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Conserved domains on  [gi|1958782513|ref|XP_038967950|]
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zinc finger protein DPF3 isoform X5 [Rattus norvegicus]

Protein Classification

PHD finger domain-containing protein( domain architecture ID 10624004)

PHD (plant homeodomain) finger domain-containing protein contains a C4HC3 zinc-finger-like motif

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
DPF1-3_N pfam14051
DPF1-3, N-terminal; This putative domain has been detected on requiem/DPF family proteins. It ...
36-102 4.38e-42

DPF1-3, N-terminal; This putative domain has been detected on requiem/DPF family proteins. It was identified as an adaptor molecule that links nuclear factor kappa-light-chain-enhancer of activated B cells (NF-kappa-B) dimer RelB/p52 and switch/sucrose-nonfermentable (SWI/SNF) chromatin remodelling factor.


:

Pssm-ID: 464074  Cd Length: 67  Bit Score: 140.08  E-value: 4.38e-42
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958782513  36 GDQFYKEAIEHCRSYNSRLCAERSVRLPFLDSQTGVAQNNCYIWMEKRHRGPGLAPGQLYTYPARCW 102
Cdd:pfam14051   1 NDSFYKDALENSSNFNSRLCIERKLRLPFLDSQTGVAQNHCYLWMKKRQRMPGLDPGQIYTYPARRW 67
PHD_SF super family cl22851
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
284-314 5.92e-17

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


The actual alignment was detected with superfamily member cd15692:

Pssm-ID: 473978  Cd Length: 57  Bit Score: 73.57  E-value: 5.92e-17
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1958782513 284 YCDFCLGGSNMNKKSGRPEELVSCADCGRSG 314
Cdd:cd15692     1 YCDFCLGGSNMNKKSGRPEELVSCADCGRSG 31
SFP1 super family cl25788
Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division ...
218-245 4.47e-08

Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning];


The actual alignment was detected with superfamily member COG5189:

Pssm-ID: 227516 [Multi-domain]  Cd Length: 423  Bit Score: 53.95  E-value: 4.47e-08
                          10        20
                  ....*....|....*....|....*...
gi 1958782513 218 DKPYVCDICGKRYKNRPGLSYHYAHTHL 245
Cdd:COG5189   396 DKPYRCEVCDKRYKNLNGLKYHRKHSHD 423
 
Name Accession Description Interval E-value
DPF1-3_N pfam14051
DPF1-3, N-terminal; This putative domain has been detected on requiem/DPF family proteins. It ...
36-102 4.38e-42

DPF1-3, N-terminal; This putative domain has been detected on requiem/DPF family proteins. It was identified as an adaptor molecule that links nuclear factor kappa-light-chain-enhancer of activated B cells (NF-kappa-B) dimer RelB/p52 and switch/sucrose-nonfermentable (SWI/SNF) chromatin remodelling factor.


Pssm-ID: 464074  Cd Length: 67  Bit Score: 140.08  E-value: 4.38e-42
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958782513  36 GDQFYKEAIEHCRSYNSRLCAERSVRLPFLDSQTGVAQNNCYIWMEKRHRGPGLAPGQLYTYPARCW 102
Cdd:pfam14051   1 NDSFYKDALENSSNFNSRLCIERKLRLPFLDSQTGVAQNHCYLWMKKRQRMPGLDPGQIYTYPARRW 67
PHD1_DPF3 cd15692
PHD finger 1 found in D4, zinc and double PHD fingers family 3 (DPF3); DPF3, also termed ...
284-314 5.92e-17

PHD finger 1 found in D4, zinc and double PHD fingers family 3 (DPF3); DPF3, also termed BRG1-associated factor 45C (BAF45C), or zinc finger protein cer-d4, is encoded by a neuro-specific gene, cer-d4. It functions as a new epigenetic key factor for heart and muscle development and may be involved in the transcription regulation of neuro-specific gene clusters. It interacts with the BAF chromatin remodeling complex and binds methylated and acetylated lysine residues of histone 3 and 4. DPF3 contains a nuclear localization signal in the N-terminal region, a Cys2His2 (C2H2) zinc finger or Kruppel-type zinc-finger and a sequence of negatively charged amino acids in the central region, and a cysteine/histidine-rich region that is composed of two adjacent plant homeodomain (PHD) fingers (d4-domain) in the C-terminal part of the molecule. This model corresponds to the first PHD finger.


Pssm-ID: 277162  Cd Length: 57  Bit Score: 73.57  E-value: 5.92e-17
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1958782513 284 YCDFCLGGSNMNKKSGRPEELVSCADCGRSG 314
Cdd:cd15692     1 YCDFCLGGSNMNKKSGRPEELVSCADCGRSG 31
SFP1 COG5189
Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division ...
218-245 4.47e-08

Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning];


Pssm-ID: 227516 [Multi-domain]  Cd Length: 423  Bit Score: 53.95  E-value: 4.47e-08
                          10        20
                  ....*....|....*....|....*...
gi 1958782513 218 DKPYVCDICGKRYKNRPGLSYHYAHTHL 245
Cdd:COG5189   396 DKPYRCEVCDKRYKNLNGLKYHRKHSHD 423
 
Name Accession Description Interval E-value
DPF1-3_N pfam14051
DPF1-3, N-terminal; This putative domain has been detected on requiem/DPF family proteins. It ...
36-102 4.38e-42

DPF1-3, N-terminal; This putative domain has been detected on requiem/DPF family proteins. It was identified as an adaptor molecule that links nuclear factor kappa-light-chain-enhancer of activated B cells (NF-kappa-B) dimer RelB/p52 and switch/sucrose-nonfermentable (SWI/SNF) chromatin remodelling factor.


Pssm-ID: 464074  Cd Length: 67  Bit Score: 140.08  E-value: 4.38e-42
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958782513  36 GDQFYKEAIEHCRSYNSRLCAERSVRLPFLDSQTGVAQNNCYIWMEKRHRGPGLAPGQLYTYPARCW 102
Cdd:pfam14051   1 NDSFYKDALENSSNFNSRLCIERKLRLPFLDSQTGVAQNHCYLWMKKRQRMPGLDPGQIYTYPARRW 67
PHD1_DPF3 cd15692
PHD finger 1 found in D4, zinc and double PHD fingers family 3 (DPF3); DPF3, also termed ...
284-314 5.92e-17

PHD finger 1 found in D4, zinc and double PHD fingers family 3 (DPF3); DPF3, also termed BRG1-associated factor 45C (BAF45C), or zinc finger protein cer-d4, is encoded by a neuro-specific gene, cer-d4. It functions as a new epigenetic key factor for heart and muscle development and may be involved in the transcription regulation of neuro-specific gene clusters. It interacts with the BAF chromatin remodeling complex and binds methylated and acetylated lysine residues of histone 3 and 4. DPF3 contains a nuclear localization signal in the N-terminal region, a Cys2His2 (C2H2) zinc finger or Kruppel-type zinc-finger and a sequence of negatively charged amino acids in the central region, and a cysteine/histidine-rich region that is composed of two adjacent plant homeodomain (PHD) fingers (d4-domain) in the C-terminal part of the molecule. This model corresponds to the first PHD finger.


Pssm-ID: 277162  Cd Length: 57  Bit Score: 73.57  E-value: 5.92e-17
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1958782513 284 YCDFCLGGSNMNKKSGRPEELVSCADCGRSG 314
Cdd:cd15692     1 YCDFCLGGSNMNKKSGRPEELVSCADCGRSG 31
PHD1_d4 cd15619
PHD finger 1 found in d4 gene family proteins; The family includes proteins coded by three ...
284-314 8.32e-15

PHD finger 1 found in d4 gene family proteins; The family includes proteins coded by three members of the d4 gene family, DPF1 (neuro-d4), DPF2 (ubi-d4/Requiem), and DPF3 (cer-d4), which function as transcription factors and are involved in transcriptional regulation of genes by changing the condensed/decondensed state of chromatin in the nucleus. DPF2 is ubiquitously expressed and it acts as a transcription factor that may participate in developmentally programmed cell death. DPF1 and DPF3 are expressed predominantly in neural tissues, and they may be involved in the transcription regulation of neuro-specific gene clusters. The d4 family proteins show distinct domain organization with domain 2/3 in the N-terminal region, a Cys2His2 (C2H2) zinc finger or Kruppel-type zinc finger in the central part and two adjacent plant homeodomain (PHD) fingers (d4-domain) in the C-terminal part of the molecule. This model corresponds to the first PHD finger.


Pssm-ID: 277091  Cd Length: 56  Bit Score: 67.87  E-value: 8.32e-15
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1958782513 284 YCDFCLGGSNMNKKSGRPEELVSCADCGRSG 314
Cdd:cd15619     1 YCDFCLGDAKENKKTGQPEELVSCSDCGRSG 31
PHD1_DPF2_like cd15691
PHD finger 1 found in D4, zinc and double PHD fingers family 2 (DPF2); DPF2 (also termed zinc ...
284-314 7.38e-14

PHD finger 1 found in D4, zinc and double PHD fingers family 2 (DPF2); DPF2 (also termed zinc finger protein ubi-d4, apoptosis response zinc finger protein, BRG1-associated factor 45D (BAF45D), or protein requiem) is a transcription factor that is encoded by the ubiquitously expressed gene, ubi-d4, and may be involved in leukemia or other cancers with other genes connected with cancer. It recognizes acetylated histone H3 and suppresses the function of estrogen-related receptor alpha (ERRalpha) through histone deacetylase 1 (HDAC1). Moreover, DPF2 functions as a linker protein between the SWI/SNF complex and RelB/p52 NF-kappaB heterodimer and plays important roles in NF-kappaB transactivation via its non-canonical pathway. It is also required as a transcriptional coactivator in SWI/SNF complex-dependent activation of NF-kappaB RelA/p50 heterodimer. DPF2 contains a nuclear localization signal in the N-terminal region, a Cys2His2 (C2H2) zinc finger or Kruppel-type zinc-finger and a sequence of negatively charged amino acids in the central region, and a cysteine/histidine-rich region that is composed of two adjacent plant homeodomain (PHD) fingers (d4-domain) in the C-terminal part of the molecule. This subfamily also includes DPF3 from zebrafish. This model describes the first PHD finger.


Pssm-ID: 277161  Cd Length: 56  Bit Score: 65.04  E-value: 7.38e-14
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1958782513 284 YCDFCLGGSNMNKKSGRPEELVSCADCGRSG 314
Cdd:cd15691     1 YCDFCLGDSKINKKTGQPEELVSCSDCGRSG 31
PHD1_MOZ_d4 cd15526
PHD finger 1 found in monocytic leukemia zinc-finger protein (MOZ), its factor (MORF), and d4 ...
284-314 7.56e-13

PHD finger 1 found in monocytic leukemia zinc-finger protein (MOZ), its factor (MORF), and d4 gene family proteins; MOZ is a MYST-type histone acetyltransferase (HAT) that functions as a coactivator for acute myeloid leukemia 1 protein (AML1)- and p53-dependent transcription. It possesses intrinsic HAT activity and to acetylate both itself and lysine (K) residues on histone H2B, histone H3 (K14) and histone H4 (K5, K8, K12 and K16) in vitro and H3K9 in vivo. MOZ-related factor (MORF) is a ubiquitously expressed transcriptional regulator with intrinsic HAT activity. It can interact with the Runt-domain transcription factor Runx2 and form a tetrameric complex with BRPFs, ING5, and EAF6. Both MOZ and MORF are catalytic subunits of HAT complexes that are required for normal developmental programs, such as hematopoiesis, neurogenesis, and skeletogenesis, and are implicated in human leukemias. MOZ is also the catalytic subunit of a tetrameric inhibitor of growth 5 (ING5) complex, which specifically acetylates nucleosomal histone H3K14. Moreover, MOZ and MORF are involved in regulating transcriptional activation mediated by Runx2 (or Cbfa1), a Runt-domain transcription factor known to play important roles in T cell lymphoma genesis and bone development, and its homologs. This family also includes three members of the d4 gene family, DPF1 (neuro-d4), DPF2 (ubi-d4/Requiem), and DPF3 (cer-d4), which function as transcription factors and are involved in transcriptional regulation of genes via changing the condensed/decondensed state of chromatin in nucleus. DPF2 is ubiquitously expressed and it acts as a transcription factor that may participate in developmentally programmed cell death. DPF1 and DPF3 are expressed predominantly in neural tissues, and they may be involved in the transcription regulation of neuro specific gene clusters. All family members contain two plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277001  Cd Length: 56  Bit Score: 62.37  E-value: 7.56e-13
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1958782513 284 YCDFCLGGSNMNKKSGRPEELVSCADCGRSG 314
Cdd:cd15526     1 ICDFCLGTDEKNNKTGEPEELISCADCGSSG 31
PHD1_DPF1 cd15690
PHD finger 1 found in D4, zinc and double PHD fingers family 1 (DPF1); DPF1, also termed zinc ...
280-314 4.98e-11

PHD finger 1 found in D4, zinc and double PHD fingers family 1 (DPF1); DPF1, also termed zinc finger protein neuro-d4, or BRG1-associated factor 45B (BAF45B), is encoded by a neuro specific gene, neuro-d4. It may be involved in the transcription regulation of neuro specific gene clusters. DPF1 contains a nuclear localization signal in the N-terminal region, a Cys2His2 (C2H2) zinc finger or Kruppel-type zinc-finger and a sequence of negatively charged amino acids in the central, and a cysteine/histidine-rich region that is composed of two adjacent plant homeodomain (PHD)-fingers (d4-domain) in the C-terminal part of the molecule. The family corresponds to the first PHD finger.


Pssm-ID: 277160  Cd Length: 58  Bit Score: 57.36  E-value: 4.98e-11
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1958782513 280 IPNNYCDFCLGGSnmnKKSGRPEELVSCADCGRSG 314
Cdd:cd15690     1 IPNGYCDFCLGGA---KKTGCPEDLISCADCGRSG 32
SFP1 COG5189
Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division ...
218-245 4.47e-08

Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning];


Pssm-ID: 227516 [Multi-domain]  Cd Length: 423  Bit Score: 53.95  E-value: 4.47e-08
                          10        20
                  ....*....|....*....|....*...
gi 1958782513 218 DKPYVCDICGKRYKNRPGLSYHYAHTHL 245
Cdd:COG5189   396 DKPYRCEVCDKRYKNLNGLKYHRKHSHD 423
PHD1_MOZ_MORF cd15618
PHD finger 1 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ ...
281-314 1.79e-06

PHD finger 1 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ (also termed histone acetyltransferase KAT6A, YBF2/SAS3, SAS2 and TIP60protein 3 (MYST-3), runt-related transcription factor-binding protein 2, or zinc finger protein 220) is a MYST-type histone acetyltransferase (HAT) that functions as a coactivator for acute myeloid leukemia 1 protein (AML1)- and p53-dependent transcription. It possesses intrinsic HAT activity to acetylate both itself and lysine (K) residues on histone H2B, histone H3 (K14) and histone H4 (K5, K8, K12 and K16) in vitro and H3K9 in vivo. MOZ-related factor (MORF), also termed MOZ2, or histone acetyltransferase KAT6B, or MOZ, YBF2/SAS3, SAS2 and TIP60 protein 4 (MYST4), is a ubiquitously expressed transcriptional regulator with intrinsic HAT activity. It can interact with the Runt-domain transcription factor Runx2 and form a tetrameric complex with BRPFs, ING5, and EAF6. Both MOZ and MORF are catalytic subunits of HAT complexes that are required for normal developmental programs, such as hematopoiesis, neurogenesis, and skeletogenesis, and are also implicated in human leukemias. MOZ is also the catalytic subunit of a tetrameric inhibitor of growth 5 (ING5) complex, which specifically acetylates nucleosomal histone H3K14. Moreover, MOZ and MORF are involved in regulating transcriptional activation mediated by Runx2 (or Cbfa1), a Runt-domain transcription factor known to play important roles in T cell lymphomagenesis and bone development, and its homologs. MOZ contains a linker histone 1 and histone 5 domains and two plant homeodomain (PHD) fingers. In contrast, MORF contains an N-terminal region containing two PHD fingers, a putative HAT domain, an acidic region, and a C-terminal Ser/Met-rich domain. The model corresponds to the first PHD finger.


