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/E02H1.3
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Query:  E02H1.3  CE01538   Yeast DEG-1 protein homolog status:Partially_confirmed SW:Q09524 protein_id:CAA87378.1

Scores for sequence family classification (score includes all domains):
Model           Description                             Score    E-value  N
--------        -----------                             -----    ------- ---
PseudoU_synth_1 tRNA pseudouridine synthase             135.7    3.1e-41   2
TRAM            TRAM domain                               6.4        3.2   1
DUF695          Family of unknown function (DUF695)       0.9        8.3   1

Parsed for domains:
Model           Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------        ------- ----- -----    ----- -----      -----  -------
DUF695            1/1      38    46 ..   244   252 .]     0.9      8.3
PseudoU_synth_1   1/2      34   161 ..     1   125 []    45.3  6.2e-13
TRAM              1/1     209   224 ..     1    16 [.     6.4      3.2
PseudoU_synth_1   2/2     184   300 ..     1   125 []    90.4  4.7e-27

Alignments of top-scoring domains:
DUF695: domain 1 of 1, from 38 to 46: score 0.9, E = 8.3
                   *->YvGWEcDai<-*
                      Y GWE D +
     E02H1.3    38    YLGWEHDGL    46

PseudoU_synth_1: domain 1 of 2, from 34 to 161: score 45.3, E = 6.2e-13
                   *->aaiaYdGtHdFtGFqrqpneskstVrgilekalsriggeeernemnq
                      + + Y+G+    G  +qp++ + tV+  + +al++ + +e+
     E02H1.3    34    IQFFYLGW-EHDGLVQQPHT-QNTVENHIMQALIKTHLIED------ 72

                   lvkiriigaGRTDkGVraivqvlhfvgpgklt........d.rd.n.k..
                   + k++++++GRTDkGV+a  q++ +v++  ++++++   +d+ ++++k +
     E02H1.3    73 WTKCDFSRCGRTDKGVSAFKQTAAMVVRSLCPgdsgvfwsDsTQeHqKvd 122

                   .n.dippedikeaLnaklpddladirvltappevlylfharys<-*
                        ++   +++Ln+ lp+    irv++++p v   f+ar++
     E02H1.3   123 yKaSGEELPYVKMLNGVLPK---TIRVFAWAP-VAQTFNARFD    161

TRAM: domain 1 of 1, from 209 to 224: score 6.4, E = 3.2
                   *->kryvGktqeVlveglg<-*
                      ++yv+k++eV+ve ++
     E02H1.3   209    QSYVRKVYEVKVEQVS    224

PseudoU_synth_1: domain 2 of 2, from 184 to 300: score 90.4, E = 4.7e-27
                   *->aaiaYdGtHdFtGFqrqpnes....kstVrgilekalsriggeeern
                       a +++G+HdF++F++ +   ++  +s Vr ++e+++++++ ++e++
     E02H1.3   184    GAELLVGEHDFSNFCQIDMNEkrllQSYVRKVYEVKVEQVSTHPEND 230

                   emnqlvkiriigaGRTDkGVraivqvlhfvgpgkltdrdnkndippedik
                    m+++v+++++g+G++++++r iv +l ++g++++         +p+ i
     E02H1.3   231 -MYSMVELTVSGSGFLWHMIRYIVTILQEIGRENE---------QPSLIS 270

                   eaLnaklpddladirvltappevlylfharys<-*
                   ++L+ k +++    + + a   +l+lf++ y
     E02H1.3   271 QLLDLKKYPS--RPQYTLASDTPLCLFDCGYK    300



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