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 CP000133  

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_2.hmm [HisKA_2]
Sequence database: CP000133.Gprot.fsa
per-sequence score cutoff: >= 32.2 [TC1]
per-domain score cutoff: >= 32.2 [TC2]
per-sequence Eval cutoff: [none]
per-domain Eval cutoff: [none]
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Query HMM: HisKA_2
Accession: PF07568.2
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
-------- ----------- ----- ------- ---
CP000133_2501 CDS_2649412-2648474 97.5 1.5e-27 1
CP000133_0423 CDS_447356-446286 81.8 4.3e-23 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP000133_2501 1/1 117 201 .. 1 94 [] 97.5 1.5e-27
CP000133_0423 1/1 160 248 .. 1 94 [] 81.8 4.3e-23

Alignments of top-scoring domains:
CP000133_2501: domain 1 of 1, from 117 to 201: score 97.5, E = 1.5e-27
*->EIHHRVKNNLQvISSLLrLQarkfkdeevikdEVleaLrEsqnRVlS
E++HR+ N+L ++ +L+r+Q+ ++d+ + ++aL+E+q R+ +
CP000133_2 117 EVNHRIANSLGLVGALIRMQSSMTRDQVA-----IDALHETQMRINA 158

mAliHEeLYksedldtvdfseYlekLtenLfqsygvgsdgisLklDl<-*
+A +H++LY+++ +++v ++eYl+ L+ +L s+++++ ++ +
CP000133_2 159 IASVHRRLYTNRQVGSVQVDEYLNSLLTELEASMRDDKRPHR----I 201

CP000133_0423: domain 1 of 1, from 160 to 248: score 81.8, E = 4.3e-23
*->EIHHRVKNNLQvISSLLrLQarkfkdeevikdEVleaLrEsqnRVlS
E +HRVKNNLQ+I++L+r++ar+++ e e + +R+ +
CP000133_0 160 ELQHRVKNNLQMITALIRMEARNAQKNEE-----SERFARLAGRIEA 201

mAliHEeLYksedldtvdfseYlekLtenLfqsygvgsdgisLklDl<-*
Al+++ L+ e +d+++Y++ ++++ + +++v++++++ k+D+
CP000133_0 202 LALLYRALSDEEKGAMIDLGSYVSQIAASVMAAHAVEGIRLDMKVDT 248


Histogram of all scores:
score obs exp (one = represents 19 sequences)
----- --- ---
-15 2 0|=
-14 15 0|=
-13 57 25|=*=
-12 201 265|=========== *
-11 1121 737|======================================*====================
-10 890 954|=============================================== *
-9 663 806|=================================== *
-8 447 541|======================== *
-7 242 321|============= *
-6 217 179|=========*==
-5 81 96|=====*
-4 43 51|==*
-3 21 26|=*
-2 14 13|*
-1 8 7|*
0 6 3|*
1 3 1|*
> 2 4 -|=


% Statistical details of theoretical EVD fit:
mu = -9.5227
lambda = 0.6548
chi-sq statistic = 333.2254
P(chi-square) = 0

Total sequences searched: 4067

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: