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/F38B7.5
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Query:  F38B7.5  CE05829   Ubiquitin carboxyl-terminal hydrolases family 2, Ubiquitin carboxyl-terminal hydrolases family 2 status:Partially_con

Scores for sequence family classification (score includes all domains):
Model         Description                               Score    E-value  N
--------      -----------                               -----    ------- ---
UCH           Ubiquitin carboxyl-terminal hydrolase     246.3    1.6e-85   1
OTU           OTU-like cysteine protease                 91.7    1.5e-23   1
LigB          Catalytic LigB subunit of aromatic ring     6.4        1.1   1
Pox_Rap94     RNA polymerase-associated transcription     3.1        4.1   1
Herpes_glycop Herpesvirus glycoprotein M                  2.7        7.5   1

Parsed for domains:
Model         Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------      ------- ----- -----    ----- -----      -----  -------
Herpes_glycop   1/1      45    91 ..   354   412 .]     2.7      7.5
Pox_Rap94       1/1     496   513 ..   815   832 .]     3.1      4.1
LigB            1/1     565   579 ..   327   341 .]     6.4      1.1
OTU             1/1     560   674 ..     1   139 []    91.7  1.5e-23
UCH             1/1     211   778 ..     1   456 []   246.3  1.6e-85

Alignments of top-scoring domains:
Herpes_glycop: domain 1 of 1, from 45 to 91: score 2.7, E = 7.5
                   *->fvrmpksrYkalvskarvRssmrSrrRpsplspkvrarrrnepslnq
                      f+ + k++ +a +sk++            p+++++ + r+++ s  +
     F38B7.5    45    FIEENKNSMQATQSKRP------------PSAASGSSSRTEKSSVRP 79

                   aprasylreees<-*
                   + ++++lre+ +
     F38B7.5    80 IFNEQILREDHE    91

Pox_Rap94: domain 1 of 1, from 496 to 513: score 3.1, E = 4.1
                   *->IdENitrIkeLYminFNN<-*
                      I E  ++ keLY+ +F+N
     F38B7.5   496    IVEDVKKRKELYFNIFSN    513

LigB: domain 1 of 1, from 565 to 579: score 6.4, E = 1.1
                   *->vveygaipesiagfg<-*
                      +++y+ai+++i+g++
     F38B7.5   565    NCFYRAISWWITGVQ    579

OTU: domain 1 of 1, from 560 to 674: score 91.7, E = 1.5e-23
                   *->vpgDGnClfhaiafllgldqdPkldielshmeLraevvkqvesnrvk
                      + +DGnC+++ai+++++++q        +hm +r++v+k++++n+
     F38B7.5   560    ITPDGNCFYRAISWWITGVQ-------SHHMIFREAVGKHLKKNELM 599

                   fePyiedvaeyfdedaveaklsqeyikniekpnaWGeeieisalsallrv
                   f             + ++ +  + y  n++ +++W++  ei a++  l+
     F38B7.5   600 FK------------KYCHNEIYEKYVENAMRDGVWATTCEIFAMANMLN- 636

                   sveivvy...dtktgrtakfkpgpekkskkivlililllegeHfd<-*
                    vei+ y +++ + +++++++++p+k++      ++l ++++H++
     F38B7.5   637 -VEIITYlgdSGWVPHSPQNNYPPRKGA------IYLKNTNMHYE    674

UCH: domain 1 of 1, from 211 to 778: score 246.3, E = 1.6e-85
                   *->egpvGLvNlGNTCYmNSvLQcLfhipelrdyllsn.........rhy
                      +  + LvN+GN+CY NS++Q+ +++++l+ +++++ +  +++ +  +
     F38B7.5   211    HENRQLVNTGNSCYYNSTMQAVSSCNPLVIRCEQLyrmvrdnieLFD 257

                   lprinnsnplgskgqllcaladlfkslqsnqyssppseaelslfeSnavs
                   ++ +n++      ++++++l++++k   + +++
     F38B7.5   258 DSMNNDQ---ADIKRKYIVLQNFLKVVICLGWHF---------------- 288

                   alnk.nsk.p.e.esisPtqflktlgkinpsFselegykliqQqDAqEfl
                     nk+n++++ e + ++  q ++++gkin++F+   +++   QqDA+Efl
     F38B7.5   289 --NKrNEGkSiElRRYDLLQYRQNVGKINEEFN---NDD---QQDAHEFL 330

                   lfLLdgLh..........EDlNrvakkpyneehepgldlaleeeeadelk
                   l+L+ ++++  +  +++ + +++v+  ++
     F38B7.5   331 LTLIGAVDdamgvmsknvKTIDNVGITLN--------------------- 359

                   dseaseeawknkstrneslisdlFqGqlesrikCaleCgkvsvtyepFld
                                      + + F++ +e+ ++C ++C +++ ++++ +d
     F38B7.5   360 -------------------PARAFKIDVETMYVC-QGCSNEELKVDSRND 389

                   LslpikpkeasdspksLeecLkaFtkeEiLKviegenkyyCdkcgkkqea
                   L + +                        +
     F38B7.5   390 LGVSV------------------------I-------------------- 395

                   sKklkisrLPpiLtihLkRFsydgetssnim.KindrvefPleeLDlspy
                              +L+i+LkR++ +g++ +++m+K ++rve  +  LD+s++
     F38B7.5   396 -----------CLIINLKRYELEGQGPPFSMkKKSCRVEPSFK-LDVSSL 433

                   ln................................................
                    n ++ ++++  ++++ +++++ ++++++  + ++++ + ++++ +++
     F38B7.5   434 GNfppvehpemfenkeysttepvnsedsrlaeittddahfndsrvsgrll 483

                   ..................................................
                   ++ +++ ++ +   ++ +++++   +  +++++ ++  ++ + +++++++
     F38B7.5   484 ggadeemsqcsvivedvkkrkelyfnifsnekdfddildemginngenqk 533

                   ..................................................
                   + + +++ ++++++  + + ++ +++ +++++   +  +   ++ ++++
     F38B7.5   534 rfhferhitgppskmyqfqlpgatrgitpdgncfyraiswwitgvqshhm 583

                   ..................................................
                     ++  +++ ++++   ++  +++  ++  ++  +++   ++ +     +
     F38B7.5   584 ifreavgkhlkknelmfkkychneiyekyvenamrdgvwattceifaman 633

                   ...........................q.k.tnkeraa.aean.sl.eee
                     + +  +  ++++  +++++++ ++++++ ++k++++++e ++sl++++
     F38B7.5   634 mlnveiitylgdsgwvphspqnnypprKgAiYLKNTNMhYEPTtSLrKNS 683

                   .qqsvnadegnnq.ee.seestksqeegenpptkYeLvaVvvHsGsslsg
                   ++ s++++e +n +++++e ++ ++ ++++ p++Y+LvaVv+H G s++
     F38B7.5   684 pERSPMKKENTNGsSMhDELDENDYLKSDIHPGTYSLVAVVCHLGDSPNK 733

                   GHYiayikk.ldnnkWykFDDsvetVgdwkvvsvvseeevlkesgggtat
                   GHY+ay+k+  +n+ W++++D+  ++      + vs+++v +  +++
     F38B7.5   734 GHYVAYTKElYKNSSWLRCSDD--NI------YAVSKNDVSEAIRSS--- 772

                   seskrlkryrwAYiLFY<-*
                              +Y+ FY
     F38B7.5   773 -----------GYLMFY    778



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