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/T11B7.4a
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Query: T11B7.4a CE03650 LIM domains status:Partially_confirmed TR:Q17878 protein_id:CAA90978.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
LIM LIM domain 147.0 2.9e-40 4
PDZ PDZ domain (Also known as DHR or GLGF) 17.7 0.0015 1
DUF678 Protein of unknown function (DUF678) 4.8 5.5 1
Polyoma_coat2 Polyomavirus coat protein 2.5 5.1 1
BK_channel_a Calcium-activated BK potassium channel 2.1 3.3 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
PDZ 1/1 5 51 .. 1 49 [. 17.7 0.0015
DUF678 1/1 233 254 .. 63 84 .. 4.8 5.5
LIM 1/4 220 267 .. 1 53 [. 25.9 7.1e-06
Polyoma_coat2 1/1 935 953 .. 335 353 .] 2.5 5.1
BK_channel_a 1/1 1041 1053 .. 1 14 [. 2.1 3.3
LIM 2/4 1251 1309 .. 1 62 [] 41.8 2.2e-10
LIM 3/4 1312 1368 .. 1 62 [] 59.5 2.1e-15
LIM 4/4 1371 1421 .. 1 54 [. 43.8 5.9e-11
Alignments of top-scoring domains:
PDZ: domain 1 of 1, from 5 to 51: score 17.7, E = 0.0015
*->evtlekevkrgglGfsikggsdkgivvsevlpGsgaAeagGrLkeGD
+v++ +++ r ++Gf + + d+ + + +v+ G + A+++G L+ GD
T11B7.4a 5 TVRMARSDRRTPWGFGVTEAPDGAVLIVNVIGG-SLADRAG-LRNGD 49
vI<-*
v+
T11B7.4a 50 VV 51
DUF678: domain 1 of 1, from 233 to 254: score 4.8, E = 5.5
*->kvagkvFggntLaCaACGSsLc<-*
+ agk g+ L+Ca CG sL+
T11B7.4a 233 RAAGKNLHGDCLSCATCGNSLR 254
LIM: domain 1 of 4, from 220 to 267: score 25.9, E = 7.1e-06
*->CagCnkpIydrevvrralnkvwHpeCFrCavCgkpLtegdefyekdg
C+ C +pI ++ r+a+ k+ H +C+ Ca+Cg L + + ++++++
T11B7.4a 220 CFMCTRPIL-GVMARAAG-KNLHGDCLSCATCGNSLRNVG-HHFIED 263
skelYC<-*
k +YC
T11B7.4a 264 -K-FYC 267
Polyoma_coat2: domain 1 of 1, from 935 to 953: score 2.5, E = 5.1
*->DiTPtWeayleElekekkk<-*
DiT+t ++eE+ ++++
T11B7.4a 935 DITSTFDIEEEEVDVVQDR 953
BK_channel_a: domain 1 of 1, from 1041 to 1053: score 2.1, E = 3.3
*->EivFLHnisPdLEL<-*
iv+L n+ P+LEL
T11B7.4a 1041 -IVYLQNLRPELEL 1053
LIM: domain 2 of 4, from 1251 to 1309: score 41.8, E = 2.2e-10
*->CagCnkpIydrevvrralnkvwHpeCFrCav..CgkpLtegdefyek
C C+++I++++v+ a +k+w+pe+F+Ca ++C++ L e + f+e
T11B7.4a 1251 CESCKQQIRGAFVL--ATGKSWCPEHFVCANssCRRRLLECG-FVEE 1294
dgskelYCkhDyyklfg<-*
dg + C++++++ +
T11B7.4a 1295 DG-Q-KFCESCFEQHIA 1309
LIM: domain 3 of 4, from 1312 to 1368: score 59.5, E = 2.1e-15
*->CagCnkpIydrevvrralnkvwHpeCFrCavCgkpLtegdefyekdg
C +C kpI + ++ al k wHp CF+Ca+C+kp++++ fy+ g
T11B7.4a 1312 CNKCSKPIISDCLN--ALQKKWHPTCFTCAHCQKPFGNSA-FYLEQG 1355
skelYCkhDyyklfg<-*
+YC++D lf
T11B7.4a 1356 -L-PYCEQDWNALFT 1368
LIM: domain 4 of 4, from 1371 to 1421: score 43.8, E = 5.9e-11
*->CagCnkpIydrevvrralnkvwHpeCFrCavCgkpLtegdefyekdg
C C pI++ ++ + al++++H +CF+Ca C+++L+ + f+ k+g
T11B7.4a 1371 CVSCRYPIEAGDRWVEALGNAFHSNCFTCARCNHNLEGES-FFAKNG 1416
skelYCk<-*
+ + C+
T11B7.4a 1417 -Q-PFCR 1421