INFERNAL1/a [1.1.5 | Sep 2023] NAME shuA_thermo ACC RF02597 DESC shuA/chuA 5' UTR thermoregulator STATES 100 NODES 27 CLEN 32 W 45 ALPH RNA RF no CONS yes MAP yes DATE Wed Jul 10 11:41:40 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/RF02597/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 5 EFFN 5.000000 CKSUM 479634926 NULL 0.000 0.000 0.000 0.000 GA 58.00 TC 58.60 NC 39.30 EFP7GF -11.1869 0.72567 ECMLC 0.50053 -8.59377 4.90976 1600000 1034094 0.001160 ECMGC 0.51802 -13.35759 1.07400 1600000 705993 0.000567 ECMLI 0.49911 -6.95886 5.76993 1600000 689089 0.001741 ECMGI 0.51069 -11.93283 2.47539 1600000 627559 0.000637 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 45 64 -7.853 -8.060 -0.028 -6.474 IL 1 1 2 1 4 1 1 50 70 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 1 49 68 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 1 ] 1 - A - - - ML 3 2 3 5 3 1 1 46 64 -8.820 -0.011 -7.474 1.917 -4.036 -3.527 -3.736 D 4 2 3 5 3 0 0 45 64 -6.174 -1.687 -0.566 IL 5 5 3 5 3 1 1 48 67 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 2 ] 2 - U - - - ML 6 5 3 8 3 1 1 44 63 -8.820 -0.011 -7.474 -3.083 -2.826 -3.864 1.877 D 7 5 3 8 3 0 0 44 62 -6.174 -1.687 -0.566 IL 8 8 3 8 3 1 1 47 66 -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 43 62 -8.820 -0.011 -7.474 -3.083 -2.826 -3.864 1.877 D 10 8 3 11 3 0 0 42 61 -6.174 -1.687 -0.566 IL 11 11 3 11 3 1 1 46 65 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 4 ] 4 - U - - - ML 12 11 3 14 3 1 1 42 61 -8.820 -0.011 -7.474 -3.083 -2.826 -3.864 1.877 D 13 11 3 14 3 0 0 41 60 -6.174 -1.687 -0.566 IL 14 14 3 14 3 1 1 45 64 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 5 ] 5 - U - - - ML 15 14 3 17 3 1 1 41 60 -8.820 -0.011 -7.474 -3.083 -2.826 -3.864 1.877 D 16 14 3 17 3 0 0 40 59 -6.174 -1.687 -0.566 IL 17 17 3 17 3 1 1 44 63 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 6 ] 6 - U - - - ML 18 17 3 20 3 1 1 40 59 -8.820 -0.011 -7.474 -3.083 -2.826 -3.864 1.877 D 19 17 3 20 3 0 0 39 58 -6.174 -1.687 -0.566 IL 20 20 3 20 3 1 1 43 62 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 7 ] 7 - U - - - ML 21 20 3 23 3 1 1 39 58 -9.168 -0.011 -7.485 -3.083 -2.826 -3.864 1.877 D 22 20 3 23 3 0 0 38 56 -5.620 -0.734 -1.403 IL 23 23 3 23 3 1 1 40 59 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 8 ] - 32 - G - - MR 24 23 3 26 3 1 1 38 57 -9.168 -0.011 -7.485 -3.201 -4.609 1.920 -3.943 D 25 23 3 26 3 0 0 36 55 -6.390 -1.568 -0.620 IR 26 26 3 26 3 1 1 39 57 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 9 ] - 31 - U - - MR 27 26 3 29 3 1 1 37 56 -9.168 -0.011 -7.485 -3.083 -2.826 -3.864 1.877 D 28 26 3 29 3 0 0 35 54 -6.390 -1.568 -0.620 IR 29 29 3 29 3 1 1 38 56 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 10 ] - 30 - A - - MR 30 29 3 32 3 1 1 36 55 -9.168 -0.011 -7.485 1.917 -4.036 -3.527 -3.736 D 31 29 3 32 3 0 0 34 53 -6.390 -1.568 -0.620 IR 32 32 3 32 3 1 1 37 55 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 11 ] - 29 - U - - MR 33 32 3 35 3 1 1 35 54 -9.168 -0.011 -7.485 -3.083 -2.826 -3.864 1.877 D 34 32 3 35 3 0 0 33 52 -6.390 -1.568 -0.620 IR 35 35 3 35 3 1 1 36 54 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 12 ] - 28 - C - - MR 36 35 3 38 3 1 1 34 53 -9.168 -0.011 -7.485 -1.343 1.658 -3.080 -1.588 D 37 35 3 38 3 0 0 32 51 -6.390 -1.568 -0.620 IR 38 38 3 38 3 1 1 35 53 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 13 ] - 27 - G - - MR 39 38 3 41 3 1 1 33 52 -9.168 -0.011 -7.485 -3.201 -4.609 1.920 -3.943 D 40 38 3 41 3 0 0 31 50 -6.390 -1.568 -0.620 IR 41 41 3 41 3 1 1 34 52 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 14 ] - 26 - C - - MR 42 41 3 44 5 1 1 32 51 -7.865 -0.023 -7.680 -7.892 -8.784 -3.685 1.899 -4.419 -2.783 D 43 41 3 44 5 0 0 31 49 -5.352 -0.707 -2.978 -4.409 -2.404 IR 44 44 3 44 5 1 1 32 51 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 15 ] 8 25 A U - - MP 45 44 3 49 6 2 2 31 50 -9.522 -9.461 -0.016 -8.238 -8.517 -8.912 -5.421 -4.170 -5.143 3.837 -6.509 -7.803 -2.118 -5.083 -5.190 -0.708 -5.803 -1.473 -2.497 -6.615 -4.039 -4.031 ML 46 44 3 49 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 47 44 3 49 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 48 44 3 49 6 0 0 27 46 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 49 49 5 49 6 1 1 31 49 -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 30 49 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 16 ] 9 24 U A - - MP 51 50 6 55 6 2 2 29 48 -9.522 -9.461 -0.016 -8.238 -8.517 -8.912 -6.530 -6.383 -6.095 -2.606 -4.670 -6.446 -0.356 -5.486 -6.084 -2.576 -6.357 -4.253 3.852 -6.538 -2.284 -4.463 ML 52 50 6 55 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 53 50 6 55 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 54 50 6 55 6 0 0 25 44 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 55 55 5 55 6 1 1 29 47 -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 28 47 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 17 ] 10 23 U A - - MP 57 56 6 61 6 2 2 27 46 -9.522 -9.461 -0.016 -8.238 -8.517 -8.912 -6.530 -6.383 -6.095 -2.606 -4.670 -6.446 -0.356 -5.486 -6.084 -2.576 -6.357 -4.253 3.852 -6.538 -2.284 -4.463 ML 58 56 6 61 6 1 1 26 44 -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 25 44 -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 27 45 -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 26 45 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 18 ] 11 22 U G - - MP 63 62 6 67 6 2 2 25 44 -9.522 -9.461 -0.016 -8.238 -8.517 -8.912 -5.569 -5.548 -4.989 -1.798 -3.446 -5.231 0.848 -4.307 -5.048 -1.823 -5.221 -3.543 -0.145 -5.527 3.615 -3.870 ML 64 62 6 67 6 1 1 24 42 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 65 62 6 67 6 1 1 24 42 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 66 62 6 67 6 0 0 21 40 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 67 67 5 67 6 1 1 25 43 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 68 68 6 68 5 1 1 24 43 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 19 ] 12 21 U A - - MP 69 68 6 73 6 2 2 23 42 -9.522 -9.461 -0.016 -8.238 -8.517 -8.912 -6.530 -6.383 -6.095 -2.606 -4.670 -6.446 -0.356 -5.486 -6.084 -2.576 -6.357 -4.253 3.852 -6.538 -2.284 -4.463 ML 70 68 6 73 6 1 1 22 41 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 71 68 6 73 6 1 1 22 41 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 72 68 6 73 6 0 0 20 39 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 73 73 5 73 6 1 1 23 41 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 74 74 6 74 5 1 1 22 41 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 20 ] 13 20 C G - - MP 75 74 6 79 6 2 2 21 40 -9.522 -9.461 -0.016 -8.238 -8.517 -8.912 -6.436 -6.502 -5.772 -2.678 -4.205 -5.936 3.874 -5.224 -5.962 -2.604 -5.938 -4.563 -0.969 -6.377 -2.038 -4.766 ML 76 74 6 79 6 1 1 21 40 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 77 74 6 79 6 1 1 21 39 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 78 74 6 79 6 0 0 19 38 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 79 79 5 79 6 1 1 21 40 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 80 80 6 80 5 1 1 21 39 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 21 ] 14 19 C G - - MP 81 80 6 85 4 2 2 19 38 -7.853 -8.060 -0.028 -6.474 -6.436 -6.502 -5.772 -2.678 -4.205 -5.936 3.874 -5.224 -5.962 -2.604 -5.938 -4.563 -0.969 -6.377 -2.038 -4.766 ML 82 80 6 85 4 1 1 20 39 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094 MR 83 80 6 85 4 1 1 20 39 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 84 80 6 85 4 0 0 19 38 -4.568 -4.250 -2.265 -0.520 IL 85 85 5 85 4 1 1 22 41 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 86 86 6 86 3 1 1 21 39 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 22 ] 15 - U - - - ML 87 86 6 89 3 1 1 16 34 -8.820 -0.011 -7.474 -3.083 -2.826 -3.864 1.877 D 88 86 6 89 3 0 0 16 34 -6.174 -1.687 -0.566 IL 89 89 3 89 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 23 ] 16 - C - - - ML 90 89 3 92 3 1 1 14 33 -8.820 -0.011 -7.474 -3.685 1.899 -4.419 -2.783 D 91 89 3 92 3 0 0 15 33 -6.174 -1.687 -0.566 IL 92 92 3 92 3 1 1 19 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 24 ] 17 - A - - - ML 93 92 3 95 3 1 1 12 31 -8.820 -0.011 -7.474 1.917 -4.036 -3.527 -3.736 D 94 92 3 95 3 0 0 13 32 -6.174 -1.687 -0.566 IL 95 95 3 95 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 25 ] 18 - U - - - ML 96 95 3 98 2 1 1 1 1 * 0.000 -3.083 -2.826 -3.864 1.877 D 97 95 3 98 2 0 0 0 0 * 0.000 IL 98 98 3 98 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 26 ] - - - - - - E 99 98 3 -1 0 0 0 0 0 // HMMER3/f [3.4 | Aug 2023] NAME shuA_thermo ACC RF02597 DESC shuA/chuA 5' UTR thermoregulator LENG 32 MAXL 100 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Wed Jul 10 11:41:40 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/RF02597/CM NSEQ 5 EFFN 4.389648 CKSUM 479634926 STATS LOCAL MSV -6.1490 0.72567 STATS LOCAL VITERBI -7.1668 0.72567 STATS LOCAL FORWARD -3.7648 0.72567 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.48600 1.74990 1.75589 0.85055 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 0.00000 * 1 0.06812 4.01613 3.67376 3.79638 1 A - - : 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 2 3.35910 3.20361 3.89743 0.10057 2 U - - : 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 3 3.35910 3.20361 3.89743 0.10057 3 U - - : 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 4 3.35910 3.20361 3.89743 0.10057 4 U - - : 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 5 3.35910 3.20361 3.89743 0.10057 5 U - - : 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 6 3.35910 3.20361 3.89743 0.10057 6 U - - : 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 7 3.35910 3.20361 3.89743 0.10057 7 U - - : 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 8 0.13366 3.77917 2.57033 3.65895 8 A - - < 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 9 3.97233 2.70300 3.81945 0.11404 9 U - - < 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 10 3.96859 2.70256 3.81736 0.11420 10 U - - < 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 11 3.57432 1.99268 3.44461 0.21851 11 U - - < 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 12 3.96210 2.70181 3.81374 0.11448 12 U - - < 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 13 4.02441 0.10496 3.89256 2.79087 13 C - - < 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 14 4.02209 0.10506 3.89123 2.79041 14 C - - < 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 15 3.35910 3.20361 3.89743 0.10057 15 U - - _ 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 16 3.75933 0.08311 4.29116 3.15220 16 C - - _ 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 17 0.06812 4.01613 3.67376 3.79638 17 A - - _ 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 18 3.35910 3.20361 3.89743 0.10057 18 U - - _ 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 19 3.07022 4.05280 0.09005 3.80176 19 G - - > 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 20 3.07137 4.05474 0.08990 3.80387 20 G - - > 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 21 0.13023 4.01107 2.53513 3.69945 21 A - - > 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 22 2.59509 3.63231 0.14809 3.30898 22 G - - > 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 23 0.12973 4.01861 2.53651 3.70716 23 A - - > 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 24 0.12932 4.02484 2.53765 3.71353 24 A - - > 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 25 3.89800 2.95429 3.59447 0.10522 25 U - - > 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 26 3.75933 0.08311 4.29116 3.15220 26 C - - : 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 27 3.45342 4.41472 0.06473 3.96620 27 G - - : 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 28 2.25523 0.26533 3.37439 2.36489 28 C - - : 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 29 3.35910 3.20361 3.89743 0.10057 29 U - - : 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 30 0.06812 4.01613 3.67376 3.79638 30 A - - : 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 31 3.35910 3.20361 3.89743 0.10057 31 U - - : 1.38629 1.38629 1.38629 1.38629 0.02817 4.27667 4.27667 1.46634 0.26236 1.09861 0.40547 32 3.45342 4.41472 0.06473 3.96620 32 G - - : 1.38629 1.38629 1.38629 1.38629 0.01418 4.26268 * 1.46634 0.26236 0.00000 * //