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

1 accessions found for Shewanella woodyi ATCC 51908  

Data for CP000961  

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: CP000961.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
-------- ----------- ----- ------- ---
CP000961_4539 CDS_5562881-5563984 91.2 1.6e-26 1
CP000961_2612 CDS_3225956-3227707 76.0 5e-22 1
CP000961_0963 CDS_1283903-1282200 62.5 4.8e-18 1
CP000961_3706 CDS_4563259-4562396 54.6 9.8e-16 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP000961_4539 1/1 178 246 .. 1 70 [] 91.2 1.6e-26
CP000961_2612 1/1 386 455 .. 1 70 [] 76.0 5e-22
CP000961_0963 1/1 363 432 .. 1 70 [] 62.5 4.8e-18
CP000961_3706 1/1 77 143 .. 1 70 [] 54.6 9.8e-16

Alignments of top-scoring domains:
CP000961_4539: domain 1 of 1, from 178 to 246: score 91.2, E = 1.6e-26
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpe.earealde
ER+RIAR+LHD g++Ls+i+l++ela++ll dk+ + +a+e+l+e
CP000961_4 178 ERERIARDLHDIMGHNLSSISLKAELAQKLL--DKNQQiQAQEQLKE 222

irelarealaevRrllgdLRpaal<-*
+ ++are+l+++R++++++++ +l
CP000961_4 223 LNQIARESLSQIRQTVSGYKHKGL 246

CP000961_2612: domain 1 of 1, from 386 to 455: score 76.0, E = 5e-22
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpe.earealde
ERa IARELHDs++QsLs +k+q++l+ r ++ + pe+++ e++d
CP000961_2 386 ERAVIARELHDSLAQSLSFLKVQMSLLTRKMQ-KGLPEeQVNETIDD 431

irelarealaevRrllgdLRpaal<-*
i++ ++ a+ ++R+ll+++R +
CP000961_2 432 IKQGLNNAYLQLRELLTTFRLKLD 455

CP000961_0963: domain 1 of 1, from 363 to 432: score 62.5, E = 4.8e-18
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpe..eareald
ER IARELHDs+gQ Ls +k+q+ l+ + l d++ +++++ +++
CP000961_0 363 ERGVIARELHDSLGQILSFLKIQVNLLSKGL--DTACRspQVEGQIA 407

eirelarealaevRrllgdLRpaal<-*
ei e +++a+ ++R+ll+++R ++
CP000961_0 408 EINEGVNTAYVQLRELLSTFRLTIN 432

CP000961_3706: domain 1 of 1, from 77 to 143: score 54.6, E = 9.8e-16
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+R +RELHD++ Q+L + k +e a +l dk e a ++l+++
CP000961_3 77 ERQRVSRELHDGIIQMLVSTKYVVENAIFRL--DKG-EVATKELTQC 120

relarealaevRrllgdLRpaal<-*
++ ++ ++++vRr+ +dL+p l
CP000961_3 121 EQYLDATINDVRRISRDLHPNLL 143


Histogram of all scores:
score obs exp (one = represents 18 sequences)
----- --- ---
-14 32 0|==
-13 162 0|=========
-12 226 54|==*==========
-11 391 447|====================== *
-10 929 1037|==================================================== *
-9 1040 1178|==========================================================*
-8 708 908|======================================== *
-7 524 571|============================== *
-6 361 323|=================*===
-5 241 173|=========*====
-4 96 90|====*=
-3 71 46|==*=
-2 49 23|=*=
-1 23 12|*=
0 11 6|*
1 7 3|*
2 2 1|*
3 2 0|=
> 4 5 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 706.6827
P(chi-square) = 0

Total sequences searched: 4880

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: