CATH Domain: 2abqA00

2abqA00

PDB 2abq, Chain A, Domain 0

CATH Code	Level Description	Links
3	Alpha Beta
3.40	3-Layer(aba) Sandwich
3.40.1190	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
3.40.1190.20		Gene3D
3.40.1190.20.15
3.40.1190.20.15.1
3.40.1190.20.15.1.1
3.40.1190.20.15.1.1.1
3.40.1190.20.15.1.1.1.1

Structure
Sequence
History

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Segment boundaries for domain 2abqA00

Domain	Start PDB Residue	Stop PDB Residue
2abqA00	2	306

What is a Structural Neighbour?

The term "structural neighbour" is used here to describe two CATH domains that share a degree of structural similarity. The SSAP algorithm is used to calculate this similarity and works by generating a structure-based pairwise alignment of the two domains then scoring this alignment using a RMSD score which has been normalised by the length of the larger domain divided by the number of aligned residues (SIMAX).

Structural Neighbourhood (7 entries)

There are 7 matching structural neighberhood comparisons for CATH ID 3.40.1190.20.15.1.1.1.1 (SIMAX score < 5)

Match	SSAP score	Match Keywords	Match Superfamily	Length	Sequence Id	Overlap	RMSD	SIMAX
2ajrA01	84.40	Thermotoga maritima1-phosphofructokinase [EC:2.7.1.56]Fructose and mannose metabolismSugar kinase, pfkB family	3.40.1190.20	259	26	82	2.18	2.64
2fv7A00	83.40	Pentose phosphate pathwayRibokinaseRibokinase [EC:2.7.1.15]Homo sapiens	3.40.1190.20	308	14	92	2.97	3.22
1tyyB00	82.34	Amino sugar and nucleotide sugar metabolismStarch and sucrose metabolismFructose and mannose metabolismMetabolic pathwaysFructokinase [EC:2.7.1.4]	3.40.1190.20	292	19	88	3.18	3.58
2afbB00	80.59	Thermotoga maritima2-dehydro-3-deoxygluconokinase [EC:2.7.1.45]Pentose phosphate pathwayPentose and glucuronate interconversions2-keto-3-deoxygluconate kinase	3.40.1190.20	319	15	89	3.11	3.48
1ub0A00	78.59	TransferaseThiamine metabolismHydroxymethylpyrimidine kinase [EC:2.7.1.49]Phosphomethylpyrimidine kinase [EC:2.7.4.7]Metabolic pathways	3.40.1190.20	246	16	74	2.95	3.98
3bf5A01	77.37	Pentose phosphate pathwayRibokinase [EC:2.7.1.15]Thermoplasma acidophilumRibokinase related protein	3.40.1190.20	221	13	69	3.28	4.74
2i5bA00	77.23	Thiamine metabolismBacillus subtilisPyridoxine kinasePhosphomethylpyrimidine kinase [EC:2.7.4.7]Metabolic pathways	3.40.1190.20	269	13	75	3.33	4.39

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Domain ATOM Sequence

>pdb|2abqA00
IYTVTLNPSIDYIVQVENFQQGVVNRSERDRKQPGGKGINVSRVLKRLGHETKALGFLGGFTGAYVRNALEKEEIGLSFI
EVEGDTRINVKIKGKQETELNGTAPLIKKEHVQALLEQLTELEKGDVLVLAGSVPQAPQTIYRSTQIAKERGAFVAVDTS
GEALHEVLAAKPSFIKPNHHELSELVSKPIASIEDAIPHVQRLIGEGIESILVSFAGDGALFASAEGFHVNVPSGEVRNS
VGAGDSVVAGFLAALQEGKSLEDAVPFAVAAGSATAFSDGFCTREEVERLQQQLQRTIKKEG

BLAST against CATH

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Domain COMBS Sequence

>pdb|2abqA00
XIYTVTLNPSIDYIVQVENFQQGVVNRSERDRKQPGGKGINVSRVLKRLGHETKALGFLGGFTGAYVRNALEKEEIGLSF
IEVEGDTRINVKIKGKQETELNGTAPLIKKEHVQALLEQLTELEKGDVLVLAGSVPQAXPQTIYRSXTQIAKERGAFVAV
DTSGEALHEVLAAKPSFIKPNHHELSELVSKPIASIEDAIPHVQRLIGEGIESILVSFAGDGALFASAEGXFHVNVPSGE
VRNSVGAGDSVVAGFLAALQEGKSLEDAVPFAVAAGSATAFSDGFCTREEVERLQQQLQRTIKKEG

BLAST against CATH

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Domain History Events (283)

Domain assigned by cuff on 04 Feb 2008 12:57

same superfamily

Domain assignment manual match h by tronnberg on 15 Jan 2008 15:24

SSAP: 83.2 OV: 94 SEQ: 18

Homcheck review by tronnberg on 15 Jan 2008 15:24

SSAP: 83.2 OV: 94 SEQ: 18

Flow stage update by tronnberg on 15 Jan 2008 15:24

SSAP: 83.2 OV: 94 SEQ: 18

Homcheck return by cuff on 14 Jan 2008 15:19

most def in same superfamily. have a look at SCOP

Flow stage update by cuff on 14 Jan 2008 15:19

most def in same superfamily. have a look at SCOP

Domain scan prc pfamcath by auto on 25 Sep 2007 12:43

Adding scan of type "DOMAIN_SCAN_PRC_PFAMCATH" with 54 results for 2abqA00

Homcheck comment by tronnberg on 14 Sep 2007 11:31

Very similar linkage and structure. None of the matches on the Scan List with a SSAP score of 70 and abve has the same function as the query.

Domain assignment manual match t by tronnberg on 28 Aug 2007 11:29

SSAP= 83, OV= 94, Seq sim= 18. Very similar linkage. I think that 2awdA00 (TBA) should be in this topology family too.

Homcheck review by tronnberg on 28 Aug 2007 11:29

SSAP= 83, OV= 94, Seq sim= 18. Very similar linkage. I think that 2awdA00 (TBA) should be in this topology family too.

Flow stage update by tronnberg on 28 Aug 2007 11:29

SSAP= 83, OV= 94, Seq sim= 18. Very similar linkage. I think that 2awdA00 (TBA) should be in this topology family too.

Homcheck allotment by tronnberg on 28 Aug 2007 11:23

User 'tronnberg' has allocated a domain to themselves for HomChecking with comment : Grabbed this domain via HomCheck's "Get Me A Domain" button.

Flow stage update by tronnberg on 28 Aug 2007 11:23

User 'tronnberg' has allocated a domain to themselves for HomChecking with comment : Grabbed this domain via HomCheck's "Get Me A Domain" button.

Flow stage update by auto on 28 Aug 2007 03:35

Domain "2abqA00" SCOP scan with no results - no SCOP mapping

Domain scan scop cath by auto on 28 Aug 2007 03:32

Adding scan of type "DOMAIN_SCAN_SCOP_CATH" with 0 results for 2abqA00

Flow stage update by auto on 28 Aug 2007 03:27

Retrieved PRC_PFAMCATH results for job ID SID9551890485305380 and results inserted.

Update comment by auto on 27 Aug 2007 23:04

PRC_PFAMCATH job SID9551890485305380 is not yet finished.

Flow stage update by auto on 27 Aug 2007 23:03

The entry "2abqA00" has been submitted to the PRC_PFAMCATH webservice.

Prc pfamcath submit by auto on 27 Aug 2007 23:03

The entry "2abqA00" has been submitted to the PRC_PFAMCATH webservice.

Flow stage update by auto on 27 Aug 2007 22:23

Retrieved SSAP results for job ID SID7758302731757728 and results inserted.

Domain scan ssap cath by auto on 27 Aug 2007 22:21

Adding scan of type "DOMAIN_SCAN_SSAP_CATH" with 595 results for 2abqA00