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
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Data for U00096  

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: U00096.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
-------- ----------- ----- ------- ---
U00096_1192 CDS_1276841-1275045 82.2 6.3e-24 1
U00096_2421 CDS_2583753-2585453 76.1 4e-22 1
U00096_3572 CDS_3848159-3846657 63.7 1.9e-18 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
U00096_1192 1/1 390 458 .. 1 70 [] 82.2 6.3e-24
U00096_2421 1/1 361 428 .. 1 70 [] 76.1 4e-22
U00096_3572 1/1 304 370 .. 1 70 [] 63.7 1.9e-18

Alignments of top-scoring domains:
U00096_1192: domain 1 of 1, from 390 to 458: score 82.2, E = 6.3e-24
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ERa IARELHDs++QsLs +k+q++ ++++ d+ pe re l +i
U00096_119 390 ERATIARELHDSIAQSLSCMKMQVSCLQMQG--DALPESSRELLSQI 434

relarealaevRrllgdLR.paal<-*
r ++ + a++R+ll+++R ++
U00096_119 435 RNELNASWAQLRELLTTFRlQLTE 458

U00096_2421: domain 1 of 1, from 361 to 428: score 76.1, E = 4e-22
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ERa IARELHDs++Q Ls +++ql l++r + ++d++ a+ ++
U00096_242 361 ERATIARELHDSLAQVLSYLRIQLTLLKRSI--PEDNATAQSIMADF 405

relarealaevRrllgdLRpaal<-*
+++++a++++R+ll+++R +
U00096_242 406 SQALNDAYRQLRELLTTFRLTLQ 428

U00096_3572: domain 1 of 1, from 304 to 370: score 63.7, E = 1.9e-18
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
R+ ARELHD +gQ+++ai+ q++ ++rl+ +d++ +++ + i
U00096_357 304 VRRDVARELHDDIGQTITAIRTQAGIVQRLA---ADNASVKQSGQLI 347

relarealaevRrllgdLRpaal<-*
++l+ ++ vRrllg+LRp +l
U00096_357 348 EQLSLGVYDAVRRLLGRLRPRQL 370


Histogram of all scores:
score obs exp (one = represents 14 sequences)
----- --- ---
-16 3 0|=
-15 1 0|=
-14 23 0|==
-13 112 0|========
-12 137 46|===*======
-11 248 378|================== *
-10 653 878|=============================================== *
-9 809 997|==========================================================*
-8 674 768|================================================= *
-7 524 483|==================================*===
-6 342 273|===================*=====
-5 269 146|==========*=========
-4 146 76|=====*=====
-3 83 39|==*===
-2 48 20|=*==
-1 26 10|*=
0 13 5|*
1 6 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 = 637.2365
P(chi-square) = 0

Total sequences searched: 4267

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: