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


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