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 Escherichia coli IHE3034  

Data for CP001969  

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: CP001969.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
-------- ----------- ----- ------- ---
CP001969_1321 CDS_1396105-1394309 79.6 4.2e-23 1
CP001969_2657 CDS_2850591-2852291 76.1 4.5e-22 1
CP001969_3961 CDS_4229046-4227553 63.7 2.1e-18 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP001969_1321 1/1 390 458 .. 1 70 [] 79.6 4.2e-23
CP001969_2657 1/1 361 428 .. 1 70 [] 76.1 4.5e-22
CP001969_3961 1/1 301 367 .. 1 70 [] 63.7 2.1e-18

Alignments of top-scoring domains:
CP001969_1321: domain 1 of 1, from 390 to 458: score 79.6, E = 4.2e-23
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ERa IARELHDs++QsLs +k+q++ ++++ d+ pe re l +i
CP001969_1 390 ERATIARELHDSIAQSLSCMKMQVSCLQMQG--DALPESSRELLSQI 434

relarealaevRrllgdLR.paal<-*
r ++ + ++R+ll+++R ++
CP001969_1 435 RNELNASWVQLRELLTTFRlQLTE 458

CP001969_2657: domain 1 of 1, from 361 to 428: score 76.1, E = 4.5e-22
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ERa IARELHDs++Q Ls +++ql l++r + ++d++ a+ ++
CP001969_2 361 ERATIARELHDSLAQVLSYLRIQLTLLKRSI--PEDNATAQSIMADF 405

relarealaevRrllgdLRpaal<-*
+++++a++++R+ll+++R +
CP001969_2 406 SQALNDAYRQLRELLTTFRLTLQ 428

CP001969_3961: domain 1 of 1, from 301 to 367: score 63.7, E = 2.1e-18
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
R+ ARELHD +gQ+++ai+ q++ ++rl+ +d++ +++ + i
CP001969_3 301 VRRDVARELHDDIGQTITAIRTQAGIVQRLA---ADNASVKQSGQLI 344

relarealaevRrllgdLRpaal<-*
++l+ ++ vRrllg+LRp +l
CP001969_3 345 EQLSLGVYDAVRRLLGRLRPRQL 367


Histogram of all scores:
score obs exp (one = represents 16 sequences)
----- --- ---
-16 2 0|=
-15 5 0|=
-14 64 0|====
-13 157 0|==========
-12 196 53|===*=========
-11 293 435|=================== *
-10 772 1011|================================================= *
-9 903 1148|========================================================= *
-8 720 885|============================================= *
-7 589 556|==================================*==
-6 387 315|===================*=====
-5 310 168|==========*=========
-4 164 88|=====*=====
-3 78 45|==*==
-2 56 23|=*==
-1 26 11|*=
0 15 5|*
1 6 3|*
2 4 1|*
3 3 0|=
4 0 0|
5 0 0|
6 1 0|=
7 1 0|=
8 0 0|
9 1 0|=
> 10 4 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 872.9938
P(chi-square) = 0

Total sequences searched: 4757

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: