4
277 Accession: [none]
278 Description: [none]
279
280 Scores for sequence family classification (score includes all domains):
281 Model Description Score E-value N
282 -------- ----------- ----- ------- ---
283 XhoI Restriction endonuclease XhoI 9.9 0.014 1
284 Endomucin Endomucin 0.1 6 1
285
286 Parsed for domains:
287 Model Domain seq-f seq-t hmm-f hmm-t score E-value
288 -------- ------- ----- ----- ----- ----- ----- -------
289 XhoI 1/1 92 122 .. 172 202 .] 9.9 0.014
290 Endomucin 1/1 113 119 .. 261 267 .] 0.1 6
291
292 Alignments of top-scoring domains:
293 XhoI: domain 1 of 1, from 92 to 122: score 9.9, E = 0.014
294 *->klvlerfytrpasllrdaqavlqGiikeprk<-*
295 ++++ ++yt ++ +d++++ qG k+ ++
296 blumeria_G 92 RSSRQKKYTPSRIACSDRSGGAQGKTKSRAI 122
297
298 Endomucin: domain 1 of 1, from 113 to 119: score 0.1, E = 6
299 *->AQGKtKN<-*
300 AQGKtK
301 blumeria_G 113 AQGKTKS 119
302
303 //
304
305 Query sequence: blumeria_Grouper_4152_12:NoCat_5
306 Accession: [none]
307 Description: [none]
308
309 Scores for sequence family classification (score includes all domains):
310 Model Description Score E-value N
311 -------- ----------- ----- ------- ---
312 SLT Transglycosylase SLT domain 4.5 1.2 1
313 DUF881 Bacterial protein of unknown function 4.0 1.6 1
314 DUF2346 Uncharacterized conserved protein (DUF 3.2 2.8 1
315 DUF1798 Bacterial domain of unknown function ( 3.0 3.3 1
316 LBP_BPI_CETP LBP / BPI / CETP family, N-terminal do 1.8 3.8 1
317 Jun Jun-like transcription factor -0.7 6.5 1
318
319 Parsed for domains:
320 Model Domain seq-f seq-t hmm-f hmm-t score E-value
321 -------- ------- ----- ----- ----- ----- ----- -------
322 DUF1798 1/1 2 19 .. 35 52 .. 3.0 3.3
323 DUF881 1/1 46 69 .. 214 237 .] 4.0 1.6
324 Jun 1/1 77 93 .. 264 284 .. -0.7 6.5
325 SLT 1/1 89 108 .. 1 20 [. 4.5 1.2
326 DUF2346 1/1 93 115 .. 63 85 .] 3.2 2.8
327 LBP_BPI_CETP 1/1 124 139 .. 191 209 .] 1.8 3.8
328
329 Alignments of top-scoring domains:
330 DUF1798: domain 1 of 1, from 2 to 19: score 3.0, E = 3.3
331 *->KPfvdevdqllaeWkelA<-*
332 +P+vd+vd++++++k+lA
333 blumeria_G 2 VPEVDMVDAEVEKLKTLA 19
334
335 DUF881: domain 1 of 1, from 46 to 69: score 4.0, E = 1.6
336 *->VeksdditiPAydgplklrYAkPv<-*
337 V + +it+PA++ p +r Ak++
338 blumeria_G 46 VAPEKRITVPALPRPAEVRPAKRA 69
339
340 Jun: domain 1 of 1, from 77 to 93: score -0.7, E = 6.5
341 *->qHheNPpgfqhsavgpPRlaa<-*
342 +++eNPp+ a++pP+l a
343 blumeria_G 77 AGAENPPL----APQPPALEA 93
344
345 SLT: domain 1 of 1, from 89 to 108: score 4.5, E = 1.2
346 CS HHHHHHHHHHTS-HHHHHHH
347 *->dliikaaekygidpsllaAi<-*
348 ++ ++a+ k+ ++p llaAi
349 blumeria_G 89 PALEAAGRKNTHPPELLAAI 108
350
351 DUF2346: domain 1 of 1, from 93 to 115: score 3.2, E = 2.8
352 *->AtKRrEkhdneLlealeeeEaKk<-*
353 A R+ h eLl+a+e eE+
354 blumeria_G 93 AAGRKNTHPPELLAAIEAEERRA 115
355
356 LBP_BPI_CETP: domain 1 of 1, from 124 to 139: score 1.8, E = 3.8
357 CS HHHHHHHCHHHH...HTTS
358 *->lCPviessVnslNvhLstl<-*
359 +C +++ssV++ L++l
360 blumeria_G 124 ICSTAISSVEAA---LQPL 139
361
362 //
363
364 Query sequence: blumeria_Grouper_4152_12:NoCat_6
365 Accession: [none]
366 Description: [none]
367
368 Scores for sequence family classification (score includes all domains):
369 Model Description Score E-value N
370 -------- ----------- ----- ------- ---
371 DUF258 Protein of unknown function, DUF258 1.5 3.8 1
372 TRAP_alpha Translocon-associated protein (TRAP), alph 0.1 4.1 1
373 DUF1289 Protein of unknown function (DUF1289) 2.8 5.3 1
374 SOCS_box SOCS box 2.4 9.7 1
375
376 Parsed for domains:
377 Model Domain seq-f seq-t hmm-f hmm-t score E-value
378 -------- ------- ----- ----- ----- ----- ----- -------
379 DUF258 1/1 50 62 .. 293 305 .] 1.5 3.8
380 SOCS_box 1/1 85 90 .. 1 6 [. 2.4 9.7
381 DUF1289 1/1 95 115 .. 36 56 .] 2.8 5.3
382 TRAP_alpha 1/1 106 116 .. 317 327 .] 0.1 4.1
383
384 Alignments of top-scoring domains:
385 DUF258: domain 1 of 1, from 50 to 62: score 1.5, E = 3.8
386 CS -HHHHHHHHHHHH
387 *->seeRYesYlklle<-*
388 s++R+++Y+ l++
389 blumeria_G 50 SASRFQHYRDLQK 62
390
391 SOCS_box: domain 1 of 1, from 85 to 90: score 2.4, E = 9.7
392 *->prSLqh<-*
393 prSLqh
394 blumeria_G 85 PRSLQH 90
395
396 DUF1289: domain 1 of 1, from 95 to 115: score 2.8, E = 5.3
397 *->dERravlqllpqRlaalglkp<-*
398 +E+ + lq+++qR +++++ +
399 blumeria_G 95 AEKIHTLQNCLQRSKRRSAGQ 115
400
401 TRAP_alpha: domain 1 of 1, from 106 to 116: score 0.1, E = 4.1
402 *->kRkvKRsvGdD<-*
403 +R +Rs+G+D
404 blumeria_G 106 QRSKRRSAGQD 116
405
406 //