2JA6D

Cpd lesion containing rna polymerase ii elongation complex b
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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publication title CPD damage recognition by transcribing RNA polymerase II.
pubmed doi rcsb
molecule keywords DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT
molecule tags Transferase
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; 2ja6D02
3PO3D 5C44D 2VUMD 2JA8D 5C3ED 4A3MD 3PO2D 1Y1VD 2R7ZD 5C4XD 1WCMD 3HOXD 4A3JD 2R92D 3H3VE 5IP7D 4A3FD 3AYHA 3HOYD 1Y14A 5FLMD 4A3GD 2JA6D 3HOUD 4A3LD 4BY7D 4BBRD 5IP9D 2JA5D 2JA7D 2C35A 3H0GD 2B63D 4A3ID 4BY1D 3HOVD 5IYBD 3I4ND 4A3CD 4A93D 3FKID 1Y1WD 4A3DD 4A3KD 4BBSD 4BXXD 3I4MD 4A3ED 4A3BD 5IYDD 3HOZD 5IYCD 2R93D 3HOWD
chains in the Genus database with same CATH superfamily
4UVMA 2L3YA 1VLKA 4YB9D 4EXPA 1PW6A 3UX9A 3HOXD 1RCBA 4A3JD 4IKWA 4YUEC 4Z5RD 4ZW9A 3BPLA 4JR9A 1GNCA 5KNHI 4BY1D 5IYBD 4D2CA 3FKID 4MHLA 5IYDD 3S9DA 1INRA 3WCYI 3SE3B 1WCMD 5A2NA 1EVSA 3BPOA 3HOYD 1Y14A 1N1FA 2INTA 1QVNA 2JA5D 1V7MV 3PIVA 4A3DD 3DGCL 1RHGA 4JA3A 4LRLA 1EKUA 3PO3D 2B5IA 3DI2A 1F6FA 1Y1VD 1HIJA 4I77Z 2B8ZA 4IU9A 3L5WI 4GBZA 2C35A 1Y6KL 3QB1A 2O6IA 4A3BD 1M4CA 1PV6A 5D72A 4APSA 1D9GA 4EXNA 1M4BA 1M4RA 5IP7D 1PVHB 4A3FD 1EMRA 4GBYA 4D2BA 2D9QA 5IP9D 1AXIA 4U4WA 4GC0A 5D71A 3LB6B 2XQBA 1Z7CA 1SCFA 3L5XA 3BESL 4TPGA 5D70A 3WDOA 4NI9A 2VUMD 4O6KA 1BGDA 2Q7NB 5C4XD 1M49A 1EERA 3UF5A 4A3GD 2PSMA 4W6VA 3SE4B 3UF2A 3DI3A 4FA8E 1ETEA 2ERJD 4XNIA 4YPGC 4A3MD 4NEJA 5D6KA 3NPZA 4Q65A 3D87A 5D59A 2KZ1A 4LDSA 1F45B 1IRLA 2E9WC 3N06A 4A3LD 4DKEA 4ZYRA 2ILKA 2Q98A 2CFPA 4IU8A 2Q14A 1HWHA 3OQ3A 5C65A 3UEZE 5IYCD 5D28B 4IKVA 4DOHA 3HOWD 3QAZA 1CNT1 1IARA 2XUTA 3QWRB 5C3ED 1IJZA 3EJJA 2R92D 3G6DA 4JREA 3NCEA 3VA2A 5TS9A 1IK0A 1CSGA 2CFQA 4A3CD 3B5KA 4IKXA 1LKIA 3I4MD 3QT2C 4DKCA 3EW3A 2B91A 2H24A 1ITIA 1KF9A 4J05A 3OG4A 1PGRA 1HGUA 5A2OA 4D2DA 3AYHA 1BUYA 5D58A 4BBRD 1ITFA 1PY2A 4A93D 1EXZA 3NCFA 2OQPA 4OH3A 1ITMA 3PO2D 1HIKA 1BGEA 5EQHA 1AX8A 3DUHC 3NCCA 3OG6A 1PW4A 2LMSA 4DKDA 4YQXA 2B8UA 2B8XA 3MZGA 4ZF7A 2D48A 1HULA 1A22A 5EQIA 3D85C 3HHRA 3IRHA 4YBQA 2Z3QA 1Y6NL 2JA6D 4YDYI 1RFBA 4A3ID 3HOVD 1Y1WD 2CYKA 2IL6A 4BBSD 4GS7A 4GRWA 1B5LA 4NN7A 1CD9A 5E4EA 1GA3A 4BY7D 1ILKA 4QIQA 4A3KD 1FG9A 1M47A 1JLIA 4NN6A 1BGCA 1LQSL 2JA8D 1BCNA 1FYHA 2V8NA 3O7QA 5GXBA 4ZS7A 4LEPA 1M48A 2O26A 4U4TA 2B90A 4ZWBA 3NCBA 3DLQI 1BP3A 3N0PA 4NEMA 2HYMB 2Z3RA 3LB6A 1V7NV 5C44D 1HZIA 3HMXB 5FUCA 4PYPA 4ZWCA 1BBNA 2O27A 1M4AA 3D48P 2Y5YA 4U4VA 4DKFA 2B8YA 5C7XA 3Q1SI 5LQBA 4XNJA 1PV7A 3PIWA 1P9MB 2R7ZD 4TPJA 1CN4C 1NBPA 5FHXA 3INKC 1I1RB 4TPHA 5EQGA 4NN5A 4IKZA 1RW5A 1A7MA 4BXXD 1CYLA 1HWGA 2GMFA 1J7VL 4O9HA 1D9CA 4J4LC 3QB7A 4OAAA 5D22A 1LK3A 1YKBA 5L6YC 3HHCA 1Z92A 4CNIC 4X51A 5FLMD 3HOUD 1HUWA 1Y6ML 2JA7D 2B63D 3H0GD 3I4ND 4IKYA 1ALUA 2L3OA 3HOZD 2LAGA 4RS1A 2R93D 4PS4A 3TGXB 4WRLB 3H3VE 3BPNA 1WU3I 4NI7A 4NKQC 1AU1A 4A3ED 1ITLA 1IL6A 3O7PA 3G9VB
chains in the Genus database with same CATH topology
1SCFA 3L5XA 2L3YA 1VLKA 2OQPA 3BESL 1HZIA 5D70A 5C44D 4NI9A 4EXPA 2VUMD 1ITMA 4O6KA 1PW6A 1HIKA 3PO2D 1BGEA 1BGDA 2Q7NB 5C4XD 3UX9A 1M49A 3HOXD 1RCBA 3HMXB 5FUCA 4A3JD 1AX8A 4YUEC 1EERA 3DUHC 3UF5A 4Z5RD 3NCCA 1BBNA 2O27A 4A3GD 1M4AA 3D48P 3BPLA 3OG6A 2PSMA 3SE4B 3UF2A 1GNCA 2LMSA 4DKFA 5KNHI 5IYBD 4BY1D 3FKID 2B8YA 4DKDA 4MHLA 4YQXA 2B8UA 3DI3A 2B8XA 5IYDD 3MZGA 4FA8E 4ZF7A 3Q1SI 5C7XA 5LQBA 1ETEA 2D48A 1HULA 3PIWA 3S9DA 1A22A 2ERJD 1INRA 3D85C 3HHRA 1P9MB 3IRHA 4YPGC 3SE3B 3WCYI 4A3MD 4NEJA 3NPZA 2R7ZD 1WCMD 1CN4C 1NBPA 3D87A 2Z3QA 1EVSA 3BPOA 5FHXA 1Y6NL 3INKC 2KZ1A 3HOYD 1F45B 1Y14A 1I1RB 1IRLA 1N1FA 2E9WC 2INTA 3N06A 4DKEA 2JA6D 1QVNA 4A3LD 2ILKA 4NN5A 4YDYI 2JA5D 2Q98A 1RW5A 1V7MV 1RFBA 4A3ID 3HOVD 3PIVA 1A7MA 1Y1WD 4A3DD 2CYKA 1HWHA 2IL6A 2Q14A 3OQ3A 4BBSD 4BXXD 3DGCL 4GS7A 3UEZE 1RHGA 1HWGA 1CYLA 2GMFA 5IYCD 1J7VL 5D28B 4DOHA 4O9HA 3HOWD 1D9CA 1CNT1 3QAZA 4J4LC 4LRLA 3QB7A 1EKUA 1IARA 3PO3D 3QWRB 4GRWA 5D22A 5C3ED 2B5IA 3DI2A 1F6FA 1B5LA 1Y1VD 1LK3A 1YKBA 1HIJA 4I77Z 1IJZA 4NN7A 1CD9A 3EJJA 2R92D 5L6YC 5E4EA 3HHCA 3G6DA 2B8ZA 1Z92A 4CNIC 4X51A 5FLMD 3HOUD 1GA3A 4BY7D 1HUWA 1Y6ML 3L5WI 3NCEA 1ILKA 3VA2A 2JA7D 2C35A 1Y6KL 3H0GD 5TS9A 3I4ND 2B63D 1ALUA 1CSGA 3NCFA 4A3CD 1IK0A 3B5KA 3QB1A 1LKIA 2O6IA 4A3KD 1FG9A 1M47A 2L3OA 3QT2C 3I4MD 4A3BD 1M4CA 4DKCA 3HOZD 2LAGA 4RS1A 1JLIA 5D72A 4NN6A 3EW3A 2R93D 1BGCA 2B91A 1LQSL 1D9GA 2H24A 4EXNA 1ITIA 1M4BA 2JA8D 1KF9A 1BCNA 1FYHA 4PS4A 3TGXB 3OG4A 4ZS7A 4WRLB 1M48A 1M4RA 1PGRA 3H3VE 1HGUA 3AYHA 1PVHB 3BPNA 5IP7D 1EMRA 4A3FD 1BUYA 2O26A 2D9QA 2B90A 3NCBA 3DLQI 4BBRD 5IP9D 1AXIA 1BP3A 1ITFA 1PY2A 3N0PA 1WU3I 4NI7A 4A93D 5D71A 4NEMA 2HYMB 3LB6B 2XQBA 4NKQC 1EXZA 1Z7CA 2Z3RA 3LB6A 1AU1A 1V7NV 4A3ED 1ITLA 1IL6A 3G9VB
chains in the Genus database with same CATH homology


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