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Conserved domains on  [gi|738093238|ref|WP_036051889|]
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porin [Burkholderia gladioli]

Protein Classification

porin( domain architecture ID 10085924)

porin forming an aqueous channel for the diffusion of small hydrophilic molecules across the outer membrane, similar to outer membrane protein P2

Gene Ontology:  GO:0009279|GO:0015288
PubMed:  31214985|31792365
TCDB:  1.B.1

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
gram_neg_porins cd00342
Porins form aqueous channels for the diffusion of small hydrophillic molecules across the ...
22-399 1.85e-84

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: 260.38  E-value: 1.85e-84
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738093238  22 SSVTLYGLIDTGFAFNSNAKGGRQYSASSGNLQGDRWGLRGIEDLGGGYAAIFRLEGGYSVNSGALGQGGALFGRKAYVG 101
Cdd:cd00342    1 SSVTLYGRIDAGVEYVNNAGGGGAGQMTSGGNNGSRWGLRGSEDLGGGLKAIFQLESGFNLNTGALGQGGRLFGRQAYVG 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738093238 102 LQTP-YGTVTLGRQYDALGDYVGDFEAAnfekfvpgteWGSIYGAHPGDMDNLDNSYRINNTVKYASRSYNGLKFGGMYS 180
Cdd:cd00342   81 LSSDtYGTLTLGRQYTPLYDVLGTTDPF----------GGSGGGSAPGDGDNLAGTGRANNSVKYTSPFFGGLTFGAMYA 150
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738093238 181 LGGQAGDVTRNQVWGLGVGYDHGPFAGGIAIERAKNPNFGVFGTnpnansataanaanvsnpvfsgfASAGAWQVISAGA 260
Cdd:cd00342  151 FGNQAGSTSNGRGYGAGLSYENGPLSLGAAYDQQRNGGGAAGGA-----------------------AGATSQRAYGAGA 207
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738093238 261 AYHLGNATIGGVYSNVAFQNLGATagaglnplhlsGTAKFNIGELSVSYLLTPSLQLGTAYTYTKGSSVGSvSGATYNQV 340
Cdd:cd00342  208 SYDFGGLKLGAGYTNTRNDNGGGG-----------GSAKFNGYELGATYQLTPALRLGAAYYYTKDRNDGG-GDGKANQV 275
                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 738093238 341 NLGADYFLSRRTDLYVVGIYQHASGVDSTGkkavaAIANLSNSSSDRQAAVVFGIRHKF 399
Cdd:cd00342  276 ALGADYALSKRTDLYAEYGYQKNSGGASTG-----LAGGGGPSSGNNQDGVAVGIRHKF 329
 
Name Accession Description Interval E-value
gram_neg_porins cd00342
Porins form aqueous channels for the diffusion of small hydrophillic molecules across the ...
22-399 1.85e-84

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: 260.38  E-value: 1.85e-84
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738093238  22 SSVTLYGLIDTGFAFNSNAKGGRQYSASSGNLQGDRWGLRGIEDLGGGYAAIFRLEGGYSVNSGALGQGGALFGRKAYVG 101
Cdd:cd00342    1 SSVTLYGRIDAGVEYVNNAGGGGAGQMTSGGNNGSRWGLRGSEDLGGGLKAIFQLESGFNLNTGALGQGGRLFGRQAYVG 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738093238 102 LQTP-YGTVTLGRQYDALGDYVGDFEAAnfekfvpgteWGSIYGAHPGDMDNLDNSYRINNTVKYASRSYNGLKFGGMYS 180
Cdd:cd00342   81 LSSDtYGTLTLGRQYTPLYDVLGTTDPF----------GGSGGGSAPGDGDNLAGTGRANNSVKYTSPFFGGLTFGAMYA 150
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738093238 181 LGGQAGDVTRNQVWGLGVGYDHGPFAGGIAIERAKNPNFGVFGTnpnansataanaanvsnpvfsgfASAGAWQVISAGA 260
Cdd:cd00342  151 FGNQAGSTSNGRGYGAGLSYENGPLSLGAAYDQQRNGGGAAGGA-----------------------AGATSQRAYGAGA 207
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738093238 261 AYHLGNATIGGVYSNVAFQNLGATagaglnplhlsGTAKFNIGELSVSYLLTPSLQLGTAYTYTKGSSVGSvSGATYNQV 340
Cdd:cd00342  208 SYDFGGLKLGAGYTNTRNDNGGGG-----------GSAKFNGYELGATYQLTPALRLGAAYYYTKDRNDGG-GDGKANQV 275
                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 738093238 341 NLGADYFLSRRTDLYVVGIYQHASGVDSTGkkavaAIANLSNSSSDRQAAVVFGIRHKF 399
Cdd:cd00342  276 ALGADYALSKRTDLYAEYGYQKNSGGASTG-----LAGGGGPSSGNNQDGVAVGIRHKF 329
OmpC COG3203
Outer membrane porin OmpC/OmpF/PhoE [Cell wall/membrane/envelope biogenesis];
15-399 2.87e-72

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


Pssm-ID: 442436 [Multi-domain]  Cd Length: 336  Bit Score: 229.50  E-value: 2.87e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738093238  15 SGVAHAQSSVTLYGLIDTGFAFNSNAkGGRQYSASSGNLQGDRWGLRGIEDLGGGYAAIFRLEGGYSVNSGALGQGGALF 94
Cdd:COG3203   12 AGAAHAQSSVTLYGRVDAGVEYVDNG-GGSLTRLTSGGDSGSRLGFKGSEDLGGGLKAIFQLESGFNADTGTSGGGGRLF 90
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738093238  95 GRKAYVGLQ-TPYGTVTLGRQYDALGDYVGDFEAanfekFVPGTEWGSIYGAhpgdmDNLDNSYRINNTVKYASRSYNGL 173
Cdd:COG3203   91 GRQAYVGLKgDDFGTLTLGRQYTPLYDVVGAFDP-----FGDSGDAGNLAGD-----DNLAGTGRADNAIKYRSPNFGGL 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738093238 174 KFGGMYSLGGQAGDVTRNQVWGLGVGYDHGPFAGGIAIERAKNPNfgvfgtnpnansataanaanvsnpvfSGFASAGAW 253
Cdd:COG3203  161 TFGAQYSFGEDAGSSSNGRGYGAGLTYANGPLSLGAAYQQSNDAQ--------------------------GATAGGDDA 214
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738093238 254 QVISAGAAYHLGNATIGGVYSNVAFQNLGATagaglnplhlsGTAKFNIGELSVSYLLTPSLQLGTAYTYTKGSsvGSVS 333
Cdd:COG3203  215 DAWGLGASYDFGNLKLAAGYGQTKNDDAGGA-----------GNAKADGYELGASYPFGPALTLSASYGYTDAK--DGAD 281
                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 738093238 334 GATYNQVNLGADYFLSRRTDLYVVGIYQHASGVdstgkkavaaiANLSNSSSDRQAAVVFGIRHKF 399
Cdd:COG3203  282 DDDANQYALGADYALSKRTSLYAEYGYNDNDGN-----------ANFTAAAGDTDDGVAVGLRHKF 336
Porin_4 pfam13609
Gram-negative porin;
15-356 5.25e-25

Gram-negative porin;


Pssm-ID: 433346 [Multi-domain]  Cd Length: 311  Bit Score: 103.67  E-value: 5.25e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738093238   15 SGVAHAQSSVTLYGLIDTGFAFNSNAKGGRQYSASSGNLQGDRWGLRGIE--DLGGGYAAIFRLEGGysvnsgaLGQGGA 92
Cdd:pfam13609   9 AGAAAAQSSVTLYGSADAGVGYVNGGAAGAGADGETGLDSNSRIGFGGSEelDNGLGFGASFELEAG-------FNGAGG 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738093238   93 LFGRKAYVGLQTPYGTVTLGRQYDALGDYVGDFeaanfekFVPGTEWGSIYGAHPGDMDNLDNSYRINNTVKYASRSYNG 172
Cdd:pfam13609  82 FNNRQAYVGLSGGFGTVTLGRQDGAFDEAGVDY-------DFDGGSLGDSGYDGSGLSGSAGFDGRDSNSIIYYSPKFGG 154
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738093238  173 LKFGGMYSLGGQ----------AGDVTRNQVWGLGVGYDHG--PFAGGIAIERAKNpnfgvfgtnpnansataanaanvs 240
Cdd:pfam13609 155 FTAGASYAFGEDgntngnnggvAGDSNDTDGYGLGAGYDFGgvGFSVAAAYQQTDN------------------------ 210
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738093238  241 npvfsgfaSAGAWQVISAGAAYHLGNATIGGVYSNVafqnlgatagaglNPLHLSGTAKFNIGELSVSYLLTPsLQLGTA 320
Cdd:pfam13609 211 --------EGGDQDAWGLGASYSLGAFTLGASYADI-------------DDDGAAAGADDNGYGVGATYTVGA-LTVGAA 268
                         330       340       350
                  ....*....|....*....|....*....|....*.
gi 738093238  321 YTYTKGssvGSVSGATYNQVNLGADYFLSRRTDLYV 356
Cdd:pfam13609 269 YGRYDD---AGGGDADATQYGLGADYNLSKRTTLYA 301
 
Name Accession Description Interval E-value
gram_neg_porins cd00342
Porins form aqueous channels for the diffusion of small hydrophillic molecules across the ...
22-399 1.85e-84

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: 260.38  E-value: 1.85e-84
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738093238  22 SSVTLYGLIDTGFAFNSNAKGGRQYSASSGNLQGDRWGLRGIEDLGGGYAAIFRLEGGYSVNSGALGQGGALFGRKAYVG 101
Cdd:cd00342    1 SSVTLYGRIDAGVEYVNNAGGGGAGQMTSGGNNGSRWGLRGSEDLGGGLKAIFQLESGFNLNTGALGQGGRLFGRQAYVG 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738093238 102 LQTP-YGTVTLGRQYDALGDYVGDFEAAnfekfvpgteWGSIYGAHPGDMDNLDNSYRINNTVKYASRSYNGLKFGGMYS 180
Cdd:cd00342   81 LSSDtYGTLTLGRQYTPLYDVLGTTDPF----------GGSGGGSAPGDGDNLAGTGRANNSVKYTSPFFGGLTFGAMYA 150
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738093238 181 LGGQAGDVTRNQVWGLGVGYDHGPFAGGIAIERAKNPNFGVFGTnpnansataanaanvsnpvfsgfASAGAWQVISAGA 260
Cdd:cd00342  151 FGNQAGSTSNGRGYGAGLSYENGPLSLGAAYDQQRNGGGAAGGA-----------------------AGATSQRAYGAGA 207
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738093238 261 AYHLGNATIGGVYSNVAFQNLGATagaglnplhlsGTAKFNIGELSVSYLLTPSLQLGTAYTYTKGSSVGSvSGATYNQV 340
Cdd:cd00342  208 SYDFGGLKLGAGYTNTRNDNGGGG-----------GSAKFNGYELGATYQLTPALRLGAAYYYTKDRNDGG-GDGKANQV 275
                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 738093238 341 NLGADYFLSRRTDLYVVGIYQHASGVDSTGkkavaAIANLSNSSSDRQAAVVFGIRHKF 399
Cdd:cd00342  276 ALGADYALSKRTDLYAEYGYQKNSGGASTG-----LAGGGGPSSGNNQDGVAVGIRHKF 329
OmpC COG3203
Outer membrane porin OmpC/OmpF/PhoE [Cell wall/membrane/envelope biogenesis];
15-399 2.87e-72

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


Pssm-ID: 442436 [Multi-domain]  Cd Length: 336  Bit Score: 229.50  E-value: 2.87e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738093238  15 SGVAHAQSSVTLYGLIDTGFAFNSNAkGGRQYSASSGNLQGDRWGLRGIEDLGGGYAAIFRLEGGYSVNSGALGQGGALF 94
Cdd:COG3203   12 AGAAHAQSSVTLYGRVDAGVEYVDNG-GGSLTRLTSGGDSGSRLGFKGSEDLGGGLKAIFQLESGFNADTGTSGGGGRLF 90
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738093238  95 GRKAYVGLQ-TPYGTVTLGRQYDALGDYVGDFEAanfekFVPGTEWGSIYGAhpgdmDNLDNSYRINNTVKYASRSYNGL 173
Cdd:COG3203   91 GRQAYVGLKgDDFGTLTLGRQYTPLYDVVGAFDP-----FGDSGDAGNLAGD-----DNLAGTGRADNAIKYRSPNFGGL 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738093238 174 KFGGMYSLGGQAGDVTRNQVWGLGVGYDHGPFAGGIAIERAKNPNfgvfgtnpnansataanaanvsnpvfSGFASAGAW 253
Cdd:COG3203  161 TFGAQYSFGEDAGSSSNGRGYGAGLTYANGPLSLGAAYQQSNDAQ--------------------------GATAGGDDA 214
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738093238 254 QVISAGAAYHLGNATIGGVYSNVAFQNLGATagaglnplhlsGTAKFNIGELSVSYLLTPSLQLGTAYTYTKGSsvGSVS 333
Cdd:COG3203  215 DAWGLGASYDFGNLKLAAGYGQTKNDDAGGA-----------GNAKADGYELGASYPFGPALTLSASYGYTDAK--DGAD 281
                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 738093238 334 GATYNQVNLGADYFLSRRTDLYVVGIYQHASGVdstgkkavaaiANLSNSSSDRQAAVVFGIRHKF 399
Cdd:COG3203  282 DDDANQYALGADYALSKRTSLYAEYGYNDNDGN-----------ANFTAAAGDTDDGVAVGLRHKF 336
Porin_4 pfam13609
Gram-negative porin;
15-356 5.25e-25

Gram-negative porin;


Pssm-ID: 433346 [Multi-domain]  Cd Length: 311  Bit Score: 103.67  E-value: 5.25e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738093238   15 SGVAHAQSSVTLYGLIDTGFAFNSNAKGGRQYSASSGNLQGDRWGLRGIE--DLGGGYAAIFRLEGGysvnsgaLGQGGA 92
Cdd:pfam13609   9 AGAAAAQSSVTLYGSADAGVGYVNGGAAGAGADGETGLDSNSRIGFGGSEelDNGLGFGASFELEAG-------FNGAGG 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738093238   93 LFGRKAYVGLQTPYGTVTLGRQYDALGDYVGDFeaanfekFVPGTEWGSIYGAHPGDMDNLDNSYRINNTVKYASRSYNG 172
Cdd:pfam13609  82 FNNRQAYVGLSGGFGTVTLGRQDGAFDEAGVDY-------DFDGGSLGDSGYDGSGLSGSAGFDGRDSNSIIYYSPKFGG 154
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738093238  173 LKFGGMYSLGGQ----------AGDVTRNQVWGLGVGYDHG--PFAGGIAIERAKNpnfgvfgtnpnansataanaanvs 240
Cdd:pfam13609 155 FTAGASYAFGEDgntngnnggvAGDSNDTDGYGLGAGYDFGgvGFSVAAAYQQTDN------------------------ 210
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738093238  241 npvfsgfaSAGAWQVISAGAAYHLGNATIGGVYSNVafqnlgatagaglNPLHLSGTAKFNIGELSVSYLLTPsLQLGTA 320
Cdd:pfam13609 211 --------EGGDQDAWGLGASYSLGAFTLGASYADI-------------DDDGAAAGADDNGYGVGATYTVGA-LTVGAA 268
                         330       340       350
                  ....*....|....*....|....*....|....*.
gi 738093238  321 YTYTKGssvGSVSGATYNQVNLGADYFLSRRTDLYV 356
Cdd:pfam13609 269 YGRYDD---AGGGDADATQYGLGADYNLSKRTTLYA 301
 
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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