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/F28B4.3
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Query: F28B4.3 CE07153 EGF-like repeat status:Partially_confirmed TR:Q19853 protein_id:AAA83584.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
vwa von Willebrand factor type A domain 68.6 1.3e-20 1
lectin_c Lectin C-type domain 36.5 4.7e-08 1
EGF EGF-like domain 28.1 3e-06 6
Complex1_17_2kD NADH:ubiquinone oxidoreductase 17.2 k 5.0 4.5 1
TSNR_N Thiostrepton-resistance methylase, N 3.8 7.4 1
Mre11_DNA_bind Mre11 DNA-binding presumed domain 3.0 9.7 1
EMP70 Endomembrane protein 70 3.0 1.9 1
Glyco_hydro_47 Glycosyl hydrolase family 47 1.5 7.6 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
EGF 1/6 87 95 .. 32 45 .] 2.8 44
EGF 2/6 347 374 .. 7 45 .] 0.4 2.1e+02
EGF 3/6 392 404 .. 28 45 .] 8.6 0.98
EMP70 1/1 587 600 .. 587 600 .] 3.0 1.9
TSNR_N 1/1 772 785 .. 44 58 .. 3.8 7.4
EGF 4/6 859 895 .. 1 45 [] 24.5 3.3e-05
lectin_c 1/1 1207 1314 .. 7 125 .] 36.5 4.7e-08
Complex1_17_2kD 1/1 1456 1464 .. 1 11 [. 5.0 4.5
EGF 5/6 1474 1503 .. 1 45 [] 10.5 0.3
EGF 6/6 1507 1532 .. 12 45 .] 17.1 0.0041
Glyco_hydro_47 1/1 1678 1687 .. 506 515 .] 1.5 7.6
Mre11_DNA_bind 1/1 2032 2044 .. 1 13 [. 3.0 9.7
vwa 1/1 2028 2211 .. 1 189 [] 68.6 1.3e-20
Alignments of top-scoring domains:
EGF: domain 1 of 6, from 87 to 95: score 2.8, E = 44
*->ppGdyylsytGkrC<-*
+pG ytG +C
F28B4.3 87 KPG-----YTGATC 95
EGF: domain 2 of 6, from 347 to 374: score 0.4, E = 2.1e+02
*->CsngGtCvntpggssdnfggytCeCppGdyylsytGkrC<-*
C+ngG+ + + g+++C C ytG++C
F28B4.3 347 CQNGGQVLKDSS------GSPYCYCFGL-----YTGRDC 374
EGF: domain 3 of 6, from 392 to 404: score 8.6, E = 0.98
*->tCeCppGdyylsytGkrC<-*
+CeCp+G +tG +C
F28B4.3 392 HCECPEG-----FTGFHC 404
EMP70: domain 1 of 1, from 587 to 600: score 3.0, E = 1.9
*->ifYfftKlkisGfv<-*
+fYf+ +++is f+
F28B4.3 587 TFYFNNRTTISNFF 600
TSNR_N: domain 1 of 1, from 772 to 785: score 3.8, E = 7.4
*->IRAGVeFiEVYGldt<-*
IR GV+ +EVYG+++
F28B4.3 772 IRDGVQ-TEVYGSSG 785
EGF: domain 4 of 6, from 859 to 895: score 24.5, E = 3.3e-05
*->Capnn...pCsngGtCvntpggssdnfggytCeCppGdyylsytGkr
C+p++++++C+n +C n++ +g +C+CppG y+G+
F28B4.3 859 CTPQFtgtYCQNI-VCYNGGT-----VSGGQCVCPPG-----YAGES 894
C<-*
C
F28B4.3 895 C 895
lectin_c: domain 1 of 1, from 1207 to 1314: score 36.5, E = 4.7e-08
*->eAelaCqkegghAHLvsIqsaeEqsfvvafltsltkksntyaWIGLt
+A+++C ++gg L+ + + +f +s++ nt +WIGL+
F28B4.3 1207 QARNFCASAGGY--LADDLGDDKN----NFYSSIAA--NTQFWIGLF 1245
dintegtwvwegwetdgspvnyt..enWapgePnnrgnhGgnEdCveiyt
n++g+++w ++ + ++ + + ++Wa geP+n + +Cv + +
F28B4.3 1246 -KNSDGQFYWDRGQGINPDLLNQpiTYWANGEPSNDPT---R-QCVYFDG 1290
dtdflaGkWnDepCdsklpyvCef<-*
++ + W + C +++p++C++
F28B4.3 1291 RSGDKSKVWTTDTCATPRPFICQK 1314
Complex1_17_2kD: domain 1 of 1, from 1456 to 1464: score 5.0, E = 4.5
*->gtlVGeDkfGN<-*
+VGeD+fGN
F28B4.3 1456 --HVGEDEFGN 1464
EGF: domain 5 of 6, from 1474 to 1503: score 10.5, E = 0.3
*->Capnn.pCsngGtCvntpggssdnfggytCeCppGdyylsytGkrC<
C+p + +C ngG+ +n+ +C+C+ +tG rC
F28B4.3 1474 CSPATiVCGNGGIRQNG-----------QCICTDY-----WTGSRC 1503
-*
F28B4.3 - -
EGF: domain 6 of 6, from 1507 to 1532: score 17.1, E = 0.0041
*->tCvntpggssdnfggytCeCppGdyylsytGkrC<-*
+Cvn++ n ++ tC+Cp G y+G +C
F28B4.3 1507 ICVNGGT---KNSDEATCTCPDG-----YAGLNC 1532
[output cut off at A = 10 top alignments]