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Chlamydiae/Verrucomicrobia Chloroflexi Cyanobacteria
Deinococcus-Thermus Deltaproteobacteria Epsilonproteobacteria
Firmicutes Fusobacteria Gammaproteobacteria
Other Bacteria Planctomycetes Spirochaetes
Thermotogae
Classification of phyla is from NCBI page
Search:
264 projects found  

1 accessions found for Pseudomonas stutzeri A1501  

Data for CP000304  

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: CP000304.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
-------- ----------- ----- ------- ---
CP000304_0881 CDS_994378-992402 70.7 1.5e-20 1
CP000304_0731 CDS_838711-840996 61.1 1e-17 1
CP000304_2229 CDS_2488217-2486955 57.4 1.3e-16 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP000304_0881 1/1 424 493 .. 1 70 [] 70.7 1.5e-20
CP000304_0731 1/1 549 616 .. 1 70 [] 61.1 1e-17
CP000304_2229 1/1 224 290 .. 1 70 [] 57.4 1.3e-16

Alignments of top-scoring domains:
CP000304_0881: domain 1 of 1, from 424 to 493: score 70.7, E = 1.5e-20
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpe..eareald
ERa IARELHDs++Q+Lsa klql +++rl+ +k+ ++ ++++ ++
CP000304_0 424 ERAVIARELHDSLAQALSAQKLQLARLKRLM--QKESGqaQLDDSVQ 468

eirelarealaevRrllgdLRpaal<-*
+i + ++ a++++R+ll+++R +
CP000304_0 469 QIDRGLNSAYRQLRELLTTFRIKVN 493

CP000304_0731: domain 1 of 1, from 549 to 616: score 61.1, E = 1e-17
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
E a+IARE HD++gQ L+++kl +++++ + ++ +++++++ld +
CP000304_0 549 EKAHIAREVHDELGQVLTVLKLETSMCELGF--AELDPALAQRLDSM 593

relarealaevRrllgdLRpaal<-*
++l+ + + vR+++++LRp++l
CP000304_0 594 KRLIAQLFQRVRDVATALRPPIL 616

CP000304_2229: domain 1 of 1, from 224 to 290: score 57.4, E = 1.3e-16
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+R+A+ LHD +gQ+L++i+ + l+r ++ + p+++re+++ +
CP000304_2 224 ERTRLAQALHDDLGQHLAGIRARACLLRVQA---DQPDAVRETAAHL 267

relarealaevRrllgdLRpaal<-*
++++ + ++ R l++dL p l
CP000304_2 268 EQHSLDLQNGFRTLVRDLYPVML 290


Histogram of all scores:
score obs exp (one = represents 12 sequences)
----- --- ---
-14 8 0|=
-13 36 0|===
-12 70 46|===*==
-11 133 378|============ *
-10 473 877|======================================== *
-9 687 996|==========================================================*
-8 595 768|================================================== *
-7 577 483|========================================*========
-6 467 273|======================*================
-5 446 146|============*=========================
-4 229 76|======*=============
-3 140 39|===*========
-2 88 20|=*======
-1 63 10|*=====
0 33 5|*==
1 28 2|*==
2 15 1|*=
3 10 0|=
4 11 0|=
5 2 0|=
6 0 0|
7 5 0|=
8 2 0|=
9 0 0|
10 3 0|=
11 1 0|=
12 1 0|=
13 0 0|
14 0 0|
> 15 5 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 2470.4827
P(chi-square) = 0

Total sequences searched: 4128

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: 21K


Acknowledgements:

This research is funded by:

Developed by: