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:
106 projects found  

2 accessions found for Mycobacterium marinum M  

Data for CP000854  

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: CP000854.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
-------- ----------- ----- ------- ---
CP000854_1497 CDS_1833042-1834799 55.8 4.8e-16 1
CP000854_3427 CDS_4286001-4284352 53.5 2.3e-15 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP000854_1497 1/1 393 459 .. 1 70 [] 55.8 4.8e-16
CP000854_3427 1/1 355 421 .. 1 70 [] 53.5 2.3e-15

Alignments of top-scoring domains:
CP000854_1497: domain 1 of 1, from 393 to 459: score 55.8, E = 4.8e-16
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpe.earealde
ER RIAR+LHD v Q+L+ai l l++ ++ e++++++l e
CP000854_1 393 ERDRIARDLHDHVIQRLFAIGLALQGSV-----PRTREpKVQQRLSE 434

irelarealaevRrllgdLR.paal<-*
+ + ++ ++e+R ++ dL++ ++
CP000854_1 435 VIDDLQGVIQEIRTTIFDLHgSSQG 459

CP000854_3427: domain 1 of 1, from 355 to 421: score 53.5, E = 2.3e-15
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+RIA +LHD v Q+L+a + l++ ++++ +++ e+ ++l +
CP000854_3 355 ERERIAHDLHDHVIQRLFASGMDLQGTLARA--RSP--EVIDRLNRT 397

relarealaevRrllgdLR.paal<-*
+ +++ ++e+R ++ +L++p++
CP000854_3 398 VDDLQTIIEEIRSTIFQLKsPSGR 421


Histogram of all scores:
score obs exp (one = represents 16 sequences)
----- --- ---
-14 8 0|=
-13 36 0|===
-12 121 60|===*====
-11 177 497|============ *
-10 575 1153|==================================== *
-9 920 1309|==========================================================*
-8 839 1009|===================================================== *
-7 719 634|=======================================*=====
-6 645 359|======================*==================
-5 586 192|===========*=========================
-4 313 100|======*=============
-3 200 51|===*=========
-2 121 26|=*======
-1 63 13|*===
0 34 6|*==
1 26 3|*=
2 19 1|*=
3 7 0|=
4 5 0|=
5 1 0|=
6 2 0|=
> 7 6 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 3245.9199
P(chi-square) = 0

Total sequences searched: 5423

Whole sequence top hits:
tophits_s report:
Total hits: 2
Satisfying E cutoff: 2
Total memory: 20K

Domain top hits:
tophits_s report:
Total hits: 2
Satisfying E cutoff: 2
Total memory: 21K


Acknowledgements:

This research is funded by:

Developed by: