3HOZD

Complete rna polymerase ii elongation complex iv with a t-u mismatch and a frayed rna 3'-guanine
Total Genus 42
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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
42
sequence length
219
structure length
179
Chain Sequence
VSTSTFQTRRRRLKKVEEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIKEALVERRRAFKRSQKKETREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKISDDELERILKELSNLETLY
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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 Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA.
pubmed doi rcsb
molecule keywords DNA-directed RNA polymerase II subunit RPB1
molecule tags Transcription,transferase/dna/rna hybrid
total genus 42
structure length 179
sequence length 219
ec nomenclature
pdb deposition date 2009-06-03

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; 3hozD02
2R7ZD 5IYDD 3H3VE 1Y1WD 2JA7D 3PO3D 2R92D 5IYCD 3I4ND 2R93D 2JA8D 2C35A 4BY1D 2B63D 4A3LD 2VUMD 1Y1VD 3I4MD 2JA5D 3HOWD 4A3CD 1Y14A 4BXXD 4A3KD 3H0GD 2JA6D 4A3GD 4A3FD 4BBSD 5IP7D 3HOVD 5C3ED 3HOZD 3FKID 3AYHA 3HOXD 4A93D 5IYBD 4A3ED 5FLMD 4BBRD 3PO2D 5IP9D 3HOUD 3HOYD 4A3JD 4A3ID 5C4XD 4BY7D 5C44D 4A3MD 4A3BD 4A3DD 1WCMD
chains in the Genus database with same CATH superfamily
3SE4B 3LB6A 2HYMB 5EQIA 5EQGA 4CNIC 1I1RB 2Q14A 2Z3RA 2B8UA 1IARA 1EVSA 1Y1VD 4U4WA 4A3FD 2O26A 1EMRA 5FLMD 1EERA 1ILKA 4RS1A 2IL6A 4A3DD 3IRHA 5E4EA 4XNJA 1BUYA 1A7MA 5IYCD 3MZGA 3BESL 3UF2A 3G6DA 4JA3A 1ITMA 2JA5D 1CN4C 1B5LA 2LAGA 4EXNA 3D85C 5C3ED 1EXZA 4D2DA 4YB9D 2OQPA 1P9MB 3I4ND 4EXPA 1PVHB 3WCYI 4DKFA 3EW3A 4NN5A 1Y14A 3TGXB 3D87A 1V7MV 4O6KA 3HOXD 3LB6B 1IRLA 2LMSA 3UF5A 5C4XD 2L3YA 2E9WC 1A22A 2R92D 1BGDA 1PW6A 1HGUA 2KZ1A 4U4VA 4DKCA 4IKZA 1GA3A 2CFQA 3EJJA 1YKBA 3OG6A 4DKDA 1JLIA 1FYHA 5C44D 4JR9A 3PO3D 4NEJA 3N06A 4O9HA 1CD9A 1HIJA 4JREA 1M48A 2B90A 1V7NV 3HOZD 4A93D 1BCNA 2Y5YA 5IP9D 5A2NA 2PSMA 1PY2A 4A3MD 3S9DA 4GBYA 4ZF7A 4YQXA 1AX8A 1RHGA 4XNIA 4Q65A 2B8ZA 1PV6A 2B5IA 1ITIA 1IL6A 4IKYA 4A3KD 4A3GD 1KF9A 5C65A 1CYLA 3DI2A 2B8YA 1Y6ML 2XQBA 5C7XA 3DI3A 4A3BD 4ZW9A 1PGRA 4PS4A 4Z5RD 1SCFA 2ERJD 2GMFA 5FUCA 4J4LC 3BPNA 3O7PA 3QWRB 4IKXA 4LDSA 3NCCA 2JA6D 1NBPA 5IP7D 1INRA 2INTA 5D71A 1BP3A 3HHRA 4ZWBA 1M47A 3QB7A 4DKEA 1HIKA 2XUTA 2D9QA 3QAZA 5EQHA 4ZS7A 4MHLA 2R93D 3O7QA 4ZYRA 3HMXB 4IKVA 3QT2C 4DOHA 1LKIA 1WU3I 4YBQA 1HWHA 4LEPA 4OH3A 1VLKA 2R7ZD 2JA7D 1D9CA 4UVMA 4FA8E 2B63D 2VUMD 3I4MD 4GBZA 5D6KA 3G9VB 4BBSD 3HOVD 1HULA 3NCFA 1ETEA 5D58A 4APSA 4NI7A 3PO2D 4YPGC 3HOUD 1Y6KL 4W6VA 3D48P 4WRLB 3INKC 5IYDD 1F45B 1HWGA 1EKUA 4TPJA 4GC0A 1M4RA 2C35A 1M4CA 1ALUA 1BGEA 5D72A 4I77Z 3BPLA 1IJZA 3DLQI 4GRWA 1BBNA 1AU1A 1Z7CA 4NN7A 4NKQC 1Z92A 1BGCA 5D59A 2CFPA 1F6FA 1RFBA 1FG9A 3NCBA 4J05A 2H24A 3BPOA 5D22A 3OG4A 4A3ID 4PYPA 4BY7D 1LQSL 3SE3B 2Q7NB 1ITFA 1M4AA 3L5XA 5GXBA 2ILKA 4TPHA 3PIWA 2L3OA 3HHCA 3DGCL 1M49A 1CSGA 2B8XA 3QB1A 4D2CA 1J7VL 4BXXD 1HZIA 5TS9A 3FKID 5A2OA 3L5WI 4A3ED 4GS7A 5D28B 4A3JD 2D48A 2Z3QA 3WDOA 4D2BA 1QVNA 2O6IA 3NPZA 1PV7A 5LQBA 4BY1D 4A3LD 1D9GA 4A3CD 4OAAA 1IK0A 3H0GD 4ZWCA 1AXIA 3Q1SI 1HUWA 3DUHC 4IU8A 4NI9A 1RCBA 3HOYD 2V8NA 4NN6A 4TPGA 1WCMD 1GNCA 2B91A 3H3VE 1RW5A 2JA8D 3HOWD 4YUEC 3VA2A 3N0PA 3UEZE 4QIQA 1PW4A 2CYKA 2Q98A 4NEMA 1LK3A 3OQ3A 1Y1WD 2O27A 4LRLA 5D70A 4IKWA 1ITLA 3B5KA 5KNHI 5FHXA 1CNT1 1N1FA 3NCEA 1M4BA 5L6YC 3UX9A 4YDYI 4U4TA 4X51A 3AYHA 3PIVA 4IU9A 5IYBD 4BBRD 1Y6NL
chains in the Genus database with same CATH topology
3SE4B 2R7ZD 2JA7D 1D9CA 1QVNA 3LB6A 3PO3D 2HYMB 2O6IA 3NPZA 4CNIC 1I1RB 4NEJA 2Q14A 2Z3RA 4FA8E 3N06A 4O9HA 2B8UA 5LQBA 4BY1D 1CD9A 1HIJA 1IARA 2B63D 1EVSA 1Y1VD 1M48A 2VUMD 3I4MD 1D9GA 4A3CD 1IK0A 3H0GD 2B90A 4A3FD 1V7NV 2O26A 1AXIA 3G9VB 4BBSD 1EMRA 3HOVD 3Q1SI 1HULA 3NCFA 3HOZD 1HUWA 4A93D 1ETEA 3DUHC 1BCNA 5FLMD 4NI9A 4NI7A 5IP9D 4YPGC 3HOUD 1RCBA 3HOYD 1EERA 3PO2D 1Y6KL 2PSMA 1ILKA 3D48P 1PY2A 4RS1A 4WRLB 2IL6A 4NN6A 3IRHA 3S9DA 5E4EA 1WCMD 4A3MD 4A3DD 1BUYA 3INKC 5IYDD 4ZF7A 1GNCA 2B91A 4YQXA 3H3VE 1F45B 1AX8A 1A7MA 1HWGA 5IYCD 1EKUA 3MZGA 1RW5A 3BESL 1M4RA 1RHGA 3UF2A 2C35A 3G6DA 1ITMA 2JA8D 2B8ZA 1M4CA 2B5IA 2JA5D 1ALUA 3HOWD 1IL6A 1CN4C 1ITIA 4A3KD 1B5LA 1BGEA 2LAGA 1KF9A 4EXNA 4A3GD 1CYLA 3D85C 3DI2A 2B8YA 5D72A 5C3ED 1Y6ML 4YUEC 3VA2A 4I77Z 1EXZA 3N0PA 3UEZE 3BPLA 1IJZA 2XQBA 3DLQI 5C7XA 3DI3A 4A3BD 2CYKA 4A3LD 2Q98A 4NEMA 1LK3A 1PGRA 4GRWA 3OQ3A 1BBNA 4PS4A 4Z5RD 1AU1A 1Y1WD 1Z7CA 4NN7A 2OQPA 4NKQC 1P9MB 3I4ND 2O27A 1SCFA 1Z92A 2ERJD 2GMFA 5FUCA 4EXPA 1BGCA 4J4LC 1PVHB 3BPNA 3WCYI 3QWRB 4DKFA 3EW3A 4NN5A 1Y14A 3NCCA 4LRLA 3TGXB 2JA6D 3D87A 1NBPA 1F6FA 1RFBA 1INRA 1V7MV 5IP7D 2INTA 1FG9A 5D70A 4O6KA 3NCBA 5D71A 3HOXD 3LB6B 1IRLA 1ITLA 2H24A 1BP3A 2LMSA 3HHRA 3UF5A 3BPOA 5D22A 1M47A 3B5KA 3OG4A 3QB7A 2L3YA 5KNHI 4A3ID 4BY7D 5C4XD 5FHXA 4DKEA 1HIKA 1LQSL 3SE3B 2Q7NB 1ITFA 1CNT1 2D9QA 2E9WC 1A22A 1M4AA 3QAZA 3L5XA 2ILKA 1N1FA 3PIWA 2R92D 2L3OA 4ZS7A 3HHCA 3DGCL 3NCEA 4MHLA 1M49A 2R93D 1BGDA 1M4BA 1PW6A 1CSGA 2B8XA 3QB1A 1J7VL 1HGUA 3HMXB 5L6YC 4BXXD 2KZ1A 3UX9A 1HZIA 3QT2C 5TS9A 4YDYI 4DKCA 4X51A 3FKID 1GA3A 3AYHA 3PIVA 4DOHA 3L5WI 5IYBD 4A3ED 4GS7A 4BBRD 3EJJA 5D28B 1LKIA 1WU3I 1YKBA 2D48A 2Z3QA 3OG6A 4DKDA 1HWHA 4A3JD 1Y6NL 1JLIA 1FYHA 5C44D 1VLKA
chains in the Genus database with same CATH homology


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