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: hmm4/seq/R05H10.6
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Query: R05H10.6 CE18108 Cadherin (3 domains) status:Partially_confirmed TR:O62328 protein_id:CAB05582.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
cadherin Cadherin domain 69.2 7.3e-19 4
Phage_holin_2 Phage holin family 2 4.5 4.7 1
RNA_pol_L RNA polymerases L / 13 to 16 kDa subuni 3.4 9.5 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
RNA_pol_L 1/1 25 49 .. 1 26 [. 3.4 9.5
Phage_holin_2 1/1 367 380 .. 1 14 [. 4.5 4.7
cadherin 1/4 396 425 .. 72 107 .] 4.1 8.7
cadherin 2/4 440 510 .. 1 82 [. 19.2 0.00033
cadherin 3/4 540 612 .. 1 84 [. 45.1 8.4e-12
cadherin 4/4 642 671 .. 1 32 [. 1.0 70
Alignments of top-scoring domains:
RNA_pol_L: domain 1 of 1, from 25 to 49: score 3.4, E = 9.5
*->ekikiLdpkdtEkdpnave...lqiekED<-*
eki+++ + +dpn v+ + +q++ ED
R05H10.6 25 EKIELIS---S-EDPNGVVvtlIQFQDED 49
Phage_holin_2: domain 1 of 1, from 367 to 380: score 4.5, E = 4.7
*->mteeEKsvLsLFvi<-*
mt +EK++ sLF i
R05H10.6 367 MTSDEKGMSSLFGI 380
cadherin: domain 1 of 4, from 396 to 425: score 4.1, E = 8.7
*->ngeYeLtveAtDadpllasgggpplsstatvtitVl<-*
+g++ ++v+A++ d +s+ atv+i V+
R05H10.6 396 EGMHKFSVLASNID------QAGVRSANATVVIDVI 425
cadherin: domain 2 of 4, from 440 to 510: score 19.2, E = 0.00033
*->ysasvpEnapvGtevltvtAtDaDdPlgpNgrirYsilggnpggwFr
+ v+En+p+ t + + + aD+ l+ + Ysi+g+n + + +
R05H10.6 440 LIFYVRENTPIDTVI---GKVSADV-LPGKCALEYSIIGPN-SEILS 481
IdpdtGdnegiisttkpLDREeifngeYeLtveAt<-*
I++++G+ ++t k+ D E++ Y Lt++++
R05H10.6 482 INSANGE----LKTSKEFDFEKQ--KSYLLTLKLV 510
cadherin: domain 3 of 4, from 540 to 612: score 45.1, E = 8.4e-12
*->ysasvpEnapvGtevltvtAtDaDdPlgpNgrirYsilggnpggwFr
+++++pE+ap +t v+tv+At D + ++Y + g+ + +F+
R05H10.6 540 QTVEIPEDAPLNTVVATVKATEGD----ESQEVFYHLKAGS-PPQFS 581
IdpdtGdnegiisttkpLDREeifngeYeLtveAtDa<-*
++++tG+ + + + LDRE+ + +e+ + A+++
R05H10.6 582 LNSKTGE----VMVEQALDREAL--DNFEIEIGASNS 612
cadherin: domain 4 of 4, from 642 to 671: score 1.0, E = 70
*->ysasvpEnapvGtevltvtAtDaDdPlgpNgr<-*
y v+ +++vG e+l ++A+D+D l + ++
R05H10.6 642 YFTVVSKDTVVGAELLELNAYDPD--LSDQEK 671