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Conserved domains on  [gi|2527201421|ref|WP_288239970|]
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ATP-binding protein [uncultured Bifidobacterium sp.]

Protein Classification

putative DNA binding domain-containing protein( domain architecture ID 1000485)

putative DNA binding domain-containing protein with a putative ATP-dependent DNA helicase RecG C-terminal domain, may bind DNA and function as a transcriptional regulator

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HATPase_c_4 pfam13749
Putative ATP-dependent DNA helicase recG C-terminal; This domain may well interact selectively ...
 319-412 2.64e-24

Putative ATP-dependent DNA helicase recG C-terminal; This domain may well interact selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.


:

Pssm-ID: 463975  Cd Length: 88  Bit Score: 96.44  E-value: 2.64e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2527201421 319 GSQVQVNMYLDRLEILNPGGLFGNVTIETLGHAGISASRNQFLSNILETTPYpgggyvVENRGTGYQVIEEELQEALMPP 398
Cdd:pfam13749   1 GAPIQIEIFDDRLEITSPGGLPGGVTVEDLGLDGVSKSRNPLLASLFRRLGL------IEERGSGIRRILEAMEEAGLPE 74

                          90
                  ....*....|....
gi 2527201421 399 PEPSNTLTYFSLTF 412
Cdd:pfam13749  75 PEFIEDGDSFRVTL 88
COG2865 COG2865
Predicted transcriptional regulator, contains HTH domain [Transcription];
4-138 7.60e-24

Predicted transcriptional regulator, contains HTH domain [Transcription];


:

Pssm-ID: 442112  Cd Length: 123  Bit Score: 96.50  E-value: 7.60e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2527201421   4 EDLEQLIAhmrqiGNDTQTCEVKEASSKlPESVVETLSAFSNGTGGTLILGLSEKNGFTPVSnfNATAMQESLAAACA-K 82
Cdd:COG2865     1 EELKELLA-----GGESETLEFKESLNE-PDEILKTVCAFANTEGGTLLIGVDDDGEIVGLD--DPDKLLERLENLIAdN 72

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2527201421  83 MTPPVRPITEILPFEGINLLVAEIPAMSkkDKPCYVTTRGRYqgsYIRTGDGDRKL 138
Cdd:COG2865    73 ISPPIRPDVEEVEIDGKRVLVIEVPPGP--SKPYYLKGKGGA---YIRVGSSSRPL 123
COG3398 super family cl28563
Predicted transcriptional regulator, contains two HTH domains [Transcription];
407-490 1.22e-07

Predicted transcriptional regulator, contains two HTH domains [Transcription];


The actual alignment was detected with superfamily member COG3398:

Pssm-ID: 442625 [Multi-domain]  Cd Length: 159  Bit Score: 51.03  E-value: 1.22e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2527201421 407 YFSltfAKRRVSESERRVIASDDVETA--IIALLHEQSSASTRELVELSGLSRSAIVNHLNRLIKADVIEPTHIARspKQ 484
Cdd:COG3398    76 YFP---NSGTYSEEEKKILAYLRRETPrrILLYLLENPGATNKELAEELGISRSTVSWHLKRLEEDGLVERERDGR--NV 150


                  ....*.
gi 2527201421 485 RYRLKR 490
Cdd:COG3398   151 RYYLNP 156
 
Name Accession Description Interval E-value
HATPase_c_4 pfam13749
Putative ATP-dependent DNA helicase recG C-terminal; This domain may well interact selectively ...
 319-412 2.64e-24

Putative ATP-dependent DNA helicase recG C-terminal; This domain may well interact selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.


Pssm-ID: 463975  Cd Length: 88  Bit Score: 96.44  E-value: 2.64e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2527201421 319 GSQVQVNMYLDRLEILNPGGLFGNVTIETLGHAGISASRNQFLSNILETTPYpgggyvVENRGTGYQVIEEELQEALMPP 398
Cdd:pfam13749   1 GAPIQIEIFDDRLEITSPGGLPGGVTVEDLGLDGVSKSRNPLLASLFRRLGL------IEERGSGIRRILEAMEEAGLPE 74

                          90
                  ....*....|....
gi 2527201421 399 PEPSNTLTYFSLTF 412
Cdd:pfam13749  75 PEFIEDGDSFRVTL 88
COG2865 COG2865
Predicted transcriptional regulator, contains HTH domain [Transcription];
4-138 7.60e-24

Predicted transcriptional regulator, contains HTH domain [Transcription];


Pssm-ID: 442112  Cd Length: 123  Bit Score: 96.50  E-value: 7.60e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2527201421   4 EDLEQLIAhmrqiGNDTQTCEVKEASSKlPESVVETLSAFSNGTGGTLILGLSEKNGFTPVSnfNATAMQESLAAACA-K 82
Cdd:COG2865     1 EELKELLA-----GGESETLEFKESLNE-PDEILKTVCAFANTEGGTLLIGVDDDGEIVGLD--DPDKLLERLENLIAdN 72

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2527201421  83 MTPPVRPITEILPFEGINLLVAEIPAMSkkDKPCYVTTRGRYqgsYIRTGDGDRKL 138
Cdd:COG2865    73 ISPPIRPDVEEVEIDGKRVLVIEVPPGP--SKPYYLKGKGGA---YIRVGSSSRPL 123
AlbA_2 pfam04326
Putative DNA-binding domain; This family belongs to the AlbA clan of DNA-binding domains.
 19-139 4.91e-19

Putative DNA-binding domain; This family belongs to the AlbA clan of DNA-binding domains.


Pssm-ID: 461263  Cd Length: 116  Bit Score: 82.73  E-value: 4.91e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2527201421  19 DTQTCEVKEASSKLPES-VVETLSAFSNGTGGTLILGLSEKNGFTPVSNFNATAMQESLAAACAKMTPPVRPITEILPFE 97
Cdd:pfam04326   1 ESETLEFKESLGKSSKKkIAKTISAFANTEGGTIVIGVDDTGKIVGVSDDEKDTEDLLKNQILDLIKPPIEVDIEEIEID 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 2527201421  98 GINLLVAEIPAMSKKDkpcYVTTRGRYqgsYIRTGDGDRKLT 139
Cdd:pfam04326  81 GKYVLVVEIPEGKLKP---YYTNKGEV---YIRVGSSSRPAS 116
COG3398 COG3398
Predicted transcriptional regulator, contains two HTH domains [Transcription];
407-490 1.22e-07

Predicted transcriptional regulator, contains two HTH domains [Transcription];


Pssm-ID: 442625 [Multi-domain]  Cd Length: 159  Bit Score: 51.03  E-value: 1.22e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2527201421 407 YFSltfAKRRVSESERRVIASDDVETA--IIALLHEQSSASTRELVELSGLSRSAIVNHLNRLIKADVIEPTHIARspKQ 484
Cdd:COG3398    76 YFP---NSGTYSEEEKKILAYLRRETPrrILLYLLENPGATNKELAEELGISRSTVSWHLKRLEEDGLVERERDGR--NV 150


                  ....*.
gi 2527201421 485 RYRLKR 490
Cdd:COG3398   151 RYYLNP 156
HTH_ARSR cd00090
Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric ...
 427-489 5.09e-05

Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.


Pssm-ID: 238042 [Multi-domain]  Cd Length: 78  Bit Score: 41.52  E-value: 5.09e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2527201421 427 SDDVETAIIALLHEqSSASTRELVELSGLSRSAIVNHLNRLIKADVIEPTHIARspKQRYRLK 489
Cdd:cd00090     5 SDPTRLRILRLLLE-GPLTVSELAERLGLSQSTVSRHLKKLEEAGLVESRREGR--RVYYSLT 64
HTH_24 pfam13412
Winged helix-turn-helix DNA-binding;
433-473 1.91e-04

Winged helix-turn-helix DNA-binding;


Pssm-ID: 404317 [Multi-domain]  Cd Length: 45  Bit Score: 38.95  E-value: 1.91e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 2527201421 433 AIIALLHEQSSASTRELVELSGLSRSAIVNHLNRLIKADVI 473
Cdd:pfam13412   5 KILNLLQENPRISQRELAERLGLSPSTVNRRLKRLEEEGVI 45
HTH_ASNC smart00344
helix_turn_helix ASNC type; AsnC: an autogenously regulated activator of asparagine synthetase ...
 428-483 3.50e-04

helix_turn_helix ASNC type; AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli)


Pssm-ID: 214628 [Multi-domain]  Cd Length: 108  Bit Score: 39.81  E-value: 3.50e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2527201421  428 DDVETAIIALLHEQSSASTRELVELSGLSRSAIVNHLNRLIKADVIEPTHIARSPK 483
Cdd:smart00344   2 DEIDRKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEEEGVIKGYTAVLNPK 57
 
Name Accession Description Interval E-value
HATPase_c_4 pfam13749
Putative ATP-dependent DNA helicase recG C-terminal; This domain may well interact selectively ...
 319-412 2.64e-24

Putative ATP-dependent DNA helicase recG C-terminal; This domain may well interact selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.


Pssm-ID: 463975  Cd Length: 88  Bit Score: 96.44  E-value: 2.64e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2527201421 319 GSQVQVNMYLDRLEILNPGGLFGNVTIETLGHAGISASRNQFLSNILETTPYpgggyvVENRGTGYQVIEEELQEALMPP 398
Cdd:pfam13749   1 GAPIQIEIFDDRLEITSPGGLPGGVTVEDLGLDGVSKSRNPLLASLFRRLGL------IEERGSGIRRILEAMEEAGLPE 74

                          90
                  ....*....|....
gi 2527201421 399 PEPSNTLTYFSLTF 412
Cdd:pfam13749  75 PEFIEDGDSFRVTL 88
COG2865 COG2865
Predicted transcriptional regulator, contains HTH domain [Transcription];
4-138 7.60e-24

Predicted transcriptional regulator, contains HTH domain [Transcription];


Pssm-ID: 442112  Cd Length: 123  Bit Score: 96.50  E-value: 7.60e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2527201421   4 EDLEQLIAhmrqiGNDTQTCEVKEASSKlPESVVETLSAFSNGTGGTLILGLSEKNGFTPVSnfNATAMQESLAAACA-K 82
Cdd:COG2865     1 EELKELLA-----GGESETLEFKESLNE-PDEILKTVCAFANTEGGTLLIGVDDDGEIVGLD--DPDKLLERLENLIAdN 72

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2527201421  83 MTPPVRPITEILPFEGINLLVAEIPAMSkkDKPCYVTTRGRYqgsYIRTGDGDRKL 138
Cdd:COG2865    73 ISPPIRPDVEEVEIDGKRVLVIEVPPGP--SKPYYLKGKGGA---YIRVGSSSRPL 123
AlbA_2 pfam04326
Putative DNA-binding domain; This family belongs to the AlbA clan of DNA-binding domains.
 19-139 4.91e-19

Putative DNA-binding domain; This family belongs to the AlbA clan of DNA-binding domains.


Pssm-ID: 461263  Cd Length: 116  Bit Score: 82.73  E-value: 4.91e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2527201421  19 DTQTCEVKEASSKLPES-VVETLSAFSNGTGGTLILGLSEKNGFTPVSNFNATAMQESLAAACAKMTPPVRPITEILPFE 97
Cdd:pfam04326   1 ESETLEFKESLGKSSKKkIAKTISAFANTEGGTIVIGVDDTGKIVGVSDDEKDTEDLLKNQILDLIKPPIEVDIEEIEID 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 2527201421  98 GINLLVAEIPAMSKKDkpcYVTTRGRYqgsYIRTGDGDRKLT 139
Cdd:pfam04326  81 GKYVLVVEIPEGKLKP---YYTNKGEV---YIRVGSSSRPAS 116
COG3398 COG3398
Predicted transcriptional regulator, contains two HTH domains [Transcription];
407-490 1.22e-07

Predicted transcriptional regulator, contains two HTH domains [Transcription];


Pssm-ID: 442625 [Multi-domain]  Cd Length: 159  Bit Score: 51.03  E-value: 1.22e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2527201421 407 YFSltfAKRRVSESERRVIASDDVETA--IIALLHEQSSASTRELVELSGLSRSAIVNHLNRLIKADVIEPTHIARspKQ 484
Cdd:COG3398    76 YFP---NSGTYSEEEKKILAYLRRETPrrILLYLLENPGATNKELAEELGISRSTVSWHLKRLEEDGLVERERDGR--NV 150


                  ....*.
gi 2527201421 485 RYRLKR 490
Cdd:COG3398   151 RYYLNP 156
HTH_ARSR cd00090
Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric ...
 427-489 5.09e-05

Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.


Pssm-ID: 238042 [Multi-domain]  Cd Length: 78  Bit Score: 41.52  E-value: 5.09e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2527201421 427 SDDVETAIIALLHEqSSASTRELVELSGLSRSAIVNHLNRLIKADVIEPTHIARspKQRYRLK 489
Cdd:cd00090     5 SDPTRLRILRLLLE-GPLTVSELAERLGLSQSTVSRHLKKLEEAGLVESRREGR--RVYYSLT 64
ArsR COG0640
DNA-binding transcriptional regulator, ArsR family [Transcription];
427-490 1.65e-04

DNA-binding transcriptional regulator, ArsR family [Transcription];


Pssm-ID: 440405 [Multi-domain]  Cd Length: 92  Bit Score: 40.64  E-value: 1.65e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2527201421 427 SDDVETAIIALLHEQSsASTRELVELSGLSRSAIVNHLNRLIKADVIEPTHIARSpkQRYRLKR 490
Cdd:COG0640    18 ADPTRLRILRLLAEGE-LCVGELAEALGLSQSTVSHHLKVLREAGLVTSRREGRW--VYYRLAD 78
HTH_24 pfam13412
Winged helix-turn-helix DNA-binding;
433-473 1.91e-04

Winged helix-turn-helix DNA-binding;


Pssm-ID: 404317 [Multi-domain]  Cd Length: 45  Bit Score: 38.95  E-value: 1.91e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 2527201421 433 AIIALLHEQSSASTRELVELSGLSRSAIVNHLNRLIKADVI 473
Cdd:pfam13412   5 KILNLLQENPRISQRELAERLGLSPSTVNRRLKRLEEEGVI 45
HTH_ASNC smart00344
helix_turn_helix ASNC type; AsnC: an autogenously regulated activator of asparagine synthetase ...
 428-483 3.50e-04

helix_turn_helix ASNC type; AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli)


Pssm-ID: 214628 [Multi-domain]  Cd Length: 108  Bit Score: 39.81  E-value: 3.50e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2527201421  428 DDVETAIIALLHEQSSASTRELVELSGLSRSAIVNHLNRLIKADVIEPTHIARSPK 483
Cdd:smart00344   2 DEIDRKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEEEGVIKGYTAVLNPK 57
Lrp COG1522
DNA-binding transcriptional regulator, Lrp family [Transcription];
428-474 4.07e-04

DNA-binding transcriptional regulator, Lrp family [Transcription];


Pssm-ID: 441131 [Multi-domain]  Cd Length: 138  Bit Score: 40.53  E-value: 4.07e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2527201421 428 DDVETAIIALLHEQSSASTRELVELSGLSRSAIVNHLNRLIKADVIE 474
Cdd:COG1522     4 DEIDRRILRLLQEDGRLSFAELAERVGLSESTVLRRVRRLEEAGVIR 50
COG2345 COG2345
Predicted transcriptional regulator, ArsR family [Transcription];
427-488 1.30e-03

Predicted transcriptional regulator, ArsR family [Transcription];


Pssm-ID: 441914 [Multi-domain]  Cd Length: 217  Bit Score: 40.29  E-value: 1.30e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2527201421 427 SDDVETAIIALLHEQSSASTRELVELSGLSRSAIVNHLNRLIKADVIEPTHIARS---PKQRYRL 488
Cdd:COG2345    11 ADPTRRRILELLKRAGPVTAAELAEALGLTPNAVRRHLDALEEEGLVERETERRGrgrPAKLYRL 75
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
396-474 4.80e-03

DNA-binding transcriptional regulator, MarR family [Transcription];


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 37.64  E-value: 4.80e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2527201421 396 MPPPEPSNTLT-YFSLTFAKRRVSESERRVIASDDVETA---IIALLHEQSSASTRELVELSGLSRSAIVNHLNRLIKAD 471
Cdd:COG1846     1 MSDEPDPAEERlGLLLRRLARALRRALDRALAELGLTPAqfrVLAALAEAGGLTQSELAERLGLTKSTVSRLLDRLEEKG 80


                  ...
gi 2527201421 472 VIE 474
Cdd:COG1846    81 LVE 83
HTH_AsnC-type pfam13404
AsnC-type helix-turn-helix domain;
428-467 8.16e-03

AsnC-type helix-turn-helix domain;


Pssm-ID: 433180 [Multi-domain]  Cd Length: 41  Bit Score: 34.27  E-value: 8.16e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 2527201421 428 DDVETAIIALLHEQSSASTRELVELSGLSRSAIVNHLNRL 467
Cdd:pfam13404   1 DEIDRKILRLLQEDARISFAELAERVGLSESTVLRRIRRL 40
MarR_2 pfam12802
MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a ...
 431-474 8.20e-03

MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR. A large number of compounds induce transcription of the mar operon. This is thought to be due to the compound binding to MarR, and the resulting complex stops MarR binding to the DNA. With the MarR repression lost, transcription of the operon proceeds. The structure of MarR is known and shows MarR as a dimer with each subunit containing a winged-helix DNA binding motif.


Pssm-ID: 432797 [Multi-domain]  Cd Length: 60  Bit Score: 34.87  E-value: 8.20e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 2527201421 431 ETAIIALLHEQSSASTRELVELSGLSRSAIVNHLNRLIKADVIE 474
Cdd:pfam12802   7 QFRVLLALARNPGLTVAELARRLGISKQTVSRLVKRLEAKGLVE 50
 
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.
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