1VHKA

Crystal structure of an hypothetical protein
Total Genus 69
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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
69
Knots found
sequence length
252
structure length
235
Chain Sequence
b'QRYFIELTKQQIEEAPTFSITGEEVHHIVNVMRMNEGDQIICCSQDGFEAKCELQSVSKDKVSCLVIEWTNENRELPIKVYIASGLPKGDKLEWIIQKGTELGAHAFIPFQAARSVVKRERWTKIAKEAAEQSYRNEVPRVMDVHSFQQLLQRMQDFDKCVVAYESAFSAIVSSLPKGSSLLIVFGPEGGLTEAEVERLTEQDGVTCGLGPRILRTETAPLYALSAISYQTELLR'
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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 keywords Hypothetical protein yqeU
publication title Structural analysis of a set of proteins resulting from a bacterial genomics project
pubmed doi rcsb
source organism Bacillus subtilis
molecule tags Structural genomics, unknown function
total genus 69
structure length 235
sequence length 252
chains with identical sequence B, C, D
other databases KnotProt 2.0: K +31
ec nomenclature ec 2.1.1.193: 16S rRNA (uracil(1498)-N(3))-methyltransferase.
pdb deposition date 2003-12-01

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF04452 Methyltrans_RNA RNA methyltransferase
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
2.40.240.20 Mainly Beta Beta Barrel Ribosomal Protein L25; Chain P Hypothetical PUA domain-like; domain 1 1vhkA01
3.40.1280.10 Alpha Beta 3-Layer(aba) Sandwich Alpha/beta knot Alpha/beta knot 1vhkA02
3OIJA 5GMCA 4YQDA 4YVIA 2YY8A 4YQ2A 4YQJA 4YQ5A 4YQLA 1UAMA 4YQ4A 4YQOA 4YQ3A 3GYQA 3BBHA 4YQSA 4YQ1A 3OINA 4YQ0A 4CNFA 3AIAA 2NWAA 5GM8A 4MCBA 4YQNA 4YQTA 1UAJA 1J85A 4FAKA 4YQCA 2V3KA 4MCCA 3BBDA 3AXZA 5CO4A 2EGWA 1NS5A 2QMMA 4YQ9A 4YVKA 2Z0YA 1V2XA 4XBOA 1X7PA 4YQPA 1Z85A 1IPAA 4YVJA 2EGVA 2V3JA 3KY7A 1MXIA 1UALA 4YQRA 2CX8A 3NK7A 3KW2A 4YVGA 3KTYA 4YPWA 1UAKA 2I6DA 4YQ6A 4YQBA 4CNEA 4H3ZA 4L69A 4JAKA 2O3AA 3L8UA 2HA8A 3NK6A 4YQKA 4YPYA 4YPXA 4IG6A 4CNDA 2QWVA 4YPZA 4YQAA 3N4JA 1TO0A 4YQQA 1VHYA 3E5YA 5D9FA 1GZ0A 3BBEA 1VHKA 3IC6A 4YQ7A 3IEFA 4KGNA 4E8BA 3N4KA 1X7OA 4CNGA 4KDZA 1VH0A 3ONPA 3AI9X 3ILKA 5GMBA 3OIIA 1P9PA 3O7BA 1V6ZA 1O6DA 5FAIA 4H3YA 4X3LA 4MCDA 4X3MA 4YVHA 1ZJRA 3QUVA 4J3CA 3DCMX 4YQIA 1OY5A 1K3RA 4PZKA 4JALA 4RG1A 4YQGA 1NXZA 3KNUA 4YQ8A
chains in the Genus database with same CATH superfamily
3OIJA 4FMWA 5BNZA 5GMCA 3DLLS 4YQDA 1D6KA 2GAEA 2YY8A 4YVIA 4UY88 4YQ2A 2PICA 4YQJA 5IZNA 5JVGS 4YQLA 3W2WB 4YQ5A 1UAMA 4YQ4A 4YQOA 3PIOS 2AE0X 4YQ3A 3GYQA 4WCES 3BBHA 4YQSA 4YQ1A 3OINA 4YQ0A 4CNFA 3AIAA 2NWAA 5GM8A 1EXDA 4JWHA 4MCBA 4YQNA 4JXZA 4YQTA 2RD2A 1UAJA 5GAEW 3X1LB 1J85A 4FAKA 4YQCA 2V3KA 5JVHS 3BBDA 4MCCA 3AXZA 1O0BA 5CO4A 3J7ZV 4JWJA 2EGWA 1NS5A 2ZJQS 2QMMA 4YQ9A 4JWFA 4WFAS 4YVKA 2Z0YA 2HZ7A 1V2XA 4XBOA 5DM7S 2PJJA 1X7PA 4YQPA 2G5DA 4JWGA 1GTSA 1Z85A 2RE8A 4P2BA 1IPAA 4YVJA 2EGVA 2V3JA 3CZBA 3KY7A 1MXIA 1UALA 4YQRA 1DFUP 2CX8A 1O0CA 4WFBS 3NK7A 3W2VB 3KW2A 4YVGA 3KTYA 4YPWA 1UAKA 1QRUA 2I6DA 4V194 4YQ6A 4YQBA 4CNEA 4H3ZA 4L69A 4JAKA 2O3AA 3L8UA 1B75A 2G6GA 2HA8A 3NK6A 4IOAS 4YQKA 4YPYA 5DM6S 4YPXA 4H4KA 4IG6A 4CNDA 1EUYA 2QWVA 4YPZA 4YQAA 4IOCS 3N4JA 1TO0A 3CF5S 4YQQA 1VHYA 4JXXA 2PI8A 4IO9S 3AIIA 3E5YA 5D9FA 4H3SA 1GZ0A 3BBEA 1VHKA 3IC6A 4YQ7A 5GAGW 4WFNS 3IEFA 2PNWA 4E8BA 4KGNA 1QTQA 1QRSA 5GADW 3N4KA 5HL7S 1X7OA 1EUQA 4WF9S 4JYZA 4KDZA 4CNGA 1NYLA 1VH0A 1GTRA 3AI9X 3ILKA 3ONPA 5GMBA 3OIIA 1P9PA 3O7BA 1V6ZA 1O6DA 2ZJPS 3PIPS 5FAIA 5GAHW 4H3YA 4X3LA 4MCDA 4X3MA 4YVHA 1ZJRA 3QUVA 4J3CA 3DCMX 4YQIA 1OY5A 1K3RA 4PZKA 1FEUA 4JALA 4RG1A 4YQGA 2ZJRS 1QRTA 1UDXA 1ZJWA 4U67S 1NXZA 3KNUA 4YQ8A
chains in the Genus database with same CATH topology
3OIJA 4FMWA 5GMCA 4YQDA 4YVIA 2YY8A 4YQ2A 4YQJA 4YQ5A 4YQLA 1UAMA 4YQ4A 4YQOA 4YQ3A 3GYQA 3BBHA 4YQSA 4YQ1A 3OINA 4YQ0A 4CNFA 3AIAA 2NWAA 5GM8A 4JWHA 4MCBA 4YQNA 4YQTA 1UAJA 1J85A 4FAKA 4YQCA 2V3KA 3BBDA 4MCCA 3AXZA 5CO4A 4JWJA 2EGWA 1NS5A 2QMMA 4YQ9A 4JWFA 4YVKA 2Z0YA 1V2XA 4XBOA 1X7PA 4YQPA 4JWGA 1Z85A 1IPAA 4YVJA 2EGVA 2V3JA 3KY7A 1MXIA 1UALA 4YQRA 2CX8A 3NK7A 3KW2A 4YVGA 3KTYA 4YPWA 1UAKA 2I6DA 4YQ6A 4YQBA 4CNEA 4H3ZA 4L69A 4JAKA 2O3AA 3L8UA 2HA8A 3NK6A 4YQKA 4YPYA 4YPXA 4IG6A 4CNDA 2QWVA 4YPZA 4YQAA 3N4JA 1TO0A 4YQQA 1VHYA 3E5YA 5D9FA 1GZ0A 3BBEA 1VHKA 3IC6A 4YQ7A 3IEFA 4KGNA 4E8BA 3N4KA 1X7OA 4CNGA 4KDZA 1VH0A 3ONPA 3AI9X 3ILKA 5GMBA 3OIIA 1P9PA 3O7BA 1V6ZA 1O6DA 5FAIA 4H3YA 4X3LA 4MCDA 4X3MA 4YVHA 1ZJRA 3QUVA 4J3CA 3DCMX 4YQIA 1OY5A 1K3RA 4PZKA 4JALA 4RG1A 4YQGA 1NXZA 3KNUA 4YQ8A
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 3OIJ A;  5GMC A;  4YQD A;  4YVI A;  2YY8 A;  4YQ2 A;  4YQJ A;  4YQ5 A;  4YQL A;  1UAM A;  4YQ4 A;  4YQO A;  4YQ3 A;  3GYQ A;  3BBH A;  4YQS A;  4YQ1 A;  3OIN A;  4YQ0 A;  4CNF A;  3AIA A;  2NWA A;  5GM8 A;  4MCB A;  4YQN A;  4YQT A;  1UAJ A;  1J85 A;  4FAK A;  4YQC A;  2V3K A;  4MCC A;  3BBD A;  3AXZ A;  5CO4 A;  2EGW A;  1NS5 A;  2QMM A;  4YQ9 A;  4YVK A;  2Z0Y A;  1V2X A;  4XBO A;  1X7P A;  4YQP A;  1Z85 A;  1IPA A;  4YVJ A;  2EGV A;  2V3J A;  3KY7 A;  1MXI A;  1UAL A;  4YQR A;  2CX8 A;  3NK7 A;  3KW2 A;  4YVG A;  3KTY A;  4YPW A;  1UAK A;  2I6D A;  4YQ6 A;  4YQB A;  4CNE A;  4H3Z A;  4L69 A;  4JAK A;  2O3A A;  3L8U A;  2HA8 A;  3NK6 A;  4YQK A;  4YPY A;  4YPX A;  4IG6 A;  4CND A;  2QWV A;  4YPZ A;  4YQA A;  3N4J A;  1TO0 A;  4YQQ A;  1VHY A;  3E5Y A;  5D9F A;  1GZ0 A;  3BBE A;  1VHK A;  3IC6 A;  4YQ7 A;  3IEF A;  4KGN A;  4E8B A;  3N4K A;  1X7O A;  4CNG A;  4KDZ A;  1VH0 A;  3ONP A;  3AI9 X;  3ILK A;  5GMB A;  3OII A;  1P9P A;  3O7B A;  1V6Z A;  1O6D A;  5FAI A;  4H3Y A;  4X3L A;  4MCD A;  4X3M A;  4YVH A;  1ZJR A;  3QUV A;  4J3C A;  3DCM X;  4YQI A;  1OY5 A;  1K3R A;  4PZK A;  4JAL A;  4RG1 A;  4YQG A;  1NXZ A;  3KNU A;  4YQ8 A; 
#chains in the Genus database with same CATH topology
 3OIJ A;  4FMW A;  5BNZ A;  5GMC A;  3DLL S;  4YQD A;  1D6K A;  2GAE A;  2YY8 A;  4YVI A;  4UY8 8;  4YQ2 A;  2PIC A;  4YQJ A;  5IZN A;  5JVG S;  4YQL A;  3W2W B;  4YQ5 A;  1UAM A;  4YQ4 A;  4YQO A;  3PIO S;  2AE0 X;  4YQ3 A;  3GYQ A;  4WCE S;  3BBH A;  4YQS A;  4YQ1 A;  3OIN A;  4YQ0 A;  4CNF A;  3AIA A;  2NWA A;  5GM8 A;  1EXD A;  4JWH A;  4MCB A;  4YQN A;  4JXZ A;  4YQT A;  2RD2 A;  1UAJ A;  5GAE W;  3X1L B;  1J85 A;  4FAK A;  4YQC A;  2V3K A;  5JVH S;  3BBD A;  4MCC A;  3AXZ A;  1O0B A;  5CO4 A;  3J7Z V;  4JWJ A;  2EGW A;  1NS5 A;  2ZJQ S;  2QMM A;  4YQ9 A;  4JWF A;  4WFA S;  4YVK A;  2Z0Y A;  2HZ7 A;  1V2X A;  4XBO A;  5DM7 S;  2PJJ A;  1X7P A;  4YQP A;  2G5D A;  4JWG A;  1GTS A;  1Z85 A;  2RE8 A;  4P2B A;  1IPA A;  4YVJ A;  2EGV A;  2V3J A;  3CZB A;  3KY7 A;  1MXI A;  1UAL A;  4YQR A;  1DFU P;  2CX8 A;  1O0C A;  4WFB S;  3NK7 A;  3W2V B;  3KW2 A;  4YVG A;  3KTY A;  4YPW A;  1UAK A;  1QRU A;  2I6D A;  4V19 4;  4YQ6 A;  4YQB A;  4CNE A;  4H3Z A;  4L69 A;  4JAK A;  2O3A A;  3L8U A;  1B75 A;  2G6G A;  2HA8 A;  3NK6 A;  4IOA S;  4YQK A;  4YPY A;  5DM6 S;  4YPX A;  4H4K A;  4IG6 A;  4CND A;  1EUY A;  2QWV A;  4YPZ A;  4YQA A;  4IOC S;  3N4J A;  1TO0 A;  3CF5 S;  4YQQ A;  1VHY A;  4JXX A;  2PI8 A;  4IO9 S;  3AII A;  3E5Y A;  5D9F A;  4H3S A;  1GZ0 A;  3BBE A;  1VHK A;  3IC6 A;  4YQ7 A;  5GAG W;  4WFN S;  3IEF A;  2PNW A;  4E8B A;  4KGN A;  1QTQ A;  1QRS A;  5GAD W;  3N4K A;  5HL7 S;  1X7O A;  1EUQ A;  4WF9 S;  4JYZ A;  4KDZ A;  4CNG A;  1NYL A;  1VH0 A;  1GTR A;  3AI9 X;  3ILK A;  3ONP A;  5GMB A;  3OII A;  1P9P A;  3O7B A;  1V6Z A;  1O6D A;  2ZJP S;  3PIP S;  5FAI A;  5GAH W;  4H3Y A;  4X3L A;  4MCD A;  4X3M A;  4YVH A;  1ZJR A;  3QUV A;  4J3C A;  3DCM X;  4YQI A;  1OY5 A;  1K3R A;  4PZK A;  1FEU A;  4JAL A;  4RG1 A;  4YQG A;  2ZJR S;  1QRT A;  1UDX A;  1ZJW A;  4U67 S;  1NXZ A;  3KNU A;  4YQ8 A; 
#chains in the Genus database with same CATH homology
 3OIJ A;  4FMW A;  5GMC A;  4YQD A;  4YVI A;  2YY8 A;  4YQ2 A;  4YQJ A;  4YQ5 A;  4YQL A;  1UAM A;  4YQ4 A;  4YQO A;  4YQ3 A;  3GYQ A;  3BBH A;  4YQS A;  4YQ1 A;  3OIN A;  4YQ0 A;  4CNF A;  3AIA A;  2NWA A;  5GM8 A;  4JWH A;  4MCB A;  4YQN A;  4YQT A;  1UAJ A;  1J85 A;  4FAK A;  4YQC A;  2V3K A;  3BBD A;  4MCC A;  3AXZ A;  5CO4 A;  4JWJ A;  2EGW A;  1NS5 A;  2QMM A;  4YQ9 A;  4JWF A;  4YVK A;  2Z0Y A;  1V2X A;  4XBO A;  1X7P A;  4YQP A;  4JWG A;  1Z85 A;  1IPA A;  4YVJ A;  2EGV A;  2V3J A;  3KY7 A;  1MXI A;  1UAL A;  4YQR A;  2CX8 A;  3NK7 A;  3KW2 A;  4YVG A;  3KTY A;  4YPW A;  1UAK A;  2I6D A;  4YQ6 A;  4YQB A;  4CNE A;  4H3Z A;  4L69 A;  4JAK A;  2O3A A;  3L8U A;  2HA8 A;  3NK6 A;  4YQK A;  4YPY A;  4YPX A;  4IG6 A;  4CND A;  2QWV A;  4YPZ A;  4YQA A;  3N4J A;  1TO0 A;  4YQQ A;  1VHY A;  3E5Y A;  5D9F A;  1GZ0 A;  3BBE A;  1VHK A;  3IC6 A;  4YQ7 A;  3IEF A;  4KGN A;  4E8B A;  3N4K A;  1X7O A;  4CNG A;  4KDZ A;  1VH0 A;  3ONP A;  3AI9 X;  3ILK A;  5GMB A;  3OII A;  1P9P A;  3O7B A;  1V6Z A;  1O6D A;  5FAI A;  4H3Y A;  4X3L A;  4MCD A;  4X3M A;  4YVH A;  1ZJR A;  3QUV A;  4J3C A;  3DCM X;  4YQI A;  1OY5 A;  1K3R A;  4PZK A;  4JAL A;  4RG1 A;  4YQG A;  1NXZ A;  3KNU A;  4YQ8 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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