fnuc Gene Table Build 14_03_12 [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) YH7053
2) YH7054
3) YH7055
4) YH7056
5) YH7199
6) animalis-4_8
7) animalis-3_1_33
8) animalis-7_1
9) animalis-D11
10) animalis-ATCC51191
11) animalis-F0419
12) animalis-21_1A
13) animalis-11_3_2
14) fusiforme-ATCC51190
15) nucleatum-ATCC23726
16) polymorphum-ATCC10953
17) polymorphum-F0401
18) vincentii-3_1_36A2
19) vincentii-4_1_13
20) 13_3C
21) CTI-5
22) CTI-6
23) CTI-7
Show genes only present in
1) YH7053
2) YH7054
3) YH7055
4) YH7056
5) YH7199
6) animalis-4_8
7) animalis-3_1_33
8) animalis-7_1
9) animalis-D11
10) animalis-ATCC51191
11) animalis-F0419
12) animalis-21_1A
13) animalis-11_3_2
14) fusiforme-ATCC51190
15) nucleatum-ATCC23726
16) polymorphum-ATCC10953
17) polymorphum-F0401
18) vincentii-3_1_36A2
19) vincentii-4_1_13
20) 13_3C
21) CTI-5
22) CTI-6
23) CTI-7
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Show genes not present in
1) YH7053
2) YH7054
3) YH7055
4) YH7056
5) YH7199
6) animalis-4_8
7) animalis-3_1_33
8) animalis-7_1
9) animalis-D11
10) animalis-ATCC51191
11) animalis-F0419
12) animalis-21_1A
13) animalis-11_3_2
14) fusiforme-ATCC51190
15) nucleatum-ATCC23726
16) polymorphum-ATCC10953
17) polymorphum-F0401
18) vincentii-3_1_36A2
19) vincentii-4_1_13
20) 13_3C
21) CTI-5
22) CTI-6
23) CTI-7


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

Fusobacterium nucleatum YH7053

Fusobacterium nucleatum YH7054

Fusobacterium nucleatum YH7055

Fusobacterium nucleatum YH7056

Fusobacterium nucleatum YH7199

Fusobacterium nucleatum subsp. animalis 4_8

Fusobacterium nucleatum subsp. animalis 3_1_33

Fusobacterium nucleatum subsp. animalis 7_1

Fusobacterium nucleatum subsp. animalis D11

Fusobacterium nucleatum subsp. animalis ATCC 51191

Fusobacterium nucleatum subsp. animalis F0419

Fusobacterium nucleatum subsp. animalis 21_1A

Fusobacterium nucleatum subsp. animalis 11_3_2

Fusobacterium nucleatum subsp. fusiforme ATCC 5119

Fusobacterium nucleatum subsp. nucleatum ATCC 2372

Fusobacterium nucleatum subsp. polymorphum ATCC 10

Fusobacterium nucleatum subsp. polymorphum F0401

Fusobacterium nucleatum subsp. vincentii 3_1_36A2

Fusobacterium nucleatum subsp. vincentii 4_1_13

Fusobacterium nucleatum 13_3C

Fusobacterium nucleatum CTI-5

Fusobacterium nucleatum CTI-6

Fusobacterium nucleatum CTI-7

1p-cluster049416 Uncategoriziedhypothetical protein77                                            *
2p-cluster000937 COG1792 [M]cell shape-determining protein MreC876                  *                         *
3p-cluster049418 Uncategoriziedhypothetical protein72                                            *
4p-cluster000405 COG0766 [M]UDP-N-acetylglucosamine 1-carboxyvi1272    *                                       *
5p-cluster000888 COG0601 [EP]ABC transporter permease978    * *           *                          
6p-cluster000015 COG1173 [EP]peptide ABC transporter permease870                  *                          
7p-cluster020029 COG1173 [EP]dipeptide ABC superfamily ATP bindi264                                             
8p-cluster031917 COG0747 [E]ABC transporter, substrate-binding 1617                                             
9p-cluster028479 COG0444 [EP]peptide ABC transporter, ATP-bindin1695* *     *         *       *                  
10p-cluster028479 COG0444 [EP]peptide ABC transporter, ATP-bindin1695* *     *         *       *                  
11p-cluster018191 COG0444 [EP]oligopeptide/dipeptide ABC transpor429                                        *    
12p-cluster024055 Uncategoriziedhypothetical protein10803* *     *                                   *
13p-cluster024055 Uncategoriziedhypothetical protein10803* *     *                                   *
14p-cluster000540 Uncategoriziedhypothetical protein411        *                                    
15p-cluster029520 Uncategoriziedhypothetical protein393        *                                    
16p-cluster001630 Uncategoriziedadhesion protein FadA390*       *                                    
17p-cluster035194 COG1346 [M]membrane protein720*     * *         *       *                  
18p-cluster000706 COG1380 [R]murein hydrolase384                  *                          
19p-cluster001354 COG2025 [C]electron transfer flavoprotein subu1176                                             
20p-cluster000708 COG2086 [C]electron transfer flavoprotein subu780                                             
21p-cluster040382 COG2086 [C]electron transfer flavoprotein subu807                                             
22p-cluster002019 COG1960 [I]hypothetical protein1914    *                     *                  
23p-cluster029526 COG1960 [I]acyl-CoA dehydrogenase912                                             
24p-cluster029527 COG1960 [I]acyl-CoA dehydrogenase111                                             
25p-cluster000710 COG0277 [C]2-hydroxy-acid oxidase1428                                             
26p-cluster000712 COG0003 [P]arsenic ABC transporter ATPase1191  *                                          
27p-cluster000712 COG0003 [P]arsenic ABC transporter ATPase1191  *                                          
28p-cluster000713 COG1556 [S](Fe-S)-binding protein552                                             
29p-cluster000714 COG0247 [C](Fe-S)-binding protein2160                                             
30p-cluster000715 COG0142 [H]heptaprenyl diphosphate synthase981                  *                          
31p-cluster000716 COG1575 [H]1,4-dihydroxy-2-naphthoate prenyltr924                                             
32p-cluster000717 COG2226 [H]ubiquinone biosynthesis methyltrans696                                             
33p-cluster016558 COG0644 [C]oxidoreductase FixC1347                                             
34p-cluster000719 COG2440 [C]ferredoxin285    *                                        
35p-cluster042304 COG0480 [J]translation elongation factor G2181    *             *       *                  
36p-cluster030801 COG0480 [J]elongation factor G216                          *                  
37p-cluster000721 COG1263 [G]PTS glucose transporter subunit IIB1470        *         *                          
38p-cluster011933 COG1585 [OU]hypothetical protein468        *         *                          
39p-cluster000723 COG0330 [O]peptidase885* *   *           *       *                  
40p-cluster049449 Uncategoriziedhypothetical protein228                                             
41p-cluster018214 Uncategoriziedhypothetical protein945                                             
42p-cluster018215 COG1106 [R]hypothetical protein1440*     *         *                            
43p-cluster012401 Uncategoriziedhypothetical protein7578* * *   *       * *     *   *           * *  
44p-cluster045169 Uncategoriziedhypothetical protein456                        *               *    
45p-cluster032433 Uncategoriziedhypothetical protein264                            *                
46p-cluster049267 Uncategoriziedhypothetical protein180                  *                       * *
47p-cluster044845 Uncategoriziedhypothetical protein77                                        *    
48p-cluster001295 COG0050 [J]elongation factor Tu1185* *   *                                 *   *
49p-cluster042304 COG0480 [J]translation elongation factor G2181    *             *       *                  
50p-cluster001297 COG0049 [J]30S ribosomal protein S7471                                             

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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