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/C34C6.4
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Query:  C34C6.4  CE03052   choline dehydrogenase status:Partially_confirmed TR:Q18429 protein_id:CAA91263.1

Scores for sequence family classification (score includes all domains):
Model       Description                                 Score    E-value  N
--------    -----------                                 -----    ------- ---
GMC_oxred_N GMC oxidoreductase                          398.6     6e-116   1
GMC_oxred_C GMC oxidoreductase                          239.8    3.8e-68   1
pyr_redox   Pyridine nucleotide-disulphide oxidoreduc    19.5    7.4e-05   1
PUA         PUA domain                                    5.7        6.6   1
Thi4        Thi4 family                                   3.7        2.1   1
EspF        EspF protein                                  1.8        9.8   1

Parsed for domains:
Model       Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------    ------- ----- -----    ----- -----      -----  -------
Thi4          1/1      41    69 ..    31    60 ..     3.7      2.1
pyr_redox     1/1      39    75 ..     1    58 [.    19.5  7.4e-05
GMC_oxred_N   1/1      41   337 ..     1   320 []   398.6   6e-116
EspF          1/1     333   353 ..   165   185 .]     1.8      9.8
GMC_oxred_C   1/1     378   577 ..     1   286 []   239.8  3.8e-68
PUA           1/1     567   590 ..     1    24 [.     5.7      6.6

Alignments of top-scoring domains:
Thi4: domain 1 of 1, from 41 to 69: score 3.7, E = 2.1
                   *->vIVGAGpSGLtAAYyLAkkRPglKVaiiEr<-*
                      +IVGAG++G + A  L +  P  +V++iE+
     C34C6.4    41    IIVGAGSAGCVLANRLTED-PSNRVLLIEA    69

pyr_redox: domain 1 of 1, from 39 to 75: score 19.5, E = 7.4e-05
                   *->dvvIIGgGpAGlaAAiraaragflGrkrlkvalvEkepplkrgtlGG
                        +I+G+G+AG + A r+ +  +      +v+l+E+
     C34C6.4    39    THIIVGAGSAGCVLANRLTE--DPS---NRVLLIEA----------- 69

                   TClNvgciprk<-*
                        g+++ k
     C34C6.4    70 -----GPVDHK    75

GMC_oxred_N: domain 1 of 1, from 41 to 337: score 398.6, E = 6e-116
                   *->yDyIivGGGSAGcvlAaRLSNeDpntsVllLEaGsepsdenpfiqlP
                         IivG+GSAGcvlA+RL+ eDp+++Vll+EaG  +   + +i++P
     C34C6.4    41    ---IIVGAGSAGCVLANRLT-EDPSNRVLLIEAGPVDHKWDWRIHMP 83

                   aafadplrserGPAkydwaYetePepalCLSSNgRritwpRGkvLGGSSs
                   aa+ ++l s+     y+w Y t  +++l     +R  +wpRG+v GGSS
     C34C6.4    84 AALMYNLCSDT----YNWHYHTTAQKNL----GNRVFYWPRGRVWGGSST 125

                   INgmvYvRgnasDydnWeseaGegWsyddVLpyfkkaEtnqrPnAKqiAa
                    N+m+YvRg+a Dy++We e++ gW+y+++LpyfkkaEt+         +
     C34C6.4   126 LNAMCYVRGHAYDYNRWEKEGASGWNYANCLPYFKKAETYS--------D 167

                   ldfvesdyHGvdGPlhVsrqkytdDlnPlskAfleAgeeaGfpvtdDlng
                     + +  y+G +GPl+V +++     nPl kA+l  g+e   + t D ng
     C34C6.4   168 ATGPNDPYRGNNGPLYVKKGDAE---NPLHKAWLNVGKEHPLGWTNDMNG 214

                   lKpdqeGfgitqvTvrndGrRsStArayLkPalrNRpNLrvltgatvdKI
                     ++qeG + +++T +n G R+S+  ay++P ++ RpNL   +g t++++
     C34C6.4   215 --EKQEGISTMDMTIHN-GERWSASKAYVHPIRN-RPNLITSSGITCTRV 260

                   iisggkavtvRAVGVeyldd.........nkghtrkvrAkkEVvlSAGav
                   +++ +     +A+G e++++ +  ++++ ++ +++k++  + V+l+ Ga+
     C34C6.4   261 LFDTN-----KAIGIEFIRKlnfvgtdsiDSYSREKIYCQGDVILAGGAI 305

                   nSPqlLllSGVGpashLaelgidvVvdlPGVG<-*
                   n+PqlL+lSGVGpa+hL+++ i+ V++lPGVG
     C34C6.4   306 NTPQLLMLSGVGPADHLRSHEIPIVANLPGVG    337

EspF: domain 1 of 1, from 333 to 353: score 1.8, E = 9.8
                   *->LPPlAqALKDHLAAYElsKKa<-*
                      LP + q L+DHL  Y +   +
     C34C6.4   333    LPGVGQNLQDHLEIYVQQEST    353

GMC_oxred_C: domain 1 of 1, from 378 to 577: score 239.8, E = 3.8e-68
                   *->lfkreglltTnlgeaggfirsrGefelatadelkfpdlqlyFlpkpd
                        +r+gl+++ + e+ggf+rs         d++  pd+q++Flp
     C34C6.4   378    FTNRTGLGASSHLETGGFARSD--------DTVTHPDIQFHFLP--- 413

                   KPLMHYSvisafaydelklpnghgaqffvflllPkSRGsvtLrSaDPlav
                            s++ +d++  ++ hg+q++v+ ++++S G++ L  +DP +
     C34C6.4   414 ---------STVHDDGRTNGTCHGYQVHVGPMRSQSKGYIMLQAKDPRR- 453

                   aPridpNYlsderDlktmvegiklareilqrmesFAGEvTafHPlyKVDS
                   aP i pNY+  + D+ +++ +i+ +re++
     C34C6.4   454 APIINPNYMEEDSDWREFRKCIRVSRELFA-------------------- 483

                   PARAleldlEdtkvAGPkakalelyfgeelipgdevqtdgdfHVTSsqvv
                                     +ka++  +g+el pg+ +q d
     C34C6.4   484 ------------------SKAFDEFRGKELAPGPDCQSD----------- 504

                   lsidlpytqeDDaaieefirehaetayHpvGTCkMGprEGsKiddpsaVV
                               a i+ f++e a++ayHp+ TCkMG++      d++aVV
     C34C6.4   505 ------------ADIDRFVKEKAASAYHPSCTCKMGSE-----NDKMAVV 537

                   DpelR.VhGvqGLRVvDaSImPtivagnthApavmiGEKa<-*
                   +pe+ +V+G ++L+VvDaS+mP+iv+gn++Ap +m++E+a
     C34C6.4   538 NPETMgVYGTENLKVVDASVMPSIVSGNLNAPVIMMAERA    577

PUA: domain 1 of 1, from 567 to 590: score 5.7, E = 6.6
                   *->glirvdvgavaadfiknGasLlap<-*
                      +++++ + + aad+ik+++ Ll+p
     C34C6.4   567    NAPVIMMAERAADLIKHKKQLLPP    590



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