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  

4 accessions found for Agrobacterium tumefaciens str. C58  

Data for AE007872  

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: AE007872.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
-------- ----------- ----- ------- ---
AE007872_0086 CDS_90312-91364 125.3 2.2e-43 1
AE007872_0526 CDS_522752-520911 105.9 8.9e-37 1
AE007872_0370 CDS_365539-366900 62.0 7.6e-22 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
AE007872_0086 1/1 155 237 .. 1 85 [] 125.3 2.2e-43
AE007872_0526 1/1 428 507 .. 1 85 [] 105.9 8.9e-37
AE007872_0370 1/1 256 345 .. 1 85 [] 62.0 7.6e-22

Alignments of top-scoring domains:
AE007872_0086: domain 1 of 1, from 155 to 237: score 125.3, E = 2.2e-43
*->ELnHRVKNtLAvVQSiarQTlRnaasldefveaFsgRLqALsraHdL
ELnHRVKN+LA+V Si+++T+R+aas++e++++F +RLqALs++H+
AE007872_0 155 ELNHRVKNILATVTSIFQMTRRGAASVEELAGDFGARLQALSGVHSA 201

VpLtrseWagAdLreLleaeLaPyggedaeRitlsGPd<-*
++++ ++ + L+ +++ ++aPy+g+++ Ri +sGPd
AE007872_0 202 --VFEAGGEEVGLSLIMATTVAPYNGDGSSRIAVSGPD 237

AE007872_0526: domain 1 of 1, from 428 to 507: score 105.9, E = 8.9e-37
*->ELnHRVKNtLAvVQSiarQTlRnaasldefveaFsgRLqALsraHdL
EL+HRVKN+LA+V +iarQT + e +eaF+ RL +Lsra+dL
AE007872_0 428 ELHHRVKNILATVTAIARQTIGRDKANHEDMEAFTSRLGSLSRAQDL 474

VpLtrseWagAdLreLleaeLaPyggedaeRitlsGPd<-*
L+ ++W+ AdLr++l+++L+Py ae +++sGP
AE007872_0 475 --LVHADWQHADLRAVLQQALSPYP---AESFQISGPG 507

AE007872_0370: domain 1 of 1, from 256 to 345: score 62.0, E = 7.6e-22
*->ELnHRVKNtLAvVQSiarQTlRnaasldefveaFsgRLqALsraHdL
E++HRVKN++++ Si++ +R+a++++e+++ RL ALs aH L
AE007872_0 256 EMHHRVKNLFTITGSIITLAARTAQTPAELADGMKNRLIALSHAHQL 302

V.p.LtrseW...agAdLreLleaeLaPyggedaeRitlsGPd<-*
p+++ e +++++ +L+ Ll+ L+P++++da+R +l+G+d
AE007872_0 303 TlPsFSGGESpseRSTTLFNLLSNLLSPFADKDAGRWHLHGED 345


Histogram of all scores:
score obs exp (one = represents 2 sequences)
----- --- ---
-14 8 0|====
-13 9 0|=====
-12 67 0|==================================
-11 60 4|=*============================
-10 69 56|===========================*=======
-9 105 140|===================================================== *
-8 85 145|=========================================== *
-7 59 97|============================== *
-6 34 53|================= *
-5 23 26|============*
-4 16 12|=====*==
-3 6 5|==*
-2 1 2|*
> -1 5 -|===


% Statistical details of theoretical EVD fit:
mu = -7.9989
lambda = 0.7843
chi-sq statistic = 60.2287
P(chi-square) = 1.359e-10

Total sequences searched: 547

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: 22K


Acknowledgements:

This research is funded by:

Developed by: