4S00A

Crystal structure of metallopeptidase-like dimethylsulphoniopropionate (dmsp) lyase rldddp mutant y366a in complex with acrylate
Total Genus 158
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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
158
sequence length
439
structure length
439
Chain Sequence
b'RKIDPSRGATLGDGTPNDNDRIEIGPTQLAFSEWAAAGLQLPNLDRMREYRWKRLTQAIVDRGYGGLLMFDPLNIRYATDSTNMQLWNTHNPFRAVLLCADGYMVIWDYKNSPFLSKFNPLVREQRSGADLFYFDRGDKVDVQADVFANEVRVLMQDHAPGHTRLAVDKIMLHGLRALEAQGFEIMEGEEVTEKTRAIKGPDEILAMRCASHACETAVAEMEKFARAHVGDGKTSEDDIWAVLHAENIKRGGEWIETRLLASGPRTNPWFQECGPRITQKNEIIAFDTDLIGSYGICVDISRTWWIGDQKPRPDMVYAMQHAHEHIMTNMEMLKPGVMIPDLTANCHRLDDKFQAQKAGCLMHGVGLCDEWPLVAYPDKAVPGSYDYPLEPGMVLCVEAAVGEVGGDFSIKLEDQVLITEDGYENLTTYPFDAALMGLA'
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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.

molecule keywords Peptidase M24
publication title Structural and molecular basis for the novel catalytic mechanism and evolution of DddP, an abundant peptidase-like bacterial Dimethylsulfoniopropionate lyase: a new enzyme from an old fold.
pubmed doi rcsb
source organism Silicibacter lacuscaerulensis iti-1157
molecule tags Lyase
total genus 158
structure length 439
sequence length 439
chains with identical sequence B, C, D
ec nomenclature
pdb deposition date 2014-12-27

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF00557 Peptidase_M24 Metallopeptidase family M24
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.40.350.10 Alpha Beta 3-Layer(aba) Sandwich Creatine Amidinohydrolase; Chain A, domain 1 Creatinase/prolidase N-terminal domain 4s00A01
3.90.230.10 Alpha Beta Alpha-Beta Complex Creatine Amidinohydrolase Creatinase/methionine aminopeptidase superfamily 4s00A02
5CDLA 4U6EA 2GA2A 2GG5A 1C27A 3BIQA 2G6PA 1XGOA 2BWYA 1KP0A 3RVAA 3S6BA 2BHCA 3FMRA 4ZWOA 3D27A 2EA2A 2EVCA 4R60A 3BITA 3IU7A 5FCHA 1W7VA 4KM3A 2P9AA 3L7GA 1A16A 1XGNA 2IW2A 5E5BA 3TAVA 2Q92A 5JI6A 4PNCA 1C21A 2ZSGA 1O0XA 1YW7A 2EVOA 5CNXA 2B3KA 1C23A 4FLIA 1XGSA 1QZYA 2P98A 3Q6DA 2BH3A 4S2RP 4IKRA 4IF7A 4U70A 2GG7A 4IKSA 1QXYA 2GU5A 2GG9A 4U6CA 1BN5A 4IPAA 4OOKA 2Q95A 1YW8A 2BHBA 2Q94A 3I7MA 5JHUA 4RGZ1 4FKCA 1QXZA 4FLKA 4FO7A 3IG4A 5CDVA 4ZWPA 3IU8A 3MATA 1BOAA 1WBQA 2B3LA 1Y1NA 1WLRA 2DFIA 1R5HA 4FUKA 2NQ6A 4FLLA 4JUQA 4U69A 2NQ7A 2OKNA 3IU9A 2ADUA 5D6FA 2GGBA 1R5GA 4IDYA 2GU4A 1YJ3A 1WN1A 2GTXA 4EGEA 3MX6A 1WY2A 2BWSA 4HXXA 3OOOA 1PV9A 1C24A 3PKBA 3BIPA 1YVMA 2V3XA 3PKAA 4IECA 2BB7A 1N51A 5E2CA 4U71A 1WKMA 2GG8A 3RORA 3CB5A 4RZYA 2EA4A 2V6CA 4U6ZA 3O5VA 1WL6A 5FCFA 3IL0A 2GG3A 2GGCA 2Q96A 4S2TP 4U76A 5CDEA 1R58A 1C22A 4FLJA 2EVMA 3FM3A 3PEBA 4RZZA 2BWUA 2GZ5A 5CE6A 1XGMA 4U75A 4U6WA 5JFRA 2BWXA 3MR1A 2BHDA 2OAZA 4U6JA 1KQ9A 2HOWA 3TB5A 1W2MA 3OVKA 2Q93A 2MATA 3PKCA 4FO8A 3PKEA 3PKDA 3CB6A 3CTZA 4B28A 4IKUA 4U1BA 3QOCA 1KQ0A 4IU6A 4Z7MA 1XNZA 3L24A 3PN9A 4A6VA 1WL9A 1B6AA 2BWWA 4S00A 4QR8A 2BHAA 5CLSA 4U73A 1QXWA 3FMQA 1MATA 4IKTA 4MATA 1M35A 2V3YA 1JAWA 4A6WA 2Q8KA 1CHMA 5CIKA 4ZWUA 2BWVA 2BWTA 2P99A 4PV4A 4S01A 4ZNGA 2GG2A 5D6EA 1B59A 1YW9A 2V3ZA 2GG0A 2B3HA 2GU7A 2BN7A 2GU6A
chains in the Genus database with same CATH superfamily
5CDLA 4U6EA 2GA2A 2GG5A 1C27A 3BIQA 2G6PA 1XGOA 2BWYA 1KP0A 3RVAA 3S6BA 2BHCA 3FMRA 4ZWOA 3D27A 2EA2A 2EVCA 4R60A 3BITA 3IU7A 5FCHA 1W7VA 4KM3A 2P9AA 3L7GA 1A16A 1XGNA 2IW2A 5E5BA 3TAVA 2Q92A 5JI6A 4PNCA 1C21A 2ZSGA 1O0XA 1YW7A 2EVOA 5CNXA 2B3KA 1C23A 4FLIA 1XGSA 1QZYA 2P98A 3Q6DA 2BH3A 4S2RP 4IKRA 4IF7A 4U70A 2GG7A 4IKSA 1QXYA 2GU5A 2GG9A 4U6CA 1BN5A 4IPAA 4OOKA 2Q95A 1YW8A 2BHBA 2Q94A 3I7MA 5JHUA 4RGZ1 4FKCA 1QXZA 4FLKA 4FO7A 3IG4A 5CDVA 4ZWPA 3IU8A 3MATA 1BOAA 1WBQA 2B3LA 1Y1NA 1WLRA 2DFIA 1R5HA 4FUKA 2NQ6A 4FLLA 4JUQA 4U69A 2NQ7A 2OKNA 3IU9A 2ADUA 5D6FA 2GGBA 1R5GA 4IDYA 2GU4A 1YJ3A 1WN1A 2GTXA 4EGEA 3MX6A 1WY2A 2BWSA 4HXXA 3OOOA 1PV9A 1C24A 3PKBA 3BIPA 1YVMA 2V3XA 3PKAA 4IECA 2BB7A 1N51A 5E2CA 4U71A 1WKMA 2GG8A 3RORA 3CB5A 4RZYA 2EA4A 2V6CA 4U6ZA 3O5VA 1WL6A 5FCFA 3IL0A 2GG3A 2GGCA 2Q96A 4S2TP 4U76A 5CDEA 1R58A 1C22A 4FLJA 2EVMA 3FM3A 3PEBA 4RZZA 2BWUA 2GZ5A 5CE6A 1XGMA 4U75A 4U6WA 5JFRA 2BWXA 3MR1A 2BHDA 2OAZA 4U6JA 1KQ9A 2HOWA 3TB5A 1W2MA 3OVKA 2Q93A 2MATA 3PKCA 4FO8A 3PKEA 3PKDA 3CB6A 3CTZA 4B28A 4IKUA 4U1BA 3QOCA 1KQ0A 4IU6A 4Z7MA 1XNZA 3L24A 3PN9A 4A6VA 1WL9A 1B6AA 2BWWA 4S00A 4QR8A 2BHAA 5CLSA 4U73A 1QXWA 3FMQA 1MATA 4IKTA 4MATA 1M35A 2V3YA 1JAWA 4A6WA 2Q8KA 1CHMA 5CIKA 4ZWUA 2BWVA 2BWTA 2P99A 4PV4A 4S01A 4ZNGA 2GG2A 5D6EA 1B59A 1YW9A 2V3ZA 2GG0A 2B3HA 2GU7A 2BN7A 2GU6A
chains in the Genus database with same CATH topology
5CDLA 4U6EA 2GA2A 2GG5A 1C27A 3BIQA 2G6PA 1XGOA 2BWYA 1KP0A 3RVAA 3S6BA 2BHCA 3FMRA 4ZWOA 3D27A 2EA2A 2EVCA 4R60A 3BITA 3IU7A 5FCHA 1W7VA 4KM3A 2P9AA 3L7GA 1A16A 1XGNA 2IW2A 5E5BA 3TAVA 2Q92A 5JI6A 4PNCA 1C21A 2ZSGA 1O0XA 1YW7A 2EVOA 5CNXA 2B3KA 1C23A 4FLIA 1XGSA 1QZYA 2P98A 3Q6DA 2BH3A 4S2RP 4IKRA 4IF7A 4U70A 2GG7A 4IKSA 1QXYA 2GU5A 2GG9A 4U6CA 1BN5A 4IPAA 4OOKA 2Q95A 1YW8A 2BHBA 2Q94A 3I7MA 5JHUA 4RGZ1 4FKCA 1QXZA 4FLKA 4FO7A 3IG4A 5CDVA 4ZWPA 3IU8A 3MATA 1BOAA 1WBQA 2B3LA 1Y1NA 1WLRA 2DFIA 1R5HA 4FUKA 2NQ6A 4FLLA 4JUQA 4U69A 2NQ7A 2OKNA 3IU9A 2ADUA 5D6FA 2GGBA 1R5GA 4IDYA 2GU4A 1YJ3A 1WN1A 2GTXA 4EGEA 3MX6A 1WY2A 2BWSA 4HXXA 3OOOA 1PV9A 1C24A 3PKBA 3BIPA 1YVMA 2V3XA 3PKAA 4IECA 2BB7A 1N51A 5E2CA 4U71A 1WKMA 2GG8A 3RORA 3CB5A 4RZYA 2EA4A 2V6CA 4U6ZA 3O5VA 1WL6A 5FCFA 3IL0A 2GG3A 2GGCA 2Q96A 4S2TP 4U76A 5CDEA 1R58A 1C22A 4FLJA 2EVMA 3FM3A 3PEBA 4RZZA 2BWUA 2GZ5A 5CE6A 1XGMA 4U75A 4U6WA 5JFRA 2BWXA 3MR1A 2BHDA 2OAZA 4U6JA 1KQ9A 2HOWA 3TB5A 1W2MA 3OVKA 2Q93A 2MATA 3PKCA 4FO8A 3PKEA 3PKDA 3CB6A 3CTZA 4B28A 4IKUA 4U1BA 3QOCA 1KQ0A 4IU6A 4Z7MA 1XNZA 3L24A 3PN9A 4A6VA 1WL9A 1B6AA 2BWWA 4S00A 4QR8A 2BHAA 5CLSA 4U73A 1QXWA 3FMQA 1MATA 4IKTA 4MATA 1M35A 2V3YA 1JAWA 4A6WA 2Q8KA 1CHMA 5CIKA 4ZWUA 2BWVA 2BWTA 2P99A 4PV4A 4S01A 4ZNGA 2GG2A 5D6EA 1B59A 1YW9A 2V3ZA 2GG0A 2B3HA 2GU7A 2BN7A 2GU6A
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 5CDL A;  4U6E A;  2GA2 A;  2GG5 A;  1C27 A;  3BIQ A;  2G6P A;  1XGO A;  2BWY A;  1KP0 A;  3RVA A;  3S6B A;  2BHC A;  3FMR A;  4ZWO A;  3D27 A;  2EA2 A;  2EVC A;  4R60 A;  3BIT A;  3IU7 A;  5FCH A;  1W7V A;  4KM3 A;  2P9A A;  3L7G A;  1A16 A;  1XGN A;  2IW2 A;  5E5B A;  3TAV A;  2Q92 A;  5JI6 A;  4PNC A;  1C21 A;  2ZSG A;  1O0X A;  1YW7 A;  2EVO A;  5CNX A;  2B3K A;  1C23 A;  4FLI A;  1XGS A;  1QZY A;  2P98 A;  3Q6D A;  2BH3 A;  4S2R P;  4IKR A;  4IF7 A;  4U70 A;  2GG7 A;  4IKS A;  1QXY A;  2GU5 A;  2GG9 A;  4U6C A;  1BN5 A;  4IPA A;  4OOK A;  2Q95 A;  1YW8 A;  2BHB A;  2Q94 A;  3I7M A;  5JHU A;  4RGZ 1;  4FKC A;  1QXZ A;  4FLK A;  4FO7 A;  3IG4 A;  5CDV A;  4ZWP A;  3IU8 A;  3MAT A;  1BOA A;  1WBQ A;  2B3L A;  1Y1N A;  1WLR A;  2DFI A;  1R5H A;  4FUK A;  2NQ6 A;  4FLL A;  4JUQ A;  4U69 A;  2NQ7 A;  2OKN A;  3IU9 A;  2ADU A;  5D6F A;  2GGB A;  1R5G A;  4IDY A;  2GU4 A;  1YJ3 A;  1WN1 A;  2GTX A;  4EGE A;  3MX6 A;  1WY2 A;  2BWS A;  4HXX A;  3OOO A;  1PV9 A;  1C24 A;  3PKB A;  3BIP A;  1YVM A;  2V3X A;  3PKA A;  4IEC A;  2BB7 A;  1N51 A;  5E2C A;  4U71 A;  1WKM A;  2GG8 A;  3ROR A;  3CB5 A;  4RZY A;  2EA4 A;  2V6C A;  4U6Z A;  3O5V A;  1WL6 A;  5FCF A;  3IL0 A;  2GG3 A;  2GGC A;  2Q96 A;  4S2T P;  4U76 A;  5CDE A;  1R58 A;  1C22 A;  4FLJ A;  2EVM A;  3FM3 A;  3PEB A;  4RZZ A;  2BWU A;  2GZ5 A;  5CE6 A;  1XGM A;  4U75 A;  4U6W A;  5JFR A;  2BWX A;  3MR1 A;  2BHD A;  2OAZ A;  4U6J A;  1KQ9 A;  2HOW A;  3TB5 A;  1W2M A;  3OVK A;  2Q93 A;  2MAT A;  3PKC A;  4FO8 A;  3PKE A;  3PKD A;  3CB6 A;  3CTZ A;  4B28 A;  4IKU A;  4U1B A;  3QOC A;  1KQ0 A;  4IU6 A;  4Z7M A;  1XNZ A;  3L24 A;  3PN9 A;  4A6V A;  1WL9 A;  1B6A A;  2BWW A;  4S00 A;  4QR8 A;  2BHA A;  5CLS A;  4U73 A;  1QXW A;  3FMQ A;  1MAT A;  4IKT A;  4MAT A;  1M35 A;  2V3Y A;  1JAW A;  4A6W A;  2Q8K A;  1CHM A;  5CIK A;  4ZWU A;  2BWV A;  2BWT A;  2P99 A;  4PV4 A;  4S01 A;  4ZNG A;  2GG2 A;  5D6E A;  1B59 A;  1YW9 A;  2V3Z A;  2GG0 A;  2B3H A;  2GU7 A;  2BN7 A;  2GU6 A; 
#chains in the Genus database with same CATH topology
 5CDL A;  4U6E A;  2GA2 A;  2GG5 A;  1C27 A;  3BIQ A;  2G6P A;  1XGO A;  2BWY A;  1KP0 A;  3RVA A;  3S6B A;  2BHC A;  3FMR A;  4ZWO A;  3D27 A;  2EA2 A;  2EVC A;  4R60 A;  3BIT A;  3IU7 A;  5FCH A;  1W7V A;  4KM3 A;  2P9A A;  3L7G A;  1A16 A;  1XGN A;  2IW2 A;  5E5B A;  3TAV A;  2Q92 A;  5JI6 A;  4PNC A;  1C21 A;  2ZSG A;  1O0X A;  1YW7 A;  2EVO A;  5CNX A;  2B3K A;  1C23 A;  4FLI A;  1XGS A;  1QZY A;  2P98 A;  3Q6D A;  2BH3 A;  4S2R P;  4IKR A;  4IF7 A;  4U70 A;  2GG7 A;  4IKS A;  1QXY A;  2GU5 A;  2GG9 A;  4U6C A;  1BN5 A;  4IPA A;  4OOK A;  2Q95 A;  1YW8 A;  2BHB A;  2Q94 A;  3I7M A;  5JHU A;  4RGZ 1;  4FKC A;  1QXZ A;  4FLK A;  4FO7 A;  3IG4 A;  5CDV A;  4ZWP A;  3IU8 A;  3MAT A;  1BOA A;  1WBQ A;  2B3L A;  1Y1N A;  1WLR A;  2DFI A;  1R5H A;  4FUK A;  2NQ6 A;  4FLL A;  4JUQ A;  4U69 A;  2NQ7 A;  2OKN A;  3IU9 A;  2ADU A;  5D6F A;  2GGB A;  1R5G A;  4IDY A;  2GU4 A;  1YJ3 A;  1WN1 A;  2GTX A;  4EGE A;  3MX6 A;  1WY2 A;  2BWS A;  4HXX A;  3OOO A;  1PV9 A;  1C24 A;  3PKB A;  3BIP A;  1YVM A;  2V3X A;  3PKA A;  4IEC A;  2BB7 A;  1N51 A;  5E2C A;  4U71 A;  1WKM A;  2GG8 A;  3ROR A;  3CB5 A;  4RZY A;  2EA4 A;  2V6C A;  4U6Z A;  3O5V A;  1WL6 A;  5FCF A;  3IL0 A;  2GG3 A;  2GGC A;  2Q96 A;  4S2T P;  4U76 A;  5CDE A;  1R58 A;  1C22 A;  4FLJ A;  2EVM A;  3FM3 A;  3PEB A;  4RZZ A;  2BWU A;  2GZ5 A;  5CE6 A;  1XGM A;  4U75 A;  4U6W A;  5JFR A;  2BWX A;  3MR1 A;  2BHD A;  2OAZ A;  4U6J A;  1KQ9 A;  2HOW A;  3TB5 A;  1W2M A;  3OVK A;  2Q93 A;  2MAT A;  3PKC A;  4FO8 A;  3PKE A;  3PKD A;  3CB6 A;  3CTZ A;  4B28 A;  4IKU A;  4U1B A;  3QOC A;  1KQ0 A;  4IU6 A;  4Z7M A;  1XNZ A;  3L24 A;  3PN9 A;  4A6V A;  1WL9 A;  1B6A A;  2BWW A;  4S00 A;  4QR8 A;  2BHA A;  5CLS A;  4U73 A;  1QXW A;  3FMQ A;  1MAT A;  4IKT A;  4MAT A;  1M35 A;  2V3Y A;  1JAW A;  4A6W A;  2Q8K A;  1CHM A;  5CIK A;  4ZWU A;  2BWV A;  2BWT A;  2P99 A;  4PV4 A;  4S01 A;  4ZNG A;  2GG2 A;  5D6E A;  1B59 A;  1YW9 A;  2V3Z A;  2GG0 A;  2B3H A;  2GU7 A;  2BN7 A;  2GU6 A; 
#chains in the Genus database with same CATH homology
 5CDL A;  4U6E A;  2GA2 A;  2GG5 A;  1C27 A;  3BIQ A;  2G6P A;  1XGO A;  2BWY A;  1KP0 A;  3RVA A;  3S6B A;  2BHC A;  3FMR A;  4ZWO A;  3D27 A;  2EA2 A;  2EVC A;  4R60 A;  3BIT A;  3IU7 A;  5FCH A;  1W7V A;  4KM3 A;  2P9A A;  3L7G A;  1A16 A;  1XGN A;  2IW2 A;  5E5B A;  3TAV A;  2Q92 A;  5JI6 A;  4PNC A;  1C21 A;  2ZSG A;  1O0X A;  1YW7 A;  2EVO A;  5CNX A;  2B3K A;  1C23 A;  4FLI A;  1XGS A;  1QZY A;  2P98 A;  3Q6D A;  2BH3 A;  4S2R P;  4IKR A;  4IF7 A;  4U70 A;  2GG7 A;  4IKS A;  1QXY A;  2GU5 A;  2GG9 A;  4U6C A;  1BN5 A;  4IPA A;  4OOK A;  2Q95 A;  1YW8 A;  2BHB A;  2Q94 A;  3I7M A;  5JHU A;  4RGZ 1;  4FKC A;  1QXZ A;  4FLK A;  4FO7 A;  3IG4 A;  5CDV A;  4ZWP A;  3IU8 A;  3MAT A;  1BOA A;  1WBQ A;  2B3L A;  1Y1N A;  1WLR A;  2DFI A;  1R5H A;  4FUK A;  2NQ6 A;  4FLL A;  4JUQ A;  4U69 A;  2NQ7 A;  2OKN A;  3IU9 A;  2ADU A;  5D6F A;  2GGB A;  1R5G A;  4IDY A;  2GU4 A;  1YJ3 A;  1WN1 A;  2GTX A;  4EGE A;  3MX6 A;  1WY2 A;  2BWS A;  4HXX A;  3OOO A;  1PV9 A;  1C24 A;  3PKB A;  3BIP A;  1YVM A;  2V3X A;  3PKA A;  4IEC A;  2BB7 A;  1N51 A;  5E2C A;  4U71 A;  1WKM A;  2GG8 A;  3ROR A;  3CB5 A;  4RZY A;  2EA4 A;  2V6C A;  4U6Z A;  3O5V A;  1WL6 A;  5FCF A;  3IL0 A;  2GG3 A;  2GGC A;  2Q96 A;  4S2T P;  4U76 A;  5CDE A;  1R58 A;  1C22 A;  4FLJ A;  2EVM A;  3FM3 A;  3PEB A;  4RZZ A;  2BWU A;  2GZ5 A;  5CE6 A;  1XGM A;  4U75 A;  4U6W A;  5JFR A;  2BWX A;  3MR1 A;  2BHD A;  2OAZ A;  4U6J A;  1KQ9 A;  2HOW A;  3TB5 A;  1W2M A;  3OVK A;  2Q93 A;  2MAT A;  3PKC A;  4FO8 A;  3PKE A;  3PKD A;  3CB6 A;  3CTZ A;  4B28 A;  4IKU A;  4U1B A;  3QOC A;  1KQ0 A;  4IU6 A;  4Z7M A;  1XNZ A;  3L24 A;  3PN9 A;  4A6V A;  1WL9 A;  1B6A A;  2BWW A;  4S00 A;  4QR8 A;  2BHA A;  5CLS A;  4U73 A;  1QXW A;  3FMQ A;  1MAT A;  4IKT A;  4MAT A;  1M35 A;  2V3Y A;  1JAW A;  4A6W A;  2Q8K A;  1CHM A;  5CIK A;  4ZWU A;  2BWV A;  2BWT A;  2P99 A;  4PV4 A;  4S01 A;  4ZNG A;  2GG2 A;  5D6E A;  1B59 A;  1YW9 A;  2V3Z A;  2GG0 A;  2B3H A;  2GU7 A;  2BN7 A;  2GU6 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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