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Conserved domains on  [gi|2096221168|ref|WP_223201064|]
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helix-turn-helix domain-containing protein [Micromonospora sp. M42]

Protein Classification

ROK family transcriptional regulator( domain architecture ID 20650276)

NagC/ROK (Repressor, ORF, Kinase) family transcriptional regulator is involved in carbohydrate-dependent transcriptional control; contains a DNA-binding helix-turn-helix (HTH) domain

CATH:  3.30.420.40|1.10.10.10
Gene Ontology:  GO:0003700|GO:0006355|GO:0005524|GO:0003677
PubMed:  20512568|17979299|7952186|15808743|2644244|8831795|7781919|8800467
SCOP:  3000034|3000092|4000330

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ASKHA_ATPase-like super family cl49607
ATPase-like domain of the ASKHA (Acetate and Sugar Kinases/Hsc70/Actin) superfamily; The ASKHA ...
 88-170 8.93e-08

ATPase-like domain of the ASKHA (Acetate and Sugar Kinases/Hsc70/Actin) superfamily; The ASKHA superfamily, also known as actin-like ATPase domain superfamily, includes acetate and sugar kinases, heat-shock cognate 70 (Hsp70) and actin family proteins. They either function as conformational hydrolases (e.g. Hsp70, actin) that perform simple ATP hydrolysis, or as metabolite kinases (e.g. glycerol kinase) that catalyze the transfer of a phosphoryl group from ATP to their cognate substrates. Both activities depend on the presence of specific metal cations. ASKHA superfamily members share a common core fold that includes an actin-like ATPase domain consisting of two subdomains (denoted I _ II) with highly similar ribonuclease (RNase) H-like folds. The fold of each subdomain is characterized by a central five strand beta-sheet and flanking alpha-helices. The two subdomains form an active site cleft in which ATP binds at the bottom. Another common feature of ASKHA superfamily members is the coupling of phosphoryl-group transfer to conformational rearrangement, leading to domain closure. Substrate binding triggers protein motion.


The actual alignment was detected with superfamily member cd24076:

Pssm-ID: 483947 [Multi-domain]  Cd Length: 303  Bit Score: 50.64  E-value: 8.93e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096221168  88 LGLRVGADELVAVAAGLGGDPVLTWRRAFPAATAgAEETVKALAALTRRAVTRANRRRfEKVLGLTVAVPGLVDA-DGDV 166
Cdd:cd24076     4 IGVELGVDYITVVVTDLAGEVLWRREVPLPASDD-PDEVLAQLAALIREALAAAPDSP-LGILGIGVGVPGLVDSeDGVV 81


                  ....
gi 2096221168 167 PAAP 170
Cdd:cd24076    82 LLAP 85
MarR_2 pfam12802
MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a ...
 20-70 1.20e-05

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: 41.42  E-value: 1.20e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2096221168  20 AAVLRHVRRHAPCSRADVAAHTGLNKATVSSLVAELIEHGLLRETGLTENR 70
Cdd:pfam12802   8 FRVLLALARNPGLTVAELARRLGISKQTVSRLVKRLEAKGLVEREPSPADR 58
 
Name Accession Description Interval E-value
ASKHA_ATPase_ROK_BsXylR-like cd24076
ATPase-like domain of Bacillus subtilis xylose repressor (XylR) and similar proteins; This ...
 88-170 8.93e-08

ATPase-like domain of Bacillus subtilis xylose repressor (XylR) and similar proteins; This subfamily includes a group of uncharacterized proteins similar to Bacillus subtilis xylose repressor (BsXylR), which belongs to the kinase (ROK) family, a group of proteins that have sugar kinase and/or transcriptional repressor activities. BsXylR acts as transcriptional repressor of xylose-utilizing enzymes.


Pssm-ID: 466926 [Multi-domain]  Cd Length: 303  Bit Score: 50.64  E-value: 8.93e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096221168  88 LGLRVGADELVAVAAGLGGDPVLTWRRAFPAATAgAEETVKALAALTRRAVTRANRRRfEKVLGLTVAVPGLVDA-DGDV 166
Cdd:cd24076     4 IGVELGVDYITVVVTDLAGEVLWRREVPLPASDD-PDEVLAQLAALIREALAAAPDSP-LGILGIGVGVPGLVDSeDGVV 81


                  ....
gi 2096221168 167 PAAP 170
Cdd:cd24076    82 LLAP 85
MarR_2 pfam12802
MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a ...
 20-70 1.20e-05

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: 41.42  E-value: 1.20e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2096221168  20 AAVLRHVRRHAPCSRADVAAHTGLNKATVSSLVAELIEHGLLRETGLTENR 70
Cdd:pfam12802   8 FRVLLALARNPGLTVAELARRLGISKQTVSRLVKRLEAKGLVEREPSPADR 58
NagC COG1940
Sugar kinase of the NBD/HSP70 family, may contain an N-terminal HTH domain [Carbohydrate ...
 88-166 1.23e-05

Sugar kinase of the NBD/HSP70 family, may contain an N-terminal HTH domain [Carbohydrate transport and metabolism, Transcription];


Pssm-ID: 441543 [Multi-domain]  Cd Length: 306  Bit Score: 44.50  E-value: 1.23e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2096221168  88 LGLRVGADELVAVAAGLGGDPVLTWRRAFPAATaGAEETVKALAALTRRAVTRANRRRfEKVLGLTVAVPGLVDADGDV 166
Cdd:COG1940     8 IGIDIGGTKIKAALVDLDGEVLARERIPTPAGA-GPEAVLEAIAELIEELLAEAGISR-GRILGIGIGVPGPVDPETGV 84
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
19-62 1.99e-03

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 36.87  E-value: 1.99e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 2096221168  19 RAAVLRHVRRHAPCSRADVAAHTGLNKATVSSLVAELIEHGLLR 62
Cdd:COG1846    40 QFRVLAALAEAGGLTQSELAERLGLTKSTVSRLLDRLEEKGLVE 83
HTH_CRP smart00419
helix_turn_helix, cAMP Regulatory protein;
31-62 8.34e-03

helix_turn_helix, cAMP Regulatory protein;


Pssm-ID: 128696 [Multi-domain]  Cd Length: 48  Bit Score: 33.18  E-value: 8.34e-03
                           10        20        30
                   ....*....|....*....|....*....|..
gi 2096221168   31 PCSRADVAAHTGLNKATVSSLVAELIEHGLLR 62
Cdd:smart00419   8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLIS 39
 
Name Accession Description Interval E-value
ASKHA_ATPase_ROK_BsXylR-like cd24076
ATPase-like domain of Bacillus subtilis xylose repressor (XylR) and similar proteins; This ...
 88-170 8.93e-08

ATPase-like domain of Bacillus subtilis xylose repressor (XylR) and similar proteins; This subfamily includes a group of uncharacterized proteins similar to Bacillus subtilis xylose repressor (BsXylR), which belongs to the kinase (ROK) family, a group of proteins that have sugar kinase and/or transcriptional repressor activities. BsXylR acts as transcriptional repressor of xylose-utilizing enzymes.


Pssm-ID: 466926 [Multi-domain]  Cd Length: 303  Bit Score: 50.64  E-value: 8.93e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096221168  88 LGLRVGADELVAVAAGLGGDPVLTWRRAFPAATAgAEETVKALAALTRRAVTRANRRRfEKVLGLTVAVPGLVDA-DGDV 166
Cdd:cd24076     4 IGVELGVDYITVVVTDLAGEVLWRREVPLPASDD-PDEVLAQLAALIREALAAAPDSP-LGILGIGVGVPGLVDSeDGVV 81


                  ....
gi 2096221168 167 PAAP 170
Cdd:cd24076    82 LLAP 85
MarR_2 pfam12802
MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a ...
 20-70 1.20e-05

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: 41.42  E-value: 1.20e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2096221168  20 AAVLRHVRRHAPCSRADVAAHTGLNKATVSSLVAELIEHGLLRETGLTENR 70
Cdd:pfam12802   8 FRVLLALARNPGLTVAELARRLGISKQTVSRLVKRLEAKGLVEREPSPADR 58
NagC COG1940
Sugar kinase of the NBD/HSP70 family, may contain an N-terminal HTH domain [Carbohydrate ...
 88-166 1.23e-05

Sugar kinase of the NBD/HSP70 family, may contain an N-terminal HTH domain [Carbohydrate transport and metabolism, Transcription];


Pssm-ID: 441543 [Multi-domain]  Cd Length: 306  Bit Score: 44.50  E-value: 1.23e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2096221168  88 LGLRVGADELVAVAAGLGGDPVLTWRRAFPAATaGAEETVKALAALTRRAVTRANRRRfEKVLGLTVAVPGLVDADGDV 166
Cdd:COG1940     8 IGIDIGGTKIKAALVDLDGEVLARERIPTPAGA-GPEAVLEAIAELIEELLAEAGISR-GRILGIGIGVPGPVDPETGV 84
ASKHA_ATPase_ROK cd23763
ATPase-like domain of the ROK (Repressor, ORF, Kinase) domain family; The ROK family ...
 88-163 6.74e-05

ATPase-like domain of the ROK (Repressor, ORF, Kinase) domain family; The ROK family corresponds to a group of proteins including sugar kinases, transcriptional repressors, and yet uncharacterized open reading frames. ROK family sugar kinases phosphorylate a range of structurally distinct hexoses including the key carbon source D-glucose, various glucose epimers, and several acetylated hexosamines. The sugar kinases include N-acetyl-D-glucosamine kinase (NAGK; EC 2.7.1.59), polyphosphate glucokinase (PPGK; EC 2.7.1.63/EC 2.7.1.2), glucokinase (GLK; EC 2.7.1.2), fructokinase (FRK; EC 2.7.1.4), hexokinase (HK; EC 2.7.1.1), D-allose kinase (AlsK; EC 2.7.1.55), bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase (GNE; EC 3.2.1.183/EC 2.7.1.60), N-acetylmannosamine kinase (NanK; EC 2.7.1.60), beta-glucoside kinase (BglK; EC 2.7.1.85), and N-acetylglucosamine kinase (EC 2.7.1.59). The family also contains the repressor proteins, such as N-acetylglucosamine repressor (NagC), xylose repressor (XylR), cyclobis-(1-6)-alpha-nigerosyl repressor (CYANR) and protein Mlc. ROK kinases harbor a conserved N-terminal ATP binding motif of sequence DxGxT, while ROK repressors possess a N-terminal extension that contains a canonical helix-turn-helix DNA binding motif. The ROK family proteins belong to the ASKHA (Acetate and Sugar Kinases/Hsc70/Actin) superfamily of phosphotransferases, all members of which share a common characteristic five-stranded beta sheet occurring in both the N- and C-terminal domains.


Pssm-ID: 466849 [Multi-domain]  Cd Length: 239  Bit Score: 42.07  E-value: 6.74e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2096221168  88 LGLRVGADELVAVAAGLGGDPVLTWRRAFPAaTAGAEETVKALAALTRRAVTRANRRrfEKVLGLTVAVPGLVDAD 163
Cdd:cd23763     1 IGIDIGGTKIRAALVDLDGEILARERVPTPA-EEGPEAVLDRIAELIEELLAEAGVR--ERILGIGIGVPGPVDPE 73
HTH_IclR pfam09339
IclR helix-turn-helix domain;
20-65 6.55e-04

IclR helix-turn-helix domain;


Pssm-ID: 430539 [Multi-domain]  Cd Length: 52  Bit Score: 36.23  E-value: 6.55e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2096221168  20 AAVLRHVRRHA-PCSRADVAAHTGLNKATVSSLVAELIEHGLLRETG 65
Cdd:pfam09339   6 LAILDALAEAPgPLTLTEIARRTGLPKSTAHRLLQTLVELGYVEQDP 52
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
19-62 1.99e-03

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 36.87  E-value: 1.99e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 2096221168  19 RAAVLRHVRRHAPCSRADVAAHTGLNKATVSSLVAELIEHGLLR 62
Cdd:COG1846    40 QFRVLAALAEAGGLTQSELAERLGLTKSTVSRLLDRLEEKGLVE 83
COG2512 COG2512
Predicted transcriptional regulator, contains CW (cell wall-binding) repeats and an HTH domain ...
 17-73 5.59e-03

Predicted transcriptional regulator, contains CW (cell wall-binding) repeats and an HTH domain [General function prediction only];


Pssm-ID: 442002 [Multi-domain]  Cd Length: 80  Bit Score: 34.50  E-value: 5.59e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2096221168  17 TNRAAVLRHVRRHAP-CSRADVAAHTGLNKATVSSLVAELIEHGLLRETgltenRVGR 73
Cdd:COG2512    15 EDERRVLELLRENGGrMTQSEIVKETGWSKSKVSRLLSRLEERGLIEKE-----RVGR 67
IclR COG1414
DNA-binding transcriptional regulator, IclR family [Transcription];
21-62 6.70e-03

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


Pssm-ID: 441024 [Multi-domain]  Cd Length: 253  Bit Score: 36.34  E-value: 6.70e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2096221168  21 AVLRHVRRHA-PCSRADVAAHTGLNKATVSSLVAELIEHGLLR 62
Cdd:COG1414    13 AILEALAEAGgGLSLSELARRLGLPKSTVHRLLATLEEEGYVE 55
COG4189 COG4189
Predicted transcriptional regulator, ArsR family [Transcription];
19-73 7.96e-03

Predicted transcriptional regulator, ArsR family [Transcription];


Pssm-ID: 443343 [Multi-domain]  Cd Length: 97  Bit Score: 34.55  E-value: 7.96e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2096221168  19 RAAVLRHVRRHaPCSRADVAAHTGLNKATVSSLVAELIEHGLLRetglTENRVGR 73
Cdd:COG4189    21 RLRILRLLAEE-PLNVNELAEALGLPKSTVSYHIRKLEEAGLIR----TEYKPGK 70
HTH_CRP smart00419
helix_turn_helix, cAMP Regulatory protein;
31-62 8.34e-03

helix_turn_helix, cAMP Regulatory protein;


Pssm-ID: 128696 [Multi-domain]  Cd Length: 48  Bit Score: 33.18  E-value: 8.34e-03
                           10        20        30
                   ....*....|....*....|....*....|..
gi 2096221168   31 PCSRADVAAHTGLNKATVSSLVAELIEHGLLR 62
Cdd:smart00419   8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLIS 39
MarR pfam01047
MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a ...
 22-70 9.71e-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: 426012 [Multi-domain]  Cd Length: 59  Bit Score: 33.29  E-value: 9.71e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2096221168  22 VLRHVRRHAPCSRADVAAHTGLNKATVSSLVAELIEHGLLRETGLTENR 70
Cdd:pfam01047   8 ILRILYEHGPLTVSELAEKLGVSKSTVTRVLDRLEKKGLIERSRSPEDR 56
ASKHA_NBD_ROK_TM1224-like cd24059
nucleotide-binding domain (NBD) of Thermotoga maritima N-acetylglucosamine kinase (TM1224) and ...
 84-162 9.97e-03

nucleotide-binding domain (NBD) of Thermotoga maritima N-acetylglucosamine kinase (TM1224) and similar proteins; This subfamily includes a group of uncharacterized proteins similar to N-acetylglucosamine kinase (Tm1224; EC 2.7.1.59) from Thermotoga maritima, which belongs to kinase (ROK) family, a group of proteins that have sugar kinase and/or transcriptional repressor activities. Tm1224 lacks the cysteine-rich zinc-binding motif, which presents in other family members.


Pssm-ID: 466909 [Multi-domain]  Cd Length: 305  Bit Score: 35.64  E-value: 9.97e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2096221168  84 RYVgLGLRVGADELVAVAAGLGGDpVLTwRRAFPAATA-GAEETVKALAALTRRAVTRANRRRfeKVLGLTVAVPGLVDA 162
Cdd:cd24059     1 PYV-IGVEIGRDLLSAVLCDLSGN-ILA-REKYPLDEKeNPEEVLEKLYELIDRLLEKENIKS--KILGIGIGAPGPLDV 75
 
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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