HHsearch 1.5 NAME c5dckA_ FAM FILE c5dckA_ COM /bmm/www/servers/phyre2/HH/hhmake -i c5dckA_.a3m DATE Sat Apr 23 08:17:32 2016 LENG 71 match states, 71 columns in multiple alignment FILT 73 out of 77 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100) NEFF 5.5 EVD 0.4394 1.4406 SEQ >ss_dssp CCCCCCCCTTCCHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHTSCHHHHHHTTTCCTTSCHHHHHHHHC >sa_dssp EDEDCEBDEECEBDDABEDACCCADEDEEEEEEBDEDCCCBACDBBCEEBDEDAEEBEDEBDCEDACEDCE >ss_pred CCCCEECCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCHHHHHHHHHCCCCCCHHHHHHHCC >ss_conf 95440017856389999999999743117433322367665365099999999860688889899997349 >Consensus xxxxIkQgpkEpfxdfVxRlxxaxxxxxxxxxxkxxxxxxLxxqNANpdCkxiLxxlxxxxtLeemlxaCq >c5dckA_ HMVQLRQGAKEDYSSFIDRLFAQIDQEQNTAEVKLYLKQSLSIANANADCKKAMSHLKPESTLEEKLRACQ >UniRef50_Q3S7Z7(11-81:147) Gag protein (Fragment) n=1 Tax=Human immunodeficiency virus 1 RepID=Q3S7Z7_9HIV1 E=9e-10 s/c=0.91 id=23% cov=100% -ILDIKQGPKDPLETMSTGSLRPSELNKLHKMCKIGWTETLLVQNANPDCKTILRALGPGLHSRKWMTACQ >UniRef50_UPI000194E898(384-455:1637) PREDICTED: similar to Gag-Pro-Pol-Env protein n=2 Tax=Taeniopygia guttata RepID=UPI000194E898 E=7e-09 s/c=0.85 id=28% cov=100% NYLSIKQDPQEAFVTFIDRLCRAIEVQVPDSNLRQGILTEVAKQNANSACKAAIlsLPLDPEPTIQDMLEVC- >UniRef50_Q9N174(490-556:708) Gag polyprotein n=1 Tax=Trichosurus vulpecula RepID=Q9N174_TRIVU E=1e-05 s/c=0.76 id=24% cov=96% ----ITQRKDEEYSDFVSRLLETAERTLGNEASDDLIIKRLAFENANGPCRSVLNGQWQDKTLNEMIKLCR >UniRef50_P0C211(265-333:1462) Integrase n=351 Tax=root RepID=POL_HTL1L E=7e-13 s/c=1.09 id=34% cov=96% ----ILQGLEEPYHTFVERLNVALDNGLPEGTPKDPILRSLAYSNANKECQKLLQARGhTNSPLGDMLRACQ >UniRef50_UPI000194E044(235-298:1106) PREDICTED: similar to pol protein n=1 Tax=Taeniopygia guttata RepID=UPI000194E044 E=2e-09 s/c=0.99 id=26% cov=92% ----VRQAESENFTQFVDRLQAAVDSSTLPAEAKGPMVADCLRQQCNSVTKDILRSLPAGASLADMIR--- >UniRef50_P04023(350-419:572) Protease n=1 Tax=Golden hamster intracisternal A-particle H18 RepID=GAG_IPHA E=5e-14 s/c=1.13 id=25% cov=100% HLTKIVQGPQEPFSDFVARMTEAASRIFGDSEQAMPLIEQLVYEQATQECRAAIAPRKSKG-LQDWLRVCR >UniRef50_Q3S7X1(4-74:133) Gag protein (Fragment) n=36 Tax=Human immunodeficiency virus 1 RepID=Q3S7X1_9HIV1 E=4e-16 s/c=1.20 id=28% cov=100% -ILDIRQGPKEPFRDYVDRFYKTLRAEQATQGGKKLDDCNLVGPKCEPRLYEYLKSIwGPAATLEEMMTACQ >UniRef50_UPI0000F2C0D3(172-238:1062) PREDICTED: similar to LOC639390 protein n=1 Tax=Monodelphis domestica RepID=UPI0000F2C0D3 E=1e-09 s/c=0.96 id=19% cov=90% ----LRQRSDQAFEDYVAEVQKAVEWTLGTVQGLEDLIKNIVKQNATPDYRQMLINLAASATLEYMI---- # 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 * * * * * * 1371 * * * * 705 * * * * * * * * 1 0 * * * * * * 2579 0 0 M 2 * 4324 * * 2272 * * 983 * 3943 4215 * * * * * * 3821 * 4397 2 0 * * * * * * 4224 0 0 V 3 * * * * 4619 * * 4592 * 922 * * * * * 3523 3619 2544 4318 * 3 0 * * * * * * 4432 0 0 Q 4 * * 1076 * * 4340 * * 3006 * * 2300 * 4025 * 3758 6229 * * * 4 0 * * * * * * 4456 0 0 L 5 * * * * * * 4839 502 * 3184 5576 * * * * * * 2965 * * 5 0 * * * * * * 5288 0 0 R 6 * * * * * * 5655 4736 1399 3611 * * * * 1400 * 3967 4689 * * 6 0 * * * * * * 5291 0 0 Q 7 * * * * * * * * * * * * * 77 * * 4261 * * * 7 0 * * * * * * 5331 0 0 G 8 5223 * 5719 5839 * 520 * * 3584 * * * * * 3731 4116 * 5429 * * 8 0 * * * * * * 5331 0 0 A 9 2974 * * 5271 * * 5795 * 5545 5547 * 5178 740 * * 2891 * 5330 * * 9 0 * * * * * * 5396 0 0 K 10 5379 * 2755 3849 * * * * 1061 * * 3686 * 3741 5280 4514 4126 * * * 10 0 * * * * * * 5735 0 0 E 11 * * 4071 391 * 4368 * * * * * 3822 * 4623 5771 * * * * * 11 0 * * * * * * 5719 0 0 D 12 3710 * 4023 4350 * * * * 4971 * * 5432 692 * 5570 3246 6296 * * * 12 0 * * * * * * 5719 0 0 Y 13 6385 * * * 980 * * * * 3850 * * * * * 4144 * * * 1494 13 0 * * * * * * 5719 0 0 S 14 3667 * * 1962 * * 5557 5223 4096 * 5386 * 4779 4513 2171 3118 3717 4620 * * 14 0 * * * * * * 5719 0 0 S 15 * * 689 4563 * * * * 5933 5990 * 7869 * 3669 5931 3672 2972 * * * 15 47 5931 5989 0 * * * 5719 1000 0 F 16 * * * * 894 * * * * * 3843 * * * * 5984 * * 5926 1474 16 0 * * * * * 0 5712 0 1000 I 17 * * * 6376 * * * 2878 * 5582 * * * * 4312 4065 * 505 * 5926 17 18 6330 * 0 * * 0 5712 1000 1000 D 18 2161 * 1238 5537 * 3399 * 5984 * * * 4833 * * 4312 3461 4507 * * * 18 52 4831 * 0 * * 0 5712 1508 1000 R 19 * * * 4602 * 3220 * * 5122 * * * 4268 * 516 4607 5760 * 6394 * 19 0 * * * * 0 * 5712 0 1000 L 20 * * * * 2138 4383 * * * 1108 4881 * * * * 3698 * 2739 * * 20 0 * * * * * * 5719 0 0 F 21 * 5056 * * 2720 * * 4247 4345 1934 5781 5557 * 2878 4634 4361 4881 4747 * 3071 21 0 * * * * * * 5719 0 0 A 22 3444 * 4384 2124 * * 6296 4499 1798 * * 6488 * 4645 4137 3147 4953 4917 * * 22 0 * * * * * * 5719 0 0 Q 23 1270 6327 * * 5222 6256 * * 5160 4892 * 3596 5877 4351 * 4400 2028 5051 * * 23 0 * * * * * * 5710 0 0 I 24 2650 * * * * * * 2438 * 1628 6519 * * * * 3001 4970 2855 * 5222 24 0 * * * * * * 5710 0 0 D 25 * * 3166 1429 * 4031 6238 * 3330 * * * * 4069 2154 4081 * * * * 25 24 5937 * 0 * * * 5735 1000 0 Q 26 2298 * * 4648 * 5863 * * 3548 3310 * 4738 5607 4929 1871 2933 7748 5960 4744 * 26 0 * * * * * * 5735 0 0 E 27 * 4152 * 2035 * 5700 * 3339 * 6165 5862 4042 4683 3064 4406 2893 3638 3853 * * 27 15 * 6565 * * * * 5737 0 0 Q 28 3531 5622 * * 3528 5929 * 2742 2857 3066 6474 * 4722 2389 * 5102 4399 3907 * * 28 0 * * * * * 0 5736 0 1000 N 29 2440 7191 6237 4278 * 2480 5929 * 4207 2652 * 5151 3410 5530 6037 3136 4744 5320 * * 29 0 * * * * * 0 5736 0 1000 T 30 6280 * 2528 4351 3974 * 3021 * 6193 4249 * 3786 4190 5357 * 2862 2353 6866 * 5775 30 0 * * * * * 0 5736 0 1000 A 31 4899 * 3254 3264 * 3925 4798 * 4041 * * * 3169 2626 4876 3120 3633 3441 * * 31 0 * * * * * 0 5736 0 1000 E 32 4132 * 3762 1349 * 3553 * * 4352 5630 4209 5211 4975 4284 3236 * 4266 * * * 32 0 * * * * * 0 5735 0 1000 V 33 2347 4179 * 5773 * 3712 * 4204 * 3697 5104 * 4494 4899 * 3173 4459 2099 5289 * 33 0 * * * * 0 * 5735 0 1000 K 34 2747 * 4553 6043 * 4727 * * 995 4686 * * * 4801 3102 3996 * * * * 34 0 * * * * * * 5656 0 0 L 35 5015 * 3681 3250 * 3041 * 3581 3084 5123 3560 2913 5569 3874 5804 5009 3970 6086 * * 35 0 * * * * * * 5656 0 0 Y 36 * * 5599 4382 5945 2880 * 2999 * 3319 * * 2745 5559 * 6031 5108 4507 2165 3790 36 0 * * * * * * 5656 0 0 L 37 * 4421 3563 * 5009 4446 * 3049 * 1644 1948 * * * * * * 4546 4353 * 37 0 * * * * * * 5656 0 0 K 38 4846 3829 4403 * 5729 5273 * 2965 4215 2872 * * * 4738 * * 1857 2550 * * 38 0 * * * * * * 5656 0 0 Q 39 5595 5791 3197 2638 * * * * 2050 4047 5120 6302 * 2564 3170 * 4546 5313 * * 39 0 * * * * * * 5656 0 0 S 40 * * 4582 4742 * * 3516 * 3138 4618 * 3849 4421 2406 4750 3872 1895 * * * 40 82 4178 * 0 * * * 5656 1501 0 L 41 * 3028 * * 6552 * * 3099 * 583 4703 * 5159 * * * * 5952 * * 41 31 * 5572 * * * * 5656 0 0 S 42 1384 5148 * * * * * 5758 * 2010 * * 5317 * * 3773 5931 3270 3269 * 42 0 * * * * * 0 5646 0 1000 I 43 * 6201 5317 5546 3409 3717 * 2834 4159 5224 5893 * * * 5562 4383 5551 2590 5148 2028 43 0 * * * * * 0 5646 0 1000 A 44 5111 * 5752 1602 * * * * 4383 * * 5546 3812 1550 * 3693 3970 * * * 44 15 * 6555 * * * 0 5646 0 1000 N 45 * * * * * * 4990 * 3072 * 4382 536 * 3418 5773 * * * * * 45 0 * * * * 0 * 5646 0 1629 A 46 376 3548 * * * * * * * 5641 4128 * 5572 5230 * * * 5703 * * 46 85 4128 * 0 * * * 5656 1714 0 N 47 * * 5595 3989 * * * 5295 * * * 431 * * * 4246 3376 * * * 47 0 * * * * * * 5673 0 0 A 48 3516 * * 3387 * 5712 * * 3740 * * * 1078 4644 * 2591 4522 * * * 48 0 * * * * * * 5673 0 0 D 49 2998 * 1237 2619 * * * 4597 5594 * * * 4647 5540 3986 * 3631 5594 * * 49 0 * * * * * * 5672 0 0 C 50 * 307 * * * * * * * 3749 * * * * 5988 * 4741 5293 * 4683 50 16 6475 * 0 * * * 5672 1000 0 K 51 * * * 5594 * * * * 1207 * * * * 1907 2072 5343 * * * 5872 51 0 * * * * * * 5672 0 0 K 52 2379 * 4594 4808 * 7185 7244 * 3251 5705 * 4621 5293 3601 3813 2534 2548 5081 * * 52 0 * * * * * * 5672 0 0 A 53 1879 * * * 4766 * 5546 1326 * 4557 5606 * * 5334 5594 * * 3047 * 4584 53 0 * * * * * * 5672 0 0 M 54 * * * * 5546 * 5795 2457 * 596 3451 * * * * * * * * 5293 54 92 4015 * 1424 673 * * 5672 2054 0 S 55 6092 6374 5334 5293 * 5731 5235 4683 1845 3999 * 5701 * 4381 1495 3725 * * * * 55 0 * * * * * * 5672 0 0 H 56 1918 * * * 5731 3146 3383 * * * * 4683 1738 * 5334 2794 * * * * 56 0 * * * * * * 5672 0 0 L 57 * * * * 4587 * 5983 2696 4545 915 6351 * * 5701 4889 6108 5334 5417 5747 3865 57 118 4416 4984 743 1313 * * 5672 2129 0 K 58 4888 * 3750 * * 1385 * * 2636 5250 * * 4012 5136 2454 5106 * * 5657 * 58 136 3638 6717 1167 850 0 * 5688 2646 1411 P 59 3659 * * 4877 * 3814 5630 * 3770 6170 5925 * 1652 2778 4356 3956 3390 5693 * * 59 31 5552 * 0 * 0 * 5680 1000 1000 E 60 5742 * 4961 2495 * 2133 6950 * 2427 * * 4439 5511 4565 3331 3630 4602 5775 * * 60 44 5065 * 672 1425 * * 5672 1537 0 S 61 1751 * 4134 * * 3296 4589 6173 5711 4008 * * 2353 5769 * 2910 4816 5331 * * 61 93 * 4001 * * * * 5527 0 0 T 62 * * 3701 5571 * 6193 4712 * * * * 5633 2886 * * 2937 959 * * 4329 62 40 5192 * 2322 322 0 * 5405 1065 1647 L 63 * * * * * * 5680 2715 * 549 4739 * * * * 4666 * 3885 * * 63 0 * * * * * * 5424 0 0 E 64 3445 * 4733 1134 * 3717 * 5372 * * 5865 4126 4547 3952 5489 3649 6218 * 5844 * 64 0 * * * * * * 5438 0 0 E 65 * * 2162 1149 * 4460 6076 * 3095 * * * 5643 4538 * * 4710 5364 * 5467 65 0 * * * * * * 5440 0 0 K 66 * * * * 4389 * * * 3067 4485 867 * * * * * 6070 * 3873 2673 66 36 * 5341 * * * * 5456 0 0 L 67 * * * * * * * 2075 * 1547 1790 * * * 4221 * * 3683 * * 67 0 * * * * * 0 5420 0 1000 R 68 5952 * 5714 2986 * * * * 2776 * * * * 2529 2267 * 1903 * 5446 5564 68 0 * * * * 0 * 5180 0 1000 A 69 814 5202 * 5038 * * * 4263 * 3720 * * 3975 4463 * * 5556 3430 * 5457 69 0 * * * * * * 5197 0 0 C 70 3975 95 * * * * * * * * * * * * * * * * * * 70 0 * * * * * * 5197 0 0 Q 71 * * * * * * * * * * * * * 682 1408 * * * * * 71 0 * * 0 * * * 4604 0 0 //