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


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