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Conserved domains on  [gi|651331199|ref|WP_026455359|]
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winged helix-turn-helix domain-containing protein [Saccharomonospora iraqiensis]

Protein Classification

winged helix-turn-helix domain-containing protein( domain architecture ID 10164212)

GntR family winged helix-turn-helix (wHTH) domain-containing protein binds DNA and may function as a transcriptional regulator

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
MngR super family cl34419
DNA-binding transcriptional regulator, GntR family [Transcription];
19-83 1.44e-21

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


The actual alignment was detected with superfamily member COG2188:

Pssm-ID: 441791 [Multi-domain]  Cd Length: 238  Bit Score: 84.14  E-value: 1.44e-21
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 651331199  19 YVLLADHLAEFIERGEWPPGSRLPGERALSAEYGVALDTIRKATQILRERGLVQTLRSKGTFVAP 83
Cdd:COG2188    7 YLQIADALRERIESGELPPGDRLPSERELAEEFGVSRMTVRKALDELVEEGLLERRQGRGTFVAE 71
 
Name Accession Description Interval E-value
MngR COG2188
DNA-binding transcriptional regulator, GntR family [Transcription];
19-83 1.44e-21

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


Pssm-ID: 441791 [Multi-domain]  Cd Length: 238  Bit Score: 84.14  E-value: 1.44e-21
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 651331199  19 YVLLADHLAEFIERGEWPPGSRLPGERALSAEYGVALDTIRKATQILRERGLVQTLRSKGTFVAP 83
Cdd:COG2188    7 YLQIADALRERIESGELPPGDRLPSERELAEEFGVSRMTVRKALDELVEEGLLERRQGRGTFVAE 71
WHTH_GntR cd07377
Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ...
19-82 2.24e-21

Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is presumed to result in a conformational change that regulates the DNA-binding affinity of the repressor. The GntR-like proteins bind as dimers, where each monomer recognizes a half-site of 2-fold symmetric DNA sequences.


Pssm-ID: 153418 [Multi-domain]  Cd Length: 66  Bit Score: 79.03  E-value: 2.24e-21
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 651331199 19 YVLLADHLAEFIERGEWPPGSRLPGERALSAEYGVALDTIRKATQILRERGLVQTLRSKGTFVA 82
Cdd:cd07377   3 YEQIADQLREAILSGELKPGDRLPSERELAEELGVSRTTVREALRELEAEGLVERRPGRGTFVA 66
HTH_GNTR smart00345
helix_turn_helix gluconate operon transcriptional repressor;
22-81 1.18e-16

helix_turn_helix gluconate operon transcriptional repressor;


Pssm-ID: 197669 [Multi-domain]  Cd Length: 60  Bit Score: 67.21  E-value: 1.18e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 651331199   22 LADHLAEFIERGEWPPGSRLPGERALSAEYGVALDTIRKATQILRERGLVQTLRSKGTFV 81
Cdd:smart00345  1 VAERLREDIVSGELRPGDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQRRPGSGTFV 60
GntR pfam00392
Bacterial regulatory proteins, gntR family; This family of regulatory proteins consists of the ...
19-81 3.40e-14

Bacterial regulatory proteins, gntR family; This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector-binding/oligomerization domain. The GntR-like proteins include the following sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA, DevA, DasR. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships. The DasR regulator has been shown to be a global regulator of primary metabolism and development in Streptomyces coelicolor.


Pssm-ID: 306822 [Multi-domain]  Cd Length: 64  Bit Score: 61.09  E-value: 3.40e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 651331199  19 YVLLADHLAEFIERGEWPPGSRLPGERALSAEYGVALDTIRKATQILRERGLVQTLRSKGTFV 81
Cdd:pfam00392  2 YEQVYARLREDILSGRLRPGDKLPSERELAAEFGVSRTTVREALRRLEAEGLVERRQGRGTFV 64
PRK10421 PRK10421
DNA-binding transcriptional repressor LldR; Provisional
22-81 2.04e-10

DNA-binding transcriptional repressor LldR; Provisional


Pssm-ID: 236690 [Multi-domain]  Cd Length: 253  Bit Score: 54.77  E-value: 2.04e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 651331199  22 LADHLAE----FIERGEWPPGSRLPGERALSAEYGVALDTIRKATQILRERGLVQTLRSKGTFV 81
Cdd:PRK10421   3 LSDEVADrvraLIEEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFI 66
C_P_lyase_phnF TIGR02325
phosphonates metabolism transcriptional regulator PhnF; All members of the seed alignment for ...
19-82 1.20e-09

phosphonates metabolism transcriptional regulator PhnF; All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond. [Transport and binding proteins, Anions, Regulatory functions, DNA interactions]


