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/C49F5.1
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Query:  C49F5.1  CE08852   s-adenosylmethionine synthetase status:Confirmed SW:O17680 protein_id:CAB03975.1

Scores for sequence family classification (score includes all domains):
Model           Description                             Score    E-value  N
--------        -----------                             -----    ------- ---
S-AdoMet_syntD2 S-adenosylmethionine synthetase, cent   297.2      2e-85   1
S-AdoMet_syntD3 S-adenosylmethionine synthetase, C-te   296.1    4.3e-85   1
S-AdoMet_synt   S-adenosylmethionine synthetase, N-te   218.2    1.3e-63   1
DUF419          Protein of unknown function (DUF419)      6.9        1.1   1
FokI_C          Restriction endonuclease FokI, cataly     2.8          5   1
HCV_NS4a        Hepatitis C virus non-structural prot     2.3        6.7   1

Parsed for domains:
Model           Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------        ------- ----- -----    ----- -----      -----  -------
S-AdoMet_synt     1/1       3   103 ..     1   101 []   218.2  1.3e-63
S-AdoMet_syntD2   1/1     115   237 ..     1   123 []   297.2    2e-85
HCV_NS4a          1/1     252   268 ..   272   288 .]     2.3      6.7
FokI_C            1/1     285   299 ..    90   104 ..     2.8        5
DUF419            1/1     327   344 ..   112   129 .]     6.9      1.1
S-AdoMet_syntD3   1/1     239   388 ..     1   150 []   296.1  4.3e-85

Alignments of top-scoring domains:
S-AdoMet_synt: domain 1 of 1, from 3 to 103: score 218.2, E = 1.3e-63
                   *->ekfLFtsesvsEGHPDKiaDqisDavLDaiLkqDPkakvACEtvvkt
                      +kfLFtsesvsEGHPDK++DqisDavLDa+LkqDP+akvACEtv+kt
     C49F5.1     3    SKFLFTSESVSEGHPDKMCDQISDAVLDAHLKQDPNAKVACETVTKT 49

                   gmvlvaGEittkavvdyekvvRetikeiGyddskkGfDaktcavLvaieq
                   gmv+++GEit+kavvdy+ +vR +i++iG++ds+ GfD ktc+vLva+eq
     C49F5.1    50 GMVMLCGEITSKAVVDYQVLVRRVIEKIGFTDSSIGFDHKTCNVLVALEQ 99

                   qspd<-*
                   qsp+
     C49F5.1   100 QSPE    103

S-AdoMet_syntD2: domain 1 of 1, from 115 to 237: score 297.2, E = 2e-85
                   *->ediGAGDQGiMFGYATdETeelMPLtilLAHKLnaklaevRkdGtLp
                      ed+GAGDQGiMFGYATdETee MPLt++L+HK na l+++R++GtLp
     C49F5.1   115    EDVGAGDQGIMFGYATDETEETMPLTLILSHKINAELHKLRRNGTLP 161

                   WLRPDgKTQVTveYdedkGavvPvRVdTVVvStQHseeitleeLreelke
                   W+RPD+K+QVT+eY++ +Ga  P+RV+TVVvStQHs+++tle Lre +++
     C49F5.1   162 WVRPDSKSQVTIEYESRHGATIPLRVHTVVVSTQHSPDVTLEKLRETILA 211

                   kVIkpViPakyLdekTifhInPsGrF<-*
                    VIk+ViPa +Lde T+fhInP+G F
     C49F5.1   212 DVIKKVIPASLLDESTVFHINPCGTF    237

HCV_NS4a: domain 1 of 1, from 252 to 268: score 2.3, E = 6.7
                   *->kvlvdiLgGYgagVsgA<-*
                      k++vd  gG+ga   gA
     C49F5.1   252    KIIVDTYGGWGAHGGGA    268

FokI_C: domain 1 of 1, from 285 to 299: score 2.8, E = 5
                   *->aRmlaGvLvklGLvk<-*
                      aR++a  Lvk+GL+k
     C49F5.1   285    ARWVATSLVKAGLAK    299

DUF419: domain 1 of 1, from 327 to 344: score 6.9, E = 1.1
                   *->vpdeelreLveqSYdLvv<-*
                      ++deel   ve+S+dL+
     C49F5.1   327    LTDEELHQIVEDSFDLTP    344

S-AdoMet_syntD3: domain 1 of 1, from 239 to 388: score 296.1, E = 4.3e-85
                   *->iGGPqGDaGLtGRKiivDtYGGwgahGgGaFsGKdptKvDRsaAYaa
                      +GGP+GDaG+tGRKiivDtYGGwgahGgGaFsGKdptKvDRsaAYaa
     C49F5.1   239    VGGPMGDAGVTGRKIIVDTYGGWGAHGGGAFSGKDPTKVDRSAAYAA 285

                   RwvAKslvaagLarrclvqlsYAiGvaePlsilvdtygtskkseeellei
                   RwvA slv+agLa+r+lvqlsYAiG+a+P+s+lv  +gts  ++eel +i
     C49F5.1   286 RWVATSLVKAGLAKRVLVQLSYAIGIAKPISVLVYAFGTSPLTDEELHQI 335

                   vrenFDlRPgvivkeLdLkkpiYkktaayGHFgreefpWekpkklkelke
                   v++ FDl Pg+i+keLdLk+piY+kta++GHFg+ efpWe+pk+lk   +
     C49F5.1   336 VEDSFDLTPGKIIKELDLKRPIYEKTAENGHFGHSEFPWEQPKALKISPA 385

                   alk<-*
                   +l+
     C49F5.1   386 LLE    388



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