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comparison commons/pyRepetUnit/hmmer/hmmOutput/tests/datas/test_hmmpfam_output @ 31:0ab839023fe4

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author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
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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: myhmms
7 Sequence file: test.fa
8 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
9
10 Query sequence: pkinase_full
11 Accession: [none]
12 Description: Dario rerio
13
14 Scores for sequence family classification (score includes all domains):
15 Model Description Score E-value N
16 -------- ----------- ----- ------- ---
17 pkinase Protein kinase domain 266.6 3.3e-80 1
18 pkinase Protein kinase domain 265.4 7.6e-80 1
19 rrm -42.5 2.5 1
20 rrm -8.7 3.7 1
21 fn3 Fibronectin type III domain -45.8 3.7 1
22 fn3 Fibronectin type III domain -9.0 3.8 1
23
24 Parsed for domains:
25 Model Domain seq-f seq-t hmm-f hmm-t score E-value
26 -------- ------- ----- ----- ----- ----- ----- -------
27 rrm 1/1 169 180 .. 66 77 .] -8.7 3.7
28 fn3 1/1 197 200 .. 81 84 .] -9.0 3.8
29 rrm 1/1 256 319 .. 1 77 [] -42.5 2.5
30 pkinase 1/1 258 540 .. 1 294 [] 266.6 3.3e-80
31 pkinase 1/1 258 537 .. 1 289 [. 265.4 7.6e-80
32 fn3 1/1 434 506 .. 1 84 [] -45.8 3.7
33
34 Alignments of top-scoring domains:
35 rrm: domain 1 of 1, from 169 to 180: score -8.7, E = 3.7
36 *->nGkelggrklrv<-*
37 n++ ++l v
38 pkinase_fu 169 NKQDPHQHRLSV 180
39
40 fn3: domain 1 of 1, from 197 to 200: score -9.0, E = 3.8
41 CS CCCC
42 *->GpeS<-*
43 G eS
44 pkinase_fu 197 GGES 200
45
46 rrm: domain 1 of 1, from 256 to 319: score -42.5, E = 2.5
47 *->lfVgNL..ppdvteedLkdlFsk.fGpivsikivkDhkektketgks
48 +N++ +d+ e + F+ + +++ +
49 pkinase_fu 256 ---NNIeyVRDIGEGAFGRVFQArAPGL----LPTE----------P 285
50
51 kGfaFVeFeseedAekAlealnG.kelggrklrv<-*
52 + V++ +ee+ ++ ++++ + l++ +
53 pkinase_fu 286 FTMVAVKMLKEEASTDMQNDFQReAALMSEFDHP 319
54
55 pkinase: domain 1 of 1, from 258 to 540: score 266.6, E = 3.3e-80
56 *->yelleklGeGsfGkVykakhkd....ktgkiVAvKilkkekesikek
57 +e ++ +GeG+fG+V++a+ +++ VAvK+lk e+ s++
58 pkinase_fu 258 IEYVRDIGEGAFGRVFQARAPGllptEPFTMVAVKMLK-EEASTDMQ 303
59
60 .rflrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdylrr
61 ++f+rE++++ +++HpNIvrl+gv+ +++++l +Eym GdL+++lrr
62 pkinase_fu 304 nDFQREAALMSEFDHPNIVRLLGVCA-VGKPMCLMFEYMAYGDLNEFLRR 352
63
64 ng........................gplsekeakkialQilrGleYLHs
65 + +++++ ++++ ++++ +++++ pls +e ++i +Q++ G++YL +
66 pkinase_fu 353 RCatqqpslsrdtltssslvseperyPPLSCQEQLSISKQVAAGMAYLSE 402
67
68 ngivHRDLKpeNILldendgtvKiaDFGLArlle..sssklttfvGTpwY
69 +++vHRDL+++N+L+ en +vKiaDFGL+r ++ +++k++ + p +
70 pkinase_fu 403 RKFVHRDLATRNCLVAEN-LVVKIADFGLSRNIYaaDYYKASENDAIPIR 451
71
72 mmAPEvilegrgysskvDvWSlGviLyElltggplfpgadlpaftggdev
73 +m+PE ++++ y+s++DvW++Gv+L+E++++g
74 pkinase_fu 452 WMPPES-IFYNRYTSESDVWAYGVVLWEIFSYG----------------- 483
75
76 dqliifvlklPfsdelpktridpleelfriikrpglrlplpsncSeelkd
77 ++P+++ + ee+ + +++ g l +p+nc+ el+
78 pkinase_fu 484 --------MQPYYG-------MAHEEVIYYVRD-GNVLSCPENCPQELYN 517
79
80 LlkkcLnkDPskRpGsatakeilnhpwf<-*
81 L++ c+ P++Rp ++ i h +
82 pkinase_fu 518 LMRLCWSGHPTDRP---SFASI--HRIL 540
83
84 pkinase: domain 1 of 1, from 258 to 537: score 265.4, E = 7.6e-80
85 *->yelleklGeGsfGkVykakhkd....ktgkiVAvKilkkekesikek
86 +e ++ +GeG+fG+V++a+ +++ VAvK+lk e+ s++
87 pkinase_fu 258 IEYVRDIGEGAFGRVFQARAPGllptEPFTMVAVKMLK-EEASTDMQ 303
88
89 .rflrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdylrr
90 ++f+rE++++ +++HpNIvrl+gv+ +++++l +Eym GdL+++lrr
91 pkinase_fu 304 nDFQREAALMSEFDHPNIVRLLGVCA-VGKPMCLMFEYMAYGDLNEFLRR 352
92
93 ng........................gplsekeakkialQilrGleYLHs
94 + +++++ ++++ ++++ +++++ pls +e ++i +Q++ G++YL +
95 pkinase_fu 353 RCatqqpslsrdtltssslvseperyPPLSCQEQLSISKQVAAGMAYLSE 402
96
97 ngivHRDLKpeNILldendgtvKiaDFGLArlle..sssklttfvGTpwY
98 +++vHRDL+++N+L+ en +vKiaDFGL+r ++ +++k++ + p +
99 pkinase_fu 403 RKFVHRDLATRNCLVAEN-LVVKIADFGLSRNIYaaDYYKASENDAIPIR 451
100
101 mmAPEvilegrgysskvDvWSlGviLyElltggplfpgadlpaftggdev
102 +m+PE ++++ y+s++DvW++Gv+L+E++++g
103 pkinase_fu 452 WMPPES-IFYNRYTSESDVWAYGVVLWEIFSYG----------------- 483
104
105 dqliifvlklPfsdelpktridpleelfriikrpglrlplpsncSeelkd
106 ++P+++ + ee+ + +++ g l +p+nc+ el+
107 pkinase_fu 484 --------MQPYYG-------MAHEEVIYYVRD-GNVLSCPENCPQELYN 517
108
109 LlkkcLnkDPskRpGsatakeil<-*
110 L++ c+ P++Rp ++ i+
111 pkinase_fu 518 LMRLCWSGHPTDRP---SFASIH 537
112
113 fn3: domain 1 of 1, from 434 to 506: score -45.8, E = 3.7
114 CS CCCCCEEEEEECCTTCCEEEEECCC CCCCCCCEEEEE.E
115 *->PsaPtnltvtdvtstsltlsWsppt........gngpitgYevtyRq
116 a ++++ + + ++W pp++ ++ + +++ Y v + +
117 pkinase_fu 434 IYAADYYKASE--NDAIPIRWMPPEsifynrytSESDVWAYGVVL-W 477
118
119 CS CCCCCC CCCCEEECCCCCECECCEEEEECCCCEEEEEECCCCCCC
120 pkngge..wneltvpgtttsytltgLkPgteYevrVqAvnggGGpeS<-*
121 + + + ++ + ++V+ +g+ S
122 pkinase_fu 478 EIFSYGmqPYYGMAHEEV--------------IYYVR--DGN--VLS 506
123
124 //
125
126 Query sequence: pkinase_part
127 Accession: [none]
128 Description: Dario rerio
129
130 Scores for sequence family classification (score includes all domains):
131 Model Description Score E-value N
132 -------- ----------- ----- ------- ---
133 pkinase Protein kinase domain 101.5 1.7e-30 1
134 pkinase Protein kinase domain -94.7 1.5e-05 1
135 rrm -42.5 2.5 1
136 rrm -8.7 3.7 1
137 fn3 Fibronectin type III domain -9.0 3.8 1
138 fn3 Fibronectin type III domain -52.2 5.9 1
139
140 Parsed for domains:
141 Model Domain seq-f seq-t hmm-f hmm-t score E-value
142 -------- ------- ----- ----- ----- ----- ----- -------
143 rrm 1/1 169 180 .. 66 77 .] -8.7 3.7
144 fn3 1/1 197 200 .. 81 84 .] -9.0 3.8
145 fn3 1/1 233 299 .. 1 84 [] -52.2 5.9
146 rrm 1/1 256 319 .. 1 77 [] -42.5 2.5
147 pkinase 1/1 258 400 .] 1 116 [. 101.5 1.7e-30
148 pkinase 1/1 258 400 .] 1 294 [] -94.7 1.5e-05
149
150 Alignments of top-scoring domains:
151 rrm: domain 1 of 1, from 169 to 180: score -8.7, E = 3.7
152 *->nGkelggrklrv<-*
153 n++ ++l v
154 pkinase_pa 169 NKQDPHQHRLSV 180
155
156 fn3: domain 1 of 1, from 197 to 200: score -9.0, E = 3.8
157 CS CCCC
158 *->GpeS<-*
159 G eS
160 pkinase_pa 197 GGES 200
161
162 fn3: domain 1 of 1, from 233 to 299: score -52.2, E = 5.9
163 CS CCCC CEEEEEECCTTCCEEEEECCCCCCCCCCEEEEE.ECCCCCCC
164 *->PsaP.tnltvtdvtstsltlsWspptgngpitgYevtyRqpknggew
165 P + ++l ++ +s ls + p + i++ +R + ++g
166 pkinase_pa 233 PNPMyQRL---PLLLNSKLLSLEYP--RNNIEY----VR-DIGEG-- 267
167
168 CS CCCEEECCCCCECECCEEEEECCCCEEEEEECCCCCCC
169 neltvpgtttsytltgLkPgteYevrVqAvnggGGpeS<-*
170 g ++ gL P + ++ + + ++S
171 pkinase_pa 268 ----AFGRVFQARAPGLLPTEPFTMVAVKMLKE--EAS 299
172
173 rrm: domain 1 of 1, from 256 to 319: score -42.5, E = 2.5
174 *->lfVgNL..ppdvteedLkdlFsk.fGpivsikivkDhkektketgks
175 +N++ +d+ e + F+ + +++ +
176 pkinase_pa 256 ---NNIeyVRDIGEGAFGRVFQArAPGL----LPTE----------P 285
177
178 kGfaFVeFeseedAekAlealnG.kelggrklrv<-*
179 + V++ +ee+ ++ ++++ + l++ +
180 pkinase_pa 286 FTMVAVKMLKEEASTDMQNDFQReAALMSEFDHP 319
181
182 pkinase: domain 1 of 1, from 258 to 400: score 101.5, E = 1.7e-30
183 *->yelleklGeGsfGkVykakhkd....ktgkiVAvKilkkekesikek
184 +e ++ +GeG+fG+V++a+ +++ VAvK+lk e+ s++
185 pkinase_pa 258 IEYVRDIGEGAFGRVFQARAPGllptEPFTMVAVKMLK-EEASTDMQ 303
186
187 .rflrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdylrr
188 ++f+rE++++ +++HpNIvrl+gv+ +++++l +Eym GdL+++lrr
189 pkinase_pa 304 nDFQREAALMSEFDHPNIVRLLGVCA-VGKPMCLMFEYMAYGDLNEFLRR 352
190
191 ng........................gplsekeakkialQilrGleYL<-
192 + +++++ ++++ ++++ +++++ pls +e ++i +Q++ G++YL
193 pkinase_pa 353 RCatqqpslsrdtltssslvseperyPPLSCQEQLSISKQVAAGMAYL 400
194
195 *
196
197 pkinase_pa - -
198
199 pkinase: domain 1 of 1, from 258 to 400: score -94.7, E = 1.5e-05
200 *->yelleklGeGsfGkVykakhkd....ktgkiVAvKilkkekesikek
201 +e ++ +GeG+fG+V++a+ +++ VAvK+lk e+ s++
202 pkinase_pa 258 IEYVRDIGEGAFGRVFQARAPGllptEPFTMVAVKMLK-EEASTDMQ 303
203
204 .rflrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdylrr
205 ++f+rE++++ +++HpNIvrl+gv+ +++++l +Eym GdL+++lrr
206 pkinase_pa 304 nDFQREAALMSEFDHPNIVRLLGVCA-VGKPMCLMFEYMAYGDLNEFLRR 352
207
208 nggplsekeakkialQilrGleYLHsngivHRDLKpeNILldendgtvKi
209 +
210 pkinase_pa 353 RC------------------------------------------------ 354
211
212 aDFGLArllesssklttfvGTpwYmmAPEvilegrgysskvDvWSlGviL
213 A++ s + +t++ ++ PE
214 pkinase_pa 355 -----ATQQP-SLSRDTLTSSSLVS-EPER-------------------- 377
215
216 yElltggplfpgadlpaftggdevdqliifvlklPfsdelpktridplee
217 +P s
218 pkinase_pa 378 --------------------------------YPPLS------------- 382
219
220 lfriikrpglrlplpsncSeelkdLlkkcLnkDPskRpGsatakeilnhp
221 + + ++S+ + +
222 pkinase_pa 383 -----CQ------EQLSISKQVAAGM-----------A------------ 398
223
224 wf<-*
225 ++
226 pkinase_pa 399 YL 400
227
228 //
229
230 Query sequence: S13421
231 Accession: [none]
232 Description: S13421 GLOBIN - BRINE SHRIMP, 1405 bases, EDBC29AF checksum.
233
234 Scores for sequence family classification (score includes all domains):
235 Model Description Score E-value N
236 -------- ----------- ----- ------- ---
237 pkinase Protein kinase domain -171.6 0.19 1
238 rrm -32.5 0.26 1
239 rrm -6.1 0.92 1
240 fn3 Fibronectin type III domain -39.7 1.2 1
241 pkinase Protein kinase domain -9.2 1.8 1
242 fn3 Fibronectin type III domain -7.5 1.9 1
243
244 Parsed for domains:
245 Model Domain seq-f seq-t hmm-f hmm-t score E-value
246 -------- ------- ----- ----- ----- ----- ----- -------
247 fn3 1/1 143 224 .. 1 84 [] -39.7 1.2
248 pkinase 1/1 233 241 .. 1 9 [. -9.2 1.8
249 rrm 1/1 440 456 .. 1 17 [. -6.1 0.92
250 rrm 1/1 669 731 .. 1 77 [] -32.5 0.26
251 pkinase 1/1 906 1127 .. 1 294 [] -171.6 0.19
252 fn3 1/1 923 934 .. 1 12 [. -7.5 1.9
253
254 Alignments of top-scoring domains:
255 fn3: domain 1 of 1, from 143 to 224: score -39.7, E = 1.2
256 CS C CCCCEEEEEECCTTCCEEEEECCCCCCCCCCEEEEE.ECCCCCCC
257 *->P.saPtnltvtdvtstsltlsWspptgngpitgYevtyRqpknggew
258 + ++t+l++ dv ++ sWs+ +g+ + tg v R + ng +
259 S13421 143 IdLEVTGLSCVDVAN--IQESWSKVSGDLKTTGSVVFQR-MINGH-P 185
260
261 CS CCCEEECCCCCECECCEEEEECCCCEEEEEECCC CCCC
262 neltvpgtttsytltgLkPgteYevrVqAvnggG.GpeS<-*
263 +++ ++ + + l L + + V v ++ +G
264 S13421 186 EYQQLFRQFRDVDLDKLGESNSFVAHVFRVVAAFdGIIH 224
265
266 pkinase: domain 1 of 1, from 233 to 241: score -9.2, E = 1.8
267 *->yelleklGe<-*
268 +l+klGe
269 S13421 233 VSTLKKLGE 241
270
271 rrm: domain 1 of 1, from 440 to 456: score -6.1, E = 0.92
272 *->lfVgNLppdvteedLkd<-*
273 + ++ L++ + d+ d
274 S13421 440 VIISFLNEGLRQADIVD 456
275
276 rrm: domain 1 of 1, from 669 to 731: score -32.5, E = 0.26
277 *->lfVgNL.ppdvteedLkdlFskfGpivsikivkDhkektketgkskG
278 V L+++d+ + + f i k++ D +
279 S13421 669 --VEELpSTDAFHYHISLVMNRFSSI--GKVIDD------------N 699
280
281 faFVeFeseedAekAlealnGkelggr.klrv<-*
282 + FV ++ + e+ ++ l k+++ +l++
283 S13421 700 VSFVYLLKKLGREHIKRGLSRKQFDQFvELYI 731
284
285 pkinase: domain 1 of 1, from 906 to 1127: score -171.6, E = 0.19
286 *->yelleklGeGsfGkVykakhkd........ktgkiVAvKilkkekes
287 ++l G++ ++ + ++ ++ ++ + ++VAv + ++
288 S13421 906 FKLMH-------GVIEEGLLQLerinpitgLSAREVAVVKQ---TWN 942
289
290 ikekrflrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdy
291 + + L+ ++ fe + + v++ +d
292 S13421 943 LVK----------PDLMGVGMRIFKSLFE-AFPAYQAVFPKFSD-VPLDK 980
293
294 lrrng....gplsekeakkialQilrGleYLHsngivHRDLKpeNILlde
295 l + +++ +s ++ Q+ lde
296 S13421 981 LEDTPavgkHSISVTTKLDELIQT-----------------------LDE 1007
297
298 ndgtvKiaDFGLArlle........sssklttfvGTpwYmmAPEvi...l
299 + ++ + LAr+l +++ + + +++++f+ +++ ++++l
300 S13421 1008 P-ANLAL----LARQLGedhivlrvNKPMFKSFGKVLVRL-----LendL 1047
301
302 egrgysskvDvW..SlGviLyElltggplfpgadlpaftggdevdqliif
303 +r s ++ W++++ vi+ ++ g
304 S13421 1048 GQRFSSFASRSWhkAYDVIVEYIEEG------------------------ 1073
305
306 vlklPfsdelpktridpleelfriikrpglrlplpsncSeelkdLlkkcL
307 l++ +++ dp + + k l + ++++ ++l+ L +k++
308 S13421 1074 -LQQSYKQ-------DPVTGITDAEKA--LVQESWDLLKPDLLGLGRKIF 1113
309
310 nkDPskRpGsatakeilnhpwf<-*
311 +k +k p +i f
312 S13421 1114 TKVFTKHP----DYQI----LF 1127
313
314 fn3: domain 1 of 1, from 923 to 934: score -7.5, E = 1.9
315 CS CCCCCEEEEEEC
316 *->PsaPtnltvtdv<-*
317 + t+l++++v
318 S13421 923 INPITGLSAREV 934
319
320 //
321