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 F1  

Data for CP000712  

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: CP000712.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
-------- ----------- ----- ------- ---
CP000712_3561 CDS_4037121-4038017 72.3 6.4e-21 2
CP000712_0436 CDS_511145-513532 64.4 1.4e-18 1
CP000712_3043 CDS_3479831-3478554 56.7 2.6e-16 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP000712_3561 2/2 87 151 .. 1 70 [] 71.7 1e-20
CP000712_0436 1/1 599 666 .. 1 70 [] 64.4 1.4e-18
CP000712_3043 1/1 229 295 .. 1 70 [] 56.7 2.6e-16

Alignments of top-scoring domains:
CP000712_3561: domain 2 of 2, from 87 to 151: score 71.7, E = 1e-20
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER++++RELHD +gQ L+a+klql++++ ++ pe ++ + d++
CP000712_3 87 ERQHLSRELHDDIGQLLTAAKLQLQWLQ-----RRMPEDLQGHCDAL 128

relarealaevRrllgdLRpaal<-*
r +++++l vR++ L p +l
CP000712_3 129 RSTLDDTLGNVRDVSALLNPRQL 151

CP000712_0436: domain 1 of 1, from 599 to 666: score 64.4, E = 1.4e-18
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
E aRIARE HD++gQ+L+++kl +++++ ++ ++ ++ + ++l+ +
CP000712_0 599 EKARIAREVHDELGQMLTVLKLEVSMCELAY--AELDPGLNDRLASM 643

relarealaevRrllgdLRpaal<-*
++l+ + + vR+++++LRp++l
CP000712_0 644 KRLIAQLFQLVRDVATALRPPIL 666

CP000712_3043: domain 1 of 1, from 229 to 295: score 56.7, E = 2.6e-16
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+ +A+ LHD +gQ L++++ ql l+r+++ + pe + ++++++
CP000712_3 229 ERTQLAQTLHDDLGQYLAGMRAQLCLLRMVA---EQPEVVTQTAQAL 272

relarealaevRrllgdLRpaal<-*
+ +++ ++ R+l+++L p al
CP000712_3 273 EFNCERLQQGFRALVHNLYPVAL 295


Histogram of all scores:
score obs exp (one = represents 15 sequences)
----- --- ---
-14 10 0|=
-13 61 0|=====
-12 117 58|===*====
-11 223 481|=============== *
-10 579 1116|======================================= *
-9 884 1268|==========================================================*
-8 803 977|====================================================== *
-7 730 614|========================================*========
-6 583 347|=======================*===============
-5 499 186|============*=====================
-4 278 97|======*============
-3 193 50|===*=========
-2 92 25|=*=====
-1 79 13|*=====
0 41 6|*==
1 25 3|*=
2 18 1|*=
3 15 0|=
4 5 0|=
5 5 0|=
6 2 0|=
7 2 0|=
8 0 0|
9 3 0|=
10 1 0|=
11 0 0|
12 0 0|
> 13 4 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 2734.8823
P(chi-square) = 0

Total sequences searched: 5252

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: