/
text_31b1_hmmscan_001.out
340 lines (287 loc) · 20.7 KB
/
text_31b1_hmmscan_001.out
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
# hmmscan :: search sequence(s) against a profile database
# HMMER 3.1b1 (May 2013); http://hmmer.org/
# Copyright (C) 2013 Howard Hughes Medical Institute.
# Freely distributed under the GNU General Public License (GPLv3).
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query sequence file: prot_multi.fa
# target HMM database: /home/bow/db/hmmer/protdb/Pfam-A.hmm
# output directed to file: hmmscan/text_31b1_hmmscan_001.out
# per-seq hits tabular output: hmmscan/tab_31b1_hmmscan_001.out
# per-dom hits tabular output: hmmscan/domtab_31b1_hmmscan_001.out
# pfam-style tabular hit output: hmmscan/pfamtab_31b1_hmmscan_001.out
# number of worker threads: 2
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: random_s00 [L=22]
Scores for complete sequence (score includes all domains):
--- full sequence --- --- best 1 domain --- -#dom-
E-value score bias E-value score bias exp N Model Description
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
[No hits detected that satisfy reporting thresholds]
Domain annotation for each model (and alignments):
[No targets detected that satisfy reporting thresholds]
Internal pipeline statistics summary:
-------------------------------------
Query sequence(s): 1 (22 residues searched)
Target model(s): 14831 (2610332 nodes)
Passed MSV filter: 57 (0.0038433); expected 296.6 (0.02)
Passed bias filter: 44 (0.00296676); expected 296.6 (0.02)
Passed Vit filter: 1 (6.74263e-05); expected 14.8 (0.001)
Passed Fwd filter: 0 (0); expected 0.1 (1e-05)
Initial search space (Z): 14831 [actual number of targets]
Domain search space (domZ): 0 [number of targets reported over threshold]
# CPU time: 0.30u 0.23s 00:00:00.53 Elapsed: 00:00:03.04
# Mc/sec: 18.89
//
Query: gi|4885477|ref|NP_005359.1| [L=154]
Description: myoglobin [Homo sapiens]
Scores for complete sequence (score includes all domains):
--- full sequence --- --- best 1 domain --- -#dom-
E-value score bias E-value score bias exp N Model Description
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
1e-22 80.5 0.3 1.6e-22 79.8 0.3 1.3 1 Globin Globin
Domain annotation for each model (and alignments):
>> Globin Globin
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 79.8 0.3 1.1e-26 1.6e-22 1 109 [. 7 112 .. 7 113 .. 0.97
Alignments for each domain:
== domain 1 score: 79.8 bits; conditional E-value: 1.1e-26
HHHHHHHHHHHHHTHHHHHHHHHHHHHHHHSGGGGGGSTTTTTTT-HHHHCTSHHHHHHHHHHHHHHHHHHHTTTSHHHHHH CS
Globin 1 dkalvkaswekvkanaeelgaeilkrlFkaypdtkklFkkfgdlssaedlksspkfkahakkvlaalgeavknldndealka 82
+++lv w+kv+a+++ +g+e+l rlFk +p+t ++F kf++l+s +++k s+++k+h+++vl+alg ++k+ ++ ++a
gi|4885477|ref|NP_005359.1| 7 EWQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASEDLKKHGATVLTALGGILKK---KGHHEA 85
5789*********************************************************************...689*** PP
HHHHHHHHHHTSTT--HHHHHHHHHHH CS
Globin 83 alkklaarHaergkvdpanFklfgeal 109
+k la++Ha+++k++ ++ + ++e++
gi|4885477|ref|NP_005359.1| 86 EIKPLAQSHATKHKIPVKYLEFISECI 112
************************998 PP
Internal pipeline statistics summary:
-------------------------------------
Query sequence(s): 1 (154 residues searched)
Target model(s): 14831 (2610332 nodes)
Passed MSV filter: 494 (0.0333086); expected 296.6 (0.02)
Passed bias filter: 402 (0.0271054); expected 296.6 (0.02)
Passed Vit filter: 35 (0.00235992); expected 14.8 (0.001)
Passed Fwd filter: 1 (6.74263e-05); expected 0.1 (1e-05)
Initial search space (Z): 14831 [actual number of targets]
Domain search space (domZ): 1 [number of targets reported over threshold]
# CPU time: 0.38u 0.31s 00:00:00.69 Elapsed: 00:00:03.72
# Mc/sec: 108.06
//
Query: gi|126362951|ref|NP_001075106.1| [L=106]
Description: leukocyte immunoglobulin-like receptor subfamily B member 1 isoform 2 precursor [Homo sapiens]
Scores for complete sequence (score includes all domains):
--- full sequence --- --- best 1 domain --- -#dom-
E-value score bias E-value score bias exp N Model Description
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
9.3e-10 38.8 0.4 1.4e-09 38.3 0.4 1.3 1 Ig_3 Immunoglobulin domain
1.6e-06 28.1 0.1 2e-06 27.8 0.1 1.1 1 Ig_2 Immunoglobulin domain
Domain annotation for each model (and alignments):
>> Ig_3 Immunoglobulin domain
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 38.3 0.4 1.8e-13 1.4e-09 1 73 [. 8 83 .. 8 87 .. 0.95
Alignments for each domain:
== domain 1 score: 38.3 bits; conditional E-value: 1.8e-13
Ig_3 1 kPvisvspsptvtsggnvtLtCsaeggpppptisWy.....ietppelqgsegssssestLtissvtsedsGtYtCva 73
kP++s++psp+v+sggnv L+C ++ + +s + +++ +++++ ++ss +++++ +v+++ + Y+C+a
gi|126362951|ref|NP_001075106.1| 8 KPTLSAQPSPVVNSGGNVILQCDSQVA--FDGFSLCkegedEHPQCLNSQPHARGSSRAIFSVGPVSPSRRWWYRCYA 83
8************************99..78888888****************************************9 PP
>> Ig_2 Immunoglobulin domain
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 27.8 0.1 2.6e-10 2e-06 1 80 [] 8 103 .. 8 103 .. 0.75
Alignments for each domain:
== domain 1 score: 27.8 bits; conditional E-value: 2.6e-10
Ig_2 1 kpvlsapp.tvvtegenvtLtCqapgnptpkvqwykdg.....eelsqsqna.......lfipnvsaedsGtYtCra 64
kp+lsa+p +vv+ g nv L C ++ ++ +++ k+g + l++++ a + + vs++ Y+C+a
gi|126362951|ref|NP_001075106.1| 8 KPTLSAQPsPVVNSGGNVILQCDSQVA-FDGFSLCKEGedehpQCLNSQPHArgssraiFSVGPVSPSRRWWYRCYA 83
799**9997779*************86.9*******98643333333333335555553444669************ PP
Ig_2 65 ....snsegskqsnsvevtv 80
s +e+s +s+ +e+ v
gi|126362951|ref|NP_001075106.1| 84 ydsnSPYEWSLPSDLLELLV 103
88554455699999999876 PP
Internal pipeline statistics summary:
-------------------------------------
Query sequence(s): 1 (106 residues searched)
Target model(s): 14831 (2610332 nodes)
Passed MSV filter: 171 (0.0115299); expected 296.6 (0.02)
Passed bias filter: 140 (0.00943969); expected 296.6 (0.02)
Passed Vit filter: 11 (0.00074169); expected 14.8 (0.001)
Passed Fwd filter: 2 (0.000134853); expected 0.1 (1e-05)
Initial search space (Z): 14831 [actual number of targets]
Domain search space (domZ): 2 [number of targets reported over threshold]
# CPU time: 0.31u 0.24s 00:00:00.55 Elapsed: 00:00:01.22
# Mc/sec: 226.80
//
Query: gi|22748937|ref|NP_065801.1| [L=1204]
Description: exportin-5 [Homo sapiens]
Scores for complete sequence (score includes all domains):
--- full sequence --- --- best 1 domain --- -#dom-
E-value score bias E-value score bias exp N Model Description
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
8.5e-34 116.6 7.8 1.2e-33 116.1 4.9 2.8 2 Xpo1 Exportin 1-like protein
0.0044 16.9 0.0 0.036 13.9 0.0 2.7 2 IBN_N Importin-beta N-terminal domain
------ inclusion threshold ------
0.095 11.7 0.3 1.3 8.0 0.3 2.3 2 Rac1 Rac1-binding domain
Domain annotation for each model (and alignments):
>> Xpo1 Exportin 1-like protein
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 116.1 4.9 2.3e-37 1.2e-33 2 148 .] 110 271 .. 109 271 .. 0.98
2 ? -1.8 0.0 0.52 2.6e+03 112 139 .. 499 525 .. 496 529 .. 0.86
Alignments for each domain:
== domain 1 score: 116.1 bits; conditional E-value: 2.3e-37
HHHHHHHHHHHHHHHHHHTTTTSTTHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHCTSXTTCSHHHHHHHHHHHHHHHHHH CS
Xpo1 2 kflrnklaealaelflqeypnqWpsffddllsllssspsglelllriLkvlpeEiadfsrskleqerrnelkdllrsqvqk 82
+++++ l+++++e++++e+p++Wp+++ +l l++++++++el++ iL++l+e++++f ++l +rr++++++l++++++
gi|22748937|ref|NP_065801.1| 110 NHIKDALSRIVVEMIKREWPQHWPDMLIELDTLSKQGETQTELVMFILLRLAEDVVTF--QTLPPQRRRDIQQTLTQNMER 188
89******************************************************99..79******************* PP
HHHHHHHHHHHHHHCC...............HHHHHHHHHHHHHHHTTTS-HHHHHSSC..HHHHHHHHTTSCCCHHHHHH CS
Xpo1 83 ilelllqileqsvskk...............sselveatLkclsswvswidiglivnsp..llsllfqlLndpelreaAve 146
i+++ll+ l+++v+k+ ++++ a+L++l+ +++w+++++i +++ ll++l+ lLn++el+ A+e
gi|22748937|ref|NP_065801.1| 189 IFSFLLNTLQENVNKYqqvktdtsqeskaqaNCRVGVAALNTLAGYIDWVSMSHITAENckLLEILCLLLNEQELQLGAAE 269
**************99*****************************************8889******************** PP
HH CS
Xpo1 147 cL 148
cL
gi|22748937|ref|NP_065801.1| 270 CL 271
*8 PP
== domain 2 score: -1.8 bits; conditional E-value: 0.52
HHTTTS-HHHHHSSCHHHHHHHHTTSCC CS
Xpo1 112 swvswidiglivnspllsllfqlLndpe 139
s+v+w ++l+++s +++ +f+ Ln++e
gi|22748937|ref|NP_065801.1| 499 SFVQWEAMTLFLES-VITQMFRTLNREE 525
899*********98.8888899998776 PP
>> IBN_N Importin-beta N-terminal domain
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 13.9 0.0 7.3e-06 0.036 4 75 .. 36 98 .. 33 100 .. 0.87
2 ? -3.5 0.0 2 1e+04 57 74 .. 168 185 .. 165 186 .. 0.84
Alignments for each domain:
== domain 1 score: 13.9 bits; conditional E-value: 7.3e-06
HHHHHHHSTTHHHHHHHHHHHTTTSTHHHHHHHHHHHHHHHHHSCCHHHHHHHHCSSHHHHHHHHHHHHHHH CS
IBN_N 4 qLnqlekqkPgflsallqilanksldlevRqlAalyLknlItkhWkseeaqrqqqlpeeekelIrnnllnll 75
++++++ P ++++ l+++ +k+ vR++++++L++ ++ +W+ ++ ek +++n++ +l+
gi|22748937|ref|NP_065801.1| 36 FCEEFKEKCPICVPCGLRLA-EKTQVAIVRHFGLQILEHVVKFRWN--------GMSRLEKVYLKNSVMELI 98
56788886699*********.6555899******************........999999****99999887 PP
== domain 2 score: -3.5 bits; conditional E-value: 2
HCSSHHHHHHHHHHHHHH CS
IBN_N 57 qqlpeeekelIrnnllnl 74
q+lp++ + +I ++l +
gi|22748937|ref|NP_065801.1| 168 QTLPPQRRRDIQQTLTQN 185
6899*******9999876 PP
>> Rac1 Rac1-binding domain
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 8.0 0.3 0.00026 1.3 94 171 .. 89 169 .. 82 254 .. 0.75
2 ? 0.8 0.0 0.041 2e+02 150 181 .. 310 341 .. 296 354 .. 0.82
Alignments for each domain:
== domain 1 score: 8.0 bits; conditional E-value: 0.00026
Rac1 94 qlrsnimksvvepslkriqkqldqshslvdia..slerar.khletllevlvtlsqqgekvssevydflyrlaevkvslsv 171
+l++ +m +++ +l+ ++++ +l+ i ++r +h +l l tls+qge + v +l rlae v++
gi|22748937|ref|NP_065801.1| 89 YLKNSVMELIANGTLNILEEENHIKDALSRIVveMIKREWpQHWPDMLIELDTLSKQGETQTELVMFILLRLAEDVVTFQT 169
788899999******9998766666666666511555543499*9*****************999999******9888642 PP
== domain 2 score: 0.8 bits; conditional E-value: 0.041
Rac1 150 kvssevydflyrlaevkvslsvrldtlkqqqe 181
+ + y fl+rl +v +l+ +l +l + +
gi|22748937|ref|NP_065801.1| 310 GLVEKHYVFLKRLCQVLCALGNQLCALLGADS 341
556678******************99977665 PP
Internal pipeline statistics summary:
-------------------------------------
Query sequence(s): 1 (1204 residues searched)
Target model(s): 14831 (2610332 nodes)
Passed MSV filter: 567 (0.0382307); expected 296.6 (0.02)
Passed bias filter: 414 (0.0279145); expected 296.6 (0.02)
Passed Vit filter: 32 (0.00215764); expected 14.8 (0.001)
Passed Fwd filter: 3 (0.000202279); expected 0.1 (1e-05)
Initial search space (Z): 14831 [actual number of targets]
Domain search space (domZ): 3 [number of targets reported over threshold]
# CPU time: 0.78u 0.28s 00:00:01.06 Elapsed: 00:00:03.60
# Mc/sec: 873.01
//
Query: gi|125490392|ref|NP_038661.2| [L=352]
Description: POU domain, class 5, transcription factor 1 isoform 1 [Mus musculus]
Scores for complete sequence (score includes all domains):
--- full sequence --- --- best 1 domain --- -#dom-
E-value score bias E-value score bias exp N Model Description
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
7.6e-37 124.8 0.5 1.5e-36 123.9 0.5 1.5 1 Pou Pou domain - N-terminal to homeobox domain
1.8e-18 65.8 1.1 3.4e-18 64.9 1.1 1.5 1 Homeobox Homeobox domain
------ inclusion threshold ------
0.013 15.6 0.0 0.18 12.0 0.0 2.2 2 HTH_31 Helix-turn-helix domain
0.043 13.5 0.0 0.1 12.2 0.0 1.6 1 Homeobox_KN Homeobox KN domain
0.15 10.5 0.1 0.28 9.6 0.1 1.4 1 DUF521 Protein of unknown function (DUF521)
Domain annotation for each model (and alignments):
>> Pou Pou domain - N-terminal to homeobox domain
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 123.9 0.5 5e-40 1.5e-36 3 75 .] 133 205 .. 131 205 .. 0.97
Alignments for each domain:
== domain 1 score: 123.9 bits; conditional E-value: 5e-40
Pou 3 eldleeleefakefkqrrikLgltqadvgsalgalyGkefsqttIcrFEalqLslknmckLkpllekWLeeae 75
++ ++ele+fak +kq+ri+Lg+tqadvg +lg+l+Gk+fsqttIcrFEalqLslknmckL+pllekW+eea+
gi|125490392|ref|NP_038661.2| 133 KALQKELEQFAKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTICRFEALQLSLKNMCKLRPLLEKWVEEAD 205
67899******************************************************************96 PP
>> Homeobox Homeobox domain
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 64.9 1.1 1.2e-21 3.4e-18 1 57 [] 224 280 .. 224 280 .. 0.98
Alignments for each domain:
== domain 1 score: 64.9 bits; conditional E-value: 1.2e-21
TT--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHHC CS
Homeobox 1 rrkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakekk 57
+rkRt++++ Le++F k+++ps ++++++A++lgL++++V+vWF+NrR+k k+
gi|125490392|ref|NP_038661.2| 224 KRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKR 280
79****************************************************997 PP
>> HTH_31 Helix-turn-helix domain
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 12.0 0.0 5.9e-05 0.18 1 35 [. 141 181 .. 141 185 .. 0.95
2 ? 0.9 0.0 0.18 5.3e+02 39 62 .. 245 268 .. 243 270 .. 0.85
Alignments for each domain:
== domain 1 score: 12.0 bits; conditional E-value: 5.9e-05
HTH_31 1 aLGarLralReraGLsqeevAerag......vSastlsriE 35
+++ +L++ R + G +q++v+ +g +S++t++r E
gi|125490392|ref|NP_038661.2| 141 QFAKLLKQKRITLGYTQADVGLTLGvlfgkvFSQTTICRFE 181
7999**************************99*******99 PP
== domain 2 score: 0.9 bits; conditional E-value: 0.18
HTH_31 39 rgrpslavlaalaralgldeaera 62
++ psl++++ +a+ lgl+ + ++
gi|125490392|ref|NP_038661.2| 245 CPKPSLQQITHIANQLGLEKDVVR 268
678**************9988765 PP
>> Homeobox_KN Homeobox KN domain
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 12.2 0.0 3.5e-05 0.1 7 39 .. 244 276 .. 241 277 .. 0.91
Alignments for each domain:
== domain 1 score: 12.2 bits; conditional E-value: 3.5e-05
Homeobox_KN 7 hnPYPskevkeelakqTglsrkqidnWFiNaRr 39
+ P Ps +++ +a+q gl + + WF N R
gi|125490392|ref|NP_038661.2| 244 KCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQ 276
56779*************************996 PP
>> DUF521 Protein of unknown function (DUF521)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 9.6 0.1 9.4e-05 0.28 273 334 .. 221 280 .. 197 294 .. 0.77
Alignments for each domain:
== domain 1 score: 9.6 bits; conditional E-value: 9.4e-05
DUF521 273 adlaavleelnkakkeevdlvvlGcPhlsleeleelaellkgrkkkvsvelvvttsravlsk 334
+ +++ + +++++ +++ ++l cP sl++++++a++l +k v+++ + r+ ++
gi|125490392|ref|NP_038661.2| 221 QARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEK--DVVRVWFCNRRQKGKR 280
345666667778888899************************99..9999999988876554 PP
Internal pipeline statistics summary:
-------------------------------------
Query sequence(s): 1 (352 residues searched)
Target model(s): 14831 (2610332 nodes)
Passed MSV filter: 663 (0.0447037); expected 296.6 (0.02)
Passed bias filter: 493 (0.0332412); expected 296.6 (0.02)
Passed Vit filter: 45 (0.00303419); expected 14.8 (0.001)
Passed Fwd filter: 5 (0.000337132); expected 0.1 (1e-05)
Initial search space (Z): 14831 [actual number of targets]
Domain search space (domZ): 5 [number of targets reported over threshold]
# CPU time: 0.43u 0.33s 00:00:00.76 Elapsed: 00:00:04.08
# Mc/sec: 225.21
//
[ok]