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/W02B12.8
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Query:  W02B12.8  CE03768   GTPase-activating (rhoGAP) like protein status:Partially_confirmed TR:Q23130 protein_id:CAA91403.1

Scores for sequence family classification (score includes all domains):
Model    Description                                    Score    E-value  N
-------- -----------                                    -----    ------- ---
RhoGAP   RhoGAP domain                                  132.9    2.7e-36   1
PdxA     Pyridoxal phosphate biosynthetic protein Pdx     4.7        2.5   1
GcpE     GcpE protein                                     2.0        2.9   1

Parsed for domains:
Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
-------- ------- ----- -----    ----- -----      -----  -------
PdxA       1/1     188   243 ..     1    60 [.     4.7      2.5
GcpE       1/1     265   283 ..   579   597 .]     2.0      2.9
RhoGAP     1/1     263   421 ..     1   170 []   132.9  2.7e-36

Alignments of top-scoring domains:
PdxA: domain 1 of 1, from 188 to 243: score 4.7, E = 2.5
                   *->lLaakegalrekctlVviaDealLeraakllglpl..dlrdiepvee
                      +  +    ++ k+++V ++  ++Le+a++++ l l++++rd+++ +
    W02B12.8   188    I--SSK--FENKFHYVMCI--DELENALSVARLNLpsPIRDHDKSFS 228

                   aqeesagllvidplp<-*
                    q +++++++++plp
    W02B12.8   229 TQSNRPETPPAQPLP    243

GcpE: domain 1 of 1, from 265 to 283: score 2.0, E = 2.9
                   *->lvEeLielieklakekepe<-*
                      +v++Lie++e +a  +e+
    W02B12.8   265    IVDQLIEYLEAHALTMEGV    283

RhoGAP: domain 1 of 1, from 263 to 421: score 132.9, E = 2.7e-36
                   *->PiivekcveyIeklYPLaerGlqeEGIYRvsGsasrvkeLreafdkd
                      P+iv++++ey+e+      ++l  EG +R+s+++ ++k+L+++++k+
    W02B12.8   263    PPIVDQLIEYLEA------HALTMEGVFRKSANIGSIKRLQDRINKG 303

                   gapdslelseke..wfDvhvvag.....lLKlYLReLPePLipydlyeef
                       ++ ++e ++++ D   va+ + + lLK ++R+L ePL ++ ly+++
    W02B12.8   304 ----EKIDFENDpeYKDNEYVASlhasvLLKTFFRSLGEPLTTNRLYPKL 349

                   iraakeqiedpderlralkellsSkLPrahynTLryLltHLnrvaeiyie
                     +++      +e+  a+ke +  +LPr++y +L+  +++L rvae
    W02B12.8   350 AALSE---VSKTEKSAAVKEFVK-LLPRENYILLKTVIKFLTRVAE---- 391

                   nsavNkMnarNLAivFgPtLlrppdkesnd<-*
                   ns+vN M+a+NL++vFgP+L +p d e  +
    W02B12.8   392 NSKVNLMTANNLSVVFGPNLTWPTDQEVPI    421



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