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/F23H12.4
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Query: F23H12.4 CE05707 locus:sqt-3 collagen status:Partially_confirmed SW:P08124 protein_id:CAA98942.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 88.0 1.1e-22 3
Col_cuticle_N Nematode cuticle collagen N-terminal do 32.3 3.5e-08 1
Melittin Melittin 5.8 4 1
AmoA Putative ammonia monooxygenase 2.6 9 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
AmoA 1/1 27 44 .. 323 340 .] 2.6 9
Melittin 1/1 22 45 .. 1 26 [] 5.8 4
Col_cuticle_N 1/1 21 84 .. 1 66 [] 32.3 3.5e-08
Collagen 1/3 104 134 .. 30 60 .] 15.8 0.0072
Collagen 2/3 153 212 .. 1 60 [] 37.4 8.4e-09
Collagen 3/3 218 277 .. 1 60 [] 50.9 1.7e-12
Alignments of top-scoring domains:
AmoA: domain 1 of 1, from 27 to 44: score 2.6, E = 9
*->lvLlllpplirylsklrg<-*
+vLl+lp+++ y+s+ r
F23H12.4 27 SVLLTLPMVYSYVSHVRQ 44
Melittin: domain 1 of 1, from 22 to 45: score 5.8, E = 4
*->GiGAiLKvLatGLPaLisWiKrKRkq<-*
i A+ vL t LP + s++ + R+q
F23H12.4 22 -IAAVASVLLT-LPMVYSYVSHVRQQ 45
Col_cuticle_N: domain 1 of 1, from 21 to 84: score 32.3, E = 3.5e-08
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
S++Av ++L+t+p++y+++++ + +++ e++++K+ a d+ e+ +
F23H12.4 21 SIAAVASVLLTLPMVYSYVSHVRQQMHHEINFCKGSAKDIFAEVNYM 67
qrnvrppskpasarfgrpf<-*
+n++p+++ +r+ r+
F23H12.4 68 KANAGPVPPR--NRTTRQA 84
Collagen: domain 1 of 3, from 104 to 134: score 15.8, E = 0.0072
*->pGppGepGpPGppGppGppGppGapGapGpp<-*
pGppG++G+PG pG+pG pG pG pG pG+p
F23H12.4 104 PGPPGPAGAPGKPGKPGRPGAPGTPGTPGKP 134
Collagen: domain 2 of 3, from 153 to 212: score 37.4, E = 8.4e-09
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
GppGppGppG+pG pG++G pG +G pG pG++GpPGp+G++G+
F23H12.4 153 GPPGPPGPPGAPGDPGEAGTPGRPGTDAAPGSPGPRGPPGPAGEAGA 199
pGppGapGapGpp<-*
pGp+G+pG p
F23H12.4 200 PGPAGEPGTPAIS 212
Collagen: domain 3 of 3, from 218 to 277: score 50.9, E = 1.7e-12
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G+pG+pG GppGppGppG+pG++G+pGppGp+G+pGp+GppG++G+
F23H12.4 218 GAPGEPGDSGPPGPPGPPGAPGNDGPPGPPGPKGAPGPDGPPGVDGQ 264
pGppGapGapGpp<-*
GppG+pG++G p
F23H12.4 265 SGPPGPPGPAGTP 277