3TMD | Genus

Total Genus 110

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	110
sequence length	305
structure length	305
Chain Sequence	DYVSIRVSTLRGDQKIDFNAYVKINDKMILYLRRGDSFEGERLKRLKDKKLRKMYILTDEENSYRTYLQKNIETAYDDTTGKDIQTRADIIQGSQQNNAEEVFENPENVESYNYCKDAAGKYVNFIMSNAQALSAVMNIENTDKTISHHGVTVSTLSIALAQKLGITDPKKTQLLTLGALLHDYGHHHSPLNLNQPLDSMSPEDLALWKKHPIEGAQKVQDKKHFDQTVINIIGQHEETINGTGPKGLREKDMDPLAVLVSSANAMDRLITFEGVPKAEAAKKLMIDHVGKHPLQHIQHLNDILK

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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

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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	Hydrolase,signaling protein
source organism	Bdellovibrio bacteriovorus
publication title	The structure of an unconventional HD-GYP protein from Bdellovibrio reveals the roles of conserved residues in this class of cyclic-di-GMP phosphodiesterases. pubmed doi rcsb
molecule keywords	Uncharacterized protein
total genus	110
structure length	305
sequence length	305
ec nomenclature
pdb deposition date	2011-08-31

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF13487	HD_5	HD domain

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

cath code	Class	Architecture	Topology	Homology	Domain
1.10.3210.10	Mainly Alpha	Orthogonal Bundle	Hypothetical protein af1432	Hypothetical protein af1432	3tmdA00

2HEKA 4TNPA 4TO5A 4BZBA 4TNQA 4RXQA 4QFXA 4TNYA 4MZ7A 3MZOA 4QFZA 3HI0A 4XDSA 1VJ7A 2Q14A 4ME4A 3I7AA 4ZWEA 3RF0A 2PAUA 2CQZA 4TNZA 5AO0A 3P3QA 4N71A 4QG4A 1U6ZA 4L7EA 5AO4A 2PAQA 5TK9A 4L1JA 5AO3A 4TO0A 4MLMA 2PGSA 4L7WA 2PARA 5AO1A 4TO3A 2OGIA 3LJXA 5TK7A 4L1JB 3U1NA 3HC1A 4RXPA 3CCGA 4R8ZA 3IRHA 1YOYA 4X9EA 2DQBA 1YNBA 3M1TA 5TK8A 4LRLA 4TNRA 4QG0A 3NR1A 4QG1A 4DMBA 2PQ7A 4TO4A 4RXRA 4MLNA 4N6WA 4MCWA 4TO6A 3TMCA 1VQRA 5TKAA 4RXSA 4MDZA 2O6IA 3KH1A 3TMDA 2O08A 4BZCA 3NQWA 2FLOA 4TNXA 3TMBA 3TM8A 4RXOA 4TO1A 1XX7A 3MEMA 4ZWGA 4Q7HA 4TO2A 4QG2A 5AO2A 4QFYA 3BG2A 2GZ4A 5TK6A
chains in the Genus database with same CATH superfamily

2HEKA 4TNPA 4TO5A 4BZBA 4TNQA 4RXQA 4QFXA 4TNYA 4MZ7A 3MZOA 4QFZA 3HI0A 4XDSA 3SKDA 1VJ7A 2Q14A 4ME4A 3I7AA 4ZWEA 3RF0A 2PAUA 2CQZA 4TNZA 5AO0A 3P3QA 4N71A 4QG4A 1U6ZA 4L7EA 5AO4A 2PAQA 5TK9A 4L1JA 5AO3A 4TO0A 4MLMA 2PGSA 4L7WA 2PARA 5AO1A 4TO3A 2OGIA 3KQ5A 3LJXA 5TK7A 4L1JB 3U1NA 3HC1A 4RXPA 3CCGA 3SK9A 4R8ZA 3IRHA 1YOYA 4X9EA 2DQBA 1YNBA 3M1TA 5TK8A 4LRLA 4TNRA 4QG0A 3NR1A 4QG1A 4DMBA 2PQ7A 4TO4A 4RXRA 4MLNA 4N6WA 4MCWA 4TO6A 4Q2CA 3TMCA 4QQYA 1VQRA 5TKAA 4RXSA 4MDZA 3S4LA 2O6IA 3KH1A 3TMDA 2O08A 4BZCA 3NQWA 2FLOA 4TNXA 3GW7A 3TMBA 4QQXA 3TM8A 4RXOA 4Q2DA 4TO1A 1XX7A 3MEMA 4ZWGA 4Q7HA 4QQWA 4TO2A 4QG2A 4QFYA 5AO2A 3BG2A 4QQZA 2GZ4A 5TK6A
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 2HEK A;  4TNP A;  4TO5 A;  4BZB A;  4TNQ A;  4RXQ A;  4QFX A;  4TNY A;  4MZ7 A;  3MZO A;  4QFZ A;  3HI0 A;  4XDS A;  1VJ7 A;  2Q14 A;  4ME4 A;  3I7A A;  4ZWE A;  3RF0 A;  2PAU A;  2CQZ A;  4TNZ A;  5AO0 A;  3P3Q A;  4N71 A;  4QG4 A;  1U6Z A;  4L7E A;  5AO4 A;  2PAQ A;  5TK9 A;  4L1J A;  5AO3 A;  4TO0 A;  4MLM A;  2PGS A;  4L7W A;  2PAR A;  5AO1 A;  4TO3 A;  2OGI A;  3LJX A;  5TK7 A;  4L1J B;  3U1N A;  3HC1 A;  4RXP A;  3CCG A;  4R8Z A;  3IRH A;  1YOY A;  4X9E A;  2DQB A;  1YNB A;  3M1T A;  5TK8 A;  4LRL A;  4TNR A;  4QG0 A;  3NR1 A;  4QG1 A;  4DMB A;  2PQ7 A;  4TO4 A;  4RXR A;  4MLN A;  4N6W A;  4MCW A;  4TO6 A;  3TMC A;  1VQR A;  5TKA A;  4RXS A;  4MDZ A;  2O6I A;  3KH1 A;  3TMD A;  2O08 A;  4BZC A;  3NQW A;  2FLO A;  4TNX A;  3TMB A;  3TM8 A;  4RXO A;  4TO1 A;  1XX7 A;  3MEM A;  4ZWG A;  4Q7H A;  4TO2 A;  4QG2 A;  5AO2 A;  4QFY A;  3BG2 A;  2GZ4 A;  5TK6 A; 
#chains in the Genus database with same CATH topology
 2HEK A;  4TNP A;  4TO5 A;  4BZB A;  4TNQ A;  4RXQ A;  4QFX A;  4TNY A;  4MZ7 A;  3MZO A;  4QFZ A;  3HI0 A;  4XDS A;  3SKD A;  1VJ7 A;  2Q14 A;  4ME4 A;  3I7A A;  4ZWE A;  3RF0 A;  2PAU A;  2CQZ A;  4TNZ A;  5AO0 A;  3P3Q A;  4N71 A;  4QG4 A;  1U6Z A;  4L7E A;  5AO4 A;  2PAQ A;  5TK9 A;  4L1J A;  5AO3 A;  4TO0 A;  4MLM A;  2PGS A;  4L7W A;  2PAR A;  5AO1 A;  4TO3 A;  2OGI A;  3KQ5 A;  3LJX A;  5TK7 A;  4L1J B;  3U1N A;  3HC1 A;  4RXP A;  3CCG A;  3SK9 A;  4R8Z A;  3IRH A;  1YOY A;  4X9E A;  2DQB A;  1YNB A;  3M1T A;  5TK8 A;  4LRL A;  4TNR A;  4QG0 A;  3NR1 A;  4QG1 A;  4DMB A;  2PQ7 A;  4TO4 A;  4RXR A;  4MLN A;  4N6W A;  4MCW A;  4TO6 A;  4Q2C A;  3TMC A;  4QQY A;  1VQR A;  5TKA A;  4RXS A;  4MDZ A;  3S4L A;  2O6I A;  3KH1 A;  3TMD A;  2O08 A;  4BZC A;  3NQW A;  2FLO A;  4TNX A;  3GW7 A;  3TMB A;  4QQX A;  3TM8 A;  4RXO A;  4Q2D A;  4TO1 A;  1XX7 A;  3MEM A;  4ZWG A;  4Q7H A;  4QQW A;  4TO2 A;  4QG2 A;  4QFY A;  5AO2 A;  3BG2 A;  4QQZ A;  2GZ4 A;  5TK6 A; 
#chains in the Genus database with same CATH homology
 2HEK A;  4TNP A;  4TO5 A;  4BZB A;  4TNQ A;  4RXQ A;  4QFX A;  4TNY A;  4MZ7 A;  3MZO A;  4QFZ A;  3HI0 A;  4XDS A;  3SKD A;  1VJ7 A;  2Q14 A;  4ME4 A;  3I7A A;  4ZWE A;  3RF0 A;  2PAU A;  2CQZ A;  4TNZ A;  5AO0 A;  3P3Q A;  4N71 A;  4QG4 A;  1U6Z A;  4L7E A;  5AO4 A;  2PAQ A;  5TK9 A;  4L1J A;  5AO3 A;  4TO0 A;  4MLM A;  2PGS A;  4L7W A;  2PAR A;  5AO1 A;  4TO3 A;  2OGI A;  3KQ5 A;  3LJX A;  5TK7 A;  4L1J B;  3U1N A;  3HC1 A;  4RXP A;  3CCG A;  3SK9 A;  4R8Z A;  3IRH A;  1YOY A;  4X9E A;  2DQB A;  1YNB A;  3M1T A;  5TK8 A;  4LRL A;  4TNR A;  4QG0 A;  3NR1 A;  4QG1 A;  4DMB A;  2PQ7 A;  4TO4 A;  4RXR A;  4MLN A;  4N6W A;  4MCW A;  4TO6 A;  4Q2C A;  3TMC A;  4QQY A;  1VQR A;  5TKA A;  4RXS A;  4MDZ A;  3S4L A;  2O6I A;  3KH1 A;  3TMD A;  2O08 A;  4BZC A;  3NQW A;  2FLO A;  4TNX A;  3GW7 A;  3TMB A;  4QQX A;  3TM8 A;  4RXO A;  4Q2D A;  4TO1 A;  1XX7 A;  3MEM A;  4ZWG A;  4Q7H A;  4QQW A;  4TO2 A;  4QG2 A;  4QFY A;  5AO2 A;  3BG2 A;  4QQZ A;  2GZ4 A;  5TK6 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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3TMDA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations