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:
76 projects found  

5 accessions found for Ralstonia pickettii 12D  

Data for CP001645  

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_3.hmm [HisKA_3]
Sequence database: CP001645.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]
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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
-------- ----------- ----- ------- ---
CP001645_1044 CDS_1166637-1168385 70.2 6.3e-21 1
CP001645_1077 CDS_1201120-1199732 67.6 3.5e-20 1
CP001645_0133 CDS_148457-150412 62.5 1.2e-18 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP001645_1044 1/1 365 432 .. 1 70 [] 70.2 6.3e-21
CP001645_1077 1/1 253 322 .. 1 70 [] 67.6 3.5e-20
CP001645_0133 1/1 446 514 .. 1 70 [] 62.5 1.2e-18

Alignments of top-scoring domains:
CP001645_1044: domain 1 of 1, from 365 to 432: score 70.2, E = 6.3e-21
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+R++RELHD+++QsL+a+k+ ++++++ l d+ +++++e+l ++
CP001645_1 365 ERRRLSRELHDELAQSLAALKVDMQMLEHKL--DATNAPVAERLSAM 409

relarealaevRrllgdLRpaal<-*
++++++ ++ +Rrl++dLRp+ l
CP001645_1 410 EHAVDDMIRATRRLASDLRPSML 432

CP001645_1077: domain 1 of 1, from 253 to 322: score 67.6, E = 3.5e-20
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+RIARELHD +gQ+Lsa+k+ ++l+++ l+ ++ + ++ ++ +++
CP001645_1 253 ERHRIARELHDDLGQRLSALKMDISLLAADLQAARSDKALIDQTQAM 299

relarealaevRrllgdLRpaal<-*
++ ++e++ vR++ dLRp+ l
CP001645_1 300 QHVIDETIVAVRHISADLRPPLL 322

CP001645_0133: domain 1 of 1, from 446 to 514: score 62.5, E = 1.2e-18
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+ A+ LHDs++Q+L ++lq++++ ++++ d++ +eare + +
CP001645_0 446 ERNLVAQGLHDSIAQGLNFLNLQVQMLDAAMR-DANLDEAREIVPLL 491

relarealaevRrllgdLRpaal<-*
r ++e++++vR+ll ++R +
CP001645_0 492 RCGVEESYQDVRELLLNFRSKLE 514


Histogram of all scores:
score obs exp (one = represents 4 sequences)
----- --- ---
-14 3 0|=
-13 17 0|=====
-12 22 13|===*==
-11 44 108|=========== *
-10 127 250|================================ *
-9 210 284|===================================================== *
-8 155 219|======================================= *
-7 172 138|==================================*========
-6 132 78|===================*=============
-5 117 41|==========*===================
-4 66 21|=====*===========
-3 50 11|==*==========
-2 16 5|=*==
-1 14 2|*===
0 14 1|*===
1 5 0|==
2 3 0|=
3 3 0|=
4 4 0|=
5 1 0|=
6 0 0|
> 7 5 -|==


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 564.5404
P(chi-square) = 0

Total sequences searched: 1180

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: 21K


Acknowledgements:

This research is funded by:

Developed by: