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/B0244.8
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Query: B0244.8 CE01755 LDL receptor status:Partially_confirmed TR:Q09967 protein_id:AAA68376.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
ldl_recept_a Low-density lipoprotein receptor domain 185.6 4.8e-55 8
toxin Snake toxin 6.1 7.4 1
integrin_B Integrin, beta chain 2.5 1.4 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
ldl_recept_a 1/8 144 184 .. 1 43 [] 42.3 2.8e-11
toxin 1/1 211 229 .. 1 19 [. 6.1 7.4
ldl_recept_a 2/8 213 237 .. 17 43 .] 15.8 0.0032
ldl_recept_a 3/8 239 274 .. 3 41 .. 35.3 3.6e-09
ldl_recept_a 4/8 275 314 .. 1 43 [] 22.4 3.2e-05
ldl_recept_a 5/8 323 352 .. 11 43 .] 29.6 1.9e-07
ldl_recept_a 6/8 394 438 .. 1 43 [] 43.2 1.4e-11
ldl_recept_a 7/8 440 478 .. 1 41 [. 24.1 9.8e-06
ldl_recept_a 8/8 479 518 .. 1 43 [] 27.0 1.2e-06
integrin_B 1/1 517 525 .. 1 9 [. 2.5 1.4
Alignments of top-scoring domains:
ldl_recept_a: domain 1 of 8, from 144 to 184: score 42.3, E = 2.8e-11
*->stCggpdeFqCgsgr.rCIprswvCDGdpDCeDGSDEslenCaa<-*
stC+ F C + + Ip+s++CDG +DCeDGSDE enC
B0244.8 144 STCS-GFGFACTGAVhMVIPSSKRCDGRRDCEDGSDE--ENCKE 184
toxin: domain 1 of 1, from 211 to 229: score 6.1, E = 7.4
*->liCyntpsqpkttktCPeG<-*
liC++ + ++ + CP+G
B0244.8 211 LICLTAQHLCDNVENCPDG 229
ldl_recept_a: domain 2 of 8, from 213 to 237: score 15.8, E = 0.0032
*->CIprswvCDGdpDCeDGSDEslenCaa<-*
C + +CD C DGSDE + C +
B0244.8 213 CLTAQHLCDNVENCPDGSDE--AVCKS 237
ldl_recept_a: domain 3 of 8, from 239 to 274: score 35.3, E = 3.6e-09
*->CggpdeFqCgsgrrCIprswvCDGdpDCeDGSDEslenC<-*
C+ d+F+C ++ C p s +CDG +DC+D SDE +nC
B0244.8 239 CS-KDQFKCPGSNACLPLSAKCDGINDCADASDE--KNC 274
ldl_recept_a: domain 4 of 8, from 275 to 314: score 22.4, E = 3.2e-05
*->stCggpdeFqCgsgrrCIprswvCDGdpDCeDGSDEslenCaa<-*
s+C+ + ++Cg + CI+ s vCDG + C+DGSDE + +C +
B0244.8 275 SKCQ-NNAHKCG-KQ-CIKASHVCDGVAQCADGSDEQQCDCQR 314
ldl_recept_a: domain 5 of 8, from 323 to 352: score 29.6, E = 1.9e-07
*->CgsgrrCIprswvCDGdpDCeDGSDEslenCaa<-*
C +g CI r +vCDG DC DG DE e+C++
B0244.8 323 CDDGT-CIMRTQVCDGKKDCTDGMDE--EDCPG 352
ldl_recept_a: domain 6 of 8, from 394 to 438: score 43.2, E = 1.4e-11
*->stCggpdeFqCgsgr....rCIprswvCDGdpDCeDGSDEslenCaa
s+C + F C +++ ++ CI+r++vCDG pDC+DG DE nC +
B0244.8 394 SKCHPKLAFTCPASKearkMCISRRKVCDGTPDCDDGADE--INCTP 438
<-*
B0244.8 - -
ldl_recept_a: domain 7 of 8, from 440 to 478: score 24.1, E = 9.8e-06
*->stCg..gpdeFqCgsgrrCIprswvCDGdpDCeDGSDEslenC<-*
+ Cg +F+C +++ C +s +CDG +DCeD SDE ++C
B0244.8 440 KECGiaKNTQFKC-DHK-CLDSSRRCDGVWDCEDKSDE--KGC 478
ldl_recept_a: domain 8 of 8, from 479 to 518: score 27.0, E = 1.2e-06
*->stCggpdeFqCgsgrrCIprswvCDGdpDCeDGSDEslenCaa<-*
++C ++ +C+ + C p +C+G +DC DGSDE C+
B0244.8 479 DKCP-SGTIKCAADKKCLPAFTRCNGVADCSDGSDE--LKCSC 518
integrin_B: domain 1 of 1, from 517 to 525: score 2.5, E = 1.4
*->SCeeCilvg<-*
SC+eC+ v+
B0244.8 517 SCQECLGVH 525
[output cut off at A = 10 top alignments]