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 Escherichia coli str. K-12 substr. DH10B  

Data for CP000948  

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: CP000948.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
-------- ----------- ----- ------- ---
CP000948_1225 CDS_1317082-1315286 82.2 6.2e-24 1
CP000948_2466 CDS_2675518-2677218 76.1 4e-22 1
CP000948_3577 CDS_3945743-3944241 63.7 1.8e-18 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP000948_1225 1/1 390 458 .. 1 70 [] 82.2 6.2e-24
CP000948_2466 1/1 361 428 .. 1 70 [] 76.1 4e-22
CP000948_3577 1/1 304 370 .. 1 70 [] 63.7 1.8e-18

Alignments of top-scoring domains:
CP000948_1225: domain 1 of 1, from 390 to 458: score 82.2, E = 6.2e-24
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ERa IARELHDs++QsLs +k+q++ ++++ d+ pe re l +i
CP000948_1 390 ERATIARELHDSIAQSLSCMKMQVSCLQMQG--DALPESSRELLSQI 434

relarealaevRrllgdLR.paal<-*
r ++ + a++R+ll+++R ++
CP000948_1 435 RNELNASWAQLRELLTTFRlQLTE 458

CP000948_2466: domain 1 of 1, from 361 to 428: score 76.1, E = 4e-22
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ERa IARELHDs++Q Ls +++ql l++r + ++d++ a+ ++
CP000948_2 361 ERATIARELHDSLAQVLSYLRIQLTLLKRSI--PEDNATAQSIMADF 405

relarealaevRrllgdLRpaal<-*
+++++a++++R+ll+++R +
CP000948_2 406 SQALNDAYRQLRELLTTFRLTLQ 428

CP000948_3577: domain 1 of 1, from 304 to 370: score 63.7, E = 1.8e-18
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
R+ ARELHD +gQ+++ai+ q++ ++rl+ +d++ +++ + i
CP000948_3 304 VRRDVARELHDDIGQTITAIRTQAGIVQRLA---ADNASVKQSGQLI 347

relarealaevRrllgdLRpaal<-*
++l+ ++ vRrllg+LRp +l
CP000948_3 348 EQLSLGVYDAVRRLLGRLRPRQL 370


Histogram of all scores:
score obs exp (one = represents 14 sequences)
----- --- ---
-16 3 0|=
-15 1 0|=
-14 23 0|==
-13 108 0|========
-12 141 46|===*=======
-11 253 378|=================== *
-10 661 877|================================================ *
-9 806 996|==========================================================*
-8 667 767|================================================ *
-7 516 482|==================================*==
-6 337 273|===================*=====
-5 267 146|==========*=========
-4 154 76|=====*=====
-3 81 39|==*===
-2 48 20|=*==
-1 26 10|*=
0 16 5|*=
1 5 2|*
2 4 1|*
3 2 0|=
4 0 0|
5 0 0|
6 1 0|=
7 1 0|=
8 0 0|
9 1 0|=
> 10 4 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 664.0865
P(chi-square) = 0

Total sequences searched: 4200

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: