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 |
107
|
sequence length |
320
|
structure length |
310
|
Chain Sequence |
MDYRKIIKEIGRGKNHARDLDRDTARGLYAHMLNGEVPDLELGGVLIALRIKGEGEAEMLGFYEAMQNHTIKLTPPAGKPMPIVIPSYNGARKQANLTPLLAILLHKLGFPVVVHGVSEDPTRVLTETIFELMGITPTLHGGQAQAKLDEHQPVFMPVGAFCPPLEKQLAMRWRMGVRNSAHTLAKLATPFAEGEALRLSSVSHPEYIGRVAKFFSDIGGRALLMHGTEGEVYANPQRCPQINLIDREGMRVLYEKQAKDPETTAQWIERCLAGSEPIPESLKIQMACCLVATGEAATISDGLARVNQAF
|
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 |
YbiB from Escherichia coli, the Defining Member of the Novel TrpD2 Family of Prokaryotic DNA-binding Proteins.
pubmed doi rcsb |
| molecule tags |
Dna binding protein
|
| source organism |
Escherichia coli
|
| molecule keywords |
Uncharacterized protein YbiB
|
| total genus |
107
|
| structure length |
310
|
| sequence length |
320
|
| chains with identical sequence |
B
|
| ec nomenclature | |
| pdb deposition date | 2013-09-23 |
| chain | Pfam Accession Code | Pfam Family Identifier | Pfam Description |
|---|---|---|---|
| A | PF02885 | Glycos_trans_3N | Glycosyl transferase family, helical bundle domain |
Image from the rcsb pdb (www.rcsb.org)
cath code
| Class | Architecture | Topology | Homology | Domain |
|---|---|---|---|---|---|
| Mainly Alpha | Up-down Bundle | Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 | Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C | ||
| Alpha Beta | 3-Layer(aba) Sandwich | Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2 | Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain |
#chains in the Genus database with same CATH superfamily 4X46 A; 1ZXY A; 4M0R A; 1ZYK A; 4OWS A; 4GA4 A; 3H5Q A; 1BRW A; 3R6C A; 4N93 A; 4X5D A; 3QSA A; 5C2L A; 4OWV A; 5BYT A; 4EAF A; 4X5C A; 1OTP A; 4GKM A; 1V8G A; 4GIU A; 3R88 A; 2WK5 A; 5BO2 A; 4OWQ A; 3QR9 A; 4YEK A; 4MUO A; 4ZOK A; 4GTN A; 1KHD A; 4N8Q A; 4YI7 A; 1KGZ A; 4XR5 A; 4OWO A; 2GVQ A; 5BO3 A; 4ZOJ A; 2DSJ A; 4LHM A; 2WK6 A; 4EAD A; 1AZY A; 4ZOF A; 4YYY A; 2ELC A; 3TWP A; 4N5V A; 2BPQ A; 4OWU A; 2J0F A; 5BNE A; 1O17 A; 4X5B A; 5EY3 A; 4X58 A; 4IJ1 A; 1UOU A; 4X5A A; 4HKM A; 4X5E A; 4GA6 A; 4ZTV A; 5C7S A; 4OWM A; 3GBR A; 2TPT A; 4OWN A; 3UU1 A; 1VQU A; 4X59 A; 1GXB A; 1ZVW A; 5C1R A; 4GA5 A; 3QS8 A; 3QQS A; 5EP8 A; #chains in the Genus database with same CATH topology 4X46 A; 1ZXY A; 4M0R A; 1ZYK A; 4OWS A; 4GA4 A; 3H5Q A; 1BRW A; 3R6C A; 4N93 A; 4X5D A; 3QSA A; 5C2L A; 4OWV A; 5BYT A; 4EAF A; 4X5C A; 1OTP A; 4GKM A; 1V8G A; 4GIU A; 3R88 A; 2WK5 A; 5BO2 A; 4OWQ A; 3QR9 A; 4YEK A; 4MUO A; 4ZOK A; 4GTN A; 1KHD A; 4N8Q A; 4YI7 A; 1KGZ A; 4XR5 A; 4OWO A; 2GVQ A; 5BO3 A; 4ZOJ A; 2DSJ A; 4LHM A; 2WK6 A; 4EAD A; 1AZY A; 4ZOF A; 1RRZ A; 4YYY A; 2ELC A; 3TWP A; 4N5V A; 2BPQ A; 4OWU A; 4F3F C; 2J0F A; 5BNE A; 1O17 A; 4X5B A; 5EY3 A; 4X58 A; 4IJ1 A; 1UOU A; 4X5A A; 4HKM A; 4GA6 A; 4X5E A; 4ZTV A; 5C7S A; 4OWM A; 3GBR A; 2TPT A; 4OWN A; 3UU1 A; 1VQU A; 4X59 A; 1GXB A; 1ZVW A; 4GA5 A; 5C1R A; 1RF8 B; 3QS8 A; 3QQS A; 5EP8 A; #chains in the Genus database with same CATH homology 4X46 A; 1ZXY A; 4M0R A; 1ZYK A; 4OWS A; 4GA4 A; 3H5Q A; 1BRW A; 3R6C A; 4N93 A; 4X5D A; 3QSA A; 5C2L A; 4OWV A; 5BYT A; 4EAF A; 4X5C A; 1OTP A; 4GKM A; 1V8G A; 4GIU A; 3R88 A; 2WK5 A; 5BO2 A; 4OWQ A; 3QR9 A; 4YEK A; 4MUO A; 4ZOK A; 4GTN A; 1KHD A; 4N8Q A; 4YI7 A; 1KGZ A; 4XR5 A; 4OWO A; 2GVQ A; 5BO3 A; 4ZOJ A; 2DSJ A; 4LHM A; 2WK6 A; 4EAD A; 1AZY A; 4ZOF A; 4YYY A; 2ELC A; 3TWP A; 4N5V A; 2BPQ A; 4OWU A; 2J0F A; 5BNE A; 1O17 A; 4X5B A; 5EY3 A; 4X58 A; 4IJ1 A; 1UOU A; 4X5A A; 4HKM A; 4X5E A; 4GA6 A; 4ZTV A; 5C7S A; 4OWM A; 3GBR A; 2TPT A; 4OWN A; 3UU1 A; 1VQU A; 4X59 A; 1GXB A; 1ZVW A; 5C1R A; 4GA5 A; 3QS8 A; 3QQS A; 5EP8 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...
