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:
76 projects found  

4 accessions found for Burkholderia ambifaria AMMD  

Data for CP000441  

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: CP000441.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
-------- ----------- ----- ------- ---
CP000441_0555 CDS_638203-636080 67.4 7.9e-20 1
CP000441_1720 CDS_1958754-1960133 66.2 1.8e-19 1
CP000441_2102 CDS_2372178-2370391 57.4 7.4e-17 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP000441_0555 1/1 494 566 .. 1 70 [] 67.4 7.9e-20
CP000441_1720 1/1 253 323 .. 1 70 [] 66.2 1.8e-19
CP000441_2102 1/1 382 449 .. 1 70 [] 57.4 7.4e-17

Alignments of top-scoring domains:
CP000441_0555: domain 1 of 1, from 494 to 566: score 67.4, E = 7.9e-20
*->ERaRIARELHDsvgQsLsaiklqlelarrllds...dkdpeeareal
E +RIARELHD +gQ+L+a+k+ l++++++l+ ++++ +++ + +l
CP000441_0 494 EKTRIARELHDDLGQQLTALKMDLSVIEQQLRApgrAQPNDDVLSHL 540

deirelarealaevRrllgdLRpaal<-*
+ +r+l++ + a vRr++ dLRp l
CP000441_0 541 QGMRRLIDATVASVRRIAADLRPVML 566

CP000441_1720: domain 1 of 1, from 253 to 323: score 66.2, E = 1.8e-19
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpe...eareal
ER+R++RELHD+++Q++ ++kl+le a++++ ++ + + +ea++al
CP000441_1 253 ERERLSRELHDGISQMMVSAKLMLESALARF--ERGATrmpEAEQAL 297

deirelarealaevRrllgdLRpaal<-*
++ + + ++l+evRr+ ++LRpa l
CP000441_1 298 ATGVGRLGDTLREVRRISHALRPAML 323

CP000441_2102: domain 1 of 1, from 382 to 449: score 57.4, E = 7.4e-17
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
E +RIARELHD+++Q+L+ +k le+++ ++ + d++++++ ++++
CP000441_2 382 EQRRIARELHDELAQTLATLKNDLEWLLDHV--PQDDAPLARKIAAM 426

relarealaevRrllgdLRpaal<-*
++lar a + +Rr+++dLRp l
CP000441_2 427 HALARGAVTATRRIASDLRPLML 449


Histogram of all scores:
score obs exp (one = represents 7 sequences)
----- --- ---
-14 2 0|=
-13 20 0|===
-12 35 26|===*=
-11 64 215|========== *
-10 274 498|======================================== *
-9 398 566|========================================================= *
-8 362 436|==================================================== *
-7 349 274|=======================================*==========
-6 273 155|======================*================
-5 255 83|===========*=========================
-4 117 43|======*==========
-3 73 22|===*=======
-2 46 11|=*=====
-1 24 5|*===
0 20 2|*==
1 12 1|*=
2 8 0|==
3 5 0|=
4 2 0|=
5 0 0|
6 2 0|=
7 1 0|=
> 8 4 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 1136.3295
P(chi-square) = 0

Total sequences searched: 2346

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: