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

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) HPS-ST41
2) HPS-ST42
3) HPS9
4) HPS10
5) HPS11
Show genes only present in
1) HPS-ST41
2) HPS-ST42
3) HPS9
4) HPS10
5) HPS11
All genomes (Core genes)
Some genomes (Variable genes)

Show genes not present in
1) HPS-ST41
2) HPS-ST42
3) HPS9
4) HPS10
5) HPS11


<< Prev    Next >>
First Page    Last Page
Go to page   / 48  

# 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         

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