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Conserved domains on  [gi|487749363|ref|WP_001831346|]
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MULTISPECIES: helix-turn-helix transcriptional regulator [Bacillota]

Protein Classification

helix-turn-helix transcriptional regulator( domain architecture ID 10787697)

helix-turn-helix (HTH) transcriptional regulator containing a XRE (Xenobiotic Response Element) family HTH domain may act as a transcriptional regulator that controls the expression of genes involved in stress response

CATH:  1.10.10.10
Gene Ontology:  GO:0003677
PubMed:  10473770|2644244
SCOP:  4000362

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-64 3.08e-24

DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];


:

Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 85.67  E-value: 3.08e-24
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 487749363  1 MRNRLKELRARDGYNQTELAKKAGISRQTVSLIERNDFTPSILTAIKIARIFGEPVEDIFIMEE 64
Cdd:COG1476   5 LGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLEE 68
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-64 3.08e-24

DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 85.67  E-value: 3.08e-24
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 487749363  1 MRNRLKELRARDGYNQTELAKKAGISRQTVSLIERNDFTPSILTAIKIARIFGEPVEDIFIMEE 64
Cdd:COG1476   5 LGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLEE 68
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
3-59 2.92e-14

Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.


Pssm-ID: 238045 [Multi-domain]  Cd Length: 58  Bit Score: 59.87  E-value: 2.92e-14
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 487749363  3 NRLKELRARDGYNQTELAKKAGISRQTVSLIERNDFTPSILTAIKIARIFGEPVEDI 59
Cdd:cd00093   2 ERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
4-59 5.57e-14

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 59.07  E-value: 5.57e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 487749363    4 RLKELRARDGYNQTELAKKAGISRQTVSLIERNDFTPSILTAIKIARIFGEPVEDI 59
Cdd:smart00530  1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
5-59 7.36e-13

Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and CI. Within the protein Swiss:Q5F9C2, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be that of a DNA-binding regulator, the function of most other members, so is not necessarily characteriztic of the whole family.


Pssm-ID: 460181 [Multi-domain]  Cd Length: 55  Bit Score: 56.39  E-value: 7.36e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 487749363   5 LKELRARDGYNQTELAKKAGISRQTVSLIERNDFTPSILTAIKIARIFGEPVEDI 59
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
PRK04140 PRK04140
transcriptional regulator;
3-66 1.05e-09

transcriptional regulator;


Pssm-ID: 235224 [Multi-domain]  Cd Length: 317  Bit Score: 51.78  E-value: 1.05e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 487749363   3 NRLKELRARDGYNQTELAKKAGISRQTVSLIERNDFTPSILTAIKIARIFGEP-VEDIFIMEEED 66
Cdd:PRK04140 129 DVLREAREELGLSLGELASELGVSRRTISKYENGGMNASIEVAIKLEEILDVPlTKPIDILEKVR 193
lysogeny_AimR NF038310
AimR family lysis-lysogeny pheromone receptor; The founding member of this family, AimR ...
5-64 1.87e-03

AimR family lysis-lysogeny pheromone receptor; The founding member of this family, AimR (arbitrium receptor), is a DNA-binding phage regulatory protein that acts as a receptor for a 6-amino acid signaling peptide cleaved from the C-terminus of AimP. AimR controls expression of AimX, the third member of the quorum sensing-like arbitrium system and an inhibitor of phage lysogeny.


Pssm-ID: 468467  Cd Length: 363  Bit Score: 34.43  E-value: 1.87e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 487749363   5 LKELRARDGYNQTELAKKAGISRQTVSLIERNDFTPSILTAIKIAR-IFGEPVEDIFIMEE 64
Cdd:NF038310   1 IKNDLESKGITNRKLAKKIGVSKSTLSKFFNGKGEISFDSLLKILRvLYPNDEERRELIRE 61
antidote_HigA TIGR02607
addiction module antidote protein, HigA family; Members of this family form a distinct clade ...
13-53 5.08e-03

addiction module antidote protein, HigA family; Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair. [Regulatory functions, DNA interactions, Regulatory functions, Protein interactions, Mobile and extrachromosomal element functions, Other]


Pssm-ID: 274228 [Multi-domain]  Cd Length: 78  Bit Score: 31.82  E-value: 5.08e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 487749363  13 GYNQTELAKKAGISRQTVSLI--ERNDFTPSilTAIKIARIFG 53
Cdd:TIGR02607 18 GLSVRALAKALGVSRSTLSRIvnGRAAITAD--MALRLAKALG 58
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-64 3.08e-24

DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 85.67  E-value: 3.08e-24
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 487749363  1 MRNRLKELRARDGYNQTELAKKAGISRQTVSLIERNDFTPSILTAIKIARIFGEPVEDIFIMEE 64
Cdd:COG1476   5 LGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLEE 68
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
3-66 1.60e-15

Transcriptional regulator, contains XRE-family HTH domain [Transcription];


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 63.86  E-value: 1.60e-15
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 487749363  3 NRLKELRARDGYNQTELAKKAGISRQTVSLIERNDFTPSILTAIKIARIFGEPVEDIFIMEEED 66
Cdd:COG1396  10 ERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEE 73
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
3-59 2.92e-14

Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.


Pssm-ID: 238045 [Multi-domain]  Cd Length: 58  Bit Score: 59.87  E-value: 2.92e-14
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 487749363  3 NRLKELRARDGYNQTELAKKAGISRQTVSLIERNDFTPSILTAIKIARIFGEPVEDI 59
Cdd:cd00093   2 ERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
4-59 5.57e-14

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 59.07  E-value: 5.57e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 487749363    4 RLKELRARDGYNQTELAKKAGISRQTVSLIERNDFTPSILTAIKIARIFGEPVEDI 59
Cdd:smart00530  1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
5-59 7.36e-13

Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and CI. Within the protein Swiss:Q5F9C2, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be that of a DNA-binding regulator, the function of most other members, so is not necessarily characteriztic of the whole family.


Pssm-ID: 460181 [Multi-domain]  Cd Length: 55  Bit Score: 56.39  E-value: 7.36e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 487749363   5 LKELRARDGYNQTELAKKAGISRQTVSLIERNDFTPSILTAIKIARIFGEPVEDI 59
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
4-58 1.54e-11

Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and HTH domains [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441418 [Multi-domain]  Cd Length: 70  Bit Score: 53.40  E-value: 1.54e-11
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 487749363  4 RLKELRARDGYNQTELAKKAGISRQTVSLIERNDFTPSILTAIKIARIFGEPVED 58
Cdd:COG1813  16 RIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGISLAE 70
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
5-67 5.23e-11

Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain CBS pair) [Transcription];


Pssm-ID: 442838 [Multi-domain]  Cd Length: 95  Bit Score: 52.71  E-value: 5.23e-11
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 487749363  5 LKELRARDGYNQTELAKKAGISRQTVSLIERNDFTPSILTAIKIARIFGEPVEDIFIMEEEDF 67
Cdd:COG3620  22 LRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAVLVVDDGKL 84
COG1395 COG1395
Predicted transcriptional regulator [Transcription];
4-66 4.53e-10

Predicted transcriptional regulator [Transcription];


Pssm-ID: 441005 [Multi-domain]  Cd Length: 313  Bit Score: 52.92  E-value: 4.53e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 487749363   4 RLKELRARDGYNQTELAKKAGISRQTVSLIERNDFTPSILTAIKIARIFGEP-VEDIFIMEEED 66
Cdd:COG1395  131 KLRELREERGLSLGELASELGVSRRTISKYERGEMDASIEVALKLEEILGEPiVKPIDILEGAE 194
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
4-60 4.63e-10

Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. This family contains many example antitoxins from bacterial toxin-antitoxin systems. These antitoxins are likely to be DNA-binding domains.


Pssm-ID: 463728 [Multi-domain]  Cd Length: 64  Bit Score: 49.59  E-value: 4.63e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 487749363   4 RLKELRARDGYNQTELAKKAGISRQTVSLIERNDFTPSILTAIKIARIFGEPVEDIF 60
Cdd:pfam12844  3 RLRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWLL 59
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
1-66 4.77e-10

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


Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 49.76  E-value: 4.77e-10
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 487749363  1 MRNRLKELRARDGYNQTELAKKAGISRQTVSLIERNDFT-PSILTAIKIARIFGEPVEDIFIMEEED 66
Cdd:COG3655   2 IYVKLDELLAERGMTKKELAEATGISRATLSRLKNGKAKaVRLDTLEKICKALDCQPGDLLEYVPDE 68
PRK04140 PRK04140
transcriptional regulator;
3-66 1.05e-09

transcriptional regulator;


Pssm-ID: 235224 [Multi-domain]  Cd Length: 317  Bit Score: 51.78  E-value: 1.05e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 487749363   3 NRLKELRARDGYNQTELAKKAGISRQTVSLIERNDFTPSILTAIKIARIFGEP-VEDIFIMEEED 66
Cdd:PRK04140 129 DVLREAREELGLSLGELASELGVSRRTISKYENGGMNASIEVAIKLEEILDVPlTKPIDILEKVR 193
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
4-65 2.23e-08

Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to DNA.


Pssm-ID: 433211 [Multi-domain]  Cd Length: 63  Bit Score: 45.22  E-value: 2.23e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 487749363   4 RLKELRARDGYNQTELAKKAGISRQTVSLIERNDF-TPSILTAIKIARIFGEPVEDIFIMEEE 65
Cdd:pfam13443  1 KLRKLMADRGISKSDLARATGISRATLSRLRKGKPkRVSLDTLDKICDALGCQPGDLLEYVPD 63
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
4-66 4.44e-08

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 46.71  E-value: 4.44e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 487749363   4 RLKELRARDGYNQTELAKKAGISRQTVSLIERNDFTPSILTAIKIARIFGEPVEDIFIMEEED 66
Cdd:PRK09943  11 RLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSEFFSEPEKP 73
PRK09726 PRK09726
type II toxin-antitoxin system antitoxin HipB;
3-48 7.77e-07

type II toxin-antitoxin system antitoxin HipB;


Pssm-ID: 182049  Cd Length: 88  Bit Score: 41.89  E-value: 7.77e-07
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 487749363  3 NRLKELRARDGYNQTELAKKAGISRQTVSLIERNDFTPSILTAIKI 48
Cdd:PRK09726 15 NAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKI 60
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
4-59 2.12e-05

Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.


Pssm-ID: 433309 [Multi-domain]  Cd Length: 64  Bit Score: 37.51  E-value: 2.12e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 487749363   4 RLKELRARDGYNQTELAKKAGISRQTVSLIER-NDFTPSILTAIKIARIFGEPVEDI 59
Cdd:pfam13560  5 RLRRLRERAGLSQEALARRLGVSRSTLSRLETgRRGRPSPAVVERLARALGVDGAER 61
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
13-57 3.45e-05

Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense mechanisms];


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 37.48  E-value: 3.45e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 487749363 13 GYNQTELAKKAGISRQTVSLIERNDFTPSILTAIKIARIFGEPVE 57
Cdd:COG3093  22 GLSQTELAKALGVSRQRISEILNGKRAITADTALRLARAFGTSAE 66
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
4-55 3.52e-05

DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 37.22  E-value: 3.52e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 487749363  4 RLKELRARDGYNQTELAKKAGISRQTVSLIERNDFTPSILTAIKIARIFGEP 55
Cdd:COG2944  10 EIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPSGAALKLLRLLEKHP 61
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
4-60 6.07e-04

Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 441035 [Multi-domain]  Cd Length: 71  Bit Score: 34.01  E-value: 6.07e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 487749363  4 RLKELRARDGYNQTELAKKAGISRQTVSLIERNDF------TPSILTAIKIARIFGEPVEDIF 60
Cdd:COG1426   9 LLRQAREAKGLSLEDVAERTKISVSYLEAIEEGDFdalpgpVYVRGFLRSYARALGLDPEELL 71
lysogeny_AimR NF038310
AimR family lysis-lysogeny pheromone receptor; The founding member of this family, AimR ...
5-64 1.87e-03

AimR family lysis-lysogeny pheromone receptor; The founding member of this family, AimR (arbitrium receptor), is a DNA-binding phage regulatory protein that acts as a receptor for a 6-amino acid signaling peptide cleaved from the C-terminus of AimP. AimR controls expression of AimX, the third member of the quorum sensing-like arbitrium system and an inhibitor of phage lysogeny.


Pssm-ID: 468467  Cd Length: 363  Bit Score: 34.43  E-value: 1.87e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 487749363   5 LKELRARDGYNQTELAKKAGISRQTVSLIERNDFTPSILTAIKIAR-IFGEPVEDIFIMEE 64
Cdd:NF038310   1 IKNDLESKGITNRKLAKKIGVSKSTLSKFFNGKGEISFDSLLKILRvLYPNDEERRELIRE 61
antidote_HigA TIGR02607
addiction module antidote protein, HigA family; Members of this family form a distinct clade ...
13-53 5.08e-03

addiction module antidote protein, HigA family; Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair. [Regulatory functions, DNA interactions, Regulatory functions, Protein interactions, Mobile and extrachromosomal element functions, Other]


Pssm-ID: 274228 [Multi-domain]  Cd Length: 78  Bit Score: 31.82  E-value: 5.08e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 487749363  13 GYNQTELAKKAGISRQTVSLI--ERNDFTPSilTAIKIARIFG 53
Cdd:TIGR02607 18 GLSVRALAKALGVSRSTLSRIvnGRAAITAD--MALRLAKALG 58
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
1-40 7.34e-03

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 32.52  E-value: 7.34e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 487749363   1 MRNRLKELrardGYNQTELAKKAGISRQTVSLIERNDFTP 40
Cdd:PRK09706  10 IRYRRKQL----KLSQRSLAKAVKVSHVSISQWERDETEP 45
 
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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