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Conserved domains on  [gi|1061385103|ref|NP_496121|]
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RNase H type-1 domain-containing protein [Caenorhabditis elegans]

Protein Classification

ribonuclease H family protein( domain architecture ID 54171)

ribonuclease H (RNase H) family protein may function as an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RNase_H_like super family cl14782
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
8-167 3.79e-16

Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of spliceosomal protein Prp8; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. It is widely present in various organisms, including bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site residues and have the same catalytic mechanism and functions in cells. RNase H is involved in DNA replication, repair and transcription. An important RNase H function is to remove Okazaki fragments during DNA replication. RNase H inhibitors have been explored as anti-HIV drug targets since RNase H inactivation inhibits reverse transcription. This model also includes the Prp8 domain IV, which adopts the RNase fold but shows low sequence homology; domain IV is implicated in key spliceosomal interactions.


The actual alignment was detected with superfamily member cd09280:

Pssm-ID: 449355 [Multi-domain]  Cd Length: 145  Bit Score: 71.44  E-value: 3.79e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061385103   8 VYTDGSTVNNGKRGARGGWAIVFPFDRSLDeyDFMKV--GKQTNNVYELTAIYEATEVVRCWDsfkcNQKLEFVR----L 81
Cdd:cd09280     2 VYTDGSCLNNGKPGARAGIGVYFGPGDPRN--VSEPLpgRKQTNNRAELLAVIHALEQAPEEG----IRKLEIRTdskyA 75
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061385103  82 KNTITpttssILIPCTRRtvspNGSTDGTNmgglriTPGILSKISRSFVPSTAiSESLDVKIEYVKGHHTNFFNCEADRL 161
Cdd:cd09280    76 INCIT-----KWIPKWKK----NGWKTSKG------KPVKNQDLIKELDKLLR-KRGIKVKFEHVKGHSGDPGNEEADRL 139

                  ....*.
gi 1061385103 162 AKKACR 167
Cdd:cd09280   140 AREGAD 145
 
Name Accession Description Interval E-value
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
8-167 3.79e-16

Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic counterparts; Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H is widely present in various organisms, including bacteria, archaea and eukaryote and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD) residues and have the same catalytic mechanism and functions in cells. Eukaryotic RNase H is longer and more complex than in prokaryotes. Almost all eukaryotic RNase HI have highly conserved regions at their N-termini called hybrid binding domain (HBD). It is speculated that the HBD contributes to binding the RNA/DNA hybrid. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability, but RNase H is essential in higher eukaryotes. RNase H knockout mice lack mitochondrial DNA replication and die as embryos.


Pssm-ID: 260012 [Multi-domain]  Cd Length: 145  Bit Score: 71.44  E-value: 3.79e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061385103   8 VYTDGSTVNNGKRGARGGWAIVFPFDRSLDeyDFMKV--GKQTNNVYELTAIYEATEVVRCWDsfkcNQKLEFVR----L 81
Cdd:cd09280     2 VYTDGSCLNNGKPGARAGIGVYFGPGDPRN--VSEPLpgRKQTNNRAELLAVIHALEQAPEEG----IRKLEIRTdskyA 75
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061385103  82 KNTITpttssILIPCTRRtvspNGSTDGTNmgglriTPGILSKISRSFVPSTAiSESLDVKIEYVKGHHTNFFNCEADRL 161
Cdd:cd09280    76 INCIT-----KWIPKWKK----NGWKTSKG------KPVKNQDLIKELDKLLR-KRGIKVKFEHVKGHSGDPGNEEADRL 139

                  ....*.
gi 1061385103 162 AKKACR 167
Cdd:cd09280   140 AREGAD 145
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
7-167 9.61e-11

RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers.


Pssm-ID: 395028 [Multi-domain]  Cd Length: 141  Bit Score: 57.00  E-value: 9.61e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061385103   7 EVYTDGSTVNNGKrgaRGGWAIVFPFDRslDEYDFMKVGKQTNNVYELTAIYEAtevvrcwdsfkcnqklefvrLKNTIT 86
Cdd:pfam00075   5 TVYTDGSCLGNPG---PGGAGAVLYRGH--ENISAPLPGRTTNNRAELQAVIEA--------------------LKALKS 59
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061385103  87 PTTSSIlipctrRTVSPNgSTDG-TNMGGLRITPGILSKISRSFVPSTAISESLD-------VKIEYVKGHHTNFFNCEA 158
Cdd:pfam00075  60 PSKVNI------YTDSQY-VIGGiTQWVHGWKKNGWPTTSEGKPVKNKDLWQLLKalckkhqVYWQWVKGHAGNPGNEMA 132

                  ....*....
gi 1061385103 159 DRLAKKACR 167
Cdd:pfam00075 133 DRLAKQGAE 141
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
7-165 1.24e-07

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 48.69  E-value: 1.24e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061385103   7 EVYTDGSTVNNGKRGargGWAIVFPFDRSLDEYdFMKVGKQTNNVYELTAIYEATEVVRcwDSFKCNqklefVRLKntit 86
Cdd:COG0328     4 EIYTDGACRGNPGPG---GWGAVIRYGGEEKEL-SGGLGDTTNNRAELTALIAALEALK--ELGPCE-----VEIY---- 68
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061385103  87 pTTSSILIpctrrtvspNGstdgtnmgglrITPGILSKISRSFVPS---------TAISESLDVKIEYVKGHHTNFFNCE 157
Cdd:COG0328    69 -TDSQYVV---------NQ-----------ITGWIHGWKKNGWKPVknpdlwqrlDELLARHKVTFEWVKGHAGHPGNER 127

                  ....*...
gi 1061385103 158 ADRLAKKA 165
Cdd:COG0328   128 ADALANKA 135
 
Name Accession Description Interval E-value
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
8-167 3.79e-16

Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic counterparts; Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H is widely present in various organisms, including bacteria, archaea and eukaryote and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD) residues and have the same catalytic mechanism and functions in cells. Eukaryotic RNase H is longer and more complex than in prokaryotes. Almost all eukaryotic RNase HI have highly conserved regions at their N-termini called hybrid binding domain (HBD). It is speculated that the HBD contributes to binding the RNA/DNA hybrid. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability, but RNase H is essential in higher eukaryotes. RNase H knockout mice lack mitochondrial DNA replication and die as embryos.


Pssm-ID: 260012 [Multi-domain]  Cd Length: 145  Bit Score: 71.44  E-value: 3.79e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061385103   8 VYTDGSTVNNGKRGARGGWAIVFPFDRSLDeyDFMKV--GKQTNNVYELTAIYEATEVVRCWDsfkcNQKLEFVR----L 81
Cdd:cd09280     2 VYTDGSCLNNGKPGARAGIGVYFGPGDPRN--VSEPLpgRKQTNNRAELLAVIHALEQAPEEG----IRKLEIRTdskyA 75
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061385103  82 KNTITpttssILIPCTRRtvspNGSTDGTNmgglriTPGILSKISRSFVPSTAiSESLDVKIEYVKGHHTNFFNCEADRL 161
Cdd:cd09280    76 INCIT-----KWIPKWKK----NGWKTSKG------KPVKNQDLIKELDKLLR-KRGIKVKFEHVKGHSGDPGNEEADRL 139

                  ....*.
gi 1061385103 162 AKKACR 167
Cdd:cd09280   140 AREGAD 145
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
7-167 9.61e-11

RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers.


Pssm-ID: 395028 [Multi-domain]  Cd Length: 141  Bit Score: 57.00  E-value: 9.61e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061385103   7 EVYTDGSTVNNGKrgaRGGWAIVFPFDRslDEYDFMKVGKQTNNVYELTAIYEAtevvrcwdsfkcnqklefvrLKNTIT 86
Cdd:pfam00075   5 TVYTDGSCLGNPG---PGGAGAVLYRGH--ENISAPLPGRTTNNRAELQAVIEA--------------------LKALKS 59
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061385103  87 PTTSSIlipctrRTVSPNgSTDG-TNMGGLRITPGILSKISRSFVPSTAISESLD-------VKIEYVKGHHTNFFNCEA 158
Cdd:pfam00075  60 PSKVNI------YTDSQY-VIGGiTQWVHGWKKNGWPTTSEGKPVKNKDLWQLLKalckkhqVYWQWVKGHAGNPGNEMA 132

                  ....*....
gi 1061385103 159 DRLAKKACR 167
Cdd:pfam00075 133 DRLAKQGAE 141
RNase_H_Dikarya_like cd13934
Fungal (dikarya) Ribonuclease H, uncharacterized; This family contains dikarya RNase H, many ...
8-82 1.12e-08

Fungal (dikarya) Ribonuclease H, uncharacterized; This family contains dikarya RNase H, many of which are uncharacterized. Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. It is widely present in various organisms, including bacteria, archaea and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site residues and have the same catalytic mechanism and functions in cells. RNase H is involved in DNA replication, repair and transcription. An important RNase H function is to remove Okazaki fragments during DNA replication.


Pssm-ID: 260014 [Multi-domain]  Cd Length: 153  Bit Score: 51.81  E-value: 1.12e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061385103   8 VYTDGSTVNNGKRGARGGWAIVF----PFDRS--LDEYDFmkvGKQTNNVYELTAIYEATEvVRCWDSFKCNQKLEFVRL 81
Cdd:cd13934     2 VYIDGACRNNGRPDARAGYGVYFgpdsSYNVSgrLEDTGG---HPQTSQRAELRAAIAALR-FRSWIIDPDGEGLKTVVI 77

                  .
gi 1061385103  82 K 82
Cdd:cd13934    78 A 78
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
7-165 4.74e-08

RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two evolutionarily unrelated families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD), residues and have the same catalytic mechanism and functions in cells. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Prokaryotic RNase H varies greatly in domain structures and substrate specificities. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability.


Pssm-ID: 260010 [Multi-domain]  Cd Length: 139  Bit Score: 49.79  E-value: 4.74e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061385103   7 EVYTDGSTVNN-GKrgarGGWAIVFPFDRSLDEyDFMKVGKQTNNVYELTAIYEATEVVrcwdsfKCNQKLEFVrlknti 85
Cdd:cd09278     3 VIYTDGACLGNpGP----GGWAAVIRYGDHEKE-LSGGEPGTTNNRMELTAAIEALEAL------KEPCPVTIY------ 65
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061385103  86 tpTTSSILIpctrrtvspNGstdgtnmgglrITPGILSKISRSFVPST--------------AISESLDVKIEYVKGHHT 151
Cdd:cd09278    66 --TDSQYVI---------NG-----------ITKWIKGWKKNGWKTADgkpvknrdlwqeldALLAGHKVTWEWVKGHAG 123
                         170
                  ....*....|....
gi 1061385103 152 NFFNCEADRLAKKA 165
Cdd:cd09278   124 HPGNERADRLANKA 137
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
7-165 1.24e-07

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 48.69  E-value: 1.24e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061385103   7 EVYTDGSTVNNGKRGargGWAIVFPFDRSLDEYdFMKVGKQTNNVYELTAIYEATEVVRcwDSFKCNqklefVRLKntit 86
Cdd:COG0328     4 EIYTDGACRGNPGPG---GWGAVIRYGGEEKEL-SGGLGDTTNNRAELTALIAALEALK--ELGPCE-----VEIY---- 68
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061385103  87 pTTSSILIpctrrtvspNGstdgtnmgglrITPGILSKISRSFVPS---------TAISESLDVKIEYVKGHHTNFFNCE 157
Cdd:COG0328    69 -TDSQYVV---------NQ-----------ITGWIHGWKKNGWKPVknpdlwqrlDELLARHKVTFEWVKGHAGHPGNER 127

                  ....*...
gi 1061385103 158 ADRLAKKA 165
Cdd:COG0328   128 ADALANKA 135
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
8-167 1.48e-04

non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). Ribonuclease HI (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as an adjunct domain to the reverse transcriptase gene in retroviruses, long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. The position of the RNase domain of non-LTR and LTR transposons is at the carboxyl terminal of the reverse transcriptase (RT) domain and their RNase domains group together, indicating a common evolutionary origin. Many non-LTR transposons have lost the RNase domain because their activity is at the nucleus and cellular RNase may suffice; however LTR retrotransposons always encode their own RNase domain because it requires RNase activity in RNA-protein particles in the cytoplasm. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260008 [Multi-domain]  Cd Length: 131  Bit Score: 39.89  E-value: 1.48e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061385103   8 VYTDGSTVNNgkrgaRGGWAIVFPfDRSLDEYDFMKVGKQTNnVY--ELTAIYEATEVVRCWDSFkcnqklefvRLKNTI 85
Cdd:cd09276     2 IYTDGSKLEG-----SVGAGFVIY-RGGEVISRSYRLGTHAS-VFdaELEAILEALELALATARR---------ARKVTI 65
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061385103  86 -TPTTSSILIPCTRRTVSPngstdgtnmgglriTPGILSKISRSFvpsTAISESLDVKIEYVKGHHTNFFNCEADRLAKK 164
Cdd:cd09276    66 fTDSQSALQALRNPRRSSG--------------QVILIRILRLLR---LLKAKGVKVRLRWVPGHVGIEGNEAADRLAKE 128

                  ...
gi 1061385103 165 ACR 167
Cdd:cd09276   129 AAS 131
RNase_HI_bacteria_like cd09277
Bacterial RNase HI containing a hybrid binding domain (HBD) at the N-terminus; Ribonuclease H ...
135-166 3.17e-04

Bacterial RNase HI containing a hybrid binding domain (HBD) at the N-terminus; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is involved in DNA replication, repair and transcription. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, Type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD) residues and have the same catalytic mechanism and functions in cells. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Prokaryotic RNase H varies greatly in domain structures and substrate specificities. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability. Some bacteria distinguished from other bacterial RNase HI in the presence of a hybrid binding domain (HBD) at the N-terminus which is commonly present at the N-termini of eukaryotic RNase HI. It has been reported that this domain is required for dimerization and processivity of RNase HI upon binding to RNA-DNA hybrids.


Pssm-ID: 260009 [Multi-domain]  Cd Length: 133  Bit Score: 39.00  E-value: 3.17e-04
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1061385103 135 ISESLDVKIEYVKGHHTNFFNCEADRLAKKAC 166
Cdd:cd09277   102 YKKKIKIEFVKVKAHSGDKYNELADKLAKKAL 133
 
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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