# List of top-scoring protein chains for t2k-100-30-o_notor2-scores 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 1fwyA 331 2.25e+00 1fwyA b.81.1.4,c.68.1.5 28064,34522 2ch8A 201 2.34e+00 1o8uA 257 2.65e+00 c.14.1.3 81194 1hv9A 456 2.68e+00 1fwyA b.81.1.4,c.68.1.5 28060,34518 1fxjA 331 2.72e+00 1fwyA b.81.1.4,c.68.1.5 28062,34520 1mkyA 439 2.90e+00 c.37.1.8,c.37.1.8,d.52.5.1 79250,79251,79252 1xt5A 135 2.98e+00 1hkfA 122 3.31e+00 b.1.1.1 83553 1om0A 274 3.58e+00 c.1.8.5 87058 1szoA 257 4.14e+00 c.14.1.3 106164 1ta3A 274 4.38e+00 c.1.8.5 106731 1oe4A 247 5.14e+00 c.18.1.3 86895 1v0wA 506 6.04e+00 d.136.1.2,d.136.1.2 108220,108221 1eft 405 6.32e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25688,25728,32123 1f0iA 504 6.48e+00 1f0iA d.136.1.2,d.136.1.2 59566,59567 1wleA 501 6.48e+00 1exmA 405 6.78e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 1krhA 338 7.52e+00 b.43.4.2,c.25.1.2,d.15.4.2 72891,72892,72893 2tbd 134 8.37e+00 2tbd d.89.1.1 40241 1aipA 405 1.02e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25697,25737,32132 1tbd 134 1.02e+01 2tbd d.89.1.1 40240 1jzuA 157 1.03e+01 b.60.1.1 84271 1ejbA 168 1.09e+01 1rvv1 c.16.1.1 59417 1zesA 125 1.22e+01 1rz1A 161 1.23e+01 b.45.1.2 98124 1aipE 405 1.23e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25699,25739,32134 1l5zA 155 1.28e+01 c.23.1.1 77722 1yal 218 1.29e+01 1cs8A d.3.1.1 37025 1ykfA 352 1.31e+01 1pedA b.35.1.2,c.2.1.1 24757,29773 1fjgP 88 1.39e+01 1emwA d.27.1.1 38444 1ha3A 405 1.49e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 2c78A 405 1.52e+01 1oaoA 674 1.53e+01 e.26.1.2 86744 1r88A 280 1.55e+01 c.69.1.3 97219 1pjcA 361 1.57e+01 1sayA c.2.1.4,c.23.12.2 30101,31361 1hqkA 154 1.65e+01 c.16.1.1 65902 1nkoA 132 1.65e+01 b.1.1.1 85829 1qkkA 155 1.78e+01 1dbwA c.23.1.1 31104 1ww9A 392 1.80e+01 1nhcA 336 1.82e+01 b.80.1.3 91879 1nmuB 104 1.86e+01 d.79.3.1 80666 1o66A 275 1.87e+01 c.1.12.8 92547 1kgsA 225 1.95e+01 a.4.6.1,c.23.1.1 68596,68597 1llfA 534 1.97e+01 c.69.1.17 78094 1przA 252 2.02e+01 d.265.1.3 95064 1kq3A 376 2.02e+01 e.22.1.2 68790 2agkA 260 2.05e+01 1xfsA 178 2.06e+01 d.129.3.5 109589 1ujpA 271 2.08e+01 c.1.2.4 99462 1x99A 145 2.15e+01 1xvwA 160 2.15e+01 1k4mA 213 2.16e+01 c.26.1.3 77258 1kgcE 242 2.18e+01 b.1.1.1,b.1.1.2 77386,77387 1qo7A 394 2.18e+01 1qo7A c.69.1.11 34697 1xc3A 302 2.32e+01 1ukuA 102 2.51e+01 d.58.5.2 99533 2ag9A 164 2.55e+01 1vq2A 193 2.56e+01 2ag4A 164 2.75e+01 2g5rA 127 2.76e+01 1v5eA 590 2.78e+01 1pjbA 361 2.79e+01 1sayA c.2.1.4,c.23.12.2 30103,31363 1u0tA 307 2.80e+01 e.52.1.1 107567 1pu5A 164 2.85e+01 b.95.1.1 104310 1iqsA 88 2.86e+01 d.214.1.1 71278 1wohA 305 2.86e+01 c.42.1.1 109446 1mjfA 281 2.87e+01 c.66.1.17 79198 1yovA 537 3.04e+01 2cbf 234 3.08e+01 1cbf c.90.1.1 35588 1vajA 214 3.15e+01 1cvrA 435 3.20e+01 1cvrA b.1.18.12,c.17.1.2 21949,31006 1emwA 88 3.22e+01 1emwA d.27.1.1 38448 1whtA 256 3.23e+01 1ivyA c.69.1.5 34646 2as9A 210 3.33e+01 1ejeA 192 3.34e+01 1ejeA b.45.1.2 25757 1dts 221 3.35e+01 1byi c.37.1.10 32200 1ehkB 168 3.40e+01 2cuaA b.6.1.2,f.17.2.1 23041,43625 3ullA 132 3.47e+01 3ullA b.40.4.3 25282 1o7sA 127 3.50e+01 b.1.1.1 86644 1hv2A 99 3.52e+01 d.42.1.1 61287 1sayA 361 3.60e+01 1sayA c.2.1.4,c.23.12.2 30102,31362 1kzhA 555 3.67e+01 c.89.1.1 73361 1b74A 254 3.69e+01 1b74A c.78.2.1,c.78.2.1 35264,35265 1e8cA 498 3.71e+01 c.98.1.1,c.59.1.1,c.72.2.1 59377,59378,59379 1efuA 385 3.72e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25682,25722,32115 2b8nA 429 3.75e+01 2bzlA 325 3.82e+01 1pk6C 129 3.84e+01 b.22.1.1 94803 1zoiA 276 3.91e+01 1o97C 264 3.92e+01 c.26.2.3 81232 2fliA 220 3.95e+01 1gq6A 313 3.99e+01 c.42.1.1 70341 1cleA 534 4.00e+01 1thg c.69.1.17 34771 1w78A 422 4.01e+01 1i86A 389 4.02e+01 c.95.1.2,c.95.1.2 66068,66069 1bj7 156 4.06e+01 1bj7 b.60.1.1 27113 1dad 224 4.07e+01 1byi c.37.1.10 32204 1p3jA 217 4.09e+01 c.37.1.1,g.41.2.1 94022,94023 1e5pA 151 4.13e+01 1bj7 b.60.1.1 59272 2b4aA 138 4.15e+01 1rljA 139 4.30e+01 c.23.5.7 104983 1rybA 212 4.31e+01 c.56.3.1 98098 1u9kA 114 4.32e+01 1x42A 232 4.39e+01 1ewjA 126 4.39e+01 1ecsA d.32.1.2 59526 1i88A 389 4.43e+01 c.95.1.2,c.95.1.2 66070,66071 1oj7A 408 4.46e+01 e.22.1.2 103971 1zmyA 142 4.52e+01 2et1A 201 4.54e+01 1klo 162 4.60e+01 1klo g.3.11.2,g.3.11.2,g.3.11.2 44326,44327,44328 1o22A 170 4.65e+01 d.238.1.1 86557 1wiwA 290 4.78e+01 1a6q 382 4.80e+01 1a6q a.159.1.1,d.219.1.1 75801,75802 1g2oA 268 4.80e+01 1b8oA c.56.2.1 60228 2a3nA 355 4.90e+01 1e9rA 437 4.91e+01 c.37.1.11 64827 1u02A 239 4.94e+01 c.108.1.15 107538 1vhoA 346 4.95e+01 b.49.3.1,c.56.5.4 100694,100695 1gph1 465 4.96e+01 1ecfB 1bi5A 389 5.06e+01 1bi5A c.95.1.2,c.95.1.2 35985,35986 1kcw 1046 5.14e+01 1kcw b.6.1.3,b.6.1.3,b.6.1.3,b.6.1.3,b.6.1.3,b.6.1.3 