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:
35 projects found  

1 accessions found for Geobacter bemidjiensis Bem  

Data for CP001124  

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: CP001124.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
-------- ----------- ----- ------- ---
CP001124_0446 CDS_541868-544210 54.5 8.6e-16 1
CP001124_1900 CDS_2217672-2219141 44.9 5.9e-13 1
CP001124_2233 CDS_2623115-2624341 38.6 4.5e-11 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP001124_0446 1/1 576 641 .. 1 70 [] 54.5 8.6e-16
CP001124_1900 1/1 286 351 .. 1 70 [] 44.9 5.9e-13
CP001124_2233 1/1 214 277 .. 1 70 [] 38.6 4.5e-11

Alignments of top-scoring domains:
CP001124_0446: domain 1 of 1, from 576 to 641: score 54.5, E = 8.6e-16
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER RIA ELHD vgQ+L ++k++l+ ++ l + e ++++ +
CP001124_0 576 ERDRIASELHDQVGQRLILAKIKLDSLASNL--PLG--ECEAEAMGV 618

relarealaevRrllgdLRpaal<-*
++l++++l+++R l ++Rp++l
CP001124_0 619 ETLIEQTLQDIRSLTFQIRPPVL 641

CP001124_1900: domain 1 of 1, from 286 to 351: score 44.9, E = 5.9e-13
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER RIA ELHD vgQ+L + k++l+++ ll +e + ++ +
CP001124_1 286 ERCRIAGELHDQVGQNLILCKMKLDALMELL----QCGEPFDVAAGL 328

relarealaevRrllgdLRpaal<-*
++++++a++++R l ++Rp++l
CP001124_1 329 ETIIDQAIQDIRSLTFQMRPSIL 351

CP001124_2233: domain 1 of 1, from 214 to 277: score 38.6, E = 4.5e-11
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+RIA ELHD v Q+L++ kl l++ ++ + + r +e+
CP001124_2 214 ERRRIATELHDDVVQHLALCKLRLDMGLKDG--T----PSRVLQEEL 254

relarealaevRrllgdLRpaal<-*
+ + ++++++Rr+ dL p++l
CP001124_2 255 VGELVRTMQQIRRICYDLSPPVL 277


Histogram of all scores:
score obs exp (one = represents 13 sequences)
----- --- ---
-16 1 0|=
-15 0 0|
-14 31 0|===
-13 92 0|========
-12 139 44|===*=======
-11 229 368|================== *
-10 581 854|============================================= *
-9 728 970|======================================================== *
-8 597 747|============================================== *
-7 487 470|====================================*=
-6 395 266|====================*==========
-5 323 142|==========*==============
-4 152 74|=====*======
-3 99 38|==*=====
-2 63 19|=*===
-1 35 9|*==
0 25 5|*=
1 11 2|*
2 13 1|*
3 4 0|=
4 5 0|=
5 2 0|=
6 2 0|=
> 7 4 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 1133.5535
P(chi-square) = 0

Total sequences searched: 4018

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: