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 putida GB-1  

Data for CP000926  

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: CP000926.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
-------- ----------- ----- ------- ---
CP000926_1655 CDS_1888801-1887905 72.5 6e-21 1
CP000926_0435 CDS_514107-516494 64.7 1.2e-18 1
CP000926_3108 CDS_3509268-3507994 55.2 7.6e-16 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP000926_1655 1/1 87 151 .. 1 70 [] 72.5 6e-21
CP000926_0435 1/1 599 666 .. 1 70 [] 64.7 1.2e-18
CP000926_3108 1/1 229 295 .. 1 70 [] 55.2 7.6e-16

Alignments of top-scoring domains:
CP000926_1655: domain 1 of 1, from 87 to 151: score 72.5, E = 6e-21
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+++ RELHD +gQ L+a+klql++++ ++ p+e++ + d++
CP000926_1 87 ERQHLGRELHDDIGQLLTAAKLQLQWLQ-----RRMPDELQNHCDAL 128

relarealaevRrllgdLRpaal<-*
r +++++l vR++ L p +l
CP000926_1 129 RSTLDDTLGNVRDVSALLNPRQL 151

CP000926_0435: domain 1 of 1, from 599 to 666: score 64.7, E = 1.2e-18
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
E aRIARE HD++gQ+L+++kl +++++ ++ ++ ++ + e+l +
CP000926_0 599 EKARIAREVHDELGQMLTVLKLEVSMCELAF--AELDPGLNERLSSM 643

relarealaevRrllgdLRpaal<-*
++l+ + + vR+++++LRp++l
CP000926_0 644 KRLIAQLFQLVRDVATALRPPIL 666

CP000926_3108: domain 1 of 1, from 229 to 295: score 55.2, E = 7.6e-16
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+ +A+ LHD +gQ L++++ ql l+r+++ + p+ + ++++++
CP000926_3 229 ERTQLAQTLHDDLGQYLAGMRAQLCLLRMVA---DQPAVVTQTAHAL 272

relarealaevRrllgdLRpaal<-*
+ +++ ++ R+l+++L p al
CP000926_3 273 EFNCERLQQGFRALVHNLYPVAL 295


Histogram of all scores:
score obs exp (one = represents 16 sequences)
----- --- ---
-14 6 0|=
-13 69 0|=====
-12 117 60|===*====
-11 215 495|============== *
-10 590 1150|===================================== *
-9 927 1306|==========================================================*
-8 862 1006|====================================================== *
-7 743 632|=======================================*=======
-6 587 358|======================*==============
-5 507 192|===========*====================
-4 279 100|======*===========
-3 203 51|===*=========
-2 111 26|=*=====
-1 78 13|*====
0 46 6|*==
1 21 3|*=
2 16 1|*
3 11 0|=
4 5 0|=
5 4 0|=
6 4 0|=
7 2 0|=
> 8 6 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 2867.5830
P(chi-square) = 0

Total sequences searched: 5409

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: