#=GF ID bCoV_NAB
#=GF AC PF16251.9
#=GF DE Betacoronavirus nucleic acid-binding (NAB)
#=GF PI NAR; bCoV_NAR;
#=GF AU Chang Y;0000-0002-2418-3433
#=GF AU Chuguransky S;0000-0002-0520-0736
#=GF SE Jackhmmer JCSG taget SARS168 and PDB 2K87
#=GF GA 25.00 25.00;
#=GF TC 26.50 25.50;
#=GF NC 22.90 24.60;
#=GF BM hmmbuild HMM.ann SEED.ann
#=GF SM hmmsearch -Z 75585367 --cpu 4 -E 1000 HMM pfamseq
#=GF TP Domain
#=GF RN [1]
#=GF RM 12730500
#=GF RT Characterization of a novel coronavirus associated with severe
#=GF RT acute respiratory syndrome
#=GF RA Rota PA, Oberste MS, Monroe SS, Nix WA, Campagnoli R, Icenogle
#=GF RA JP, Peñaranda S, Bankamp B, Maher K, Chen MH, Tong S, Tamin A,
#=GF RA Lowe L, Frace M, DeRisi JL, Chen Q, Wang D, Erdman DD, Peret TC,
#=GF RA Burns C, Ksiazek TG, Rollin PE, Sanchez A, Liffick S, Holloway
#=GF RA B, Limor J, McCaustland K, Olsen-Rasmussen M, Fouchier R,
#=GF RA Günther S, Osterhaus AD, Drosten C, Pallansch MA, Anderson LJ,
#=GF RA Bellini WJ.
#=GF RL Science 300 (5624), 1394-1399 (2003)
#=GF RN [2]
#=GF RM 29128390
#=GF RT Nsp3 of coronaviruses: Structures and functions of a large
#=GF RT multi-domain protein.
#=GF RA Lei J, Kusov Y, Hilgenfeld R;
#=GF RL Antiviral Res. 2018;149:58-74.
#=GF RN [3]
#=GF RM 19828617
#=GF RT Nuclear magnetic resonance structure of the nucleic acid-binding
#=GF RT domain of severe acute respiratory syndrome coronavirus
#=GF RT nonstructural protein 3.
#=GF RA Serrano P, Johnson MA, Chatterjee A, Neuman BW, Joseph JS,
#=GF RA Buchmeier MJ, Kuhn P, Wüthrich K.
#=GF RL J. Virol. 83 (24), 12998-13008 (2009).
#=GF RN [4]
#=GF RM 32770392
#=GF RT (1)H, (13)C, and (15)N backbone chemical shift assignments of
#=GF RT the nucleic acid-binding domain of SARS-CoV-2 non-structural
#=GF RT protein 3e.
#=GF RA Korn SM, Dhamotharan K, Furtig B, Hengesbach M, Lohr F, Qureshi
#=GF RA NS, Richter C, Saxena K, Schwalbe H, Tants JN, Weigand JE,
#=GF RA Wohnert J, Schlundt A;
#=GF RL Biomol NMR Assign. 2020;14:329-333.
#=GF DR INTERPRO; IPR032592;
#=GF DR SO; 0000417; polypeptide_domain;
#=GF CC This is the nucleic acid-binding domain (NAB) from the
#=GF CC multidomain nonstructural protein NSP3, and described as NSP3e
#=GF CC domain. NSP3 is part of Orf1a polyproteins in SARS-CoV [1]. It
#=GF CC is an essential component of the replication/transcription
#=GF CC complex [2]. The global domain of the NAB represents a new fold,
#=GF CC with a parallel four-strand beta-sheet holding two alpha-helices
#=GF CC of three and four turns that are oriented antiparallel to the
#=GF CC beta-strands and a group of residues form a positively charged
#=GF CC patch on the protein surface as the binding site responsible for
#=GF CC binding affinity for nucleic acids. When binding to ssRNA, the
#=GF CC NAB prefers sequences with repeats of three consecutive Gs, such
#=GF CC as (GGGA)5 and (GGGA)2. A positively charged surface patch
#=GF CC (Lys75, Lys76, Lys99, and Arg106) is involved in RNA binding
#=GF CC [2,3,4].
#=GF SQ 42
#=GS R1A_BCHK5/1904-2031 AC P0C6T5.1
#=GS R1A_CVM2/1885-2008 AC P0C6U9.1
#=GS I7B5F2_9BETC/1937-2060 AC I7B5F2.1
#=GS E0ZN59_BCHK9/1739-1854 AC E0ZN59.1
#=GS Q6UZF1_SARS/1884-1996 AC Q6UZF1.1
#=GS R1A_BCHK9/1764-1879 AC P0C6T6.1
#=GS R1AB_SARS/1884-1996 AC P0C6X7.1
#=GS R1AB_BCHK5/1904-2031 AC P0C6W4.1
#=GS Q6UZF5_SARS/1884-1996 AC Q6UZF5.1
#=GS Q0ZJK7_CVHK1/1979-2102 AC Q0ZJK7.1
#=GS R1A_CVHN5/1929-2052 AC P0C6U5.1
#=GS Q2QKN6_9BETC/1894-2016 AC Q2QKN6.1
#=GS A0A023YA54_MERS/1933-2060 AC A0A023YA54.1
#=GS B7U2M9_9BETC/1894-2016 AC B7U2M9.1
#=GS A0A0U1WHL2_BCHK5/1904-2031 AC A0A0U1WHL2.1
#=GS T2B9I2_MERS/1841-1952 AC T2B9I2.1
#=GS U5LR11_9BETC/1900-2014 AC U5LR11.1
#=GS R1A_SARS/1884-1996 AC P0C6U8.1
#=GS R1AB_BCHK4/1865-1993 AC P0C6W3.1
#=GS R1A_CVMA5/1938-2061 AC P0C6V0.1
#=GS A0A0K2RW65_9BETC/1898-2020 AC A0A0K2RW65.1
#=GS R1AB_BCHK9/1764-1879 AC P0C6W5.1
#=GS A0A0K1YZY7_SARS/1884-1996 AC A0A0K1YZY7.1
#=GS A0A0A7UXS1_9BETC/1947-2068 AC A0A0A7UXS1.1
#=GS A0A0K1Z0N1_SARS/1884-1996 AC A0A0K1Z0N1.1
#=GS I7AWB5_9BETC/1937-2060 AC I7AWB5.1
#=GS A3EXH3_BCHK9/1739-1854 AC A3EXH3.1
#=GS T2B9U0_MERS/1841-1952 AC T2B9U0.1
#=GS A0A2Z4EVM4_9NIDO/1723-1838 AC A0A2Z4EVM4.1
#=GS R1AB_CVM2/1885-2008 AC P0C6X8.1
#=GS U5KNA9_9BETC/1900-2014 AC U5KNA9.1
#=GS R1AB_CVHN5/1929-2052 AC P0C6X4.1
#=GS Q0Q485_SARS/1880-1992 AC Q0Q485.1
#=GS A0A088DIE1_9BETC/2028-2147 AC A0A088DIE1.1
#=GS A0A0K2RVJ3_9BETC/1898-2020 AC A0A0K2RVJ3.1
#=GS R1A_SARS2/1907-2019 AC P0DTC1.1
#=GS R9QTB2_SARS/1876-1988 AC R9QTB2.1
#=GS A7BKB9_9BETC/1894-2016 AC A7BKB9.1
#=GS R1AB_SARS2/1907-2019 AC P0DTD1.1
#=GS C0KYT7_9BETC/1938-2061 AC C0KYT7.1
#=GS R1A_BCHK4/1865-1993 AC P0C6T4.1
#=GS R1AB_CVMA5/1938-2061 AC P0C6X9.1
R1A_BCHK5/1904-2031 ...............ymkdgkyftk-----------KPVIEYSPATI-.LSGSVYTNSCL.V.G.....HdgtigSDAIS..SSFNNLLGFDNSKPVSKKLTYSFFPDFEGDVILTEYSTYDPIYKNGAMLHGKPILW---VNNSKFDSAL-NKFNRATLRQVYDIAPV................................
R1A_CVM2/1885-2008 .................yycesgky---------YTKPIIKAQFRTFE.KVEGVYTNFKL.V.-.....-.....GHSIA..EKFNAKLGFDCNSPFT-EYKITEWPTATGDVVLASDDLYVSRYSGGCVTFGKPVIWLGHEEASLKSLTYFNRPSVVC-ENKFNVLPV................................
I7B5F2_9BETC/1937-2060 .................yycesgky---------YTKPIIKAQFRTFE.KVEGVYTNFKL.V.-.....-.....GHDIA..EKLNAKLGFDCNSPFM-EYKITEWPTATGDVVLASDDLYVSRYSGGCVTFGKPVIWRGHEEASLKSLTYFNRPSVVC-ENKFNVLPV................................
E0ZN59_BCHK9/1739-1854 ...........yyfttapievvaap-----------------------.KLVTPYDGFYL.SsC.....Q.....NPQLA..ESFNKAINATKKGPMK---LLTMYPNIAGDVVAISDDNV-TAHPYGSLHMGKPVLFVTRPNTW-KKLVPLLSTLVVNTTNNYDVLPV................................
Q6UZF1_SARS/1884-1996 .........................YTEQPIDLVPTQPLPNASF----.------DNFKL.T.C.....S.....NTKFA..DDLNQMTGF--TKPASRELSVTFFPDLNGDVVAIDYRHYSASFKKGAKLLHKPIVW--HINQATTKTTF--KPNTWCLRCLWSTKPV................................
R1A_BCHK9/1764-1879 ...........yyfttapievvaap-----------------------.KLVTSYDGFYL.SsC.....Q.....NPQLA..ESFNKAINATKTGPMK---LLTMYPNVAGDVVAISDDNVVA-HPYGSLHMGKPVLFVTRPNTWKK----------------------lvpllstvvvntpntydvlav...........
R1AB_SARS/1884-1996 .........................YTEQPIDLVPTQPLPNASF----.------DNFKL.T.C.....S.....NTKFA..DDLNQMTGF--TKPASRELSVTFFPDLNGDVVAIDYRHYSASFKKGAKLLHKPIVW--HINQATTKTTF--KPNTWCLRCLWSTKPV................................
R1AB_BCHK5/1904-2031 ...............ymkdgkyftk-----------KPVIEYSPATI-.LSGSVYTNSCL.V.G.....HdgtigSDAIS..SSFNNLLGFDNSKPVSKKLTYSFFPDFEGDVILTEYSTYDPIYKNGAMLHGKPILW---VNNSKFDSAL-NKFNRATLRQVYDIAPV................................
Q6UZF5_SARS/1884-1996 .........................YTEQPIDLVPTQPLPNASF----.------DNFKL.T.C.....S.....NTKFA..DDLNQMTGF--TKPASRELSVTFFPDLNGDVVAIDYRHYSASFKKGAKLLHKPIVW--HINQATTKTTF--KPNTWCLRCLWSTKPV................................
Q0ZJK7_CVHK1/1979-2102 .................yycdngky---------YTKPIIKAQFKPFA.KVDGVYTNFKL.V.-.....-.....GHDIC..AQLNDKLGFNVDLPFV-EYKVTVWPVATGDVVLASDDLYVKRYFKGCETFGKPVIWFCHDEASLNSLTYFNKPSFKS-ENRYSVLSV................................
R1A_CVHN5/1929-2052 .................yycdngky---------YTKPIIKAQFKPFA.KVDGVYTNFKL.V.-.....-.....GHDIC..AQLNDKLGFNVDLPFV-EYKVTVWPVATGDVVLASDDLYVKRYFKGCETFGKPVIWFCHDEASLNSLTYFNKPSFKS-ENRYSVLSV................................
Q2QKN6_9BETC/1894-2016 ..................ycdggky---------YTQRIIKAQFKTFE.KVDGVYTNFKL.V.-.....-.....GHTIC..DSLNAKLGFDSSKEFV-EYKVTEWPTATGDVVLATDDLYVKRYERGCITFGKPVIWLSHEKASLNSLTYFNRPSLVD-DNKFAVLKV................................
A0A023YA54_MERS/1933-2060 .........tstppvsyspatviag-----------------------.---SVYTNSCL.I.AadgqvS.....GDPIS..LAFNNMLGYDPSKPTSKKYTYSVLPDENGDILMAEYSTYDPIYKNGAMLNGKPVLWVSN----------------------------glfdaalsrfnrasirqiydpepvelenkftp
B7U2M9_9BETC/1894-2016 ..................ycdggky---------YTQRIIKAQFKTFE.KVDGVYTNFKL.I.-.....-.....GHTIC..DILNAKLGFDSSKEFV-EYKVTEWPTATGDVVLATDDLYVKRYERGCITFGKPVIWLSHEQASLNSLTYFNRPLLVD-ENKFDVLKV................................
A0A0U1WHL2_BCHK5/1904-2031 ...............ymkdgkyftk-----------KPVIEYSPATI-.LSGSVYTNSCL.V.G.....HdgtigSDAIS..SSFNNLLGFDNSKPVSKKLTYSFFPDFEGDVILTEYSTYDPIYKNGAMLHGKPILW---VNNSKFDSAL-NKFNRATLRQVYDIAPV................................
T2B9I2_MERS/1841-1952 .................spatilag-----------------------.---SVYTNSCL.V.S.....SdgqpgGDAIS..LSFNNLLGFDSSKPVTKKYTYSFLPKEDGDVLLAEFDTYDPIYKNGAMYKGKPILW---VNKASYDTNL-NKFNRASLRQIFDVAPI................................
U5LR11_9BETC/1900-2014 ..........nkpsleftpatvssg-----------------------.---VVYTNSCFiV.N.....D.....GDAIG..SAFNKLLGFDKNKPASKQLTYSLLPNEDGDVLLAEFKSYDPMYKNGAAYKGKPILW---VNNGLYDSKL-NKYNRASLRQIFDIQPV................................
R1A_SARS/1884-1996 .........................YTEQPIDLVPTQPLPNASF----.------DNFKL.T.C.....S.....NTKFA..DDLNQMTGF--TKPASRELSVTFFPDLNGDVVAIDYRHYSASFKKGAKLLHKPIVW--HINQATTKTTF--KPNTWCLRCLWSTKPV................................
R1AB_BCHK4/1865-1993 yymkdgkyytskptikyspatilpg-----------------------.---SVYSNSCL.V.G.....VdgtpgSDTIS..KFFNDLLGFDETKPISKKLTYSLLPNEDGDVLLSEFSNYNPVYKKGVMLKGKPILW---VNNGVCDSAL-NKPNRASLRQLYDVAPI................................
R1A_CVMA5/1938-2061 .................yycesgky---------YTKPIIKAQFRTFE.KVDGVYTNFKL.V.-.....-.....GHSIA..EKLNAKLGFDCNSPFV-EYKITEWPTATGDVVLASDDLYVSRYSSGCITFGKPVVWLGHEEASLKSLTYFNRPSVVC-ENKFNVLPV................................
A0A0K2RW65_9BETC/1898-2020 ..................yceggky---------YTQRIVKAQFRTFE.KVDGAYINFKL.V.-.....-.....GHTVC..DSLNAKLGFDSSKEFV-EYKVTEWPTATGDVVLANDDLYVKRYERGCITFGKPVIWYNHEQASLNSLTYFNRPSLVD-VNKFDVLKV................................
R1AB_BCHK9/1764-1879 ...........yyfttapievvaap-----------------------.KLVTSYDGFYL.SsC.....Q.....NPQLA..ESFNKAINATKTGPMK---LLTMYPNVAGDVVAISDDNVVA-HPYGSLHMGKPVLFVTRPNTWKK----------------------lvpllstvvvntpntydvlav...........
A0A0K1YZY7_SARS/1884-1996 .........................YTEQPIDLVPTQPLPNASF----.------DNFKL.T.C.....S.....NTKFA..DDLNQMTGF--TKPASRELSVTFFPDLNGDVVAIDYRHYSASFKKGAKLLHKPIVW--HINQATTKTTF--KPNTWCLRCLWSTKPV................................
A0A0A7UXS1_9BETC/1947-2068 ..................ceggryy----------TQRIVKAQFKTFE.AVDGVYTNFEL.V.-.....-.....GHALC..DTLNVKLGFDSTKDSV-QYKVTVWPDATGDVVLADDDLYVKRYKKGCITFGKPVIWQSHMEASLASLTYFNRPSLID-KNKFDVLTV................................
A0A0K1Z0N1_SARS/1884-1996 .........................YTEQPIDLVPTQPLPNASF----.------DNFKL.T.C.....S.....NTKFA..DDLNQMTGF--TKPASRELSVTFFPDLNGDVVAIDYRHYSASFKKGAKLLHKPIVW--HINQATTKTTF--KPNTWCLRCLWSTKPV................................
I7AWB5_9BETC/1937-2060 .................yycesgky---------YTKPIIKAQFRTFE.KVEGVYTNFKL.V.-.....-.....GHDIA..EKLNAKLGFDCNSPFM-EYKITEWPTATGDVVLASDDLYVSRYSGGCVTFGKPVIWRGHEEASLKSLTYFNRPSVVC-ENKFNVLPV................................
A3EXH3_BCHK9/1739-1854 ...........yyfttapievvaap-----------------------.KLVTPYDGFYL.SsC.....Q.....NPQLA..ESFNKAINATKKGPMK---LLTMYPNIAGDVVAISDDNV-TAHPYGSLHMGKPVLFVTRPNTW-KKLVPLLSTLVVNTTNNYDVLPV................................
T2B9U0_MERS/1841-1952 .................spatilag-----------------------.---SVYTNSCL.V.S.....SdgqpgGDAIS..LSFNNLLGFDSSKPVTKKYTYSFLPKEDGDVLLAEFDTYDPIYKNGAMYKGKPILW---VNKASYDTNL-NKFNRASLRQIFDVAPI................................
A0A2Z4EVM4_9NIDO/1723-1838 ..........yyfttvpvesvaapr-----------------------.-LKTKFDNFYL.T.S.....S.....GE-LAevESFNKVIGTDFSGPKK---VVTRYPDCSGDVVAILDE-IVTMHPHGTLIQGKPVLFLTKPNT-WKKLVPLLSASVIEVGNKYEVLPV................................
R1AB_CVM2/1885-2008 .................yycesgky---------YTKPIIKAQFRTFE.KVEGVYTNFKL.V.-.....-.....GHSIA..EKFNAKLGFDCNSPFT-EYKITEWPTATGDVVLASDDLYVSRYSGGCVTFGKPVIWLGHEEASLKSLTYFNRPSVVC-ENKFNVLPV................................
U5KNA9_9BETC/1900-2014 ..........nkpsleftpatvssg-----------------------.---VVYTNSCFiV.N.....D.....GDAIG..SAFNKLLGFDKNKPASKQLTYSLLPNEDGDVLLAEFKSYDPMYKNGAAYKGKPILW---VNNGLYDSKL-NKYNRASLRQIFDIQPV................................
R1AB_CVHN5/1929-2052 .................yycdngky---------YTKPIIKAQFKPFA.KVDGVYTNFKL.V.-.....-.....GHDIC..AQLNDKLGFNVDLPFV-EYKVTVWPVATGDVVLASDDLYVKRYFKGCETFGKPVIWFCHDEASLNSLTYFNKPSFKS-ENRYSVLSV................................
Q0Q485_SARS/1880-1992 .........................YTEQPIDLVPTQPLPNASF----.------DNFKL.T.C.....S.....NIKFA..DDLNQMTGF--KKPASRELSVTFFPDLNGDVVAIDYRHYSASFKKGAKLLHKPIIW--HINQTTNKTTY--KPNIWCLRCLWSTKPV................................
A0A088DIE1_9BETC/2028-2147 .........................YTSAPIDLTPTEPLSGAEYDNFHlKLVGTLDDNKV.K.-.....-.....---FV..QEFNHMVKYDKTKPTR-PVTISFYPEMEGDVVALSADKLQQHFKKGAKFGSKFIVW--HTGYKITRDLV--KPNMAAMRCITTSKPV................................
A0A0K2RVJ3_9BETC/1898-2020 ..................yceggky---------YTQRIVKAQFRTFE.KVDGAYINFKL.V.-.....-.....GHTVC..DSLNAKLGFDSSKEFV-EYKVTEWPTATGDVVLANDDLYVKRYERGCITFGKPVIWYNHEQASLNSLTYFNRPSLVD-VNKFDVLKV................................
R1A_SARS2/1907-2019 .........................FTEQPIDLVPNQPYPNASF----.------DNFKF.V.C.....D.....NIKFA..DDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW--HVNNATNKATY--KPNTWCIRCLWSTKPV................................
R9QTB2_SARS/1876-1988 .........................YTEQPIDLVPTQPLPNASF----.------DNFKL.T.C.....A.....NTKFA..DDLNQMTGF--KKPASRELSVTFFPDLNGDVVAIDYRHYSASFKKGAKLLHKPIIW--HINQTTNKTTY--KPNTWCLRCLWSTKPV................................
A7BKB9_9BETC/1894-2016 ..................ycdggky---------YTQRIIKAQFKTFE.KVDGVYTNFKL.I.-.....-.....GHTVC..DILNAKLGFDSSKEFV-EYKVTEWPTATGDVVLATDDLYVKRYERGCITFGKPVIWLSHEQASLNSLTYFNRPLLVD-ENKFDVLKV................................
R1AB_SARS2/1907-2019 .........................FTEQPIDLVPNQPYPNASF----.------DNFKF.V.C.....D.....NIKFA..DDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW--HVNNATNKATY--KPNTWCIRCLWSTKPV................................
C0KYT7_9BETC/1938-2061 .................yycesgky---------YTKPIIKAQFRTFE.KVDGVYTNFKL.V.-.....-.....GHSIA..EKLNAKLGFDCNSPFV-EYKITEWPTATGDVVLASDDLYVSRYSSGCITFGKPVVWLGHEEASLKSLTYFNRPSVVC-ENKFNVLPV................................
R1A_BCHK4/1865-1993 yymkdgkyytskptikyspatilpg-----------------------.---SVYSNSCL.V.G.....VdgtpgSDTIS..KFFNDLLGFDETKPISKKLTYSLLPNEDGDVLLSEFSNYNPVYKKGVMLKGKPILW---VNNGVCDSAL-NKPNRASLRQLYDVAPI................................
R1AB_CVMA5/1938-2061 .................yycesgky---------YTKPIIKAQFRTFE.KVDGVYTNFKL.V.-.....-.....GHSIA..EKLNAKLGFDCNSPFV-EYKITEWPTATGDVVLASDDLYVSRYSSGCITFGKPVVWLGHEEASLKSLTYFNRPSVVC-ENKFNVLPV................................
#=GC seq_cons ...................st.hth..........sp.l.pApF........ssYsNFKL.l.............ucslu..-shNphLGFspsKPhs.chplThaPshsGDVVhss.chYsspYcpGshhhGKPllW..H.psuhpphTa..+Pshhs.cshaslhPV................................
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