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 Shewanella halifaxensis HAW-EB4  

Data for CP000931  

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: CP000931.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
-------- ----------- ----- ------- ---
CP000931_0175 CDS_204961-203201 77.7 1.4e-22 1
CP000931_0884 CDS_1105141-1103429 71.2 1.1e-20 1
CP000931_1969 CDS_2388257-2385051 52.9 2.7e-15 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP000931_0175 1/1 389 458 .. 1 70 [] 77.7 1.4e-22
CP000931_0884 1/1 366 435 .. 1 70 [] 71.2 1.1e-20
CP000931_1969 1/1 870 933 .. 1 70 [] 52.9 2.7e-15

Alignments of top-scoring domains:
CP000931_0175: domain 1 of 1, from 389 to 458: score 77.7, E = 1.4e-22
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpe.earealde
ERa IARELHDs++QsLs +k+q++l+ r ++ +k pe++++e++ e
CP000931_0 389 ERAIIARELHDSLAQSLSFLKVQMSLLTRKME-KKLPEeQIEETIVE 434

irelarealaevRrllgdLRpaal<-*
i+ +++a+ ++R+ll+++R +
CP000931_0 435 IKSGLNKAYLQLRELLTTFRLKLD 458

CP000931_0884: domain 1 of 1, from 366 to 435: score 71.2, E = 1.1e-20
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpe..eareald
ER IARELHDs+gQ Ls +k+q+ l+ + l dk +++a+e+l+
CP000931_0 366 ERGVIARELHDSLGQLLSFLKIQVNLLSKEL--DKTSKspRAAEQLQ 410

eirelarealaevRrllgdLRpaal<-*
ei e +++a+ ++R+ll+++R ++
CP000931_0 411 EINEGVNTAYVQLRELLSTFRLTIK 435

CP000931_1969: domain 1 of 1, from 870 to 933: score 52.9, E = 2.7e-15
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+ I+RELHD gQ+L+a k+ l+l +k + + +e+++ +
CP000931_1 870 ERKSISRELHDQFGQTLTATKINLQLY------KKFNYQEQERIESA 910

relarealaevRrllgdLRpaal<-*
+ ++ ++++R + +LRpa l
CP000931_1 911 ISITHTMIQQMRSISFNLRPALL 933


Histogram of all scores:
score obs exp (one = represents 17 sequences)
----- --- ---
-14 18 0|==
-13 99 0|======
-12 218 47|==*==========
-11 316 392|=================== *
-10 807 909|================================================ *
-9 951 1033|======================================================== *
-8 638 796|====================================== *
-7 454 500|=========================== *
-6 311 283|================*==
-5 220 151|========*====
-4 113 79|====*==
-3 53 40|==*=
-2 28 20|=*
-1 19 10|*=
0 12 5|*
1 10 2|*
2 3 1|*
3 4 0|=
> 4 4 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 743.3147
P(chi-square) = 0

Total sequences searched: 4278

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: