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 |
40
|
sequence length |
229
|
structure length |
229
|
Chain Sequence |
MLDSKLKAPVFTVRTQGREYGEFVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNLKELVVRFLNPSLQTVTLLLKAEGPKEVKARDFLPVADVEIMNPDLHIATLEEGGRLNMEVRVDRGVGYVPAEKHGIKDRINAIPVDAVFSPVRRVAFQVEDTRLGQRTDLDKLTLRIWTDGSVTPLEALNQAVEILREHLTYFSNPQ
|
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 |
Structural basis for transcription regulation by alarmone ppGpp
pubmed doi rcsb |
| molecule keywords |
DNA-directed RNA polymerase alpha chain
|
| molecule tags |
Transferase
|
| total genus |
40
|
| structure length |
229
|
| sequence length |
229
|
| chains with identical sequence |
B, K, L
|
| ec nomenclature |
ec
2.7.7.6: DNA-directed RNA polymerase. |
| pdb deposition date | 2004-03-10 |
| chain | Pfam Accession Code | Pfam Family Identifier | Pfam Description |
|---|---|---|---|
| A | PF01000 | RNA_pol_A_bac | RNA polymerase Rpb3/RpoA insert domain |
| A | PF01193 | RNA_pol_L | RNA polymerase Rpb3/Rpb11 dimerisation domain |
| A | PF03118 | RNA_pol_A_CTD | Bacterial RNA polymerase, alpha chain C terminal domain |
Image from the rcsb pdb (www.rcsb.org)
cath code
| Class | Architecture | Topology | Homology | Domain |
|---|---|---|---|---|---|
| Mainly Beta | Beta Complex | RNA Polymerase Alpha Subunit; Chain A, domain 2 | DNA-directed RNA polymerase, insert domain | ||
| Alpha Beta | 2-Layer Sandwich | Gyrase A; domain 2 | RNA polymerase, RBP11-like subunit |
#chains in the Genus database with same CATH superfamily 2NVQ C; 3RZO C; 3S1N K; 1BDF A; 1YNJ A; 4LK1 A; 4YG2 A; 4C2M C; 3RZO K; 4MEX A; 3S2D K; 4A93 C; 2WB1 L; 5C4J K; 3H0G K; 4ZH4 A; 1TWA C; 2NVX C; 3I4N C; 4A93 K; 4Y7N C; 4C3J C; 1TWA K; 4MQ9 A; 1R9T C; 3S2H C; 3GTG K; 3S15 C; 4C3J K; 4OIO A; 1R9T K; 3S2H K; 3HOV C; 4XSX A; 5FJ8 K; 3GTK C; 4JK1 A; 4C3H C; 3HOV K; 5C44 C; 4A3F K; 4QJV A; 2WAQ D; 1I6H C; 3FKI K; 5D4D A; 5C44 K; 3GTK K; 3S1R C; 3S14 C; 2CW0 A; 3S1R K; 1TWC C; 2Y0S D; 4YFN A; 5TMC A; 3HKZ D; 2A69 A; 3PO2 C; 4XLN A; 2E2I K; 3GTL K; 1IW7 A; 4A3L K; 3HOX C; 5IYD C; 3S16 C; 3S17 C; 3M3Y C; 3HOX K; 1SFO C; 5IYD K; 2PA8 D; 2JA6 C; 1Y1V C; 1YNN A; 4GZY A; 5M3F K; 3RZD K; 1SFO K; 2B63 K; 2VUM K; 3M3Y K; 1Y1V K; 4KN4 A; 5IYB C; 2NVQ K; 2JA7 C; 4XLP A; 1I3Q C; 4C2M K; 5IYB K; 4A3C C; 4A3E C; 1I3Q K; 4OIP A; 3I4N K; 4BBS C; 4A3E K; 2NVX K; 3GTM C; 5FLM C; 4Y7N K; 3HOY C; 4G7Z A; 1K83 C; 2E2H C; 3GTM K; 4AYB D; 1TWF C; 4A3M C; 3S15 K; 1K83 K; 3WOD A; 3M4O C; 5M3M K; 4A3M K; 3EQL A; 3PO3 C; 2E2H K; 3H3V L; 2R93 C; 3M4O K; 4C3H K; 3PO3 K; 2PMZ L; 1I6H K; 4BXX C; 1Y1W C; 5IP7 C; 2A6H A; 4LJZ A; 4YFX A; 1XPP A; 2R92 C; 3S14 K; 4BXX K; 1Y1W K; 5IP7 K; 2R92 K; 1TWC K; 2JA5 C; 4A3D C; 5C4X C; 2YU9 C; 3PO2 K; 4A3D K; 5IP9 C; 4A3G K; 5C4X K; 2R7Z C; 4A3B C; 5M5X K; 2YU9 K; 1TWG C; 2NVT C; 3GTQ C; 4XSZ A; 3S16 K; 3S17 K; 4A3B K; 3HOW C; 4MEY A; 1HQM A; 3DXJ A; 1TWG K; 2JA6 K; 2NVT K; 3GTJ C; 3HOW K; 4QIW D; 3GTJ K; 2PPB A; 2JA8 C; 4C3I C; 3S1Q C; 5TMF A; 2WB1 D; 5M5W K; 4NOI A; 2JA7 K; 4BY1 C; 2JA8 K; 4C3I K; 4A3C K; 3S1Q K; 2WAQ L; 4BBR C; 4BY1 K; 4A3J C; 1TWH C; 4KN7 A; 4BBS K; 4BBR K; 5FLM K; 4A3J K; 3HOY K; 1TWH K; 1WCM C; 1TWF K; 2Y0S L; 1WCM K; 3S1M C; 2R93 K; 3S1M K; 4BY7 C; 1I50 C; 3GTP C; 2PA8 L; 4BY7 K; 3GTP K; 4A3K C; 4A3I C; 2JA5 K; 2O5I A; 3HOU C; 3S2D C; 2O5J A; 5C4J C; 3H0G C; 4A3I K; 5IP9 K; 4A3K K; 5M5Y K; 3HOU K; 4OIR A; 2R7Z K; 3GTQ K; 5C3E C; 3GTG C; 1SMY A; 5C3E K; 4OIN A; 4Q4Z A; 4AYB L; 4Y52 C; 4Q5S A; 3CQZ C; 1I6V A; 4A3F C; 4X6A C; 3FKI C; 2NVY C; 3GTO C; 2A68 A; 4Y52 K; 3CQZ K; 4X6A K; 4QJV B; 2NVY K; 3GTO K; 3K7A C; 5IYC C; 4KMU A; 4G7O A; 3K7A K; 5IYC K; 4YFK A; 4LLG A; 2BE5 A; 4OIQ A; 3GTL C; 2A6E A; 3H3V D; 4A3L C; 3HKZ L; 4LK0 A; 3I4M C; 2PMZ D; 3I4M K; 3HOZ C; 4G7H A; 2B63 C; 3RZD C; 2E2I C; 2E2J C; 2VUM C; 4A3G C; 1I50 K; 3HOZ K; 1ZYR A; 2E2J K; 3S1N C; 4QIW L; #chains in the Genus database with same CATH topology 2NVQ C; 1BDF A; 4LK1 A; 4YG2 A; 3RZO K; 3GSI A; 4ZH4 A; 1TWA C; 2NVX C; 4Y7N C; 2RGR A; 3L4J A; 4C3J K; 3TTG A; 3HOV C; 3LPX A; 4WFA S; 3FKI K; 5C44 K; 5D4D A; 1PJ5 A; 1USO A; 2GAH C; 2PHC B; 1XZP A; 2FQT A; 2Y0S D; 5TMC A; 2A69 A; 4GTB A; 4XLN A; 1IW7 A; 4WIL A; 3ERE D; 1SFO C; 4KM9 A; 2JA6 C; 3M3Y K; 5M3F K; 3RZD K; 3GEI A; 2JA7 C; 4XLP A; 5IYB K; 4C2M K; 2ZJP S; 5DM6 S; 1J6V A; 1I3Q K; 5IOQ A; 3I4N K; 1YX2 A; 4BBS C; 1O27 A; 3AQO A; 4G7Z A; 1K83 C; 4AYB D; 2CFA B; 4GTL A; 2E2H K; 5M3M K; 4A3M K; 3PIP S; 1WOP A; 4ILD A; 2PMZ L; 4LR2 A; 1GE9 A; 4BXX C; 1USM A; 4LJZ A; 1EH1 A; 2R92 K; 4A3D C; 3QX3 A; 3CQZ A; 3PO2 K; 3FKI A; 5IP9 C; 2R7Z C; 3IPJ A; 4A3B C; 2YU9 K; 1TWG C; 2NVT C; 3S17 K; 4LQY A; 2V6S A; 1IE0 A; 2PPB A; 2JA8 C; 4C3I C; 3AD9 C; 1EI6 A; 3S1Q K; 3N0C A; 2WAQ L; 4A3J C; 5JVO A; 4KN7 A; 4BBR K; 1TWH K; 1WQF A; 1WCM K; 1X31 C; 1VRQ C; 2R93 K; 2XCO A; 3S1M K; 2KWA A; 2ZFZ A; 4O2D A; 3AQP A; 1I50 C; 1R9T A; 1C0A A; 3G4C A; 1O2B A; 1ISE A; 1EQR A; 1WQG A; 3AH5 A; 3MML B; 4KAR A; 5C4J C; 3HOU K; 5L46 A; 1SMY A; 4GFQ A; 3V4G A; 4A3F C; 4KMA A; 4Y52 K; 4QJV B; 2L5N A; 3GTO K; 5IYC C; 5HL7 S; 4WFN S; 5IOS A; 4OIQ A; 3GTL C; 4IOA S; 2A6E A; 4A3L C; 1L0W A; 3DLL S; 4FM9 A; 4LK0 A; 2PMZ D; 4IO9 S; 3HOZ C; 3GTM A; 2VUM C; 1ZYR A; 4A3G K; 2RH6 A; 3S1N K; 2R93 A; 3S2D K; 1Y1W A; 1TWA K; 4P5A A; 4MQ9 A; 3GTG K; 3S15 C; 3GTK C; 4C3H C; 3HOV K; 2WAQ D; 1I6H C; 3L4K A; 3JST A; 2XCQ A; 3GTJ A; 3PIO S; 1TWC C; 3LAP A; 4KB2 A; 1BGW A; 1Y1V C; 1SFO K; 1XXB A; 3TFI A; 2B63 K; 1ZBS A; 3GTP A; 2ZUE A; 5FLM C; 1HI9 A; 3HOY C; 1TWF C; 5JVG S; 1K83 K; 4WFB S; 3EQL A; 2JH3 A; 3H3V L; 3GEH A; 1FEU A; 4BLA A; 3GTG A; 5IP7 C; 3S14 K; 2ZJQ S; 1XPP A; 3Q3Q A; 4BXX K; 1UV7 A; 1G51 A; 4A3D K; 2NVY A; 1WQH A; 5M5X K; 3S16 K; 2ZJR S; 4A3B K; 3HOW C; 1TWG K; 3DXJ A; 2NVT K; 4GT9 A; 3G4A A; 1DCP A; 1O2A A; 3BP3 A; 5M5W K; 5TMF A; 4BY1 C; 4P5B A; 4C3I K; 2JA8 K; 4A3C K; 1O24 A; 1XZQ B; 4GTC A; 2B63 A; 2E2I A; 3T02 A; 4A3J K; 4PAB A; 2CFA A; 4U67 S; 1KQ4 A; 1PJ7 A; 4BY7 C; 5EGE A; 3LAJ A; 4KMD A; 4KDD A; 1K83 A; 4A3K C; 2JA5 K; 2O5I A; 2O5J A; 1VGX A; 1WSR A; 3GTQ K; 1O25 A; 4OIN A; 2GAG C; 3ADA C; 3OEP A; 4Q5S A; 3CQZ C; 1I6V A; 3FKI C; 4KMU A; 1WIH A; 5JVH S; 4YFK A; 5IYC K; 2BE5 A; 3A8K A; 3H3V D; 1I3Q A; 1O29 A; 3I4M C; 2L3U A; 3N0B A; 1ZXO A; 3HOZ K; 3RZD C; 2E2H A; 4BKW A; 3HXA A; 1YNJ A; 4C2M C; 3A8I A; 3FHZ A; 4MEX A; 4A93 C; 5HL8 A; 3H0G K; 3I4N C; 1DCH A; 2R92 A; 1R9T C; 3S2H C; 4GTA A; 1F7V A; 5TJ3 A; 2JA5 A; 4C45 A; 5FJ8 K; 2YU9 A; 3GTK K; 4QJV A; 3GTQ A; 3S1R C; 1DCO A; 5IOT A; 1B4B A; 4KAT A; 4YFN A; 4WJ3 M; 3PO2 C; 1AB4 A; 3HOX C; 5IYD C; 3S17 C; 1VLO A; 1WOO A; 1TWH A; 3CAG A; 3TFJ A; 4GZY A; 1YNN A; 4AH6 A; 2V6T A; 4DDQ A; 1WCM A; 1J98 A; 1Y1V K; 1B4A A; 4KN4 A; 1BJT A; 2NVQ K; 5HQH A; 4A3E C; 4OIP A; 2NVX K; 3GTM C; 4Y7N K; 3WOD A; 3M4O C; 3PO3 C; 2R93 C; 3H0G A; 3ORE A; 1Y1W C; 1JQW A; 1O28 A; 1PJ6 A; 4M1X A; 5IP7 K; 2GSN A; 5C4X C; 3GTK A; 3GTO A; 1VH2 A; 4G0U A; 1IS1 A; 2JA6 K; 3GTJ C; 1XXC A; 4G0W A; 3HOW K; 1J6W A; 2JA7 K; 2GSU A; 4BY1 K; 4BBS K; 4WF9 S; 1EFW A; 5CJ9 A; 1TWA A; 2NVX A; 3SZY A; 5E68 A; 3GTP C; 2PA8 L; 5CHP A; 4BY7 K; 3T00 A; 3N3Y A; 4A3I C; 1DD5 A; 3S2D C; 5IOR A; 4A3K K; 5IP9 K; 2R7Z K; 5C3E C; 3GTG C; 3A8J A; 2KQ1 A; 4Q4Z A; 2FQO A; 4X6A C; 4WJ4 A; 2NVY C; 1XZQ A; 3CQZ K; 1SFO A; 1WSV A; 3FOF A; 2JA6 A; 3LYW A; 3K7A C; 1ZQ1 C; 4RMF A; 1RU0 A; 1INN A; 4LOW A; 1XZP B; 4LLG A; 2JA7 A; 2ZUF A; 4GTF A; 3T01 A; 1WOS A; 2D6F C; 3I4M K; 4GTD A; 3CF5 S; 2B63 C; 2E2I C; 2E2J C; 1I50 K; 3BUE A; 4QIW L; 3RZO C; 4BLB A; 1ZVU A; 1IQ0 A; 2WB1 L; 5C4J K; 4A93 K; 4C3J C; 3OPF A; 3GDZ A; 4OIO A; 1R9T K; 4KC6 A; 3S2H K; 4KAS A; 4XSX A; 4JK1 A; 1YCL A; 2Y3P A; 5C44 C; 2R7Z A; 4A3F K; 1TWG A; 4KB4 A; 3S14 C; 2CW0 A; 2EBB A; 3S1R K; 1F93 A; 2P8T A; 4GTE A; 3HKZ D; 2E2I K; 3GTL K; 3VA7 A; 4A3L K; 3S16 C; 3M3Y C; 3GIR A; 3HOX K; 4G0V A; 2PA8 D; 5IYD K; 3NUH A; 1IL2 A; 2VUM K; 3S0X A; 5IYB C; 4PAA A; 1I3Q C; 4A3C C; 5JFE A; 1I50 A; 4A3E K; 2E2H C; 3GTM K; 4A3M C; 3S15 K; 1O2F B; 3M4O K; 4C3H K; 3PO3 K; 3FOE A; 1O26 A; 1JVI A; 2V6U A; 1I6H K; 1VJE A; 1EK8 A; 2A6H A; 4YFX A; 2R92 C; 5DM7 S; 1V5V A; 1Y1W K; 1TWC K; 2JA5 C; 1J6X A; 2YU9 C; 1JOE A; 5C4X K; 3GEE A; 3GTQ C; 4XSZ A; 1WOR A; 4MEY A; 1HQM A; 1F9N A; 4QIW D; 3GTL A; 3GTJ K; 2P5M A; 3S1Q C; 2WB1 D; 4IOC S; 4NOI A; 4WCE S; 4BBR C; 4KMH A; 2VUM A; 1TWH C; 5FLM K; 3HOY K; 1WCM C; 4FZB A; 1TWF K; 2Y0S L; 3S1M C; 3BP8 C; 2GSO A; 3TFH A; 3GTP K; 1F7U A; 3HOU C; 4XCH A; 1XXA A; 1IBA A; 3H0G C; 3AD8 C; 5EGH A; 4A3I K; 5M5Y K; 4OIR A; 3AD7 C; 5C3E K; 1TWC A; 4AYB L; 4Y52 C; 4KM8 A; 3GTO C; 2A68 A; 1BS2 A; 4KAW X; 3SZZ A; 4X6A K; 2NVY K; 1Y1V A; 4J3N A; 4G7O A; 2KPU A; 3K7A K; 2KXY A; 3HKZ L; 2XCR B; 4G7H A; 4A3G C; 1TWF A; 2E2J K; 3S1N C; 2W7V A; 4P9S A; #chains in the Genus database with same CATH homology 2NVQ C; 3RZO C; 3S1N K; 1BDF A; 1YNJ A; 4LK1 A; 4YG2 A; 4C2M C; 3RZO K; 4MEX A; 3S2D K; 4A93 C; 2WB1 L; 5C4J K; 3H0G K; 4ZH4 A; 1TWA C; 2NVX C; 3I4N C; 4A93 K; 4Y7N C; 4C3J C; 1TWA K; 4MQ9 A; 1R9T C; 3S2H C; 3GTG K; 3S15 C; 4C3J K; 4OIO A; 1R9T K; 3S2H K; 3HOV C; 4XSX A; 5FJ8 K; 3GTK C; 4JK1 A; 4C3H C; 3HOV K; 5C44 C; 4A3F K; 4QJV A; 2WAQ D; 1I6H C; 3FKI K; 5D4D A; 5C44 K; 3GTK K; 3S1R C; 3S14 C; 2CW0 A; 3S1R K; 1TWC C; 2Y0S D; 4YFN A; 5TMC A; 3HKZ D; 2A69 A; 3PO2 C; 4XLN A; 2E2I K; 3GTL K; 1IW7 A; 4A3L K; 3HOX C; 5IYD C; 3S16 C; 3S17 C; 3M3Y C; 3HOX K; 1SFO C; 5IYD K; 2PA8 D; 2JA6 C; 1Y1V C; 1YNN A; 4GZY A; 5M3F K; 3RZD K; 1SFO K; 2B63 K; 2VUM K; 3M3Y K; 1Y1V K; 4KN4 A; 5IYB C; 2NVQ K; 2JA7 C; 4XLP A; 1I3Q C; 4C2M K; 5IYB K; 4A3C C; 4A3E C; 1I3Q K; 4OIP A; 3I4N K; 4BBS C; 4A3E K; 2NVX K; 3GTM C; 5FLM C; 4Y7N K; 3HOY C; 4G7Z A; 1K83 C; 2E2H C; 3GTM K; 4AYB D; 1TWF C; 4A3M C; 3S15 K; 1K83 K; 3WOD A; 3M4O C; 5M3M K; 4A3M K; 3EQL A; 3PO3 C; 2E2H K; 3H3V L; 2R93 C; 3M4O K; 4C3H K; 3PO3 K; 2PMZ L; 1I6H K; 4BXX C; 1Y1W C; 5IP7 C; 2A6H A; 4LJZ A; 4YFX A; 1XPP A; 2R92 C; 3S14 K; 4BXX K; 1Y1W K; 5IP7 K; 2R92 K; 1TWC K; 2JA5 C; 4A3D C; 5C4X C; 2YU9 C; 3PO2 K; 4A3D K; 5IP9 C; 4A3G K; 5C4X K; 2R7Z C; 4A3B C; 5M5X K; 2YU9 K; 1TWG C; 2NVT C; 3GTQ C; 4XSZ A; 3S16 K; 3S17 K; 4A3B K; 3HOW C; 4MEY A; 1HQM A; 3DXJ A; 1TWG K; 2JA6 K; 2NVT K; 3GTJ C; 3HOW K; 4QIW D; 3GTJ K; 2PPB A; 2JA8 C; 4C3I C; 3S1Q C; 5TMF A; 2WB1 D; 5M5W K; 4NOI A; 2JA7 K; 4BY1 C; 2JA8 K; 4C3I K; 4A3C K; 3S1Q K; 2WAQ L; 4BBR C; 4BY1 K; 4A3J C; 1TWH C; 4KN7 A; 4BBS K; 4BBR K; 5FLM K; 4A3J K; 3HOY K; 1TWH K; 1WCM C; 1TWF K; 2Y0S L; 1WCM K; 3S1M C; 2R93 K; 3S1M K; 4BY7 C; 1I50 C; 3GTP C; 2PA8 L; 4BY7 K; 3GTP K; 4A3K C; 4A3I C; 2JA5 K; 2O5I A; 3HOU C; 3S2D C; 2O5J A; 5C4J C; 3H0G C; 4A3I K; 5IP9 K; 4A3K K; 5M5Y K; 3HOU K; 4OIR A; 2R7Z K; 3GTQ K; 5C3E C; 3GTG C; 1SMY A; 5C3E K; 4OIN A; 4Q4Z A; 4AYB L; 4Y52 C; 4Q5S A; 3CQZ C; 1I6V A; 4A3F C; 4X6A C; 3FKI C; 2NVY C; 3GTO C; 2A68 A; 4Y52 K; 3CQZ K; 4X6A K; 4QJV B; 2NVY K; 3GTO K; 3K7A C; 5IYC C; 4KMU A; 4G7O A; 3K7A K; 5IYC K; 4YFK A; 4LLG A; 2BE5 A; 4OIQ A; 3GTL C; 2A6E A; 3H3V D; 4A3L C; 3HKZ L; 4LK0 A; 3I4M C; 2PMZ D; 3I4M K; 3HOZ C; 4G7H A; 2B63 C; 3RZD C; 2E2I C; 2E2J C; 2VUM C; 4A3G C; 1I50 K; 3HOZ K; 1ZYR A; 2E2J K; 3S1N C; 4QIW L;
#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...
