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).
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file:                 /home/niguts/usr02/tshini/ykclst/db/Pfam_fs
Sequence file:            hmm2/seq/F09E8.3
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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



[DB home][top]