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


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