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



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