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/F13B10.2
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Query: F13B10.2 CE05598 locus:rpl-3 60S ribosomal protein L3 status:Confirmed SW:P50880 protein_id:CAA90183.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Ribosomal_L3 Ribosomal protein L3 576.4 1.9e-169 1
RNA_pol_Rpb2_6 RNA polymerase Rpb2, domain 6 3.6 1.3 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
RNA_pol_Rpb2_6 1/1 84 100 .. 1 17 [. 3.6 1.3
Ribosomal_L3 1/1 50 345 .. 1 299 [] 576.4 1.9e-169
Alignments of top-scoring domains:
RNA_pol_Rpb2_6: domain 1 of 1, from 84 to 100: score 3.6, E = 1.3
RF xxxxxxxxxxxxxxxxx
*->gvvAsligfvehnqSpr<-*
+v+A+++g+v+ q+pr
F13B10.2 84 MVIAGVTGYVDTPQGPR 100
Ribosomal_L3: domain 1 of 1, from 50 to 345: score 576.4, E = 1.9e-169
*->KaGMThifredgkPGSKmhKkEelvpVTvietpPmvVvqvktyeeTp
KaGMThi+r+++kPGSK++KkE++++VT++etpPmv+ +v++y++Tp
F13B10.2 50 KAGMTHIVRDVDKPGSKVNKKEVVEAVTIVETPPMVIAGVTGYVDTP 96
dGyralqvgwaehkseevnrrllghfaKskKKAftkyakkyetedGKksI
+G ral+++waeh+see++rr++ ++aKskKKAftkyakk+++edGKk I
F13B10.2 97 QGPRALTTIWAEHLSEEARRRFYSNWAKSKKKAFTKYAKKWQDEDGKKLI 146
ereLeriKKYcsViRViaHTqvrpkrgLaqKKAhvmEirvnGGtnadkie
e++++++KKYcs iRViaHTq+ +r +qKKAh+ Ei+vnGGt+ +k++
F13B10.2 147 EADFAKLKKYCSSIRVIAHTQMKILR-RRQKKAHLVEIQVNGGTIEQKVD 195
vgqeikektvavedvFregeyVDVtGvTKGKGFqGvvKRWGfkrlPasHg
+++e+ ek+v v+ vF+++e++D +GvT+G+GF+Gv+ RW++k+lP ++
F13B10.2 196 WAREHLEKQVQVDTVFAQDEMIDTIGVTRGHGFKGVTSRWHTKKLP--RK 243
tskghRkvGsiGawhppGRVfkgvkmaGqmGnhhrTeqNlkivridqeq.
t+kg+Rkv++iGawhp+ RV ++v++aGq+G hhrT++N ki+ri+++
F13B10.2 244 THKGLRKVACIGAWHPS-RVAFTVARAGQKGFHHRTIINNKIYRIGKSAl 292
..dDGkaknaeTefDlTeKtItPmGGFvhYGeVknnlllVKGsVPGpkkr
+++ ++n++TefDlT KtItPmGGF++YG+V +++++ G+V Gpkkr
F13B10.2 293 teEG--KNNGSTEFDLTQKTITPMGGFPRYGIVNQDYIMLRGAVLGPKKR 340
lVtir<-*
l t+r
F13B10.2 341 LITLR 345