CATH Domain: 2ibdA01

2ibdA01

PDB 2ibd, Chain A, Domain 1

CATH Code	Level Description	Links
1	Mainly Alpha
1.10	Orthogonal Bundle
1.10.10	Arc Repressor Mutant, subunit A
1.10.10.60	Homeodomain-like	Gene3D
1.10.10.60.15
1.10.10.60.15.1
1.10.10.60.15.1.1
1.10.10.60.15.1.1.1
1.10.10.60.15.1.1.1.1

Structure
Sequence
History

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Segment boundaries for domain 2ibdA01

Domain	Start PDB Residue	Stop PDB Residue
2ibdA01	11	55
2ibdA02	56	202

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 (41 entries)

There are 41 matching structural neighberhood comparisons for CATH ID 1.10.10.60.15.1.1.1.1 (SIMAX score < 5)

Match	SSAP score	Match Keywords	Match Superfamily	Length	Sequence Id	Overlap	RMSD	SIMAX
2raeA01	95.34	Rhodococcus jostii RHA1Transcriptional regulator, AcrR family protein	1.10.10.60	43	30	93	0.62	0.66
3ccyA01	94.18	Bordetella parapertussisPutative TetR-family transcriptional regulator	1.10.10.60	44	34	95	0.71	0.74
1zkgA01	93.08	Thermotoga maritimaTranscriptional regulator, TetR family	1.10.10.60	46	28	95	2.38	2.49
2fd5A01	92.86	Probable transcriptional regulatorPseudomonas aeruginosa	1.10.10.60	48	33	93	1.24	1.32
1t56A01	92.79	TRANSCRIPTIONAL REGULATORY REPRESSOR PROTEIN (TETR-FAMILY) ETHRMycobacterium tuberculosis	1.10.10.60	46	31	95	1.31	1.37
2fq4A01	92.57	Transcriptional regulator, TetR familyBacillus cereus ATCC 14579	1.10.10.60	47	24	95	1.47	1.54
2hyjA01	92.10	Streptomyces coelicolorPutative tetR-family transcriptional regulator	1.10.10.60	46	24	97	1.29	1.32
3bqzA01	91.84	HTH-type transcriptional regulator qacRStaphylococcus aureus subsp. aureus Mu50	1.10.10.60	49	31	85	1.26	1.47
2id6A01	91.58	Thermotoga maritimaTranscriptional regulator, TetR family	1.10.10.60	46	26	95	2.57	2.69
1zk8A01	91.24	Transcriptional regulator, TetR familyBacillus cereus ATCC 14579	1.10.10.60	46	26	93	2.14	2.29
1rktA01	91.04	Bacillus subtilisUncharacterized HTH-type transcriptional regulator yfiR	1.10.10.60	52	33	84	1.30	1.54
3c2bA01	89.79	Agrobacterium tumefaciens str. C58Transcriptional regulator, TetR family	1.10.10.60	51	37	82	1.12	1.36
3bqyA01	89.41	Putative transcriptional regulatorStreptomyces coelicolor	1.10.10.60	48	28	77	0.91	1.18
2np3B01	88.28	Streptomyces coelicolorPutative TetR-family regulator	1.10.10.60	60	35	75	1.43	1.91
1gv2A02	85.74	Transcriptional activator MybNucleusEmbryonic digestive tract developmentProtein bindingMus musculus	1.10.10.60	46	13	86	3.09	3.55
3f0cA01	84.09	Cytophaga hutchinsonii ATCC 33406Transcriptional regulator	1.10.10.60	47	22	87	2.78	3.19
1hlvA01	82.39	Centromere protein BMajor centromere autoantigen BHomo sapiensChromosome, centromeric region	1.10.10.60	58	8	65	1.89	2.88
1ng6A02	81.03	Hypothetical proteinBacillus subtilisUncharacterized protein yqeY	1.10.10.410	57	11	71	3.54	4.92
1hcrA00	80.95	Salmonella enterica subsp. enterica serovar TyphimuriumDNA-invertase hin	1.10.10.60	52	13	71	2.95	4.15
1tc3C00	80.93	Caenorhabditis elegansTransposable element Tc3 transposase	1.10.10.60	51	2	80	3.67	4.57
1bl0A01	80.64	Multiple antibiotic resistance protein marAAraC family transcriptional regulator, multiple antibiotic resistance protein MarAEscherichia coli K-12	1.10.10.60	56	8	71	1.76	2.46
2hxoA01	80.53	Streptomyces coelicolorPutative TetR-family transcriptional regulator	1.10.10.60	63	24	66	1.72	2.58
1sauA02	80.39	Archaeoglobus fulgidusSulfite reductase, desulfoviridin-type subunit gamma (DsvC)	1.10.10.370	70	15	61	2.19	3.57
1gdtB03	80.33	Transposon gamma-delta resolvaseEscherichia coli K-12	1.10.10.60	45	6	80	2.86	3.58
1b8iB00	79.64	Oenocyte developmentLeg disc proximal/distal pattern formationTranscription factor complexBrain developmentDrosophila melanogaster	1.10.10.60	58	13	75	3.76	4.96
1w1wE00	78.86	Nuclear mitotic cohesin complexProtein acetylationChromatin bindingCohesin complex subunit SCC1Establishment of mitotic sister chromatid cohesion	1.10.10.580	70	6	57	2.25	3.94
1irzA00	78.27	Regulation of anthocyanin metabolic processCytokinin mediated signaling pathwayNucleusSequence-specific DNA binding transcription factor activityArabidopsis thaliana	1.10.10.60	64	13	70	3.26	4.64
1k6yA01	77.79	POL polyproteinHuman immunodeficiency virus 1	1.10.10.200	46	4	80	3.78	4.70
1etxA00	77.17	DNA-binding protein fisFis family transcriptional regulator, factor for inversion stimulation proteinProtein bindingEscherichia coli K-12	1.10.10.60	74	13	51	1.69	3.29
1fipA00	77.15	Escherichia coli O157:H7DNA-binding protein fisFis family transcriptional regulator, factor for inversion stimulation protein	1.10.10.60	73	13	52	1.64	3.15
1d5yA02	76.24	Right origin-binding proteinRight origin-binding proteinEscherichia coli K-12	1.10.10.60	66	11	54	2.32	4.25
1g2hA00	75.37	Transcriptional regulator of aroF, aroG, tyrA and aromatic amino acid transportHaemophilus influenzaeTranscriptional regulatory protein tyrR	1.10.10.60	61	11	60	2.10	3.46
1tkvA00	72.68	10 kDa anti-sigma factorEnterobacteria phage T4	1.10.1810.10	88	8	51	2.50	4.89
3b81A00	66.59	Transcriptional regulator, AcrR familyClostridium acetobutylicum	1.10.357.10	175	35	25	1.24	4.93
3cjdA00	65.73	Jannaschia sp. CCS1Transcriptional regulator, TetR family	1.10.357.10	175	31	25	1.24	4.93
2qguA02	65.32	Probable signal peptide proteinRalstonia solanacearum	1.10.10.640	77	11	23	0.42	1.80
2genA00	65.21	Probable transcriptional regulatorPseudomonas aeruginosa	1.10.357.10	186	44	21	0.89	4.14
2qibB00	64.78	Streptomyces coelicolorPutative tetR-family transcriptional regulator	1.10.357.10	204	35	20	0.71	3.53
3colB00	64.54	Transcription regulator (Putative)Lactobacillus plantarum	1.10.357.10	170	17	24	1.17	4.85
3c07B00	63.42	Streptomyces coelicolorPutative tetR-family transcriptional regulator	1.10.357.10	210	40	20	0.79	3.86
1nu5A01	58.25	Chloromuconate cycloisomerasePseudomonas sp. P51	3.30.390.10	116	2	17	0.49	2.84

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Domain ATOM Sequence

>pdb|2ibdA01
GKSGRRTELLDIAATLFAERGLRATTVRDIADAAGILSGSLYHHF

BLAST against CATH

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Domain COMBS Sequence

>pdb|2ibdA01
XTPPPADDTSGKSGRRTELLDIAATLFAERGLRATTVRDIADAAGILSGSLYHHF

BLAST against CATH

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Domain History Events (63)

Domain assigned by cuff on 24 Jul 2008 17:58

same superfamily

Homcheck review by yan on 16 Jun 2008 16:11

same super family

Flow stage update by yan on 16 Jun 2008 16:11

same super family

Domain assignment manual match h by yan on 16 Jun 2008 16:08

very high ssap score, same function, very nicely overlapped, same PFAM

Homcheck allotment by yan on 16 Jun 2008 16:02

User 'yan' 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 yan on 16 Jun 2008 16:02

User 'yan' 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 24 Feb 2008 09:17

Domain "2ibdA01" SCOP scan with no results - no SCOP mapping

Domain scan scop cath by auto on 24 Feb 2008 09:01

Adding scan of type "DOMAIN_SCAN_SCOP_CATH" with 0 results for 2ibdA01

Flow stage update by auto on 24 Feb 2008 08:59

Retrieved PRC_PFAMCATH results for job ID SID4626421450960160 and results inserted.

Domain scan prc pfamcath by auto on 24 Feb 2008 08:59

Adding scan of type "DOMAIN_SCAN_PRC_PFAMCATH" with 40 results for 2ibdA01

Update comment by auto on 24 Feb 2008 00:10

PRC_PFAMCATH job SID4626421450960160 is not yet finished.

Flow stage update by auto on 24 Feb 2008 00:08

The entry "2ibdA01" has been submitted to the PRC_PFAMCATH webservice.

Prc pfamcath submit by auto on 24 Feb 2008 00:07

The entry "2ibdA01" has been submitted to the PRC_PFAMCATH webservice.

Flow stage update by auto on 23 Feb 2008 23:42

Retrieved SSAP results for job ID SID5516527882658304 and results inserted.

Domain scan ssap cath by auto on 23 Feb 2008 23:36

Adding scan of type "DOMAIN_SCAN_SSAP_CATH" with 2064 results for 2ibdA01

Update comment by auto on 23 Feb 2008 12:36

SSAP job SID5516527882658304 is not yet finished.

Flow stage update by auto on 23 Feb 2008 12:35

The entry "2ibdA01" has been submitted to the SSAP webservice.

Ssap cath submit by auto on 23 Feb 2008 12:34

The entry "2ibdA01" has been submitted to the SSAP webservice.

Flow stage update by auto on 23 Feb 2008 12:34

Retrieved PRC results for job ID SID2330546628192048 and inserted them into the database.

Domain scan prc cath by auto on 23 Feb 2008 12:33

Adding scan of type "DOMAIN_SCAN_PRC_CATH" with 32 results for 2ibdA01

Update comment by auto on 22 Feb 2008 21:34

PRC job SID2330546628192048 is not yet finished.

Flow stage update by auto on 22 Feb 2008 21:34

The entry "2ibdA01" has been submitted to the PRC webservice.

Prc cath submit by auto on 22 Feb 2008 21:34

The entry "2ibdA01" has been submitted to the PRC webservice.

Flow stage update by auto on 22 Feb 2008 21:33

Retrieved HMM(SAM) results for job ID SID0938041447057903 and inserted them into the database.

Domain scan sam cath by auto on 22 Feb 2008 21:33

Adding scan of type "DOMAIN_SCAN_SAM_CATH" with 30 results for 2ibdA01