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Database: Pfam
Entry: Peptidase_S3
LinkDB: Peptidase_S3
Original site: Peptidase_S3 
#=GF ID   Peptidase_S3
#=GF AC   PF00944.16
#=GF DE   Alphavirus core protein 
#=GF PI   Alpha_core; 
#=GF AU   Finn RD, Bateman A
#=GF SE   Pfam-B_266 (release 3.0)
#=GF GA   20.70 20.70;
#=GF TC   20.80 22.00;
#=GF NC   20.40 19.60;
#=GF BM   hmmbuild HMM.ann SEED.ann
#=GF SM   hmmsearch -Z 11927849 -E 1000 --cpu 4 HMM pfamseq
#=GF TP   Domain
#=GF RN   [1]
#=GF RM   8450538
#=GF RT   Refined structure of Sindbis virus core protein and comparison
#=GF RT   with other chymotrypsin-like serine proteinase structures. 
#=GF RA   Tong L, Wengler G, Rossmann MG; 
#=GF RL   J Mol Biol 1993;230:228-247.
#=GF RN   [2]
#=GF RM   7867069
#=GF RT   Nucleocapsid and glycoprotein organization in an enveloped
#=GF RT   virus. 
#=GF RA   Cheng RH, Kuhn RJ, Olson NH, Rossmann MG, Choi HK, Smith TJ,
#=GF RA   Baker TS; 
#=GF RL   Cell 1995;80:621-630.
#=GF RN   [3]
#=GF RM   8831786
#=GF RT   Structural analysis of Sindbis virus capsid mutants involving
#=GF RT   assembly and catalysis. 
#=GF RA   Choi HK, Lee S, Zhang YP, McKinney BR, Wengler G, Rossmann MG,
#=GF RA   Kuhn RJ; 
#=GF RL   J Mol Biol 1996;262:151-167.
#=GF DR   INTERPRO; IPR000930;
#=GF DR   MEROPS; S3;
#=GF DR   SCOP; 1kxf; fa;
#=GF DR   HOMSTRAD; vprotease;
#=GF DR   TC; 1.A.34;
#=GF CC   Also known as coat protein C and capsid protein C. This makes
#=GF CC   the literature very confusing.  Alphaviruses consist of a
#=GF CC   nucleoprotein core, a lipid membrane which envelopes the core,
#=GF CC   and glycoprotein spikes protruding from the lipid membrane.
#=GF SQ   4
#=GS POLS_CHIKS/106-262    AC Q8JUX5.3
#=GS POLS_SINDV/107-265    AC P03316.1
#=GS POLS_SINDV/107-265    DR PDB; 1LD4 D; 107-6264;
#=GS POLS_SINDV/107-265    DR PDB; 1KXA A; 107-264;
#=GS POLS_SINDV/107-265    DR PDB; 1KXE A; 107-264;
#=GS POLS_SINDV/107-265    DR PDB; 1KXD A; 107-264;
#=GS POLS_SINDV/107-265    DR PDB; 1Z8Y Q; 107-264;
#=GS POLS_SINDV/107-265    DR PDB; 2SNW B; 107-264;
#=GS POLS_SINDV/107-265    DR PDB; 1SVP A; 107-265;
#=GS POLS_SINDV/107-265    DR PDB; 1KXF A; 107-264;
#=GS POLS_SINDV/107-265    DR PDB; 1LD4 A; 107-1264;
#=GS POLS_SINDV/107-265    DR PDB; 1LD4 B; 107-4264;
#=GS POLS_SINDV/107-265    DR PDB; 1Z8Y T; 107-264;
#=GS POLS_SINDV/107-265    DR PDB; 1Z8Y S; 107-264;
#=GS POLS_SINDV/107-265    DR PDB; 2SNV A; 107-264;
#=GS POLS_SINDV/107-265    DR PDB; 1SVP B; 107-265;
#=GS POLS_SINDV/107-265    DR PDB; 1KXC A; 107-264;
#=GS POLS_SINDV/107-265    DR PDB; 1KXB A; 107-264;
#=GS POLS_SINDV/107-265    DR PDB; 1Z8Y R; 107-264;
#=GS POLS_SINDV/107-265    DR PDB; 2SNW A; 107-264;
#=GS POLS_SINDV/107-265    DR PDB; 1LD4 C; 107-5264;
#=GS C5FTE2_ARTOC/485-559  AC C5FTE2.1
#=GS POLS_SFV/112-268      AC P03315.1
#=GS POLS_SFV/112-268      DR PDB; 1VCP B; 119-267;
#=GS POLS_SFV/112-268      DR PDB; 1VCP C; 119-267;
#=GS POLS_SFV/112-268      DR PDB; 1DYL A; 119-267;
#=GS POLS_SFV/112-268      DR PDB; 1VCQ B; 119-267;
#=GS POLS_SFV/112-268      DR PDB; 1DYL D; 119-267;
#=GS POLS_SFV/112-268      DR PDB; 1VCQ A; 119-267;
#=GS POLS_SFV/112-268      DR PDB; 1VCP A; 119-267;
#=GS POLS_SFV/112-268      DR PDB; 1DYL C; 119-267;
#=GS POLS_SFV/112-268      DR PDB; 1DYL B; 119-267;
POLS_CHIKS/106-262               .............CMKIENDCIFEVKHE-GKVTGYACLVGDKVMKPAHVKGTIDNADLAKLAFKRSSKYDLECAQIPVHMKSDASKFTHEKPEGYYNWHHGAVQYSGGRFTIPTGAGKPGDSGRPIFDNKGRVVAIVLGG.ANEGARTALSVVTWN-KDIVTKITPEGAEEWS..........
#=GR POLS_CHIKS/106-262    AS    ...............................................*.....*...................................................................*.............................................................
POLS_SINDV/107-265               .............ALKLEADRLFDVKNEDGDVIGHALAMEGKVMKPLHVKGTIDHPVLSKLKFTKSSAYDMEFAQLPVNMRSEAFTYTSEHPEGFYNWHHGAVQYSGGRFTIPRGVGGRGDSGRPIMDNSGRVVAIVLGG.ADEGTRTALSVVTWNSKGKTIKTTPEGTEEWS..........
#=GR POLS_SINDV/107-265    SS    .............ETTSEEEEEEEEETTEEEEETTS-SEESSTTGGGS--EEEGGGTEEEEE--GGGSTTSB-B-S---SEEEEETTEEEEEETTEEEEETTS--TT-TT-EEE-TTS-EEEEEEEEEEESSEEEEEEEE.-TTS-EEEEE-TTEEESXXXXXXXXXXXXXXX..........
#=GR POLS_SINDV/107-265    AS    ...............................................*.....*...................................................................*.............................................................
C5FTE2_ARTOC/485-559             .egypgglhhrgw----------------------------------------------------------------------------------------------GVFNPSTHFAKPGDSGSWVLDMSGRVVAIVIAGdSSDGSTLTLPMTELV-KDVE------------imvklpagaf
POLS_SFV/112-268                 .............CMKIENDCIFEVKHE-GKVTGYACLVGDKVMKPAHVKGVIDNADLAKLAFKKSSKYDLECAQIPVHMRSDASKYTHEKPEGHYNWHHGAVQYSGGRFTIPTGAGKPGDSGRPIFDNKGRVVAIVLGG.ANEGSRTALSVVTWN-KDMVTRVTPEGSEEWS..........
#=GR POLS_SFV/112-268      SS    .............ETTEEEEEEEEETTE-EEBTT--SEESSHHHHTSEEEEETTTTEEEEE--GGGGGG-B-B-S---SEEEEETTEEEEEESSEEEEETTS--TT-TT-EEE-TTS-EEEEEEEEEEETTEEEEEEEEE.SSEEEEE--TTEEE--XXXXXXXXXXXXXXXX..........
#=GR POLS_SFV/112-268      AS    ...............................................*.....*...................................................................*.............................................................
#=GC SS_cons                     .............ETTCEEEEEEEECTCEEEECTTSSCECSCCCHCCCEEEECCCCCEEEEE-GGGGCCTCBBBSS--SCEEEECTCEEEEECTCEEEECTTS-TTTTTTEEEETTTSEEEEEEEEEEECTCEEEEEEEE.STCCEEEEECTCCEEESXXXXXXXXXXXXXXX..........
#=GC seq_cons                    .............shKlEsDplF-VKpE.GcVhGaAhhhtsKVMKPhHVKGsIDpssLuKLtFp+SStYDhEhAQlPVpM+S-A.paTpE+PEGaYNWHHGAVQYSGGRFTIPTGsGKPGDSGRPIhDNpGRVVAIVLGG.AsEGoRTALSVVTWN.KDhsh+hTPEGsEEWS..........
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