5IPLE

Sigmas-transcription initiation complex with 4-nt nascent rna
Total Genus 24
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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
24
sequence length
79
structure length
79
Chain Sequence
ARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLINNQILDVRERQEQQEQEAAEL
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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.

Structure visualization

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Chord Diagram
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publication title Structures of E. coli sigma S-transcription initiation complexes provide new insights into polymerase mechanism.
pubmed doi rcsb
source organism Escherichia coli
molecule tags Transcription, transferase/dna/rna
molecule keywords DNA-directed RNA polymerase subunit alpha
total genus 24
structure length 79
sequence length 79
ec nomenclature ec 2.7.7.6: DNA-directed RNA polymerase.
pdb deposition date 2016-03-09

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
E PF01192 RNA_pol_Rpb6 RNA polymerase Rpb6
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.90.940.10 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit Eukaryotic RPB6 RNA polymerase subunit 5iplE00
2PMZK 2JA6F 1WCMF 4XSZE 4JK1E 4KMUE 2A69E 1TWGF 5IYDF 4GZYE 5IYBF 5M3MF 4Y52F 1R9TF 4A3BF 3M3YF 5TMFE 4C3HF 2Y0SI 5M5YF 5IP7F 4XLNE 4OIRE 2R92F 1QKLA 3S15F 2O5JE 1Y1VF 4LK1E 2NVQF 4YG2E 3HOZF 1YNJK 3HOWF 5IYCF 3WODE 4BXXF 4G7ZE 4OIQE 1I6VE 3DXJE 4A3CF 5TMCE 1TWAF 3PO3F 3S2HF 1IW7E 3I4MF 4OIPE 4BY7F 3HOYF 4LK0E 4A3LF 2JA8F 2WB1I 2R93F 3GTQF 3H3VG 2JA7F 3EQLE 3HOXF 4A3KF 2E2IF 2E2HF 3PO2F 4C3IF 2A68E 4YFNE 3RZDF 3M4OF 4A3IF 5C4JF 4Q5SE 3CQZF 3GTMF 4XSXE 4KN7E 3GTOF 5D4EE 1TWHF 1TWCF 4LLGE 3GTKF 5C4XF 1I50F 1HQME 1I3QF 4AYBK 3GTJF 5IP9F 3S1MF 3GTGF 4YFKE 5FLMF 4BBSF 1ZYRE 3H0GF 4MQ9E 3S1NF 2R7ZF 4ZH4E 4LJZE 3K7AF 3HKZK 2B63F 2NVTF 5E17E 3GTLF 2BE5E 4A3DF 5E18E 5C3EF 5D4CE 4XLPE 3GTPF 4BY1F 4MEXE 5D4DE 1TWFF 4G7HE 3S16F 3S1RF 2O5IE 1Y1WF 3I4NF 2A6HE 5M5XF 3FKIF 2PPBE 4X6AF 2A6EE 3HOUF 3S14F 1SFOF 5IPLE 2YU9F 3HOVF 5C44F 4A3FF 2WAQK 5BYHE 4OINE 2E2JF 4A3JF 2VUMF 4G7OE 1SMYE 4OIOE 1I6HF 2NVYF 2CW0E 4C2MF 5FJ8F 4Q4ZE 4YFXE 4A3MF 4C3JF 3S17F 4MEYE 2JA5F 1YNNK 4KN4E 5M3FF 3RZOF 4A93F 4Y7NF 2NVXF 1K83F 4A3GF 3S2DF 3S1QF 4A3EF 4BBRF 5M5WF
chains in the Genus database with same CATH superfamily
1TWCE 2PMZK 4C2ME 4A3ME 2JA6F 3S17E 1WCMF 4XSZE 4JK1E 4KMUE 2A69E 1TWGF 5IYDF 4GZYE 2VUME 4A3JE 5IYBF 5M3MF 4Y52F 5C4JE 1R9TF 4A3BF 5C44E 3RZDE 3HOVE 4C3IE 3M3YF 5TMFE 4C3HF 1SFOE 2Y0SI 3S14E 3HOUE 5M5YF 5IP7F 4XLNE 4OIRE 2PMZH 2R92F 1QKLA 2E2IE 3S15F 1Y1VF 3HOXE 2O5JE 4X6AE 4LK1E 1Y1WE 3S1RE 2NVQF 4YG2E 3HOZF 3S16E 1YNJK 4QIWH 1TWFE 3HOWF 3S17F 2R93E 5IYCF 3WODE 4BXXF 1EIKA 4G7ZE 4OIQE 1I6VE 3DXJE 2JA8E 3GTPE 4A3CF 3HOYE 4A3LE 4BY7E 5TMCE 3GTLE 1TWAF 2NVTE 3I4ME 3PO3F 1DZFA 2B63E 3S2HE 3S2HF 1IW7E 2R7ZE 3S1NE 1TWAE 3I4MF 4OIPE 4BY7F 3HOYF 4LK0E 4A3LF 2JA8F 4A3CE 2Y0SH 3S1ME 2WB1I 2R93F 3HOWE 3GTQF 3GTJE 3H3VG 1I3QE 2JA7F 3EQLE 1Y1VE 3HOXF 4A3KF 2E2IF 3S15E 5IP7E 2E2HF 2R92E 5C4XE 5M5YE 1TWHE 4C3HE 3PO2F 4C3IF 2A68E 4YFNE 3RZDF 3GTOE 3M4OF 4A3IF 5C4JF 1R9TE 5M3ME 3M3YE 5IYBE 4A3BE 4Y52E 4Q5SE 3CQZF 3GTMF 3GTME 1TWGE 3CQZE 4XSXE 5IYDE 2WAQH 4A3IE 4KN7E 3GTOF 3M4OE 1WCME 5D4EE 1TWHF 1TWCF 4LLGE 3PO2E 3GTKF 2E2HE 1I50F 5C4XF 4QIWK 4A3KE 1HQME 3S1QE 1I3QF 2JA7E 4AYBK 3GTJF 1K83E 3GTQE 5IP9F 3S1MF 3GTGF 4YFKE 3RZOE 5FLMF 2JA5E 4BBSF 1ZYRE 4C3JE 3H0GF 4MQ9E 5FJ8E 2R7ZF 4ZH4E 4LJZE 2NVYE 3S1NF 3K7AF 1I6HE 3HKZK 2B63F 3PO3E 2NVTF 5E17E 3GTLF 2BE5E 4A3DF 5E18E 5C3EF 2E2JE 5D4CE 4XLPE 3GTPF 4BY1F 4MEXE 4A3FE 5IYCE 4BXXE 5D4DE 2YU9E 1TWFF 4G7HE 3S16F 3S1RF 2NVQE 1Y1WF 2O5IE 3FKIE 2A6HE 3FKIF 5M5XE 5M5XF 2PPBE 3I4NE 3I4NF 4X6AF 2A6EE 3H3VF 3HOUF 3S14F 1SFOF 5IPLE 2YU9F 3HOVF 5C44F 4A3FF 2WAQK 5BYHE 4BY1E 4OINE 5C3EE 4A3JF 2E2JF 2VUMF 4G7OE 4A3DE 4BBRF 1SMYE 3K7AE 4OIOE 1I6HF 2NVYF 2CW0E 2JA6E 4C2MF 5FJ8F 4Q4ZE 3H0GE 4YFXE 4C3JF 5M5WE 4MEYE 4BBRE 4A3MF 4AYBH 2JA5F 3HOZE 1YNNK 4KN4E 5FLME 2WB1H 5M3FF 4A3EE 4BBSE 3RZOF 4A93F 3GTGE 4Y7NF 2NVXF 3S2DE 4A3GE 5IP9E 1K83F 4A3GF 2NVXE 3S2DF 3S1QF 4Y7NE 4A93E 5M3FE 4A3EF 1I50E 3GTKE 3HKZH 2KRXA 5M5WF
chains in the Genus database with same CATH topology
2PMZK 2JA6F 1WCMF 4XSZE 4JK1E 4KMUE 2A69E 1TWGF 5IYDF 4GZYE 5IYBF 5M3MF 4Y52F 1R9TF 4A3BF 3M3YF 5TMFE 4C3HF 2Y0SI 5M5YF 5IP7F 4XLNE 4OIRE 2R92F 1QKLA 3S15F 2O5JE 1Y1VF 4LK1E 2NVQF 4YG2E 3HOZF 1YNJK 3HOWF 5IYCF 3WODE 4BXXF 4G7ZE 4OIQE 1I6VE 3DXJE 4A3CF 5TMCE 1TWAF 3PO3F 3S2HF 1IW7E 3I4MF 4OIPE 4BY7F 3HOYF 4LK0E 4A3LF 2JA8F 2WB1I 2R93F 3GTQF 3H3VG 2JA7F 3EQLE 3HOXF 4A3KF 2E2IF 2E2HF 3PO2F 4C3IF 2A68E 4YFNE 3RZDF 3M4OF 4A3IF 5C4JF 4Q5SE 3CQZF 3GTMF 4XSXE 4KN7E 3GTOF 5D4EE 1TWHF 1TWCF 4LLGE 3GTKF 5C4XF 1I50F 4QIWK 1HQME 1I3QF 4AYBK 3GTJF 5IP9F 3S1MF 3GTGF 4YFKE 5FLMF 4BBSF 1ZYRE 3H0GF 4MQ9E 3S1NF 2R7ZF 4ZH4E 4LJZE 3K7AF 3HKZK 2B63F 2NVTF 5E17E 3GTLF 2BE5E 4A3DF 5E18E 5C3EF 5D4CE 4XLPE 3GTPF 4BY1F 4MEXE 5D4DE 1TWFF 4G7HE 3S16F 3S1RF 2O5IE 1Y1WF 3I4NF 2A6HE 5M5XF 3FKIF 2PPBE 4X6AF 2A6EE 3HOUF 3S14F 1SFOF 5IPLE 2YU9F 3HOVF 5C44F 4A3FF 2WAQK 5BYHE 4OINE 2E2JF 4A3JF 2VUMF 4G7OE 1SMYE 4OIOE 1I6HF 2NVYF 2CW0E 4C2MF 5FJ8F 4Q4ZE 4YFXE 4A3MF 4C3JF 3S17F 4MEYE 2JA5F 1YNNK 4KN4E 5M3FF 3RZOF 4A93F 4Y7NF 2NVXF 1K83F 4A3GF 3S2DF 3S1QF 4A3EF 4BBRF 2KRXA 5M5WF
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 2PMZ K;  2JA6 F;  1WCM F;  4XSZ E;  4JK1 E;  4KMU E;  2A69 E;  1TWG F;  5IYD F;  4GZY E;  5IYB F;  5M3M F;  4Y52 F;  1R9T F;  4A3B F;  3M3Y F;  5TMF E;  4C3H F;  2Y0S I;  5M5Y F;  5IP7 F;  4XLN E;  4OIR E;  2R92 F;  1QKL A;  3S15 F;  2O5J E;  1Y1V F;  4LK1 E;  2NVQ F;  4YG2 E;  3HOZ F;  1YNJ K;  3HOW F;  5IYC F;  3WOD E;  4BXX F;  4G7Z E;  4OIQ E;  1I6V E;  3DXJ E;  4A3C F;  5TMC E;  1TWA F;  3PO3 F;  3S2H F;  1IW7 E;  3I4M F;  4OIP E;  4BY7 F;  3HOY F;  4LK0 E;  4A3L F;  2JA8 F;  2WB1 I;  2R93 F;  3GTQ F;  3H3V G;  2JA7 F;  3EQL E;  3HOX F;  4A3K F;  2E2I F;  2E2H F;  3PO2 F;  4C3I F;  2A68 E;  4YFN E;  3RZD F;  3M4O F;  4A3I F;  5C4J F;  4Q5S E;  3CQZ F;  3GTM F;  4XSX E;  4KN7 E;  3GTO F;  5D4E E;  1TWH F;  1TWC F;  4LLG E;  3GTK F;  5C4X F;  1I50 F;  1HQM E;  1I3Q F;  4AYB K;  3GTJ F;  5IP9 F;  3S1M F;  3GTG F;  4YFK E;  5FLM F;  4BBS F;  1ZYR E;  3H0G F;  4MQ9 E;  3S1N F;  2R7Z F;  4ZH4 E;  4LJZ E;  3K7A F;  3HKZ K;  2B63 F;  2NVT F;  5E17 E;  3GTL F;  2BE5 E;  4A3D F;  5E18 E;  5C3E F;  5D4C E;  4XLP E;  3GTP F;  4BY1 F;  4MEX E;  5D4D E;  1TWF F;  4G7H E;  3S16 F;  3S1R F;  2O5I E;  1Y1W F;  3I4N F;  2A6H E;  5M5X F;  3FKI F;  2PPB E;  4X6A F;  2A6E E;  3HOU F;  3S14 F;  1SFO F;  5IPL E;  2YU9 F;  3HOV F;  5C44 F;  4A3F F;  2WAQ K;  5BYH E;  4OIN E;  2E2J F;  4A3J F;  2VUM F;  4G7O E;  1SMY E;  4OIO E;  1I6H F;  2NVY F;  2CW0 E;  4C2M F;  5FJ8 F;  4Q4Z E;  4YFX E;  4A3M F;  4C3J F;  3S17 F;  4MEY E;  2JA5 F;  1YNN K;  4KN4 E;  5M3F F;  3RZO F;  4A93 F;  4Y7N F;  2NVX F;  1K83 F;  4A3G F;  3S2D F;  3S1Q F;  4A3E F;  4BBR F;  5M5W F; 
#chains in the Genus database with same CATH topology
 1TWC E;  2PMZ K;  4C2M E;  4A3M E;  2JA6 F;  3S17 E;  1WCM F;  4XSZ E;  4JK1 E;  4KMU E;  2A69 E;  1TWG F;  5IYD F;  4GZY E;  2VUM E;  4A3J E;  5IYB F;  5M3M F;  4Y52 F;  5C4J E;  1R9T F;  4A3B F;  5C44 E;  3RZD E;  3HOV E;  4C3I E;  3M3Y F;  5TMF E;  4C3H F;  1SFO E;  2Y0S I;  3S14 E;  3HOU E;  5M5Y F;  5IP7 F;  4XLN E;  4OIR E;  2PMZ H;  2R92 F;  1QKL A;  2E2I E;  3S15 F;  1Y1V F;  3HOX E;  2O5J E;  4X6A E;  4LK1 E;  1Y1W E;  3S1R E;  2NVQ F;  4YG2 E;  3HOZ F;  3S16 E;  1YNJ K;  4QIW H;  1TWF E;  3HOW F;  3S17 F;  2R93 E;  5IYC F;  3WOD E;  4BXX F;  1EIK A;  4G7Z E;  4OIQ E;  1I6V E;  3DXJ E;  2JA8 E;  3GTP E;  4A3C F;  3HOY E;  4A3L E;  4BY7 E;  5TMC E;  3GTL E;  1TWA F;  2NVT E;  3I4M E;  3PO3 F;  1DZF A;  2B63 E;  3S2H E;  3S2H F;  1IW7 E;  2R7Z E;  3S1N E;  1TWA E;  3I4M F;  4OIP E;  4BY7 F;  3HOY F;  4LK0 E;  4A3L F;  2JA8 F;  4A3C E;  2Y0S H;  3S1M E;  2WB1 I;  2R93 F;  3HOW E;  3GTQ F;  3GTJ E;  3H3V G;  1I3Q E;  2JA7 F;  3EQL E;  1Y1V E;  3HOX F;  4A3K F;  2E2I F;  3S15 E;  5IP7 E;  2E2H F;  2R92 E;  5C4X E;  5M5Y E;  1TWH E;  4C3H E;  3PO2 F;  4C3I F;  2A68 E;  4YFN E;  3RZD F;  3GTO E;  3M4O F;  4A3I F;  5C4J F;  1R9T E;  5M3M E;  3M3Y E;  5IYB E;  4A3B E;  4Y52 E;  4Q5S E;  3CQZ F;  3GTM F;  3GTM E;  1TWG E;  3CQZ E;  4XSX E;  5IYD E;  2WAQ H;  4A3I E;  4KN7 E;  3GTO F;  3M4O E;  1WCM E;  5D4E E;  1TWH F;  1TWC F;  4LLG E;  3PO2 E;  3GTK F;  2E2H E;  1I50 F;  5C4X F;  4QIW K;  4A3K E;  1HQM E;  3S1Q E;  1I3Q F;  2JA7 E;  4AYB K;  3GTJ F;  1K83 E;  3GTQ E;  5IP9 F;  3S1M F;  3GTG F;  4YFK E;  3RZO E;  5FLM F;  2JA5 E;  4BBS F;  1ZYR E;  4C3J E;  3H0G F;  4MQ9 E;  5FJ8 E;  2R7Z F;  4ZH4 E;  4LJZ E;  2NVY E;  3S1N F;  3K7A F;  1I6H E;  3HKZ K;  2B63 F;  3PO3 E;  2NVT F;  5E17 E;  3GTL F;  2BE5 E;  4A3D F;  5E18 E;  5C3E F;  2E2J E;  5D4C E;  4XLP E;  3GTP F;  4BY1 F;  4MEX E;  4A3F E;  5IYC E;  4BXX E;  5D4D E;  2YU9 E;  1TWF F;  4G7H E;  3S16 F;  3S1R F;  2NVQ E;  1Y1W F;  2O5I E;  3FKI E;  2A6H E;  3FKI F;  5M5X E;  5M5X F;  2PPB E;  3I4N E;  3I4N F;  4X6A F;  2A6E E;  3H3V F;  3HOU F;  3S14 F;  1SFO F;  5IPL E;  2YU9 F;  3HOV F;  5C44 F;  4A3F F;  2WAQ K;  5BYH E;  4BY1 E;  4OIN E;  5C3E E;  4A3J F;  2E2J F;  2VUM F;  4G7O E;  4A3D E;  4BBR F;  1SMY E;  3K7A E;  4OIO E;  1I6H F;  2NVY F;  2CW0 E;  2JA6 E;  4C2M F;  5FJ8 F;  4Q4Z E;  3H0G E;  4YFX E;  4C3J F;  5M5W E;  4MEY E;  4BBR E;  4A3M F;  4AYB H;  2JA5 F;  3HOZ E;  1YNN K;  4KN4 E;  5FLM E;  2WB1 H;  5M3F F;  4A3E E;  4BBS E;  3RZO F;  4A93 F;  3GTG E;  4Y7N F;  2NVX F;  3S2D E;  4A3G E;  5IP9 E;  1K83 F;  4A3G F;  2NVX E;  3S2D F;  3S1Q F;  4Y7N E;  4A93 E;  5M3F E;  4A3E F;  1I50 E;  3GTK E;  3HKZ H;  2KRX A;  5M5W F; 
#chains in the Genus database with same CATH homology
 2PMZ K;  2JA6 F;  1WCM F;  4XSZ E;  4JK1 E;  4KMU E;  2A69 E;  1TWG F;  5IYD F;  4GZY E;  5IYB F;  5M3M F;  4Y52 F;  1R9T F;  4A3B F;  3M3Y F;  5TMF E;  4C3H F;  2Y0S I;  5M5Y F;  5IP7 F;  4XLN E;  4OIR E;  2R92 F;  1QKL A;  3S15 F;  2O5J E;  1Y1V F;  4LK1 E;  2NVQ F;  4YG2 E;  3HOZ F;  1YNJ K;  3HOW F;  5IYC F;  3WOD E;  4BXX F;  4G7Z E;  4OIQ E;  1I6V E;  3DXJ E;  4A3C F;  5TMC E;  1TWA F;  3PO3 F;  3S2H F;  1IW7 E;  3I4M F;  4OIP E;  4BY7 F;  3HOY F;  4LK0 E;  4A3L F;  2JA8 F;  2WB1 I;  2R93 F;  3GTQ F;  3H3V G;  2JA7 F;  3EQL E;  3HOX F;  4A3K F;  2E2I F;  2E2H F;  3PO2 F;  4C3I F;  2A68 E;  4YFN E;  3RZD F;  3M4O F;  4A3I F;  5C4J F;  4Q5S E;  3CQZ F;  3GTM F;  4XSX E;  4KN7 E;  3GTO F;  5D4E E;  1TWH F;  1TWC F;  4LLG E;  3GTK F;  5C4X F;  1I50 F;  4QIW K;  1HQM E;  1I3Q F;  4AYB K;  3GTJ F;  5IP9 F;  3S1M F;  3GTG F;  4YFK E;  5FLM F;  4BBS F;  1ZYR E;  3H0G F;  4MQ9 E;  3S1N F;  2R7Z F;  4ZH4 E;  4LJZ E;  3K7A F;  3HKZ K;  2B63 F;  2NVT F;  5E17 E;  3GTL F;  2BE5 E;  4A3D F;  5E18 E;  5C3E F;  5D4C E;  4XLP E;  3GTP F;  4BY1 F;  4MEX E;  5D4D E;  1TWF F;  4G7H E;  3S16 F;  3S1R F;  2O5I E;  1Y1W F;  3I4N F;  2A6H E;  5M5X F;  3FKI F;  2PPB E;  4X6A F;  2A6E E;  3HOU F;  3S14 F;  1SFO F;  5IPL E;  2YU9 F;  3HOV F;  5C44 F;  4A3F F;  2WAQ K;  5BYH E;  4OIN E;  2E2J F;  4A3J F;  2VUM F;  4G7O E;  1SMY E;  4OIO E;  1I6H F;  2NVY F;  2CW0 E;  4C2M F;  5FJ8 F;  4Q4Z E;  4YFX E;  4A3M F;  4C3J F;  3S17 F;  4MEY E;  2JA5 F;  1YNN K;  4KN4 E;  5M3F F;  3RZO F;  4A93 F;  4Y7N F;  2NVX F;  1K83 F;  4A3G F;  3S2D F;  3S1Q F;  4A3E F;  4BBR F;  2KRX A;  5M5W F; 
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similar chains in the Genus database (?% sequence similarity)
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similar chains in the pdb database (?% sequence similarity)

 
#similar chains in the Genus database (?% sequence similarity)
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#similar chains, but unknotted
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#similar chains in the pdb database (?% sequence similarity)
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