hpar Gene Table Build 14_03_11 [A quick tutorial]

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) HPS-ST41
2) HPS-ST42
3) HPS9
4) HPS10
5) HPS11
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1) HPS-ST41
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# Cluster ID COG Function Annotation Expected gene Length (bp)

Haemophilus parasuis ST4-1

Haemophilus parasuis ST4-2

Haemophilus parasuis HPS9

Haemophilus parasuis HPS10

Haemophilus parasuis HPS11

1p-cluster000883 COG0621 [J](dimethylallyl)adenosine tRNA methy1428* * *   *
2p-cluster000940 COG0317 [TK](p)ppGpp synthetase2208      *  
3p-cluster001820 COG1575 [H]1,4-dihydroxy-2-naphthoate prenyltr906         
4p-cluster007350 COG0106 [E]1-(5-phosphoribosyl)-5-[(5- phospho750         
5p-cluster000941 COG0743 [I]1-deoxy-D-xylulose 5-phosphate redu1191         
6p-cluster000797 COG1154 [HI]1-deoxy-D-xylulose-5-phosphate synt1848         
7rrna-cluster000009 Uncategorizied16S ribosomal RNA436  * *    
8rrna-cluster000016 Uncategorizied16S ribosomal RNA71    *    
9rrna-cluster000020 Uncategorizied16S ribosomal RNA1542* * * * *
10p-cluster000475 COG1385 [S]16S rRNA methyltransferase735         
11p-cluster000533 COG0144 [J]16S rRNA methyltransferase1299         
12p-cluster000800 COG0275 [M]16S rRNA methyltransferase939         
13p-cluster001277 COG0357 [M]16S rRNA methyltransferase612         
14p-cluster002825 COG0742 [L]16S rRNA methyltransferase591         
15p-cluster000129 COG1187 [J]16S rRNA pseudouridylate synthase693         
16p-cluster001724 COG0806 [J]16S rRNA-processing protein RimM528         
17p-cluster006184 COG0737 [F]2, 3-cyclic nucleotide 2-phosphodie1974         
18p-cluster008911 COG0617 [J]2, 3-cyclic nucleotide 2-phosphodie1257         
19p-cluster001034 COG2171 [E]2,3,4,5-tetrahydropyridine-2,6-carb825         
20p-cluster000986 COG2055 [C]2,3-diketo-L-gulonate reductase999         
21p-cluster006737 COG0076 [E]2,4-diaminobutyrate decarboxylase1533         
22p-cluster000953 COG0245 [I]2-C-methyl-D-erythritol 2,4-cyclodi504         
23p-cluster000952 COG1211 [I]2-C-methyl-D-erythritol 4-phosphate681         
24p-cluster001160 COG2877 [M]2-dehydro-3-deoxyphosphooctonate al855         
25p-cluster000526 COG0119 [E]2-isopropylmalate synthase1566        *
26p-cluster005438 COG0654 [HC]2-octaprenyl-3-methyl-6-methoxy-1,41173         
27p-cluster001899 COG0654 [HC]2-octaprenyl-6-methoxyphenyl hydrox1200  *      
28p-cluster001891 COG0567 [C]2-oxoglutarate dehydrogenase2808         
29p-cluster000404 COG1165 [H]2-succinyl-5-enolpyruvyl-6-hydroxy-1710         
30p-cluster000403 COG0596 [R]2-succinyl-6-hydroxy-2, 4-cyclohexa768         
31rrna-cluster000004 Uncategorizied23S ribosomal RNA338*        
32rrna-cluster000021 Uncategorizied23S ribosomal RNA3032* * * * *
33p-cluster000114 COG0293 [J]23S rRNA methyltransferase627  *      
34p-cluster000479 COG2265 [J]23S rRNA methyltransferase1341         
35p-cluster001109 COG2265 [J]23S rRNA methyltransferase1170         
36p-cluster001289 COG0566 [J]23S rRNA methyltransferase735    * *  
37p-cluster001874 COG1092 [R]23S rRNA methyltransferase2178        *
38p-cluster000472 COG0564 [J]23S rRNA pseudouridylate synthase978    *    
39p-cluster000753 COG0633 [C]2Fe-2S ferredoxin342         
40p-cluster001565 COG1409 [R]3,5-cyclic-nucleotide phosphodieste828         
41p-cluster001123 COG0483 [G]3-5-bisphosphate nucleotidase813         
42p-cluster000824 COG0757 [E]3-dehydroquinate dehydratase444        *
43p-cluster001424 COG0337 [E]3-dehydroquinate synthase1089         
44p-cluster000165 COG2227 [H]3-demethylubiquinone-9 3-methyltran711*   * * *
45p-cluster001644 COG1778 [R]3-deoxy-D-manno-octulosonate 8-phos540         
46p-cluster001368 COG0515 [RTKL]3-deoxy-D-manno-octulosonic acid ki702         
47p-cluster000566 COG1519 [M]3-deoxy-D-manno-octulosonic acid tr1284         
48p-cluster000897 COG1212 [M]3-deoxy-manno-octulosonate cytidyly768    *    
49p-cluster001014 COG0764 [I]3-hydroxyacyl-ACP dehydratase468         
50p-cluster001685 COG0764 [I]3-hydroxydecanoyl-ACP dehydratase531         

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Gene Completeness


: Similar sequence present
: Not present

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