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:            hmm5/seq/Y76B12C.7
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Query:  Y76B12C.7  CE29932    status:Partially_confirmed SW:Q9N4C2 protein_id:AAF36067.2

Scores for sequence family classification (score includes all domains):
Model      Description                                  Score    E-value  N
--------   -----------                                  -----    ------- ---
CPSF_A     CPSF A subunit region                        179.6    4.9e-50   1
FKBP       FKBP-type peptidyl-prolyl cis-trans isomer     4.2        3.8   1
Pep3_Vps18 Pep3/Vps18/deep orange family                  4.0        6.7   1
adh_short  short chain dehydrogenase                      2.9        9.3   1

Parsed for domains:
Model      Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------   ------- ----- -----    ----- -----      -----  -------
adh_short    1/1     597   657 ..   214   271 .]     2.9      9.3
Pep3_Vps18   1/1    1208  1224 ..     1    20 [.     4.0      6.7
CPSF_A       1/1    1079  1387 ..     1   345 []   179.6  4.9e-50
FKBP         1/1    1403  1427 ..     1    26 [.     4.2      3.8

Alignments of top-scoring domains:
adh_short: domain 1 of 1, from 597 to 657: score 2.9, E = 9.3
                   *->e.vadiadpeleerits.titplgrygvtpeeianavlfLasdgasy
                      ++v   +   +++ + + ++ + gr++ + e ++++++ L + + s+
   Y76B12C.7   597    FpV---IQASIVDPYVAlLT-QNGRLL-LYELVMEPYVQLREVDISA 638

                   s......vtgqtlnvdggi<-*
                   ++  + ++t+q l+   +i
   Y76B12C.7   639 TsfatwhATAQNLTQLTSI    657

Pep3_Vps18: domain 1 of 1, from 1208 to 1224: score 4.0, E = 6.7
                   *->GIvfGdlsEKqiyvnpasnl<-*
                      GI+f+d +   +yv+ +++l
   Y76B12C.7  1208    GISFLDMH---YYVYQLHSL    1224

CPSF_A: domain 1 of 1, from 1079 to 1387: score 179.6, E = 4.9e-50
                   *->ekeassirlidpntfevih.asyklqqnEtalSmasvkfsneettkd
                          + + l++++++  +++ ++++++ E+++ ++ v +++e+t ++
   Y76B12C.7  1079    ---KYTLNLFSSQDWAAVPnTEISFEDMEAVTACEDVALKSESTISG 1122

                   kntYlvVGTalnlpeeietvqadhliIcPsrGRilifelieVvPepgkpk
                   ++t l+ GT +n++ee+            +rGRi++ e+ieVvPep +p
   Y76B12C.7  1123 LETLLAMGTVNNYGEEVL-----------VRGRIILCEVIEVVPEPDQPT 1161

                   tgnkLklvhetevkGpVyalcefnGrlLagiGqkvrlydltkdkekkeLr
                    + k+k+++ +e+kGpV+ lc  nG lL g+Gqkv+++++ +    + L+
   Y76B12C.7  1162 SNRKIKVLFDKEQKGPVTGLCAINGLLLCGMGQKVFIWQFKD---ND-LM 1207

                   keafidtpvyildiksmHQWgnrIlVgDvmkSvtllrYkeeenqLievAr
                   + +f d ++y+ ++ s    ++  ++ D ++S++l+r++e  + +++ +r
   Y76B12C.7  1208 GISFLDMHYYVYQLHSL---RTIAIACDARESMSLIRFQEDNKAMSIASR 1254

                   D...tnprwvtavefLdddtnLyfagaDasGNlfvlrydpeapkdvdedP
                   D++++++  +++  +++d+   +f+ +D  GN+    y peap
   Y76B12C.7  1255 DdrkCAQPPMAS-QLVVDGAHVGFLLSDETGNITMFNYAPEAP------- 1296

                   tesKslwdrgltsserqkLelvghFHlGeivnsfq....kgslvmknlnd
                              +s+++++L ++++  +G  +n f + ++++sl  ++ n+
   Y76B12C.7  1297 -----------ESNGGERLTVRAAINIGTNINAFVrlrgHTSLL-QLNNE 1334

                   ssssdtgasptllygTldGsIGvivpllseeeyrfLeqlqnhLrkeipsa
                   + +  ++++ t++++ ldGs G + pl  e+ yr+L+ lq  + ++ p
   Y76B12C.7  1335 DEKEAIEQRMTTVFASLDGSFGFVRPL-TEKSYRRLHFLQTFIGSVTP-- 1381

                   plgGld<-*
                   +++Gl+
   Y76B12C.7  1382 QIAGLH    1387

FKBP: domain 1 of 1, from 1403 to 1427: score 4.2, E = 3.8
                   *->GdGpekpkkGDtVevhYtGtLedGgk<-*
                      G  +++ ++GD+Ve+ +  +L d ++
   Y76B12C.7  1403    GRNARNLIDGDVVEQYLHLSLYD-KT    1427



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