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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4) HPS10
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4) HPS10
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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-cluster000012 COG0811 [U]energy transducer TonB453         
12p-cluster000013 COG0848 [U]biopolymer transporter ExbD387         
13p-cluster000015 COG4390 [S]RNA polymerase subunit sigma-32321         
14p-cluster000016 COG3087 [D]cell division protein720         
15p-cluster000018 Uncategoriziedhypothetical protein204         
16p-cluster000019 COG0861 [P]membrane protein729         
17p-cluster000020 COG3066 [L]DNA mismatch repair protein MutH681  *     *
18p-cluster000022 COG0497 [L]recombination and repair protein1680         
19p-cluster000023 COG0620 [E]5-methyltetrahydropteroyltriglutama2271        *
20p-cluster000024 COG0323 [L]DNA mismatch repair protein MutL1848        *
21p-cluster000025 COG0268 [J]30S ribosomal protein S20264         
22p-cluster000026 COG0728 [R]multidrug transporter MurJ1572      *  
23p-cluster000027 COG0031 [E]cysteine synthase951      *  
24p-cluster000028 COG3719 [J]ribonuclease747         
25p-cluster000030 COG0632 [L]Holliday junction ATP-dependent DNA609         
26p-cluster000031 COG1584 [S]hypothetical protein567         
27p-cluster000032 COG0687 [E]spermidine/putrescine ABC transport1050      * *
28p-cluster000033 COG0209 [F]ribonucleotide-diphosphate reductas1710         
29p-cluster000034 COG0208 [F]ribonucleotide reductase978         
30p-cluster000035 COG1012 [C]proline dehydrogenase3612         
31p-cluster000036 COG0591 [ER]proline:sodium symporter PutP1506      *  
32p-cluster000037 COG0316 [S]amino acid ABC transporter substrat594* * * * *
33p-cluster000038 COG1726 [C]Na(+)-translocating NADH-quinone re1347         
34p-cluster000039 COG4658 [C]Na(+)-translocating NADH-quinone re1239         
35p-cluster000040 COG2869 [C]Na(+)-translocating NADH-quinone re777         
36p-cluster000043 COG0543 [HC]Na(+)-translocating NADH-quinone re1233        *
37p-cluster000044 Uncategoriziedhypothetical protein429         
38p-cluster000045 COG1708 [R]hypothetical protein300         
39p-cluster000046 COG1178 [P]thiamine transporter1578         
40p-cluster000047 COG3303 [P]cytochrome C nitrite reductase1458         
41p-cluster000048 Uncategoriziedcysteine dioxygenase624         
42p-cluster000050 COG3301 [P]nitrite reductase954         
43p-cluster000051 COG3774 [M]glycosyl transferase789         
44p-cluster000052 COG0560 [E]phosphoserine phosphatase864         
45p-cluster000054 COG0361 [J]translation initiation factor IF-1219         
46p-cluster000055 COG1162 [R]GTPase RsgA1032         
47p-cluster000056 COG0803 [P]iron-binding protein879         
48p-cluster000057 COG1120 [PH]manganese transporter762         
49p-cluster000058 COG1108 [P]membrane protein873      * *
50p-cluster000060 COG4316 [S]hypothetical protein414        *

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Gene Completeness


: Similar sequence present
: Not present

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