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Conserved domains on  [gi|291334214|gb|ADD93880|]
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hypothetical protein [uncultured marine bacterium MedDCM-OCT-S08-C1463]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
OM_channels super family cl21487
Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in ...
 194-310 1.75e-10

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 TIGR01783:

Pssm-ID: 473880 [Multi-domain]  Cd Length: 651  Bit Score: 61.66  E-value: 1.75e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291334214  194 TGNSMPF-PELTVSMGIGYTAQAGNLELTPRLDYYYQSDFYngFYNIESRKSPAWDEWNFSLR-IVPTDADWNIRFYVQN 271
Cdd:TIGR01783 539 QGNTVPFvPKHTASLWASYAPPVGDNGLTLGGGVQYTGKAY--VDGGNTGKVPSYTVVDLSVRyDLTKKKNLTLALNVNN 616

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 291334214  272 LTDERNITgmglSASSQGFFSAISLREPRSWGMSFGIDF 310
Cdd:TIGR01783 617 LFDRDYYT----SGYRWGPSAYIYPGAPRTVGLSVSYDF 651
 
Name Accession Description Interval E-value
TonB-siderophor TIGR01783
TonB-dependent siderophore receptor; This subfamily model encompasses a wide variety of ...
 194-310 1.75e-10

TonB-dependent siderophore receptor; This subfamily model encompasses a wide variety of TonB-dependent outer membrane siderophore receptors. It has no overlap with TonB receptors known to transport other substances, but is likely incomplete due to lack of characterizations. It is likely that genuine siderophore receptors will be identified which score below the noise cutoff to this model at which point the model should be updated. [Transport and binding proteins, Cations and iron carrying compounds, Transport and binding proteins, Porins]


Pssm-ID: 273805 [Multi-domain]  Cd Length: 651  Bit Score: 61.66  E-value: 1.75e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291334214  194 TGNSMPF-PELTVSMGIGYTAQAGNLELTPRLDYYYQSDFYngFYNIESRKSPAWDEWNFSLR-IVPTDADWNIRFYVQN 271
Cdd:TIGR01783 539 QGNTVPFvPKHTASLWASYAPPVGDNGLTLGGGVQYTGKAY--VDGGNTGKVPSYTVVDLSVRyDLTKKKNLTLALNVNN 616

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 291334214  272 LTDERNITgmglSASSQGFFSAISLREPRSWGMSFGIDF 310
Cdd:TIGR01783 617 LFDRDYYT----SGYRWGPSAYIYPGAPRTVGLSVSYDF 651
TonB_dep_Rec pfam00593
TonB dependent receptor; This model now only covers the conserved part of the barrel structure.
 186-309 3.73e-08

TonB dependent receptor; This model now only covers the conserved part of the barrel structure.


Pssm-ID: 395474 [Multi-domain]  Cd Length: 475  Bit Score: 54.39  E-value: 3.73e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291334214  186 STGLPTDITGNSMPF-PELTVSMGIGYTAQAGNLELTPRLDYYYQSDFYNGFYNiESRKSPAWDEWNFSLRIVPTDaDWN 264
Cdd:pfam00593 357 DDDADADDTGNPLPNvPRHTANLGLTYDFPLGGWGARLGARYVGSGERRYGDAA-NTFKTPGYTLVDLSAGYRLNK-NLT 434

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 291334214  265 IRFYVQNLTDERNITGMGLSASSQGFFSAislrEPRSWGMSFGID 309
Cdd:pfam00593 435 LRLGVNNLFDKYYKRYYSSGGGNLGGYPG----PGRTFYLGLSYK 475
CirA COG1629
Outer membrane receptor protein, Fe transport [Inorganic ion transport and metabolism];
186-291 1.20e-07

Outer membrane receptor protein, Fe transport [Inorganic ion transport and metabolism];


Pssm-ID: 441236 [Multi-domain]  Cd Length: 644  Bit Score: 52.91  E-value: 1.20e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291334214 186 STGLPTDITGNSMPF-PELTVSMGIGYTAQAGnleLTPRLDYYYQSDFYNGFYNiESRKSPAWDEWNFSLRIVPTDaDWN 264
Cdd:COG1629  542 DTDGSADLDGNRLPGvPPLTANLGLTYEFPGG---WSLGLGVRYVGDRYLDDAN-TQGAPGGYTLVDLGAGYRFGD-NLT 616

                         90       100
                 ....*....|....*....|....*..
gi 291334214 265 IRFYVQNLTDERNITGMGLSASSQGFF 291
Cdd:COG1629  617 LSLGVDNLFDKKYATSLSVRASNVRGF 643
ligand_gated_channel cd01347
TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) ...
 187-310 1.26e-06

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: 49.76  E-value: 1.26e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291334214 187 TGLPTDITGNSMPF-PELTVSMGIGYtaQAGNLELTPRLDYYYQSDFYNGFYNIESR-KSPAWDEWNFSLRIVPTDaDWN 264
Cdd:cd01347  517 KRTDGATTGNRLPGiPKHTANLGLDY--ELPDEGLTAGGGVRYRGKQYADTANGNNTvKVPGYTLVDLSASYQFTK-NLT 593

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 291334214 265 IRFYVQNLTDERNITGMGLSASSqgffSAISLREPRSWGMSFGIDF 310
Cdd:cd01347  594 LRLGVNNLFDKDYYTSLSVRGSG----LYGYYGPGRTYYLSVSYKF 635
 
Name Accession Description Interval E-value
TonB-siderophor TIGR01783
TonB-dependent siderophore receptor; This subfamily model encompasses a wide variety of ...
 194-310 1.75e-10

TonB-dependent siderophore receptor; This subfamily model encompasses a wide variety of TonB-dependent outer membrane siderophore receptors. It has no overlap with TonB receptors known to transport other substances, but is likely incomplete due to lack of characterizations. It is likely that genuine siderophore receptors will be identified which score below the noise cutoff to this model at which point the model should be updated. [Transport and binding proteins, Cations and iron carrying compounds, Transport and binding proteins, Porins]


Pssm-ID: 273805 [Multi-domain]  Cd Length: 651  Bit Score: 61.66  E-value: 1.75e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291334214  194 TGNSMPF-PELTVSMGIGYTAQAGNLELTPRLDYYYQSDFYngFYNIESRKSPAWDEWNFSLR-IVPTDADWNIRFYVQN 271
Cdd:TIGR01783 539 QGNTVPFvPKHTASLWASYAPPVGDNGLTLGGGVQYTGKAY--VDGGNTGKVPSYTVVDLSVRyDLTKKKNLTLALNVNN 616

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 291334214  272 LTDERNITgmglSASSQGFFSAISLREPRSWGMSFGIDF 310
Cdd:TIGR01783 617 LFDRDYYT----SGYRWGPSAYIYPGAPRTVGLSVSYDF 651
TonB_dep_Rec pfam00593
TonB dependent receptor; This model now only covers the conserved part of the barrel structure.
 186-309 3.73e-08

TonB dependent receptor; This model now only covers the conserved part of the barrel structure.


Pssm-ID: 395474 [Multi-domain]  Cd Length: 475  Bit Score: 54.39  E-value: 3.73e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291334214  186 STGLPTDITGNSMPF-PELTVSMGIGYTAQAGNLELTPRLDYYYQSDFYNGFYNiESRKSPAWDEWNFSLRIVPTDaDWN 264
Cdd:pfam00593 357 DDDADADDTGNPLPNvPRHTANLGLTYDFPLGGWGARLGARYVGSGERRYGDAA-NTFKTPGYTLVDLSAGYRLNK-NLT 434

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 291334214  265 IRFYVQNLTDERNITGMGLSASSQGFFSAislrEPRSWGMSFGID 309
Cdd:pfam00593 435 LRLGVNNLFDKYYKRYYSSGGGNLGGYPG----PGRTFYLGLSYK 475
CirA COG1629
Outer membrane receptor protein, Fe transport [Inorganic ion transport and metabolism];
186-291 1.20e-07

Outer membrane receptor protein, Fe transport [Inorganic ion transport and metabolism];


Pssm-ID: 441236 [Multi-domain]  Cd Length: 644  Bit Score: 52.91  E-value: 1.20e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291334214 186 STGLPTDITGNSMPF-PELTVSMGIGYTAQAGnleLTPRLDYYYQSDFYNGFYNiESRKSPAWDEWNFSLRIVPTDaDWN 264
Cdd:COG1629  542 DTDGSADLDGNRLPGvPPLTANLGLTYEFPGG---WSLGLGVRYVGDRYLDDAN-TQGAPGGYTLVDLGAGYRFGD-NLT 616

                         90       100
                 ....*....|....*....|....*..
gi 291334214 265 IRFYVQNLTDERNITGMGLSASSQGFF 291
Cdd:COG1629  617 LSLGVDNLFDKKYATSLSVRASNVRGF 643
ligand_gated_channel cd01347
TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) ...
 187-310 1.26e-06

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: 49.76  E-value: 1.26e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291334214 187 TGLPTDITGNSMPF-PELTVSMGIGYtaQAGNLELTPRLDYYYQSDFYNGFYNIESR-KSPAWDEWNFSLRIVPTDaDWN 264
Cdd:cd01347  517 KRTDGATTGNRLPGiPKHTANLGLDY--ELPDEGLTAGGGVRYRGKQYADTANGNNTvKVPGYTLVDLSASYQFTK-NLT 593

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 291334214 265 IRFYVQNLTDERNITGMGLSASSqgffSAISLREPRSWGMSFGIDF 310
Cdd:cd01347  594 LRLGVNNLFDKDYYTSLSVRGSG----LYGYYGPGRTYYLSVSYKF 635
FecA COG4772
Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism];
191-310 3.41e-06

Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism];


Pssm-ID: 443804 [Multi-domain]  Cd Length: 681  Bit Score: 48.39  E-value: 3.41e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291334214 191 TDITGNSMPF-PELTVSMGIGYtaQAGNLELTprLDYYYQSDFY----NGFYNIESRKSPAWDEWNFSLRIvptDADWNI 265
Cdd:COG4772  567 PVFAGNRLPYvPRHQLTAGLGY--EHGGWTAN--LNGRYVSEQFtdaaNTVADGSFGKIPSYTVLDLSASY---DFGKNL 639

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 291334214 266 RFY--VQNLTDERNITGmGLSASSQGFFSAislrEPRSWGMSFGIDF 310
Cdd:COG4772  640 SLFagVNNLFDKRYIAS-RAPNYAAGIRPG----PPRTVYAGLRLKF 681
Fiu COG4774
Outer membrane receptor for monomeric catechols [Inorganic ion transport and metabolism];
191-310 4.23e-05

Outer membrane receptor for monomeric catechols [Inorganic ion transport and metabolism];


Pssm-ID: 443806 [Multi-domain]  Cd Length: 639  Bit Score: 44.87  E-value: 4.23e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291334214 191 TDITGNSMPF-PELTVSMGIGYTAQAGNLELTprLDYYYQSDFYNGFYNieSRKSPAWDEWNFSLRIVPTDaDWNIRFYV 269
Cdd:COG4774  531 AANVGNRLPNvPRHSASLWTTYDLPLPGLTLG--GGVRYVGSRYADAAN--TVKLPSYTRFDAGASYRLNK-NLTLRLNV 605

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 291334214 270 QNLTDERNITgmglSASSQGFfsaISLREPRSWGMSFGIDF 310
Cdd:COG4774  606 NNLTDKRYYA----SAYGSGY---VTPGAPRTVLLSASYRF 639
FhuE COG4773
Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion ...
 190-310 4.81e-04

Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism];


Pssm-ID: 443805 [Multi-domain]  Cd Length: 692  Bit Score: 41.80  E-value: 4.81e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291334214 190 PTDITGNSMPF-PELTVSMGIGYTAQAGNLE-LTPRLDYYYQSDFYNGFYNieSRKSPAWDEWNFSLRIVPTDaDWNIRF 267
Cdd:COG4773  580 ADALEGKRLTNvPRHTASLWTTYRFPSGALKgLGLGGGVRYVGERYGDAAN--TFTLPSYTLVDAGARYDLGK-NWTLQL 656

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 291334214 268 YVQNLTDERNITgmglsasSQGFFSAISLREPRSWGMSFGIDF 310
Cdd:COG4773  657 NVNNLFDKKYYA-------SSGSRGYVYYGAPRNVRLSLSYKF 692
 
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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