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 Pseudomonas fluorescens Pf0-1  

Data for CP000094  

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: CP000094.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
-------- ----------- ----- ------- ---
CP000094_3951 CDS_4483747-4484718 66.9 2.8e-19 1
CP000094_5122 CDS_5762377-5759978 64.2 1.8e-18 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP000094_3951 1/1 113 177 .. 1 70 [] 66.9 2.8e-19
CP000094_5122 1/1 600 667 .. 1 70 [] 64.2 1.8e-18

Alignments of top-scoring domains:
CP000094_3951: domain 1 of 1, from 113 to 177: score 66.9, E = 2.8e-19
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+R++RELHD +gQ L+a+klq+e+++ ++ p+ +e+ +
CP000094_3 113 ERHRLSRELHDDIGQLLTAAKLQSEWLK-----RRLPADMQEHCSVL 154

relarealaevRrllgdLRpaal<-*
e+++e+l+ vR++ L p +l
CP000094_3 155 CETLEETLNKVRDVSAILNPRQL 177

CP000094_5122: domain 1 of 1, from 600 to 667: score 64.2, E = 1.8e-18
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
E aRIARE HD++gQ+L+++kl +++++ ++ + ++ + e+l +
CP000094_5 600 EKARIAREVHDELGQMLTVLKLETSMCELAY--AQLDPGLNERLNSM 644

relarealaevRrllgdLRpaal<-*
++l+ + + vR+++++LRp++l
CP000094_5 645 KRLIAQLFQLVRDVATALRPPIL 667


Histogram of all scores:
score obs exp (one = represents 19 sequences)
----- --- ---
-14 10 0|=
-13 65 0|====
-12 142 64|===*====
-11 263 525|============== *
-10 748 1219|======================================== *
-9 1065 1385|========================================================= *
-8 851 1067|============================================= *
-7 742 671|===================================*====
-6 595 379|===================*============
-5 522 203|==========*=================
-4 268 106|=====*=========
-3 166 54|==*======
-2 117 27|=*=====
-1 66 14|*===
0 51 7|*==
1 16 3|*
2 14 1|*
3 9 0|=
4 9 0|=
5 4 0|=
6 1 0|=
7 1 0|=
8 2 0|=
9 2 0|=
10 1 0|=
11 1 0|=
12 2 0|=
13 0 0|
> 14 3 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 2361.9285
P(chi-square) = 0

Total sequences searched: 5736

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: