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  

4 accessions found for Nitrobacter hamburgensis X14  

Data for CP000319  

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/HWE_HK.hmm [HWE_HK]
Sequence database: CP000319.Gprot.fsa
per-sequence score cutoff: >= 60.0 [TC1]
per-domain score cutoff: >= 60.0 [TC2]
per-sequence Eval cutoff: [none]
per-domain Eval cutoff: [none]
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query HMM: HWE_HK
Accession: PF07536.4
Description: HWE 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
-------- ----------- ----- ------- ---
CP000319_3400 CDS_3931214-3929544 124.6 2.6e-42 1
CP000319_1096 CDS_1309078-1308251 112.4 3.9e-38 1
CP000319_3623 CDS_4195228-4196229 87.6 1.1e-29 1
CP000319_1139 CDS_1368994-1370805 73.5 6.4e-25 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP000319_3400 1/1 347 425 .. 1 85 [] 124.6 2.6e-42
CP000319_1096 1/1 76 158 .. 1 85 [] 112.4 3.9e-38
CP000319_3623 1/1 140 227 .. 1 85 [] 87.6 1.1e-29
CP000319_1139 1/1 411 495 .. 1 85 [] 73.5 6.4e-25

Alignments of top-scoring domains:
CP000319_3400: domain 1 of 1, from 347 to 425: score 124.6, E = 2.6e-42
*->ELnHRVKNtLAvVQSiarQTlRnaasldefveaFsgRLqALsraHdL
ELnHRVKN+LAv+QSi++ TlR+ +++ ++e ++gR++A+s++ +L
CP000319_3 347 ELNHRVKNILAVIQSIVTRTLRHGSDIEVARELLIGRIHAMSNVVSL 393

VpLtrseWagAdLreLleaeLaPyggedaeRitlsGPd<-*
L++s+W+g+ Lr L ea P+ +Ri + GPd
CP000319_3 394 --LSESQWQGVKLRGLFEARAIPH----TDRIAVNGPD 425

CP000319_1096: domain 1 of 1, from 76 to 158: score 112.4, E = 3.9e-38
*->ELnHRVKNtLAvVQSiarQTlRnaasldefveaFsgRLqALsraHdL
EL+HR+KNtLA+V++ia+Q+lR+ + +++ a++gRLqAL+raHdL
CP000319_1 76 ELHHRIKNTLATVSAIATQSLRHVQGTEHAQHAIAGRLQALGRAHDL 122

VpLtrseWagAdLreLleaeLaPyggedaeRitlsGPd<-*
L +++W +AdL+ +++++ ++++ +d + + + GPd
CP000319_1 123 --LLQARWNSADLSHIVRSATEAFDNPDVPKFSIAGPD 158

CP000319_3623: domain 1 of 1, from 140 to 227: score 87.6, E = 1.1e-29
*->ELnHRVKNtLAvVQSiarQTlRnaasldefveaFsgRLqALsraHdL
E++HRVKN+LA+ +++ T+R+++s e++ ++ RL AL+raHdL
CP000319_3 140 EMSHRVKNLLAIASGLTSITSRSTTSTVEMAKELTLRLTALGRAHDL 186

V.pLtrseWagAdLreLleaeLaPygged..aeRitlsGPd<-*
++pL +e+ A L++Ll+ LaPy++ + ++Ri++s P+
CP000319_3 187 IrPLPGHEGKAALLGDLLTVLLAPYDDLGafSGRIRVSVPR 227

CP000319_1139: domain 1 of 1, from 411 to 495: score 73.5, E = 6.4e-25
*->ELnHRVKNtLAvVQSiarQTlRnaasldefveaFsgRLqALsraHdL
EL+HR+KN++++ ++++ ++R+a+ + ++++++gR++ALs aHd
CP000319_1 411 ELHHRIKNLFSIFGALVNLSARSAQNVGTYATDLTGRIMALSKAHDF 457

VpLtrseWagAdLreLleaeLaPyggedaeRitlsGPd<-*
V+ t + a +L +L+++ L+Py+g+ + R+ +G+d
CP000319_1 458 VRPTSALLAAQTLQALVQRLLSPYAGAHGSRLFCEGED 495


Histogram of all scores:
score obs exp (one = represents 12 sequences)
----- --- ---
-17 1 0|=
-16 0 0|
-15 1 0|=
-14 9 0|=
-13 76 0|=======
-12 334 0|============================
-11 389 31|==*==============================
-10 575 393|================================*===============
-9 693 973|==========================================================*
-8 667 1010|======================================================== *
-7 410 679|=================================== *
-6 246 370|===================== *
-5 164 183|============== *
-4 97 87|=======*=
-3 61 40|===*==
-2 35 18|=*=
-1 15 8|*=
0 12 3|*
1 7 1|*
2 4 0|=
3 0 0|
4 0 0|
5 1 0|=
6 1 0|=
7 0 0|
> 8 6 -|=


% Statistical details of theoretical EVD fit:
mu = -7.9989
lambda = 0.7843
chi-sq statistic = 4583.9873
P(chi-square) = 0

Total sequences searched: 3804

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: