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:
14 projects found  

1 accessions found for Dehalococcoides sp. VS  

Data for CP001827  

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: CP001827.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
-------- ----------- ----- ------- ---
CP001827_0873 CDS_871826-868146 68.0 3.3e-20 1
CP001827_0348 CDS_361143-360070 57.2 4.9e-17 1
CP001827_0568 CDS_565278-564133 54.0 4.5e-16 2

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP001827_0873 1/1 1020 1084 .. 1 70 [] 68.0 3.3e-20
CP001827_0348 1/1 147 214 .. 1 70 [] 57.2 4.9e-17
CP001827_0568 2/2 171 238 .. 1 70 [] 53.9 4.7e-16

Alignments of top-scoring domains:
CP001827_0873: domain 1 of 1, from 1020 to 1084: score 68.0, E = 3.3e-20
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER IARELHD vgQsL+++kl+l+ a+ d p++a+e l+e+
CP001827_0 1020 ERSIIARELHDQVGQSLTVLKLMLDKAK-----DGLPDKAEELLAEA 1061

relarealaevRrllgdLRpaal<-*
+ l++e ++ vR++ dLRp l
CP001827_0 1062 QPLVSELISSVRNMSLDLRPRML 1084

CP001827_0348: domain 1 of 1, from 147 to 214: score 57.2, E = 4.9e-17
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+RI+RELHD+v+ L +++ +++ + ++ ++d + + +ld++
CP001827_0 147 ERKRISRELHDEVAPLLLLLMQKIDNLGKQS--ERDIADCKPQLDAL 191

relarealaevRrllgdLRpaal<-*
r ++eal+ +Rr+++dLRp +l
CP001827_0 192 RSQSEEALESLRRIAQDLRPRIL 214

CP001827_0568: domain 2 of 2, from 171 to 238: score 53.9, E = 4.7e-16
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpe...eareal
ER+RIA+ELHD +Q L +i+ +++ + +p ++ ++l
CP001827_0 171 ERRRIAQELHDDTAQDLIVISRAIDRFV-----TQNPNlgeDNLAEL 212

deirelarealaevRrllgdLRpaal<-*
+e++ +++++l+evRr ++dLRp++l
CP001827_0 213 EELQNHVNRTLSEVRRFAQDLRPSVL 238


Histogram of all scores:
score obs exp (one = represents 6 sequences)
----- --- ---
-14 9 0|==
-13 50 0|=========
-12 78 16|==*==========
-11 111 131|=================== *
-10 258 305|=========================================== *
-9 301 347|=================================================== *
-8 208 267|=================================== *
-7 153 168|========================== *
-6 102 95|===============*=
-5 67 51|========*===
-4 49 26|====*====
-3 16 13|==*
-2 9 7|=*
-1 7 3|*=
0 2 1|*
1 5 0|=
2 4 0|=
> 3 9 -|==


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 295.5589
P(chi-square) = 0

Total sequences searched: 1438

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: