2KKDA

Nmr structure of ni substitued desulfovibrio vulgaris rubredoxin
Total Genus 2
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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
2
sequence length
52
structure length
52
Chain Sequence
MKKYVCTVCGYEYDPAEGDPDNGVKPGTSFDDLPADWVCPVCGAPKSEFEAA
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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 An NMR structural study of nickel-substituted rubredoxin
pubmed doi rcsb
molecule tags Electron transport
source organism Desulfovibrio vulgaris str. hildenborough
molecule keywords Rubredoxin
total genus 2
structure length 52
sequence length 52
ec nomenclature
pdb deposition date 2009-06-18

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF00301 Rubredoxin Rubredoxin
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
2.20.28.10 Mainly Beta Single Sheet Rubrerythrin, domain 2 Rubrerythrin, domain 2 2kkdA00
1S30A 4TPUA 3RZTA 4POGA 1B13A 3PWFA 1YUXA 4AR4A 4YWMA 4AR6A 4POFA 2DSXA 2PVXA 1LTLA 1QYBA 1YV1A 4RXNA 1CAAA 1QCVA 1RWDA 1T9QA 6RXNA 7RXNA 1RB9A 1H7VA 2M4YA 3KYVA 1BFYA 1NNQA 1IU6A 1YUZA 4YWLA 1S2ZA 1T9OA 3MPSA 2V3BB 1BQ8A 1BE7A 2LCQA 5RXNA 3RZ6A 1ZRPA 1LKOA 1B2OA 2KN9A 2HR5A 1SMUA 1IROA 1CADA 1BRFA 1S24A 3KYWA 1IRNA 3QVDA 1R0JA 2MS3A 3KYUA 4ME3A 2GMGA 1JYBA 3RYGA 1FHHA 2RDVA 3PZAA 2K2DA 8RXNA 1R0GA 5IY0A 1E8JA 2KKDA 1VCXA 1IU5A 1FHMA 5AI3A 1YK5A 1B2JA 1SMMA 1DVBA 1R0IA 2PYAA 1SMWA 1R0FA 1DX8A 1YK4A 1B71A 1LKMA 2VL6A 4K9FA 1RYTA 3KYXA 1T9PA 1RDGA 5AI2A 3A44A 1R0HA 1RDVA 2QL0A 1BQ9A 4AR3A 2PVEA 3SS2A 1LKPA 1C09A 4AR5A 3KYYA
chains in the Genus database with same CATH superfamily
2XJQA 5C4JL 4TPUA 2V0FA 2A69D 3PO2L 4A93L 3PIO1 3GTJL 5JVG1 1VZIA 3ZG6A 4POFA 2DSXA 4JADA 5GAGc 3S1ML 1H7VA 3K35A 4LHLA 5IP9L 3CQZL 1PZXA 1R9TL 1P7PA 1I3QL 2V3BB 2ZIXA 3PKIA 4LHNA 5M5XL 1WJVA 3LWVB 2LCQA 3RZ6A 4C2M1 2A68D 1IROA 1IRNA 4ME3A 2NVYL 2Z3RB 2L0ZA 3NFPI 3RYGA 4AHXA 2RDVA 3LNLA 5IY0A 2KKDA 5GADc 1VCXA 5JVH1 1FHMA 1SMMA 2NYDA 3VPBE 2PPTA 1DVBA 3J7Z1 4A3CL 1SMWA 4AHWA 3I4NL 1DX8A 3S1RL 1B71A 3KYXA 3LWRB 1T9PA 1RDGA 4A3LL 1R0HA 1TWCL 2QL0A 5FLML 2PVEA 3HJWB 5DM71 5M3FL 1LKPA 3GTML 1PFWA 4BBRL 5DM61 4AR5A 2NVQL 2NVXL 1I50L 4C3JL 5IYCL 3H0GL 4AR4A 2JA7L 4AR6A 2ERJA 2PVXA 5EIOC 1LTLA 4X6AL 3FDJA 2XJTA 1YV1A 4JAGA 1RWDA 4A3ML 5GAEc 5MF6A 7RXNA 5MLC3 1TWFL 1NXEA 4ZN3B 4YWLA 4BBSL 1S2ZA 1T9OA 2WAQP 3MPSA 5C3EL 1I6HL 1NXGA 4AI3A 3LWOB 5C4XL 3HKZP 3LWQB 1SMUA 3RZDL 3M3YL 3H99A 1R0JA 3HOVL 3S2DL 2C6BA 1JYBA 3FKIL 2RFKB 1VZGA 3K7AL 5M3ML 2K2DA 8RXNA 1TWHL 4A3IL 5K2ME 3J7Y1 5AI3A 3B0AB 2C6AA 3S1QL 3GTKL 1R0FA 2A6ED 1OWBA 1YK4A 3B08B 2VL6A 3H9BA 3A44A 2JA8L 1BQ9A 4AR3A 3MSUA 4A3EL 1VZHA 4C3HL 5AN9H 2JI1A 2VUML 1C09A 2R92L 2NVTL 4JAFA 4A3GL 4AI0A 3RZTA 4A3JL 4G6BA 1B13A 4XXBB 2PMZP 1YUXA 3HJYB 2ERSA 3HOWL 4YWMA 3HAXC 2B5ID 3HOUL 4AYBP 2M6PA 4RXNA 1T9QA 1ODHA 3LWPB 2O5JD 2E2HL 4Y52L 2M4YA 4BY1L 3S1NL 1NNQA 3LPEB 4QIWP 2JI3A 2E2JL 2WB1P 2V0EA 2CKCA 3GTGL 3HOZL 1F4LA 2HVYC 1BE7A 5RXNA 2H12A 1B2OA 4UY81 4Y7NL 5GAHc 4A3FL 3P2AA 3P8BA 3S14L 4WFN1 4A3BL 4B8CD 5M5WL 3S17L 1S24A 1QQTA 3QVDA 5FJ8L 2MS3A 2YU9L 3KYUA 1Y1WL 2GMGA 4C3IL 1OWCA 2B63L 5MFPA 3H9CA 1R0GA 4ZN1B 1E8JA 3S2HL 5M5YL 3H3VM 1B2JA 2BE5D 1PFVA 1R0IA 2PYAA 1IW7D 1TWGL 2J9UB 3WWNB 3PO3L 5AI2A 1WCML 2CR8A 1RDVA 5IYBL 2AUSB 3GTQL 4AI1A 3IU3I 4AHYA 1S30A 2R93L 4POGA 3PWFA 3GTOL 2Y0SP 5IYDL 2XJPA 4BXXL 1QYBA 1CAAA 3MQKB 2AQCA 1QCVA 5MFZA 6RXNA 5MGNA 2AYJA 1RB9A 1TWAL 2JA6L 4V196 3M4OL 2JI2A 3KYVA 4GS7D 2JA5L 1BFYA 1IU6A 4XGHA 1YUZA 3QQCE 4TVMA 4E6YA 3HOYL 5EINC 5IP7L 5H1Sc 1BQ8A 1RYQA 4A3DL 1Z92B 2CKAA 1ZRPA 1LKOA 3S16L 2KN9A 2M4VA 3H97A 1SFOL 2HR5A 2Z3QB 2E2IL 1CADA 1BRFA 2XJSA 2XJVA 3KYWA 3PL5A 3WWLA 3S15L 1Y1VL 1PFUA 4JAEA 3RZOL 1FHHA 4AHZA 3PZAA 2A6HD 4BY7L 3I4ML 3PKJA 4AI2A 1IU5A 4A3KL 2EY4E 1YK5A 2APOB 2PSMC 1PFYA 3HOXL 1K83L 3GTLL 2XJRA 2R7ZL 1LKMA 3JR7A 4K9FA 1RYTA 3GTPL 5C44L 3SS2A 2XJUA 2M6OA 4U671 3PIP1 3KYYA
chains in the Genus database with same CATH topology
3IU3I 4JAFA 4AHYA 2XJQA 4AI0A 1S30A 4TPUA 3RZTA 4POGA 2V0FA 2A69D 4G6BA 1B13A 4XXBB 3PIO1 3PWFA 1YUXA 1VZIA 3ZG6A 5JVG1 2ERSA 4AR4A 4YWMA 4AR6A 2B5ID 2ERJA 4POFA 2DSXA 2XJPA 2PVXA 5EIOC 1LTLA 1QYBA 2M6PA 2XJTA 1YV1A 4RXNA 1CAAA 4JAGA 1QCVA 1RWDA 1T9QA 6RXNA 5MF6A 5MFZA 5GAEc 4JADA 5MGNA 5GAGc 2AYJA 1ODHA 7RXNA 1RB9A 2O5JD 1H7VA 3K35A 2M4YA 5MLC3 4V196 4LHLA 2JI2A 3KYVA 4GS7D 1BFYA 1NXEA 1NNQA 4ZN3B 3LPEB 1IU6A 4XGHA 1YUZA 2JI3A 3QQCE 4TVMA 4YWLA 4E6YA 2V0EA 5EINC 2CKCA 1S2ZA 1T9OA 5H1Sc 3MPSA 2V3BB 2ZIXA 3PKIA 1BQ8A 4LHNA 1RYQA 1BE7A 1WJVA 1Z92B 2LCQA 2CKAA 5RXNA 2H12A 3RZ6A 1NXGA 1ZRPA 1LKOA 4AI3A 1B2OA 2KN9A 2M4VA 4UY81 5GAHc 3P2AA 3P8BA 4WFN1 2HR5A 1SMUA 2A68D 1IROA 2Z3QB 1CADA 4B8CD 1BRFA 2XJSA 2XJVA 1S24A 3KYWA 1IRNA 3QVDA 1R0JA 3WWLA 2MS3A 3KYUA 4ME3A 2Z3RB 2C6BA 2L0ZA 2GMGA 1JYBA 4JAEA 3NFPI 3RYGA 1FHHA 4AHXA 1OWCA 1VZGA 4AHZA 5MFPA 2RDVA 3PZAA 2K2DA 2A6HD 8RXNA 3PKJA 3LNLA 1R0GA 4ZN1B 5IY0A 1E8JA 2KKDA 4AI2A 5GADc 1VCXA 1IU5A 5K2ME 3J7Y1 5JVH1 1FHMA 5AI3A 3B0AB 1YK5A 1B2JA 2BE5D 1SMMA 2PSMC 2NYDA 3VPBE 2PPTA 2C6AA 1DVBA 1R0IA 2PYAA 3J7Z1 1SMWA 4AHWA 1R0FA 1DX8A 2A6ED 2XJRA 1OWBA 1IW7D 1YK4A 1B71A 1LKMA 3B08B 2VL6A 4K9FA 2J9UB 1RYTA 3KYXA 1T9PA 1RDGA 3WWNB 5AI2A 3A44A 2CR8A 1R0HA 1RDVA 2QL0A 1BQ9A 4AR3A 3MSUA 2PVEA 3SS2A 1VZHA 2XJUA 2M6OA 5DM71 5AN9H 1LKPA 2JI1A 5DM61 1C09A 4AI1A 4AR5A 4U671 3PIP1 3KYYA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 1S30 A;  4TPU A;  3RZT A;  4POG A;  1B13 A;  3PWF A;  1YUX A;  4AR4 A;  4YWM A;  4AR6 A;  4POF A;  2DSX A;  2PVX A;  1LTL A;  1QYB A;  1YV1 A;  4RXN A;  1CAA A;  1QCV A;  1RWD A;  1T9Q A;  6RXN A;  7RXN A;  1RB9 A;  1H7V A;  2M4Y A;  3KYV A;  1BFY A;  1NNQ A;  1IU6 A;  1YUZ A;  4YWL A;  1S2Z A;  1T9O A;  3MPS A;  2V3B B;  1BQ8 A;  1BE7 A;  2LCQ A;  5RXN A;  3RZ6 A;  1ZRP A;  1LKO A;  1B2O A;  2KN9 A;  2HR5 A;  1SMU A;  1IRO A;  1CAD A;  1BRF A;  1S24 A;  3KYW A;  1IRN A;  3QVD A;  1R0J A;  2MS3 A;  3KYU A;  4ME3 A;  2GMG A;  1JYB A;  3RYG A;  1FHH A;  2RDV A;  3PZA A;  2K2D A;  8RXN A;  1R0G A;  5IY0 A;  1E8J A;  2KKD A;  1VCX A;  1IU5 A;  1FHM A;  5AI3 A;  1YK5 A;  1B2J A;  1SMM A;  1DVB A;  1R0I A;  2PYA A;  1SMW A;  1R0F A;  1DX8 A;  1YK4 A;  1B71 A;  1LKM A;  2VL6 A;  4K9F A;  1RYT A;  3KYX A;  1T9P A;  1RDG A;  5AI2 A;  3A44 A;  1R0H A;  1RDV A;  2QL0 A;  1BQ9 A;  4AR3 A;  2PVE A;  3SS2 A;  1LKP A;  1C09 A;  4AR5 A;  3KYY A; 
#chains in the Genus database with same CATH topology
 2XJQ A;  5C4J L;  4TPU A;  2V0F A;  2A69 D;  3PO2 L;  4A93 L;  3PIO 1;  3GTJ L;  5JVG 1;  1VZI A;  3ZG6 A;  4POF A;  2DSX A;  4JAD A;  5GAG c;  3S1M L;  1H7V A;  3K35 A;  4LHL A;  5IP9 L;  3CQZ L;  1PZX A;  1R9T L;  1P7P A;  1I3Q L;  2V3B B;  2ZIX A;  3PKI A;  4LHN A;  5M5X L;  1WJV A;  3LWV B;  2LCQ A;  3RZ6 A;  4C2M 1;  2A68 D;  1IRO A;  1IRN A;  4ME3 A;  2NVY L;  2Z3R B;  2L0Z A;  3NFP I;  3RYG A;  4AHX A;  2RDV A;  3LNL A;  5IY0 A;  2KKD A;  5GAD c;  1VCX A;  5JVH 1;  1FHM A;  1SMM A;  2NYD A;  3VPB E;  2PPT A;  1DVB A;  3J7Z 1;  4A3C L;  1SMW A;  4AHW A;  3I4N L;  1DX8 A;  3S1R L;  1B71 A;  3KYX A;  3LWR B;  1T9P A;  1RDG A;  4A3L L;  1R0H A;  1TWC L;  2QL0 A;  5FLM L;  2PVE A;  3HJW B;  5DM7 1;  5M3F L;  1LKP A;  3GTM L;  1PFW A;  4BBR L;  5DM6 1;  4AR5 A;  2NVQ L;  2NVX L;  1I50 L;  4C3J L;  5IYC L;  3H0G L;  4AR4 A;  2JA7 L;  4AR6 A;  2ERJ A;  2PVX A;  5EIO C;  1LTL A;  4X6A L;  3FDJ A;  2XJT A;  1YV1 A;  4JAG A;  1RWD A;  4A3M L;  5GAE c;  5MF6 A;  7RXN A;  5MLC 3;  1TWF L;  1NXE A;  4ZN3 B;  4YWL A;  4BBS L;  1S2Z A;  1T9O A;  2WAQ P;  3MPS A;  5C3E L;  1I6H L;  1NXG A;  4AI3 A;  3LWO B;  5C4X L;  3HKZ P;  3LWQ B;  1SMU A;  3RZD L;  3M3Y L;  3H99 A;  1R0J A;  3HOV L;  3S2D L;  2C6B A;  1JYB A;  3FKI L;  2RFK B;  1VZG A;  3K7A L;  5M3M L;  2K2D A;  8RXN A;  1TWH L;  4A3I L;  5K2M E;  3J7Y 1;  5AI3 A;  3B0A B;  2C6A A;  3S1Q L;  3GTK L;  1R0F A;  2A6E D;  1OWB A;  1YK4 A;  3B08 B;  2VL6 A;  3H9B A;  3A44 A;  2JA8 L;  1BQ9 A;  4AR3 A;  3MSU A;  4A3E L;  1VZH A;  4C3H L;  5AN9 H;  2JI1 A;  2VUM L;  1C09 A;  2R92 L;  2NVT L;  4JAF A;  4A3G L;  4AI0 A;  3RZT A;  4A3J L;  4G6B A;  1B13 A;  4XXB B;  2PMZ P;  1YUX A;  3HJY B;  2ERS A;  3HOW L;  4YWM A;  3HAX C;  2B5I D;  3HOU L;  4AYB P;  2M6P A;  4RXN A;  1T9Q A;  1ODH A;  3LWP B;  2O5J D;  2E2H L;  4Y52 L;  2M4Y A;  4BY1 L;  3S1N L;  1NNQ A;  3LPE B;  4QIW P;  2JI3 A;  2E2J L;  2WB1 P;  2V0E A;  2CKC A;  3GTG L;  3HOZ L;  1F4L A;  2HVY C;  1BE7 A;  5RXN A;  2H12 A;  1B2O A;  4UY8 1;  4Y7N L;  5GAH c;  4A3F L;  3P2A A;  3P8B A;  3S14 L;  4WFN 1;  4A3B L;  4B8C D;  5M5W L;  3S17 L;  1S24 A;  1QQT A;  3QVD A;  5FJ8 L;  2MS3 A;  2YU9 L;  3KYU A;  1Y1W L;  2GMG A;  4C3I L;  1OWC A;  2B63 L;  5MFP A;  3H9C A;  1R0G A;  4ZN1 B;  1E8J A;  3S2H L;  5M5Y L;  3H3V M;  1B2J A;  2BE5 D;  1PFV A;  1R0I A;  2PYA A;  1IW7 D;  1TWG L;  2J9U B;  3WWN B;  3PO3 L;  5AI2 A;  1WCM L;  2CR8 A;  1RDV A;  5IYB L;  2AUS B;  3GTQ L;  4AI1 A;  3IU3 I;  4AHY A;  1S30 A;  2R93 L;  4POG A;  3PWF A;  3GTO L;  2Y0S P;  5IYD L;  2XJP A;  4BXX L;  1QYB A;  1CAA A;  3MQK B;  2AQC A;  1QCV A;  5MFZ A;  6RXN A;  5MGN A;  2AYJ A;  1RB9 A;  1TWA L;  2JA6 L;  4V19 6;  3M4O L;  2JI2 A;  3KYV A;  4GS7 D;  2JA5 L;  1BFY A;  1IU6 A;  4XGH A;  1YUZ A;  3QQC E;  4TVM A;  4E6Y A;  3HOY L;  5EIN C;  5IP7 L;  5H1S c;  1BQ8 A;  1RYQ A;  4A3D L;  1Z92 B;  2CKA A;  1ZRP A;  1LKO A;  3S16 L;  2KN9 A;  2M4V A;  3H97 A;  1SFO L;  2HR5 A;  2Z3Q B;  2E2I L;  1CAD A;  1BRF A;  2XJS A;  2XJV A;  3KYW A;  3PL5 A;  3WWL A;  3S15 L;  1Y1V L;  1PFU A;  4JAE A;  3RZO L;  1FHH A;  4AHZ A;  3PZA A;  2A6H D;  4BY7 L;  3I4M L;  3PKJ A;  4AI2 A;  1IU5 A;  4A3K L;  2EY4 E;  1YK5 A;  2APO B;  2PSM C;  1PFY A;  3HOX L;  1K83 L;  3GTL L;  2XJR A;  2R7Z L;  1LKM A;  3JR7 A;  4K9F A;  1RYT A;  3GTP L;  5C44 L;  3SS2 A;  2XJU A;  2M6O A;  4U67 1;  3PIP 1;  3KYY A; 
#chains in the Genus database with same CATH homology
 3IU3 I;  4JAF A;  4AHY A;  2XJQ A;  4AI0 A;  1S30 A;  4TPU A;  3RZT A;  4POG A;  2V0F A;  2A69 D;  4G6B A;  1B13 A;  4XXB B;  3PIO 1;  3PWF A;  1YUX A;  1VZI A;  3ZG6 A;  5JVG 1;  2ERS A;  4AR4 A;  4YWM A;  4AR6 A;  2B5I D;  2ERJ A;  4POF A;  2DSX A;  2XJP A;  2PVX A;  5EIO C;  1LTL A;  1QYB A;  2M6P A;  2XJT A;  1YV1 A;  4RXN A;  1CAA A;  4JAG A;  1QCV A;  1RWD A;  1T9Q A;  6RXN A;  5MF6 A;  5MFZ A;  5GAE c;  4JAD A;  5MGN A;  5GAG c;  2AYJ A;  1ODH A;  7RXN A;  1RB9 A;  2O5J D;  1H7V A;  3K35 A;  2M4Y A;  5MLC 3;  4V19 6;  4LHL A;  2JI2 A;  3KYV A;  4GS7 D;  1BFY A;  1NXE A;  1NNQ A;  4ZN3 B;  3LPE B;  1IU6 A;  4XGH A;  1YUZ A;  2JI3 A;  3QQC E;  4TVM A;  4YWL A;  4E6Y A;  2V0E A;  5EIN C;  2CKC A;  1S2Z A;  1T9O A;  5H1S c;  3MPS A;  2V3B B;  2ZIX A;  3PKI A;  1BQ8 A;  4LHN A;  1RYQ A;  1BE7 A;  1WJV A;  1Z92 B;  2LCQ A;  2CKA A;  5RXN A;  2H12 A;  3RZ6 A;  1NXG A;  1ZRP A;  1LKO A;  4AI3 A;  1B2O A;  2KN9 A;  2M4V A;  4UY8 1;  5GAH c;  3P2A A;  3P8B A;  4WFN 1;  2HR5 A;  1SMU A;  2A68 D;  1IRO A;  2Z3Q B;  1CAD A;  4B8C D;  1BRF A;  2XJS A;  2XJV A;  1S24 A;  3KYW A;  1IRN A;  3QVD A;  1R0J A;  3WWL A;  2MS3 A;  3KYU A;  4ME3 A;  2Z3R B;  2C6B A;  2L0Z A;  2GMG A;  1JYB A;  4JAE A;  3NFP I;  3RYG A;  1FHH A;  4AHX A;  1OWC A;  1VZG A;  4AHZ A;  5MFP A;  2RDV A;  3PZA A;  2K2D A;  2A6H D;  8RXN A;  3PKJ A;  3LNL A;  1R0G A;  4ZN1 B;  5IY0 A;  1E8J A;  2KKD A;  4AI2 A;  5GAD c;  1VCX A;  1IU5 A;  5K2M E;  3J7Y 1;  5JVH 1;  1FHM A;  5AI3 A;  3B0A B;  1YK5 A;  1B2J A;  2BE5 D;  1SMM A;  2PSM C;  2NYD A;  3VPB E;  2PPT A;  2C6A A;  1DVB A;  1R0I A;  2PYA A;  3J7Z 1;  1SMW A;  4AHW A;  1R0F A;  1DX8 A;  2A6E D;  2XJR A;  1OWB A;  1IW7 D;  1YK4 A;  1B71 A;  1LKM A;  3B08 B;  2VL6 A;  4K9F A;  2J9U B;  1RYT A;  3KYX A;  1T9P A;  1RDG A;  3WWN B;  5AI2 A;  3A44 A;  2CR8 A;  1R0H A;  1RDV A;  2QL0 A;  1BQ9 A;  4AR3 A;  3MSU A;  2PVE A;  3SS2 A;  1VZH A;  2XJU A;  2M6O A;  5DM7 1;  5AN9 H;  1LKP A;  2JI1 A;  5DM6 1;  1C09 A;  4AI1 A;  4AR5 A;  4U67 1;  3PIP 1;  3KYY 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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