3TM8 | Genus

Total Genus 126

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	126
sequence length	309
structure length	309
Chain Sequence	HMDYVSIRVSTLRGDQKIDFNAYVKINDKMILYLRRGDSFEGERLKRLKDKKLRKMYILTDEENSYRTYLQKNIETAYDDTTGKDIQTRADIIQGSQQNNAEEVFENPENVESYNYCKDAAGKYVNFIMSNAQALSAVMNIENTDKTISHHGVTVSTLSIALAQKLGITDPKKTQLLTLGALLHDYGHHHSPLNLNQPLDSMSPEDLALWKKHPIEGAQKVQDKKHFDQTVINIIGQHEETINGTGPKGLREKDMDPLAVLVSSANAMDRLITFEGVPKAEAAKKLMIDHVGKHPLQHIQHLNDILKGL

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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	126
structure length	309
sequence length	309
chains with identical sequence	B
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	3tm8A00

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

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

#chains in the Genus database with same CATH superfamily
 4N71 A;  3U1N A;  4QFY A;  4ME4 A;  2DQB A;  3NR1 A;  5AO3 A;  4TNX A;  3IRH A;  3HC1 A;  4TO4 A;  1YOY A;  4TNQ A;  4TO5 A;  5TK9 A;  4TO2 A;  4TO1 A;  4ZWE A;  4QG2 A;  5AO1 A;  4TNP A;  3NQW A;  4RXR A;  4N6W A;  4X9E A;  5TK6 A;  4QG4 A;  4L1J A;  5TK8 A;  2HEK A;  3MEM A;  1U6Z A;  4DMB A;  4TNY A;  4MZ7 A;  3TMD A;  5TK7 A;  5AO4 A;  2PQ7 A;  4TO3 A;  3TM8 A;  4MDZ A;  4TO0 A;  4BZB A;  3RF0 A;  4XDS A;  3BG2 A;  3I7A A;  4BZC A;  2OGI A;  4MLM A;  2Q14 A;  3KH1 A;  4TNZ A;  3M1T A;  2GZ4 A;  5TKA A;  3P3Q A;  4MLN A;  4L7W A;  2O6I A;  5AO2 A;  1YNB A;  4ZWG A;  4MCW A;  2CQZ A;  1VQR A;  5AO0 A;  2PAR A;  4L7E A;  2FLO A;  3CCG A;  3HI0 A;  2O08 A;  2PGS A;  4L1J B;  4QFZ A;  4TO6 A;  2PAQ A;  4RXP A;  4QFX A;  4RXQ A;  1VJ7 A;  4LRL A;  3TMB A;  2PAU A;  3MZO A;  4RXS A;  3LJX A;  4QG0 A;  4RXO A;  1XX7 A;  4TNR A;  3TMC A;  4Q7H A;  4R8Z A;  4QG1 A; 
#chains in the Genus database with same CATH topology
 4N71 A;  3U1N A;  4QFY A;  4ME4 A;  2DQB A;  3NR1 A;  5AO3 A;  4TNX A;  3IRH A;  3KQ5 A;  3HC1 A;  4TO4 A;  1YOY A;  4TNQ A;  4TO5 A;  5TK9 A;  4TO2 A;  4TO1 A;  4ZWE A;  4QG2 A;  5AO1 A;  4TNP A;  3NQW A;  4RXR A;  4N6W A;  4X9E A;  5TK6 A;  4QQW A;  4QG4 A;  4L1J A;  5TK8 A;  2HEK A;  3MEM A;  1U6Z A;  4DMB A;  4TNY A;  4MZ7 A;  3S4L A;  3TMD A;  5TK7 A;  4QQX A;  5AO4 A;  2PQ7 A;  4TO3 A;  3TM8 A;  4MDZ A;  4TO0 A;  4BZB A;  3RF0 A;  3BG2 A;  4XDS A;  3I7A A;  4Q2D A;  4BZC A;  2OGI A;  4MLM A;  2Q14 A;  3KH1 A;  4TNZ A;  3M1T A;  2GZ4 A;  5TKA A;  3P3Q A;  3GW7 A;  4MLN A;  4L7W A;  2O6I A;  5AO2 A;  1YNB A;  4ZWG A;  4MCW A;  2CQZ A;  1VQR A;  5AO0 A;  2PAR A;  4L7E A;  2FLO A;  3CCG A;  3SKD A;  3HI0 A;  2O08 A;  2PGS A;  4L1J B;  4QQZ A;  4QFZ A;  4TO6 A;  2PAQ A;  4RXP A;  4QFX A;  3SK9 A;  4RXQ A;  1VJ7 A;  4QQY A;  4LRL A;  3TMB A;  2PAU A;  3MZO A;  4RXS A;  3LJX A;  4QG0 A;  4RXO A;  1XX7 A;  4TNR A;  4Q2C A;  3TMC A;  4Q7H A;  4R8Z A;  4QG1 A; 
#chains in the Genus database with same CATH homology
 4N71 A;  3U1N A;  4QFY A;  4ME4 A;  2DQB A;  3NR1 A;  5AO3 A;  4TNX A;  3IRH A;  3KQ5 A;  3HC1 A;  4TO4 A;  1YOY A;  4TNQ A;  4TO5 A;  5TK9 A;  4TO2 A;  4TO1 A;  4ZWE A;  4QG2 A;  5AO1 A;  4TNP A;  3NQW A;  4RXR A;  4N6W A;  4X9E A;  5TK6 A;  4QQW A;  4QG4 A;  4L1J A;  5TK8 A;  2HEK A;  3MEM A;  1U6Z A;  4DMB A;  4TNY A;  4MZ7 A;  3S4L A;  3TMD A;  5TK7 A;  4QQX A;  5AO4 A;  2PQ7 A;  4TO3 A;  3TM8 A;  4MDZ A;  4TO0 A;  4BZB A;  3RF0 A;  3BG2 A;  4XDS A;  3I7A A;  4Q2D A;  4BZC A;  2OGI A;  4MLM A;  2Q14 A;  3KH1 A;  4TNZ A;  3M1T A;  2GZ4 A;  5TKA A;  3P3Q A;  3GW7 A;  4MLN A;  4L7W A;  2O6I A;  5AO2 A;  1YNB A;  4ZWG A;  4MCW A;  2CQZ A;  1VQR A;  5AO0 A;  2PAR A;  4L7E A;  2FLO A;  3CCG A;  3SKD A;  3HI0 A;  2O08 A;  2PGS A;  4L1J B;  4QQZ A;  4QFZ A;  4TO6 A;  2PAQ A;  4RXP A;  4QFX A;  3SK9 A;  4RXQ A;  1VJ7 A;  4QQY A;  4LRL A;  3TMB A;  2PAU A;  3MZO A;  4RXS A;  3LJX A;  4QG0 A;  4RXO A;  1XX7 A;  4TNR A;  4Q2C A;  3TMC A;  4Q7H A;  4R8Z A;  4QG1 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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3TM8A

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations