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/F38A6.1
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Query: F38A6.1 CE15998 locus:pha-4 Fork head domain, eukaryotic transcription factors status:Confirmed TR:Q17381 protein_id:CAB07378.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Fork_head Fork head domain 233.9 2.2e-66 1
RFX_DNA_binding RFX DNA-binding domain 3.6 4.7 1
FemAB FemAB family 3.1 5.2 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
RFX_DNA_binding 1/1 227 236 .. 75 84 .] 3.6 4.7
FemAB 1/1 214 241 .. 1 28 [. 3.1 5.2
Fork_head 1/1 236 331 .. 1 101 [] 233.9 2.2e-66
Alignments of top-scoring domains:
RFX_DNA_binding: domain 1 of 1, from 227 to 236: score 3.6, E = 4.7
*->RRLGtRGqSK<-*
RR Gt GqSK
F38A6.1 227 RRHGTYGQSK 236
FemAB: domain 1 of 1, from 214 to 241: score 3.1, E = 5.2
*->LtaleFenftnkmpvysH..ftQsienyel<-*
Lt++eFe+ t k ++H++++Qs+ +y +
F38A6.1 214 LTIQEFETVTEKI--RRHgtYGQSKPPYSY 241
Fork_head: domain 1 of 1, from 236 to 331: score 233.9, E = 2.2e-66
*->KPPYSYiaLItmAIqqySpekrLtLseIYkfImdrFPYYRqnkqgWQ
KPPYSYi+LItmAIq+ S ++LtLseIY +Imd+FPYY n+q+WQ
F38A6.1 236 KPPYSYISLITMAIQK-SNSRQLTLSEIYNWIMDLFPYYQNNQQRWQ 281
NSIRHNLSLNkcFiKVpRspdkpGKGsyWtldPeaedmFenkkkkgsflk
NSIRH+LS+N+cF+KV+RspdkpGKGs+Wtl++ ++mFen g++l+
F38A6.1 282 NSIRHSLSFNDCFVKVARSPDKPGKGSFWTLHEHCGNMFEN----GCYLR 327
rrrr<-*
r++r
F38A6.1 328 RQKR 331