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/H12C20.2a
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Query:  H12C20.2a  CE19915  locus:pms-2 DNA mismatch repair protein (PMS2) status:Partially_confirmed TR:Q9TVL8 protein_id:CAA98478.1

Scores for sequence family classification (score includes all domains):
Model          Description                              Score    E-value  N
--------       -----------                              -----    ------- ---
DNA_mis_repair DNA mismatch repair protein, C-termina   121.2    1.3e-32   1
HATPase_c      Histidine kinase-, DNA gyrase B-, and     29.8      4e-07   1
RecT           RecT family                               10.6      0.091   1
dNK            Deoxynucleoside kinase                     7.4       0.86   1

Parsed for domains:
Model          Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------       ------- ----- -----    ----- -----      -----  -------
HATPase_c        1/1      21    82 ..     1    71 [.    29.8    4e-07
DNA_mis_repair   1/1     270   363 ..    45   148 .]   121.2  1.3e-32
dNK              1/1     565   593 ..   141   170 .]     7.4     0.86
RecT             1/1     558   598 ..   202   256 .]    10.6    0.091

Alignments of top-scoring domains:
HATPase_c: domain 1 of 1, from 21 to 82: score 29.8, E = 4e-07
                   *->gdedrLrqvlsNLldNAikhapaggritvrlerdgdrlritVeDnGp
                       + + L  +++ L+dN+i+++ +   i++r++   +  +i+V+DnG
   H12C20.2a    21    QVVVSLSSAIRQLIDNSIDAGST--IIDIRVKNN-GFESIEVQDNGS 64

                   GIppehkisiedleriFepFyrtd<-*
                   GI +       + + +  p+ +++
   H12C20.2a    65 GIEA------RNFDALCKPHSTSK    82

DNA_mis_repair: domain 1 of 1, from 270 to 363: score 121.2, E = 1.3e-32
                   *->gFISqctlgn.rskrdrqflFINgRpVedkldrgkSLlkairevYad
                      gF S+c +g++r   drqf +IN+RpVe++      ++ +i++vY++
   H12C20.2a   270    GFVSSCEHGCgRGTSDRQFVYINNRPVEYSR-----VCSVINDVYKQ 311

                   ylprgrkLrysyPvfvLnlelppelvDvNVHPdKkeVrllneeeilelik
                   ++ +++     yP++vL++++ppe++DvNV+PdKk V+l +e+++l++++
   H12C20.2a   312 FN-KKQ-----YPIIVLFIDVPPEKIDVNVTPDKKTVMLEKERHLLAVVR 355

                   ealkslla<-*
                    ++  ++
   H12C20.2a   356 ASMMKTYL    363

dNK: domain 1 of 1, from 565 to 593: score 7.4, E = 0.86
                   *->aspvlvidgdklDfvedeediknkineive<-*
                      +sp++++ +d+ +++++++++k+++nei++
   H12C20.2a   565    YSPKTDETDDN-TEEAEVSAEKDVLNEITT    593

RecT: domain 1 of 1, from 558 to 598: score 10.6, E = 0.091
                   *->kqlLrkAylplsvemqgaytedEmerteripaEregekdvtpaefvs
                      + lLr+Ay+p   e     t+d+ e++e+      +ekdv+ ++
   H12C20.2a   558    MKLLREAYSPKTDE-----TDDNTEEAEVS-----AEKDVLNEI--- 591

                   edeeidee<-*
                    +  i++e
   H12C20.2a   592 -TTKINKE    598



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