3KTY | Genus

Total Genus 48

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	48
Knots found	KnotProt 2.0: K +3₁
sequence length	173
structure length	167
Chain Sequence	SNAMTQAFSRVRFIMTQPSHPGNVGSAARAIKTMGFGELVLVAPRFPDMTAQPEAVALASGALDVLERAAVHDTLEEALAPVTLAFALTTRPPPCDIREAAGLARRHLDDTEAGVVAIVLGTERGLTNAQIELCHRICHIPANPQYSSLNVAQALQLAAWELRYALL

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

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The Resolver thinks Pdb

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Time for openFile(/file/5cff6457004e681d81150bc9/pdb.gz): 2197 ms

reading 167 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Jmol

167 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

Time for creating model: 19 ms

Adding embedded #jmolscript: select ({0:166});backbone only;select *;

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Genus data interpretation

Chord Diagram

publication title	Crystal Structure of Probable Methyltransferase SpoU from Bordetella pertussis Tohama I rcsb
molecule keywords	Probable methyltransferase
molecule tags	Transferase
source organism	Bordetella pertussis
total genus	48
structure length	167
sequence length	173
chains with identical sequence	B, C
other databases	KnotProt 2.0: K +3₁
ec nomenclature
pdb deposition date	2009-11-26

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	Class	Architecture	Topology	Homology	Domain
3.40.1280.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha/beta knot	Alpha/beta knot	3ktyA01

2EGVA 2O3AA 4CNFA 2V3JA 2YY8A 1Z85A 5GMBA 1IPAA 4YQSA 4H3ZA 4YQ5A 4YQ6A 4YQ8A 4XBOA 4X3LA 4YQ4A 3IC6A 3L8UA 3GYQA 1UAJA 3BBDA 4MCBA 4YQ0A 3AIAA 3OIJA 3IEFA 1J85A 2Z0YA 3KNUA 3AI9X 4YQLA 4YQTA 1NS5A 3BBHA 4YVHA 1GZ0A 4L69A 4CNGA 4JALA 4X3MA 1P9PA 1VHYA 5CO4A 4YQ3A 3DCMX 4YQAA 4YPYA 1K3RA 4PZKA 3ONPA 1VHKA 1OY5A 1ZJRA 1X7OA 3N4JA 4CNEA 1V2XA 4FAKA 1TO0A 4YQGA 3OIIA 4MCCA 4RG1A 4MCDA 4YQJA 3KTYA 3QUVA 5GMCA 1X7PA 4IG6A 3KY7A 3O7BA 4KDZA 4YQOA 4YQ9A 2EGWA 3N4KA 2CX8A 2I6DA 4YQDA 3AXZA 4YQKA 4E8BA 4YVJA 1UALA 3ILKA 4YQBA 4YQRA 4KGNA 4H3YA 4JAKA 2QWVA 4YVIA 1O6DA 1V6ZA 5D9FA 3KW2A 1MXIA 1UAKA 4J3CA 5GM8A 1NXZA 4YQ2A 2HA8A 1VH0A 4YQCA 2V3KA 3NK7A 3BBEA 5FAIA 4YPZA 4YPXA 3E5YA 3OINA 3NK6A 4YVGA 4YQ7A 4YQNA 4CNDA 2QMMA 4YQIA 4YQQA 1UAMA 4YQ1A 4YPWA 4YQPA 4YVKA
chains in the Genus database with same CATH superfamily

2EGVA 2O3AA 4CNFA 2V3JA 2YY8A 1Z85A 5GMBA 1IPAA 4YQSA 4H3ZA 4YQ5A 4YQ6A 4YQ8A 4XBOA 4X3LA 4YQ4A 3IC6A 3L8UA 3GYQA 1UAJA 3BBDA 4MCBA 4YQ0A 3AIAA 3OIJA 3IEFA 1J85A 2Z0YA 3KNUA 3AI9X 4YQLA 4YQTA 1NS5A 3BBHA 4YVHA 1GZ0A 4L69A 4CNGA 4JALA 4JWHA 4X3MA 1P9PA 1VHYA 5CO4A 4YQ3A 3DCMX 4YQAA 4JWFA 4YPYA 1K3RA 4PZKA 4FMWA 3ONPA 1VHKA 1OY5A 1ZJRA 1X7OA 3N4JA 4CNEA 1V2XA 4FAKA 1TO0A 4YQGA 3OIIA 4MCCA 4RG1A 4MCDA 4YQJA 3KTYA 3QUVA 5GMCA 1X7PA 4IG6A 3KY7A 3O7BA 4KDZA 4YQOA 4YQ9A 2EGWA 3N4KA 2CX8A 2I6DA 4YQDA 3AXZA 4YQKA 4E8BA 4YVJA 1UALA 3ILKA 4YQBA 4YQRA 4KGNA 4H3YA 4JAKA 2QWVA 4JWJA 4YVIA 1O6DA 1V6ZA 5D9FA 3KW2A 1MXIA 1UAKA 4J3CA 5GM8A 1NXZA 4YQ2A 2HA8A 1VH0A 4YQCA 2V3KA 3NK7A 3BBEA 5FAIA 4YPZA 4YPXA 3E5YA 3OINA 3NK6A 4YVGA 4YQ7A 4YQNA 4CNDA 2QMMA 4YQIA 4JWGA 4YQQA 1UAMA 4YQ1A 4YPWA 4YQPA 4YVKA
chains in the Genus database with same CATH topology

2EGVA 2O3AA 4CNFA 2V3JA 2YY8A 1Z85A 5GMBA 1IPAA 4YQSA 4H3ZA 4YQ5A 4YQ6A 4YQ8A 4XBOA 4X3LA 4YQ4A 3IC6A 3L8UA 3GYQA 1UAJA 3BBDA 4MCBA 4YQ0A 3AIAA 3OIJA 3IEFA 1J85A 2Z0YA 3KNUA 3AI9X 4YQLA 4YQTA 1NS5A 3BBHA 4YVHA 1GZ0A 4L69A 4CNGA 4JALA 4JWHA 4X3MA 1P9PA 1VHYA 5CO4A 4YQ3A 3DCMX 4YQAA 4JWFA 4YPYA 1K3RA 4PZKA 4FMWA 3ONPA 1VHKA 1OY5A 1ZJRA 1X7OA 3N4JA 4CNEA 1V2XA 4FAKA 1TO0A 4YQGA 3OIIA 4MCCA 4RG1A 4MCDA 4YQJA 3KTYA 3QUVA 5GMCA 1X7PA 4IG6A 3KY7A 3O7BA 4KDZA 4YQOA 4YQ9A 2EGWA 3N4KA 2CX8A 2I6DA 4YQDA 3AXZA 4YQKA 4E8BA 4YVJA 1UALA 3ILKA 4YQBA 4YQRA 4KGNA 4H3YA 4JAKA 2QWVA 4JWJA 4YVIA 1O6DA 1V6ZA 5D9FA 3KW2A 1MXIA 1UAKA 4J3CA 5GM8A 1NXZA 4YQ2A 2HA8A 1VH0A 4YQCA 2V3KA 3NK7A 3BBEA 5FAIA 4YPZA 4YPXA 3E5YA 3OINA 3NK6A 4YVGA 4YQ7A 4YQNA 4CNDA 2QMMA 4YQIA 4JWGA 4YQQA 1UAMA 4YQ1A 4YPWA 4YQPA 4YVKA
chains in the Genus database with same CATH homology

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

Total Genus

Knots found

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations