NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2273501554|ref|WP_254772065|]
View 

DUF3108 domain-containing protein [Pseudoalteromonas sp. DSM 26666]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
DUF3108 super family cl20412
Protein of unknown function (DUF3108); This is a bacterial family of putative lipoproteins. ...
 98-230 3.47e-11

Protein of unknown function (DUF3108); This is a bacterial family of putative lipoproteins. The structure for Swiss:Q64U78, PDB:3fzx, the first structural template for this large family including several homologs in the human gut microbiome and in metagenomic datasets, folds into a beta barrel that topologically looks like a small-scale porin (such as FepA). Swiss:Q64U78 is a putative exported protein, and this fold is of the YmcC-like type, with a predicted signal peptide SpI cleavage site AGAMA|QNQDC, and a Phobius server prediction of non-cytoplasmic localization for amino acids 21-236. The possibility of it being a membrane protein can be ruled out by the hydrophilic nature of the solvent exposed surface outside the barrels. Analysis of sequence conservation suggests that an area near Glu172/Trp206 is potentially interesting. These two residues are also conserved in Dali hit PDB:2in5, a hypothetical lipoprotein classified as a new YmcC-like fold in SCOP (SCOP:159271, with a 12-stranded meander beta-sheet folded into a deformed beta-barrel) despite large structural differences between the two structures, suggesting similarity in function.


The actual alignment was detected with superfamily member pfam11306:

Pssm-ID: 431801  Cd Length: 225  Bit Score: 61.24  E-value: 3.47e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2273501554  98 DKVEPIQYSMIRTGTGPDKKYEINF--DRQTQTVTSNTSDYPLKCQWHDNFQDGISYQVQVREGLKKGKTSFSFPLVDKK 175
Cdd:pfam11306  72 GDLVPLRFRKSAREGGRYRVDEVTFddDRGAVKVTDVEPDKTRTPPLPAGVQDPLSAFYYLRSLDLKVGDSITLPVFDGR 151

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2273501554 176 gNCRDYDFEVVETEMISLPIGNVEAIKVKRL-----YDNDKRQALAWFAPEMDYMLVRMW 230
Cdd:pfam11306 152 -KRYDLRLRYLGRETVKTPLGKYRTLVVVPVvryggVFKEKRDIEVWLADDENRIPVRIE 210
 
Name Accession Description Interval E-value
DUF3108 pfam11306
Protein of unknown function (DUF3108); This is a bacterial family of putative lipoproteins. ...
 98-230 3.47e-11

Protein of unknown function (DUF3108); This is a bacterial family of putative lipoproteins. The structure for Swiss:Q64U78, PDB:3fzx, the first structural template for this large family including several homologs in the human gut microbiome and in metagenomic datasets, folds into a beta barrel that topologically looks like a small-scale porin (such as FepA). Swiss:Q64U78 is a putative exported protein, and this fold is of the YmcC-like type, with a predicted signal peptide SpI cleavage site AGAMA|QNQDC, and a Phobius server prediction of non-cytoplasmic localization for amino acids 21-236. The possibility of it being a membrane protein can be ruled out by the hydrophilic nature of the solvent exposed surface outside the barrels. Analysis of sequence conservation suggests that an area near Glu172/Trp206 is potentially interesting. These two residues are also conserved in Dali hit PDB:2in5, a hypothetical lipoprotein classified as a new YmcC-like fold in SCOP (SCOP:159271, with a 12-stranded meander beta-sheet folded into a deformed beta-barrel) despite large structural differences between the two structures, suggesting similarity in function.


Pssm-ID: 431801  Cd Length: 225  Bit Score: 61.24  E-value: 3.47e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2273501554  98 DKVEPIQYSMIRTGTGPDKKYEINF--DRQTQTVTSNTSDYPLKCQWHDNFQDGISYQVQVREGLKKGKTSFSFPLVDKK 175
Cdd:pfam11306  72 GDLVPLRFRKSAREGGRYRVDEVTFddDRGAVKVTDVEPDKTRTPPLPAGVQDPLSAFYYLRSLDLKVGDSITLPVFDGR 151

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2273501554 176 gNCRDYDFEVVETEMISLPIGNVEAIKVKRL-----YDNDKRQALAWFAPEMDYMLVRMW 230
Cdd:pfam11306 152 -KRYDLRLRYLGRETVKTPLGKYRTLVVVPVvryggVFKEKRDIEVWLADDENRIPVRIE 210
 
Name Accession Description Interval E-value
DUF3108 pfam11306
Protein of unknown function (DUF3108); This is a bacterial family of putative lipoproteins. ...
 98-230 3.47e-11

Protein of unknown function (DUF3108); This is a bacterial family of putative lipoproteins. The structure for Swiss:Q64U78, PDB:3fzx, the first structural template for this large family including several homologs in the human gut microbiome and in metagenomic datasets, folds into a beta barrel that topologically looks like a small-scale porin (such as FepA). Swiss:Q64U78 is a putative exported protein, and this fold is of the YmcC-like type, with a predicted signal peptide SpI cleavage site AGAMA|QNQDC, and a Phobius server prediction of non-cytoplasmic localization for amino acids 21-236. The possibility of it being a membrane protein can be ruled out by the hydrophilic nature of the solvent exposed surface outside the barrels. Analysis of sequence conservation suggests that an area near Glu172/Trp206 is potentially interesting. These two residues are also conserved in Dali hit PDB:2in5, a hypothetical lipoprotein classified as a new YmcC-like fold in SCOP (SCOP:159271, with a 12-stranded meander beta-sheet folded into a deformed beta-barrel) despite large structural differences between the two structures, suggesting similarity in function.


Pssm-ID: 431801  Cd Length: 225  Bit Score: 61.24  E-value: 3.47e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2273501554  98 DKVEPIQYSMIRTGTGPDKKYEINF--DRQTQTVTSNTSDYPLKCQWHDNFQDGISYQVQVREGLKKGKTSFSFPLVDKK 175
Cdd:pfam11306  72 GDLVPLRFRKSAREGGRYRVDEVTFddDRGAVKVTDVEPDKTRTPPLPAGVQDPLSAFYYLRSLDLKVGDSITLPVFDGR 151

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2273501554 176 gNCRDYDFEVVETEMISLPIGNVEAIKVKRL-----YDNDKRQALAWFAPEMDYMLVRMW 230
Cdd:pfam11306 152 -KRYDLRLRYLGRETVKTPLGKYRTLVVVPVvryggVFKEKRDIEVWLADDENRIPVRIE 210
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH