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  

2 accessions found for Campylobacter lari RM2100  

Data for CP000932  

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: CP000932.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
-------- ----------- ----- ------- ---
CP000932_0560 CDS_567689-568705 39.9 2.1e-11 1
CP000932_0740 CDS_741874-743118 33.2 1.6e-09 1
CP000932_0762 CDS_763406-764695 30.8 8e-09 1
CP000932_1056 CDS_1056719-1055496 30.6 9e-09 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP000932_0560 1/1 131 195 .. 1 87 [] 39.9 2.1e-11
CP000932_0740 1/1 210 268 .. 1 87 [] 33.2 1.6e-09
CP000932_0762 1/1 227 292 .. 1 87 [] 30.8 8e-09
CP000932_1056 1/1 198 262 .. 1 87 [] 30.6 9e-09

Alignments of top-scoring domains:
CP000932_0560: domain 1 of 1, from 131 to 195: score 39.9, E = 2.1e-11
*->akseflanlsHELRTPLtaIrgyaelLleeldkvlagdtelseeqrl
+++ +a+l+HE+R+P+ +I++++++L e +se ++
CP000932_0 131 SMGTVAAHLAHEIRNPIGSISLLSSTLFE-----------RSELKN- 165

peLRledpeyreyletilreaerllrLindlLdlsrieag<-*
+ ++ i++++ r +r++n L +++ +
CP000932_0 166 ----------KHIVLEIQKAISRVERIVNSTLLFTKGVHV 195

CP000932_0740: domain 1 of 1, from 210 to 268: score 33.2, E = 1.6e-09
*->akseflanlsHELRTPLtaIrgyaelLleeldkvlagdtelseeqrl
+++ fl+n+ HEL+TP+t + ++e+L++
CP000932_0 210 SRQFFLRNIMHELKTPITKGLITLEMLED------------------ 238

peLRledpeyreyletilreaerllrLindlLdlsrieag<-*
+y +++ + +rl+ Lin++ +++i +g
CP000932_0 239 ----------SKYKKRLVGAFNRLEILINEFAAIEQITSG 268

CP000932_0762: domain 1 of 1, from 227 to 292: score 30.8, E = 8e-09
*->akseflanlsHELRTPLtaIrgyaelLleeldkvlagdtelseeqrl
++s ++++sHE+++P+++I + ++ L+e t+ +
CP000932_0 227 QLSNIISAISHEIKNPISVIDLSLQSLKE---------TNDENMK-- 262

peLRledpeyreyletilreaerllrLindlLdlsrieag<-*
+le+i++++ +++L l + +
CP000932_0 263 ----------LFLLEKIHKQSIKINQLTHKLNFVFNLNFN 292

CP000932_1056: domain 1 of 1, from 198 to 262: score 30.6, E = 9e-09
*->akseflanlsHELRTPLtaIrgyaelLleeldkvlagdtelseeqrl
++ f+ + HE++TP++aI++ +e L++ +++ e+
CP000932_1 198 FLNNFIKDTTHEINTPISAILMSVENLER----------KKNFEE-- 232

peLRledpeyreyletilreaerllrLindlLdlsrieag<-*
++l++++ +a l++L +dl l +a
CP000932_1 233 ----------VKALKRVKIAALTLSHLYSDLTFLNFSQAY 262


Histogram of all scores:
score obs exp (one = represents 5 sequences)
----- --- ---
-15 1 0|=
-14 3 0|=
-13 14 1|*==
-12 70 34|======*=======
-11 165 178|================================= *
-10 281 330|========================================================= *
-9 280 341|======================================================== *
-8 239 255|================================================ *
-7 164 161|================================*
-6 112 92|==================*====
-5 62 50|=========*===
-4 52 27|=====*=====
-3 30 14|==*===
-2 9 7|=*
-1 2 3|*
0 10 2|*=
1 2 1|*
2 1 0|=
> 3 7 -|==


% Statistical details of theoretical EVD fit:
mu = -8.9758
lambda = 0.6525
chi-sq statistic = 103.8289
P(chi-square) = 9.309e-18

Total sequences searched: 1504

Whole sequence top hits:
tophits_s report:
Total hits: 4
Satisfying E cutoff: 4
Total memory: 20K

Domain top hits:
tophits_s report:
Total hits: 4
Satisfying E cutoff: 4
Total memory: 22K


Acknowledgements:

This research is funded by:

Developed by: