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/R11F4.1
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Query:  R11F4.1  CE04828   Glycerol kinase status:Confirmed SW:Q21944 protein_id:AAA79749.1

Scores for sequence family classification (score includes all domains):
Model      Description                                  Score    E-value  N
--------   -----------                                  -----    ------- ---
FGGY       FGGY family of carbohydrate kinases, N-ter   338.5    7.4e-98   1
FGGY_C     FGGY family of carbohydrate kinases, C-ter   153.8    2.9e-42   1
proteasome Proteasome A-type and B-type                   5.9        1.7   1
FlgM       Anti-sigma-28 factor, FlgM                     4.6        4.7   1
GSPII_E    Type II/IV secretion system protein            3.9        2.2   1

Parsed for domains:
Model      Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------   ------- ----- -----    ----- -----      -----  -------
proteasome   1/1      45    76 ..   161   194 .]     5.9      1.7
GSPII_E      1/1      62    85 ..   275   300 ..     3.9      2.2
FGGY         1/1       3   253 ..     1   262 []   338.5  7.4e-98
FlgM         1/1     410   427 ..    85   102 .]     4.6      4.7
FGGY_C       1/1     256   477 ..     1   227 [.   153.8  2.9e-42

Alignments of top-scoring domains:
proteasome: domain 1 of 1, from 45 to 76: score 5.9, E = 1.7
                   *->nlteeeavelakkalkialdrdvysggnievaei<-*
                      +++++e+ ++++ +++++++  ++ +  i++ ei
     R11F4.1    45    EMDPMELYDTVVSCISKTIE--KLENLGISADEI    76

GSPII_E: domain 1 of 1, from 62 to 85: score 3.9, E = 2.2
                   *->altRLldmGveafllaSsllliiAQR<-*
                      ++ +L ++G++a++++S   +++ QR
     R11F4.1    62    TIEKLENLGISADEIKS--VGVANQR    85

FGGY: domain 1 of 1, from 3 to 253: score 338.5, E = 7.4e-98
                   *->yvlGiDcGTtstKAivfdskqGkvvasasakyalisPkpssgwaEqD
                      +  +iD+GT+s++++vf   +G++v s++++  + +P+   gw+E D
     R11F4.1     3    LLAAIDQGTSSSRFLVFEADTGELVTSHQIEVRQLFPHG--GWVEMD 47

                   PeeiwqallqairkileqskqsgisakqIkgIgiSgQmhglvllDkndGk
                   P+e+++++ ++i k++e++ ++gisa++Ik +g+++Q+++ +++Dk++Gk
     R11F4.1    48 PMELYDTVVSCISKTIEKLENLGISADEIKSVGVANQRETSIVWDKETGK 97

                   PLypAIlWnDtRTaeiveeLkek..lggadklyeiTGltllpgfTlsKLr
                   PLy+AI+W DtRT++ ++e ++++   + d ++++TGl+++p+f++ KL+
     R11F4.1    98 PLYNAIVWLDTRTSSLADEAISRtaSKSKDEFRAKTGLPIHPYFSALKLK 147

                   WlkenePeiferirkgelkfllikdYLrwrLTGvGkqftTDysdASgtmm
                   Wl +n+Pe+ ++ + g l f++++++L+w+LTG    ++TD+s+AS+t +
     R11F4.1   148 WLFQNVPEVKKAYADGNLMFGTVDTWLIWKLTG---AYVTDVSNASRTLL 194

                   fniktleWDeelLailGIppdielLPplvesseiyGtlnpeaaallGLde
                   +++++++W+++l++++++p +  +LP++++s+e+yG+   +  ++
     R11F4.1   195 LDLHKRKWSTQLCEFFDLPIE--ILPEIRSSAEVYGHFDKGPLEG----- 237

                   niPVvgGggDnaaaalG<-*
                    +P +g++gD++aa +G
     R11F4.1   238 -VPLSGCLGDQQAAMVG    253

FlgM: domain 1 of 1, from 410 to 427: score 4.6, E = 4.7
                   *->eYkVDteklAkklldFek<-*
                      ++kVD + +A kl+++++
     R11F4.1   410    TLKVDGGMIANKLFNEIQ    427

FGGY_C: domain 1 of 1, from 256 to 477: score 153.8, E = 2.9e-42
                   *->aidegqavvSlGTsgvllavtqkkdtdsegglayfahaldGrdnpgn
                      +  +gq ++++GT+ ++l++++ +++ s++gl++++    G d+p+
     R11F4.1   256    CLNAGQTKNTYGTGTFMLCNIGTRPIISKNGLLTTVGFQFGADSPVV 302

                   wylmgvvlnaggvleWlrdllgslvlinfdelneaaaqaveganGvlflP
                   ++l+g+  ++g v++ lrd+++    i+++   e + ++ve ++G +f+P
     R11F4.1   303 YALEGSGSIGGNVVRFLRDNFK---FISDAKEMEGLCRSVEDTSGAYFVP 349

                   yldGeraPlwdpsvrGsffGLtsnttrghllRAaLEGviyslrdgLdamq
                    ++G+++P+wd ++rG + GLt+ t+r+h++ AaL +v+++ ++ + a++
     R11F4.1   350 SFTGLYTPYWDSTARGTILGLTQVTQREHICLAALRAVAFQSAEMIAAVE 399

                   ad..sgikastlrviGGgAksnlWmQmqADilnlpVvvpeieEttaLGAA
                   +d ++g+k+ tl v+GG+  ++l + +qADi+++ +v+p+i E ++ GAA
     R11F4.1   400 QDleGGTKVTTLKVDGGMIANKLFNEIQADIMGRDIVTPKITEISGWGAA 449

                   mlAaaaeVGvfeslaEasqalnlerkkhyPpe<-*
                    ++++++ +   sl+E +q+  ++ +  y p+
     R11F4.1   450 VAGGIGA-QQ-ISLDEFLQQSSEDNR--YTPQ    477



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