4S01A

Crystal structure of metallopeptidase-like dimethylsulphoniopropionate (dmsp) lyase rldddp mutant d377n 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'RKIDPSRGATLGDGTPNDNDRIEIGPTQLAFSEWAAAGLQLPNLDRMREYRWKRLTQAIVDRGYGGLLMFDPLNIRYATDSTNMQLWNTHNPFRAVLLCADGYMVIWDYKNSPFLSKFNPLVREQRSGADLFYFDRGDKVDVQADVFANEVRVLMQDHAPGHTRLAVDKIMLHGLRALEAQGFEIMEGEEVTEKTRAIKGPDEILAMRCASHACETAVAEMEKFARAHVGDGKTSEDDIWAVLHAENIKRGGEWIETRLLASGPRTNPWFQECGPRITQKNEIIAFDTDLIGSYGICVDISRTWWIGDQKPRPDMVYAMQHAHEHIMTNMEMLKPGVMIPDLTANCHRLDDKFQAQKYGCLMHGVGLCNEWPLVAYPDKAVPGSYDYPLEPGMVLCVEAAVGEVGGDFSIKLEDQVLITEDGYENLTTYPFDAALMGLA'
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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 4s01A01
3.90.230.10 Alpha Beta Alpha-Beta Complex Creatine Amidinohydrolase Creatinase/methionine aminopeptidase superfamily 4s01A02
4PNCA 1WN1A 4Z7MA 3MR1A 2GGBA 1A16A 2V6CA 3MX6A 4FO7A 3PN9A 2ZSGA 2P9AA 2NQ7A 2GA2A 4FKCA 1YJ3A 3PKBA 2Q8KA 2NQ6A 4B28A 1BOAA 3D27A 2GGCA 3PKCA 1M35A 2V3XA 2Q93A 3CB5A 2EVCA 1WKMA 4IKTA 2GG7A 2GU4A 4S2TP 3PKEA 4IKSA 4U75A 4FLKA 1KQ0A 4QR8A 4IPAA 1QXWA 4IDYA 3O5VA 2BHAA 3Q6DA 2BN7A 1QXZA 2B3LA 2OKNA 2GU6A 1WY2A 4U76A 2ADUA 3RORA 5D6FA 4IU6A 2B3KA 1KP0A 4U1BA 5FCHA 5JFRA 1WL6A 4A6VA 1WL9A 1XNZA 2GG2A 4U71A 4MATA 1YW8A 4R60A 4IKUA 3BIPA 2BWSA 2DFIA 1KQ9A 5CNXA 1R5HA 5CIKA 2V3ZA 1CHMA 1QXYA 4KM3A 2GG5A 4IF7A 4OOKA 1C24A 3IG4A 4RZZA 3OVKA 3QOCA 3L24A 4FLJA 2BH3A 2IW2A 4S00A 5E2CA 2EVOA 1BN5A 5CDVA 3IL0A 2GTXA 4U6ZA 4FO8A 2HOWA 2BWYA 2P99A 4FLIA 4PV4A 3TB5A 5JHUA 5FCFA 5JI6A 3IU7A 2GZ5A 3I7MA 3S6BA 2BWVA 2V3YA 2MATA 1JAWA 2Q92A 4EGEA 3MATA 1YW7A 3BIQA 2BHBA 1PV9A 3OOOA 3FMRA 4RGZ1 4U6JA 4S2RP 3BITA 5CDEA 1O0XA 1B59A 5CLSA 2BWTA 2GG0A 1W2MA 3IU9A 1QZYA 2OAZA 2BHCA 4S01A 1XGMA 1W7VA 4U6EA 4U73A 5CE6A 2BHDA 1YVMA 2Q94A 5CDLA 2Q95A 1XGNA 1Y1NA 2G6PA 2BWUA 2GG8A 4FUKA 3L7GA 3CTZA 2P98A 4A6WA 5E5BA 4ZWOA 1WLRA 4ZWPA 1B6AA 2GG3A 2BWXA 3IU8A 1XGOA 2Q96A 4ZWUA 3RVAA 1C22A 2B3HA 3PEBA 2GU7A 4FLLA 3TAVA 2GG9A 1YW9A 3FM3A 4JUQA 4U6CA 4U70A 2BWWA 4IECA 1N51A 4RZYA 5D6EA 1R5GA 1R58A 4IKRA 1C27A 4U69A 3PKDA 1WBQA 3CB6A 4ZNGA 4HXXA 3PKAA 2EA4A 2EA2A 3FMQA 1MATA 4U6WA 1C23A 2BB7A 1XGSA 2EVMA 1C21A 2GU5A
chains in the Genus database with same CATH superfamily
4PNCA 1WN1A 4Z7MA 3MR1A 2GGBA 1A16A 2V6CA 3MX6A 4FO7A 3PN9A 2ZSGA 2P9AA 2NQ7A 2GA2A 4FKCA 1YJ3A 3PKBA 2Q8KA 2NQ6A 4B28A 1BOAA 3D27A 2GGCA 3PKCA 1M35A 2V3XA 2Q93A 3CB5A 2EVCA 1WKMA 4IKTA 2GG7A 2GU4A 4S2TP 3PKEA 4IKSA 4U75A 4FLKA 1KQ0A 4QR8A 4IPAA 1QXWA 4IDYA 3O5VA 2BHAA 3Q6DA 2BN7A 1QXZA 2B3LA 2OKNA 2GU6A 1WY2A 4U76A 2ADUA 3RORA 5D6FA 4IU6A 2B3KA 1KP0A 4U1BA 5FCHA 5JFRA 1WL6A 4A6VA 1WL9A 1XNZA 2GG2A 4U71A 4MATA 1YW8A 4R60A 4IKUA 3BIPA 2BWSA 2DFIA 1KQ9A 5CNXA 1R5HA 5CIKA 2V3ZA 1CHMA 1QXYA 4KM3A 2GG5A 4IF7A 4OOKA 1C24A 3IG4A 4RZZA 3OVKA 3QOCA 3L24A 4FLJA 2BH3A 2IW2A 4S00A 5E2CA 2EVOA 1BN5A 5CDVA 3IL0A 2GTXA 4U6ZA 4FO8A 2HOWA 2BWYA 2P99A 4FLIA 4PV4A 3TB5A 5JHUA 5FCFA 5JI6A 3IU7A 2GZ5A 3I7MA 3S6BA 2BWVA 2V3YA 2MATA 1JAWA 2Q92A 4EGEA 3MATA 1YW7A 3BIQA 2BHBA 1PV9A 3OOOA 3FMRA 4RGZ1 4U6JA 4S2RP 3BITA 5CDEA 1O0XA 1B59A 5CLSA 2BWTA 2GG0A 1W2MA 3IU9A 1QZYA 2OAZA 2BHCA 4S01A 1XGMA 1W7VA 4U6EA 4U73A 5CE6A 2BHDA 1YVMA 2Q94A 5CDLA 2Q95A 1XGNA 1Y1NA 2G6PA 2BWUA 2GG8A 4FUKA 3L7GA 3CTZA 2P98A 4A6WA 5E5BA 4ZWOA 1WLRA 4ZWPA 1B6AA 2GG3A 2BWXA 3IU8A 1XGOA 2Q96A 4ZWUA 3RVAA 1C22A 2B3HA 3PEBA 2GU7A 4FLLA 3TAVA 2GG9A 1YW9A 3FM3A 4JUQA 4U6CA 4U70A 2BWWA 4IECA 1N51A 4RZYA 5D6EA 1R5GA 1R58A 4IKRA 1C27A 4U69A 3PKDA 1WBQA 3CB6A 4ZNGA 4HXXA 3PKAA 2EA4A 2EA2A 3FMQA 1MATA 4U6WA 1C23A 2BB7A 1XGSA 2EVMA 1C21A 2GU5A
chains in the Genus database with same CATH topology
4PNCA 1WN1A 4Z7MA 3MR1A 2GGBA 1A16A 2V6CA 3MX6A 4FO7A 3PN9A 2ZSGA 2P9AA 2NQ7A 2GA2A 4FKCA 1YJ3A 3PKBA 2Q8KA 2NQ6A 4B28A 1BOAA 3D27A 2GGCA 3PKCA 1M35A 2V3XA 2Q93A 3CB5A 2EVCA 1WKMA 4IKTA 2GG7A 2GU4A 4S2TP 3PKEA 4IKSA 4U75A 4FLKA 1KQ0A 4QR8A 4IPAA 1QXWA 4IDYA 3O5VA 2BHAA 3Q6DA 2BN7A 1QXZA 2B3LA 2OKNA 2GU6A 1WY2A 4U76A 2ADUA 3RORA 5D6FA 4IU6A 2B3KA 1KP0A 4U1BA 5FCHA 5JFRA 1WL6A 4A6VA 1WL9A 1XNZA 2GG2A 4U71A 4MATA 1YW8A 4R60A 4IKUA 3BIPA 2BWSA 2DFIA 1KQ9A 5CNXA 1R5HA 5CIKA 2V3ZA 1CHMA 1QXYA 4KM3A 2GG5A 4IF7A 4OOKA 1C24A 3IG4A 4RZZA 3OVKA 3QOCA 3L24A 4FLJA 2BH3A 2IW2A 4S00A 5E2CA 2EVOA 1BN5A 5CDVA 3IL0A 2GTXA 4U6ZA 4FO8A 2HOWA 2BWYA 2P99A 4FLIA 4PV4A 3TB5A 5JHUA 5FCFA 5JI6A 3IU7A 2GZ5A 3I7MA 3S6BA 2BWVA 2V3YA 2MATA 1JAWA 2Q92A 4EGEA 3MATA 1YW7A 3BIQA 2BHBA 1PV9A 3OOOA 3FMRA 4RGZ1 4U6JA 4S2RP 3BITA 5CDEA 1O0XA 1B59A 5CLSA 2BWTA 2GG0A 1W2MA 3IU9A 1QZYA 2OAZA 2BHCA 4S01A 1XGMA 1W7VA 4U6EA 4U73A 5CE6A 2BHDA 1YVMA 2Q94A 5CDLA 2Q95A 1XGNA 1Y1NA 2G6PA 2BWUA 2GG8A 4FUKA 3L7GA 3CTZA 2P98A 4A6WA 5E5BA 4ZWOA 1WLRA 4ZWPA 1B6AA 2GG3A 2BWXA 3IU8A 1XGOA 2Q96A 4ZWUA 3RVAA 1C22A 2B3HA 3PEBA 2GU7A 4FLLA 3TAVA 2GG9A 1YW9A 3FM3A 4JUQA 4U6CA 4U70A 2BWWA 4IECA 1N51A 4RZYA 5D6EA 1R5GA 1R58A 4IKRA 1C27A 4U69A 3PKDA 1WBQA 3CB6A 4ZNGA 4HXXA 3PKAA 2EA4A 2EA2A 3FMQA 1MATA 4U6WA 1C23A 2BB7A 1XGSA 2EVMA 1C21A 2GU5A
chains in the Genus database with same CATH homology


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