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Conserved domains on  [gi|2264344984|gb|UTB60204|]
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D-alanine:D-alanine ligase, partial [Staphylococcus lugdunensis]

Protein Classification

D-alanine--D-alanine ligase( domain architecture ID 1000172)

D-alanine--D-alanine ligase catalyzes the synthesis of D-alanyl-D-alanine, an essential component of bacterial peptidoglycan, and is involved in cell wall formation

EC:  6.3.2.4
Gene Ontology:  GO:0009252|GO:0008716|GO:0046872|GO:0005524
SCOP:  4002041|4003870

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ddl super family cl35171
D-alanine--D-alanine ligase;
1-134 1.51e-52

D-alanine--D-alanine ligase;


The actual alignment was detected with superfamily member PRK01966:

Pssm-ID: 234993 [Multi-domain]  Cd Length: 333  Bit Score: 168.76  E-value: 1.51e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344984   1 QNVLNAIDKEKYLVDIIYITNDGLWKKKGnitatiESPEELTLTDVEPEDITLLLKQSSAGEAYDAVFPLLHGPNGEDGT 80
Cdd:PRK01966   25 KSVLKALDKEKYEVVPIGITKDGRWYLID------ADNMELADDDNDKEDLSLLILPSGGSEEVDVVFPVLHGPPGEDGT 98

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2264344984  81 IQGLFEVLDIPYVGNGVLAASSSMDKLVMKQLFEHRGLPQLPYISFLRSEYEKY 134
Cdd:PRK01966   99 IQGLLELLGIPYVGCGVLASALSMDKILTKRLLAAAGIPVAPYVVLTRGDWEEA 152
 
Name Accession Description Interval E-value
ddl PRK01966
D-alanine--D-alanine ligase;
1-134 1.51e-52

D-alanine--D-alanine ligase;


Pssm-ID: 234993 [Multi-domain]  Cd Length: 333  Bit Score: 168.76  E-value: 1.51e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344984   1 QNVLNAIDKEKYLVDIIYITNDGLWKKKGnitatiESPEELTLTDVEPEDITLLLKQSSAGEAYDAVFPLLHGPNGEDGT 80
Cdd:PRK01966   25 KSVLKALDKEKYEVVPIGITKDGRWYLID------ADNMELADDDNDKEDLSLLILPSGGSEEVDVVFPVLHGPPGEDGT 98

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2264344984  81 IQGLFEVLDIPYVGNGVLAASSSMDKLVMKQLFEHRGLPQLPYISFLRSEYEKY 134
Cdd:PRK01966   99 IQGLLELLGIPYVGCGVLASALSMDKILTKRLLAAAGIPVAPYVVLTRGDWEEA 152
DdlA COG1181
D-alanine-D-alanine ligase or related ATP-grasp enzyme [Cell wall/membrane/envelope biogenesis, ...
 1-132 4.39e-34

D-alanine-D-alanine ligase or related ATP-grasp enzyme [Cell wall/membrane/envelope biogenesis, General function prediction only]; D-alanine-D-alanine ligase or related ATP-grasp enzyme is part of the Pathway/BioSystem: Mureine biosynthesis


Pssm-ID: 440794 [Multi-domain]  Cd Length: 303  Bit Score: 120.21  E-value: 4.39e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344984   1 QNVLNAIDKEKYLVDIIYITNDGLwkkkgnitatiesPEELTLTDVepeditlllkqssageayDAVFPLLHGPNGEDGT 80
Cdd:COG1181    22 RAVAAALDKAGYDVVPIGIDVEDL-------------PAALKELKP------------------DVVFPALHGRGGEDGT 70

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2264344984  81 IQGLFEVLDIPYVGNGVLAASSSMDKLVMKQLFEHRGLPQLPYISFLRSEYE 132
Cdd:COG1181    71 IQGLLELLGIPYTGSGVLASALAMDKALTKRVLAAAGLPTPPYVVLRRGELA 122
D_ala_D_alaTIGR TIGR01205
D-alanine--D-alanine ligase; This model describes D-Ala--D-Ala ligase, an enzyme that makes a ...
 1-130 6.13e-33

D-alanine--D-alanine ligase; This model describes D-Ala--D-Ala ligase, an enzyme that makes a required precursor of the bacterial cell wall. It also describes some closely related proteins responsible for resistance to glycopeptide antibiotics such as vancomycin. The mechanism of glyopeptide antibiotic resistance involves the production of D-alanine-D-lactate (VanA and VanB families) or D-alanine-D-serine (VanC). The seed alignment contains only chromosomally encoded D-ala--D-ala ligases, but a number of antibiotic resistance proteins score above the trusted cutoff of this model. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan]


Pssm-ID: 273498 [Multi-domain]  Cd Length: 315  Bit Score: 117.77  E-value: 6.13e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344984   1 QNVLNAIDKEKYLVDIIYITNDGLWKKKGNITATIESPEELtltdvepeditlllkqssagEAYDAVFPLLHGPNGEDGT 80
Cdd:TIGR01205  21 AAVLKALRDLGYDVYPVDIDKMGSWTYKDLPQLILELGALL--------------------EGIDVVFPVLHGRYGEDGT 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 2264344984  81 IQGLFEVLDIPYVGNGVLAASSSMDKLVMKQLFEHRGLPQLPYISFLRSE 130
Cdd:TIGR01205  81 IQGLLELMGIPYTGSGVLASALSMDKLLTKLLWKALGLPTPDYIVLTQNR 130
Dala_Dala_lig_N pfam01820
D-ala D-ala ligase N-terminus; This family represents the N-terminal region of the ...
 1-94 2.14e-32

D-ala D-ala ligase N-terminus; This family represents the N-terminal region of the D-alanine--D-alanine ligase enzyme EC:6.3.2.4 which is thought to be involved in substrate binding. D-Alanine is one of the central molecules of the cross-linking step of peptidoglycan assembly. There are three enzymes involved in the D-alanine branch of peptidoglycan biosynthesis: the pyridoxal phosphate-dependent D-alanine racemase (Alr), the ATP-dependent D-alanine:D-alanine ligase (Ddl), and the ATP-dependent D-alanine:D-alanine-adding enzyme (MurF). This domain is structurally related to the PreATP-grasp domain.


Pssm-ID: 460346 [Multi-domain]  Cd Length: 118  Bit Score: 110.77  E-value: 2.14e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344984   1 QNVLNAIDKEKYLVDIIYITNDGLWKKKGNITATIESPEELTLTDVEPEDITLLLKQSSAGEAY---DAVFPLLHGPNGE 77
Cdd:pfam01820  21 RSVLKALDKEKYEVIPIGITKDGRLGEAALRELASDDGLLLEVDDAPDGGPAGLLFGPNVLELLievDVVFPVLHGPNGE 100

                          90
                  ....*....|....*..
gi 2264344984  78 DGTIQGLFEVLDIPYVG 94
Cdd:pfam01820 101 DGTLQGLLELAGIPYVG 117
 
Name Accession Description Interval E-value
ddl PRK01966
D-alanine--D-alanine ligase;
1-134 1.51e-52

D-alanine--D-alanine ligase;


Pssm-ID: 234993 [Multi-domain]  Cd Length: 333  Bit Score: 168.76  E-value: 1.51e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344984   1 QNVLNAIDKEKYLVDIIYITNDGLWKKKGnitatiESPEELTLTDVEPEDITLLLKQSSAGEAYDAVFPLLHGPNGEDGT 80
Cdd:PRK01966   25 KSVLKALDKEKYEVVPIGITKDGRWYLID------ADNMELADDDNDKEDLSLLILPSGGSEEVDVVFPVLHGPPGEDGT 98

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2264344984  81 IQGLFEVLDIPYVGNGVLAASSSMDKLVMKQLFEHRGLPQLPYISFLRSEYEKY 134
Cdd:PRK01966   99 IQGLLELLGIPYVGCGVLASALSMDKILTKRLLAAAGIPVAPYVVLTRGDWEEA 152
DdlA COG1181
D-alanine-D-alanine ligase or related ATP-grasp enzyme [Cell wall/membrane/envelope biogenesis, ...
 1-132 4.39e-34

D-alanine-D-alanine ligase or related ATP-grasp enzyme [Cell wall/membrane/envelope biogenesis, General function prediction only]; D-alanine-D-alanine ligase or related ATP-grasp enzyme is part of the Pathway/BioSystem: Mureine biosynthesis


Pssm-ID: 440794 [Multi-domain]  Cd Length: 303  Bit Score: 120.21  E-value: 4.39e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344984   1 QNVLNAIDKEKYLVDIIYITNDGLwkkkgnitatiesPEELTLTDVepeditlllkqssageayDAVFPLLHGPNGEDGT 80
Cdd:COG1181    22 RAVAAALDKAGYDVVPIGIDVEDL-------------PAALKELKP------------------DVVFPALHGRGGEDGT 70

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2264344984  81 IQGLFEVLDIPYVGNGVLAASSSMDKLVMKQLFEHRGLPQLPYISFLRSEYE 132
Cdd:COG1181    71 IQGLLELLGIPYTGSGVLASALAMDKALTKRVLAAAGLPTPPYVVLRRGELA 122
D_ala_D_alaTIGR TIGR01205
D-alanine--D-alanine ligase; This model describes D-Ala--D-Ala ligase, an enzyme that makes a ...
 1-130 6.13e-33

D-alanine--D-alanine ligase; This model describes D-Ala--D-Ala ligase, an enzyme that makes a required precursor of the bacterial cell wall. It also describes some closely related proteins responsible for resistance to glycopeptide antibiotics such as vancomycin. The mechanism of glyopeptide antibiotic resistance involves the production of D-alanine-D-lactate (VanA and VanB families) or D-alanine-D-serine (VanC). The seed alignment contains only chromosomally encoded D-ala--D-ala ligases, but a number of antibiotic resistance proteins score above the trusted cutoff of this model. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan]


Pssm-ID: 273498 [Multi-domain]  Cd Length: 315  Bit Score: 117.77  E-value: 6.13e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344984   1 QNVLNAIDKEKYLVDIIYITNDGLWKKKGNITATIESPEELtltdvepeditlllkqssagEAYDAVFPLLHGPNGEDGT 80
Cdd:TIGR01205  21 AAVLKALRDLGYDVYPVDIDKMGSWTYKDLPQLILELGALL--------------------EGIDVVFPVLHGRYGEDGT 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 2264344984  81 IQGLFEVLDIPYVGNGVLAASSSMDKLVMKQLFEHRGLPQLPYISFLRSE 130
Cdd:TIGR01205  81 IQGLLELMGIPYTGSGVLASALSMDKLLTKLLWKALGLPTPDYIVLTQNR 130
Dala_Dala_lig_N pfam01820
D-ala D-ala ligase N-terminus; This family represents the N-terminal region of the ...
 1-94 2.14e-32

D-ala D-ala ligase N-terminus; This family represents the N-terminal region of the D-alanine--D-alanine ligase enzyme EC:6.3.2.4 which is thought to be involved in substrate binding. D-Alanine is one of the central molecules of the cross-linking step of peptidoglycan assembly. There are three enzymes involved in the D-alanine branch of peptidoglycan biosynthesis: the pyridoxal phosphate-dependent D-alanine racemase (Alr), the ATP-dependent D-alanine:D-alanine ligase (Ddl), and the ATP-dependent D-alanine:D-alanine-adding enzyme (MurF). This domain is structurally related to the PreATP-grasp domain.


Pssm-ID: 460346 [Multi-domain]  Cd Length: 118  Bit Score: 110.77  E-value: 2.14e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344984   1 QNVLNAIDKEKYLVDIIYITNDGLWKKKGNITATIESPEELTLTDVEPEDITLLLKQSSAGEAY---DAVFPLLHGPNGE 77
Cdd:pfam01820  21 RSVLKALDKEKYEVIPIGITKDGRLGEAALRELASDDGLLLEVDDAPDGGPAGLLFGPNVLELLievDVVFPVLHGPNGE 100

                          90
                  ....*....|....*..
gi 2264344984  78 DGTIQGLFEVLDIPYVG 94
Cdd:pfam01820 101 DGTLQGLLELAGIPYVG 117
PRK14573 PRK14573
bifunctional UDP-N-acetylmuramate--L-alanine ligase/D-alanine--D-alanine ligase;
1-123 3.44e-22

bifunctional UDP-N-acetylmuramate--L-alanine ligase/D-alanine--D-alanine ligase;


Pssm-ID: 184752 [Multi-domain]  Cd Length: 809  Bit Score: 91.03  E-value: 3.44e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344984   1 QNVLNAIDKEKYLVDIIYITNDGLWKKKGNITATIESPEELTLTDVEPeditlllkqSSAGEAYDAVFPLLHGPNGEDGT 80
Cdd:PRK14573  473 KNIAKYLSPEFYDVSYFLINRQGLWETVSSLETAIEEDSGKSVLSSEI---------AQALAKVDVVLPILHGPFGEDGT 543

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2264344984  81 IQGLFEVLDIPYVGNGVLAASSSMDKLVMKQLFEHRGLPQLPY 123
Cdd:PRK14573  544 MQGFLEIIGKPYTGPSLAFSAIAMDKVLTKRFASDVGVPVVPY 586
ddl PRK01372
D-alanine--D-alanine ligase; Reviewed
 45-130 7.52e-22

D-alanine--D-alanine ligase; Reviewed


Pssm-ID: 234948 [Multi-domain]  Cd Length: 304  Bit Score: 88.24  E-value: 7.52e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344984  45 DVEPEDITLLLKQssageAYDAVFPLLHGPNGEDGTIQGLFEVLDIPYVGNGVLAASSSMDKLVMKQLFEHRGLPQLPYI 124
Cdd:PRK01372   43 DPGEDIAAQLKEL-----GFDRVFNALHGRGGEDGTIQGLLELLGIPYTGSGVLASALAMDKLRTKLVWQAAGLPTPPWI 117


                  ....*.
gi 2264344984 125 SFLRSE 130
Cdd:PRK01372  118 VLTREE 123
PRK14572 PRK14572
D-alanyl-alanine synthetase A; Provisional
 7-131 6.46e-18

D-alanyl-alanine synthetase A; Provisional


Pssm-ID: 173036 [Multi-domain]  Cd Length: 347  Bit Score: 78.02  E-value: 6.46e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344984   7 IDKEKYLVDIIYITNDGLW-----------KKKGNitATIESPEELTLTDV--EPEDITLLlkqssageAYDAVFPLLHG 73
Cdd:PRK14572   29 LHTMGHSVKPILLTPDGGWvvptvyrpsipDESGN--SEDLFLEEFQKANGvsEPADISQL--------DADIAFLGLHG 98

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2264344984  74 PNGEDGTIQGLFEVLDIPYVGNGVLAASSSMDKLVMKQLFEHRGLPQLPYISFLRSEY 131
Cdd:PRK14572   99 GAGEDGRIQGFLDTLGIPYTGSGVLASALAMDKTRANQIFLQSGQKVAPFFELEKLKY 156
PRK14570 PRK14570
D-alanyl-alanine synthetase A; Provisional
 65-131 1.58e-13

D-alanyl-alanine synthetase A; Provisional


Pssm-ID: 173034 [Multi-domain]  Cd Length: 364  Bit Score: 66.01  E-value: 1.58e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2264344984  65 DAVFPLLHGPNGEDGTIQGLFEVLDIPYVGNGVLAASSSMDKLVMKQLFEHRGLPQLPYISFLRSEY 131
Cdd:PRK14570   89 DVVFPIVHGRTGEDGAIQGFLKVMDIPCVGAGILGSAISINKYFCKLLLKSFNIPLVPFIGFRKYDY 155
PRK14571 PRK14571
D-alanyl-alanine synthetase A; Provisional
 40-108 9.39e-09

D-alanyl-alanine synthetase A; Provisional


Pssm-ID: 184751 [Multi-domain]  Cd Length: 299  Bit Score: 52.13  E-value: 9.39e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2264344984  40 ELTLTDVEpEDitlLLKQSSAGEAYDAVFPLLHGPNGEDGTIQGLFEVLDIPYVGNGVLAASSSMDKLV 108
Cdd:PRK14571   34 EVTVFDVD-ED---FLKKVDQLKSFDVVFNVLHGTFGEDGTLQAILDFLGIRYTGSDAFSSMICFDKLL 98
PRK14569 PRK14569
D-alanyl-alanine synthetase A; Provisional
 65-127 7.70e-07

D-alanyl-alanine synthetase A; Provisional


Pssm-ID: 173033 [Multi-domain]  Cd Length: 296  Bit Score: 46.59  E-value: 7.70e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2264344984  65 DAVFPLLHGPNGEDGTIQGLFEVLDIPYVGNGVLAASSSMDKLVMKQLFEHRGLPQlPYISFL 127
Cdd:PRK14569   58 DKCFVALHGEDGENGRVSALLEMLEIKHTSSSMKSSVITMDKMISKEILMHHRMPT-PMAKFL 119
 
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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