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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  

6 accessions found for Shigella boydii CDC 3083-94  

Data for CP001063  

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: CP001063.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
-------- ----------- ----- ------- ---
CP001063_1184 CDS_1267159-1265363 80.2 2.5e-23 1
CP001063_2439 CDS_2633428-2635128 71.9 6.9e-21 1
CP001063_3666 CDS_3972286-3973779 63.7 1.9e-18 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP001063_1184 1/1 390 458 .. 1 70 [] 80.2 2.5e-23
CP001063_2439 1/1 361 428 .. 1 70 [] 71.9 6.9e-21
CP001063_3666 1/1 301 367 .. 1 70 [] 63.7 1.9e-18

Alignments of top-scoring domains:
CP001063_1184: domain 1 of 1, from 390 to 458: score 80.2, E = 2.5e-23
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ERa IARELHDs++QsLs +k+q++ ++++ d+ p+ re l +i
CP001063_1 390 ERATIARELHDSIAQSLSCMKMQVSCLQMQG--DALPASSRELLSQI 434

relarealaevRrllgdLR.paal<-*
r ++ + a++R+ll+++R ++
CP001063_1 435 RNELNASWAQLRELLTTFRlQLTE 458

CP001063_2439: domain 1 of 1, from 361 to 428: score 71.9, E = 6.9e-21
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ERa IARELHDs++Q Ls +++ql l++r + ++d++ a+ ++
CP001063_2 361 ERATIARELHDSLAQVLSYLRIQLTLLKRSI--PEDNATAQSIMADF 405

relarealaevRrllgdLRpaal<-*
++++a++++R+ll+++R +
CP001063_2 406 SLALNDAYRQLRELLTTFRLTLQ 428

CP001063_3666: domain 1 of 1, from 301 to 367: score 63.7, E = 1.9e-18
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
R+ ARELHD +gQ+++ai+ q++ ++rl+ +d++ +++ + i
CP001063_3 301 VRRDVARELHDDIGQTITAIRTQAGIVQRLA---ADNASVKQSGQLI 344

relarealaevRrllgdLRpaal<-*
++l+ ++ vRrllg+LRp +l
CP001063_3 345 EQLSLGVYDAVRRLLGRLRPRQL 367


Histogram of all scores:
score obs exp (one = represents 14 sequences)
----- --- ---
-15 3 0|=
-14 37 0|===
-13 119 0|=========
-12 147 47|===*=======
-11 358 389|========================== *
-10 623 902|============================================= *
-9 758 1025|======================================================= *
-8 772 790|========================================================*
-7 458 496|================================= *
-6 360 281|====================*=====
-5 281 150|==========*==========
-4 159 78|=====*======
-3 62 40|==*==
-2 46 20|=*==
-1 35 10|*==
0 12 5|*
1 4 2|*
2 3 1|*
3 3 0|=
4 0 0|
5 0 0|
6 1 0|=
7 1 0|=
8 0 0|
9 0 0|
> 10 4 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 695.3348
P(chi-square) = 0

Total sequences searched: 4246

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: