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  

1 accessions found for Mycobacterium avium 104  

Data for CP000479  

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: CP000479.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
-------- ----------- ----- ------- ---
CP000479_5090 CDS_5436113-5434893 58.2 9.4e-17 1
CP000479_3954 CDS_4231760-4230105 54.4 1.2e-15 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP000479_5090 1/1 190 254 .. 1 65 [. 58.2 9.4e-17
CP000479_3954 1/1 357 423 .. 1 70 [] 54.4 1.2e-15

Alignments of top-scoring domains:
CP000479_5090: domain 1 of 1, from 190 to 254: score 58.2, E = 9.4e-17
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+RIARE HD++++sLs l++ +arr+l++d+d + a eal+++
CP000479_5 190 ERRRIAREVHDVIAHSLSITLLHVTGARRALQQDRDVDDAVEALEQA 236

relarealaevRrllgdL<-*
++l+r+a+a++Rr++g L
CP000479_5 237 ERLGRQAMADIRRTVGLL 254

CP000479_3954: domain 1 of 1, from 357 to 423: score 54.4, E = 1.2e-15
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+RIA +LHD v Q+L+a+ + l++ ++++ +++ e++++l +
CP000479_3 357 ERERIAHDLHDHVIQRLFAAGMDLQGTLARA--RSP--EVADRLNRT 399

relarealaevRrllgdLR.paal<-*
+ +++ ++e+R ++ +LR+paa
CP000479_3 400 LDDLQTIIEEIRTTIFALRsPAAV 423


Histogram of all scores:
score obs exp (one = represents 15 sequences)
----- --- ---
-14 9 0|=
-13 72 0|=====
-12 120 57|===*====
-11 184 469|============= *
-10 476 1088|================================ *
-9 830 1236|======================================================== *
-8 741 952|================================================== *
-7 733 599|=======================================*=========
-6 611 339|======================*==================
-5 585 181|============*==========================
-4 283 94|======*============
-3 155 48|===*=======
-2 137 24|=*========
-1 68 12|*====
0 50 6|*===
1 20 3|*=
2 15 1|*
3 12 0|=
4 4 0|=
5 3 0|=
6 2 0|=
7 3 0|=
8 1 0|=
9 0 0|
10 1 0|=
11 1 0|=
12 0 0|
> 13 4 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 3550.7278
P(chi-square) = 0

Total sequences searched: 5120

Whole sequence top hits:
tophits_s report:
Total hits: 2
Satisfying E cutoff: 2
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: