3TFJA

Dmsp-dependent demethylase from p. ubique - with cofactor thf
Total Genus 110
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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
110
sequence length
369
structure length
369
Chain Sequence
MKNFSIAKSRRLRSTPYTSRIEKQGVTAYTIYNHMLLPAAFGSIEDSYKHLKEHVQIWDVAAERQVEISGKDSAELVQLMTCRDLSKSKIGRCYYCPIIDENGNLVNDPVVLKLDENKWWISIADSDVIFFAKGLASGHKFDVKIVEPVVDIMAIQGPKSFALMEKVFGKKITELKFFGFDYFDFEGTKHLIARSGWSKQGGYEVYVENTQSGQKLYDHLFEVGKEFNVGPGCPNLIERIESALLSYGNDFDNNDNPFECGFDQYVSLDSDINFLGKEKLKEIKLKGPQKKLRGVKIDIKEISLTGSKNIYDENNNVIGELRSACYSPHFQKVIGIAMIKKSHWEASQGFKIQINDNTINGNVCDLPFI
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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 Structures of dimethylsulfoniopropionate-dependent demethylase from the marine organism Pelagabacter ubique.
pubmed doi rcsb
source organism Candidatus pelagibacter ubique
molecule tags Transferase
molecule keywords GcvT-like Aminomethyltransferase protein
total genus 110
structure length 369
sequence length 369
chains with identical sequence B
ec nomenclature ec 2.1.1.269: Dimethylsulfoniopropionate demethylase.
pdb deposition date 2011-08-15

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF01571 GCV_T Aminomethyltransferase folate-binding domain
A PF08669 GCV_T_C Glycine cleavage T-protein C-terminal barrel domain
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.30.1360.120 Alpha Beta 2-Layer Sandwich Gyrase A; domain 2 Probable tRNA modification gtpase trme; domain 1 3tfjA00
1YX2A 1XZPB 3AD8C 3GEEA 4P9SA 3AD9C 3A8KA 1X31C 1WOOA 2GAGC 2GAHC 1WORA 3TFHA 1PJ7A 3GIRA 3GEIA 3TTGA 1VLOA 3GSIA 3ADAC 4PAAA 1WOPA 3A8JA 4PABA 3AD7C 3TFIA 1WSVA 3TFJA 1PJ5A 5L46A 1PJ6A 3A8IA 1V5VA 1XZQA 3GEHA 1XZPA 1VRQC 1WSRA 1XZQB 1WOSA
chains in the Genus database with same CATH superfamily
1Y1VK 1R9TK 1EI6A 3SZYA 4KDDA 1GE9A 4MQ9A 2R7ZK 1I3QC 1IQ0A 3ERED 1XXAA 3M3YC 1K83A 5TJ3A 4BLAA 3AH5A 5FLMC 3PO3C 5C4JK 1TWCK 3K7AC 3TFIA 3TFJA 2R93A 4KB2A 4OIOA 1PJ6A 5M3MK 2VUMK 1I6HK 2PPBA 4BY7K 3AD8C 4KMDA 4XSZA 3GDZA 1I50A 4Y7NC 4BY7C 1BDFA 3GTGC 1G51A 3N3YA 4C2MC 3SZZA 1XXBA 1EFWA 1WOPA 4XLNA 3OREA 4G0WA 3HOUC 2R92C 1TWFK 3S15K 3AQPA 5C3EK 5M5YK 3LAJA 2PHCB 2WB1L 2E2HK 3HOXC 3GTKA 1F7UA 3NUHA 1I50C 5TMCA 2NVXC 3OEPA 4X6AC 5E68A 3I4MK 2A6HA 3GTJK 1VLOA 1F7VA 5HL8A 4P5BA 3I4NC 5CHPA 2NVTC 3I4MC 1USOA 3RZDC 4KN4A 1PJ5A 3FHZA 1TWHK 3GTMA 2XCOA 1J6WA 2R93C 1XZQA 1WSRA 3RZOC 3GTMC 3BP3A 4KM8A 3CQZC 3LPXA 1YNNA 3A8KA 4KN7A 1X31C 2GAGC 1Y1VA 4G0UA 2PA8D 3HKZL 4BBRC 2Y0SD 4GT9A 1IW7A 4YG2A 1IS1A 3JSTA 2D6FC 5M5XK 2BE5A 2A68A 5M5WK 2JA6C 4MEYA 3GTLA 1IBAA 1SFOC 1TWFC 3GEHA 1I50K 2NVYK 3N0CA 1TWFA 4BBSK 5IP7K 1BGWA 5M3FK 3AD9C 2YU9K 4OIQA 1WCMC 2B63K 2P8TA 5IOQA 5EGHA 4A3IK 4A3DC 5CJ9A 4OINA 5C4JC 4C3IK 4A3KC 4G7OA 3GEIA 3S1QK 1R9TC 1XPPA 3EQLA 4LOWA 5C44C 1F93A 1R9TA 1I3QK 4C3JK 2GSOA 3FKIA 4FZBA 4A3LC 4XCHA 4KMUA 2RH6A 4Y7NK 3HOYC 3H0GA 4C3JC 4ZH4A 3RZOK 4G7ZA 3CQZK 1I6HC 3L4KA 1BS2A 3GTQA 3OPFA 4KASA 1O2BA 3GTQC 3BUEA 2E2JC 1DCHA 3S1RK 4KM9A 5IYCK 3L4JA 4KB4A 4AYBL 1Y1VC 5C3EC 1O29A 3S16C 1WCMK 2PA8L 3HKZD 1EH1A 4C3HC 5C44K 3GTLK 2WB1D 1WQFA 2R7ZC 5EGEA 4A3BK 3GTGA 2E2IK 3HOWK 2JA5K 3GTLC 3HOYK 3T01A 3GTKK 2A69A 4A3BC 2ZUEA 2E2IC 3HOWC 1VRQC 4BY1K 3BP8C 4GTFA 4MEXA 3RZDK 4GTBA 3H0GC 4A3EC 1WIHA 4A3GK 1WOOA 2GAHC 1WORA 4QJVA 2NVXA 2JA8K 2JA6K 4KMHA 1TWHA 1PJ7A 1TWGA 1DCPA 3GTMK 1K83C 3ADAC 2JA7K 2E2JK 4AYBD 4WILA 5JVOA 3GTQK 1IE0A 3HOXK 1K83K 2GSUA 4RMFA 3VA7A 5IYDK 3S15C 2VUMA 4WJ3M 1XZPB 2CW0A 2V6SA 3LAPA 1ZQ1C 1TWCA 5IYBK 4G7HA 1YNJA 3S0XA 1TWGC 2O5JA 3G4CA 1J98A 2CFAB 1TWAA 3S16K 3I4NK 4YFKA 3GTOK 1I3QA 2WAQL 4XLPA 3GTJC 4FM9A 1EQRA 4O2DA 3WODA 4LJZA 4WJ4A 2ZFZA 3S1QC 4KARA 3V4GA 3S17C 4DDQA 1O28A 4Y52K 5D4DA 1XZQB 1WOSA 4LK1A 1YX2A 1TWCC 2ZUFA 1ZYRA 4A3CK 2NVYA 2JA8C 3Q3QA 1INNA 2JA7A 3AQOA 4BLBA 4A3MK 2JH3A 1Y1WK 2JA7C 5C4XC 4GFQA 4A3CC 3GSIA 5IYCC 2JA6A 4A3FK 2Y3PA 2R92A 3M4OK 4A3MC 3DXJA 4KAWX 3MMLB 1O26A 5C4XK 1JVIA 5IYDC 4A93C 4A3FC 5IP9C 4AH6A 4BBSC 1YCLA 1WCMA 3H3VD 3S14K 4P9SA 1ZBSA 1WQHA 4JK1A 1HQMA 3S2DC 4YFXA 4A3DK 5FLMK 2GSNA 3PO3K 2KWAA 2R93K 2XCQA 3GTPA 3GTPK 1B4BA 4YFNA 3S2DK 4LR2A 3AD7C 1J6XA 2EBBA 5FJ8K 4ILDA 2CFAA 3G4AA 4OIPA 4P5AA 4QJVB 1L0WA 1F9NA 3S1NK 3M4OC 1B4AA 4QIWD 2PMZD 1HI9A 3H3VL 4Q5SA 2P5MA 3HOVC 1JOEA 3A8JA 4A93K 1VH2A 1SFOA 5IP9K 2XCRB 2YU9C 2B63C 2RGRA 4A3IC 3HOVK 1ZVUA 3S1RC 1EK8A 1ISEA 1ZXOA 1BJTA 3PO2K 3GEEA 3FOFA 2W7VA 5JFEA 2E2HC 4NOIA 3HOZC 4A3JC 2R7ZA 3TFHA 3GIRA 4X6AK 2NVQC 3FOEA 4G0VA 2YU9A 2B63A 2E2IA 3M3YK 3CAGA 3GTPC 4GTEA 2Y0SL 4GTLA 1VJEA 3GTOC 3A8IA 1AB4A 2PMZL 4QIWL 4J3NA 4BKWA 3S1MK 4GTAA 1O2AA 3H0GK 4KC6A 4A3EK 3T02A 3TTGA 1XXCA 5TMFA 4C45A 4BBRK 4PAAA 2A6EA 4PABA 3N0BA 4LQYA 1JQWA 3S2HC 1USMA 5L46A 1DD5A 4C2MK 1O2FB 1XZPA 3HXAA 3CQZA 4KMAA 2JA5A 4C3HK 4BXXK 2R92K 4A3JK 1WQGA 5IORA 2NVYC 3IPJA 1I6VA 4A3KK 5IP7C 1Y1WA 2E2HA 3S14C 3GTJA 1TWGK 4GTCA 2WAQD 2NVXK 3FKIK 4GZYA 2NVQK 1O25A 3S17K 4BY1C 4A3LK 2V6TA 3K7AK 1O27A 1V5VA 3FKIC 3QX3A 5IOSA 2FQOA 2JA5C 4M1XA 3S1NC 2VUMC 2NVTK 4Y52C 3GTKC 2V6UA 1TWHC 3S1MC 4KATA 1Y1WC 1SMYA 1C0AA 1J6VA 3GTGK 2O5IA 1IL2A 1O24A 4XSXA 2FQTA 3HOUK 3T00A 1TWAC 4A3GC 1SFOK 3S2HK 4Q4ZA 1KQ4A 5IOTA 3PO2C 1WSVA 3GTOA 4GTDA 4LLGA 5IYBC 1TWAK 1DCOA 1UV7A 1VGXA 4OIRA 1RU0A 4BXXC 3HOZK 4LK0A 4C3IC
chains in the Genus database with same CATH topology
1YX2A 1XZPB 3AD8C 3GEEA 4P9SA 3AD9C 3A8KA 1X31C 1WOOA 2GAGC 2GAHC 1WORA 3TFHA 1PJ7A 3GIRA 3GEIA 3TTGA 1VLOA 3GSIA 3ADAC 4PAAA 1WOPA 3A8JA 4PABA 3AD7C 3TFIA 1WSVA 3TFJA 1PJ5A 5L46A 1PJ6A 3A8IA 1V5VA 1XZQA 3GEHA 1XZPA 1VRQC 1WSRA 1XZQB 1WOSA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 1YX2 A;  1XZP B;  3AD8 C;  3GEE A;  4P9S A;  3AD9 C;  3A8K A;  1X31 C;  1WOO A;  2GAG C;  2GAH C;  1WOR A;  3TFH A;  1PJ7 A;  3GIR A;  3GEI A;  3TTG A;  1VLO A;  3GSI A;  3ADA C;  4PAA A;  1WOP A;  3A8J A;  4PAB A;  3AD7 C;  3TFI A;  1WSV A;  3TFJ A;  1PJ5 A;  5L46 A;  1PJ6 A;  3A8I A;  1V5V A;  1XZQ A;  3GEH A;  1XZP A;  1VRQ C;  1WSR A;  1XZQ B;  1WOS A; 
#chains in the Genus database with same CATH topology
 1Y1V K;  1R9T K;  1EI6 A;  3SZY A;  4KDD A;  1GE9 A;  4MQ9 A;  2R7Z K;  1I3Q C;  1IQ0 A;  3ERE D;  1XXA A;  3M3Y C;  1K83 A;  5TJ3 A;  4BLA A;  3AH5 A;  5FLM C;  3PO3 C;  5C4J K;  1TWC K;  3K7A C;  3TFI A;  3TFJ A;  2R93 A;  4KB2 A;  4OIO A;  1PJ6 A;  5M3M K;  2VUM K;  1I6H K;  2PPB A;  4BY7 K;  3AD8 C;  4KMD A;  4XSZ A;  3GDZ A;  1I50 A;  4Y7N C;  4BY7 C;  1BDF A;  3GTG C;  1G51 A;  3N3Y A;  4C2M C;  3SZZ A;  1XXB A;  1EFW A;  1WOP A;  4XLN A;  3ORE A;  4G0W A;  3HOU C;  2R92 C;  1TWF K;  3S15 K;  3AQP A;  5C3E K;  5M5Y K;  3LAJ A;  2PHC B;  2WB1 L;  2E2H K;  3HOX C;  3GTK A;  1F7U A;  3NUH A;  1I50 C;  5TMC A;  2NVX C;  3OEP A;  4X6A C;  5E68 A;  3I4M K;  2A6H A;  3GTJ K;  1VLO A;  1F7V A;  5HL8 A;  4P5B A;  3I4N C;  5CHP A;  2NVT C;  3I4M C;  1USO A;  3RZD C;  4KN4 A;  1PJ5 A;  3FHZ A;  1TWH K;  3GTM A;  2XCO A;  1J6W A;  2R93 C;  1XZQ A;  1WSR A;  3RZO C;  3GTM C;  3BP3 A;  4KM8 A;  3CQZ C;  3LPX A;  1YNN A;  3A8K A;  4KN7 A;  1X31 C;  2GAG C;  1Y1V A;  4G0U A;  2PA8 D;  3HKZ L;  4BBR C;  2Y0S D;  4GT9 A;  1IW7 A;  4YG2 A;  1IS1 A;  3JST A;  2D6F C;  5M5X K;  2BE5 A;  2A68 A;  5M5W K;  2JA6 C;  4MEY A;  3GTL A;  1IBA A;  1SFO C;  1TWF C;  3GEH A;  1I50 K;  2NVY K;  3N0C A;  1TWF A;  4BBS K;  5IP7 K;  1BGW A;  5M3F K;  3AD9 C;  2YU9 K;  4OIQ A;  1WCM C;  2B63 K;  2P8T A;  5IOQ A;  5EGH A;  4A3I K;  4A3D C;  5CJ9 A;  4OIN A;  5C4J C;  4C3I K;  4A3K C;  4G7O A;  3GEI A;  3S1Q K;  1R9T C;  1XPP A;  3EQL A;  4LOW A;  5C44 C;  1F93 A;  1R9T A;  1I3Q K;  4C3J K;  2GSO A;  3FKI A;  4FZB A;  4A3L C;  4XCH A;  4KMU A;  2RH6 A;  4Y7N K;  3HOY C;  3H0G A;  4C3J C;  4ZH4 A;  3RZO K;  4G7Z A;  3CQZ K;  1I6H C;  3L4K A;  1BS2 A;  3GTQ A;  3OPF A;  4KAS A;  1O2B A;  3GTQ C;  3BUE A;  2E2J C;  1DCH A;  3S1R K;  4KM9 A;  5IYC K;  3L4J A;  4KB4 A;  4AYB L;  1Y1V C;  5C3E C;  1O29 A;  3S16 C;  1WCM K;  2PA8 L;  3HKZ D;  1EH1 A;  4C3H C;  5C44 K;  3GTL K;  2WB1 D;  1WQF A;  2R7Z C;  5EGE A;  4A3B K;  3GTG A;  2E2I K;  3HOW K;  2JA5 K;  3GTL C;  3HOY K;  3T01 A;  3GTK K;  2A69 A;  4A3B C;  2ZUE A;  2E2I C;  3HOW C;  1VRQ C;  4BY1 K;  3BP8 C;  4GTF A;  4MEX A;  3RZD K;  4GTB A;  3H0G C;  4A3E C;  1WIH A;  4A3G K;  1WOO A;  2GAH C;  1WOR A;  4QJV A;  2NVX A;  2JA8 K;  2JA6 K;  4KMH A;  1TWH A;  1PJ7 A;  1TWG A;  1DCP A;  3GTM K;  1K83 C;  3ADA C;  2JA7 K;  2E2J K;  4AYB D;  4WIL A;  5JVO A;  3GTQ K;  1IE0 A;  3HOX K;  1K83 K;  2GSU A;  4RMF A;  3VA7 A;  5IYD K;  3S15 C;  2VUM A;  4WJ3 M;  1XZP B;  2CW0 A;  2V6S A;  3LAP A;  1ZQ1 C;  1TWC A;  5IYB K;  4G7H A;  1YNJ A;  3S0X A;  1TWG C;  2O5J A;  3G4C A;  1J98 A;  2CFA B;  1TWA A;  3S16 K;  3I4N K;  4YFK A;  3GTO K;  1I3Q A;  2WAQ L;  4XLP A;  3GTJ C;  4FM9 A;  1EQR A;  4O2D A;  3WOD A;  4LJZ A;  4WJ4 A;  2ZFZ A;  3S1Q C;  4KAR A;  3V4G A;  3S17 C;  4DDQ A;  1O28 A;  4Y52 K;  5D4D A;  1XZQ B;  1WOS A;  4LK1 A;  1YX2 A;  1TWC C;  2ZUF A;  1ZYR A;  4A3C K;  2NVY A;  2JA8 C;  3Q3Q A;  1INN A;  2JA7 A;  3AQO A;  4BLB A;  4A3M K;  2JH3 A;  1Y1W K;  2JA7 C;  5C4X C;  4GFQ A;  4A3C C;  3GSI A;  5IYC C;  2JA6 A;  4A3F K;  2Y3P A;  2R92 A;  3M4O K;  4A3M C;  3DXJ A;  4KAW X;  3MML B;  1O26 A;  5C4X K;  1JVI A;  5IYD C;  4A93 C;  4A3F C;  5IP9 C;  4AH6 A;  4BBS C;  1YCL A;  1WCM A;  3H3V D;  3S14 K;  4P9S A;  1ZBS A;  1WQH A;  4JK1 A;  1HQM A;  3S2D C;  4YFX A;  4A3D K;  5FLM K;  2GSN A;  3PO3 K;  2KWA A;  2R93 K;  2XCQ A;  3GTP A;  3GTP K;  1B4B A;  4YFN A;  3S2D K;  4LR2 A;  3AD7 C;  1J6X A;  2EBB A;  5FJ8 K;  4ILD A;  2CFA A;  3G4A A;  4OIP A;  4P5A A;  4QJV B;  1L0W A;  1F9N A;  3S1N K;  3M4O C;  1B4A A;  4QIW D;  2PMZ D;  1HI9 A;  3H3V L;  4Q5S A;  2P5M A;  3HOV C;  1JOE A;  3A8J A;  4A93 K;  1VH2 A;  1SFO A;  5IP9 K;  2XCR B;  2YU9 C;  2B63 C;  2RGR A;  4A3I C;  3HOV K;  1ZVU A;  3S1R C;  1EK8 A;  1ISE A;  1ZXO A;  1BJT A;  3PO2 K;  3GEE A;  3FOF A;  2W7V A;  5JFE A;  2E2H C;  4NOI A;  3HOZ C;  4A3J C;  2R7Z A;  3TFH A;  3GIR A;  4X6A K;  2NVQ C;  3FOE A;  4G0V A;  2YU9 A;  2B63 A;  2E2I A;  3M3Y K;  3CAG A;  3GTP C;  4GTE A;  2Y0S L;  4GTL A;  1VJE A;  3GTO C;  3A8I A;  1AB4 A;  2PMZ L;  4QIW L;  4J3N A;  4BKW A;  3S1M K;  4GTA A;  1O2A A;  3H0G K;  4KC6 A;  4A3E K;  3T02 A;  3TTG A;  1XXC A;  5TMF A;  4C45 A;  4BBR K;  4PAA A;  2A6E A;  4PAB A;  3N0B A;  4LQY A;  1JQW A;  3S2H C;  1USM A;  5L46 A;  1DD5 A;  4C2M K;  1O2F B;  1XZP A;  3HXA A;  3CQZ A;  4KMA A;  2JA5 A;  4C3H K;  4BXX K;  2R92 K;  4A3J K;  1WQG A;  5IOR A;  2NVY C;  3IPJ A;  1I6V A;  4A3K K;  5IP7 C;  1Y1W A;  2E2H A;  3S14 C;  3GTJ A;  1TWG K;  4GTC A;  2WAQ D;  2NVX K;  3FKI K;  4GZY A;  2NVQ K;  1O25 A;  3S17 K;  4BY1 C;  4A3L K;  2V6T A;  3K7A K;  1O27 A;  1V5V A;  3FKI C;  3QX3 A;  5IOS A;  2FQO A;  2JA5 C;  4M1X A;  3S1N C;  2VUM C;  2NVT K;  4Y52 C;  3GTK C;  2V6U A;  1TWH C;  3S1M C;  4KAT A;  1Y1W C;  1SMY A;  1C0A A;  1J6V A;  3GTG K;  2O5I A;  1IL2 A;  1O24 A;  4XSX A;  2FQT A;  3HOU K;  3T00 A;  1TWA C;  4A3G C;  1SFO K;  3S2H K;  4Q4Z A;  1KQ4 A;  5IOT A;  3PO2 C;  1WSV A;  3GTO A;  4GTD A;  4LLG A;  5IYB C;  1TWA K;  1DCO A;  1UV7 A;  1VGX A;  4OIR A;  1RU0 A;  4BXX C;  3HOZ K;  4LK0 A;  4C3I C; 
#chains in the Genus database with same CATH homology
 1YX2 A;  1XZP B;  3AD8 C;  3GEE A;  4P9S A;  3AD9 C;  3A8K A;  1X31 C;  1WOO A;  2GAG C;  2GAH C;  1WOR A;  3TFH A;  1PJ7 A;  3GIR A;  3GEI A;  3TTG A;  1VLO A;  3GSI A;  3ADA C;  4PAA A;  1WOP A;  3A8J A;  4PAB A;  3AD7 C;  3TFI A;  1WSV A;  3TFJ A;  1PJ5 A;  5L46 A;  1PJ6 A;  3A8I A;  1V5V A;  1XZQ A;  3GEH A;  1XZP A;  1VRQ C;  1WSR A;  1XZQ B;  1WOS 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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