5C44D

Crystal structure of a transcribing rna polymerase ii complex reveals a complete transcription bubble
Total Genus 39
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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
39
sequence length
218
structure length
178
Chain Sequence
STSTFQTRRRRLKKVEEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIKEALVERRRAFKRSQKKETREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKISDDELERILKELSNLETLY
Loading diagram...

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/dna/rna
molecule keywords DNA-directed RNA polymerase II subunit RPB1
publication title Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble.
pubmed doi rcsb
source organism Saccharomyces cerevisiae (strain atcc 204508 / s288c)
total genus 39
structure length 178
sequence length 218
ec nomenclature
pdb deposition date 2015-06-17

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; 5c44D02
5C44D 3I4ND 3HOXD 4BBSD 2JA5D 3PO3D 2JA7D 4A3LD 4A3GD 2JA6D 3HOVD 4BBRD 4A3CD 2R92D 2VUMD 5IYBD 4A3BD 3HOZD 4A93D 3HOUD 1Y1VD 5FLMD 1Y14A 1WCMD 5IYDD 5C3ED 3H3VE 3H0GD 4A3MD 4A3JD 3HOYD 5IP7D 4A3KD 4BY1D 4A3DD 4BY7D 5C4XD 3AYHA 2B63D 3HOWD 3I4MD 4A3FD 5IP9D 3PO2D 4A3ED 1Y1WD 2JA8D 2R7ZD 4BXXD 3FKID 4A3ID 2R93D 5IYCD 2C35A
chains in the Genus database with same CATH superfamily
4NN7A 1CD9A 4W6VA 4GC0A 1Z7CA 3O7PA 1ITFA 1CYLA 4J4LC 4YUEC 4NI7A 3LB6A 1M4BA 4IKZA 3QWRB 2C35A 4TPHA 1EERA 5D71A 5C44D 4BBSD 1F45B 3QB1A 3HHRA 3SE4B 2ERJD 3L5WI 2CFPA 2Z3QA 1BCNA 1ETEA 2CYKA 2B8UA 5D28B 5D22A 1D9CA 5D72A 3VA2A 3FKID 3NCCA 1BP3A 4WRLB 4XNJA 1BGEA 4JA3A 2Y5YA 4DKCA 5EQHA 1HZIA 2PSMA 3QAZA 1Y14A 2D9QA 4U4VA 1J7VL 1LQSL 2R7ZD 3BESL 2JA5D 1VLKA 4EXNA 1V7NV 5D6KA 4A93D 1Y6ML 5IP7D 1GNCA 2Q98A 1PVHB 1F6FA 4NN6A 3OQ3A 2LAGA 3WDOA 1M48A 1HGUA 2O6IA 1HIKA 1HULA 1AU1A 1P9MB 1EXZA 3DGCL 4YDYI 4J05A 4DKDA 5FLMD 1EKUA 3O7QA 4A3DD 4JR9A 2Q7NB 4TPGA 3Q1SI 4NEJA 4A3ED 1HUWA 3D85C 2JA8D 1AXIA 3D87A 4Z5RD 3L5XA 1IJZA 3HHCA 2LMSA 1IRLA 2IL6A 5D70A 2KZ1A 1CNT1 3EJJA 5FHXA 5C4XD 2B8ZA 4A3FD 4PYPA 4DKFA 3I4ND 4IKXA 2R92D 4Q65A 4NI9A 1M4RA 1Y1VD 3H0GD 3PIWA 4OAAA 4UVMA 3OG6A 3HOWD 3I4MD 1JLIA 1PW6A 1V7MV 5IYCD 3MZGA 3D48P 4I77Z 5LQBA 4A3CD 2B91A 4YBQA 1M47A 2HYMB 1PV6A 5C3ED 2E9WC 4A3MD 4A3KD 3NCEA 1AX8A 4ZWBA 4APSA 5IP9D 1EVSA 1N1FA 2V8NA 1A22A 2B5IA 1RFBA 3S9DA 3HOXD 4A3LD 1Z92A 1GA3A 1HIJA 1IARA 1IK0A 1ITLA 4IKYA 2B8YA 3NCFA 4QIQA 4LEPA 3HOYD 4GBYA 3G9VB 4LDSA 4X51A 4A3ID 2B90A 1PGRA 3HMXB 3PIVA 2JA7D 5KNHI 4IU8A 2Q14A 4D2BA 4CNIC 3DUHC 1BGCA 1LK3A 2H24A 1ILKA 1PY2A 2GMFA 4BY7D 2L3YA 3BPOA 3LB6B 1D9GA 5FUCA 2Z3RA 1RHGA 3HOVD 1ITMA 1WU3I 4NN5A 4PS4A 5EQIA 3N06A 2O26A 3G6DA 1KF9A 1HWHA 4DOHA 3QB7A 4DKEA 1I1RB 5A2NA 1QVNA 2D48A 4XNIA 4GS7A 1PV7A 4U4WA 1M49A 1Y6KL 4ZWCA 3PO3D 5D58A 4MHLA 4NKQC 2XQBA 1A7MA 3HOZD 5IYDD 3DI2A 3DLQI 1CSGA 4JREA 3DI3A 1FYHA 1Y6NL 3B5KA 5E4EA 4YPGC 4IU9A 4A3GD 4YB9D 1RCBA 5TS9A 5GXBA 4U4TA 4FA8E 1IL6A 2XUTA 1INRA 5C65A 4A3JD 3EW3A 4LRLA 2B63D 4ZW9A 3NPZA 1Y1WD 5L6YC 1SCFA 2R93D 3TGXB 4IKVA 1HWGA 3UX9A 4GBZA 4BBRD 1BUYA 2CFQA 2ILKA 5IYBD 1ITIA 1WCMD 1PW4A 1NBPA 2OQPA 1YKBA 2INTA 4D2CA 4ZS7A 3N0PA 1ALUA 1FG9A 4OH3A 3UF2A 4ZF7A 1EMRA 1RW5A 2O27A 2VUMD 5EQGA 5D59A 4EXPA 3WCYI 4ZYRA 1BGDA 4RS1A 2B8XA 3H3VE 1LKIA 1M4AA 4BY1D 4D2DA 4GRWA 1B5LA 3NCBA 4BXXD 5A2OA 3IRHA 4IKWA 3QT2C 2JA6D 4TPJA 3UEZE 4O9HA 4A3BD 2L3OA 4YQXA 3HOUD 1CN4C 3OG4A 4O6KA 1M4CA 3INKC 3BPLA 1BBNA 3AYHA 3SE3B 3PO2D 4NEMA 3UF5A 5C7XA 3BPNA
chains in the Genus database with same CATH topology
1RFBA 1HIKA 1HULA 4NN7A 5E4EA 4YPGC 3S9DA 1AU1A 3HOXD 1CD9A 1P9MB 4A3LD 1EXZA 1Z92A 3DGCL 4A3GD 1GA3A 1RCBA 5TS9A 1HIJA 1IARA 4FA8E 1IK0A 1ITLA 4YDYI 1Z7CA 1IL6A 1ITFA 1INRA 4DKDA 5FLMD 1EKUA 2B8YA 3NCFA 4A3JD 3HOYD 1CYLA 4J4LC 4YUEC 4NI7A 3G9VB 1M4BA 3LB6A 3EW3A 4LRLA 4A3DD 2B63D 2Q7NB 3NPZA 3Q1SI 4X51A 3QWRB 4NEJA 4A3ED 1HUWA 3D85C 5L6YC 1Y1WD 1SCFA 2JA8D 4A3ID 2R93D 2B90A 1AXIA 3D87A 1PGRA 2C35A 4Z5RD 1EERA 3L5XA 5D71A 1IJZA 3HMXB 1HWGA 3TGXB 5C44D 3HHCA 3PIVA 4BBSD 3UX9A 1F45B 2LMSA 2JA7D 3QB1A 3HHRA 5KNHI 3SE4B 2Q14A 4BBRD 2ERJD 1BUYA 3L5WI 1IRLA 2ILKA 5IYBD 2Z3QA 1ITIA 4CNIC 1WCMD 2IL6A 3DUHC 1BCNA 5D70A 1BGCA 2KZ1A 1NBPA 1ETEA 1LK3A 2H24A 2OQPA 1YKBA 2CYKA 2B8UA 1ILKA 2INTA 4ZS7A 1CNT1 3EJJA 1PY2A 3N0PA 5D28B 2GMFA 5D22A 5FHXA 1D9CA 4BY7D 5C4XD 2B8ZA 2L3YA 5D72A 3VA2A 1ALUA 4A3FD 3BPOA 3LB6B 1D9GA 1FG9A 1M48A 3FKID 4DKFA 3NCCA 1BP3A 4WRLB 3UF2A 1EMRA 4ZF7A 1A22A 1BGEA 5FUCA 2Z3RA 3I4ND 1RHGA 1RW5A 3HOVD 1ITMA 4DKCA 1WU3I 2O27A 2R92D 4NN5A 2VUMD 4PS4A 1HZIA 4NI9A 4EXPA 1M4RA 1Y1VD 2PSMA 3QAZA 3WCYI 1Y14A 1BGDA 3BPNA 3N06A 4RS1A 2B8XA 3H3VE 1LKIA 2D9QA 3H0GD 2O26A 3G6DA 1KF9A 3PIWA 1M4AA 3OG6A 4BY1D 1HWHA 4DOHA 4GRWA 3QB7A 1J7VL 3HOWD 1B5LA 3I4MD 1LQSL 4DKEA 3NCBA 2R7ZD 4BXXD 1I1RB 1JLIA 1PW6A 1V7MV 1QVNA 3BESL 5IYCD 3MZGA 2D48A 4GS7A 3D48P 3IRHA 2JA5D 1M49A 1Y6KL 3QT2C 4I77Z 3PO3D 2JA6D 1VLKA 5LQBA 4EXNA 4MHLA 4A3CD 3UEZE 4O9HA 2B91A 1V7NV 4NKQC 2XQBA 1A7MA 4A3BD 3HOZD 1M47A 2L3OA 4YQXA 3HOUD 4A93D 1CN4C 3OG4A 5IYDD 4O6KA 1M4CA 1Y6ML 2HYMB 3INKC 2E9WC 3BPLA 5C3ED 3DI2A 3DLQI 1CSGA 4A3MD 5IP7D 4A3KD 1GNCA 3NCEA 1BBNA 1AX8A 2Q98A 1PVHB 3DI3A 1F6FA 3AYHA 1FYHA 4NN6A 3OQ3A 3SE3B 3PO2D 5IP9D 4NEMA 1EVSA 3UF5A 1Y6NL 1N1FA 2LAGA 3B5KA 5C7XA 1HGUA 2B5IA 2O6IA
chains in the Genus database with same CATH homology


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