Conserved Protein Domain Family
CoV_nucleocap

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pfam00937: CoV_nucleocap 
Coronavirus nucleocapsid
Coronavirus (CoV) nucleocapsid (N) proteins have 3 highly conserved domains. The N-terminal domain (NTD) (N1b), the C-terminal domain (CTD)(N2b) and the N3 region. The N1b and N2b domains from SARS CoV, infectious bronchitis virus (IBV), human CoV 229E and mouse hepatic virus (MHV) display similar topological organisations. N proteins form dimers, which are asymmetrically arranged into octamers via their N2b domains. Domains N1b and N2b are linked by another domain N2a that contains an SR-rich region in which phosphorylation of specific serine residues allows the N protein to associate with the RNA helicase DDX1 permitting template read-through, and enabling the transition from discontinuous transcription of subgenomic mRNAs (sgmRNAs) to continuous synthesis of longer sgmRNAs and genomic RNA (gRNA). It has been shown that N proteins interact with nonstructural protein 3 (NSP3) and thus are recruited to the replication-transcription complexes (RTCs).
Statistics
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PSSM-Id: 484538
Aligned: 22 rows
Threshold Bit Score: 312.382
Created: 12-Feb-2025
Updated: 28-Apr-2025
Structure
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Aligned Rows:
PubMed ReferencesClick to see Conserved Features Help

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
YP_009201734  13 AARGRSGRVPFSFYMPVINNSSQPFYKVMPQNAVPKGQG-NKDQQIGYWNEQVR--WRMVKGTRKDLPSKWHFYYLGTGP 89 
YP_009113031  49 QASGGNVVPFYSWFSGITQFQKGQEFGFEQGQGVPLTNGvPPSEEKGYWYRHNRksYRTADGQQRQLLPRWYFYYLGTGP 128
YP_001876448  26 QAPALPTSGNVSWFQAIKGRKAGEEGITFKGPGVPVNENvSKNQNHGYWIQRSR--TTPGG---KKLAPLYYFYYTGTGP 100
YP_005352850   1 MATPSVPTTDASWFQVLKAQNKKATHPQFRGNGVPLNSAiKPAENHGYWLRYTR--QKPGGT---QIPPSYAFYYTGTGP 75 
YP_005352885   1 MATPTVPVADASWFQPLKAQNKKNTTPSFKGDGVPINTSlDHKAAHGYWLRFNR--QKPGGA---QLPPSFAFYYTGTGP 75 
YP_005352875   1 MAVPSVPKADCSWFQIIKAQNKKVQPLAFKGDGVPINTTlPKEMCHGYWLRYKR--VKPGGA---PLPPSYSFYYTGTGP 75 
YP_009273009  50 EKPRAAPMQNVSWFAPLVQTGK-SDLKFAHGEGVPVSQGvDGTYQHGYWLRTQR--NFTKGGKSLTANPRWYFYYTGTGR 126
YP_009072446  35 RKPRPAPQNNVSWFTPLTQHGK-QALTFNPGQGVPLNANdDPDSRIGYWRRNIR--TVTKNGKPQKLDPRWYFYYLGTGP 111
YP_009513018  31 PKPRPAPNVSVSWYTGITQHGK-QPLAFPAGQGVPLNANsTPKQNAGYWRRQDRk-LNTGNG-VKQLAPRWYFYYTGTGP 107
A3EXA1        31 PKPRPAPNNTVSWYTGLTQHGK-NPLAFPPGQGVPLNANsTTAQNAGYWRRQDRk-INTGNG-VKQLAPRWFFYYTGTGP 107 Tylonycteris ba...
YP_009201734  90 HADLKFRQRQ--------QGVFWVAKEGAKAEPTG-LGTRGR---NAELTTPIFNPG--LPDSIEIV-DQysr--pnsRA 152
YP_009113031 129 YANKQYGSDI--------DGVVWVASPNVDVRSPAdVPDRDPt--SHQAEPTRFAPGtvLPKGYYVE-GSg-------RS 190
YP_001876448 101 RDQAKYGQEI--------PYVTWVKGDGAKTSQLSeAGSRDVn-kFPNAFPLIFPTGdgPERGFFIErSRs-------RS 164
YP_005352850  76 RGNLKYGELPpndt-qatTRVTWVKGPGADTSIKPhVAKRNPnnpKHQLLPLRFPTGdgPAQGF--------------RV 140
YP_005352885  76 RGNLKYGEFPpnes-kgnSRITWVHVKDADTSIKPkVAKRNPqnpKHALLPLRFPPGdgPAQGF--------------RI 140
YP_005352875  76 RATLKYGELQdsdnqdnvNRVLWVKSPDADTSIKPkVAKRNPd--KHPLLPLRFKPGdgPVQGF--------------RI 139
YP_009273009 127 YADLRFGTRQ--------PDILWVGRNGANVNKVGnMGTRNPn--NDSAIPVQLPEG--IPKGFYAE-GT--------RS 185
YP_009072446 112 EQNLKYLQQK--------DGIVWVAAHGALNVPVKtVGTRNPa--NDQAIVAAFAPGteLPKGFYVE-GSrst--ssaSS 178
YP_009513018 108 EANLPFRTVK--------DGIYWVWEEGASEAPSD-FGTRNPa--NDAAIVTQFAPGtqLPKNCHIE-GTggnsqsssRA 175
A3EXA1       108 EANLPFRSVK--------DGIVWVYEEGATDAPSV-FGTRNPa--NDAAIVCQFAPGtlIPKNFHIE-GTggnsqsssRA 175 Tylonycteris ba...
YP_009201734 153 SSRARSQSndqgnRSRSQsnn--raqSNNRSQSRGRQNQNqnnqptgdggsngqrnqprnrsnsrnrsgnqgrnggsQQD 230
YP_009113031 191 APSSRSSS-----RASSRass--vggSRSRNNSASRNNTS---------------------------------------E 224
YP_001876448 165 RSNSQADN-----RSKSRers--qssDKPRKEDRGRSKSP---------------------------------------- 197
YP_005352850 141 DPFN-ARG-----RPQERg-------SGPRSQSANPRGTN---------------------------------------- 167
YP_005352885 141 DPFQPQRG-----RGMERg-------PTQRSQSANPRQND---------------------------------------- 168
YP_005352875 140 DPF----------QSRGR--------SVERGQQDRRAQSAe--------------------------------------- 162
YP_009273009 186 RNSSRSSS-----RGSSRntsasnsrANSRASSPGRNLPPqa----------------------------------gSEP 226
YP_009072446 179 AASSRSNS-----RSRNSsls--rssSPGRGLPPATDPNG---------------------------------------V 212
YP_009513018 176 SSASRNSS-----RSNSRgs-----qPGSRSHSPGSVGPS--------------------------------------DA 207
A3EXA1       176 SSNSRNSS-----RSSSRggr---stSNSRGTSPVSHGVGsa----------------------------------eSLA 213 Tylonycteris ba...
YP_009201734 231 LVAAVREALAGMGFKPNTSGsgRNTPVKVPKGDKPLNKptkapASQVEKPVWKRTPHSQeNVEVCFGPRDTYQ---NFGD 307
YP_009113031 225 VTPDMADQIASLVLAKLNKE--SGKPVQVTKQTAKEIK-----QKILNKPRQKRTPNKQcTVQQCFGKRGPSQ---NFGG 294
YP_001876448 198 ------------AQKNPGSG------GKITKEKAALMV---------SRAYSKRTLPPNkPVDQVFGSRDTEK---NFGD 247
YP_005352850 168 -----------------------NQPRKRDQSAPAAVR------RKTQHQAPKRTLPKGkTISQVFGNRSRTGa--NVGS 216
YP_005352885 169 -----------------------AGNRRRAASAPGTNR-----SKTHTHAIPKRTLQKGkTISAVFGKRSPAGs--NVGS 218
YP_005352875 163 ----------------------PQRPKQRERSRSAPSR-----AAPKQHAIPKRVLLKGkTISGTFGKRSPAKa--NVGS 213
YP_009273009 227 WMAYLVQKLQALESKVDGKKp-EKTPQKVTKQGAANMA---------DKLRHKRTPHKGsGVTQNFGRRGPGDlegNFGD 296
YP_009072446 213 LAALLLTKLEALDAKVNGPK----QPPVVTKKTAAEIA---------AKPRQKRVAHKGyNVNAAYGRRGPGPyqgNFGT 279
YP_009513018 208 SALLYLELAKRLEALEAGKS--KSAPKVITKKDAADAK---------KKMRHKRVATKAyNPTQAFGLRGPGDlqgNFGD 276
A3EXA1       214 ALPLLLDLQKRLADLESGKS---KQPKVVTKKDAAAAK---------NKMRHKRVATKGfNVTQAFGLRGPGPlqgNFGD 281 Tylonycteris ba...
YP_009201734 308 SQLVRLGVDYPHYPQIGELIPSQAALLFGSEITAH---------ERGD-NI------QLTYIYKMEVPKDHKSLAAFLPH 371
YP_009113031 295 GSMLKLGTSDPQFPILAELAPTAGAFFFGSKLELAkvnnmsgaaDEPQkDVy-----ELRYSGAIRFDSTLPGFETIMKV 369
YP_001876448 248 AEMIKKGMSDPRFTAALIPTPGPQAALFGSHVTLK---------EKPD-GL------EITYKYRTLFPKTDERYEEVKHA 311
YP_005352850 217 ADTEKTGMADPRIMALARHVPGVQEMLFAGHLESN---------FQAG-AI------TLTFSYSITVKEGSPDYERLKDA 280
YP_005352885 219 ADTEKAGMADGRIMALARQVPGVQEMLFAGHLSHQ---------FQAD-AV------TLTWTYSITIKSDSSDYDRIKQA 282
YP_005352875 214 PDTEKTGLGDPRLMALMRFVPGTQELLFAGHLKHK---------MQPE-GV------QLTFTYDITVKRDNKDFDRIVEA 277
YP_009273009 297 LEMLKLGTDDPRFPAAAQMAPTAAAFLFMSHFDTR---------EEND-AT------WLNYRGAIKLPKDNPNYATWMKL 360
YP_009072446 280 QEFNKLGTDYPKWPQIAQLAPTPSAFFGMSRFAVQ---------KNDD-GT------WLTYHGHIKMDESDPNFQVWMTE 343
YP_009513018 277 LKYCKEGVDDPRWPQMAELAPSASAFLSMSQLKLV---------HHSN-DTdnkpvyMLRYSGAIKLDPKNPNYSKWLEI 346
A3EXA1       282 MNYNKFGTEDPRWPQMAELAPSASAFMSMSQFKLT---------HQSN-DDkgdpiyFLSYSGAIKLDPKNPNYKKWLEL 351 Tylonycteris ba...
YP_009201734 372 IGAYADSTed------vTLPPALPPKQQRLRrsa---------------steVLADTTS 409
YP_009113031 370 MNENLDAYqhte--egaQLLSPKFQRKQKKGqve---------------kdnVSAATPK 411
YP_001876448 312 YLSNVPLQ-----------DGGQPLHSSGVQkklksrs-------ksrdrtdDGVENPT 352
YP_005352850 281 LNTVVNQT---------YEPPTKPTKDKKPEkqdqs------------akpkQQKKPKK 318
YP_005352885 283 LDTVVDQT---------YEAPIKEKKQPAKQqpkqd-----------kpkpqRSPKKQD 321
YP_005352875 278 LNSVVDMVyepegeirkDQQSKKDTQPKKKAekk---------------tptNPQKQPD 321
YP_009273009 361 LKENVDAY---------KDFPQTPERETKKKkkd---------------vvvEDVTVVE 395
YP_009072446 344 LQQNIDAY---------KNFPQKEEKKSrkp------------------ktkNVDMAPQ 375
YP_009513018 347 LEGNIDAY---------KNFPKKEKKQKQSQikqeaedpewdstdlfsqplqDPDNQPK 396
A3EXA1       352 LESNIDAY---------KTFPKKERKPKTTEdgavasssa----sqmedvdaKPQRKPK 397 Tylonycteris bat coronavirus HKU4
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