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  

Data for CP001680  

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: CP001680.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
-------- ----------- ----- ------- ---
CP001680_0228 CDS_259230-258085 43.5 1.9e-12 1
CP001680_0033 CDS_36743-37855 31.5 4.7e-09 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP001680_0228 1/1 170 234 .. 1 87 [] 43.5 1.9e-12
CP001680_0033 1/1 163 221 .. 1 87 [] 31.5 4.7e-09

Alignments of top-scoring domains:
CP001680_0228: 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++
CP001680_0 170 SMGKISAHLAHEIRNPVGSISLLASVLLK----------HANEKT-- 204

peLRledpeyreyletilreaerllrLindlLdlsrieag<-*
+ ++ +++++ r +r+i L +s+ +
CP001680_0 205 ----------KPIVVELQKALWRVERIIKATLLFSKGIQA 234

CP001680_0033: domain 1 of 1, from 163 to 221: score 31.5, E = 4.7e-09
*->akseflanlsHELRTPLtaIrgyaelLleeldkvlagdtelseeqrl
+ + fl n HEL+TP++a+ + +++L++
CP001680_0 163 RIDHFLKNTTHELNTPMSALVLSLKTLED------------------ 191

peLRledpeyreyletilreaerllrLindlLdlsrieag<-*
+ ++i+ +++r++ L + l l + +
CP001680_0 192 ----------NQQHRRIKIAIQRMSFLYRSLSYLVMQDIE 221


Histogram of all scores:
score obs exp (one = represents 5 sequences)
----- --- ---
-14 3 0|=
-13 19 1|*===
-12 61 32|======*======
-11 134 166|=========================== *
-10 264 308|===================================================== *
-9 269 319|====================================================== *
-8 225 238|============================================= *
-7 175 150|=============================*=====
-6 110 86|=================*====
-5 63 47|=========*===
-4 38 25|====*===
-3 14 13|==*
-2 10 7|=*
-1 7 3|*=
0 6 1|*=
1 3 1|*
> 2 4 -|=


% Statistical details of theoretical EVD fit:
mu = -8.9758
lambda = 0.6525
chi-sq statistic = 70.3208
P(chi-square) = 3.844e-11

Total sequences searched: 1405

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: