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 Pseudomonas fluorescens Pf-5  

Data for CP000076  

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: CP000076.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
-------- ----------- ----- ------- ---
CP000076_3771 CDS_4419683-4420843 73.9 2.6e-21 1
CP000076_4146 CDS_4891646-4892638 72.6 6.5e-21 1
CP000076_5549 CDS_6426584-6424188 63.8 2.5e-18 1
CP000076_2166 CDS_2470832-2472103 50.7 1.8e-14 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP000076_3771 1/1 184 251 .. 1 70 [] 73.9 2.6e-21
CP000076_4146 1/1 120 184 .. 1 70 [] 72.6 6.5e-21
CP000076_5549 1/1 599 666 .. 1 70 [] 63.8 2.5e-18
CP000076_2166 1/1 224 290 .. 1 70 [] 50.7 1.8e-14

Alignments of top-scoring domains:
CP000076_3771: domain 1 of 1, from 184 to 251: score 73.9, E = 2.6e-21
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+R A +LHD+++Q+L+++ l++ + + + pe++ ++l++i
CP000076_3 184 ERKRVAYDLHDGLAQTLAGLHQRLQGFAGRC--PPLPEPLHDELQTI 228

relarealaevRrllgdLRpaal<-*
+la+ + e R+l+g+LRp +l
CP000076_3 229 LQLAQGCVGEGRQLIGGLRPHVL 251

CP000076_4146: domain 1 of 1, from 120 to 184: score 72.6, E = 6.5e-21
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+R++RELHD +gQ L+a+klq+++++ ++ p+e++e+ + +
CP000076_4 120 ERHRLSRELHDDIGQLLTAAKLQTDWLK-----RRLPDELQEHCAVL 161

relarealaevRrllgdLRpaal<-*
++++e+la vR++ L p +l
CP000076_4 162 GTTLEETLAKVRDVSAILNPRQL 184

CP000076_5549: domain 1 of 1, from 599 to 666: score 63.8, E = 2.5e-18
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
E aRIARE HD++gQ+L+++kl +++++ ++ + ++ + e+l +
CP000076_5 599 EKARIAREVHDELGQMLTVLKLETSMCELAY--AQLDPGLHERLNSM 643

relarealaevRrllgdLRpaal<-*
++l+ + + vR+++++LRp++l
CP000076_5 644 KRLIAQLFQLVRDVATALRPPIL 666

CP000076_2166: domain 1 of 1, from 224 to 290: score 50.7, E = 1.8e-14
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+ +A+ LHD +gQ L++i+ q+ l+r++ p ++++++++
CP000076_2 224 ERTYLAQTLHDDLGQYLAGIRAQACLLRMVS---NQPTVVEQTAQAL 267

relarealaevRrllgdLRpaal<-*
+ +++ ++ R+l++dL p +l
CP000076_2 268 ELNCERLQQGFRALVQDLYPVVL 290


Histogram of all scores:
score obs exp (one = represents 18 sequences)
----- --- ---
-14 12 0|=
-13 62 0|====
-12 117 68|===*===
-11 224 562|============= *
-10 727 1305|========================================= *
-9 1047 1482|==========================================================*
-8 941 1142|===================================================== *
-7 861 718|=======================================*========
-6 677 406|======================*===============
-5 578 218|============*====================
-4 344 113|======*=============
-3 204 58|===*========
-2 132 29|=*======
-1 76 15|*====
0 46 7|*==
1 38 3|*==
2 10 1|*
3 15 1|*
4 9 0|=
5 3 0|=
6 0 0|
7 3 0|=
8 2 0|=
9 0 0|
10 1 0|=
11 2 0|=
12 1 0|=
13 0 0|
14 1 0|=
> 15 5 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 3067.5098
P(chi-square) = 0

Total sequences searched: 6138

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: