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Conserved domains on  [gi|1462843245|emb|SXF32754|]
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outer membrane protein C [Klebsiella variicola]

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
OM_channels super family cl21487
Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in ...
 11-104 3.58e-49

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 PRK10554:

Pssm-ID: 473880  Cd Length: 355  Bit Score: 159.23  E-value: 3.58e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1462843245  11 FPNKAQNLEMVAQYQFDSGLQPSIAYLQSKGKDI-----EGFGDQDLLKYIDVGTTYNINKNISTYVDYKINLLKDNDFT 85
Cdd:PRK10554  257 FANKAQNFEVVAQYQFDFGLRPSVAYLQSKGKDLgningRNYGDQDILKYVDVGATYYFNKNMSTYVDYKINLLDDNQFT 336

                          90
                  ....*....|....*....
gi 1462843245  86 QRAGISTDNIVAVGLAYQF 104
Cdd:PRK10554  337 RDAGINTDDIVALGLVYQF 355
 
Name Accession Description Interval E-value
PRK10554 PRK10554
outer membrane porin protein C; Provisional
 11-104 3.58e-49

outer membrane porin protein C; Provisional


Pssm-ID: 182543  Cd Length: 355  Bit Score: 159.23  E-value: 3.58e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1462843245  11 FPNKAQNLEMVAQYQFDSGLQPSIAYLQSKGKDI-----EGFGDQDLLKYIDVGTTYNINKNISTYVDYKINLLKDNDFT 85
Cdd:PRK10554  257 FANKAQNFEVVAQYQFDFGLRPSVAYLQSKGKDLgningRNYGDQDILKYVDVGATYYFNKNMSTYVDYKINLLDDNQFT 336

                          90
                  ....*....|....*....
gi 1462843245  86 QRAGISTDNIVAVGLAYQF 104
Cdd:PRK10554  337 RDAGINTDDIVALGLVYQF 355
Porin_1 pfam00267
Gram-negative porin;
11-104 2.13e-38

Gram-negative porin;


Pssm-ID: 395205  Cd Length: 335  Bit Score: 130.64  E-value: 2.13e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1462843245  11 FPNKAQNLEMVAQYQFDSGLQPSIAYLQSKGKDIEG-FGDQDLLKYIDVGTTYNINKNISTYVDYKINLLKDNDftqRAG 89
Cdd:pfam00267 244 FANKTQNTEVVAQYQFDFGLRPSISYAQSKGKDLEGaYGDNDLVKYVDVGATYYFNKNMSTYVDYKINLLDKGD---DLG 320

                          90
                  ....*....|....*
gi 1462843245  90 ISTDNIVAVGLAYQF 104
Cdd:pfam00267 321 INTDDAVAVGLRYQF 335
OM_channels cd01345
Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in ...
 9-102 4.04e-22

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.


Pssm-ID: 238655 [Multi-domain]  Cd Length: 253  Bit Score: 86.72  E-value: 4.04e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1462843245   9 RTFPNKAQNLEMVAQYQFDSGLQPSIAYLQSKGKDIEGFGDQDLLKYIDVGTTYNINKNISTYVDYKINLLKDNDFTQRA 88
Cdd:cd01345   145 RLSIIPEYTLNVTLSWQAREDLS*QVTYTWYKKQQPKKYKEIDPYSIVGLSATWDVTKNVSLTGGYDNLFDKRLWRAGNA 224

                          90
                  ....*....|....*
gi 1462843245  89 GISTD-NIVAVGLAY 102
Cdd:cd01345   225 QTTGDaNYIAGAGAY 239
OmpC COG3203
Outer membrane porin OmpC/OmpF/PhoE [Cell wall/membrane/envelope biogenesis];
2-104 3.64e-17

Outer membrane porin OmpC/OmpF/PhoE [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442436 [Multi-domain]  Cd Length: 336  Bit Score: 74.27  E-value: 3.64e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1462843245   2 GRNDLLIRTFPNKAQNLEMVAQYQFDSGLQPSIAYLQSKGKDiegFGDQDLLKYIDVGTTYNINKNISTYVDYKINLLKD 81
Cdd:COG3203   237 TKNDDAGGAGNAKADGYELGASYPFGPALTLSASYGYTDAKD---GADDDDANQYALGADYALSKRTSLYAEYGYNDNDG 313

                          90       100
                  ....*....|....*....|...
gi 1462843245  82 NDFTQRAGISTDNIVAVGLAYQF 104
Cdd:COG3203   314 NANFTAAAGDTDDGVAVGLRHKF 336
 
Name Accession Description Interval E-value
PRK10554 PRK10554
outer membrane porin protein C; Provisional
 11-104 3.58e-49

outer membrane porin protein C; Provisional


Pssm-ID: 182543  Cd Length: 355  Bit Score: 159.23  E-value: 3.58e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1462843245  11 FPNKAQNLEMVAQYQFDSGLQPSIAYLQSKGKDI-----EGFGDQDLLKYIDVGTTYNINKNISTYVDYKINLLKDNDFT 85
Cdd:PRK10554  257 FANKAQNFEVVAQYQFDFGLRPSVAYLQSKGKDLgningRNYGDQDILKYVDVGATYYFNKNMSTYVDYKINLLDDNQFT 336

                          90
                  ....*....|....*....
gi 1462843245  86 QRAGISTDNIVAVGLAYQF 104
Cdd:PRK10554  337 RDAGINTDDIVALGLVYQF 355
PRK10159 PRK10159
phosphoporin PhoE;
11-104 1.96e-39

phosphoporin PhoE;


Pssm-ID: 182275  Cd Length: 351  Bit Score: 133.90  E-value: 1.96e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1462843245  11 FPNKAQNLEMVAQYQFDSGLQPSIAYLQSKGKDIEGFGDQDLLKYIDVGTTYNINKNISTYVDYKINLLKDNDftqRAGI 90
Cdd:PRK10159  261 FANKTQNFEAVAQYQFDFGLRPSLGYVLSKGKDIEGIGDEDLVNYIDVGATYYFNKNMSAFVDYKINQLDSDN---KLNI 337

                          90
                  ....*....|....
gi 1462843245  91 STDNIVAVGLAYQF 104
Cdd:PRK10159  338 NNDDIVAVGMTYQF 351
Porin_1 pfam00267
Gram-negative porin;
11-104 2.13e-38

Gram-negative porin;


Pssm-ID: 395205  Cd Length: 335  Bit Score: 130.64  E-value: 2.13e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1462843245  11 FPNKAQNLEMVAQYQFDSGLQPSIAYLQSKGKDIEG-FGDQDLLKYIDVGTTYNINKNISTYVDYKINLLKDNDftqRAG 89
Cdd:pfam00267 244 FANKTQNTEVVAQYQFDFGLRPSISYAQSKGKDLEGaYGDNDLVKYVDVGATYYFNKNMSTYVDYKINLLDKGD---DLG 320

                          90
                  ....*....|....*
gi 1462843245  90 ISTDNIVAVGLAYQF 104
Cdd:pfam00267 321 INTDDAVAVGLRYQF 335
PRK10002 PRK10002
porin OmpF;
11-104 1.82e-34

porin OmpF;


Pssm-ID: 236639  Cd Length: 362  Bit Score: 121.14  E-value: 1.82e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1462843245  11 FPNKAQNLEMVAQYQFDSGLQPSIAYLQSKGKDIEGFGDQDLLKYIDVGTTYNINKNISTYVDYKINLLKDNDftqRAGI 90
Cdd:PRK10002  272 FANKTQDVLLVAQYQFDFGLRPSIAYTKSKAKDVEGIGDVDLVNYFEVGATYYFNKNMSTYVDYIINQIDSDN---KLGV 348

                          90
                  ....*....|....
gi 1462843245  91 STDNIVAVGLAYQF 104
Cdd:PRK10002  349 GSDDTVAVGIVYQF 362
OM_channels cd01345
Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in ...
 9-102 4.04e-22

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.


Pssm-ID: 238655 [Multi-domain]  Cd Length: 253  Bit Score: 86.72  E-value: 4.04e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1462843245   9 RTFPNKAQNLEMVAQYQFDSGLQPSIAYLQSKGKDIEGFGDQDLLKYIDVGTTYNINKNISTYVDYKINLLKDNDFTQRA 88
Cdd:cd01345   145 RLSIIPEYTLNVTLSWQAREDLS*QVTYTWYKKQQPKKYKEIDPYSIVGLSATWDVTKNVSLTGGYDNLFDKRLWRAGNA 224

                          90
                  ....*....|....*
gi 1462843245  89 GISTD-NIVAVGLAY 102
Cdd:cd01345   225 QTTGDaNYIAGAGAY 239
OmpC COG3203
Outer membrane porin OmpC/OmpF/PhoE [Cell wall/membrane/envelope biogenesis];
2-104 3.64e-17

Outer membrane porin OmpC/OmpF/PhoE [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442436 [Multi-domain]  Cd Length: 336  Bit Score: 74.27  E-value: 3.64e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1462843245   2 GRNDLLIRTFPNKAQNLEMVAQYQFDSGLQPSIAYLQSKGKDiegFGDQDLLKYIDVGTTYNINKNISTYVDYKINLLKD 81
Cdd:COG3203   237 TKNDDAGGAGNAKADGYELGASYPFGPALTLSASYGYTDAKD---GADDDDANQYALGADYALSKRTSLYAEYGYNDNDG 313

                          90       100
                  ....*....|....*....|...
gi 1462843245  82 NDFTQRAGISTDNIVAVGLAYQF 104
Cdd:COG3203   314 NANFTAAAGDTDDGVAVGLRHKF 336
gram_neg_porins cd00342
Porins form aqueous channels for the diffusion of small hydrophillic molecules across the ...
 2-104 1.81e-11

Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers are stabilized by hytrophillic clamping of Loop L2. Loop 3 bends into the pore, creating an elliptical constriction of about 7 x 11A, large enough to allow passage of a glucose molecule without steric hindrance. Removal of the C-terminal residue (usuallly F) destabilizes the trimer and removal of the 16th beta-sheet abolishes trimerization. Unlike typical membrane proteins, porins lack long hydrophobic stretches. Short turns are found at the smooth, periplasmic end, longer irregular loops are found at the rough, extracellular end. C-terminal residue forms salt bridge with N-terminus.


Pssm-ID: 238208 [Multi-domain]  Cd Length: 329  Bit Score: 58.54  E-value: 1.81e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1462843245   2 GRNDLLIRTFPNKAQNLEMVAQYQFDSGLQPSIAYLQSKGKDIEGFGDQdlLKYIDVGTTYNINKNISTYVDYKINLLKD 81
Cdd:cd00342   223 TRNDNGGGGGSAKFNGYELGATYQLTPALRLGAAYYYTKDRNDGGGDGK--ANQVALGADYALSKRTDLYAEYGYQKNSG 300

                          90       100
                  ....*....|....*....|....*....
gi 1462843245  82 NDFT------QRAGISTDNIVAVGLAYQF 104
Cdd:cd00342   301 GASTglagggGPSSGNNQDGVAVGIRHKF 329
 
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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