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Conserved domains on  [gi|379139148|gb|AFC95876|]
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VanY (plasmid) [Enterococcus faecium]

Protein Classification

D-alanyl-D-alanine carboxypeptidase family protein( domain architecture ID 11449003)

D-alanyl-D-alanine carboxypeptidase family protein such as Streptococcus pneumoniae L,D-carboxypeptidase Dacb and Enterococcus faecium D-alanyl-D-alanine carboxypeptidase, which removes C-terminal D-alanyl residues from sugar-peptide cell wall precursors

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LdcB COG1876
LD-carboxypeptidase LdcB, LAS superfamily [Cell wall/membrane/envelope biogenesis];
86-240 2.38e-56

LD-carboxypeptidase LdcB, LAS superfamily [Cell wall/membrane/envelope biogenesis];


:

Pssm-ID: 441480  Cd Length: 168  Bit Score: 179.31  E-value: 2.38e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379139148  86 IVNLS---KHDELINgygLLDSNIYMSKEIAQKFSEMVNDAVKGGVsHFIINSGYRDFDEQSVLY----QEMGAEYAL-- 156
Cdd:COG1876    1 LVNKDhplPADDLVP---LPGGGHRLRKEAAAAFEAMQAAAKKDGI-DLVIVSGYRSYERQEALYnrkvARYGIEAALry 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379139148 157 --PAGYSEHNSGLSLDVGSS------LTKMERAPEGKWIEENAWKYGFILRYPEDKTELTGIQYEPWHIRYVGLPHSAIM 228
Cdd:COG1876   77 saPPGTSEHHTGLAIDIGDPdpgtdlEEEFEETPAGKWLAANAAKYGFILRYPKGKEDITGYAYEPWHWRYVGVEAAKEI 156

                        170
                 ....*....|..
gi 379139148 229 KEKNFVLEEYMD 240
Cdd:COG1876  157 FEKGLTLEEYLG 168
 
Name Accession Description Interval E-value
LdcB COG1876
LD-carboxypeptidase LdcB, LAS superfamily [Cell wall/membrane/envelope biogenesis];
86-240 2.38e-56

LD-carboxypeptidase LdcB, LAS superfamily [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 441480  Cd Length: 168  Bit Score: 179.31  E-value: 2.38e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379139148  86 IVNLS---KHDELINgygLLDSNIYMSKEIAQKFSEMVNDAVKGGVsHFIINSGYRDFDEQSVLY----QEMGAEYAL-- 156
Cdd:COG1876    1 LVNKDhplPADDLVP---LPGGGHRLRKEAAAAFEAMQAAAKKDGI-DLVIVSGYRSYERQEALYnrkvARYGIEAALry 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379139148 157 --PAGYSEHNSGLSLDVGSS------LTKMERAPEGKWIEENAWKYGFILRYPEDKTELTGIQYEPWHIRYVGLPHSAIM 228
Cdd:COG1876   77 saPPGTSEHHTGLAIDIGDPdpgtdlEEEFEETPAGKWLAANAAKYGFILRYPKGKEDITGYAYEPWHWRYVGVEAAKEI 156

                        170
                 ....*....|..
gi 379139148 229 KEKNFVLEEYMD 240
Cdd:COG1876  157 FEKGLTLEEYLG 168
LD-carboxypeptidase cd14852
L,D-carboxypeptidase DacB and LdcB, and related proteins; This L,D-carboxypeptidase family ...
 69-228 1.62e-53

L,D-carboxypeptidase DacB and LdcB, and related proteins; This L,D-carboxypeptidase family includes LdcB LD-Carboxypeptidase from Streptococcus pneumoniae, Bacillus anthracis, and Bacillus subtilis, and L,D-carboxypeptidase DacB from Streptococcus pneumonia and Lactococcus lactis. These enzymes are active against cell-wall-derived tetrapeptides and synthetic tetrapeptides lacking the sugar moiety but are inactive against tetrapeptides terminating in L-alanine. L,D-carboxypeptidase DacB plays a key role in the remodeling of S. pneumoniae peptidoglycan during cell division. It adopts a zinc-dependent carboxypeptidase fold and acts as an L,D-carboxypeptidase towards the tetrapeptide L-Ala-D-iGln-L-Lys-D-Ala of the peptidoglycan stem. This family also includes vanY D-Ala-D-Ala carboxypeptidase which is vancomycin-inducible and penicillin-resistant. VanY hydrolyzes depsipeptide- and D-alanyl-D-alanine-containing peptidoglycan precursors; it is insensitive to beta-lactams. All these enzymes belong to the MEROPS family M15 subfamily B.


Pssm-ID: 350624  Cd Length: 162  Bit Score: 172.04  E-value: 1.62e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379139148  69 LLINSKYPVRQESVKSDIVNlskhdelingYGLLDSNIYMSKEIAQKFSEMVNDAVKGGVsHFIINSGYRDFDEQSVLY- 147
Cdd:cd14852    1 VLVNKDHPLPEDYVPEDLVP----------YVLLDNGLYLRKEAAEALEEMFDAAKKDGI-DLTIVSGYRSYEYQQELYn 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379139148 148 -------QEMGAEYALPAGYSEHNSGLSLDVGSS-----LTKMERAPEGKWIEENAWKYGFILRYPEDKTELTGIQYEPW 215
Cdd:cd14852   70 nyvarygKEEADRYSARPGYSEHQTGLAVDIGSTdgpclEESFEDTPAGKWLAENAHKYGFILRYPKGKENITGYSYEPW 149

                        170
                 ....*....|...
gi 379139148 216 HIRYVGLPHSAIM 228
Cdd:cd14852  150 HFRYVGKEAAKKI 162
VanY pfam02557
D-alanyl-D-alanine carboxypeptidase;
105-222 1.50e-41

D-alanyl-D-alanine carboxypeptidase;


Pssm-ID: 426830 [Multi-domain]  Cd Length: 131  Bit Score: 140.06  E-value: 1.50e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379139148  105 NIYMSKEIAQKFSEMVNDAVKGGVSHFIInSGYRDFDEQSVLYQEMGAEYALPA--------GYSEHNSGLSLDVGSSLT 176
Cdd:pfam02557   1 GIYLRKEAAEALEELFAAAKKEGINLRAI-SGFRSYEYQEALFKKYVKGEGKKAilrwsappGTSEHHTGLAIDIGDPDN 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 379139148  177 KM------ERAPEGKWIEENAWKYGFILRYPEDKTELTGIQYEPWHIRYVGL 222
Cdd:pfam02557  80 PWeleesfEDTAAFKWLQANAHKYGFVLRYPKGKEQITGVSYEPWHWRYVGI 131
LD_carboxy_LdcB NF041194
LD-carboxypeptidase LdcB/DacB;
135-238 6.10e-21

LD-carboxypeptidase LdcB/DacB;


Pssm-ID: 469098  Cd Length: 180  Bit Score: 87.87  E-value: 6.10e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379139148 135 SGYRDFDEQSVLYQ--------EMGAEYALPAGYSEHNSGLSLD-VGSSLTKMERAPEGKWIEENAWKYGFILRYPEDKT 205
Cdd:NF041194  61 SGFRSYETQTELYQnyvnqdgkEAADRYSARPGYSEHQTGLAFDlIDTSGNLLEEPKASQWLLDHAADYGFIVRYLKGKE 140

                         90       100       110
                 ....*....|....*....|....*....|...
gi 379139148 206 ELTGIQYEPWHIRYVGLPHSAIMKEkNFVLEEY 238
Cdd:NF041194 141 ASTGYMPESWHLRYIGKEAKEIADS-GLSLEEY 172
 
Name Accession Description Interval E-value
LdcB COG1876
LD-carboxypeptidase LdcB, LAS superfamily [Cell wall/membrane/envelope biogenesis];
86-240 2.38e-56

LD-carboxypeptidase LdcB, LAS superfamily [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 441480  Cd Length: 168  Bit Score: 179.31  E-value: 2.38e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379139148  86 IVNLS---KHDELINgygLLDSNIYMSKEIAQKFSEMVNDAVKGGVsHFIINSGYRDFDEQSVLY----QEMGAEYAL-- 156
Cdd:COG1876    1 LVNKDhplPADDLVP---LPGGGHRLRKEAAAAFEAMQAAAKKDGI-DLVIVSGYRSYERQEALYnrkvARYGIEAALry 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379139148 157 --PAGYSEHNSGLSLDVGSS------LTKMERAPEGKWIEENAWKYGFILRYPEDKTELTGIQYEPWHIRYVGLPHSAIM 228
Cdd:COG1876   77 saPPGTSEHHTGLAIDIGDPdpgtdlEEEFEETPAGKWLAANAAKYGFILRYPKGKEDITGYAYEPWHWRYVGVEAAKEI 156

                        170
                 ....*....|..
gi 379139148 229 KEKNFVLEEYMD 240
Cdd:COG1876  157 FEKGLTLEEYLG 168
LD-carboxypeptidase cd14852
L,D-carboxypeptidase DacB and LdcB, and related proteins; This L,D-carboxypeptidase family ...
 69-228 1.62e-53

L,D-carboxypeptidase DacB and LdcB, and related proteins; This L,D-carboxypeptidase family includes LdcB LD-Carboxypeptidase from Streptococcus pneumoniae, Bacillus anthracis, and Bacillus subtilis, and L,D-carboxypeptidase DacB from Streptococcus pneumonia and Lactococcus lactis. These enzymes are active against cell-wall-derived tetrapeptides and synthetic tetrapeptides lacking the sugar moiety but are inactive against tetrapeptides terminating in L-alanine. L,D-carboxypeptidase DacB plays a key role in the remodeling of S. pneumoniae peptidoglycan during cell division. It adopts a zinc-dependent carboxypeptidase fold and acts as an L,D-carboxypeptidase towards the tetrapeptide L-Ala-D-iGln-L-Lys-D-Ala of the peptidoglycan stem. This family also includes vanY D-Ala-D-Ala carboxypeptidase which is vancomycin-inducible and penicillin-resistant. VanY hydrolyzes depsipeptide- and D-alanyl-D-alanine-containing peptidoglycan precursors; it is insensitive to beta-lactams. All these enzymes belong to the MEROPS family M15 subfamily B.


Pssm-ID: 350624  Cd Length: 162  Bit Score: 172.04  E-value: 1.62e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379139148  69 LLINSKYPVRQESVKSDIVNlskhdelingYGLLDSNIYMSKEIAQKFSEMVNDAVKGGVsHFIINSGYRDFDEQSVLY- 147
Cdd:cd14852    1 VLVNKDHPLPEDYVPEDLVP----------YVLLDNGLYLRKEAAEALEEMFDAAKKDGI-DLTIVSGYRSYEYQQELYn 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379139148 148 -------QEMGAEYALPAGYSEHNSGLSLDVGSS-----LTKMERAPEGKWIEENAWKYGFILRYPEDKTELTGIQYEPW 215
Cdd:cd14852   70 nyvarygKEEADRYSARPGYSEHQTGLAVDIGSTdgpclEESFEDTPAGKWLAENAHKYGFILRYPKGKENITGYSYEPW 149

                        170
                 ....*....|...
gi 379139148 216 HIRYVGLPHSAIM 228
Cdd:cd14852  150 HFRYVGKEAAKKI 162
VanY pfam02557
D-alanyl-D-alanine carboxypeptidase;
105-222 1.50e-41

D-alanyl-D-alanine carboxypeptidase;


Pssm-ID: 426830 [Multi-domain]  Cd Length: 131  Bit Score: 140.06  E-value: 1.50e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379139148  105 NIYMSKEIAQKFSEMVNDAVKGGVSHFIInSGYRDFDEQSVLYQEMGAEYALPA--------GYSEHNSGLSLDVGSSLT 176
Cdd:pfam02557   1 GIYLRKEAAEALEELFAAAKKEGINLRAI-SGFRSYEYQEALFKKYVKGEGKKAilrwsappGTSEHHTGLAIDIGDPDN 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 379139148  177 KM------ERAPEGKWIEENAWKYGFILRYPEDKTELTGIQYEPWHIRYVGL 222
Cdd:pfam02557  80 PWeleesfEDTAAFKWLQANAHKYGFVLRYPKGKEQITGVSYEPWHWRYVGI 131
DD-dipeptidase_VanXYc cd14849
D-Ala-D-Ala dipeptidase/D-Ala-D-Ala carboxypeptidase (VanXYc) and related proteins; VanXYc ...
 126-221 2.11e-23

D-Ala-D-Ala dipeptidase/D-Ala-D-Ala carboxypeptidase (VanXYc) and related proteins; VanXYc peptidase (also known as vanXY(C) peptidase, D-alanyl-D-alanine carboxypeptidase D,D-dipeptidase/D,D-carboxypeptidase, vancomycin resistance D,D-dipeptidase) is a Zn2+-dependent enzyme that mediates resistance to the antibiotic vancomycin in Enterococci. Some of the vancomycin resistance operons encode VanXY D,D-carboxypeptidase which hydrolyzes both, dipeptide (D-Ala-D-Ala) or pentapeptide (UDP-MurNac-L-Ala-D-Glu-L-Lys-D-Ala-D-Ala). It is a bifunctional enzyme that catalyzes D,D-peptidase and D,D-carboxypeptidase activities. VanXY has higher sequence similarity to VanY than with VanX and hydrolyzes D,D-dipeptides such as D-Ala-D-Ala, whereas VanY is inactive against this substrate; thus having a less restrictive active site to accommodate larger substrates such as UDP-MurNAc-pentapeptide[Ala]. This family belongs to the MEROPS family M15, subfamily B, and includes the D,D-dipeptidases VanXYg and VanXYe.


Pssm-ID: 350623 [Multi-domain]  Cd Length: 127  Bit Score: 92.71  E-value: 2.11e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379139148 126 GGVSHFIINSGYRDFDEQSVLYQ----EMGAEY-----ALPaGYSEHNSGLSLDVGSSLTKM-------ERAPEGKWIEE 189
Cdd:cd14849   17 GGEDEIVPVSGYRSKEEQTAIYDdslnENGEEFtekyvALP-GHSEHQTGLAIDLGLNKKDIdficpsfPDSGICDLFRE 95

                         90       100       110
                 ....*....|....*....|....*....|..
gi 379139148 190 NAWKYGFILRYPEDKTELTGIQYEPWHIRYVG 221
Cdd:cd14849   96 QAADYGFIERYPKDKEEITGISYEPWHFRYVG 127
Peptidase_M15 cd14814
Metalloproteases including zinc D-Ala-D-Ala carboxypeptidase, L-Ala-D-Glu peptidase, L, ...
 110-220 7.17e-23

Metalloproteases including zinc D-Ala-D-Ala carboxypeptidase, L-Ala-D-Glu peptidase, L,D-carboxypeptidase, bacteriophage endolysins, and related proteins; This family summarizes zinc-binding metallopeptidases which are mostly carboxypeptidases and dipeptidases, and includes zinc-dependent D-Ala-D-Ala carboxypeptidases, VanX, L-Ala-D-Glu peptidase, L,D-carboxypeptidase and bacteriophage endolysins, amongst other family members. These peptidases belong to MEROPS family M15 which are involved in bacterial cell wall biosynthesis and metabolism.


Pssm-ID: 350615 [Multi-domain]  Cd Length: 111  Bit Score: 90.96  E-value: 7.17e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379139148 110 KEIAQKFSEMVNDAVKGGVsHFIINSGYRDFDEQSVLYQEMGAEY-----ALPAGYSEHNSGLSLDVGSSlTKMERAPEG 184
Cdd:cd14814    1 PDAAEALARMIAAAGAEGR-TLTINSGYRTYAQQLRLFAAKGKGSggrrwAAPPGTSNHQWGLAIDLGDG-GGWRETQGY 78

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 379139148 185 KWIEENAWKYGFilRYPEDKtELTGIQYEPWHIRYV 220
Cdd:cd14814   79 RWLKANAPRYGF--DNPGGA-RRGGAFQEPWHWEYV 111
LD_carboxy_LdcB NF041194
LD-carboxypeptidase LdcB/DacB;
135-238 6.10e-21

LD-carboxypeptidase LdcB/DacB;


Pssm-ID: 469098  Cd Length: 180  Bit Score: 87.87  E-value: 6.10e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379139148 135 SGYRDFDEQSVLYQ--------EMGAEYALPAGYSEHNSGLSLD-VGSSLTKMERAPEGKWIEENAWKYGFILRYPEDKT 205
Cdd:NF041194  61 SGFRSYETQTELYQnyvnqdgkEAADRYSARPGYSEHQTGLAFDlIDTSGNLLEEPKASQWLLDHAADYGFIVRYLKGKE 140

                         90       100       110
                 ....*....|....*....|....*....|...
gi 379139148 206 ELTGIQYEPWHIRYVGLPHSAIMKEkNFVLEEY 238
Cdd:NF041194 141 ASTGYMPESWHLRYIGKEAKEIADS-GLSLEEY 172
DD-carboxypeptidase_like cd14847
Uncharacterized proteins of the MEROPS peptidase family M15, subfamily B; This family of ...
 110-219 4.24e-10

Uncharacterized proteins of the MEROPS peptidase family M15, subfamily B; This family of uncharacterized proteins similar to D-Ala-D-Ala carboxypeptidase pdcA (Myxococcus-type) are zinc-binding enzymes that belong to the peptidase M15 subfamily B. The enzyme D-Ala-D-Ala carbozypeptidase catalyzes carboxypeptidation reactions involved in bacterial cell wall metabolism.


Pssm-ID: 350622  Cd Length: 162  Bit Score: 57.59  E-value: 4.24e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379139148 110 KEIAQKFSEMVNDAVKGGVsHFIINSGYRDFDEQS-----------VLYQEMGAEY------------------ALPaGY 160
Cdd:cd14847    3 PDAAEAFLALQAAAAKDGF-DLQIASSFRSFERQLaiwnrkwsgerPVLDDNGQPLdisslspeekihailrwsALP-GA 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 379139148 161 SEHNSGLSLDV----------GSSLTKMERAPEG------KWIEENAWKYGFILRYPEDKtelTGIQYEPWHIRY 219
Cdd:cd14847   81 SRHHWGTDIDVydanalpagyQLQLTPSEYEEGGpfaklyQWLDENAAKFGFFRPYTQDR---GGVAPEPWHLSY 152
L-Ala-D-Glu_peptidase_like cd14845
L-Ala-D-Glu peptidase, also known as L-alanyl-D-glutamate endopeptidase; This L-Ala-D-Glu ...
 111-193 6.32e-03

L-Ala-D-Glu peptidase, also known as L-alanyl-D-glutamate endopeptidase; This L-Ala-D-Glu peptidase family includes L-alanyl-D-glutamate peptidase (bacteriophage T5) (also known as L-alanoyl-D-glutamate endopeptidase), and Ply118 and Ply500 L-Ala-D-Glu peptidase. Bacteriophage endolysin degrades the peptidoglycan of the bacterial host from within, leading to cell lysis and release of progeny virions. The bacteriophage endolysin Ply118 cleaves between L-Ala and D-Glu residues of Listeria cell wall peptidoglycan. This family belongs to the MEROPS peptidase M15 subfamily C.


Pssm-ID: 350620 [Multi-domain]  Cd Length: 126  Bit Score: 36.19  E-value: 6.32e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379139148 111 EIAQKFSEMVNDAVKGGVsHFIINSGYRDFDEQSVLYQ------EMGAEYAlPAGYSEHNSGLSLDVGSSLTKMERAPEG 184
Cdd:cd14845   11 EVRAVVKELIELAEEEGI-DFRITEGYRSPARQAALYAqgrtkpGLIVTNA-RGGQSYHNYGLAVDIVPLVNGKLSTGGA 88


                 ....*....
gi 379139148 185 KWIEENAWK 193
Cdd:cd14845   89 DPWVSKAYQ 97
Peptidase_M15_like cd14846
Uncharacterized family of the peptidase family M15, subfamily B; This family of ...
 116-216 7.69e-03

Uncharacterized family of the peptidase family M15, subfamily B; This family of uncharacterized proteins, similar to endolysin lys (Clavibacter phage CMP1) and VanYn peptidase, are zinc-binding enzymes that belong to the peptidase M15 subfamily B, involved in bacterial cell wall metabolism.


Pssm-ID: 350621  Cd Length: 104  Bit Score: 35.36  E-value: 7.69e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379139148 116 FSEMVNDAVKGGVShFIINSGYRDFDEQSVLYQEMGAEYA---------LPAGYSEHNSGLSLDVGssltkmeRAPEGKW 186
Cdd:cd14846    9 LTAAATAAAADGVT-LRITSGWRSPAEQQRLLDDAVRTYGseeearrwvAPPEDSAHVTGEAVDIG-------PADAAQW 80

                         90       100       110
                 ....*....|....*....|....*....|
gi 379139148 187 IEENAWKYGFILRYPEdkteltgiqyEPWH 216
Cdd:cd14846   81 LERHGARYGLCRIYAN----------EWWH 100
 
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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