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  

2 accessions found for Vibrio cholerae M66-2  

Data for CP001233  

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: CP001233.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
-------- ----------- ----- ------- ---
CP001233_1211 CDS_1308215-1309570 59.0 2.8e-17 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP001233_1211 1/1 250 315 .. 1 70 [] 59.0 2.8e-17

Alignments of top-scoring domains:
CP001233_1211: domain 1 of 1, from 250 to 315: score 59.0, E = 2.8e-17
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
E +++ARELHD++ Q L + k +lel++ +l ++ + +l+
CP001233_1 250 EKKHLARELHDGINQLLVSSKCHLELLANQL--NDP--KQIVHLEKS 292

relarealaevRrllgdLRpaal<-*
++ + +a++evRr+ ++LRp+al
CP001233_1 293 QHSLMTAINEVRRISHHLRPSAL 315


Histogram of all scores:
score obs exp (one = represents 10 sequences)
----- --- ---
-15 2 0|=
-14 56 0|======
-13 94 0|==========
-12 106 29|==*========
-11 151 242|================ *
-10 404 563|========================================= *
-9 545 639|======================================================= *
-8 399 493|======================================== *
-7 313 310|==============================*=
-6 203 175|=================*===
-5 161 94|=========*=======
-4 85 49|====*====
-3 53 25|==*===
-2 35 12|=*==
-1 16 6|*=
0 6 3|*
1 8 1|*
2 6 0|=
3 2 0|=
4 1 0|=
5 1 0|=
> 6 3 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 468.9502
P(chi-square) = 0

Total sequences searched: 2650

Whole sequence top hits:
tophits_s report:
Total hits: 1
Satisfying E cutoff: 1
Total memory: 20K

Domain top hits:
tophits_s report:
Total hits: 1
Satisfying E cutoff: 1
Total memory: 21K


Acknowledgements:

This research is funded by:

Developed by: