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/F07A11.4
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Query:  F07A11.4  CE03146   ubiquitin carboxyl-terminal hydrolase status:Partially_confirmed TR:Q19132 protein_id:CAA91317.1

Scores for sequence family classification (score includes all domains):
Model    Description                                    Score    E-value  N
-------- -----------                                    -----    ------- ---
UCH      Ubiquitin carboxyl-terminal hydrolase          487.8   1.4e-169   2
zf-MYND  MYND finger                                     64.4      5e-20   1
PHD      PHD-finger                                       6.5       0.66   1
TIR      TIR domain                                       2.6        9.7   1

Parsed for domains:
Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
-------- ------- ----- -----    ----- -----      -----  -------
UCH        1/2      14   404 ..    45    58 ..   -24.2  5.9e+04
TIR        1/1     507   534 ..     1    35 [.     2.6      9.7
zf-MYND    1/1     716   756 ..     1    43 []    64.4    5e-20
PHD        1/1     925   937 ..    39    51 .]     6.5     0.66
UCH        2/2     420  1067 ..     1   456 []   501.8   2e-174

Alignments of top-scoring domains:
UCH: domain 1 of 2, from 14 to 404: score -24.2, E = 5.9e+04
                   *->snplgs.........................................
                      s++++s ++++ +++ +++ ++ + ++++ +++ +++ +++++++++
    F07A11.4    14    SSSCSSirssnysrsytpsfntfkyspssytpnisrnlnttstgstt 60

                   ..................................................
                   +++++ ++++ ++++ + +++++++++ ++++ +++++  +++   + +
    F07A11.4    61 sdtpklssssaprsrlsfttpsststnlprtsitshktlysspaaarvsv 110

                   ..................................................
                   +++++ ++++++++ ++ ++ ++ ++++  ++++  ++ +++ +++ +++
    F07A11.4   111 stndslshstphntyrgiskystierstvadtkpyyssatsslsstydsr 160

                   ..................................................
                   +++++++ ++++ ++ + +++++++++  ++++++ +++++ +++++ +
    F07A11.4   161 rhsrsdrissstlpdvkietgpttrthmvhptsshirsrssygrsntvsm 210

                   ..................................................
                     ++ +++ ++++++++ ++  +++++++++ + ++  ++++++++ +++
    F07A11.4   211 faqqareradreekdrdykewmqkekdretelgletlypttsssssaqss 260

                   ..................................................
                    +++ +++  +++++++++++ ++++ ++ ++++++++  + ++  +++
    F07A11.4   261 aqsefrrsvapsptststttpyrsnryssatrggnsssaaplddimstsy 310

                   ..................................................
                   ++   ++++  ++ ++++++  ++++++ +++++++++++ ++++++  +
    F07A11.4   311 ssvaatpppaysqlstststllrtrrerlereeegrnsssmtpqpqslvp 360

                   ....................................kgqllcal<-*
                   +++++++++++  ++++++  +++ +    ++ +++++++++a+
    F07A11.4   361 ppppppppppsaasngrsgylprsvsaavissasssSVYKPTAM    404

TIR: domain 1 of 1, from 507 to 534: score 2.6, E = 9.7
                   *->vFisfsgksrsnddrdtFvshllkeLeekkqpgin<-*
                       F +f+      +d ++F+s ll  L+e+  ++++
    F07A11.4   507    -FANFAQ-----HDAHEFLSFLLDGLHED-VNRVK    534

zf-MYND: domain 1 of 1, from 716 to 756: score 64.4, E = 5e-20
                   *->CanCgkeatksrqLkkCsrCknarYCSkeCQrkdWll.gHkreC<-*
                      C++Cg++++k   Lk C++C++a YCSkeCQ+++W+++gH++eC
    F07A11.4   716    CHECGNSKLK---LKACEECYDAVYCSKECQVANWSTgGHREEC    756

PHD: domain 1 of 1, from 925 to 937: score 6.5, E = 0.66
                   *->pegkWlCpeCtpk<-*
                      pe+ W+C  C++
    F07A11.4   925    PEESWYCSTCKEN    937

UCH: domain 2 of 2, from 420 to 1067: score 501.8, E = 2e-174
                   *->egpvGLvNlGNTCYmNSvLQcLfhipelrdyllsnrhylprinnsnp
                      +g++GL+N+GNTC+mN+vLQ+L+++ elr+y+l+n hy+p+in++np
    F07A11.4   420    QGYTGLRNIGNTCFMNAVLQMLVNNIELREYFLRN-HYQPEINETNP 465

                   lgskgqllcaladlfkslqsnqyssppseaelslfeSnavsalnknskpe
                   lgs+g+l++a+ad++++++s+++
    F07A11.4   466 LGSEGRLAKAFADFMHQMWSGHQ--------------------------- 488

                   esisPtqflktlgkinpsFselegykliqQqDAqEfllfLLdgLhEDlNr
                   ++i+Ptq++++++  +++F+   ++    Q+DA+Efl fLLdgLhED+Nr
    F07A11.4   489 KAIEPTQIKNIVAEKASQFA---NFA---QHDAHEFLSFLLDGLHEDVNR 532

                   vakkpyneehepgldlalee.ee.adelkdseaseeawknkstrneslis
                   v+kkp+              +++++++++d  +s+eawkn+++rn+s+++
    F07A11.4   533 VKKKPL-------------TgTVeSHGRHDLDVSNEAWKNHILRNDSIFV 569

                   dlFqGqlesrikCaleCgkvsvtyepFldLslpi................
                   dlF+Gql+s+++C ++C++vs+t++pF +L++p ++++++++    + ++
    F07A11.4   570 DLFHGQLKSHVQC-PNCDRVSITFDPFVYLPVPFpknkqstdlifwplen 618

                   ..................................................
                   ++++ + + + +++++  +  +  +++ + ++++ +  +   ++ ++  +
    F07A11.4   619 qtkpykltvsystegtvadflsvvsetvrvptrnlraceaichkfdkiys 668

                   ..................................................
                    + + ++  ++++    +++++ + +++    +  +++  ++++++  ++
    F07A11.4   669 ldmkvsdivspdrlfvfqthdemefneeivilhvlqrelyrkntkhache 718

                   ..................................................
                    ++++ + +  ++  +    +++ +  + ++++++++ ++++++++ +++
    F07A11.4   719 cgnsklklkaceecydavycskecqvanwstgghreecskrkpsetvghp 768

                   ..................................................
                      + ++++ + ++  +  + +++++++++++++++ ++++++++   ++
    F07A11.4   769 livslprsqltyqhlyrvleaksrhtppgessssssvsstprrrsvaaep 818

                   ..................................................
                   ++++++  + ++ ++++++ ++++ ++++  ++ ++++  + +  +++++
    F07A11.4   819 rtknqkmfeirklsgqndsfgshsisddeacqslesggyvsvnwinqrng 868

                   ..............................kpkeasdspksLeecLkaFt
                   ++  + +++++ + + +++++ ++++ ++  ++++s+ ++ L+++L++F+
    F07A11.4   869 kpyitienrkdidvdveksrqmnsrnmngyVKSNNSETNPHLTQMLDLFS 918

                   keEiLKviegenkyyCdkcgkkqeasKklkisrLPpiLtihLkRFsydge
                   ++E L   ++e+ +yC++c++ +ea+Kkl+++rLPp+L+i+LkRF y  +
    F07A11.4   919 ETERL---KPEESWYCSTCKENVEATKKLQLYRLPPVLIIQLKRFVYTAF 965

                   tssnim....KindrvefPleeLDlspylnqktnkeraaaeansleeeqq
                   t++ +m +++K  ++ve+Ple+LD+sp+l+
    F07A11.4   966 TYQSSMarrsKDTRSVEYPLESLDMSPFLA-------------------- 995

                   svnadegnnqeeseestksqeegenpptkYeLvaVvvHsGsslsgGHYia
                                       + +  ++t+Y+L++Vv+HsG +++ GHYi+
    F07A11.4   996 -------------------ETSPHPNSTMYDLTGVVCHSG-NSYFGHYIS 1025

                   yikk......ldnnkWykFDDsvetVgdwkvvsvvseeevlkesgggtat
                   + +  + ++++ + +W+ FDDs  tV       ++s+++ ++e+
    F07A11.4  1026 MGRLadfdssKTKIEWRNFDDS--TV------ARQSTSTLQTED------ 1061

                   seskrlkryrwAYiLFY<-*
                              AY+LFY
    F07A11.4  1062 -----------AYLLFY    1067



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