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: hmm5c/seq/ZK863.7
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Query: ZK863.7 CE15447 locus:rnp-1 RNP-1 protein status:Confirmed SW:Q10667 protein_id:CAB01455.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
rrm RNA recognition motif. (a.k.a. RRM, RBD, 35.9 4.2e-09 1
zf-CCHC Zinc knuckle 12.1 0.22 1
DbpA DbpA RNA binding domain 8.8 0.36 1
NIR_SIR_ferr Nitrite/Sulfite reductase ferredoxin-lik 6.8 2.1 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
NIR_SIR_ferr 1/1 37 58 .. 54 75 .] 6.8 2.1
rrm 1/1 5 67 .. 1 77 [] 35.9 4.2e-09
DbpA 1/1 33 71 .. 51 89 .] 8.8 0.36
zf-CCHC 1/1 82 99 .. 1 18 [] 12.1 0.22
Alignments of top-scoring domains:
NIR_SIR_ferr: domain 1 of 1, from 37 to 58: score 6.8, E = 2.1
*->niqlhgikkedlpailaeLaea<-*
n + +i+++d+++i+++L +
ZK863.7 37 NYAFVHIEEDDVDPIITRLTGY 58
rrm: domain 1 of 1, from 5 to 67: score 35.9, E = 4.2e-09
*->lfVgNLppdvteedLkdlFskfGpivsikivkDhiekpketgkskGf
lfVgNLp +v+ +Lk+ F++f ++++++ivk ++
ZK863.7 5 LFVGNLPDNVDSNKLKQVFQPFCKVTECDIVK-------------NY 38
aFVeFeseedAekAlealnGkelggrklrv<-*
aFV +e+d++ + l G++++g+++ +
ZK863.7 39 AFVH-IEEDDVDPIITRLTGYTIDGKVVNI 67
DbpA: domain 1 of 1, from 33 to 71: score 8.8, E = 0.36
*->kIfddfsfVevpegmadavLkklkgtrikGkqlrvrllk<-*
+I +++fV ++e++ d ++++l g +i Gk ++++++
ZK863.7 33 DIVKNYAFVHIEEDDVDPIITRLTGYTIDGKVVNIKKST 71
zf-CCHC: domain 1 of 1, from 82 to 99: score 12.1, E = 0.22
*->rkCynCGkpGHiardCpe<-*
++C++C H+ +Cp+
ZK863.7 82 NRCFRCQSDEHRTPQCPQ 99