Pssm-ID: 277090  Cd Length: 58  Bit Score: 44.40  E-value: 1.79e-06
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1958782513 281 PNNYCDFCLGGSNMNKkSGRPEELVSCADCGRSG 314
Cdd:cd15618     1 PIPICSFCLGTAEKNR-DGKPEELLSCADCGNSG 33
PHD1_MOZ cd15688
PHD finger 1 found in monocytic leukemia zinc-finger protein (MOZ); MOZ, also termed histone ...
281-314 4.64e-05

PHD finger 1 found in monocytic leukemia zinc-finger protein (MOZ); MOZ, also termed histone acetyltransferase KAT6A, YBF2/SAS3, SAS2 and TIP60 protein 3 (MYST-3), or runt-related transcription factor-binding protein 2, or zinc finger protein 220, is a MYST-type histone acetyltransferase (HAT) that functions as a coactivator for acute myeloid leukemia 1 protein (AML1)- and p53-dependent transcription. It possesses intrinsic HAT activity to acetylate both itself and lysine (K) residues on histone H2B, histone H3 (K14) and histone H4 (K5, K8, K12 and K16) in vitro and H3K9 in vivo. MOZ and MOZ-related factor (MORF) are catalytic subunits of histone acetyltransferase (HAT) complexes that are required for normal developmental programs, such as hematopoiesis, neurogenesis, and skeletogenesis, and implicated in human leukemias. It is also the catalytic subunit of a tetrameric inhibitor of growth 5 (ING5) complex, which specifically acetylates nucleosomal histone H3K14. Moreover, MOZ and MORF are involved in regulating transcriptional activation mediated by Runx2 (or Cbfa1), a Runt-domain transcription factor known to play important roles in T cell lymphomagenesis and bone development, and its homologs. MOZ contains a linker histone 1 and histone 5 domains and two plant homeodomain (PHD) fingers. The model corresponds to the first PHD finger.


Pssm-ID: 277158  Cd Length: 59  Bit Score: 40.45  E-value: 4.64e-05
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1958782513 281 PNNYCDFCLGGSNMNKKSgRPEELVSCADCGRSG 314
Cdd:cd15688     1 PIPICSFCLGTKEQNREK-KPEELISCADCGNSG 33
PHD1_MORF cd15689
PHD finger 1 found in monocytic leukemia zinc finger protein-related factor (MORF); MORF, also ...
281-314 1.01e-04

PHD finger 1 found in monocytic leukemia zinc finger protein-related factor (MORF); MORF, also termed MOZ2, or histone acetyltransferase KAT6B, or MOZ, YBF2/SAS3, SAS2 and TIP60 protein 4 (MYST4), is a ubiquitously expressed transcriptional regulator with intrinsic histone acetyltransferase (HAT) activity. It can interact with the Runt-domain transcription factor Runx2 and form a tetrameric complex with BRPFs, ING5, and EAF6. MORF and monocytic leukemia zinc-finger protein (MOZ) are catalytic subunits of HAT complexes that are required for normal developmental programs, such as hematopoiesis, neurogenesis, and skeletogenesis, and are also implicated in human leukemias. MORF contains an N-terminal region containing two plant homeodomain (PHD) fingers, a putative HAT domain, an acidic region, and a C-terminal Ser/Met-rich domain. The model corresponds to the first PHD finger.


Pssm-ID: 277159  Cd Length: 59  Bit Score: 39.64  E-value: 1.01e-04
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1958782513 281 PNNYCDFCLGGSNMNKKSgRPEELVSCADCGRSG 314
Cdd:cd15689     1 PIPICSFCLGTKESNREK-KPEELLSCADCGSSG 33
SFP1 COG5189
Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division ...
219-244 5.70e-03

Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning];


Pssm-ID: 227516 [Multi-domain]  Cd Length: 423  Bit Score: 38.16  E-value: 5.70e-03
                          10        20
                  ....*....|....*....|....*...
gi 1958782513 219 KPYVCDI--CGKRYKNRPGLSYHYAHTH 244
Cdd:COG5189   348 KPYKCPVegCNKKYKNQNGLKYHMLHGH 375
PHD1_PHF10 cd15528
PHD finger 1 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed ...
285-314 6.70e-03

PHD finger 1 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed BRG1-associated factor 45a (BAF45a), or XAP135, is a ubiquitously expressed transcriptional regulator that is required for maintaining the undifferentiated status of neuroblasts. It contains a SAY (supporter of activation of yellow) domain and two adjacent plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277003  Cd Length: 54  Bit Score: 34.31  E-value: 6.70e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 1958782513 285 CDFCLGGSNMNKksGRPEELVSCADCGRSG 314
Cdd:cd15528     2 CGICEKGGKSNK--GEPEELIHCSQCGNSG 29
 
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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