INFERNAL1/a [1.1.5 | Sep 2023] NAME SBRMV1_UPD-PKd ACC RF01109 DESC Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR STATES 67 NODES 20 CLEN 21 W 35 ALPH RNA RF no CONS yes MAP yes DATE Fri Jul 12 14:13:24 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/RF01109/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 4170216555 NULL 0.000 0.000 0.000 0.000 GA 33.00 TC 35.50 NC 32.00 EFP7GF -2.6888 0.78265 ECMLC 0.56237 -7.44365 3.73316 1600000 644106 0.001863 ECMGC 0.52956 -7.54116 5.01457 1600000 308811 0.001295 ECMLI 0.58420 -5.46766 4.60695 1600000 431766 0.002779 ECMGI 0.53361 -6.73440 5.38894 1600000 257981 0.001551 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 35 54 -6.891 -8.136 -0.079 -4.590 IL 1 1 2 1 4 1 1 36 55 -2.817 -4.319 -0.613 -2.698 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 1 37 56 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 1 ] - 21 - G - - MR 3 2 3 5 3 1 1 35 54 -8.380 -0.018 -6.697 -1.638 -2.867 1.736 -2.254 D 4 2 3 5 3 0 0 33 52 -6.390 -1.568 -0.620 IR 5 5 3 5 3 1 1 36 55 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 2 ] - 20 - G - - MR 6 5 3 8 3 1 1 34 53 -8.380 -0.018 -6.697 -1.638 -2.867 1.736 -2.254 D 7 5 3 8 3 0 0 32 51 -6.390 -1.568 -0.620 IR 8 8 3 8 3 1 1 35 54 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 3 ] - 19 - U - - MR 9 8 3 11 3 1 1 33 52 -8.380 -0.018 -6.697 -1.535 -1.523 -2.271 1.632 D 10 8 3 11 3 0 0 31 50 -6.390 -1.568 -0.620 IR 11 11 3 11 3 1 1 34 53 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 4 ] - 18 - A - - MR 12 11 3 14 3 1 1 32 51 -8.380 -0.018 -6.697 1.730 -2.426 -2.052 -1.973 D 13 11 3 14 3 0 0 30 49 -6.390 -1.568 -0.620 IR 14 14 3 14 3 1 1 33 52 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 5 ] - 17 - G - - MR 15 14 3 17 3 1 1 31 50 -8.380 -0.018 -6.697 -1.638 -2.867 1.736 -2.254 D 16 14 3 17 3 0 0 29 48 -6.390 -1.568 -0.620 IR 17 17 3 17 3 1 1 32 51 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 6 ] - 16 - A - - MR 18 17 3 20 3 1 1 30 49 -8.380 -0.018 -6.697 1.730 -2.426 -2.052 -1.973 D 19 17 3 20 3 0 0 28 47 -6.390 -1.568 -0.620 IR 20 20 3 20 3 1 1 31 50 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 7 ] - 15 - U - - MR 21 20 3 23 3 1 1 29 48 -8.380 -0.018 -6.697 -1.535 -1.523 -2.271 1.632 D 22 20 3 23 3 0 0 27 46 -6.390 -1.568 -0.620 IR 23 23 3 23 3 1 1 30 49 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 8 ] - 14 - A - - MR 24 23 3 26 5 1 1 28 47 -7.117 -0.038 -6.932 -7.144 -8.036 1.730 -2.426 -2.052 -1.973 D 25 23 3 26 5 0 0 27 46 -5.352 -0.707 -2.978 -4.409 -2.404 IR 26 26 3 26 5 1 1 28 47 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 9 ] 1 13 C G - - MP 27 26 3 31 6 2 2 27 46 -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 28 26 3 31 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 29 26 3 31 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 30 26 3 31 6 0 0 24 42 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 31 31 5 31 6 1 1 27 46 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 32 32 6 32 5 1 1 26 45 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 10 ] 2 12 G C - - MP 33 32 6 37 6 2 2 25 44 -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 34 32 6 37 6 1 1 24 43 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 35 32 6 37 6 1 1 24 43 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 36 32 6 37 6 0 0 23 42 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 37 37 5 37 6 1 1 25 44 -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 24 43 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 11 ] 3 11 U A - - MP 39 38 6 43 4 2 2 23 42 -6.977 -7.184 -0.052 -5.598 -4.256 -4.083 -4.087 -0.373 -3.015 -4.645 1.315 -3.716 -4.092 -0.129 -4.462 -1.980 3.359 -4.405 -0.690 -2.909 ML 40 38 6 43 4 1 1 24 43 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 41 38 6 43 4 1 1 23 42 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 42 38 6 43 4 0 0 22 41 -4.568 -4.250 -2.265 -0.520 IL 43 43 5 43 4 1 1 25 44 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 44 44 6 44 3 1 1 24 43 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 12 ] 4 - G - - - ML 45 44 6 47 3 1 1 20 39 -7.991 -0.020 -6.645 -1.638 -2.867 1.736 -2.254 D 46 44 6 47 3 0 0 19 38 -6.174 -1.687 -0.566 IL 47 47 3 47 3 1 1 23 42 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 13 ] 5 - G - - - ML 48 47 3 50 3 1 1 19 37 -7.991 -0.020 -6.645 -1.638 -2.867 1.736 -2.254 D 49 47 3 50 3 0 0 18 37 -6.174 -1.687 -0.566 IL 50 50 3 50 3 1 1 22 41 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 14 ] 6 - C - - - ML 51 50 3 53 3 1 1 18 36 -7.991 -0.020 -6.645 -1.806 1.641 -2.632 -1.207 D 52 50 3 53 3 0 0 17 36 -6.174 -1.687 -0.566 IL 53 53 3 53 3 1 1 21 40 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 15 ] 7 - C - - - ML 54 53 3 56 3 1 1 16 35 -7.991 -0.020 -6.645 -1.806 1.641 -2.632 -1.207 D 55 53 3 56 3 0 0 16 34 -6.174 -1.687 -0.566 IL 56 56 3 56 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 16 ] 8 - A - - - ML 57 56 3 59 3 1 1 15 33 -7.991 -0.020 -6.645 1.730 -2.426 -2.052 -1.973 D 58 56 3 59 3 0 0 15 33 -6.174 -1.687 -0.566 IL 59 59 3 59 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 17 ] 9 - U - - - ML 60 59 3 62 3 1 1 13 31 -7.991 -0.020 -6.645 -1.535 -1.523 -2.271 1.632 D 61 59 3 62 3 0 0 13 32 -6.174 -1.687 -0.566 IL 62 62 3 62 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 18 ] 10 - C - - - ML 63 62 3 65 2 1 1 1 1 * 0.000 -1.806 1.641 -2.632 -1.207 D 64 62 3 65 2 0 0 0 0 * 0.000 IL 65 65 3 65 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 19 ] - - - - - - E 66 65 3 -1 0 0 0 0 0 // HMMER3/f [3.4 | Aug 2023] NAME SBRMV1_UPD-PKd ACC RF01109 DESC Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR LENG 21 MAXL 90 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Fri Jul 12 14:13:24 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/RF01109/CM NSEQ 2 EFFN 1.527344 CKSUM 4170216555 STATS LOCAL MSV -6.6178 0.78265 STATS LOCAL VITERBI -7.5907 0.78265 STATS LOCAL FORWARD -2.2481 0.78265 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.38888 1.46837 1.18506 1.53890 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * 1 2.76574 0.37402 2.48481 1.79719 1 C - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 2 2.31083 2.78022 0.25677 2.72947 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 2.53484 1.59415 2.22754 0.49454 3 U - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 4 2.24246 3.04809 0.25660 2.62171 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 2.24246 3.04809 0.25660 2.62171 5 G - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 6 2.32678 0.34540 2.88662 1.97551 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 2.32678 0.34540 2.88662 1.97551 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 0.25032 2.80613 2.57354 2.46808 8 A - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 9 2.21356 2.24758 2.71030 0.33056 9 U - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 10 2.32678 0.34540 2.88662 1.97551 10 C - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 11 0.56353 2.40374 1.43055 2.29019 11 A - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 12 2.95569 0.29845 2.61243 2.02018 12 C - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 13 2.07331 2.65569 0.32222 2.53275 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 0.25032 2.80613 2.57354 2.46808 14 A - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 15 2.21356 2.24758 2.71030 0.33056 15 U - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 16 0.25032 2.80613 2.57354 2.46808 16 A - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 17 2.24246 3.04809 0.25660 2.62171 17 G - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 18 0.25032 2.80613 2.57354 2.46808 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 2.21356 2.24758 2.71030 0.33056 19 U - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 20 2.24246 3.04809 0.25660 2.62171 20 G - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 21 2.24246 3.04809 0.25660 2.62171 21 G - - : 1.38629 1.38629 1.38629 1.38629 0.02469 3.71357 * 1.46634 0.26236 0.00000 * //