INFERNAL1/a [1.1.5 | Sep 2023] NAME UPD-PK2 ACC RF01083 DESC Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR STATES 67 NODES 18 CLEN 21 W 35 ALPH RNA RF no CONS yes MAP yes DATE Sun Jul 7 12:38:46 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/RF01083/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 4 EFFN 4.000000 CKSUM 1338229757 NULL 0.000 0.000 0.000 0.000 GA 32.00 TC 32.00 NC 31.90 EFP7GF -5.1622 0.75030 ECMLC 0.54929 -8.02089 3.71458 1600000 756373 0.001587 ECMGC 0.48534 -11.70833 2.74721 1600000 445636 0.000898 ECMLI 0.57464 -6.42484 4.31472 1600000 574590 0.002088 ECMGI 0.49187 -10.67573 3.31596 1600000 389842 0.001026 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 35 54 -7.615 -7.822 -0.033 -6.236 IL 1 1 2 1 4 1 1 39 59 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 1 38 58 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 1 ] 1 - C - - - ML 3 2 3 5 3 1 1 35 54 -8.593 -0.013 -7.247 -1.122 1.151 -0.395 -0.840 D 4 2 3 5 3 0 0 34 53 -6.174 -1.687 -0.566 IL 5 5 3 5 3 1 1 37 56 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 2 ] 2 - G - - - ML 6 5 3 8 3 1 1 34 52 -8.593 -0.013 -7.247 -0.999 -0.489 1.240 -1.233 D 7 5 3 8 3 0 0 33 52 -6.174 -1.687 -0.566 IL 8 8 3 8 3 1 1 36 55 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 3 ] 3 - U - - - ML 9 8 3 11 3 1 1 33 51 -8.593 -0.013 -7.247 -2.677 -2.478 -3.451 1.837 D 10 8 3 11 3 0 0 32 51 -6.174 -1.687 -0.566 IL 11 11 3 11 3 1 1 35 54 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 4 ] 4 - G - - - ML 12 11 3 14 3 1 1 31 50 -8.593 -0.013 -7.247 -2.823 -4.195 1.895 -3.558 D 13 11 3 14 3 0 0 30 49 -6.174 -1.687 -0.566 IL 14 14 3 14 3 1 1 34 53 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 5 ] 5 - G - - - ML 15 14 3 17 5 1 1 30 49 -7.656 -0.026 -7.471 -7.683 -8.575 -2.823 -4.195 1.895 -3.558 D 16 14 3 17 5 0 0 29 48 -4.959 -0.803 -4.221 -2.596 -2.508 IL 17 17 3 17 5 1 1 31 49 -2.408 -0.496 -4.087 -5.920 -5.193 0.000 0.000 0.000 0.000 [ MATP 6 ] 6 21 U A - - MP 18 17 3 22 6 2 2 29 48 -9.400 -9.339 -0.017 -8.115 -8.395 -8.790 -5.885 -5.729 -5.521 -1.951 -4.171 -5.925 0.158 -4.961 -5.516 -1.872 -5.808 -3.591 3.777 -5.942 -1.807 -4.074 ML 19 17 3 22 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 20 17 3 22 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 21 17 3 22 6 0 0 25 44 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 22 22 5 22 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 23 23 6 23 5 1 1 29 47 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 7 ] 7 20 G C - - MP 24 23 6 28 6 2 2 27 46 -9.400 -9.339 -0.017 -8.115 -8.395 -8.790 -5.941 -3.685 -6.268 -0.655 -6.883 -5.136 -1.953 -6.515 -5.029 3.829 -5.299 -1.454 -2.316 -5.228 -4.074 -5.128 ML 25 23 6 28 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 26 23 6 28 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 27 23 6 28 6 0 0 24 42 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 28 28 5 28 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 29 29 6 29 5 1 1 27 45 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 8 ] 8 19 C G - - MP 30 29 6 34 6 2 2 25 44 -9.400 -9.339 -0.017 -8.115 -8.395 -8.790 -5.950 -5.973 -5.383 -2.142 -3.866 -5.609 3.825 -4.822 -5.519 -2.037 -5.588 -3.985 -0.541 -5.921 -1.647 -4.326 ML 31 29 6 34 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 32 29 6 34 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 33 29 6 34 6 0 0 22 41 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 34 34 5 34 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 35 35 6 35 5 1 1 25 44 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 9 ] 9 18 A U - - MP 36 35 6 40 6 2 2 23 42 -9.400 -9.339 -0.017 -8.115 -8.395 -8.790 -5.003 -3.794 -4.847 3.771 -5.908 -7.143 -1.529 -4.807 -4.794 -0.246 -5.395 -1.126 -1.928 -6.065 -3.460 -3.682 ML 37 35 6 40 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 38 35 6 40 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 39 35 6 40 6 0 0 21 40 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 40 40 5 40 6 1 1 23 42 -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 23 42 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 10 ] 10 17 U A - - MP 42 41 6 46 4 2 2 21 40 -7.615 -7.822 -0.033 -6.236 -5.885 -5.729 -5.521 -1.951 -4.171 -5.925 0.158 -4.961 -5.516 -1.872 -5.808 -3.591 3.777 -5.942 -1.807 -4.074 ML 43 41 6 46 4 1 1 23 41 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 44 41 6 46 4 1 1 22 41 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 45 41 6 46 4 0 0 21 40 -4.568 -4.250 -2.265 -0.520 IL 46 46 5 46 4 1 1 24 43 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 47 47 6 47 3 1 1 23 42 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 11 ] 11 - A - - - ML 48 47 6 50 3 1 1 18 37 -8.593 -0.013 -7.247 1.889 -3.622 -3.140 -3.290 D 49 47 6 50 3 0 0 18 37 -6.174 -1.687 -0.566 IL 50 50 3 50 3 1 1 22 40 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 12 ] 12 - C - - - ML 51 50 3 53 3 1 1 17 36 -8.593 -0.013 -7.247 -3.231 1.864 -4.018 -2.379 D 52 50 3 53 3 0 0 17 35 -6.174 -1.687 -0.566 IL 53 53 3 53 3 1 1 21 39 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 13 ] 13 - G - - - ML 54 53 3 56 3 1 1 16 34 -8.593 -0.013 -7.247 -2.823 -4.195 1.895 -3.558 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 14 ] 14 - A - - - ML 57 56 3 59 3 1 1 14 33 -8.593 -0.013 -7.247 1.889 -3.622 -3.140 -3.290 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 15 ] 15 - U - - - ML 60 59 3 62 3 1 1 13 31 -8.593 -0.013 -7.247 -2.677 -2.478 -3.451 1.837 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 16 ] 16 - A - - - ML 63 62 3 65 2 1 1 1 1 * 0.000 1.889 -3.622 -3.140 -3.290 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 17 ] - - - - - - E 66 65 3 -1 0 0 0 0 0 // HMMER3/f [3.4 | Aug 2023] NAME UPD-PK2 ACC RF01083 DESC Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR LENG 21 MAXL 86 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Sun Jul 7 12:38:46 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/RF01083/CM NSEQ 4 EFFN 3.496094 CKSUM 1338229757 STATS LOCAL MSV -6.3033 0.75030 STATS LOCAL VITERBI -6.7626 0.75030 STATS LOCAL FORWARD -2.9358 0.75030 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.26790 1.64401 1.26812 1.41052 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 0.00000 * 1 2.05866 0.63620 1.65715 1.88130 1 C - - : 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 2 1.98703 1.72523 0.56837 2.13438 2 G - - : 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 3 3.07441 2.96196 3.60659 0.13362 3 U - - : 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 4 3.18130 4.11623 0.08663 3.68300 4 G - - : 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 5 3.18130 4.11623 0.08663 3.68300 5 G - - : 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 6 3.58252 2.36959 3.38624 0.16861 6 U - - < 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 7 2.90814 3.72412 0.11016 3.66528 7 G - - < 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 8 3.71369 0.14374 3.54339 2.51845 8 C - - < 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 9 0.18944 3.39456 2.28268 3.29662 9 A - - < 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 10 3.56642 2.36799 3.37790 0.16966 10 U - - < 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 11 0.09234 3.72461 3.40426 3.47862 11 A - - _ 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 12 3.42780 0.11419 3.98874 2.86596 12 C - - _ 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 13 3.18130 4.11623 0.08663 3.68300 13 G - - _ 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 14 0.09234 3.72461 3.40426 3.47862 14 A - - _ 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 15 3.07441 2.96196 3.60659 0.13362 15 U - - _ 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 16 0.09234 3.72461 3.40426 3.47862 16 A - - _ 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 17 0.19263 3.56964 2.20343 3.30702 17 A - - > 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 18 3.51263 2.63247 3.20006 0.15371 18 U - - > 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 19 2.79864 3.70610 0.12375 3.47597 19 G - - > 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 20 3.83288 0.13309 3.56541 2.59457 20 C - - > 1.38629 1.38629 1.38629 1.38629 0.03279 4.12713 4.12713 1.46634 0.26236 1.09861 0.40547 21 0.19251 3.57078 2.20362 3.30825 21 A - - > 1.38629 1.38629 1.38629 1.38629 0.01653 4.11087 * 1.46634 0.26236 0.00000 * //