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  

7 accessions found for Rhizobium etli CFN 42  

Data for CP000136  

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_1.hmm [HisKA]
Sequence database: CP000136.Gprot.fsa
per-sequence score cutoff: >= 26.8 [TC1]
per-domain score cutoff: >= 26.8 [TC2]
per-sequence Eval cutoff: [none]
per-domain Eval cutoff: [none]
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Query HMM: HisKA
Accession: PF00512.12
Description: His Kinase A (phosphoacceptor) domain
[HMM has been calibrated; E-values are empirical estimates]

Scores for complete sequences (score includes all domains):
Sequence Description Score E-value N
-------- ----------- ----- ------- ---
CP000136_0058 CDS_56390-57685 59.2 1.1e-17 1
CP000136_0094 CDS_96282-102188 40.7 2e-12 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP000136_0058 1/1 202 265 .. 1 87 [] 59.2 1.1e-17
CP000136_0094 1/1 1744 1814 .. 1 87 [] 40.7 2e-12

Alignments of top-scoring domains:
CP000136_0058: domain 1 of 1, from 202 to 265: score 59.2, E = 1.1e-17
*->akseflanlsHELRTPLtaIrgyaelLleeldkvlagdtelseeqrl
a+++++ ++sHELR PL+ +++++ +L+ s+ ++
CP000136_0 202 AQQRLFHDVSHELRSPLSRLQAAVGVLRQ------------SPAKL- 235

peLRledpeyreyletilreaerllrLindlLdlsrieag<-*
+l++++re+erl+ L+ ++L+l+r+ ag
CP000136_0 236 ----------GVMLDRMDREVERLDTLVGEVLTLARLTAG 265

CP000136_0094: domain 1 of 1, from 1744 to 1814: score 40.7, E = 2e-12
*->akseflanlsHELRTPLtaIrgyaelLleeldkvlagdtelseeqrl
++e++a+++HE R+PLt++ ++l++ld ++++ +
CP000136_0 1744 TMGELVASIAHEVRQPLTGLVSSGNACLRYLD-----ADPRDIVSA- 1784

peLRledpeyreyletilreaerllrLindlLdlsrieag<-*
r+++e+++++a r ++ i++++ +++ +
CP000136_0 1785 ----------RRAIERMISDAFRASEVIDRIRAMAKKSPE 1814


Histogram of all scores:
score obs exp (one = represents 1 sequences)
----- --- ---
-12 5 5|====*
-11 18 27|================== *
-10 38 51|====================================== *
-9 51 52|===================================================*
-8 46 39|======================================*=======
-7 37 24|=======================*=============
-6 15 14|=============*=
-5 7 7|======*
-4 3 4|===*
-3 5 2|=*===
-2 0 1|*
-1 3 0|===
0 0 0|
> 1 4 -|====


% Statistical details of theoretical EVD fit:
mu = -8.9758
lambda = 0.6525
chi-sq statistic = 13.8180
P(chi-square) = 0.05452

Total sequences searched: 234

Whole sequence top hits:
tophits_s report:
Total hits: 2
Satisfying E cutoff: 2
Total memory: 20K

Domain top hits:
tophits_s report:
Total hits: 2
Satisfying E cutoff: 2
Total memory: 21K


Acknowledgements:

This research is funded by:

Developed by: