# List of top-scoring protein chains for t2k.100-30-str 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 2ny1B 184 2.23e-01 b.1.1.1 138764 b.1.1.3 138765 3cbnA 151 3.05e-01 1z4vA 532 5.09e-01 1iwmA 186 7.21e-01 b.125.1.2 83758 2hzqA 174 7.75e-01 2obtA 327 1.63e+00 1cdy 178 1.96e+00 1cdy 1d2eA 397 2.62e+00 1efcA b.43.3.1 25701 b.44.1.1 25741 c.37.1.8 32136 2qklA 127 2.77e+00 1xf1A 926 3.58e+00 1ddzA 496 3.65e+00 1ddzA c.53.2.1 33372 c.53.2.1 33373 2hf2A 283 4.13e+00 1ctn 540 4.68e+00 1ctn 1z9nA 177 4.76e+00 1k9tA 540 4.99e+00 b.1.18.2 77298 c.1.8.5 77299 d.26.3.1 77300 1edqA 540 5.00e+00 1ctn b.1.18.2 21873 c.1.8.5 29002 d.26.3.1 38436 2rmpA 361 5.19e+00 2rmpA b.50.1.2 26825 1gmuA 143 5.42e+00 b.107.1.1 65335 d.58.38.1 65336 1um5H 217 5.66e+00 b.1.1.1 113302 b.1.1.2 113303 1y8xA 160 6.13e+00 d.20.1.1 122769 2ix2A 249 6.64e+00 3cniA 156 6.77e+00 1olrA 224 6.90e+00 b.29.1.11 93330 1x3cA 73 7.14e+00 g.37.1.1 121660 1rloA 271 7.32e+00 c.108.1.10 111864 1mdaH 368 7.58e+00 2bbkH b.69.2.1 27637 2hx0A 154 8.89e+00 d.290.1.3 136830 2apsA 162 8.99e+00 1yaiA b.1.8.1 22298 2uxyA 341 9.13e+00 1qz8A 113 9.29e+00 b.140.1.1 96619 1rlmA 271 9.31e+00 c.108.1.10 111860 2ghsA 326 9.43e+00 b.68.6.1 135209 2hr0A 645 9.55e+00 2uubL 135 9.73e+00 b.40.4.5 139943 1qftA 175 1.01e+01 1qftA b.60.1.1 27151 1eagA 342 1.05e+01 1eagA b.50.1.2 26826 1wosA 364 1.10e+01 b.44.2.1 109468 d.250.1.1 109469 1hl9A 449 1.11e+01 b.71.1.3 90650 c.1.8.11 90651 1oi0A 124 1.16e+01 c.97.3.1 93045 1pzsA 208 1.20e+01 b.1.8.1 104397 1ft9A 222 1.20e+01 1ft9A a.4.5.4 16107 b.82.3.1 28131 2z4tA 514 1.24e+01 2aqpA 164 1.26e+01 1o7iA 119 1.27e+01 b.40.4.3 86642 1z9pA 155 1.27e+01 2axwA 134 1.27e+01 1tf6A 190 1.27e+01 1tf6A g.37.1.1 45060 g.37.1.1 45061 g.37.1.1 45062 g.37.1.1 45063 g.37.1.1 45064 g.37.1.1 45065 1rztA 331 1.30e+01 a.60.6.1 98224 a.60.12.1 98225 d.218.1.2 98226 3cswA 285 1.50e+01 1dt9A 437 1.53e+01 1dt9A c.55.4.2 33738 d.79.3.2 39815 d.91.1.1 40257 1xaoA 121 1.55e+01 2dscA 212 1.61e+01 2dg1A 333 1.65e+01 b.68.6.1 131493 2cwsA 237 1.68e+01 3cnqP 80 1.70e+01 1mgpA 313 1.71e+01 c.119.1.1 79098 2o4uX 334 1.74e+01 3tssA 194 1.76e+01 b.40.2.2 25160 d.15.6.1 37749 3bm4A 210 1.76e+01 1fx5A 242 1.80e+01 1led b.29.1.1 24135 3c0fB 91 1.85e+01 2eklA 313 1.87e+01 2c78A 405 1.87e+01 b.43.3.1 130037 b.44.1.1 130038 c.37.1.8 130039 2aqqA 164 1.95e+01 1ywhA 313 1.99e+01 1o12A 376 2.02e+01 b.92.1.5 80758 c.1.9.10 80759 1rl5A 60 2.03e+01 1xsoA 150 2.06e+01 1mfmA b.1.8.1 22273 1qq1A 559 2.07e+01 1tyv b.80.1.6 28041 1qa1A 554 2.07e+01 1tyv b.80.1.6 28047 1aipA 405 2.11e+01 1efcA b.43.3.1 25697 b.44.1.1 25737 c.37.1.8 32132 1exmA 405 2.22e+01 1efcA b.43.3.1 25696 b.44.1.1 25736 c.37.1.8 32131 2qh0A 138 2.23e+01 2o5nA 319 2.26e+01 1fjgL 135 2.26e+01 1fjfL b.40.4.5 25346 1uzxA 169 2.33e+01 d.20.1.2 100238 1vkyA 347 2.34e+01 e.53.1.1 108696 2dyuA 334 2.36e+01 1rxxA 421 2.40e+01 d.126.1.4 98061 1rd5A 262 2.41e+01 c.1.2.4 111772 2a74A 643 2.44e+01 1gsjA 258 2.46e+01 c.73.1.2 70397 1gvhA 396 2.46e+01 a.1.1.2 70601 b.43.4.2 70602 c.25.1.5 70603 1i6pA 220 2.47e+01 1ddzA c.53.2.1 61848 1zm0A 114 2.49e+01 b.55.1.1 125276 1zxuA 217 2.51e+01 d.23.1.2 125796 1mkmA 249 2.53e+01 a.4.5.33 79242 d.110.2.2 79243 1jj2A 239 2.57e+01 1rl2A b.34.5.3 63084 b.40.4.5 63085 2fliA 220 2.59e+01 c.1.2.2 133714 2fn9A 290 2.60e+01 1aw7A 194 2.62e+01 1aw7A b.40.2.2 25164 d.15.6.1 37753 2e27L 119 2.63e+01 1qh0A 295 2.66e+01 b.43.4.2 68891 c.25.1.1 68892 2e27H 126 2.71e+01 1ts3A 194 2.75e+01 1aw7A b.40.2.2 25168 d.15.6.1 37757 3b9eA 584 2.76e+01 1tyvA 554 2.77e+01 b.80.1.6 28038 1tyv 542 2.77e+01 1tyv 1ru0A 105 2.83e+01 d.74.1.1 111937 2agyA 361 2.83e+01 2oizA 361 2.84e+01 1yh2A 175 2.85e+01 d.20.1.1 123158 1h4uA 265 2.88e+01 1h4uA d.22.1.2 60622 g.3.11.5 60623 3bijA 285 2.90e+01 2fug7 129 2.91e+01 1iz6A 138 2.93e+01 b.34.5.2 76976 b.40.4.5 76977 1mzyA 333 2.96e+01 b.6.1.3 103848 b.6.1.3 103849 1nqbA 256 2.96e+01 1mfa b.1.1.1 20043 b.1.1.1 20042 2pqvA 154 2.99e+01 2i75A 320 3.00e+01 3c99A 432 3.04e+01 1w34A 304 3.05e+01 b.43.4.2 120620 c.25.1.1 120621 1o7dD 282 3.05e+01 1kw3B 292 3.06e+01 d.32.1.3 77549 d.32.1.3 77550 1p42A 270 3.07e+01 d.14.1.7 87754 d.14.1.7 87755 1ej6D 418 3.08e+01 i.7.1.1 45970 1w6tA 444 3.18e+01 c.1.11.1 120670 d.54.1.1 120671 1xccA 220 3.18e+01 c.47.1.10 115113 1k4iA 233 3.19e+01 d.115.1.2 72056 2bsaA 303 3.21e+01 b.43.4.2 129078 c.25.1.1 129079 2i5fA 109 3.24e+01 1ug4A 60 3.25e+01 3c26A 266 3.26e+01 1b3cA 64 3.28e+01 1aho g.3.7.1 44121 1ylvA 342 3.34e+01 1b4kA c.1.10.3 29180 1d9eA 284 3.35e+01 1d9eA c.1.10.4 29195 2go3A 267 3.40e+01 d.14.1.7 135422 d.14.1.7 135423 2j22A 148 3.41e+01 2viuB 175 3.49e+01 1hgeB h.3.1.1 45676 2q4mA 217 3.50e+01 d.23.1.2 139870 1yudA 170 3.51e+01 b.82.1.16 124046 1ohlA 342 3.56e+01 c.1.10.3 87035 1ncwL 219 3.62e+01 b.1.1.1 85557 b.1.1.2 85558 1gs5A 258 3.65e+01 c.73.1.2 70395 2f4wA 187 3.66e+01 d.20.1.1 132958 1fzyA 149 3.71e+01 d.20.1.1 65072 2ejwA 332 3.73e+01 1hgeB 175 3.74e+01 1hgeB h.3.1.1 45680 1h3fA 432 3.76e+01 c.26.1.1 76631 d.66.1.4 76632 1qhlA 227 3.81e+01 1qhlA c.37.1.12 32382 1gkkA 297 3.81e+01 c.69.1.2 65248 2oqkA 117 3.85e+01 1tcrA 202 3.85e+01 1tcrA b.1.1.1 20605 b.1.1.2 21549 1ogiA 303 3.86e+01 b.43.4.2 92914 c.25.1.1 92915 2bmwA 304 3.86e+01 b.43.4.2 128815 c.25.1.1 128816 1b2rA 304 3.88e+01 1fnc b.43.4.2 25648 c.25.1.1 31538 2co7B 221 3.89e+01 1i4uA 181 3.89e+01 b.60.1.1 61732 2p3yA 491 3.89e+01 2bcqA 335 3.90e+01 a.60.6.1 128304 a.60.12.1 128305 d.218.1.2 128306 2pa6A 427 3.90e+01 1efuA 385 3.93e+01 1efcA b.43.3.1 25682 b.44.1.1 25722 c.37.1.8 32115 1r64A 481 3.94e+01 b.18.1.20 97140 c.41.1.1 97141