2JA8D

Cpd lesion containing rna polymerase ii elongation complex d
Total Genus 40
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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
40
sequence length
218
structure length
177
Chain Sequence
STSTFQTRRRRLKKVEEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIKEALVERRRAFKRSQKKTREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKISDDELERILKELSNLETLY
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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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molecule tags Transferase
molecule keywords DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT
publication title Cpd Damage Recognition by Transcribing RNA Polymerase II.
pubmed doi rcsb
total genus 40
structure length 177
sequence length 218
ec nomenclature
pdb deposition date 2006-11-23

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
D PF03874 RNA_pol_Rpb4 RNA polymerase Rpb4
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
1.20.1250.40 Mainly Alpha Up-down Bundle Growth Hormone; Chain: A; Growth Hormone; Chain: A; 2ja8D02
4BY1D 3I4MD 4BY7D 2JA6D 3I4ND 4A3GD 4A3MD 2JA8D 5C44D 5C3ED 4A3ID 4BBSD 5C4XD 4A3KD 2C35A 4A93D 2R93D 4A3JD 5IP7D 2JA7D 3FKID 1WCMD 4A3ED 5IYCD 3HOXD 2JA5D 4BXXD 4A3CD 4A3DD 1Y1VD 3H3VE 3HOWD 4BBRD 4A3FD 1Y1WD 4A3BD 3AYHA 2B63D 5FLMD 3HOYD 5IP9D 5IYDD 3PO2D 4A3LD 1Y14A 2R92D 3H0GD 3PO3D 3HOUD 3HOZD 5IYBD 2VUMD 2R7ZD 3HOVD
chains in the Genus database with same CATH superfamily
2B8UA 2LAGA 5EQGA 1LQSL 2B90A 1AU1A 3UX9A 1B5LA 1F45B 4NKQC 4QIQA 3DI2A 4IKYA 4J4LC 2B5IA 3DI3A 3G6DA 2VUMD 1Y6KL 5E4EA 1LK3A 5C44D 5C3ED 3NCBA 2O26A 3N0PA 1EMRA 4ZS7A 4JREA 4UVMA 5D22A 4EXPA 1M4CA 1ETEA 3G9VB 1HWGA 2XQBA 3NCCA 3FKID 1ITMA 5IYCD 4O6KA 1Z92A 2B8ZA 3WCYI 1M49A 1EVSA 4TPHA 2Z3RA 2V8NA 3D87A 1PY2A 1V7NV 2R92D 1RHGA 4ZYRA 3DLQI 3SE3B 1IJZA 2IL6A 5TS9A 3PIVA 4PYPA 2Q14A 4RS1A 2C35A 1WCMD 3BESL 1ALUA 4NN5A 1IK0A 2D9QA 5FUCA 4XNIA 1V7MV 4DKCA 5GXBA 1J7VL 1HUWA 1IRLA 2JA6D 3B5KA 4IKVA 1A7MA 1D9GA 3D85C 2JA5D 5D72A 4YDYI 3OQ3A 3NCFA 3BPNA 1CNT1 1ITLA 4GS7A 4YB9D 1HZIA 4NI7A 2GMFA 4D2CA 1LKIA 4FA8E 4NN6A 1PW6A 4YPGC 4YUEC 3UF5A 2L3YA 4MHLA 2L3OA 1QVNA 4IKZA 4PS4A 4D2DA 5C7XA 1ITIA 1PV7A 1EERA 3NPZA 1Y1WD 3QB7A 4GRWA 4OH3A 3UF2A 1F6FA 4YBQA 4GC0A 2B63D 1RCBA 5FHXA 3BPLA 4NN7A 1IARA 4DKFA 4BBSD 4BY7D 2HYMB 4A3GD 4A3ID 3N06A 2CFQA 4BXXD 2CYKA 4NEMA 2Q7NB 1WU3I 3D48P 2H24A 4NEJA 4A3BD 1JLIA 1P9MB 4YQXA 5IYDD 5D59A 4ZWBA 3WDOA 3TGXB 3HOZD 2B91A 2LMSA 3PIWA 5D28B 4D2BA 2Q98A 3HMXB 5C65A 4U4WA 3UEZE 3HOXD 3O7QA 5EQHA 3QT2C 1HIKA 4Z5RD 4OAAA 4DKDA 1AXIA 5A2NA 1Y6ML 1EXZA 4A3LD 3BPOA 3HOUD 5IYBD 1KF9A 4LRLA 3HOVD 2JA8D 4XNJA 4A3KD 4EXNA 2E9WC 2JA7D 1Z7CA 3DUHC 1M48A 2KZ1A 3OG4A 3SE4B 3NCEA 1BBNA 3OG6A 1I1RB 3O7PA 4X51A 5LQBA 2Y5YA 1M4RA 1A22A 1GA3A 4A3MD 5C4XD 3QAZA 2Z3QA 2R93D 4A93D 1VLKA 5D6KA 2XUTA 3DGCL 1HGUA 4JA3A 4ZWCA 1ILKA 4IU9A 3PO3D 3MZGA 2R7ZD 4BY1D 4LEPA 3I4MD 5A2OA 1EKUA 4GBYA 1IL6A 3HHCA 1AX8A 5D70A 1HWHA 3L5WI 4LDSA 3HHRA 1CN4C 1N1FA 2ERJD 1GNCA 3Q1SI 3LB6B 3L5XA 1RFBA 4CNIC 3LB6A 1PGRA 4DOHA 3QWRB 2O27A 4JR9A 2ILKA 4I77Z 1NBPA 1CD9A 3VA2A 1M4AA 3QB1A 4APSA 4U4VA 1D9CA 1BP3A 4NI9A 1Y14A 3H0GD 1RW5A 1BCNA 4TPJA 4ZW9A 1M47A 1M4BA 3S9DA 1CSGA 4A3CD 1BGEA 4U4TA 3HOWD 3AYHA 1ITFA 2D48A 2INTA 5FLMD 1PW4A 1BUYA 1FG9A 1PVHB 5L6YC 5KNHI 4DKEA 1HULA 2O6IA 4WRLB 2OQPA 4J05A 3IRHA 1HIJA 4W6VA 3H3VE 4A3FD 4ZF7A 3PO2D 2CFPA 3EJJA 4TPGA 1CYLA 1YKBA 5EQIA 4A3DD 2B8YA 1BGDA 4BBRD 1PV6A 3HOYD 5IP9D 1Y6NL 3I4ND 1FYHA 4Q65A 1INRA 2B8XA 4A3JD 2PSMA 5IP7D 4A3ED 5D71A 1BGCA 1Y1VD 3EW3A 4IKXA 4O9HA 4GBZA 5D58A 4IKWA 3INKC 4IU8A 1SCFA
chains in the Genus database with same CATH topology
2B8UA 2LAGA 2JA6D 3B5KA 1A7MA 2JA8D 1LQSL 1D9GA 4A3KD 2B90A 3D85C 1M47A 4EXNA 2E9WC 1AU1A 2JA7D 1M4BA 2JA5D 3UX9A 1B5LA 1Z7CA 3S9DA 1CSGA 5D72A 4YDYI 3DUHC 4A3CD 3OQ3A 1BGEA 1M48A 2KZ1A 1F45B 3NCFA 4NKQC 3OG4A 3SE4B 3HOWD 3NCEA 3DI2A 3AYHA 1ITFA 4J4LC 3BPNA 1BBNA 2D48A 1CNT1 2INTA 1ITLA 5FLMD 3OG6A 1I1RB 2B5IA 4GS7A 4X51A 1HZIA 1BUYA 5LQBA 4NI7A 1FG9A 2GMFA 1LKIA 4FA8E 3DI3A 3G6DA 1PW6A 1PVHB 4NN6A 2VUMD 1M4RA 1A22A 1Y6KL 4YPGC 5E4EA 1GA3A 5L6YC 1LK3A 4YUEC 3UF5A 2L3YA 3QAZA 5C44D 2Z3QA 4MHLA 5KNHI 5C3ED 5C4XD 2R93D 2L3OA 4A93D 4DKEA 1QVNA 1HULA 3NCBA 4PS4A 1VLKA 5C7XA 2O6IA 4WRLB 1ITIA 3DGCL 2OQPA 2O26A 3N0PA 3IRHA 1HIJA 3H3VE 1EMRA 1HGUA 1EERA 3NPZA 4A3FD 1Y1WD 3QB7A 4GRWA 3UF2A 4ZF7A 1F6FA 4ZS7A 2B63D 1RCBA 5D22A 5FHXA 3PO2D 4EXPA 1ILKA 3BPLA 1M4CA 3PO3D 5IYBD 3MZGA 4NN7A 1ETEA 3G9VB 2R7ZD 1IARA 4DKFA 3EJJA 4BY1D 4BBSD 1HWGA 3I4MD 4BY7D 2XQBA 1EKUA 3NCCA 2HYMB 3I4ND 4A3GD 4A3ID 1IL6A 3HHCA 1CYLA 1AX8A 5D70A 1HWHA 3N06A 3FKID 1ITMA 1YKBA 2CYKA 5IYCD 4NEMA 4O6KA 4BXXD 1Z92A 4A3DD 2B8ZA 3WCYI 2B8YA 1M49A 1EVSA 3L5WI 2Q7NB 1BGDA 1CN4C 1WU3I 2H24A 2Z3RA 3D48P 3HHRA 4NEJA 3D87A 4BBRD 4A3BD 1JLIA 1P9MB 4YQXA 1N1FA 3HOYD 5IP9D 5IYDD 2ERJD 1PY2A 1Y6NL 1V7NV 2R92D 1RHGA 3TGXB 3Q1SI 1GNCA 3DLQI 3SE3B 3LB6B 3L5XA 2B91A 3HOZD 1RFBA 2LMSA 3PIWA 4A3MD 5D28B 1IJZA 4LRLA 2IL6A 2Q98A 4CNIC 3HMXB 1FYHA 3LB6A 1PGRA 3PIVA 3QWRB 5TS9A 4DOHA 1INRA 2B8XA 2Q14A 2C35A 4RS1A 4A3JD 2PSMA 2O27A 5IP7D 1WCMD 3UEZE 4A3ED 3BESL 3HOXD 1ALUA 2ILKA 4I77Z 4NN5A 1BGCA 1Y1VD 1NBPA 2D9QA 3EW3A 5D71A 1CD9A 1IK0A 3VA2A 3QT2C 1HIKA 4O9HA 5FUCA 4Z5RD 1V7MV 4DKCA 1AXIA 4DKDA 1M4AA 3QB1A 1Y6ML 1EXZA 4A3LD 3INKC 3BPOA 1D9CA 1BP3A 1J7VL 1Y14A 1HUWA 3H0GD 4NI9A 1SCFA 1RW5A 3HOUD 1BCNA 1KF9A 1IRLA 3HOVD
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 4BY1 D;  3I4M D;  4BY7 D;  2JA6 D;  3I4N D;  4A3G D;  4A3M D;  2JA8 D;  5C44 D;  5C3E D;  4A3I D;  4BBS D;  5C4X D;  4A3K D;  2C35 A;  4A93 D;  2R93 D;  4A3J D;  5IP7 D;  2JA7 D;  3FKI D;  1WCM D;  4A3E D;  5IYC D;  3HOX D;  2JA5 D;  4BXX D;  4A3C D;  4A3D D;  1Y1V D;  3H3V E;  3HOW D;  4BBR D;  4A3F D;  1Y1W D;  4A3B D;  3AYH A;  2B63 D;  5FLM D;  3HOY D;  5IP9 D;  5IYD D;  3PO2 D;  4A3L D;  1Y14 A;  2R92 D;  3H0G D;  3PO3 D;  3HOU D;  3HOZ D;  5IYB D;  2VUM D;  2R7Z D;  3HOV D; 
#chains in the Genus database with same CATH topology
 2B8U A;  2LAG A;  5EQG A;  1LQS L;  2B90 A;  1AU1 A;  3UX9 A;  1B5L A;  1F45 B;  4NKQ C;  4QIQ A;  3DI2 A;  4IKY A;  4J4L C;  2B5I A;  3DI3 A;  3G6D A;  2VUM D;  1Y6K L;  5E4E A;  1LK3 A;  5C44 D;  5C3E D;  3NCB A;  2O26 A;  3N0P A;  1EMR A;  4ZS7 A;  4JRE A;  4UVM A;  5D22 A;  4EXP A;  1M4C A;  1ETE A;  3G9V B;  1HWG A;  2XQB A;  3NCC A;  3FKI D;  1ITM A;  5IYC D;  4O6K A;  1Z92 A;  2B8Z A;  3WCY I;  1M49 A;  1EVS A;  4TPH A;  2Z3R A;  2V8N A;  3D87 A;  1PY2 A;  1V7N V;  2R92 D;  1RHG A;  4ZYR A;  3DLQ I;  3SE3 B;  1IJZ A;  2IL6 A;  5TS9 A;  3PIV A;  4PYP A;  2Q14 A;  4RS1 A;  2C35 A;  1WCM D;  3BES L;  1ALU A;  4NN5 A;  1IK0 A;  2D9Q A;  5FUC A;  4XNI A;  1V7M V;  4DKC A;  5GXB A;  1J7V L;  1HUW A;  1IRL A;  2JA6 D;  3B5K A;  4IKV A;  1A7M A;  1D9G A;  3D85 C;  2JA5 D;  5D72 A;  4YDY I;  3OQ3 A;  3NCF A;  3BPN A;  1CNT 1;  1ITL A;  4GS7 A;  4YB9 D;  1HZI A;  4NI7 A;  2GMF A;  4D2C A;  1LKI A;  4FA8 E;  4NN6 A;  1PW6 A;  4YPG C;  4YUE C;  3UF5 A;  2L3Y A;  4MHL A;  2L3O A;  1QVN A;  4IKZ A;  4PS4 A;  4D2D A;  5C7X A;  1ITI A;  1PV7 A;  1EER A;  3NPZ A;  1Y1W D;  3QB7 A;  4GRW A;  4OH3 A;  3UF2 A;  1F6F A;  4YBQ A;  4GC0 A;  2B63 D;  1RCB A;  5FHX A;  3BPL A;  4NN7 A;  1IAR A;  4DKF A;  4BBS D;  4BY7 D;  2HYM B;  4A3G D;  4A3I D;  3N06 A;  2CFQ A;  4BXX D;  2CYK A;  4NEM A;  2Q7N B;  1WU3 I;  3D48 P;  2H24 A;  4NEJ A;  4A3B D;  1JLI A;  1P9M B;  4YQX A;  5IYD D;  5D59 A;  4ZWB A;  3WDO A;  3TGX B;  3HOZ D;  2B91 A;  2LMS A;  3PIW A;  5D28 B;  4D2B A;  2Q98 A;  3HMX B;  5C65 A;  4U4W A;  3UEZ E;  3HOX D;  3O7Q A;  5EQH A;  3QT2 C;  1HIK A;  4Z5R D;  4OAA A;  4DKD A;  1AXI A;  5A2N A;  1Y6M L;  1EXZ A;  4A3L D;  3BPO A;  3HOU D;  5IYB D;  1KF9 A;  4LRL A;  3HOV D;  2JA8 D;  4XNJ A;  4A3K D;  4EXN A;  2E9W C;  2JA7 D;  1Z7C A;  3DUH C;  1M48 A;  2KZ1 A;  3OG4 A;  3SE4 B;  3NCE A;  1BBN A;  3OG6 A;  1I1R B;  3O7P A;  4X51 A;  5LQB A;  2Y5Y A;  1M4R A;  1A22 A;  1GA3 A;  4A3M D;  5C4X D;  3QAZ A;  2Z3Q A;  2R93 D;  4A93 D;  1VLK A;  5D6K A;  2XUT A;  3DGC L;  1HGU A;  4JA3 A;  4ZWC A;  1ILK A;  4IU9 A;  3PO3 D;  3MZG A;  2R7Z D;  4BY1 D;  4LEP A;  3I4M D;  5A2O A;  1EKU A;  4GBY A;  1IL6 A;  3HHC A;  1AX8 A;  5D70 A;  1HWH A;  3L5W I;  4LDS A;  3HHR A;  1CN4 C;  1N1F A;  2ERJ D;  1GNC A;  3Q1S I;  3LB6 B;  3L5X A;  1RFB A;  4CNI C;  3LB6 A;  1PGR A;  4DOH A;  3QWR B;  2O27 A;  4JR9 A;  2ILK A;  4I77 Z;  1NBP A;  1CD9 A;  3VA2 A;  1M4A A;  3QB1 A;  4APS A;  4U4V A;  1D9C A;  1BP3 A;  4NI9 A;  1Y14 A;  3H0G D;  1RW5 A;  1BCN A;  4TPJ A;  4ZW9 A;  1M47 A;  1M4B A;  3S9D A;  1CSG A;  4A3C D;  1BGE A;  4U4T A;  3HOW D;  3AYH A;  1ITF A;  2D48 A;  2INT A;  5FLM D;  1PW4 A;  1BUY A;  1FG9 A;  1PVH B;  5L6Y C;  5KNH I;  4DKE A;  1HUL A;  2O6I A;  4WRL B;  2OQP A;  4J05 A;  3IRH A;  1HIJ A;  4W6V A;  3H3V E;  4A3F D;  4ZF7 A;  3PO2 D;  2CFP A;  3EJJ A;  4TPG A;  1CYL A;  1YKB A;  5EQI A;  4A3D D;  2B8Y A;  1BGD A;  4BBR D;  1PV6 A;  3HOY D;  5IP9 D;  1Y6N L;  3I4N D;  1FYH A;  4Q65 A;  1INR A;  2B8X A;  4A3J D;  2PSM A;  5IP7 D;  4A3E D;  5D71 A;  1BGC A;  1Y1V D;  3EW3 A;  4IKX A;  4O9H A;  4GBZ A;  5D58 A;  4IKW A;  3INK C;  4IU8 A;  1SCF A; 
#chains in the Genus database with same CATH homology
 2B8U A;  2LAG A;  2JA6 D;  3B5K A;  1A7M A;  2JA8 D;  1LQS L;  1D9G A;  4A3K D;  2B90 A;  3D85 C;  1M47 A;  4EXN A;  2E9W C;  1AU1 A;  2JA7 D;  1M4B A;  2JA5 D;  3UX9 A;  1B5L A;  1Z7C A;  3S9D A;  1CSG A;  5D72 A;  4YDY I;  3DUH C;  4A3C D;  3OQ3 A;  1BGE A;  1M48 A;  2KZ1 A;  1F45 B;  3NCF A;  4NKQ C;  3OG4 A;  3SE4 B;  3HOW D;  3NCE A;  3DI2 A;  3AYH A;  1ITF A;  4J4L C;  3BPN A;  1BBN A;  2D48 A;  1CNT 1;  2INT A;  1ITL A;  5FLM D;  3OG6 A;  1I1R B;  2B5I A;  4GS7 A;  4X51 A;  1HZI A;  1BUY A;  5LQB A;  4NI7 A;  1FG9 A;  2GMF A;  1LKI A;  4FA8 E;  3DI3 A;  3G6D A;  1PW6 A;  1PVH B;  4NN6 A;  2VUM D;  1M4R A;  1A22 A;  1Y6K L;  4YPG C;  5E4E A;  1GA3 A;  5L6Y C;  1LK3 A;  4YUE C;  3UF5 A;  2L3Y A;  3QAZ A;  5C44 D;  2Z3Q A;  4MHL A;  5KNH I;  5C3E D;  5C4X D;  2R93 D;  2L3O A;  4A93 D;  4DKE A;  1QVN A;  1HUL A;  3NCB A;  4PS4 A;  1VLK A;  5C7X A;  2O6I A;  4WRL B;  1ITI A;  3DGC L;  2OQP A;  2O26 A;  3N0P A;  3IRH A;  1HIJ A;  3H3V E;  1EMR A;  1HGU A;  1EER A;  3NPZ A;  4A3F D;  1Y1W D;  3QB7 A;  4GRW A;  3UF2 A;  4ZF7 A;  1F6F A;  4ZS7 A;  2B63 D;  1RCB A;  5D22 A;  5FHX A;  3PO2 D;  4EXP A;  1ILK A;  3BPL A;  1M4C A;  3PO3 D;  5IYB D;  3MZG A;  4NN7 A;  1ETE A;  3G9V B;  2R7Z D;  1IAR A;  4DKF A;  3EJJ A;  4BY1 D;  4BBS D;  1HWG A;  3I4M D;  4BY7 D;  2XQB A;  1EKU A;  3NCC A;  2HYM B;  3I4N D;  4A3G D;  4A3I D;  1IL6 A;  3HHC A;  1CYL A;  1AX8 A;  5D70 A;  1HWH A;  3N06 A;  3FKI D;  1ITM A;  1YKB A;  2CYK A;  5IYC D;  4NEM A;  4O6K A;  4BXX D;  1Z92 A;  4A3D D;  2B8Z A;  3WCY I;  2B8Y A;  1M49 A;  1EVS A;  3L5W I;  2Q7N B;  1BGD A;  1CN4 C;  1WU3 I;  2H24 A;  2Z3R A;  3D48 P;  3HHR A;  4NEJ A;  3D87 A;  4BBR D;  4A3B D;  1JLI A;  1P9M B;  4YQX A;  1N1F A;  3HOY D;  5IP9 D;  5IYD D;  2ERJ D;  1PY2 A;  1Y6N L;  1V7N V;  2R92 D;  1RHG A;  3TGX B;  3Q1S I;  1GNC A;  3DLQ I;  3SE3 B;  3LB6 B;  3L5X A;  2B91 A;  3HOZ D;  1RFB A;  2LMS A;  3PIW A;  4A3M D;  5D28 B;  1IJZ A;  4LRL A;  2IL6 A;  2Q98 A;  4CNI C;  3HMX B;  1FYH A;  3LB6 A;  1PGR A;  3PIV A;  3QWR B;  5TS9 A;  4DOH A;  1INR A;  2B8X A;  2Q14 A;  2C35 A;  4RS1 A;  4A3J D;  2PSM A;  2O27 A;  5IP7 D;  1WCM D;  3UEZ E;  4A3E D;  3BES L;  3HOX D;  1ALU A;  2ILK A;  4I77 Z;  4NN5 A;  1BGC A;  1Y1V D;  1NBP A;  2D9Q A;  3EW3 A;  5D71 A;  1CD9 A;  1IK0 A;  3VA2 A;  3QT2 C;  1HIK A;  4O9H A;  5FUC A;  4Z5R D;  1V7M V;  4DKC A;  1AXI A;  4DKD A;  1M4A A;  3QB1 A;  1Y6M L;  1EXZ A;  4A3L D;  3INK C;  3BPO A;  1D9C A;  1BP3 A;  1J7V L;  1Y14 A;  1HUW A;  3H0G D;  4NI9 A;  1SCF A;  1RW5 A;  3HOU D;  1BCN A;  1KF9 A;  1IRL A;  3HOV D; 
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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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