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Conserved domains on  [gi|26324874|dbj|BAC26191|]
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unnamed protein product [Mus musculus]

Protein Classification

PIN_FAM120B-like and PRK13042 domain-containing protein( domain architecture ID 13036706)

PIN_FAM120B-like and PRK13042 domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PIN_FAM120B-like cd18672
FEN-like PIN domains of FAM120B (family with sequence similarity 120B) and related proteins; ...
 5-213 1.57e-133

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: 384.72  E-value: 1.57e-133
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26324874   5 GLQGFVGSTCPHICTIVNIHELAERHRNKYPGCTPTIVVDAMCCLRYWYTAE-SWVCGGQWREYYCALRNFVAAFTSAGI 83
Cdd:cd18672   1 GLQSFVESHCPNACVQVNLKKLAREHRRKPPGSTPVLVVDAMCCLRYLYGGYlDWVCGGQWNEMLRNLSNFVSAFQAAGI 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26324874  84 KLIFFFDGMVEPGKRDEWVKRRLKNNREISKIFHYIKSKRDQPGRNMFFIPSGLAIFTRFALKTLGQETFCSLQEADYEV 163
Cdd:cd18672  81 QLVFFFDGVVESQKRDEWVKRRLKNNKKVSKVFNHIKKKGTQPPKNLFFLPSGLATFTRFALRSLGVEVICSMDEADQEV 160

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|
gi 26324874 164 ASYGLQHNCLGILGEDTDYLIYDTCPYFSIGDLCLESLQTIMLCREKLCE 213
Cdd:cd18672 161 ASYCRQNNCFGILGQDSDYLIFDTPPYLSISKLKLTSLKTVLESRERLCD 210
PRK13042 super family cl32851
superantigen-like protein SSL4; Reviewed;
350-494 7.93e-05

superantigen-like protein SSL4; Reviewed;


The actual alignment was detected with superfamily member PRK13042:

Pssm-ID: 183854 [Multi-domain]  Cd Length: 291  Bit Score: 44.62  E-value: 7.93e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26324874  350 EVPVCTNPESMQEVPMCMDPE-PNQEASMCTDPESKQEVPMCTDSESKPEVSQYTNPES--KQKLPSGIDTEFNLEALMC 426
Cdd:PRK13042  31 TTPSSTKVEAPQSTPPSTKVEaPQSKPNATTPPSTKVEAPQQTPNATTPSSTKVETPQSptTKQVPTEINPKFKDLRAYY 110

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26324874  427 THP--EFKQEDVMDMEP--EIKQVTMVSESEILKAS-----DCASPTSVHN-----VVIESvptNGFDREKRTVGGCRRE 492
Cdd:PRK13042 111 TKPslEFKNEIGIILKKwtTIRFMNVVPDYFIYKIAlvgkdDKKYGEGVHRnvdvfVVLEE---NKYNLEKYSVGGITKS 187


                 ..
gi 26324874  493 TS 494
Cdd:PRK13042 188 NS 189
 
Name Accession Description Interval E-value
PIN_FAM120B-like cd18672
FEN-like PIN domains of FAM120B (family with sequence similarity 120B) and related proteins; ...
 5-213 1.57e-133

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: 384.72  E-value: 1.57e-133
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26324874   5 GLQGFVGSTCPHICTIVNIHELAERHRNKYPGCTPTIVVDAMCCLRYWYTAE-SWVCGGQWREYYCALRNFVAAFTSAGI 83
Cdd:cd18672   1 GLQSFVESHCPNACVQVNLKKLAREHRRKPPGSTPVLVVDAMCCLRYLYGGYlDWVCGGQWNEMLRNLSNFVSAFQAAGI 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26324874  84 KLIFFFDGMVEPGKRDEWVKRRLKNNREISKIFHYIKSKRDQPGRNMFFIPSGLAIFTRFALKTLGQETFCSLQEADYEV 163
Cdd:cd18672  81 QLVFFFDGVVESQKRDEWVKRRLKNNKKVSKVFNHIKKKGTQPPKNLFFLPSGLATFTRFALRSLGVEVICSMDEADQEV 160

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|
gi 26324874 164 ASYGLQHNCLGILGEDTDYLIYDTCPYFSIGDLCLESLQTIMLCREKLCE 213
Cdd:cd18672 161 ASYCRQNNCFGILGQDSDYLIFDTPPYLSISKLKLTSLKTVLESRERLCD 210
PRK13042 PRK13042
superantigen-like protein SSL4; Reviewed;
350-494 7.93e-05

superantigen-like protein SSL4; Reviewed;


Pssm-ID: 183854 [Multi-domain]  Cd Length: 291  Bit Score: 44.62  E-value: 7.93e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26324874  350 EVPVCTNPESMQEVPMCMDPE-PNQEASMCTDPESKQEVPMCTDSESKPEVSQYTNPES--KQKLPSGIDTEFNLEALMC 426
Cdd:PRK13042  31 TTPSSTKVEAPQSTPPSTKVEaPQSKPNATTPPSTKVEAPQQTPNATTPSSTKVETPQSptTKQVPTEINPKFKDLRAYY 110

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26324874  427 THP--EFKQEDVMDMEP--EIKQVTMVSESEILKAS-----DCASPTSVHN-----VVIESvptNGFDREKRTVGGCRRE 492
Cdd:PRK13042 111 TKPslEFKNEIGIILKKwtTIRFMNVVPDYFIYKIAlvgkdDKKYGEGVHRnvdvfVVLEE---NKYNLEKYSVGGITKS 187


                 ..
gi 26324874  493 TS 494
Cdd:PRK13042 188 NS 189
 
Name Accession Description Interval E-value
PIN_FAM120B-like cd18672
FEN-like PIN domains of FAM120B (family with sequence similarity 120B) and related proteins; ...
 5-213 1.57e-133

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: 384.72  E-value: 1.57e-133
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26324874   5 GLQGFVGSTCPHICTIVNIHELAERHRNKYPGCTPTIVVDAMCCLRYWYTAE-SWVCGGQWREYYCALRNFVAAFTSAGI 83
Cdd:cd18672   1 GLQSFVESHCPNACVQVNLKKLAREHRRKPPGSTPVLVVDAMCCLRYLYGGYlDWVCGGQWNEMLRNLSNFVSAFQAAGI 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26324874  84 KLIFFFDGMVEPGKRDEWVKRRLKNNREISKIFHYIKSKRDQPGRNMFFIPSGLAIFTRFALKTLGQETFCSLQEADYEV 163
Cdd:cd18672  81 QLVFFFDGVVESQKRDEWVKRRLKNNKKVSKVFNHIKKKGTQPPKNLFFLPSGLATFTRFALRSLGVEVICSMDEADQEV 160

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|
gi 26324874 164 ASYGLQHNCLGILGEDTDYLIYDTCPYFSIGDLCLESLQTIMLCREKLCE 213
Cdd:cd18672 161 ASYCRQNNCFGILGQDSDYLIFDTPPYLSISKLKLTSLKTVLESRERLCD 210
PIN_FEN-like cd09853
FEN-like PIN domains of structure-specific 5' nucleases (or Flap endonuclease-1-like) involved ...
 42-212 8.19e-44

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: 152.25  E-value: 8.19e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26324874  42 VVDAMCCLRYWYTAESWV---CGGQWREYYCALRNFVAAFTSaGIKLIFFFDGMVEPGKRDEWVKRRLKNNREISKIFHY 118
Cdd:cd09853   1 VIDGMNIAFNFAHPVRNLkeeEGSDFQGYFSAVDDLVKKLKP-GIKPILLFDGGKPKAKKGNRDKRRERRAREEDRKKGQ 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26324874 119 IKSKRDQPGRNMFFIPSGLAIFTRFALKTLGQETFCSLQEADYEVASYGLQHN----CLGILGEDTDYLIYDT-CPYFSI 193
Cdd:cd09853  80 LKEHKEFDKRLIELGPEYLIRLFELLKHFMGIPVMDAPGEAEDEIAYLVKKHKhlgtVHLIISTDGDFLLLGTdHPYIPR 159

                       170
                ....*....|....*....
gi 26324874 194 GDLCleslQTIMLCREKLC 212
Cdd:cd09853 160 NLLT----VKEETFQEFHL 174
PIN_asteroid-like cd18676
FEN-like PIN domain of Drosophila melanogaster asteroid and related proteins; This subfamily ...
 41-186 3.33e-06

FEN-like PIN domain of Drosophila melanogaster asteroid and related proteins; This subfamily includes Drosophila melanogaster asteroid protein which may function in EGF receptor signaling, and may play a role in compound eye morphogenesis. 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: 350243 [Multi-domain]  Cd Length: 164  Bit Score: 47.25  E-value: 3.33e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26324874  41 IVVDA---MCCLRYWYTAESWVCGGQWREYYCALRNFVAAFTSAGIKLIFFFDGMVEPGKRdEWVKRRLKNNREISKIFH 117
Cdd:cd18676   1 LVIDGnnlCYQLYFDSNLDNSAFGGDYDKYARVVREFFELLSKCNVTPYVILDGGYEDRKL-KTVTSRLRAKIKIAKAKT 79

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 26324874 118 YIkskrdqPGRNMFFIPsglaIFTR--F--ALKTLGQETFCSLQEADYEVASYGLQHNClGILGEDTDYLIYD 186
Cdd:cd18676  80 PS------TGGSGSILP----LLLKevFvdVLKELNVKVVQCDFEADDEIAALARKLNC-PVLSYDSDFYIFD 141
PRK13042 PRK13042
superantigen-like protein SSL4; Reviewed;
350-494 7.93e-05

superantigen-like protein SSL4; Reviewed;


Pssm-ID: 183854 [Multi-domain]  Cd Length: 291  Bit Score: 44.62  E-value: 7.93e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26324874  350 EVPVCTNPESMQEVPMCMDPE-PNQEASMCTDPESKQEVPMCTDSESKPEVSQYTNPES--KQKLPSGIDTEFNLEALMC 426
Cdd:PRK13042  31 TTPSSTKVEAPQSTPPSTKVEaPQSKPNATTPPSTKVEAPQQTPNATTPSSTKVETPQSptTKQVPTEINPKFKDLRAYY 110

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26324874  427 THP--EFKQEDVMDMEP--EIKQVTMVSESEILKAS-----DCASPTSVHN-----VVIESvptNGFDREKRTVGGCRRE 492
Cdd:PRK13042 111 TKPslEFKNEIGIILKKwtTIRFMNVVPDYFIYKIAlvgkdDKKYGEGVHRnvdvfVVLEE---NKYNLEKYSVGGITKS 187


                 ..
gi 26324874  493 TS 494
Cdd:PRK13042 188 NS 189
PIN_EXO1 cd09857
FEN-like PIN domains of Exonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' ...
 1-111 7.12e-04

FEN-like PIN domains of Exonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs; exonuclease-1 (EXO1) is involved in multiple, eukaryotic DNA metabolic pathways, including DNA replication processes (5' flap DNA endonuclease activity and double stranded DNA 5'-exonuclease activity), DNA repair processes (DNA mismatch repair (MMR) and post-replication repair (PRR)), recombination, and telomere integrity. EXO1 functions in the MMS2 error-free branch of the PRR pathway in the maintenance and repair of stalled replication forks. Studies also suggest that EXO1 plays both structural and catalytic roles during MMR-mediated mutation avoidance. These nucleases are members of 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), 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. EXO1 nucleases also have C-terminal Mlh1- and Msh2-binding domains which allow interaction with MMR and PRR proteins, respectively.


Pssm-ID: 350207 [Multi-domain]  Cd Length: 202  Bit Score: 40.85  E-value: 7.12e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26324874   1 MGVRGLQGFVGStcphICTIVNIHELAerhrnkypGCTptIVVDAMCclryW-----YT-AESWVCGGQWREY--YCalR 72
Cdd:cd09857   1 MGIQGLLPFLKP----IQRPVHISEYA--------GKT--VAVDAYC----WlhrgaYScAEELALGKPTDKYidYC--M 60

                        90       100       110       120
                ....*....|....*....|....*....|....*....|.
gi 26324874  73 NFVAAFTSAGIKLIFFFDGMVEPGKRDEWVKRRLK--NNRE 111
Cdd:cd09857  61 KRVNMLLHHGITPILVFDGAPLPSKAGTEEERRERreEALE 101
 
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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