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Conserved domains on  [gi|254951741|gb|ACT96441|]
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peptidase C39 bacteriocin processing [Dyadobacter fermentans DSM 18053]

Protein Classification

vitamin K epoxide reductase family protein; glutaredoxin family protein( domain architecture ID 10218940)

vitamin K epoxide reductase (VKOR) family protein containing a thioredoxin domain, is a membrane protein that functions as a thiol-disulfide oxidoreductase catalyzing disulfide bond formation, similar to Synechococcus sp. vitamin K epoxide reductase homolog and Arabidopsis thaliana thiol-disulfide oxidoreductase LTO1; glutaredoxin family protein with similarity to redoxin NrdH, a glutaredoxin-like protein with a thioredoxin-like activity profile

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
VKOR_4 cd12921
Vitamin K epoxide reductase (VKOR) family in bacteria; This family includes vitamin K epoxide ...
 179-307 9.72e-34

Vitamin K epoxide reductase (VKOR) family in bacteria; This family includes vitamin K epoxide reductase (VKOR) present only in bacteria. VKOR (also named VKORC1) is an integral membrane protein that catalyzes the reduction of vitamin K 2,3-epoxide and vitamin K to vitamin K hydroquinone, an essential co-factor subsequently used in the gamma-carboxylation of glutamic acid residues in blood coagulation enzymes. All homologs of VKOR contain an active site CXXC motif, which is switched between reduced and disulfide-bonded states during the reaction cycle. In some bacterial homologs, the VKOR domain is fused with domains of the thioredoxin family of oxidoreductases which may function as redox partners in initiating the reduction cascade. This family also has a cysteine peptidase domain present at the N-terminus of the VKOR domain.


:

Pssm-ID: 240604  Cd Length: 128  Bit Score: 124.36  E-value: 9.72e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254951741 179 WLLFFTKISGLFFTGLLIAKQLGSKNDLTDRLCRINDKTSCENVLNSPGAKLfGWLNWSDLGLLYFAGGSSALLFTGEQH 258
Cdd:cd12921    1 LLLLLLSLIGLLISILLLLKELGKSNKILKKFCSIGKKVDCNAVLKSKGAKI-GGISLSELGLLYFFGLLLLLLLSPLNS 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 254951741 259 NEFNLLNALALLAMPYVAFSIYYQAYKVRQWCTLCLGVQVILIVEGVIA 307
Cdd:cd12921   80 SLLFLLSLLLLLALPAELYSIYYQKFVIKKWCPLCLSIQAILWLLFLLL 128
Peptidase_C39_like super family cl00296
Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The ...
 68-128 1.49e-10

Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is not conserved in all sub-families.


The actual alignment was detected with superfamily member pfam03412:

Pssm-ID: 469710 [Multi-domain]  Cd Length: 133  Bit Score: 59.16  E-value: 1.49e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 254951741   68 EQLREIPVPFITQIKKKGGWYILINQIREKHIQYTDSEQGEVTLSLSDFEKRWTGIVLLTE 128
Cdd:pfam03412  69 SELKELPLPFIAHWDGNGGHFVVVYGIKKNKVLIADPAVGKIKLSREEFEKEWTGVALLVA 129
Thioredoxin_like super family cl00388
Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin ...
 382-531 3.95e-05

Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; The thioredoxin (TRX)-like superfamily is a large, diverse group of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others.


The actual alignment was detected with superfamily member pfam13462:

Pssm-ID: 469754 [Multi-domain]  Cd Length: 164  Bit Score: 44.25  E-value: 3.95e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254951741  382 IYPLVLGNPDAEIKITMVTNPYCSSCSRAHKELEQLV---LQDENVSVTTI---FSTTGDSSPATKVVTHLLALARHETS 455
Cdd:pfam13462   2 PTDPVIGNPDAPVTVVEYADLRCPHCAKFHEEVLKLLeeyIDTGKVRFIIRdfpLDGEGESLLAAMAARCAGDQSPEYFL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254951741  456 ARSALT-----EWYSQKEKDYNAWAK--------SHPTTTDptEMMAICRNQRlwchEADIALTPTIYINGYKMPEIYKL 522
Cdd:pfam13462  82 VIDKLLysqqeEWAQDLELAALAGLKdeefeaclEEEDFLA--LVMADVKEAR----AAGINFTPTFIINGKKVDGPLTY 155


                  ....*....
gi 254951741  523 ESLQWILKR 531
Cdd:pfam13462 156 EELKKLIDD 164
 
Name Accession Description Interval E-value
VKOR_4 cd12921
Vitamin K epoxide reductase (VKOR) family in bacteria; This family includes vitamin K epoxide ...
 179-307 9.72e-34

Vitamin K epoxide reductase (VKOR) family in bacteria; This family includes vitamin K epoxide reductase (VKOR) present only in bacteria. VKOR (also named VKORC1) is an integral membrane protein that catalyzes the reduction of vitamin K 2,3-epoxide and vitamin K to vitamin K hydroquinone, an essential co-factor subsequently used in the gamma-carboxylation of glutamic acid residues in blood coagulation enzymes. All homologs of VKOR contain an active site CXXC motif, which is switched between reduced and disulfide-bonded states during the reaction cycle. In some bacterial homologs, the VKOR domain is fused with domains of the thioredoxin family of oxidoreductases which may function as redox partners in initiating the reduction cascade. This family also has a cysteine peptidase domain present at the N-terminus of the VKOR domain.


Pssm-ID: 240604  Cd Length: 128  Bit Score: 124.36  E-value: 9.72e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254951741 179 WLLFFTKISGLFFTGLLIAKQLGSKNDLTDRLCRINDKTSCENVLNSPGAKLfGWLNWSDLGLLYFAGGSSALLFTGEQH 258
Cdd:cd12921    1 LLLLLLSLIGLLISILLLLKELGKSNKILKKFCSIGKKVDCNAVLKSKGAKI-GGISLSELGLLYFFGLLLLLLLSPLNS 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 254951741 259 NEFNLLNALALLAMPYVAFSIYYQAYKVRQWCTLCLGVQVILIVEGVIA 307
Cdd:cd12921   80 SLLFLLSLLLLLALPAELYSIYYQKFVIKKWCPLCLSIQAILWLLFLLL 128
VKOR pfam07884
Vitamin K epoxide reductase family; Vitamin K epoxide reductase (VKOR) recycles reduced ...
 179-308 4.85e-15

Vitamin K epoxide reductase family; Vitamin K epoxide reductase (VKOR) recycles reduced vitamin K, which is used subsequently as a co-factor in the gamma-carboxylation of glutamic acid residues in blood coagulation enzymes. VKORC1 is a member of a large family of predicted enzymes that are present in vertebrates, Drosophila, plants, bacteria and archaea. Four cysteine residues and one residue, which is either serine or threonine, are identified as likely active-site residues. In some plant and bacterial homologs the VKORC1 homologous domain is fused with domains of the thioredoxin family of oxidoreductases.


Pssm-ID: 429714  Cd Length: 132  Bit Score: 71.87  E-value: 4.85e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254951741  179 WLLFFTKISGLFFTGLLIAKQLGSKNDLTDrLCRINDKTSCENVLNSPGAKLFGwLNWSDLGLLYFAG----GSSALLFT 254
Cdd:pfam07884   1 LLLLVLALIGLLASAYLTLEKLGPDPGYAA-SCDINGVVSCGKVLTSPYASVFG-IPNALLGLLAYAVvavlALAGLAGA 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 254951741  255 GEQHNEFNLLNALALLAMPYVAFSIYYQAYKVRQWCTLCLGVQVILIVEGVIAL 308
Cdd:pfam07884  79 RLPRWPWLLLLLGSLAGVVFSLYLIYISLFVIGALCPYCLVSAVVSLLLFVLTL 132
COG4243 COG4243
Vitamin K epoxide reductase (VKOR) family protein, predicted involvement in disulfide bond ...
 168-308 6.36e-15

Vitamin K epoxide reductase (VKOR) family protein, predicted involvement in disulfide bond formation [General function prediction only];


Pssm-ID: 443385  Cd Length: 161  Bit Score: 72.34  E-value: 6.36e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254951741 168 MFAGRSFST-PEWLLFFTKISGLFFTGLLIAKQLGSKNDLTDRLCRINDKTSCENVLNSPGAKLFGwLNWSDLGLLYFAG 246
Cdd:COG4243    1 MTSTRRRSRwLAWLLLVLALIGLLASFYLTLEKLTLLAPGGVLSCDINPVVSCGSVLNSPQASVFG-FPNALLGLAAFAV 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 254951741 247 --GSSALLFTGEQHNEFNLLNALALLA--MPYVAFSIYYQAYKVRQWCTLCLGVQVILIVEGVIAL 308
Cdd:COG4243   80 viTLAVALLAGARLPRWLWLALLAGALagVVFSVWLIYQSLFVIGALCPYCLVVWAVTIPLFVLTT 145
Peptidase_C39 pfam03412
Peptidase C39 family; Lantibiotic and non-lantibiotic bacteriocins are synthesized as ...
 68-128 1.49e-10

Peptidase C39 family; Lantibiotic and non-lantibiotic bacteriocins are synthesized as precursor peptides containing N-terminal extensions (leader peptides) which are cleaved off during maturation. Most non-lantibiotics and also some lantibiotics have leader peptides of the so-called double-glycine type. These leader peptides share consensus sequences and also a common processing site with two conserved glycine residues in positions -1 and -2. The double- glycine-type leader peptides are unrelated to the N-terminal signal sequences which direct proteins across the cytoplasmic membrane via the sec pathway. Their processing sites are also different from typical signal peptidase cleavage sites, suggesting that a different processing enzyme is involved. Peptide bacteriocins are exported across the cytoplasmic membrane by a dedicated ATP-binding cassette (ABC) transporter. The ABC transporter is the maturation protease and its proteolytic domain resides in the N-terminal part of the protein. This peptidase domain is found in a wide range of ABC transporters, however the presumed catalytic cysteine and histidine are not conserved in all members of this family.


Pssm-ID: 367483 [Multi-domain]  Cd Length: 133  Bit Score: 59.16  E-value: 1.49e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 254951741   68 EQLREIPVPFITQIKKKGGWYILINQIREKHIQYTDSEQGEVTLSLSDFEKRWTGIVLLTE 128
Cdd:pfam03412  69 SELKELPLPFIAHWDGNGGHFVVVYGIKKNKVLIADPAVGKIKLSREEFEKEWTGVALLVA 129
C39G COG3271
Predicted double-glycine leader peptidase, C39-like (CLD) domain [Intracellular trafficking, ...
 66-126 7.29e-07

Predicted double-glycine leader peptidase, C39-like (CLD) domain [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 442502 [Multi-domain]  Cd Length: 179  Bit Score: 49.61  E-value: 7.29e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 254951741  66 TVEQLREIPVPFITQIKKKGGW-YILINQIREKHIQYTDSEQGEVTLSLSDFEKRWTGIVLL 126
Cdd:COG3271  113 TLDDLAQLGIPAIVLINLGGYKhFVVVKGVDDGRVLLADPALGNRSLSREEFEKMWDGNVLF 174
Peptidase_C39B cd02418
A sub-family of peptidase family C39. Peptidase family C39 mostly contains ...
 68-132 1.25e-06

A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.


Pssm-ID: 239099 [Multi-domain]  Cd Length: 136  Bit Score: 47.97  E-value: 1.25e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 254951741  68 EQLREIPVPFITQIKKKGGW--YILINQIREKHIQYTDSEQGEVTLSLSDFEKRWTGIVLLTEINEQ 132
Cdd:cd02418   70 FELKDIPLPFIAHVIKEWKLnhYVVVYKIKKKKILIADPAVGITKISKEEFEKEWTGVALFLEPTPN 136
Thioredoxin_4 pfam13462
Thioredoxin;
382-531 3.95e-05

Thioredoxin;


Pssm-ID: 433227 [Multi-domain]  Cd Length: 164  Bit Score: 44.25  E-value: 3.95e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254951741  382 IYPLVLGNPDAEIKITMVTNPYCSSCSRAHKELEQLV---LQDENVSVTTI---FSTTGDSSPATKVVTHLLALARHETS 455
Cdd:pfam13462   2 PTDPVIGNPDAPVTVVEYADLRCPHCAKFHEEVLKLLeeyIDTGKVRFIIRdfpLDGEGESLLAAMAARCAGDQSPEYFL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254951741  456 ARSALT-----EWYSQKEKDYNAWAK--------SHPTTTDptEMMAICRNQRlwchEADIALTPTIYINGYKMPEIYKL 522
Cdd:pfam13462  82 VIDKLLysqqeEWAQDLELAALAGLKdeefeaclEEEDFLA--LVMADVKEAR----AAGINFTPTFIINGKKVDGPLTY 155


                  ....*....
gi 254951741  523 ESLQWILKR 531
Cdd:pfam13462 156 EELKKLIDD 164
VKc smart00756
Family of likely enzymes that includes the catalytic subunit of vitamin K epoxide reductase; ...
 175-308 4.66e-05

Family of likely enzymes that includes the catalytic subunit of vitamin K epoxide reductase; Bacterial homologues are fused to members of the thioredoxin family of oxidoreductases.


Pssm-ID: 214805  Cd Length: 142  Bit Score: 43.48  E-value: 4.66e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254951741   175 STPEWLLFFTKISGLFFTGLLIAKQLGSKNDLTDRL-CRINDKTSCENVLNSPGAKLFGWLNwSDLGLLYFAG--GSSAL 251
Cdd:smart00756   2 RWTRWILLILGLIGLLASLYLTYEKLTLLEDPDYVAsCDINPVVSCGKVLSSPYASIFGIPL-SLLGIAAYLVvlALAVL 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 254951741   252 LFTGEQHNEFNLLNALALLAMpYVAFSIY--YQA-YKVRQWCTLCLGVQVILIVEGVIAL 308
Cdd:smart00756  81 GLLGVTLPRWTWRLLFLGSLA-GAVFSVYliYLLvFVIKALCLYCILSAVVSISLFILVT 139
DsbG COG1651
Protein thiol-disulfide isomerase DsbC [Posttranslational modification, protein turnover, ...
 394-532 5.56e-05

Protein thiol-disulfide isomerase DsbC [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 441257 [Multi-domain]  Cd Length: 152  Bit Score: 43.45  E-value: 5.56e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254951741 394 IKITMVTNPYCSSCSRAHKELEQLV--LQDENVsvttifsttgdsspatKVVTHLLALArHETSARSALTEWYSQKEKDY 471
Cdd:COG1651    2 VTVVEFFDYQCPYCARFHPELPELLkkYVDGKV----------------RVVYRPFPLL-HPDSLRAARAALCAADQGKF 64

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254951741 472 NAWA----KSHPTTTDPT----------------------EMMAICRNQRLWCHEADIALTPTIYINGYKMPEIYKLESL 525
Cdd:COG1651   65 WAFHdalfANQPALTDDDlreiakeagldaakfdaclnsgAVAAKVEADTALAQALGVTGTPTFVVNGKLVSGAVPYEEL 144


                 ....*..
gi 254951741 526 QWILKRV 532
Cdd:COG1651  145 EAALDAA 151
DsbA_Com1_like cd03023
DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer ...
 388-474 1.78e-04

DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a CXXC motif, assumed to be imbedded in a DsbA-like structure. Its homology to DsbA suggests that the protein is a protein disulfide oxidoreductase. The role of such a protein in pathogenesis is unknown.


Pssm-ID: 239321 [Multi-domain]  Cd Length: 154  Bit Score: 42.20  E-value: 1.78e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254951741 388 GNPDAEIKITMVTNPYCSSCSRAHKELEQLVLQDENVSVTTI-FSTTGDSSpatkvvthllalarhETSARSALTEWYSQ 466
Cdd:cd03023    1 GNPNGDVTIVEFFDYNCGYCKKLAPELEKLLKEDPDVRVVFKeFPILGESS---------------VLAARVALAVWKNG 65


                 ....*...
gi 254951741 467 KEKdYNAW 474
Cdd:cd03023   66 PGK-YLEF 72
PRK14889 PRK14889
VKOR family protein; Provisional
 210-312 2.58e-03

VKOR family protein; Provisional


Pssm-ID: 184883  Cd Length: 143  Bit Score: 38.53  E-value: 2.58e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254951741 210 LCRINDKTSCENVLNSPGAKLFGwLNWSDLGLLYFAG--GSSALLFTGEQHNEFNLLNALALLAMPYVAFSIYYQAYKVR 287
Cdd:PRK14889  39 FCTINSVINCSSVLSSPYARFLG-IPLDYLGAAWFSAniALALLGVGTLKRILGRVISLWSIIGLAIVPYLVYLEVFVLG 117

                         90       100
                 ....*....|....*....|....*
gi 254951741 288 QWCTLCLGVQVILIVEGVIALTQLK 312
Cdd:PRK14889 118 AICIYCTIAHVSILAAFILILIKLK 142
 
Name Accession Description Interval E-value
VKOR_4 cd12921
Vitamin K epoxide reductase (VKOR) family in bacteria; This family includes vitamin K epoxide ...
 179-307 9.72e-34

Vitamin K epoxide reductase (VKOR) family in bacteria; This family includes vitamin K epoxide reductase (VKOR) present only in bacteria. VKOR (also named VKORC1) is an integral membrane protein that catalyzes the reduction of vitamin K 2,3-epoxide and vitamin K to vitamin K hydroquinone, an essential co-factor subsequently used in the gamma-carboxylation of glutamic acid residues in blood coagulation enzymes. All homologs of VKOR contain an active site CXXC motif, which is switched between reduced and disulfide-bonded states during the reaction cycle. In some bacterial homologs, the VKOR domain is fused with domains of the thioredoxin family of oxidoreductases which may function as redox partners in initiating the reduction cascade. This family also has a cysteine peptidase domain present at the N-terminus of the VKOR domain.


Pssm-ID: 240604  Cd Length: 128  Bit Score: 124.36  E-value: 9.72e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254951741 179 WLLFFTKISGLFFTGLLIAKQLGSKNDLTDRLCRINDKTSCENVLNSPGAKLfGWLNWSDLGLLYFAGGSSALLFTGEQH 258
Cdd:cd12921    1 LLLLLLSLIGLLISILLLLKELGKSNKILKKFCSIGKKVDCNAVLKSKGAKI-GGISLSELGLLYFFGLLLLLLLSPLNS 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 254951741 259 NEFNLLNALALLAMPYVAFSIYYQAYKVRQWCTLCLGVQVILIVEGVIA 307
Cdd:cd12921   80 SLLFLLSLLLLLALPAELYSIYYQKFVIKKWCPLCLSIQAILWLLFLLL 128
VKOR pfam07884
Vitamin K epoxide reductase family; Vitamin K epoxide reductase (VKOR) recycles reduced ...
 179-308 4.85e-15

Vitamin K epoxide reductase family; Vitamin K epoxide reductase (VKOR) recycles reduced vitamin K, which is used subsequently as a co-factor in the gamma-carboxylation of glutamic acid residues in blood coagulation enzymes. VKORC1 is a member of a large family of predicted enzymes that are present in vertebrates, Drosophila, plants, bacteria and archaea. Four cysteine residues and one residue, which is either serine or threonine, are identified as likely active-site residues. In some plant and bacterial homologs the VKORC1 homologous domain is fused with domains of the thioredoxin family of oxidoreductases.


Pssm-ID: 429714  Cd Length: 132  Bit Score: 71.87  E-value: 4.85e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254951741  179 WLLFFTKISGLFFTGLLIAKQLGSKNDLTDrLCRINDKTSCENVLNSPGAKLFGwLNWSDLGLLYFAG----GSSALLFT 254
Cdd:pfam07884   1 LLLLVLALIGLLASAYLTLEKLGPDPGYAA-SCDINGVVSCGKVLTSPYASVFG-IPNALLGLLAYAVvavlALAGLAGA 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 254951741  255 GEQHNEFNLLNALALLAMPYVAFSIYYQAYKVRQWCTLCLGVQVILIVEGVIAL 308
Cdd:pfam07884  79 RLPRWPWLLLLLGSLAGVVFSLYLIYISLFVIGALCPYCLVSAVVSLLLFVLTL 132
COG4243 COG4243
Vitamin K epoxide reductase (VKOR) family protein, predicted involvement in disulfide bond ...
 168-308 6.36e-15

Vitamin K epoxide reductase (VKOR) family protein, predicted involvement in disulfide bond formation [General function prediction only];


Pssm-ID: 443385  Cd Length: 161  Bit Score: 72.34  E-value: 6.36e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254951741 168 MFAGRSFST-PEWLLFFTKISGLFFTGLLIAKQLGSKNDLTDRLCRINDKTSCENVLNSPGAKLFGwLNWSDLGLLYFAG 246
Cdd:COG4243    1 MTSTRRRSRwLAWLLLVLALIGLLASFYLTLEKLTLLAPGGVLSCDINPVVSCGSVLNSPQASVFG-FPNALLGLAAFAV 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 254951741 247 --GSSALLFTGEQHNEFNLLNALALLA--MPYVAFSIYYQAYKVRQWCTLCLGVQVILIVEGVIAL 308
Cdd:COG4243   80 viTLAVALLAGARLPRWLWLALLAGALagVVFSVWLIYQSLFVIGALCPYCLVVWAVTIPLFVLTT 145
VKOR cd10546
Vitamin K epoxide reductase (VKOR) family; VKOR (also named VKORC1) is an integral membrane ...
 179-302 7.80e-12

Vitamin K epoxide reductase (VKOR) family; VKOR (also named VKORC1) is an integral membrane protein that catalyzes the reduction of vitamin K 2,3-epoxide and vitamin K to vitamin K hydroquinone, an essential co-factor subsequently used in the gamma-carboxylation of glutamic acid residues in blood coagulation enzymes. This family includes enzymes that are present in vertebrates, Drosophila, plants, bacteria, and archaea. All homologs of VKOR contain an active site CXXC motif, which is switched between reduced and disulfide-bonded states during the reaction cycle. In some plant and bacterial homologs, the VKOR domain is fused with domains of the thioredoxin family of oxidoreductases which may function as redox partners in initiating the reduction cascade. Warfarin, a widely used oral anticoagulant used in medicine as well as rodenticides, inhibits the activity of VKOR, resulting in decreased levels of reduced vitamin K, which is required for the function of several clotting factors. However, anticoagulation effect of warfarin is significantly associated with polymorphism of certain genes, including VKORC1. Interestingly, in rodents, an adaptive trait appears to have evolved convergently by selection on new or standing genetic polymorphisms in VKORC1 as well as by adaptive introgressive hybridization between species, likely brought about by human-mediated dispersal.


Pssm-ID: 240598  Cd Length: 126  Bit Score: 62.44  E-value: 7.80e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254951741 179 WLLFFTKISGLFFTGLLIAKQLGSKNDLtdrLCRINDKTSCENVLNSPGAKLFGwLNWSDLGLLYFAGGSSALLFTGEQH 258
Cdd:cd10546    1 LILLLLAAIGLLVSLYLTYYELTEGAVA---GCDAGPSSSCDLVLTSRWSRIFG-VPLSLLGALYYLVVLGLLLSPPAGA 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 254951741 259 NEFNLLNALALLAM-PYVAFSIYYQAYKVRQWCTLCLGVQVILIV 302
Cdd:cd10546   77 RLRWTALAAATFAGlGAAAWLIYLQLFVLGAFCPYCLVAHAAGLA 121
Peptidase_C39 pfam03412
Peptidase C39 family; Lantibiotic and non-lantibiotic bacteriocins are synthesized as ...
 68-128 1.49e-10

Peptidase C39 family; Lantibiotic and non-lantibiotic bacteriocins are synthesized as precursor peptides containing N-terminal extensions (leader peptides) which are cleaved off during maturation. Most non-lantibiotics and also some lantibiotics have leader peptides of the so-called double-glycine type. These leader peptides share consensus sequences and also a common processing site with two conserved glycine residues in positions -1 and -2. The double- glycine-type leader peptides are unrelated to the N-terminal signal sequences which direct proteins across the cytoplasmic membrane via the sec pathway. Their processing sites are also different from typical signal peptidase cleavage sites, suggesting that a different processing enzyme is involved. Peptide bacteriocins are exported across the cytoplasmic membrane by a dedicated ATP-binding cassette (ABC) transporter. The ABC transporter is the maturation protease and its proteolytic domain resides in the N-terminal part of the protein. This peptidase domain is found in a wide range of ABC transporters, however the presumed catalytic cysteine and histidine are not conserved in all members of this family.


Pssm-ID: 367483 [Multi-domain]  Cd Length: 133  Bit Score: 59.16  E-value: 1.49e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 254951741   68 EQLREIPVPFITQIKKKGGWYILINQIREKHIQYTDSEQGEVTLSLSDFEKRWTGIVLLTE 128
Cdd:pfam03412  69 SELKELPLPFIAHWDGNGGHFVVVYGIKKNKVLIADPAVGKIKLSREEFEKEWTGVALLVA 129
C39G COG3271
Predicted double-glycine leader peptidase, C39-like (CLD) domain [Intracellular trafficking, ...
 66-126 7.29e-07

Predicted double-glycine leader peptidase, C39-like (CLD) domain [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 442502 [Multi-domain]  Cd Length: 179  Bit Score: 49.61  E-value: 7.29e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 254951741  66 TVEQLREIPVPFITQIKKKGGW-YILINQIREKHIQYTDSEQGEVTLSLSDFEKRWTGIVLL 126
Cdd:COG3271  113 TLDDLAQLGIPAIVLINLGGYKhFVVVKGVDDGRVLLADPALGNRSLSREEFEKMWDGNVLF 174
Peptidase_C39B cd02418
A sub-family of peptidase family C39. Peptidase family C39 mostly contains ...
 68-132 1.25e-06

A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.


Pssm-ID: 239099 [Multi-domain]  Cd Length: 136  Bit Score: 47.97  E-value: 1.25e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 254951741  68 EQLREIPVPFITQIKKKGGW--YILINQIREKHIQYTDSEQGEVTLSLSDFEKRWTGIVLLTEINEQ 132
Cdd:cd02418   70 FELKDIPLPFIAHVIKEWKLnhYVVVYKIKKKKILIADPAVGITKISKEEFEKEWTGVALFLEPTPN 136
Thioredoxin_4 pfam13462
Thioredoxin;
382-531 3.95e-05

Thioredoxin;


Pssm-ID: 433227 [Multi-domain]  Cd Length: 164  Bit Score: 44.25  E-value: 3.95e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254951741  382 IYPLVLGNPDAEIKITMVTNPYCSSCSRAHKELEQLV---LQDENVSVTTI---FSTTGDSSPATKVVTHLLALARHETS 455
Cdd:pfam13462   2 PTDPVIGNPDAPVTVVEYADLRCPHCAKFHEEVLKLLeeyIDTGKVRFIIRdfpLDGEGESLLAAMAARCAGDQSPEYFL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254951741  456 ARSALT-----EWYSQKEKDYNAWAK--------SHPTTTDptEMMAICRNQRlwchEADIALTPTIYINGYKMPEIYKL 522
Cdd:pfam13462  82 VIDKLLysqqeEWAQDLELAALAGLKdeefeaclEEEDFLA--LVMADVKEAR----AAGINFTPTFIINGKKVDGPLTY 155


