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: BA000019.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
-------- ----------- ----- ------- ---
BA000019_4633 CDS_5541100-5539895 98.4 1.4e-28 1
BA000019_2134 CDS_2564524-2567358 83.5 3.4e-24 1
Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
BA000019_4633 1/1 203 270 .. 1 70 [] 98.4 1.4e-28
BA000019_2134 1/1 745 812 .. 1 70 [] 83.5 3.4e-24
Alignments of top-scoring domains:
BA000019_4633: domain 1 of 1, from 203 to 270: score 98.4, E = 1.4e-28
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+RIARE+HDs+g+sL+a++lqle+a++l+ +++p +a++ l ++
BA000019_4 203 ERNRIAREIHDSLGHSLTALNLQLETALKLA--QSNPNKAQTFLVRA 247
relarealaevRrllgdLRpaal<-*
+el+++al++vR+ ++++R l
BA000019_4 248 KELGSKALQDVRNSVSAMRSHPL 270
BA000019_2134: domain 1 of 1, from 745 to 812: score 83.5, E = 3.4e-24
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+R+ARE+HD+++Q++++i q+++a+++l ++d e+ + +ld i
BA000019_2 745 ERNRMAREIHDTLAQAFTGILAQVGAAKQVL--TDDLEATESHLDLI 789
relarealaevRrllgdLRpaal<-*
+elar++l e+Rr + +LRp+ l
BA000019_2 790 KELARTGLVEARRSVVALRPQLL 812
Histogram of all scores:
score obs exp (one = represents 17 sequences)
----- --- ---
-14 49 0|===
-13 147 0|=========
-12 250 59|===*===========
-11 379 491|======================= *
-10 915 1141|====================================================== *
-9 989 1296|==========================================================*
-8 803 999|================================================ *
-7 615 628|====================================*
-6 414 355|====================*====
-5 361 190|===========*==========
-4 188 99|=====*======
-3 113 51|==*====
-2 77 26|=*===
-1 31 13|*=
0 13 6|*
1 4 3|*
2 9 1|*
3 3 0|=
4 2 0|=
5 1 0|=
6 2 0|=
7 0 0|
8 0 0|
> 9 3 -|=
% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 1227.9536
P(chi-square) = 0
Total sequences searched: 5368
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
