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Conserved domains on  [gi|149062788|gb|EDM13211|]
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retinol binding protein 4, plasma, isoform CRA_b [Rattus norvegicus]

Protein Classification

lipocalin/fatty acid-binding family protein( domain architecture ID 3669)

lipocalin/fatty acid-binding family protein contains a large beta-barrel cavity that binds hydrophobic ligands

CATH:  2.40.128.20
Gene Ontology:  GO:0036094
PubMed:  11058745|11058743
SCOP:  3001332

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
lipocalin_FABP super family cl10502
lipocalin/cytosolic fatty acid-binding protein family; Lipocalins are diverse, mainly low ...
 1-122 3.03e-83

lipocalin/cytosolic fatty acid-binding protein family; Lipocalins are diverse, mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules as well as membrane bound-receptors. They have a large beta-barrel ligand-binding cavity. Members include retinol-binding protein, retinoic acid-binding protein, complement protein C8 gamma, Can f 2, apolipoprotein D, extracellular fatty acid-binding protein, beta-lactoglobulin, oderant-binding protein, and bacterial lipocalin Blc. Lipocalins are involved in many important processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty acid-binding proteins also bind hydrophobic ligands in a non-covalent, reversible manner, and are involved in protection and shuttling of fatty acids within the cell, and in acquisition and removal of fatty acids from intracellular sites.


The actual alignment was detected with superfamily member cd00743:

Pssm-ID: 471979  Cd Length: 171  Bit Score: 241.20  E-value: 3.03e-83
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149062788   1 MSATAKGRVRLLSNWEVCADMVGTFTDTEDPAKFKMKYWGVASFLQRGNDDHWIIDTDYDTFALQYSCRLQNLDGTCADS 80
Cdd:cd00743   50 MTATAKGRVRLLNNWDVCADMVGTFTDTEDPAKFKMKYWGVASYLQKGNDDHWVIDTDYDTYAITYSCRLLNLDGTCADS 129

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 149062788  81 YSFVFSRDPNGLTPETRRLVRQRQEELCLERQYRWIEHNGYC 122
Cdd:cd00743  130 YSFVFSRDPNGLPPEVQKIVRQRQEELCLARQYRLVVHNGYC 171
 
Name Accession Description Interval E-value
lipocalin_RBP_like cd00743
retinol-binding protein 4 and similar proteins; Retinol-Binding Protein 4 (RBP4) is a plasma ...
 1-122 3.03e-83

retinol-binding protein 4 and similar proteins; Retinol-Binding Protein 4 (RBP4) is a plasma protein that transports retinol (vitamin A) from the liver stores to the peripheral tissues. The RBP4-retinol complex interacts with transthyretin (TTR - transports thyroxine and retinol) which protects it from renal excretion. In addition to retinol, other endogenous and synthetic retinoids bind RBP4, including all-trans and 13-cis retinoic acid, retinyl acetate, N-(ethyl)retinamide, and fenretinide. This group also includes purpurin, a retinol-specific protein that plays a role in neural retina cell adhesion during development of the chicken retina; it also binds retinol and may participate in retinol transporter in the retina. This group belongs to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development.


Pssm-ID: 381184  Cd Length: 171  Bit Score: 241.20  E-value: 3.03e-83
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149062788   1 MSATAKGRVRLLSNWEVCADMVGTFTDTEDPAKFKMKYWGVASFLQRGNDDHWIIDTDYDTFALQYSCRLQNLDGTCADS 80
Cdd:cd00743   50 MTATAKGRVRLLNNWDVCADMVGTFTDTEDPAKFKMKYWGVASYLQKGNDDHWVIDTDYDTYAITYSCRLLNLDGTCADS 129

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 149062788  81 YSFVFSRDPNGLTPETRRLVRQRQEELCLERQYRWIEHNGYC 122
Cdd:cd00743  130 YSFVFSRDPNGLPPEVQKIVRQRQEELCLARQYRLVVHNGYC 171
Lipocalin pfam00061
Lipocalin / cytosolic fatty-acid binding protein family; Lipocalins are transporters for small ...
 16-107 6.68e-12

Lipocalin / cytosolic fatty-acid binding protein family; Lipocalins are transporters for small hydrophobic molecules, such as lipids, steroid hormones, bilins, and retinoids. The family also encompasses the enzyme prostaglandin D synthase (EC:5.3.99.2). Alignment subsumes both the lipocalin and fatty acid binding protein signatures from PROSITE. This is supported on structural and functional grounds. The structure is an eight-stranded beta barrel.


Pssm-ID: 395015  Cd Length: 143  Bit Score: 58.61  E-value: 6.68e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149062788   16 EVCADMVGTFTDTEDPAKFKMKYWGVAsflqrGNDDHWIIDTDYDTFALQYSCrlqNLDGTCADSYSFVFSRDPNgLTPE 95
Cdd:pfam00061  47 GKCKTVSVTFKKTEEPGKLGVEFDEYA-----GGRKVKVLTTDYDNYLIFYQK---GDKDGKTTIVRELYGRDPE-LSPE 117

                          90
                  ....*....|..
gi 149062788   96 TRRLVRQRQEEL 107
Cdd:pfam00061 118 LLEKFKKFLKEL 129
 
Name Accession Description Interval E-value
lipocalin_RBP_like cd00743
retinol-binding protein 4 and similar proteins; Retinol-Binding Protein 4 (RBP4) is a plasma ...
 1-122 3.03e-83

retinol-binding protein 4 and similar proteins; Retinol-Binding Protein 4 (RBP4) is a plasma protein that transports retinol (vitamin A) from the liver stores to the peripheral tissues. The RBP4-retinol complex interacts with transthyretin (TTR - transports thyroxine and retinol) which protects it from renal excretion. In addition to retinol, other endogenous and synthetic retinoids bind RBP4, including all-trans and 13-cis retinoic acid, retinyl acetate, N-(ethyl)retinamide, and fenretinide. This group also includes purpurin, a retinol-specific protein that plays a role in neural retina cell adhesion during development of the chicken retina; it also binds retinol and may participate in retinol transporter in the retina. This group belongs to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development.


Pssm-ID: 381184  Cd Length: 171  Bit Score: 241.20  E-value: 3.03e-83
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149062788   1 MSATAKGRVRLLSNWEVCADMVGTFTDTEDPAKFKMKYWGVASFLQRGNDDHWIIDTDYDTFALQYSCRLQNLDGTCADS 80
Cdd:cd00743   50 MTATAKGRVRLLNNWDVCADMVGTFTDTEDPAKFKMKYWGVASYLQKGNDDHWVIDTDYDTYAITYSCRLLNLDGTCADS 129

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 149062788  81 YSFVFSRDPNGLTPETRRLVRQRQEELCLERQYRWIEHNGYC 122
Cdd:cd00743  130 YSFVFSRDPNGLPPEVQKIVRQRQEELCLARQYRLVVHNGYC 171
lipocalin_FABP cd00301
lipocalin/cytosolic fatty acid-binding protein family; Lipocalins are diverse, mainly low ...
 17-87 4.61e-13

lipocalin/cytosolic fatty acid-binding protein family; Lipocalins are diverse, mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules as well as membrane bound-receptors. They have a large beta-barrel ligand-binding cavity. Members include retinol-binding protein, retinoic acid-binding protein, complement protein C8 gamma, Can f 2, apolipoprotein D, extracellular fatty acid-binding protein, beta-lactoglobulin, oderant-binding protein, and bacterial lipocalin Blc. Lipocalins are involved in many important processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty acid-binding proteins also bind hydrophobic ligands in a non-covalent, reversible manner, and are involved in protection and shuttling of fatty acids within the cell, and in acquisition and removal of fatty acids from intracellular sites.


Pssm-ID: 381182  Cd Length: 109  Bit Score: 61.02  E-value: 4.61e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 149062788  17 VCADMVGTFTDTEDPAKFKMKYWGVAsflqrGNDDHWIIDTDYDTFALQYSCrlqNLDGTCADSYSFVFSR 87
Cdd:cd00301   47 VCKSITGTLKKTDGPGKFTVTYPGYT-----GKNELYVLSTDYDNYAIVYSC---KNLDGGHTVVAWLLSR 109
Lipocalin pfam00061
Lipocalin / cytosolic fatty-acid binding protein family; Lipocalins are transporters for small ...
 16-107 6.68e-12

Lipocalin / cytosolic fatty-acid binding protein family; Lipocalins are transporters for small hydrophobic molecules, such as lipids, steroid hormones, bilins, and retinoids. The family also encompasses the enzyme prostaglandin D synthase (EC:5.3.99.2). Alignment subsumes both the lipocalin and fatty acid binding protein signatures from PROSITE. This is supported on structural and functional grounds. The structure is an eight-stranded beta barrel.


Pssm-ID: 395015  Cd Length: 143  Bit Score: 58.61  E-value: 6.68e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149062788   16 EVCADMVGTFTDTEDPAKFKMKYWGVAsflqrGNDDHWIIDTDYDTFALQYSCrlqNLDGTCADSYSFVFSRDPNgLTPE 95
Cdd:pfam00061  47 GKCKTVSVTFKKTEEPGKLGVEFDEYA-----GGRKVKVLTTDYDNYLIFYQK---GDKDGKTTIVRELYGRDPE-LSPE 117

                          90
                  ....*....|..
gi 149062788   96 TRRLVRQRQEEL 107
Cdd:pfam00061 118 LLEKFKKFLKEL 129
lipocalin_apoD-like cd19437
apolipoprotein D and similar proteins; Human apolipoprotein D (ApoD) is a small glycoprotein ...
 22-102 2.92e-08

apolipoprotein D and similar proteins; Human apolipoprotein D (ApoD) is a small glycoprotein associated with high density lipoproteins (HDL) in plasma. It appears promiscuous since it can bind hydrophobic ligands belonging to different lipid groups, with different shapes and biochemical properties; however, it exhibits specificity between very similar lipidic species. Some ligands, such as progesterone and arachidonic acid, bind to the ligand-binding pocket with high affinity, while others may interact with ApoD via its region of surface hydrophobicity. This hydrophobic surface cluster may facilitate its association with HDL particles and facilitate its insertion into cellular lipid membranes. Drosophila NLaz and Schistocerca Laz belong to this group, and share functional properties with human ApoD, including regulation of lifespan, lipid and carbohydrate metabolism control, and protection against oxidative stress or starvation. This group also includes Sandercyanin, a blue protein secreted in the skin mucus of blue forms of walleye, Sander vitreus. Walleye is an important golden yellow commercial and sport fish; the findings of blue walleye are recent. This group belongs to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development.


Pssm-ID: 381212 [Multi-domain]  Cd Length: 160  Bit Score: 49.17  E-value: 2.92e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149062788  22 VGTFTDTEDPAKFKMKYwgvASFLQRGNddHWIIDTDYDTFALQYSC----RLQNLDgtcadsYSFVFSRDPNgLTPETR 97
Cdd:cd19437   71 SARCPDPNEPAKLGVSF---PGFPPAGP--YWVLDTDYDNYAIVYSCtdvlGLFKVE------YAWILSRQRT-LSAETL 138


                 ....*
gi 149062788  98 RLVRQ 102
Cdd:cd19437  139 TKAKE 143
lipocalin_crustacyanin cd19436
crustacyanin Type I CRTC and Type II CRTA subunits; Alpha crustacyanin bound with the ...
 54-98 4.83e-05

crustacyanin Type I CRTC and Type II CRTA subunits; Alpha crustacyanin bound with the carotenoid astaxanthisn (AXT) is the predominant cartenoprotein generating the slate-grey/blue color of the lobster carapace. Crustacyanin forms heterodimers (beta-crustacyanin) or complexes of 16 subunits (alpha-crustacyanin) assembled from beta-crustacyanin. Beta-crustacyanin is formed from one type I CRTC lipocalin subunit, and one type II CRTA lipocalin subunit (and two bound astaxanthin molecules). Homarus gammarus (European lobster) crustacyanin has of five distinct subunits evident on 6 M urea-PAGE gels: type I CRTC ( A1, C1, C2) and type II CRTA ( A2, A3). Homarus americanus crustacyanin consists of only two major subunits, namely type I CRTC (H1) and type II CRTA (H2), both of which behave like Ax subunits on a 6 M urea-PAGE gel. This family includes both type I CRTC subunit and type II CRTA subunits and belongs to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development.


Pssm-ID: 381211  Cd Length: 169  Bit Score: 40.53  E-value: 4.83e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 149062788  54 IIDTDYDTFALQYSCrlQNLDGTCADsYSFVFSRDPNGLTPETRR 98
Cdd:cd19436  103 VIETDYENYSCVYSC--IDTDGYKSE-FGFVFSRSPQLAGPAVEK 144
lipocalin_LTBP1-like cd19423
Triatominae salivary lipocalins such as Rhodnius prolixus LTBP1 and Meccus pallidipennis ...
 54-88 1.55e-03

Triatominae salivary lipocalins such as Rhodnius prolixus LTBP1 and Meccus pallidipennis triabin, and similar proteins; This subfamily includes various insect proteins found in the saliva of Triatominae (kissing bugs), including Rhodnius prolixus leukotriene-binding LTBP1. Rhodnius prolixus, a vector of the pathogen Trypanosoma cruzi, sequesters cysteinyl leukotrienes during feeding to inhibit immediate inflammatory responses; LTBP1 binds leukotrienes C4 (LTC4), D4 (LTD4), and E4 (LTE4). Meccus pallidipennis (syn Triatoma pallidipennis) triabin is a potent and selective thrombin inhibitor. It also includes Triatoma protracta procalin, a major salivary allergen which causes an allergic reaction in humans. It belongs to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development.


Pssm-ID: 381198  Cd Length: 132  Bit Score: 36.18  E-value: 1.55e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 149062788  54 IIDTDYDTFALQYSCrLQNLDGTCADSYsFVFSRD 88
Cdd:cd19423  100 VIDTDYDNYALVYRC-VTYGSGKKKDNY-LVLQRD 132
 
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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