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/K02F2.3
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Query:  K02F2.3  CE17155    status:Partially_confirmed TR:O44985 protein_id:AAB97566.1

Scores for sequence family classification (score includes all domains):
Model          Description                              Score    E-value  N
--------       -----------                              -----    ------- ---
CPSF_A         CPSF A subunit region                    517.6   9.1e-152   1
FlaG           FlaG protein                               5.7        4.6   1
HTH_3          Helix-turn-helix                           5.1        9.5   1
DUF665         Putative RNA binding domain                5.0        5.9   1
B-block_TFIIIC B-block binding subunit of TFIIIC          1.4        6.8   1

Parsed for domains:
Model          Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------       ------- ----- -----    ----- -----      -----  -------
B-block_TFIIIC   1/1     514   524 ..     1    11 [.     1.4      6.8
DUF665           1/1     976  1005 ..    41    82 .]     5.0      5.9
CPSF_A           1/1     854  1162 ..     1   345 []   517.6 9.1e-152
HTH_3            1/1    1190  1209 ..    13    34 ..     5.1      9.5
FlaG             1/1    1188  1216 ..    28    60 ..     5.7      4.6

Alignments of top-scoring domains:
B-block_TFIIIC: domain 1 of 1, from 514 to 524: score 1.4, E = 6.8
                   *->DeLvrivSdkI<-*
                      D+Lv+i S+ I
     K02F2.3   514    DSLVQIYSEGI    524

DUF665: domain 1 of 1, from 976 to 1005: score 5.0, E = 5.9
                   *->gglsgigkketdddgaSldregnvivPynkakVvkiGdiiiv<-*
                      g+ ++++k+e+          +n+ v     ++++ G +iiv
     K02F2.3   976    GQKKLLAKCEN----------KNFPVSIV--NIQSTGQRIIV    1005

CPSF_A: domain 1 of 1, from 854 to 1162: score 517.6, E = 9.1e-152
                   *->ekeassirlidpntfevihasyklqqnEtalSmasvkfsneettkdk
                      +k+as i+li+++++++++ +++l+q+E+a+++a+v+fs+++    +
     K02F2.3   854    GKWASAISLISATSGDKLS-YFELPQDENAKCVALVQFSKHP----N 895

                   ntYlvVGTalnlpeeietvqadhliIcPsrGRilifelieVvPepgkpkt
                   + +++VG+++n+ ++++++++++++I+P+rG++++f+l+          +
     K02F2.3   896 EAMVLVGCGVNEVLNVHDIDPNDTSIRPTRGCVYTFHLSA---------N 936

                   gnkLklvhetevkGpVyalcefnGrlLagiGqkvrlydltkdkekkeLrk
                   g++++++h+te++ pV+a+++f+G+ L+g+G+++r+yd+++   kk+L k
     K02F2.3   937 GDRFDFLHRTETPLPVGAIHDFRGMALVGFGRFLRMYDIGQ---KKLLAK 983

                   eafidtpvyildiksmHQWgnrIlVgDvmkSvtllrYkeeenqLievArD
                   ++++++pv+i++i+s+   g+rI+V+D+++Sv++lrY++ +nqL+++A+D
     K02F2.3   984 CENKNFPVSIVNIQST---GQRIIVSDSQESVHFLRYRKGDNQLVVFADD 1030

                   tnprwvtavefLdddtnLyfagaDasGNlfvlrydpeapkdvdedPtesK
                   t pr+vt+v+ Ld++t   +a+aD++GNl+v+r+++++++dv++dPt+sK
     K02F2.3  1031 TTPRYVTCVCVLDYHT---VAVADKFGNLAVVRLPERVNEDVQDDPTVSK 1077

                   slwdrgltsserqkLelvghFHlGeivnsfqkgslvmknlndssssdtga
                   s+wdrg++++++qk+elv++F++G++++s+qk+sl+           +ga
     K02F2.3  1078 SVWDRGWLNGASQKVELVSNFFIGDTITSLQKTSLM-----------PGA 1116

                   sptllygTldGsIGvivpllseeeyrfLeqlqnhLrkeipsaplgGld<-
                   +++l+y+T+ G+IG++v+++s++e++f+ +l++h r+e+p  pl+G+d
     K02F2.3  1117 NEALVYTTIGGAIGCLVSFMSKDEVDFFTNLEMHVRSEYP--PLCGRD   1162

                   *

     K02F2.3     -   -

HTH_3: domain 1 of 1, from 1190 to 1209: score 5.1, E = 9.5
                   *->sqlseeLAeklGskvsrstisk<-*
                      +q+++++Ae+lG   ++s isk
     K02F2.3  1190    TQKQKDVAEELG--KTVSEISK    1209

FlaG: domain 1 of 1, from 1188 to 1216: score 5.7, E = 4.6
                   *->naaeeqkiskedlekaveeineflesLsKlint<-*
                      +++++qk   e+l k+v+ei+++le     i+t
     K02F2.3  1188    MDTQKQKDVAEELGKTVSEISKKLED----IRT    1216



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