                  ....*....
gi 254951741  523 ESLQWILKR 531
Cdd:pfam13462 156 EELKKLIDD 164
VKc smart00756
Family of likely enzymes that includes the catalytic subunit of vitamin K epoxide reductase; ...
 175-308 4.66e-05

Family of likely enzymes that includes the catalytic subunit of vitamin K epoxide reductase; Bacterial homologues are fused to members of the thioredoxin family of oxidoreductases.


Pssm-ID: 214805  Cd Length: 142  Bit Score: 43.48  E-value: 4.66e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254951741   175 STPEWLLFFTKISGLFFTGLLIAKQLGSKNDLTDRL-CRINDKTSCENVLNSPGAKLFGWLNwSDLGLLYFAG--GSSAL 251
Cdd:smart00756   2 RWTRWILLILGLIGLLASLYLTYEKLTLLEDPDYVAsCDINPVVSCGKVLSSPYASIFGIPL-SLLGIAAYLVvlALAVL 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 254951741   252 LFTGEQHNEFNLLNALALLAMpYVAFSIY--YQA-YKVRQWCTLCLGVQVILIVEGVIAL 308
Cdd:smart00756  81 GLLGVTLPRWTWRLLFLGSLA-GAVFSVYliYLLvFVIKALCLYCILSAVVSISLFILVT 139
DsbG COG1651
Protein thiol-disulfide isomerase DsbC [Posttranslational modification, protein turnover, ...
 394-532 5.56e-05

Protein thiol-disulfide isomerase DsbC [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 441257 [Multi-domain]  Cd Length: 152  Bit Score: 43.45  E-value: 5.56e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254951741 394 IKITMVTNPYCSSCSRAHKELEQLV--LQDENVsvttifsttgdsspatKVVTHLLALArHETSARSALTEWYSQKEKDY 471
Cdd:COG1651    2 VTVVEFFDYQCPYCARFHPELPELLkkYVDGKV----------------RVVYRPFPLL-HPDSLRAARAALCAADQGKF 64

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254951741 472 NAWA----KSHPTTTDPT----------------------EMMAICRNQRLWCHEADIALTPTIYINGYKMPEIYKLESL 525
Cdd:COG1651   65 WAFHdalfANQPALTDDDlreiakeagldaakfdaclnsgAVAAKVEADTALAQALGVTGTPTFVVNGKLVSGAVPYEEL 144


                 ....*..
gi 254951741 526 QWILKRV 532
Cdd:COG1651  145 EAALDAA 151
Peptidase_C39G cd02423
A sub-family of peptidase family C39. Peptidase family C39 mostly contains ...
 68-126 9.13e-05

A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family of proteins with a single peptidase domain, which are lacking the nucleotide-binding transporter signature.


Pssm-ID: 239103 [Multi-domain]  Cd Length: 129  Bit Score: 42.25  E-value: 9.13e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 254951741  68 EQLREIPVPFITQIKKKG-GWYILINQIREKHIQYTDSEQGEVTLSLSDFEKRWTGIVLL 126
Cdd:cd02423   69 DKLNALQIPVIVLVNNGGyGHFVVIKGIDGDRVLVGDPALGNISMSREEFERIWTGNALF 128
DsbA_Com1_like cd03023
DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer ...
 388-474 1.78e-04

DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a CXXC motif, assumed to be imbedded in a DsbA-like structure. Its homology to DsbA suggests that the protein is a protein disulfide oxidoreductase. The role of such a protein in pathogenesis is unknown.


Pssm-ID: 239321 [Multi-domain]  Cd Length: 154  Bit Score: 42.20  E-value: 1.78e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254951741 388 GNPDAEIKITMVTNPYCSSCSRAHKELEQLVLQDENVSVTTI-FSTTGDSSpatkvvthllalarhETSARSALTEWYSQ 466
Cdd:cd03023    1 GNPNGDVTIVEFFDYNCGYCKKLAPELEKLLKEDPDVRVVFKeFPILGESS---------------VLAARVALAVWKNG 65


                 ....*...
gi 254951741 467 KEKdYNAW 474
Cdd:cd03023   66 PGK-YLEF 72
VKOR_arc cd12918
Vitamin K epoxide reductase family in archaea and some bacteria; This family includes vitamin ...
 210-307 6.56e-04

Vitamin K epoxide reductase family in archaea and some bacteria; This family includes vitamin K epoxide reductase (VKOR) mostly present in archaea and some bacteria. VKOR (also named VKORC1) is an integral membrane protein that catalyzes the reduction of vitamin K 2,3-epoxide and vitamin K to vitamin K hydroquinone, an essential co-factor subsequently used in the gamma-carboxylation of glutamic acid residues in blood coagulation enzymes. All homologs of VKOR contain an active site CXXC motif, which is switched between reduced and disulfide-bonded states during the reaction cycle. In some bacterial homologs, the VKOR domain is fused with domains of the thioredoxin family of oxidoreductases which may function as redox partners in initiating the reduction cascade.


Pssm-ID: 240601  Cd Length: 126  Bit Score: 39.99  E-value: 6.56e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254951741 210 LCRINDKTSCENVLNSPGAKLFGwLNWSDLGLLYFAGGSSALLFTGEQHNEFNLLNALALLA-MPYVAFSIYYQAYKVRQ 288
Cdd:cd12918   29 ACTISGVINCEKVLSSPYSRILG-VPLAVLGLAWFAVLLVLSLLAALRVRLLLGALLYWSILgIAFVPYLVYLELFLIGA 107

                         90
                 ....*....|....*....
gi 254951741 289 WCTLCLGVQVILIVEGVIA 307
Cdd:cd12918  108 ICLYCTVAHVIILALFIII 126
Peptidase_C39E cd02424
A sub-family of peptidase family C39. Peptidase family C39 mostly contains ...
 55-125 6.69e-04

A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family, which contains Colicin V perocessing peptidase.


Pssm-ID: 239104 [Multi-domain]  Cd Length: 129  Bit Score: 40.01  E-value: 6.69e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 254951741  55 WNIDNAALQLnTVEQLREIPVPFITQIKKKGG-WYILINQIREKHIQYTDSEQGEVTLSLSDFEKRWTGIVL 125
Cdd:cd02424   57 FGLETESYQG-SFLEFLELKNKFIILLKSNGLnHFVIVKKIKKNKFIVLDPKKGKYKITYKEFEKIFNNIII 127
PRK14889 PRK14889
VKOR family protein; Provisional
 210-312 2.58e-03

VKOR family protein; Provisional


Pssm-ID: 184883  Cd Length: 143  Bit Score: 38.53  E-value: 2.58e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254951741 210 LCRINDKTSCENVLNSPGAKLFGwLNWSDLGLLYFAG--GSSALLFTGEQHNEFNLLNALALLAMPYVAFSIYYQAYKVR 287
Cdd:PRK14889  39 FCTINSVINCSSVLSSPYARFLG-IPLDYLGAAWFSAniALALLGVGTLKRILGRVISLWSIIGLAIVPYLVYLEVFVLG 117

                         90       100
                 ....*....|....*....|....*
gi 254951741 288 QWCTLCLGVQVILIVEGVIALTQLK 312
Cdd:PRK14889 118 AICIYCTIAHVSILAAFILILIKLK 142
VKOR_3 cd12920
Vitamin K epoxide reductase family in bacteria; This family includes vitamin K epoxide ...
 188-295 7.18e-03

Vitamin K epoxide reductase family in bacteria; This family includes vitamin K epoxide reductase (VKOR) present in proteobacteria and spirochetes. VKOR (also named VKORC1) is an integral membrane protein that catalyzes the reduction of vitamin K 2,3-epoxide and vitamin K to vitamin K hydroquinone, an essential co-factor subsequently used in the gamma-carboxylation of glutamic acid residues in blood coagulation enzymes. All homologs of VKOR contain an active site CXXC motif, which is switched between reduced and disulfide-bonded states during the reaction cycle. In some bacterial homologs, the VKOR domain is fused with domains of the thioredoxin family of oxidoreductases which may function as redox partners in initiating the reduction cascade.


Pssm-ID: 240603  Cd Length: 134  Bit Score: 36.90  E-value: 7.18e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254951741 188 GLFFTGLLIAKQLGSKNDLT-DRLCRINDKTSCENVLNSPGAKLFGwLNWSDLGLLY---FAGGSSALLFTGEQHNEFNL 263
Cdd:cd12920   10 GLAFSGLLTYHHYGILTDGVgSSFCAINEVVNCDKVAQSPYSAIGG-VPIALWGLLAygfLAALFLLALISREDSERAAG 88

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 254951741 264 LNALALLAMpyVAFSIY---YQAYKVRQWCTLCLG 295
Cdd:cd12920   89 LLFLVLLVG--LVADLVlglISVTAIGALCILCAG 121
 
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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