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