INFERNAL1/a [1.1.5 | Sep 2023] NAME SBWMV2_UPD-PKl ACC RF01105 DESC Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR STATES 85 NODES 25 CLEN 27 W 41 ALPH RNA RF no CONS yes MAP yes DATE Mon Jul 8 04:49:13 2024 COM [1] /hps/software/users/agb/rfam/bin/cmbuild -F CM SEED COM [2] /hps/software/users/agb/rfam/bin/cmcalibrate --cpu 8 /nfs/production/agb/rfam/15/rescan/families/RF01105/CM PBEGIN 0.05 PEND 0.05 WBETA 1e-07 QDBBETA1 1e-07 QDBBETA2 1e-15 N2OMEGA 1.52588e-05 N3OMEGA 1.52588e-05 ELSELF -0.08926734 NSEQ 2 EFFN 2.000000 CKSUM 2085579491 NULL 0.000 0.000 0.000 0.000 GA 39.00 TC 45.40 NC 35.70 EFP7GF -3.0763 0.76565 ECMLC 0.49851 -7.54547 5.00729 1600000 626412 0.001916 ECMGC 0.50108 -6.48775 6.75640 1600000 304941 0.001312 ECMLI 0.50846 -5.32709 6.06903 1600000 394175 0.003044 ECMGI 0.52276 -4.95233 7.50326 1600000 269090 0.001486 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 41 60 -6.891 -8.136 -0.079 -4.590 IL 1 1 2 1 4 1 1 43 62 -2.817 -4.319 -0.613 -2.698 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 1 43 62 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 1 ] - 27 - A - - MR 3 2 3 5 3 1 1 41 60 -8.380 -0.018 -6.697 1.730 -2.426 -2.052 -1.973 D 4 2 3 5 3 0 0 39 58 -6.390 -1.568 -0.620 IR 5 5 3 5 3 1 1 42 61 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 2 ] - 26 - G - - MR 6 5 3 8 3 1 1 40 59 -8.380 -0.018 -6.697 -1.638 -2.867 1.736 -2.254 D 7 5 3 8 3 0 0 38 57 -6.390 -1.568 -0.620 IR 8 8 3 8 3 1 1 41 60 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 3 ] - 25 - U - - MR 9 8 3 11 3 1 1 39 58 -8.380 -0.018 -6.697 -1.535 -1.523 -2.271 1.632 D 10 8 3 11 3 0 0 37 56 -6.390 -1.568 -0.620 IR 11 11 3 11 3 1 1 40 59 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 4 ] - 24 - A - - MR 12 11 3 14 3 1 1 38 57 -8.380 -0.018 -6.697 1.730 -2.426 -2.052 -1.973 D 13 11 3 14 3 0 0 36 55 -6.390 -1.568 -0.620 IR 14 14 3 14 3 1 1 39 58 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 5 ] - 23 - U - - MR 15 14 3 17 3 1 1 37 56 -8.380 -0.018 -6.697 -1.535 -1.523 -2.271 1.632 D 16 14 3 17 3 0 0 35 54 -6.390 -1.568 -0.620 IR 17 17 3 17 3 1 1 38 57 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 6 ] - 22 - C - - MR 18 17 3 20 3 1 1 36 55 -8.380 -0.018 -6.697 -1.806 1.641 -2.632 -1.207 D 19 17 3 20 3 0 0 34 53 -6.390 -1.568 -0.620 IR 20 20 3 20 3 1 1 37 56 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 7 ] - 21 - A - - MR 21 20 3 23 3 1 1 35 54 -8.380 -0.018 -6.697 1.730 -2.426 -2.052 -1.973 D 22 20 3 23 3 0 0 33 52 -6.390 -1.568 -0.620 IR 23 23 3 23 3 1 1 36 55 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 8 ] - 20 - A - - MR 24 23 3 26 3 1 1 34 53 -8.380 -0.018 -6.697 1.730 -2.426 -2.052 -1.973 D 25 23 3 26 3 0 0 32 51 -6.390 -1.568 -0.620 IR 26 26 3 26 3 1 1 35 54 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 9 ] - 19 - A - - MR 27 26 3 29 3 1 1 33 52 -8.380 -0.018 -6.697 1.730 -2.426 -2.052 -1.973 D 28 26 3 29 3 0 0 31 50 -6.390 -1.568 -0.620 IR 29 29 3 29 3 1 1 34 53 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 10 ] - 18 - U - - MR 30 29 3 32 3 1 1 32 51 -8.380 -0.018 -6.697 -1.535 -1.523 -2.271 1.632 D 31 29 3 32 3 0 0 31 49 -6.390 -1.568 -0.620 IR 32 32 3 32 3 1 1 33 52 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 11 ] - 17 - A - - MR 33 32 3 35 5 1 1 31 50 -7.117 -0.038 -6.932 -7.144 -8.036 1.730 -2.426 -2.052 -1.973 D 34 32 3 35 5 0 0 30 49 -5.352 -0.707 -2.978 -4.409 -2.404 IR 35 35 3 35 5 1 1 31 50 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 12 ] 1 16 A U - - MP 36 35 3 40 6 2 2 30 49 -9.118 -9.058 -0.021 -7.834 -8.114 -8.509 -3.842 -2.861 -3.857 3.364 -4.221 -5.288 0.082 -3.896 -3.747 1.023 -4.297 -0.328 -0.335 -4.467 -1.858 -2.688 ML 37 35 3 40 6 1 1 29 48 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 38 35 3 40 6 1 1 29 47 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 39 35 3 40 6 0 0 26 45 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 40 40 5 40 6 1 1 30 49 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 41 41 6 41 5 1 1 29 48 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 13 ] 2 15 G C - - MP 42 41 6 46 6 2 2 28 47 -9.118 -9.058 -0.021 -7.834 -8.114 -8.509 -4.798 -3.121 -4.902 0.163 -5.312 -4.716 -0.662 -5.149 -4.364 3.651 -4.697 -0.822 -1.046 -4.505 -2.702 -3.778 ML 43 41 6 46 6 1 1 27 46 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 44 41 6 46 6 1 1 27 46 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 45 41 6 46 6 0 0 25 44 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 46 46 5 46 6 1 1 28 47 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 47 47 6 47 5 1 1 27 46 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 14 ] 3 14 A U - - MP 48 47 6 52 6 2 2 26 45 -9.118 -9.058 -0.021 -7.834 -8.114 -8.509 -3.842 -2.861 -3.857 3.364 -4.221 -5.288 0.082 -3.896 -3.747 1.023 -4.297 -0.328 -0.335 -4.467 -1.858 -2.688 ML 49 47 6 52 6 1 1 26 45 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 50 47 6 52 6 1 1 25 44 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 51 47 6 52 6 0 0 24 43 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 52 52 5 52 6 1 1 26 45 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 53 53 6 53 5 1 1 26 45 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 15 ] 4 13 G C - - MP 54 53 6 58 4 2 2 24 43 -6.977 -7.184 -0.052 -5.598 -4.798 -3.121 -4.902 0.163 -5.312 -4.716 -0.662 -5.149 -4.364 3.651 -4.697 -0.822 -1.046 -4.505 -2.702 -3.778 ML 55 53 6 58 4 1 1 25 44 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 56 53 6 58 4 1 1 24 43 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 57 53 6 58 4 0 0 23 42 -4.568 -4.250 -2.265 -0.520 IL 58 58 5 58 4 1 1 26 45 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 59 59 6 59 3 1 1 25 44 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 16 ] 5 - U - - - ML 60 59 6 62 3 1 1 21 40 -7.991 -0.020 -6.645 -1.535 -1.523 -2.271 1.632 D 61 59 6 62 3 0 0 20 39 -6.174 -1.687 -0.566 IL 62 62 3 62 3 1 1 24 43 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 17 ] 6 - U - - - ML 63 62 3 65 3 1 1 20 39 -7.991 -0.020 -6.645 -1.535 -1.523 -2.271 1.632 D 64 62 3 65 3 0 0 19 38 -6.174 -1.687 -0.566 IL 65 65 3 65 3 1 1 23 42 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 18 ] 7 - A - - - ML 66 65 3 68 3 1 1 19 37 -7.991 -0.020 -6.645 1.730 -2.426 -2.052 -1.973 D 67 65 3 68 3 0 0 18 37 -6.174 -1.687 -0.566 IL 68 68 3 68 3 1 1 22 41 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 19 ] 8 - U - - - ML 69 68 3 71 3 1 1 18 36 -7.991 -0.020 -6.645 -1.535 -1.523 -2.271 1.632 D 70 68 3 71 3 0 0 17 36 -6.174 -1.687 -0.566 IL 71 71 3 71 3 1 1 21 40 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 20 ] 9 - C - - - ML 72 71 3 74 3 1 1 16 35 -7.991 -0.020 -6.645 -1.806 1.641 -2.632 -1.207 D 73 71 3 74 3 0 0 16 34 -6.174 -1.687 -0.566 IL 74 74 3 74 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 21 ] 10 - A - - - ML 75 74 3 77 3 1 1 15 33 -7.991 -0.020 -6.645 1.730 -2.426 -2.052 -1.973 D 76 74 3 77 3 0 0 15 33 -6.174 -1.687 -0.566 IL 77 77 3 77 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 22 ] 11 - U - - - ML 78 77 3 80 3 1 1 13 31 -7.991 -0.020 -6.645 -1.535 -1.523 -2.271 1.632 D 79 77 3 80 3 0 0 13 32 -6.174 -1.687 -0.566 IL 80 80 3 80 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 23 ] 12 - A - - - ML 81 80 3 83 2 1 1 1 1 * 0.000 1.730 -2.426 -2.052 -1.973 D 82 80 3 83 2 0 0 0 0 * 0.000 IL 83 83 3 83 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 24 ] - - - - - - E 84 83 3 -1 0 0 0 0 0 // HMMER3/f [3.4 | Aug 2023] NAME SBWMV2_UPD-PKl ACC RF01105 DESC Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR LENG 27 MAXL 100 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Mon Jul 8 04:49:13 2024 COM [1] /hps/software/users/agb/rfam/bin/cmbuild -F CM SEED COM [2] /hps/software/users/agb/rfam/bin/cmcalibrate --cpu 8 /nfs/production/agb/rfam/15/rescan/families/RF01105/CM NSEQ 2 EFFN 1.496094 CKSUM 2085579491 STATS LOCAL MSV -6.9896 0.76565 STATS LOCAL VITERBI -8.0832 0.76565 STATS LOCAL FORWARD -2.4566 0.76565 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.05803 1.66870 1.74922 1.23630 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * 1 0.57945 2.27144 1.47766 2.22136 1 A - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 2 2.29961 2.76025 0.26149 2.71017 2 G - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 3 0.57875 2.27286 1.47759 2.22378 3 A - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 4 2.30089 2.76142 0.26108 2.71191 4 G - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 5 2.19729 2.23435 2.69294 0.33666 5 U - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 6 2.19729 2.23435 2.69294 0.33666 6 U - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 7 0.25557 2.78789 2.55713 2.44824 7 A - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 8 2.19729 2.23435 2.69294 0.33666 8 U - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 9 2.30545 0.35353 2.86415 1.95866 9 C - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 10 0.25557 2.78789 2.55713 2.44824 10 A - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 11 2.19729 2.23435 2.69294 0.33666 11 U - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 12 0.25557 2.78789 2.55713 2.44824 12 A - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 13 2.93363 0.30425 2.59101 2.00862 13 C - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 14 2.45768 1.72258 2.09007 0.49089 14 U - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 15 2.93674 0.30379 2.59219 2.00923 15 C - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 16 2.45963 1.72263 2.09061 0.49049 16 U - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 17 0.25557 2.78789 2.55713 2.44824 17 A - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 18 2.19729 2.23435 2.69294 0.33666 18 U - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 19 0.25557 2.78789 2.55713 2.44824 19 A - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 20 0.25557 2.78789 2.55713 2.44824 20 A - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 21 0.25557 2.78789 2.55713 2.44824 21 A - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 22 2.30545 0.35353 2.86415 1.95866 22 C - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 23 2.19729 2.23435 2.69294 0.33666 23 U - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 24 0.25557 2.78789 2.55713 2.44824 24 A - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 25 2.19729 2.23435 2.69294 0.33666 25 U - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 26 2.22280 3.02490 0.26300 2.59843 26 G - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 27 0.25557 2.78789 2.55713 2.44824 27 A - - : 1.38629 1.38629 1.38629 1.38629 0.02469 3.71357 * 1.46634 0.26236 0.00000 * //