HHsearch 1.5 NAME d2f76x1 FAM FILE d2f76x1 COM /bmm/www/servers/phyre/brandnew/HH/hhmake -i d2f76x1.a3m DATE Mon Mar 8 19:06:04 2010 LENG 94 match states, 94 columns in multiple alignment FILT 36 out of 40 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100) NEFF 4.5 EVD 0.4052 -0.0911 SEQ >ss_dssp CCCSSCHHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHHHHHCCCCCCCSSCHHHHHHHHHHHHHHHHHHHSCCSSCTHHHHHHHHHHHHHHHHC >sa_dssp EEEEECEEBEDACECCEDADECDAEBECCCACDACDABEEDBEEDDEDEECBCDDAAECACDDADEDCEEEDEDACEDBDDCBEDACDCCDEEE >ss_pred CCCCHHHHHHHHHHHHHHHHHCCEEECHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCC >ss_conf 9863011279999999999653837159999999999999689721177517999999999999999837987577466679999999732589 >Consensus MGxxxSkxxxxixxLkxlLkxrgvkVxxxxLxxfxxxIxxxcPWFpxxGtLxxxxWekvGxxLxxxxxxxxxxxipxxxxxxWxlIrxxLexxe >d2f76x1 MGQELSQHERYVEQLKQALKTRGVKVKYADLLKFFDFVKDTCPWFPQEGTIDIKRWRRVGDCFQDYYNTFGPEKVPVTAFSYWNLIKELIDKKE >UniRef50_Q8AGY0(1-95:1637) Gag polyprotein n=4 Tax=root RepID=Q8AGY0_9RETR E=1e-05 s/c=0.54 id=24% cov=90% MGGKFSQQQtAHLKELRELTessskisSNGGKtlpRLKNKELIGLLSYIWQQCPSYPEKGSLKISTWTKLGEYF------HAAPRAPVQILTSWRVVMEC L---- >UniRef50_UPI0000D65A16(1-86:280) PREDICTED: similar to putative retrovirus-related gag protein n=1 Tax=Mus musculus RepID=UPI0000D65A16 E=0.0003 s/c=0.54 id=23% cov=93% MG--SSQSHPIFSALDELLRVKSAKLKKHTIQAFLEECDKVAPWFAVSGHLTPASWGRLGRDL-DFSWEQG--VLKEGTRAVWKLVNSCLE--- >UniRef50_A8BDN3(1-91:507) Gag protein n=1 Tax=Bos taurus RepID=A8BDN3_BOVIN E=3e-19 s/c=1.06 id=28% cov=96% MGQHSSKIP-FISIMHHFLKQNAVNVSRDQLNDCYHILLEHNPWFPEEGTLDLDIWKRVKNNVLRAY--QQGVRIPPQWWLTWSLIWAVTEQ-- >UniRef50_UPI00017972D8(2-92:879) PREDICTED: similar to Gag-Pro-Pol-Env protein n=1 Tax=Equus caballus RepID=UPI00017972D8 E=2e-17 s/c=0.99 id=27% cov=97% MGQQwRTQQKLYFKTLQRLLKVISVSVSLSELQKLLLAISTHCPWFPEDGTLDIELWERARKALKSRFEHGLLKYV--HILTTWGTVRTELFP-- >UniRef50_Q7M6W5(3-80:576) Gag protein n=4 Tax=Mus musculus RepID=Q7M6W5_MOUSE E=8e-14 s/c=1.00 id=25% cov=72% ----------------ELFQARGVRLEVQLVKNFLGKIDSCCPWFKEEETLDCETWEKVGEALKITQTD-------NFTLGLWALVNDAI---- >UniRef50_UPI0000F2C7C6(328-403:436) PREDICTED: similar to MOG alpha-7Cj n=2 Tax=Monodelphis domestica RepID=UPI0000F2C7C6 E=1e-12 s/c=0.98 id=31% cov=79% --------------LRTVLGLHGVKVKRRQLKDFIRYVRRLAPWLPDKNRVTIEDWEWIGSKFK-------GNEEPQPLFALiYNVVKLCLEDKE >UniRef50_UPI0000F2B625(175-267:917) PREDICTED: similar to gag polyprotein n=13 Tax=Monodelphis domestica RepID=UPI0000F2B625 E=1e-23 s/c=1.18 id=33% cov=99% MGKTLSKEALFIKELKERIKERNVEVKKRDLLRFFSFIEQRCPWLILHGPgIHPLTWEKVGRDLNDFARSGQP--IPEDFFTFYGLIRDILKEAD >UniRef50_UPI00017EFE87(1-88:821) PREDICTED: similar to Gag-Pro-Pol protein n=1 Tax=Sus scrofa RepID=UPI00017EFE87 E=2e-17 s/c=1.02 id=30% cov=88% ----------YICLFGQLLKKGGAKTSESKLLKLFQTIERHCDWLFTSETLYLKIWEMVGMELRILQDEGI--RIPESIWSTWNLIKSVLELPE >UniRef50_UPI0000F2B8BF(721-797:850) PREDICTED: similar to chromosome 20 open reading frame 12, n=1 Tax=Monodelphis domestica RepID=UPI0000F2B8BF E=2e-11 s/c=0.91 id=22% cov=83% -----------IRLLKSLTEKKGIKVSEAKIKALIKIIIRAYPDFPAAGVLNMQDWELIGDKMRQYQKEGQ--KISQVSWNTWEIIRMTL---- # 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 * * * * M 1 * * * * * * * * * * 0 * * * * * * * * * 1 0 * * * * * * 4157 0 0 G 2 * * * * * 0 * * * * * * * * * * * * * * 2 85 * 4125 * * * * 4152 0 0 Q 3 * * * * * 3836 3382 * 3512 * * 3221 * 1225 * 3211 3276 * * * 3 94 * 3984 * * * 0 4051 0 1000 E 4 3293 * * 4018 * 4753 3633 * 2665 * 4103 * 4396 3412 * 3089 2337 4445 * * 4 140 3432 * 1026 975 968 1033 3940 1470 1403 L 5 * * * 2343 3867 * 3279 * 4892 1896 * 4809 * * 4208 2064 * * * * 5 0 * * * * * 0 4077 0 1000 S 6 4863 * * * * * * * * * * * * * * 216 3255 * * * 6 146 4863 4010 0 * * 0 4077 1000 1000 Q 7 * * * * * * 4441 * 1033 * * 3754 * 1691 3616 * * * * * 7 180 4803 3616 0 * 1000 1000 3977 1000 1299 H 8 * * * 1875 * * 3957 3588 * * * * * 2257 * 2448 * * * 2416 8 121 3638 * 0 * 670 1429 4062 1092 1722 E 9 2370 * * 3701 * * 4014 * 3555 4361 * * 3749 1300 * * * * * 4222 9 290 3217 3749 458 1878 * 0 4167 1612 1000 R 10 2102 * * * * * * 5803 * 1483 4060 * 3932 * 4664 2856 * 3500 * * 10 0 * * * * 0 * 3982 0 1611 Y 11 * * * * 1127 * 4026 4199 * * * * * * * * * 3303 * 1622 11 0 * * * * * * 4359 0 0 V 12 * * * * 3034 * * 1020 * 2105 * * * * * * * 2714 * * 12 0 * * * * * * 4488 0 0 E 13 * 3397 * 3547 * 3436 4155 * 2065 * * 4646 * 4794 4130 2285 3415 * * * 13 0 * * * * * * 4488 0 0 Q 14 2795 * 4776 2955 3426 4723 4830 3070 * 3247 4155 * * 4411 * * 3800 3673 * 4420 14 0 * * * * * * 4488 0 0 L 15 * * * * 4481 * * 2442 * 557 3451 * * * * * * * * * 15 0 * * * * * * 4598 0 0 K 16 * * 5081 * 5261 4481 4058 * 1272 3504 * * * 2653 2722 5228 * * * * 16 0 * * * * * * 4598 0 0 Q 17 * * 5159 2058 * 5028 3266 4516 * 4778 * * * 2453 4650 3179 2988 4104 * * 17 0 * * * * * * 4659 0 0 A 18 3866 * * * 4074 * * * * 926 3439 * * * 4994 3497 * 2903 * * 18 0 * * * * * * 4659 0 0 L 19 * * * * 3974 * * 4994 * 304 * * * * * * 3400 * * * 19 67 4455 * 2807 222 * * 4659 1000 0 K 20 4487 * * 4346 * 4054 * * 725 * * 4301 * 4834 3571 3814 * * * * 20 0 * * * * * * 4659 0 0 T 21 4159 * * 2692 * 5504 3832 6675 2681 4592 * 4455 * 2411 3759 5035 5250 2994 * * 21 0 * * * * * * 4659 0 0 R 22 * 4980 * * * 2327 4592 4041 3244 * * 4074 * * 1070 * 5294 * * * 22 0 * * * * * * 4659 0 0 G 23 4074 * 5016 5078 * 514 * * 5052 * * 4994 * * 5090 3488 * * * * 23 0 * * * * * * 4659 0 0 V 24 3829 * * * * * * 1603 4455 3020 * * * * * * * 1212 * * 24 67 4455 * 1585 585 * * 4659 1000 0 K 25 * * * 4074 * * 5504 * 1029 * * 4074 * * 2021 4041 5287 * 4778 * 25 0 * * * * * * 4659 0 0 V 26 5427 * * * 5294 * * 2725 * 2868 * * * * * * 4574 687 * * 26 37 * 5294 * * * * 4659 0 0 K 27 3973 * * 3907 * * * * 1503 * * 5454 4753 5014 5067 1336 * * * * 27 0 * * * * * 0 4659 0 1000 Y 28 * * * 3420 * 6659 * 5495 1712 4626 4753 4416 4244 * 2595 * 2612 4789 * 5217 28 0 * * * * * 0 4659 0 1000 A 29 3060 * 4039 3035 * 4438 5106 * 1812 5454 * 6659 * 4789 2873 3248 5236 * * * 29 0 * * * * * 0 4659 0 1000 D 30 5556 * 2381 3517 * * * 5036 2308 4789 * 3264 * 2978 4438 * 2703 * * * 30 0 * * * * * 0 4659 0 1000 L 31 * * * * * * * 3319 * 410 4753 * * * * 5550 5014 4109 * * 31 0 * * * * * 0 4659 0 1000 L 32 * * * 2791 6659 * * 2217 2951 2927 * 4039 * 2597 * 3706 * 3902 * * 32 0 * * * * * 0 4659 0 1000 K 33 3663 * 3264 4958 * 3660 * * 1727 * * 2683 * * 4233 3274 3454 * * * 33 0 * * * * 0 * 4659 0 1000 F 34 * 4074 * * 715 * * 5579 * 1688 * * * * * * * * * * 34 0 * * * * * * 4659 0 0 F 35 * * * * 1296 * * 3056 * 1512 5016 * * * * * * 4980 * 4074 35 31 5579 * 5615 30 * * 4659 1000 0 D 36 * 5028 3370 4059 * 4834 4074 2981 3210 4015 * * * 3545 2845 2505 5602 * * * 36 0 * * * * * * 4659 0 0 F 37 4041 * * 2464 1533 * * 2954 4834 * * * * * * * 3938 3380 * 3522 37 0 * * * * * * 4659 0 0 V 38 * 3494 * * * * * 955 * 3390 * * * * * * * 1737 * * 38 0 * * * * * * 4659 0 0 K 39 * * 1598 2173 5222 * * 4395 3973 4086 * * * 3228 4653 4073 * * 4465 * 39 0 * * * * * * 4673 0 0 D 40 5052 * 4501 1762 * * * * 3609 5002 * * * 2520 2003 4851 4073 * * * 40 0 * * * * * * 4673 0 0 T 41 3664 3955 * * 4546 * 2074 4072 * 3817 * * * 2963 4147 * 3817 2394 * * 41 0 * * * * * * 4673 0 0 C 42 2195 705 * * * 4972 * * * * * 4077 * * * 5087 * * * 4389 42 0 * * * * * * 4667 0 0 P 43 * * 4597 * * * * * * * * * 96 * * 5449 * * * * 43 0 * * * * * * 4667 0 0 W 44 * * 4397 * * * * * * * * * * * * 4474 * * 140 * 44 0 * * * * * * 4742 0 0 F 45 * * * * 538 * * * * 2511 * * * * * * * * * 2882 45 0 * * * * * * 4742 0 0 P 46 3075 * * 5099 4773 * * 2885 4832 * * * 758 * * 5200 * 5222 * * 46 0 * * * * * * 4742 0 0 Q 47 4397 3463 3601 1395 * * * 4972 * 3759 * * * 3970 5532 * 3893 2829 * * 47 0 * * * * * * 4742 0 0 E 48 4397 * 3455 1686 * * 4409 * 2791 * * 4210 * 3960 * 2054 * * * * 48 0 * * * * * * 4742 0 0 G 49 * * 5422 3802 * 207 * * * * * 4692 * * * * * * * * 49 0 * * * * * * 4742 0 0 T 50 4972 * * * * * 4212 * 4857 * 5422 5042 3750 * 4692 2082 1220 4397 * * 50 206 2911 * 0 * * * 4742 2028 0 I 51 * * * * * * * 2188 * 695 * * * * * * * 2619 * * 51 0 * * * * * * 4742 0 0 D 52 * * 1654 5024 * * 2911 * 4474 * * 2534 * * * 5534 2042 * * 4773 52 0 * * * * * * 4742 0 0 I 53 * 3900 * 5248 * 5200 * 2476 * 1431 4397 * 2967 * * 5207 * 2984 * * 53 0 * * * * * * 4742 0 0 K 54 2786 * 3638 1781 * 5198 * * 2494 3307 * * * 4397 4152 3753 * * * * 54 0 * * * * * * 4742 0 0 R 55 4172 * 2658 * * * * 3418 4080 3413 * * * * 3967 2758 1820 4491 * * 55 0 * * * * * * 4742 0 0 W 56 * * * * * * * * * * * * * * * * * * 0 * 56 0 * * * * * * 4742 0 0 R 57 * * 3397 1185 * 4216 * 4972 3063 * * 3707 * 5198 4766 * 3499 5024 * * 57 0 * * * * * * 4742 0 0 R 58 * * * 5024 * * * * 988 4397 4773 * * * 1662 5248 * * 4692 * 58 0 * * * * * * 4742 0 0 V 59 4075 * * * * * * 2436 * 2005 * * * * * * * 981 * * 59 0 * * * * * * 4742 0 0 G 60 * * * * * 278 * * 3503 * * * * * 3523 * * * * * 60 39 * 5222 * * * * 4742 0 0 D 61 4836 * 2658 2909 * 4977 * * 1616 * 4746 4122 * * 2465 4654 * * * * 61 0 * * * * * 0 4720 0 1000 C 62 3384 3916 1919 2591 * * * * 3030 * * 4122 * 2456 * * * * * 4458 62 0 * * * * * 0 4720 0 1000 F 63 * * * * 2519 * * 4339 * 576 4389 * * * * * * 4122 * * 63 208 * 2896 * * 0 * 4720 0 1000 Q 64 * * 3036 * * * 4390 * 1348 3949 * 3164 * 3286 3027 4792 * * * * 64 123 * 3614 * * 1854 467 4553 0 2064 D 65 * * 2791 2746 * * * 2634 4704 4338 * * * 3216 3246 3536 2659 * * * 65 0 * * * * 2155 367 4378 0 2412 Y 66 2384 * * 4818 2761 * 5347 3904 4484 3244 * * * * 3599 * 4623 * 4978 2127 66 0 * * * * 1165 852 4488 0 2168 Y 67 3007 * * * 4328 5537 3108 3459 * 3999 * 4238 * 2889 * 5089 * 4840 4925 2003 67 94 * 3993 * * * 0 4554 0 1629 N 68 3016 * 4545 3085 * * * 5494 2433 4992 * 4507 4530 * 2717 4150 2732 * 5021 * 68 56 * 4705 * * * 0 4383 0 2212 T 69 * * 4573 1207 * * 4195 * 3962 2907 * * * 3920 * 3290 4442 4100 * * 69 62 * 4573 * * 931 1072 4341 0 2476 F 70 * * * 5016 3842 1351 2000 5032 * * * * * 2139 * * * * * * 70 240 * 2705 * * 1532 612 4548 0 2022 G 71 4252 * 3590 * * 1372 * 4336 3159 4158 * * * 1940 * * * * * * 71 491 * 1793 * * 1656 550 4461 0 3065 P 72 3920 * 4691 * * 2333 * * 3999 3896 * 4212 1309 4576 * 3886 * * * * 72 68 * 4450 * * 2567 267 4079 0 3569 E 73 * * 4365 1284 * 3154 4420 * 3984 * * 2487 3955 * * * * 3724 * * 73 53 4784 * 2000 415 512 1742 4168 1000 3505 K 74 4796 * 4968 3942 4901 * * 3647 1678 * * * * 5189 2310 4934 5079 3993 * 3524 74 0 * * * * 526 1710 4609 0 2206 V 75 4447 * * 4666 5517 * * 1511 * 2227 * * * * * * * 1607 * * 75 70 * 4402 * * * 0 4644 0 1000 P 76 5085 4927 * * * * * * 2955 * * * 503 * 4951 3823 * * * * 76 0 * * * * 1102 904 4539 0 1531 V 77 3348 * 5579 2710 4710 4958 * 4136 5125 3701 * 3606 3024 3474 * * 5547 2484 * * 77 0 * * * * 0 * 4636 0 1000 T 78 * * 2684 4594 4780 2273 4450 * 5243 * * 4063 3925 3271 * 4759 2528 4381 * * 78 0 * * * * * * 4739 0 0 A 79 2511 * * * 4174 * * 2166 * 4684 5014 * * * * 3693 2210 3249 4100 5677 79 0 * * * * * * 4739 0 0 F 80 * * * * 1453 * * 4995 4048 2300 5091 * * * 4099 * * * 1988 * 80 0 * * * * * * 4739 0 0 S 81 2537 * * * * 3798 * * * 4100 5243 3090 3090 * * 1815 2719 * * * 81 0 * * * * * * 4739 0 0 Y 82 * * 3685 * 3704 * * 4008 * 1644 * * * * * 4465 2404 3543 * 2802 82 57 4684 * 0 * * * 4739 1000 0 W 83 * * * * * * * * * * * * * * * * * * 175 3131 83 0 * * * * * * 4739 0 0 N 84 2784 * * 4381 5243 3051 * * 2493 * * 2025 * * 3744 3463 3812 * * * 84 0 * * * * * * 4739 0 0 L 85 * * * * * * * 2412 * 916 3398 * * * * 5009 4450 3177 * * 85 0 * * * * * * 4739 0 0 I 86 * * * * * * * 833 * * * * * * * * * 1188 * * 86 0 * * * * * * 4739 0 0 K 87 * 4816 * * * * 5009 * 2123 * 4465 3454 * 5188 1054 * * * 4100 * 87 0 * * * * * * 4739 0 0 E 88 2596 * 1360 3880 * * * * * 4684 4381 5007 * 5243 * 2419 4450 * * * 88 0 * * * * * * 4739 0 0 L 89 3286 1579 5408 4450 * * * 3171 * 3372 * * * * * * 3828 2215 * * 89 0 * * * * * * 4739 0 0 I 90 * * * * * * * 2635 * 357 * * * * * * 4100 * * * 90 0 * * * * * * 4739 0 0 D 91 * * 1723 1074 4067 * * * 3932 * * * * 4346 * 4388 * * * * 91 0 * * * * * * 4328 0 0 K 92 * * 2393 3501 * * * * 3767 3901 * * 1610 2434 * 3874 * * * * 92 0 * * * * * * 4040 0 0 K 93 1080 * * * * * * * 1540 * * * 3421 * 3479 * * * * * 93 0 * * * * * * 3678 0 0 E 94 * * 2397 304 * * * * * * * * * * * * * * * * 94 0 * * 0 * * * 3219 0 0 //