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Classification of phyla is from NCBI page
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106 projects found  

1 accessions found for Frankia sp. CcI3  

Data for CP000249  

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: CP000249.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
-------- ----------- ----- ------- ---
CP000249_1467 CDS_1777591-1779330 58.3 7.4e-17 1
CP000249_0297 CDS_352739-351807 56.9 2e-16 1
CP000249_0084 CDS_105374-103611 52.9 3e-15 1
CP000249_1541 CDS_1872249-1870483 48.2 7.1e-14 1
CP000249_3213 CDS_3850593-3848815 41.0 9.2e-12 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP000249_1467 1/1 368 432 .. 1 70 [] 58.3 7.4e-17
CP000249_0297 1/1 194 253 .. 1 62 [. 56.9 2e-16
CP000249_0084 1/1 401 466 .. 1 70 [] 52.9 3e-15
CP000249_1541 1/1 393 458 .. 1 70 [] 48.2 7.1e-14
CP000249_3213 1/1 400 464 .. 1 70 [] 41.0 9.2e-12

Alignments of top-scoring domains:
CP000249_1467: domain 1 of 1, from 368 to 432: score 58.3, E = 7.4e-17
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER RIAR+LHD+v Q+L+a l+l+ ++r++ + +a+e+ld++
CP000249_1 368 ERDRIARDLHDVVIQRLFATGLHLQSLARAV---DS--RAAERLDAA 409

relarealaevRrllgdLRpaal<-*
++ ++++++++R+++ L a
CP000249_1 410 AGELDQTISDIRQTIFSLTSNAA 432

CP000249_0297: domain 1 of 1, from 194 to 253: score 56.9, E = 2e-16
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER R+ARE HD+vg+s s i+lq+ +a+++l d+ pe+a+ al++i
CP000249_0 194 ERLRMAREVHDVVGHSRSIISLQAAVALHVL--DRRPEQAQVALEAI 238

relarealaevRrll<-*
r+++ +al+e+R++l
CP000249_0 239 RRTSVDALDELRATL 253

CP000249_0084: domain 1 of 1, from 401 to 466: score 52.9, E = 3e-15
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+R+ R+LHD+v Q+L a++ l+lar+ ++ ++ a++++
CP000249_0 401 ERRRLERDLHDGVQQRLLALATRLGLART----KTSDPDTISAIEAA 443

relarealaevRrllgdLRpaal<-*
re +++al+++R l+++++pa l
CP000249_0 444 REDLHHALQDLRSLARGIHPAML 466

CP000249_1541: domain 1 of 1, from 393 to 458: score 48.2, E = 7.1e-14
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
R RIAR+LHD v Q+L+a++++l+++++ +++ +e++ +
CP000249_1 393 DRDRIARDLHDHVMQRLFAVAMGLQGLAASE--ERP--TRAERMNTY 435

relarealaevRrllgdLRpaal<-*
e ++e+ +e+R+++ +LR a
CP000249_1 436 VEDLDETVREIRHTIFELRGRAA 458

CP000249_3213: domain 1 of 1, from 400 to 464: score 41.0, E = 9.2e-12
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
R RIAR+LHD v Q+++a++l+l+ ++ ++ +++ +e++ +
CP000249_3 400 DRGRIARDLHDHVIQRMFAVALGLQDIA-QY--ERP--SNAERINQY 441

relarealaevRrllgdLRpaal<-*
e ++ +++++Rr + +LR ++
CP000249_3 442 VEDLDVTIKDIRRSIFELRASGA 464


Histogram of all scores:
score obs exp (one = represents 12 sequences)
----- --- ---
-14 1 0|=
-13 24 0|==
-12 60 50|====*
-11 114 412|========== *
-10 360 956|============================== *
-9 592 1086|================================================== *
-8 625 837|===================================================== *
-7 687 526|===========================================*==============
-6 545 297|========================*=====================
-5 595 159|=============*====================================
-4 346 83|======*======================
-3 202 42|===*=============
-2 127 21|=*=========
-1 109 11|*=========
0 42 5|*===
1 20 2|*=
2 14 1|*=
3 13 0|==
4 6 0|=
5 4 0|=
6 4 0|=
7 1 0|=
8 1 0|=
9 0 0|
10 0 0|
> 11 7 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 5318.1323
P(chi-square) = 0

Total sequences searched: 4499

Whole sequence top hits:
tophits_s report:
Total hits: 5
Satisfying E cutoff: 5
Total memory: 20K

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


Acknowledgements:

This research is funded by:

Developed by: