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