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Chlamydiae/Verrucomicrobia Chloroflexi Cyanobacteria
Deinococcus-Thermus Deltaproteobacteria Epsilonproteobacteria
Firmicutes Fusobacteria Gammaproteobacteria
Other Bacteria Planctomycetes Spirochaetes
Thermotogae
Classification of phyla is from NCBI page
Search:
132 projects found  

3 accessions found for Rhizobium sp. NGR234  

Data for CP001389  

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/HWE_HK.hmm [HWE_HK]
Sequence database: CP001389.Gprot.fsa
per-sequence score cutoff: >= 60.0 [TC1]
per-domain score cutoff: >= 60.0 [TC2]
per-sequence Eval cutoff: [none]
per-domain Eval cutoff: [none]
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query HMM: HWE_HK
Accession: PF07536.4
Description: HWE 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
-------- ----------- ----- ------- ---
CP001389_3438 CDS_3733315-3735666 152.4 8.2e-52 1
CP001389_2416 CDS_2558960-2557461 144.8 3.3e-49 1
CP001389_3490 CDS_3788363-3790069 116.4 1.6e-39 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP001389_3438 1/1 592 674 .. 1 85 [] 152.4 8.2e-52
CP001389_2416 1/1 313 395 .. 1 85 [] 144.8 3.3e-49
CP001389_3490 1/1 376 458 .. 1 85 [] 116.4 1.6e-39

Alignments of top-scoring domains:
CP001389_3438: domain 1 of 1, from 592 to 674: score 152.4, E = 8.2e-52
*->ELnHRVKNtLAvVQSiarQTlRnaasldefveaFsgRLqALsraHdL
EL+HRVKNtLAvVQS+arQTlR+++s ++fve+F+gRL+AL++aH L
CP001389_3 592 ELSHRVKNTLAVVQSLARQTLRTTDSGEDFVERFDGRLAALAGAHKL 638

VpLtrseWagAdLreLleaeLaPyggedaeRitlsGPd<-*
L++seWagA+L++L+ +L++y g d++R++++G++
CP001389_3 639 --LVESEWAGAELGALAFDQLRAYSGGDPGRLQFEGDR 674

CP001389_2416: domain 1 of 1, from 313 to 395: score 144.8, E = 3.3e-49
*->ELnHRVKNtLAvVQSiarQTlRnaasldefveaFsgRLqALsraHdL
ELnHRVKNtLA+ QS+arQTlR++ +++ef++aF+gRLqA s+aH+L
CP001389_2 313 ELNHRVKNTLAMLQSLARQTLRQTSDPAEFMTAFAGRLQAISEAHGL 359

VpLtrseWagAdLreLleaeLaPyggedaeRitlsGPd<-*
L++ eW+ +L+eL++ +L Py +++ae+++++ ++
CP001389_2 360 --LSDYEWGTIRLAELISKQLKPYVSDYAEQVEIHKDE 395

CP001389_3490: domain 1 of 1, from 376 to 458: score 116.4, E = 1.6e-39
*->ELnHRVKNtLAvVQSiarQTlRnaasldefveaFsgRLqALsraHdL
E+ HR+KN+L+v+QS+ +Q++ ++++ efv+aF+ RL+ L+r+ dL
CP001389_3 376 EVAHRSKNQLTVIQSMLAQSAWSSEDTSEFVDAFRKRLAGLARSTDL 422

VpLtrseWagAdLreLleaeLaPyggedaeRitlsGPd<-*
+ ++g+d+reL+e++L+P++++ ++Ri+l+GP+
CP001389_3 423 --MIANAAMGVDFRELAEEQLQPFAPDEPGRIVLDGPA 458


Histogram of all scores:
score obs exp (one = represents 12 sequences)
----- --- ---
-15 1 0|=
-14 13 0|==
-13 47 0|====
-12 246 0|=====================
-11 409 29|==*================================
-10 579 375|===============================*=================
-9 661 929|======================================================== *
-8 645 965|====================================================== *
-7 413 648|=================================== *
-6 233 353|==================== *
-5 159 175|==============*
-4 108 83|======*==
-3 52 38|===*=
-2 34 17|=*=
-1 14 8|*=
0 6 3|*
1 3 1|*
2 1 0|=
3 2 0|=
4 1 0|=
> 5 6 -|=


% Statistical details of theoretical EVD fit:
mu = -7.9989
lambda = 0.7843
chi-sq statistic = 5299.6040
P(chi-square) = 0

Total sequences searched: 3633

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: 22K


Acknowledgements:

This research is funded by:

Developed by: