# List of top-scoring protein chains for t2k-100-30-bys 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 1.18e-04 d.58.4.3 78129 1iujA 106 2.12e-04 unknown_sccs -9953 1g0cA 364 1.27e-02 7a3hA c.1.8.3 60165 1edt 271 1.84e-02 2ebn c.1.8.5 28993 1g01A 364 2.67e-02 7a3hA c.1.8.3 60161 1q8bA 105 5.53e-02 unknown_sccs -9958 1qysA 106 6.94e-02 unknown_sccs -13432 2scuB 388 1.11e-01 2scuB c.23.4.1 31141 d.142.1.4 41562 1q4rA 112 1.54e-01 d.58.4.4 -9943 1tr1A 447 1.64e-01 1e70M c.1.8.4 28957 1f2fA 104 2.47e-01 1fmk d.93.1.1 40455 1a4iA 301 3.11e-01 1a4iA c.2.1.7 30278 c.58.1.2 33926 1diaA 306 3.51e-01 1a4iA c.2.1.7 30280 c.58.1.2 33928 1g60A 260 3.77e-01 c.66.1.11 70151 1q53A 112 3.91e-01 d.58.4.4 -9944 1e4iA 447 4.72e-01 1e70M c.1.8.4 59225 1bc5A 269 4.93e-01 1af7 a.58.1.1 17929 c.66.1.8 34204 1cvjA 190 5.09e-01 1cvjB d.58.7.1 39191 d.58.7.1 39192 1g7eA 122 5.55e-01 1g7eA c.47.1.7 33055 1j0wA 103 5.95e-01 b.55.1.2 -4364 1af7 274 6.00e-01 1af7 a.58.1.1 17928 c.66.1.8 34203 1qb0A 211 6.23e-01 1c25 c.46.1.1 32699 1ordA 730 6.63e-01 1ordA c.23.1.4 31274 c.67.1.5 34503 d.125.1.1 41124 1bix 287 6.73e-01 1bix d.151.1.1 41781 1o4rA 108 6.82e-01 d.93.1.1 -10624 1c4kA 730 7.13e-01 1ordA c.23.1.4 31273 c.67.1.5 34502 d.125.1.1 41123 1a4iB 301 7.17e-01 1a4iA c.2.1.7 30279 c.58.1.2 33927 1shbA 104 7.76e-01 1fmk d.93.1.1 40425 1shdA 107 7.84e-01 1fmk d.93.1.1 40440 1shaA 104 9.81e-01 1fmk d.93.1.1 40424 1cnt3 187 1.32e+00 1cnt3 1jae 471 1.56e+00 1smd b.71.1.1 27773 c.1.8.1 28760 1bm9A 122 1.78e+00 1bm9A a.4.5.7 16116 1g7vA 284 1.78e+00 1d9eA c.1.10.4 60335 1cbg 490 1.82e+00 1e70M c.1.8.4 28933 1fjcA 96 1.96e+00 1fjcA d.58.7.1 39212 1pauB 102 2.00e+00 1pauB 1kc0A 299 2.04e+00 1n2sA 299 2.14e+00 c.2.1.2 79857 1vjtA 483 2.36e+00 c.2.1.5 -5941 d.162.1.2 -11508 1cnt1 187 2.84e+00 1cnt3 1colA 204 2.85e+00 1a87 f.1.1.1 43378 1dtdA 303 2.92e+00 1aye c.56.5.1 33823 1egzA 291 3.04e+00 7a3hA c.1.8.3 28828 1mwqA 101 3.19e+00 unknown_sccs -9962 1k9dA 679 3.20e+00 c.1.8.10 77292 d.92.2.2 77293 1d9eA 284 3.35e+00 1d9eA c.1.10.4 29195 1forL 210 3.48e+00 8fabA b.1.1.1 19988 b.1.1.2 21044 1qmeA 702 3.58e+00 1pmd d.11.1.1 37487 d.11.1.1 37488 d.175.1.1 42560 e.3.1.1 42769 1akz 223 3.63e+00 3eugA c.18.1.1 31007 1ug6A 431 3.96e+00 c.1.8.4 88490 1rt8A 513 3.96e+00 1ll7A 392 3.99e+00 c.1.8.5 78085 d.26.3.1 78086 1bag 425 4.03e+00 1bag b.71.1.1 27720 c.1.8.1 28707 1uahA 431 4.08e+00 1d2kA 392 4.29e+00 1d2kA c.1.8.5 29008 d.26.3.1 38442 1b31A 302 4.59e+00 1taxA c.1.8.3 28892 1jmtA 104 4.84e+00 d.58.7.3 63180 1aye 401 4.84e+00 1aye c.56.5.1 33824 d.58.3.1 39065 1cvjB 190 4.93e+00 1cvjB d.58.7.1 39193 d.58.7.1 39194 1inp 400 4.96e+00 1inp e.7.1.1 42972 1b5tA 275 4.99e+00 1b5tA c.1.23.1 29676 1h09A 338 5.08e+00 b.109.1.1 83420 c.1.8.8 83421 1jayA 212 5.54e+00 c.2.1.6 66478 1nox 205 5.75e+00 1nox d.90.1.1 40242 1cp3A 277 5.88e+00 1pauA c.17.1.1 30992 1bg4 302 6.00e+00 1taxA c.1.8.3 28806 1sspE 223 6.05e+00 3eugA c.18.1.1 31009 1s2dA 167 6.26e+00 c.23.14.1 -6469 1fgyA 127 6.48e+00 1faoA b.55.1.1 26976 1g8kA 825 7.15e+00 1g8jA b.52.2.2 26920 c.81.1.1 35328 1fmk 452 7.22e+00 1fmk b.34.2.1 24511 d.93.1.1 40436 d.144.1.7 41690 1c25 161 7.26e+00 1c25 c.46.1.1 32698 1tvlA 454 7.42e+00 1nmeB 92 7.53e+00 1bn7A 294 7.82e+00 1bn6A c.69.1.8 34677 1es4A 262 8.07e+00 1skf e.3.1.1 42683 1f4kA 122 8.14e+00 1bm9A a.4.5.7 59646 1jaxA 212 8.30e+00 c.2.1.6 66476 1e44B 96 8.35e+00 1e44B b.101.1.1 59220 1umhA 184 8.42e+00 unknown_sccs -3127 1fjeB 175 8.90e+00 1fj7A d.58.7.1 39210 d.58.7.1 39211 1ibvB 229 9.11e+00 1pyaB 228 9.14e+00 1pyaB 1cb8A 678 9.55e+00 1cb8A a.102.3.2 18849 b.24.1.1 23898 b.30.5.2 24422 1miuA 738 9.61e+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 1v0wA 506 9.70e+00 1hm2A 700 9.70e+00 1cb8A a.102.3.2 61083 b.24.1.1 61084 b.30.5.2 61085 1icrA 217 9.96e+00 1vfrA d.90.1.1 62274 1esiA 262 1.00e+01 1skf e.3.1.1 42682 2fokA 579 1.01e+01 2fokA a.4.5.12 16131 a.4.5.12 16132 a.4.5.12 16133 c.52.1.12 33323 1bn6A 294 1.01e+01 1bn6A c.69.1.8 34678 1j34B 123 1.02e+01 d.169.1.1 84049 1f3fA 155 1.04e+01 1npk d.58.6.1 39101 2jhbA 143 1.04e+01 2jhbA b.54.1.1 26950 1h9dB 134 1.07e+01 2jhbA b.54.1.1 60822 1e50B 134 1.17e+01 2jhbA b.54.1.1 59245 1v02A 565 1.17e+01 1g8jA 825 1.18e+01 1g8jA b.52.2.2 26924 c.81.1.1 35332 1otgA 125 1.20e+01 1otgA d.80.1.2 39831 1ckeA 227 1.21e+01 1ckeA c.37.1.1 31846 1eceA 358 1.22e+01 1eceA c.1.8.3 28813 1cnt2 187 1.24e+01 1cnt3 1oef 24 1.24e+01 j.39.1.1 46299 1jclA 260 1.25e+01 c.1.10.1 66501 1pgx 83 1.31e+01 2igd d.15.7.1 37823 1bjx 110 1.34e+01 1bjx c.47.1.2 32774 2bjxA 110 1.34e+01 1bjx c.47.1.2 32776 1gdhA 320 1.34e+01 1gdhA c.2.1.4 30095 c.23.12.1 31355 1p1xA 260 1.38e+01 1js3A 486 1.39e+01 c.67.1.6 67215 1gqeA 365 1.40e+01 e.38.1.1 70351 1lkkA 105 1.40e+01 1lckA d.93.1.1 40412 1uzcA 71 1.41e+01 a.159.2.1 -339 2igd 61 1.43e+01 2igd d.15.7.1 37821 1ly1A 181 1.44e+01 c.37.1.1 74334 1necA 216 1.44e+01 1vfrA d.90.1.1 40249 1a99A 344 1.47e+01 1pot c.94.1.1 35812 1cxlA 686 1.50e+01 1cxlA b.1.18.2 21829 b.3.1.1 22498 b.71.1.1 27736 c.1.8.1 28723 1igd 61 1.52e+01 2igd d.15.7.1 37822 1cgt 684 1.55e+01 1cxlA b.1.18.2 21815 b.3.1.1 22484 b.71.1.1 27722 c.1.8.1 28709 2irfG 113 1.61e+01 2irfG a.4.5.23 16185 2mprA 421 1.61e+01 2mprA f.4.3.2 43788 1pamA 686 1.62e+01 1cxlA b.1.18.2 21846 b.3.1.1 22515 b.71.1.1 27753 c.1.8.1 28740 1uedA 406 1.64e+01 a.104.1.1 -1459 1qkmA 255 1.66e+01 3erdA a.123.1.1 19309 1i37A 260 1.67e+01 1a28A a.123.1.1 61583 1yprA 125 1.70e+01 3nul d.110.1.1 40888 1v84A 253 1.77e+01 1kpgA 287 1.82e+01 c.66.1.18 68735 1jw9B 249 1.82e+01 c.111.1.1 67377 1h40A 71 1.83e+01 1jjoC 261 1.83e+01 1l2iA 261 1.91e+01 a.123.1.1 73503 1ixxB 123 1.95e+01 1ixxB d.169.1.1 42336 1cqwA 295 1.96e+01 1b6g c.69.1.8 34679 1jsmB 176 1.96e+01 h.3.1.1 63265 1aw0 72 1.99e+01 1aw0 d.58.17.1 39342 1kdoA 227 2.04e+01 c.37.1.1 68478 1fi4A 416 2.04e+01 1fi4A d.14.1.5 59847 d.58.26.2 59848 1v7oA 165 2.05e+01 unknown_sccs -10249 1o60A 292 2.09e+01 c.1.10.4 -5549 3erdA 261 2.09e+01 3erdA a.123.1.1 19293 1es5A 262 2.10e+01 1skf e.3.1.1 42679 1es2A 262 2.10e+01 1skf e.3.1.1 42680 1pydA 556 2.11e+01 1zpdA c.31.1.3 31735 c.36.1.5 31773 c.36.1.9 31774 1uroA 367 2.11e+01 1uroA c.1.22.1 29675 1iibA 106 2.13e+01 1iibA c.44.2.1 32648 1egxA 115 2.15e+01 1evhA b.55.1.4 27000 1ot1A 686 2.17e+01 b.1.18.2 87392 b.3.1.1 87393 b.71.1.1 87394 c.1.8.1 87395 1ash 150 2.17e+01 1ash a.1.1.2 15622 1f0iA 504 2.18e+01 1f0iA d.136.1.2 59566 d.136.1.2 59567 1l8nA 679 2.19e+01 c.1.8.10 84564 d.92.2.2 84565 1ltqA 301 2.20e+01 c.108.1.9 78208 c.37.1.1 78209 1mwpA 96 2.22e+01 1mwpA d.170.2.1 42453 1r3sA 367 2.23e+01 c.1.22.1 -5648 1e3uA 246 2.25e+01 1fofA e.3.1.1 42755 1iybA 208 2.26e+01 d.124.1.1 -10977 1lvmA 229 2.27e+01 b.47.1.3 78243 1skf 262 2.36e+01 1skf e.3.1.1 42684 1uc2A 481 2.36e+01 unknown_sccs -11725 1twdA 256 2.38e+01 1e55A 512 2.41e+01 1e70M c.1.8.4 28934 1k55A 246 2.45e+01 e.3.1.1 68156 1h49A 512 2.47e+01 c.1.8.4 83477 1pbgA 468 2.49e+01 1e70M c.1.8.4 28946 1kp9B 287 2.53e+01 c.66.1.18 68734 1vrtA 560 2.55e+01 1rthA c.55.3.1 33574 e.8.1.2 43023 1nu0A 138 2.56e+01 unknown_sccs -7658 1gt91 357 2.56e+01 1dciA 275 2.57e+01 1dciA c.14.1.3 30918 1cb0A 283 2.57e+01 1cb0A c.56.2.1 33790 1usmA 80 2.57e+01 d.74.1.1 -10334 1gr2A 279 2.60e+01 1gr2A c.94.1.1 35825 1btkB 169 2.60e+01 1btkA b.55.1.1 26960 1o6uA 403 2.69e+01 a.5.3.1 -366 unknown_sccs -3048 c.13.1.1 -6221 2cmkA 227 2.72e+01 1ckeA c.37.1.1 31847 1fmeA 28 2.75e+01 k.12.1.1 59878 1qpbA 563 2.76e+01 1zpdA c.31.1.3 31739 c.36.1.5 31781 c.36.1.9 31782 1ftkA 279 2.82e+01 1gr2A c.94.1.1 35819 3ertA 261 2.82e+01 3erdA a.123.1.1 19292 1c0dA 358 2.83e+01 1eceA c.1.8.3 28815 1vhh 162 2.84e+01 1vhh d.65.1.2 39550 1ovnA 248 2.84e+01 a.71.1.1 -1096 c.47.1.7 -7477 1vhsA 175 2.86e+01 d.108.1.1 -10794 1mqdA 261 2.88e+01 c.94.1.1 85049 1mkeA 152 2.89e+01 b.55.1.4 79231 1hzoA 271 2.91e+01 e.3.1.1 71092 1u02A 239 2.91e+01 1ffkM 148 2.93e+01 1ffkM a.94.1.1 18740 1fshA 105 2.93e+01 1fshA a.4.5.31 60006 1bh9B 89 2.97e+01 1bh9B a.22.1.3 16485 4eugA 229 2.97e+01 3eugA c.18.1.1 31019 1pvdA 537 3.00e+01 1zpdA c.31.1.3 31737 c.36.1.5 31777 c.36.1.9 31778 1n0wA 243 3.06e+01 c.37.1.11 79772 1j5vA 351 3.06e+01 c.72.1.1 71585 1pk6B 132 3.06e+01 b.22.1.1 -3290 1oflA 481 3.06e+01 1shuX 182 3.29e+01 c.62.1.1 -7982 1m5dA 263 3.29e+01 c.94.1.1 78641 1v4vA 376 3.32e+01 c.87.1.3 -8583 1n13B 113 3.35e+01 1k4jA 230 3.42e+01 d.108.1.3 72057 1dbgA 506 3.46e+01 1dbgA b.80.1.4 28033 1qk9A 92 3.47e+01 1qk9A d.10.1.3 37485 1on3A 523 3.53e+01 c.14.1.4 87107 c.14.1.4 87108 1vjzA 341 3.53e+01 c.1.8.3 -5318 1a28A 256 3.54e+01 1a28A a.123.1.1 19290 1azwA 313 3.54e+01 1qtrA c.69.1.7 34658 1e5rA 290 3.56e+01 1e5rA b.82.2.4 59276 1mqiA 263 3.58e+01 c.94.1.1 -8681 1s72P 149 3.61e+01 1srrA 124 3.62e+01 1dz3A c.23.1.1 31110 1b3tA 147 3.63e+01 1b3tA d.58.8.1 39228 1goiA 499 3.63e+01 b.72.2.1 65413 c.1.8.5 65414 d.26.3.1 65415 1lcjA 109 3.64e+01 1qadA d.93.1.1 40414 1jj2O 148 3.65e+01 1ffkM a.94.1.1 63100 1udh 244 3.67e+01 3eugA c.18.1.1 31015 1s71A 316 3.68e+01 1sgvA 316 3.68e+01 b.122.1.1 -5120 unknown_sccs -10148 1kzfA 230 3.68e+01 d.108.1.3 73354 1h5vA 304 3.68e+01 c.1.8.3 70898 1q7zA 566 3.69e+01 c.1.21.2 -5638 c.1.26.1 -5666 1jsdB 176 3.70e+01 h.3.1.1 63259 1jkvA 266 3.73e+01 unknown_sccs 71719 1m5eA 263 3.75e+01 c.94.1.1 78642 1v6fA 151 3.79e+01 1ako 268 3.81e+01 1ako d.151.1.1 41779 1nseA 444 3.82e+01 1nseA d.174.1.1 42534 1sr7A 259 3.82e+01 2cpb 50 3.84e+01 2cpb h.1.4.1 45568 1g7rA 594 3.85e+01 1g7rA b.43.3.1 25716 b.43.3.1 25717 c.20.1.1 31034 c.37.1.8 32149 1o9iA 266 3.88e+01 unknown_sccs -698 1k1xA 659 3.89e+01 a.8.3.2 84279 b.30.5.8 84280 c.6.2.2 84281 1qd1A 325 3.90e+01 1qd1A d.58.34.1 39493 d.58.34.1 39494 1oapA 109 3.91e+01 unknown_sccs -10428 1fcyA 236 3.91e+01 2lbd a.123.1.1 19282 1rj9A 304 3.91e+01 a.24.13.1 -631 c.37.1.10 -7129 1mjfA 281 3.94e+01 c.66.1.17 79198 1d1vA 444 3.96e+01 1nseA d.174.1.1 59101 1d3cA 686 3.97e+01 1cxlA b.1.18.2 21827 b.3.1.1 22496 b.71.1.1 27734 c.1.8.1 28721