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-cluster008189 COG1349 [KG]DeoR faimly transcriptional regulat759    *    
2p-cluster001350 COG2084 [I]oxidoreductase909         
3p-cluster001351 COG3395 [S]membrane protein1242         
4p-cluster001352 COG0235 [G]aldolase633         
5p-cluster001353 COG3622 [G]hypothetical protein783         
6p-cluster001354 COG0451 [MG]hypothetical protein948         
7p-cluster001355 COG2610 [GE]gluconate permease1467         
8p-cluster001356 COG4099 [R]phospholipase1347    * * *
9p-cluster000698 COG1053 [C]fumarate reductase1785        *
10p-cluster000699 COG0479 [C]fumarate reductase771         
11p-cluster006256 COG3029 [C]fumarate reductase396         
12p-cluster000701 COG3080 [C]fumarate reductase351         
13p-cluster000702 COG2981 [E]sulfate transport protein CysZ756         
14p-cluster000703 COG3115 [D]cell division protein ZipA819         
15p-cluster004115 COG0272 [L]NAD-dependent DNA ligase LigA2070         
16p-cluster000705 COG0513 [LKJ]ATP-dependent DNA helicase RecQ1830        *
17p-cluster000706 COG1965 [P]frataxin309        *
18p-cluster000707 COG1974 [KT]LexA family transcriptional regulat630         
19p-cluster003969 Uncategoriziedhypothetical protein1005         
20p-cluster004120 Uncategoriziedhypothetical protein585         
21p-cluster000710 COG0790 [R]hypothetical protein759         
22p-cluster000711 COG2937 [I]glycerol-3-phosphate acyltransferas2436         
23p-cluster000712 COG0503 [F]adenine phosphoribosyltransferase543         
24p-cluster000713 COG2812 [L]DNA polymerase III subunit gamma/ta2019         
25p-cluster000714 COG1131 [V]ABC transporter897         
26p-cluster000715 COG0842 [V]hypothetical protein756  *      
27p-cluster000716 COG2161 [D]plasmid stabilization protein255         
28p-cluster000717 COG2026 [JD]addiction module toxin RelE285         
29p-cluster000718 COG2925 [L]exonuclease I1551         
30p-cluster000719 COG1912 [S]DNA-directed RNA polymerase subunit960         
31p-cluster000720 COG3663 [L]DNA glycosylase597         
32p-cluster000721 COG0613 [R]S-adenosylmethionine tRNA ribosyltr822         
33p-cluster000722 COG0440 [E]acetolactate synthase 3 regulatory 492         
34p-cluster000723 COG0028 [EH]acetolactate synthase 3 catalytic s1722      *  
35p-cluster000724 COG0473 [CE]3-isopropylmalate dehydrogenase1083      *  
36p-cluster000725 COG0841 [V]transporter3090  *   * *
37p-cluster000726 COG0845 [M]membrane protein1206         
38p-cluster007481 COG1309 [K]TetR family transcriptional regulat567         
39p-cluster000728 COG0138 [F]phosphoribosylaminoimidazolecarboxa1599         
40p-cluster000729 COG0626 [E]cystathionine beta-lyase1191         
41p-cluster000730 COG0350 [L]cysteine methyltransferase564* * *    
42p-cluster001288 COG0050 [J]elongation factor Tu1188* * * * *
43p-cluster008786 Uncategoriziedhypothetical protein381        *
44p-cluster002040 Uncategoriziedhypothetical protein432*       *
45p-cluster001245 Uncategoriziedhypothetical protein1413* * * *  
46p-cluster001246 COG0212 [H]hypothetical protein579         
47p-cluster001247 COG3027 [S]cell division protein ZapA330         
48p-cluster001248 COG3079 [S]hypothetical protein546         
49p-cluster001249 COG1328 [F]ribonucleoside-triphosphate reducta1782         
50p-cluster001250 Uncategoriziedribonucleoside-triphosphate reducta471         

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