compactor work
[jalview.git] / forester / test_data / hmmpfam_output
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/yye/db/pfam20.0/Pfam_ls
7 Sequence file:            Human.fasta.1
8 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
9
10 Query sequence: ENSP00000285681
11 Accession:      acc_ENSP00000285681    
12 Description:    pep:known chromosome:NCBI36:21:16024215:16174248:1 gene:ENSG00000155313 transcript:ENST00000285681
13
14 Scores for sequence family classification (score includes all domains):
15 Model    Description                                    Score    E-value  N 
16 -------- -----------                                    -----    ------- ---
17 UCH      Ubiquitin carboxyl-terminal hydrolase          176.2    7.7e-50   1
18 UIM      Ubiquitin interaction motif                     38.8    1.7e-08   2
19 UBA      UBA/TS-N domain                                 23.2    0.00084   1
20
21 Parsed for domains:
22 Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
23 -------- ------- ----- -----    ----- -----      -----  -------
24 UBA        1/1      16    57 ..     1    41 []    23.2  0.00084
25 UIM        1/2      96   113 ..     1    18 []    24.5  0.00035
26 UIM        2/2     123   140 ..     1    18 []    14.3  7.7e-50
27 UCH        1/1     166   654 ..     1   318 []   176.2  0.3
28
29 Alignments of top-scoring domains:
30 UBA: domain 1 of 1, from 16 to 57: score 23.2, E = 0.00084
31                    *->ideeavkqLreMTGf.dreeakkALeatngnverAvewLleh<-*
32                        ++  + qLre TG +d +  ++AL+ +ngn+e Av +L  +   
33   ENSP000002    16    HQQTFLNQLREITGInDTQILQQALKDSNGNLELAVAFLTAK    57   
34
35 UIM: domain 1 of 2, from 96 to 113: score 24.5, E = 0.00035
36                    *->mdEEedLqlALalSlqea<-*
37                       +d+ +dLq+A+alSl+e+   
38   ENSP000002    96    GDDKDDLQRAIALSLAES    113  
39
40 UIM: domain 2 of 2, from 123 to 140: score 14.3, E = 0.3
41                    *->mdEEedLqlALalSlqea<-*
42                       +dEE+ + + L+ S++e+   
43   ENSP000002   123    TDEEQAISRVLEASIAEN    140  
44
45 UCH: domain 1 of 1, from 166 to 654: score 176.2, E = 7.7e-50
46                 RF    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx   xx
47                    *->pgptGLvNlGNTCYmNSvLQcLfsipplrdyflsdsyesein...es
48                         p+GL+N GNTC+ ++v+Q+Lf+  ++r+ +l++++ s  ++ ++ 
49   ENSP000002   166    KAPVGLKNVGNTCWFSAVIQSLFNLLEFRRLVLNYKPPSNAQdlpRN 212  
50
51                 RF xxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxx
52                    nplgskgsllcaladLfnalqsg.yksvapsplkflqfkltlgkineefs
53                    ++++++  + ++l+ Lf+ l   ++k+v ps+     ++ +l+  +++ +
54   ENSP000002   213 QKEHRNLPFMRELRYLFALLVGTkRKYVDPSR-----AVEILKDAFKS-N 256  
55
56                 RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxx
57                    gymQQDAhEFllfLLdgLhedlnrvnkkpytepessdkrpdkaa.eawkn
58                     ++QQD+ EF   LLd+L+++++                  ka++e ++ 
59   ENSP000002   257 DSQQQDVSEFTHKLLDWLEDAFQM-----------------KAEeETDE- 288  
60
61                 RF xxxxxxxxxxxxxxxxxxx                               
62                    hltrnesiitdlFqGqlks...............................
63                      ++ +++ ++lF G++   +  ++++ ++++  ++ + + ++ ++ +++
64   ENSP000002   289 --EKPKNPMVELFYGRFLAvgvlegkkfentemfgqyplqvngfkdlhec 336  
65
66                 RF                        xxxxxxxxxxxxxxxxxxxxxxxxxxx
67                    .......................klkikrLPpvLiihLKRFsyngetgln
68                     +    +++ ++ ++++++++++ + ++ LPpvL++ L+RF++n  +g++
69   ENSP000002   337 leaamiegeieslhsensgksgqEHWFTELPPVLTFELSRFEFNQALGRP 386  
70
71                 RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xx xxxxxxxxxx    
72                    kKiddkVefPleLdlssycnaelkekevlrkd.ek.ieklkeerqr....
73                    +Ki++k+efP  L+l++y+ ++ +   ++r++ ++ ++ l++ +qr ++ 
74   ENSP000002   387 EKIHNKLEFPQVLYLDRYMHRNREITRIKREEiKRlKDYLTVLQQRlery 436  
75
76                 RF                                                   
77                    ..................................................
78                     + ++++++ +  +  +   +  ++++  +++ ++ + +++++++ ++++
79   ENSP000002   437 lsygsgpkrfplvdvlqyalefasskpvctspvddidassppsgsipsqt 486  
80
81                 RF                                                   
82                    ..................................................
83                     ++++++++  +++ +++++++    ++++  +++ ++++ +++ + ++ 
84   ENSP000002   487 lpstteqqgalsselpstspssvaaissrsvihkpftqsrippdlpmhpa 536  
85
86                 RF                                        xxxxx xx xx
87                    .......................................dedgn.ne.ee
88                    +++ ++++ +  ++  ++ +++ ++++++ +++ ++ +++ +++ +++ +
89   ENSP000002   537 prhiteeelsvlesclhrwrteiendtrdlqesisrihrTIELMySDkSM 586  
90
91                 RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
92                    peeeekdneegenpptkYeLyaVvvHsGsslssGHYiayikkkkengkWy
93                                  +  Y+L+aV+vH G +++ GHY+ayi  +  +++W 
94   ENSP000002   587 -------------IQVPYRLHAVLVHEG-QANAGHYWAYIF-DHRESRWM 621  
95
96                 RF xxxxxxxxxxxxxxxxx      xxxxxxxxxx   
97                    kfDDekVsevteeevle......rsssAYiLFY<-*
98                    k++D  V+ ++ ee  +++ ++ r+ sAY L+Y   
99   ENSP000002   622 KYNDIAVTKSSWEELVRdsfggyRNASAYCLMY    654  
100
101 //
102
103 hmmpfam - search one or more sequences against HMM database
104 HMMER 2.3.2 (Oct 2003)
105 Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
106 Freely distributed under the GNU General Public License (GPL)
107 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
108 HMM file:                 /home/yye/db/pfam20.0/Pfam_ls
109 Sequence file:            Human.fasta.1
110 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
111
112 Query sequence: ENSP00000310334
113 Accession:      [none]
114 Description:    pep:known chromosome:NCBI36:21:16364713:16901413:1 gene:ENSG00000174496 transcript:ENST00000308787
115
116 Scores for sequence family classification (score includes all domains):
117 Model    Description                                    Score    E-value  N 
118 -------- -----------                                    -----    ------- ---
119         [no hits above thresholds]
120
121 Parsed for domains:
122 Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
123 -------- ------- ----- -----    ----- -----      -----  -------
124         [no hits above thresholds]
125
126 Alignments of top-scoring domains:
127         [no hits above thresholds]
128 //