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  

2 accessions found for Burkholderia pseudomallei 1710b  

Data for CP000125  

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)
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file: /home/projects/MicrobialGenomicsGroup/Packages/hmmdata-1.0.0.package/Resources/noarch/TCS/HisKA_3.hmm [HisKA_3]
Sequence database: CP000125.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]
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

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
-------- ----------- ----- ------- ---
CP000125_1460 CDS_1781778-1783178 64.0 9.3e-19 1
CP000125_0126 CDS_153824-155683 62.0 3.5e-18 1
CP000125_0380 CDS_540635-539244 54.6 5.3e-16 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP000125_1460 1/1 253 323 .. 1 70 [] 64.0 9.3e-19
CP000125_0126 1/1 400 476 .. 1 70 [] 62.0 3.5e-18
CP000125_0380 1/1 256 324 .. 1 70 [] 54.6 5.3e-16

Alignments of top-scoring domains:
CP000125_1460: domain 1 of 1, from 253 to 323: score 64.0, E = 9.3e-19
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpe...eareal
ERaR+ARELHD+++Q++ ++kl+ e a+ +l + p+++++a++al
CP000125_1 253 ERARLARELHDGISQMMVSAKLMFESALERL--AHLPArenAAQAAL 297

deirelarealaevRrllgdLRpaal<-*
+ + ++l+evRr+ ++LRp+ l
CP000125_1 298 SKGIARLGDTLREVRRISHALRPTML 323

CP000125_0126: domain 1 of 1, from 400 to 476: score 62.0, E = 3.5e-18
*->ERaRIARELHDsvgQsLsaiklqlelarrllds......dkdpe..e
E +RIARELHD +gQ+L+a+k+ +++++ +l + +++++++p+ +
CP000125_0 400 EKTRIARELHDDLGQQLTALKMDVSAVAIAL-AryrdtqADAPPiaA 445

arealdeirelarealaevRrllgdLRpaal<-*
++++l+ +r+l++ + a vRr++ dLRp l
CP000125_0 446 VEQQLHGMRRLIDSTVASVRRIAADLRPVML 476

CP000125_0380: domain 1 of 1, from 256 to 324: score 54.6, E = 5.3e-16
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpe..eareald
E +RIARELHD +gQ+L+a+k+ + l+ l kd++ +l
CP000125_0 256 EKTRIARELHDDLGQQLTALKMAVTLVDNEL---KDAGwaSRTSRLP 299

eirelarealaevRrllgdLRpaal<-*
++ +l+ + l+ vRr++ dLRp l
CP000125_0 300 NVYALIGQLLDSVRRIAADLRPVML 324


Histogram of all scores:
score obs exp (one = represents 7 sequences)
----- --- ---
-15 1 0|=
-14 10 0|==
-13 33 0|=====
-12 44 29|====*==
-11 82 239|============ *
-10 220 555|================================ *
-9 361 630|==================================================== *
-8 354 485|=================================================== *
-7 356 305|===========================================*=======
-6 276 172|========================*===============
-5 324 92|=============*=================================
-4 174 48|======*==================
-3 124 24|===*==============
-2 81 12|=*==========
-1 68 6|*=========
0 29 3|*====
1 23 1|*===
2 10 0|==
3 11 0|==
4 7 0|=
5 5 0|=
6 8 0|==
7 0 0|
8 4 0|=
9 1 0|=
10 1 0|=
> 11 4 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 2781.6572
P(chi-square) = 0

Total sequences searched: 2611

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: