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Conserved domains on  [gi|824464058|gb|AKI86336|]
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protein ygiW precursor [Escherichia phage PA11]

Protein Classification

NirD/YgiW/YdeI family stress tolerance protein( domain architecture ID 16671237)

NirD/YgiW/YdeI family stress tolerance protein may function to bind proteins, small molecules, or other typical OB-fold ligands

PubMed:  15178340|12504685|12769718
SCOP:  2000100

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YdeI super family cl42375
Predicted periplasmic protein YdeI with OB-fold, BOF family [Function unknown];
3-112 3.24e-52

Predicted periplasmic protein YdeI with OB-fold, BOF family [Function unknown];


The actual alignment was detected with superfamily member NF033674:

Pssm-ID: 478165  Cd Length: 110  Bit Score: 159.56  E-value: 3.24e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 824464058   3 KVLIAALISGVSFGAFAQQGGFQGPEAERSTVAQAKELKDDAWVILEGSIVKKVGDERYEFRDNSGTIVTDIDDSIWAGQ 82
Cdd:NF033674   1 KLLLAALLALLSAPAFAADGGFTGPAANVTTVAQALKAKDDTPVTLTGNIVKQLGDDKYEFRDATGTITVEIDDDLWRGQ 80

                         90       100       110
                 ....*....|....*....|....*....|
gi 824464058  83 NVSPKDKVRIEGEIDKDLSSVEVDVKALKL 112
Cdd:NF033674  81 TVTPKDKVRITGEVDKDWKPTEIDVDRIEK 110
 
Name Accession Description Interval E-value
stress_OB_fold NF033674
NirD/YgiW/YdeI family stress tolerance protein; Members of this family possess an N-terminal ...
 3-112 3.24e-52

NirD/YgiW/YdeI family stress tolerance protein; Members of this family possess an N-terminal signal peptide, and are associated with tolerance to various toxic stresses. These include antimicrobial peptides (YdeI), hydrogen peroxide (YgiW and YdeI), and nickel (NcrY and NirD).


Pssm-ID: 468134  Cd Length: 110  Bit Score: 159.56  E-value: 3.24e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 824464058   3 KVLIAALISGVSFGAFAQQGGFQGPEAERSTVAQAKELKDDAWVILEGSIVKKVGDERYEFRDNSGTIVTDIDDSIWAGQ 82
Cdd:NF033674   1 KLLLAALLALLSAPAFAADGGFTGPAANVTTVAQALKAKDDTPVTLTGNIVKQLGDDKYEFRDATGTITVEIDDDLWRGQ 80

                         90       100       110
                 ....*....|....*....|....*....|
gi 824464058  83 NVSPKDKVRIEGEIDKDLSSVEVDVKALKL 112
Cdd:NF033674  81 TVTPKDKVRITGEVDKDWKPTEIDVDRIEK 110
YdeI COG3111
Predicted periplasmic protein YdeI with OB-fold, BOF family [Function unknown];
1-112 5.00e-50

Predicted periplasmic protein YdeI with OB-fold, BOF family [Function unknown];


Pssm-ID: 442345  Cd Length: 125  Bit Score: 154.68  E-value: 5.00e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 824464058   1 MKK-VLIAALISGVSFGAFAQQGGFQGP------------EAERSTVAQAKELKDDAWVILEGSIVKKVGDERYEFRDNS 67
Cdd:COG3111    1 MKKtLALAALLALASAPAFAADGGFKGPpsaqdggftgpsDAAVTTVAQALAMRDDAWVTLEGNIVKQLGDDKYLFRDAT 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 824464058  68 GTIVTDIDDSIWAGQNVSPKDKVRIEGEIDKDLSSVEVDVKALKL 112
Cdd:COG3111   81 GTIKVEIDDKVWNGQTVTPKDKVRISGEVDKDWNKVEIDVKRIQK 125
BOF pfam04076
Bacterial OB fold (BOF) protein; Proteins in this family form an OB-fold. Analysis of the ...
 19-108 3.65e-33

Bacterial OB fold (BOF) protein; Proteins in this family form an OB-fold. Analysis of the predicted binding site of BOF family proteins implies that they lack nucleic acid-binding properties. They contain an predicted N-terminal signal peptide which indicates that they localize in the periplasm where they may function to bind proteins, small molecules, or other typical OB-fold ligands. As hypothesized for the distantly related OB-fold containing bacterial enterotoxins, the loss of nucleotide-binding function and the rapid evolution of the BOF ligand-binding site may be associated with the presence of BOF proteins in mobile genetic elements and their potential role in bacterial pathogenicity.


Pssm-ID: 281996  Cd Length: 103  Bit Score: 111.10  E-value: 3.65e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 824464058   19 AQQGGFQGPEAERSTVAQAKELKDDAWVILEGSIVKKVGDERYEFRDNSGTIVTDIDDSIWAGQNVSPKDKVRIEGEIDK 98
Cdd:pfam04076  10 AIEGGFQGANAKKTTVKAALSAADDTPVSLRGNIVSQIDGDEYVFRDATGEIKVEIDDRVWNGREVQPKDMVKIQGKVDK 89

                          90
                  ....*....|
gi 824464058   99 DLSSVEVDVK 108
Cdd:pfam04076  90 DWNKAEIDVK 99
TIGR00156 TIGR00156
TIGR00156 family protein; As of the last revision, this family consists only of two proteins ...
 1-111 2.79e-31

TIGR00156 family protein; As of the last revision, this family consists only of two proteins from Escherichia coli and one from the related species Haemophilus influenzae. [Hypothetical proteins, Conserved]


Pssm-ID: 129260  Cd Length: 126  Bit Score: 107.31  E-value: 2.79e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 824464058    1 MKK---VLIAALISGVSFGAF-----------AQQGGFQGPEAERSTVAQAKELKDDAWVILEGSIVKKVGDERYEFRDN 66
Cdd:TIGR00156   1 MKFqaiVLASALVMPYALADDqgglsapppphAIEGGFQGTDAKKMTVDFAKSMHDGASVTLRGNIISHIGDDRYVFRDK 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 824464058   67 SGTIVTDIDDSIWAGQNVSPKDKVRIEGEIDKDLSSVEVDVKALK 111
Cdd:TIGR00156  81 SGEINVVIPAAVWNGREVQPKDMVNISGSLDKKSAPAEVDVTHIQ 125
PRK10053 PRK10053
YdeI family stress tolerance OB fold protein;
1-110 2.29e-17

YdeI family stress tolerance OB fold protein;


Pssm-ID: 182212  Cd Length: 130  Bit Score: 71.72  E-value: 2.29e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 824464058   1 MKKVLIAALISGVSFGAFAQ-QGGFQGPEA-----------------ERSTVAQAKELKDDAWVILEGSIVKKVGDERYE 62
Cdd:PRK10053   1 MKLQAIALASFLVMPYALADdQGGLKQDAApppphaiedgyrgtddaRKMTVEQAKTMHDGATVSLRGNLIDHKGDDRYV 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 824464058  63 FRDNSGTIVTDIDDSIWAGQNVSPKDKVRIEGEIDKDLSSVEVDVKAL 110
Cdd:PRK10053  81 FRDKSGEINVIIPAAVFDGREVQPDQMININGSLDKKSAPPVVRVTHL 128
 
Name Accession Description Interval E-value
stress_OB_fold NF033674
NirD/YgiW/YdeI family stress tolerance protein; Members of this family possess an N-terminal ...
 3-112 3.24e-52

NirD/YgiW/YdeI family stress tolerance protein; Members of this family possess an N-terminal signal peptide, and are associated with tolerance to various toxic stresses. These include antimicrobial peptides (YdeI), hydrogen peroxide (YgiW and YdeI), and nickel (NcrY and NirD).


Pssm-ID: 468134  Cd Length: 110  Bit Score: 159.56  E-value: 3.24e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 824464058   3 KVLIAALISGVSFGAFAQQGGFQGPEAERSTVAQAKELKDDAWVILEGSIVKKVGDERYEFRDNSGTIVTDIDDSIWAGQ 82
Cdd:NF033674   1 KLLLAALLALLSAPAFAADGGFTGPAANVTTVAQALKAKDDTPVTLTGNIVKQLGDDKYEFRDATGTITVEIDDDLWRGQ 80

                         90       100       110
                 ....*....|....*....|....*....|
gi 824464058  83 NVSPKDKVRIEGEIDKDLSSVEVDVKALKL 112
Cdd:NF033674  81 TVTPKDKVRITGEVDKDWKPTEIDVDRIEK 110
YdeI COG3111
Predicted periplasmic protein YdeI with OB-fold, BOF family [Function unknown];
1-112 5.00e-50

Predicted periplasmic protein YdeI with OB-fold, BOF family [Function unknown];


Pssm-ID: 442345  Cd Length: 125  Bit Score: 154.68  E-value: 5.00e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 824464058   1 MKK-VLIAALISGVSFGAFAQQGGFQGP------------EAERSTVAQAKELKDDAWVILEGSIVKKVGDERYEFRDNS 67
Cdd:COG3111    1 MKKtLALAALLALASAPAFAADGGFKGPpsaqdggftgpsDAAVTTVAQALAMRDDAWVTLEGNIVKQLGDDKYLFRDAT 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 824464058  68 GTIVTDIDDSIWAGQNVSPKDKVRIEGEIDKDLSSVEVDVKALKL 112
Cdd:COG3111   81 GTIKVEIDDKVWNGQTVTPKDKVRISGEVDKDWNKVEIDVKRIQK 125
BOF pfam04076
Bacterial OB fold (BOF) protein; Proteins in this family form an OB-fold. Analysis of the ...
 19-108 3.65e-33

Bacterial OB fold (BOF) protein; Proteins in this family form an OB-fold. Analysis of the predicted binding site of BOF family proteins implies that they lack nucleic acid-binding properties. They contain an predicted N-terminal signal peptide which indicates that they localize in the periplasm where they may function to bind proteins, small molecules, or other typical OB-fold ligands. As hypothesized for the distantly related OB-fold containing bacterial enterotoxins, the loss of nucleotide-binding function and the rapid evolution of the BOF ligand-binding site may be associated with the presence of BOF proteins in mobile genetic elements and their potential role in bacterial pathogenicity.


Pssm-ID: 281996  Cd Length: 103  Bit Score: 111.10  E-value: 3.65e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 824464058   19 AQQGGFQGPEAERSTVAQAKELKDDAWVILEGSIVKKVGDERYEFRDNSGTIVTDIDDSIWAGQNVSPKDKVRIEGEIDK 98
Cdd:pfam04076  10 AIEGGFQGANAKKTTVKAALSAADDTPVSLRGNIVSQIDGDEYVFRDATGEIKVEIDDRVWNGREVQPKDMVKIQGKVDK 89

                          90
                  ....*....|
gi 824464058   99 DLSSVEVDVK 108
Cdd:pfam04076  90 DWNKAEIDVK 99
TIGR00156 TIGR00156
TIGR00156 family protein; As of the last revision, this family consists only of two proteins ...
 1-111 2.79e-31

TIGR00156 family protein; As of the last revision, this family consists only of two proteins from Escherichia coli and one from the related species Haemophilus influenzae. [Hypothetical proteins, Conserved]


Pssm-ID: 129260  Cd Length: 126  Bit Score: 107.31  E-value: 2.79e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 824464058    1 MKK---VLIAALISGVSFGAF-----------AQQGGFQGPEAERSTVAQAKELKDDAWVILEGSIVKKVGDERYEFRDN 66
Cdd:TIGR00156   1 MKFqaiVLASALVMPYALADDqgglsapppphAIEGGFQGTDAKKMTVDFAKSMHDGASVTLRGNIISHIGDDRYVFRDK 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 824464058   67 SGTIVTDIDDSIWAGQNVSPKDKVRIEGEIDKDLSSVEVDVKALK 111
Cdd:TIGR00156  81 SGEINVVIPAAVWNGREVQPKDMVNISGSLDKKSAPAEVDVTHIQ 125
PRK10053 PRK10053
YdeI family stress tolerance OB fold protein;
1-110 2.29e-17

YdeI family stress tolerance OB fold protein;


Pssm-ID: 182212  Cd Length: 130  Bit Score: 71.72  E-value: 2.29e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 824464058   1 MKKVLIAALISGVSFGAFAQ-QGGFQGPEA-----------------ERSTVAQAKELKDDAWVILEGSIVKKVGDERYE 62
Cdd:PRK10053   1 MKLQAIALASFLVMPYALADdQGGLKQDAApppphaiedgyrgtddaRKMTVEQAKTMHDGATVSLRGNLIDHKGDDRYV 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 824464058  63 FRDNSGTIVTDIDDSIWAGQNVSPKDKVRIEGEIDKDLSSVEVDVKAL 110
Cdd:PRK10053  81 FRDKSGEINVIIPAAVFDGREVQPDQMININGSLDKKSAPPVVRVTHL 128
 
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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