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Conserved domains on  [gi|1622723368|gb|QCD41419|]
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acyloxyacyl hydrolase [Duncaniella dubosii]

Protein Classification

porin family protein( domain architecture ID 229388)

porin family protein is a member of a large superfamily consisting of classical (gram-negative ) porins which are non-specific channels for small hydrophillic molecules, maltoporin-like channels which have specificities for various sugars, and ligand-gated protein channels which cooperate with a TonB associated inner membrane complex to actively transport ligands via the proton motive force

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PagL super family cl48058
Lipid A 3-O-deacylase (PagL); PagL is an outer membrane protein with lipid A 3-O-deacylase ...
 171-225 1.09e-05

Lipid A 3-O-deacylase (PagL); PagL is an outer membrane protein with lipid A 3-O-deacylase activity. It forms an 8 stranded beta barrel structure.


The actual alignment was detected with superfamily member pfam09411:

Pssm-ID: 462791  Cd Length: 129  Bit Score: 44.78  E-value: 1.09e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1622723368 171 GSPINAYINLGFMLSYrldAKWNLTAGIDLTHYSNGNTALPNPGVNTLGGRVGVT 225
Cdd:pfam09411  78 GTRFQFRDQAGLGYRF---GEGNLSLGLRFQHYSNAGIKDPNPGLNSLGLNLGYR 129
OM_channels super family cl21487
Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in ...
 89-322 2.75e-03

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: 39.74  E-value: 2.75e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622723368  89 FGYSETTRTGRLYPGAYQGIGVGSTTFFANNLTGMPVTAYlfqgapivRLAKGLTFDYEWNFGASFGWKKY-NEDSNPIN 167
Cdd:cd01347   399 ASYSQGFRAPSLGELYGGGSHGGTAAVGNPNLKPEKSKQY--------ELGLKYDPGDGLTLSAALFRIDIkNEIVSTPT 470

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622723368 168 VIVGSPINAYINLG--------FMLSYRLDAKWNLTAGIDLTH-----YSNGNTALPNPGVNTLGGRVGVTYTLNGDRRT 234
Cdd:cd01347   471 NTGLGLVTVYVNGGkarirgveLEASYDLTDGLGLTGSYTYTDtevkrTDGATTGNRLPGIPKHTANLGLDYELPDEGLT 550

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622723368 235 GALADNFeiepmkphlsydlviYGAVRKKVADLNGPEELPGhFGIAGLNFApmYNFNR--FLRAGVS--LDVQYDESSDI 310
Cdd:cd01347   551 AGGGVRY---------------RGKQYADTANGNNTVKVPG-YTLVDLSAS--YQFTKnlTLRLGVNnlFDKDYYTSLSV 612

                         250
                  ....*....|..
gi 1622723368 311 RSYWIEGTYGDE 322
Cdd:cd01347   613 RGSGLYGYYGPG 624
 
Name Accession Description Interval E-value
PagL pfam09411
Lipid A 3-O-deacylase (PagL); PagL is an outer membrane protein with lipid A 3-O-deacylase ...
 171-225 1.09e-05

Lipid A 3-O-deacylase (PagL); PagL is an outer membrane protein with lipid A 3-O-deacylase activity. It forms an 8 stranded beta barrel structure.


Pssm-ID: 462791  Cd Length: 129  Bit Score: 44.78  E-value: 1.09e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1622723368 171 GSPINAYINLGFMLSYrldAKWNLTAGIDLTHYSNGNTALPNPGVNTLGGRVGVT 225
Cdd:pfam09411  78 GTRFQFRDQAGLGYRF---GEGNLSLGLRFQHYSNAGIKDPNPGLNSLGLNLGYR 129
ligand_gated_channel cd01347
TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) ...
 89-322 2.75e-03

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: 39.74  E-value: 2.75e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622723368  89 FGYSETTRTGRLYPGAYQGIGVGSTTFFANNLTGMPVTAYlfqgapivRLAKGLTFDYEWNFGASFGWKKY-NEDSNPIN 167
Cdd:cd01347   399 ASYSQGFRAPSLGELYGGGSHGGTAAVGNPNLKPEKSKQY--------ELGLKYDPGDGLTLSAALFRIDIkNEIVSTPT 470

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622723368 168 VIVGSPINAYINLG--------FMLSYRLDAKWNLTAGIDLTH-----YSNGNTALPNPGVNTLGGRVGVTYTLNGDRRT 234
Cdd:cd01347   471 NTGLGLVTVYVNGGkarirgveLEASYDLTDGLGLTGSYTYTDtevkrTDGATTGNRLPGIPKHTANLGLDYELPDEGLT 550

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622723368 235 GALADNFeiepmkphlsydlviYGAVRKKVADLNGPEELPGhFGIAGLNFApmYNFNR--FLRAGVS--LDVQYDESSDI 310
Cdd:cd01347   551 AGGGVRY---------------RGKQYADTANGNNTVKVPG-YTLVDLSAS--YQFTKnlTLRLGVNnlFDKDYYTSLSV 612

                         250
                  ....*....|..
gi 1622723368 311 RSYWIEGTYGDE 322
Cdd:cd01347   613 RGSGLYGYYGPG 624
 
Name Accession Description Interval E-value
PagL pfam09411
Lipid A 3-O-deacylase (PagL); PagL is an outer membrane protein with lipid A 3-O-deacylase ...
 171-225 1.09e-05

Lipid A 3-O-deacylase (PagL); PagL is an outer membrane protein with lipid A 3-O-deacylase activity. It forms an 8 stranded beta barrel structure.


Pssm-ID: 462791  Cd Length: 129  Bit Score: 44.78  E-value: 1.09e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1622723368 171 GSPINAYINLGFMLSYrldAKWNLTAGIDLTHYSNGNTALPNPGVNTLGGRVGVT 225
Cdd:pfam09411  78 GTRFQFRDQAGLGYRF---GEGNLSLGLRFQHYSNAGIKDPNPGLNSLGLNLGYR 129
ligand_gated_channel cd01347
TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) ...
 89-322 2.75e-03

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: 39.74  E-value: 2.75e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622723368  89 FGYSETTRTGRLYPGAYQGIGVGSTTFFANNLTGMPVTAYlfqgapivRLAKGLTFDYEWNFGASFGWKKY-NEDSNPIN 167
Cdd:cd01347   399 ASYSQGFRAPSLGELYGGGSHGGTAAVGNPNLKPEKSKQY--------ELGLKYDPGDGLTLSAALFRIDIkNEIVSTPT 470

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622723368 168 VIVGSPINAYINLG--------FMLSYRLDAKWNLTAGIDLTH-----YSNGNTALPNPGVNTLGGRVGVTYTLNGDRRT 234
Cdd:cd01347   471 NTGLGLVTVYVNGGkarirgveLEASYDLTDGLGLTGSYTYTDtevkrTDGATTGNRLPGIPKHTANLGLDYELPDEGLT 550

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622723368 235 GALADNFeiepmkphlsydlviYGAVRKKVADLNGPEELPGhFGIAGLNFApmYNFNR--FLRAGVS--LDVQYDESSDI 310
Cdd:cd01347   551 AGGGVRY---------------RGKQYADTANGNNTVKVPG-YTLVDLSAS--YQFTKnlTLRLGVNnlFDKDYYTSLSV 612

                         250
                  ....*....|..
gi 1622723368 311 RSYWIEGTYGDE 322
Cdd:cd01347   613 RGSGLYGYYGPG 624
ligand_gated_channel cd01347
TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) ...
 82-229 4.51e-03

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: 39.36  E-value: 4.51e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622723368  82 SWHLKYSFGYSETTRTGRLYPGAYQGIGVGSTTFFANNLTGMPVTAYLFQGAPIVRLAKGLtFDYEWNFGASFGWKKYNE 161
Cdd:cd01347   254 GWTLRANLSYSYTDNDGDPLILNGGNNAAGGDLGRSGYSSERDTTQLGFDAGLNAPFGTGP-VAHTLTLGVEYRREELDE 332

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1622723368 162 DSNpinvivgspiNAYInlgfMLSYRLDAKWNLTAGIDLTHYSNGNTALPNPGV------NTLGGRVGVTYTLN 229
Cdd:cd01347   333 KQT----------ALYA----QDTIELTDDLTLTLGLRYDHYDQDSKDTIAGGTtakksySHWSPSLGLVYKLT 392
 
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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