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

Keyword search
Search for
Also include clusters with significant sequence similarity
Also include clusters containing upstream and downstream genes (Must sort rows by Gene position in a genome first)

BLAST search
Sequence type

Row sorting and cell coloring options
Sort rows by Order rows in
Color cells by Display rows

Row filtering options
 Show COG of type
 Show clusters with minimum expected length of bp
Show clusters containing genes near the ends of contigs
Show clusters containing genes with frameshift mutation

Display column
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
All genomes (Core genes)
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


<< Prev    Next >>
First Page    Last Page
Go to page   / 108  

# 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-cluster035139 Uncategoriziedhypothetical protein90                              *              
2p-cluster035140 Uncategoriziedhypothetical protein384                              *              
3p-cluster043359 Uncategoriziedhypothetical protein891                                             
4p-cluster043900 Uncategoriziedhypothetical protein657                                             
5p-cluster006022 COG1132 [V]ABC transporter1758  *   * *         *                          
6p-cluster014907 COG1132 [V]ABC transporter1692                                             
7p-cluster032866 Uncategoriziedhypothetical protein180                                             
8p-cluster000186 COG0716 [C]flavodoxin510                  *                          
9p-cluster000773 COG1309 [K]TetR family transcriptional regulat471                  *                          
10p-cluster043905 Uncategoriziedhypothetical protein723                                             
11p-cluster035147 Uncategoriziedhypothetical protein234                                             
12p-cluster032031 COG1227 [C]DHHA2 domain protein1635                  *                          
13p-cluster032030 Uncategoriziedhypothetical protein462                                             
14p-cluster032029 COG0826 [O]peptidase, U32 family1233*                                            
15p-cluster000302 COG0305 [L]DNA helicase1341                                             
16p-cluster030007 COG0359 [J]50S ribosomal protein L9453                                             
17p-cluster000304 Uncategoriziedhypothetical protein831                                             
18p-cluster030009 COG0470 [L]DNA polymerase III subunits gamma/t1455                                             
19p-cluster001036 COG2204 [T]transcriptional regulator1716* *               *       *                  
20p-cluster020266 COG0810 [M]TonB protein840                                             
21p-cluster000308 COG0848 [U]biopolymer transporter ExbD444                          *                  
22p-cluster000309 COG0811 [U]biopolymer transporter ExbB612                          *                  
23p-cluster000310 Uncategoriziedhypothetical protein378  *   * *                                    
24p-cluster020927 Uncategoriziedhypothetical protein234        *                                    
25p-cluster000311 COG0457 [R]hypothetical protein2811  *     *                                    
26p-cluster000312 COG1852 [S]DNA-binding protein531                                             
27p-cluster028577 COG2202 [T]methyl-accepting chemotaxis sensory807                  *                          
28p-cluster031434 COG0745 [TK]response regulator receiver domain 702                  *                          
29p-cluster006002 COG0642 [T]histidine kinase1872*                                            
30p-cluster020047 COG1454 [C]1,3-propanediol dehydrogenase1149* *               *         *                
31p-cluster035390 Uncategoriziedhypothetical protein207                                             
32p-cluster017714 COG4816 [E]propanediol utilization protein Pdu813                                             
33p-cluster031629 Uncategoriziedhypothetical protein432                            *                
34p-cluster005999 COG4909 [Q]propanediol dehydratase1665                                             
35p-cluster035168 COG4909 [Q]propanediol dehydratase medium subu681                                             
36p-cluster020280 COG4910 [Q]propanediol dehydratase small subun537                                             
37p-cluster005996 Uncategoriziedglycerol dehydratase1815                                             
38p-cluster005995 Uncategoriziedhypothetical protein378                                             
39p-cluster028872 COG4577 [QC]ethanolamine utilization protein Eu474                                             
40p-cluster001688 COG4577 [QC]carboxysome structural protein EutM294                                             
41p-cluster005992 COG4869 [Q]phosphate propanoyltransferase621                                             
42p-cluster005991 Uncategoriziedflavoprotein711                                             
43p-cluster003007 COG4576 [QC]ethanolamine utilization protein Eu270                                             
44p-cluster017703 COG3193 [R]hypothetical protein951                                             
45p-cluster001687 COG1012 [C]hypothetical protein1449                  *                          
46p-cluster020292 COG1012 [C]CoA-dependent propionaldehyde dehyd384                                             
47p-cluster003010 COG0580 [G]glycerol transporter732                                             
48p-cluster003011 COG0554 [C]glycerol kinase1494                                             
49p-cluster003012 COG2376 [G]dihydroxyacetone kinase987  *                                          
50p-cluster023672 COG0675 [L]hypothetical protein119                                             

Please send any comment/suggestion to kitticho@uw.edu
Compatible browswer

tumblr site counter

 

Gene Completeness

>=100%
=70%
<70%

: Similar sequence present
: Not present

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