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/C04H5.6
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Query:  C04H5.6  CE15592  locus:mog-4 Helicases conserved C-terminal domain status:Confirmed SW:O45244 protein_id:CAB03845.1

Scores for sequence family classification (score includes all domains):
Model           Description                             Score    E-value  N
--------        -----------                             -----    ------- ---
HA2             Helicase associated domain (HA2)        153.3    4.3e-42   1
helicase_C      Helicase conserved C-terminal domain     51.7    3.4e-13   1
Thymidylate_kin Thymidylate kinase                        4.3        1.2   1
OTCace          Aspartate/ornithine carbamoyltransfer     3.4        6.6   1
Lyase_8         Polysaccharide lyase family 8, super-     3.2        3.5   1
InvE            InvE invasion protein                     2.4        3.4   1
HSP70           Hsp70 protein                             1.2          9   1

Parsed for domains:
Model           Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------        ------- ----- -----    ----- -----      -----  -------
Thymidylate_kin   1/1     385   397 ..     1    13 [.     4.3      1.2
HSP70             1/1     584   607 ..   597   620 .]     1.2        9
Lyase_8           1/1     679   695 ..   287   303 .]     3.2      3.5
helicase_C        1/1     607   696 ..     1    72 []    51.7  3.4e-13
InvE              1/1     708   717 ..   361   370 .]     2.4      3.4
OTCace            1/1     770   785 ..   129   143 ..     3.4      6.6
HA2               1/1     755   850 ..     1   114 []   153.3  4.3e-42

Alignments of top-scoring domains:
Thymidylate_kin: domain 1 of 1, from 385 to 397: score 4.3, E = 1.2
                   *->iEGiDGaGKTTqa<-*
                      iEG  G+GKTTq+
     C04H5.6   385    IEGETGSGKTTQL    397

HSP70: domain 1 of 1, from 584 to 607: score 1.2, E = 9
                   *->keeikakteeLqkvvqkigekmyq<-*
                      +eei++ +e+L + + ++g+k+ +
     C04H5.6   584    QEEIETVQEALMERSKALGSKIKE    607

Lyase_8: domain 1 of 1, from 679 to 695: score 3.2, E = 3.5
                   *->gisRaefkklaTkanke<-*
                      +is+a+ +++a +a+++
     C04H5.6   679    TISKAAANQRAGRAGRT    695

helicase_C: domain 1 of 1, from 607 to 696: score 51.7, E = 3.4e-13
                   *->gikvarlhGglsqeeReeilekFrngkskvLvaTdvaarGiDipdvn
                      ++  ++++++l+++ + +i+e   ++ +kv++aT++a+++++i ++n
     C04H5.6   607    ELIPLPVYANLPSDLQAKIFEPTPKDARKVVLATNIAETSVTIDGIN 653

                   lVInydl..................pwnpesyiQRiGRaGRaG<-*
                   +VI+ +++++++ + +++ ++ +    +++   QR+GRaGR G
     C04H5.6   654 YVIDPGFskqnsfdarsgvehlhvvTISKAAANQRAGRAGRTG    696

InvE: domain 1 of 1, from 708 to 717: score 2.4, E = 3.4
                   *->AYKkElaEqR<-*
                      AYK+El Eq
     C04H5.6   708    AYKHELEEQP    717

OTCace: domain 1 of 1, from 770 to 785: score 3.4, E = 6.6
                   *->hRv.eTkVGkkiaEFG<-*
                      hR++ Tk+G+++aEF+
     C04H5.6   770    HRGeLTKLGRRMAEFP    785

HA2: domain 1 of 1, from 755 to 850: score 153.3, E = 4.3e-42
                   *->llrAlelLyaLGALDppkeekddgeLTppLGrqmaelPldPrLsKML
                      l+ Ale+LyaLGAL+      ++geLT+ LGr+mae+P+dP +sKM+
     C04H5.6   755    LVIALEQLYALGALN------HRGELTK-LGRRMAEFPCDPCMSKMI 794

                   llaaefgCldeiltIaAmLSvqspffgrpkekkeeearadearrkdslkF
                   +++ ++ C++ei+tIaAmLS+   +f+rpk++   +  ad+ar+     F
     C04H5.6   795 IASEKYECSEEIVTIAAMLSCNAAVFYRPKAQVI-H--ADSARK----GF 837

                   aspsgregDehltllnv<-*
                    sp    gD h+tl nv
     C04H5.6   838 WSP---AGD-HITLMNV    850



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