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Conserved domains on  [gi|1025608575|ref|NP_001311339|]
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RNA pseudouridylate synthase domain-containing protein 1 isoform 3 [Homo sapiens]

Protein Classification

pseudouridine synthase family protein( domain architecture ID 10120734)

pseudouridine synthase family protein may catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines

CATH:  3.30.2350.10
EC:  5.4.99.-
Gene Ontology:  GO:0003723|GO:0001522|GO:0009982
PubMed:  17113994|12756329|12762017

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PseudoU_synth_RluA_like cd02869
Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and ...
 9-89 1.55e-28

Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli.


:

Pssm-ID: 211346 [Multi-domain]  Cd Length: 185  Bit Score: 104.73  E-value: 1.55e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025608575   9 VAGCENPKPSLTDLVVLEHGlyagDPVSKVLLKPLTGRTHQLRVHCSALGHPVVGDLTYGEVSGREDRPFRMMLHAFYLR 88
Cdd:cd02869   109 VVVSEDGKPAITHYKVLERF----GNVTLVELQLETGRTHQIRVHLASIGHPIVGDPKYGGKASDSPGLKRLALHAYRLS 184


                  .
gi 1025608575  89 I 89
Cdd:cd02869   185 F 185
 
Name Accession Description Interval E-value
PseudoU_synth_RluA_like cd02869
Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and ...
 9-89 1.55e-28

Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli.


Pssm-ID: 211346 [Multi-domain]  Cd Length: 185  Bit Score: 104.73  E-value: 1.55e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025608575   9 VAGCENPKPSLTDLVVLEHGlyagDPVSKVLLKPLTGRTHQLRVHCSALGHPVVGDLTYGEVSGREDRPFRMMLHAFYLR 88
Cdd:cd02869   109 VVVSEDGKPAITHYKVLERF----GNVTLVELQLETGRTHQIRVHLASIGHPIVGDPKYGGKASDSPGLKRLALHAYRLS 184


                  .
gi 1025608575  89 I 89
Cdd:cd02869   185 F 185
RluA COG0564
Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific [Translation, ribosomal structure and ...
 13-103 5.84e-24

Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific [Translation, ribosomal structure and biogenesis]; Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific is part of the Pathway/BioSystem: 23S rRNA modification


Pssm-ID: 440330 [Multi-domain]  Cd Length: 218  Bit Score: 93.66  E-value: 5.84e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025608575  13 ENPKPSLTDLVVLEHGlyagDPVSKVLLKPLTGRTHQLRVHCSALGHPVVGDLTYGevSGREDRPF---RMMLHAFYLRI 89
Cdd:COG0564   120 EDGKPAVTHYRVLERF----GGYSLVEVRLETGRTHQIRVHLAHIGHPIVGDPLYG--GDRSNRLLgldRQALHAYRLGF 193

                          90
                  ....*....|....*.
gi 1025608575  90 --PTDTECVEVCTPDP 103
Cdd:COG0564   194 phPVTGEPLEFEAPLP 209
PRK10158 PRK10158
bifunctional tRNA pseudouridine(32) synthase/23S rRNA pseudouridine(746) synthase RluA;
13-89 2.73e-15

bifunctional tRNA pseudouridine(32) synthase/23S rRNA pseudouridine(746) synthase RluA;


Pssm-ID: 236659 [Multi-domain]  Cd Length: 219  Bit Score: 70.79  E-value: 2.73e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1025608575  13 ENPKPSLTDLVVLEhglYAGDPVSKVLLKPLTGRTHQLRVHCSALGHPVVGDLTYGEVSGREDRPfRMMLHAFYLRI 89
Cdd:PRK10158  130 ETGKPAQTEYEVVE---YAADNTARVVLKPITGRSHQLRVHMLALGHPILGDRFYASPEARAMAP-RLLLHAEMLTI 202
rluA_subfam TIGR00005
pseudouridine synthase, RluA family; In E. coli, RluD (SfhB) modifies uridine to pseudouridine ...
 16-103 1.32e-12

pseudouridine synthase, RluA family; In E. coli, RluD (SfhB) modifies uridine to pseudouridine at 23S RNA U1911, 1915, and 1917, RluC modifies 955, 2504 and 2580, and RluA modifies U746 and tRNA U32. An additional homolog from E. coli outside this family, TruC (SP|Q46918), modifies uracil-65 in transfer RNAs to pseudouridine. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 161659 [Multi-domain]  Cd Length: 299  Bit Score: 64.27  E-value: 1.32e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025608575  16 KPSLTDLVVLEHGLYAgdpvSKVLLKPLTGRTHQLRVHCSALGHPVVGDLTYGevSGREDRPF--------RMMLHAFYL 87
Cdd:TIGR00005 197 KPAVTHFRVLERFGNA----SLVECELETGRTHQIRVHLQYLGHPLAGDPLYG--NKPVPGNNlngllnfdRQALHAYEL 270

                          90
                  ....*....|....*...
gi 1025608575  88 RI--PTDTECVEVCTPDP 103
Cdd:TIGR00005 271 GFihPATGEILEFEAPLP 288
PseudoU_synth_2 pfam00849
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ...
 12-56 2.23e-07

RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA molecules. They carry out the conversion of uracil bases to pseudouridine. This family includes RluD, a pseudouridylate synthase that converts specific uracils to pseudouridine in 23S rRNA. RluA from E. coli converts bases in both rRNA and tRNA.


Pssm-ID: 459961 [Multi-domain]  Cd Length: 151  Bit Score: 48.17  E-value: 2.23e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1025608575  12 CENPKPSLTDLVVLEHGLYAgdPVSKVLLKPLTGRTHQLRVHCSA 56
Cdd:pfam00849 109 ELGGKKAVTHLKVLKSGSKG--DYSLLELELVTGRKHQIRAHLAA 151
 
Name Accession Description Interval E-value
PseudoU_synth_RluA_like cd02869
Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and ...
 9-89 1.55e-28

Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli.


Pssm-ID: 211346 [Multi-domain]  Cd Length: 185  Bit Score: 104.73  E-value: 1.55e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025608575   9 VAGCENPKPSLTDLVVLEHGlyagDPVSKVLLKPLTGRTHQLRVHCSALGHPVVGDLTYGEVSGREDRPFRMMLHAFYLR 88
Cdd:cd02869   109 VVVSEDGKPAITHYKVLERF----GNVTLVELQLETGRTHQIRVHLASIGHPIVGDPKYGGKASDSPGLKRLALHAYRLS 184


                  .
gi 1025608575  89 I 89
Cdd:cd02869   185 F 185
RluA COG0564
Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific [Translation, ribosomal structure and ...
 13-103 5.84e-24

Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific [Translation, ribosomal structure and biogenesis]; Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific is part of the Pathway/BioSystem: 23S rRNA modification


Pssm-ID: 440330 [Multi-domain]  Cd Length: 218  Bit Score: 93.66  E-value: 5.84e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025608575  13 ENPKPSLTDLVVLEHGlyagDPVSKVLLKPLTGRTHQLRVHCSALGHPVVGDLTYGevSGREDRPF---RMMLHAFYLRI 89
Cdd:COG0564   120 EDGKPAVTHYRVLERF----GGYSLVEVRLETGRTHQIRVHLAHIGHPIVGDPLYG--GDRSNRLLgldRQALHAYRLGF 193

                          90
                  ....*....|....*.
gi 1025608575  90 --PTDTECVEVCTPDP 103
Cdd:COG0564   194 phPVTGEPLEFEAPLP 209
PRK10158 PRK10158
bifunctional tRNA pseudouridine(32) synthase/23S rRNA pseudouridine(746) synthase RluA;
13-89 2.73e-15

bifunctional tRNA pseudouridine(32) synthase/23S rRNA pseudouridine(746) synthase RluA;


Pssm-ID: 236659 [Multi-domain]  Cd Length: 219  Bit Score: 70.79  E-value: 2.73e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1025608575  13 ENPKPSLTDLVVLEhglYAGDPVSKVLLKPLTGRTHQLRVHCSALGHPVVGDLTYGEVSGREDRPfRMMLHAFYLRI 89
Cdd:PRK10158  130 ETGKPAQTEYEVVE---YAADNTARVVLKPITGRSHQLRVHMLALGHPILGDRFYASPEARAMAP-RLLLHAEMLTI 202
rluA_subfam TIGR00005
pseudouridine synthase, RluA family; In E. coli, RluD (SfhB) modifies uridine to pseudouridine ...
 16-103 1.32e-12

pseudouridine synthase, RluA family; In E. coli, RluD (SfhB) modifies uridine to pseudouridine at 23S RNA U1911, 1915, and 1917, RluC modifies 955, 2504 and 2580, and RluA modifies U746 and tRNA U32. An additional homolog from E. coli outside this family, TruC (SP|Q46918), modifies uracil-65 in transfer RNAs to pseudouridine. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 161659 [Multi-domain]  Cd Length: 299  Bit Score: 64.27  E-value: 1.32e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025608575  16 KPSLTDLVVLEHGLYAgdpvSKVLLKPLTGRTHQLRVHCSALGHPVVGDLTYGevSGREDRPF--------RMMLHAFYL 87
Cdd:TIGR00005 197 KPAVTHFRVLERFGNA----SLVECELETGRTHQIRVHLQYLGHPLAGDPLYG--NKPVPGNNlngllnfdRQALHAYEL 270

                          90
                  ....*....|....*...
gi 1025608575  88 RI--PTDTECVEVCTPDP 103
Cdd:TIGR00005 271 GFihPATGEILEFEAPLP 288
PseudoU_synth_ScRIB2 cd02557
Pseudouridine synthases similar to Saccharomyces cerevisiae RIB2; Pseudouridine synthase, ...
 11-85 4.07e-12

Pseudouridine synthases similar to Saccharomyces cerevisiae RIB2; Pseudouridine synthase, Saccharomyces cerevisiae RIB2_like. This group is comprised of eukaryotic and bacterial proteins similar to Saccharomyces cerevisiae RIB2, S. cerevisiae Pus6p and human hRPUDSD2. S. cerevisiae RIB2 displays two distinct catalytic activities. The N-terminal domain of RIB2 is RNA:psi-synthase which makes psi32 on cytoplasmic tRNAs. Psi32 is highly phylogenetically conserved. The C-terminal domain of RIB2 has a DRAP deaminase activity which catalyses the formation of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate from 2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate during riboflavin biosynthesis. S. cerevisiae Pus6p makes the psi31 of cytoplasmic and mitochondrial tRNAs.


Pssm-ID: 211331 [Multi-domain]  Cd Length: 213  Bit Score: 62.26  E-value: 4.07e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1025608575  11 GCENPKPSLTdlvVLEHGLYAGDP-VSKVLLKPLTGRTHQLRVHCSALGHPVVGDLTYGevsgredrPFRMMLHAF 85
Cdd:cd02557   131 VDEKGKDART---IFKRLSYNGDLnTSVVLCKPITGRTHQIRVHLQYLGHPIVNDPIYN--------NLGIYLHAL 195
PRK11112 PRK11112
tRNA pseudouridine synthase C; Provisional
 15-88 1.45e-11

tRNA pseudouridine synthase C; Provisional


Pssm-ID: 182971 [Multi-domain]  Cd Length: 257  Bit Score: 61.22  E-value: 1.45e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025608575  15 PKPSLTDLVVLEH-------GLYAGDPVSKVLLKPLTGRTHQLRVHCSALGHPVVGDLTYGEvsGREDRPF-------RM 80
Cdd:PRK11112  122 PQPAVTHYRGLATvempvatGRYPTTRYSLVELEPKTGRKHQLRRHMAHLRHPIIGDTKHGD--LRQNRSLaehfgcsRL 199


                  ....*...
gi 1025608575  81 MLHAFYLR 88
Cdd:PRK11112  200 MLHASELS 207
PseudoU_synth_TruC cd02563
tRNA pseudouridine isomerase C; Pseudouridine synthases catalyze the isomerization of specific ...
 36-90 1.77e-10

tRNA pseudouridine isomerase C; Pseudouridine synthases catalyze the isomerization of specific uridines in an tRNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. TruC makes psi65 in tRNAs. This psi residue is not universally conserved.


Pssm-ID: 211333 [Multi-domain]  Cd Length: 223  Bit Score: 57.73  E-value: 1.77e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1025608575  36 SKVLLKPLTGRTHQLRVHCSALGHPVVGDLTYGEvsGREDRPF-------RMMLHAFYLRIP 90
Cdd:cd02563   149 SLVELTPHTGRKHQLRRHLAHIRHPIIGDTTHGD--GRHNRFFrehfgchRLLLAATRLEFT 208
rluD PRK11180
23S rRNA pseudouridine(1911/1915/1917) synthase RluD;
16-130 1.40e-09

23S rRNA pseudouridine(1911/1915/1917) synthase RluD;


Pssm-ID: 183020 [Multi-domain]  Cd Length: 325  Bit Score: 55.84  E-value: 1.40e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025608575  16 KPSLTDLVVLEH-GLYagdpvSKVLLKPLTGRTHQLRVHCSALGHPVVGDLTYGevsGREdRP-------FRMM------ 81
Cdd:PRK11180  206 KPAVTHYRIMEHfRVH-----TRLRLRLETGRTHQIRVHMAHITHPLVGDQVYG---GRP-RPpkgaseeFISTlrkfdr 276

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1025608575  82 --LHAFYLRI--PTDTECVEVCTPDPflpsldacwsphtllQSLDQLVQALRA 130
Cdd:PRK11180  277 qaLHATMLRLyhPITGIEMEWHAPLP---------------QDMVELIEALRA 314
PSRA_1 cd02558
Pseudouridine synthase, a subgroup of the RluA family; This group is comprised of bacterial ...
 18-83 6.66e-09

Pseudouridine synthase, a subgroup of the RluA family; This group is comprised of bacterial proteins assigned to the RluA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. The RluA family is comprised of proteins related to Escherichia coli RluA.


Pssm-ID: 211332 [Multi-domain]  Cd Length: 246  Bit Score: 53.43  E-value: 6.66e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025608575  18 SLTDLVVLEH----GLYAgdpvskvlLKPLTGRTHQLRVHCSALGHPVVGDLTYGEVSGREDRPFRMMLH 83
Cdd:cd02558   160 AETRIELLARrggwGLYR--------LSPHTGKTHQLRVHMAALGVPILNDPFYPVLLDKDPDDFSRPLQ 221
PRK11025 PRK11025
23S rRNA pseudouridine(955/2504/2580) synthase RluC;
16-88 2.49e-08

23S rRNA pseudouridine(955/2504/2580) synthase RluC;


Pssm-ID: 182909 [Multi-domain]  Cd Length: 317  Bit Score: 52.43  E-value: 2.49e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025608575  16 KPSLTDLVVLEHGLYAgdpvSKVLLKPLTGRTHQLRVHCSALGHPVVGDLTYGevsgreDRPF----------RMMLHAF 85
Cdd:PRK11025  214 KPSETRFKVEERYAFA----TLVRASPVTGRTHQIRVHTQYAGHPIAFDDRYG------DREFdqqltgtglnRLFLHAA 283


                  ...
gi 1025608575  86 YLR 88
Cdd:PRK11025  284 ALK 286
PseudoU_synth_2 pfam00849
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ...
 12-56 2.23e-07

RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA molecules. They carry out the conversion of uracil bases to pseudouridine. This family includes RluD, a pseudouridylate synthase that converts specific uracils to pseudouridine in 23S rRNA. RluA from E. coli converts bases in both rRNA and tRNA.


Pssm-ID: 459961 [Multi-domain]  Cd Length: 151  Bit Score: 48.17  E-value: 2.23e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1025608575  12 CENPKPSLTDLVVLEHGLYAgdPVSKVLLKPLTGRTHQLRVHCSA 56
Cdd:pfam00849 109 ELGGKKAVTHLKVLKSGSKG--DYSLLELELVTGRKHQIRAHLAA 151
PseudoU_synth_Rsu_Rlu_like cd02550
Pseudouridine synthase, Rsu/Rlu family; This group is comprised of eukaryotic, bacterial and ...
 13-62 4.46e-06

Pseudouridine synthase, Rsu/Rlu family; This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli.


Pssm-ID: 211325 [Multi-domain]  Cd Length: 154  Bit Score: 44.67  E-value: 4.46e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1025608575  13 ENPKPSLTDLVVLEHGlyagDPVSKVLLKPLTGRTHQLRVHCSALGHPVV 62
Cdd:cd02550   102 EGVPLAVTKVRVIGEH----GGTGRLRLTLKTGRTHQIRRHCAAVGFPVL 147
 
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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