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
Loading diagram...

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


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