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

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1) BL
2) DJ-1
3) BFTR-1
4) DAB
5) BFTR-2
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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
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1) BL
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4) DAB
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6) DJ-2
7) D12
8) ATCC51357
9) Fnf1007


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# 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-cluster000417 COG0579 [R](2Fe-2S)-binding protein1434                 
2p-cluster000538 COG0743 [I]1-deoxy-D-xylulose 5-phosphate redu1155                 
3p-cluster002712 COG1154 [HI]1-deoxy-D-xylulose-5-phosphate synt1782  *              
4rrna-cluster000001 Uncategorizied16S ribosomal RNA1510* * * * * * * * *
5p-cluster000159 COG0357 [M]16S rRNA methyltransferase705                 
6p-cluster000769 COG0275 [M]16S rRNA methyltransferase942        *        
7p-cluster001417 COG0030 [J]16S rRNA methyltransferase807                 
8p-cluster002193 COG0313 [R]16S rRNA methyltransferase684  *              
9p-cluster000943 COG0656 [R]2,5-diketo-D-gluconic acid reductas846                 
10p-cluster002013 COG0801 [H]2-amino-4-hydroxy-6- hydroxymethyld828                 
11p-cluster002219 COG0245 [I]2-C-methyl-D-erythritol 2,4-cyclodi477                 
12p-cluster001497 COG1211 [I]2-C-methyl-D-erythritol 4-phosphate699                 
13p-cluster004428 COG1211 [I]2-C-methyl-D-erythritol 4-phosphate723  * * *   *      
14p-cluster007473 COG0800 [G]2-dehydro-3-deoxyphosphogluconate a663  *              
15p-cluster000680 COG2877 [M]2-dehydro-3-deoxyphosphooctonate al837                 
16p-cluster001677 COG1028 [IQR]2-deoxy-D-gluconate 3-dehydrogenase774                 
17p-cluster001544 COG0277 [C]2-hydroxy-acid oxidase1428                 
18p-cluster001501 COG0111 [HE]2-hydroxyacid dehydrogenase999    *            
19p-cluster001648 COG1052 [CHR]2-hydroxyacid dehydrogenase1071                 
20p-cluster000620 COG1775 [E]2-hydroxyglutaryl-CoA dehydratase1149* * * * * *   * *
21p-cluster000621 COG1775 [E]2-hydroxyglutaryl-CoA dehydratase1326                 
22p-cluster001044 COG3581 [S]2-hydroxyglutaryl-CoA dehydratase1203                 
23p-cluster001045 COG1924 [I]2-hydroxyglutaryl-CoA dehydratase2943                 
24p-cluster002047 COG2070 [R]2-nitropropane dioxygenase948*                
25p-cluster002285 COG0493 [ER]2-polyprenylphenol hydroxylase2286        *        
26rrna-cluster000023 Uncategorizied23S ribosomal RNA112          *      
27rrna-cluster000036 Uncategorizied23S ribosomal RNA2913* * * * * *   * *
28p-cluster016617 COG2265 [J]23S rRNA (uracil-5-)-methyltransfer1446        *        
29p-cluster000278 COG0108 [H]3,4-dihydroxy-2-butanone 4-phosphat1212*                
30p-cluster000440 Uncategorizied3-aminobutyryl-CoA ammonia lyase384  *     *        
31p-cluster000986 COG0757 [E]3-dehydroquinate dehydratase435                 
32p-cluster000600 COG0337 [E]3-dehydroquinate synthase1980                 
33p-cluster002452 COG1778 [R]3-deoxy-D-manno-octulosonate 8-phos522                 
34p-cluster000784 COG1519 [M]3-deoxy-D-manno-octulosonic acid tr1230      *          
35p-cluster002278 COG1212 [M]3-deoxy-manno-octulosonate cytidyly744                 
36p-cluster005371 COG1257 [I]3-hydroxy-3-methylglutaryl-CoA redu1257                 
37p-cluster002066 COG0764 [I]3-hydroxyacyl-ACP dehydratase426                 
38p-cluster001107 COG1250 [I]3-hydroxybutyryl-CoA dehydrogenase834                 
39p-cluster009981 COG3246 [S]3-keto-5-aminohexanoate cleavage en837                 
40p-cluster000980 COG0183 [I]3-ketoacyl-CoA thiolase1209  *              
41p-cluster002240 COG0413 [H]3-methyl-2-oxobutanoate hydroxymeth825                 
42p-cluster001458 COG1028 [IQR]3-oxoacyl-ACP reductase690                 
43p-cluster000314 COG0332 [I]3-oxoacyl-ACP synthase987                 
44p-cluster000317 COG0304 [IQ]3-oxoacyl-ACP synthase1248                 
45p-cluster000982 COG0128 [E]3-phosphoshikimate 1-carboxyvinyltr1227                 
46p-cluster001898 COG0051 [J]30S ribosomal protein S10312                 
47p-cluster000357 COG0100 [J]30S ribosomal protein S11390                 
48p-cluster000579 COG0048 [J]30S ribosomal protein S12369                 
49p-cluster000356 COG0099 [J]30S ribosomal protein S13357                 
50p-cluster001912 COG0199 [J]30S ribosomal protein S14288        *        

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Gene Completeness

>=100%
=70%
<70%

: Similar sequence present
: Not present

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