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/ZK1320.6
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Query:  ZK1320.6  CE30716  locus:arc-1 ADP-ribosylation factors (Arf family) (contains ATP\/GTP binding P-loop), Zinc finger, C3HC4 type (RING fi

Scores for sequence family classification (score includes all domains):
Model           Description                             Score    E-value  N
--------        -----------                             -----    ------- ---
arf             ADP-ribosylation factor family          126.7    9.9e-35   1
zf-B_box        B-box zinc finger                        31.4    3.1e-06   2
Thymidylate_kin Thymidylate kinase                        9.8      0.013   1
spectrin        Spectrin repeat                           5.7          4   1
Apolipoprotein  Apolipoprotein A1/A4/E family             5.5        2.4   1
SKI             Shikimate kinase                          4.7        3.7   1
ABC_tran        ABC transporter                           4.0        5.2   1
PBP_dimer       Penicillin-binding Protein dimerisati     4.0        5.8   1

Parsed for domains:
Model           Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------        ------- ----- -----    ----- -----      -----  -------
zf-B_box          1/2     119   153 ..    12    48 .]    27.5  3.1e-05
zf-B_box          2/2     180   205 ..    17    48 .]     9.3      1.5
Apolipoprotein    1/1     205   226 ..   116   137 ..     5.5      2.4
spectrin          1/1     208   273 ..    35   101 ..     5.7        4
PBP_dimer         1/1     317   334 ..     1    18 [.     4.0      5.8
ABC_tran          1/1     373   391 ..     1    19 [.     4.0      5.2
SKI               1/1     374   393 ..     1    20 [.     4.7      3.7
Thymidylate_kin   1/1     380   395 ..     1    18 [.     9.8    0.013
arf               1/1     373   472 ..    18   114 ..   126.7  9.9e-35

Alignments of top-scoring domains:
zf-B_box: domain 1 of 2, from 119 to 153: score 27.5, E = 3.1e-05
                   *->plslfCedDqallCvvCdlsgeHsanklargHtvvpl<-*
                      ++ ++C  ++  lC  C +s  H   +++++H++ pl
    ZK1320.6   119    VAVIYCTVCDSNLCERCSES-TH-STNVLSKHRRIPL    153

zf-B_box: domain 2 of 2, from 180 to 205: score 9.3, E = 1.5
                   *->CedDqallCvvCdlsgeHsanklargHtvvpl<-*
                      C + + l+C +C+  g+H      +gH  v++
    ZK1320.6   180    CDTESPLMCMMCRDYGRH------KGHSHVLI    205

Apolipoprotein: domain 1 of 1, from 205 to 226: score 5.5, E = 2.4
                   *->lgkDlEdvrnrlaPyrdEvqam<-*
                      ++k++Ed+r++++ +++E++++
    ZK1320.6   205    IEKEVEDLREKVREHLGELSKQ    226

spectrin: domain 1 of 1, from 208 to 273: score 5.7, E = 4
                   *->svqaLlkkHealeaelaaheqdrvkqlnelaqkLieegeahpdseei
                      +v+ L +k +++  el  +  + + +  +  +++i e +++++   +
    ZK1320.6   208    EVEDLREKVREHLGELSKQS-ETIGNALHSIDSVIHELTPGQEDGSL 253

                   kerleeLnerWeaLlelaae<-*
                   +e+++e++ ++++L++++++
    ZK1320.6   254 EETRQEVRNHFRRLRTALDR    273

PBP_dimer: domain 1 of 1, from 317 to 334: score 4.0, E = 5.8
                   *->pipapRGsIyDRnGvaLA<-*
                       +  +RG+I+DR+ ++LA
    ZK1320.6   317    ALIMERGKILDRKDDLLA    334

ABC_tran: domain 1 of 1, from 373 to 391: score 4.0, E = 5.2
                   *->GevlalvGpNGaGKSTLLk<-*
                        +++l+G  GaGK+++ +
    ZK1320.6   373    ESRVVLLGLDGAGKTSIVR    391

SKI: domain 1 of 1, from 374 to 393: score 4.7, E = 3.7
                   *->rnifLIGmmGaGKsTvGrlL<-*
                        ++L G+ GaGK+++ r+L
    ZK1320.6   374    SRVVLLGLDGAGKTSIVRRL    393

Thymidylate_kin: domain 1 of 1, from 380 to 395: score 9.8, E = 0.013
                   *->iEGiDGaGKTTqaelLke<-*
                        G+DGaGKT+++++Lk+
    ZK1320.6   380    --GLDGAGKTSIVRRLKK    395

arf: domain 1 of 1, from 373 to 472: score 126.7, E = 9.9e-35
                   *->EmRILiLGLDnAGKTTILykLk...lgeivttiPTiGFNvEtveykN
                      E R+++LGLD+AGKT I+ +Lk+ +++ ++   PTiGFN+Et+ ykN
    ZK1320.6   373    ESRVVLLGLDGAGKTSIVRRLKkvqMDTVMAPHPTIGFNIETIHYKN 419

                   ikFtvWDvGGQeslRPlWrnYfpnTdavIfVVDSaDreRieeakeELhaL
                   +++++WDvGG  +lR lW++Y++n +a+ +V+D +  eR++ea +EL++
    ZK1320.6   420 YRLNFWDVGGLPKLRHLWKHYYSNAQAIFYVIDGYAVERFSEAIKELNRV 469

                   Lne<-*
                   + +
    ZK1320.6   470 MSD    472



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