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/T21C12.1b
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Query: T21C12.1b CE28082 locus:unc-49 gamma-aminobutyric-acid receptor status:Confirmed TR:Q9Y0I6 protein_id:CAC42346.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Neur_chan_LBD Neurotransmitter-gated ion-channel lig 276.2 4.1e-79 1
Neur_chan_memb Neurotransmitter-gated ion-channel tra 156.0 3.8e-45 2
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Neur_chan_LBD 1/1 34 247 .. 1 246 [] 276.2 4.1e-79
Neur_chan_memb 1/2 254 337 .. 1 84 [. 133.0 2.3e-38
Neur_chan_memb 2/2 448 468 .. 271 291 .] 26.2 7e-07
Alignments of top-scoring domains:
Neur_chan_LBD: domain 1 of 1, from 34 to 247: score 276.2, E = 4.1e-79
*->etrLlddLlentvsgYdkrvRPvnggdvPpvtVsvgltlqqiisVdE
+ +ld+L t +Ydkr+RP +g++ P v+V++ +++++i+ V+E
T21C12.1b 34 LSSVLDRLTNRT--TYDKRLRPRYGEK-P-VDVGITIHVSSISAVSE 76
knqdlttnvwlrqgqWtDpRLaWnpsdplddeddyggikslrlpsddehd
+++d+t++ ++rq +W+DpRLa+ +d ++++ i+sl++ d
T21C12.1b 77 VDMDFTLDFYMRQ-TWQDPRLAFGSLD----LGLSKEIDSLTVGVD---- 117
mldkIWlPDiflyNqttskadgnhdvttpntnvrvypglkdGtVlwsppa
+ld++W+PD+f+ N +k++++h tt+n+++r++ dGtV++s ++
T21C12.1b 118 YLDRLWKPDTFFPN---EKKSFFHLATTHNSFLRIEG---DGTVYTSQRL 161
iykssCpmdltyFPFDqQnCslkFgSwtYngdevdlqwkdd....leeid
+++++Cpmdl++FP+D+Q+C+l+++S++Y+ ++ ++ ++++ ++e+ +
T21C12.1b 162 TVTATCPMDLKLFPMDSQHCKLEIESYGYSILDIMYVSHEKksvsTESYE 211
LpdFtengeWdlldvpakrnekpygcyselsgagLnklvYpditfyfvlr
Lp+F + ++ +++ +++ + g+ys+l +f ++
T21C12.1b 212 LPQFVLQSI-KVVN--HTQKLS-SGEYSRLC-------------WFFLFK 244
Rkp<-*
R++
T21C12.1b 245 RNI 247
Neur_chan_memb: domain 1 of 2, from 254 to 337: score 133.0, E = 2.3e-38
*->liiPCvLIsfLswLvFyLPsDaGPeKvtLgIsvLLtlTvFlllirei
+++P+vLI++ sw++F+L +Da+P++v+Lg++++Lt+T++++ + +
T21C12.1b 254 IYLPSVLIVVISWVSFWLSRDATPARVALGVTTVLTMTTLMTMTNSS 300
lPkTSlvvPLigkYllFtMfvvtasieyavvvlnvhh<-*
+Pk+S+v+ +++++ +++M+v+ +++eya+v ++ ++
T21C12.1b 301 MPKVSYVKSIDIFLGVCFMMVFCSLLEYAAVGYISKR 337
Neur_chan_memb: domain 2 of 2, from 448 to 468: score 26.2, E = 7e-07
*->IDRlflwiFpivfvlGTlgyf<-*
ID++++ +Fp fvl+++gy+
T21C12.1b 448 IDKYSRSLFPSIFVLFNVGYW 468