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Conserved domains on  [gi|218750610|gb|ACL01369|]
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transferrin, partial [Notropis stilbius]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Periplasmic_Binding_Protein_Type_2 super family cl21456
Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent ...
 1-51 1.26e-16

Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent the ligand-binding domains found in solute binding proteins that serve as initial receptors in the transport, signal transduction and channel gating. The PBP2 proteins share the same architecture as periplasmic binding proteins type 1 (PBP1), but have a different topology. They are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The origin of PBP module can be traced across the distant phyla, including eukaryotes, archebacteria, and prokaryotes. The majority of PBP2 proteins are involved in the uptake of a variety of soluble substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the family includes ionotropic glutamate receptors and unorthodox sensor proteins involved in signal transduction. The substrate binding domain of the LysR transcriptional regulators and the oligopeptide-like transport systems also contain the type 2 periplasmic binding fold and thus they are significantly homologous to that of the PBP2; however, these two families are grouped into a separate hierarchy of the PBP2 superfamily due to the large number of protein sequences.


The actual alignment was detected with superfamily member cd13617:

Pssm-ID: 473866  Cd Length: 331  Bit Score: 70.51  E-value: 1.26e-16
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 218750610   1 PSSYHVVAVVRKGSGK-TWSNLKGSKSCHTGLNRNAGWKVPDSVICGKTPDC 51
Cdd:cd13617   89 EEGYLAVAVVKKSDSDlTWNNLKGKKSCHTAVGRTAGWNIPMGLIYNQTGSC 140
 
Name Accession Description Interval E-value
PBP2_transferrin_C cd13617
The C-lobe of transferrin, a member of the type 2 periplasmic binding protein fold superfamily; ...
 1-51 1.26e-16

The C-lobe of transferrin, a member of the type 2 periplasmic binding protein fold superfamily; Transferrins are iron-binding blood plasma glycoproteins that regulate the level of free iron in biological fluids. Vertebrate transferrins are made of a single polypeptide chain with a molecular weight of about 80 kDa. The polypeptide is folded into two homologous lobes (the N-lobe and C-lobe), and each lobe is further subdivided into two similar alpha helices and beta sheets domains separated by a deep cleft that forms the binding site for ferric iron. Thus, the transferrin protein contains two homologous metal-binding sites with high affinities for ferric iron. The modern transferrin proteins are thought to be evolved from an ancestral gene coding for a protein of 40 kDa containing a single binding site by means of a gene duplication event. Vertebrate transferrins are found in a variety of bodily fluids, including serum transferrins, ovotransferrins, lactoferrins, and melanotransferrins. Transferrin-like proteins are also found in the circulatory fluid of certain invertebrates. The transferrins have the same structural fold as the type 2 periplasmic-binding proteins, many of which are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor.


Pssm-ID: 270335  Cd Length: 331  Bit Score: 70.51  E-value: 1.26e-16
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 218750610   1 PSSYHVVAVVRKGSGK-TWSNLKGSKSCHTGLNRNAGWKVPDSVICGKTPDC 51
Cdd:cd13617   89 EEGYLAVAVVKKSDSDlTWNNLKGKKSCHTAVGRTAGWNIPMGLIYNQTGSC 140
TR_FER smart00094
Transferrin;
1-40 1.75e-16

Transferrin;


Pssm-ID: 214514  Cd Length: 332  Bit Score: 70.02  E-value: 1.75e-16
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 218750610     1 PSSYHVVAVVRKGSGK-TWSNLKGSKSCHTGLNRNAGWKVP 40
Cdd:smart00094  83 ETGYYAVAVVKKGSAIfTWNQLRGKKSCHTGVGRTAGWNIP 123
Transferrin pfam00405
Transferrin;
2-40 2.94e-15

Transferrin;


Pssm-ID: 395328 [Multi-domain]  Cd Length: 328  Bit Score: 66.72  E-value: 2.94e-15
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 218750610    2 SSYHVVAVVRKGSGKTWSNLKGSKSCHTGLNRNAGWKVP 40
Cdd:pfam00405  85 THYYAVAVVKKGSNFQLNQLQGKKSCHTGLGRSAGWNIP 123
 
Name Accession Description Interval E-value
PBP2_transferrin_C cd13617
The C-lobe of transferrin, a member of the type 2 periplasmic binding protein fold superfamily; ...
 1-51 1.26e-16

The C-lobe of transferrin, a member of the type 2 periplasmic binding protein fold superfamily; Transferrins are iron-binding blood plasma glycoproteins that regulate the level of free iron in biological fluids. Vertebrate transferrins are made of a single polypeptide chain with a molecular weight of about 80 kDa. The polypeptide is folded into two homologous lobes (the N-lobe and C-lobe), and each lobe is further subdivided into two similar alpha helices and beta sheets domains separated by a deep cleft that forms the binding site for ferric iron. Thus, the transferrin protein contains two homologous metal-binding sites with high affinities for ferric iron. The modern transferrin proteins are thought to be evolved from an ancestral gene coding for a protein of 40 kDa containing a single binding site by means of a gene duplication event. Vertebrate transferrins are found in a variety of bodily fluids, including serum transferrins, ovotransferrins, lactoferrins, and melanotransferrins. Transferrin-like proteins are also found in the circulatory fluid of certain invertebrates. The transferrins have the same structural fold as the type 2 periplasmic-binding proteins, many of which are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor.


Pssm-ID: 270335  Cd Length: 331  Bit Score: 70.51  E-value: 1.26e-16
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 218750610   1 PSSYHVVAVVRKGSGK-TWSNLKGSKSCHTGLNRNAGWKVPDSVICGKTPDC 51
Cdd:cd13617   89 EEGYLAVAVVKKSDSDlTWNNLKGKKSCHTAVGRTAGWNIPMGLIYNQTGSC 140
TR_FER smart00094
Transferrin;
1-40 1.75e-16

Transferrin;


Pssm-ID: 214514  Cd Length: 332  Bit Score: 70.02  E-value: 1.75e-16
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 218750610     1 PSSYHVVAVVRKGSGK-TWSNLKGSKSCHTGLNRNAGWKVP 40
Cdd:smart00094  83 ETGYYAVAVVKKGSAIfTWNQLRGKKSCHTGVGRTAGWNIP 123
Transferrin pfam00405
Transferrin;
2-40 2.94e-15

Transferrin;


Pssm-ID: 395328 [Multi-domain]  Cd Length: 328  Bit Score: 66.72  E-value: 2.94e-15
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 218750610    2 SSYHVVAVVRKGSGKTWSNLKGSKSCHTGLNRNAGWKVP 40
Cdd:pfam00405  85 THYYAVAVVKKGSNFQLNQLQGKKSCHTGLGRSAGWNIP 123
PBP2_transferrin cd13529
Transferrin family of the type 2 periplasmic-binding protein superfamily; Transferrins are ...
 1-40 1.68e-14

Transferrin family of the type 2 periplasmic-binding protein superfamily; Transferrins are iron-binding blood plasma glycoproteins that regulate the level of free iron in biological fluids. Vertebrate transferrins are made of a single polypeptide chain with a molecular weight of about 80 kDa. The polypeptide is folded into two homologous lobes (the N-lobe and C-lobe), and each lobe is further subdivided into two similar alpha helical and beta sheet domains separated by a deep cleft that forms the binding site for ferric iron. Thus, the transferrin protein contains two homologous metal-binding sites with high affinities for ferric iron. The modern transferrin proteins are thought to be evolved from an ancestral gene coding for a protein of 40 kDa containing a single binding site by means of a gene duplication event. Vertebrate transferrins are found in a variety of bodily fluids, including serum transferrins, ovotransferrins, lactoferrins, and melanotransferrins. Transferrin-like proteins are also found in the circulatory fluid of certain invertebrates. The transferrins have the same structural fold as the type 2 periplasmic-binding proteins, many of which are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor.


Pssm-ID: 270247  Cd Length: 298  Bit Score: 64.35  E-value: 1.68e-14
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 218750610   1 PSSYHVVAVVRKGSG-KTWSNLKGSKSCHTGLNRNAGWKVP 40
Cdd:cd13529   83 EASYYAVAVVKKSSNiTSLKDLRGKKSCHTGYGRTAGWNVP 123
PBP2_transferrin_N cd13618
The N-lobe of transferrin, a member of the type 2 periplasmic binding protein fold superfamily; ...
 2-40 3.75e-14

The N-lobe of transferrin, a member of the type 2 periplasmic binding protein fold superfamily; Transferrins are iron-binding blood plasma glycoproteins that regulate the level of free iron in biological fluids. Vertebrate transferrins are made of a single polypeptide chain with a molecular weight of about 80 kDa. The polypeptide is folded into two homologous lobes (the N-lobe and C-lobe), and each lobe is further subdivided into two similar alpha helices and beta sheets domains separated by a deep cleft that forms the binding site for ferric iron. Thus, the transferrin protein contains two homologous metal-binding sites with high affinities for ferric iron. The modern transferrin proteins are thought to be evolved from an ancestral gene coding for a protein of 40 kDa containing a single binding site by means of a gene duplication event. Vertebrate transferrins are found in a variety of bodily fluids, including serum transferrins, ovotransferrins, lactoferrins, and melanotransferrins. Transferrin-like proteins are also found in the circulatory fluid of certain invertebrates. The transferrins have the same structural fold as the type 2 periplasmic-binding proteins, many of which are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor.


Pssm-ID: 270336  Cd Length: 324  Bit Score: 63.60  E-value: 3.75e-14
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 218750610   2 SSYHVVAVVRKGSGKTWSNLKGSKSCHTGLNRNAGWKVP 40
Cdd:cd13618   86 THYYAVAVVKKGSGFQLNQLQGKKSCHTGLGRSAGWNIP 124
PBP2_PhnD_like cd01071
Substrate binding domain of phosphonate uptake system-like, a member of the type 2 ...
 2-40 4.31e-03

Substrate binding domain of phosphonate uptake system-like, a member of the type 2 periplasmic-binding fold superfamily; This family includes alkylphosphonate binding domain PhnD. These domains are found in PhnD-like proteins that are predicted to function as initial receptors in hypophosphite, phosphonate, or phosphate ABC transport in archaea and eubacteria. PhnD is the periplasmic binding component of an ABC-type phosphonate uptake system (PhnCDE) that recognizes and binds phosphonate. PhnD belongs to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. The PBP2 have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.


Pssm-ID: 270232 [Multi-domain]  Cd Length: 253  Bit Score: 32.62  E-value: 4.31e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 218750610   2 SSYHVVAVVRKGSG-KTWSNLKGSKSCHTGLNRNAGWKVP 40
Cdd:cd01071   89 PGYYSVIIVRKDSPiKSLEDLKGKTVAFVDPSSTSGYLFP 128
Phosphonate-bd pfam12974
ABC transporter, phosphonate, periplasmic substrate-binding protein; This is a family of ...
 3-40 5.08e-03

ABC transporter, phosphonate, periplasmic substrate-binding protein; This is a family of periplasmic proteins which are part of the transport system for alkylphosphonate uptake.


Pssm-ID: 432911 [Multi-domain]  Cd Length: 243  Bit Score: 32.24  E-value: 5.08e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 218750610    3 SYHVVAVVRKGSG-KTWSNLKGSKSCHTGLNRNAGWKVP 40
Cdd:pfam12974  84 GYRSVIIVRKDSPiQSLEDLKGKTVAFGDPSSTSGYLVP 122
 
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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