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

1trna-cluster000001 UncategoriziedtRNA-Met78* * * *                                      
2trna-cluster000002 UncategoriziedtRNA-Arg77* * * *                                      
3trna-cluster000003 UncategoriziedtRNA-Lys76* *   *                                      
4p-cluster046402 COG0608 [L]single-stranded-DNA-specific exonuc2559*     *           *                          
5p-cluster033536 COG1840 [P]iron(III)-binding protein1062                  *       *                  
6p-cluster028479 COG0444 [EP]peptide ABC transporter, ATP-bindin1695  *     *         *       *                  
7p-cluster015093 COG1176 [E]iron ABC transporter permease1656                  *                          
8p-cluster030378 COG3315 [Q]tetracenomycin polyketide synthesis810                  *                          
9p-cluster021633 Uncategoriziedhypothetical protein441                  *                          
10p-cluster011295 Uncategoriziedhypothetical protein213                                             
11p-cluster029487 COG5015 [S]hypothetical protein492                                             
12p-cluster017112 COG0561 [R]Cof-like hydrolase813      *                     *                
13p-cluster021630 COG0561 [R]cof family hydrolase489                  *                          
14p-cluster021629 COG0561 [R]cof family hydrolase273                  *                          
15p-cluster000009 COG1032 [C]methyltransferase894                  *                          
16p-cluster000010 COG0726 [G]polysaccharide deacetylase1803                  *                          
17p-cluster018723 UncategoriziedSMI1 / KNR4 family protein984                                             
18p-cluster000012 COG0697 [GER]membrane protein864                  *                          
19p-cluster015102 COG0747 [E]diguanylate phosphodiesterase1539      *           *                          
20p-cluster000888 COG0601 [EP]ABC transporter permease978    * *           *                          
21p-cluster000015 COG1173 [EP]peptide ABC transporter permease870                  *                          
22p-cluster028479 COG0444 [EP]peptide ABC transporter, ATP-bindin1695  *     *         *       *                  
23p-cluster028479 COG0444 [EP]peptide ABC transporter, ATP-bindin1695  *     *         *       *                  
24p-cluster020139 COG4608 [E]oligopeptide ABC superfamily ATP bi864    *                                   *    
25p-cluster015112 COG4115 [S]addiction module protein255                                             
26p-cluster040957 Uncategoriziedtoxin-antitoxin system, toxin compo138                                             
27p-cluster027699 Uncategoriziedtoxin-antitoxin system, antitoxin c303                  *                          
28p-cluster020142 Uncategoriziedhypothetical protein129                  *                          
29p-cluster031669 COG1862 [U]preprotein translocase, YajC subuni330  *                       *                  
30p-cluster000020 COG0860 [M]N-acetylmuramoyl-L-alanine amidase1029                                             
31p-cluster000021 Uncategoriziedhypothetical protein447                                             
32p-cluster031666 COG0216 [J]peptide chain release factor 11098                                             
33p-cluster000023 COG2890 [J]SAM-dependent methyltransferase1152                                             
34p-cluster015126 COG0809 [J]S-adenosylmethionine tRNA ribosyltr1056                                             
35p-cluster000025 COG0742 [L]methyltransferase549                  *                          
36p-cluster021344 Uncategoriziedhypothetical protein144                  *                          
37p-cluster000026 COG1722 [L]exodeoxyribonuclease VII small subu213                                             
38p-cluster000715 COG0142 [H]heptaprenyl diphosphate synthase981                  *                          
39p-cluster000028 COG0020 [I]UDP pyrophosphate synthase693                  *                          
40p-cluster006092 COG0575 [I]phosphatidate cytidylyltransferase891                                             
41p-cluster015132 COG0743 [I]1-deoxy-D-xylulose 5-phosphate redu1173                                             
42p-cluster026519 COG0125 [F]hypothetical protein687*     *                   *               *  
43p-cluster016772 Uncategoriziedhypothetical protein117                                             
44p-cluster000032 Uncategoriziedhypothetical protein549                                             
45p-cluster000033 Uncategoriziedhypothetical protein738                                      *      
46p-cluster046475 Uncategoriziedhypothetical protein1047                    *                 *      
47p-cluster024518 Uncategoriziedhypothetical protein219                    *                 *      
48p-cluster000034 UncategoriziedCopG family transcriptional regulat315                    *                 *      
49p-cluster000035 Uncategoriziedhypothetical protein246                                *     * *    
50p-cluster024514 COG5527 [L]hypothetical protein1512              *     *                 *      

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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