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  

4 accessions found for Cupriavidus metallidurans CH34  

Data for CP000352  

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: CP000352.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
-------- ----------- ----- ------- ---
CP000352_0092 CDS_100625-99240 68.1 7.9e-20 1
CP000352_2079 CDS_2264669-2266684 64.8 7.2e-19 1
CP000352_3561 CDS_3878196-3879623 61.6 6.5e-18 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP000352_0092 1/1 250 317 .. 1 70 [] 68.1 7.9e-20
CP000352_2079 1/1 455 523 .. 1 70 [] 64.8 7.2e-19
CP000352_3561 1/1 262 332 .. 1 70 [] 61.6 6.5e-18

Alignments of top-scoring domains:
CP000352_0092: domain 1 of 1, from 250 to 317: score 68.1, E = 7.9e-20
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
E +R+ARELHD++g L+aikl l+++r+++ ++ +ear+ l+++
CP000352_0 250 EKTRLARELHDELGAILTAIKLDLHWVRMRV--QDTHPEARDKLTRV 294

relarealaevRrllgdLRpaal<-*
+++a++a++ R+l+ dLRp++l
CP000352_0 295 MQHADQAIQIKRQLIEDLRPTVL 317

CP000352_2079: domain 1 of 1, from 455 to 523: score 64.8, E = 7.2e-19
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+ A+ LHDs++Q+L ++lq++l+ +++ + d++e re + +
CP000352_2 455 ERNLVAQGLHDSIAQGLNFLNLQVQLLGDAVE-RNDNAETREIVPLL 500

relarealaevRrllgdLRpaal<-*
r+ ++e++++vR+ll+++R
CP000352_2 501 RHGVEESYQDVRELLHNFRSRLT 523

CP000352_3561: domain 1 of 1, from 262 to 332: score 61.6, E = 6.5e-18
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpe...eareal
ERaR++RELHD+++Q L ++kl le+a ++ + +p ++ ++ l
CP000352_3 262 ERARLSRELHDGISQLLVSVKLVLEAATNRI--RLAPTegaSVAPIL 306

deirelarealaevRrllgdLRpaal<-*
++ ++ +evRr++++LRpa l
CP000352_3 307 GMALNRLDSVFNEVRRVARNLRPALL 332


Histogram of all scores:
score obs exp (one = represents 11 sequences)
----- --- ---
-14 6 0|=
-13 38 0|====
-12 72 40|===*===
-11 123 330|============ *
-10 436 765|======================================== *
-9 626 869|========================================================= *
-8 541 670|================================================== *
-7 532 421|======================================*==========
-6 378 238|=====================*=============
-5 358 127|===========*=====================
-4 184 66|=====*===========
-3 120 34|===*=======
-2 67 17|=*=====
-1 39 8|*===
0 27 4|*==
1 16 2|*=
2 13 1|*=
3 7 0|=
4 7 0|=
5 3 0|=
6 0 0|
7 1 0|=
8 0 0|
9 1 0|=
10 1 0|=
11 0 0|
> 12 5 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 1574.8334
P(chi-square) = 0

Total sequences searched: 3601

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: