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 Haemophilus influenzae PittGG  

Data for CP000672  

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: CP000672.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
-------- ----------- ----- ------- ---
CP000672_0603 CDS_698228-696432 74.8 3e-21 1
CP000672_0105 CDS_125268-123991 70.8 4.2e-20 1
CP000672_0374 CDS_410956-409601 46.3 3.5e-13 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP000672_0603 1/1 121 186 .. 1 87 [] 74.8 3e-21
CP000672_0105 1/1 194 260 .. 1 87 [] 70.8 4.2e-20
CP000672_0374 1/1 234 300 .. 1 87 [] 46.3 3.5e-13

Alignments of top-scoring domains:
CP000672_0603: domain 1 of 1, from 121 to 186: score 74.8, E = 3e-21
*->akseflanlsHELRTPLtaIrgyaelLleeldkvlagdtelseeqrl
ks +la++sHE+RTPL++I g++++Ll+ +el++ q
CP000672_0 121 DKSTLLATISHEFRTPLNGIVGLSQILLD---------DELDDLQ-- 156

peLRledpeyreyletilreaerllrLindlLdlsrieag<-*
r yl+ti +a +l + +d+ dl++i+a
CP000672_0 157 ----------RNYLKTINISAVSLGYIFSDIIDLEKIDAS 186

CP000672_0105: domain 1 of 1, from 194 to 260: score 70.8, E = 4.2e-20
*->akseflanlsHELRTPLtaIrgyaelLleeldkvlagdtelseeqrl
++++fl+n+ HELRTPLt+++gy+e+L ++ +++ q
CP000672_0 194 SRQKFLSNINHELRTPLTVLQGYLEILADN--------NIQNPLQ-- 230

peLRledpeyreyletilreaerllrLindlLdlsrieag<-*
++++ ++++++r+++L++++ l++ie+
CP000672_0 231 ----------KKAIFAMQEQSQRMEHLLQQFNFLAKIETT 260

CP000672_0374: domain 1 of 1, from 234 to 300: score 46.3, E = 3.5e-13
*->akseflanlsHELRTPLtaIrgyaelLleeldkvlagdtelseeqrl
+ ++f+++++HELR PL+a+r +e+++ + + r
CP000672_0 234 RERRFTSDAAHELRSPLAALRIQTEVAQL---------AGDDVALR- 270

peLRledpeyreyletilreaerllrLindlLdlsrieag<-*
+++l + + ++r ++Li++lL+lsr+++
CP000672_0 271 ----------EQALLHLTQGIDRASQLIEQLLTLSRLDNL 300


Histogram of all scores:
score obs exp (one = represents 6 sequences)
----- --- ---
-15 3 0|=
-14 17 0|===
-13 32 1|*=====
-12 95 38|======*=========
-11 189 197|================================*
-10 310 367|==================================================== *
-9 305 379|=================================================== *
-8 271 283|============================================== *
-7 174 178|=============================*
-6 124 102|================*====
-5 57 56|=========*
-4 39 30|====*==
-3 26 15|==*==
-2 11 8|=*
-1 7 4|*=
0 1 2|*
1 4 1|*
2 0 0|
3 1 0|=
4 0 0|
5 0 0|
> 6 4 -|=


% Statistical details of theoretical EVD fit:
mu = -8.9758
lambda = 0.6525
chi-sq statistic = 123.1659
P(chi-square) = 1.151e-21

Total sequences searched: 1670

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: