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
Search:
32 projects found  

1 accessions found for Helicobacter pylori 51  

Data for CP000012  

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_1.hmm [HisKA]
Sequence database: CP000012.Gprot.fsa
per-sequence score cutoff: >= 26.8 [TC1]
per-domain score cutoff: >= 26.8 [TC2]
per-sequence Eval cutoff: [none]
per-domain Eval cutoff: [none]
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Query HMM: HisKA
Accession: PF00512.12
Description: His Kinase A (phosphoacceptor) domain
[HMM has been calibrated; E-values are empirical estimates]

Scores for complete sequences (score includes all domains):
Sequence Description Score E-value N
-------- ----------- ----- ------- ---
CP000012_0234 CDS_263794-262649 43.5 1.9e-12 1
CP000012_0038 CDS_44347-45459 31.1 6.2e-09 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP000012_0234 1/1 170 234 .. 1 87 [] 43.5 1.9e-12
CP000012_0038 1/1 163 221 .. 1 87 [] 31.1 6.2e-09

Alignments of top-scoring domains:
CP000012_0234: domain 1 of 1, from 170 to 234: score 43.5, E = 1.9e-12
*->akseflanlsHELRTPLtaIrgyaelLleeldkvlagdtelseeqrl
++++ a+l+HE+R+P+ +I+++a++Ll+ +++e++
CP000012_0 170 SMGKISAHLAHEIRNPVGSISLLASVLLK----------HANEKT-- 204

peLRledpeyreyletilreaerllrLindlLdlsrieag<-*
+ ++ +++++ r +r+i L +s+ +
CP000012_0 205 ----------KPIVVELQKALWRVERIIKATLLFSKGIQA 234

CP000012_0038: domain 1 of 1, from 163 to 221: score 31.1, E = 6.2e-09
*->akseflanlsHELRTPLtaIrgyaelLleeldkvlagdtelseeqrl
+ + fl n HEL+TP++++ + +++L++
CP000012_0 163 RIDHFLKNTTHELNTPMSTLVLSLKTLED------------------ 191

peLRledpeyreyletilreaerllrLindlLdlsrieag<-*
+ ++i+ +++r++ L + l l + +
CP000012_0 192 ----------NQQHHRIKIAIQRMSFLYRSLSYLVMQDIE 221


Histogram of all scores:
score obs exp (one = represents 5 sequences)
----- --- ---
-15 1 0|=
-14 8 0|==
-13 16 1|*===
-12 60 32|======*=====
-11 141 167|============================= *
-10 258 311|==================================================== *
-9 282 321|========================================================= *
-8 217 240|============================================ *
-7 175 151|==============================*====
-6 115 87|=================*=====
-5 63 47|=========*===
-4 29 25|====*=
-3 21 13|==*==
-2 10 7|=*
-1 7 3|*=
0 5 1|*
1 2 1|*
> 2 5 -|=


% Statistical details of theoretical EVD fit:
mu = -8.9758
lambda = 0.6525
chi-sq statistic = 67.0883
P(chi-square) = 1.613e-10

Total sequences searched: 1415

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


Acknowledgements:

This research is funded by:

Developed by: