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 //