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).
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HMM file:                 /home/niguts/usr02/tshini/ykclst/db/Pfam_fs
Sequence file:            hmm3/seq/F54F3.4
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Query:  F54F3.4  CE19894   dehydrogenase status:Partially_confirmed TR:Q93790 protein_id:CAB01974.1

Scores for sequence family classification (score includes all domains):
Model       Description                                 Score    E-value  N
--------    -----------                                 -----    ------- ---
adh_short   short chain dehydrogenase                   228.4      1e-64   1
Radical_SAM Radical SAM superfamily                       5.1        3.3   1
SWIB        BAF60b domain of the SWIB complex             4.4        8.5   1
Dor1        Dor1-like family                              3.9        3.9   1
N6_N4_Mtase DNA methylase                                 2.9        6.5   1
Mtap_PNP    Phosphorylase family 2                        2.7        7.9   1

Parsed for domains:
Model       Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------    ------- ----- -----    ----- -----      -----  -------
Dor1          1/1      38    52 ..   422   436 .]     3.9      3.9
N6_N4_Mtase   1/1      27    58 ..     1    33 [.     2.9      6.5
Mtap_PNP      1/1      43    71 ..   253   281 .]     2.7      7.9
Radical_SAM   1/1      38    82 ..   114   163 .]     5.1      3.3
SWIB          1/1     125   140 ..    66    81 .]     4.4      8.5
adh_short     1/1       9   256 ..     1   271 []   228.4    1e-64

Alignments of top-scoring domains:
Dor1: domain 1 of 1, from 38 to 52: score 3.9, E = 3.9
                   *->tvlrrfetnveeaie<-*
                      ++ +r+++nv+eaie
     F54F3.4    38    VIGSRNQKNVDEAIE    52

N6_N4_Mtase: domain 1 of 1, from 27 to 58: score 2.9, E = 6.5
                   *->arrvlkpdGsififggksqknifrfidilqelG<-*
                      a r+l+++ s +i   + qkn++ +i++l+++G
     F54F3.4    27    AERLLDEGASVVIGS-RNQKNVDEAIEYLKNKG    58

Mtap_PNP: domain 1 of 1, from 43 to 71: score 2.7, E = 7.9
                   *->ahaevleaikqlaanelslicaillriAv<-*
                      +++ v+eai++l+++ l  +++i+  iA
     F54F3.4    43    NQKNVDEAIEYLKNKGLTKVAGIAGHIAS    71

Radical_SAM: domain 1 of 1, from 38 to 82: score 5.1, E = 3.3
                   *->iinrkhtfeevleaiellreaGipvvivvdnivglpGendedleell
                      +i +  + + v eaie+l+++G+     v +i g+   +d++ ++l+
     F54F3.4    38    VI-GSRNQKNVDEAIEYLKNKGLT---KVAGIAGHIASTDDQ-KKLV 79

                   ell<-*
                   ++
     F54F3.4    80 DFT    82

SWIB: domain 1 of 1, from 125 to 140: score 4.4, E = 8.5
                   *->fempKlLtkHllkpep<-*
                      f+m+Kl ++H+ k+
     F54F3.4   125    FQMTKLVHPHIAKEGG    140

adh_short: domain 1 of 1, from 9 to 256: score 228.4, E = 1e-64
                   *->tgKvaLvTGassGIGlaiAkrLakeGakVvvvdrreekaeqvaaelk
                      +gKva+vT a++GIGlaiA+rL+ eGa Vv++ r++ + +++++ lk
     F54F3.4     9    EGKVAIVTAATKGIGLAIAERLLDEGASVVIGSRNQKNVDEAIEYLK 55

                   aelG.dralfiqlDvtdeeqvkaavaqaverlGdrlDvLVNNAGilgdgp
                      G  ++ +i++ +++ ++ k++v++ ++++G ++++LVNN Gi++  +
     F54F3.4    56 N-KGlTKVAGIAGHIASTDDQKKLVDFTLQKFG-KINILVNNHGINPAFG 103

                   pfeelseedwervidvNltGvflltravlpamdhmlkrkgGrIvNisSva
                    + e s++ w+++++vN+++ f++t++v p   h+ k +gG I++ +S +
     F54F3.4   104 HILEVSDQVWDKLFEVNVKAGFQMTKLVHP---HIAKEGGGAIIFNASYS 150

                   GlrvgvpglsaYsASKaavigltrsLAlElaphgtgIrVnavaPGgvdTd
                   +  +  pg +aY+ +K  ++gltr+LA+ la+++  IrVn++aPG ++T
     F54F3.4   151 AY-KSPPGIAAYGVTKTTLVGLTRALAMGLAKDN--IRVNGIAPGVIKT- 196

                   mtkalrsrlieakkkvrevadiadpeleerits..titplgrygvtpeei
                    +  + ++                ++ e+ +t+ ++i +lgr+g  p+++
     F54F3.4   197 KMSQVLWD--------------GGEDAEKELTDiqEI-ALGRLG-VPDDC 230

                   anavlfLasdgasysvtgqtlnvdggi<-*
                   a+ v++Lasd++sy +tg+++ ++gg
     F54F3.4   231 AGTVAYLASDDSSY-ITGEMIIIAGGV    256



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