fnec Gene Table Build 14_03_11 [A quick tutorial]

Citation
Kittichotirat W, Bumgarner RE, Asikainen S, Chen C, 2011
Identification of the Pangenome and Its Components in 14 Distinct Aggregatibacter actinomycetemcomitans Strains by Comparative Genomic Analysis
PLoS ONE 6(7): e22420. doi:10.1371/journal.pone.0022420

Keyword search
Search for
Also include clusters with significant sequence similarity
Also include clusters containing upstream and downstream genes (Must sort rows by Gene position in a genome first)

BLAST search
Sequence type

Row sorting and cell coloring options
Sort rows by Order rows in
Color cells by Display rows

Row filtering options
 Show COG of type
 Show clusters with minimum expected length of bp
Show clusters containing genes near the ends of contigs
Show clusters containing genes with frameshift mutation

Display column
1) BL
2) DJ-1
3) BFTR-1
4) DAB
5) BFTR-2
6) DJ-2
7) D12
8) ATCC51357
9) Fnf1007
Show genes only present in
1) BL
2) DJ-1
3) BFTR-1
4) DAB
5) BFTR-2
6) DJ-2
7) D12
8) ATCC51357
9) Fnf1007
All genomes (Core genes)
Some genomes (Variable genes)

Show genes not present in
1) BL
2) DJ-1
3) BFTR-1
4) DAB
5) BFTR-2
6) DJ-2
7) D12
8) ATCC51357
9) Fnf1007


<< Prev    Next >>
First Page    Last Page
Go to page   / 63  

# Cluster ID COG Function Annotation Expected gene Length (bp)

Fusobacterium necrophorum BL

Fusobacterium necrophorum DJ-1

Fusobacterium necrophorum BFTR-1

Fusobacterium necrophorum DAB

Fusobacterium necrophorum BFTR-2

Fusobacterium necrophorum DJ-2

Fusobacterium necrophorum D12

Fusobacterium necrophorum subsp. funduliforme ATCC

Fusobacterium necrophorum subsp. funduliforme Fnf

1p-cluster000004 COG0601 [EP]peptide ABC transporter permease915                 
2p-cluster000005 COG0747 [E]diguanylate phosphodiesterase1488                 
3p-cluster000006 Uncategoriziedhypothetical protein1401        *        
4p-cluster000008 COG1073 [R]lysophospholipase864  *              
5p-cluster000010 Uncategoriziedhypothetical protein222                 
6p-cluster000011 COG0736 [I]4-phosphopantetheinyl transferase345                 
7p-cluster000012 COG0084 [L]hydrolase TatD759                 
8p-cluster000013 COG1281 [O]molecular chaperone Hsp33861                 
9p-cluster000014 COG1555 [L]competence protein522                 
10p-cluster000015 COG0635 [H]coproporphyrinogen III oxidase1383                 
11p-cluster000017 COG0606 [O]magnesium transporter1503                 
12p-cluster000018 COG1971 [S]hypothetical protein558                 
13p-cluster000019 COG0781 [K]nitrogen utilization protein B417                 
14p-cluster000020 Uncategoriziedmembrane protein225                 
15p-cluster000021 Uncategoriziedhypothetical protein537                 
16p-cluster000022 COG1302 [S]alkaline-shock protein363                 
17p-cluster000023 COG0439 [I]acetyl-CoA carboxylase biotin carbo1344                 
18p-cluster000026 Uncategoriziedhypothetical protein1761        *        
19p-cluster000027 COG0553 [KL]helicase SNF3405    *            
20p-cluster000028 COG0614 [P]hemin receptor876                 
21p-cluster000031 COG1120 [PH]heme ABC transporter ATP-binding pr801        *        
22p-cluster000032 COG0635 [H]oxygen-independent coproporphyrinog1227                 
23p-cluster000033 COG3775 [G]PTS galactitol transporter subunit 1260            *    
24p-cluster000034 COG3414 [G]PTS lactose transporter subunit IIB393                 
25p-cluster000035 COG1762 [GT]PTS sugar transporter subunit IIA438                 
26p-cluster000037 COG1762 [GT]phosphoenolpyruvate-dependent sugar2061  *     *   *    
27p-cluster000038 COG3629 [T]hypothetical protein1152  *         *    
28p-cluster000040 COG1574 [R]exoenzyme regulatory protein aepA p1629  *         *    
29p-cluster000041 COG1757 [C]sodium:proton antiporter1428  *              
30p-cluster000042 COG0441 [J]threonyl-tRNA synthetase1914                 
31p-cluster000043 Uncategoriziedhypothetical protein3633      *          
32p-cluster000044 COG0526 [OC]thioredoxin321* * * *       * *
33p-cluster000045 COG1214 [O]O-sialoglycoprotein endopeptidase669                 
34p-cluster000046 COG0802 [R]ATP/GTP hydrolase468                 
35p-cluster000048 COG0494 [LR]phosphohydrolase597  *       *   *  
36p-cluster000049 Uncategoriziedhypothetical protein120*         *      
37p-cluster000050 COG1902 [C]NADH oxidase957*                
38p-cluster000052 Uncategoriziedhypothetical protein216                 
39p-cluster000053 COG4394 [S]hypothetical protein1029                 
40p-cluster000054 COG0231 [J]elongation factor P564                 
41p-cluster000055 COG0326 [O]heat shock protein 901818              * *
42p-cluster000056 Uncategoriziedantitoxin231    *            
43p-cluster000057 COG2026 [JD]pirin270  * *   *        
44p-cluster000058 COG1362 [E]aminopeptidase1389  * *            
45p-cluster000059 COG1609 [K]transcriptional regulator1035    *            
46p-cluster000063 COG1082 [G]endonuclease786            *    
47p-cluster000064 COG1597 [IR]lipid kinase882            *    
48p-cluster000069 COG4750 [M]cholinephosphate cytidylyltransfera870                 
49p-cluster000072 COG4938 [S]ATPase AAA1407      *     *    
50p-cluster000073 Uncategoriziedhypothetical protein699      *          

Please send any comment/suggestion to kitticho@uw.edu
Compatible browswer

tumblr site counter

 

Gene Completeness

>=100%
=70%
<70%

: Similar sequence present
: Not present

* : Within 300 bp from ends
F : Possible frameshift
I : Island genes