Pssm-ID: 131378 [Multi-domain]  Cd Length: 238  Bit Score: 52.48  E-value: 1.20e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 651331199   19 YVLLADHLAEFIERGEWPPGSRLPGERALSAEYGVALDTIRKATQILRERGLVQTLRSKGTFVA 82
Cdd:TIGR02325  10 WRQIADKIEQEIAAGHLRAGDYLPAEMQLAERFGVNRHTVRRAIAALVERGLLRAEQGRGTFVA 73
 
Name Accession Description Interval E-value
MngR COG2188
DNA-binding transcriptional regulator, GntR family [Transcription];
19-83 1.44e-21

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


Pssm-ID: 441791 [Multi-domain]  Cd Length: 238  Bit Score: 84.14  E-value: 1.44e-21
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 651331199  19 YVLLADHLAEFIERGEWPPGSRLPGERALSAEYGVALDTIRKATQILRERGLVQTLRSKGTFVAP 83
Cdd:COG2188    7 YLQIADALRERIESGELPPGDRLPSERELAEEFGVSRMTVRKALDELVEEGLLERRQGRGTFVAE 71
WHTH_GntR cd07377
Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ...
19-82 2.24e-21

Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is presumed to result in a conformational change that regulates the DNA-binding affinity of the repressor. The GntR-like proteins bind as dimers, where each monomer recognizes a half-site of 2-fold symmetric DNA sequences.


Pssm-ID: 153418 [Multi-domain]  Cd Length: 66  Bit Score: 79.03  E-value: 2.24e-21
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 651331199 19 YVLLADHLAEFIERGEWPPGSRLPGERALSAEYGVALDTIRKATQILRERGLVQTLRSKGTFVA 82
Cdd:cd07377   3 YEQIADQLREAILSGELKPGDRLPSERELAEELGVSRTTVREALRELEAEGLVERRPGRGTFVA 66
YhcF COG1725
DNA-binding transcriptional regulator YhcF, GntR family [Transcription];
19-86 1.51e-19

DNA-binding transcriptional regulator YhcF, GntR family [Transcription];


Pssm-ID: 441331 [Multi-domain]  Cd Length: 114  Bit Score: 75.99  E-value: 1.51e-19
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 651331199  19 YVLLADHLAEFIERGEWPPGSRLPGERALSAEYGVALDTIRKATQILRERGLVQTLRSKGTFVAPGGR 86
Cdd:COG1725   12 YEQIADQIKEAIASGELKPGDRLPSVRELAAELGVNPNTVAKAYRELEDEGLIETRRGKGTFVAEDAR 79
ARO8 COG1167
DNA-binding transcriptional regulator, MocR family, contains an aminotransferase domain ...
19-90 3.30e-18

DNA-binding transcriptional regulator, MocR family, contains an aminotransferase domain [Transcription, Amino acid transport and metabolism]; DNA-binding transcriptional regulator, MocR family, contains an aminotransferase domain is part of the Pathway/BioSystem: Lysine biosynthesis


Pssm-ID: 440781 [Multi-domain]  Cd Length: 471  Bit Score: 77.18  E-value: 3.30e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 651331199  19 YVLLADHLAEFIERGEWPPGSRLPGERALSAEYGVALDTIRKATQILRERGLVQTLRSKGTFVAPGGRTTDP 90
Cdd:COG1167   14 YLQLADALREAILSGRLPPGDRLPSSRELAAQLGVSRSTVVRAYEELEAEGLIESRPGSGTFVAARLPAPAP 85
FadR COG2186
DNA-binding transcriptional regulator, FadR family [Transcription];
12-83 1.13e-17

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


Pssm-ID: 441789 [Multi-domain]  Cd Length: 232  Bit Score: 73.81  E-value: 1.13e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 651331199  12 ESKTGYEYVllADHLAEFIERGEWPPGSRLPGERALSAEYGVALDTIRKATQILRERGLVQTLRSKGTFVAP 83
Cdd:COG2186    4 RRRSLAEQV--AEQLRELILSGELKPGDRLPSERELAEQLGVSRTTVREALRALEALGLVEVRQGGGTFVRE 73
HTH_GNTR smart00345
helix_turn_helix gluconate operon transcriptional repressor;
22-81 1.18e-16

helix_turn_helix gluconate operon transcriptional repressor;


Pssm-ID: 197669 [Multi-domain]  Cd Length: 60  Bit Score: 67.21  E-value: 1.18e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 651331199   22 LADHLAEFIERGEWPPGSRLPGERALSAEYGVALDTIRKATQILRERGLVQTLRSKGTFV 81
Cdd:smart00345  1 VAERLREDIVSGELRPGDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQRRPGSGTFV 60
GntR pfam00392
Bacterial regulatory proteins, gntR family; This family of regulatory proteins consists of the ...
19-81 3.40e-14

Bacterial regulatory proteins, gntR family; This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector-binding/oligomerization domain. The GntR-like proteins include the following sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA, DevA, DasR. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships. The DasR regulator has been shown to be a global regulator of primary metabolism and development in Streptomyces coelicolor.


Pssm-ID: 306822 [Multi-domain]  Cd Length: 64  Bit Score: 61.09  E-value: 3.40e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 651331199  19 YVLLADHLAEFIERGEWPPGSRLPGERALSAEYGVALDTIRKATQILRERGLVQTLRSKGTFV 81
Cdd:pfam00392  2 YEQVYARLREDILSGRLRPGDKLPSERELAAEFGVSRTTVREALRRLEAEGLVERRQGRGTFV 64
PRK10421 PRK10421
DNA-binding transcriptional repressor LldR; Provisional
22-81 2.04e-10

DNA-binding transcriptional repressor LldR; Provisional


Pssm-ID: 236690 [Multi-domain]  Cd Length: 253  Bit Score: 54.77  E-value: 2.04e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 651331199  22 LADHLAE----FIERGEWPPGSRLPGERALSAEYGVALDTIRKATQILRERGLVQTLRSKGTFV 81
Cdd:PRK10421   3 LSDEVADrvraLIEEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFI 66
GntR COG1802
DNA-binding transcriptional regulator, GntR family [Transcription];
23-83 3.75e-10

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


Pssm-ID: 441407 [Multi-domain]  Cd Length: 222  Bit Score: 53.77  E-value: 3.75e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 651331199  23 ADHLAEFIERGEWPPGSRLPgERALSAEYGVALDTIRKATQILRERGLVQTLRSKGTFVAP 83
Cdd:COG1802   17 YEALREAILSGELPPGERLS-EAELAERLGVSRTPVREALRRLEAEGLVEIRPNRGARVAP 76
PRK09764 PRK09764
GntR family transcriptional regulator;
19-81 8.16e-10

GntR family transcriptional regulator;


Pssm-ID: 182065 [Multi-domain]  Cd Length: 240  Bit Score: 52.91  E-value: 8.16e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 651331199  19 YVLLADHLAEFIERGEWPPGSRLPGERALSAEYGVALDTIRKATQILRERGLVQTLRSKGTFV 81
Cdd:PRK09764   7 YRQIADRIREQIARGELKPGDALPTESALQTEFGVSRVTVRQALRQLVEQQILESIQGSGTYV 69
PRK03837 PRK03837
transcriptional regulator NanR; Provisional
24-72 8.39e-10

transcriptional regulator NanR; Provisional


Pssm-ID: 235166 [Multi-domain]  Cd Length: 241  Bit Score: 53.10  E-value: 8.39e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 651331199  24 DHLAEFIERGEWPPGSRLPGERALSAEYGVALDTIRKATQILRERGLVQ 72
Cdd:PRK03837  20 ERLEQMIRSGEFGPGDQLPSERELMAFFGVGRPAVREALQALKRKGLVQ 68
C_P_lyase_phnF TIGR02325
phosphonates metabolism transcriptional regulator PhnF; All members of the seed alignment for ...
19-82 1.20e-09

phosphonates metabolism transcriptional regulator PhnF; All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond. [Transport and binding proteins, Anions, Regulatory functions, DNA interactions]


Pssm-ID: 131378 [Multi-domain]  Cd Length: 238  Bit Score: 52.48  E-value: 1.20e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 651331199   19 YVLLADHLAEFIERGEWPPGSRLPGERALSAEYGVALDTIRKATQILRERGLVQTLRSKGTFVA 82
Cdd:TIGR02325  10 WRQIADKIEQEIAAGHLRAGDYLPAEMQLAERFGVNRHTVRRAIAALVERGLLRAEQGRGTFVA 73
PRK09990 PRK09990
DNA-binding transcriptional regulator GlcC; Provisional
22-89 5.02e-09

DNA-binding transcriptional regulator GlcC; Provisional


Pssm-ID: 182186 [Multi-domain]  Cd Length: 251  Bit Score: 50.92  E-value: 5.02e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 651331199  22 LADHLAEFIER----GEWPPGSRLPGERALSAEYGVALDTIRKATQILRERGLVQTLRSKGTFVAPGGRTTD 89
Cdd:PRK09990   8 IADVVAERIERlivdGVLKVGQALPSERRLCEKLGFSRSALREGLTVLRGRGIIETAQGRGSFVARLNRVQD 79
PRK11402 PRK11402
transcriptional regulator PhoB;
19-81 1.55e-08

transcriptional regulator PhoB;


Pssm-ID: 183118 [Multi-domain]  Cd Length: 241  Bit Score: 49.45  E-value: 1.55e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 651331199  19 YVLLADHLAEFIERGEWPPGSRLPGERALSAEYGVALDTIRKATQILRERGLVQTLRSKGTFV 81
Cdd:PRK11402  11 YATVRQRLLDDIAQGVYQAGQQIPTENELCTQYNVSRITIRKAISDLVADGVLIRWQGKGTFV 73
PRK14999 PRK14999
histidine utilization repressor; Provisional
26-87 3.18e-08

histidine utilization repressor; Provisional


Pssm-ID: 184961 [Multi-domain]  Cd Length: 241  Bit Score: 48.78  E-value: 3.18e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 651331199  26 LAEFIERGEWPPGSRLPGERALSAEYGVALDTIRKATQILRERGLVQTLRSKGTFVA-PGGRT 87
Cdd:PRK14999  21 ICKKIAGGVWQPHDRIPSEAELVAQYGFSRMTINRALRELTDEGWLVRLQGVGTFVAePKGQS 83
PRK11523 PRK11523
transcriptional regulator ExuR;
19-81 6.01e-06

transcriptional regulator ExuR;


Pssm-ID: 183176 [Multi-domain]  Cd Length: 253  Bit Score: 42.52  E-value: 6.01e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 651331199  19 YVLLADHLAEFIERGEWPPGSRLPGERALSAEYGVALDTIRKATQILRERGLVQTLRSKGTFV 81
Cdd:PRK11523  10 YQQLAAELKERIEQGVYLVGDKLPAERFIADEKNVSRTVVREAIIMLEVEGYVEVRKGSGIHV 72
pdhR PRK09464
pyruvate dehydrogenase complex transcriptional repressor PdhR;
25-81 4.98e-05

pyruvate dehydrogenase complex transcriptional repressor PdhR;


Pssm-ID: 181879 [Multi-domain]  Cd Length: 254  Bit Score: 39.62  E-value: 4.98e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 651331199  25 HLAEFIERGEWPPGSRLPGERALSAEYGVALDTIRKATQILRERGLVQTLRSKGTFV 81
Cdd:PRK09464  18 QLEFLILEGTLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRRQGGGTFV 74
PRK10225 PRK10225
Uxu operon transcriptional regulator;
28-81 5.15e-05

Uxu operon transcriptional regulator;


Pssm-ID: 182318 [Multi-domain]  Cd Length: 257  Bit Score: 39.62  E-value: 5.15e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 651331199  28 EFIERGEWPPGSRLPGERALSAEYGVALDTIRKATQILRERGLVQTLRSKGTFV 81
Cdd:PRK10225  20 DLIIKTPYNPGERLPPEREIAEMLDVTRTVVREALIMLEIKGLVEVRRGAGIYV 73
PRK15481 PRK15481
transcriptional regulatory protein PtsJ; Provisional
24-81 1.03e-04

transcriptional regulatory protein PtsJ; Provisional


Pssm-ID: 185378 [Multi-domain]  Cd Length: 431  Bit Score: 38.87  E-value: 1.03e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 651331199  24 DHLAEFIERGEWPPGSRLPGERALSAEYGVALDTIRKATQILRERGLVQTLRSKGTFV 81
Cdd:PRK15481  12 DSIRQLIQAGRLRPGDSLPPVRELASELGVNRNTVAAAYKRLVTAGLAQSQGRNGTVI 69
PRK10079 PRK10079
phosphonate metabolism transcriptional regulator PhnF; Provisional
32-81 5.14e-04

phosphonate metabolism transcriptional regulator PhnF; Provisional


Pssm-ID: 182227 [Multi-domain]  Cd Length: 241  Bit Score: 37.06  E-value: 5.14e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 651331199  32 RGEWPPGSRLPGERALSAEYGVALDTIRKATQILRERGLVQTLRSKGTFV 81
Cdd:PRK10079  26 RQHYRCGDYLPAEQQLAARYEVNRHTLRRAIDQLVEKGWVQRRQGVGVLV 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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