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:
132 projects found  

1 accessions found for Rhodopseudomonas palustris HaA2  

Data for CP000250  

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: CP000250.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
-------- ----------- ----- ------- ---
CP000250_3053 CDS_3496354-3498759 58.8 5.5e-17 1
CP000250_4015 CDS_4603290-4605617 57.5 1.3e-16 1
CP000250_4424 CDS_5039903-5041033 48.8 5e-14 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP000250_3053 1/1 603 670 .. 1 70 [] 58.8 5.5e-17
CP000250_4015 1/1 578 644 .. 1 70 [] 57.5 1.3e-16
CP000250_4424 1/1 176 242 .. 1 70 [] 48.8 5e-14

Alignments of top-scoring domains:
CP000250_3053: domain 1 of 1, from 603 to 670: score 58.8, E = 5.5e-17
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER RI+ +LHD v+Q+L+++ l +e++ + ++d +a++ l+ +
CP000250_3 603 ERSRISSDLHDAVSQTLFSAVLIAETLPEQW--KRDRTKAEALLTDL 647

relarealaevRrllgdLRpaal<-*
++l r al+e+R+ll++ R +l
CP000250_3 648 ARLNRSALDEMRDLLSRVRSRDL 670

CP000250_4015: domain 1 of 1, from 578 to 644: score 57.5, E = 1.3e-16
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER RIARELHD++gQsL+++ l+ e + +++ d++e++ +++ +
CP000250_4 578 ERLRIARELHDTLGQSLTLLQLGFENLGQVA---PDNGELQNRIAGM 621

relarealaevRrllgdLRpaal<-*
r l + ++v rl++++Rp+al
CP000250_4 622 RSLTADIGQQVNRLAWEIRPTAL 644

CP000250_4424: domain 1 of 1, from 176 to 242: score 48.8, E = 5e-14
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+RIARE+HD +gQs +++ l+l+ ++r + + ++ ++ +
CP000250_4 176 ERQRIAREMHDNLGQSVTLVQLGLDSIARSAS-AQS--DIASKAASL 219

relarealaevRrllgdLRpaal<-*
+++ ++ + + r++++ Rp+al
CP000250_4 220 KRITHDMSRSLHRIAWEVRPTAL 242


Histogram of all scores:
score obs exp (one = represents 14 sequences)
----- --- ---
-14 7 0|=
-13 50 0|====
-12 101 52|===*====
-11 174 429|============= *
-10 546 995|======================================= *
-9 798 1130|========================================================= *
-8 714 871|=================================================== *
-7 670 547|=======================================*========
-6 551 310|======================*=================
-5 431 166|===========*===================
-4 236 86|======*==========
-3 158 44|===*========
-2 90 22|=*=====
-1 60 11|*====
0 34 5|*==
1 18 2|*=
2 18 1|*=
3 14 0|=
4 5 0|=
5 1 0|=
6 2 0|=
> 7 5 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 2238.9373
P(chi-square) = 0

Total sequences searched: 4683

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: