3HOWD

Complete rna polymerase ii elongation complex iii with a t-u mismatch and a frayed rna 3'-uridine
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
178
Chain Sequence
b'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 keywords DNA-directed RNA polymerase II subunit RPB1
publication title Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA.
pubmed doi rcsb
molecule tags Transcription,transferase/dna/rna hybrid
total genus 42
structure length 178
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; 3howD02
2R7ZD 2C35A 2JA5D 1Y1WD 3H0GD 2JA6D 5IP7D 3HOWD 4A3ID 4BBSD 3PO3D 2VUMD 4A93D 2R92D 1Y14A 5C44D 4A3GD 4BBRD 4A3DD 4A3CD 4A3KD 5IYDD 4A3ED 4A3MD 2JA7D 3HOXD 4A3LD 5C4XD 3I4MD 3HOZD 4BY1D 5IP9D 2B63D 3PO2D 5IYCD 3HOVD 4A3BD 3I4ND 4BXXD 4A3FD 3HOUD 1WCMD 5FLMD 2R93D 1Y1VD 3HOYD 4BY7D 3FKID 3H3VE 2JA8D 5C3ED 4A3JD 5IYBD 3AYHA
chains in the Genus database with same CATH superfamily
1M4CA 4NI7A 4DKCA 1BP3A 4BBSD 2VUMD 4YDYI 2R92D 1NBPA 4A3GD 2Q98A 4A3DD 1PGRA 4JR9A 3OG4A 3QB7A 1F45B 4A3BD 4MHLA 1HWHA 3TGXB 5GXBA 1HGUA 1EKUA 4ZWCA 1B5LA 2LMSA 5D6KA 1SCFA 1WU3I 4IKVA 4A3KD 1M49A 3HHCA 4EXPA 2Z3RA 4TPJA 3N06A 1M47A 1IK0A 1AU1A 4A3JD 4TPHA 3OG6A 2E9WC 4JA3A 3HOWD 1FYHA 1M4AA 4BBRD 1RFBA 4GC0A 4Q65A 5D72A 3QT2C 5IYCD 4RS1A 1D9CA 4A3FD 4IU8A 1BGCA 3BPNA 1EMRA 3NCFA 2D9QA 1IARA 1ALUA 1Y14A 2JA7D 4DKFA 1PW6A 3INKC 4CNIC 4QIQA 3DUHC 4NKQC 5L6YC 2B8UA 1Z7CA 1KF9A 1M4RA 1P9MB 4GS7A 2Q7NB 2O6IA 4PYPA 3DI2A 5C4XD 3NCCA 4DOHA 3NPZA 3DLQI 3L5WI 4PS4A 1HIKA 3H3VE 4XNIA 3WCYI 2O26A 3B5KA 3D48P 1HUWA 2V8NA 1CSGA 1YKBA 3Q1SI 1A7MA 1M48A 1PVHB 2ERJD 2L3OA 3IRHA 4IKZA 4W6VA 5TS9A 4U4WA 1BUYA 1HULA 3QB1A 4GBZA 2JA5D 4O9HA 4DKEA 1PW4A 1ITMA 4NN7A 5D58A 4A3LD 3I4MD 2GMFA 3HOVD 3BESL 4U4TA 1GNCA 4X51A 3L5XA 2OQPA 4D2DA 2D48A 3LB6A 4NI9A 1ITLA 4A3ID 4WRLB 2ILKA 4J05A 5C44D 3O7QA 1IJZA 3WDOA 5EQGA 3UEZE 1LK3A 3HOUD 4BY7D 1CYLA 4Z5RD 1BGEA 2HYMB 3PIWA 2IL6A 3PIVA 1ITFA 4D2BA 3I4ND 3UF2A 4BXXD 1BGDA 5FLMD 3NCEA 4IKWA 2JA8D 4YBQA 3UF5A 1D9GA 2Q14A 5D70A 2JA6D 2B5IA 1JLIA 3SE3B 1ILKA 3BPLA 4ZS7A 1PV7A 4APSA 4A3MD 4U4VA 3HOXD 1IL6A 4OAAA 1CNT1 1AXIA 3PO2D 2B8ZA 1INRA 1EVSA 1Y6KL 1HWGA 3DGCL 5C3ED 3D85C 4YB9D 3AYHA 2R7ZD 2PSMA 1Y1WD 5C7XA 1ITIA 5IP7D 1LQSL 4LEPA 5EQIA 1EERA 3O7PA 5EQHA 4A3ED 2B91A 3SE4B 4GRWA 2L3YA 2CFQA 4NN5A 1BCNA 2B90A 3HMXB 3QAZA 2B8YA 3H0GD 4IKYA 3LB6B 2XUTA 3EW3A 3UX9A 4JREA 1RCBA 4DKDA 4LRLA 1N1FA 5D22A 1FG9A 2INTA 4OH3A 1CD9A 1WCMD 5D59A 4GBYA 1CN4C 2O27A 2XQBA 4I77Z 3BPOA 3OQ3A 3PO3D 4J4LC 4NN6A 4YPGC 5A2OA 2H24A 4A3CD 1PY2A 5IYDD 1AX8A 3HOZD 5KNHI 4BY1D 3VA2A 4D2CA 1QVNA 1A22A 1HZIA 4ZF7A 4NEMA 3QWRB 4NEJA 3D87A 5A2NA 1HIJA 1BBNA 2KZ1A 1PV6A 5LQBA 4TPGA 1M4BA 4XNJA 5IP9D 4LDSA 3MZGA 3EJJA 3G6DA 1Z92A 2CYKA 4FA8E 1IRLA 1ETEA 1EXZA 5IYBD 4ZWBA 1LKIA 5D71A 4IKXA 4A93D 3N0PA 3HHRA 4YQXA 2B63D 5FHXA 2R93D 5E4EA 1I1RB 2CFPA 4YUEC 3DI3A 2Y5YA 4EXNA 4O6KA 1VLKA 2B8XA 1V7MV 1Y6NL 2C35A 3G9VB 5FUCA 3S9DA 1F6FA 1V7NV 5D28B 1GA3A 4IU9A 2Z3QA 4ZW9A 1RW5A 4ZYRA 1J7VL 4UVMA 1Y1VD 3HOYD 2LAGA 5C65A 3FKID 1Y6ML 1RHGA 3NCBA
chains in the Genus database with same CATH topology
1M4CA 2XQBA 4I77Z 1CYLA 4NI7A 3BPOA 4DKCA 3OQ3A 1BP3A 4BBSD 3PO3D 4J4LC 4NN6A 2VUMD 4YDYI 2R92D 4YPGC 1NBPA 4A3GD 2Q98A 4Z5RD 1BGEA 2H24A 2HYMB 1PGRA 1PY2A 4A3CD 5IYDD 4A3DD 3DI2A 3PIWA 5C4XD 2IL6A 3OG4A 3PIVA 1AX8A 3HOZD 5KNHI 4BY1D 3QB7A 3NCCA 1F45B 3VA2A 1ITFA 4A3BD 4MHLA 1HWHA 3UF2A 3I4ND 4DOHA 4BXXD 1BGDA 3TGXB 3NPZA 1QVNA 5FLMD 1A22A 3DLQI 3NCEA 3L5WI 4PS4A 1HIKA 1HGUA 3H3VE 2JA8D 1EKUA 3WCYI 3UF5A 2O26A 1HZIA 4ZF7A 1D9GA 2Q14A 4NEMA 5D70A 2JA6D 2B5IA 1B5LA 1JLIA 3SE3B 1ILKA 2LMSA 3D87A 3QWRB 4NEJA 3BPLA 1HIJA 3B5KA 4ZS7A 1BBNA 2KZ1A 1SCFA 5LQBA 1WU3I 3D48P 4A3KD 1HUWA 1M49A 3HOXD 4A3MD 1CSGA 3HHCA 1IL6A 1CNT1 1YKBA 1M4BA 5IP9D 1AXIA 3Q1SI 3PO2D 1A7MA 2B8ZA 4EXPA 1M48A 3MZGA 1INRA 1PVHB 1EVSA 2ERJD 2L3OA 2Z3RA 3EJJA 1Y6KL 3G6DA 3IRHA 1Z92A 3N06A 2CYKA 4FA8E 1IRLA 1M47A 1BUYA 5TS9A 1HWGA 1ETEA 1EXZA 3DGCL 1IK0A 5C3ED 1AU1A 4A3JD 3D85C 5IYBD 1HULA 3QB1A 3AYHA 2R7ZD 2PSMA 3OG6A 2E9WC 4O9HA 5C7XA 5IP7D 4DKEA 1Y1WD 2JA5D 3HOWD 1ITIA 1LQSL 1LKIA 5D71A 1ITMA 4A93D 1FYHA 1EERA 1M4AA 4BBRD 1RFBA 3N0PA 4NN7A 4A3ED 4A3LD 3HHRA 4YQXA 2B91A 3I4MD 3SE4B 5D72A 4GRWA 2GMFA 3QT2C 2B63D 5IYCD 4RS1A 2L3YA 3HOVD 1D9CA 5FHXA 3BESL 4NN5A 4A3FD 1BCNA 2B90A 5E4EA 2R93D 1I1RB 4YUEC 3HMXB 3DI3A 1GNCA 4X51A 4EXNA 3L5XA 4O6KA 3QAZA 2OQPA 2B8YA 1BGCA 2D48A 3BPNA 1VLKA 1EMRA 2B8XA 3LB6A 3NCFA 2D9QA 1V7MV 1Y6NL 2C35A 4NI9A 3H0GD 1IARA 3G9VB 5FUCA 3S9DA 1ITLA 4A3ID 3LB6B 4WRLB 1ALUA 2ILKA 1F6FA 1V7NV 1Y14A 5C44D 3EW3A 5D28B 1GA3A 3UX9A 4DKDA 1RCBA 4LRLA 1N1FA 5D22A 2JA7D 1FG9A 4DKFA 1IJZA 1PW6A 3INKC 2INTA 2Z3QA 1RW5A 4CNIC 3UEZE 1LK3A 1J7VL 1CD9A 3HOUD 1WCMD 3DUHC 4NKQC 5L6YC 2B8UA 1Y1VD 3HOYD 1Z7CA 2LAGA 4BY7D 3FKID 1KF9A 1M4RA 1Y6ML 1P9MB 1RHGA 3NCBA 4GS7A 2Q7NB 1CN4C 2O6IA 2O27A
chains in the Genus database with same CATH homology


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