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 Dickeya dadantii Ech586  

Data for CP001836  

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: CP001836.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
-------- ----------- ----- ------- ---
CP001836_1852 CDS_2143815-2145281 84.4 1.4e-24 1
CP001836_1779 CDS_2054849-2053041 79.0 5.4e-23 1
CP001836_0559 CDS_625986-627497 56.0 3.4e-16 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP001836_1852 1/1 290 357 .. 1 70 [] 84.4 1.4e-24
CP001836_1779 1/1 393 461 .. 1 70 [] 79.0 5.4e-23
CP001836_0559 1/1 304 370 .. 1 70 [] 56.0 3.4e-16

Alignments of top-scoring domains:
CP001836_1852: domain 1 of 1, from 290 to 357: score 84.4, E = 1.4e-24
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER++IARE+HD++gQ+L+++++ l+l r+++ ++d++ ++l+++
CP001836_1 290 ERKHIAREIHDELGQHLTSMRMSLSLMRMQF--ARDNPHMLTQLQNL 334

relarealaevRrllgdLRpaal<-*
++l++++++ vR+++++LRp +l
CP001836_1 335 MALSDKTIQVVRHVATRLRPNVL 357

CP001836_1779: domain 1 of 1, from 393 to 461: score 79.0, E = 5.4e-23
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+ IARELHDs++QsLs +k+q++ ++++ ++ +e++++ld++
CP001836_1 393 ERTTIARELHDSIAQSLSCLKIQVSCLQMQH--TSLTPEIQQQLDAM 437

relarealaevRrllgdLR.paal<-*
r+ +++a++++R+ll+++R +
CP001836_1 438 RDEINTAYRQLRELLTTFRlKLSE 461

CP001836_0559: domain 1 of 1, from 304 to 370: score 56.0, E = 3.4e-16
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpe..eareald
R+ ARELHD +gQ+++ai+ q++ ++rl+ pe++ +r+ +
CP001836_0 304 VRRDVARELHDDIGQTITAIRTQAGILQRLA-----PEsrHVRQSST 345

eirelarealaevRrllgdLRpaal<-*
i++l+ ++ vRrl g+LRp +l
CP001836_0 346 LIEQLSLSVYDSVRRLMGRLRPRQL 370


Histogram of all scores:
score obs exp (one = represents 14 sequences)
----- --- ---
-14 27 0|==
-13 71 0|======
-12 116 46|===*=====
-11 188 379|============== *
-10 561 881|========================================= *
-9 801 1000|==========================================================*
-8 643 771|============================================== *
-7 558 484|==================================*=====
-6 403 274|===================*=========
-5 309 147|==========*============
-4 181 76|=====*=======
-3 111 39|==*=====
-2 75 20|=*====
-1 36 10|*==
0 27 5|*=
1 13 2|*
2 11 1|*
3 6 0|=
4 0 0|
5 1 0|=
6 1 0|=
7 0 0|
> 8 5 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 1202.8815
P(chi-square) = 0

Total sequences searched: 4144

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: