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Conserved domains on  [gi|459495029|gb|EMG88303|]
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outer membrane protein [Helicobacter pylori GAM114Ai]

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 ...
 94-241 9.50e-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 pfam01856:

Pssm-ID: 473880  Cd Length: 154  Bit Score: 38.41  E-value: 9.50e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 459495029   94 TGLEHFLRNHPKVGFRIFSVYNYFHSVSLSQPQILMVQN--YGGALDFSWIFVDKKTYRFRSYLGIALeQGVLLVDTIKT 171
Cdd:pfam01856   4 VGYKQFFGKKKWFGLRYYGFFDYGHANFGSQSGKQAVNMftYGVGTDLLYNFFNNKKASFGFFGGIQL-AGNTWTSSNNS 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 459495029  172 GAITTIIPRTKK--TFFQAPFRFGFIVDFIGYLSLQLGIEMPLVRNVSYIYNNHQERFKPRFNANLSLIVSF 241
Cdd:pfam01856  83 FLKIANDWNAKVspTNFQFLFNFGVRLNFAKHHGIEFGVKIPTINNNYYKTLGYTLDFRRLYSFYVNYTYNF 154
 
Name Accession Description Interval E-value
HP_OMP pfam01856
Helicobacter outer membrane protein; This family seems confined to Helicobacter. It is ...
 94-241 9.50e-04

Helicobacter outer membrane protein; This family seems confined to Helicobacter. It is predicted to be an outer membrane protein based on its pattern of alternating hydrophobic amino acids similar to porins.


Pssm-ID: 280099  Cd Length: 154  Bit Score: 38.41  E-value: 9.50e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 459495029   94 TGLEHFLRNHPKVGFRIFSVYNYFHSVSLSQPQILMVQN--YGGALDFSWIFVDKKTYRFRSYLGIALeQGVLLVDTIKT 171
Cdd:pfam01856   4 VGYKQFFGKKKWFGLRYYGFFDYGHANFGSQSGKQAVNMftYGVGTDLLYNFFNNKKASFGFFGGIQL-AGNTWTSSNNS 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 459495029  172 GAITTIIPRTKK--TFFQAPFRFGFIVDFIGYLSLQLGIEMPLVRNVSYIYNNHQERFKPRFNANLSLIVSF 241
Cdd:pfam01856  83 FLKIANDWNAKVspTNFQFLFNFGVRLNFAKHHGIEFGVKIPTINNNYYKTLGYTLDFRRLYSFYVNYTYNF 154
 
Name Accession Description Interval E-value
HP_OMP pfam01856
Helicobacter outer membrane protein; This family seems confined to Helicobacter. It is ...
 94-241 9.50e-04

Helicobacter outer membrane protein; This family seems confined to Helicobacter. It is predicted to be an outer membrane protein based on its pattern of alternating hydrophobic amino acids similar to porins.


Pssm-ID: 280099  Cd Length: 154  Bit Score: 38.41  E-value: 9.50e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 459495029   94 TGLEHFLRNHPKVGFRIFSVYNYFHSVSLSQPQILMVQN--YGGALDFSWIFVDKKTYRFRSYLGIALeQGVLLVDTIKT 171
Cdd:pfam01856   4 VGYKQFFGKKKWFGLRYYGFFDYGHANFGSQSGKQAVNMftYGVGTDLLYNFFNNKKASFGFFGGIQL-AGNTWTSSNNS 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 459495029  172 GAITTIIPRTKK--TFFQAPFRFGFIVDFIGYLSLQLGIEMPLVRNVSYIYNNHQERFKPRFNANLSLIVSF 241
Cdd:pfam01856  83 FLKIANDWNAKVspTNFQFLFNFGVRLNFAKHHGIEFGVKIPTINNNYYKTLGYTLDFRRLYSFYVNYTYNF 154
 
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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