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:
76 projects found  

1 accessions found for Delftia acidovorans SPH-1  

Data for CP000884  

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: CP000884.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
-------- ----------- ----- ------- ---
CP000884_1103 CDS_1223846-1225744 69.7 4.5e-20 1
CP000884_5303 CDS_5901367-5902779 62.3 6.9e-18 1
CP000884_1803 CDS_2006767-2005382 52.9 3.9e-15 1
CP000884_0651 CDS_714612-713464 51.7 8.8e-15 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP000884_1103 1/1 421 489 .. 1 70 [] 69.7 4.5e-20
CP000884_5303 1/1 249 320 .. 1 70 [] 62.3 6.9e-18
CP000884_1803 1/1 252 319 .. 1 70 [] 52.9 3.9e-15
CP000884_0651 1/1 174 239 .. 1 70 [] 51.7 8.8e-15

Alignments of top-scoring domains:
CP000884_1103: domain 1 of 1, from 421 to 489: score 69.7, E = 4.5e-20
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpe.earealde
ER IARELHDs++QsL+ +k+q++l+r ++ +k +++ ++ l e
CP000884_1 421 ERGLIARELHDSIAQSLAFLKIQTQLLRDAV--AKGRDeARDRSLGE 465

irelarealaevRrllgdLRpaal<-*
++ +re++a+vR+ll ++R+ +
CP000884_1 466 LEVGVRECYADVRELLVHFRTRTS 489

CP000884_5303: domain 1 of 1, from 249 to 320: score 62.3, E = 6.9e-18
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpe....earea
ER+R AR+LHD+v Q L + k le+a+++l ++ +++++ a++
CP000884_5 249 ERTRVARDLHDGVVQVLVSSKFLLETAQAQL--RRLAAqdpaTAQRM 293

ldeirelarealaevRrllgdLRpaal<-*
+d+ e +++al e+Rr+ ++LRpa l
CP000884_5 294 VDQGLEQLNHALVEIRRVSHGLRPALL 320

CP000884_1803: domain 1 of 1, from 252 to 319: score 52.9, E = 3.9e-15
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER ++ARELHD++g L+a+kl + +++ + d ++ + e++ +
CP000884_1 252 ERGHLARELHDELGSLLTAAKLDVARLKSKI--DLSAPDVGERVSHL 296

relarealaevRrllgdLRpaal<-*
e+++ ++a Rr++ dLRp+ l
CP000884_1 297 VETLNSGIALKRRIIEDLRPSSL 319

CP000884_0651: domain 1 of 1, from 174 to 239: score 51.7, E = 8.8e-15
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ERa IARE+HD +g sL+++k + +++r + ++ +re++ ++
CP000884_0 174 ERASIAREIHDDIGGSLTSVKFDVAWIARNA--PEG--GLREHALAA 216

relarealaevRrllgdLRpaal<-*
e++++al r+ +LRp++l
CP000884_0 217 LEMLEHALGASQRIMMNLRPPVL 239


Histogram of all scores:
score obs exp (one = represents 16 sequences)
----- --- ---
-14 10 0|=
-13 48 0|===
-12 106 67|====*==
-11 174 553|=========== *
-10 663 1284|========================================== *
-9 933 1458|==========================================================*
-8 860 1124|====================================================== *
-7 869 706|============================================*==========
-6 724 400|========================*=====================
-5 621 214|=============*=========================
-4 358 111|======*================
-3 237 57|===*===========
-2 178 29|=*==========
-1 104 14|*======
0 60 7|*===
1 39 3|*==
2 14 1|*
3 18 0|==
4 6 0|=
5 4 0|=
6 3 0|=
> 7 11 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 4642.1714
P(chi-square) = 0

Total sequences searched: 6040

Whole sequence top hits:
tophits_s report:
Total hits: 4
Satisfying E cutoff: 4
Total memory: 20K

Domain top hits:
tophits_s report:
Total hits: 4
Satisfying E cutoff: 4
Total memory: 22K


Acknowledgements:

This research is funded by:

Developed by: