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 Agrobacterium vitis S4  

Data for CP000636  

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/HWE_HK.hmm [HWE_HK]
Sequence database: CP000636.Gprot.fsa
per-sequence score cutoff: >= 60.0 [TC1]
per-domain score cutoff: >= 60.0 [TC2]
per-sequence Eval cutoff: [none]
per-domain Eval cutoff: [none]
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Query HMM: HWE_HK
Accession: PF07536.4
Description: HWE 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
-------- ----------- ----- ------- ---
CP000636_0049 CDS_58425-55855 105.5 3.9e-37 1
CP000636_0005 CDS_6113-7192 72.6 6.3e-26 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP000636_0049 1/1 522 603 .. 1 85 [] 105.5 3.9e-37
CP000636_0005 1/1 162 251 .. 1 85 [] 72.6 6.3e-26

Alignments of top-scoring domains:
CP000636_0049: domain 1 of 1, from 522 to 603: score 105.5, E = 3.9e-37
*->ELnHRVKNtLAvVQSiarQTlRnaasldefveaFsgRLqALsraHdL
ELnHRV+N+LA++ S+++ T++ a ++ ++v+++sgR qAL+raHd
CP000636_0 522 ELNHRVRNILALIRSLVTKTSQAAVDVTSYVDSLSGRVQALARAHDR 568

VpLtrseWagAdLreLleaeLaPyggedaeRitlsGPd<-*
+tr +W++A L+ L e e+a++ +++++R+ l GP+
CP000636_0 569 --ITRQSWGPAPLAGLFEDEIAAH-DNARGRLSLKGPN 603

CP000636_0005: domain 1 of 1, from 162 to 251: score 72.6, E = 6.3e-26
*->ELnHRVKNtLAvVQSiarQTlRnaasldefveaFsgRLqALsraHdL
E++HRVKN++A+ Si++ +R+a+++ e++ + +RL+ALs+aH +
CP000636_0 162 EMHHRVKNLFAITGSIITLAARTAQTPGELASSMKDRLVALSQAHEM 208

V.p.LtrseW...agAdLreLleaeLaPyggedaeRitlsGPd<-*
p++t +e+ ++++ +L+eLl++ L+Pyg ++R +l+G+d
CP000636_0 209 TlPsFTGDEAfqeRSTTLFELLSSLLSPYGEGEEGRWRLHGED 251


Histogram of all scores:
score obs exp (one = represents 1 sequences)
----- --- ---
-13 1 0|=
-12 16 0|================
-11 18 1|*=================
-10 29 18|=================*===========
-9 26 45|========================== *
-8 30 47|============================== *
-7 20 31|==================== *
-6 12 17|============ *
-5 12 8|=======*====
-4 7 4|===*===
-3 3 1|*==
-2 0 0|
> -1 4 -|====


% Statistical details of theoretical EVD fit:
mu = -7.9989
lambda = 0.7843
chi-sq statistic = 28.1748
P(chi-square) = 3.364e-05

Total sequences searched: 178

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: