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Conserved domains on  [gi|523414721|ref|WP_020750043|]
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MULTISPECIES: peptide deformylase [Ralstonia solanacearum species complex]

Protein Classification

peptide deformylase( domain architecture ID 10791807)

peptide deformylase catalyzes the removal of the N-terminal formyl group in a growing polypeptide chain following translation initiation during protein synthesis

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
def PRK00150
peptide deformylase; Reviewed
1-164 3.46e-91

peptide deformylase; Reviewed


:

Pssm-ID: 234668  Cd Length: 165  Bit Score: 262.37  E-value: 3.46e-91
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 523414721   1 MALLNILQYPDPRLHKVAKPVAVVDDRIRKLVADMAETMYDAPGIGLAATQVDVHERVITIDISESRDELRVFINPEIVW 80
Cdd:PRK00150   1 MAILPILRYGDPVLRKVAKPVEEVDDELRKLIDDMFETMYAAPGVGLAAPQVGVSKRIIVIDVEDKEGEPLVLINPEIIS 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 523414721  81 AS-DARKVWDEGCLSVPDIYDKVERPDRVRVRALNEKGESFELETDGLLAVCIQHEMDHLMGKVFVEYLSPLKQNRIKIK 159
Cdd:PRK00150  81 ESsEEYLTYEEGCLSVPGVYGEVPRPERVTVKALDRDGKPFELEADGLLARCIQHEIDHLNGVLFIDRLSPLKRFRIKKK 160

                 ....*
gi 523414721 160 LKKHQ 164
Cdd:PRK00150 161 LKKIE 165
 
Name Accession Description Interval E-value
def PRK00150
peptide deformylase; Reviewed
1-164 3.46e-91

peptide deformylase; Reviewed


Pssm-ID: 234668  Cd Length: 165  Bit Score: 262.37  E-value: 3.46e-91
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 523414721   1 MALLNILQYPDPRLHKVAKPVAVVDDRIRKLVADMAETMYDAPGIGLAATQVDVHERVITIDISESRDELRVFINPEIVW 80
Cdd:PRK00150   1 MAILPILRYGDPVLRKVAKPVEEVDDELRKLIDDMFETMYAAPGVGLAAPQVGVSKRIIVIDVEDKEGEPLVLINPEIIS 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 523414721  81 AS-DARKVWDEGCLSVPDIYDKVERPDRVRVRALNEKGESFELETDGLLAVCIQHEMDHLMGKVFVEYLSPLKQNRIKIK 159
Cdd:PRK00150  81 ESsEEYLTYEEGCLSVPGVYGEVPRPERVTVKALDRDGKPFELEADGLLARCIQHEIDHLNGVLFIDRLSPLKRFRIKKK 160

                 ....*
gi 523414721 160 LKKHQ 164
Cdd:PRK00150 161 LKKIE 165
Def COG0242
Peptide deformylase [Translation, ribosomal structure and biogenesis];
1-161 2.17e-90

Peptide deformylase [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440012  Cd Length: 163  Bit Score: 260.41  E-value: 2.17e-90
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 523414721   1 MALLNILQYPDPRLHKVAKPVAVVDDRIRKLVADMAETMYDAPGIGLAATQVDVHERVITIDISES--RDELRVFINPEI 78
Cdd:COG0242    1 MAILPILQYGDPVLRKVAKPVTEFDDELRALIDDMFETMYAAPGVGLAAPQVGVSLRLFVIDVSDEdgKGEPLVLINPEI 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 523414721  79 VWASDARKVWDEGCLSVPDIYDKVERPDRVRVRALNEKGESFELETDGLLAVCIQHEMDHLMGKVFVEYLSPLKQNRIKI 158
Cdd:COG0242   81 VEASGETVEGEEGCLSVPGIRGEVPRPERVRVRYLDLDGEPVELEAEGLLARCIQHEIDHLDGILFIDRLSPLKRERILK 160

                 ...
gi 523414721 159 KLK 161
Cdd:COG0242  161 KLE 163
Pep_deformylase cd00487
Polypeptide or peptide deformylase; a family of metalloenzymes that catalyzes the removal of ...
6-144 5.63e-73

Polypeptide or peptide deformylase; a family of metalloenzymes that catalyzes the removal of the N-terminal formyl group in a growing polypeptide chain following translation initiation during protein synthesis in prokaryotes. These enzymes utilize Fe(II) as the catalytic metal ion, which can be replaced with a nickel or cobalt ion with no loss of activity. There are two types of peptide deformylases, types I and II, which differ in structure only in the outer surface of the domain. Because these enzymes are essential only in prokaryotes (although eukaryotic gene sequences have been found), they are a target for a new class of antibacterial agents.


Pssm-ID: 238271  Cd Length: 141  Bit Score: 215.43  E-value: 5.63e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 523414721   6 ILQYPDPRLHKVAKPVAVVDDRIRKLVADMAETMYDAPGIGLAATQVDVHERVITIDISESR--DELRVFINPEIVWASD 83
Cdd:cd00487    1 IVQYPDPVLRKKAKPVEEFDDELKQLIDDMFETMYAAPGVGLAAPQIGVSKRIFVIDVPDEEnkEPPLVLINPEIIESSG 80
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 523414721  84 ARKVWDEGCLSVPDIYDKVERPDRVRVRALNEKGESFELETDGLLAVCIQHEMDHLMGKVF 144
Cdd:cd00487   81 ETEYGEEGCLSVPGYRGEVERPKKVTVRYLDEDGNPIELEAEGFLARCIQHEIDHLNGILF 141
Pep_deformylase pfam01327
Polypeptide deformylase;
4-153 2.94e-66

Polypeptide deformylase;


Pssm-ID: 426202  Cd Length: 153  Bit Score: 198.96  E-value: 2.94e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 523414721    4 LNILQYPDPRLHKVAKPVAVVDDR-IRKLVADMAETMYDAPGIGLAATQVDVHERVITIDISESRDE--LRVFINPEIVW 80
Cdd:pfam01327   1 LPIVTYPDPVLRKKAEPVEEFDDKeLKKLIDDMLETMYAADGVGLAAPQVGVSKRIFVIDLPDGEEEpdPLVLINPEIIS 80
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 523414721   81 ASDARKVWDEGCLSVPDIYDKVERPDRVRVRALNEKGESFELETDGLLAVCIQHEMDHLMGKVFVEYLSPLKQ 153
Cdd:pfam01327  81 KSEETVTDEEGCLSVPGIRGEVERPKRITVKYLDLNGKEIELEAEGFLARVLQHEIDHLNGILFIDRLSPLKR 153
pept_deformyl TIGR00079
peptide deformylase; Peptide deformylase (EC 3.5.1.88), also called polypeptide deformylase, ...
3-162 5.59e-55

peptide deformylase; Peptide deformylase (EC 3.5.1.88), also called polypeptide deformylase, is a metalloenzyme that uses water to release formate from the N-terminal formyl-L-methionine of bacterial and chloroplast peptides. This enzyme should not be confused with formylmethionine deformylase (EC 3.5.1.31) which is active on free N-formyl methionine and has been reported from rat intestine. [Protein fate, Protein modification and repair]


Pssm-ID: 272895  Cd Length: 161  Bit Score: 170.64  E-value: 5.59e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 523414721    3 LLNILQYPDPRLHKVAKPVAVVDDRIRKLVADMAETMYDAPGIGLAATQVDVHERVITIDISESRDELRVF-INPEIVWA 81
Cdd:TIGR00079   1 MLEVFHYPDDLLRKTAKPVEIVDKKIDQQLDDMIETMIAEKGIGLAAPQVGILKRMIVIELEDADKEPLLFlINPKIIES 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 523414721   82 SDARKVWDEGCLSVPDIYDKVERPDRVRVRALNEKGESFELETDGLLAVCIQHEMDHLMGKVFVEYLSPLKQNRIKIKLK 161
Cdd:TIGR00079  81 SEESSYLEEGCLSVPVYYGLVPRKEKVKIRGDDRFGKPIILEADGLLAICIQHEIDHLNGVFFVDYISPLNPKKLKKEMK 160

                  .
gi 523414721  162 K 162
Cdd:TIGR00079 161 E 161
 
Name Accession Description Interval E-value
def PRK00150
peptide deformylase; Reviewed
1-164 3.46e-91

peptide deformylase; Reviewed


Pssm-ID: 234668  Cd Length: 165  Bit Score: 262.37  E-value: 3.46e-91
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 523414721   1 MALLNILQYPDPRLHKVAKPVAVVDDRIRKLVADMAETMYDAPGIGLAATQVDVHERVITIDISESRDELRVFINPEIVW 80
Cdd:PRK00150   1 MAILPILRYGDPVLRKVAKPVEEVDDELRKLIDDMFETMYAAPGVGLAAPQVGVSKRIIVIDVEDKEGEPLVLINPEIIS 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 523414721  81 AS-DARKVWDEGCLSVPDIYDKVERPDRVRVRALNEKGESFELETDGLLAVCIQHEMDHLMGKVFVEYLSPLKQNRIKIK 159
Cdd:PRK00150  81 ESsEEYLTYEEGCLSVPGVYGEVPRPERVTVKALDRDGKPFELEADGLLARCIQHEIDHLNGVLFIDRLSPLKRFRIKKK 160

                 ....*
gi 523414721 160 LKKHQ 164
Cdd:PRK00150 161 LKKIE 165
Def COG0242
Peptide deformylase [Translation, ribosomal structure and biogenesis];
1-161 2.17e-90

Peptide deformylase [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440012  Cd Length: 163  Bit Score: 260.41  E-value: 2.17e-90
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 523414721   1 MALLNILQYPDPRLHKVAKPVAVVDDRIRKLVADMAETMYDAPGIGLAATQVDVHERVITIDISES--RDELRVFINPEI 78
Cdd:COG0242    1 MAILPILQYGDPVLRKVAKPVTEFDDELRALIDDMFETMYAAPGVGLAAPQVGVSLRLFVIDVSDEdgKGEPLVLINPEI 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 523414721  79 VWASDARKVWDEGCLSVPDIYDKVERPDRVRVRALNEKGESFELETDGLLAVCIQHEMDHLMGKVFVEYLSPLKQNRIKI 158
Cdd:COG0242   81 VEASGETVEGEEGCLSVPGIRGEVPRPERVRVRYLDLDGEPVELEAEGLLARCIQHEIDHLDGILFIDRLSPLKRERILK 160

                 ...
gi 523414721 159 KLK 161
Cdd:COG0242  161 KLE 163
PRK12846 PRK12846
peptide deformylase; Reviewed
1-164 1.32e-74

peptide deformylase; Reviewed


Pssm-ID: 237227  Cd Length: 165  Bit Score: 220.45  E-value: 1.32e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 523414721   1 MALLNILQYPDPRLHKVAKPVAVVD-DRIRKLVADMAETMYDAPGIGLAATQVDVHERVITIDISESRDELRVFINPEIV 79
Cdd:PRK12846   1 MAVRPILKMPDPRLRRPAEPVTAFDtEELQALIDDMFETMRAADGVGLAAPQIGVSLRVVVIDLGDDRVPPTVLINPEIT 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 523414721  80 WASDARKVWDEGCLSVPDIYDKVERPDRVRVRALNEKGESFELETDGLLAVCIQHEMDHLMGKVFVEYLSPLKQNRIKIK 159
Cdd:PRK12846  81 ELSPEEEVGWEGCLSVPGLRGEVERPARVRVRAQDRDGKPIEIEAEGFLARVLQHEIDHLDGILYTDRLSRLKRERALKK 160

                 ....*
gi 523414721 160 LKKHQ 164
Cdd:PRK12846 161 VEKYD 165
Pep_deformylase cd00487
Polypeptide or peptide deformylase; a family of metalloenzymes that catalyzes the removal of ...
6-144 5.63e-73

Polypeptide or peptide deformylase; a family of metalloenzymes that catalyzes the removal of the N-terminal formyl group in a growing polypeptide chain following translation initiation during protein synthesis in prokaryotes. These enzymes utilize Fe(II) as the catalytic metal ion, which can be replaced with a nickel or cobalt ion with no loss of activity. There are two types of peptide deformylases, types I and II, which differ in structure only in the outer surface of the domain. Because these enzymes are essential only in prokaryotes (although eukaryotic gene sequences have been found), they are a target for a new class of antibacterial agents.


Pssm-ID: 238271  Cd Length: 141  Bit Score: 215.43  E-value: 5.63e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 523414721   6 ILQYPDPRLHKVAKPVAVVDDRIRKLVADMAETMYDAPGIGLAATQVDVHERVITIDISESR--DELRVFINPEIVWASD 83
Cdd:cd00487    1 IVQYPDPVLRKKAKPVEEFDDELKQLIDDMFETMYAAPGVGLAAPQIGVSKRIFVIDVPDEEnkEPPLVLINPEIIESSG 80
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 523414721  84 ARKVWDEGCLSVPDIYDKVERPDRVRVRALNEKGESFELETDGLLAVCIQHEMDHLMGKVF 144
Cdd:cd00487   81 ETEYGEEGCLSVPGYRGEVERPKKVTVRYLDEDGNPIELEAEGFLARCIQHEIDHLNGILF 141
Pep_deformylase pfam01327
Polypeptide deformylase;
4-153 2.94e-66

Polypeptide deformylase;


Pssm-ID: 426202  Cd Length: 153  Bit Score: 198.96  E-value: 2.94e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 523414721    4 LNILQYPDPRLHKVAKPVAVVDDR-IRKLVADMAETMYDAPGIGLAATQVDVHERVITIDISESRDE--LRVFINPEIVW 80
Cdd:pfam01327   1 LPIVTYPDPVLRKKAEPVEEFDDKeLKKLIDDMLETMYAADGVGLAAPQVGVSKRIFVIDLPDGEEEpdPLVLINPEIIS 80
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 523414721   81 ASDARKVWDEGCLSVPDIYDKVERPDRVRVRALNEKGESFELETDGLLAVCIQHEMDHLMGKVFVEYLSPLKQ 153
Cdd:pfam01327  81 KSEETVTDEEGCLSVPGIRGEVERPKRITVKYLDLNGKEIELEAEGFLARVLQHEIDHLNGILFIDRLSPLKR 153
pept_deformyl TIGR00079
peptide deformylase; Peptide deformylase (EC 3.5.1.88), also called polypeptide deformylase, ...
3-162 5.59e-55

peptide deformylase; Peptide deformylase (EC 3.5.1.88), also called polypeptide deformylase, is a metalloenzyme that uses water to release formate from the N-terminal formyl-L-methionine of bacterial and chloroplast peptides. This enzyme should not be confused with formylmethionine deformylase (EC 3.5.1.31) which is active on free N-formyl methionine and has been reported from rat intestine. [Protein fate, Protein modification and repair]


Pssm-ID: 272895  Cd Length: 161  Bit Score: 170.64  E-value: 5.59e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 523414721    3 LLNILQYPDPRLHKVAKPVAVVDDRIRKLVADMAETMYDAPGIGLAATQVDVHERVITIDISESRDELRVF-INPEIVWA 81
Cdd:TIGR00079   1 MLEVFHYPDDLLRKTAKPVEIVDKKIDQQLDDMIETMIAEKGIGLAAPQVGILKRMIVIELEDADKEPLLFlINPKIIES 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 523414721   82 SDARKVWDEGCLSVPDIYDKVERPDRVRVRALNEKGESFELETDGLLAVCIQHEMDHLMGKVFVEYLSPLKQNRIKIKLK 161
Cdd:TIGR00079  81 SEESSYLEEGCLSVPVYYGLVPRKEKVKIRGDDRFGKPIILEADGLLAICIQHEIDHLNGVFFVDYISPLNPKKLKKEMK 160

                  .
gi 523414721  162 K 162
Cdd:TIGR00079 161 E 161
PRK14595 PRK14595
peptide deformylase; Provisional
1-146 1.36e-19

peptide deformylase; Provisional


Pssm-ID: 184757  Cd Length: 162  Bit Score: 80.24  E-value: 1.36e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 523414721   1 MALLNILQYPDPRLHKVAKPVAVVDDRIRKLVADMAETMYDAPGIGLAATQVDVHERVITIDISEsrDELRVFINPEIVW 80
Cdd:PRK14595   1 MAIKKLVPASHPILTKKAQAVKTFDDSLKRLLQDLEDTMYAQEAAALCAPQIGQSLQVAIIDMEM--EGLLQLVNPKIIS 78
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 523414721  81 ASDARKVWDEGCLSVPDIYDKVERPDRVRVRALNEKGESFELETDGLLAVCIQHEMDHLMGKVFVE 146
Cdd:PRK14595  79 QSNETITDLEGSITLPDVYGEVTRSKMIVVESYDVNGNKVELTAYDDVARMILHIIDQMNGIPFTE 144
PRK09218 PRK09218
peptide deformylase; Validated
45-142 2.88e-10

peptide deformylase; Validated


Pssm-ID: 181704  Cd Length: 136  Bit Score: 55.31  E-value: 2.88e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 523414721  45 IGLAATQVDVHERVITIDISeSRDelRVFINPEIVWASDARKVwDEGCLSVPDiYDKVERPDRVRVRALNEKGESFELET 124
Cdd:PRK09218  42 VGMAANMIGVQKRIIIFSLG-FVP--VVMFNPVIVSKSGPYET-EEGCLSLTG-ERPTKRYEEITVKYLDRNWREQTQTF 116
                         90
                 ....*....|....*...
gi 523414721 125 DGLLAVCIQHEMDHLMGK 142
Cdd:PRK09218 117 TGFTAQIIQHELDHCEGI 134
 
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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