# List of top-scoring protein chains for T0413.t2k-w0.5 hidden Markov model. # HMM and HMM E-value scores computed by SAM (c) 1992-2001 Regents of the University of California, Santa Cruz # Sequence Alignment and Modeling Software System # http://www.soe.ucsc.edu/research/compbio/sam.html # ----------------- Citations (SAM, SAM-T99, HMMs) -------------------- # R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: # Extension and analysis of the basic method, CABIOS 12:95-107, 1996. # K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting # remote protein homologies, Bioinformatics 14(10):846-856, 1998. # A. Krogh et al., Hidden Markov models in computational biology: # Applications to protein modeling, JMB 235:1501-1531, Feb 1994. # # FSSP representative for each protein chain taken from FSSP: # ------------------Citations (FSSP) ----------------------------------- # L. Holm and C. Sander (1996) Mapping the protein universe. Science 273:595-602. # #SCOP domains found in each protein chain taken from SCOP: # ------------------Citations (SCOP) ----------------------------------- #Murzin A. G., Brenner S. E., Hubbard T., Chothia C. (1995). #SCOP: a structural classification of proteins database for the investigation of sequences and structures. #J. Mol. Biol. 247, 536-540. Sequence_ID Length Target_Evalue FSSP-rep SCOP_domain SCOP_suid 5S 5N 12S 6S 12S 10N 1hlgA 371 1.01e-17 1hlgA c.69.1.6 34656 1k4yA 534 1.28e-17 c.69.1.1 72069 2ecfA 741 2.37e-16 1k8qA 377 2.62e-16 c.69.1.6 72177 1qe3A 489 4.51e-16 2bce c.69.1.1 34630 1c7jA 489 4.60e-16 2bce c.69.1.1 34631 2bceA 579 4.92e-16 c.69.1.1 34625 1c7iA 489 5.32e-16 1thg c.69.1.1 34632 1aqlA 532 6.55e-16 2bce c.69.1.1 34627 1aknA 579 6.68e-16 c.69.1.1 34626 2hrrA 532 7.54e-16 c.69.1.1 136696 2h7cA 542 7.66e-16 c.69.1.1 136207 1mx1A 548 7.79e-16 c.69.1.1 85165 2pm8A 574 1.19e-15 2ogtA 498 1.29e-15 2ogsA 498 1.30e-15 1jmyA 522 3.16e-15 c.69.1.1 63182 1p0iA 529 3.92e-15 c.69.1.1 93867 2j4cA 529 4.01e-15 1f6wA 533 4.26e-15 2bce c.69.1.1 34629 1w6rA 543 7.89e-15 c.69.1.1 114283 1ut6A 537 8.57e-15 c.69.1.1 119698 1gqrA 532 8.59e-15 c.69.1.1 70374 1ea5A 537 8.59e-15 2bce c.69.1.1 34592 2dfpA 534 8.61e-15 2bce c.69.1.1 34597 2cekA 535 8.63e-15 c.69.1.1 130347 1eeaA 534 8.63e-15 2bce c.69.1.1 34609 2qzpA 562 9.73e-15 2hu5A 582 1.21e-14 b.69.7.2,c.69.1.33 136763,136764 3be8A 588 2.58e-14 2vh8A 562 2.87e-14 2c58A 537 3.32e-14 c.69.1.1 129891 2fj0A 551 3.71e-14 2d5lA 706 4.80e-14 1b41A 539 5.08e-14 2bce c.69.1.1 34621 1f8uA 583 6.00e-14 2bce c.69.1.1 34620 1n5mA 541 6.37e-14 c.69.1.1 80031 1c2oA 539 6.37e-14 2bce c.69.1.1 34610 1c2bA 540 6.37e-14 2bce c.69.1.1 34614 2ha2A 543 6.38e-14 c.69.1.1 136274 1ku6A 549 6.39e-14 c.69.1.1 91037 1maaA 547 6.40e-14 2bce c.69.1.1 34615 2c0pA 548 6.40e-14 c.69.1.1 129600 2z3zA 706 6.41e-14 1q84A 580 6.51e-14 c.69.1.1 96156 3bixA 574 8.43e-14 3b3qA 577 8.56e-14 3bwxA 285 1.04e-13 2hu8A 582 1.16e-13 b.69.7.2,c.69.1.33 136772,136773 1zoiA 276 1.83e-13 3bl8A 580 1.98e-13 1va4A 279 2.15e-13 c.69.1.12 108458 2jf0A 548 2.46e-13 1thgA 544 2.89e-13 c.69.1.17 34763 2dcmA 706 4.65e-13 2og1A 286 5.43e-13 2ha5A 543 6.32e-13 1a8sA 273 6.69e-13 c.69.1.12 34710 1a88A 275 6.83e-13 1brt c.69.1.12 34707 1c4xA 285 1.52e-12 1c4xA c.69.1.10 34684 2cjpA 328 1.67e-12 1hkhA 279 2.21e-12 c.69.1.12 90628 1jjfA 268 3.19e-12 c.69.1.2 66765 1gz7A 534 4.29e-12 c.69.1.17 83401 2pujA 286 5.22e-12 2puhA 286 5.60e-12 2rhwA 283 5.75e-12 2uz0A 263 6.41e-12 1cleA 534 6.76e-12 1thg c.69.1.17 34771 1llfA 534 6.87e-12 c.69.1.17 78094 1lppA 549 1.10e-11 c.69.1.17 34764 1crlA 534 1.10e-11 c.69.1.17 34765 1dx4A 585 1.48e-11 2bce c.69.1.1 34622 1evqA 310 2.00e-11 1jkmA c.69.1.2 34635 1u4nA 310 2.05e-11 c.69.1.2 113021 1a8qA 274 2.16e-11 c.69.1.12 34702 1xroA 293 2.28e-11 1mtzA 293 2.37e-11 c.69.1.7 79467 1xrlA 293 2.38e-11 1xrrA 293 2.85e-11 1z68A 719 3.29e-11 1auoA 218 3.29e-11 1auoA c.69.1.14 34716 1orvA 728 3.80e-11 b.70.3.1,c.69.1.24 87354,87355 2hm7A 310 4.32e-11 1ehyA 294 4.33e-11 1ehyA c.69.1.11 34693 2r11A 306 4.44e-11 1xqvA 293 4.68e-11 1a8uA 277 4.89e-11 1brt c.69.1.12 34703 1broA 277 5.53e-11 1brt c.69.1.12 34700 1jt2A 268 5.55e-11 c.69.1.2 71858 1u2eA 289 6.39e-11 1pv1A 299 6.42e-11 c.69.1.34 111639 3bdiA 207 8.00e-11 3c45A 728 9.41e-11 2g63A 726 9.42e-11 b.70.3.1,c.69.1.24 134686,134687 1tk3A 728 9.43e-11 b.70.3.1,c.69.1.24 107069,107070 2oncA 731 9.44e-11 2ripA 729 9.46e-11 1pfqA 731 9.53e-11 b.70.3.1,c.69.1.24 88061,88062 2rguA 734 9.56e-11 2bgrA 738 9.70e-11 b.70.3.1,c.69.1.24 128496,128497 1wcyA 740 9.74e-11 b.70.3.1,c.69.1.24 120903,120904 1r9mA 733 9.92e-11 b.70.3.1,c.69.1.24 104870,104871 1jjiA 311 1.02e-10 c.69.1.2 66766 2gbcA 730 1.03e-10 1r9nA 739 1.04e-10 b.70.3.1,c.69.1.24 118745,118746 1r3dA 264 1.11e-10 c.69.1.35 111680 2h1iA 226 1.24e-10 2qt9A 766 1.42e-10 1y37A 304 1.60e-10 1ukcA 522 1.61e-10 c.69.1.17 107911 1xqwA 293 2.38e-10 1lzlA 323 2.43e-10 c.69.1.2 78306 2d0dA 282 2.58e-10 1u8eA 728 3.12e-10 b.70.3.1,c.69.1.24 107733,107734 1brtA 277 3.21e-10 c.69.1.12 34699 2zjfA 362 3.34e-10 2e3jA 356 3.57e-10 2c7bA 311 3.69e-10 3c5vA 316 4.18e-10 1j1iA 296 4.21e-10 c.69.1.10 83977 2ockA 254 4.45e-10 2o7rA 338 6.58e-10 1zd3A 555 8.78e-10 c.108.1.2,c.69.1.11 124930,124931 2r8bA 251 9.99e-10 2ocgA 254 1.00e-09 1womA 271 1.02e-09 2qm0A 275 1.05e-09 1q0rA 298 1.76e-09 c.69.1.28 95508 1uk8A 282 2.43e-09 c.69.1.10 107907 2i3dA 249 3.04e-09 2vf2A 311 4.23e-09 3c5wP 310 5.83e-09 1ufoA 238 6.01e-09 c.69.1.27 99344 1fj2A 232 6.25e-09 1auoA c.69.1.14 34720 1wm1A 317 9.56e-09 c.69.1.7 109405 1bn7A 294 9.61e-09 1bn6A c.69.1.8 34677 1cqwA 295 9.86e-09 1b6g c.69.1.8 34679 2oclA 254 1.20e-08 1r1dA 247 1.47e-08 c.69.1.29 96813 1tqhA 247 1.58e-08 c.69.1.29 107225 1m33A 258 1.62e-08 c.69.1.26 78514 1vlqA 337 1.63e-08 c.69.1.25 108848 3bf7A 255 1.67e-08 3bf8A 255 1.99e-08 1jfrA 262 2.15e-08 1jfrA c.69.1.16 34724 1cr6A 554 2.52e-08 1cr6B c.69.1.11,c.108.1.2 34687,43337 2bklA 695 5.04e-08 2pshA 319 1.08e-07 2psdA 318 1.11e-07 2psjA 319 1.13e-07 2psfA 310 1.16e-07 1l7aA 318 1.25e-07 c.69.1.25 77772 2pblA 262 1.31e-07 1jkmA 361 1.44e-07 1jkmA c.69.1.2 34633 1hdeA 310 1.86e-07 1b6g c.69.1.8 34675 1bezA 310 1.91e-07 c.69.1.8 34666 1b6gA 310 1.93e-07 c.69.1.8 34661 2yxpX 310 1.93e-07 1azwA 313 2.52e-07 1qtrA c.69.1.7 34658 1odsA 318 3.96e-07 c.69.1.25 86877 2yysA 286 4.21e-07 3b5eA 223 5.12e-07 2gzsA 278 6.46e-07 3bdvA 191 1.55e-06 2fukA 220 2.66e-06 1odtC 318 2.87e-06 c.69.1.25 86885 2jbwA 386 2.88e-06 3bjrA 283 3.58e-06 1gkkA 297 4.07e-06 c.69.1.2 65248 2d80A 318 4.40e-06 2o2gA 223 9.25e-06 1imjA 210 1.89e-05 c.69.1.23 71246 3bxpA 277 2.12e-05 1zixA 236 2.42e-05 2rauA 354 2.55e-05 1zi8A 236 3.03e-05 1zi9A 236 3.14e-05 1wb4A 297 3.85e-05 c.69.1.2 120827 1zi6A 236 4.20e-05 1ivyA 452 5.25e-05 1ivyA c.69.1.5 34654 1zicA 236 7.08e-05 1qgeD 222 7.59e-05 1cvl c.69.1.18 34773 2d81A 318 7.70e-05 1ys1X 320 7.92e-05 1cvlA 319 9.79e-05 c.69.1.18 34786 1tahA 318 9.98e-05 1cvl c.69.1.18 34775 2hdwA 367 1.18e-04 1zj5A 236 1.71e-04 1zj4A 236 1.77e-04 1mnaA 298 1.94e-04 c.69.1.22 79322 2h7xA 319 1.97e-04 c.69.1.22 136227 1xklA 273 2.25e-04 c.69.1.20 115410 1y7iA 268 2.28e-04 c.69.1.20 116546 2fx5A 258 2.31e-04 1ziyA 236 2.39e-04 4lipD 320 2.42e-04 1cvl c.69.1.18 34783 1ggvA 232 2.52e-04 1din c.69.1.9 34683 1dinA 236 2.80e-04 c.69.1.9 34682 1dqyA 283 3.15e-04 1dqyA c.69.1.3 34640 1dqzA 280 3.19e-04 1dqyA c.69.1.3 34638 1va5A 303 5.12e-04 c.69.1.3 108464 1r88A 280 5.96e-04 c.69.1.3 97219 1wpxA 421 6.05e-04 c.69.1.5 121156 1ycdA 243 6.66e-04 1xfdA 723 7.40e-04 b.70.3.1,c.69.1.24 115251,115252 1yr2A 741 9.31e-04 1cpyA 421 1.38e-03 c.69.1.5 34651 2qubA 615 2.16e-03 2qmqA 286 2.20e-03 3c8dA 403 2.32e-03 2qruA 274 2.61e-03 1sfrA 304 2.76e-03 c.69.1.3 105500 2oxeA 466 3.21e-03 2pvsA 452 4.20e-03 1t2nA 181 4.22e-03 c.69.1.18 112226 2hfkA 319 4.24e-03 1t4mA 181 4.61e-03 c.69.1.18 112243 1ispA 181 4.95e-03 c.69.1.18 76778 2qxuA 179 5.37e-03 1w52X 452 7.88e-03 1mo2A 294 9.52e-03 c.69.1.22 79331 1kezA 300 9.54e-03 c.69.1.22 68546 1pjaA 302 9.56e-03 c.69.1.13 94758 1f0nA 285 1.07e-02 1dqyA c.69.1.3 34636 1vkhA 273 1.14e-02 c.69.1.32 108662 1rp1A 450 1.25e-02 b.12.1.2,c.69.1.19 23646,34794 1gplA 432 1.26e-02 b.12.1.2,c.69.1.19 23645,34793 2o2iA 300 1.28e-02 2qvbA 297 1.29e-02 2qs9A 194 1.74e-02 1lpbB 449 1.82e-02 1gpl b.12.1.2,c.69.1.19 23643,34791 2pl5A 366 2.23e-02 1g42A 296 3.49e-02 c.69.1.8 65139 1iz7A 295 3.49e-02 c.69.1.8 76982 1cv2A 296 3.51e-02 1bn6A c.69.1.8 34680 1ryyA 652 3.54e-02 b.18.1.13,c.69.1.21 118821,118822 1mj5A 302 3.62e-02 c.69.1.8 91285 1bu8A 452 5.57e-02 1gpl b.12.1.2,c.69.1.19 23647,34795 2qjwA 176 6.39e-02 2z8zA 617 6.79e-02 1ex9A 285 7.08e-02 1cvl c.69.1.18 34785 2b9vA 652 8.05e-02 b.18.1.13,c.69.1.21 128199,128200 2z8xA 617 8.66e-02 2q0xA 335 8.91e-02 1sckA 257 9.70e-02 c.69.1.20 105421 1yb6A 256 1.29e-01 c.69.1.20 122870 1qj4A 257 1.30e-01 1qj4A c.69.1.20 34796 1whsA 255 1.38e-01 1ivyA c.69.1.5 34649 1gxsA 270 1.45e-01 c.69.1.5 76375 1whtA 256 1.46e-01 1ivyA c.69.1.5 34646 1mpxA 615 1.58e-01 b.18.1.13,c.69.1.21 85041,85042 1bcsA 263 1.66e-01 1ivyA c.69.1.5 34647 3sc2A 259 2.18e-01 1ivyA c.69.1.5 34648 2pplA 485 2.77e-01 2b61A 377 3.34e-01 1dwqA 262 3.79e-01 1qj4A c.69.1.20 34808 1tibA 269 4.02e-01 c.69.1.17 34738 3tglA 269 4.26e-01 c.69.1.17 34733 1tglA 269 5.73e-01 c.69.1.17 34734 4tglA 269 5.74e-01 c.69.1.17 34735 5tglA 269 5.89e-01 c.69.1.17 34736 1uw7A 143 6.10e-01 b.140.1.1 100099 1qz8A 113 9.68e-01 b.140.1.1 96619 1tiaA 279 1.11e+00 c.69.1.17 34737 2o8nA 265 1.22e+00 1ji3A 388 1.30e+00 c.69.1.18 77115 2i5nL 273 1.40e+00 f.26.1.1 137066 1dxrL 273 1.44e+00 6prcL f.26.1.1 43431 1dwoA 262 1.54e+00 1qj4A c.69.1.20 34804 1eb8A 262 1.60e+00 c.69.1.20 64896 1ku0A 388 1.75e+00 c.69.1.18 72994 2hihA 431 1.77e+00 1vz3A 710 1.81e+00 b.69.7.1,c.69.1.4 108947,108948 1jmkC 230 1.81e+00 c.69.1.22 71747 1h2wA 710 1.97e+00 b.69.7.1,c.69.1.4 76596,76597 1ethA 448 2.04e+00 1gpl b.12.1.2,c.69.1.19 23641,34789 2dsnA 387 2.25e+00 1vz2A 710 2.52e+00 b.69.7.1,c.69.1.4 108945,108946 1nx9A 652 2.66e+00 b.18.1.13,c.69.1.21 92285,92286 2z5gA 387 2.76e+00 1qo7A 394 3.09e+00 1qo7A c.69.1.11 34697 1qlwA 328 3.59e+00 1qlwA c.69.1.15 34722 2is6A 680 3.90e+00 1e5tA 710 4.17e+00 1qfmA b.69.7.1,c.69.1.4 27676,34644 1h2xA 710 5.17e+00 b.69.7.1,c.69.1.4 76598,76599 1gwmA 153 5.24e+00 b.18.1.19 83348 1w8wA 149 5.30e+00 1hplA 449 6.85e+00 1gpl b.12.1.2,c.69.1.19 23639,34787 2cb9A 244 7.04e+00 2jgpA 520 7.58e+00 1l7rA 574 7.81e+00 b.18.1.13,c.69.1.21 77793,77794 2ihxA 61 8.52e+00 3crkA 407 8.94e+00 1lgyA 269 9.00e+00 3tgl c.69.1.17 34758 1jn0A 335 9.90e+00 c.2.1.3,d.81.1.1 66915,66916 1qozA 207 1.01e+01 1bs9 c.69.1.30 31332 1w8uA 149 1.01e+01 1gxsB 158 1.02e+01 1z5gA 214 1.08e+01 c.108.1.12 124476 2jfzA 255 1.11e+01 1a6cA 513 1.12e+01 1a6cA b.121.4.2,b.121.4.2,b.121.4.2 23296,23297,23298 2ip1A 432 1.13e+01 1wlyA 333 1.19e+01 1w8tA 149 1.20e+01 2autA 214 1.31e+01 1w90A 153 1.34e+01 2eisA 133 1.34e+01 2reiA 318 1.38e+01 1gt6A 269 1.38e+01 c.69.1.17 76342 1z7aA 308 1.41e+01 c.6.2.6 124591 1eiwA 111 1.43e+01 1eiwA c.23.3.1 31130 1z88A 214 1.54e+01 c.108.1.12 124691 1rliA 184 1.55e+01 c.23.5.6 97647 1g66A 207 1.59e+01 1bs9 c.69.1.30 31329 1g0uK 212 1.64e+01 d.153.1.4 41893 2qeeA 437 1.64e+01 1x6vA 630 1.64e+01 b.122.1.3,c.26.1.5,c.37.1.4 121755,121756,121757 1g65K 211 1.66e+01 d.153.1.4 41907 1ju3A 583 1.70e+01 b.18.1.13,c.69.1.21 67300,67301 1v5rA 97 1.79e+01 d.82.4.1 119854 1e8nA 710 1.82e+01 1qfmA b.69.7.1,c.69.1.4 27675,34643 2p4hX 322 1.87e+01 1h4fA 406 1.94e+01 c.95.1.1,c.95.1.1 90609,90610 1pjrA 724 1.96e+01 c.37.1.19,c.37.1.19 32391,32392 1xw8A 252 1.99e+01 c.6.2.5 116111 2mysB 166 1.99e+01 1wdcB a.39.1.5 17308 2q2eB 621 2.13e+01 1w8zA 149 2.18e+01 1w9fA 149 2.22e+01 1rypL 212 2.27e+01 d.153.1.4 41880 2hegA 211 2.27e+01 2rfeA 324 2.32e+01 1rmtA 212 2.50e+01 c.108.1.12 111888 2b82A 211 2.51e+01 c.108.1.12 128057 2aq4A 434 2.53e+01 1qzgA 187 2.55e+01 b.40.4.3 96643 1gs5A 258 2.56e+01 c.73.1.2 70395 2floA 524 2.64e+01 a.211.1.5,c.55.1.8,c.55.1.8 133733,133734,133735 1u6zA 513 2.79e+01 a.211.1.5,c.55.1.8,c.55.1.8 119608,119609,119610 2e3dA 302 2.79e+01 1uswA 260 2.83e+01 c.69.1.17 99895 2q08A 427 2.86e+01 1x05A 129 2.87e+01 b.55.1.1 121543 2pnkA 428 2.89e+01 1zm0A 114 2.89e+01 b.55.1.1 125276 1uwcA 261 2.93e+01 c.69.1.17 100101 1biaA 321 2.96e+01 a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 2hl6A 260 3.00e+01 c.69.1.17 136561 2i5fA 109 3.01e+01 1xx0A 127 3.07e+01 b.55.1.1 122412 1rlrA 761 3.12e+01 a.98.1.1,c.7.1.2 18753,30679 2ca4A 373 3.22e+01 1uxoA 192 3.22e+01 c.69.1.31 108121 1o6fA 710 3.23e+01 b.69.7.1,c.69.1.4 81085,81086 1k89A 449 3.33e+01 c.2.1.7,c.58.1.1 30218,33866 2dksA 130 3.48e+01 1ka9H 200 3.55e+01 c.23.16.1 77308 2dkhA 639 3.61e+01 1rm5A 337 3.77e+01 c.2.1.3,d.81.1.1 105006,105007 2o8gI 206 3.88e+01 2oebA 155 4.00e+01 1aupA 449 4.05e+01 c.2.1.7,c.58.1.1 30222,33870 2yvuA 186 4.12e+01 2pq0A 258 4.13e+01 2bz3A 418 4.19e+01 c.95.1.1,c.95.1.1 129534,129535 1mzpA 217 4.23e+01 e.24.1.1 79710 1iayA 428 4.44e+01 1b8gA c.67.1.4 62130 2e0aA 394 4.55e+01 1t4bA 367 4.55e+01 c.2.1.3,d.81.1.1 106406,106407 1brmA 367 4.55e+01 1brmA c.2.1.3,d.81.1.1 30030,39945 1iy9A 275 4.59e+01 c.66.1.17 76943 1rm4A 337 4.60e+01 c.2.1.3,d.81.1.1 105000,105001 2bz4A 418 4.63e+01 c.95.1.1,c.95.1.1 129542,129543 1bgvA 449 4.65e+01 1k89 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123942,123943 2blnA 305 6.40e+01 b.46.1.1,c.65.1.1 128734,128735 1ax4A 467 6.42e+01 1ax4A c.67.1.2 34391 2ed1A 76 6.46e+01 3b8kA 239 6.47e+01 2ywbA 503 6.50e+01 1ei9A 279 6.57e+01 1ei9A c.69.1.13 34713 2fn0A 437 6.61e+01 d.161.1.1 133799 1qdbA 473 6.68e+01 1qdbA a.138.1.3 19688 1iirA 415 6.69e+01 1iirA c.87.1.5 62453 1jpaA 312 6.80e+01 d.144.1.7 67011 3cssA 267 7.14e+01 1tpvA 247 7.17e+01 1amk c.1.1.1 28443 1uf1A 128 7.22e+01 b.36.1.1 99288 1bqyA 234 7.23e+01 5ptp b.47.1.2 26332 3ch7A 266 7.29e+01 1rjvA 110 7.30e+01 a.39.1.4 104964 1mg8A 78 7.30e+01 d.15.1.1 84958 1w7bA 339 7.37e+01 a.65.1.1 114317 1ug6A 431 7.47e+01 c.1.8.4 88490 2adfA 196 7.76e+01 c.62.1.1 126584 1fp3A 402 7.78e+01 1fp3A a.102.1.3 18842 1kaoA 167 7.92e+01 c.37.1.8 32014