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: hmm4/seq/T21C12.1a
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Query: T21C12.1a CE02346 locus:unc-49 gamma-aminobutyric-acid receptor status:Partially_confirmed TR:Q22637 protein_id:CAA90318.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Neur_chan_memb Neurotransmitter-gated ion-channel tr 294.1 7.5e-86 4
Neur_chan_LBD Neurotransmitter-gated ion-channel li 269.6 4.2e-77 2
Mob_Pre Plasmid recombination enzyme 3.4 2.9 1
mRNA_cap_enzyme mRNA capping enzyme, catalytic domain -0.3 8.5 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Neur_chan_LBD 1/2 34 259 .. 1 246 [] 261.9 8.5e-75
Neur_chan_memb 1/4 266 349 .. 1 84 [. 133.0 2.3e-38
Neur_chan_LBD 2/2 463 527 .. 175 246 .] 9.1 0.24
Neur_chan_memb 2/4 534 614 .. 1 81 [. 117.6 7.8e-34
Mob_Pre 1/1 614 629 .. 1 16 [. 3.4 2.9
mRNA_cap_enzyme 1/1 906 925 .. 46 66 .. -0.3 8.5
Neur_chan_memb 3/4 919 998 .. 1 80 [. 51.7 2.1e-14
Neur_chan_memb 4/4 1059 1079 .. 271 291 .] 13.3 0.0045
Alignments of top-scoring domains:
Neur_chan_LBD: domain 1 of 2, from 34 to 259: score 261.9, E = 8.5e-75
*->etrLlddLlentvsgYdkrvRPvnggdvPpvtVsvgltlqqiisVdE
+ +ld+L t +Ydkr+RP +g++ P v+V++ +++++i+ V+E
T21C12.1a 34 LSSVLDRLTNRT--TYDKRLRPRYGEK-P-VDVGITIHVSSISAVSE 76
knqdlttnvwlrqgqWtDpRLaWnpsdplddeddyggikslrlpsddehd
+++d+t++ ++rq +W+DpRLa+ +d ++++ i+sl++ d
T21C12.1a 77 VDMDFTLDFYMRQ-TWQDPRLAFGSLD----LGLSKEIDSLTVGVD---- 117
mldkIWlPDiflyNqttskadgnhdvttpntnvrvypglkdGtVlwsppa
+ld++W+PD+f+ N +k++++h tt+n+++r++ dGtV++s ++
T21C12.1a 118 YLDRLWKPDTFFPN---EKKSFFHLATTHNSFLRIEG---DGTVYTSQRL 161
iykssCpmdltyFPFDqQnCslkFgS............wtYngdevdlqw
+++++Cpmdl++FP+D+Q+C+l+++S ++ +++ ++ +Y+ ++ ++
T21C12.1a 162 TVTATCPMDLKLFPMDSQHCKLEIESckslcspdifspNGYSILDIMYVS 211
kdd....leeidLpdFtengeWdlldvpakrnekpygcyselsgagLnkl
++++ ++e+ +Lp+F + ++ +++ +++ + g+ys+l
T21C12.1a 212 HEKksvsTESYELPQFVLQSI-KVVN--HTQKLS-SGEYSRLC------- 250
vYpditfyfvlrRkp<-*
+f ++R++
T21C12.1a 251 ------WFFLFKRNI 259
Neur_chan_memb: domain 1 of 4, from 266 to 349: score 133.0, E = 2.3e-38
*->liiPCvLIsfLswLvFyLPsDaGPeKvtLgIsvLLtlTvFlllirei
+++P+vLI++ sw++F+L +Da+P++v+Lg++++Lt+T++++ + +
T21C12.1a 266 IYLPSVLIVVISWVSFWLSRDATPARVALGVTTVLTMTTLMTMTNSS 312
lPkTSlvvPLigkYllFtMfvvtasieyavvvlnvhh<-*
+Pk+S+v+ +++++ +++M+v+ +++eya+v ++ ++
T21C12.1a 313 MPKVSYVKSIDIFLGVCFMMVFCSLLEYAAVGYISKR 349
Neur_chan_LBD: domain 2 of 2, from 463 to 527: score 9.1, E = 0.24
*->tYngdevdlqwkdd..........leeidLpdFtengeWdlldvpak
+Y ++++d++w +++++ + + + + Lp+F+++ + + +
T21C12.1a 463 GYETKDIDYYWGKKrtdleitavkFDTFQLPQFQPTLYFVNTT---- 505
rnekpygcyselsgagLnklvYpditfyfvlrRkp<-*
+ e++ g y +l +++l R++
T21C12.1a 506 KAETSSGKYVRLA-------------LEVILVRNM 527
Neur_chan_memb: domain 2 of 4, from 534 to 614: score 117.6, E = 7.8e-34
*->liiPCvLIsfLswLvFyLPsDaGPeKvtLgIsvLLtlTvFlllirei
+ iP++LI+ sw++F+L+++a+P++v Lg++++Lt+T++ + +++
T21C12.1a 534 IVIPSILIVTISWVSFWLNREASPARVGLGVTTVLTMTTLITTTNNS 580
lPkTSlvvPLigkYllFtMfvvtasieyavvvln<-*
+Pk+S+v+ L++++ ++++v+++++eya+v ++
T21C12.1a 581 MPKVSYVKGLDVFLNFCFVMVFASLLEYAIVSYM 614
Mob_Pre: domain 1 of 1, from 614 to 629: score 3.4, E = 2.9
*->MsnyaiaRmqKvKagn<-*
M++++++R +K+++ +
T21C12.1a 614 MNKRLVLRREKRRKAA 629
mRNA_cap_enzyme: domain 1 of 1, from 906 to 925: score -0.3, E = 8.5
*->yliDRdnevylvenlrfPlkl<-*
+++DRd +y+++ ++fP +l
T21C12.1a 906 FIFDRDSGFYFLQ-IFFPASL 925
Neur_chan_memb: domain 3 of 4, from 919 to 998: score 51.7, E = 2.1e-14
*->liiPCvLIsfLswLvFyLPsDaGPeKvtLgIsvLLtlTvFlllirei
+ +P L ++Lsw +F++++D+ P ++ g ++Lt T ++++ + +
T21C12.1a 919 IFFPASLVVVLSWISFWINRDSAPSRTLIGTMTVLTETHLMTGTNRR 965
lPkTSlvvPLigkYllFtMfvvtasieyavvvl<-*
lP++++v++ ++++ +++ v +a+ieya v +
T21C12.1a 966 LPPVAYVKAVDVFLGFCYLLVILALIEYACVAY 998
Neur_chan_memb: domain 4 of 4, from 1059 to 1079: score 13.3, E = 0.0045
*->IDRlflwiFpivfvlGTlgyf<-*
ID ++++Fp+vf+l++ +
T21C12.1a 1059 IDIVSRAAFPLVFILFNTLFW 1079