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:
132 projects found  

6 accessions found for Rhizobium leguminosarum bv. trifolii WSM1325  

Data for CP001625  

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_1.hmm [HisKA]
Sequence database: CP001625.Gprot.fsa
per-sequence score cutoff: >= 26.8 [TC1]
per-domain score cutoff: >= 26.8 [TC2]
per-sequence Eval cutoff: [none]
per-domain Eval cutoff: [none]
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Query HMM: HisKA
Accession: PF00512.12
Description: His Kinase A (phosphoacceptor) domain
[HMM has been calibrated; E-values are empirical estimates]

Scores for complete sequences (score includes all domains):
Sequence Description Score E-value N
-------- ----------- ----- ------- ---
CP001625_0300 CDS_326247-331784 43.8 5.4e-13 1
CP001625_0286 CDS_313112-310929 36.5 6.3e-11 1
CP001625_0316 CDS_346729-348855 29.6 5.7e-09 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP001625_0300 1/1 1605 1675 .. 1 87 [] 43.8 5.4e-13
CP001625_0286 1/1 356 423 .. 1 87 [] 36.5 6.3e-11
CP001625_0316 1/1 332 400 .. 1 87 [] 29.6 5.7e-09

Alignments of top-scoring domains:
CP001625_0300: domain 1 of 1, from 1605 to 1675: score 43.8, E = 5.4e-13
*->akseflanlsHELRTPLtaIrgyaelLleeldkvlagdtelseeqrl
+++++a+++HE ++PL+a +++a+++l++l + + e++
CP001625_0 1605 TMGQLTASIAHEVNQPLAASLTNAQAALRWLA-----TRPPNLEEV- 1645

peLRledpeyreyletilreaerllrLindlLdlsrieag<-*
++l++i + a+r + i +++ l + e
CP001625_0 1646 ----------TQALDRIVENANRAGDVIGRIRALVKKEPT 1675

CP001625_0286: domain 1 of 1, from 356 to 423: score 36.5, E = 6.3e-11
*->akseflanlsHELRTPLtaIrgyaelLleeldkvlagdtelseeqrl
a ++++ +++H++++ L I g++++L + +l++e
CP001625_0 356 AVGQLTGGVAHDFNNLLQIIVGNLDTLMR----------TLPPEA-- 390

peLRledpeyreyletilreaerllrLindlLdlsrieag<-*
+Rl r++ + + + a+r +L ++lL ++r +a
CP001625_0 391 --GRL-----RRAASQAMNGARRAAALTQRLLAFARRQAL 423

CP001625_0316: domain 1 of 1, from 332 to 400: score 29.6, E = 5.7e-09
*->akseflanlsHELRTPLtaIrgyaelLleeldkvlagdtelseeqrl
a ++++ +++H++++ Lt+I+g + ++++ + + + ++
CP001625_0 332 AVGQLTGGIAHDFNNMLTGIIGGINVAKR------RIAGGRLDDV-- 370

peLRledpeyreyletilreaerllrLindlLdlsrieag<-*
++ + + ++a+r +Li +lL +sr ++
CP001625_0 371 ----------DRFMDAAADAANRAAALIARLLAFSRRQTL 400


Histogram of all scores:
score obs exp (one = represents 2 sequences)
----- --- ---
-14 5 0|===
-13 14 0|=======
-12 32 11|=====*==========
-11 52 58|========================== *
-10 81 108|========================================= *
-9 90 112|============================================= *
-8 73 83|===================================== *
-7 60 52|=========================*====
-6 34 30|==============*==
-5 18 16|=======*=
-4 13 8|===*===
-3 4 4|=*
-2 6 2|*==
-1 3 1|*=
0 2 0|=
1 0 0|
2 1 0|=
3 1 0|=
4 0 0|
> 5 5 -|===


% Statistical details of theoretical EVD fit:
mu = -8.9758
lambda = 0.6525
chi-sq statistic = 54.8666
P(chi-square) = 4.687e-09

Total sequences searched: 494

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: