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   / 54  

# 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-cluster003731 COG4143 [H]thiamine ABC transporter substrate-984         
2p-cluster001000 COG1198 [L]primosomal protein N2199        *
3p-cluster001002 COG2962 [R]permease882*       *
4p-cluster001002 COG2962 [R]permease882*       *
5p-cluster001003 COG0436 [E]aminotransferase1218*        
6p-cluster001004 COG0147 [EH]isochorismate synthase1275         
7p-cluster001005 COG0671 [I]phosphatidylglycerophosphatase723         
8p-cluster001006 COG1940 [KG]N-acetylglucosamine kinase915         
9p-cluster001007 COG0491 [R]hydroxyacylglutathione hydrolase708         
10p-cluster001008 COG0020 [I]UDP pyrophosphate synthase714        *
11p-cluster001009 COG0575 [I]phosphatidate cytidylyltransferase870         
12p-cluster001010 COG0750 [M]zinc metallopeptidase RseP1320        *
13p-cluster001011 COG4775 [M]outer membrane protein assembly pro2418         
14p-cluster001012 COG2825 [M]membrane protein804         
15p-cluster001013 COG1044 [M]UDP-3-O-(3-hydroxymyristoyl) glucos1026         
16p-cluster001014 COG0764 [I]3-hydroxyacyl-ACP dehydratase468         
17p-cluster001013 COG1044 [M]UDP-3-O-(3-hydroxymyristoyl) glucos1026         
18p-cluster001016 COG0527 [E]aspartate kinase2445    *    
19p-cluster001017 COG0083 [E]serine kinase948         
20p-cluster001018 COG0287 [E]prephenate dehydrogenase1122         
21p-cluster000621 COG0722 [E]phospho-2-dehydro-3-deoxyheptonate 1068         
22p-cluster001020 COG0859 [M]glycosyl transferase1029        *
23p-cluster001021 COG2920 [P]sulfur transfer protein TusE339        *
24p-cluster006184 COG0737 [F]2, 3-cyclic nucleotide 2-phosphodie1974         
25p-cluster001022 COG0737 [F]hypothetical protein339         
26p-cluster001023 COG1115 [E]sodium:alanine symporter1449         
27p-cluster001024 COG2215 [R]cobalt transporter978         
28p-cluster001025 COG3683 [R]ABC transporter substrate-binding p642         
29p-cluster006188 COG3630 [C]Oxaloacetate decarboxylase gamma ch255      *  
30p-cluster006189 COG5016 [C]oxaloacetate decarboxylase1806        *
31p-cluster006190 COG1883 [C]oxaloacetate decarboxylase subunit 1305         
32p-cluster000066 COG2824 [P]hypothetical protein321         
33p-cluster001210 COG0299 [F]formyltetrahydrofolate deformylase837        *
34p-cluster000068 COG0114 [C]aspartate ammonia-lyase1428         
35p-cluster006194 Uncategoriziedhypothetical protein204         
36p-cluster000069 COG0326 [O]heat shock protein 901887    *    
37p-cluster002113 COG2027 [M]D-alanyl-D-alanine carboxypeptidase1440    *    
38p-cluster003344 COG0782 [K]transcription elongation factor Gre489* * *   *
39p-cluster004746 COG3328 [L]transposase183         
40p-cluster005626 COG3328 [L]transposase344*   * * *
41p-cluster002438 COG0463 [M]glycosyltransferase888      *  
42p-cluster001651 Uncategoriziedhypothetical protein507         
43p-cluster006200 Uncategoriziedmembrane protein1191         
44p-cluster006201 COG3306 [M]Lsg locus protein 4777         
45p-cluster004376 UncategoriziedCMP-N-acetylneuraminate-beta-galact969        *
46p-cluster007473 COG2244 [R]Lsg locus protein 12136         
47p-cluster000734 COG1083 [M]acylneuraminate cytidylyltransferas681         
48p-cluster001649 COG1434 [S]hypothetical protein744         
49p-cluster001648 Uncategoriziedmembrane protein708         
50p-cluster001647 COG0860 [M]N-acetylmuramoyl-L-alanine amidase1113         

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