# List of top-scoring protein chains for t2k-100-30-dssp-ebghstl 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.cse.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 1lq9A 112 2.01e-05 d.58.4.3 78129 1iujA 106 3.09e-05 unknown_sccs -9953 1q8bA 105 5.57e-03 unknown_sccs -9958 1g0cA 364 2.75e-02 7a3hA c.1.8.3 60165 1q4rA 112 3.74e-02 d.58.4.4 -9943 1g01A 364 3.92e-02 7a3hA c.1.8.3 60161 1edt 271 5.50e-02 2ebn c.1.8.5 28993 1q53A 112 8.04e-02 d.58.4.4 -9944 1cvjA 190 9.63e-02 1cvjB d.58.7.1 39191 d.58.7.1 39192 1qysA 106 1.30e-01 unknown_sccs -13432 1bm9A 122 1.43e-01 1bm9A a.4.5.7 16116 1qb0A 211 1.97e-01 1c25 c.46.1.1 32699 1fjcA 96 2.40e-01 1fjcA d.58.7.1 39212 1jmtA 104 4.37e-01 d.58.7.3 63180 1j5yA 187 4.47e-01 a.4.5.1 71592 d.94.2.1 71593 1a4iA 301 4.62e-01 1a4iA c.2.1.7 30278 c.58.1.2 33926 1g7eA 122 4.82e-01 1g7eA c.47.1.7 33055 1cnt1 187 4.90e-01 1cnt3 1a4iB 301 4.98e-01 1a4iA c.2.1.7 30279 c.58.1.2 33927 1diaA 306 4.98e-01 1a4iA c.2.1.7 30280 c.58.1.2 33928 1j27A 102 5.14e-01 unknown_sccs -10116 1o0uA 429 5.36e-01 c.118.1.1 80743 1v02A 565 5.60e-01 1j0wA 103 6.10e-01 b.55.1.2 -4364 1f4kA 122 6.98e-01 1bm9A a.4.5.7 59646 1g7vA 284 9.38e-01 1d9eA c.1.10.4 60335 1c25 161 9.89e-01 1c25 c.46.1.1 32698 1jclA 260 1.12e+00 c.1.10.1 66501 1p1xA 260 1.14e+00 1fjeB 175 1.17e+00 1fj7A d.58.7.1 39210 d.58.7.1 39211 1bix 287 1.17e+00 1bix d.151.1.1 41781 1d9eA 284 1.21e+00 1d9eA c.1.10.4 29195 1af7 274 1.33e+00 1af7 a.58.1.1 17928 c.66.1.8 34203 1cx0A 95 1.43e+00 1urnA d.58.7.1 39158 1aye 401 1.45e+00 1aye c.56.5.1 33824 d.58.3.1 39065 1bc5A 269 1.58e+00 1af7 a.58.1.1 17929 c.66.1.8 34204 1e50B 134 1.74e+00 2jhbA b.54.1.1 59245 1urnA 97 1.95e+00 1urnA d.58.7.1 39153 1h9dB 134 2.14e+00 2jhbA b.54.1.1 60822 1dtdA 303 2.17e+00 1aye c.56.5.1 33823 1f2fA 104 2.34e+00 1fmk d.93.1.1 40455 1v1aA 309 2.67e+00 c.72.1.1 -8400 1o60A 292 2.91e+00 c.1.10.4 -5549 1h49A 512 2.94e+00 c.1.8.4 83477 1e55A 512 3.00e+00 1e70M c.1.8.4 28934 1g60A 260 3.02e+00 c.66.1.11 70151 1m5oC 100 3.13e+00 d.58.7.1 78654 1e44B 96 3.23e+00 1e44B b.101.1.1 59220 1h2vZ 156 3.43e+00 d.58.7.1 76595 1shdA 107 3.43e+00 1fmk d.93.1.1 40440 1o4rA 108 3.53e+00 d.93.1.1 -10624 1cnt3 187 3.74e+00 1cnt3 1b7fA 168 3.88e+00 1b7fA d.58.7.1 39169 d.58.7.1 39170 1a6cA 513 3.96e+00 1a6cA b.121.4.2 23296 b.121.4.2 23297 b.121.4.2 23298 2jhbA 143 4.02e+00 2jhbA b.54.1.1 26950 1a3h 300 4.19e+00 7a3hA c.1.8.3 28819 7a3hA 303 4.19e+00 7a3hA c.1.8.3 28817 1shbA 104 4.38e+00 1fmk d.93.1.1 40425 1n13B 113 4.39e+00 1cg2A 393 4.45e+00 1cg2A c.56.5.4 33844 d.58.19.1 39360 1iibA 106 4.45e+00 1iibA c.44.2.1 32648 1cvjB 190 4.51e+00 1cvjB d.58.7.1 39193 d.58.7.1 39194 1fxlA 167 4.62e+00 1b7fA d.58.7.1 39183 d.58.7.1 39184 1shaA 104 4.68e+00 1fmk d.93.1.1 40424 1v84A 253 4.92e+00 1h5vA 304 5.08e+00 c.1.8.3 70898 1c4kA 730 5.38e+00 1ordA c.23.1.4 31273 c.67.1.5 34502 d.125.1.1 41123 1ovnA 248 5.51e+00 a.71.1.1 -1096 c.47.1.7 -7477 1whsA 255 5.87e+00 1ivyA c.69.1.5 34649 1cbg 490 5.92e+00 1e70M c.1.8.4 28933 1ordA 730 6.68e+00 1ordA c.23.1.4 31274 c.67.1.5 34503 d.125.1.1 41124 1mo9A 523 6.71e+00 c.3.1.5 79341 c.3.1.5 79342 d.87.1.1 79343 1o0pA 104 6.80e+00 d.58.7.1 86535 1ubeA 349 6.87e+00 c.37.1.11 88412 d.48.1.1 88413 1ro2A 216 6.88e+00 unknown_sccs -11391 1ekeA 230 6.92e+00 1ekeA c.55.3.1 33572 1luzA 88 6.95e+00 b.40.4.5 74271 1bag 425 7.15e+00 1bag b.71.1.1 27720 c.1.8.1 28707 1jcjA 260 7.17e+00 c.1.10.1 66499 1n7hA 381 7.42e+00 c.2.1.2 80250 1egzA 291 7.89e+00 7a3hA c.1.8.3 28828 1ro0A 216 8.09e+00 unknown_sccs -11390 1js3A 486 8.20e+00 c.67.1.6 67215 1vjtA 483 8.35e+00 c.2.1.5 -5941 d.162.1.2 -11508 1urrA 102 8.48e+00 1dw9A 156 8.54e+00 1dw9A a.35.1.4 17065 d.72.1.1 39596 1dwkA 156 8.70e+00 1dw9A a.35.1.4 17075 d.72.1.1 39606 1vgvA 384 8.73e+00 c.87.1.3 -8575 1fi4A 416 8.74e+00 1fi4A d.14.1.5 59847 d.58.26.2 59848 1whtA 256 8.92e+00 1ivyA c.69.1.5 34646 1umhA 184 9.07e+00 unknown_sccs -3127 1kmmA 424 9.12e+00 1adjA c.51.1.1 33174 d.104.1.1 40723 1btkB 169 9.20e+00 1btkA b.55.1.1 26960 1dcpA 104 9.20e+00 1dcpA d.74.1.1 39672 1tca 317 9.27e+00 1tca c.69.1.17 34726 2ptd 298 9.78e+00 2plc c.1.18.2 29605 1sek 378 9.99e+00 1sek e.1.1.1 42675 3sxlA 184 1.00e+01 1b7fA d.58.7.1 39173 d.58.7.1 39174 1nu0A 138 1.03e+01 unknown_sccs -7658 1l9vA 317 1.05e+01 d.13.2.1 73760 d.216.1.1 73761 1s2dA 167 1.05e+01 c.23.14.1 -6469 1g19A 350 1.08e+01 2reb c.37.1.11 32284 d.48.1.1 38770 1k9dA 679 1.09e+01 c.1.8.10 77292 d.92.2.2 77293 1f93A 104 1.11e+01 1dcpA d.74.1.1 39688 1gy8A 397 1.11e+01 c.2.1.2 83376 1f6dA 376 1.11e+01 1f6dA c.87.1.3 35467 1bcsA 263 1.17e+01 1ivyA c.69.1.5 34647 1uuqA 440 1.18e+01 c.1.8.3 -5321 1dv2A 452 1.21e+01 1bncA b.84.2.1 28238 c.30.1.1 31645 d.142.1.2 41490 1oiaA 95 1.25e+01 d.58.7.1 87051 1vjzA 341 1.30e+01 c.1.8.3 -5318 1tkaA 678 1.32e+01 1trkA c.36.1.6 31816 c.36.1.10 31815 c.48.1.1 33096 1dboA 506 1.34e+01 1dbgA b.80.1.4 28034 1dbgA 506 1.34e+01 1dbgA b.80.1.4 28033 1forL 210 1.35e+01 8fabA b.1.1.1 19988 b.1.1.2 21044 1egxA 115 1.36e+01 1evhA b.55.1.4 27000 1ic6A 279 1.37e+01 1gci c.41.1.1 62257 2scuB 388 1.37e+01 2scuB c.23.4.1 31141 d.142.1.4 41562 1cb0A 283 1.37e+01 1cb0A c.56.2.1 33790 1oflA 481 1.38e+01 1puiA 210 1.41e+01 c.37.1.8 88292 1dyr 206 1.42e+01 1aoeA c.71.1.1 34916 1jae 471 1.45e+01 1smd b.71.1.1 27773 c.1.8.1 28760 1mwqA 101 1.49e+01 unknown_sccs -9962 1pgx 83 1.51e+01 2igd d.15.7.1 37823 2u1a 88 1.54e+01 2u1a d.58.7.1 39164 1f0iA 504 1.57e+01 1f0iA d.136.1.2 59566 d.136.1.2 59567 1ltqA 301 1.57e+01 c.108.1.9 78208 c.37.1.1 78209 1igd 61 1.59e+01 2igd d.15.7.1 37822 2igd 61 1.59e+01 2igd d.15.7.1 37821 1d2kA 392 1.59e+01 1d2kA c.1.8.5 29008 d.26.3.1 38442 1qfxA 460 1.60e+01 1qfxA c.60.1.2 33994 1btkA 169 1.60e+01 1btkA b.55.1.1 26959 1p8xA 344 1.62e+01 d.109.1.1 -10813 d.109.1.1 -10814 d.109.1.1 -10815 1ako 268 1.62e+01 1ako d.151.1.1 41779 1ll7A 392 1.63e+01 c.1.8.5 78085 d.26.3.1 78086 1l8nA 679 1.63e+01 c.1.8.10 84564 d.92.2.2 84565 1jwqA 179 1.64e+01 unknown_sccs -7897 1q7zA 566 1.64e+01 c.1.21.2 -5638 c.1.26.1 -5666 1l2rA 458 1.65e+01 1nthA 458 1.65e+01 c.1.25.1 80730 1d5rA 324 1.66e+01 1d5rA b.7.1.1 23181 c.45.1.1 32697 1dchA 104 1.66e+01 1dcpA d.74.1.1 39692 1gdhA 320 1.67e+01 1gdhA c.2.1.4 30095 c.23.12.1 31355 1p1mA 406 1.67e+01 b.92.1.4 87696 c.1.9.9 87697 1qk9A 92 1.68e+01 1qk9A d.10.1.3 37485 1thfD 253 1.70e+01 1thfD c.1.2.1 28535 1ha1 184 1.73e+01 1ha1 d.58.7.1 39147 d.58.7.1 39148 1nseA 444 1.73e+01 1nseA d.174.1.1 42534 1l3kA 196 1.74e+01 d.58.7.1 73539 d.58.7.1 73540 1vkbA 161 1.75e+01 1mwpA 96 1.75e+01 1mwpA d.170.2.1 42453 1fgyA 127 1.77e+01 1faoA b.55.1.1 26976 1gpuA 680 1.78e+01 c.36.1.6 65455 c.36.1.10 65454 c.48.1.1 65456 1ivnA 190 1.78e+01 c.23.10.5 83719 1l2qA 458 1.78e+01 c.1.25.1 73510 1qdlA 422 1.79e+01 1qdlA d.161.1.1 42088 1trkA 680 1.82e+01 1trkA c.36.1.6 31804 c.36.1.10 31803 c.48.1.1 33090 1omzA 293 1.85e+01 c.68.1.15 87093 1j6pA 418 1.86e+01 b.92.1.4 77089 c.1.9.9 77090 1d0cA 444 1.88e+01 d.174.1.1 64769 1gr2A 279 1.91e+01 1gr2A c.94.1.1 35825 1pbn 289 1.94e+01 1b8oA c.56.2.1 33771 1ftkA 279 1.95e+01 1gr2A c.94.1.1 35819 1v7oA 165 1.96e+01 unknown_sccs -10249 1qy1A 174 1.98e+01 b.60.1.1 -4445 1ehiA 377 1.98e+01 1iow c.30.1.2 31716 d.142.1.1 41484 1cmiA 85 1.98e+01 1cmiA d.39.1.1 38551 1mp9A 198 2.04e+01 a.74.1.2 -1127 a.74.1.2 -1128 1uedA 406 2.04e+01 a.104.1.1 -1459 1h5wA 309 2.06e+01 e.27.1.1 65635 1jyhA 157 2.07e+01 d.60.1.3 71956 1lvmA 229 2.07e+01 b.47.1.3 78243 1iybA 208 2.08e+01 d.124.1.1 -10977 1akz 223 2.09e+01 3eugA c.18.1.1 31007 1rkuA 206 2.10e+01 unknown_sccs -6823 1irf 112 2.10e+01 2irfG a.4.5.23 16192 1a0cA 438 2.10e+01 1a0cA c.1.15.3 29529 1miuA 738 2.11e+01 a.170.1.1 79153 a.171.1.1 79154 b.40.4.3 79155 b.40.4.3 79156 b.40.4.3 79157 1g8kA 825 2.11e+01 1g8jA b.52.2.2 26920 c.81.1.1 35328 1mup 166 2.14e+01 1mup b.60.1.1 27133 1lqvA 193 2.14e+01 d.19.1.1 74206 1kp9B 287 2.16e+01 c.66.1.18 68734 1hg3A 225 2.17e+01 1hg3A c.1.1.1 61025 1mml 265 2.18e+01 1mml e.8.1.2 43015 1sspE 223 2.19e+01 3eugA c.18.1.1 31009 5nseA 444 2.19e+01 d.174.1.1 74644 1bjx 110 2.20e+01 1bjx c.47.1.2 32774 2bjxA 110 2.20e+01 1bjx c.47.1.2 32776 1jsdB 176 2.21e+01 h.3.1.1 63259 1kpgA 287 2.23e+01 c.66.1.18 68735 1d1vA 444 2.24e+01 1nseA d.174.1.1 59101 1jv4A 162 2.25e+01 b.60.1.1 67343 1df3A 162 2.26e+01 1mup b.60.1.1 27134 1ucdA 190 2.27e+01 1ub1A 133 2.28e+01 d.10.1.3 -8969 1cnt2 187 2.29e+01 1cnt3 1bk7A 190 2.30e+01 1bk7A d.124.1.1 41121 1ucaA 190 2.31e+01 d.124.1.1 88462 1bhgA 613 2.32e+01 1bhgA b.1.4.1 22161 b.18.1.5 23766 c.1.8.3 28889 1i05A 180 2.33e+01 1mup b.60.1.1 27130 2irfG 113 2.34e+01 2irfG a.4.5.23 16185 1on3A 523 2.36e+01 c.14.1.4 87107 c.14.1.4 87108 1oef 24 2.36e+01 j.39.1.1 46299 1i06A 180 2.41e+01 1mup b.60.1.1 27131 1b8oA 284 2.45e+01 1b8oA c.56.2.1 33762 1n6jG 35 2.46e+01 1gt91 357 2.46e+01 1dad 224 2.47e+01 1byi c.37.1.10 32204 1m5eA 263 2.47e+01 c.94.1.1 78642 1dbs 224 2.48e+01 1byi c.37.1.10 32209 1colA 204 2.52e+01 1a87 f.1.1.1 43378 1ddwA 120 2.52e+01 1evhA b.55.1.4 27001 1c4zA 358 2.53e+01 1c4zA d.148.1.1 41766 1tidB 119 2.54e+01 1dcoA 104 2.55e+01 1dcpA d.74.1.1 39680 1mqiA 263 2.58e+01 c.94.1.1 -8681 1m5dA 263 2.60e+01 c.94.1.1 78641 1e4iA 447 2.62e+01 1e70M c.1.8.4 59225 1mqdA 261 2.63e+01 c.94.1.1 85049 1im8A 244 2.65e+01 c.66.1.14 66212 1v6fA 151 2.67e+01 1ed5A 444 2.68e+01 1nseA d.174.1.1 42530 2fokA 579 2.70e+01 2fokA a.4.5.12 16131 a.4.5.12 16132 a.4.5.12 16133 c.52.1.12 33323 1byrA 155 2.71e+01 1byrA d.136.1.1 41450 1yprA 125 2.75e+01 3nul d.110.1.1 40888 1jjoC 261 2.76e+01 1mkeA 152 2.76e+01 b.55.1.4 79231 1inp 400 2.77e+01 1inp e.7.1.1 42972 1rj9A 304 2.77e+01 a.24.13.1 -631 c.37.1.10 -7129 1hvyA 288 2.83e+01 1bkpA d.117.1.1 41049 1h09A 338 2.84e+01 b.109.1.1 83420 c.1.8.8 83421 1g8jA 825 2.86e+01 1g8jA b.52.2.2 26924 c.81.1.1 35332 1qpbA 563 2.92e+01 1zpdA c.31.1.3 31739 c.36.1.5 31781 c.36.1.9 31782 1b31A 302 2.94e+01 1taxA c.1.8.3 28892 1bg4 302 2.94e+01 1taxA c.1.8.3 28806 1j5vA 351 2.96e+01 c.72.1.1 71585 1pls 113 2.97e+01 1pls b.55.1.1 26965 3pnp 289 3.00e+01 1b8oA c.56.2.1 33763 1eikA 77 3.02e+01 1eikA d.78.1.1 39751 1ckeA 227 3.10e+01 1ckeA c.37.1.1 31846 3pbgA 468 3.11e+01 1e70M c.1.8.4 28951 1byi 224 3.12e+01 1byi c.37.1.10 32199 1isaA 192 3.14e+01 1avmA a.2.11.1 15731 d.44.1.1 38724 1iv0A 98 3.16e+01 unknown_sccs -7667 1iscA 192 3.18e+01 1avmA a.2.11.1 15733 d.44.1.1 38726 1bn6A 294 3.19e+01 1bn6A c.69.1.8 34678 1ez0A 510 3.21e+01 1eyyA c.82.1.1 35385 1ly1A 181 3.22e+01 c.37.1.1 74334 1o54A 277 3.23e+01 c.66.1.13 -8095 1ew3A 159 3.25e+01 1mup b.60.1.1 27114 1tux 301 3.27e+01 1taxA c.1.8.3 28907 1i3cA 149 3.31e+01 c.23.1.1 71112 1lwdA 413 3.38e+01 c.77.1.1 78265 1pbgA 468 3.46e+01 1e70M c.1.8.4 28946 1t0iA 191 3.51e+01 1ta3A 274 3.51e+01 1i8jA 323 3.52e+01 1b4kA c.1.10.3 61968 1pvuA 154 3.53e+01 3pviA c.52.1.6 33306 2mprA 421 3.57e+01 2mprA f.4.3.2 43788 1uc8A 280 3.62e+01 unknown_sccs -6718 unknown_sccs -11230 1rk8A 165 3.62e+01 d.58.7.1 -10018 1hl8A 449 3.62e+01 unknown_sccs -4690 unknown_sccs -5361 1b3tA 147 3.63e+01 1b3tA d.58.8.1 39228 1tr1A 447 3.63e+01 1e70M c.1.8.4 28957 1v4vA 376 3.65e+01 c.87.1.3 -8583 1kanA 253 3.67e+01 1knyA a.24.16.1 75878 d.218.1.1 75879 1obbA 480 3.69e+01 c.2.1.5 86760 d.162.1.2 86761 1f37A 110 3.70e+01 1f37A c.47.1.11 33088 1jw9B 249 3.74e+01 c.111.1.1 67377 1va4A 279 3.81e+01 1ctn 540 3.88e+01 1ctn b.1.18.2 21876 c.1.8.5 29005 d.26.3.1 38439 2prk 279 3.94e+01 1gci c.41.1.1 32548 1fht 116 3.96e+01 1urnA d.58.7.1 39157 2fmr 65 3.97e+01 2fmr d.51.1.1 38808 1iv3A 152 3.98e+01 d.79.5.1 76828 1kdgA 546 4.00e+01 c.3.1.2 77337 d.16.1.1 77338