INFERNAL1/a [1.1.5 | Sep 2023] NAME BMV3_UPD-PK1 ACC RF01108 DESC Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR STATES 82 NODES 23 CLEN 26 W 40 ALPH RNA RF no CONS yes MAP yes DATE Tue Jul 9 07:31:19 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/RF01108/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 213448415 NULL 0.000 0.000 0.000 0.000 GA 38.00 TC 43.70 NC 37.40 EFP7GF -3.8691 0.76646 ECMLC 0.61431 -6.57114 3.60845 1600000 623720 0.001924 ECMGC 0.53916 -8.16612 4.13643 1600000 303926 0.001316 ECMLI 0.65415 -4.40576 4.57206 1600000 426316 0.002815 ECMGI 0.56882 -6.57441 4.78397 1600000 255848 0.001563 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 40 59 -6.977 -7.184 -0.052 -5.598 IL 1 1 2 1 4 1 1 45 64 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 1 44 63 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 1 ] 1 - G - - - ML 3 2 3 5 3 1 1 40 59 -8.380 -0.018 -6.697 -1.638 -2.867 1.736 -2.254 D 4 2 3 5 3 0 0 39 58 -5.620 -0.734 -1.403 IL 5 5 3 5 3 1 1 41 60 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 2 ] - 26 - A - - MR 6 5 3 8 3 1 1 39 58 -8.380 -0.018 -6.697 1.730 -2.426 -2.052 -1.973 D 7 5 3 8 3 0 0 37 56 -6.390 -1.568 -0.620 IR 8 8 3 8 3 1 1 40 59 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 3 ] - 25 - C - - MR 9 8 3 11 3 1 1 38 57 -8.380 -0.018 -6.697 -1.806 1.641 -2.632 -1.207 D 10 8 3 11 3 0 0 36 55 -6.390 -1.568 -0.620 IR 11 11 3 11 3 1 1 39 58 -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 37 56 -8.380 -0.018 -6.697 1.730 -2.426 -2.052 -1.973 D 13 11 3 14 3 0 0 35 54 -6.390 -1.568 -0.620 IR 14 14 3 14 3 1 1 38 57 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 5 ] - 23 - C - - MR 15 14 3 17 3 1 1 36 55 -8.380 -0.018 -6.697 -1.806 1.641 -2.632 -1.207 D 16 14 3 17 3 0 0 34 53 -6.390 -1.568 -0.620 IR 17 17 3 17 3 1 1 37 56 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 6 ] - 22 - U - - MR 18 17 3 20 3 1 1 35 54 -8.380 -0.018 -6.697 -1.535 -1.523 -2.271 1.632 D 19 17 3 20 3 0 0 33 52 -6.390 -1.568 -0.620 IR 20 20 3 20 3 1 1 36 55 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 7 ] - 21 - G - - MR 21 20 3 23 3 1 1 34 53 -8.380 -0.018 -6.697 -1.638 -2.867 1.736 -2.254 D 22 20 3 23 3 0 0 32 51 -6.390 -1.568 -0.620 IR 23 23 3 23 3 1 1 35 54 -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 33 52 -8.380 -0.018 -6.697 1.730 -2.426 -2.052 -1.973 D 25 23 3 26 3 0 0 31 50 -6.390 -1.568 -0.620 IR 26 26 3 26 3 1 1 34 53 -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 32 51 -8.380 -0.018 -6.697 1.730 -2.426 -2.052 -1.973 D 28 26 3 29 3 0 0 30 49 -6.390 -1.568 -0.620 IR 29 29 3 29 3 1 1 33 52 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 10 ] - 18 - A - - MR 30 29 3 32 5 1 1 31 50 -7.117 -0.038 -6.932 -7.144 -8.036 1.730 -2.426 -2.052 -1.973 D 31 29 3 32 5 0 0 30 48 -5.352 -0.707 -2.978 -4.409 -2.404 IR 32 32 3 32 5 1 1 31 50 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 11 ] 2 17 A U - - MP 33 32 3 37 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 34 32 3 37 6 1 1 28 47 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 35 32 3 37 6 1 1 28 47 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 36 32 3 37 6 0 0 26 45 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 37 37 5 37 6 1 1 30 48 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 38 38 6 38 5 1 1 29 48 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 12 ] 3 16 G U - - MP 39 38 6 43 6 2 2 28 47 -9.118 -9.058 -0.021 -7.834 -8.114 -8.509 -3.651 -2.410 -3.821 1.112 -4.567 -5.291 -0.165 -3.840 -3.474 1.309 -3.997 3.120 -0.523 -4.491 -2.107 -2.514 ML 40 38 6 43 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 41 38 6 43 6 1 1 26 45 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 42 38 6 43 6 0 0 24 43 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 43 43 5 43 6 1 1 28 46 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 44 44 6 44 5 1 1 27 46 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 13 ] 4 15 C G - - MP 45 44 6 49 6 2 2 26 45 -9.118 -9.058 -0.021 -7.834 -8.114 -8.509 -4.612 -4.524 -4.292 -0.750 -2.996 -4.695 3.570 -3.812 -4.343 -0.519 -4.597 -2.472 0.512 -4.677 -0.704 -3.181 ML 46 44 6 49 6 1 1 25 44 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 47 44 6 49 6 1 1 25 43 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 48 44 6 49 6 0 0 22 41 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 49 49 5 49 6 1 1 26 44 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 50 50 6 50 5 1 1 25 44 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 14 ] 5 14 C G - - MP 51 50 6 55 6 2 2 24 43 -9.118 -9.058 -0.021 -7.834 -8.114 -8.509 -4.612 -4.524 -4.292 -0.750 -2.996 -4.695 3.570 -3.812 -4.343 -0.519 -4.597 -2.472 0.512 -4.677 -0.704 -3.181 ML 52 50 6 55 6 1 1 23 42 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 53 50 6 55 6 1 1 23 42 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 54 50 6 55 6 0 0 22 40 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 55 55 5 55 6 1 1 24 43 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 56 56 6 56 5 1 1 23 42 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 15 ] 6 13 C G - - MP 57 56 6 61 4 2 2 22 41 -6.977 -7.184 -0.052 -5.598 -4.612 -4.524 -4.292 -0.750 -2.996 -4.695 3.570 -3.812 -4.343 -0.519 -4.597 -2.472 0.512 -4.677 -0.704 -3.181 ML 58 56 6 61 4 1 1 23 42 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 59 56 6 61 4 1 1 22 41 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 60 56 6 61 4 0 0 21 40 -4.568 -4.250 -2.265 -0.520 IL 61 61 5 61 4 1 1 24 43 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 62 62 6 62 3 1 1 23 42 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 16 ] 7 - C - - - ML 63 62 6 65 3 1 1 19 37 -7.991 -0.020 -6.645 -1.806 1.641 -2.632 -1.207 D 64 62 6 65 3 0 0 18 37 -6.174 -1.687 -0.566 IL 65 65 3 65 3 1 1 22 41 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 17 ] 8 - U - - - ML 66 65 3 68 3 1 1 18 36 -7.991 -0.020 -6.645 -1.535 -1.523 -2.271 1.632 D 67 65 3 68 3 0 0 17 36 -6.174 -1.687 -0.566 IL 68 68 3 68 3 1 1 21 40 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 18 ] 9 - G - - - ML 69 68 3 71 3 1 1 16 35 -7.991 -0.020 -6.645 -1.638 -2.867 1.736 -2.254 D 70 68 3 71 3 0 0 16 34 -6.174 -1.687 -0.566 IL 71 71 3 71 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 19 ] 10 - A - - - ML 72 71 3 74 3 1 1 15 33 -7.991 -0.020 -6.645 1.730 -2.426 -2.052 -1.973 D 73 71 3 74 3 0 0 15 33 -6.174 -1.687 -0.566 IL 74 74 3 74 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 20 ] 11 - C - - - ML 75 74 3 77 3 1 1 13 31 -7.991 -0.020 -6.645 -1.806 1.641 -2.632 -1.207 D 76 74 3 77 3 0 0 13 32 -6.174 -1.687 -0.566 IL 77 77 3 77 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 21 ] 12 - U - - - ML 78 77 3 80 2 1 1 1 1 * 0.000 -1.535 -1.523 -2.271 1.632 D 79 77 3 80 2 0 0 0 0 * 0.000 IL 80 80 3 80 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 22 ] - - - - - - E 81 80 3 -1 0 0 0 0 0 // HMMER3/f [3.4 | Aug 2023] NAME BMV3_UPD-PK1 ACC RF01108 DESC Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR LENG 26 MAXL 98 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Tue Jul 9 07:31:19 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/RF01108/CM NSEQ 2 EFFN 1.597656 CKSUM 213448415 STATS LOCAL MSV -6.7214 0.76646 STATS LOCAL VITERBI -7.8912 0.76646 STATS LOCAL FORWARD -2.2978 0.76646 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.29789 1.38331 1.35188 1.52606 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * 1 2.28616 3.09952 0.24302 2.67335 1 G - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 2 0.54258 2.33012 1.51888 2.27778 2 A - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 3 1.76060 2.49666 0.42401 2.39384 3 G - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 4 2.81083 0.35796 2.53199 1.82484 4 C - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 5 2.81120 0.35790 2.53214 1.82489 5 C - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 6 2.81101 0.35793 2.53206 1.82486 6 C - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 7 2.37450 0.32802 2.93676 2.01325 7 C - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 8 2.24990 2.27720 2.74898 0.31742 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 2.28616 3.09952 0.24302 2.67335 9 G - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 10 0.23907 2.84674 2.61008 2.51231 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 2.37450 0.32802 2.93676 2.01325 11 C - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 12 2.24990 2.27720 2.74898 0.31742 12 U - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 13 2.09843 2.69830 0.31014 2.56798 13 G - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 14 2.09883 2.69877 0.30997 2.56860 14 G - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 15 2.09933 2.69932 0.30976 2.56935 15 G - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 16 2.61804 1.58541 2.30535 0.47407 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 2.51604 1.76995 2.14890 0.45844 17 U - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 18 0.23907 2.84674 2.61008 2.51231 18 A - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 19 0.23907 2.84674 2.61008 2.51231 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 0.23907 2.84674 2.61008 2.51231 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 2.28616 3.09952 0.24302 2.67335 21 G - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 22 2.24990 2.27720 2.74898 0.31742 22 U - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 23 2.37450 0.32802 2.93676 2.01325 23 C - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 24 0.23907 2.84674 2.61008 2.51231 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 2.37450 0.32802 2.93676 2.01325 25 C - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 26 0.23907 2.84674 2.61008 2.51231 26 A - - : 1.38629 1.38629 1.38629 1.38629 0.02469 3.71357 * 1.46634 0.26236 0.00000 * //