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:
76 projects found  

1 accessions found for Acidovorax ebreus TPSY  

Data for CP001392  

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: CP001392.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
-------- ----------- ----- ------- ---
CP001392_0418 CDS_431593-433509 69.9 2.3e-20 1
CP001392_3011 CDS_3279697-3280818 55.8 3.2e-16 1
CP001392_2778 CDS_3017010-3018353 55.0 5.6e-16 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP001392_0418 1/1 422 490 .. 1 70 [] 69.9 2.3e-20
CP001392_3011 1/1 168 233 .. 1 70 [] 55.8 3.2e-16
CP001392_2778 1/1 250 317 .. 1 70 [] 55.0 5.6e-16

Alignments of top-scoring domains:
CP001392_0418: domain 1 of 1, from 422 to 490: score 69.9, E = 2.3e-20
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpe.earealde
ER IARELHDs++QsL+ +k+q++l+r ++ +k + ++ ++ ++e
CP001392_0 422 ERSLIARELHDSIAQSLAFLKIQTQLLRDAV--AKGNTeARDRSMAE 466

irelarealaevRrllgdLRpaal<-*
+ + +re++a+vR+ll ++R+ +
CP001392_0 467 LDTGVRECYADVRELLVHFRTRTQ 490

CP001392_3011: domain 1 of 1, from 168 to 233: score 55.8, E = 3.2e-16
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ERa IARE+HD +g +L+a+k l ++ r++ +d +re++ ++
CP001392_3 168 ERAAIAREIHDDIGGALAAVKFDLAWIGRHA--GED--GLREHAGTA 210

relarealaevRrllgdLRpaal<-*
e++++a++ + rl +LRp++l
CP001392_3 211 TEMLQHAIDAAQRLMMNLRPPVL 233

CP001392_2778: domain 1 of 1, from 250 to 317: score 55.0, E = 5.6e-16
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ERa++ARELHD++g L+a+kl + +++ ++ d + +e +e+++ +
CP001392_2 250 ERAHLARELHDELGALLTAAKLDVARLKSRI--DLHTPENAERVQHL 294

relarealaevRrllgdLRpaal<-*
e+++ ++a Rr++ dLRp+ l
CP001392_2 295 TETLNSGIALKRRIIEDLRPSSL 317


Histogram of all scores:
score obs exp (one = represents 10 sequences)
----- --- ---
-14 9 0|=
-13 23 0|===
-12 60 38|===*==
-11 115 318|============ *
-10 397 739|======================================== *
-9 540 840|====================================================== *
-8 513 647|==================================================== *
-7 481 407|========================================*========
-6 399 230|======================*=================
-5 372 123|============*=========================
-4 193 64|======*=============
-3 137 33|===*==========
-2 78 16|=*======
-1 56 8|*=====
0 42 4|*====
1 25 2|*==
2 11 1|*=
3 4 0|=
4 5 0|=
5 5 0|=
6 6 0|=
7 1 0|=
8 1 0|=
9 0 0|
10 1 0|=
> 11 5 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 2132.7073
P(chi-square) = 0

Total sequences searched: 3479

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: