# List of top-scoring protein chains for t04-100-30-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 1mkmA 249 9.02e-05 a.4.5.33 79242 d.110.2.2 79243 1in4A 334 1.03e-03 1hqcA a.4.5.11 62597 c.37.1.20 62598 1j5yA 187 1.62e-03 a.4.5.1 71592 d.94.2.1 71593 1in6A 334 1.68e-03 1hqcA a.4.5.11 62601 c.37.1.20 62602 1jhfA 202 2.92e-03 a.4.5.2 63057 b.87.1.1 63058 1j75A 67 1.96e-02 a.4.5.19 62673 1je8A 82 3.18e-02 a.4.6.2 77108 1s3jA 155 6.17e-02 a.4.5.28 -227 1a04A 215 8.94e-02 1a04A a.4.6.2 16234 c.23.1.1 31089 1fseA 74 9.76e-02 1fseA a.4.6.2 60000 1bjaA 95 1.34e-01 1bjaA a.4.5.9 16122 1mzbA 136 1.44e-01 unknown_sccs -266 1q1hA 110 1.51e-01 unknown_sccs -262 1hw1A 239 1.87e-01 1e2xA a.4.5.6 16111 a.78.1.1 18441 1okrA 123 2.00e-01 unknown_sccs -235 1lnwA 147 2.27e-01 a.4.5.28 78104 1lj9A 144 2.46e-01 a.4.5.28 78035 1lvaA 258 2.70e-01 a.4.5.35 74276 a.4.5.35 74277 a.4.5.35 74278 a.4.5.35 74279 1rvkA 382 2.99e-01 c.1.11.2 -5568 d.54.1.1 -9826 2mnr 357 3.32e-01 2mnr c.1.11.2 29245 d.54.1.1 38889 1mdl 359 3.52e-01 2mnr c.1.11.2 29247 d.54.1.1 38891 1fp2A 352 4.09e-01 1fpxA a.4.5.29 59941 c.66.1.12 59942 1hw5A 210 5.75e-01 2cgpA a.4.5.4 16098 b.82.3.2 28137 1on2A 142 8.07e-01 a.4.5.24 87103 a.76.1.1 87104 1qbjA 81 8.67e-01 1qbjA a.4.5.19 16155 1kgsA 225 1.27e+00 a.4.6.1 68596 c.23.1.1 68597 1bj7 156 1.33e+00 1bj7 b.60.1.1 27113 1ad3A 452 1.40e+00 1ad3A c.82.1.1 35335 1pq4A 291 1.63e+00 c.92.2.2 -8633 1bia 321 1.64e+00 1bia a.4.5.1 16083 b.34.1.1 24447 d.104.1.2 40787 1o04A 500 1.75e+00 c.82.1.1 86508 1jpmA 366 1.78e+00 c.1.11.2 67031 d.54.1.1 67032 1e0bA 68 1.86e+00 1e0bA b.34.13.2 37476 1q48A 134 1.96e+00 unknown_sccs -9776 1btl 263 2.22e+00 1btl e.3.1.1 42691 1fipA 98 2.33e+00 1fipA unknown_sccs 18980 1vi9A 299 2.36e+00 c.72.1.5 -8393 1j09A 468 2.91e+00 a.97.1.1 77025 c.26.1.1 77026 1j8yF 297 2.97e+00 1ng1 a.24.13.1 62747 c.37.1.10 62748 5rubA 490 3.04e+00 1burA c.1.14.1 29382 d.58.9.1 39288 1gln 468 3.35e+00 1gln a.97.1.1 18752 c.26.1.1 31588 1ermA 263 3.60e+00 1btl e.3.1.1 42690 1mp8A 281 3.87e+00 d.144.1.7 -11361 1sczA 233 4.11e+00 c.43.1.1 -7326 1g8iA 190 4.17e+00 1rec a.39.1.5 60363 1aj8A 371 4.22e+00 1aj8A a.103.1.1 18900 1e8cA 498 4.26e+00 c.98.1.1 59377 c.59.1.1 59378 c.72.2.1 59379 1n9lA 109 4.30e+00 d.110.3.6 85468 1rypG 244 4.34e+00 d.153.1.4 41938 1lucA 355 4.51e+00 1lucA c.1.16.1 29547 1su8A 636 4.81e+00 e.26.1.2 -12015 1qb5D 99 5.03e+00 b.40.2.1 88357 1j8mF 297 5.43e+00 1ng1 a.24.13.1 62742 c.37.1.10 62743 1r4vA 171 5.47e+00 unknown_sccs -1221 1jx4A 352 5.77e+00 unknown_sccs -10188 unknown_sccs -11898 1kxpD 458 6.25e+00 a.126.1.1 73160 a.126.1.1 73161 a.126.1.1 73162 1mj5A 302 6.28e+00 c.69.1.8 -8326 2ak3A 226 6.74e+00 1zin c.37.1.1 31892 g.41.2.1 45193 1ohuA 175 6.77e+00 f.1.4.1 -12058 1pwxA 254 6.84e+00 c.2.1.2 -5858 1uu1A 335 6.95e+00 c.67.1.1 -8146 1tml 286 7.10e+00 1tml c.6.1.1 30656 1uylA 236 7.19e+00 1ihoA 283 7.27e+00 1ihoA c.26.1.4 62390 1k32A 1045 7.75e+00 b.36.1.3 68068 b.68.7.1 68069 b.69.9.1 68070 c.14.1.2 68071 1b0uA 262 7.75e+00 1b0uA c.37.1.12 32370 1i6iA 366 7.80e+00 1bg2 c.37.1.9 61844 1jjyA 636 7.81e+00 1jjyA 1kk8B 139 8.08e+00 a.39.1.5 77430 2fokA 579 8.20e+00 2fokA a.4.5.12 16131 a.4.5.12 16132 a.4.5.12 16133 c.52.1.12 33323 1o0sA 605 8.42e+00 c.2.1.7 86540 c.58.1.3 86541 1oz9A 150 8.51e+00 unknown_sccs -10588 1oi2A 366 8.64e+00 c.32.1.2 87039 d.79.2.2 87040 1tiiD 99 9.09e+00 1tiiD b.40.2.1 24965 1m40A 263 9.23e+00 e.3.1.1 74437 1cv2A 296 9.39e+00 1bn6A c.69.1.8 34680 1vyrA 364 9.49e+00 1ae9A 179 9.64e+00 1ae9A d.163.1.1 42153 1dozA 309 9.99e+00 1ak1 c.92.1.1 35592 1e3oC 160 9.99e+00 1au7A a.4.1.1 59197 a.35.1.1 59198 1qc7A 101 1.04e+01 1qc7A a.118.14.1 18456 1hs6A 611 1.04e+01 1hs6A a.118.1.7 61233 b.98.1.1 61234 d.92.1.13 61235 1paqA 189 1.06e+01 unknown_sccs -1557 1olrA 224 1.08e+01 b.29.1.11 -3489 1us6A 102 1.11e+01 1nxuA 333 1.12e+01 c.122.1.1 86389 1f2tB 148 1.13e+01 1f2tB 1cpcA 162 1.19e+01 1cpcA a.1.1.3 15643 1d2zA 108 1.21e+01 1d2zA a.77.1.2 18437 1vypX 364 1.21e+01 1pfvA 551 1.22e+01 a.27.1.1 -727 c.26.1.1 -6603 g.41.1.1 -12765 1r6uA 437 1.26e+01 c.26.1.1 -6594 1f4lA 551 1.27e+01 1qqtA a.27.1.1 59648 c.26.1.1 59649 g.41.1.1 59650 1n9bA 265 1.27e+01 e.3.1.1 85463 1nt4A 391 1.28e+01 c.60.1.2 -7942 1p4xA 250 1.30e+01 a.4.5.28 87784 a.4.5.28 87785 1p9bA 442 1.32e+01 c.37.1.10 -7115 1fsz 372 1.34e+01 1fsz c.32.1.1 31750 d.79.2.1 39802 1a9xA 1058 1.34e+01 a.92.1.1 18550 c.24.1.1 31479 c.30.1.1 31657 c.30.1.1 31658 d.142.1.2 41502 d.142.1.2 41503 1hu3A 260 1.36e+01 1hu3A unknown_sccs 19137 1ukz 203 1.39e+01 1zin c.37.1.1 31840 1jb9A 316 1.40e+01 1fnc b.43.4.2 62840 c.25.1.1 62841 1kay 381 1.44e+01 1ba1 c.55.1.1 33385 c.55.1.1 33386 1mgtA 174 1.44e+01 1mgtA a.4.2.1 16078 c.55.7.1 33753 1ub9A 100 1.48e+01 a.4.5.28 -231 1byqA 228 1.50e+01 1yer d.122.1.1 41100 1kit 757 1.55e+01 1kit b.29.1.8 24272 b.29.1.8 24273 b.68.1.1 27616 1obbA 480 1.57e+01 c.2.1.5 86760 d.162.1.2 86761 1ecmA 109 1.57e+01 1ecmA a.130.1.1 19492 1b79A 119 1.59e+01 1b79A a.81.1.1 18451 1hf8A 289 1.61e+01 1hg5A unknown_sccs -399 unknown_sccs -1628 1kblA 873 1.64e+01 c.1.12.2 68384 c.8.1.1 68385 d.142.1.5 68386 1qf5A 431 1.66e+01 1adeA c.37.1.10 32212 1qsdA 106 1.66e+01 1qsdA a.7.5.1 16335 1q06A 135 1.68e+01 a.6.1.3 -375 1h61A 364 1.70e+01 1oyc c.1.4.1 60657 1a8b 318 1.70e+01 1avc a.65.1.1 18171 1squA 155 1.71e+01 unknown_sccs -10229 1f39A 101 1.72e+01 1umuA b.87.1.1 28386 1hn2A 159 1.74e+01 b.60.1.1 65890 1aisB 200 1.75e+01 1aisB a.74.1.2 18384 a.74.1.2 18385 1ec7A 446 1.76e+01 1bqg c.1.11.2 29218 d.54.1.1 38862 1ig8A 486 1.78e+01 2yhx c.55.1.3 64746 c.55.1.3 64747 2dtr 226 1.79e+01 1bi0 a.4.5.24 16193 a.76.1.1 18399 b.34.1.2 24450 1k8kA 418 1.80e+01 c.55.1.1 68305 c.55.1.1 68306 1pujA 282 1.80e+01 c.37.1.8 88294 1moq 368 1.80e+01 1moq c.80.1.1 35302 2rmcA 182 1.81e+01 2cpl b.62.1.1 27491 1dik 874 1.81e+01 1dik c.1.12.2 29304 c.8.1.1 30702 d.142.1.5 41572 1p2fA 220 1.84e+01 a.4.6.1 87720 c.23.1.1 87721 1puoA 170 1.85e+01 a.101.1.1 -1318 a.101.1.1 -1322 1vimA 200 1.91e+01 c.80.1.3 -8532 1gt1A 159 1.92e+01 b.60.1.1 -4436 1j5wA 298 1.98e+01 d.104.1.1 71589 1n81A 186 1.98e+01 a.185.1.1 85388 1ezvA 430 2.00e+01 1be3A d.185.1.1 59541 d.185.1.1 59542 6paxA 133 2.00e+01 6paxA a.4.1.5 64758 a.4.1.5 64759 1h0pA 182 2.05e+01 b.62.1.1 76450 1s1dA 331 2.06e+01 unknown_sccs -4566 1r26A 125 2.09e+01 c.47.1.1 -7389 1dbtA 239 2.12e+01 1dbtA c.1.2.3 28539 1o5oA 221 2.12e+01 c.61.1.1 -7954 1uzbA 516 2.12e+01 c.82.1.1 -8552 1khdA 345 2.15e+01 a.46.2.1 77400 c.27.1.1 77401 1fts 295 2.18e+01 1ng1 a.24.13.1 16968 c.37.1.10 32279 1p7gA 222 2.18e+01 a.2.11.1 -108 d.44.1.1 -9742 1j2aA 166 2.30e+01 b.62.1.1 -4538 1apxA 249 2.31e+01 1ryc a.93.1.1 18669 1a73A 163 2.31e+01 1a73A d.4.1.3 37145 1q35A 320 2.32e+01 c.94.1.1 -8658 1fkmA 396 2.32e+01 1fkmA a.69.2.1 18315 a.69.2.1 18316 1tvxA 75 2.35e+01 1tvxA d.9.1.1 37441 1aa7A 158 2.37e+01 1aa7A a.95.1.1 18741 2ran 316 2.37e+01 1avc a.65.1.1 18170 1rcd 173 2.40e+01 2fha a.25.1.1 16687 1obpA 159 2.46e+01 1obpA b.60.1.1 27092 1gvoA 364 2.48e+01 c.1.4.1 76357 1bupA 386 2.50e+01 1ba1 c.55.1.1 33377 c.55.1.1 33378 1czaN 917 2.54e+01 1qhaA c.55.1.3 33463 c.55.1.3 33464 c.55.1.3 33465 c.55.1.3 33466 1j31A 262 2.55e+01 d.160.1.2 -11473 1a59 378 2.56e+01 1aj8A a.103.1.1 18902 1r1tA 122 2.60e+01 1jboA 162 2.63e+01 a.1.1.3 84150 1bjwA 382 2.64e+01 1bjwA c.67.1.1 34349 1smtA 122 2.72e+01 1smtA a.4.5.5 16109 1oktA 211 2.75e+01 a.45.1.1 -942 c.47.1.5 -7467 1rcwA 231 2.77e+01 unknown_sccs -1921 1a76 326 2.77e+01 1a76 a.60.7.1 18091 c.120.1.2 33361 1rypC 244 2.77e+01 1rypC d.153.1.4 41934 1lldA 319 2.88e+01 3ldh c.2.1.5 30177 d.162.1.1 42144 1blxA 326 2.88e+01 1hcl d.144.1.7 41596 1nu5A 370 2.90e+01 c.1.11.2 -5565 d.54.1.1 -9823 1k8kB 394 2.91e+01 c.55.1.1 68307 1r71A 178 2.93e+01 1top 162 2.95e+01 1ncx a.39.1.5 17223 1kn1A 160 2.96e+01 a.1.1.3 77455 1ewqA 765 2.99e+01 1ewqA a.113.1.1 19069 c.37.1.12 32383 c.55.6.1 33740 d.75.2.1 39743 1gnlA 544 3.00e+01 e.26.1.1 70287 1iw7C 1119 3.02e+01 e.29.1.1 71474 1ua4A 455 3.05e+01 c.72.1.3 -8416 1ad2 228 3.05e+01 1ad2 e.24.1.1 43353 1jcfA 344 3.06e+01 c.55.1.1 62878 c.55.1.1 62879 1l2yA 20 3.11e+01 k.32.1.1 73530 1b4pA 217 3.14e+01 a.45.1.1 83158 c.47.1.5 83159 1csh 435 3.15e+01 1csh a.103.1.1 18880 1rypB 250 3.20e+01 1rypB d.153.1.4 41933 1eqoA 158 3.22e+01 1hka 1f52A 468 3.23e+01 1lgr d.15.9.1 37839 d.128.1.1 41169 1s5lU 134 3.27e+01 1c7qA 445 3.27e+01 2pgi c.80.1.2 35307 1om1A 332 3.29e+01 d.144.1.7 -11318 1h8mA 140 3.29e+01 1h8mA d.110.4.1 60782 1gc5A 467 3.38e+01 1gc5A c.72.1.3 60429 1pieA 419 3.42e+01 d.14.1.5 -9075 unknown_sccs -10120 1mu5A 471 3.46e+01 a.156.1.3 79472 d.14.1.3 79473 d.122.1.2 79474 1ub0A 258 3.50e+01 c.72.1.2 88394 1guzA 310 3.52e+01 c.2.1.5 65586 d.162.1.1 65587 1qazA 351 3.52e+01 1qazA a.102.3.1 18848 1eswA 500 3.54e+01 1cwyA c.1.8.1 59500 1q45A 391 3.56e+01 c.1.4.1 -5199 1hdhA 536 3.59e+01 c.76.1.2 65805 1qydA 313 3.62e+01 c.2.1.2 -5786 1pixA 587 3.62e+01 c.14.1.4 -6282 1bw0A 416 3.65e+01 1bw0A c.67.1.1 34385 2kinA 238 3.67e+01 1bg2 c.37.1.9 32190 1iupA 282 3.67e+01 c.69.1.10 76815 1hr6A 475 3.69e+01 1hr6A d.185.1.1 61164 d.185.1.1 61165 1s7oA 113 3.71e+01 1o1yA 239 3.80e+01 c.23.16.1 86554 1o70A 324 3.80e+01 b.118.1.1 81115 b.118.1.1 81116 1a70 97 3.80e+01 1awd d.15.4.1 37678 1oacA 727 3.81e+01 1oacA b.30.2.1 24390 d.17.2.1 38007 d.17.2.1 38008 d.82.1.1 40003 1kf6C 130 3.85e+01 f.21.2.2 72399 1a8d 452 3.90e+01 1a8d b.29.1.6 24262 b.42.4.2 25607 1ois 223 3.91e+01 1a36A e.15.1.1 43267 1kyqA 274 3.92e+01 c.2.1.11 73281 e.37.1.1 73282 1kkoA 413 3.94e+01 c.1.11.2 68675 d.54.1.1 68676 1h99A 224 3.96e+01 a.142.1.1 60814 a.142.1.1 60815 1gk8A 475 3.97e+01 c.1.14.1 65234 d.58.9.1 65235