HHsearch 1.5 NAME c2m9uA_ FAM FILE c2m9uA_ COM /bmm/www/servers/phyre2/HH/hhmake -i c2m9uA_.a3m DATE Sat Jan 11 09:26:54 2014 LENG 89 match states, 89 columns in multiple alignment FILT 41 out of 45 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100) NEFF 3.5 EVD 0.4388 0.2275 SEQ >ss_dssp CCCCCSCCCTTEEEEEEECCSSSSCCEEEEEEEEEEEETTEEEETTSSSCEEGGGEEECCCCSSTTTSSSCCTTCCTTTSCCCCCCCCC >sa_dssp EEEEDEACBBABBACAEECEEEEEEDEEDDECBABCBDEECCCBDECEDDCDCDDBDDBCCEDCDCBEECEEEDDDEECAEDEEDEECE >ss_pred CCCEECCCCCCCEEEEEECCCCCCCCEECCCEEEEEECCCEEEECCCCCCEEEHHEEECCCCCCCCCCCEEEEECCCCCEEEEEEECCC >ss_conf 97500663789899998167887674452857999952525992786771641205645788787776416872478843899992588 >Consensus xxxxxHxxxpGdxVxvKxxxxxxlxPrWxGPyxVlLtTpTAVkvxgxxxWiHxSxxKxappxxxxxxxxxWxxxxxxxplklxlxrxxx >c2m9uA_ HHHHHHSHMVGDTVWVRRHQTKNLEPRWKGPYTVLLTTPTALKVDGIAAWIHAAHVKAADPGGGPSSRLTWRVQRSQNPLKIRLTREAP >UniRef50_Q14263(62-128:163) Pol gene protein; Xxx (Fragment) n=1 Tax=Homo sapiens RepID=Q14263_HUMAN E=2e-09 s/c=0.95 id=35% cov=73% -----HPFKPRDSLWVKKXNPTTLGPIWDGLHTVILSIPTVVKVAGIVPWIHPS------SQLKPAAQDKWTSQQ-------------- >UniRef50_UPI000175F85A(1043-1129:1161) PREDICTED: similar to gag-pro-pol polyprotein n=1 Tax=Danio rerio RepID=UPI000175F85A E=1e-20 s/c=1.15 id=36% cov=94% -----HNLRPGDFVVIRDLRRKSWRAkRWLGPFQMLLTTETAVKVAERATWVHAGHCRKIPPPEEDSTREfiSWSVGRlITSTTSLQMVKMA- >UniRef50_UPI000194E476(1125-1207:1210) PREDICTED: similar to Pro-Pol polyprotein n=3 Tax=Taeniopygia guttata RepID=UPI000194E476 E=2e-19 s/c=1.17 id=31% cov=91% -----HQVQPGDWVLIRSWKEDSITPKWDGPYLVLITTDSAVRTAEKG-WTHASRIKgPVDPTRfhTASRETSWKIDGKPGDLKLTVKK--- >UniRef50_UPI000179CCC3(1006-1070:1092) Protease n=2 Tax=Bos taurus RepID=UPI000179CCC3 E=1e-15 s/c=1.29 id=34% cov=72% -------FEPGTEVLIKTLGFGgpSLKPLWEGPYHVILSSPTAVKVPGIDSWVHHTRVKRWHPDQKEQTEPS------------------- >UniRef50_Q9UNM4(28-109:114) Pol protein (Fragment) n=3 Tax=Homo sapiens RepID=Q9UNM4_HUMAN E=3e-15 s/c=1.01 id=31% cov=91% ----YEDNLAGRSVLVKNLTPQTLQPRWTGPYLVIYSTPTAVCLQNPPHWVHHSRIKLCPSDSQPnPSSSSWKSQ-VLSPTSLKLT---- >UniRef50_Q2VF30(2065-2127:2146) Polyprotein n=1 Tax=Atlantic salmon swim bladder sarcoma virus RepID=Q2VF30_9RETR E=3e-13 s/c=1.20 id=38% cov=63% --------KVGDWVRIKVHKRKWADPRWTGPYEVKEVTSHSVQVKGKsgAPWHHLTHCTPAPAPD-------------------------- >UniRef50_Q4TFN9(91-145:147) Chromosome undetermined SCAF4341, whole genome shotgun sequence. (Fragment) n=1 Tax=Tetraodon nigroviridis RepID=Q4TFN9_TETNG E=2e-05 s/c=0.91 id=24% cov=62% -----HDLRPGDWIMVKKLNNGrKKRLIWDGPHQVLQSSNSGVMIAEGATWLDTSEFKRA------------------------------ >UniRef50_Q88285(1887-1956:2017) Gag-pol polyprotein n=3 Tax=Snakehead retrovirus RepID=Q88285_9RETR E=9e-08 s/c=0.83 id=39% cov=49% -------------VLVRKFTGDAFSPKWEGPYVITETTKYAAKVQamsdkvtQHSGWIHRTHL--------------------------------- # 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 * * * * * * 0 * * * * * * * * * * * * * 1 0 * * * * * * 1000 0 0 H 2 * * * * * * 0 * * * * * * * * * * * * * 2 0 * * * * * * 1000 0 0 H 3 * * * * * * 0 * * * * * * * * * * * * * 3 0 * * * * * * 1000 0 0 H 4 * * * * * * 0 * * * * * * * * * * * * * 4 0 * * * * * * 1000 0 0 H 5 * * * * * * 1190 * * * * * * * * * * * * 832 5 0 * * * * * * 1628 0 0 H 6 * * * 3520 * * 132 * * * * * * * * * * * * * 6 0 * * * * * * 3328 0 0 S 7 * * 1961 * * 5450 * * 3706 * * 4257 1867 2717 * 5175 2862 * * * 7 0 * * * * * * 3328 0 0 H 8 4275 * * * 1747 * 5213 2410 * 3037 * 3580 * * * * * 3219 * 3029 8 0 * * * * * * 3362 0 0 M 9 * * * 3357 * * * 4198 2818 3281 5416 * * 2001 1839 4816 6066 * * * 9 0 * * * * * * 3532 0 0 V 10 3281 * * * * * * * * * * * 649 * * * 4360 2247 * * 10 0 * * * * * * 3532 0 0 G 11 * * * * * 77 * * * * * * * * 4266 * * * * * 11 0 * * * * * * 3571 0 0 D 12 * * 661 * * * 4397 * * * * 3501 * 3625 4475 4296 4184 * * * 12 0 * * * * * * 3573 0 0 T 13 5474 * * 5223 4831 * * * 3347 4687 5154 * * 4311 4664 2796 3991 * 1214 5461 13 0 * * * * * * 3795 0 0 V 14 * 4460 * * 4957 * * 3172 * 4781 * * * * * * * 368 * * 14 0 * * * * * * 3865 0 0 W 15 * * * * 4957 * * * * 1412 3145 * * * 3462 * * 4862 2890 2191 15 0 * * * * * * 3865 0 0 V 16 * * * * * * * 1611 * 2458 * * * * 5054 * * 1220 * 4998 16 0 * * * * * * 3865 0 0 R 17 * * * * * * * * 556 * * 4500 * * 2016 * * * 5146 * 17 0 * * * * * * 3865 0 0 R 18 * * 3518 4500 * * * 4412 2618 * * 2667 * 4139 2410 3260 3722 3718 * * 18 0 * * * * * * 3865 0 0 H 19 4472 * * * 2592 * 1614 * * 1970 * * 5308 * * * * * 2459 * 19 117 3687 * 0 * * * 3833 1470 0 Q 20 4412 * 4957 * * 5252 * * 2003 * * 3060 * 2703 2369 5184 2732 * * * 20 0 * * * * * * 3865 0 0 T 21 4506 * 5417 2971 4097 3950 * * 2768 * * 3494 2832 5146 2616 6338 3723 5243 * * 21 56 4719 * 0 * * * 3865 1090 0 K 22 5322 * 2896 4184 * 1874 5242 * 1912 * * * * 3000 * 4313 4457 * * * 22 109 3784 * 465 1861 * * 3883 1604 0 N 23 2993 * * 5523 * * * * 3473 * * 2880 4092 4944 * 2024 2675 * 2908 * 23 228 3021 5454 791 1244 * * 3883 1973 0 L 24 4873 * * 4556 4786 * * 3862 4352 816 * * 5499 * * 4100 3976 5504 4827 * 24 0 * * * * * 0 3875 0 1000 E 25 * 5298 4873 2202 * 3672 * * 4476 * * * 5565 1854 3570 3042 3793 5368 * * 25 35 * 5368 * * * 0 3875 0 1000 P 26 4779 * * * * 4536 * * * 3915 * * 327 * * * 5274 4993 * * 26 54 4779 * 0 * 1032 969 3873 1000 1254 R 27 * * * * * 4363 * 3452 2837 5355 * 4476 * 5561 917 4735 5539 * 4608 * 27 0 * * * * 0 * 3902 0 1000 W 28 * * * * * * * * * * * * * * 3513 * * * 132 * 28 0 * * * * * * 3897 0 0 K 29 * * 2541 2056 * * * 4425 2189 3561 * * * * * 4172 2829 4608 * * 29 0 * * * * * * 3897 0 0 G 30 * * * 4172 * 82 * * * * * * * * * * * * * * 30 0 * * * * * * 3897 0 0 P 31 * * * * * * * * * 4145 * * 138 * * 4859 * * * * 31 0 * * * * * * 3897 0 0 Y 32 * * * * 2760 * 2095 * * 4205 * * * 5336 * * * * * 891 32 0 * * * * * * 3897 0 0 T 33 * * 4339 4962 * * 5393 4310 * 2444 * * 5583 1617 3619 * 2503 4157 * * 33 0 * * * * * * 3897 0 0 V 34 * * * * * * * 2851 * 4339 5030 * * * * * 5469 398 * * 34 0 * * * * * * 3897 0 0 L 35 4339 * * * * * * 1751 4962 1166 4776 * * 5639 * * 3512 4980 * * 35 0 * * * * * * 3897 0 0 L 36 4205 * * 3932 5469 * * 5654 * 467 * * * 4309 * 5103 * * * 4839 36 0 * * * * * * 3897 0 0 T 37 5639 * * * * * * 4776 * * * * * * 4205 1536 1119 3573 * * 37 0 * * * * * * 3897 0 0 T 38 * * * * * * * 4754 * * * 5091 * * * 3405 253 * * * 38 0 * * * * * * 3897 0 0 P 39 4776 * 4644 3948 5609 * 4633 * 4224 * * 4309 769 * * 3222 * * * * 39 0 * * * * * * 3897 0 0 T 40 4776 * * * * * 3535 5103 * * 5145 * * * * 3032 590 * * 4902 40 0 * * * * * * 3897 0 0 A 41 472 4205 * * * 4309 * * * * * * * * * 3090 5639 4754 * * 41 0 * * * * * * 3897 0 0 L 42 3504 * * * * * * 2890 * 3502 * * * * * * * 538 * * 42 0 * * * * * * 3897 0 0 K 43 * 4839 * * * 5103 * * 652 4776 3667 * * 3265 3642 * * * * * 43 0 * * * * * * 3897 0 0 V 44 4961 4737 * * * * * 3356 * 2143 * * * * * * 4055 873 * * 44 0 * * * * * * 3856 0 0 D 45 1711 * 2702 3177 * 5352 * * 3218 3715 * * 4541 2656 5603 * * * * * 45 51 4844 * 2807 222 * * 3856 1000 0 G 46 * * 4204 2025 * 728 * * * * * 4827 * 4844 5258 * * * * * 46 0 * * * * * * 3856 0 0 I 47 * * * * * 4223 3254 1843 2085 5603 * * 3942 3993 2696 * * 5353 * * 47 134 3495 * 491 1792 * * 3856 1336 0 A 48 2628 * 3890 3030 * 3584 5815 * 4737 5600 * 5258 2682 * * 3532 2449 4734 * * 48 90 * 4055 * * * * 3856 0 0 A 49 2413 * * * * 4774 3866 * * * * 5469 2606 * * 2051 1842 * * * 49 0 * * * * 0 * 3824 0 1504 W 50 * * * * * * * * * * * * * * * * * * 0 * 50 0 * * * * * * 3856 0 0 I 51 * * * * 4292 * 4913 1162 * 4223 * * * * * * 2754 2241 * 4172 51 0 * * * * * * 3856 0 0 H 52 * * 4223 * * * 199 * * * * * * 4292 5355 * * * * * 52 0 * * * * * * 3856 0 0 A 53 2220 5352 5877 * * * 2505 4334 * 2433 * * 4734 * 4174 * 3400 3974 * 3616 53 0 * * * * * * 3856 0 0 A 54 4749 * 4451 * * 4421 * * * * * 5314 * * * 548 2632 * * * 54 61 * 4589 * * * * 3856 0 0 H 55 * * * 3952 * * 1115 * * * * 4039 * 4229 1584 * * * * 5274 55 0 * * * * * 0 3671 0 1000 V 56 * 2059 * * 3828 * * 2261 * 2624 * * * * * * * 1649 * * 56 0 * * * * * 0 3628 0 1000 K 57 * * * * * * * * 293 * * * * * 2965 * 4159 * * * 57 172 4137 4171 530 1701 * 0 3638 1549 1000 A 58 4013 * * * * * * * 1857 2710 * * 1847 * 2478 * * 4275 * * 58 49 * 4912 * * * 0 3458 0 1765 A 59 847 3788 * * 4328 * * 3771 * 4555 * * * * * 5098 4858 3343 4507 * 59 190 5379 3330 0 * * 0 3592 1000 2051 D 60 5132 * 2535 * * * 4122 4202 * * 4484 * 817 * * * 5101 4453 * * 60 65 * 4509 * * 2416 299 3362 0 2278 P 61 3733 * * * * * * * 4680 4272 * * 827 * * 2207 4217 * * * 61 44 * 5066 * * * 0 3429 0 2307 G 62 3548 * 2817 4495 * 4067 4216 * * * * * 1418 2907 * 4223 4213 * * * 62 160 4410 4103 2322 322 1892 453 3437 1000 2365 G 63 3268 4096 2674 3370 * 3704 * * * 3816 * * 3560 4151 4291 3423 2725 * * * 63 82 4175 * 1000 1000 2766 229 3420 1000 2186 G 64 * * * 2890 * 2545 * 4042 2963 4303 * 4721 3631 3373 * 3382 3576 4080 * * 64 0 * * * * 598 1559 3459 0 2258 P 65 4182 * 3643 2774 * * * * * 4208 * * 1191 3376 * 4253 5013 4415 * * 65 133 3506 * 0 * * 0 3448 1085 1401 S 66 3500 * 3535 3226 * * * * 4454 * * 3523 2621 3375 * 2152 3885 4872 * * 66 0 * * * * 980 1020 3448 0 1401 S 67 2830 * 2432 * * * 4961 3942 4400 * * 4504 * * 4300 2351 2067 * * * 67 174 * 3135 * * * 0 3520 0 1000 R 68 * * * 2638 4066 3571 * * 4727 4465 * * 3196 2759 2501 2975 4274 * * * 68 145 4066 4788 0 * 1862 464 3483 1000 1941 L 69 * 4179 2812 3084 * * * 4282 4274 3615 * 4652 1725 * * 3302 4157 * * * 69 104 3844 * 1000 1000 400 2046 3507 1000 2054 T 70 4395 * * 2504 * * 4674 * 3195 * * 4912 * * 4293 1524 2804 4243 * * 70 0 * * * * 0 * 3472 0 1000 W 71 4287 * * * * * * * * * * * * * * * * 4314 154 * 71 0 * * * * * * 3622 0 0 R 72 * * * 5075 * * * * 1356 * * 4552 * * 4241 3100 1444 * * * 72 76 4287 * 0 * * * 3622 1000 0 V 73 4299 * * * * * * 2799 * 2558 * * * * * 1882 * 1456 * * 73 0 * * * * * * 3622 0 0 Q 74 4744 * 4001 4957 * 3811 4434 * 2325 * * * * 1716 * 3320 4485 3299 * * 74 184 * 3059 * * * * 3605 0 0 R 75 4528 * * * * 2767 * * 2373 * 4225 * 2183 4035 2142 4173 * * * * 75 471 1843 * 0 * 0 * 3426 2249 1142 S 76 * * * * * 4438 * 3778 3048 * 4141 * 2601 * * 2895 2146 2489 * * 76 71 * 4374 * * * * 3485 0 0 Q 77 * * 1983 * * * * 4163 * 2868 * 4433 3938 2834 * 2545 2931 * * * 77 0 * * * * 0 * 3444 0 1000 N 78 * * 3067 * * 2598 4812 * * * * 1784 * 3906 * 1632 * * * * 78 0 * * * * * * 3344 0 0 P 79 * * 3909 3092 * * * * * * * * 558 * * 4085 3680 * * * 79 93 * 4008 * * * * 3344 0 0 L 80 * * * * * * * * * 630 * * * * * * 1498 * * * 80 0 * * * * 0 * 3305 0 1000 K 81 * * * * * * * * 638 * * * * * 2875 2177 * * * * 81 0 * * * * * * 3376 0 0 I 82 * * * * 3984 * * 2513 * 523 * * * * * * * 3931 * * 82 0 * * * * * * 3377 0 0 R 83 * * * * * * 3774 * 1625 * * * * 2800 1376 * 3763 * * * 83 0 * * * * * * 3377 0 0 L 84 * * * * 4208 * * * * 542 3519 * * * * * * 2541 * * 84 0 * * * * * * 3377 0 0 T 85 4122 * * * * * * 3806 3673 * * * * * 2036 * 1136 3414 * * 85 0 * * * * * * 3345 0 0 R 86 3409 * * * * * 3388 * 2197 * * * * * 756 * * * * * 86 0 * * * * * * 2997 0 0 E 87 1937 * * 3698 * 2741 * * * * 2600 * * * 3033 2151 * * * * 87 0 * * * * * * 2749 0 0 A 88 584 * * * * * * * * * * * 2387 * * 2821 * * * * 88 0 * * * * * * 2469 0 0 P 89 * * * * * * * * * * * * 0 * * * * * * * 89 0 * * 0 * * * 1690 0 0 //