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 |
87
|
sequence length |
231
|
structure length |
231
|
Chain Sequence |
VPMHPFVKALQEHFTAHQNPEKAEPMARYMKNHFLFLGIQTPERRQLLKDIIQIHTLPDQKDFQIIIRELWDLPEREFQAAALDIMQKYKKHINETHIPFLEELIVTKSWWDSVDSIVPTFLGDIFLKHPELISAYIPKWIASDNIWLQRAAILFQLKYKQKMDEELLFWIIGQLHSSKEFFIQKAIGWVLREYAKTNPDVVWEYVQNNELAPLSKREAIKHIKQNYGINN
|
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 |
The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions.
pubmed doi rcsb |
| molecule keywords |
AlkD
|
| molecule tags |
Hydrolase/dna
|
| source organism |
Bacillus cereus
|
| total genus |
87
|
| structure length |
231
|
| sequence length |
231
|
| ec nomenclature |
ec
3.2.2.-: |
| pdb deposition date | 2015-07-16 |
| chain | Pfam Accession Code | Pfam Family Identifier | Pfam Description |
|---|---|---|---|
| A | PF08713 | DNA_alkylation | DNA alkylation repair enzyme |
Image from the rcsb pdb (www.rcsb.org)
cath code
| Class | Architecture | Topology | Homology | Domain |
|---|---|---|---|---|---|
| Mainly Alpha | Alpha Horseshoe | Leucine-rich Repeat Variant | Leucine-rich Repeat Variant |
#chains in the Genus database with same CATH superfamily 5CL7 A; 5KUB A; 5CL4 A; 5CLE A; 5CLC A; 5CL6 A; 5CL3 A; 5CL9 A; 5CLA A; 3BVS A; 5CL8 A; 5CL5 A; 3JY1 A; 5CLB A; 3JX7 A; 3JXY A; 3JXZ A; 5CLD A; #chains in the Genus database with same CATH topology 4I8M A; 4PLQ A; 4QMI A; 2NYM A; 3K5Y A; 1IBR B; 2IX3 A; 2GL7 A; 4CB9 A; 3IBV A; 1Z2C B; 5CLD A; 2IE3 A; 4RZP A; 2BNX A; 4U5O A; 3OPB A; 1HO8 A; 4I2W A; 4U5V A; 4YGX A; 3K7V A; 1XM9 A; 4PLS A; 4I5N A; 4HM9 A; 3TT9 A; 1EE5 A; 4JW2 A; 1B3U A; 1TE4 A; 3IFQ A; 3DW8 A; 4B18 A; 4U3J C; 3T7U A; 1Q1S C; 2JKR A; 1G3J A; 4DB9 A; 2YNR A; 2YNS A; 4MZ6 E; 2BAP A; 5BYM A; 2NYM B; 5CLB A; 3DAD A; 1UN0 A; 2Z6G A; 5CL7 A; 3Q0Q A; 4ZDU A; 3VE6 A; 3L6Y A; 5B56 A; 3O4X A; 4O27 A; 1T08 A; 3ZIR A; 4PVZ A; 3WYF C; 1EJY I; 3BTR C; 4BQK A; 3ZIL A; 3BX2 A; 4EVP A; 5FC8 E; 5CLE A; 4Y5J A; 3Q0S A; 4FQ3 A; 4B8O A; 4OO6 A; 4BPL A; 3L3F X; 2F31 A; 3PSP A; 4GMO A; 4IMI A; 3ND2 A; 2PF4 A; 2IAE B; 1U6G C; 3K5Q A; 1F59 A; 4UQI A; 1QZ7 A; 4UAF B; 3QHE A; 3ZIP A; 1PJM B; 3BCT A; 3VLF A; 4A3T A; 1Y2A C; 3QG9 A; 5HUY C; 5HHG E; 3BSB A; 4FFB C; 4GMN A; 3WPT A; 3ZIK A; 3JX7 A; 5LSW A; 5KUB A; 1JPW A; 2RU4 B; 4L4H A; 4H3H A; 3LWW A; 4EV9 A; 4JKQ A; 3GS3 A; 2QK1 A; 3FGA B; 4RV1 A; 2Z5N A; 5H2W A; 5HUW C; 3OQS A; 4L4I A; 5EWP A; 2PKG A; 3K64 A; 3NMX A; 4FZA A; 3UKZ B; 5K9S A; 1N4K A; 3NOW A; 5KLR B; 3TPO A; 3K5Z A; 4G3A A; 4DB6 A; 2NYL A; 4FZF A; 4A3V A; 4UQI B; 3Q0M A; 1LRV A; 1I7W A; 4V3R A; 1WA5 C; 4CT6 B; 3JY1 A; 1IAL A; 2YJY A; 5K6S A; 5BZV A; 2JKT B; 5SW9 A; 5CL9 A; 5E6Q B; 4A0C A; 4CRV B; 1Q1T C; 3LTJ A; 3EG5 B; 4JLQ A; 3TJ3 A; 2VGL A; 5CL5 A; 4R11 A; 4UAD A; 1XQR A; 3WOY A; 5KL8 A; 2XA7 A; 3GAE A; 3GNI A; 5EKF A; 3ZIN A; 4OIH A; 2P8Q A; 4E4V A; 5KLT B; 5CLC A; 4ADY A; 4I5L A; 2NYL B; 3Q0L A; 3TJZ B; 2IE4 A; 3UKY B; 2Z5O A; 3ODR A; 3OUW A; 4CBA A; 4U5U A; 1QBK B; 4KZG A; 4D49 A; 5H2X A; 5KL1 A; 5JJA A; 5CTT A; 1I7X A; 4WV6 A; 4H3K A; 4RXH B; 3UKW B; 4CRU B; 5BZ1 A; 2C1T A; 2DB0 A; 1GCJ A; 5J3V A; 4XZR B; 1W9C A; 3GRL A; 1OYZ A; 4V3Q A; 3RZX A; 3AU3 A; 2XA7 B; 1UPK A; 3BX3 A; 3EBB A; 4JW2 B; 3SLA A; 4DBA A; 3PST A; 1BK6 A; 4UAE A; 4I2Z A; 4CT7 B; 3BWT A; 3WOZ A; 3ODS A; 2JKR B; 1O6P A; 1IB2 A; 1LSH A; 4DVG B; 1EE4 A; 5SVZ A; 3GQ2 A; 4I0Y A; 4I3N A; 4UWX A; 2Z5K A; 4FZD A; 5AEI A; 1W63 A; 4U2X D; 2OF3 A; 4HXT A; 4R0Z A; 3Q0R A; 4MFU A; 4DZS A; 1PJN B; 4LAC A; 3VWA A; 2XOA A; 4EVA A; 2BKU B; 5CL8 A; 3V71 A; 3W3U A; 3C2H A; 5KLA A; 4V3O A; 3K61 A; 3Q5U A; 1O6O A; 4MZ5 E; 3C2G A; 3OBV A; 3RZ9 A; 2OT8 A; 3QML C; 4U54 A; 3K62 A; 5EKG A; 3UKX B; 3K4E A; 4B8P A; 3GVO A; 4MFV A; 3Q0P A; 1JPP A; 1JDH A; 2Q5D A; 4CB8 A; 3Q0N A; 4EV8 A; 4JW3 C; 3BSX A; 2BCT A; 2NPP A; 3FEY C; 4B8J A; 3A6P A; 4QMH A; 3O2Q A; 2QMR A; 5SWF A; 3SL9 A; 3KND A; 1WA5 B; 3QGB A; 4FP7 A; 3TPM A; 3EA5 B; 4I37 A; 2QNA A; 4I2S A; 1UKL A; 3OUX A; 1W63 B; 4FDD A; 4YJL A; 3K49 A; 4QMJ A; 2Z6H A; 4YI0 C; 2IWH A; 2FV2 A; 3L3Q A; 3ZHP A; 2Z5J A; 1LUJ A; 4PLR A; 1EJL I; 3UVU A; 4EVT A; 1XQS A; 2WTK A; 4CV5 B; 3QGC A; 4I6I A; 4K6J A; 1M5N S; 4P6Z G; 3T8S A; 2IAE A; 1M8Y A; 4U5L A; 3UJ4 A; 4BA3 A; 1QGK A; 3UL1 B; 4DB8 A; 3GVT A; 2NPP B; 2RU4 A; 3UL0 B; 2JAK A; 5CL4 A; 1UPL A; 5BZU A; 1M8W A; 3FGA A; 4U5N A; 4R10 A; 2C1M A; 3O2T A; 1IQ1 C; 3V6Y A; 2VGL B; 3NMW A; 2IW3 A; 5D5K C; 3GB8 A; 3ZIQ A; 3K7W A; 4P6Z B; 5DN7 A; 1M8Z A; 1QGR A; 4U5S A; 3UJ0 A; 4DJS A; 1M1E A; 2X19 B; 3O2S A; 1TH1 A; 4U58 A; 4HTV A; 5CL6 A; 4I96 A; 4NEE A; 4L7M A; 4K92 A; 3BVS A; 4IMJ A; 3NMZ A; 3V74 A; 1M8X A; 3VLE A; 3FEX C; 2JKT A; 3ZIO A; 4I1E A; 4HNM A; 3JXY A; 3ZKV A; 3Q0O A; 3TX7 A; 2QK2 A; 1V18 A; 1BK5 A; 2X1G F; 3LTM A; 4YJE A; 4D4E A; 2JDQ A; 5CL3 A; 2Z5M A; 4I7I A; 4TNM A; 2H4M A; 3JXZ A; 2W3C A; 5CLA A; 4NZW A; 3L6X A; 3VLD A; 3C5W A; 4YK6 A; 5BZ5 A; 3H3D X; #chains in the Genus database with same CATH homology 4I8M A; 4PLQ A; 4QMI A; 2NYM A; 3K5Y A; 1IBR B; 2IX3 A; 2GL7 A; 4CB9 A; 3IBV A; 1Z2C B; 5CLD A; 2IE3 A; 4RZP A; 2BNX A; 4U5O A; 3OPB A; 1HO8 A; 4I2W A; 4U5V A; 4YGX A; 3K7V A; 1XM9 A; 4PLS A; 4I5N A; 4HM9 A; 3TT9 A; 1EE5 A; 4JW2 A; 1B3U A; 1TE4 A; 3IFQ A; 3DW8 A; 4B18 A; 4U3J C; 3T7U A; 1Q1S C; 2JKR A; 1G3J A; 4DB9 A; 2YNR A; 2YNS A; 4MZ6 E; 2BAP A; 5BYM A; 2NYM B; 5CLB A; 3DAD A; 1UN0 A; 2Z6G A; 5CL7 A; 3Q0Q A; 4ZDU A; 3VE6 A; 3L6Y A; 5B56 A; 3O4X A; 4O27 A; 1T08 A; 3ZIR A; 4PVZ A; 3WYF C; 1EJY I; 3BTR C; 4BQK A; 3ZIL A; 3BX2 A; 4EVP A; 5FC8 E; 5CLE A; 4Y5J A; 3Q0S A; 4FQ3 A; 4B8O A; 4OO6 A; 4BPL A; 3L3F X; 2F31 A; 3PSP A; 4GMO A; 4IMI A; 3ND2 A; 2PF4 A; 2IAE B; 1U6G C; 3K5Q A; 1F59 A; 4UQI A; 1QZ7 A; 4UAF B; 3QHE A; 3ZIP A; 1PJM B; 3BCT A; 3VLF A; 4A3T A; 1Y2A C; 3QG9 A; 5HUY C; 5HHG E; 3BSB A; 4FFB C; 4GMN A; 3WPT A; 3ZIK A; 3JX7 A; 5LSW A; 5KUB A; 1JPW A; 2RU4 B; 4L4H A; 4H3H A; 3LWW A; 4EV9 A; 4JKQ A; 3GS3 A; 2QK1 A; 3FGA B; 4RV1 A; 2Z5N A; 5H2W A; 5HUW C; 3OQS A; 4L4I A; 5EWP A; 2PKG A; 3K64 A; 3NMX A; 4FZA A; 3UKZ B; 5K9S A; 3NOW A; 5KLR B; 3TPO A; 3K5Z A; 4G3A A; 4DB6 A; 2NYL A; 4FZF A; 4A3V A; 4UQI B; 3Q0M A; 1LRV A; 1I7W A; 4V3R A; 1WA5 C; 4CT6 B; 3JY1 A; 1IAL A; 2YJY A; 5K6S A; 5BZV A; 2JKT B; 5SW9 A; 5CL9 A; 5E6Q B; 4A0C A; 4CRV B; 1Q1T C; 3LTJ A; 3EG5 B; 4JLQ A; 3TJ3 A; 2VGL A; 5CL5 A; 4R11 A; 4UAD A; 1XQR A; 3WOY A; 5KL8 A; 2XA7 A; 3GAE A; 3GNI A; 5EKF A; 3ZIN A; 4OIH A; 2P8Q A; 4E4V A; 5KLT B; 5CLC A; 4ADY A; 4I5L A; 2NYL B; 3Q0L A; 3TJZ B; 2IE4 A; 3UKY B; 2Z5O A; 3ODR A; 3OUW A; 4CBA A; 4U5U A; 1QBK B; 4KZG A; 4D49 A; 5H2X A; 5KL1 A; 5JJA A; 5CTT A; 1I7X A; 4WV6 A; 4H3K A; 4RXH B; 3UKW B; 4CRU B; 5BZ1 A; 2C1T A; 2DB0 A; 1GCJ A; 5J3V A; 4XZR B; 1W9C A; 3GRL A; 1OYZ A; 4V3Q A; 3RZX A; 3AU3 A; 2XA7 B; 1UPK A; 3BX3 A; 3EBB A; 4JW2 B; 3SLA A; 4DBA A; 3PST A; 1BK6 A; 4UAE A; 4I2Z A; 4CT7 B; 3BWT A; 3WOZ A; 3ODS A; 2JKR B; 1O6P A; 1IB2 A; 4DVG B; 1EE4 A; 5SVZ A; 3GQ2 A; 4I0Y A; 4I3N A; 4UWX A; 2Z5K A; 4FZD A; 5AEI A; 1W63 A; 4U2X D; 2OF3 A; 4HXT A; 4R0Z A; 3Q0R A; 4MFU A; 4DZS A; 1PJN B; 3VWA A; 4LAC A; 2XOA A; 4EVA A; 2BKU B; 5CL8 A; 3V71 A; 3W3U A; 3C2H A; 5KLA A; 4V3O A; 3K61 A; 3Q5U A; 1O6O A; 4MZ5 E; 3C2G A; 3OBV A; 3RZ9 A; 2OT8 A; 3QML C; 4U54 A; 3K62 A; 5EKG A; 3UKX B; 3K4E A; 4B8P A; 3GVO A; 4MFV A; 3Q0P A; 1JPP A; 1JDH A; 2Q5D A; 4CB8 A; 3Q0N A; 4EV8 A; 4JW3 C; 3BSX A; 2BCT A; 2NPP A; 3FEY C; 4B8J A; 3A6P A; 4QMH A; 3O2Q A; 2QMR A; 5SWF A; 3SL9 A; 3KND A; 1WA5 B; 3QGB A; 4FP7 A; 3TPM A; 3EA5 B; 4I37 A; 2QNA A; 4I2S A; 1UKL A; 3OUX A; 1W63 B; 4FDD A; 4YJL A; 3K49 A; 4QMJ A; 2Z6H A; 4YI0 C; 2IWH A; 2FV2 A; 3L3Q A; 3ZHP A; 2Z5J A; 1LUJ A; 4PLR A; 1EJL I; 3UVU A; 4EVT A; 1XQS A; 2WTK A; 4CV5 B; 3QGC A; 4I6I A; 4K6J A; 1M5N S; 4P6Z G; 2IAE A; 1M8Y A; 4U5L A; 4BA3 A; 1QGK A; 3UL1 B; 4DB8 A; 3GVT A; 2NPP B; 2RU4 A; 3UL0 B; 2JAK A; 5CL4 A; 1UPL A; 5BZU A; 1M8W A; 3FGA A; 4U5N A; 4R10 A; 2C1M A; 3O2T A; 1IQ1 C; 3V6Y A; 2VGL B; 3NMW A; 2IW3 A; 5D5K C; 3GB8 A; 3ZIQ A; 3K7W A; 4P6Z B; 5DN7 A; 1M8Z A; 1QGR A; 4U5S A; 4DJS A; 1M1E A; 2X19 B; 3O2S A; 1TH1 A; 4U58 A; 4HTV A; 5CL6 A; 4I96 A; 4NEE A; 4L7M A; 4K92 A; 3BVS A; 4IMJ A; 3NMZ A; 3V74 A; 1M8X A; 3VLE A; 3FEX C; 2JKT A; 3ZIO A; 4I1E A; 4HNM A; 3JXY A; 3ZKV A; 3Q0O A; 3TX7 A; 2QK2 A; 1V18 A; 1BK5 A; 2X1G F; 3LTM A; 4YJE A; 4D4E A; 2JDQ A; 5CL3 A; 2Z5M A; 4I7I A; 4TNM A; 2H4M A; 3JXZ A; 2W3C A; 5CLA A; 4NZW A; 3L6X A; 3VLD A; 3C5W A; 4YK6 A; 5BZ5 A; 3H3D X;
#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...
