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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  

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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_3.hmm [HisKA_3]
Sequence database: BA000040.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
-------- ----------- ----- ------- ---
BA000040_5280 CDS_5831008-5832390 64.8 1.6e-18 1
BA000040_6184 CDS_6807700-6806189 64.6 1.9e-18 1
BA000040_5687 CDS_6247190-6248560 52.1 9.1e-15 1
BA000040_1179 CDS_1297250-1295910 45.8 6.9e-13 1
BA000040_7308 CDS_8042616-8041423 30.1 2.8e-08 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
BA000040_5280 1/1 253 321 .. 1 70 [] 64.8 1.6e-18
BA000040_6184 1/1 296 366 .. 1 70 [] 64.6 1.9e-18
BA000040_5687 1/1 252 322 .. 1 70 [] 52.1 9.1e-15
BA000040_1179 1/1 243 309 .. 1 70 [] 45.8 6.9e-13
BA000040_7308 1/1 172 236 .. 3 70 .] 30.1 2.8e-08

Alignments of top-scoring domains:
BA000040_5280: domain 1 of 1, from 253 to 321: score 64.8, E = 1.6e-18
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+++ARELHD+ gQsL+ai+ + ar+ + d + + + d i
BA000040_5 253 ERRHLARELHDEFGQSLAAIRALAASARQTA--VQDCPSLLSECDGI 297

relarealaevRrllgdLR.paal<-*
+++a ++ +R +l +LR+p+++
BA000040_5 298 ARTATGMMEMLRGTLFRLRpPDVE 321

BA000040_6184: domain 1 of 1, from 296 to 366: score 64.6, E = 1.9e-18
*->ERaRIARELHDsvgQsLsaiklqlelarrllds.dkdpeearealde
ER+ IARELHD+ g L++++ +++++++++d+++ ++++r++ +
BA000040_6 296 ERKEIARELHDEFGPYLFSLRAHASALAKQADGrAPSADAVRKHGSA 342

irelarealaevRrllgdLRpaal<-*
+ e ++ ++ +Rr+l +LRp +l
BA000040_6 343 MLEQINALQQFTRRVLERLRPVGL 366

BA000040_5687: domain 1 of 1, from 252 to 322: score 52.1, E = 9.1e-15
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpe..eareald
ER+ +ARELHD+ gQ+L+ai +++++++ +k + ++ +++ ++
BA000040_5 252 ERRALARELHDEFGQNLAAILAFADTIETAS--AKQNRedGIAQDAR 296

eirelarealaevRrllgdLR.paal<-*
+i ++ ++ +a +R++l +LR+p +
BA000040_5 297 MISQATHHLMASLRDALKRLRnPLPE 322

BA000040_1179: domain 1 of 1, from 243 to 309: score 45.8, E = 6.9e-13
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpe..eareald
ER+ +ARELHD++g L++i+ ++ ++ ++ p+ + + +++
BA000040_1 243 ERRDLARELHDELGPLLFSIRAGTIALI-----EASPPvgHLGNTAQ 284

eirelarealaevRrllgdLRpaal<-*
e+ + ++ ++ Rr+l +LRp
BA000040_1 285 EVLQSVEALQQTNRRILDRLRPLYI 309

BA000040_7308: domain 1 of 1, from 172 to 236: score 30.1, E = 2.8e-08
*->aRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdeire
+RIA +LHDs Q+L a++l+l ++rr + ++ a++ ei +
BA000040_7 172 QRIASDLHDSTCQHLIAASLGLMRLRREM--SDAV-GAERLCGEIDA 215

larealaevRrllgdLRpaal<-*
++eal+e+R+ L+p+ l
BA000040_7 216 SIDEALREIRAFSYLLHPQNL 236


Histogram of all scores:
score obs exp (one = represents 26 sequences)
----- --- ---
-14 9 0|=
-13 101 1|*===
-12 174 92|===*===
-11 340 762|============== *
-10 1049 1768|========================================= *
-9 1531 2008|==========================================================*
-8 1330 1547|==================================================== *
-7 1086 973|=====================================*====
-6 887 550|=====================*=============
-5 785 295|===========*===================
-4 377 154|=====*=========
-3 259 79|===*======
-2 153 40|=*====
-1 96 20|*===
0 53 10|*==
1 32 5|*=
2 20 2|*
3 13 1|*
4 9 0|=
5 2 0|=
6 4 0|=
7 0 0|
8 0 0|
> 9 7 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 3393.6431
P(chi-square) = 0

Total sequences searched: 8317

Whole sequence top hits:
tophits_s report:
Total hits: 5
Satisfying E cutoff: 5
Total memory: 21K

Domain top hits:
tophits_s report:
Total hits: 5
Satisfying E cutoff: 5
Total memory: 22K


Acknowledgements:

This research is funded by:

Developed by: