INFERNAL1/a [1.1.5 | Sep 2023] NAME L31-Firmicutes ACC RF03156 DESC L31-Firmicutes ribosomal protein leader STATES 100 NODES 26 CLEN 32 W 64 ALPH RNA RF no CONS yes MAP yes DATE Sat Jul 13 16:54:47 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/RF03156/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 1083 EFFN 1083.000000 CKSUM 3760353181 NULL 0.000 0.000 0.000 0.000 GA 33.30 TC 33.30 NC 33.20 EFP7GF -13.6888 0.73578 ECMLC 0.56624 -10.11946 1.26770 1600000 757665 0.001584 ECMGC 0.43038 -19.53820 -5.16971 1600000 193942 0.002062 ECMLI 0.58858 -8.65389 2.05591 1600000 655833 0.001830 ECMGI 0.41227 -18.48207 -4.01129 1600000 155960 0.002565 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 4 1 1 64 100 -15.009 -16.255 -0.000 -12.708 IL 1 1 2 1 4 1 10 66 101 -2.817 -4.319 -0.613 -2.698 0.000 0.000 0.000 0.000 IR 2 2 3 2 3 1 11 66 102 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 1 ] - 75 - G - - MR 3 2 3 5 3 2 11 65 100 -16.418 -0.000 -14.735 -2.979 -11.797 1.917 -3.386 D 4 2 3 5 3 0 7 63 98 -6.390 -1.568 -0.620 IR 5 5 3 5 3 1 10 65 101 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 2 ] - 74 - A - - MR 6 5 3 8 3 2 10 64 99 -16.418 -0.000 -14.735 1.965 -11.889 -3.399 -11.332 D 7 5 3 8 3 0 6 62 97 -6.390 -1.568 -0.620 IR 8 8 3 8 3 1 10 64 100 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 3 ] - 73 - G - - MR 9 8 3 11 3 1 9 63 98 -16.418 -0.000 -14.735 -10.649 -12.407 2.000 -11.397 D 10 8 3 11 3 0 6 61 96 -6.390 -1.568 -0.620 IR 11 11 3 11 3 1 9 63 99 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 4 ] - 72 - G - - MR 12 11 3 14 3 1 8 62 97 -16.418 -0.002 -9.258 -0.616 -10.635 1.718 -4.158 D 13 11 3 14 3 0 5 59 95 -6.390 -1.568 -0.620 IR 14 14 3 14 3 1 8 62 98 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 5 ] - 71 - A - - MR 15 14 3 17 3 1 7 61 96 -16.415 -0.000 -14.733 1.953 -4.613 -3.533 -10.621 D 16 14 3 17 3 0 5 58 94 -8.579 -3.756 -0.115 IR 17 17 3 17 3 1 7 61 97 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 6 ] - 70 - A - - MR 18 17 3 20 3 1 6 60 95 -16.415 -0.000 -14.733 1.923 -11.609 -2.268 -11.214 D 19 17 3 20 3 0 5 58 94 -8.579 -0.765 -1.290 IR 20 20 3 20 3 1 6 60 96 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 7 ] - 69 - G - - MR 21 20 3 23 3 1 5 59 94 -16.417 -0.314 -2.353 0.806 -4.246 1.079 -3.551 D 22 20 3 23 3 0 4 57 93 -7.537 -0.513 -1.766 IR 23 23 3 23 3 1 7 59 95 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 8 ] - 68 - G - - MR 24 23 3 26 3 1 7 58 93 -2.746 -0.233 -14.421 -0.111 -2.892 1.491 -2.973 D 25 23 3 26 3 0 3 57 92 -15.161 -0.002 -9.391 IR 26 26 3 26 3 1 5 58 93 -5.381 -0.036 -10.919 0.000 0.000 0.000 0.000 [ MATR 9 ] - 65 - C - - MR 27 26 3 29 5 1 6 57 92 -10.851 -0.001 -14.873 -15.085 -15.977 -3.781 1.973 -11.128 -10.149 D 28 26 3 29 5 0 0 55 91 -5.352 -0.707 -2.978 -4.409 -2.404 IR 29 29 3 29 5 1 2 57 92 -2.851 -0.348 -6.362 -4.530 -5.636 0.000 0.000 0.000 0.000 [ MATP 10 ] 1 63 C G - - MP 30 29 3 34 6 2 7 56 91 -15.992 -15.931 -0.000 -14.708 -14.988 -15.383 -13.044 -13.326 -12.361 -9.562 -10.712 -12.506 3.943 -11.627 -12.465 -9.534 -12.585 -11.729 -7.444 -12.878 -0.716 -11.267 ML 31 29 3 34 6 1 1 54 89 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 32 29 3 34 6 1 1 54 89 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 33 29 3 34 6 0 0 50 86 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 34 34 5 34 6 1 2 55 91 -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 2 55 90 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 11 ] 2 62 U G - - MP 36 35 6 40 6 2 7 54 89 -15.992 -15.931 -0.000 -14.708 -14.988 -15.383 -13.043 -13.322 -12.361 -9.559 -10.712 -12.506 -1.196 -11.627 -12.465 -9.532 -12.585 -11.722 -7.445 -12.878 3.959 -11.267 ML 37 35 6 40 6 1 1 52 87 -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 52 87 -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 48 84 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 40 40 5 40 6 1 2 53 89 -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 2 53 88 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 12 ] 3 61 C G - - MP 42 41 6 46 6 2 6 52 87 -15.992 -15.931 -0.000 -14.708 -14.988 -15.383 -11.936 -11.817 -11.646 1.813 -10.243 -12.113 3.431 -11.038 -11.617 -2.000 -11.944 -9.568 0.071 -11.984 -2.676 -2.051 ML 43 41 6 46 6 1 1 50 85 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 44 41 6 46 6 1 1 50 85 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 45 41 6 46 6 0 0 47 82 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 46 46 5 46 6 1 1 51 87 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 47 47 6 47 5 1 2 51 86 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 13 ] 4 60 U A - - MP 48 47 6 52 6 2 4 50 85 -15.992 -15.931 -0.013 -6.940 -14.988 -10.172 -2.052 -13.320 -12.361 -9.557 -10.713 -12.507 -1.232 -11.628 -12.464 -9.530 -12.585 -11.716 3.938 -12.878 -8.416 -11.267 ML 49 47 6 52 6 1 1 48 83 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 50 47 6 52 6 1 1 48 84 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 51 47 6 52 6 0 0 45 81 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 IL 52 52 5 52 6 1 1 49 85 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 53 53 6 53 5 1 1 49 84 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 14 ] 5 59 G C - - MP 54 53 6 58 4 2 2 48 83 -15.202 -15.409 -0.885 -1.125 -13.376 -6.501 -14.349 0.006 -14.727 -4.435 -9.315 -14.617 -11.805 3.795 -12.000 -1.956 -0.859 -2.046 -11.609 -13.359 ML 55 53 6 58 4 1 1 45 80 -7.148 -7.331 -3.897 -0.121 -4.673 1.949 -5.248 -3.750 MR 56 53 6 58 4 1 1 47 82 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 57 53 6 58 4 0 0 44 80 -5.934 -5.615 -3.631 -0.180 IL 58 58 5 58 4 1 1 49 85 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 59 59 6 59 3 1 1 48 84 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 15 ] 6 - U - - - ML 60 59 6 62 3 1 2 47 82 -0.146 -3.376 -13.838 -1.305 -2.383 -1.015 1.540 D 61 59 6 62 3 0 0 43 78 -15.165 -3.774 -0.110 IL 62 62 3 62 3 1 1 46 81 -3.178 -0.207 -5.421 0.000 0.000 0.000 0.000 [ MATR 16 ] - 58 - U - - MR 63 62 3 65 5 1 2 44 80 -0.183 -3.071 -14.031 -14.243 -15.135 -2.514 -1.721 -3.019 1.765 D 64 62 3 65 5 0 0 42 78 -8.310 -0.023 -12.090 -13.521 -6.320 IR 65 65 3 65 5 1 1 44 79 -3.221 -0.170 -14.518 -12.686 -8.144 0.000 0.000 0.000 0.000 [ MATP 17 ] 13 51 u a - - MP 66 65 3 70 6 2 2 42 78 -15.981 -15.921 -0.003 -9.779 -14.977 -10.711 -6.171 -8.990 -4.444 1.666 -8.588 -9.947 1.293 -9.098 -5.807 0.535 -2.404 1.110 2.588 -9.253 -1.398 -3.301 ML 67 65 3 70 6 1 1 41 77 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 68 65 3 70 6 1 1 40 76 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 69 65 3 70 6 0 0 34 70 -13.008 -11.707 -7.504 -8.186 -8.203 -0.019 IL 70 70 5 70 6 1 1 42 77 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 71 71 6 71 5 1 1 42 77 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 18 ] 14 50 C G - - MP 72 71 6 76 6 2 2 40 76 -15.979 -15.918 -0.427 -7.226 -14.975 -2.004 -10.274 -4.213 -10.275 0.572 -6.350 -11.119 3.209 -9.795 -10.133 0.360 -10.647 -1.672 1.251 -5.456 0.220 -5.084 ML 73 71 6 76 6 1 1 40 76 -7.692 -8.038 -2.752 -0.295 -7.888 -5.417 -1.022 1.354 -1.809 -0.586 MR 74 71 6 76 6 1 1 38 74 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 75 71 6 76 6 0 0 33 69 -13.110 -11.809 -7.606 -8.288 -8.305 -0.017 IL 76 76 5 76 6 1 1 40 76 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 77 77 6 77 5 1 1 40 76 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 19 ] 15 49 u a - - MP 78 77 6 82 4 2 2 39 75 -1.091 -2.564 -1.469 -13.394 -7.725 -7.863 -3.271 1.909 -2.653 -8.747 1.878 -8.093 -4.931 0.468 -3.062 0.229 2.237 -8.043 -0.436 -2.963 ML 79 77 6 82 4 1 1 39 75 -0.140 -7.260 -3.826 -5.989 -0.511 -0.864 -0.763 1.111 MR 80 77 6 82 4 1 1 34 69 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 81 77 6 82 4 0 0 33 68 -8.755 -2.525 -0.282 -9.420 IL 82 82 5 82 4 1 1 38 74 -1.392 -0.694 -10.709 -14.446 0.000 0.000 0.000 0.000 IR 83 83 6 83 3 1 1 36 72 -0.746 -1.308 -13.892 0.000 0.000 0.000 0.000 [ MATL 20 ] 26 - g - - - ML 84 83 6 86 3 1 1 12 30 -16.124 -0.000 -14.778 0.381 -1.944 0.734 -0.369 D 85 83 6 86 3 0 0 16 35 -6.174 -1.687 -0.566 IL 86 86 3 86 3 1 1 20 39 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 21 ] 27 - a - - - ML 87 86 3 89 3 1 1 10 29 -16.124 -0.000 -14.778 0.418 0.050 0.124 -0.892 D 88 86 3 89 3 0 0 15 34 -6.174 -1.687 -0.566 IL 89 89 3 89 3 1 1 19 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 22 ] 28 - A - - - ML 90 89 3 92 3 1 1 9 27 -16.124 -0.281 -2.500 1.359 -1.350 -1.772 -0.415 D 91 89 3 92 3 0 0 14 32 -6.174 -1.687 -0.566 IL 92 92 3 92 3 1 1 18 37 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 23 ] 29 - a - - - ML 93 92 3 95 3 1 1 8 26 -15.844 -0.563 -1.631 0.972 -1.667 -1.269 0.388 D 94 92 3 95 3 0 0 7 26 -15.046 -10.559 -0.001 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 24 ] 30 - A - - - ML 96 95 3 98 2 1 1 1 1 * 0.000 1.411 -2.382 -1.821 -0.208 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 25 ] - - - - - - E 99 98 3 -1 0 0 0 0 0 // HMMER3/f [3.4 | Aug 2023] NAME L31-Firmicutes ACC RF03156 DESC L31-Firmicutes ribosomal protein leader LENG 32 MAXL 75 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Sat Jul 13 16:54:47 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/RF03156/CM NSEQ 1083 EFFN 365.039062 CKSUM 3760353181 STATS LOCAL MSV -6.8877 0.73578 STATS LOCAL VITERBI -7.9286 0.73578 STATS LOCAL FORWARD -2.8902 0.73578 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.25921 1.68282 1.11228 1.60213 1.38629 1.38629 1.38629 1.38629 0.00018 9.29210 9.29210 1.46634 0.26236 0.00000 * 1 7.81890 0.04116 7.76911 3.23139 1 C - - < 1.38629 1.38629 1.38629 1.38629 0.00018 9.29210 9.29210 1.46634 0.26236 1.09861 0.40547 2 7.81306 3.54506 7.76385 0.03015 2 U - - < 1.38629 1.38629 1.38629 1.38629 0.00018 9.29210 9.29210 1.46634 0.26236 1.09861 0.40547 3 1.51967 0.39893 4.05758 2.37633 3 C - - < 1.38629 1.38629 1.38629 1.38629 0.00018 9.29210 9.29210 1.46634 0.26236 1.09861 0.40547 4 4.17208 3.56838 7.75554 0.04505 4 U - - < 1.38629 1.38629 1.38629 1.38629 0.00106 9.29210 6.94549 1.46634 0.26236 1.09861 0.40547 5 2.75375 4.53872 0.13244 3.00230 5 G - - < 1.38629 1.38629 1.38629 1.38629 0.63598 9.29123 0.75398 1.46634 0.26236 2.52173 0.08373 6 2.27441 2.99544 2.09470 0.32293 6 U - - - 1.38629 1.38629 1.38629 1.38629 2.27586 0.10857 8.65560 0.10124 2.34042 0.01223 4.40958 7 1.59848 1.85399 1.43622 0.90792 13 u - - < 1.38629 1.38629 1.38629 1.38629 0.00280 9.28654 5.91395 1.46634 0.26236 4.14587 0.01596 8 2.32950 0.55429 2.28672 1.48467 14 C - - < 1.38629 1.38629 1.38629 1.38629 0.29355 9.28393 1.36926 1.46634 0.26236 2.51649 0.08419 9 1.42461 1.42914 1.76398 1.05405 15 u - - < 1.38629 1.38629 1.38629 1.38629 0.66661 0.72066 8.99143 0.48213 0.96093 0.00071 7.25173 10 1.12378 2.70763 0.88355 1.63503 26 g - - _ 1.38629 1.38629 1.38629 1.38629 0.00018 9.29210 9.29210 1.46634 0.26236 1.09861 0.40547 11 1.09775 1.35601 1.30541 1.98317 27 a - - _ 1.38629 1.38629 1.38629 1.38629 0.00018 9.29210 9.29210 1.46634 0.26236 1.09861 0.40547 12 0.44990 2.31130 2.59721 1.66761 28 A - - _ 1.38629 1.38629 1.38629 1.38629 0.19491 9.29211 1.73160 1.46634 0.26236 1.09861 0.40547 13 0.71913 2.51528 2.25096 1.11876 29 a - - _ 1.38629 1.38629 1.38629 1.38629 0.27546 9.09742 1.42436 1.46634 0.26236 0.53211 0.88519 14 0.41576 2.98309 2.62212 1.52842 30 A - - _ 1.38629 1.38629 1.38629 1.38629 1.04311 0.59163 2.36212 1.00425 0.45621 0.78377 0.61006 15 1.18976 2.39151 1.23647 1.15898 49 u - - > 1.38629 1.38629 1.38629 1.38629 0.00311 9.04906 5.81288 1.46634 0.26236 0.03390 3.40137 16 1.88656 2.44867 0.43649 2.15678 50 G - - > 1.38629 1.38629 1.38629 1.38629 0.00019 9.28279 9.28279 1.46634 0.26236 0.91700 0.51035 17 0.98218 2.37207 1.63396 1.08748 51 a - - > 1.38629 1.38629 1.38629 1.38629 2.70627 0.72567 0.80026 0.11208 2.24402 4.14587 0.01596 18 3.10754 2.57400 3.46343 0.16519 58 U - - - 1.38629 1.38629 1.38629 1.38629 0.01036 8.69031 4.59144 1.46634 0.26236 0.00912 4.70216 19 3.36552 0.12222 7.01653 2.53068 59 C - - > 1.38629 1.38629 1.38629 1.38629 0.00019 9.28268 9.28268 1.46634 0.26236 0.01926 3.95922 20 0.02993 7.89219 3.55395 7.59468 60 A - - > 1.38629 1.38629 1.38629 1.38629 0.00018 9.29210 9.29210 1.46634 0.26236 1.09861 0.40547 21 2.69337 4.07825 0.38379 1.45187 61 G - - > 1.38629 1.38629 1.38629 1.38629 0.00018 9.29210 9.29210 1.46634 0.26236 1.09861 0.40547 22 6.64990 7.91393 0.00215 7.61821 62 G - - > 1.38629 1.38629 1.38629 1.38629 0.00018 9.29210 9.29210 1.46634 0.26236 1.09861 0.40547 23 6.65825 7.93534 0.00212 7.64149 63 G - - > 1.38629 1.38629 1.38629 1.38629 0.00071 7.38545 9.29210 0.27454 1.42678 1.09861 0.40547 24 4.00209 0.01955 7.87466 7.25424 65 C - - : 1.38629 1.38629 1.38629 1.38629 0.37518 2.09385 1.66272 0.02059 3.89308 1.09861 0.40547 25 1.46706 3.36592 0.35431 3.40491 68 G - - : 1.38629 1.38629 1.38629 1.38629 0.00092 9.08196 7.11934 1.46634 0.26236 0.00097 6.93720 26 0.83086 4.27413 0.63836 3.80567 69 G - - : 1.38629 1.38629 1.38629 1.38629 0.00127 9.29154 6.74217 1.46634 0.26236 2.21025 0.11617 27 0.05327 8.28134 2.97004 8.03524 70 A - - : 1.38629 1.38629 1.38629 1.38629 0.00018 9.29045 9.29045 1.46634 0.26236 3.04056 0.04899 28 0.03308 4.57657 3.83142 7.47300 71 A - - : 1.38629 1.38629 1.38629 1.38629 0.00018 9.29045 9.29045 1.46634 0.26236 0.10050 2.34741 29 1.81718 7.35465 0.19555 4.23403 72 G - - : 1.38629 1.38629 1.38629 1.38629 0.00018 9.29210 9.29210 1.46634 0.26236 1.09861 0.40547 30 7.68848 8.91421 0.00086 8.21263 73 G - - : 1.38629 1.38629 1.38629 1.38629 0.00018 9.29210 9.29210 1.46634 0.26236 1.09861 0.40547 31 0.02405 8.50681 3.76051 8.14620 74 A - - : 1.38629 1.38629 1.38629 1.38629 0.00018 9.29210 9.29210 1.46634 0.26236 1.09861 0.40547 32 3.44914 8.23054 0.05755 3.73462 75 G - - : 1.38629 1.38629 1.38629 1.38629 0.00009 9.29201 * 1.46634 0.26236 0.00000 * //