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: hmm5/seq/Y47G6A.8
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Query: Y47G6A.8 CE22109 endonuclease status:Partially_confirmed TR:Q9N3T2 protein_id:AAF60653.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
XPG_N XPG N-terminal domain 187.6 2e-52 1
XPG_I XPG I-region 136.8 4e-37 1
5_3_exonuclease 5'-3' exonuclease, C-terminal SAM fol 29.4 1.4e-07 1
DGPF DGPF domain 4.1 6.8 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
XPG_N 1/1 1 107 [. 1 111 [] 187.6 2e-52
DGPF 1/1 81 111 .. 113 143 .] 4.1 6.8
XPG_I 1/1 146 237 .. 1 104 [] 136.8 4e-37
5_3_exonuclease 1/1 238 265 .. 24 52 .. 29.4 1.4e-07
Alignments of top-scoring domains:
XPG_N: domain 1 of 1, from 1 to 107: score 187.6, E = 2e-52
*->MGIkGLlpiLkpvapeairsvsiEalegYYkvLAiDasiwLyqfLka
MGIkGL +++++ ap+ai+ + +a++g +++AiDas+ LyqfL+a
Y47G6A.8 1 MGIKGLSQVIADNAPSAIKVNEMKAFFG--RTVAIDASMCLYQFLIA 45
vRdqlgnnlenEeGettshlmglfsRlcrLldfgIkPifVFDGgapndlK
vR q+g +l++E+Gettshlmg++ R+ r+ ++g+kP++VFDG++p d K
Y47G6A.8 46 VR-QDGSQLQSEDGETTSHLMGMLNRTVRMFENGVKPVYVFDGKPP-DMK 93
aetlqKRsarrqea<-*
++l+KRs+rr+ea
Y47G6A.8 94 GGELEKRSERRAEA 107
DGPF: domain 1 of 1, from 81 to 111: score 4.1, E = 6.8
*->PVfefsdfgedvt.kvlrefeepLRAELEKgk<-*
PV++f ++d+++ +l+ + e+ RAE EK+
Y47G6A.8 81 PVYVFDGKPPDMKgGELEKRSER-RAEAEKAL 111
XPG_I: domain 1 of 1, from 146 to 237: score 136.8, E = 4e-37
*->rlmGIpyIvAPgvEAEAQcayLekkglvdgiiTeDsDvLLFGaprll
lmGIp+++AP+ EAEAQca L+k+g+v g++TeD+D L FG+++ll
Y47G6A.8 146 GLMGIPVVEAPC-EAEAQCAHLVKAGKVFGTVTEDMDALTFGSTVLL 191
rnLtlsgkksgPsitslkveieeidlesllreLgLgklsreqLidlaiLl
r++ +k k++i e++l+ l+e +L s e++idl+iLl
Y47G6A.8 192 RHFLAPVAK--------KIPIKEFNLSLALEEMKL---SVEEFIDLCILL 230
GcDYteG<-*
GcDY+
Y47G6A.8 231 GCDYCGT 237
5_3_exonuclease: domain 1 of 1, from 238 to 265: score 29.4, E = 1.4e-07
*->VpGIGeKTAakLLkeyGSlEniyeiNldk<-*
++G+G+K+A++L++++ ++E i+e N+d+
Y47G6A.8 238 IRGVGPKKAVELIRQHKNIETILE-NIDQ 265