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:
132 projects found  

7 accessions found for Agrobacterium vitis S4  

Data for CP000633  

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_2.hmm [HisKA_2]
Sequence database: CP000633.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]
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

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
-------- ----------- ----- ------- ---
CP000633_0294 CDS_329270-328236 108.3 1e-30 1
CP000633_0884 CDS_1007844-1009019 101.3 1e-28 1
CP000633_1206 CDS_1367090-1368118 46.3 4.3e-13 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP000633_0294 1/1 150 238 .. 1 94 [] 108.3 1e-30
CP000633_0884 1/1 189 272 .. 1 94 [] 101.3 1e-28
CP000633_1206 1/1 150 233 .. 1 94 [] 46.3 4.3e-13

Alignments of top-scoring domains:
CP000633_0294: domain 1 of 1, from 150 to 238: score 108.3, E = 1e-30
*->EIHHRVKNNLQvISSLLrLQarkfkdeevikdEVleaLrEsqnRVlS
E++HRV N+L++++SLLrLQ ++++ ev ++ L E+q R+ +
CP000633_0 150 EVNHRVANSLALVASLLRLQIANARSDEV-----KAELTETQARITA 191

mAliHEeLYksedldtvdfseYlekLtenLfqsygvgsdgisLklDl<-*
+A H+ LY+s+d+++vd++ Y+ +L++++ s + ++ i L +D
CP000633_0 192 IAGMHRSLYTSDDVSRVDMDIYIANLVREIGGSLANPDKPITLTVDA 238

CP000633_0884: domain 1 of 1, from 189 to 272: score 101.3, E = 1e-28
*->EIHHRVKNNLQvISSLLrLQarkfkdeevikdEVleaLrEsqnRVlS
E++HRV N+LQ+I+S L+ ar++++ee+ + +L+++++R++S
CP000633_0 189 EVQHRVANSLQIIASVLMQSARRVQSEEA-----RGHLHDARQRIMS 230

mAliHEeLYksedldtvdfseYlekLtenLfqsygvgsdgisLklDl<-*
+A ++++L+ s + ++v++s+Y++ L+ +L s+ + +++s +
CP000633_0 231 IAALQRQLSASPG-GSVELSAYFTQLCQSLGASMIADPERLS----I 272

CP000633_1206: domain 1 of 1, from 150 to 233: score 46.3, E = 4.3e-13
*->EIHHRVKNNLQvISSLLrLQarkfkdeevikdEVleaLrEsqnRVlS
E HR+KN+LQ+ISS ++ + r++ ++ + e + q R+++
CP000633_1 150 ELAHRIKNSLQIISSFVSHEIRRAAEP-C-----AEGYKAMQARIRA 190

mAliHEeLYksedldtvdfseYlekLtenLfqsygvgsdgisLklDl<-*
+A +++ +s ++ v++ Yl+ + + +++s +++i +
CP000633_1 191 VAELYDVIAQSSAFGPVNMETYLRGINNTIRKSLLSPNSNIT----I 233


Histogram of all scores:
score obs exp (one = represents 15 sequences)
----- --- ---
-15 3 0|=
-14 11 0|=
-13 28 20|=*
-12 153 212|=========== *
-11 832 591|=======================================*================
-10 745 765|==================================================*
-9 569 646|====================================== *
-8 392 433|=========================== *
-7 196 257|============== *
-6 157 143|=========*=
-5 61 77|=====*
-4 47 40|==*=
-3 16 21|=*
-2 8 11|*
-1 5 5|*
0 4 3|*
> 1 7 -|=


% Statistical details of theoretical EVD fit:
mu = -9.5227
lambda = 0.6548
chi-sq statistic = 153.9997
P(chi-square) = 8.738e-27

Total sequences searched: 3234

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: 22K


Acknowledgements:

This research is funded by:

Developed by: