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:
264 projects found  

1 accessions found for Shewanella piezotolerans WP3  

Data for CP000472  

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: CP000472.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
-------- ----------- ----- ------- ---
CP000472_0299 CDS_317456-316386 86.9 3.1e-25 1
CP000472_3781 CDS_4175937-4177535 71.2 1.3e-20 1
CP000472_1729 CDS_1862509-1863909 38.8 4.5e-11 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP000472_0299 1/1 171 239 .. 1 70 [] 86.9 3.1e-25
CP000472_3781 1/1 329 398 .. 1 70 [] 71.2 1.3e-20
CP000472_1729 1/1 251 317 .. 1 70 [] 38.8 4.5e-11

Alignments of top-scoring domains:
CP000472_0299: domain 1 of 1, from 171 to 239: score 86.9, E = 3.1e-25
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+RIAR+LHD g+sLs+i+l++ela++l+ e+ar++l+e+
CP000472_0 171 ERERIARDLHDIMGHSLSSISLKAELAEKLIA-NNQTEQARQQLTEL 216

relarealaevRrllgdLRpaal<-*
+ar++l+++R++++++++ +l
CP000472_0 217 NSIARDSLSQIRQTVSGYKHKGL 239

CP000472_3781: domain 1 of 1, from 329 to 398: score 71.2, E = 1.3e-20
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpe..eareald
ER IARELHDs+gQ Ls +k+q+ l+ + l dk +++a+e+l+
CP000472_3 329 ERGVIARELHDSLGQLLSFLKIQVNLLSKEL--DKTSKspRAAEQLQ 373

eirelarealaevRrllgdLRpaal<-*
ei e +++a+ ++R+ll+++R ++
CP000472_3 374 EINEGVNTAYVQLRELLSTFRLTIK 398

CP000472_1729: domain 1 of 1, from 251 to 317: score 38.8, E = 4.5e-11
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
E +R +RELHD+v+Q+++a+ +e+a+ + d ++l+
CP000472_1 251 ECKRVSRELHDGVSQTIAAALFSMETAQLKQE-YGD--DSSKELEKS 294

relarealaevRrllgdLRpaal<-*
+l r+ + e+R++ ++L+pa+l
CP000472_1 295 ITLTRQIMLEIRNISHQLHPAIL 317


Histogram of all scores:
score obs exp (one = represents 17 sequences)
----- --- ---
-15 4 0|=
-14 116 0|=======
-13 297 0|==================
-12 313 55|===*===============
-11 419 452|========================= *
-10 906 1049|====================================================== *
-9 970 1191|==========================================================*
-8 638 918|====================================== *
-7 499 577|============================== *
-6 321 326|===================*
-5 218 175|==========*==
-4 108 91|=====*=
-3 46 47|==*
-2 27 24|=*
-1 28 12|*=
0 9 6|*
1 3 3|*
2 3 1|*
> 3 8 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 1401.6643
P(chi-square) = 0

Total sequences searched: 4933

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: