Lipoprotein amino terminal region; This family contains regions from: Vitellogenin, Microsomal ...
46-597
1.64e-125
Lipoprotein amino terminal region; This family contains regions from: Vitellogenin, Microsomal triglyceride transfer protein and apolipoprotein B-100. These proteins are all involved in lipid transport. This family contains the LV1n chain from lipovitellin, that contains two structural domains.
:
Pssm-ID: 460170 [Multi-domain] Cd Length: 582 Bit Score: 410.13 E-value: 1.64e-125
Vitellinogen, open beta-sheet; This entry represents the open beta-sheet domain found in ...
632-937
9.04e-79
Vitellinogen, open beta-sheet; This entry represents the open beta-sheet domain found in vitellinogen, which generally corresponds to a domain within the lipovitellin-1 peptide product. This domain adopts a structure consisting of several large open beta-sheets.
:
Pssm-ID: 462702 Cd Length: 300 Bit Score: 264.20 E-value: 9.04e-79
Apolipoprotein B100 C terminal; This domain family is found in eukaryotes, and is ...
4494-4550
4.96e-29
Apolipoprotein B100 C terminal; This domain family is found in eukaryotes, and is approximately 60 amino acids in length. There are two conserved sequence motifs: QLS and LIDL. ApoB100 has an essential role in the assembly and secretion of triglyceride-rich lipoproteins and lipids transport.
:
Pssm-ID: 463606 Cd Length: 57 Bit Score: 111.74 E-value: 4.96e-29
reticulocyte binding/rhoptry protein; This model represents a group of paralogous families in ...
2060-2490
4.82e-09
reticulocyte binding/rhoptry protein; This model represents a group of paralogous families in plasmodium species alternately annotated as reticulocyte binding protein, 235-kDa family protein and rhoptry protein. Rhoptry protein is localized on the cell surface and is extremely large (although apparently lacking in repeat structure) and is important for the process of invasion of the RBCs by the parasite. These proteins are found in P. falciparum, P. vivax and P. yoelii.
The actual alignment was detected with superfamily member TIGR01612:
Pssm-ID: 130673 [Multi-domain] Cd Length: 2757 Bit Score: 63.15 E-value: 4.82e-09
Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in ...
1448-1865
1.91e-04
Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20), which associate as trimers. Maltoporin-like channels have specificities for various sugars and form 18 beta-stranded barrels (18,22), which associate as trimers. Ligand-gated protein channels cooperate with a TonB associated inner membrane complex to actively transport ligands via the proton motive force and they form monomeric, (22,24) barrels. The 150-200 N-terminal residues form a plug that blocks the channel from the periplasmic end.
The actual alignment was detected with superfamily member cd01347:
Pssm-ID: 473880 [Multi-domain] Cd Length: 635 Bit Score: 47.83 E-value: 1.91e-04
Lipoprotein amino terminal region; This family contains regions from: Vitellogenin, Microsomal ...
46-597
1.64e-125
Lipoprotein amino terminal region; This family contains regions from: Vitellogenin, Microsomal triglyceride transfer protein and apolipoprotein B-100. These proteins are all involved in lipid transport. This family contains the LV1n chain from lipovitellin, that contains two structural domains.
Pssm-ID: 460170 [Multi-domain] Cd Length: 582 Bit Score: 410.13 E-value: 1.64e-125
Vitellinogen, open beta-sheet; This entry represents the open beta-sheet domain found in ...
632-937
9.04e-79
Vitellinogen, open beta-sheet; This entry represents the open beta-sheet domain found in vitellinogen, which generally corresponds to a domain within the lipovitellin-1 peptide product. This domain adopts a structure consisting of several large open beta-sheets.
Pssm-ID: 462702 Cd Length: 300 Bit Score: 264.20 E-value: 9.04e-79
Apolipoprotein B100 C terminal; This domain family is found in eukaryotes, and is ...
4494-4550
4.96e-29
Apolipoprotein B100 C terminal; This domain family is found in eukaryotes, and is approximately 60 amino acids in length. There are two conserved sequence motifs: QLS and LIDL. ApoB100 has an essential role in the assembly and secretion of triglyceride-rich lipoproteins and lipids transport.
Pssm-ID: 463606 Cd Length: 57 Bit Score: 111.74 E-value: 4.96e-29
reticulocyte binding/rhoptry protein; This model represents a group of paralogous families in ...
2060-2490
4.82e-09
reticulocyte binding/rhoptry protein; This model represents a group of paralogous families in plasmodium species alternately annotated as reticulocyte binding protein, 235-kDa family protein and rhoptry protein. Rhoptry protein is localized on the cell surface and is extremely large (although apparently lacking in repeat structure) and is important for the process of invasion of the RBCs by the parasite. These proteins are found in P. falciparum, P. vivax and P. yoelii.
Pssm-ID: 130673 [Multi-domain] Cd Length: 2757 Bit Score: 63.15 E-value: 4.82e-09
TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) ...
1448-1865
1.91e-04
TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel. Energy (proton-motive force) and TonB-dependent conformational alteration of channel (parts of plug, and loops 7 and 8) allow passage of ligand. FepA residues 12-18 form the TonB box, which mediates the interaction with the TonB-containing inner membrane complex. TonB preferentially interacts with ligand-bound receptors. Transport thru the channel may resemble passage thru an air lock. In this model, ligand binding leads to closure of the extracellular end of pore, then a TonB-mediated signal facillitates opening of the interior side of pore, deforming the N-terminal plug and allowing passage of the ligand to the periplasm. Such a mechanism would prevent the free diffusion of small molecules thru the pore.
Pssm-ID: 238657 [Multi-domain] Cd Length: 635 Bit Score: 47.83 E-value: 1.91e-04
LXG domain of WXG superfamily; This domain is present is the N-terminal region of a group of ...
2341-2552
3.30e-03
LXG domain of WXG superfamily; This domain is present is the N-terminal region of a group of polymorphic toxin proteins in bacteria. It is predicted to use Type VII secretion pathway to mediate export of bacterial toxins.
Pssm-ID: 428100 [Multi-domain] Cd Length: 202 Bit Score: 42.24 E-value: 3.30e-03
Lipoprotein amino terminal region; This family contains regions from: Vitellogenin, Microsomal ...
46-597
1.64e-125
Lipoprotein amino terminal region; This family contains regions from: Vitellogenin, Microsomal triglyceride transfer protein and apolipoprotein B-100. These proteins are all involved in lipid transport. This family contains the LV1n chain from lipovitellin, that contains two structural domains.
Pssm-ID: 460170 [Multi-domain] Cd Length: 582 Bit Score: 410.13 E-value: 1.64e-125
Vitellinogen, open beta-sheet; This entry represents the open beta-sheet domain found in ...
632-937
9.04e-79
Vitellinogen, open beta-sheet; This entry represents the open beta-sheet domain found in vitellinogen, which generally corresponds to a domain within the lipovitellin-1 peptide product. This domain adopts a structure consisting of several large open beta-sheets.
Pssm-ID: 462702 Cd Length: 300 Bit Score: 264.20 E-value: 9.04e-79
Apolipoprotein B100 C terminal; This domain family is found in eukaryotes, and is ...
4494-4550
4.96e-29
Apolipoprotein B100 C terminal; This domain family is found in eukaryotes, and is approximately 60 amino acids in length. There are two conserved sequence motifs: QLS and LIDL. ApoB100 has an essential role in the assembly and secretion of triglyceride-rich lipoproteins and lipids transport.
Pssm-ID: 463606 Cd Length: 57 Bit Score: 111.74 E-value: 4.96e-29
reticulocyte binding/rhoptry protein; This model represents a group of paralogous families in ...
2060-2490
4.82e-09
reticulocyte binding/rhoptry protein; This model represents a group of paralogous families in plasmodium species alternately annotated as reticulocyte binding protein, 235-kDa family protein and rhoptry protein. Rhoptry protein is localized on the cell surface and is extremely large (although apparently lacking in repeat structure) and is important for the process of invasion of the RBCs by the parasite. These proteins are found in P. falciparum, P. vivax and P. yoelii.
Pssm-ID: 130673 [Multi-domain] Cd Length: 2757 Bit Score: 63.15 E-value: 4.82e-09
TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) ...
1448-1865
1.91e-04
TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel. Energy (proton-motive force) and TonB-dependent conformational alteration of channel (parts of plug, and loops 7 and 8) allow passage of ligand. FepA residues 12-18 form the TonB box, which mediates the interaction with the TonB-containing inner membrane complex. TonB preferentially interacts with ligand-bound receptors. Transport thru the channel may resemble passage thru an air lock. In this model, ligand binding leads to closure of the extracellular end of pore, then a TonB-mediated signal facillitates opening of the interior side of pore, deforming the N-terminal plug and allowing passage of the ligand to the periplasm. Such a mechanism would prevent the free diffusion of small molecules thru the pore.
Pssm-ID: 238657 [Multi-domain] Cd Length: 635 Bit Score: 47.83 E-value: 1.91e-04
reticulocyte binding/rhoptry protein; This model represents a group of paralogous families in ...
2037-2593
5.34e-04
reticulocyte binding/rhoptry protein; This model represents a group of paralogous families in plasmodium species alternately annotated as reticulocyte binding protein, 235-kDa family protein and rhoptry protein. Rhoptry protein is localized on the cell surface and is extremely large (although apparently lacking in repeat structure) and is important for the process of invasion of the RBCs by the parasite. These proteins are found in P. falciparum, P. vivax and P. yoelii.
Pssm-ID: 130673 [Multi-domain] Cd Length: 2757 Bit Score: 46.58 E-value: 5.34e-04
LXG domain of WXG superfamily; This domain is present is the N-terminal region of a group of ...
2341-2552
3.30e-03
LXG domain of WXG superfamily; This domain is present is the N-terminal region of a group of polymorphic toxin proteins in bacteria. It is predicted to use Type VII secretion pathway to mediate export of bacterial toxins.
Pssm-ID: 428100 [Multi-domain] Cd Length: 202 Bit Score: 42.24 E-value: 3.30e-03
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.
of the residues that compose this conserved feature have been mapped to the query sequence.
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