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   / 71  

# 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-cluster000556 COG2610 [GE]citrate transporter1380* * * * * *   * *
2p-cluster000395 COG4670 [I]CoA transferase1560* *         *    
3p-cluster001988 COG1024 [I]enoyl-CoA hydratase1047                 
4p-cluster000397 COG2030 [I]enoyl-CoA hydratase456  *              
5p-cluster000398 COG2025 [C]electron transfer flavoprotein subu1038  *   * *        
6p-cluster000399 COG2086 [C]electron transfer flavoprotein subu801                 
7p-cluster000989 COG1960 [I]acyl-CoA dehydrogenase1914* * * *         *
8p-cluster000585 COG1804 [C]carnitine dehydratase1212                 
9p-cluster000556 COG2610 [GE]citrate transporter1380* * * * *     * *
10p-cluster000403 COG1024 [I]crotonase789                 
11p-cluster000230 COG2204 [T]transcriptional regulator1716  * *   *   *   *
12p-cluster011700 COG2204 [T]hypothetical protein553        *        
13p-cluster011821 COG2204 [T]hypothetical protein665        *        
14p-cluster000405 COG3051 [C]citrate lyase subunit alpha1542  *              
15p-cluster000406 COG2301 [G]citrate lyase subunit beta903                 
16p-cluster000407 COG3052 [C]citrate lyase subunit gamma285                 
17p-cluster000627 COG1883 [C]glutaconyl-CoA decarboxylase subuni1143                 
18p-cluster000628 COG4770 [I]biotin carboxyl carrier protein of 420                 
19p-cluster000410 Uncategoriziedoxaloacetate decarboxylase336                 
20p-cluster000411 COG5016 [C]oxaloacetate decarboxylase1392                 
21p-cluster011813 COG3493 [C]citrate-sodium symport1391        *        
22p-cluster000413 COG1802 [K]GntR family transcriptional regulat654        *        
23p-cluster000414 COG4574 [R]ecotin480                 
24p-cluster000415 COG3862 [S]molybdopterin oxidoreductase345    *            
25p-cluster000416 COG0446 [R]FAD-dependent pyridine nucleotide-d1317    *            
26p-cluster000417 COG0579 [R](2Fe-2S)-binding protein1434                 
27p-cluster000418 COG0554 [C]glycerol kinase1500                 
28p-cluster000419 COG0580 [G]glycerol transporter750                 
29p-cluster000424 COG3412 [S]diguanylate cyclase405                 
30p-cluster000425 COG2376 [G]diguanylate cyclase612                 
31p-cluster000426 COG2376 [G]dihydroxyacetone kinase subunit K987                 
32p-cluster000427 COG1954 [K]glycerol uptake operon antiterminat561                 
33p-cluster000428 COG1838 [C]fumarate hydratase555                 
34p-cluster000429 COG1951 [C]fumarate hydratase846  *              
35p-cluster009280 COG1448 [E]aspartate aminotransferase1284  *              
36p-cluster001311 COG2885 [M]membrane protein654              *  
37p-cluster017016 Uncategoriziedbacterial SH3 domain protein1203                 
38p-cluster000433 COG5012 [R]L-beta-lysine 5,6-aminomutase subun798    *            
39p-cluster000434 Uncategorizieddioxygenase1566                 
40p-cluster000435 COG0249 [L]methionine ABC transporter substrat1470                 
41p-cluster000436 Uncategoriziedhypothetical protein1083                 
42p-cluster000437 COG1509 [E]lysine 2,3-aminomutase1260                 
43p-cluster000438 UncategoriziedL-erythro-3,5-diaminohexanoate dehy1038                 
44p-cluster009981 COG3246 [S]3-keto-5-aminohexanoate cleavage en837                 
45p-cluster000440 Uncategorizied3-aminobutyryl-CoA ammonia lyase384  *     *        
46p-cluster000441 Uncategoriziedhypothetical protein285  *     *        
47p-cluster000442 Uncategoriziedhypothetical protein138                 
48p-cluster000443 Uncategoriziedhypothetical protein153                 
49p-cluster000788 COG0776 [L]DNA-binding protein318* *   *          
50p-cluster004560 COG1028 [IQR]L-allo-threonine dehydrogenase832  *              

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