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/F09E8.3
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Query: F09E8.3 CE26678 locus:msh-5 Yeast DNA mismatch repair protein MSH5 like status:Confirmed SW:Q19272 protein_id:CAA98059.2
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
MutS_V MutS domain V 141.7 1.1e-43 2
MutS_IV MutS family domain IV 80.4 5.9e-23 1
MutS_III MutS domain III 34.8 2.2e-08 2
Peptidase_A8 Signal peptidase (SPase) II 3.2 8 1
ECH Enoyl-CoA hydratase/isomerase family 2.8 9.7 1
FokI_C Restriction endonuclease FokI, catalytic 2.0 8.8 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
MutS_III 1/2 275 350 .. 1 73 [. 31.7 1.6e-07
MutS_IV 1/1 449 543 .. 1 103 [] 80.4 5.9e-23
MutS_III 2/2 574 588 .. 200 214 .] 3.2 11
ECH 1/1 670 680 .. 166 176 .] 2.8 9.7
MutS_V 1/2 591 732 .. 1 151 [. 136.7 3.9e-42
FokI_C 1/1 777 789 .. 136 148 .] 2.0 8.8
MutS_V 2/2 774 829 .. 191 245 .] 5.2 0.98
Peptidase_A8 1/1 927 939 .. 149 161 .] 3.2 8
Alignments of top-scoring domains:
MutS_III: domain 1 of 2, from 275 to 350: score 31.7, E = 1.6e-07
RF xxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxx
*->edymllDaaTrrNLELtenl...srdggkegSLlsvLDrTvTaMGsR
++ +++D+ T ++L +++ ++++++ g + SL++++D+++ + G+
F09E8.3 275 GNLVEIDFNTIQALDILPKEtenKKTFGQGRSLYQLMDKCRSTVGKK 321
RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxx
LLrrWLlqPLrdreeInaRldaVeelled<-*
Lr+W ++P +dr+ + R+ +V +++d
F09E8.3 322 CLRKWFRNPTTDRDDLVSRQKCVHYFKQD 350
MutS_IV: domain 1 of 1, from 449 to 543: score 80.4, E = 5.9e-23
*->gfdeeLDelrdlleeleeeleeleakererlgidpkksLkvgynkvl
g+deeLDe+rd++e++ ++l + ++e++rlg++p++++ ++y+ ++
F09E8.3 449 GIDEELDEIRDTYENMPMVLTAIAKQEEARLGLPPYSNVACVYIPLV 495
GYyievtrseakkvRktLPkGnnsdyirrqtlKnseRFtTpeLkeledel
G+++ v+r++ + d++++ +++ R +++++++l+de+
F09E8.3 496 GFVLSVPRDYGVES----QP----DMTLLYSTHEDLRVRNATTSRLDDEF 537
leaeee<-*
++ ++
F09E8.3 538 GDILMR 543
MutS_III: domain 2 of 2, from 574 to 588: score 3.2, E = 11
RF xxxxxxxxxxxxxxx
*->AeLDvlvSLAelAee<-*
+ +Dvl+S+ +A++
F09E8.3 574 SRIDVLISFGLIAAQ 588
ECH: domain 1 of 1, from 670 to 680: score 2.8, E = 9.7
*->lkmGlVdkVVp<-*
+k+G+Vd++V+
F09E8.3 670 AKIGIVDRIVT 680
MutS_V: domain 1 of 2, from 591 to 732: score 136.7, E = 3.9e-42
*->YvRPeftesdgagelhIegGRHPVVEavlkrdagnFVpNDvsLdker
+ +P + +++ + ++ HP+ v+k ++FVpN vs +++
F09E8.3 591 WNCPALVDEPV---IEAVELYHPISVLVVK---KSFVPNQVSSGRDG 631
avnsrillITGPNMgGKSTYlRQvALIvlMAQiGSFVPAesAeIgivDrI
+ITGPN GKS+Y++ +++ v + +iGSFVPA++A+IgivDrI
F09E8.3 632 ---IKASIITGPNACGKSVYMKSIGIMVFLSHIGSFVPARHAKIGIVDRI 678
FTRIGAsDdLasGrSTFMVEMlETAnILhnATdkSLVlLDElGRGTSTyD
TR+ D+ G+STF + +A L++AT +SLV++DE G GT T+
F09E8.3 679 VTRMFTVDSVLDGMSTFAKDVEQVALALRKATGNSLVIIDEFGKGTMTEV 728
GlaI<-*
Gl++
F09E8.3 729 GLSL 732
FokI_C: domain 1 of 1, from 777 to 789: score 2.0, E = 8.8
*->kvLkrvkGkskyt<-*
+vL+++ Gk ky
F09E8.3 777 TVLREAGGKIKYL 789
MutS_V: domain 2 of 2, from 774 to 829: score 5.2, E = 0.98
*->lHmaaketd.gdivFLykvkpGaadkSYGIhVAklAGlPesVverAr
l+++++++++g i +L + +pG d S+ + VAk G+P +V+ rA+
F09E8.3 774 LTFTVLREAgGKIKYLFRMTPGLVDCSFALSVAKEEGIPPPVIGRAC 820
evLaeLEer<-*
++ + L+
F09E8.3 821 RIYKALKAG 829
Peptidase_A8: domain 1 of 1, from 927 to 939: score 3.2, E = 8
*->llasffdsskkkk<-*
+l+++++++kkkk
F09E8.3 927 VLDALLPKKKKKK 939