# List of top-scoring protein chains for t2k-100-30-alpha 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 2.49e-05 d.58.4.3 78129 1iujA 106 8.33e-05 unknown_sccs -9953 1edt 271 6.18e-03 2ebn c.1.8.5 28993 1qysA 106 9.24e-03 unknown_sccs -13432 1q8bA 105 2.27e-02 unknown_sccs -9958 1g0cA 364 2.37e-02 7a3hA c.1.8.3 60165 1cvjA 190 2.78e-02 1cvjB d.58.7.1 39191 d.58.7.1 39192 1g01A 364 2.89e-02 7a3hA c.1.8.3 60161 1q4rA 112 5.18e-02 d.58.4.4 -9943 1a4iB 301 6.93e-02 1a4iA c.2.1.7 30279 c.58.1.2 33927 1qb0A 211 9.70e-02 1c25 c.46.1.1 32699 1q53A 112 1.26e-01 d.58.4.4 -9944 1diaA 306 1.29e-01 1a4iA c.2.1.7 30280 c.58.1.2 33928 1a4iA 301 1.36e-01 1a4iA c.2.1.7 30278 c.58.1.2 33926 1j0wA 103 1.74e-01 b.55.1.2 -4364 1cvjB 190 2.49e-01 1cvjB d.58.7.1 39193 d.58.7.1 39194 1f2fA 104 2.92e-01 1fmk d.93.1.1 40455 1jmtA 104 3.44e-01 d.58.7.3 63180 1v84A 253 3.75e-01 1cnt3 187 4.11e-01 1cnt3 1g7eA 122 4.27e-01 1g7eA c.47.1.7 33055 1af7 274 4.94e-01 1af7 a.58.1.1 17928 c.66.1.8 34203 1shdA 107 6.19e-01 1fmk d.93.1.1 40440 1cnt1 187 6.37e-01 1cnt3 1o4rA 108 7.05e-01 d.93.1.1 -10624 1egzA 291 7.07e-01 7a3hA c.1.8.3 28828 1c25 161 7.94e-01 1c25 c.46.1.1 32698 1bg4 302 8.60e-01 1taxA c.1.8.3 28806 1a8y 367 8.63e-01 1a8y c.47.1.3 32781 c.47.1.3 32782 c.47.1.3 32783 1shaA 104 8.75e-01 1fmk d.93.1.1 40424 1g60A 260 8.92e-01 c.66.1.11 70151 1shbA 104 9.21e-01 1fmk d.93.1.1 40425 1v02A 565 9.52e-01 1ll7A 392 1.04e+00 c.1.8.5 78085 d.26.3.1 78086 1d2kA 392 1.07e+00 1d2kA c.1.8.5 29008 d.26.3.1 38442 1o0uA 429 1.08e+00 c.118.1.1 80743 1bc5A 269 1.12e+00 1af7 a.58.1.1 17929 c.66.1.8 34204 1mwqA 101 1.25e+00 unknown_sccs -9962 1s2dA 167 1.42e+00 c.23.14.1 -6469 1fjeB 175 1.76e+00 1fj7A d.58.7.1 39210 d.58.7.1 39211 1vjtA 483 1.80e+00 c.2.1.5 -5941 d.162.1.2 -11508 1b31A 302 1.81e+00 1taxA c.1.8.3 28892 1c4kA 730 1.85e+00 1ordA c.23.1.4 31273 c.67.1.5 34502 d.125.1.1 41123 1cnt2 187 1.87e+00 1cnt3 1bix 287 1.91e+00 1bix d.151.1.1 41781 1miuA 738 1.93e+00 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 1bag 425 2.11e+00 1bag b.71.1.1 27720 c.1.8.1 28707 1tr1A 447 2.18e+00 1e70M c.1.8.4 28957 1colA 204 2.19e+00 1a87 f.1.1.1 43378 1jayA 212 2.34e+00 c.2.1.6 66478 1forL 210 2.50e+00 8fabA b.1.1.1 19988 b.1.1.2 21044 1h49A 512 2.58e+00 c.1.8.4 83477 1fjcA 96 2.62e+00 1fjcA d.58.7.1 39212 1f4kA 122 2.62e+00 1bm9A a.4.5.7 59646 2scuB 388 2.76e+00 2scuB c.23.4.1 31141 d.142.1.4 41562 1udsA 255 2.82e+00 d.14.1.4 -9055 d.101.1.1 -10745 1bm9A 122 2.99e+00 1bm9A a.4.5.7 16116 1uedA 406 3.08e+00 a.104.1.1 -1459 1sspE 223 3.23e+00 3eugA c.18.1.1 31009 1fgyA 127 3.29e+00 1faoA b.55.1.1 26976 1e4iA 447 3.30e+00 1e70M c.1.8.4 59225 1j5vA 351 3.31e+00 c.72.1.1 71585 1akz 223 3.44e+00 3eugA c.18.1.1 31007 1cbg 490 3.64e+00 1e70M c.1.8.4 28933 2fokA 579 3.72e+00 2fokA a.4.5.12 16131 a.4.5.12 16132 a.4.5.12 16133 c.52.1.12 33323 1jae 471 3.85e+00 1smd b.71.1.1 27773 c.1.8.1 28760 1v7oA 165 4.06e+00 unknown_sccs -10249 1ta3B 303 4.13e+00 1e55A 512 4.14e+00 1e70M c.1.8.4 28934 1m5dA 263 4.39e+00 c.94.1.1 78641 1ftkA 279 4.46e+00 1gr2A c.94.1.1 35819 1mqdA 261 4.49e+00 c.94.1.1 85049 1pamA 686 4.51e+00 1cxlA b.1.18.2 21846 b.3.1.1 22515 b.71.1.1 27753 c.1.8.1 28740 1mqiA 263 4.52e+00 c.94.1.1 -8681 1m5eA 263 4.52e+00 c.94.1.1 78642 1oef 24 4.86e+00 j.39.1.1 46299 1nu0A 138 4.89e+00 unknown_sccs -7658 1es4A 262 5.04e+00 1skf e.3.1.1 42683 1iw0A 215 5.23e+00 a.132.1.1 83720 1ivnA 190 5.36e+00 c.23.10.5 83719 1cxvA 164 5.36e+00 1ck7A d.92.1.11 40404 1hg3A 225 5.50e+00 1hg3A c.1.1.1 61025 1jaxA 212 5.53e+00 c.2.1.6 66476 1cgt 684 5.54e+00 1cxlA b.1.18.2 21815 b.3.1.1 22484 b.71.1.1 27722 c.1.8.1 28709 1n7kA 234 5.58e+00 c.1.10.1 85374 1dcpA 104 5.68e+00 1dcpA d.74.1.1 39672 1d9eA 284 5.74e+00 1d9eA c.1.10.4 29195 1gr2A 279 5.79e+00 1gr2A c.94.1.1 35825 1yprA 125 5.82e+00 3nul d.110.1.1 40888 1lzlA 323 5.85e+00 c.69.1.2 78306 1rt8A 513 6.10e+00 1vkbA 161 6.14e+00 1vjzA 341 6.28e+00 c.1.8.3 -5318 7a3hA 303 6.42e+00 7a3hA c.1.8.3 28817 1ordA 730 6.43e+00 1ordA c.23.1.4 31274 c.67.1.5 34503 d.125.1.1 41124 1h5vA 304 6.47e+00 c.1.8.3 70898 1ot1A 686 6.68e+00 b.1.18.2 87392 b.3.1.1 87393 b.71.1.1 87394 c.1.8.1 87395 1f93A 104 6.76e+00 1dcpA d.74.1.1 39688 1pls 113 6.89e+00 1pls b.55.1.1 26965 1bcsA 263 6.93e+00 1ivyA c.69.1.5 34647 1b5tA 275 7.10e+00 1b5tA c.1.23.1 29676 1kdgA 546 7.43e+00 c.3.1.2 77337 d.16.1.1 77338 1bn6A 294 7.45e+00 1bn6A c.69.1.8 34678 1bn7A 294 7.56e+00 1bn6A c.69.1.8 34677 1idm 343 7.57e+00 1cnzA c.77.1.1 35035 1ehiA 377 7.58e+00 1iow c.30.1.2 31716 d.142.1.1 41484 1uzcA 71 7.62e+00 a.159.2.1 -339 1cqwA 295 7.62e+00 1b6g c.69.1.8 34679 1vh7A 265 7.92e+00 c.1.2.1 -5159 1dr8B 344 8.22e+00 1cnzA c.77.1.1 35052 1s71A 316 8.38e+00 1sgvA 316 8.38e+00 b.122.1.1 -5120 unknown_sccs -10148 1shuX 182 8.46e+00 c.62.1.1 -7982 1j5yA 187 8.50e+00 a.4.5.1 71592 d.94.2.1 71593 1v1aA 309 8.65e+00 c.72.1.1 -8400 1mb4A 370 8.74e+00 c.2.1.3 78908 d.81.1.1 78909 1dchA 104 8.77e+00 1dcpA d.74.1.1 39692 1ovnA 248 8.85e+00 a.71.1.1 -1096 c.47.1.7 -7477 1a3h 300 8.87e+00 7a3hA c.1.8.3 28819 1k3eA 156 8.89e+00 d.198.1.1 68103 1ro2A 216 8.90e+00 unknown_sccs -11391 1h40A 71 9.10e+00 1cxlA 686 9.17e+00 1cxlA b.1.18.2 21829 b.3.1.1 22498 b.71.1.1 27736 c.1.8.1 28723 1jjoC 261 9.19e+00 1p9rA 418 9.35e+00 c.37.1.11 -7142 1igd 61 9.47e+00 2igd d.15.7.1 37822 1dcoA 104 9.53e+00 1dcpA d.74.1.1 39680 1whsA 255 9.57e+00 1ivyA c.69.1.5 34649 2igd 61 9.60e+00 2igd d.15.7.1 37821 1e44B 96 9.67e+00 1e44B b.101.1.1 59220 1bjx 110 9.69e+00 1bjx c.47.1.2 32774 2bjxA 110 9.69e+00 1bjx c.47.1.2 32776 1fmk 452 9.76e+00 1fmk b.34.2.1 24511 d.93.1.1 40436 d.144.1.7 41690 1va4A 279 9.77e+00 1pvdA 537 1.01e+01 1zpdA c.31.1.3 31737 c.36.1.5 31777 c.36.1.9 31778 1ixxB 123 1.02e+01 1ixxB d.169.1.1 42336 1whtA 256 1.03e+01 1ivyA c.69.1.5 34646 1pgx 83 1.05e+01 2igd d.15.7.1 37823 1n8jA 186 1.09e+01 c.47.1.10 85401 1a99A 344 1.11e+01 1pot c.94.1.1 35812 1pydA 556 1.12e+01 1zpdA c.31.1.3 31735 c.36.1.5 31773 c.36.1.9 31774 1gy8A 397 1.15e+01 c.2.1.2 83376 1skf 262 1.18e+01 1skf e.3.1.1 42684 1n13B 113 1.21e+01 1a0rP 245 1.23e+01 1b9yC c.47.1.6 33054 1k9dA 679 1.24e+01 c.1.8.10 77292 d.92.2.2 77293 1clxA 347 1.34e+01 1taxA c.1.8.3 28899 1ubeA 349 1.37e+01 c.37.1.11 88412 d.48.1.1 88413 1ox0A 430 1.44e+01 c.95.1.1 87495 c.95.1.1 87496 1psdA 409 1.45e+01 1psdA c.2.1.4 30097 c.23.12.1 31357 d.58.18.1 39354 1j34B 123 1.46e+01 d.169.1.1 84049 1atiB 505 1.46e+01 1atiA c.51.1.1 33197 d.104.1.1 40746 1d3gA 367 1.46e+01 1d3gA c.1.4.1 28600 1s6yA 450 1.48e+01 1qpbA 563 1.52e+01 1zpdA c.31.1.3 31739 c.36.1.5 31781 c.36.1.9 31782 1atiA 505 1.54e+01 1atiA c.51.1.1 33196 d.104.1.1 40745 1g19A 350 1.54e+01 2reb c.37.1.11 32284 d.48.1.1 38770 1goiA 499 1.55e+01 b.72.2.1 65413 c.1.8.5 65414 d.26.3.1 65415 1l9vA 317 1.56e+01 d.13.2.1 73760 d.216.1.1 73761 1tvlA 454 1.56e+01 830cA 168 1.59e+01 1ck7A d.92.1.11 40400 1d3cA 686 1.59e+01 1cxlA b.1.18.2 21827 b.3.1.1 22496 b.71.1.1 27734 c.1.8.1 28721 1ipd 345 1.60e+01 1cnzA c.77.1.1 35038 1pauB 102 1.66e+01 1pauB 1jj2O 148 1.68e+01 1ffkM a.94.1.1 63100 1lvmA 229 1.70e+01 b.47.1.3 78243 1s72P 149 1.71e+01 1ltqA 301 1.74e+01 c.108.1.9 78208 c.37.1.1 78209 1v4vA 376 1.74e+01 c.87.1.3 -8583 1ash 150 1.76e+01 1ash a.1.1.2 15622 1i17A 107 1.80e+01 1i17A d.6.1.1 61519 1i1wA 303 1.80e+01 c.1.8.3 76732 1icrA 217 1.81e+01 1vfrA d.90.1.1 62274 1nmeB 92 1.83e+01 1esiA 262 1.84e+01 1skf e.3.1.1 42682 1a8s 273 1.85e+01 1brt c.69.1.12 34710 1usmA 80 1.85e+01 d.74.1.1 -10334 1dtdA 303 1.86e+01 1aye c.56.5.1 33823 1tidB 119 1.86e+01 1kmmA 424 1.87e+01 1adjA c.51.1.1 33174 d.104.1.1 40723 1ffkM 148 1.88e+01 1ffkM a.94.1.1 18740 1es2A 262 1.90e+01 1skf e.3.1.1 42680 1kp9B 287 1.90e+01 c.66.1.18 68734 1n7hA 381 1.90e+01 c.2.1.2 80250 1btkB 169 1.92e+01 1btkA b.55.1.1 26960 1jf3A 147 1.97e+01 a.1.1.2 71642 1mli 96 2.00e+01 1mli d.58.4.1 39070 1es5A 262 2.06e+01 1skf e.3.1.1 42679 1l2uA 245 2.07e+01 c.1.2.3 73516 2irfG 113 2.15e+01 2irfG a.4.5.23 16185 1ro0A 216 2.19e+01 unknown_sccs -11390 1fsd 28 2.20e+01 k.14.1.1 46439 1a4uA 254 2.21e+01 1b16A c.2.1.2 29878 1g8kA 825 2.22e+01 1g8jA b.52.2.2 26920 c.81.1.1 35328 1vhh 162 2.23e+01 1vhh d.65.1.2 39550 1h5qA 265 2.24e+01 1cydA c.2.1.2 60643 1kpgA 287 2.24e+01 c.66.1.18 68735 1o54A 277 2.25e+01 c.66.1.13 -8095 1umhA 184 2.28e+01 unknown_sccs -3127 1fokA 568 2.28e+01 2fokA a.4.5.12 16137 a.4.5.12 16138 a.4.5.12 16139 c.52.1.12 33325 1fggA 261 2.28e+01 1fggA c.68.1.7 34576 1gqeA 365 2.29e+01 e.38.1.1 70351 1if1A 113 2.31e+01 2irfG a.4.5.23 16183 1kwsA 261 2.32e+01 c.68.1.7 73083 1s0uA 408 2.36e+01 b.43.3.1 -4053 b.44.1.1 -4061 c.37.1.8 -7096 1acc 735 2.36e+01 1acc f.11.1.1 43828 1ofuA 320 2.37e+01 c.32.1.1 86972 d.79.2.1 86973 1egxA 115 2.39e+01 1evhA b.55.1.4 27000 1v6fA 151 2.40e+01 1e15A 499 2.45e+01 1e15A b.72.2.1 27810 c.1.8.5 29006 d.26.3.1 38440 1httA 423 2.46e+01 1adjA c.51.1.1 33178 d.104.1.1 40727 1b16A 254 2.50e+01 1b16A c.2.1.2 29875 1ucdA 190 2.50e+01 1qdlA 422 2.55e+01 1qdlA d.161.1.1 42088 3pbgA 468 2.55e+01 1e70M c.1.8.4 28951 1e6pA 499 2.57e+01 1e15A b.72.2.1 59314 c.1.8.5 59315 d.26.3.1 59316 2ebn 289 2.58e+01 2ebn c.1.8.5 28990 1f3cA 89 2.59e+01 1cmiA d.39.1.1 38557 1ucaA 190 2.60e+01 d.124.1.1 88462 1ako 268 2.65e+01 1ako d.151.1.1 41779 1ckeA 227 2.66e+01 1ckeA c.37.1.1 31846 1bk7A 190 2.67e+01 1bk7A d.124.1.1 41121 1eywA 331 2.69e+01 1pscA c.1.9.3 29057 1vgvA 384 2.79e+01 c.87.1.3 -8575 1r1mA 164 2.79e+01 unknown_sccs -10431 1nq6A 302 2.82e+01 c.1.8.3 -5332 1a48 306 2.85e+01 1a48 d.143.1.1 41590 1qmvA 197 2.87e+01 1qq2A c.47.1.10 33066 1lwdA 413 2.87e+01 c.77.1.1 78265 1lqvA 193 2.90e+01 d.19.1.1 74206 1aye 401 2.91e+01 1aye c.56.5.1 33824 d.58.3.1 39065 1hl9A 449 2.92e+01 unknown_sccs -4694 unknown_sccs -5365 1p8xA 344 2.92e+01 d.109.1.1 -10813 d.109.1.1 -10814 d.109.1.1 -10815 1hb6A 86 2.92e+01 a.11.1.1 70959 1evhA 112 2.94e+01 1evhA b.55.1.4 26997 1bd3A 243 2.95e+01 1bd3A c.61.1.1 34098 1i0dA 332 2.96e+01 1pscA c.1.9.3 61487 1pscA 365 2.98e+01 1pscA c.1.9.3 29058 1g8jA 825 3.02e+01 1g8jA b.52.2.2 26924 c.81.1.1 35332 1f7wA 144 3.04e+01 1f46A d.129.4.1 59679 1sb8A 352 3.08e+01 1l8nA 679 3.09e+01 c.1.8.10 84564 d.92.2.2 84565 1uwwA 191 3.10e+01 1ufiA 64 3.11e+01 unknown_sccs -773 1n0wA 243 3.14e+01 c.37.1.11 79772 1f0iA 504 3.15e+01 1f0iA d.136.1.2 59566 d.136.1.2 59567 1tux 301 3.21e+01 1taxA c.1.8.3 28907 1f47B 144 3.28e+01 1f46A d.129.4.1 59645 1lfpA 249 3.29e+01 e.39.1.1 73885 1e5rA 290 3.31e+01 1e5rA b.82.2.4 59276 1qhkA 47 3.31e+01 1qhkA d.100.1.2 40694 1oen 540 3.33e+01 1ayl c.91.1.1 64750 c.109.1.1 64751 1qwzA 235 3.35e+01 b.100.1.1 -4543 1twdA 256 3.36e+01 1nijA 318 3.40e+01 c.37.1.10 85741 d.237.1.1 85742 1w1kA 560 3.40e+01 1cd9B 215 3.44e+01 1cto b.1.2.1 22041 b.1.2.1 22042 1jdpA 441 3.45e+01 c.93.1.1 62906 1fxlA 167 3.46e+01 1b7fA d.58.7.1 39183 d.58.7.1 39184 1hjp 203 3.48e+01 1hjp a.5.1.1 16274 a.60.2.1 17947 b.40.4.2 25266 1cg2A 393 3.48e+01 1cg2A c.56.5.4 33844 d.58.19.1 39360 1hstA 90 3.49e+01 1hstA a.4.5.13 16140 1necA 216 3.49e+01 1vfrA d.90.1.1 40249 2u1a 88 3.51e+01 2u1a d.58.7.1 39164 1lfkA 398 3.51e+01 a.104.1.1 77926 1rj9A 304 3.52e+01 a.24.13.1 -631 c.37.1.10 -7129 1e8gA 560 3.54e+01 1qltA d.58.32.1 39455 d.145.1.1 41718 1qltA 560 3.55e+01 1qltA d.58.32.1 39457 d.145.1.1 41720 1uroA 367 3.57e+01 1uroA c.1.22.1 29675 1mwpA 96 3.60e+01 1mwpA d.170.2.1 42453 1ffyA 917 3.61e+01 1qu2A a.27.1.1 16926 b.51.1.1 26891 c.26.1.1 31593 1qu2A 917 3.61e+01 1qu2A a.27.1.1 16925 b.51.1.1 26890 c.26.1.1 31592 1pta 318 3.62e+01 1pscA c.1.9.3 29064 1m55A 197 3.63e+01 d.89.1.3 74469 1thfD 253 3.67e+01 1thfD c.1.2.1 28535 1h70A 255 3.68e+01 1h70A d.126.1.3 60711 1khcA 147 3.69e+01 b.34.9.2 68608 1ddwA 120 3.71e+01 1evhA b.55.1.4 27001 1r3sA 367 3.75e+01 c.1.22.1 -5648 1hl8A 449 3.76e+01 unknown_sccs -4690 unknown_sccs -5361 1sr9A 644 3.83e+01 8rucI 123 3.84e+01 1rboC d.73.1.1 39629 1aw0 72 3.87e+01 1aw0 d.58.17.1 39342 1b74A 254 3.87e+01 1b74A c.78.2.1 35264 c.78.2.1 35265 1lrzA 426 3.90e+01 a.2.7.4 78167 d.108.1.4 78168 d.108.1.4 78169 1c44A 123 3.91e+01 1qndA d.106.1.1 40795 1qba 858 3.93e+01 1qba b.1.18.2 21810 b.2.2.3 22406 c.1.8.6 29009 d.92.2.1 40408 1f37A 110 3.93e+01 1f37A c.47.1.11 33088 1dioB 224 3.94e+01 1dioB c.51.3.1 33219 1rboC 123 3.95e+01 1rboC d.73.1.1 39634 1eexB 224 3.96e+01 1dioB c.51.3.1 33213 1t0iA 191 4.00e+01