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Conserved domains on  [gi|1070093054|ref|WP_069707638|]
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MULTISPECIES: YdeI family protein [Novosphingobium]

Protein Classification

YdeI/OmpD-associated family protein( domain architecture ID 11468231)

YdeI/OmpD-associated family protein may play a role in antimicrobial peptide (bacteriocin) resistance; similar to Bacillus subtilis protein YdeI

PubMed:  19767429

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YdeI COG4430
Uncharacterized conserved protein YdeI, YjbR/CyaY-like superfamily, DUF1801 family [Function ...
 11-186 1.61e-28

Uncharacterized conserved protein YdeI, YjbR/CyaY-like superfamily, DUF1801 family [Function unknown];


:

Pssm-ID: 443542 [Multi-domain]  Cd Length: 189  Bit Score: 105.03  E-value: 1.61e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070093054  11 IAKAADFARPILEHLRELAHrALHDAEEaIKWgmphfLVNAKNVAGM------AAFKAHCTFV-IHGDGRQGDAMGQLGR 83
Cdd:COG4430     2 NPEVPVLYFESAAEWRAWLE-ANHDTET-GKW-----LVFYKKGSGKpsytynEAVKEALCFGwIDGVLKKLDDESYLQR 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070093054  84 ITaiadlPDEA---------ELVRKLQAArGRVQAKGTAVNQARK--------PKPEIAMPDDFAAALDGVPAARTHYDA 146
Cdd:COG4430    75 FT-----PRRPksqwsrvnkERVERLIAE-GRMTPAGLEAIEAAKadgrwaayEVEELEVPEDLQAALDANPAAKAFFEA 148

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1070093054 147 FSPAARRDYLEWITEAKTAATREKRMAQAVEWIAEGKKRN 186
Cdd:COG4430   149 LTPSYRRAYLLWISSAKRPETRAKRIEKIIEMLARGKKLN 188
 
Name Accession Description Interval E-value
YdeI COG4430
Uncharacterized conserved protein YdeI, YjbR/CyaY-like superfamily, DUF1801 family [Function ...
 11-186 1.61e-28

Uncharacterized conserved protein YdeI, YjbR/CyaY-like superfamily, DUF1801 family [Function unknown];


Pssm-ID: 443542 [Multi-domain]  Cd Length: 189  Bit Score: 105.03  E-value: 1.61e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070093054  11 IAKAADFARPILEHLRELAHrALHDAEEaIKWgmphfLVNAKNVAGM------AAFKAHCTFV-IHGDGRQGDAMGQLGR 83
Cdd:COG4430     2 NPEVPVLYFESAAEWRAWLE-ANHDTET-GKW-----LVFYKKGSGKpsytynEAVKEALCFGwIDGVLKKLDDESYLQR 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070093054  84 ITaiadlPDEA---------ELVRKLQAArGRVQAKGTAVNQARK--------PKPEIAMPDDFAAALDGVPAARTHYDA 146
Cdd:COG4430    75 FT-----PRRPksqwsrvnkERVERLIAE-GRMTPAGLEAIEAAKadgrwaayEVEELEVPEDLQAALDANPAAKAFFEA 148

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1070093054 147 FSPAARRDYLEWITEAKTAATREKRMAQAVEWIAEGKKRN 186
Cdd:COG4430   149 LTPSYRRAYLLWISSAKRPETRAKRIEKIIEMLARGKKLN 188
OmdA pfam13376
Bacteriocin-protection, YdeI or OmpD-Associated; This is a family of archaeal and bacterial ...
 123-182 1.23e-20

Bacteriocin-protection, YdeI or OmpD-Associated; This is a family of archaeal and bacterial proteins predicted to be periplasmic. YdeI is important for resistance to polymyxin B in broth and for bacterial survival in mice upon oral, but not intraperitoneal inoculation, suggesting a role for YdeI in the gastrointestinal tract of mice. Production of the ydeI gene is regulated by the Rcs (regulator of capsule synthesis) phospho-relay system pathway independently of RcsA, and additionally transcription of the protein is regulated by the stationary-phase sigma factor, RpoS (sigma-S). YdeI confers protection against cationic AMPs (Antimicrobial peptides) or bacteriocins in conjunction with the general porin Omp, thus justifying its name of OmdA, for OmpD-Associated protein.


Pssm-ID: 433158  Cd Length: 60  Bit Score: 80.58  E-value: 1.23e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070093054 123 EIAMPDDFAAALDGVPAARTHYDAFSPAARRDYLEWITEAKTAATREKRMAQAVEWIAEG 182
Cdd:pfam13376   1 EAEVPEDLAAALAANPAAKAFFEALTPSYRREYLLWISSAKRPETRAKRIAKFVEMLAEG 60
 
Name Accession Description Interval E-value
YdeI COG4430
Uncharacterized conserved protein YdeI, YjbR/CyaY-like superfamily, DUF1801 family [Function ...
 11-186 1.61e-28

Uncharacterized conserved protein YdeI, YjbR/CyaY-like superfamily, DUF1801 family [Function unknown];


Pssm-ID: 443542 [Multi-domain]  Cd Length: 189  Bit Score: 105.03  E-value: 1.61e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070093054  11 IAKAADFARPILEHLRELAHrALHDAEEaIKWgmphfLVNAKNVAGM------AAFKAHCTFV-IHGDGRQGDAMGQLGR 83
Cdd:COG4430     2 NPEVPVLYFESAAEWRAWLE-ANHDTET-GKW-----LVFYKKGSGKpsytynEAVKEALCFGwIDGVLKKLDDESYLQR 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070093054  84 ITaiadlPDEA---------ELVRKLQAArGRVQAKGTAVNQARK--------PKPEIAMPDDFAAALDGVPAARTHYDA 146
Cdd:COG4430    75 FT-----PRRPksqwsrvnkERVERLIAE-GRMTPAGLEAIEAAKadgrwaayEVEELEVPEDLQAALDANPAAKAFFEA 148

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1070093054 147 FSPAARRDYLEWITEAKTAATREKRMAQAVEWIAEGKKRN 186
Cdd:COG4430   149 LTPSYRRAYLLWISSAKRPETRAKRIEKIIEMLARGKKLN 188
OmdA pfam13376
Bacteriocin-protection, YdeI or OmpD-Associated; This is a family of archaeal and bacterial ...
 123-182 1.23e-20

Bacteriocin-protection, YdeI or OmpD-Associated; This is a family of archaeal and bacterial proteins predicted to be periplasmic. YdeI is important for resistance to polymyxin B in broth and for bacterial survival in mice upon oral, but not intraperitoneal inoculation, suggesting a role for YdeI in the gastrointestinal tract of mice. Production of the ydeI gene is regulated by the Rcs (regulator of capsule synthesis) phospho-relay system pathway independently of RcsA, and additionally transcription of the protein is regulated by the stationary-phase sigma factor, RpoS (sigma-S). YdeI confers protection against cationic AMPs (Antimicrobial peptides) or bacteriocins in conjunction with the general porin Omp, thus justifying its name of OmdA, for OmpD-Associated protein.


Pssm-ID: 433158  Cd Length: 60  Bit Score: 80.58  E-value: 1.23e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070093054 123 EIAMPDDFAAALDGVPAARTHYDAFSPAARRDYLEWITEAKTAATREKRMAQAVEWIAEG 182
Cdd:pfam13376   1 EAEVPEDLAAALAANPAAKAFFEALTPSYRREYLLWISSAKRPETRAKRIAKFVEMLAEG 60
DUF1801 pfam08818
Domain of unknown function (DU1801); This domain is found in the Intracellular iron chaperone ...
 19-98 2.47e-17

Domain of unknown function (DU1801); This domain is found in the Intracellular iron chaperone frataxin YdhG and the uncharacterized protein YdeI from Bacillus subtilis.


Pssm-ID: 430236  Cd Length: 94  Bit Score: 73.06  E-value: 2.47e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070093054  19 RPILEHLRELAHRALHDAEEAIKWGMPHFLVNAKNVAGMAAFKAHCTFVIHGDGRQGDAMGQLG-----------RITAI 87
Cdd:pfam08818   2 REILERLRALILEALPELEETIKWGMPVYTYNGGNIGGFSAFKNHVSLYFFKGALLEDPKGLLEklkygkgkrciRFKSL 81

                          90
                  ....*....|...
gi 1070093054  88 ADLPDEA--ELVR 98
Cdd:pfam08818  82 DDIDEELlkALIR 94
Fra COG5646
Iron-binding protein Fra/YdhG, frataxin family (Fe-S cluster biosynthesis) [Posttranslational ...
 7-66 1.63e-16

Iron-binding protein Fra/YdhG, frataxin family (Fe-S cluster biosynthesis) [Posttranslational modification, protein turnover, chaperones, Inorganic ion transport and metabolism];


Pssm-ID: 444369  Cd Length: 112  Bit Score: 71.77  E-value: 1.63e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070093054   7 VDEYIAKAADFARPILEHLRELAHRALHDAEEAIKWGMPHFLVNAKNVAGMAAFKAHCTF 66
Cdd:COG5646     4 VDEYIASLPEEDRERLERLRALIREAAPEAEEKISYGMPAFKLDGKFLVGFAAAKKHISL 63
COG5649 COG5649
Uncharacterized conserved protein, DUF1801 domain [Function unknown];
4-63 3.51e-12

Uncharacterized conserved protein, DUF1801 domain [Function unknown];


Pssm-ID: 444370  Cd Length: 120  Bit Score: 60.25  E-value: 3.51e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070093054   4 DPRVDEYIAKAADFARPILEHLRELAHRALHDAEEAIKWGMPHFLVNAkNVAGMAAFKAH 63
Cdd:COG5649     8 DAPVDAYIAALPGWRGEIARRLRALILEAVPDVEEEVKWGSPVYSVDG-WFCGGEAYKKH 66
DUF5655 pfam18899
Domain of unknown function (DUF5655); This family of proteins is found in bacteria, archaea, ...
 7-93 5.27e-06

Domain of unknown function (DUF5655); This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 122 and 304 amino acids in length.


Pssm-ID: 465903  Cd Length: 110  Bit Score: 43.51  E-value: 5.27e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070093054   7 VDEYIAKAADFARPILEHLRELAHRALHDAEEAIKWGMPHFLVNaKNVAGMAAFKAHC-----------TFVIHGDGRQG 75
Cdd:pfam18899   1 VDDQFSGKPAKLKPLYDALRERILELGPDVEEEPKKSYIAFKRK-KTFAAVPAKKGRLrlglalgelpsDPKISEDVQNS 79

                          90
                  ....*....|....*....
gi 1070093054  76 DAMGQ-LGRITAIADLPDE 93
Cdd:pfam18899  80 GTRVThHVRITSLSDIDEE 98
 
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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