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
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132 projects found  

1 accessions found for Hyphomicrobium denitrificans ATCC 51888  

Data for CP002083  

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: CP002083.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
-------- ----------- ----- ------- ---
CP002083_0590 CDS_628857-630716 59.9 1.9e-17 1
CP002083_0804 CDS_854564-853200 56.2 2.4e-16 1
CP002083_1361 CDS_1429616-1428252 44.9 5.3e-13 1
CP002083_1309 CDS_1349025-1350497 32.3 2.7e-09 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP002083_0590 1/1 412 484 .. 1 70 [] 59.9 1.9e-17
CP002083_0804 1/1 247 314 .. 1 70 [] 56.2 2.4e-16
CP002083_1361 1/1 240 308 .. 1 70 [] 44.9 5.3e-13
CP002083_1309 1/1 262 333 .. 1 70 [] 32.3 2.7e-09

Alignments of top-scoring domains:
CP002083_0590: domain 1 of 1, from 412 to 484: score 59.9, E = 1.9e-17
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpe.....eare
ERa IARELHDs++QsLs +k+ql +++ + + + ++++++ ++
CP002083_0 412 ERAAIARELHDSLAQSLSFMKIQLARLQ-SY--QNNVTsesreQTKA 455

aldeirelarealaevRrllgdLR.paal<-*
e+r+ ++ a++e+R+ll ++R +++
CP002083_0 456 ITSELRHGLDNAYRELRELLATFRvHMDV 484

CP002083_0804: domain 1 of 1, from 247 to 314: score 56.2, E = 2.4e-16
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER +IARELHD v+Q+Ls+i+ + +r + + ++ a + ++e+
CP002083_0 247 ERLHIARELHDDVAQQLSGINAVAACVRSKV--NRKDPSATQDATEL 291

relarealaevRrllgdLRpaal<-*
+++ ++ + +R +l+ LRp++
CP002083_0 292 ETMTSKLMISLRKTLTYLRPPEI 314

CP002083_1361: domain 1 of 1, from 240 to 308: score 44.9, E = 5.3e-13
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpe.earealde
ER IAR+LHD++g L+a+ + ++ + +l ++++ + + ++ +
CP002083_1 240 ERSEIARDLHDEIGPFLFAVDVDAQSIPLML--ARNATdDVNSRAGA 284

irelarealaevRrllgdLRpaal<-*
ir+ +++ + +R +l++LRpa l
CP002083_1 285 IRQSVQHMQVHLRGILSRLRPAML 308

CP002083_1309: domain 1 of 1, from 262 to 333: score 32.3, E = 2.7e-09
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpe...eareal
ER+ IARELHD+ g L++i+ +e + r+ + d+e+ +++ ++
CP002083_1 262 ERREIARELHDEAGPCLFGITASAESINRISI-KLDDEsarRITTRT 307

deirelarealaevRrllgdLRpaal<-*
dei +a++ a R+ll +L+p
CP002083_1 308 DEILSIADRLKAMNRALLKRLHPVSI 333


Histogram of all scores:
score obs exp (one = represents 11 sequences)
----- --- ---
-14 19 0|==
-13 58 0|======
-12 119 39|===*=======
-11 170 321|================ *
-10 515 746|=============================================== *
-9 648 848|==========================================================*
-8 507 653|=============================================== *
-7 466 410|=====================================*=====
-6 311 232|=====================*=======
-5 293 124|===========*===============
-4 148 65|=====*========
-3 103 33|==*=======
-2 61 17|=*====
-1 37 8|*===
0 22 4|*=
1 14 2|*=
2 6 1|*
3 7 0|=
4 0 0|
> 5 8 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 1100.8427
P(chi-square) = 0

Total sequences searched: 3512

Whole sequence top hits:
tophits_s report:
Total hits: 4
Satisfying E cutoff: 4
Total memory: 20K

Domain top hits:
tophits_s report:
Total hits: 4
Satisfying E cutoff: 4
Total memory: 22K


Acknowledgements:

This research is funded by:

Developed by: