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 Pseudomonas aeruginosa PAO1  

Data for AE004091  

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: AE004091.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
-------- ----------- ----- ------- ---
AE004091_3878 CDS_4345010-4346878 77.6 2e-22 1
AE004091_0601 CDS_660315-662708 67.2 2.2e-19 1
AE004091_1981 CDS_2165213-2165863 39.7 2.9e-11 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
AE004091_3878 1/1 411 481 .. 1 70 [] 77.6 2e-22
AE004091_0601 1/1 596 663 .. 1 70 [] 67.2 2.2e-19
AE004091_1981 1/1 22 85 .. 1 70 [] 39.7 2.9e-11

Alignments of top-scoring domains:
AE004091_3878: domain 1 of 1, from 411 to 481: score 77.6, E = 2e-22
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpe..eareald
ER IARELHDs++QsLs +k+q++++ +ll +++++ ++++++ld
AE004091_3 411 ERGTIARELHDSLAQSLSYLKIQVSRLGTLL--KREAPaeKIEDTLD 455

eirelarealaevRrllgdLR.paal<-*
e+re ++ a++++R+ll+++R ++
AE004091_3 456 ELREGLNGAYRQLRELLTTFRlSLDE 481

AE004091_0601: domain 1 of 1, from 596 to 663: score 67.2, E = 2.2e-19
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
E aRIARE HD++gQ L+++kl +++++ ++ +++ e +re+l ++
AE004091_0 596 EKARIAREVHDELGQVLTVLKLETSMCELAY--ADAQEGLRERLGNM 640

relarealaevRrllgdLRpaal<-*
++l+ + + vR+++++LRp++l
AE004091_0 641 KKLIAQLFQLVRDVATALRPPIL 663

AE004091_1981: domain 1 of 1, from 22 to 85: score 39.7, E = 2.9e-11
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+ +A+ HD +gQ L++i+ ql l+r + + al+++
AE004091_1 22 ERRLLAQAVHDDIGQYLTGIRTQLLLLRCTA--G----DGQPALARL 62

relarealaevRrllgdLRpaal<-*
++ ++ + R+ll++L p+al
AE004091_1 63 ERYCQGLDDSFRALLRGLPPPAL 85


Histogram of all scores:
score obs exp (one = represents 14 sequences)
----- --- ---
-14 8 0|=
-13 37 0|===
-12 85 62|====*==
-11 163 510|============ *
-10 536 1184|======================================= *
-9 825 1344|==========================================================*
-8 813 1036|==========================================================*
-7 778 651|==============================================*=========
-6 661 368|==========================*=====================
-5 655 197|==============*================================
-4 361 103|=======*==================
-3 233 53|===*=============
-2 149 27|=*=========
-1 93 13|*======
0 56 7|*===
1 39 3|*==
2 32 1|*==
3 19 0|==
4 7 0|=
5 3 0|=
6 4 0|=
7 1 0|=
8 2 0|=
9 3 0|=
10 1 0|=
11 0 0|
12 0 0|
> 13 4 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 4757.5962
P(chi-square) = 0

Total sequences searched: 5568

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: