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:
132 projects found  

1 accessions found for Methylobacterium extorquens PA1  

Data for CP000908  

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: CP000908.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
-------- ----------- ----- ------- ---
CP000908_4284 CDS_4833187-4831973 50.3 1.8e-14 1
CP000908_4391 CDS_4958834-4960363 40.5 1.4e-11 1
CP000908_1637 CDS_1874931-1876085 31.3 7.6e-09 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP000908_4284 1/1 205 266 .. 1 70 [] 50.3 1.8e-14
CP000908_4391 1/1 282 353 .. 1 70 [] 40.5 1.4e-11
CP000908_1637 1/1 175 240 .. 1 70 [] 31.3 7.6e-09

Alignments of top-scoring domains:
CP000908_4284: domain 1 of 1, from 205 to 266: score 50.3, E = 1.8e-14
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+R+ARELHD+ gQ+L+ +klql+++rr + p ++++ l+++
CP000908_4 205 ERERLARELHDEAGQQLAWLKLQLDRLRR----APSPTQVEAMLKQV 247

relarealaevRrllgdLRpaal<-*
+++ a +R+++++LRp +l
CP000908_4 248 DAIS----ASLRQVVRELRPVTL 266

CP000908_4391: domain 1 of 1, from 282 to 353: score 40.5, E = 1.4e-11
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpe....earea
ERaRIA ELHD+ g L+a+ + ++rl+ +++ e ++++++++
CP000908_4 282 ERARIALELHDEFGPCLFALEANAASVARLA--ASPGEidrgRLAAR 326

ldeirelarealaevRrllgdLRpaal<-*
+ i ++ + + R+ll +LRp +l
CP000908_4 327 AGDIGSIVGQVQVLNRDLLNRLRPHGL 353

CP000908_1637: domain 1 of 1, from 175 to 240: score 31.3, E = 7.6e-09
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+R+AR+LHD gQ+L ++ +l ++ +l + a +++++
CP000908_1 175 ERRRLARDLHDHAGQQLVTLTFGLRKIASRL----SCPTAIHEVEQL 217

relarealaevRrllgdLRpaal<-*
++ ++ + +Rr+ +LRpaal
CP000908_1 218 LRHTQDIGQSLRRVTLELRPAAL 240


Histogram of all scores:
score obs exp (one = represents 14 sequences)
----- --- ---
-14 5 0|=
-13 44 0|====
-12 89 53|===*===
-11 148 442|=========== *
-10 486 1026|=================================== *
-9 777 1166|======================================================== *
-8 714 898|=================================================== *
-7 664 565|========================================*=======
-6 577 319|======================*===================
-5 545 171|============*==========================
-4 270 89|======*=============
-3 186 46|===*==========
-2 123 23|=*=======
-1 69 11|*====
0 56 6|*===
1 24 3|*=
2 17 1|*=
3 14 0|=
4 3 0|=
5 6 0|=
6 3 0|=
7 1 0|=
8 1 0|=
9 1 0|=
10 1 0|=
> 11 5 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 3598.8767
P(chi-square) = 0

Total sequences searched: 4829

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: