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 Shewanella sediminis HAW-EB3  

Data for CP000821  

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: CP000821.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
-------- ----------- ----- ------- ---
CP000821_1948 CDS_2357477-2355702 74.2 1.5e-21 1
CP000821_0928 CDS_1113203-1111500 66.2 3.5e-19 1
CP000821_0904 CDS_1083196-1081787 38.4 5.6e-11 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP000821_1948 1/1 394 463 .. 1 70 [] 74.2 1.5e-21
CP000821_0928 1/1 364 433 .. 1 70 [] 66.2 3.5e-19
CP000821_0904 1/1 254 320 .. 1 70 [] 38.4 5.6e-11

Alignments of top-scoring domains:
CP000821_1948: domain 1 of 1, from 394 to 463: score 74.2, E = 1.5e-21
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpe.earealde
ERa IARELHDs++QsLs +k+q++l+ r ++ + pe+++ e++
CP000821_1 394 ERAVIARELHDSLAQSLSFLKVQMSLLTRKMQ-KGLPEeQVNETIND 439

irelarealaevRrllgdLRpaal<-*
i++ +++a+ ++R+ll+++R +
CP000821_1 440 IKQGLNHAYLQLRELLTTFRLKLD 463

CP000821_0928: domain 1 of 1, from 364 to 433: score 66.2, E = 3.5e-19
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpe..eareald
ER IARELHDs+gQ Ls +k+q+ l+ + l d++ +++++++l
CP000821_0 364 ERGVIARELHDSLGQLLSFLKIQVNLLSKGL--DSACRspQVEQQLS 408

eirelarealaevRrllgdLRpaal<-*
ei e +++a+ ++R+ll+++R ++
CP000821_0 409 EINEGVNTAYVQLRELLSTFRLTIK 433

CP000821_0904: domain 1 of 1, from 254 to 320: score 38.4, E = 5.6e-11
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpe..eareald
E +R +RELHD+v+Q+++a+ +e+a+ k ++ +l+
CP000821_0 254 ECKRVSRELHDGVSQTIAAALFAMETAQ-----LKKEYggDSGPELE 295

eirelarealaevRrllgdLRpaal<-*
+ ++ r+ + ++R++ ++L+p++l
CP000821_0 296 KAITMTRQIMLDIRNISHQLHPSIL 320


Histogram of all scores:
score obs exp (one = represents 18 sequences)
----- --- ---
-14 25 0|==
-13 119 0|=======
-12 186 50|==*========
-11 310 412|================== *
-10 816 956|============================================== *
-9 1012 1086|========================================================= *
-8 683 836|====================================== *
-7 500 526|============================ *
-6 328 297|================*==
-5 245 159|========*=====
-4 115 83|====*==
-3 57 42|==*=
-2 35 21|=*
-1 25 11|*=
0 17 5|*
1 10 2|*
2 5 1|*
3 3 0|=
> 4 6 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 560.4023
P(chi-square) = 0

Total sequences searched: 4497

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: