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: hmm5/seq/Y56A3A.27
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Query: Y56A3A.27 CE28138 locus:top-3 DNA topoisomerase III status:Confirmed SW:O61660 protein_id:CAB60518.2
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Topoisom_bac DNA topoisomerase 360.7 1.5e-104 1
Toprim Toprim domain 93.0 5.8e-24 1
HR1 Hr1 repeat 5.3 3.2 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Toprim 1/1 3 147 .. 1 151 [] 93.0 5.8e-24
Topoisom_bac 1/1 161 568 .. 1 455 [] 360.7 1.5e-104
HR1 1/1 591 623 .. 55 87 .] 5.3 3.2
Alignments of top-scoring domains:
Toprim: domain 1 of 1, from 3 to 147: score 93.0, E = 5.8e-24
*->kvliiVEgpsdakalakalgkpskrki............vyelp.gg
++l+++E++ ak +a +l++++ +++++++ ++ + + el+++
Y56A3A.27 3 RALFVAEKNDVAKGVAAILSNGTANRRegrskfnkiytlNTELFgQQ 49
kdgnvvaslGhlvdLptpegyddky.kw.lw.lpivdvkkgfep.yqie.
+ v+++ Gh+ +++ +++++++w+ ++ +++++ +++ +++
Y56A3A.27 50 TAISVTSVSGHM-------MNFQFHeNMsNWqTASMVELFRAPVrHVVTp 92
f.dqlckcskkidlkkeqlkllkklakkadevilatDpDreGeaiawkll
+ + l++++l++ ++ + ++++tD+DreGeai+ ++
Y56A3A.27 93 EmK----------LIEQTLREQAQRHDI---LVVWTDCDREGEAIGAEIV 129
ellkpygpveleddkkvrriflp<-*
++++ +++ +++++r++++
Y56A3A.27 130 KVCRDSNR-----RLDIFRARFS 147
Topoisom_bac: domain 1 of 1, from 161 to 568: score 360.7, E = 1.5e-104
*->preidmglvdAqlARqilDrlvGynlSRlltkklragg........y
++d++ v A+ R +lD+++G +++Rl+t++lr+ +++ ++++
Y56A3A.27 161 LIRLDEKTVAAVDCRSELDLRIGSAFTRLQTLHLRNRFrdllgqndT 207
kglLSaGRVQsPaLrLvveRErEIraFkpekYweidAtlevGeaegfeak
++++S+G +Q+P+L++v +R + I++F+ e++w++ ++++
Y56A3A.27 208 SQVISYGSCQFPTLGFVTDRYKMIENFVSEPFWKLIVEHTR--------- 248
ltvkgkkiaaewkakesselklkdvderlldeeaaeavvkrvtgrpaeVa
+ k+ + w++++++++ ++v +l de+ +++ + ++++
Y56A3A.27 249 ---ESHKVEFLWDRNRLFDR--DTV-DILHDECKETKEAHVEKVA----- 287
sykekpkkksaPlPFttstLQqdAsrkLgfSAkkTmdiAQkLYEggdtkh
+kpk+k++P++++t++L+++ ++kL++SAk+Tm++A+kLY +g
Y56A3A.27 288 ---KKPKSKWRPQALDTVELEKLGISKLRMSAKQTMQVAEKLYSKG---- 330
ghtalITYpRTDStrLseeivlaleearaaidqhygseylseqksinpkq
+I+YpRT++++++ ++ + ++++ + + +e +++
Y56A3A.27 331 ----FISYPRTETNKFPAGLN-LTPLVQQQTQSNIWGDFANEV---LQNG 372
ykpksnnkkqeAHeAIrPTGdvfatpeelkdelkkiedEqkLYeLIwrRf
+p++++k +eAH++I+P ++ k +l++ d +k+YeL++r+f
Y56A3A.27 373 VNPRNGRKSDEAHPPIHPL------KFTEKHQLQG--DDWKVYELVVRHF 414
lAsqmadAvyeqtsveldiagGekFkasGkrvlleaGwlevyeeaegdeE
lA+ ++dA++e+t v l+++ ekF asG r +++ G+l+vy +
Y56A3A.27 415 LACVSQDAQGEETMVNLTVGT-EKFHASGLR-IRDMGYLKVYVY------ 456
ldeeeddedelLPklkkGdeltiekielkeheTkPPaRYTEAsLikaLEk
e+++ +lLP + +G+++t ++++ +++T+ P TEA+Li++++k
Y56A3A.27 457 ----EKWGNRLLPTYTEGERFTDFELKIGDGKTQAPDFLTEADLISLMDK 502
eGIGRPsTyaeiikkllidRgY.glgteatlaptilglsvielLekkfek
GIG+++T+ae+i+k+ R Y g+ +++l p++lgl+ +++++ ++
Y56A3A.27 503 YGIGTDATHAEHIEKIK-TREYiGVRPDGKLIPSFLGLALVDGYDDMGFA 551
IistdftaemEkdLdei<-*
+ ++d++a +E L+ei
Y56A3A.27 552 MSKPDLRANLEIGLKEI 568
HR1: domain 1 of 1, from 591 to 623: score 5.3, E = 3.2
*->vESnqklelLkqsLerLeelhqdsdpegesdte<-*
vES++k+ L qsL+r+ +++ ++ ++ ++
Y56A3A.27 591 VESERKIGVLSQSLQRYLDKNNQAGGGPGGPGG 623