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  

3 accessions found for Pseudomonas syringae pv. tomato str. DC3000  

Data for AE016853  

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: AE016853.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
-------- ----------- ----- ------- ---
AE016853_2092 CDS_2305321-2304137 71.4 1.2e-20 1
AE016853_0544 CDS_614343-616358 69.1 6.1e-20 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
AE016853_2092 1/1 189 256 .. 1 70 [] 71.4 1.2e-20
AE016853_0544 1/1 467 534 .. 1 70 [] 69.1 6.1e-20

Alignments of top-scoring domains:
AE016853_2092: domain 1 of 1, from 189 to 256: score 71.4, E = 1.2e-20
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+R A +LHD+++Q+L+++ l++ + + ++ p+++++ l++i
AE016853_2 189 ERKRVAYDLHDGLAQTLAGLHQRLQGFAGRC--PELPAQLDADLQAI 233

relarealaevRrllgdLRpaal<-*
+la+++ e R+l+++LRpa+l
AE016853_2 234 LKLAQHCVGEGRQLISGLRPAVL 256

AE016853_0544: domain 1 of 1, from 467 to 534: score 69.1, E = 6.1e-20
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
E aRIARE HD++gQ+L+++kl +++++ ++ ++ ++ + e+ld +
AE016853_0 467 EKARIAREVHDELGQMLTVLKLETSMCELAY--ADLDPGLSERLDSM 511

relarealaevRrllgdLRpaal<-*
++l+++ + vR+++++LRp++l
AE016853_0 512 KRLISQLFQLVRDVATALRPPIL 534


Histogram of all scores:
score obs exp (one = represents 16 sequences)
----- --- ---
-15 1 0|=
-14 21 0|==
-13 91 0|======
-12 151 61|===*======
-11 241 501|================ *
-10 718 1164|============================================= *
-9 938 1322|==========================================================*
-8 898 1019|========================================================= *
-7 714 640|=======================================*=====
-6 549 362|======================*============
-5 467 194|============*=================
-4 258 101|======*==========
-3 175 52|===*=======
-2 102 26|=*=====
-1 62 13|*===
0 37 6|*==
1 18 3|*=
2 13 1|*
3 6 0|=
4 4 0|=
5 2 0|=
6 2 0|=
7 4 0|=
8 1 0|=
9 0 0|
10 0 0|
> 11 3 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 2096.8269
P(chi-square) = 0

Total sequences searched: 5476

Whole sequence top hits:
tophits_s report:
Total hits: 2
Satisfying E cutoff: 2
Total memory: 20K

Domain top hits:
tophits_s report:
Total hits: 2
Satisfying E cutoff: 2
Total memory: 21K


Acknowledgements:

This research is funded by:

Developed by: