hmmsearch - search a sequence database with a profile HMM
HMMER 2.3.2 (Oct 2003)
Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
Freely distributed under the GNU General Public License (GPL)
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HMM file: /home/projects/MicrobialGenomicsGroup/Packages/hmmdata-1.0.0.package/Resources/noarch/TCS/HisKA_3.hmm [HisKA_3]
Sequence database: CP001103.Gprot.fsa
per-sequence score cutoff: >= 30.1 [TC1]
per-domain score cutoff: >= 30.1 [TC2]
per-sequence Eval cutoff: [none]
per-domain Eval cutoff: [none]
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Query HMM: HisKA_3
Accession: PF07730.2
Description: Histidine kinase
[HMM has been calibrated; E-values are empirical estimates]
Scores for complete sequences (score includes all domains):
Sequence Description Score E-value N
-------- ----------- ----- ------- ---
CP001103_3818 CDS_4148916-4150682 68.0 9.1e-20 1
CP001103_3336 CDS_3618577-3619845 65.8 4.2e-19 1
CP001103_1504 CDS_1624607-1625950 36.6 1.7e-10 2
Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP001103_3818 1/1 376 445 .. 1 70 [] 68.0 9.1e-20
CP001103_3336 1/1 223 291 .. 1 70 [] 65.8 4.2e-19
CP001103_1504 2/2 242 307 .. 1 70 [] 33.1 1.8e-09
Alignments of top-scoring domains:
CP001103_3818: domain 1 of 1, from 376 to 445: score 68.0, E = 9.1e-20
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpe..eareald
ER+ IARELHDs++Q+Ls +k+q+ +++rl +k+ +++++++ +d
CP001103_3 376 ERTVIARELHDSLAQALSYLKIQVTRLQRLQ--QKESAqeQIDQVID 420
eirelarealaevRrllgdLRpaal<-*
e++ + a++e+R+ll+++R +
CP001103_3 421 ELKNGLGAAYSELRELLTTFRLKLD 445
CP001103_3336: domain 1 of 1, from 223 to 291: score 65.8, E = 4.2e-19
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+RI R+LHD+ g++Ls+i+l+++la +l+ ++ eea ++++++
CP001103_3 223 ERERIGRDLHDVAGHALSSISLKAQLADKLIS-KDKIEEAHREVRAL 268
relarealaevRrllgdLRpaal<-*
++l++ l+++R++++d++ l
CP001103_3 269 AQLSQSLLSDIRQAVSDIKQLSL 291
CP001103_1504: domain 2 of 2, from 242 to 307: score 33.1, E = 1.8e-09
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+ +ARELHD vgQ L+ ik ++ + ++ ++ ++ +
CP001103_1 242 ERNYLARELHDNVGQLLTTIKAHAYILVNTK--ERS--VVELSAQKV 284
relarealaevRrllgdLRpaal<-*
+ ++++ + +R l +L+p +l
CP001103_1 285 QVMSHQISDAIRKLTAHLHPLVL 307
Histogram of all scores:
score obs exp (one = represents 15 sequences)
----- --- ---
-15 3 0|=
-14 82 0|======
-13 181 0|=============
-12 216 45|==*============
-11 268 373|================== *
-10 754 865|=================================================== *
-9 862 983|==========================================================*
-8 583 757|======================================= *
-7 421 476|============================= *
-6 265 269|=================*
-5 230 144|=========*======
-4 100 75|====*==
-3 41 38|==*
-2 35 19|=*=
-1 11 10|*
0 7 5|*
1 2 2|*
2 2 1|*
3 2 0|=
4 2 0|=
5 1 0|=
> 6 4 -|=
% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 816.0625
P(chi-square) = 0
Total sequences searched: 4072
Whole sequence top hits:
tophits_s report:
Total hits: 3
Satisfying E cutoff: 3
Total memory: 20K
Domain top hits:
tophits_s report:
Total hits: 3
Satisfying E cutoff: 3
Total memory: 21K
