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Conserved domains on  [gi|1063732901|ref|NP_001331938|]
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PRLI-interacting factor [Arabidopsis thaliana]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Extensin_2 super family cl25884
Extensin-like region;
10-67 2.57e-03

Extensin-like region;


The actual alignment was detected with superfamily member pfam04554:

Pssm-ID: 252669 [Multi-domain]  Cd Length: 57  Bit Score: 36.28  E-value: 2.57e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1063732901  10 PPPPQQMIGQPPPQQRMNPPPPSQVPRIMNQSPLLGQSHPimgmnqqPPQVMMNSNQP 67
Cdd:pfam04554   6 PPPPVKQYSPPPPYYYKSPPPPVKSPVYKSPPPPVYKSPP-------PPKYVYKSPPP 56
PABP-1234 super family cl31127
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 14-162 2.61e-03

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


The actual alignment was detected with superfamily member TIGR01628:

Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 40.18  E-value: 2.61e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063732901  14 QQMIGQPPPQQRmNPPPPSQVPRIMNQsPLLGQSHPIMGMNQQPPQVMMNSNQPMMMNPRNFNLNQSLSSEYQQNLAPNN 93
Cdd:TIGR01628 372 QDQFMQLQPRMR-QLPMGSPMGGAMGQ-PPYYGQGPQQQFNGQPLGWPRMSMMPTPMGPGGPLRPNGLAPMNAVRAPSRN 449

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1063732901  94 FGSKMSRNnwkgkkitsDKRPMMEQQQQQirrmhnsGIPMYNPQQLPgsgSIQVGAGGYKPPTLNELQS 162
Cdd:TIGR01628 450 AQNAAQKP---------PMQPVMYPPNYQ-------SLPLSQDLPQP---QSTASQGGQNKKLAQVLAS 499
COG4026 super family cl26606
Uncharacterized conserved protein, contains TOPRIM domain, potential nuclease [General ...
 276-354 8.92e-03

Uncharacterized conserved protein, contains TOPRIM domain, potential nuclease [General function prediction only];


The actual alignment was detected with superfamily member COG4026:

Pssm-ID: 443204 [Multi-domain]  Cd Length: 287  Bit Score: 38.17  E-value: 8.92e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1063732901 276 EEHVEVERRLDHDLSRFEMIYpnyggsEYNNVLENRVDDQDSHIAQLEEENLTLKERLFLMERELGDMRRRLQYLERRD 354
Cdd:COG4026   135 EELLELKEKIDEIAKEKEKLT------KENEELESELEELREEYKKLREENSILEEEFDNIKSEYSDLKSRFEELLKKR 207
 
Name Accession Description Interval E-value
Extensin_2 pfam04554
Extensin-like region;
10-67 2.57e-03

Extensin-like region;


Pssm-ID: 252669 [Multi-domain]  Cd Length: 57  Bit Score: 36.28  E-value: 2.57e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1063732901  10 PPPPQQMIGQPPPQQRMNPPPPSQVPRIMNQSPLLGQSHPimgmnqqPPQVMMNSNQP 67
Cdd:pfam04554   6 PPPPVKQYSPPPPYYYKSPPPPVKSPVYKSPPPPVYKSPP-------PPKYVYKSPPP 56
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 14-162 2.61e-03

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 40.18  E-value: 2.61e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063732901  14 QQMIGQPPPQQRmNPPPPSQVPRIMNQsPLLGQSHPIMGMNQQPPQVMMNSNQPMMMNPRNFNLNQSLSSEYQQNLAPNN 93
Cdd:TIGR01628 372 QDQFMQLQPRMR-QLPMGSPMGGAMGQ-PPYYGQGPQQQFNGQPLGWPRMSMMPTPMGPGGPLRPNGLAPMNAVRAPSRN 449

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1063732901  94 FGSKMSRNnwkgkkitsDKRPMMEQQQQQirrmhnsGIPMYNPQQLPgsgSIQVGAGGYKPPTLNELQS 162
Cdd:TIGR01628 450 AQNAAQKP---------PMQPVMYPPNYQ-------SLPLSQDLPQP---QSTASQGGQNKKLAQVLAS 499
Amelogenin smart00818
Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem ...
 10-68 4.67e-03

Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem to regulate formation of crystallites during the secretory stage of tooth enamel development and are thought to play a major role in the structural organisation and mineralisation of developing enamel. The extracellular matrix of the developing enamel comprises two major classes of protein: the hydrophobic amelogenins and the acidic enamelins. Circular dichroism studies of porcine amelogenin have shown that the protein consists of 3 discrete folding units: the N-terminal region appears to contain beta-strand structures, while the C-terminal region displays characteristics of a random coil conformation. Subsequent studies on the bovine protein have indicated the amelogenin structure to contain a repetitive beta-turn segment and a "beta-spiral" between Gln112 and Leu138, which sequester a (Pro, Leu, Gln) rich region. The beta-spiral offers a probable site for interactions with Ca2+ ions. Muatations in the human amelogenin gene (AMGX) cause X-linked hypoplastic amelogenesis imperfecta, a disease characterised by defective enamel. A 9bp deletion in exon 2 of AMGX results in the loss of codons for Ile5, Leu6, Phe7 and Ala8, and replacement by a new threonine codon, disrupting the 16-residue (Met1-Ala16) amelogenin signal peptide.


Pssm-ID: 197891 [Multi-domain]  Cd Length: 165  Bit Score: 37.85  E-value: 4.67e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1063732901   10 PPPPQQMIgQPPPQQRMNPPPPSQvprimNQSPLlgqsHPIMGMNQQPPQVMMNSNQPM 68
Cdd:smart00818  93 PQPAQQPF-QPQPLQPPQPQQPMQ-----PQPPV----HPIPPLPPQPPLPPMFPMQPL 141
COG4026 COG4026
Uncharacterized conserved protein, contains TOPRIM domain, potential nuclease [General ...
 276-354 8.92e-03

Uncharacterized conserved protein, contains TOPRIM domain, potential nuclease [General function prediction only];


Pssm-ID: 443204 [Multi-domain]  Cd Length: 287  Bit Score: 38.17  E-value: 8.92e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1063732901 276 EEHVEVERRLDHDLSRFEMIYpnyggsEYNNVLENRVDDQDSHIAQLEEENLTLKERLFLMERELGDMRRRLQYLERRD 354
Cdd:COG4026   135 EELLELKEKIDEIAKEKEKLT------KENEELESELEELREEYKKLREENSILEEEFDNIKSEYSDLKSRFEELLKKR 207
 
Name Accession Description Interval E-value
Extensin_2 pfam04554
Extensin-like region;
10-67 2.57e-03

Extensin-like region;


Pssm-ID: 252669 [Multi-domain]  Cd Length: 57  Bit Score: 36.28  E-value: 2.57e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1063732901  10 PPPPQQMIGQPPPQQRMNPPPPSQVPRIMNQSPLLGQSHPimgmnqqPPQVMMNSNQP 67
Cdd:pfam04554   6 PPPPVKQYSPPPPYYYKSPPPPVKSPVYKSPPPPVYKSPP-------PPKYVYKSPPP 56
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 14-162 2.61e-03

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 40.18  E-value: 2.61e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063732901  14 QQMIGQPPPQQRmNPPPPSQVPRIMNQsPLLGQSHPIMGMNQQPPQVMMNSNQPMMMNPRNFNLNQSLSSEYQQNLAPNN 93
Cdd:TIGR01628 372 QDQFMQLQPRMR-QLPMGSPMGGAMGQ-PPYYGQGPQQQFNGQPLGWPRMSMMPTPMGPGGPLRPNGLAPMNAVRAPSRN 449

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1063732901  94 FGSKMSRNnwkgkkitsDKRPMMEQQQQQirrmhnsGIPMYNPQQLPgsgSIQVGAGGYKPPTLNELQS 162
Cdd:TIGR01628 450 AQNAAQKP---------PMQPVMYPPNYQ-------SLPLSQDLPQP---QSTASQGGQNKKLAQVLAS 499
Amelogenin smart00818
Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem ...
 10-68 4.67e-03

Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem to regulate formation of crystallites during the secretory stage of tooth enamel development and are thought to play a major role in the structural organisation and mineralisation of developing enamel. The extracellular matrix of the developing enamel comprises two major classes of protein: the hydrophobic amelogenins and the acidic enamelins. Circular dichroism studies of porcine amelogenin have shown that the protein consists of 3 discrete folding units: the N-terminal region appears to contain beta-strand structures, while the C-terminal region displays characteristics of a random coil conformation. Subsequent studies on the bovine protein have indicated the amelogenin structure to contain a repetitive beta-turn segment and a "beta-spiral" between Gln112 and Leu138, which sequester a (Pro, Leu, Gln) rich region. The beta-spiral offers a probable site for interactions with Ca2+ ions. Muatations in the human amelogenin gene (AMGX) cause X-linked hypoplastic amelogenesis imperfecta, a disease characterised by defective enamel. A 9bp deletion in exon 2 of AMGX results in the loss of codons for Ile5, Leu6, Phe7 and Ala8, and replacement by a new threonine codon, disrupting the 16-residue (Met1-Ala16) amelogenin signal peptide.


Pssm-ID: 197891 [Multi-domain]  Cd Length: 165  Bit Score: 37.85  E-value: 4.67e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1063732901   10 PPPPQQMIgQPPPQQRMNPPPPSQvprimNQSPLlgqsHPIMGMNQQPPQVMMNSNQPM 68
Cdd:smart00818  93 PQPAQQPF-QPQPLQPPQPQQPMQ-----PQPPV----HPIPPLPPQPPLPPMFPMQPL 141
COG4026 COG4026
Uncharacterized conserved protein, contains TOPRIM domain, potential nuclease [General ...
 276-354 8.92e-03

Uncharacterized conserved protein, contains TOPRIM domain, potential nuclease [General function prediction only];


Pssm-ID: 443204 [Multi-domain]  Cd Length: 287  Bit Score: 38.17  E-value: 8.92e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1063732901 276 EEHVEVERRLDHDLSRFEMIYpnyggsEYNNVLENRVDDQDSHIAQLEEENLTLKERLFLMERELGDMRRRLQYLERRD 354
Cdd:COG4026   135 EELLELKEKIDEIAKEKEKLT------KENEELESELEELREEYKKLREENSILEEEFDNIKSEYSDLKSRFEELLKKR 207
 
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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