2FIO | Genus

Total Genus 43

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	43
sequence length	123
structure length	123
Chain Sequence	PKTQRGIYHNLKESEYVASNTDVTFFFSSELYLNKFLDGYQEYRKKFNKKIERVAVTPWNMDMLADITFYSEVEKRGFHAWLKGDNATWREVHVYALRIMTKPNTLDWSRIQKPRLRERRKSM

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/5d252aa43ae3aa23095315d3/pdb.gz

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The Resolver thinks Pdb

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Time for openFile(/file/5d252aa43ae3aa23095315d3/pdb.gz): 1129 ms

reading 123 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

123 atoms created

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

Time for creating model: 18 ms

Adding embedded #jmolscript: select ({0:122});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	Transcription/dna
source organism	Bacillus phage phi29
publication title	The structure of phage phi29 transcription regulator p4-DNA complex reveals an N-hook motif for DNA pubmed doi rcsb
molecule keywords	DNA (41-MER)
total genus	43
structure length	123
sequence length	123
chains with identical sequence	B
ec nomenclature
pdb deposition date	2005-12-30

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

cath code	Class	Architecture	Topology	Homology	Domain
1.10.274.40	Mainly Alpha	Orthogonal Bundle	Enzyme I; Chain A, domain 2	Enzyme I; Chain A, domain 2	2fioA00

2FIPA 2FIOA
chains in the Genus database with same CATH superfamily

1TWFA 2R7ZA 1ZYMA 2A69D 4FBSA 1I6VD 4CQ5A 2O5JD 1SFOA 2LKMB 1I3QA 1ZYRD 5IZ2A 2MX8A 2CW0D 2X0OA 2EZBA 4C6GA 2FIPA 2NVXA 1W27A 4C5UA 2LTHA 2VK9A 3EZBA 2N3EA 4CEHA 2K3OA 2NVYA 3FKIA 1WCMA 4CEIA 3GTQA 3GTOA 2K3QA 2HWGA 2A6HD 1EZAA 2A68D 2VUMA 1R9TA 2MQAA 3EZEA 1Y2MA 2MX9A 2MP0A 1K83A 1Y1WA 4V2QA 4C5SA 1Y1VA 2Y0NA 2E2IA 2AQLA 3GTGA 3LRDA 2JA6A 3NZ4A 2F5JA 2N1DB 3CQZA 2X0QA 3GTMA 1I50A 2YU9A 2B63A 2K3NA 2LPJA 1TWAA 2R93A 3U44A 1YNND 2EZAA 1EZBA 2YIIA 2EZCA 4QIWA 4C2MA 1SMYD 2A6ED 3H0GA 2X0PA 3GTLA 4CEJA 3U4QA 4BAAA 2FIOA 2BE5D 1TWGA 1T6JA 2LPIA 2JA7A 3LR2A 1HQMD 3GTPA 2LYIA 2JA5A 1TWCA 4V2RA 4C5RA 1T6PA 1IW7D 3GTJA 3LR6A 2E2HA 3LR8A 2R92A 3GTKA 1TWHA 3EZAA 2HROA 1YNJD 4BABA
chains in the Genus database with same CATH topology

1TWFA 2R7ZA 2A69D 4FBSA 1I6VD 2O5JD 1SFOA 2LKMB 1I3QA 1ZYRD 5IZ2A 2MX8A 2CW0D 2X0OA 2FIPA 2NVXA 2LTHA 2VK9A 2N3EA 4CEHA 2K3OA 2NVYA 3FKIA 1WCMA 4CEIA 3GTQA 3GTOA 2K3QA 2A6HD 2A68D 2VUMA 1R9TA 2MQAA 2MX9A 1K83A 1Y1WA 1Y1VA 2Y0NA 2E2IA 2AQLA 3GTGA 3LRDA 2JA6A 2F5JA 2N1DB 3CQZA 3GTMA 2X0QA 1I50A 2YU9A 2B63A 2K3NA 2LPJA 1TWAA 2R93A 3U44A 1YNND 4QIWA 4C2MA 2A6ED 3H0GA 2X0PA 3GTLA 4CEJA 3U4QA 2FIOA 2BE5D 1TWGA 2LPIA 2JA7A 3LR2A 1HQMD 3GTPA 2LYIA 2JA5A 1TWCA 1IW7D 3GTJA 3LR6A 2E2HA 3LR8A 2R92A 3GTKA 1TWHA 1SMYD 1YNJD
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 2FIP A;  2FIO A; 
#chains in the Genus database with same CATH topology
 1TWF A;  2R7Z A;  1ZYM A;  2A69 D;  4FBS A;  1I6V D;  4CQ5 A;  2O5J D;  1SFO A;  2LKM B;  1I3Q A;  1ZYR D;  5IZ2 A;  2MX8 A;  2CW0 D;  2X0O A;  2EZB A;  4C6G A;  2FIP A;  2NVX A;  1W27 A;  4C5U A;  2LTH A;  2VK9 A;  3EZB A;  2N3E A;  4CEH A;  2K3O A;  2NVY A;  3FKI A;  1WCM A;  4CEI A;  3GTQ A;  3GTO A;  2K3Q A;  2HWG A;  2A6H D;  1EZA A;  2A68 D;  2VUM A;  1R9T A;  2MQA A;  3EZE A;  1Y2M A;  2MX9 A;  2MP0 A;  1K83 A;  1Y1W A;  4V2Q A;  4C5S A;  1Y1V A;  2Y0N A;  2E2I A;  2AQL A;  3GTG A;  3LRD A;  2JA6 A;  3NZ4 A;  2F5J A;  2N1D B;  3CQZ A;  2X0Q A;  3GTM A;  1I50 A;  2YU9 A;  2B63 A;  2K3N A;  2LPJ A;  1TWA A;  2R93 A;  3U44 A;  1YNN D;  2EZA A;  1EZB A;  2YII A;  2EZC A;  4QIW A;  4C2M A;  1SMY D;  2A6E D;  3H0G A;  2X0P A;  3GTL A;  4CEJ A;  3U4Q A;  4BAA A;  2FIO A;  2BE5 D;  1TWG A;  1T6J A;  2LPI A;  2JA7 A;  3LR2 A;  1HQM D;  3GTP A;  2LYI A;  2JA5 A;  1TWC A;  4V2R A;  4C5R A;  1T6P A;  1IW7 D;  3GTJ A;  3LR6 A;  2E2H A;  3LR8 A;  2R92 A;  3GTK A;  1TWH A;  3EZA A;  2HRO A;  1YNJ D;  4BAB A; 
#chains in the Genus database with same CATH homology
 1TWF A;  2R7Z A;  2A69 D;  4FBS A;  1I6V D;  2O5J D;  1SFO A;  2LKM B;  1I3Q A;  1ZYR D;  5IZ2 A;  2MX8 A;  2CW0 D;  2X0O A;  2FIP A;  2NVX A;  2LTH A;  2VK9 A;  2N3E A;  4CEH A;  2K3O A;  2NVY A;  3FKI A;  1WCM A;  4CEI A;  3GTQ A;  3GTO A;  2K3Q A;  2A6H D;  2A68 D;  2VUM A;  1R9T A;  2MQA A;  2MX9 A;  1K83 A;  1Y1W A;  1Y1V A;  2Y0N A;  2E2I A;  2AQL A;  3GTG A;  3LRD A;  2JA6 A;  2F5J A;  2N1D B;  3CQZ A;  3GTM A;  2X0Q A;  1I50 A;  2YU9 A;  2B63 A;  2K3N A;  2LPJ A;  1TWA A;  2R93 A;  3U44 A;  1YNN D;  4QIW A;  4C2M A;  2A6E D;  3H0G A;  2X0P A;  3GTL A;  4CEJ A;  3U4Q A;  2FIO A;  2BE5 D;  1TWG A;  2LPI A;  2JA7 A;  3LR2 A;  1HQM D;  3GTP A;  2LYI A;  2JA5 A;  1TWC A;  1IW7 D;  3GTJ A;  3LR6 A;  2E2H A;  3LR8 A;  2R92 A;  3GTK A;  1TWH A;  1SMY D;  1YNJ 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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2FIOA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN