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


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