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  

2 accessions found for Geobacter lovleyi SZ  

Data for CP001089  

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)
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file: /home/projects/MicrobialGenomicsGroup/Packages/hmmdata-1.0.0.package/Resources/noarch/TCS/HisKA_3.hmm [HisKA_3]
Sequence database: CP001089.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]
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

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
-------- ----------- ----- ------- ---
CP001089_1537 CDS_1652925-1654634 51.1 8.2e-15 1
CP001089_1541 CDS_1655952-1657139 46.9 1.4e-13 1
CP001089_2886 CDS_3131989-3130013 30.3 1.1e-08 2

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP001089_1537 1/1 373 440 .. 1 70 [] 51.1 8.2e-15
CP001089_1541 1/1 193 258 .. 1 70 [] 46.9 1.4e-13

Alignments of top-scoring domains:
CP001089_1537: domain 1 of 1, from 373 to 440: score 51.1, E = 8.2e-15
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+RI+RELHD++gQ+L a+ l l l++ + + ++ r a+ e+
CP001089_1 373 ERTRISRELHDGIGQALHAVLLRLKLLLGTI--EPGRGAERIAIGEL 417

relarealaevRrllgdLRpaal<-*
+ ++ a ae+R+l+ LRp l
CP001089_1 418 IQDIQNASAELRNLVISLRPLPL 440

CP001089_1541: domain 1 of 1, from 193 to 258: score 46.9, E = 1.4e-13
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+ IAR++HD +gQ+L+a+ l + + ++ +++ + +l +
CP001089_1 193 ERRSIARDIHDDLGQTLTAMHLEITAMLH----ADNVIDLTPRLCDL 235

relarealaevRrllgdLRpaal<-*
++ ++ a+ v r+++++Rp++l
CP001089_1 236 KKQVDAAIGTVQRIISTMRPQVL 258


Histogram of all scores:
score obs exp (one = represents 12 sequences)
----- --- ---
-15 1 0|=
-14 23 0|==
-13 74 0|=======
-12 131 40|===*=======
-11 171 330|=============== *
-10 511 766|=========================================== *
-9 679 870|========================================================= *
-8 510 671|=========================================== *
-7 448 421|===================================*==
-6 340 238|===================*=========
-5 290 128|==========*==============
-4 148 66|=====*=======
-3 106 34|==*======
-2 56 17|=*===
-1 48 8|*===
0 29 4|*==
1 11 2|*
2 12 1|*
3 6 0|=
4 3 0|=
5 1 0|=
6 3 0|=
> 7 5 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 1198.8689
P(chi-square) = 0

Total sequences searched: 3606

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: 2
Satisfying E cutoff: 2
Total memory: 21K


Acknowledgements:

This research is funded by:

Developed by: