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:
106 projects found  

3 accessions found for Nocardia farcinica IFM 10152  

Data for AP006618  

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_2.hmm [HisKA_2]
Sequence database: AP006618.Gprot.fsa
per-sequence score cutoff: >= 32.2 [TC1]
per-domain score cutoff: >= 32.2 [TC2]
per-sequence Eval cutoff: [none]
per-domain Eval cutoff: [none]
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Query HMM: HisKA_2
Accession: PF07568.2
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
-------- ----------- ----- ------- ---
AP006618_4590 CDS_4766067-4764553 121.8 2.5e-34 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
AP006618_4590 1/1 305 388 .. 1 94 [] 121.8 2.5e-34

Alignments of top-scoring domains:
AP006618_4590: domain 1 of 1, from 305 to 388: score 121.8, E = 2.5e-34
*->EIHHRVKNNLQvISSLLrLQarkfkdeevikdEVleaLrEsqnRVlS
EIHHRVKNNLQ++++LLrLQar++++ee+ + aL Es++RV S
AP006618_4 305 EIHHRVKNNLQTVAALLRLQARRTENEEA-----QVALTESVRRVTS 346

mAliHEeLYksedldtvdfseYlekLtenLfqsygvgsdgisLklDl<-*
+A +HE+L++s d + vd++e++++L+ + + ++v +i+ +
AP006618_4 347 IASVHEMLSMSVD-EEVDLDEVVDRLLPIMADVATVHTTRIK----V 388


Histogram of all scores:
score obs exp (one = represents 31 sequences)
----- --- ---
-15 8 0|=
-14 36 0|==
-13 95 35|=*==
-12 397 373|============*
-11 1788 1039|=================================*========================
-10 1282 1345|========================================== *
-9 774 1135|========================= *
-8 617 762|==================== *
-7 270 452|========= *
-6 220 252|========*
-5 81 135|=== *
-4 41 71|==*
-3 33 37|=*
-2 21 19|*
-1 11 10|*
0 2 5|*
1 1 2|*
2 1 1|*
3 1 0|=
4 1 0|=
5 1 0|=
> 6 2 -|=


% Statistical details of theoretical EVD fit:
mu = -9.5227
lambda = 0.6548
chi-sq statistic = 899.7961
P(chi-square) = 0

Total sequences searched: 5683

Whole sequence top hits:
tophits_s report:
Total hits: 1
Satisfying E cutoff: 1
Total memory: 20K

Domain top hits:
tophits_s report:
Total hits: 1
Satisfying E cutoff: 1
Total memory: 21K


Acknowledgements:

This research is funded by:

Developed by: