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/D2024.8
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Query: D2024.8 CE27897 cuticle collagen status:Partially_confirmed TR:Q18975 protein_id:AAA82291.2
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copi 54.5 1.7e-13 4
Col_cuticle_N Nematode cuticle collagen N-terminal 9.8 0.17 1
CDP-OH_P_transf CDP-alcohol phosphatidyltransferase 3.7 7.8 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CDP-OH_P_transf 1/1 12 44 .. 123 164 .] 3.7 7.8
Col_cuticle_N 1/1 23 85 .. 1 66 [] 9.8 0.17
Collagen 1/4 122 150 .. 6 34 .. 7.6 1.3
Collagen 2/4 172 231 .. 1 60 [] 41.6 5.9e-10
Collagen 3/4 237 288 .. 9 60 .] 32.9 1.5e-07
Collagen 4/4 289 301 .. 1 13 [. -4.0 2e+03
Alignments of top-scoring domains:
CDP-OH_P_transf: domain 1 of 1, from 12 to 44: score 3.7, E = 7.8
*->anwllalglvlaallfilqmgviaailtlisvleyllaaykl<-*
++w+ +++++a++ +++++++s+ ++++ +
D2024.8 12 YQWVANIAMCFAIV---------SVLTVCVSMPAIYMYMFHV 44
Col_cuticle_N: domain 1 of 1, from 23 to 85: score 9.8, E = 0.17
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
++v+vl++++++p iy ++ + + e+ ++ + a+++W+e+ +
D2024.8 23 AIVSVLTVCVSMPAIYMYMFHVKQLINTEVVSCEDHAREIWREVEIM 69
qrnvrppskpasarfgrpf<-*
+ + +rf+r+
D2024.8 70 KNLPFT---NRTSRFPRQA 85
Collagen: domain 1 of 4, from 122 to 150: score 7.6, E = 1.3
*->pGppGppGppGppGppGpaGapGppGppG<-*
pG+pGp G pG+pG pG +GapG pG pG
D2024.8 122 PGGPGPNGKPGKPGRPGKPGAPGLPGVPG 150
Collagen: domain 2 of 4, from 172 to 231: score 41.6, E = 5.9e-10
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G pG++G G+pG +Gp+G+pG +G+ Gp+G pG++GpPG+pG++G+
D2024.8 172 GMPGEQGVTGAPGDKGPAGQPGRNGPDGPNGEPGPKGPPGQPGADGQ 218
pGppGapGapGpp<-*
pG pG+pG p
D2024.8 219 PGMPGEPGKDAPQ 231
Collagen: domain 3 of 4, from 237 to 288: score 32.9, E = 1.5e-07
*->pGppGppGppGppGpaGapGppGppGepGpPGppGppGppGppGapG
pG+pGppG++G pGp+G+pG++Gp G pG G++G++Gp GppGa+G
D2024.8 237 PGDPGPPGDSGIPGPPGPPGMAGPDGIPGMGGAKGQNGPDGPPGASG 283
apGpp<-*
+ Gp+
D2024.8 284 ESGPN 288
Collagen: domain 4 of 4, from 289 to 301: score -4.0, E = 2e+03
*->GppGppGppGppG<-*
GppG+ G++G+ G
D2024.8 289 GPPGSGGGAGEKG 301