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
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
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1) BL
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4) DAB
5) BFTR-2
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-cluster010159 COG1131 [V]hypothetical protein936*     *          
2p-cluster000515 COG0444 [EP]ATPase813  *              
3p-cluster001715 COG1173 [EP]diguanylate cyclase867                 
4p-cluster000004 COG0601 [EP]peptide ABC transporter permease915                 
5p-cluster000005 COG0747 [E]diguanylate phosphodiesterase1488                 
6p-cluster000006 Uncategoriziedhypothetical protein1401        *        
7p-cluster018611 COG0008 [J]glutamate--tRNA ligase1557        *        
8p-cluster016857 Uncategoriziedhypothetical protein114                 
9p-cluster000008 COG1073 [R]lysophospholipase864  *              
10p-cluster001005 COG0216 [J]peptide chain release factor 11080  *              
11p-cluster000010 Uncategoriziedhypothetical protein222                 
12p-cluster000011 COG0736 [I]4-phosphopantetheinyl transferase345                 
13p-cluster000012 COG0084 [L]hydrolase TatD759                 
14p-cluster000013 COG1281 [O]molecular chaperone Hsp33861                 
15p-cluster000014 COG1555 [L]competence protein522                 
16p-cluster000015 COG0635 [H]coproporphyrinogen III oxidase1383                 
17p-cluster004193 COG2804 [NU]general secretion pathway protein E1476        *        
18p-cluster000017 COG0606 [O]magnesium transporter1503                 
19p-cluster000018 COG1971 [S]hypothetical protein558                 
20p-cluster000019 COG0781 [K]nitrogen utilization protein B417                 
21p-cluster000020 Uncategoriziedmembrane protein225                 
22p-cluster000021 Uncategoriziedhypothetical protein537                 
23p-cluster000022 COG1302 [S]alkaline-shock protein363                 
24p-cluster000023 COG0439 [I]acetyl-CoA carboxylase biotin carbo1344                 
25p-cluster000084 COG0511 [I]carboxylesterase444                 
26p-cluster002144 COG0847 [L]DNA polymerase III subunit alpha4353                 
27p-cluster000026 Uncategoriziedhypothetical protein1761        *        
28p-cluster000027 COG0553 [KL]helicase SNF3405    *            
29p-cluster000028 COG0614 [P]hemin receptor876                 
30p-cluster016826 COG1629 [P]TonB-dependent receptor plug domain2256  *              
31p-cluster014749 COG0609 [P]iron chelate uptake ABC transporter1080  *              
32p-cluster000031 COG1120 [PH]heme ABC transporter ATP-binding pr801        *        
33p-cluster000032 COG0635 [H]oxygen-independent coproporphyrinog1227                 
34p-cluster000033 COG3775 [G]PTS galactitol transporter subunit 1260            *    
35p-cluster000034 COG3414 [G]PTS lactose transporter subunit IIB393                 
36p-cluster000035 COG1762 [GT]PTS sugar transporter subunit IIA438                 
37p-cluster000517 COG0235 [G]fuculose phosphate aldolase669                 
38p-cluster015665 COG0235 [G]L-fuculose-1-phosphate aldolase dom297                 
39p-cluster000037 COG1762 [GT]phosphoenolpyruvate-dependent sugar2061  *     *   *    
40p-cluster000038 COG3629 [T]hypothetical protein1152  *         *    
41p-cluster016105 COG3629 [T]hypothetical protein261            *    
42p-cluster000040 COG1574 [R]exoenzyme regulatory protein aepA p1629  *         *    
43p-cluster000040 COG1574 [R]exoenzyme regulatory protein aepA p1629  *         *    
44p-cluster000041 COG1757 [C]sodium:proton antiporter1428  *              
45p-cluster000042 COG0441 [J]threonyl-tRNA synthetase1914                 
46p-cluster000043 Uncategoriziedhypothetical protein3633      *          
47p-cluster000044 COG0526 [OC]thioredoxin321  * * *       * *
48p-cluster000045 COG1214 [O]O-sialoglycoprotein endopeptidase669                 
49p-cluster000046 COG0802 [R]ATP/GTP hydrolase468                 
50p-cluster015657 COG2870 [M]bifunctional protein RfaE, domain I477                 

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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