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Classification of phyla is from NCBI page
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132 projects found  

1 accessions found for Bradyrhizobium japonicum USDA 110  

Data for BA000040  

Available Atlases
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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_2.hmm [HisKA_2]
Sequence database: BA000040.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]
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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
-------- ----------- ----- ------- ---
BA000040_4287 CDS_4729278-4728163 113.4 9.3e-32 1
BA000040_2180 CDS_2356412-2357656 103.4 6.5e-29 1
BA000040_6988 CDS_7697408-7696203 102.7 1e-28 1
BA000040_6266 CDS_6892954-6892289 42.7 1.2e-11 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
BA000040_4287 1/1 168 251 .. 1 94 [] 113.4 9.3e-32
BA000040_2180 1/1 225 306 .. 1 94 [] 103.4 6.5e-29
BA000040_6988 1/1 206 288 .. 1 94 [] 102.7 1e-28
BA000040_6266 1/1 34 119 .. 1 94 [] 42.7 1.2e-11

Alignments of top-scoring domains:
BA000040_4287: domain 1 of 1, from 168 to 251: score 113.4, E = 9.3e-32
*->EIHHRVKNNLQvISSLLrLQarkfkdeevikdEVleaLrEsqnRVlS
E++HRV N+LQ+I+SLL LQa ++ eev ++aL + +RV++
BA000040_4 168 EVNHRVGNSLQIIASLLHLQASSAGQEEV-----KAALTNAMGRVAA 209

mAliHEeLYksedldtvdfseYlekLtenLfqsygvgsdgisLklDl<-*
+A++H++LY+s dl++v + +Yl+ L+e+L++s+++ + l
BA000040_4 210 VAQVHRRLYTSQDLKSVVLNQYLDSLLEDLRRSAEGNRMSR-----L 251

BA000040_2180: domain 1 of 1, from 225 to 306: score 103.4, E = 6.5e-29
*->EIHHRVKNNLQvISSLLrLQarkfkdeevikdEVleaLrEsqnRVlS
E+ HRVKN+L+ + +LLr Q+r++++eev ++aL+++ +R+ +
BA000040_2 225 EMSHRVKNSLASVVGLLRVQSRSAQSEEV-----QNALKDAASRITT 266

mAliHEeLYksedldtvdfseYlekLtenLfqsygvgsdgisLklDl<-*
+A++H++L++s ++ vd++++ +L++ L ++ + + d +
BA000040_2 267 IAQVHDHLWRSTRIGFVDIADFAGELCRKLQETLAYKID-------C 306

BA000040_6988: domain 1 of 1, from 206 to 288: score 102.7, E = 1e-28
*->EIHHRVKNNLQvISSLLrLQarkfkdeevikdEVleaLrEsqnRVlS
E+ HRVKN+L + +LLr Qar++++eev ++aL ++ RV +
BA000040_6 206 EMSHRVKNSLTSVVGLLRVQARSAQSEEV-----RNALDDASARVET 247

mAliHEeLYksedldtvdfseYlekLtenLfqsygvgsdgisLklDl<-*
+A++H++L+++ ++ vd+ +++++L++ L+ + ++ s + +
BA000040_6 248 IAQVHDHLWRGSQIGFVDLEDFMTELCKKLKGATEGLSLH------C 288

BA000040_6266: domain 1 of 1, from 34 to 119: score 42.7, E = 1.2e-11
*->EIHHRVKNNLQvISSLLrLQarkfkdeevikdEVleaLrEsqnRVlS
E HHR KN L + + +r ++ ++v a +++RV +
BA000040_6 34 ESHHRMKNTLTLLGASVRRDFTRAGTRDV-----SLAVDRFERRVVA 75

mAliHEeLYksedldtvdfseYlekLtenLfqsygvgsdgisLklDl<-*
+++ L+ ++d + v +++++e+L++ L ++ ++ ++++
BA000040_6 76 FGRLYQLLSDNDDDSAVPVGAFFENLCGALSEAVLEPAG---VRCEA 119


Histogram of all scores:
score obs exp (one = represents 39 sequences)
----- --- ---
-15 4 0|=
-14 29 0|=
-13 132 52|=*==
-12 527 546|=============*
-11 2291 1521|======================================*====================
-10 1859 1968|================================================ *
-9 1299 1662|================================== *
-8 989 1115|========================== *
-7 510 662|============== *
-6 391 368|=========*=
-5 136 198|==== *
-4 68 105|==*
-3 34 55|=*
-2 19 28|*
-1 11 15|*
0 5 7|*
1 2 4|*
2 1 2|*
3 1 1|*
4 0 0|
5 0 0|
> 6 9 -|=


% Statistical details of theoretical EVD fit:
mu = -9.5227
lambda = 0.6548
chi-sq statistic = 695.8885
P(chi-square) = 0

Total sequences searched: 8317

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: