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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Some genomes (Variable genes)

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-cluster000726 COG0006 [E]Xaa-Pro aminopeptidase1389                  *         *               *
2p-cluster000726 COG0006 [E]Xaa-Pro aminopeptidase1389                            *               *
3p-cluster020569 COG2110 [R]appr-1-p processing enzyme family d798        *                                    
4p-cluster033016 COG1115 [E]amino acid carrier protein1536* *   * *                                    
5p-cluster031095 COG1115 [E]hypothetical protein303                                             
6p-cluster019003 COG0584 [C]glycerophosphodiester phosphodieste780                                             
7p-cluster029208 Uncategoriziedhypothetical protein357                                             
8p-cluster019441 Uncategoriziedhypothetical protein261                                             
9p-cluster032102 COG1343 [L]CRISPR-associated protein Cas2321                                        *    
10p-cluster029047 COG1518 [L]CRISPR-associated protein Cas11020                                             
11p-cluster032104 COG1468 [L]CRISPR-associated protein Cas4495                                             
12p-cluster000734 COG1203 [R]CRISPR-associated protein Cas32538                                             
13p-cluster000734 COG1203 [R]CRISPR-associated protein Cas32538                  *                          
14p-cluster000734 COG1203 [R]CRISPR-associated protein Cas32538                  *                          
15p-cluster000735 UncategoriziedCRISPR-associated protein Cas5771                                             
16p-cluster000735 UncategoriziedCRISPR-associated protein Cas5771                                             
17p-cluster000736 UncategoriziedCRISPR-associated protein948                                             
18p-cluster000736 UncategoriziedCRISPR-associated protein948                                             
19p-cluster000736 UncategoriziedCRISPR-associated protein948                                             
20p-cluster000737 Uncategoriziedhypothetical protein1728                  *                          
21p-cluster000737 Uncategoriziedhypothetical protein1728                  *                          
22p-cluster000737 Uncategoriziedhypothetical protein1728                                             
23p-cluster000738 UncategoriziedCRISPR-associated protein744      *                                      
24p-cluster000738 UncategoriziedCRISPR-associated protein744      *                                      
25trna-cluster000006 UncategoriziedtRNA-Gln75    * * *                                 *  
26trna-cluster000031 UncategoriziedtRNA-Leu84    * * *                                 *  
27trna-cluster000003 UncategoriziedtRNA-Lys76* *   *                                      
28trna-cluster000029 UncategoriziedtRNA-His76* * * * *         *                          
29trna-cluster000028 UncategoriziedtRNA-Gly76* * * * *         *                          
30trna-cluster000007 UncategoriziedtRNA-Pro77* * * * *         *                          
31p-cluster029209 COG0457 [R]O-linked GlcNAc transferase2448    *             *                   * * * *
32p-cluster004836 Uncategoriziedhypothetical protein213                                             
33p-cluster000170 Uncategoriziedendonuclease951* *   * *         *                          
34p-cluster001581 COG3839 [G]spermidine/putrescine ABC transport1131* * * * *         *                         *
35p-cluster032346 COG0609 [P]iron chelate uptake ABC transporter1059                                             
36p-cluster019463 COG0614 [P]heme ABC superfamily ATP binding ca894                                             
37p-cluster032866 Uncategoriziedhypothetical protein180                                             
38p-cluster027807 Uncategoriziedhypothetical protein216                                             
39p-cluster020548 COG1629 [P]hemin receptor2276    *                     *                 *
40p-cluster046781 COG1629 [P]iron complex outermembrane recepter1974                                             
41p-cluster019465 Uncategoriziedhypothetical protein141                                             
42p-cluster018513 Uncategoriziedhypothetical protein219                          *                  
43p-cluster017061 COG0251 [J]endoribonuclease L-PSP387* *   *                                      
44p-cluster001662 COG1061 [KL]DNA helicase2829* *   *           *                          
45p-cluster035322 COG0513 [LKJ]RNA helicase1590                  *                          
46p-cluster035322 COG0513 [LKJ]RNA helicase1590                                             
47p-cluster001664 COG2184 [D]cell division protein Fic657                                             
48p-cluster019472 COG1559 [R]aminodeoxychorismate lyase975                                          *  
49p-cluster034031 Uncategoriziedhypothetical protein123                                             
50p-cluster035387 Uncategoriziedhypothetical protein147                                             

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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