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:
264 projects found  

1 accessions found for Salmonella enterica subsp. arizonae serovar 62:z4,z23:--  

Data for CP000880  

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: CP000880.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
-------- ----------- ----- ------- ---
CP000880_1138 CDS_1152979-1151081 77.1 2.1e-22 1
CP000880_0385 CDS_408413-406716 70.1 2.5e-20 1
CP000880_3700 CDS_3791353-3792855 65.1 7.7e-19 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP000880_1138 1/1 424 492 .. 1 70 [] 77.1 2.1e-22
CP000880_0385 1/1 361 428 .. 1 70 [] 70.1 2.5e-20
CP000880_3700 1/1 304 370 .. 1 70 [] 65.1 7.7e-19

Alignments of top-scoring domains:
CP000880_1138: domain 1 of 1, from 424 to 492: score 77.1, E = 2.1e-22
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ERa IARELHDs++QsLs +k+q++ ++++ d+ pe re l +i
CP000880_1 424 ERATIARELHDSIAQSLSCMKMQVSCLQMQG--DALPESSRELLSQI 468

relarealaevRrllgdLR.paal<-*
r ++ + a++R+ll+++R ++
CP000880_1 469 RNELNCSWAQLRELLTTFRlQLTE 492

CP000880_0385: domain 1 of 1, from 361 to 428: score 70.1, E = 2.5e-20
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ERa IARELHDs++Q Ls +++ql l++r++ ++d++ a+ ++
CP000880_0 361 ERATIARELHDSLAQVLSYLRIQLTLLKRAI--PEDNACAQSIMTDF 405

relarealaevRrllgdLRpaal<-*
+++++a++++R+ll+++R +
CP000880_0 406 SRALNDAYRQLRELLTTFRLTLQ 428

CP000880_3700: domain 1 of 1, from 304 to 370: score 65.1, E = 7.7e-19
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
R+ ARELHD +gQ+++ai+ q++ ++rl+ +d++ +++ + i
CP000880_3 304 VRRDVARELHDDIGQTITAIRTQAGIVQRLA---ADNGGVKQSGQLI 347

relarealaevRrllgdLRpaal<-*
++l+ ++ vRrllg+LRp +l
CP000880_3 348 EQLSLGVYDAVRRLLGRLRPRQL 370


Histogram of all scores:
score obs exp (one = represents 14 sequences)
----- --- ---
-15 4 0|=
-14 69 0|=====
-13 204 0|===============
-12 227 50|===*=============
-11 323 413|======================== *
-10 730 959|===================================================== *
-9 799 1089|==========================================================*
-8 638 839|============================================== *
-7 500 527|==================================== *
-6 373 298|=====================*=====
-5 282 160|===========*=========
-4 137 83|=====*====
-3 88 43|===*===
-2 57 21|=*===
-1 39 11|*==
0 21 5|*=
1 6 2|*
2 4 1|*
3 2 0|=
4 1 0|=
> 5 6 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 1179.1954
P(chi-square) = 0

Total sequences searched: 4510

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: