# STOCKHOLM 1.0
#=GF ID 2.40.10.10/FF/20656
#=GF DE Replicase polyprotein 1ab
#=GF AC 2.40.10.10/FF/20656
#=GF TP FunFam
#=GF DR CATH: 4.2
#=GF DR DOPS: 23.763
#=GS 2q6dC01/1-16_100-199            AC P0C6Y3
#=GS 2q6dC01/1-16_100-199            OS Avian infectious bronchitis virus (strain M41)
#=GS 2q6dC01/1-16_100-199            DE Replicase polyprotein 1ab
#=GS 2q6dC01/1-16_100-199            DR CATH; 2q6d; C:6-14; C:98-197; 
#=GS 2q6dC01/1-16_100-199            DR ORG; Viruses; Nidovirales; Coronaviridae; Coronavirinae; Gammacoronavirus; Avian coronavirus; 
#=GS 2q6dC01/1-16_100-199            DR EC; 2.7.7.48; 3.6.4.12; 3.6.4.13; 
#=GS P0C6Y1/2780-2793_2879-2969      AC P0C6Y1
#=GS P0C6Y1/2780-2793_2879-2969      OS Avian infectious bronchitis virus (strain Beaudette)
#=GS P0C6Y1/2780-2793_2879-2969      DE Replicase polyprotein 1ab
#=GS P0C6Y1/2780-2793_2879-2969      DR GENE3D; 5243b6d1879cb4abb49d01ae13e401f0/2780-2793_2879-2969; 
#=GS P0C6Y1/2780-2793_2879-2969      DR ORG; Viruses; Nidovirales; Coronaviridae; Coronavirinae; Gammacoronavirus; Avian coronavirus; 
#=GS P0C6Y1/2780-2793_2879-2969      DR EC; 2.7.7.48; 3.6.4.12; 3.6.4.13; 
#=GS P0C6Y2/2780-2793_2879-2969      AC P0C6Y2
#=GS P0C6Y2/2780-2793_2879-2969      OS Avian infectious bronchitis virus (strain Beaudette CK)
#=GS P0C6Y2/2780-2793_2879-2969      DE Replicase polyprotein 1ab
#=GS P0C6Y2/2780-2793_2879-2969      DR GENE3D; db280800c1fb0e81c0f6d85640d4f811/2780-2793_2879-2969; 
#=GS P0C6Y2/2780-2793_2879-2969      DR ORG; Viruses; Nidovirales; Coronaviridae; Coronavirinae; Gammacoronavirus; Avian coronavirus; 
#=GS P0C6Y2/2780-2793_2879-2969      DR EC; 2.7.7.48; 3.6.4.12; 3.6.4.13; 
#=GS P0C6Y3/2783-2795_2881-2971      AC P0C6Y3
#=GS P0C6Y3/2783-2795_2881-2971      OS Avian infectious bronchitis virus (strain M41)
#=GS P0C6Y3/2783-2795_2881-2971      DE Replicase polyprotein 1ab
#=GS P0C6Y3/2783-2795_2881-2971      DR GENE3D; f2c75b19c67e9ed2c37cb03f1f3c49bf/2783-2795_2881-2971; 
#=GS P0C6Y3/2783-2795_2881-2971      DR ORG; Viruses; Nidovirales; Coronaviridae; Coronavirinae; Gammacoronavirus; Avian coronavirus; 
#=GS P0C6Y3/2783-2795_2881-2971      DR EC; 2.7.7.48; 3.6.4.12; 3.6.4.13; 
#=GS Q3Y5H1/1-14_100-190             AC Q3Y5H1
#=GS Q3Y5H1/1-14_100-190             OS Infectious bronchitis virus
#=GS Q3Y5H1/1-14_100-190             DE 3C-like protease
#=GS Q3Y5H1/1-14_100-190             DR GENE3D; 02c26b927bf90910116d2e4061744884/1-14_100-190; 
#=GS Q3Y5H1/1-14_100-190             DR ORG; Viruses; Nidovirales; Coronaviridae; Coronavirinae; Gammacoronavirus; Avian coronavirus; 
#=GS A0A1L2FT79/2804-2816_2902-2992  AC A0A1L2FT79
#=GS A0A1L2FT79/2804-2816_2902-2992  OS Infectious bronchitis virus
#=GS A0A1L2FT79/2804-2816_2902-2992  DE 1ab pol protein
#=GS A0A1L2FT79/2804-2816_2902-2992  DR GENE3D; 088cd1da461337f472ba21da5e86f966/2804-2816_2902-2992; 
#=GS A0A1L2FT79/2804-2816_2902-2992  DR ORG; Viruses; Nidovirales; Coronaviridae; Coronavirinae; Gammacoronavirus; Avian coronavirus; 
#=GS B4UTZ9/2804-2816_2902-2992      AC B4UTZ9
#=GS B4UTZ9/2804-2816_2902-2992      OS Infectious bronchitis virus
#=GS B4UTZ9/2804-2816_2902-2992      DE Pol protein
#=GS B4UTZ9/2804-2816_2902-2992      DR GENE3D; 0fa5892b85dd4e268083d783a60e6b8e/2804-2816_2902-2992; 
#=GS B4UTZ9/2804-2816_2902-2992      DR ORG; Viruses; Nidovirales; Coronaviridae; Coronavirinae; Gammacoronavirus; Avian coronavirus; 
#=GS A0A0F6SKM6/2810-2822_2908-2998  AC A0A0F6SKM6
#=GS A0A0F6SKM6/2810-2822_2908-2998  OS Duck coronavirus
#=GS A0A0F6SKM6/2810-2822_2908-2998  DE ORF1a
#=GS A0A0F6SKM6/2810-2822_2908-2998  DR GENE3D; 126d15aae49e43e5a0a5f001396b1415/2810-2822_2908-2998; 
#=GS A0A0F6SKM6/2810-2822_2908-2998  DR ORG; Viruses; Nidovirales; Coronaviridae; Coronavirinae; Gammacoronavirus; Avian coronavirus; 
#=GS A0A0F6WGL5/2810-2822_2908-2998  AC A0A0F6WGL5
#=GS A0A0F6WGL5/2810-2822_2908-2998  OS Duck coronavirus
#=GS A0A0F6WGL5/2810-2822_2908-2998  DE ORF1ab polyprotein
#=GS A0A0F6WGL5/2810-2822_2908-2998  DR GENE3D; 56c3e474426de45f084a7acc6240aa78/2810-2822_2908-2998; 
#=GS A0A0F6WGL5/2810-2822_2908-2998  DR ORG; Viruses; Nidovirales; Coronaviridae; Coronavirinae; Gammacoronavirus; Avian coronavirus; 
#=GS G3FER5/2781-2793_2879-2969      AC G3FER5
#=GS G3FER5/2781-2793_2879-2969      OS Duck coronavirus
#=GS G3FER5/2781-2793_2879-2969      DE 1a polyprotein
#=GS G3FER5/2781-2793_2879-2969      DR GENE3D; 655e11097f92f3572475f7831f590beb/2781-2793_2879-2969; 
#=GS G3FER5/2781-2793_2879-2969      DR ORG; Viruses; Nidovirales; Coronaviridae; Coronavirinae; Gammacoronavirus; Avian coronavirus; 
#=GS B8QAY7/2762-2774_2860-2950      AC B8QAY7
#=GS B8QAY7/2762-2774_2860-2950      OS Infectious bronchitis virus
#=GS B8QAY7/2762-2774_2860-2950      DE 1a
#=GS B8QAY7/2762-2774_2860-2950      DR GENE3D; 6937aa7a7a26d858d0f067e2ef5e2cd1/2762-2774_2860-2950; 
#=GS B8QAY7/2762-2774_2860-2950      DR ORG; Viruses; Nidovirales; Coronaviridae; Coronavirinae; Gammacoronavirus; Avian coronavirus; 
#=GS A0A0M5J8L2/2759-2771_2857-2947  AC A0A0M5J8L2
#=GS A0A0M5J8L2/2759-2771_2857-2947  OS Infectious bronchitis virus
#=GS A0A0M5J8L2/2759-2771_2857-2947  DE 1a protein
#=GS A0A0M5J8L2/2759-2771_2857-2947  DR GENE3D; 74efff6816c9b198d22ce38f5dd199c8/2759-2771_2857-2947; 
#=GS A0A0M5J8L2/2759-2771_2857-2947  DR ORG; Viruses; Nidovirales; Coronaviridae; Coronavirinae; Gammacoronavirus; Avian coronavirus; 
#=GS P0C6V3/2780-2793_2879-2969      AC P0C6V3
#=GS P0C6V3/2780-2793_2879-2969      OS Avian infectious bronchitis virus (strain Beaudette)
#=GS P0C6V3/2780-2793_2879-2969      DE Replicase polyprotein 1a
#=GS P0C6V3/2780-2793_2879-2969      DR GENE3D; 776e256905ffdb93d40d137d7f51cde6/2780-2793_2879-2969; 
#=GS P0C6V3/2780-2793_2879-2969      DR ORG; Viruses; Nidovirales; Coronaviridae; Coronavirinae; Gammacoronavirus; Avian coronavirus; 
#=GS P0C6V4/2780-2793_2879-2969      AC P0C6V4
#=GS P0C6V4/2780-2793_2879-2969      OS Avian infectious bronchitis virus (strain Beaudette CK)
#=GS P0C6V4/2780-2793_2879-2969      DE Replicase polyprotein 1a
#=GS P0C6V4/2780-2793_2879-2969      DR GENE3D; 776e256905ffdb93d40d137d7f51cde6/2780-2793_2879-2969; 
#=GS P0C6V4/2780-2793_2879-2969      DR ORG; Viruses; Nidovirales; Coronaviridae; Coronavirinae; Gammacoronavirus; Avian coronavirus; 
#=GS C7S7Y8/2778-2790_2876-2966      AC C7S7Y8
#=GS C7S7Y8/2778-2790_2876-2966      OS Infectious bronchitis virus
#=GS C7S7Y8/2778-2790_2876-2966      DE 1ab polyprotein
#=GS C7S7Y8/2778-2790_2876-2966      DR GENE3D; 8786b3f2654ac4c0154923eb669c12ea/2778-2790_2876-2966; 
#=GS C7S7Y8/2778-2790_2876-2966      DR ORG; Viruses; Nidovirales; Coronaviridae; Coronavirinae; Gammacoronavirus; Avian coronavirus; 
#=GS P0C6V5/2783-2795_2881-2971      AC P0C6V5
#=GS P0C6V5/2783-2795_2881-2971      OS Avian infectious bronchitis virus (strain M41)
#=GS P0C6V5/2783-2795_2881-2971      DE Replicase polyprotein 1a
#=GS P0C6V5/2783-2795_2881-2971      DR GENE3D; 88289917fe53a8c18e85071e1a539dd8/2783-2795_2881-2971; 
#=GS P0C6V5/2783-2795_2881-2971      DR ORG; Viruses; Nidovirales; Coronaviridae; Coronavirinae; Gammacoronavirus; Avian coronavirus; 
#=GS A0A023PMZ4/2762-2774_2860-2950  AC A0A023PMZ4
#=GS A0A023PMZ4/2762-2774_2860-2950  OS Infectious bronchitis virus
#=GS A0A023PMZ4/2762-2774_2860-2950  DE ORF1ab
#=GS A0A023PMZ4/2762-2774_2860-2950  DR GENE3D; ae33f6095d7bca9de3286aad545dbb94/2762-2774_2860-2950; 
#=GS A0A023PMZ4/2762-2774_2860-2950  DR ORG; Viruses; Nidovirales; Coronaviridae; Coronavirinae; Gammacoronavirus; Avian coronavirus; 
#=GS I1YZH5/2783-2795_2881-2971      AC I1YZH5
#=GS I1YZH5/2783-2795_2881-2971      OS Infectious bronchitis virus
#=GS I1YZH5/2783-2795_2881-2971      DE ORF1a
#=GS I1YZH5/2783-2795_2881-2971      DR GENE3D; bea133402b1a969f9d8d1f6039cea2fe/2783-2795_2881-2971; 
#=GS I1YZH5/2783-2795_2881-2971      DR ORG; Viruses; Nidovirales; Coronaviridae; Coronavirinae; Gammacoronavirus; Avian coronavirus; 
#=GS I1U336/2780-2792_2878-2968      AC I1U336
#=GS I1U336/2780-2792_2878-2968      OS Infectious bronchitis virus
#=GS I1U336/2780-2792_2878-2968      DE 1a
#=GS I1U336/2780-2792_2878-2968      DR GENE3D; d0dc213cc935dbc8ed48205f4578f150/2780-2792_2878-2968; 
#=GS I1U336/2780-2792_2878-2968      DR ORG; Viruses; Nidovirales; Coronaviridae; Coronavirinae; Gammacoronavirus; Avian coronavirus; 
#=GS B2MWL8/2771-2783_2869-2959      AC B2MWL8
#=GS B2MWL8/2771-2783_2869-2959      OS Infectious bronchitis virus
#=GS B2MWL8/2771-2783_2869-2959      DE 1a protein
#=GS B2MWL8/2771-2783_2869-2959      DR GENE3D; 2571ca807798c1ec425a6805300b9a52/2771-2783_2869-2959; 
#=GS B2MWL8/2771-2783_2869-2959      DR ORG; Viruses; Nidovirales; Coronaviridae; Coronavirinae; Gammacoronavirus; Avian coronavirus; 
#=GS Q6VMD6/2800-2812_2898-2988      AC Q6VMD6
#=GS Q6VMD6/2800-2812_2898-2988      OS Infectious bronchitis virus
#=GS Q6VMD6/2800-2812_2898-2988      DE 1ab polyprotein
#=GS Q6VMD6/2800-2812_2898-2988      DR GENE3D; 937e000ab169d865e047d0a33e9a3c74/2800-2812_2898-2988; 
#=GS Q6VMD6/2800-2812_2898-2988      DR ORG; Viruses; Nidovirales; Coronaviridae; Coronavirinae; Gammacoronavirus; Avian coronavirus; 
#=GS Q6VMD5/2800-2812_2898-2988      AC Q6VMD5
#=GS Q6VMD5/2800-2812_2898-2988      OS Infectious bronchitis virus
#=GS Q6VMD5/2800-2812_2898-2988      DE 1a protein
#=GS Q6VMD5/2800-2812_2898-2988      DR GENE3D; aa50e7e977ea9f66c7a0195ca9baf0f6/2800-2812_2898-2988; 
#=GS Q6VMD5/2800-2812_2898-2988      DR ORG; Viruses; Nidovirales; Coronaviridae; Coronavirinae; Gammacoronavirus; Avian coronavirus; 
#=GS A0A059SFS7/2777-2789_2875-2965  AC A0A059SFS7
#=GS A0A059SFS7/2777-2789_2875-2965  OS Infectious bronchitis virus
#=GS A0A059SFS7/2777-2789_2875-2965  DE ORF1ab
#=GS A0A059SFS7/2777-2789_2875-2965  DR GENE3D; 0337706a3e1855f4770013b57a9e776b/2777-2789_2875-2965; 
#=GS A0A059SFS7/2777-2789_2875-2965  DR ORG; Viruses; Nidovirales; Coronaviridae; Coronavirinae; Gammacoronavirus; Avian coronavirus; 
#=GF TC 230.3 2.1E-72
#=GF SQ 23
2q6dC01/1-16_100-199                    GSSGFKKLVSPSSAVEKYKFVKANCGDSFTIACSYGGTVIGLYPVTMRSNGTIRASFLAGACGSVGFNIEKGVVNFFYMHHLELPNALHTGTDLMGEFYGGYVDEEVAQRVPPDNL
P0C6Y1/2780-2793_2879-2969              --SGFKKLVSPSSAVE--KFIKANCGDSFTIACAYGGTVVGLYPVTMRSNGTIRASFLAGACGSVGFNIEKGVVNFFYMHHLELPNALHTGTDLMGEFYGGYVDEEVAQ-------
P0C6Y2/2780-2793_2879-2969              --SGFKKLVSPSSAVE--KFIKANCGDSFTIACAYGGTVVGLYPVTMRSNGTIRASFLAGACGSVGFNIEKGVVNFFYMHHLELPNALHTGTDLMGEFYGGYVDEEVAQ-------
P0C6Y3/2783-2795_2881-2971              ---GFKKLVSPSSAVE--KFVKANCGDSFTIACSYGGTVIGLYPVTMRSNGTIRASFLAGACGSVGFNIEKGVVNFFYMHHLELPNALHTGTDLMGEFYGGYVDEEVAQ-------
Q3Y5H1/1-14_100-190                     --SGFKKLVSPSSAVE--KFVKANCGDSFTIACSYGGTVIGLYPVTMRSNGTIRASFLAGACGSVGFNIEKGVVNFFYMHHLELPNALHTGTDLMGEFYGGYVDEEVAQ-------
A0A1L2FT79/2804-2816_2902-2992          ---GFKKLVFPSSAVE--KFLKANCGDSFTIACSYGGTVVGLYPVTMRSNGTIRASFLAGACGSVGFNIEKGVVNFFYMHHLELPNALHTGTDLMGEFYGGYVDEEVAQ-------
B4UTZ9/2804-2816_2902-2992              ---GFKKLVSPSSAVE--KFLKANCGDSFTIACSYGGTVVGLYPVTMRSNGTIRASFLAGACGSVGFNIEKGVVNFFYMHHLELPNALHTGTDLMGEFYGGYVDEEVAQ-------
A0A0F6SKM6/2810-2822_2908-2998          ---GFKKFVSPSSAVE--KFLKANCGDSFTIACSYGGIVIGLYPVTMRSNGTIRASFLAGACGSVGFNIEKGVVNFYYMHHLELPNALHTGTDLMGEFYGGYIDEEVAQ-------
A0A0F6WGL5/2810-2822_2908-2998          ---GFKKFVSPSSAVE--KFLKANCGDSFTIACSYGGIVIGLYPVTMRSNGTIRASFLAGACGSVGFNIEKGVVNFYYMHHLELPNALHTGTDLMGEFYGGYIDEEVAQ-------
G3FER5/2781-2793_2879-2969              ---GFKKLVCPSSAVE--KFLKANCGDSFTIACSYGGTVVGLYPVTMRSNGTIRASFLAGACGSVGFNIEKGVVNFFYMHHLELPNALHTGTDLMGEFYGGYVDEEVAQ-------
B8QAY7/2762-2774_2860-2950              ---GFKKLVFPSSAVE--KFVKANCGDSFTIACSYGGTVVGLYPVTMRSNGTIRASFLAGACGSVGFNIEKGVVNFFYMHHLELPNALHTGTDLMGDFYGGYVDEEVAQ-------
A0A0M5J8L2/2759-2771_2857-2947          ---GFKKLVFPSSAVE--KFVKANCGDSFTIACSYGGTVVGLYPVTMRSNGTIRASFLAGACGSVGFNIEKGVVNFFYMHHLELPNALHTGTDLMGDFYGGYVDEEVAQ-------
P0C6V3/2780-2793_2879-2969              --SGFKKLVSPSSAVE--KFIKANCGDSFTIACAYGGTVVGLYPVTMRSNGTIRASFLAGACGSVGFNIEKGVVNFFYMHHLELPNALHTGTDLMGEFYGGYVDEEVAQ-------
P0C6V4/2780-2793_2879-2969              --SGFKKLVSPSSAVE--KFIKANCGDSFTIACAYGGTVVGLYPVTMRSNGTIRASFLAGACGSVGFNIEKGVVNFFYMHHLELPNALHTGTDLMGEFYGGYVDEEVAQ-------
C7S7Y8/2778-2790_2876-2966              ---GFKKLVSPSSAVE--KFVKANCGDSFTIACSYGGTVVGLYPVTMRSNGTIRASFLAGACGSVGFNIEKGVVNFYYMHHLELPNALHTGTDLMGVFYGGYVDEEVAQ-------
P0C6V5/2783-2795_2881-2971              ---GFKKLVSPSSAVE--KFVKANCGDSFTIACSYGGTVIGLYPVTMRSNGTIRASFLAGACGSVGFNIEKGVVNFFYMHHLELPNALHTGTDLMGEFYGGYVDEEVAQ-------
A0A023PMZ4/2762-2774_2860-2950          ---GFKKLVSPSSVVE--KFVKANCGDSFTIACSYGGTVVGLYPVTMRSNGTIRASFLAGACGSPGFNIEKGVVNFYYMHHLELPNALHTGTDLMGEFYGGYVDEEVAQ-------
I1YZH5/2783-2795_2881-2971              ---GFKKLVSPSSAVE--KFVKANCGDSFTIACSYGGTVVGLYPVTMRSNGTIRASFLAGACGSVGFNIEKGVVNFFYMHHLELPNALHTGTDLQGEFYGGYVDEEVAQ-------
I1U336/2780-2792_2878-2968              ---GFKKLVSPSSAVE--KFLKANCGDSFTIACSYGGTVIGLYPVTMRSNGTIRASFLAGACGSVGFNIEKGVVNFYYMHHLELPNALHTGTDLLGEFYGGYIDEEVAQ-------
B2MWL8/2771-2783_2869-2959              ---GFKKLVSPSSAVE--KFLKANCGDSFTIACSYGGTVVGLYPVTMRSNGTIRASFLAGACGSVGFNIERGVVNFFYMHHLELPNALHTGTDLSGEFYGGYVDEEVAQ-------
Q6VMD6/2800-2812_2898-2988              ---GFKKLAAPSSAVE--KFMKANCGDSFTIACSYGGTVIGLYPVTMRSNGTIRASFLAGACGSVGFNIERGVVNFYYMHHLELPNALHTGTDLNGAFYGGCVDEEVAQ-------
Q6VMD5/2800-2812_2898-2988              ---GFKKLAAPSSAVE--KFMKANCGDSFTIACSYGGTVIGLYPVTMRSNGTIRASFLAGACGSVGFNIERGVVNFYYMHHLELPNALHTGTDLNGAFYGGCVDEEVAQ-------
A0A059SFS7/2777-2789_2875-2965          ---GFKKLVSPSSAVE--KFLKANCGDSFTIACSYGGTVIGLYPVTMRSNGTIRASFLAGACGSVGFSIEKGVVNFFYMHHLELPNALHTGTDLAGEFYGGYIDEEVAQ-------
#=GC scorecons                          00099998769998990099599999999999979998979999999999999999999999998998997999997999999999999999995969999779999990000000
#=GC scorecons_70                       ___******_******__**_*************************************************************************_**************_______
#=GC scorecons_80                       ___******_******__**_******************_******************************************************_*_************_______
#=GC scorecons_90                       ___*****__******__**_************_***_*_******************************_*****_*****************_*_****__******_______
//