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 BW2952  

Data for CP001396  

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: CP001396.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
-------- ----------- ----- ------- ---
CP001396_1050 CDS_1165562-1163766 82.2 6e-24 1
CP001396_2226 CDS_2469558-2471258 76.1 3.8e-22 1
CP001396_3353 CDS_3736492-3734990 63.7 1.8e-18 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP001396_1050 1/1 390 458 .. 1 70 [] 82.2 6e-24
CP001396_2226 1/1 361 428 .. 1 70 [] 76.1 3.8e-22
CP001396_3353 1/1 304 370 .. 1 70 [] 63.7 1.8e-18

Alignments of top-scoring domains:
CP001396_1050: domain 1 of 1, from 390 to 458: score 82.2, E = 6e-24
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ERa IARELHDs++QsLs +k+q++ ++++ d+ pe re l +i
CP001396_1 390 ERATIARELHDSIAQSLSCMKMQVSCLQMQG--DALPESSRELLSQI 434

relarealaevRrllgdLR.paal<-*
r ++ + a++R+ll+++R ++
CP001396_1 435 RNELNASWAQLRELLTTFRlQLTE 458

CP001396_2226: domain 1 of 1, from 361 to 428: score 76.1, E = 3.8e-22
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ERa IARELHDs++Q Ls +++ql l++r + ++d++ a+ ++
CP001396_2 361 ERATIARELHDSLAQVLSYLRIQLTLLKRSI--PEDNATAQSIMADF 405

relarealaevRrllgdLRpaal<-*
+++++a++++R+ll+++R +
CP001396_2 406 SQALNDAYRQLRELLTTFRLTLQ 428

CP001396_3353: domain 1 of 1, from 304 to 370: score 63.7, E = 1.8e-18
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
R+ ARELHD +gQ+++ai+ q++ ++rl+ +d++ +++ + i
CP001396_3 304 VRRDVARELHDDIGQTITAIRTQAGIVQRLA---ADNASVKQSGQLI 347

relarealaevRrllgdLRpaal<-*
++l+ ++ vRrllg+LRp +l
CP001396_3 348 EQLSLGVYDAVRRLLGRLRPRQL 370


Histogram of all scores:
score obs exp (one = represents 14 sequences)
----- --- ---
-16 3 0|=
-15 1 0|=
-14 25 0|==
-13 105 0|========
-12 135 45|===*======
-11 254 374|=================== *
-10 652 868|=============================================== *
-9 784 986|======================================================== *
-8 661 760|================================================ *
-7 518 477|==================================*==
-6 345 270|===================*=====
-5 266 145|==========*========
-4 148 75|=====*=====
-3 84 38|==*===
-2 47 19|=*==
-1 24 10|*=
0 13 5|*
1 5 2|*
2 5 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 = 635.8829
P(chi-square) = 0

Total sequences searched: 4084

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: