NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2624454|pdb|2AAC|A]
View 

Chain A, ARAC

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PRK10572 super family cl35928
arabinose operon transcriptional regulator AraC;
1-177 1.67e-123

arabinose operon transcriptional regulator AraC;


The actual alignment was detected with superfamily member PRK10572:

Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 349.27  E-value: 1.67e-123
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2AAC_A         1 AEAQNDPLLPGYSFNAHLVAGLTPIEANGYLDFFIDRPLGMKGYILNLTIRGQGVVKNQGREFVCRPGDILLFPPGEIHH 80
Cdd:PRK10572   7 AEAQNNPLLPGYSFNAHLVAGLTPIEAGGYLDFFIDRPLGMKGYILNLTIRGQGVIFNGGRAFVCRPGDLLLFPPGEIHH 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2AAC_A        81 YGRHPEAREWYHQWVYFRPRAYWHEWLNWPSIFANTGFFR-PDEAHQPHFSDLFGQIINAGQGEGRYSELLAINLLEQLL 159
Cdd:PRK10572  87 YGRHPDSDEWYHQWVYFRPRAYWADWLNWPSIFAGVGRLRiPDEALQPEFSDLFGQIEQAGQSEGRYSELLAMNLLERLL 166

                        170
                 ....*....|....*...
2AAC_A       160 LRRMEAINESLHPPMDNR 177
Cdd:PRK10572 167 LRCMEAIPESLHPPMDPR 184
 
Name Accession Description Interval E-value
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
1-177 1.67e-123

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 349.27  E-value: 1.67e-123
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2AAC_A         1 AEAQNDPLLPGYSFNAHLVAGLTPIEANGYLDFFIDRPLGMKGYILNLTIRGQGVVKNQGREFVCRPGDILLFPPGEIHH 80
Cdd:PRK10572   7 AEAQNNPLLPGYSFNAHLVAGLTPIEAGGYLDFFIDRPLGMKGYILNLTIRGQGVIFNGGRAFVCRPGDLLLFPPGEIHH 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2AAC_A        81 YGRHPEAREWYHQWVYFRPRAYWHEWLNWPSIFANTGFFR-PDEAHQPHFSDLFGQIINAGQGEGRYSELLAINLLEQLL 159
Cdd:PRK10572  87 YGRHPDSDEWYHQWVYFRPRAYWADWLNWPSIFAGVGRLRiPDEALQPEFSDLFGQIEQAGQSEGRYSELLAMNLLERLL 166

                        170
                 ....*....|....*...
2AAC_A       160 LRRMEAINESLHPPMDNR 177
Cdd:PRK10572 167 LRCMEAIPESLHPPMDPR 184
AraC_binding pfam02311
AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization ...
 20-155 1.25e-24

AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization domain of the bacterial gene regulatory protein AraC. The domain is found in conjunction with the helix-turn-helix (HTH) DNA-binding motif pfam00165. This domain is distantly related to the Cupin domain pfam00190.


Pssm-ID: 396749 [Multi-domain]  Cd Length: 134  Bit Score: 92.88  E-value: 1.25e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2AAC_A         20 AGLTPIEANGYLDFFIDRPLGmkGYILNLTIRGQGVVKNQGREFVCRPGDILLFPPGEIHHYGRHPEArEWYHQWVYFRP 99
Cdd:pfam02311   2 PGLEGIEARYPGHSFPPHVHD--FYVIGYIERGVGRFRLNGRTYHLGPGDLFLLPPGEPHDYEPESED-GWRYRWLYFEP 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
2AAC_A        100 RAYWHEWLNWPSIFANTGFFRPDEAHQPHFSDLFGQIINAGQGEGRYSELLAINLL 155
Cdd:pfam02311  79 ELLERILADISILAGGPLPLLRDPELAALLRALFRLLEEAGRSDDLLAEALLYQLL 134
cupin_MmsR-like_N cd06986
AraC/XylS family transcriptional regulators similar to MmsR, N-terminal cupin domain; This ...
 25-100 5.93e-17

AraC/XylS family transcriptional regulators similar to MmsR, N-terminal cupin domain; This family contains bacterial proteins containing an AraC/XylS family helix-turn-helix (HTH) DNA-binding domain C-terminal to a cupin domain, and may be possible transcriptional regulators. Included is MmsR, a bacterial transcriptional regulator thought to positively regulate the expression of the mmsAB operon. The mmsAB operon contains two structural genes involved in valine metabolism: mmsA which encodes methylmalonate-semialdehyde dehydrogenase, and mmsB which encodes 3-hydroxyisobutyrate dehydrogenase. The cupin domain of members of this subfamily does not contain a metal binding site.


Pssm-ID: 380391 [Multi-domain]  Cd Length: 84  Bit Score: 71.36  E-value: 5.93e-17
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
2AAC_A       25 IEANGYLDF---FIDRPLGMKGYILNLTIRGQGVVKNQGREFVCRPGDILLFPPGEIHHYGRHPEaREWYHQWVYFRPR 100
Cdd:cd06986   7 LTDCGYEPCepgHSYGPAVRDYYILHYVLSGKGTFSVNGKTYHLKAGQGFLIPPGEPHSYGADED-DPWTYYWIGFSGS 84
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
50-87 2.97e-03

Cupin domain protein related to quercetin dioxygenase [General function prediction only];


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 35.59  E-value: 2.97e-03
                        10        20        30
                ....*....|....*....|....*....|....*...
2AAC_A       50 IRGQGVVKNQGREFVCRPGDILLFPPGEIHHYGRHPEA 87
Cdd:COG1917  50 LEGEGEVEVGGEEYELKPGDVVFIPPGVPHAFRNLGDE 87
 
Name Accession Description Interval E-value
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
1-177 1.67e-123

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 349.27  E-value: 1.67e-123
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2AAC_A         1 AEAQNDPLLPGYSFNAHLVAGLTPIEANGYLDFFIDRPLGMKGYILNLTIRGQGVVKNQGREFVCRPGDILLFPPGEIHH 80
Cdd:PRK10572   7 AEAQNNPLLPGYSFNAHLVAGLTPIEAGGYLDFFIDRPLGMKGYILNLTIRGQGVIFNGGRAFVCRPGDLLLFPPGEIHH 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2AAC_A        81 YGRHPEAREWYHQWVYFRPRAYWHEWLNWPSIFANTGFFR-PDEAHQPHFSDLFGQIINAGQGEGRYSELLAINLLEQLL 159
Cdd:PRK10572  87 YGRHPDSDEWYHQWVYFRPRAYWADWLNWPSIFAGVGRLRiPDEALQPEFSDLFGQIEQAGQSEGRYSELLAMNLLERLL 166

                        170
                 ....*....|....*...
2AAC_A       160 LRRMEAINESLHPPMDNR 177
Cdd:PRK10572 167 LRCMEAIPESLHPPMDPR 184
AraC_binding pfam02311
AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization ...
 20-155 1.25e-24

AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization domain of the bacterial gene regulatory protein AraC. The domain is found in conjunction with the helix-turn-helix (HTH) DNA-binding motif pfam00165. This domain is distantly related to the Cupin domain pfam00190.


Pssm-ID: 396749 [Multi-domain]  Cd Length: 134  Bit Score: 92.88  E-value: 1.25e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2AAC_A         20 AGLTPIEANGYLDFFIDRPLGmkGYILNLTIRGQGVVKNQGREFVCRPGDILLFPPGEIHHYGRHPEArEWYHQWVYFRP 99
Cdd:pfam02311   2 PGLEGIEARYPGHSFPPHVHD--FYVIGYIERGVGRFRLNGRTYHLGPGDLFLLPPGEPHDYEPESED-GWRYRWLYFEP 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
2AAC_A        100 RAYWHEWLNWPSIFANTGFFRPDEAHQPHFSDLFGQIINAGQGEGRYSELLAINLL 155
Cdd:pfam02311  79 ELLERILADISILAGGPLPLLRDPELAALLRALFRLLEEAGRSDDLLAEALLYQLL 134
cupin_MmsR-like_N cd06986
AraC/XylS family transcriptional regulators similar to MmsR, N-terminal cupin domain; This ...
 25-100 5.93e-17

AraC/XylS family transcriptional regulators similar to MmsR, N-terminal cupin domain; This family contains bacterial proteins containing an AraC/XylS family helix-turn-helix (HTH) DNA-binding domain C-terminal to a cupin domain, and may be possible transcriptional regulators. Included is MmsR, a bacterial transcriptional regulator thought to positively regulate the expression of the mmsAB operon. The mmsAB operon contains two structural genes involved in valine metabolism: mmsA which encodes methylmalonate-semialdehyde dehydrogenase, and mmsB which encodes 3-hydroxyisobutyrate dehydrogenase. The cupin domain of members of this subfamily does not contain a metal binding site.


Pssm-ID: 380391 [Multi-domain]  Cd Length: 84  Bit Score: 71.36  E-value: 5.93e-17
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
2AAC_A       25 IEANGYLDF---FIDRPLGMKGYILNLTIRGQGVVKNQGREFVCRPGDILLFPPGEIHHYGRHPEaREWYHQWVYFRPR 100
Cdd:cd06986   7 LTDCGYEPCepgHSYGPAVRDYYILHYVLSGKGTFSVNGKTYHLKAGQGFLIPPGEPHSYGADED-DPWTYYWIGFSGS 84
cupin_TM1459-like cd02222
Thermotoga maritima TM1459 and related proteins, cupin domain; This family includes bacterial ...
 50-81 2.07e-03

Thermotoga maritima TM1459 and related proteins, cupin domain; This family includes bacterial and archaeal proteins homologous to Thermotoga maritima TM1459, a manganese-containing cupin that has been shown to cleave C=C bonds in the presence of alkylperoxide as oxidant in vitro. Its biological function is still unknown. This family also includes Halorhodospira halophila Hhal_0468. Structures of these proteins show a cupin fold with a conserved "jelly roll-like" beta-barrel fold that form a homodimer.


Pssm-ID: 380351 [Multi-domain]  Cd Length: 91  Bit Score: 35.89  E-value: 2.07e-03
                        10        20        30
                ....*....|....*....|....*....|..
2AAC_A       50 IRGQGVVKNQGREFVCRPGDILLFPPGEIHHY 81
Cdd:cd02222  44 LRGKGVVVIGGEEYPVKPGDVVYIPPNEPHQF 75
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
50-87 2.97e-03

Cupin domain protein related to quercetin dioxygenase [General function prediction only];


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 35.59  E-value: 2.97e-03
                        10        20        30
                ....*....|....*....|....*....|....*...
2AAC_A       50 IRGQGVVKNQGREFVCRPGDILLFPPGEIHHYGRHPEA 87
Cdd:COG1917  50 LEGEGEVEVGGEEYELKPGDVVFIPPGVPHAFRNLGDE 87
AraC_binding_2 pfam14525
AraC-binding-like domain; This domain is related to the AraC ligand binding domain pfam02311.
 44-77 7.82e-03

AraC-binding-like domain; This domain is related to the AraC ligand binding domain pfam02311.


Pssm-ID: 434015  Cd Length: 173  Bit Score: 35.36  E-value: 7.82e-03
                          10        20        30
                  ....*....|....*....|....*....|....
2AAC_A         44 YILNLTIRGQGVVKNQGREFVCRPGDILLFPPGE 77
Cdd:pfam14525  56 YLLQLPLSGSAEIEQGGREVVLGPGDAVLLDPGR 89
cupin_YbfI-like_N cd07001
AraC/XylS family transcriptional regulators similar to Bacillus subtilis YbfI, N-terminal ...
 44-79 8.73e-03

AraC/XylS family transcriptional regulators similar to Bacillus subtilis YbfI, N-terminal cupin domain; This family contains bacterial proteins containing an AraC/XylS family helix-turn-helix (HTH) DNA-binding domain C-terminal to a cupin domain, and may be possible transcriptional regulators, including YbfI, an uncharacterized Bacillus subtilis. In Pseudomonas putida, this protein is thought to regulate the expression of phenylserine aldolase. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380405 [Multi-domain]  Cd Length: 76  Bit Score: 33.90  E-value: 8.73e-03
                        10        20        30
                ....*....|....*....|....*....|....*.
2AAC_A       44 YILNLTIRGQGVVKNQGREFVCRPGDILLFPPGEIH 79
Cdd:cd07001  23 YVIGFIESGQRTLFCEGKEYTVEPGDLLLINPRDVH 58
cupin_RmlC-like cd02208
RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP ...
 43-81 9.23e-03

RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP (deoxythymidine diphosphates)-4-dehydrorhamnose 3,5-epimerase)-like cupins. RmlC is a dTDP-sugar isomerase involved in the synthesis of L-rhamnose, a saccharide required for the virulence of some pathogenic bacteria. Cupins are a functionally diverse superfamily originally discovered based on the highly conserved motif found in germin and germin-like proteins. This conserved motif forms a beta-barrel fold found in all of the cupins, giving rise to the name cupin ('cupa' is the Latin term for small barrel). The active site of members of this superfamily is generally located at the center of a conserved barrel and usually includes a metal ion. The different functional classes in this superfamily include single domain bacterial isomerases and epimerases involved in the modification of cell wall carbohydrates, two domain bicupins such as the desiccation-tolerant seed storage globulins, and multidomain nuclear transcription factors involved in legume root nodulation.


Pssm-ID: 380338 [Multi-domain]  Cd Length: 73  Bit Score: 33.61  E-value: 9.23e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|
2AAC_A       43 GYILNLTIRGQGVVK-NQGREFVCRPGDILLFPPGEIHHY 81
Cdd:cd02208  20 QDEIFYVLSGEGELTlDDGETVELKAGDIVLIPPGVPHSF 59
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH