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:
35 projects found  

1 accessions found for Geobacter uraniireducens Rf4  

Data for CP000698  

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: CP000698.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
-------- ----------- ----- ------- ---
CP000698_0751 CDS_899254-901086 80.1 2.8e-23 1
CP000698_0735 CDS_875426-877408 40.5 1.3e-11 2
CP000698_2739 CDS_3238691-3237150 37.3 1.1e-10 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP000698_0751 1/1 400 467 .. 1 70 [] 80.1 2.8e-23
CP000698_0735 2/2 452 518 .. 1 70 [] 39.6 2.3e-11
CP000698_2739 1/1 306 371 .. 1 70 [] 37.3 1.1e-10

Alignments of top-scoring domains:
CP000698_0751: domain 1 of 1, from 400 to 467: score 80.1, E = 2.8e-23
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+RIAR++HD+v+Q L+++++ +++ ++l+ +++ e+ e+++
CP000698_0 400 ERRRIARDIHDGVAQDLAMMNMRASVWEHLV--HSNREKMTEEIKLF 444

relarealaevRrllgdLRpaal<-*
r+l+++ + evRr++ ++Rp +l
CP000698_0 445 RKLLHKNIGEVRRAIFAMRPVEL 467

CP000698_0735: domain 2 of 2, from 452 to 518: score 39.6, E = 2.3e-11
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+RI+ +LHD++ Q+L++++l+ ++++r l + +++ + +++++
CP000698_0 452 ERRRISHDLHDGLCQQLTGARLHFSVLERKL---EGAGRQQPEMTQL 495

relarealaevRrllgdLRpaal<-*
l++e+ + + +l ++L p ++
CP000698_0 496 SSLLEESVNHAYDLSRGLWPVEH 518

CP000698_2739: domain 1 of 1, from 306 to 371: score 37.3, E = 1.1e-10
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+RIA ELHD +gQ L +++++l++++++ +d e + l +
CP000698_2 306 ERRRIAAELHDNIGQDLVLARIKLGMLAKMP--LTD--EEAGILGNT 348

relarealaevRrllgdLRpaal<-*
re++ ++ vR l + + p++l
CP000698_2 349 REILGGMIQRVRFLTHMISPPIL 371


Histogram of all scores:
score obs exp (one = represents 16 sequences)
----- --- ---
-14 19 0|==
-13 92 0|======
-12 148 48|==*=======
-11 271 399|================= *
-10 707 926|============================================= *
-9 921 1052|==========================================================*
-8 634 810|======================================== *
-7 525 509|===============================*=
-6 366 288|=================*=====
-5 293 154|=========*=========
-4 146 80|====*=====
-3 98 41|==*====
-2 67 21|=*===
-1 31 10|*=
0 20 5|*=
1 7 2|*
> 2 12 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 799.6879
P(chi-square) = 0

Total sequences searched: 4357

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: