3TFIA

Dmsp-dependent demethylase from p. ubique - with substrate dmsp
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 3tfiA00
3A8KA 1WOPA 1XZPB 1XZPA 3GIRA 3TFJA 1PJ6A 1X31C 3AD9C 1VLOA 1V5VA 3TFHA 1WOOA 5L46A 1WSVA 2GAHC 1WOSA 3TFIA 3TTGA 1VRQC 3GEIA 1YX2A 1WORA 3A8IA 1XZQA 1PJ5A 1XZQB 3ADAC 3GEHA 4PABA 4P9SA 3A8JA 3AD8C 4PAAA 2GAGC 1PJ7A 3GEEA 1WSRA 3GSIA 3AD7C
chains in the Genus database with same CATH superfamily
3LAJA 4C3JK 4C3HC 2JA6K 3M4OC 3S1NC 1PJ6A 1X31C 2E2IK 3S17K 3S2DK 1IW7A 2NVQC 5FLMK 4KB2A 5EGEA 1ZBSA 1I3QK 1TWAA 4A3KC 2PA8L 2NVXC 1VRQC 5TJ3A 5E68A 4AYBL 4XSZA 1XZQA 3HOXC 4G7HA 4C45A 4A3BK 3EQLA 3N3YA 4OIRA 1K83C 2JA7K 1IS1A 1WCMA 3AH5A 3GTLC 3AQPA 1F93A 4GT9A 4A3FC 3HXAA 1Y1VC 1EI6A 5C3EK 1Y1VK 5C3EC 3K7AK 3GTLA 4M1XA 3T01A 4BBRK 5IYDC 1TWCK 3LAPA 1K83K 2JA7C 3Q3QA 5C4JC 3HOWK 1USOA 1RU0A 1TWFK 2JA5K 3GTQC 4LLGA 3FOEA 4KASA 4MEXA 2R93K 4A3MK 3OREA 1EFWA 5CHPA 4KMUA 3GEHA 4C3IC 3HKZD 5TMFA 3OEPA 1I6HK 1V5VA 2NVXA 5IOTA 2XCRB 3GTJA 3GTMK 2V6SA 3I4MC 4GTBA 3S1MC 5M3FK 1WQFA 1YCLA 1ZXOA 4A93K 4MQ9A 4BKWA 2YU9A 2NVTC 4Y52K 2FQTA 4Y7NK 3A8JA 2BE5A 1I50A 1EK8A 4QJVA 3GTPK 4P5BA 1JQWA 3GTJK 3GSIA 1VH2A 1I50C 4XLNA 1ISEA 4G0VA 4A3LK 1VLOA 2NVQK 3GTGC 4YFKA 3GTGK 3MMLB 3S17C 4GTEA 5JVOA 3RZOC 4A3LC 4QJVB 5IORA 1Y1WK 4C3JC 1YX2A 2PMZL 4OINA 4GFQA 5C44C 1J6VA 3S1RC 2O5IA 4WJ3M 1WQHA 4GTCA 3H0GK 4P9SA 4LJZA 2O5JA 3BP8C 1J6XA 1AB4A 2ZUFA 5TMCA 4KM9A 2E2HC 2A69A 1TWCA 3G4AA 3GTLK 4GTFA 4ILDA 4A3GC 5JFEA 2YU9C 1WOSA 1GE9A 2RH6A 4AH6A 3S16C 1WORA 1O2FB 3L4JA 4A3KK 4YFXA 4XLPA 1F7UA 1I3QC 3S1QK 2GSOA 3CAGA 5M5WK 2R92A 3T02A 4C3IK 5D4DA 2GAGC 1BS2A 2E2IC 2WB1L 1I3QA 1TWHC 2WB1D 2ZFZA 4A3MC 2R92C 3GTPC 5CJ9A 4OIPA 2Y3PA 5IYBK 4GTAA 1JOEA 4X6AC 3V4GA 1WOOA 5IYDK 5L46A 4Y52C 2NVTK 2CFAA 3I4NC 3GTOA 3HOVK 3S2HK 3GTMC 4G0UA 3AD8C 4QIWL 2B63C 4KN4A 3HOXK 4BLBA 1O2BA 4DDQA 2NVXK 3OPFA 1XZPA 2WAQD 3M3YC 4BXXC 5M3MK 1WSVA 4NOIA 4C3HK 1O29A 3S1NK 4O2DA 3M4OK 2FQOA 4KB4A 2R7ZK 2JA5C 1TWAC 1XXCA 4Q5SA 1F7VA 3HOWC 3PO3C 3BUEA 3BP3A 3G4CA 1TWFA 2JA5A 5IP9C 4LR2A 1XXAA 1IE0A 1SMYA 4A3DC 2CFAB 2A6EA 4BY7K 3TFIA 1B4AA 1WCMK 2JA7A 4RMFA 4FZBA 3GTQA 5FLMC 3CQZK 3HOZK 2EBBA 2P5MA 3AQOA 1TWGK 2VUMK 3HKZL 3HOVC 1EH1A 2XCOA 3RZDK 1R9TK 4LQYA 1O27A 3GEEA 2E2JK 2Y0SD 4A3IC 5C4XC 1XZPB 3QX3A 3PO2C 5IYCC 4JK1A 3DXJA 4ZH4A 1C0AA 4P5AA 1BJTA 4A3EK 4A3JC 3S15K 3PO2K 4A3CK 2PA8D 2R7ZC 4BBSC 1TWGA 4A3IK 1B4BA 3CQZA 4BY1K 4C2MC 4PABA 1TWGC 3FKIK 3FOFA 2JA8C 3CQZC 4GTLA 3S1QC 2PPBA 4OIOA 1ZQ1C 1O2AA 1IL2A 2GSNA 1WCMC 3ERED 2B63K 2NVYC 1J98A 4MEYA 2GSUA 4C2MK 4YG2A 1O24A 1WQGA 3HOYK 1F9NA 4A3EC 3S15C 4KMHA 5IP7C 5EGHA 4Q4ZA 1EQRA 3H3VL 1PJ7A 3AD7C 4BLAA 4KC6A 1HQMA 3RZOK 4G7OA 2E2HA 4G7ZA 4BXXK 2NVYK 2GAHC 1VGXA 1UV7A 2WAQL 2YU9K 3WODA 4A3DK 3IPJA 3GTOK 3S14C 1IBAA 1SFOC 4Y7NC 2NVYA 2CW0A 2E2HK 3I4NK 2XCQA 1TWHA 3AD9C 3N0CA 1DCOA 5IP7K 3HOUC 1YNNA 1DCPA 3HOYC 1WIHA 4KMAA 3TTGA 5C44K 1J6WA 2JH3A 3H3VD 3GEIA 2A68A 2R92K 2E2JC 2PMZD 3RZDC 1R9TC 4GZYA 2VUMC 1SFOK 3L4KA 1G51A 3GTOC 3S14K 3M3YK 5M5XK 1WSRA 4YFNA 5IOQA 1IQ0A 3S16K 3A8KA 3GTJC 2B63A 3JSTA 4A3GK 1BGWA 5C4JK 4QIWD 4XSXA 4LK1A 1TWCC 2RGRA 2D6FC 3K7AC 1I6VA 5IP9K 3H0GA 1SFOA 4BBSK 1ZVUA 1JVIA 3I4MK 2PHCB 3ADAC 4GTDA 3HOUK 4KAWX 4X6AK 4KMDA 4A3BC 1Y1WA 1I6HC 2W7VA 4KATA 1ZYRA 4KDDA 3GTGA 1USMA 2E2IA 1Y1WC 3GIRA 1TWHK 4XCHA 2JA6A 4WILA 1XPPA 5IOSA 3GTPA 1O28A 1O26A 1R9TA 2JA6C 2VUMA 1I50K 4LOWA 4KN7A 1INNA 1PJ5A 3GTQK 4BY7C 1YNJA 2JA8K 3GTKA 3FKIC 3FHZA 4BBRC 5HL8A 4BY1C 3GTMA 4LK0A 3VA7A 4KM8A 5FJ8K 4A3JK 4KARA 3H0GC 5IYBC 1VJEA 5IYCK 2Y0SL 3GDZA 4AYBD 4J3NA 3N0BA 3LPXA 3SZZA 1XZQB 2R7ZA 2R93A 1DCHA 3S2DC 3HOZC 3T00A 3S0XA 4WJ4A 2R93C 1HI9A 2ZUEA 1K83A 5M5YK 3SZYA 4G0WA 1WOPA 2A6HA 1TWFC 3TFJA 1L0WA 1BDFA 1KQ4A 1XXBA 1Y1VA 3TFHA 3S2HC 4A93C 1DD5A 3GTKC 3A8IA 3GTKK 3FKIA 4A3FK 4OIQA 3S1MK 4A3CC 1O25A 2V6TA 4PAAA 3PO3K 2V6UA 1TWAK 2KWAA 4FM9A 3S1RK 3NUHA 2P8TA 5C4XK
chains in the Genus database with same CATH topology
3A8KA 1WOPA 1XZPB 1XZPA 3GIRA 3TFJA 1PJ6A 1X31C 3AD9C 1VLOA 1V5VA 3TFHA 1WOOA 5L46A 1WSVA 2GAHC 1WOSA 3TFIA 3TTGA 1VRQC 3GEIA 1YX2A 1WORA 3A8IA 1XZQA 1PJ5A 1XZQB 3ADAC 3GEHA 4PABA 4P9SA 3A8JA 3AD8C 4PAAA 2GAGC 1PJ7A 3GEEA 1WSRA 3GSIA 3AD7C
chains in the Genus database with same CATH homology


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