INFERNAL1/a [1.1 | October 2013] NAME T-loop DESC T-loop STATES 55 NODES 13 CLEN 17 W 59 ALPH RNA RF no CONS yes MAP yes DATE Tue Jul 1 13:30:59 2014 COM [1] /share/data/bin/cmbuild -F /share/data/people/ppg15/motifs/T-loop/CM /share/data/people/ppg15/motifs/T-loop/SEED COM [2] /share/data/bin/cmcalibrate --mpi --seed 1 /share/data/people/ppg15/motifs/T-loop/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 90 EFFN 90.000000 CKSUM 112567387 NULL 0.000 0.000 0.000 0.000 GA 9.20 EFP7GF -0.5175 1.04830 ECMLC 0.77565 -0.71069 6.46578 1600000 313799 0.003824 ECMGC 0.95659 1.13417 7.77599 1600000 229806 0.001741 ECMLI 0.83068 0.58716 7.06294 1600000 260243 0.004611 ECMGI 0.99399 1.90243 8.18387 1600000 205900 0.001943 CM [ ROOT 0 ] - - - - - - S 0 -1 0 1 6 1 1 59 104 -12.506 -12.445 -0.368 -11.222 -11.501 -2.159 IL 1 1 2 1 6 1 1 61 106 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 IR 2 2 3 2 5 1 1 60 106 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 1 ] 7 44 c g - - MP 3 2 3 7 6 2 4 59 105 -2.663 -12.080 -0.285 -10.856 -5.618 -11.531 -6.481 -6.017 -6.463 0.346 -5.489 -7.283 2.583 -6.090 -6.379 1.889 -6.869 0.511 1.737 -6.610 -2.941 -5.087 ML 4 2 3 7 6 1 1 56 102 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 5 2 3 7 6 1 1 58 103 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 6 2 3 7 6 0 0 56 101 -14.404 -13.102 -0.616 -9.582 -9.599 -1.536 IL 7 7 5 7 6 1 2 60 105 -1.815 -0.704 -3.374 -8.735 -9.511 -9.171 0.000 0.000 0.000 0.000 IR 8 8 6 8 5 1 1 58 103 -1.732 -0.536 -9.391 -7.559 -8.665 0.000 0.000 0.000 0.000 [ MATP 2 ] 10 41 c g - - MP 9 8 6 13 6 2 3 57 102 -2.679 -4.753 -0.438 -3.885 -11.365 -11.760 -6.698 -6.364 -6.694 -0.167 0.092 -7.529 2.241 -6.242 -6.568 2.229 -7.076 -1.919 2.050 -6.867 -3.062 -5.287 ML 10 8 6 13 6 1 1 53 98 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 11 8 6 13 6 1 1 58 103 -0.608 -7.245 -3.154 -7.223 -2.357 -5.437 -1.335 1.493 -2.141 -0.833 D 12 8 6 13 6 0 0 51 96 -12.889 -11.587 -1.093 -8.066 -8.084 -0.934 IL 13 13 5 13 6 1 1 58 103 -2.330 -1.473 -1.198 -8.915 -9.692 -9.352 0.000 0.000 0.000 0.000 IR 14 14 6 14 5 1 1 58 103 -0.660 -1.465 -10.274 -8.441 -9.547 0.000 0.000 0.000 0.000 [ MATP 3 ] 13 36 g c - - MP 15 14 6 19 6 2 2 52 97 -3.497 -12.295 -0.136 -11.072 -11.352 -11.747 -6.500 -5.492 -6.393 1.324 -1.853 -7.078 1.783 -6.536 -6.586 2.858 -6.955 -1.326 0.909 -6.363 -2.925 -5.208 ML 16 14 6 19 6 1 1 51 96 -9.509 -9.855 -0.093 -4.264 -9.705 -7.235 -3.398 -3.101 -4.184 1.901 MR 17 14 6 19 6 1 1 49 94 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 18 14 6 19 6 0 0 50 95 -11.992 -10.690 -0.328 -7.169 -7.187 -2.407 IL 19 19 5 19 6 1 1 52 97 -1.845 -6.496 -0.510 -8.151 -8.927 -8.587 0.000 0.000 0.000 0.000 IR 20 20 6 20 5 1 1 51 96 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 4 ] 16 35 g c - - MP 21 20 6 25 6 2 2 50 95 -2.770 -12.440 -0.231 -11.216 -11.496 -11.891 -6.639 -5.854 -6.577 0.102 -1.972 -7.312 2.168 -2.680 -6.662 2.750 -7.085 0.863 -0.160 -6.611 -1.041 -5.337 ML 22 20 6 25 6 1 1 43 88 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094 MR 23 20 6 25 6 1 1 42 87 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094 D 24 20 6 25 6 0 0 36 81 -9.770 -8.469 -1.166 -4.948 -4.965 -1.041 IL 25 25 5 25 6 1 1 53 98 -0.594 -1.632 -6.321 -10.059 -10.835 -10.495 0.000 0.000 0.000 0.000 IR 26 26 6 26 5 1 1 41 78 -0.727 -1.353 -10.575 -8.743 -9.849 0.000 0.000 0.000 0.000 [ MATP 5 ] 21 31 g c - - MP 27 26 6 31 4 2 2 20 38 -4.423 -12.693 -0.545 -1.901 -6.645 -5.562 -6.522 0.963 -6.538 -7.190 2.318 -6.744 -6.756 2.679 -7.103 0.057 0.085 -6.470 -1.190 -5.359 ML 28 26 6 31 4 1 1 19 38 -2.408 -4.532 -1.293 -1.473 0.368 -0.385 -0.191 0.094 MR 29 26 6 31 4 1 1 19 37 -4.102 -12.528 -0.390 -2.485 0.368 -0.385 -0.191 0.094 D 30 26 6 31 4 0 0 17 36 -12.737 -14.007 -2.036 -0.404 IL 31 31 5 31 4 1 1 19 37 -5.106 -6.609 -0.790 -1.387 0.000 0.000 0.000 0.000 IR 32 32 6 32 3 1 1 20 38 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 [ MATR 6 ] - 30 - a - - MR 33 32 6 35 5 1 1 18 36 -11.020 -0.469 -1.855 -11.048 -11.940 0.767 -0.101 -0.636 -0.468 D 34 32 6 35 5 0 0 17 36 -10.319 -0.714 -1.388 -9.377 -7.371 IR 35 35 3 35 5 1 1 19 38 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 [ MATP 7 ] 23 29 u a - - MP 36 35 3 40 4 2 2 17 35 -11.111 -11.318 -0.003 -9.732 -0.904 -1.841 0.896 -0.738 0.833 -4.439 0.825 -3.939 1.322 -0.730 -0.883 -1.141 1.593 -0.474 -0.273 -1.332 ML 37 35 3 40 4 1 1 17 36 -8.740 -8.923 -0.014 -7.652 0.790 -2.237 0.205 -0.142 MR 38 35 3 40 4 1 1 20 39 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094 D 39 35 3 40 4 0 0 19 38 -4.568 -4.250 -2.265 -0.520 IL 40 40 5 40 4 1 1 22 41 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 IR 41 41 6 41 3 1 1 21 39 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 8 ] 24 - U - - - ML 42 41 6 44 3 1 1 13 31 -12.563 -0.001 -11.217 -2.476 -3.647 -1.368 1.745 D 43 41 6 44 3 0 0 16 34 -6.174 -1.687 -0.566 IL 44 44 3 44 3 1 1 20 38 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 9 ] 25 - a - - - ML 45 44 3 47 3 1 1 11 30 -2.421 -0.299 -11.217 0.496 -0.415 0.163 -0.473 D 46 44 3 47 3 0 0 13 31 -6.174 -1.687 -0.566 IL 47 47 3 47 3 1 1 11 29 -4.964 -0.054 -7.665 0.000 0.000 0.000 0.000 [ MATL 10 ] 27 - A - - - ML 48 47 3 50 3 1 1 10 28 -12.563 -0.001 -11.217 1.181 -0.942 -0.267 -1.390 D 49 47 3 50 3 0 0 13 32 -6.174 -1.687 -0.566 IL 50 50 3 50 3 1 1 18 36 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 [ MATL 11 ] 28 - a - - - ML 51 50 3 53 2 1 1 1 1 * 0.000 0.519 -0.036 -1.061 0.154 D 52 50 3 53 2 0 0 0 0 * 0.000 IL 53 53 3 53 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000 [ END 12 ] - - - - - - E 54 53 3 -1 0 0 0 0 0 // HMMER3/f [i1.1 | October 2013] NAME T-loop DESC T-loop LENG 17 MAXL 66 ALPH RNA RF no MM no CONS yes CS yes MAP yes DATE Tue Jul 1 13:30:59 2014 COM [1] /share/data/bin/cmbuild -F /share/data/people/ppg15/motifs/T-loop/CM /share/data/people/ppg15/motifs/T-loop/SEED NSEQ 90 EFFN 83.213196 CKSUM 112567387 STATS LOCAL MSV -9.1079 1.04830 STATS LOCAL VITERBI -10.7993 1.04830 STATS LOCAL FORWARD -1.5853 1.04830 HMM A C G U m->m m->i m->d i->m i->i d->m d->d COMPO 1.47513 1.34618 1.26604 1.47372 1.38629 1.38629 1.38629 1.38629 2.57966 0.08294 5.57539 1.16451 0.37407 0.00000 * 1 2.49290 0.97657 1.13668 1.51482 7 c - - < 1.38629 1.38629 1.38629 1.38629 0.18870 1.76878 6.55728 0.35381 1.21069 1.09861 0.40547 2 2.83220 1.01426 1.17247 1.31362 10 c - - < 1.38629 1.38629 1.38629 1.38629 0.18029 1.80916 6.74455 0.25561 1.48919 1.09861 0.40547 3 1.89237 1.51386 0.80311 1.70764 13 g - - < 1.38629 1.38629 1.38629 1.38629 0.09411 2.42260 6.78619 0.35558 1.20652 1.09861 0.40547 4 2.63666 1.18473 0.63138 2.40007 16 G - - < 1.38629 1.38629 1.38629 1.38629 0.17043 1.86039 6.82270 1.12066 0.39462 1.09861 0.40547 5 2.07336 1.16564 0.76556 2.32850 21 g - - < 1.38629 1.38629 1.38629 1.38629 0.04947 3.05373 6.82655 0.04536 3.11579 1.09861 0.40547 6 1.29380 1.73814 1.32721 1.25629 23 u - - < 1.38629 1.38629 1.38629 1.38629 0.00217 6.82655 6.82655 1.46634 0.26236 1.09861 0.40547 7 3.09688 3.89222 2.33706 0.17698 24 U - - _ 1.38629 1.38629 1.38629 1.38629 0.00217 6.82655 6.82655 1.46634 0.26236 1.09861 0.40547 8 1.04358 1.67416 1.27550 1.70896 25 a - - _ 1.38629 1.38629 1.38629 1.38629 0.20832 1.67684 6.82655 0.01156 4.46580 1.09861 0.40547 9 0.57005 2.03723 1.57224 2.33786 27 A - - _ 1.38629 1.38629 1.38629 1.38629 0.00217 6.82655 6.82655 1.46634 0.26236 1.09861 0.40547 10 1.02780 1.41273 2.11781 1.27858 28 a - - _ 1.38629 1.38629 1.38629 1.38629 0.37313 6.82655 1.17009 1.46634 0.26236 1.09861 0.40547 11 0.72412 2.25566 1.16386 2.32109 29 a - - > 1.38629 1.38629 1.38629 1.38629 0.29439 6.45656 1.37261 1.46634 0.26236 0.45182 1.01189 12 0.85738 1.45839 1.82581 1.70358 30 a - - - 1.38629 1.38629 1.38629 1.38629 0.00304 6.49049 6.49049 1.46634 0.26236 0.00754 4.89094 13 2.65976 0.91212 1.08293 1.66200 31 c - - > 1.38629 1.38629 1.38629 1.38629 0.17043 1.86039 6.82270 0.97431 0.47394 1.09861 0.40547 14 2.58762 0.86650 1.16561 1.64687 35 c - - > 1.38629 1.38629 1.38629 1.38629 0.07199 6.78619 2.68337 1.46634 0.26236 1.09861 0.40547 15 1.98535 0.79158 1.49266 1.68866 36 c - - > 1.38629 1.38629 1.38629 1.38629 0.14378 2.02000 6.67191 1.06874 0.42074 0.03252 3.44219 16 1.13353 1.20089 1.20337 2.56399 41 a - - > 1.38629 1.38629 1.38629 1.38629 0.16907 1.86994 6.55728 0.38516 1.14051 1.09861 0.40547 17 1.55337 1.45623 0.95767 1.76278 44 g - - > 1.38629 1.38629 1.38629 1.38629 3.09645 0.04626 * 1.54864 0.23894 0.00000 * //