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Firmicutes Fusobacteria Gammaproteobacteria
Other Bacteria Planctomycetes Spirochaetes
Thermotogae
Classification of phyla is from NCBI page
Search:
264 projects found  

5 accessions found for Shigella sonnei Ss046  

Data for CP000038  

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_3.hmm [HisKA_3]
Sequence database: CP000038.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
-------- ----------- ----- ------- ---
CP000038_1825 CDS_2057139-2058935 82.2 6.2e-24 1
CP000038_2381 CDS_2687798-2689498 76.1 4e-22 1
CP000038_3375 CDS_3793156-3791651 63.7 1.8e-18 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP000038_1825 1/1 390 458 .. 1 70 [] 82.2 6.2e-24
CP000038_2381 1/1 361 428 .. 1 70 [] 76.1 4e-22
CP000038_3375 1/1 305 371 .. 1 70 [] 63.7 1.8e-18

Alignments of top-scoring domains:
CP000038_1825: domain 1 of 1, from 390 to 458: score 82.2, E = 6.2e-24
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ERa IARELHDs++QsLs +k+q++ ++++ d+ pe re l +i
CP000038_1 390 ERATIARELHDSIAQSLSCMKMQVSCLQMQG--DALPESSRELLSQI 434

relarealaevRrllgdLR.paal<-*
r ++ + a++R+ll+++R ++
CP000038_1 435 RNELNASWAQLRELLTTFRlQLTE 458

CP000038_2381: domain 1 of 1, from 361 to 428: score 76.1, E = 4e-22
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ERa IARELHDs++Q Ls +++ql l++r + ++d++ a+ ++
CP000038_2 361 ERATIARELHDSLAQVLSYLRIQLTLLKRSI--PEDNATAQSIMADF 405

relarealaevRrllgdLRpaal<-*
+++++a++++R+ll+++R +
CP000038_2 406 SQALNDAYRQLRELLTTFRLTLQ 428

CP000038_3375: domain 1 of 1, from 305 to 371: score 63.7, E = 1.8e-18
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
R+ ARELHD +gQ+++ai+ q++ ++rl+ +d++ +++ + i
CP000038_3 305 VRRDVARELHDDIGQTITAIRTQAGIVQRLA---ADNASVKQSGQLI 348

relarealaevRrllgdLRpaal<-*
++l+ ++ vRrllg+LRp +l
CP000038_3 349 EQLSLGVYDAVRRLLGRLRPRQL 371


Histogram of all scores:
score obs exp (one = represents 15 sequences)
----- --- ---
-16 2 0|=
-15 0 0|
-14 23 0|==
-13 86 0|======
-12 129 47|===*=====
-11 246 387|================= *
-10 569 898|====================================== *
-9 827 1019|======================================================== *
-8 845 785|====================================================*====
-7 495 494|================================*
-6 354 279|==================*=====
-5 310 149|=========*===========
-4 149 78|=====*====
-3 76 40|==*===
-2 47 20|=*==
-1 29 10|*=
0 15 5|*
1 7 2|*
2 4 1|*
3 3 0|=
4 0 0|
5 0 0|
6 1 0|=
7 1 0|=
8 0 0|
9 1 0|=
> 10 4 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 725.0574
P(chi-square) = 0

Total sequences searched: 4224

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: