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: hmm1/seq/C33F10.5a
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Query: C33F10.5a CE04138 fibronectin, IG-like domains of NCAM status:Partially_confirmed TR:Q18382 protein_id:AAK31481.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
ig Immunoglobulin domain 74.9 4.4e-19 3
fn3 Fibronectin type III domain 65.8 1.6e-17 4
DNA_ligase_OB NAD-dependent DNA ligase OB-fold doma 7.0 1.5 1
AFP Insect antifreeze protein 6.9 9 1
PseudoU_synth_2 RNA pseudouridylate synthase 4.6 2.8 1
PKD PKD domain 3.6 6.2 1
Connexin50 Gap junction alpha-8 protein (Cx50) 2.3 9.3 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Connexin50 1/1 67 74 .. 62 69 .] 2.3 9.3
ig 1/3 133 190 .. 1 50 [] 32.2 3e-07
ig 2/3 223 287 .. 1 50 [] 26.9 8.7e-06
PKD 1/1 286 302 .. 82 99 .] 3.6 6.2
ig 3/3 323 380 .. 1 50 [] 15.8 0.0099
PseudoU_synth_2 1/1 392 400 .. 1 9 [. 4.6 2.8
AFP 1/1 420 431 .. 1 12 [] 6.9 9
DNA_ligase_OB 1/1 541 558 .. 66 85 .] 7.0 1.5
fn3 1/4 523 601 .. 17 84 .] 36.5 4.5e-09
fn3 2/4 614 658 .. 1 41 [. 6.3 2.3
fn3 3/4 738 815 .. 9 84 .] 17.1 0.0018
fn3 4/4 910 926 .. 69 84 .] 5.7 3.5
Alignments of top-scoring domains:
Connexin50: domain 1 of 1, from 67 to 74: score 2.3, E = 9.3
*->tLPSYAQv<-*
tL SYAQ+
C33F10.5a 67 TLWSYAQT 74
ig: domain 1 of 3, from 133 to 190: score 32.2, E = 3e-07
*->GesvtLtCsvsgfgpp.p.vtWl.rngk.le......tsslslti.s
G+s L C + ++p p+++W + +gk+++ +++ ++++ +l i++
C33F10.5a 133 GDSIYLECFAY--ASPlPqYKWSrVDGKpIParshisNYGRVLKIeK 177
vtpeDsgGtYtCvv<-*
v+++D+ G Y Cv+
C33F10.5a 178 VNYGDA-GKYKCVA 190
ig: domain 2 of 3, from 223 to 287: score 26.9, E = 8.7e-06
*->GesvtLtCsvsgfgpp.p.vtWlrngk.le.............tssl
+ v++ C s +++ +v W+++ k++ + + +++++ + +
C33F10.5a 223 ESNVSFECLLS-NADSySsVEWFKDAKpIVplllpaekrkrlkIDHN 268
slti.svtpeDsgGtYtCvv<-*
+l+++ + + Ds G+Y Cv+
C33F10.5a 269 VLHLkFADETDS-GVYQCVA 287
PKD: domain 1 of 1, from 286 to 302: score 3.6, E = 6.2
*->tvsNgvgsasattttvtV<-*
++sN+vgs+s++ + +tV
C33F10.5a 286 VASNDVGSSSSS-ALLTV 302
ig: domain 3 of 3, from 323 to 380: score 15.8, E = 0.0099
*->GesvtLtCsvsgfgpp.p.vtWl.rngk.le......tsslslti.s
G++v+++C + ++p+ + +W + +g++l+++++ + ++ i++
C33F10.5a 323 GSTVSIPCIFE--ASPrFhGKWAdAGGSkLPqkgrirDEEGVISIeK 367
vtpeDsgGtYtCvv<-*
v eD+ G ++C++
C33F10.5a 368 VLHEDA-GLFFCTA 380
PseudoU_synth_2: domain 1 of 1, from 392 to 400: score 4.6, E = 2.8
*->dllVvNKPa<-*
+l+VvNKP+
C33F10.5a 392 QLIVVNKPS 400
AFP: domain 1 of 1, from 420 to 431: score 6.9, E = 9
*->tCTgStnCteAt<-*
tC +S+ C+eA
C33F10.5a 420 TCENSAECPEAL 431
DNA_ligase_OB: domain 1 of 1, from 541 to 558: score 7.0, E = 1.5
*->PkvvgVvlrvekRtgdekpi<-*
Pkv+g ++ e+Rt ++++
C33F10.5a 541 PKVEGYLV--ELRTRKNRKW 558
fn3: domain 1 of 4, from 523 to 601: score 36.5, E = 4.5e-09
*->ltlsWsppt.......gngpitgYevtyRqpkngge.wneltvpgt.
++l+W p++++++++++ +++gY v++R kn ++ e+++ g+
C33F10.5a 523 FRLRWRLPPqhrdtrdHSPKVEGYLVELRTRKNRKWrAAERQLVGNm 569
.ttsytltgLkPgteYevrVqAvnggG.GpeS<-*
+++s t+++L P+teY++rV++v + G++S
C33F10.5a 570 eKDSITVENLLPNTEYQFRVRSVESAAiGEPS 601
fn3: domain 2 of 4, from 614 to 658: score 6.3, E = 2.3
*->PsaP.tnltvtdvtstsltlsWsppt....gngpitgYevtyRqpk<
Ps+ nl+ +++ s +l ++W+p + +++ +g+ +Y+v++ +++
C33F10.5a 614 PSETiDNLKWRSLDSQTLLVEWQPIEigqeSSGDNLRYRVSW-SEA 658
-*
C33F10.5a - -
[output cut off at A = 10 top alignments]