The genus trace: a function that shows values of genus (vertical axis) for subchains spanned between the first residue, and all other residues (shown on horizontal axis). The number of the latter residue and the genus of a given subchain are shown interactively.
Total Genus |
199
|
sequence length |
688
|
structure length |
648
|
Chain Sequence |
SAYPFFRRDMSWLSFNERVLMEAADRTLPVYDRIKFLSIFSSNLEEFYTVRVAYHQAVLQKHILQAIRETVIRQDELYYRIFYDQILPTLEEHGIRLRTHAPTHPDHKAYLRRFFHEEIFPLLYPMLLLPSKVRTFIRSGRVYLAVRLKEKETDEAYSYALLNVPTDGLPRFVELPRLQTDTFYYYSFLEDIIKEHLDVVFPGYEVMDSYSIKVSRDADLLLDAPTRFMYDGRMPDEVLRYICSSCDIDPEEAIRSGNYVNLQDLAMLPNPFAPRLETLTPEPLLSKHLEQAPSLMEGIRRKDYLIHVPYYTYDYVVRLLMEAAISPDVSEIRLTQYRVAENSSIISALEAAAQSGKKVSVFVELKARFNLRLSERMRRSGIRIVYSMPGLKVHAKTALILYHTPAGERPQGIALLSTGNFNETTARIYSDTTLMTANTDIVHDVYRLFRILDGDPEPARFSRLLVARYNMGEAITNLIEREIENVKRGKRGYMLLKMNGLQDKNVITQLYRASEAGVEIDLIVRGICCLVPDMPQSRNIRVTRLVDMYLEHSRIWCFHNGGKEEVFISSADWMKRNLYNRIETACPVLDPTLRREIIDILEIQLRDNIKACRIDSSLNNIYKHNSDEKPVRAQAAIYRYLKGKEETT
|
The genus matrix. At position (x,y) a genus value for a subchain spanned between x’th and y’th residue is shown. Values of the genus are represented by color, according to the scale given on the right.
After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.
| publication title |
Crystal Structure of Polyphosphate Kinase from Porphyromonas Gingivalis
rcsb |
| molecule tags |
Transferase
|
| source organism |
Porphyromonas gingivalis
|
| molecule keywords |
Polyphosphate kinase
|
| total genus |
199
|
| structure length |
648
|
| sequence length |
688
|
| chains with identical sequence |
B
|
| ec nomenclature |
ec
2.7.4.1: Polyphosphate kinase. |
| pdb deposition date | 2006-12-12 |
| chain | Pfam Accession Code | Pfam Family Identifier | Pfam Description |
|---|---|---|---|
| A | PF02503 | PP_kinase | Polyphosphate kinase middle domain |
| A | PF13089 | PP_kinase_N | Polyphosphate kinase N-terminal domain |
| A | PF13090 | PP_kinase_C | Polyphosphate kinase C-terminal domain 2 |
| A | PF17941 | PP_kinase_C_1 | Polyphosphate kinase C-terminal domain 1 |
Image from the rcsb pdb (www.rcsb.org)
cath code
| Class | Architecture | Topology | Homology | Domain |
|---|---|---|---|---|---|
| Alpha Beta | 2-Layer Sandwich | Endonuclease; Chain A | Endonuclease Chain A | ||
| Alpha Beta | 2-Layer Sandwich | Endonuclease; Chain A | Endonuclease Chain A | ||
| Alpha Beta | 2-Layer Sandwich | polyphosphate kinase like | Polyphosphate kinase middle domain |
#chains in the Genus database with same CATH superfamily 1V0R A; 5LZK A; 5BOX A; 1NOP A; 1MU9 A; 1RH0 A; 1QZQ A; 1RG2 A; 3SQ8 A; 5BPI A; 4URJ A; 1V0V A; 4GEL A; 3SQ3 A; 1RG1 A; 4GGK A; 5BPD A; 1V0U A; 1Q32 A; 2F5T X; 2ZE4 A; 4H4A A; 1XDO A; 2ZE9 A; 1JY1 A; 5BQT A; 1MU7 A; 1F0I A; 1V0Y A; 2O8R A; 1XDP A; 4RCT A; 1V0T A; 1BYS A; 1BYR A; 3SQ5 A; 1RGU A; 4GGJ A; 2C1L A; 3QPH A; 4GEM A; 1V0W A; 1V0S A; 4GEN A; 1RFI A; 3SQ7 A; 3HSI A; 1RFF A; 1RGT A; #chains in the Genus database with same CATH topology 1V0R A; 5LZK A; 5BOX A; 1NOP A; 1MU9 A; 1RH0 A; 1QZQ A; 2YMB A; 1RG2 A; 3SQ8 A; 5BPI A; 4URJ A; 1V0V A; 4GEL A; 3SQ3 A; 1RG1 A; 4GGK A; 5BPD A; 1V0U A; 1Q32 A; 2F5T X; 2ZE4 A; 4H4A A; 1XDO A; 2ZE9 A; 1JY1 A; 5BQT A; 3R3P A; 1MU7 A; 1F0I A; 1V0Y A; 2O8R A; 1XDP A; 4RCT A; 1V0T A; 1BYS A; 1BYR A; 1VSR A; 3SQ5 A; 3HRL A; 1CW0 A; 1ODG A; 4A5Z A; 1RGU A; 4GGJ A; 2C1L A; 3QPH A; 4GEM A; 1V0W A; 1V0S A; 4GEN A; 1RFI A; 3SQ7 A; 3HSI A; 1RFF A; 1RGT A; #chains in the Genus database with same CATH homology 1V0R A; 5LZK A; 5BOX A; 1NOP A; 1MU9 A; 1RH0 A; 1QZQ A; 1RG2 A; 3SQ8 A; 5BPI A; 4URJ A; 1V0V A; 4GEL A; 3SQ3 A; 1RG1 A; 4GGK A; 5BPD A; 1V0U A; 1Q32 A; 2F5T X; 2ZE4 A; 4H4A A; 1XDO A; 2ZE9 A; 1JY1 A; 5BQT A; 1MU7 A; 1F0I A; 1V0Y A; 2O8R A; 1XDP A; 4RCT A; 1V0T A; 1BYS A; 1BYR A; 3SQ5 A; 1RGU A; 4GGJ A; 2C1L A; 3QPH A; 4GEM A; 1V0W A; 1V0S A; 4GEN A; 1RFI A; 3SQ7 A; 3HSI A; 1RFF A; 1RGT A;
#similar chains in the Genus database (?% sequence similarity) ...loading similar chains, please wait... #similar chains, but unknotted ...loading similar chains, please wait... #similar chains in the pdb database (?% sequence similarity) ...loading similar chains, please wait...
