HHsearch 1.5 NAME c9mnmB_ FAM FILE c9mnmB_ COM /bmm/www/servers/phyre2/HH/hhmake -i c9mnmB_.a3m DATE Sat Jan 17 10:48:57 2026 LENG 128 match states, 128 columns in multiple alignment FILT 19 out of 21 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100) NEFF 3.3 EVD 0.4168 0.0244 SEQ >ss_pred CCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHCCCCCHHHHHHHHHCC CCCCHHHHHHHHHHHHHHHHHHHHCCCC >ss_conf 9676478999999999965888889999999834857899999997267614649999999999999898618899886245431675899999864223 5873788789999999999999747799 >Consensus hxplsPRtlxxWvkxveexgxxxevvpxFxalSxxxtpxDinxmLnxvxghqaaxQilkdxInEeaxewDrxHplrxPxxsdIxGxtstxqeQxxwxxxx xxvxxgxiyrxWiixglxkxvkxxxpxx >c9mnmB_ HQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHQMREPRGSDIAGTTSTLQEQIGWMTHN PPIPVGEIYKRWIILGLNKIVRMYSPTS >UniRef50_Q99FI2(143-273:482) Gag polyprotein n=1 Tax=Simian immunodeficiency virus RepID=Q99FI2_SIVCZ E=4e-24 s/c=0.85 id=47% cov=96% HQPLSPRTLGAWVKCV-EGGIAPSLAPMFLAYSTGAIAYDMNLMLNILDTHQGFPQVLKDEINKKAEEYDLLHpvqqpqqqgALRQPTASDITGNTSSVA EQVAWGE-----PIANIYRGWIVQSLEKVIQIARPSS >UniRef50_B7UES0(128-263:480) Gag polyprotein n=1 Tax=Simian immunodeficiency virus - olc RepID=B7UES0_SIVCZ E=3e-52 s/c=1.51 id=55% cov=99% HVPLATRTLQSWVKALEDRGFKSEIVPLFSAFAEGLLPEEINTLLNVVGDYQGAMQVLKEAINEEAEEYDRQHpqpigplpvgQIPPPRASDIVGTTSNL QQQLAWV--NAGIDVGALYKRWVIIGLQKLVKMYSPVT >UniRef50_Q05313(146-275:450) Nucleocapsid protein p13 n=119 Tax=Feline lentivirus group RepID=GAG_FIVWO E=2e-05 s/c=0.39 id=26% cov=96% YVALDPKMVSIFMEKAREGLGGEEVQLWFTAFSANLTPTDMATLIMARPGCAADKEILDESLKQLTAEYDRTHPPDGPRplpyftAAEIMGIGLTQEQQA EARFAPARMQC----RAWYLEALGKLaaIKAKSP-- >UniRef50_B7FCA1(133-268:513) Gag polyprotein n=2 Tax=Simian immunodeficiency virus RepID=B7FCA1_SIVCZ E=2e-43 s/c=1.29 id=51% cov=99% --PLSPRTIQTWVKHIEDRGFGAECVPFFSALTDRALAHDINTLLNNIGDHQAAMQIIKEIVNEEIQDWDRTHPqpagpiapgqMRQPTGSDIAGVTASV EDELAWLAQNPPIDVGAVYKRWVLRGLQKVVQIYVPVS >UniRef50_P69730(138-267:486) p9 n=167 Tax=Equine infectious anemia virus RepID=GAG_EIAV9 E=2e-27 s/c=0.95 id=23% cov=92% --PLTPRGYTTWVNTIQTNGLLNEASQnLFGILSVDCTSEEMNAFLDVVPGQAGQKQILLDAIDKIADDWDNRHPLPNAplvappqgpipmTARFIRGLG VPRERQMEPAFDQFR----QTYRQWIIEAMSEGIKV----- >UniRef50_C0K090(145-250:250) Gag protein (Fragment) n=2 Tax=Leporidae RepID=C0K090_LEPGR E=3e-20 s/c=0.94 id=31% cov=59% YEPVGPGLIGAWLKQVQEHGLThPATITYYAVISVNFTSVDINVLLNVTPGFAAEKQLVIDKIKEKAIAWDEMHP------------------------- ----------------------------- >UniRef50_P19560(166-284:1475) Integrase n=30 Tax=Bovine immunodeficiency virus RepID=POL_BIV29 E=5e-07 s/c=0.47 id=14% cov=88% ------KQLKIWSDATERNGVDLHAVNILGVITANLVQEEIKLLLNSTPKWRLDVQLIESKVREKENAhrtWKQHHP-EAPKTDEIIGKGLSSAEQATLI S----VECRETFRQWVLQAAMEVAQ------ >UniRef50_Q699V2(166-304:561) Gag polyprotein n=8 Tax=Simian immunodeficiency virus RepID=Q699V2_SIVCZ E=7e-40 s/c=1.18 id=53% cov=101% HVGVNTRTLKTWVEAVNSKKFDASLVPLFQILTEGFIPYDLNDMLNAIGDHQGAMQVIKDVINEEGSEWDlqhpqpqqqqPVAGLRDPSASDIAGTTSTI QEQIEWITrQNNPIQVGQIYRQWIILGLQKCVQVYNPVN >UniRef50_P03352(170-276:442) Nucleocapsid protein p14 n=445 Tax=Lentivirus RepID=GAG_VILV E=1e-15 s/c=0.79 id=24% cov=69% -------------------------------YATTWTSKDILEVLAMMPGNRAQKELIQGKLNEEAERWVRQNP-PGPnvlTVDQIMGVGQTNQQASQAN MDQAR----QICLQWVITALRSVRHM----- # NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665 HMM A C D E F G H I K L M N P Q R S T V W Y M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D 0 * * 0 * 0 * * * * H 1 * * * * * * 680 * * * * * * * * * * * * 1412 1 0 * * * * * * 2778 0 0 Q 2 * * * 2745 * * * * * * * * * 1565 * * 4097 1138 * * 2 0 * * * * * * 2825 0 0 A 3 2387 * * * * 4046 * * * * * * 535 * * 4105 * * * * 3 0 * * * * * * 3045 0 0 I 4 * * * * * * * 2452 * 541 * * * * * * * 2947 * * 4 0 * * * * * * 3045 0 0 S 5 4060 * 3411 * * 3854 * * * * * 2721 * * * 1126 2582 * * * 5 0 * * * * * * 3045 0 0 P 6 * * * * * * * * * * * * 185 * * * 3053 * * * 6 0 * * * * * * 3045 0 0 R 7 * * * * * 4142 * * 2367 * * * * * 416 * * * * * 7 0 * * * * * * 3327 0 0 T 8 * * * * * 3487 * 4557 * 4142 2636 * * 3163 * * 891 * * * 8 0 * * * * * * 3327 0 0 L 9 * * * * * * * 2428 * 826 * * * * * * * 2636 * 3487 9 0 * * * * * * 3327 0 0 N 10 3666 * * * * 3043 * * 2594 * * 1837 * 2450 * 3606 3487 * * * 10 0 * * * * * * 3327 0 0 A 11 1318 * * * * * * 1875 * * * * * * * 4215 1876 * * * 11 0 * * * * * * 3327 0 0 W 12 * * * * 2636 * * * * * * * * * * * * * 253 * 12 0 * * * * * * 3327 0 0 V 13 * * * * * * * * * 4142 3606 * * * * 3163 * 416 * * 13 0 * * * * * * 3327 0 0 K 14 * * 3163 2218 * * * * 865 * * 3487 * * 4828 * * * * * 14 0 * * * * * * 3327 0 0 V 15 1978 3950 * * * * 3528 * 2636 4665 * * * 4142 * * 2925 2279 * * 15 0 * * * * * * 3327 0 0 V 16 2636 * * * * * * 1920 * 4215 * * * * * * 3163 1289 * * 16 96 * 3950 * * * * 3327 0 0 E 17 * * * 696 * * * * * * * 4096 * 2688 2563 * * * * * 17 0 * * * * 0 * 3255 0 1000 E 18 * * 2831 726 * * * * * * * * * * 3163 4211 3487 * * * 18 0 * * * * * * 3327 0 0 K 19 * * * * * 2148 4142 * 1410 * * 2316 * * 2831 * * * * * 19 0 * * * * * * 3327 0 0 A 20 2815 * * * * 925 * * 2554 2636 * * * * * * * * * * 20 0 * * * * * * 3327 0 0 F 21 * * * * 1076 2636 * 3950 * 2778 * * * * * * * 3163 4557 * 21 0 * * * * * * 3327 0 0 S 22 3950 * 2594 * * 2043 * * 3376 3487 * 3966 * * * 2815 2885 * * * 22 84 4142 * 0 * * * 3327 1000 0 P 23 2221 * * 2636 * * * * * 3163 * 3487 1435 * * 4215 * * * * 23 0 * * * * * * 3327 0 0 E 24 4142 * * 488 * * 3163 * * * * * * * * 3075 * * * * 24 0 * * * * * * 3327 0 0 V 25 2316 3528 * * * * * 3502 * 3075 * * * * * * 4142 1156 * * 25 0 * * * * * * 3327 0 0 I 26 3950 * * * * * * 1712 * 3666 * * * 3606 * 3487 * 1396 * * 26 0 * * * * * * 3327 0 0 P 27 * * * * * * * * * 2636 * 3163 782 3487 * * 4142 * * * 27 135 3487 * 0 * * * 3327 1000 0 M 28 * * * * 3528 4665 * 3163 * 2062 1712 * * * * * * * 2636 4142 28 0 * * * * * * 3327 0 0 F 29 * * * * 266 * * * * 3163 * * * * * * * * * 4142 29 0 * * * * * * 3327 0 0 S 30 4142 * * * * 2316 * * * 3950 * * * 2968 * 1703 2041 * * * 30 0 * * * * * * 3327 0 0 A 31 538 * * * * * * 2804 * * * * * * * * * 2571 * * 31 0 * * * * * * 3327 0 0 L 32 * * * * 2355 * * 2654 * 958 * * * * * * * * * 2935 32 0 * * * * * * 3494 0 0 S 33 3113 * * * * * * * * * * * * * * 718 1855 * * * 33 0 * * * * * * 3494 0 0 E 34 1972 * 3593 1338 * * * * * * * * * * * * 2935 2880 * * 34 0 * * * * * * 3494 0 0 G 35 * * 2677 * * 1127 * * * * * 2093 * * 3593 * 3865 * * * 35 0 * * * * * * 3494 0 0 A 36 1403 2711 * * 3340 * * * * 1728 * * * * * * * * 3865 * 36 0 * * * * * * 3494 0 0 T 37 * * * * * * * 2744 * 2946 * * * * * * 702 3233 * * 37 0 * * * * * * 3494 0 0 P 38 3253 * * * * * * * * * * * 991 3233 * 2027 4640 * * * 38 0 * * * * * * 3494 0 0 Q 39 * * * 2079 * * 3015 * 3865 * * * * 2655 * * 2751 4252 * 2243 39 0 * * * * * * 3494 0 0 D 40 * * 390 2079 * * * * * * * * * * * * * * * * 40 0 * * * * * * 3494 0 0 L 41 * * * * * * * 1229 * 1840 1766 * * * * * * * * * 41 0 * * * * * * 3494 0 0 N 42 2751 * * * * * * * 3233 3865 * 564 * * * * * * * * 42 0 * * * * * * 3494 0 0 T 43 3585 * 4435 3865 * * * 4613 * 2155 * * * 3848 * 4903 1392 4252 * * 43 0 * * * * * * 3494 0 0 M 44 * * * * 3585 * * 3775 * 1457 1283 * * * * * * 3865 * * 44 0 * * * * * * 3494 0 0 L 45 * * * * * * * 3728 * 113 * * * * * * * * * * 45 0 * * * * * * 3494 0 0 N 46 3865 * 3585 * * * * * * * 2751 516 * * * * * * * * 46 0 * * * * * * 3494 0 0 T 47 2351 4762 * * * * * 4009 * * 3865 3593 * * * 2478 2655 2215 * * 47 0 * * * * * * 3494 0 0 V 48 3775 * * * * * * 2953 * 3400 3865 * * * 3728 * 2654 1321 * * 48 0 * * * * * * 3494 0 0 G 49 * * 4009 * * 1063 * * * * * * 1122 * * * * * * * 49 0 * * * * * * 3494 0 0 G 50 * * 1804 4903 * 967 * * 3233 * * * * * * * 4009 * * * 50 0 * * * * * * 3494 0 0 H 51 * 2751 * * 4252 * 1018 * * * * 3865 * 3585 * * * * 3233 4414 51 0 * * * * * * 3494 0 0 Q 52 1814 * * * * * * * * * * * * 887 2514 * * * * * 52 0 * * * * * * 3494 0 0 A 53 976 * * * * 1680 * * * 3233 * * * * * 3775 * * * * 53 0 * * * * * * 3494 0 0 A 54 1063 * 1972 4252 4009 * * * * * * * * 2718 * * * * * * 54 0 * * * * * * 3494 0 0 M 55 * * * * * * * * 1502 4940 1165 * 4009 * * * * 3233 * * 55 0 * * * * * * 3494 0 0 Q 56 * * * 2203 * * * * * * * * * 353 * * * * * * 56 0 * * * * * * 3494 0 0 M 57 * * * * * * * 1380 * 1858 2796 * * * * * * 2350 * * 57 0 * * * * * * 3494 0 0 L 58 * * * * * * * 1419 * 997 * * * * * * * 2998 * * 58 0 * * * * * * 3494 0 0 K 59 * * 2751 3233 * * * 4252 989 3585 * * * 3865 4762 * * * * * 59 0 * * * * * * 3494 0 0 E 60 * * 1262 1578 * 3865 * * * * * * * * * 3233 3775 * * * 60 0 * * * * * * 3494 0 0 T 61 2941 * * 4009 * * * 2715 1734 * * * * * * 3728 2655 3053 * * 61 0 * * * * * * 3494 0 0 I 62 * * * * * * * 752 * 2203 * * * * * * * 2402 * * 62 0 * * * * * * 3494 0 0 N 63 * * 3585 * * * * * 2315 * * 715 * * 3233 * * * * * 63 0 * * * * * * 3494 0 0 E 64 * * * 360 * * * * 2782 * * * * 3728 * * * * * * 64 0 * * * * * * 3494 0 0 E 65 * * * 1126 * * * 3585 2178 2751 * * * 3488 * * * * * * 65 0 * * * * * * 3494 0 0 A 66 699 * * 3233 * 4435 * 3593 * * * * * * * * 2751 * * * 66 0 * * * * * * 3494 0 0 A 67 1635 * 3585 2493 * * * 4252 * * * 3233 * 4548 4156 3068 4640 * * * 67 0 * * * * * * 3494 0 0 E 68 2654 * 2191 941 * * * * * * * * * 4940 3865 * * * * * 68 162 3233 * 1585 585 * * 3494 1000 0 W 69 * * * * * * * * * * * * * * * * * * 543 1673 69 83 4156 * 0 * * * 3494 1000 0 D 70 * * 411 3775 * * * * 3233 * * * * * * * * 3865 * * 70 68 4435 * 3322 152 * * 3494 1000 0 R 71 * * * 4252 * * * 4940 * 3279 * 3585 4435 3233 891 4762 * * * * 71 0 * * * * * * 3494 0 0 L 72 3921 * * * 4156 * 3233 * * 2601 4252 * * 2714 3585 * 1877 4435 * * 72 0 * * * * * * 3494 0 0 H 73 4435 * * * 4156 * 270 * * * * 3865 * * * * * * * * 73 356 2194 * 3254 160 * * 3494 1899 0 Q 74 3290 * * * * 4435 * * 4156 * * * 617 2803 * * * * * * 74 856 1929 2437 2990 194 * * 3494 1796 0 M 75 * * * * * * * 4019 * 991 2093 * 3290 * * 3344 * * * * 75 0 * * * * 0 * 2965 0 1612 R 76 * * 2679 3089 * * * * * * * * 2232 * 962 * * * * * 76 0 * * * * * * 3455 0 0 E 77 2535 * 3040 2806 * 2116 * * * * * 2916 4393 3195 * * 4542 * * * 77 0 * * * * * * 3455 0 0 P 78 3463 * * 4184 * * * * * * * * 227 * * * * * * * 78 261 2597 * 2850 215 * * 3455 1653 0 R 79 * * * * * * * * 3089 * * * * 4184 1376 3453 1511 * * * 79 245 2679 * 2585 263 * * 3455 1219 0 G 80 1110 * * * * 1537 * * * * * * * * * * 3089 3745 * * 80 0 * * * * * * 3455 0 0 S 81 3139 * 2380 * * * * * * * * * * * 2573 1085 4184 * * * 81 82 * 4184 * * * * 3455 0 0 D 82 * * 871 1831 3405 * * * * * * * * 3685 * * * * * * 82 0 * * * * * 0 3415 0 1000 I 83 * * * * * * * 0 * * * * * * * * * * * * 83 0 * * * * * 0 3415 0 1000 A 84 1226 * * * * * * 3061 * * 2065 * * * 3405 * 3848 4328 * * 84 0 * * * * * 0 3415 0 1000 G 85 * * * * * 0 * * * * * * * * * * * * * * 85 0 * * * * * 0 3415 0 1000 T 86 * * * * * * * 3613 3061 2523 * 3848 * * * * 1372 2568 * * 86 0 * * * * * 0 3415 0 1000 T 87 * * 3651 * * 1420 * * * * * * * * * * 871 * * * 87 0 * * * * * 0 3415 0 1000 S 88 4426 * * * * * * * * 1831 * * * 3685 * 1000 * 3405 * * 88 0 * * * * * 0 3415 0 1000 T 89 * * * * * * * * * * * 3611 3405 * * 2084 766 * * * 89 0 * * * * * 0 3415 0 1000 L 90 * * * * * * * 4271 * 2256 4493 3685 * 2632 3405 3061 * 2052 * * 90 0 * * * * 0 * 3415 0 1000 Q 91 2451 * 3108 1746 * * * * * * * * * 1311 * * * * * * 91 0 * * * * * * 3455 0 0 E 92 * * 4512 768 * * * * * * * * * 2315 2573 * * * * * 92 0 * * * * * * 3455 0 0 Q 93 2999 * * 3547 * * * * * * * * * 445 * * * 4184 * * 93 0 * * * * * * 3455 0 0 I 94 1869 * * 4308 * * * 2787 4184 2247 3463 * * * * 3745 * 3322 * * 94 0 * * * * * * 3455 0 0 G 95 1437 * * 1986 * 5129 * * * 4850 * 4184 * 3143 * * 2768 * * * 95 0 * * * * * * 3455 0 0 W 96 2705 * * * * * * * * 3089 4308 * 2573 * * * * * 970 * 96 0 * * * * * * 3455 0 0 M 97 3463 * * * * 3936 3692 2319 * 3547 2126 3745 * * 3665 4308 * 4393 * * 97 124 4856 4393 0 * * * 3455 1000 0 T 98 3435 * * 3890 1959 * * * * * 3676 4452 * 4256 * 3045 2033 * * 4606 98 560 2908 2406 595 1565 * 0 3441 1536 1000 H 99 1962 * 1846 * * * 2903 * * * * * * 2038 4332 4709 * * * * 99 73 4332 * 0 * 1572 591 3009 1000 2096 N 100 * * * * * * * * * * * 1498 2394 1357 * * 3938 * * * 100 0 * * * * * 0 3030 0 1724 P 101 1569 * * * 3176 4577 * * * 3938 * 2132 2204 * * * * * * * 101 90 * 4048 * * * 0 3030 0 1724 P 102 4083 * * * * 3217 * * * 3795 * * 1679 * 1155 * * * * * 102 335 * 2270 * * 1445 661 2992 0 2135 I 103 * * * * * * * 1305 * * 3206 * * * * * * 1038 * * 103 0 * * * * 1024 976 2954 0 2489 P 104 * * 2321 2850 * * * * * * * 4275 2133 1633 * * 4082 * * * 104 0 * * * * * 0 3079 0 1655 V 105 * 1589 * * * * * 3018 * * * 3964 * * * 4082 * 1248 * * 105 311 * 2368 * * * 0 3079 0 1655 G 106 2578 * * * * 634 * * * * * * * * 2409 * * * * * 106 0 * * * * 821 1204 2689 0 2131 E 107 2361 * 3749 2477 * * * * * * * 2460 * 1924 * * 4341 4139 * * 107 0 * * * * * 0 3166 0 1219 I 108 * * * * * * * 959 * 4111 4139 * 4036 * * * 1942 4333 * * 108 0 * * * * * 0 3166 0 1219 Y 109 * 3431 4036 * 2778 * * * * * 4139 * * * * * * * * 635 109 0 * * * * 0 * 3166 0 1219 K 110 * 4184 * * * * * * 1897 3745 * * * 4308 859 * * * * * 110 0 * * * * * * 3455 0 0 R 111 2679 * * * * 3936 * * 4184 * * * * 1594 1517 4542 * * * * 111 0 * * * * * * 3455 0 0 W 112 * * * * * * * * * * * * * * * 4308 4184 * 161 * 112 0 * * * * * * 3455 0 0 I 113 * * * * * * * 972 * * * 4308 * * * * * 1818 * 2679 113 0 * * * * * * 3455 0 0 I 114 * * * * 4308 * * 1080 * 1424 * * * 4693 * * * 3936 * * 114 0 * * * * * * 3455 0 0 L 115 * * * 2018 * * * 3535 4308 2195 * * * 2451 2830 * 3745 * * * 115 0 * * * * * * 3455 0 0 G 116 1188 * * * * 1013 * * * * * * * * * 3936 * * * * 116 0 * * * * * * 3455 0 0 L 117 3089 * * * * * * * * 518 2904 * * * * 4308 * * * * 117 0 * * * * * * 3455 0 0 N 118 * * * 3848 * 3613 * * 4123 * 3061 2749 * 1512 3685 3405 * * * * 118 0 * * * * * * 3415 0 0 K 119 * * * 2223 * * * * 931 * * * * * 3266 3685 * * * 3651 119 0 * * * * * * 3415 0 0 I 120 * 2939 * * * 3405 * 3040 * 1758 * * * * * * * 1482 * * 120 123 3613 * 1000 1000 * * 3415 1000 0 V 121 3061 * * * * * * 2026 * * 3651 * * * 3685 * * 1067 * * 121 0 * * * * * * 3415 0 0 R 122 * * * * * * 3685 * 1165 * * * * 1591 2793 * * * * * 122 0 * * * * * * 3415 0 0 M 123 3389 3976 * * * * * 2477 4453 * 1736 * * * * 4277 * 1922 * * 123 0 * * * * * * 3062 0 0 Y 124 3282 * * * 3628 * 3806 * 2447 * * * * * * * * * * 833 124 0 * * * * * * 2553 0 0 S 125 * 3806 * * * * * * * * * 1826 * * 3282 1277 * 2931 * * 125 0 * * * * * * 2553 0 0 P 126 * * * * * * * * * * * * 0 * * * * * * * 126 0 * * * * * * 2495 0 0 T 127 * * * * * * * 3336 * * * * * * * 2856 2082 925 * * 127 0 * * * * * * 2103 0 0 S 128 * * * * * * * * * * * 2382 * * * 524 3146 * * * 128 0 * * 0 * * * 2103 0 0 //