2VQF | Genus

Total Genus 60

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
sequence length	208
structure length	208
Chain Sequence	GRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLREKQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQNLEAMKGRKVGPWLSLDVEGMKGKFLRLPDREDLALPVNEQLVIEFYSR

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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Viewer cachePut cache://localLOAD_/file/5d186b0484b14465c90ea684/pdb.gz

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The Resolver thinks Pdb

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Time for openFile(/file/5d186b0484b14465c90ea684/pdb.gz): 1535 ms

reading 208 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

208 atoms created

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

Time for creating model: 58 ms

Adding embedded #jmolscript: select ({0:207});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

molecule tags	Ribosome
publication title	Modified Uridines with C5-Methylene Substituents at the First Position of the tRNA Anticodon Stabilize U.G Wobble Pairing During Decoding. pubmed doi rcsb
molecule keywords	16S RRNA
total genus	60
structure length	208
sequence length	208
ec nomenclature
pdb deposition date	2008-03-14

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
D	PF00163	Ribosomal_S4	Ribosomal protein S4/S9 N-terminal domain
D	PF01479	S4	S4 domain

Image from the rcsb pdb (www.rcsb.org)

cath code	Class	Architecture	Topology	Homology	Domain
1.10.1050.10	Mainly Alpha	Orthogonal Bundle	Ribosomal Protein S4 Delta 41; Chain A, domain 1	Ribosomal Protein S4 Delta 41; Chain A, domain 1	2vqfD01
3.10.290.10	Alpha Beta	Roll	Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A	RNA-binding S4 domain	2vqfD02

3OTOD 1XNQD 4LF5D 3T1HD 1DM9A 4OUDA 2F4VD 2ZM6D 4DR3D 2K6PA 4YY3D 4X64D 1JH3A 4DUZD 2HHHD 4DV4D 1IBLD 4DV7D 1FKAD 3HP7A 1H3EA 4AQYD 4NXMD 4LFCD 1XMQD 3DH3A 4JI5D 4DR2D 4LFBD 2VQED 1XNRD 4DV2D 4B3MD 4JI8D 1H3FA 1N32D 4JI0D 4JI2D 4X66D 5IWAD 1N36D 2UXCD 4DR1D 4DR7D 5LMUD 1HNZD 2UXDD 4JI7D 1FJGD 2UUCD 4LFAD 1IBKD 1HR0D 2UXBD 1HNWD 1XMOD 4X62D 1KSLA 5LMND 4B3TD 1VIOA 4DV1D 4LF4D 4DR4D 3KBGA 4JV5D 4B3RD 4OX9D 4KHPD 1HNXD 2JANA 4B3SD 4LF7D 4GKJD 4JYAD 1IBMD 4DV5D 4YHHD 2ISTA 1C06A 4JI6D 4DV3D 4DUYD 4DR5D 4GKKD 1I94D 4K0KD 1J5ED 2VQFD 1KSVA 4JI1D 4NXND 4JI4D 1P9KA 2UUBD 5BR8D 4LF9D 4JI3D 2UUAD 4DV0D 2KTLA 1KSKA 2E5LD 3T1YD 4DR6D 4LGTA 4DV6D 1N34D 2UU9D 1N33D 4LF6D 4X65D 1C05A 4LF8D
chains in the Genus database with same CATH superfamily

3OTOD 1XNQD 4LF5D 3T1HD 1DM9A 4OUDA 2F4VD 2ZM6D 1Y8XB 4DR3D 5FLXE 2K6PA 5IT9E 3CMMA 4YY3D 3ONHA 4X64D 1JH3A 4DUZD 1Y8RB 2HHHD 4DV4D 1IBLD 3JAME 4DV7D 1FKAD 3HP7A 1H3EA 4AQYD 4NXMD 4LFCD 1XMQD 3DH3A 4JI5D 2ZTBA 4DR2D 4LFBD 2VQED 1XNRD 4DV2D 4B3MD 4JI8D 1H3FA 1N32D 4JI0D 4JI2D 4X66D 2I1SA 5IWAD 2L3NA 1N36D 2LQ7A 2UXCD 4II2A 4W5VB 4DR1D 4DR7D 5LMUD 1HNZD 5A2QE 1Y8QB 2UXDD 4JI7D 1FJGD 2UUCD 4LFAD 1IBKD 1HR0D 2UXBD 1HNWD 1XMOD 4X62D 1KSLA 5LMND 4B3TD 1VIOA 4DV1D 4LF4D 4DR4D 3KBGA 4JV5D 4B3RD 3KYDB 4OX9D 4KHPD 3J80E 5FQ2B 1HNXD 2JANA 4B3SD 4LF7D 4GKJD 4JYAD 1IBMD 3J7AF 4DV5D 4YHHD 2ISTA 1C06A 3ONGA 4JI6D 4DV3D 2NVUB 4DUYD 4DR5D 4GKKD 1I94D 4K0KD 1J5ED 2VQFD 1KSVA 4JI1D 4NXND 4JI4D 1P9KA 2UUBD 5BR8D 4LF9D 3J81E 4JI3D 2UUAD 4DV0D 2KTLA 1KSKA 2E5LD 3T1YD 4DR6D 4LGTA 4DV6D 1N34D 5LL6S 2UU9D 3FN1A 1N33D 5KNLA 3KYCB 4LF6D 4X65D 4NNJA 1C05A 4II3A 4LF8D
chains in the Genus database with same CATH topology

3OTOD 1XNQD 4LF5D 3T1HD 1DM9A 4OUDA 2F4VD 2ZM6D 4DR3D 2K6PA 4YY3D 4X64D 1JH3A 4DUZD 2HHHD 4DV4D 1IBLD 4DV7D 1FKAD 3HP7A 1H3EA 4AQYD 4NXMD 4LFCD 1XMQD 3DH3A 4JI5D 4DR2D 4LFBD 2VQED 1XNRD 4DV2D 4B3MD 4JI8D 1H3FA 1N32D 4JI0D 4JI2D 4X66D 5IWAD 2L3NA 1N36D 2UXCD 4DR1D 4DR7D 5LMUD 1HNZD 2UXDD 4JI7D 1FJGD 2UUCD 4LFAD 1IBKD 1HR0D 2UXBD 1HNWD 1XMOD 4X62D 1KSLA 5LMND 4B3TD 1VIOA 4DV1D 4LF4D 4DR4D 3KBGA 4JV5D 4B3RD 4OX9D 4KHPD 1HNXD 2JANA 4B3SD 4LF7D 4GKJD 4JYAD 1IBMD 4DV5D 4YHHD 2ISTA 1C06A 4JI6D 4DV3D 4DUYD 4DR5D 4GKKD 1I94D 4K0KD 1J5ED 2VQFD 1KSVA 4JI1D 4NXND 4JI4D 1P9KA 2UUBD 5BR8D 4LF9D 4JI3D 2UUAD 4DV0D 2KTLA 1KSKA 2E5LD 3T1YD 4DR6D 4LGTA 4DV6D 1N34D 2UU9D 1N33D 4LF6D 4X65D 1C05A 4LF8D
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 3OTO D;  1XNQ D;  4LF5 D;  3T1H D;  1DM9 A;  4OUD A;  2F4V D;  2ZM6 D;  4DR3 D;  2K6P A;  4YY3 D;  4X64 D;  1JH3 A;  4DUZ D;  2HHH D;  4DV4 D;  1IBL D;  4DV7 D;  1FKA D;  3HP7 A;  1H3E A;  4AQY D;  4NXM D;  4LFC D;  1XMQ D;  3DH3 A;  4JI5 D;  4DR2 D;  4LFB D;  2VQE D;  1XNR D;  4DV2 D;  4B3M D;  4JI8 D;  1H3F A;  1N32 D;  4JI0 D;  4JI2 D;  4X66 D;  5IWA D;  1N36 D;  2UXC D;  4DR1 D;  4DR7 D;  5LMU D;  1HNZ D;  2UXD D;  4JI7 D;  1FJG D;  2UUC D;  4LFA D;  1IBK D;  1HR0 D;  2UXB D;  1HNW D;  1XMO D;  4X62 D;  1KSL A;  5LMN D;  4B3T D;  1VIO A;  4DV1 D;  4LF4 D;  4DR4 D;  3KBG A;  4JV5 D;  4B3R D;  4OX9 D;  4KHP D;  1HNX D;  2JAN A;  4B3S D;  4LF7 D;  4GKJ D;  4JYA D;  1IBM D;  4DV5 D;  4YHH D;  2IST A;  1C06 A;  4JI6 D;  4DV3 D;  4DUY D;  4DR5 D;  4GKK D;  1I94 D;  4K0K D;  1J5E D;  2VQF D;  1KSV A;  4JI1 D;  4NXN D;  4JI4 D;  1P9K A;  2UUB D;  5BR8 D;  4LF9 D;  4JI3 D;  2UUA D;  4DV0 D;  2KTL A;  1KSK A;  2E5L D;  3T1Y D;  4DR6 D;  4LGT A;  4DV6 D;  1N34 D;  2UU9 D;  1N33 D;  4LF6 D;  4X65 D;  1C05 A;  4LF8 D; 
#chains in the Genus database with same CATH topology
 3OTO D;  1XNQ D;  4LF5 D;  3T1H D;  1DM9 A;  4OUD A;  2F4V D;  2ZM6 D;  1Y8X B;  4DR3 D;  5FLX E;  2K6P A;  5IT9 E;  3CMM A;  4YY3 D;  3ONH A;  4X64 D;  1JH3 A;  4DUZ D;  1Y8R B;  2HHH D;  4DV4 D;  1IBL D;  3JAM E;  4DV7 D;  1FKA D;  3HP7 A;  1H3E A;  4AQY D;  4NXM D;  4LFC D;  1XMQ D;  3DH3 A;  4JI5 D;  2ZTB A;  4DR2 D;  4LFB D;  2VQE D;  1XNR D;  4DV2 D;  4B3M D;  4JI8 D;  1H3F A;  1N32 D;  4JI0 D;  4JI2 D;  4X66 D;  2I1S A;  5IWA D;  2L3N A;  1N36 D;  2LQ7 A;  2UXC D;  4II2 A;  4W5V B;  4DR1 D;  4DR7 D;  5LMU D;  1HNZ D;  5A2Q E;  1Y8Q B;  2UXD D;  4JI7 D;  1FJG D;  2UUC D;  4LFA D;  1IBK D;  1HR0 D;  2UXB D;  1HNW D;  1XMO D;  4X62 D;  1KSL A;  5LMN D;  4B3T D;  1VIO A;  4DV1 D;  4LF4 D;  4DR4 D;  3KBG A;  4JV5 D;  4B3R D;  3KYD B;  4OX9 D;  4KHP D;  3J80 E;  5FQ2 B;  1HNX D;  2JAN A;  4B3S D;  4LF7 D;  4GKJ D;  4JYA D;  1IBM D;  3J7A F;  4DV5 D;  4YHH D;  2IST A;  1C06 A;  3ONG A;  4JI6 D;  4DV3 D;  2NVU B;  4DUY D;  4DR5 D;  4GKK D;  1I94 D;  4K0K D;  1J5E D;  2VQF D;  1KSV A;  4JI1 D;  4NXN D;  4JI4 D;  1P9K A;  2UUB D;  5BR8 D;  4LF9 D;  3J81 E;  4JI3 D;  2UUA D;  4DV0 D;  2KTL A;  1KSK A;  2E5L D;  3T1Y D;  4DR6 D;  4LGT A;  4DV6 D;  1N34 D;  5LL6 S;  2UU9 D;  3FN1 A;  1N33 D;  5KNL A;  3KYC B;  4LF6 D;  4X65 D;  4NNJ A;  1C05 A;  4II3 A;  4LF8 D; 
#chains in the Genus database with same CATH homology
 3OTO D;  1XNQ D;  4LF5 D;  3T1H D;  1DM9 A;  4OUD A;  2F4V D;  2ZM6 D;  4DR3 D;  2K6P A;  4YY3 D;  4X64 D;  1JH3 A;  4DUZ D;  2HHH D;  4DV4 D;  1IBL D;  4DV7 D;  1FKA D;  3HP7 A;  1H3E A;  4AQY D;  4NXM D;  4LFC D;  1XMQ D;  3DH3 A;  4JI5 D;  4DR2 D;  4LFB D;  2VQE D;  1XNR D;  4DV2 D;  4B3M D;  4JI8 D;  1H3F A;  1N32 D;  4JI0 D;  4JI2 D;  4X66 D;  5IWA D;  2L3N A;  1N36 D;  2UXC D;  4DR1 D;  4DR7 D;  5LMU D;  1HNZ D;  2UXD D;  4JI7 D;  1FJG D;  2UUC D;  4LFA D;  1IBK D;  1HR0 D;  2UXB D;  1HNW D;  1XMO D;  4X62 D;  1KSL A;  5LMN D;  4B3T D;  1VIO A;  4DV1 D;  4LF4 D;  4DR4 D;  3KBG A;  4JV5 D;  4B3R D;  4OX9 D;  4KHP D;  1HNX D;  2JAN A;  4B3S D;  4LF7 D;  4GKJ D;  4JYA D;  1IBM D;  4DV5 D;  4YHH D;  2IST A;  1C06 A;  4JI6 D;  4DV3 D;  4DUY D;  4DR5 D;  4GKK D;  1I94 D;  4K0K D;  1J5E D;  2VQF D;  1KSV A;  4JI1 D;  4NXN D;  4JI4 D;  1P9K A;  2UUB D;  5BR8 D;  4LF9 D;  4JI3 D;  2UUA D;  4DV0 D;  2KTL A;  1KSK A;  2E5L D;  3T1Y D;  4DR6 D;  4LGT A;  4DV6 D;  1N34 D;  2UU9 D;  1N33 D;  4LF6 D;  4X65 D;  1C05 A;  4LF8 D;

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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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2VQFD

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations