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Conserved domains on  [gi|1998277091|ref|WP_206546545|]
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MULTISPECIES: cytidine deaminase [Alphaproteobacteria]

Protein Classification

cytidine/deoxycytidylate deaminase family protein( domain architecture ID 923)

cytidine/deoxycytidylate deaminase family protein similar to Bacillus subtilis cytidine deaminase that scavenges exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
cytidine_deaminase-like super family cl00269
Cytidine and deoxycytidylate deaminase zinc-binding region. The family contains cytidine ...
1-131 2.82e-58

Cytidine and deoxycytidylate deaminase zinc-binding region. The family contains cytidine deaminases, nucleoside deaminases, deoxycytidylate deaminases and riboflavin deaminases. Also included are the apoBec family of mRNA editing enzymes. All members are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate.


The actual alignment was detected with superfamily member PRK05578:

Pssm-ID: 444801 [Multi-domain]  Cd Length: 131  Bit Score: 176.26  E-value: 2.82e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998277091   1 MSAEDLFAAASAAMQNAYAPYSRFPVGAAVKTEAGAIHAGCNIENASYPEGWCAETTALGHLVMAGGGRVTEIAVVAEKM 80
Cdd:PRK05578    1 MDWKELIEAAIEASEKAYAPYSKFPVGAALLTDDGRIYTGCNIENASYGLTNCAERTAIFKAISEGGGRLVAIACVGETG 80
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1998277091  81 PKIMPCGGCRQRLAEFVTDDACLHLCDTNGVLETVPFSAVFPRGFSFEDGK 131
Cdd:PRK05578   81 EPLSPCGRCRQVLAEFGGPDLLVTLVAKDGPTGEMTLGELLPYAFTPDDLG 131
 
Name Accession Description Interval E-value
PRK05578 PRK05578
cytidine deaminase; Validated
1-131 2.82e-58

cytidine deaminase; Validated


Pssm-ID: 180142 [Multi-domain]  Cd Length: 131  Bit Score: 176.26  E-value: 2.82e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998277091   1 MSAEDLFAAASAAMQNAYAPYSRFPVGAAVKTEAGAIHAGCNIENASYPEGWCAETTALGHLVMAGGGRVTEIAVVAEKM 80
Cdd:PRK05578    1 MDWKELIEAAIEASEKAYAPYSKFPVGAALLTDDGRIYTGCNIENASYGLTNCAERTAIFKAISEGGGRLVAIACVGETG 80
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1998277091  81 PKIMPCGGCRQRLAEFVTDDACLHLCDTNGVLETVPFSAVFPRGFSFEDGK 131
Cdd:PRK05578   81 EPLSPCGRCRQVLAEFGGPDLLVTLVAKDGPTGEMTLGELLPYAFTPDDLG 131
Cdd COG0295
Cytidine deaminase [Nucleotide transport and metabolism]; Cytidine deaminase is part of the ...
1-129 1.60e-53

Cytidine deaminase [Nucleotide transport and metabolism]; Cytidine deaminase is part of the Pathway/BioSystem: Pyrimidine salvage


Pssm-ID: 440064 [Multi-domain]  Cd Length: 130  Bit Score: 164.17  E-value: 1.60e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998277091   1 MSAEDLFAAASAAMQNAYAPYSRFPVGAAVKTEAGAIHAGCNIENASYPEGWCAETTALGHLVMAGGGRVTEIAVVAEKM 80
Cdd:COG0295     1 MDDEELIEAAREARENAYAPYSKFPVGAALLTEDGRIYTGCNVENASYGLTLCAERTAIFAAVAAGEREIKAIAVVADTG 80
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1998277091  81 PKIMPCGGCRQRLAEFVTDDACLHLCDTNGVLETVPFSAVFPRGFSFED 129
Cdd:COG0295    81 EPVSPCGACRQVLAEFAGPDLEVILPNGDGEVKTVTLSELLPDAFGPED 129
cyt_deam_tetra TIGR01354
cytidine deaminase, homotetrameric; This small, homotetrameric zinc metalloprotein is found in ...
4-129 1.26e-47

cytidine deaminase, homotetrameric; This small, homotetrameric zinc metalloprotein is found in humans and most bacteria. A related, homodimeric form with a much larger subunit is found in E. coli and in Arabidopsis. Both types may act on deoxycytidine as well as cytidine. [Purines, pyrimidines, nucleosides, and nucleotides, Salvage of nucleosides and nucleotides]


Pssm-ID: 273572 [Multi-domain]  Cd Length: 127  Bit Score: 149.34  E-value: 1.26e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998277091   4 EDLFAAASAAMQNAYAPYSRFPVGAAVKTEAGAIHAGCNIENASYPEGWCAETTALGHLVMAGGGRVTEIAVVAEKMPKI 83
Cdd:TIGR01354   1 DKLFKAAQEARKNAYAPYSNFKVGAALLTKDGRIFTGVNVENASYPLTICAERSAIGKAISAGYRKFVAIAVADSADDPV 80
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1998277091  84 MPCGGCRQRLAEFVTDDACLHLCDTNGVLETVPFSAVFPRGFSFED 129
Cdd:TIGR01354  81 SPCGACRQVLAEFAGPDTPIYMTNNDGTYKVYTVGELLPFGFGPSD 126
cytidine_deaminase cd01283
Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the ...
14-118 1.88e-35

Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate. Cytidine deaminases catalyze the deamination of cytidine to uridine and are important in the pyrimadine salvage pathway in many cell types, from bacteria to humans. This family also includes the apoBec proteins, which are a mammal specific expansion of RNA editing enzymes, and the closely related phorbolins, and the AID (activation-induced) enzymes.


Pssm-ID: 238610 [Multi-domain]  Cd Length: 112  Bit Score: 117.83  E-value: 1.88e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998277091  14 MQNAYAPYSRFPVGAAVKTEAGAIHAGCNIENASYPEGWCAETTALGHLVMAGGGRVTEIAVVAEKMPKIMPCGGCRQRL 93
Cdd:cd01283     8 AEFAYAPYSNFTVGAALLTKDGRIFTGVNVENASYGLTLCAERTAIGKAVSEGLRRYLVTWAVSDEGGVWSPCGACRQVL 87
                          90       100
                  ....*....|....*....|....*
gi 1998277091  94 AEFVTDDACLHLCDTNGVLETVPFS 118
Cdd:cd01283    88 AEFLPSRLYIIIDNPKGEEFAYTLS 112
dCMP_cyt_deam_1 pfam00383
Cytidine and deoxycytidylate deaminase zinc-binding region;
14-96 6.48e-10

Cytidine and deoxycytidylate deaminase zinc-binding region;


Pssm-ID: 395307 [Multi-domain]  Cd Length: 100  Bit Score: 52.30  E-value: 6.48e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998277091  14 MQNAYaPYSRFPVGAA-VKTEAGAIHAGCNIENASYPEGWCAETTALGHLVMAGGGRV---TEIAVVAEkmpkimPCGGC 89
Cdd:pfam00383  13 AKRAY-PYSNFPVGAViVKKDGEIIATGYNGENAGYDPTIHAERNAIRQAGKRGEGVRlegATLYVTLE------PCGMC 85

                  ....*..
gi 1998277091  90 RQRLAEF 96
Cdd:pfam00383  86 AQAIIES 92
 
Name Accession Description Interval E-value
PRK05578 PRK05578
cytidine deaminase; Validated
1-131 2.82e-58

cytidine deaminase; Validated


Pssm-ID: 180142 [Multi-domain]  Cd Length: 131  Bit Score: 176.26  E-value: 2.82e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998277091   1 MSAEDLFAAASAAMQNAYAPYSRFPVGAAVKTEAGAIHAGCNIENASYPEGWCAETTALGHLVMAGGGRVTEIAVVAEKM 80
Cdd:PRK05578    1 MDWKELIEAAIEASEKAYAPYSKFPVGAALLTDDGRIYTGCNIENASYGLTNCAERTAIFKAISEGGGRLVAIACVGETG 80
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1998277091  81 PKIMPCGGCRQRLAEFVTDDACLHLCDTNGVLETVPFSAVFPRGFSFEDGK 131
Cdd:PRK05578   81 EPLSPCGRCRQVLAEFGGPDLLVTLVAKDGPTGEMTLGELLPYAFTPDDLG 131
Cdd COG0295
Cytidine deaminase [Nucleotide transport and metabolism]; Cytidine deaminase is part of the ...
1-129 1.60e-53

Cytidine deaminase [Nucleotide transport and metabolism]; Cytidine deaminase is part of the Pathway/BioSystem: Pyrimidine salvage


Pssm-ID: 440064 [Multi-domain]  Cd Length: 130  Bit Score: 164.17  E-value: 1.60e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998277091   1 MSAEDLFAAASAAMQNAYAPYSRFPVGAAVKTEAGAIHAGCNIENASYPEGWCAETTALGHLVMAGGGRVTEIAVVAEKM 80
Cdd:COG0295     1 MDDEELIEAAREARENAYAPYSKFPVGAALLTEDGRIYTGCNVENASYGLTLCAERTAIFAAVAAGEREIKAIAVVADTG 80
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1998277091  81 PKIMPCGGCRQRLAEFVTDDACLHLCDTNGVLETVPFSAVFPRGFSFED 129
Cdd:COG0295    81 EPVSPCGACRQVLAEFAGPDLEVILPNGDGEVKTVTLSELLPDAFGPED 129
cyt_deam_tetra TIGR01354
cytidine deaminase, homotetrameric; This small, homotetrameric zinc metalloprotein is found in ...
4-129 1.26e-47

cytidine deaminase, homotetrameric; This small, homotetrameric zinc metalloprotein is found in humans and most bacteria. A related, homodimeric form with a much larger subunit is found in E. coli and in Arabidopsis. Both types may act on deoxycytidine as well as cytidine. [Purines, pyrimidines, nucleosides, and nucleotides, Salvage of nucleosides and nucleotides]


Pssm-ID: 273572 [Multi-domain]  Cd Length: 127  Bit Score: 149.34  E-value: 1.26e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998277091   4 EDLFAAASAAMQNAYAPYSRFPVGAAVKTEAGAIHAGCNIENASYPEGWCAETTALGHLVMAGGGRVTEIAVVAEKMPKI 83
Cdd:TIGR01354   1 DKLFKAAQEARKNAYAPYSNFKVGAALLTKDGRIFTGVNVENASYPLTICAERSAIGKAISAGYRKFVAIAVADSADDPV 80
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1998277091  84 MPCGGCRQRLAEFVTDDACLHLCDTNGVLETVPFSAVFPRGFSFED 129
Cdd:TIGR01354  81 SPCGACRQVLAEFAGPDTPIYMTNNDGTYKVYTVGELLPFGFGPSD 126
cytidine_deaminase cd01283
Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the ...
14-118 1.88e-35

Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate. Cytidine deaminases catalyze the deamination of cytidine to uridine and are important in the pyrimadine salvage pathway in many cell types, from bacteria to humans. This family also includes the apoBec proteins, which are a mammal specific expansion of RNA editing enzymes, and the closely related phorbolins, and the AID (activation-induced) enzymes.


Pssm-ID: 238610 [Multi-domain]  Cd Length: 112  Bit Score: 117.83  E-value: 1.88e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998277091  14 MQNAYAPYSRFPVGAAVKTEAGAIHAGCNIENASYPEGWCAETTALGHLVMAGGGRVTEIAVVAEKMPKIMPCGGCRQRL 93
Cdd:cd01283     8 AEFAYAPYSNFTVGAALLTKDGRIFTGVNVENASYGLTLCAERTAIGKAVSEGLRRYLVTWAVSDEGGVWSPCGACRQVL 87
                          90       100
                  ....*....|....*....|....*
gi 1998277091  94 AEFVTDDACLHLCDTNGVLETVPFS 118
Cdd:cd01283    88 AEFLPSRLYIIIDNPKGEEFAYTLS 112
PRK12411 PRK12411
cytidine deaminase; Provisional
1-129 2.07e-30

cytidine deaminase; Provisional


Pssm-ID: 183511 [Multi-domain]  Cd Length: 132  Bit Score: 105.81  E-value: 2.07e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998277091   1 MSAEDLFAAASAAMQNAYAPYSRFPVGAAVKTEAGAIHAGCNIENASYPEGWCAETTALGHLVMAGGGRVTEIAVVAEKM 80
Cdd:PRK12411    1 MNSKQLIQEAIEARKQAYVPYSKFQVGAALLTQDGKVYRGCNVENASYGLCNCAERTALFKAVSEGDKEFVAIAIVADTK 80
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1998277091  81 PKIMPCGGCRQRLAEFVTDDACLHLCDTNGVLETVPFSAVFPRGFSFED 129
Cdd:PRK12411   81 RPVPPCGACRQVMVELCKQDTKVYLSNLHGDVQETTVGELLPGAFLAED 129
dCMP_cyt_deam_1 pfam00383
Cytidine and deoxycytidylate deaminase zinc-binding region;
14-96 6.48e-10

Cytidine and deoxycytidylate deaminase zinc-binding region;


Pssm-ID: 395307 [Multi-domain]  Cd Length: 100  Bit Score: 52.30  E-value: 6.48e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998277091  14 MQNAYaPYSRFPVGAA-VKTEAGAIHAGCNIENASYPEGWCAETTALGHLVMAGGGRV---TEIAVVAEkmpkimPCGGC 89
Cdd:pfam00383  13 AKRAY-PYSNFPVGAViVKKDGEIIATGYNGENAGYDPTIHAERNAIRQAGKRGEGVRlegATLYVTLE------PCGMC 85

                  ....*..
gi 1998277091  90 RQRLAEF 96
Cdd:pfam00383  86 AQAIIES 92
cyt_deam_dimer TIGR01355
cytidine deaminase, homodimeric; This homodimeric zinc metalloprotein is found in Arabidopis ...
17-129 1.48e-08

cytidine deaminase, homodimeric; This homodimeric zinc metalloprotein is found in Arabidopis and some Proteobacteria. A related, homotetrameric form with a much smaller subunit is found most bacteria and in animals. Both types may act on deoxycytidine as well as cytidine. [Purines, pyrimidines, nucleosides, and nucleotides, Salvage of nucleosides and nucleotides]


Pssm-ID: 273573 [Multi-domain]  Cd Length: 283  Bit Score: 51.37  E-value: 1.48e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998277091  17 AYAPYSRFPVGAAVKTEAGAIHAGCNIENASYPEGWC--AETTALGHLVMAGGGRVTEIAVVAEkmpkimPCGGCRQRLA 94
Cdd:TIGR01355  36 ARAPISKFNVGAVGRGSSGRFYLGVNVEFPGLPLHHSihAEQFLISHLALNGERGLNDLAVSFA------PCGHCRQFLN 109
                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1998277091  95 EFVT-DDACLHLCDTNGVlETVPFSAVFPRGFSFED 129
Cdd:TIGR01355 110 EIRNaSSIKILLPDPHNK-RDMSLQSYLPDRFGPDD 144
cytidine_deaminase-like cd00786
Cytidine and deoxycytidylate deaminase zinc-binding region. The family contains cytidine ...
17-100 1.28e-07

Cytidine and deoxycytidylate deaminase zinc-binding region. The family contains cytidine deaminases, nucleoside deaminases, deoxycytidylate deaminases and riboflavin deaminases. Also included are the apoBec family of mRNA editing enzymes. All members are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate.


Pssm-ID: 238406 [Multi-domain]  Cd Length: 96  Bit Score: 46.39  E-value: 1.28e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998277091  17 AYAPYSRFPVGAAV--KTEAGAIHAGCNIENASYPEGWCAETTALGHLVMAGGGRVTEIAVVAEkmpkimPCGGCRQRLA 94
Cdd:cd00786    11 GYAKESNFQVGACLvnKKDGGKVGRGCNIENAAYSMCNHAERTALFNAGSEGDTKGQMLYVALS------PCGACAQLII 84

                  ....*.
gi 1998277091  95 EFVTDD 100
Cdd:cd00786    85 ELGIKD 90
PRK06848 PRK06848
cytidine deaminase;
26-128 2.75e-07

cytidine deaminase;


Pssm-ID: 235875 [Multi-domain]  Cd Length: 139  Bit Score: 46.27  E-value: 2.75e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998277091  26 VGAAVKTEAGAIHAGCNIENASYPEGWCAETTALGHLVMAGGGRVTEIavVAEKMPK----------IMPCGGCRQRLAE 95
Cdd:PRK06848   29 VGAALRTKTGRIYAAVHLEAYVGRITVCAEAIAIGKAISEGDHEIDTI--VAVRHPKpheddreiwvVSPCGACRELISD 106
                          90       100       110
                  ....*....|....*....|....*....|...
gi 1998277091  96 FvtDDACLHLCDTNGVLETVPFSAVFPRGFSFE 128
Cdd:PRK06848  107 Y--GKNTNVIVPYNDELVKVNIMELLPNKYTRE 137
dCMP_cyt_deam_2 pfam08211
Cytidine and deoxycytidylate deaminase zinc-binding region;
14-79 5.78e-07

Cytidine and deoxycytidylate deaminase zinc-binding region;


Pssm-ID: 429867 [Multi-domain]  Cd Length: 122  Bit Score: 45.22  E-value: 5.78e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1998277091  14 MQNAYAPYSRFPVGAAVKTEAGAIHAGCNIENASYPEGWCAETTALGHLVMAGGGrVTEI--AVVAEK 79
Cdd:pfam08211  44 ANRSYAPYSKCPSGVALQDGDGRVYRGRYAENAAFNPSLPPLQAALVDFVAGGKD-FEDIvrAVLVEK 110
PRK09027 PRK09027
cytidine deaminase; Provisional
17-105 4.16e-06

cytidine deaminase; Provisional


Pssm-ID: 181614 [Multi-domain]  Cd Length: 295  Bit Score: 44.44  E-value: 4.16e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998277091  17 AYAPYSRFPVGAAVKTEAGAIHAGCNIENASYPEGWC--AETTALGHLVMAGGGRVTEIAVVAEkmpkimPCGGCRQRLA 94
Cdd:PRK09027   64 AVTPISHFNVGAIARGVSGNFYFGANMEFAGAALQQTvhAEQSAISHAWLRGEKAIADITVNYT------PCGHCRQFMN 137
                          90
                  ....*....|..
gi 1998277091  95 EFVT-DDACLHL 105
Cdd:PRK09027  138 ELNSaSDLRIHL 149
PRK09027 PRK09027
cytidine deaminase; Provisional
17-79 5.88e-04

cytidine deaminase; Provisional


Pssm-ID: 181614 [Multi-domain]  Cd Length: 295  Bit Score: 38.28  E-value: 5.88e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1998277091  17 AYAPYSRFPVGAAVKTEAGAIHAGCNIENA----SYPegwcAETTALGHLVMAgGGRVTEI--AVVAEK 79
Cdd:PRK09027  203 SHAPYSQSYSGVALETKDGRIYTGRYAENAafnpSLP----PLQGALNLLNLS-GEDFSDIqrAVLVEK 266
PLN02182 PLN02182
cytidine deaminase
14-95 5.43e-03

cytidine deaminase


Pssm-ID: 177837  Cd Length: 339  Bit Score: 35.42  E-value: 5.43e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1998277091  14 MQNAYAPYSRFPVGAAVKTEAGAIHAGCNIENASYP--EGWCAETTALGHLVMAGGGRVTEIAVV--AEKMPKIMPCGGC 89
Cdd:PLN02182   56 MCLARAPISKYKVGAVGRASSGRVYLGVNVDFPGLPlhHSIHAEQFLVTNLALNSEKDLCELAVAisTDGKEFGTPCGHC 135

                  ....*.
gi 1998277091  90 RQRLAE 95
Cdd:PLN02182  136 LQFLME 141
 
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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