Acidobacteria Actinobacteria Alphaproteobacteria
Aquificae Bacteroidetes/Chlorobi Betaproteobacteria
Chlamydiae/Verrucomicrobia Chloroflexi Cyanobacteria
Deinococcus-Thermus Deltaproteobacteria Epsilonproteobacteria
Firmicutes Fusobacteria Gammaproteobacteria
Other Bacteria Planctomycetes Spirochaetes
Thermotogae
Classification of phyla is from NCBI page
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Data for CP000481  

Available Atlases
Other Plots
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: CP000481.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
-------- ----------- ----- ------- ---
CP000481_0192 CDS_206252-207448 76.5 1.6e-22 1
CP000481_0513 CDS_548922-550100 52.0 2.6e-15 1
CP000481_0971 CDS_1074246-1072492 45.1 2.7e-13 2

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP000481_0192 1/1 192 259 .. 1 70 [] 76.5 1.6e-22
CP000481_0513 1/1 182 247 .. 1 70 [] 52.0 2.6e-15
CP000481_0971 2/2 348 414 .. 1 70 [] 44.9 3.3e-13

Alignments of top-scoring domains:
CP000481_0192: domain 1 of 1, from 192 to 259: score 76.5, E = 1.6e-22
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER RIAR+LHD +g+sL+ i++++ la+rl+ d+d +ar +++ +
CP000481_0 192 ERLRIARDLHDLLGHSLTTITVKAALAARLA--DRDLTRARNEIADV 236

relarealaevRrllgdLRpaal<-*
++lar++la+vR+++ ++R+ l
CP000481_0 237 EALARRTLADVRAAVAGYRDVRL 259

CP000481_0513: domain 1 of 1, from 182 to 247: score 52.0, E = 2.6e-15
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
R+RIARELHD+v Q+L+a l l+ + ++ + + ++r+++ e
CP000481_0 182 DRERIARELHDTVIQRLFATGLALQSVVPIT--EVP--AVRKQILET 224

relarealaevRrllgdLRpaal<-*
+ ++e+++++R ++ L p+ +
CP000481_0 225 VADLDETIRQIRTTIFSLEPPPE 247

CP000481_0971: domain 2 of 2, from 348 to 414: score 44.9, E = 3.3e-13
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+R+ARE+HD+++Q L+++ ++ + + +++p +++ l++i
CP000481_0 348 ERRRLAREIHDGIAQELASLGYRIDDQIANA--TAAP-GLAADLRAI 391

relarealaevRrllgdLRpaal<-*
r+ +++ ++e+R + dLR +
CP000481_0 392 RADVSRLITELRLSIFDLRSEVG 414


Histogram of all scores:
score obs exp (one = represents 6 sequences)
----- --- ---
-14 1 0|=
-13 8 0|==
-12 28 24|===*=
-11 53 197|========= *
-10 176 458|============================== *
-9 287 520|================================================ *
-8 303 401|=================================================== *
-7 320 252|=========================================*============
-6 269 142|=======================*=====================
-5 255 76|============*==============================
-4 164 39|======*=====================
-3 93 20|===*============
-2 66 10|=*=========
-1 42 5|*======
0 32 2|*=====
1 21 1|*===
2 14 0|===
3 9 0|==
4 1 0|=
5 2 0|=
6 0 0|
7 2 0|=
8 2 0|=
9 1 0|=
10 2 0|=
11 1 0|=
12 0 0|
13 0 0|
> 14 5 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 2138.2515
P(chi-square) = 0

Total sequences searched: 2157

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


Acknowledgements:

This research is funded by:

Developed by: