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 Shewanella frigidimarina NCIMB 400  

Data for CP000447  

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: CP000447.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
-------- ----------- ----- ------- ---
CP000447_0358 CDS_387395-386301 74.0 1.6e-21 1
CP000447_0618 CDS_725345-723630 73.0 3.1e-21 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP000447_0358 1/1 176 244 .. 1 70 [] 74.0 1.6e-21
CP000447_0618 1/1 366 435 .. 1 70 [] 73.0 3.1e-21

Alignments of top-scoring domains:
CP000447_0358: domain 1 of 1, from 176 to 244: score 74.0, E = 1.6e-21
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpe.earealde
ER+RI R+LHD+ g++L+ai+l++ela +l+ ++ ++a++++++
CP000447_0 176 ERERIGRDLHDVMGHHLAAIALKAELADKLI--ASGKIdQAQQQIHQ 220

irelarealaevRrllgdLRpaal<-*
+ + r++l+++R++++++++++l
CP000447_0 221 VSVITRDCLSQIRHTVSGYKHQGL 244

CP000447_0618: domain 1 of 1, from 366 to 435: score 73.0, E = 3.1e-21
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpe..eareald
ERa IARELHDs+gQ Ls +k+q++l+r+ l d ++e++ +l+
CP000447_0 366 ERAVIARELHDSIGQLLSFLKIQVSLLRKSL--DHSCRspEVEGQLT 410

eirelarealaevRrllgdLRpaal<-*
ei e +++a+ ++R+ll+++R ++
CP000447_0 411 EINEGVSTAYVQLRELLSTFRLTIK 435


Histogram of all scores:
score obs exp (one = represents 15 sequences)
----- --- ---
-14 22 0|==
-13 100 0|=======
-12 204 45|==*===========
-11 330 369|====================== *
-10 761 856|=================================================== *
-9 845 972|========================================================= *
-8 601 749|========================================= *
-7 429 471|============================= *
-6 295 266|=================*==
-5 213 143|=========*=====
-4 98 74|====*==
-3 56 38|==*=
-2 31 19|=*=
-1 21 9|*=
0 6 5|*
1 7 2|*
2 5 1|*
3 1 0|=
4 1 0|=
> 5 3 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 698.1097
P(chi-square) = 0

Total sequences searched: 4029

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: