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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76 projects found  

1 accessions found for Thiobacillus denitrificans ATCC 25259  

Data for CP000116  

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)
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file: /home/projects/MicrobialGenomicsGroup/Packages/hmmdata-1.0.0.package/Resources/noarch/TCS/HisKA_3.hmm [HisKA_3]
Sequence database: CP000116.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]
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

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
-------- ----------- ----- ------- ---
CP000116_1289 CDS_1357301-1360807 82.8 2.9e-24 1
CP000116_1400 CDS_1481524-1479590 64.8 5.6e-19 1
CP000116_1587 CDS_1672042-1673523 49.5 1.8e-14 1
CP000116_2235 CDS_2313456-2314829 44.7 4.9e-13 1
CP000116_2463 CDS_2536185-2537432 37.9 4.8e-11 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP000116_1289 1/1 964 1031 .. 1 70 [] 82.8 2.9e-24
CP000116_1400 1/1 431 500 .. 1 70 [] 64.8 5.6e-19
CP000116_1587 1/1 288 355 .. 1 70 [] 49.5 1.8e-14
CP000116_2235 1/1 260 328 .. 1 70 [] 44.7 4.9e-13
CP000116_2463 1/1 203 271 .. 1 70 [] 37.9 4.8e-11

Alignments of top-scoring domains:
CP000116_1289: domain 1 of 1, from 964 to 1031: score 82.8, E = 2.9e-24
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER++IARE+HD++gQ L+a+++ ++++ +++ +d++e++e ++ +
CP000116_1 964 ERKHIAREIHDELGQLLTALRMEVSAVGMAF--GRDNPELDEKVRSM 1008

relarealaevRrllgdLRpaal<-*
++ ++++++ vR++++ LRpaal
CP000116_1 1009 KTVINQTIQTVRQVATSLRPAAL 1031

CP000116_1400: domain 1 of 1, from 431 to 500: score 64.8, E = 5.6e-19
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpe.earealde
ERa +AR+LHDs++QsL+ +k+q+++++ l++ + +++ea + l+e
CP000116_1 431 ERAALARDLHDSLAQSLAYMKIQVSRLKPLVE-GSGAGsEAGDVLAE 476

irelarealaevRrllgdLRpaal<-*
+re ++ a++++R+ll+++R ++
CP000116_1 477 LREGLNSAYRQLRELLTTFRLRIE 500

CP000116_1587: domain 1 of 1, from 288 to 355: score 49.5, E = 1.8e-14
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER +ARE HD +g +L+ ik++l+ ++r++ +++ ++ e+++ +
CP000116_1 288 ERLYLAREVHDDLGGNLTTIKIGLSCLARQF--PSESTPLTERVRYL 332

relarealaevRrllgdLRpaal<-*
l++++ + + r++++LRpaal
CP000116_1 333 DNLVDQTFEAAHRIASNLRPAAL 355

CP000116_2235: domain 1 of 1, from 260 to 328: score 44.7, E = 4.9e-13
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpe....earea
E ++ARELHD++g L+a+kl +++++ +k p++ + ++++
CP000116_2 260 EKLHLARELHDELGALLTAAKLDADWIE-----RKLPPemraLVEQR 301

ldeirelarealaevRrllgdLRpaal<-*
l+++r+ + +++ Rr+ +LRpa l
CP000116_2 302 LTRLRQSLVGGITLKRRITNNLRPALL 328

CP000116_2463: domain 1 of 1, from 203 to 271: score 37.9, E = 4.8e-11
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpe.earealde
ER+ +A +HDs++Q+L+ +k+ l ++ ++ + ++ +a + l
CP000116_2 203 ERQMLANQIHDSLAQTLAYAKMRLTVLSDAM--RHEDYaKANRFLGD 247

irelarealaevRrllgdLRpaal<-*
++e+++ a+a++R+l++++R+ +
CP000116_2 248 VEEAVDLAYADLRDLITQYRDRIN 271


Histogram of all scores:
score obs exp (one = represents 9 sequences)
----- --- ---
-14 9 0|=
-13 32 0|====
-12 54 31|===*==
-11 117 259|============= *
-10 314 601|=================================== *
-9 500 682|======================================================== *
-8 422 526|=============================================== *
-7 375 330|====================================*=====
-6 330 187|====================*================
-5 263 100|===========*==================
-4 140 52|=====*==========
-3 92 26|==*========
-2 61 13|=*=====
-1 51 7|*=====
0 15 3|*=
1 22 1|*==
2 8 0|=
3 5 0|=
4 8 0|=
5 2 0|=
6 1 0|=
7 0 0|
> 8 6 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 1419.5541
P(chi-square) = 0

Total sequences searched: 2827

Whole sequence top hits:
tophits_s report:
Total hits: 5
Satisfying E cutoff: 5
Total memory: 21K

Domain top hits:
tophits_s report:
Total hits: 5
Satisfying E cutoff: 5
Total memory: 22K


Acknowledgements:

This research is funded by:

Developed by: