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  

5 accessions found for Methylobacterium extorquens AM1  

Data for CP001510  

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: CP001510.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
-------- ----------- ----- ------- ---
CP001510_2543 CDS_2881527-2880082 56.0 4.1e-16 1
CP001510_4396 CDS_4869414-4868200 50.3 1.8e-14 1
CP001510_4532 CDS_5012796-5014283 40.1 1.9e-11 1
CP001510_1498 CDS_1692272-1693564 31.3 7.8e-09 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP001510_2543 1/1 252 318 .. 1 70 [] 56.0 4.1e-16
CP001510_4396 1/1 205 266 .. 1 70 [] 50.3 1.8e-14
CP001510_4532 1/1 268 339 .. 1 70 [] 40.1 1.9e-11
CP001510_1498 1/1 221 286 .. 1 70 [] 31.3 7.8e-09

Alignments of top-scoring domains:
CP001510_2543: domain 1 of 1, from 252 to 318: score 56.0, E = 4.1e-16
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+ +ARELHD+ gQ L+a + ++++ + + p + e +++i
CP001510_2 252 ERRALARELHDEFGQCLTATGALAAAIEAGA--GDRP-DLHEDAQAI 295

relarealaevRrllgdLRpaal<-*
++ r+ ++ +R++l +LRp++l
CP001510_2 296 SRITRQMMQTLREALAHLRPPDL 318

CP001510_4396: 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+++
CP001510_4 205 ERERLARELHDEAGQQLAWLKLQLDRLRR----APSPTQVEAMLKQV 247

relarealaevRrllgdLRpaal<-*
+++ a +R+++++LRp +l
CP001510_4 248 DAIS----ASLRQVVRELRPVTL 266

CP001510_4532: domain 1 of 1, from 268 to 339: score 40.1, E = 1.9e-11
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpe....earea
ERaRIA ELHD+ g L+a+ + ++rl+ +++ e ++++++ +
CP001510_4 268 ERARIALELHDEFGPCLFALEANAASVARLA--ASPGEidrgRLASR 312

ldeirelarealaevRrllgdLRpaal<-*
+ i ++ + + R+ll +LRp +l
CP001510_4 313 AGDIGSIVGQVQVLNRDLLNRLRPHGL 339

CP001510_1498: domain 1 of 1, from 221 to 286: score 31.3, E = 7.8e-09
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+R+AR+LHD gQ+L ++ +l ++ +l + a +++++
CP001510_1 221 ERRRLARDLHDHAGQQLVTLTFGLRKIASRL----SCPTAIHEVEQL 263

relarealaevRrllgdLRpaal<-*
++ ++ + +Rr+ +LRpaal
CP001510_1 264 LRHTQDIGQSLRRVTLELRPAAL 286


Histogram of all scores:
score obs exp (one = represents 14 sequences)
----- --- ---
-16 1 0|=
-15 2 0|=
-14 15 0|==
-13 62 0|=====
-12 96 55|===*===
-11 190 455|============== *
-10 515 1056|===================================== *
-9 801 1200|==========================================================*
-8 728 925|==================================================== *
-7 663 581|=========================================*======
-6 559 329|=======================*================
-5 543 176|============*==========================
-4 264 92|======*============
-3 193 47|===*==========
-2 130 24|=*========
-1 71 12|*=====
0 54 6|*===
1 29 3|*==
2 12 1|*
3 16 0|==
4 4 0|=
5 7 0|=
6 2 0|=
7 2 0|=
8 2 0|=
9 0 0|
10 1 0|=
> 11 8 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 3441.9705
P(chi-square) = 0

Total sequences searched: 4970

Whole sequence top hits:
tophits_s report:
Total hits: 4
Satisfying E cutoff: 4
Total memory: 20K

Domain top hits:
tophits_s report:
Total hits: 4
Satisfying E cutoff: 4
Total memory: 22K


Acknowledgements:

This research is funded by:

Developed by: