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: hmm5/seq/ZC101.1
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Query: ZC101.1 CE16690 low-density lipoprotein receptor status:Predicted TR:O18260 protein_id:CAB07705.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
ldl_recept_a Low-density lipoprotein receptor domai 220.0 1.6e-65 7
EB EB module 10.9 0.33 1
DNA_ligase_ZBD NAD-dependent DNA ligase C4 zinc finge 6.0 3.9 1
squash Squash family serine protease inhibito 2.4 6.2 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
DNA_ligase_ZBD 1/1 155 167 .. 18 30 .] 6.0 3.9
ldl_recept_a 1/7 138 180 .. 1 43 [] 33.0 1.8e-08
ldl_recept_a 2/7 288 326 .. 1 43 [] 20.9 9.3e-05
ldl_recept_a 3/7 327 366 .. 1 43 [] 42.7 2.1e-11
EB 1/1 336 443 .. 1 63 [] 10.9 0.33
ldl_recept_a 4/7 429 467 .. 1 43 [] 53.4 1.1e-14
ldl_recept_a 5/7 511 552 .. 1 43 [] 34.3 7.4e-09
squash 1/1 577 606 .. 1 30 [] 2.4 6.2
ldl_recept_a 6/7 577 616 .. 1 43 [] 33.2 1.6e-08
ldl_recept_a 7/7 765 803 .. 1 43 [] 50.8 6.8e-14
Alignments of top-scoring domains:
DNA_ligase_ZBD: domain 1 of 1, from 155 to 167: score 6.0, E = 3.9
*->vviRCpNpliCPA<-*
+++RC + ++CP
ZC101.1 155 ADQRCDGRRNCPD 167
ldl_recept_a: domain 1 of 7, from 138 to 180: score 33.0, E = 1.8e-08
*->stCggpdeFqCgsgrrCIprswvCDGdpDCeDGSDEslen..Caa<-
C+ eF C + + CIp +++CDG + C DGSDE+ e+++C +
ZC101.1 138 IACA-TTEFTCLDKS-CIPADQRCDGRRNCPDGSDEHKEHgkCKQ 180
*
ZC101.1 - -
ldl_recept_a: domain 2 of 7, from 288 to 326: score 20.9, E = 9.3e-05
*->stCggpdeFqCgsgrrCIprswvCDGdpDCeDGSDEslenCaa<-*
+ C ++e C+sg+ C p + CD C DG DE e+C+
ZC101.1 288 DECP-SGERACKSGH-CLPVAQFCDRRVQCPDGDDE--EHCSE 326
ldl_recept_a: domain 3 of 7, from 327 to 366: score 42.7, E = 2.1e-11
*->stCggpdeFqCgsgrrCIprswvCDGdpDCeDGSDEslenCaa<-*
++C+ ++eF+C+s C+p vCDG DC+DGSDE + C+
ZC101.1 327 VQCK-SNEFRCESTNVCVPTVVVCDGWKDCHDGSDE--KKCSH 366
EB: domain 1 of 1, from 336 to 443: score 10.9, E = 0.33
*->ClsgqVlingqCva.................................
C+s+ V++ v+++ ++ ++++++++ ++++++ ++++ ++ + +
ZC101.1 336 CESTNVCVPTVVVCdgwkdchdgsdekkcshprktykphhvhhvkvn 382
.....k.elnkvnpGesgCeaseQCqggwpgSvCingmC...........
++++e+ +++ G+s C ++ C+++ + C g C + ++++++++
ZC101.1 383 avcqdGsEPEFSLHGSSYCWSNKVCPAM---TECVAGLCcsisktrkrqs 429
eCpegvpkttrvngvC<-*
eC eg +++ g+C
ZC101.1 430 ECLEG--QFKCGTGQC 443
ldl_recept_a: domain 4 of 7, from 429 to 467: score 53.4, E = 1.1e-14
*->stCggpdeFqCgsgrrCIprswvCDGdpDCeDGSDEslenCaa<-*
s C ++F+Cg+g+ CI s++C+ +DC+DGSDE +C
ZC101.1 429 SECL-EGQFKCGTGQ-CIEESLKCNRKYDCADGSDE--ITCEY 467
ldl_recept_a: domain 5 of 7, from 511 to 552: score 34.3, E = 7.4e-09
*->stCggpdeFqCgsgr..rCIprswvCDGdpDCeDGSDEslenCaa<-
C eF+C ++rC +++ +CDG +DC+DGSDE nC +
ZC101.1 511 LVCN-DQEFRCPYLAetRCFHYDRLCDGTDDCGDGSDE--TNCDS 552
*
ZC101.1 - -
squash: domain 1 of 1, from 577 to 606: score 2.4, E = 6.2
*->riCPrilmeCkrDsDClaeCvCleegeyCG<-*
+C + eCkrD C+ + + ++ C
ZC101.1 577 SRCSSVQFECKRDGKCIDKALECNHKYDCE 606
ldl_recept_a: domain 6 of 7, from 577 to 616: score 33.2, E = 1.6e-08
*->stCggpdeFqC.gsgrrCIprswvCDGdpDCeDGSDEslenCaa<-*
s+C+ + +F C+++g+ CI + + C+ +DCeDGSDE C
ZC101.1 577 SRCS-SVQFECkRDGK-CIDKALECNHKYDCEDGSDE--TECEY 616
ldl_recept_a: domain 7 of 7, from 765 to 803: score 50.8, E = 6.8e-14
*->stCggpdeFqCgsgrrCIprswvCDGdpDCeDGSDEslenCaa<-*
+ C +eFqC+ g+ CI ++ vCD pDC D SDE +nCa
ZC101.1 765 VGCL-EHEFQCAIGE-CIDKRRVCDTRPDCLDASDE--QNCAD 803
[output cut off at A = 10 top alignments]