Motif confirmation by HMMer


hmmpfam - search a single seq against HMM database
HMMER 2.1.1 (Dec 1998)
Copyright (C) 1992-1998 Washington University School of Medicine
HMMER is freely distributed under the GNU General Public License (GPL).
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file:                 /home/niguts/usr02/tshini/ykclst/db/Pfam_fs
Sequence file:            hmm1/seq/C39E9.3
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query:  C39E9.3  CE05386   collagen status:Partially_confirmed TR:Q18537 protein_id:CAA94329.1

Scores for sequence family classification (score includes all domains):
Model         Description                               Score    E-value  N
--------      -----------                               -----    ------- ---
Collagen      Collagen triple helix repeat (20 copies    68.6    2.2e-17   3
Col_cuticle_N Nematode cuticle collagen N-terminal do     7.1        1.1   1
B56           Protein phosphatase 2A regulatory B sub     2.5        5.5   1

Parsed for domains:
Model         Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------      ------- ----- -----    ----- -----      -----  -------
Col_cuticle_N   1/1      11    42 ..     1    32 [.     7.1      1.1
B56             1/1      28    59 ..   381   412 .]     2.5      5.5
Collagen        1/3     110   138 ..    32    60 .]    20.8  0.00032
Collagen        2/3     155   213 ..     1    60 []    34.8  4.4e-08
Collagen        3/3     225   284 ..     1    60 []    29.2  1.5e-06

Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 11 to 42: score 7.1, E = 1.1
                   *->SgvAvlacLftvpsiyndInsfqdevmdemde<-*
                      S+++ l++L++v++  nd+++ + e+++e+ e
     C39E9.3    11    SLFVFLSVLVFVLQTKNDLDQVWAEFDQEVQE    42

B56: domain 1 of 1, from 28 to 59: score 2.5, E = 5.5
                   *->EctaqYkeerqkekqreeeReelWkkLEelak<-*
                      ++++ + e  q+ +++ + Re+ W+ L +la
     C39E9.3    28    DLDQVWAEFDQEVQEVTVLREASWNTLRNLAT    59

Collagen: domain 1 of 3, from 110 to 138: score 20.8, E = 0.00032
                   *->ppGepGpPGppGppGppGppGapGapGpp<-*
                      p+G++Gp G pG++G+pG+pG++G +G++
     C39E9.3   110    PAGPSGPKGLPGQDGAPGEPGPAGKMGQN    138

Collagen: domain 2 of 3, from 155 to 213: score 34.8, E = 4.4e-08
                   *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
                       p+G++GppG+pG  Gp+G+ G++G++G pG+ G+pG  G  Gp G+
     C39E9.3   155    -PAGEMGPPGAPGKIGPRGQRGQSGGAGTPGNNGAPGHNGELGPCGQ 200

                   pGppGapGapGpp<-*
                   +GppG++Ga G +
     C39E9.3   201 AGPPGPAGAIGRR    213

Collagen: domain 3 of 3, from 225 to 284: score 29.2, E = 1.5e-06
                   *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
                      Gp G pGp Gp G+ G++G  G  G  Gp G  G  GpPG  G  G
     C39E9.3   225    GPIGAPGPVGPVGMEGDRGNRGGLGVDGPLGSIGLQGPPGRTGSTGD 271

                   pGppGapGapGpp<-*
                    G+ G++G+ G+
     C39E9.3   272 VGESGPIGPNGQD    284



[DB home][top]