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Other Bacteria Planctomycetes Spirochaetes
Thermotogae
Classification of phyla is from NCBI page
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132 projects found  

1 accessions found for Methylocella silvestris BL2  

Data for CP001280  

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/HisKA_3.hmm [HisKA_3]
Sequence database: CP001280.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
-------- ----------- ----- ------- ---
CP001280_1975 CDS_2192969-2190654 64.6 9e-19 1
CP001280_2221 CDS_2466237-2464822 57.6 1e-16 1
CP001280_3727 CDS_4194266-4192776 41.7 4.9e-12 1
CP001280_3075 CDS_3465200-3466561 35.3 3.9e-10 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP001280_1975 1/1 571 637 .. 1 70 [] 64.6 9e-19
CP001280_2221 1/1 257 325 .. 1 70 [] 57.6 1e-16
CP001280_3727 1/1 255 328 .. 1 70 [] 41.7 4.9e-12
CP001280_3075 1/1 241 309 .. 1 70 [] 35.3 3.9e-10

Alignments of top-scoring domains:
CP001280_1975: domain 1 of 1, from 571 to 637: score 64.6, E = 9e-19
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+RIARELHDs+gQ L+++ l l+++ r + d+ p +++++++ +
CP001280_1 571 ERQRIARELHDSLGQYLTVMQLDLDGIGRDV--DSSP-AVKRRVADL 614

relarealaevRrllgdLRpaal<-*
+ l +ev rl++++Rp+al
CP001280_1 615 KNLTANLGKEVNRLAWEIRPTAL 637

CP001280_2221: domain 1 of 1, from 257 to 325: score 57.6, E = 1e-16
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER ++ARELHD+ gQ L+ai ++ a + + ++d ++++ + i
CP001280_2 257 ERLHLARELHDEFGQCLAAIGAMAASAGQTA--RRDCPALEPPCQSI 301

relarealaevRrllgdLR.paal<-*
++a + ++ +R +l +LR+p+++
CP001280_2 302 GRTAAHMMQALRGALLRLRpPDVE 325

CP001280_3727: domain 1 of 1, from 255 to 328: score 41.7, E = 4.9e-12
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpe......ear
ER+ +ARELHD+ g sL++i++ ++ + ++ ++ ++++ +++e+
CP001280_3 255 ERKELARELHDEFGASLFGIRVAASCVVEAA--AAGAGtpaekdEII 299

ealdeirelarealaevRrllgdLRpaal<-*
+++++i +la+ +++ r+l ++Rp +l
CP001280_3 300 DRAKNISALADAIQKQNYRILERIRPVVL 328

CP001280_3075: domain 1 of 1, from 241 to 309: score 35.3, E = 3.9e-10
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ERa +AR+LHD+v+ L+++ + ++r+ l+ + +++ ++d+i
CP001280_3 241 ERAELARDLHDEVAPFLFSVGADAAMIRQFLQ-TGMGDQVGPRADAI 286

relarealaevRrllgdLRpaal<-*
+++r+ ++ +R++l++L p+al
CP001280_3 287 SDAVRHMQRHLRDVLRRLAPGAL 309


Histogram of all scores:
score obs exp (one = represents 12 sequences)
----- --- ---
-14 8 0|=
-13 48 0|====
-12 98 42|===*=====
-11 163 349|============== *
-10 472 811|======================================== *
-9 694 922|==========================================================*
-8 542 710|============================================== *
-7 525 446|=====================================*======
-6 402 252|====================*=============
-5 381 135|===========*====================
-4 185 70|=====*==========
-3 117 36|==*=======
-2 60 18|=*===
-1 49 9|*====
0 32 4|*==
1 11 2|*
2 14 1|*=
3 2 0|=
4 5 0|=
5 1 0|=
6 1 0|=
7 0 0|
8 1 0|=
9 1 0|=
10 0 0|
11 0 0|
> 12 6 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 1575.7998
P(chi-square) = 0

Total sequences searched: 3818

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: