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: AE009952.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
-------- ----------- ----- ------- ---
AE009952_2313 CDS_2590748-2592553 71.7 7.9e-21 1
AE009952_3769 CDS_4249083-4249820 55.2 5.6e-16 1
Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
AE009952_2313 1/1 400 467 .. 1 70 [] 71.7 7.9e-21
AE009952_3769 1/1 45 110 .. 1 70 [] 55.2 5.6e-16
Alignments of top-scoring domains:
AE009952_2313: domain 1 of 1, from 400 to 467: score 71.7, E = 7.9e-21
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER IARELHDs++QsLs +k+q++ +++++ ++ pe ++++
AE009952_2 400 ERSAIARELHDSIAQSLSCLKIQISCLQMQT--PDLPENSNLLIKQM 444
relarealaevRrllgdLRpaal<-*
r+ ++ a++++R+ll+++R
AE009952_2 445 RDELNIAYRQLRELLTTFRLKLN 467
AE009952_3769: domain 1 of 1, from 45 to 110: score 55.2, E = 5.6e-16
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
R+ ARELHD+vgQ+ ++i+ q++ ++rl+ + ++ + +++i
AE009952_3 45 TRHDVARELHDEVGQTVTVIRTQASIIKRLT--TQQ--PVLTSAEMI 87
relarealaevRrllgdLRpaal<-*
+++a + ++ v ++l L paal
AE009952_3 88 ETAALRVYDGVHDVLAKLWPAAL 110
Histogram of all scores:
score obs exp (one = represents 14 sequences)
----- --- ---
-16 1 0|=
-15 2 0|=
-14 53 0|====
-13 152 0|===========
-12 180 45|===*=========
-11 337 374|========================= *
-10 595 869|=========================================== *
-9 807 987|==========================================================*
-8 595 761|=========================================== *
-7 474 478|==================================*
-6 349 270|===================*=====
-5 250 145|==========*=======
-4 115 75|=====*===
-3 69 39|==*==
-2 44 19|=*==
-1 30 10|*==
0 18 5|*=
1 12 2|*
2 2 1|*
3 0 0|
4 2 0|=
> 5 3 -|=
% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 796.1375
P(chi-square) = 0
Total sequences searched: 4090
Whole sequence top hits:
tophits_s report:
Total hits: 2
Satisfying E cutoff: 2
Total memory: 20K
Domain top hits:
tophits_s report:
Total hits: 2
Satisfying E cutoff: 2
Total memory: 21K
