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:            hmm2/seq/F09B9.2a
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Query:  F09B9.2a  CE15759  locus:unc-115 LIM domains status:Confirmed TR:Q19240 protein_id:CAA90057.1

Scores for sequence family classification (score includes all domains):
Model    Description                                    Score    E-value  N
-------- -----------                                    -----    ------- ---
LIM      LIM domain                                     102.4    1.4e-27   3
VHP      Villin headpiece domain                         75.8    1.8e-23   2
IATP     Mitochondrial ATPase inhibitor, IATP             5.5        6.6   1
DC1      DC1 domain                                       5.2          3   2
Xlink    Extracellular link domain                        2.2        2.2   1

Parsed for domains:
Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
-------- ------- ----- -----    ----- -----      -----  -------
DC1        1/2       3    14 ..     1    12 [.     4.5      5.3
LIM        1/3       5    44 ..     1    43 [.    36.9  5.3e-09
DC1        2/2      29    45 ..     1    20 [.     3.3       12
VHP        1/2      51    60 ..     1    10 [.     0.7  1.2e+02
Xlink      1/1     137   142 ..    99   104 .]     2.2      2.2
LIM        2/3     117   173 ..     1    62 []    57.0  1.1e-14
LIM        3/3     176   222 ..     1    51 [.    25.1  1.2e-05
IATP       1/1     526   550 ..     1    27 [.     5.5      6.6
VHP        2/2     590   625 .]     1    36 []    72.4  2.5e-22

Alignments of top-scoring domains:
DC1: domain 1 of 2, from 3 to 14: score 4.5, E = 5.3
                   *->fsCdvCerkidp<-*
                      ++CdvC++k+++
    F09B9.2a     3    KKCDVCRKKCSG    14

LIM: domain 1 of 3, from 5 to 44: score 36.9, E = 5.3e-09
                   *->CagCnkpIydrevvrralnkvwHpeCFrCavCgkpLtegdefy<-*
                      C  C k++ + ++   a++k++H++CF+C  Cg++L+e++ fy
    F09B9.2a     5    CDVCRKKCSGDVLK--ANDKYFHINCFQCKKCGRNLGETG-FY    44

DC1: domain 2 of 2, from 29 to 45: score 3.3, E = 12
                   *->fsCdvCerkidpgsngffYs<-*
                      f C  C+r++ +    +fY+
    F09B9.2a    29    FQCKKCGRNLGE---TGFYT    45

VHP: domain 1 of 2, from 51 to 60: score 0.7, E = 1.2e+02
                   *->YLsdeDFeev<-*
                      YL ++DF+ v
    F09B9.2a    51    YLCPDDFRAV    60

Xlink: domain 1 of 1, from 137 to 142: score 2.2, E = 2.2
                   *->YDvYCF<-*
                      ++vYCF
    F09B9.2a   137    WHVYCF    142

LIM: domain 2 of 3, from 117 to 173: score 57.0, E = 1.1e-14
                   *->CagCnkpIydrevvrralnkvwHpeCFrCavCgkpLtegdefyekdg
                      Ca+C++  ++ +v+  al+ +wH+ CF+C++C   L     ++++ g
    F09B9.2a   117    CAACDQALHSGQVLL-ALGLSWHVYCFKCSECSAVLHGE--YMSHHG 160

                   skelYCkhDyyklfg<-*
                    k ++C +Dy ++fg
    F09B9.2a   161 -K-PLCLRDYNEKFG    173

LIM: domain 3 of 3, from 176 to 222: score 25.1, E = 1.2e-05
                   *->CagCnkpIydrevvrralnkvwHpeCFrCavCgkpLtegdefyekdg
                      C+ C k I++ ++   a++  +Hp C rC+ Cg ++++g e y+  +
    F09B9.2a   176    CYECEKFIAGKVLQ--AGGYKFHPTCARCSRCGSHFGDGEEMYMQGD 220

                   skel<-*
                    + +
    F09B9.2a   221 -E-I    222

IATP: domain 1 of 1, from 526 to 550: score 5.5, E = 6.6
                   *->msarGfgSdggegvggggGSiReAGGa<-*
                      +s+  ++S+ +++  g +G +R+AGGa
    F09B9.2a   526    ISS--HYSEHSTTESGTAGGPRSAGGA    550

VHP: domain 2 of 2, from 590 to 625: score 72.4, E = 2.5e-22
                   *->YLsdeDFeevFgMtkeEFykLPlWKqnqLKKklgLF<-*
                      +L++++Fee+F+M+  EFykLP+WK+ +LK+k++LF
    F09B9.2a   590    HLPRDQFEEIFKMSLIEFYKLPEWKRINLKRKHKLF    625



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