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Conserved domains on  [gi|557878677|ref|NP_001273653|]
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constitutive coactivator of PPAR-gamma-like protein 1 isoform d [Homo sapiens]

Protein Classification

PIN domain-containing protein( domain architecture ID 1000090)

PIN (PilT N terminus) domain-containing protein may function as a nuclease

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PIN_SF super family cl28905
PIN (PilT N terminus) domain: Superfamily; The PIN (PilT N terminus) domain belongs to a large ...
 5-220 3.90e-77

PIN (PilT N terminus) domain: Superfamily; The PIN (PilT N terminus) domain belongs to a large nuclease superfamily, and were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. The PIN domain superfamily includes: the FEN-like PIN domain family such as the PIN domains of Flap endonuclease-1 (FEN1), exonuclease-1 (EXO1), Mkt1, Gap Endonuclease 1 (GEN1), and Xeroderma pigmentosum complementation group G (XPG) nuclease, 5'-3' exonucleases of DNA polymerase I and bacteriophage T4- and T5-5' nucleases; the VapC-like PIN domain family which includes toxins of prokaryotic toxin/antitoxin operons FitAB and VapBC, as well as eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1; the LabA-like PIN domain family which includes the PIN domains of Synechococcus elongatus LabA (low-amplitude and bright); the PRORP-Zc3h12a-like PIN domain family which includes the PIN domains of RNase P (PRORP), ribonuclease Zc3h12a; and Bacillus subtilis YacP/Rae1-like PIN domains. It also includes the Mut7-C PIN domain family, which is not represented here as it is a shortened version of the PIN fold and lacks a core strand and helix (H3 and S3). The Mut7-C PIN domain family includes the C-terminus of Caenorhabditis elegans exonuclease Mut-7.


The actual alignment was detected with superfamily member cd18672:

Pssm-ID: 475124 [Multi-domain]  Cd Length: 210  Bit Score: 244.12  E-value: 3.90e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557878677   5 GFQDYIEKHCPSAVVPVELQKLARGslvggGRQRPPQTPLRLLVDADNCLHRLYGGfYTDWVSGGQWNHMLGYLAALAKA 84
Cdd:cd18672    1 GLQSFVESHCPNACVQVNLKKLARE-----HRRKPPGSTPVLVVDAMCCLRYLYGG-YLDWVCGGQWNEMLRNLSNFVSA 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557878677  85 CFGGNIELFVFFNGALEKARLHEWVKRQGNERQTAQQIVSHVQNKGTPPPKVWFLPPVCMAHCIRLALIRFHVKVAQSIE 164
Cdd:cd18672   75 FQAAGIQLVFFFDGVVESQKRDEWVKRRLKNNKKVSKVFNHIKKKGTQPPKNLFFLPSGLATFTRFALRSLGVEVICSMD 154

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 557878677 165 DHHQEVIGFCRENGFHGLVAYDSDYALCNIPYYFSAHALKLSRNGKSLTTSQYLMH 220
Cdd:cd18672  155 EADQEVASYCRQNNCFGILGQDSDYLIFDTPPYLSISKLKLTSLKTVLESRERLCD 210
PHA03378 super family cl33729
EBNA-3B; Provisional
 330-527 7.37e-03

EBNA-3B; Provisional


The actual alignment was detected with superfamily member PHA03378:

Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 39.67  E-value: 7.37e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557878677 330 ATSKPMSFHPPhylAARPGPFGMPGMVPPHVPPQMLNIPQTSlqakpvAPQVPSPGGAPGQGPYPYSLSEPAPLTLDTSG 409
Cdd:PHA03378 682 NTMLPIQWAPG---TMQPPPRAPTPMRPPAAPPGRAQRPAAA------TGRARPPAAAPGRARPPAAAPGRARPPAAAPG 752

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557878677 410 KNLTEQNSYSNIP----HEGKHTPLYERSSPINPAQ--SGSPNHVDSAYFPGSSTSSSSDNDEGSGGATNHISGNKIgwe 483
Cdd:PHA03378 753 RARPPAAAPGRARppaaAPGAPTPQPPPQAPPAPQQrpRGAPTPQPPPQAGPTSMQLMPRAAPGQQGPTKQILRQLL--- 829

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 557878677 484 ktgshSEPQARGDPGDQTKAEGSSTASSGSQLAEGKGSQMGTVQ 527
Cdd:PHA03378 830 -----TGGVKRGRPSLKKPAALERQAAAGPTPSPGSGTSDKIVQ 868
 
Name Accession Description Interval E-value
PIN_FAM120B-like cd18672
FEN-like PIN domains of FAM120B (family with sequence similarity 120B) and related proteins; ...
 5-220 3.90e-77

FEN-like PIN domains of FAM120B (family with sequence similarity 120B) and related proteins; FAM120B (also known as CCPG, "constitutive coactivator of PPAR-gamma", PGCC1, "PPARgamma constitutive coactivator 1") is a constitutive coactivator of peroxisome proliferator-activated receptor (PPARgamma) that promotes adipogenesis in a PPARgamma-dependent manner. This subfamily belongs to the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), the helical arch/clamp region is involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350239 [Multi-domain]  Cd Length: 210  Bit Score: 244.12  E-value: 3.90e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557878677   5 GFQDYIEKHCPSAVVPVELQKLARGslvggGRQRPPQTPLRLLVDADNCLHRLYGGfYTDWVSGGQWNHMLGYLAALAKA 84
Cdd:cd18672    1 GLQSFVESHCPNACVQVNLKKLARE-----HRRKPPGSTPVLVVDAMCCLRYLYGG-YLDWVCGGQWNEMLRNLSNFVSA 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557878677  85 CFGGNIELFVFFNGALEKARLHEWVKRQGNERQTAQQIVSHVQNKGTPPPKVWFLPPVCMAHCIRLALIRFHVKVAQSIE 164
Cdd:cd18672   75 FQAAGIQLVFFFDGVVESQKRDEWVKRRLKNNKKVSKVFNHIKKKGTQPPKNLFFLPSGLATFTRFALRSLGVEVICSMD 154

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 557878677 165 DHHQEVIGFCRENGFHGLVAYDSDYALCNIPYYFSAHALKLSRNGKSLTTSQYLMH 220
Cdd:cd18672  155 EADQEVASYCRQNNCFGILGQDSDYLIFDTPPYLSISKLKLTSLKTVLESRERLCD 210
PHA03378 PHA03378
EBNA-3B; Provisional
 330-527 7.37e-03

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 39.67  E-value: 7.37e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557878677 330 ATSKPMSFHPPhylAARPGPFGMPGMVPPHVPPQMLNIPQTSlqakpvAPQVPSPGGAPGQGPYPYSLSEPAPLTLDTSG 409
Cdd:PHA03378 682 NTMLPIQWAPG---TMQPPPRAPTPMRPPAAPPGRAQRPAAA------TGRARPPAAAPGRARPPAAAPGRARPPAAAPG 752

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557878677 410 KNLTEQNSYSNIP----HEGKHTPLYERSSPINPAQ--SGSPNHVDSAYFPGSSTSSSSDNDEGSGGATNHISGNKIgwe 483
Cdd:PHA03378 753 RARPPAAAPGRARppaaAPGAPTPQPPPQAPPAPQQrpRGAPTPQPPPQAGPTSMQLMPRAAPGQQGPTKQILRQLL--- 829

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 557878677 484 ktgshSEPQARGDPGDQTKAEGSSTASSGSQLAEGKGSQMGTVQ 527
Cdd:PHA03378 830 -----TGGVKRGRPSLKKPAALERQAAAGPTPSPGSGTSDKIVQ 868
 
Name Accession Description Interval E-value
PIN_FAM120B-like cd18672
FEN-like PIN domains of FAM120B (family with sequence similarity 120B) and related proteins; ...
 5-220 3.90e-77

FEN-like PIN domains of FAM120B (family with sequence similarity 120B) and related proteins; FAM120B (also known as CCPG, "constitutive coactivator of PPAR-gamma", PGCC1, "PPARgamma constitutive coactivator 1") is a constitutive coactivator of peroxisome proliferator-activated receptor (PPARgamma) that promotes adipogenesis in a PPARgamma-dependent manner. This subfamily belongs to the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), the helical arch/clamp region is involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350239 [Multi-domain]  Cd Length: 210  Bit Score: 244.12  E-value: 3.90e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557878677   5 GFQDYIEKHCPSAVVPVELQKLARGslvggGRQRPPQTPLRLLVDADNCLHRLYGGfYTDWVSGGQWNHMLGYLAALAKA 84
Cdd:cd18672    1 GLQSFVESHCPNACVQVNLKKLARE-----HRRKPPGSTPVLVVDAMCCLRYLYGG-YLDWVCGGQWNEMLRNLSNFVSA 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557878677  85 CFGGNIELFVFFNGALEKARLHEWVKRQGNERQTAQQIVSHVQNKGTPPPKVWFLPPVCMAHCIRLALIRFHVKVAQSIE 164
Cdd:cd18672   75 FQAAGIQLVFFFDGVVESQKRDEWVKRRLKNNKKVSKVFNHIKKKGTQPPKNLFFLPSGLATFTRFALRSLGVEVICSMD 154

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 557878677 165 DHHQEVIGFCRENGFHGLVAYDSDYALCNIPYYFSAHALKLSRNGKSLTTSQYLMH 220
Cdd:cd18672  155 EADQEVASYCRQNNCFGILGQDSDYLIFDTPPYLSISKLKLTSLKTVLESRERLCD 210
PIN_FEN-like cd09853
FEN-like PIN domains of structure-specific 5' nucleases (or Flap endonuclease-1-like) involved ...
 47-205 1.01e-06

FEN-like PIN domains of structure-specific 5' nucleases (or Flap endonuclease-1-like) involved in DNA replication, repair, and recombination; Structure-specific 5' nucleases are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner. The family includes the PIN (PilT N terminus) domains of Flap endonuclease-1 (FEN1), exonuclease-1 (EXO1), Mkt1, Gap Endonuclease 1 (GEN1), and Xeroderma pigmentosum complementation group G (XPG) nuclease. Also included are the PIN domains of the 5'-3' exonucleases of DNA polymerase I and single domain protein homologs, as well as, the bacteriophage T4- and T5-5' nucleases, and other homologs. Canonical members of this FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350204 [Multi-domain]  Cd Length: 174  Bit Score: 49.40  E-value: 1.01e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557878677  47 LVDADNCLHRLYggFYTDWVS---GGQWNHMLGYLAALAKAcFGGNIELFVFFNGALEKARLHEWVKRQGNERQTAQQIV 123
Cdd:cd09853    1 VIDGMNIAFNFA--HPVRNLKeeeGSDFQGYFSAVDDLVKK-LKPGIKPILLFDGGKPKAKKGNRDKRRERRAREEDRKK 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557878677 124 SHVQNKGTPPPKVWFLPPVCMAHCIRLAL--IRFHVKVAQSIEDHHQEVIG--FCRENGFHGLVAYDSDYALCNIPY-YF 198
Cdd:cd09853   78 GQLKEHKEFDKRLIELGPEYLIRLFELLKhfMGIPVMDAPGEAEDEIAYLVkkHKHLGTVHLIISTDGDFLLLGTDHpYI 157


                 ....*..
gi 557878677 199 SAHALKL 205
Cdd:cd09853  158 PRNLLTV 164
PHA03378 PHA03378
EBNA-3B; Provisional
 330-527 7.37e-03

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 39.67  E-value: 7.37e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557878677 330 ATSKPMSFHPPhylAARPGPFGMPGMVPPHVPPQMLNIPQTSlqakpvAPQVPSPGGAPGQGPYPYSLSEPAPLTLDTSG 409
Cdd:PHA03378 682 NTMLPIQWAPG---TMQPPPRAPTPMRPPAAPPGRAQRPAAA------TGRARPPAAAPGRARPPAAAPGRARPPAAAPG 752

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557878677 410 KNLTEQNSYSNIP----HEGKHTPLYERSSPINPAQ--SGSPNHVDSAYFPGSSTSSSSDNDEGSGGATNHISGNKIgwe 483
Cdd:PHA03378 753 RARPPAAAPGRARppaaAPGAPTPQPPPQAPPAPQQrpRGAPTPQPPPQAGPTSMQLMPRAAPGQQGPTKQILRQLL--- 829

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 557878677 484 ktgshSEPQARGDPGDQTKAEGSSTASSGSQLAEGKGSQMGTVQ 527
Cdd:PHA03378 830 -----TGGVKRGRPSLKKPAALERQAAAGPTPSPGSGTSDKIVQ 868
 
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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