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  

1 accessions found for Bifidobacterium dentium Bd1  

Data for CP001750  

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: CP001750.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
-------- ----------- ----- ------- ---
CP001750_0779 CDS_943798-941261 86.0 2.5e-25 2
CP001750_1345 CDS_1618401-1617232 59.3 1.9e-17 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP001750_0779 1/2 237 304 .. 1 70 [] 68.8 2.9e-20
CP001750_1345 1/1 196 264 .. 1 70 [] 59.3 1.9e-17

Alignments of top-scoring domains:
CP001750_0779: domain 1 of 2, from 237 to 304: score 68.8, E = 2.9e-20
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ERaRIAR++HD+v+++Ls i++q+++ r++ + dp ar ++++i
CP001750_0 237 ERARIARDMHDVVAHTLSIIIVQSDGGRYAG--ANDPVVARSTMETI 281

relarealaevRrllgdLRpaal<-*
r+ +++al ++ rllg++ + +
CP001750_0 282 RHESEHALHDMTRLLGVFGGSPH 304

CP001750_1345: domain 1 of 1, from 196 to 264: score 59.3, E = 1.9e-17
*->ERaRIARELHDsvgQsLsaiklqlelarrllds..dkdpeeareald
ER+RIARE+HD vg+ L+ +++q+e+ + ++ + + +d + ++ ++
CP001750_1 196 ERTRIAREIHDNVGHLLTRAIMQSEASQVVA-QisGRD--ADARGFE 239

eirelarealaevRrllgdLRpaal<-*
i+++++ea++ vRr ++dL++ +
CP001750_1 240 DIHATVNEAMTMVRRSVHDLKEEGA 264


Histogram of all scores:
score obs exp (one = represents 8 sequences)
----- --- ---
-14 17 0|===
-13 50 0|=======
-12 48 23|==*===
-11 98 195|============= *
-10 311 452|======================================= *
-9 423 514|===================================================== *
-8 311 396|======================================= *
-7 256 249|===============================*
-6 203 140|=================*========
-5 178 75|=========*=============
-4 95 39|====*=======
-3 54 20|==*====
-2 33 10|=*===
-1 22 5|*==
0 10 2|*=
1 5 1|*
2 6 0|=
3 2 0|=
4 1 0|=
5 1 0|=
6 0 0|
7 2 0|=
> 8 3 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 554.2505
P(chi-square) = 0

Total sequences searched: 2129

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: