INFERNAL1/a [1.1.5 | Sep 2023] NAME UPD-PKc ACC RF01103 DESC Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR STATES 91 NODES 26 CLEN 29 W 43 ALPH RNA RF no CONS yes MAP yes DATE Fri Jul 12 14:05:07 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/RF01103/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 1378388257 NULL 0.000 0.000 0.000 0.000 GA 40.00 TC 47.50 NC 36.00 EFP7GF -3.1724 0.76215 ECMLC 0.49527 -9.73412 3.29745 1600000 762351 0.001574 ECMGC 0.42560 -11.18459 4.34943 1600000 297351 0.001345 ECMLI 0.51549 -7.14038 4.42997 1600000 467179 0.002569 ECMGI 0.45210 -8.92368 5.22358 1600000 239782 0.001668 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 43 62 -6.891 -8.136 -0.079 -4.590 IL 1 1 2 1 4 1 1 45 63 -2.817 -4.319 -0.613 -2.698 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 1 45 64 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 1 ] - 29 - G - - MR 3 2 3 5 3 1 1 43 62 -8.380 -0.018 -6.697 -1.638 -2.867 1.736 -2.254 D 4 2 3 5 3 0 0 41 60 -6.390 -1.568 -0.620 IR 5 5 3 5 3 1 1 44 63 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 2 ] - 28 - A - - MR 6 5 3 8 3 1 1 42 61 -8.380 -0.018 -6.697 1.730 -2.426 -2.052 -1.973 D 7 5 3 8 3 0 0 40 59 -6.390 -1.568 -0.620 IR 8 8 3 8 3 1 1 43 62 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 3 ] - 27 - a - - MR 9 8 3 11 3 1 1 41 60 -8.380 -0.018 -6.697 0.713 -1.419 0.512 -0.832 D 10 8 3 11 3 0 0 39 58 -6.390 -1.568 -0.620 IR 11 11 3 11 3 1 1 42 61 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 4 ] - 26 - G - - MR 12 11 3 14 3 1 1 40 59 -8.380 -0.018 -6.697 -1.638 -2.867 1.736 -2.254 D 13 11 3 14 3 0 0 38 57 -6.390 -1.568 -0.620 IR 14 14 3 14 3 1 1 41 60 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 5 ] - 25 - C - - MR 15 14 3 17 3 1 1 39 58 -8.380 -0.018 -6.697 -1.806 1.641 -2.632 -1.207 D 16 14 3 17 3 0 0 37 56 -6.390 -1.568 -0.620 IR 17 17 3 17 3 1 1 40 59 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 6 ] - 24 - U - - MR 18 17 3 20 3 1 1 38 57 -8.380 -0.018 -6.697 -1.535 -1.523 -2.271 1.632 D 19 17 3 20 3 0 0 36 55 -6.390 -1.568 -0.620 IR 20 20 3 20 3 1 1 39 58 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 7 ] - 23 - A - - MR 21 20 3 23 3 1 1 37 56 -8.380 -0.018 -6.697 1.730 -2.426 -2.052 -1.973 D 22 20 3 23 3 0 0 35 54 -6.390 -1.568 -0.620 IR 23 23 3 23 3 1 1 38 57 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 8 ] - 22 - A - - MR 24 23 3 26 3 1 1 36 55 -8.380 -0.018 -6.697 1.730 -2.426 -2.052 -1.973 D 25 23 3 26 3 0 0 34 53 -6.390 -1.568 -0.620 IR 26 26 3 26 3 1 1 37 56 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 9 ] - 21 - A - - MR 27 26 3 29 3 1 1 35 54 -8.380 -0.018 -6.697 1.730 -2.426 -2.052 -1.973 D 28 26 3 29 3 0 0 33 52 -6.390 -1.568 -0.620 IR 29 29 3 29 3 1 1 36 55 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 10 ] - 20 - U - - MR 30 29 3 32 3 1 1 34 53 -8.380 -0.018 -6.697 -1.535 -1.523 -2.271 1.632 D 31 29 3 32 3 0 0 32 51 -6.390 -1.568 -0.620 IR 32 32 3 32 3 1 1 35 54 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 11 ] - 19 - G - - MR 33 32 3 35 3 1 1 33 52 -8.380 -0.018 -6.697 -1.638 -2.867 1.736 -2.254 D 34 32 3 35 3 0 0 31 50 -6.390 -1.568 -0.620 IR 35 35 3 35 3 1 1 34 53 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 12 ] - 18 - U - - MR 36 35 3 38 5 1 1 32 51 -7.117 -0.038 -6.932 -7.144 -8.036 -1.535 -1.523 -2.271 1.632 D 37 35 3 38 5 0 0 31 50 -5.352 -0.707 -2.978 -4.409 -2.404 IR 38 38 3 38 5 1 1 32 51 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 13 ] 1 17 U A - - MP 39 38 3 43 6 2 2 31 50 -9.118 -9.058 -0.021 -7.834 -8.114 -8.509 -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 3 43 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 41 38 3 43 6 1 1 29 48 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 42 38 3 43 6 0 0 27 46 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 43 43 5 43 6 1 1 31 50 -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 30 49 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 14 ] 2 16 C G - - MP 45 44 6 49 6 2 2 29 48 -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 28 46 -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 27 46 -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 25 44 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 49 49 5 49 6 1 1 29 48 -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 28 47 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 15 ] 3 15 U A - - MP 51 50 6 55 6 2 2 27 46 -9.118 -9.058 -0.021 -7.834 -8.114 -8.509 -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 52 50 6 55 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 53 50 6 55 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 54 50 6 55 6 0 0 24 42 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 55 55 5 55 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 56 56 6 56 5 1 1 26 45 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 16 ] 4 14 G C - - MP 57 56 6 61 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 58 56 6 61 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 59 56 6 61 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 60 56 6 61 6 0 0 23 42 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 61 61 5 61 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 62 62 6 62 5 1 1 24 43 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 17 ] 5 13 U A - - MP 63 62 6 67 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 64 62 6 67 4 1 1 24 43 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 65 62 6 67 4 1 1 23 42 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 66 62 6 67 4 0 0 22 41 -4.568 -4.250 -2.265 -0.520 IL 67 67 5 67 4 1 1 25 44 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 68 68 6 68 3 1 1 24 43 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 18 ] 6 - U - - - ML 69 68 6 71 3 1 1 20 39 -7.991 -0.020 -6.645 -1.535 -1.523 -2.271 1.632 D 70 68 6 71 3 0 0 19 38 -6.174 -1.687 -0.566 IL 71 71 3 71 3 1 1 23 42 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 19 ] 7 - U - - - ML 72 71 3 74 3 1 1 19 37 -7.991 -0.020 -6.645 -1.535 -1.523 -2.271 1.632 D 73 71 3 74 3 0 0 18 37 -6.174 -1.687 -0.566 IL 74 74 3 74 3 1 1 22 41 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 20 ] 8 - U - - - ML 75 74 3 77 3 1 1 18 36 -7.991 -0.020 -6.645 -1.535 -1.523 -2.271 1.632 D 76 74 3 77 3 0 0 17 36 -6.174 -1.687 -0.566 IL 77 77 3 77 3 1 1 21 40 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 21 ] 9 - U - - - ML 78 77 3 80 3 1 1 16 35 -7.991 -0.020 -6.645 -1.535 -1.523 -2.271 1.632 D 79 77 3 80 3 0 0 16 34 -6.174 -1.687 -0.566 IL 80 80 3 80 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 22 ] 10 - C - - - ML 81 80 3 83 3 1 1 15 33 -7.991 -0.020 -6.645 -1.806 1.641 -2.632 -1.207 D 82 80 3 83 3 0 0 15 33 -6.174 -1.687 -0.566 IL 83 83 3 83 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 23 ] 11 - G - - - ML 84 83 3 86 3 1 1 13 31 -7.991 -0.020 -6.645 -1.638 -2.867 1.736 -2.254 D 85 83 3 86 3 0 0 13 32 -6.174 -1.687 -0.566 IL 86 86 3 86 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 24 ] 12 - A - - - ML 87 86 3 89 2 1 1 1 1 * 0.000 1.730 -2.426 -2.052 -1.973 D 88 86 3 89 2 0 0 0 0 * 0.000 IL 89 89 3 89 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 25 ] - - - - - - E 90 89 3 -1 0 0 0 0 0 // HMMER3/f [3.4 | Aug 2023] NAME UPD-PKc ACC RF01103 DESC Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR LENG 29 MAXL 103 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Fri Jul 12 14:05:07 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/RF01103/CM NSEQ 2 EFFN 1.589844 CKSUM 1378388257 STATS LOCAL MSV -6.6716 0.76215 STATS LOCAL VITERBI -8.0774 0.76215 STATS LOCAL FORWARD -2.5908 0.76215 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.30291 1.68459 1.40928 1.20925 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 * 1 2.56236 1.61602 2.26345 0.47772 1 U - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 2 2.80475 0.35988 2.52633 1.82159 2 C - - < 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 3 2.56718 1.61597 2.26512 0.47685 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 2.33459 2.82100 0.24729 2.76964 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 2.56736 1.61596 2.26518 0.47682 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 2.24588 2.27392 2.74471 0.31884 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 2.24588 2.27392 2.74471 0.31884 7 U - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 8 2.24588 2.27392 2.74471 0.31884 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 2.24588 2.27392 2.74471 0.31884 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 2.36922 0.32989 2.93122 2.00907 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 2.28134 3.09386 0.24448 2.66766 11 G - - _ 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 12 0.24029 2.84226 2.60604 2.50743 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 0.54329 2.44148 1.45249 2.32128 13 A - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 14 2.98988 0.28865 2.65114 2.04130 14 C - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 15 0.54305 2.44214 1.45245 2.32222 15 A - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 16 2.09687 2.69500 0.31092 2.56596 16 G - - > 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 17 0.54271 2.44306 1.45240 2.32355 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 2.24588 2.27392 2.74471 0.31884 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 2.28134 3.09386 0.24448 2.66766 19 G - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 20 2.24588 2.27392 2.74471 0.31884 20 U - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 21 0.24029 2.84226 2.60604 2.50743 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 0.24029 2.84226 2.60604 2.50743 22 A - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 23 0.24029 2.84226 2.60604 2.50743 23 A - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 24 2.24588 2.27392 2.74471 0.31884 24 U - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 25 2.36922 0.32989 2.93122 2.00907 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 2.28134 3.09386 0.24448 2.66766 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 0.91610 2.27487 1.07259 1.86438 27 a - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 28 0.24029 2.84226 2.60604 2.50743 28 A - - : 1.38629 1.38629 1.38629 1.38629 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547 29 2.28134 3.09386 0.24448 2.66766 29 G - - : 1.38629 1.38629 1.38629 1.38629 0.02469 3.71357 * 1.46634 0.26236 0.00000 * //