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/C08F1.4a
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Query:  C08F1.4a  CE27059    status:Partially_confirmed TR:O17175 protein_id:AAK31407.1

Scores for sequence family classification (score includes all domains):
Model         Description                               Score    E-value  N
--------      -----------                               -----    ------- ---
MATH          MATH domain                               387.0   1.8e-112   5
Ribosomal_L31 Ribosomal protein L31                       6.3        4.2   1

Parsed for domains:
Model         Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------      ------- ----- -----    ----- -----      -----  -------
MATH            1/5       2    31 ..   127   159 .]    18.9  0.00065
Ribosomal_L31   1/1      69    77 ..    63    71 .]     6.3      4.2
MATH            2/5      53   169 ..     1   159 []   111.8  1.3e-29
MATH            3/5     200   314 ..     1   159 []    89.8  1.9e-23
MATH            4/5     336   449 ..     1   159 []   141.8  1.3e-38
MATH            5/5     466   520 .]     1    78 [.    45.5  2.9e-11

Alignments of top-scoring domains:
MATH: domain 1 of 5, from 2 to 31: score 18.9, E = 0.00065
                   *->sGfkkFisWddLeddyngylvdDsiiiEaeVkI<-*
                      +G+ k+++W++L ++    lv+Ds+++Ea  ++
    C08F1.4a     2    KGYRKLMKWEKLVSNH---LVNDSVTVEADLNV    31

Ribosomal_L31: domain 1 of 1, from 69 to 77: score 6.3, E = 4.2
                   *->RFnkKYnik<-*
                      RF+k++ni+
    C08F1.4a    69    RFEKRFNIP    77

MATH: domain 2 of 5, from 53 to 169: score 111.8, E = 1.3e-29
                   *->tiknfSkikeeakeGregeeyytspyeerfnipWrlnvlriyrnggg
                       + ++S+i+       ege++++   e+rfnipWr   + ++r  g
    C08F1.4a    53    QFSDVSRIE-------EGESRFS-RFEKRFNIPWR---IELQRVSG- 87

                   egrsgkflglyLhClkeekdsptienlkWsieteftlklvsdnGksirrm
                         fl+++Lh   e +++     +   i +++++ lvs nGk
    C08F1.4a    88 ------FLEIHLHRGIEIEKP---DDVFTIIKADCWFNLVSTNGKN---- 124

                   ssttltkktkdaknnshvFekptgegwgksGfkkFisWddLeddyngylv
                       l+++++       vF++  + ++ k    k i+Wdd+++dy   ++
    C08F1.4a   125 ----LMRQMS------AVFCRDVDMESLK----KVIRWDDMMTDY---VI 157

                   dDsiiiEaeVkI<-*
                   +Ds+iiEa+++I
    C08F1.4a   158 NDSFIIEAHIEI    169

MATH: domain 3 of 5, from 200 to 314: score 89.8, E = 1.9e-23
                   *->tiknfSkikeeakeGregeeyytspyeerfnipWrlnvlriyrnggg
                      ++ n+S++        +ge     ++e r++ipWr   ++ +r  +
    C08F1.4a   200    KVNNVSRFQ-------DGEKQWG-NTELRYDIPWR---IQTKRSLD- 234

                   egrsgkflglyLhClkeekdsptienlkWsieteftlklvsdnGksirrm
                         fl+lyL C+  ++ s      k  i+t++t+ lvs nG+
    C08F1.4a   235 ------FLELYLFCDEDDNVS------KKLIQTKCTFNLVSTNGNN---- 268

                   ssttltkktkdaknnshvFekptgegwgksGfkkFisWddLeddyngylv
                         ++ k       +Fekp g g ++     F++W+d+ + +   l+
    C08F1.4a   269 ----YRRTSK------LCFEKPGGQGISG-----FFKWNDMIESF---LN 300

                   ..dDsiiiEaeVkI<-*
                   + +Ds+i+Ea+VkI
    C08F1.4a   301 plEDSLIVEAHVKI    314

MATH: domain 4 of 5, from 336 to 449: score 141.8, E = 1.3e-38
                   *->tiknfSkikeeakeGregeeyytspyeerfnipWrlnvlriyrnggg
                      +++n+S++        eg+  ++  ++e+++ipW+   ++++  +g
    C08F1.4a   336    VVRNVSNMV-------EGGVIFS-ASQEWYDIPWS---ISMKYING- 370

                   egrsgkflglyLhClkeekdsptienlkWsieteftlklvsdnGksirrm
                         f++l L C+ke ++        Wsiet f+l lv +nGk+
    C08F1.4a   371 ------FVELLLSCDKELNAH-----EAWSIETNFQLILVGANGKR---- 405

                   ssttltkktkdaknnshvFekptgegwgksGfkkFisWddLeddyngylv
                       lt   +      h+Fekp+++g +k     +i+W+d++d+y    v
    C08F1.4a   406 ----LTDYFE------HTFEKPDSIGDSK-----LIRWEDMLDQY---AV 437

                   dDsiiiEaeVkI<-*
                   +Ds+++Ea+V+
    C08F1.4a   438 EDSLTVEARVNF    449

MATH: domain 5 of 5, from 466 to 520: score 45.5, E = 2.9e-11
                   *->tiknfSkikeeakeGregeeyytspyeerfnipWrlnvlriyrnggg
                      t+kn S++        ege +++ ++e++ + pWr   ++++++
    C08F1.4a   466    TVKNLSNVH-------EGEFHFS-KTEKHCDAPWR---ISLKKEEM- 500

                   egrsgkflglyLhClkeekdsptienlkWsi<-*
                          l +yLhC+k+  +s   +   Ws+
    C08F1.4a   501 ------CLLIYLHCDKL--LS---NDEHWSV    520



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