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  

3 accessions found for Thiomonas intermedia K12  

Data for CP002021  

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: CP002021.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
-------- ----------- ----- ------- ---
CP002021_2403 CDS_2630835-2632766 67.0 1.4e-19 1
CP002021_0190 CDS_209530-208337 62.4 3.1e-18 1
CP002021_1211 CDS_1323857-1322724 58.3 5.3e-17 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP002021_2403 1/1 425 493 .. 1 70 [] 67.0 1.4e-19
CP002021_0190 1/1 179 244 .. 1 70 [] 62.4 3.1e-18
CP002021_1211 1/1 168 231 .. 1 70 [] 58.3 5.3e-17

Alignments of top-scoring domains:
CP002021_2403: domain 1 of 1, from 425 to 493: score 67.0, E = 1.4e-19
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ERa +ARELHDs++QsL+ +k+ql+l+r++l+ + +++++ + e+
CP002021_2 425 ERAFLARELHDSIAQSLAFMKIQLQLLRTALQ-AGKVGKIEQVVSEL 470

relarealaevRrllgdLRpaal<-*
+ ++e+la+vR+ll ++R+ +
CP002021_2 471 EVGVKESLADVRELLLHFRTRTQ 493

CP002021_0190: domain 1 of 1, from 179 to 244: score 62.4, E = 3.1e-18
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ERaR+AR+LHD +gQ L+a+ + + l+r+++ ++ +a e + ++
CP002021_0 179 ERARMARDLHDDLGQVLTALQMDVALLRKQF--GAA--QAPELFGNV 221

relarealaevRrllgdLRpaal<-*
+l++ a + Rr++++LRp++l
CP002021_0 222 DKLIHAAAEAGRRVASELRPSVL 244

CP002021_1211: domain 1 of 1, from 168 to 231: score 58.3, E = 5.3e-17
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ERaR+AR++HD++gQ L+a+k+ ++l+rr+l + +++l +
CP002021_1 168 ERARLARDMHDELGQLLTALKMDISLLRRRL--G----PDDAQLNSM 208

relarealaevRrllgdLRpaal<-*
+l++ a a Rr++ +LRpa+l
CP002021_1 209 TQLVDAATAAGRRVAAQLRPAVL 231


Histogram of all scores:
score obs exp (one = represents 9 sequences)
----- --- ---
-14 6 0|=
-13 27 0|===
-12 66 34|===*====
-11 151 284|================= *
-10 343 660|======================================= *
-9 492 750|======================================================= *
-8 431 578|================================================ *
-7 400 363|========================================*====
-6 351 205|======================*================
-5 314 110|============*======================
-4 179 57|======*=============
-3 142 29|===*============
-2 69 15|=*======
-1 48 7|*=====
0 24 3|*==
1 20 1|*==
2 12 1|*=
3 6 0|=
4 9 0|=
5 4 0|=
6 3 0|=
7 1 0|=
8 1 0|=
9 0 0|
> 10 7 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 1936.8804
P(chi-square) = 0

Total sequences searched: 3106

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: