5GMCA

Methylation at position 32 of trna catalyzed by trmj alters oxidative stress response in pseudomonas aeruiginosa
Total Genus 60
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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
60
Knots found
sequence length
174
structure length
174
Chain Sequence
NLYFQSMMLDRIRVVLVNTSHPGNIGGAARAMKNMGLSQLVLVQPESFPHGDAVARASGATDILDAARVVDTLEEALSGCSVVLGTSARDRRIPWPLLDPRECATTCLEHLEANGEVALVFGREYAGLTNEELQRCQFHVHIPSDPEFGSLNLAAAVQVLTYEVRMAWLAAQGK
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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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molecule tags Transferase
molecule keywords tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ
publication title Methylation at position 32 of tRNA catalyzed by TrmJ alters oxidative stress response in Pseudomonas aeruginosa.
pubmed doi rcsb
source organism Pseudomonas aeruginosa
total genus 60
structure length 174
sequence length 174
chains with identical sequence B, C, D
other databases KnotProt 2.0: K +31
ec nomenclature ec 2.1.1.200: tRNA (cytidine(32)/uridine(32)-2'-O)-methyltransferase.
pdb deposition date 2016-07-13

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF00588 SpoU_methylase SpoU rRNA Methylase family
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.40.1280.10 Alpha Beta 3-Layer(aba) Sandwich Alpha/beta knot Alpha/beta knot 5gmcA01
5GMBA 1Z85A 4JAKA 3AXZA 2V3KA 3KNUA 2EGVA 4MCDA 2O3AA 3L8UA 4CNEA 4YPYA 1V2XA 4YQ9A 4YQ3A 4CNDA 1UALA 4YQTA 4H3ZA 1X7OA 4YQGA 4CNGA 4YQSA 4PZKA 3GYQA 3NK7A 4YPWA 4YQLA 4KGNA 4YPZA 4YQ4A 4YQOA 3O7BA 4YQBA 2CX8A 4YQDA 4CNFA 2YY8A 1NXZA 4MCBA 4MCCA 2V3JA 4YVJA 3IEFA 4YQNA 2HA8A 4YQ8A 1VHKA 4XBOA 5GM8A 4YQIA 4X3LA 1NS5A 3KY7A 1VH0A 3ILKA 3N4JA 3IC6A 3AI9X 4YVGA 4FAKA 1K3RA 1UAJA 4YQQA 4YVHA 3DCMX 5GMCA 4YQKA 2QWVA 1VHYA 4JALA 3BBEA 1TO0A 3KTYA 1UAMA 1ZJRA 4YVKA 1UAKA 2I6DA 1X7PA 4YQPA 1O6DA 3AIAA 5CO4A 4YPXA 4YQ2A 4YQ6A 3OIJA 2EGWA 4YQAA 4YQ1A 3N4KA 3E5YA 3BBHA 1J85A 5D9FA 4IG6A 4YQRA 4L69A 3BBDA 4E8BA 4YVIA 4YQJA 3QUVA 4YQCA 1IPAA 4H3YA 5FAIA 3KW2A 3ONPA 4KDZA 4X3MA 4J3CA 1V6ZA 3OIIA 1OY5A 1GZ0A 4RG1A 4YQ0A 1P9PA 4YQ7A 2QMMA 4YQ5A 1MXIA 2Z0YA 3NK6A 3OINA
chains in the Genus database with same CATH superfamily
5GMBA 1Z85A 4JAKA 4JWHA 3AXZA 2V3KA 3KNUA 2EGVA 4MCDA 2O3AA 3L8UA 4CNEA 4YPYA 1V2XA 4YQ9A 4YQ3A 4CNDA 1UALA 4YQTA 4H3ZA 1X7OA 4YQGA 4CNGA 4YQSA 4PZKA 3GYQA 3NK7A 4YPWA 4YQLA 4KGNA 4YPZA 4YQ4A 4YQOA 3O7BA 4YQBA 2CX8A 4YQDA 4CNFA 2YY8A 4FMWA 1NXZA 4MCBA 4MCCA 2V3JA 4YVJA 3IEFA 4YQNA 2HA8A 4YQ8A 1VHKA 4XBOA 5GM8A 4YQIA 4X3LA 1NS5A 3KY7A 1VH0A 3ILKA 3N4JA 3IC6A 3AI9X 4YVGA 4FAKA 1K3RA 1UAJA 4YQQA 4YVHA 3DCMX 5GMCA 4YQKA 2QWVA 1VHYA 4JALA 3BBEA 1TO0A 4JWJA 3KTYA 1UAMA 1ZJRA 4YVKA 1UAKA 2I6DA 1X7PA 4YQPA 1O6DA 3AIAA 5CO4A 4YPXA 4YQ2A 4YQ6A 3OIJA 4JWGA 2EGWA 4YQAA 4YQ1A 3N4KA 3E5YA 3BBHA 1J85A 5D9FA 4IG6A 4YQRA 4L69A 3BBDA 4E8BA 4YVIA 4YQJA 3QUVA 4YQCA 1IPAA 4H3YA 5FAIA 3KW2A 3ONPA 4KDZA 4X3MA 4J3CA 1V6ZA 3OIIA 1OY5A 1GZ0A 4RG1A 4YQ0A 4JWFA 1P9PA 4YQ7A 2QMMA 4YQ5A 1MXIA 2Z0YA 3NK6A 3OINA
chains in the Genus database with same CATH topology
5GMBA 1Z85A 4JAKA 4JWHA 3AXZA 2V3KA 3KNUA 2EGVA 4MCDA 2O3AA 3L8UA 4CNEA 4YPYA 1V2XA 4YQ9A 4YQ3A 4CNDA 1UALA 4YQTA 4H3ZA 1X7OA 4YQGA 4CNGA 4YQSA 4PZKA 3GYQA 3NK7A 4YPWA 4YQLA 4KGNA 4YPZA 4YQ4A 4YQOA 3O7BA 4YQBA 2CX8A 4YQDA 4CNFA 2YY8A 4FMWA 1NXZA 4MCBA 4MCCA 2V3JA 4YVJA 3IEFA 4YQNA 2HA8A 4YQ8A 1VHKA 4XBOA 5GM8A 4YQIA 4X3LA 1NS5A 3KY7A 1VH0A 3ILKA 3N4JA 3IC6A 3AI9X 4YVGA 4FAKA 1K3RA 1UAJA 4YQQA 4YVHA 3DCMX 5GMCA 4YQKA 2QWVA 1VHYA 4JALA 3BBEA 1TO0A 4JWJA 3KTYA 1UAMA 1ZJRA 4YVKA 1UAKA 2I6DA 1X7PA 4YQPA 1O6DA 3AIAA 5CO4A 4YPXA 4YQ2A 4YQ6A 3OIJA 4JWGA 2EGWA 4YQAA 4YQ1A 3N4KA 3E5YA 3BBHA 1J85A 5D9FA 4IG6A 4YQRA 4L69A 3BBDA 4E8BA 4YVIA 4YQJA 3QUVA 4YQCA 1IPAA 4H3YA 5FAIA 3KW2A 3ONPA 4KDZA 4X3MA 4J3CA 1V6ZA 3OIIA 1OY5A 1GZ0A 4RG1A 4YQ0A 4JWFA 1P9PA 4YQ7A 2QMMA 4YQ5A 1MXIA 2Z0YA 3NK6A 3OINA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 5GMB A;  1Z85 A;  4JAK A;  3AXZ A;  2V3K A;  3KNU A;  2EGV A;  4MCD A;  2O3A A;  3L8U A;  4CNE A;  4YPY A;  1V2X A;  4YQ9 A;  4YQ3 A;  4CND A;  1UAL A;  4YQT A;  4H3Z A;  1X7O A;  4YQG A;  4CNG A;  4YQS A;  4PZK A;  3GYQ A;  3NK7 A;  4YPW A;  4YQL A;  4KGN A;  4YPZ A;  4YQ4 A;  4YQO A;  3O7B A;  4YQB A;  2CX8 A;  4YQD A;  4CNF A;  2YY8 A;  1NXZ A;  4MCB A;  4MCC A;  2V3J A;  4YVJ A;  3IEF A;  4YQN A;  2HA8 A;  4YQ8 A;  1VHK A;  4XBO A;  5GM8 A;  4YQI A;  4X3L A;  1NS5 A;  3KY7 A;  1VH0 A;  3ILK A;  3N4J A;  3IC6 A;  3AI9 X;  4YVG A;  4FAK A;  1K3R A;  1UAJ A;  4YQQ A;  4YVH A;  3DCM X;  5GMC A;  4YQK A;  2QWV A;  1VHY A;  4JAL A;  3BBE A;  1TO0 A;  3KTY A;  1UAM A;  1ZJR A;  4YVK A;  1UAK A;  2I6D A;  1X7P A;  4YQP A;  1O6D A;  3AIA A;  5CO4 A;  4YPX A;  4YQ2 A;  4YQ6 A;  3OIJ A;  2EGW A;  4YQA A;  4YQ1 A;  3N4K A;  3E5Y A;  3BBH A;  1J85 A;  5D9F A;  4IG6 A;  4YQR A;  4L69 A;  3BBD A;  4E8B A;  4YVI A;  4YQJ A;  3QUV A;  4YQC A;  1IPA A;  4H3Y A;  5FAI A;  3KW2 A;  3ONP A;  4KDZ A;  4X3M A;  4J3C A;  1V6Z A;  3OII A;  1OY5 A;  1GZ0 A;  4RG1 A;  4YQ0 A;  1P9P A;  4YQ7 A;  2QMM A;  4YQ5 A;  1MXI A;  2Z0Y A;  3NK6 A;  3OIN A; 
#chains in the Genus database with same CATH topology
 5GMB A;  1Z85 A;  4JAK A;  4JWH A;  3AXZ A;  2V3K A;  3KNU A;  2EGV A;  4MCD A;  2O3A A;  3L8U A;  4CNE A;  4YPY A;  1V2X A;  4YQ9 A;  4YQ3 A;  4CND A;  1UAL A;  4YQT A;  4H3Z A;  1X7O A;  4YQG A;  4CNG A;  4YQS A;  4PZK A;  3GYQ A;  3NK7 A;  4YPW A;  4YQL A;  4KGN A;  4YPZ A;  4YQ4 A;  4YQO A;  3O7B A;  4YQB A;  2CX8 A;  4YQD A;  4CNF A;  2YY8 A;  4FMW A;  1NXZ A;  4MCB A;  4MCC A;  2V3J A;  4YVJ A;  3IEF A;  4YQN A;  2HA8 A;  4YQ8 A;  1VHK A;  4XBO A;  5GM8 A;  4YQI A;  4X3L A;  1NS5 A;  3KY7 A;  1VH0 A;  3ILK A;  3N4J A;  3IC6 A;  3AI9 X;  4YVG A;  4FAK A;  1K3R A;  1UAJ A;  4YQQ A;  4YVH A;  3DCM X;  5GMC A;  4YQK A;  2QWV A;  1VHY A;  4JAL A;  3BBE A;  1TO0 A;  4JWJ A;  3KTY A;  1UAM A;  1ZJR A;  4YVK A;  1UAK A;  2I6D A;  1X7P A;  4YQP A;  1O6D A;  3AIA A;  5CO4 A;  4YPX A;  4YQ2 A;  4YQ6 A;  3OIJ A;  4JWG A;  2EGW A;  4YQA A;  4YQ1 A;  3N4K A;  3E5Y A;  3BBH A;  1J85 A;  5D9F A;  4IG6 A;  4YQR A;  4L69 A;  3BBD A;  4E8B A;  4YVI A;  4YQJ A;  3QUV A;  4YQC A;  1IPA A;  4H3Y A;  5FAI A;  3KW2 A;  3ONP A;  4KDZ A;  4X3M A;  4J3C A;  1V6Z A;  3OII A;  1OY5 A;  1GZ0 A;  4RG1 A;  4YQ0 A;  4JWF A;  1P9P A;  4YQ7 A;  2QMM A;  4YQ5 A;  1MXI A;  2Z0Y A;  3NK6 A;  3OIN A; 
#chains in the Genus database with same CATH homology
 5GMB A;  1Z85 A;  4JAK A;  4JWH A;  3AXZ A;  2V3K A;  3KNU A;  2EGV A;  4MCD A;  2O3A A;  3L8U A;  4CNE A;  4YPY A;  1V2X A;  4YQ9 A;  4YQ3 A;  4CND A;  1UAL A;  4YQT A;  4H3Z A;  1X7O A;  4YQG A;  4CNG A;  4YQS A;  4PZK A;  3GYQ A;  3NK7 A;  4YPW A;  4YQL A;  4KGN A;  4YPZ A;  4YQ4 A;  4YQO A;  3O7B A;  4YQB A;  2CX8 A;  4YQD A;  4CNF A;  2YY8 A;  4FMW A;  1NXZ A;  4MCB A;  4MCC A;  2V3J A;  4YVJ A;  3IEF A;  4YQN A;  2HA8 A;  4YQ8 A;  1VHK A;  4XBO A;  5GM8 A;  4YQI A;  4X3L A;  1NS5 A;  3KY7 A;  1VH0 A;  3ILK A;  3N4J A;  3IC6 A;  3AI9 X;  4YVG A;  4FAK A;  1K3R A;  1UAJ A;  4YQQ A;  4YVH A;  3DCM X;  5GMC A;  4YQK A;  2QWV A;  1VHY A;  4JAL A;  3BBE A;  1TO0 A;  4JWJ A;  3KTY A;  1UAM A;  1ZJR A;  4YVK A;  1UAK A;  2I6D A;  1X7P A;  4YQP A;  1O6D A;  3AIA A;  5CO4 A;  4YPX A;  4YQ2 A;  4YQ6 A;  3OIJ A;  4JWG A;  2EGW A;  4YQA A;  4YQ1 A;  3N4K A;  3E5Y A;  3BBH A;  1J85 A;  5D9F A;  4IG6 A;  4YQR A;  4L69 A;  3BBD A;  4E8B A;  4YVI A;  4YQJ A;  3QUV A;  4YQC A;  1IPA A;  4H3Y A;  5FAI A;  3KW2 A;  3ONP A;  4KDZ A;  4X3M A;  4J3C A;  1V6Z A;  3OII A;  1OY5 A;  1GZ0 A;  4RG1 A;  4YQ0 A;  4JWF A;  1P9P A;  4YQ7 A;  2QMM A;  4YQ5 A;  1MXI A;  2Z0Y A;  3NK6 A;  3OIN 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)

 
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#similar chains, but unknotted
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