4BBSD

Structure of an initially transcribing rna polymerase ii-tfiib complex
Total Genus 57
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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
57
sequence length
219
structure length
178
Chain Sequence
VSTSTFQTRRRRLKKVEEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIKEALVERRRAFKRSQKKTREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKISDDELERILKELSNLETLY
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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 Transcription
molecule keywords DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1
publication title Structure and Function of the Initially Transcribing RNA Polymerase II-TFIIB Complex
pubmed doi rcsb
source organism Saccharomyces cerevisiae
total genus 57
structure length 178
sequence length 219
ec nomenclature
pdb deposition date 2012-09-27

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; 4bbsD02
2C35A 2R92D 2JA6D 2JA8D 4A3CD 2R93D 2B63D 3PO3D 3HOWD 3I4MD 4A3BD 1Y14A 2R7ZD 1WCMD 5IYBD 5IYCD 3HOVD 4BBSD 5C4XD 3PO2D 2JA5D 4BY1D 4A93D 4BY7D 5IYDD 3HOXD 4A3MD 4A3DD 4BBRD 3I4ND 4BXXD 3FKID 1Y1WD 4A3ED 5C44D 2VUMD 3HOZD 5IP7D 4A3JD 3HOUD 4A3KD 4A3LD 3AYHA 5C3ED 3HOYD 2JA7D 4A3ID 3H0GD 3H3VE 5IP9D 4A3FD 4A3GD 5FLMD 1Y1VD
chains in the Genus database with same CATH superfamily
2Z3RA 2CFQA 4U4VA 4ZF7A 3HOVD 1HIKA 1D9CA 1YKBA 4U4WA 3SE4B 3DGCL 4A3ED 4O6KA 4PS4A 1HIJA 1RW5A 3H3VE 1PGRA 4LDSA 4PYPA 1V7NV 2B63D 3PO3D 1WCMD 2ERJD 4XNIA 2JA5D 1J7VL 4A3DD 3D48P 3S9DA 3EW3A 5A2NA 4A3LD 3G9VB 5EQIA 5FLMD 3HOWD 1PW4A 4GRWA 2Y5YA 4DKDA 4A3MD 1PV7A 2XQBA 1AU1A 2LAGA 4LRLA 3BESL 2O6IA 1AX8A 3BPLA 1JLIA 4I77Z 1ILKA 4IKVA 5IYCD 2D9QA 1IL6A 1ITIA 4EXNA 3Q1SI 5L6YC 1M4CA 4MHLA 1A22A 3UF2A 1Y1WD 4DKCA 4GBZA 3DUHC 1V7MV 3AYHA 2ILKA 3PIWA 1BP3A 4DKFA 2O27A 4A3FD 2Q14A 3WDOA 1BBNA 2R92D 3QB1A 4A3CD 3DI2A 2R93D 4YBQA 1IARA 3N06A 5FHXA 4A3BD 1ITMA 4BY1D 5IYDD 3HOXD 5EQGA 1AXIA 1M4RA 4IKYA 4Q65A 5TS9A 1F45B 1CYLA 4EXPA 1CSGA 1BGEA 2Q98A 3LB6A 5D70A 4DKEA 4DOHA 3O7PA 3NCCA 4BY7D 5LQBA 5E4EA 3NCBA 3QAZA 4YB9D 4JR9A 1PY2A 4IU8A 5C65A 4JA3A 4GC0A 2B91A 4A3GD 1HWGA 1Y1VD 3WCYI 5IYBD 4XNJA 5KNHI 4A93D 4WRLB 2B8YA 3OG4A 4NEJA 1LK3A 1PW6A 1BUYA 4NKQC 1FG9A 2JA7D 1WU3I 4O9HA 1LKIA 2V8NA 4ZW9A 3IRHA 2B8XA 2JA8D 1CN4C 1M47A 5D58A 2Q7NB 1F6FA 4YPGC 3UX9A 1BGDA 1EERA 5D6KA 1EXZA 2IL6A 3BPNA 1PV6A 3PIVA 3HOUD 3G6DA 4X51A 1RCBA 4IKXA 1HUWA 1HGUA 1M4AA 4D2DA 4YQXA 4U4TA 4W6VA 4GBYA 3NCFA 1M4BA 4APSA 1GA3A 3INKC 4IKZA 1I1RB 2E9WC 4QIQA 1B5LA 3HOZD 4J4LC 4FA8E 4NEMA 3H0GD 2XUTA 1ALUA 1Y6ML 4NI7A 1EVSA 2L3OA 3O7QA 3N0PA 2PSMA 4NI9A 4Z5RD 5D72A 1Y6NL 5D59A 4JREA 3VA2A 4CNIC 4ZYRA 2L3YA 5D71A 3MZGA 4BBSD 1M49A 2B8ZA 3L5XA 2VUMD 3UF5A 5IP7D 3QWRB 3D87A 5C3ED 2D48A 3HHRA 5C7XA 5IP9D 1HWHA 4NN5A 1NBPA 1EKUA 4IKWA 3B5KA 1ETEA 2CFPA 3HHCA 4J05A 2OQPA 5A2OA 1RHGA 3DI3A 3HMXB 1HULA 1CNT1 4NN7A 3QT2C 1Y6KL 1ITLA 3D85C 2GMFA 3EJJA 3QB7A 3HOYD 4OAAA 1LQSL 1IJZA 3OG6A 1PVHB 2JA6D 4UVMA 2LMSA 4GS7A 2B8UA 2B90A 1SCFA 3PO2D 1IK0A 1A7MA 1M48A 4NN6A 3SE3B 1Z7CA 2C35A 1EMRA 1P9MB 3I4MD 1KF9A 5D22A 4D2CA 2H24A 5C4XD 4ZWCA 4OH3A 4BXXD 3DLQI 4A3JD 1FYHA 1N1FA 4RS1A 4YDYI 3NPZA 4TPGA 4TPJA 4A3ID 1D9GA 1RFBA 1VLKA 1GNCA 1Y14A 2R7ZD 4ZWBA 2INTA 3LB6B 2Z3QA 1IRLA 3I4ND 5D28B 3OQ3A 3UEZE 5C44D 1BCNA 4A3KD 4IU9A 5FUCA 4D2BA 2KZ1A 4TPHA 4LEPA 5EQHA 2CYKA 5GXBA 4YUEC 1BGCA 3NCEA 2B5IA 3TGXB 1CD9A 1INRA 4BBRD 3FKID 2HYMB 1HZIA 1QVNA 1ITFA 2O26A 3BPOA 1Z92A 4ZS7A 3L5WI
chains in the Genus database with same CATH topology
1BBNA 2Z3RA 3QB1A 2JA6D 2R92D 1M4AA 3DI2A 4A3CD 5FHXA 1IARA 2LMSA 3N06A 4A3BD 2R93D 1ITMA 4YQXA 4ZF7A 4GS7A 2B8UA 3HOVD 2B90A 1SCFA 3PO2D 1IK0A 1HIKA 4BY1D 1A7MA 3NCFA 1D9CA 1M4BA 5IYDD 3HOXD 1M48A 1YKBA 1GA3A 3INKC 3SE4B 3DGCL 1AXIA 1I1RB 2E9WC 4A3ED 1B5LA 3HOZD 4NN6A 4O6KA 3SE3B 1M4RA 4PS4A 1HIJA 1RW5A 1F45B 4J4LC 5TS9A 1CYLA 4FA8E 4EXPA 4NEMA 1CSGA 3H0GD 1BGEA 2Q98A 3H3VE 3LB6A 1ALUA 1PGRA 1Y6ML 1Z7CA 5D70A 4DKEA 2C35A 1EMRA 1P9MB 1V7NV 3I4MD 4DOHA 2B63D 3PO3D 1KF9A 1WCMD 1EVSA 4NI7A 5D22A 2ERJD 2H24A 3NCCA 5C4XD 2L3OA 2JA5D 1J7VL 4BY7D 5LQBA 4A3DD 5E4EA 3D48P 3NCBA 3N0PA 3QAZA 2PSMA 3S9DA 4BXXD 3EW3A 4NI9A 3DLQI 4Z5RD 5D72A 4A3JD 1FYHA 1PY2A 1N1FA 4A3LD 1Y6NL 3G9VB 4RS1A 4YDYI 3NPZA 4A3ID 1D9GA 1RFBA 2B91A 4A3GD 3VA2A 5FLMD 1HWGA 1Y1VD 4CNIC 3HOUD 3WCYI 1VLKA 1GNCA 2L3YA 3HOWD 1Y14A 2R7ZD 5IYBD 4GRWA 5D71A 3MZGA 4BBSD 1M49A 2B8ZA 2INTA 3LB6B 4DKDA 5KNHI 4A93D 2Z3QA 1IRLA 4WRLB 4A3MD 3L5XA 2B8YA 3OG4A 4NEJA 3I4ND 5D28B 2XQBA 3OQ3A 3UF5A 3UEZE 5C44D 2VUMD 1BCNA 1LK3A 1PW6A 5IP7D 1BUYA 3QWRB 1AU1A 4NKQC 3D87A 4A3KD 5C3ED 5FUCA 2KZ1A 1FG9A 2D48A 3HHRA 5C7XA 2JA7D 2CYKA 1WU3I 2LAGA 1HWHA 4O9HA 5IP9D 1LKIA 4LRLA 4NN5A 3IRHA 2B8XA 3BESL 1NBPA 1EKUA 2JA8D 2O6IA 3B5KA 1CN4C 1AX8A 1ETEA 1JLIA 3BPLA 1ILKA 1M47A 4I77Z 4YUEC 5IYCD 1BGCA 2D9QA 3NCEA 2Q7NB 3HHCA 1F6FA 1IL6A 2B5IA 2OQPA 1CD9A 3TGXB 1ITIA 4YPGC 3UX9A 1BGDA 4EXNA 1EERA 1RHGA 3Q1SI 1INRA 5L6YC 4BBRD 3DI3A 1M4CA 1EXZA 4MHLA 1A22A 2IL6A 3HMXB 3FKID 3UF2A 2HYMB 1HULA 1Y1WD 3BPNA 4DKCA 1HZIA 1QVNA 1CNT1 3PIVA 4NN7A 1ITFA 2O26A 3QT2C 1Y6KL 1ITLA 3D85C 2GMFA 3DUHC 3EJJA 3G6DA 1V7MV 3AYHA 3QB7A 2ILKA 3PIWA 4X51A 3HOYD 1BP3A 3BPOA 1Z92A 1RCBA 1LQSL 1IJZA 2O27A 4DKFA 4ZS7A 4A3FD 1HUWA 3OG6A 2Q14A 1HGUA 3L5WI 1PVHB
chains in the Genus database with same CATH homology


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