hpar 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) HPS-ST41
2) HPS-ST42
3) HPS9
4) HPS10
5) HPS11
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1) HPS-ST41
2) HPS-ST42
3) HPS9
4) HPS10
5) HPS11
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1) HPS-ST41
2) HPS-ST42
3) HPS9
4) HPS10
5) HPS11


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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-cluster000001 COG1295 [S]hypothetical protein849*     * *
2p-cluster000002 COG1490 [J]D-tyrosyl-tRNA(Tyr) deacylase435         
3p-cluster000003 COG0037 [D]tRNA(Ile)-lysidine synthetase1269         
4p-cluster000004 COG3012 [S]preprotein translocase subunit SecA465        *
5p-cluster000005 COG0661 [R]ubiquinone biosynthesis protein Ubi1650        *
6p-cluster000006 COG3165 [S]hypothetical protein627         
7p-cluster000007 COG0500 [QR]ubiquinone biosynthesis methyltrans774         
8p-cluster000008 COG2901 [KL]Fis family transcriptional regulato297         
9p-cluster000009 COG0042 [J]tRNA-dihydrouridine synthase B978  *   * *
10p-cluster000010 COG0616 [OU]peptidase1056         
11p-cluster005126 COG0607 [P]hypothetical protein465         
12p-cluster000012 COG0811 [U]energy transducer TonB453         
13p-cluster000013 COG0848 [U]biopolymer transporter ExbD387         
14p-cluster002506 COG0810 [M]energy transducer TonB774         
15p-cluster000015 COG4390 [S]RNA polymerase subunit sigma-32321         
16p-cluster000016 COG3087 [D]cell division protein720         
17p-cluster001394 COG3839 [G]maltose/maltodextrin transporter AT1140         
18p-cluster000018 Uncategoriziedhypothetical protein204         
19p-cluster000019 COG0861 [P]membrane protein729         
20p-cluster000020 COG3066 [L]DNA mismatch repair protein MutH681  *     *
21p-cluster002561 COG3676 [L]transposase357        *
22p-cluster002588 Uncategoriziedmembrane protein942  *   * *
23p-cluster000022 COG0497 [L]recombination and repair protein1680         
24p-cluster000023 COG0620 [E]5-methyltetrahydropteroyltriglutama2271        *
25p-cluster007144 COG0620 [E]hypothetical protein201         
26p-cluster000024 COG0323 [L]DNA mismatch repair protein MutL1848        *
27p-cluster000025 COG0268 [J]30S ribosomal protein S20264         
28p-cluster000026 COG0728 [R]multidrug transporter MurJ1572      *  
29p-cluster000027 COG0031 [E]cysteine synthase951      *  
30p-cluster000028 COG3719 [J]ribonuclease747         
31p-cluster004205 COG3091 [S]sprT507         
32p-cluster000030 COG0632 [L]Holliday junction ATP-dependent DNA609         
33p-cluster000031 COG1584 [S]hypothetical protein567         
34p-cluster000032 COG0687 [E]spermidine/putrescine ABC transport1050      * *
35p-cluster000033 COG0209 [F]ribonucleotide-diphosphate reductas1710         
36p-cluster000034 COG0208 [F]ribonucleotide reductase978         
37p-cluster000035 COG1012 [C]proline dehydrogenase3612         
38p-cluster000036 COG0591 [ER]proline:sodium symporter PutP1506      *  
39p-cluster000037 COG0316 [S]amino acid ABC transporter substrat594* * * * *
40p-cluster000038 COG1726 [C]Na(+)-translocating NADH-quinone re1347         
41p-cluster000039 COG4658 [C]Na(+)-translocating NADH-quinone re1239         
42p-cluster000040 COG2869 [C]Na(+)-translocating NADH-quinone re777         
43p-cluster000669 COG4660 [C]elongation factor G690      * *
44p-cluster000669 COG4660 [C]elongation factor G690      * *
45p-cluster000043 COG0543 [HC]Na(+)-translocating NADH-quinone re1233        *
46p-cluster000044 Uncategoriziedhypothetical protein429         
47p-cluster000045 COG1708 [R]hypothetical protein300         
48p-cluster000046 COG1178 [P]thiamine transporter1578         
49p-cluster000047 COG3303 [P]cytochrome C nitrite reductase1458         
50p-cluster000048 Uncategoriziedcysteine dioxygenase624         

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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