23151,23152,23153,23154,23155,23156 1pytC 253 5.16e+01 5ptp b.47.1.2 26233 2arhA 203 5.18e+01 1g13A 162 5.18e+01 1g13A b.95.1.1 60194 1zxmA 400 5.19e+01 1x1gA 129 5.27e+01 2b9wA 424 5.27e+01 2fgoA 82 5.29e+01 1w0pA 781 5.30e+01 b.29.1.8,b.29.1.8,b.68.1.1 109038,109039,109040 2biiA 424 5.31e+01 2asuB 234 5.35e+01 2c1cA 312 5.35e+01 1kqfB 294 5.36e+01 d.58.1.5,f.23.22.1 75900,75901 1guiA 155 5.40e+01 b.18.1.14 76351 1a8s 273 5.41e+01 1brt c.69.1.12 34710 2cuaA 135 5.41e+01 2cuaA b.6.1.2 23039 2cxcA 144 5.41e+01 1cb6A 691 5.42e+01 1cb6A c.94.1.2,c.94.1.2 35840,35841 1vj0A 380 5.47e+01 b.35.1.2,c.2.1.1 100786,100787 1w6uA 302 5.48e+01 1ei9A 279 5.52e+01 1ei9A c.69.1.13 34713 1b73A 254 5.55e+01 1b74A c.78.2.1,c.78.2.1 35266,35267 1uuyA 167 5.57e+01 c.57.1.1 108059 1kfwA 435 5.64e+01 c.1.8.5,d.26.3.1 77376,77377 1byi 224 5.64e+01 1byi c.37.1.10 32199 2evwX 166 5.65e+01 1srrA 124 5.65e+01 1dz3A c.23.1.1 31110 1ptmA 329 5.66e+01 c.77.1.3 95104 1lcf 691 5.67e+01 1cb6A c.94.1.2,c.94.1.2 35838,35839 1pjr 724 5.74e+01 1pjr c.37.1.19,c.37.1.19 32391,32392 1nt4A 391 5.77e+01 c.60.1.2 92102 1h3fA 432 5.82e+01 c.26.1.1,d.66.1.4 76631,76632 1ej8A 140 5.86e+01 1qupA b.1.8.1 22300 1a8q 274 5.91e+01 1brt c.69.1.12 34702 1vdwA 254 5.96e+01 e.7.1.1 100569 2fdsA 352 6.01e+01 1jiwI 106 6.01e+01 1smpI b.61.2.1 63078 1tc5A 194 6.02e+01 c.110.1.1 106752 1kewA 361 6.03e+01 c.2.1.2 68544 1gw5S 142 6.03e+01 d.110.4.2 70633 1pedA 351 6.04e+01 1pedA b.35.1.2,c.2.1.1 24753,29769 1fonA 240 6.05e+01 5ptp b.47.1.2 26231 1b00A 127 6.08e+01 3chy c.23.1.1 31122 1s6yA 450 6.08e+01 c.2.1.5,d.162.1.2 105314,105315 1k1gA 131 6.15e+01 d.51.1.1 68015 1wcuA 153 6.19e+01 2b6dA 345 6.19e+01 1efcA 393 6.30e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25680,25720,32113 1tluA 130 6.41e+01 d.156.1.2 107139 1l5jA 865 6.47e+01 a.118.15.1,c.8.2.1,c.83.1.1 73592,73593,73594 1qfjA 232 6.52e+01 1qfjA b.43.4.2,c.25.1.1 25655,31545 1tn3 137 6.60e+01 1htn d.169.1.1 42423 1thg 544 6.75e+01 1thg c.69.1.17 34763 1hnf 182 6.76e+01 1qa9A b.1.1.1,b.1.1.3 19741,21680 1zedA 484 6.85e+01 1ecsA 126 6.88e+01 1ecsA d.32.1.2 59407 1ck9A 104 6.89e+01 1ck9A d.79.3.1 39806 1nkxA 348 6.95e+01 c.94.1.2 91943 1czfA 362 7.01e+01 1czfA b.80.1.3 28031 1qupA 222 7.06e+01 1qupA b.1.8.1,d.58.17.1 22301,39352 1tzbA 302 7.08e+01 c.80.1.1 107470 2an1A 292 7.18e+01 1tllA 688 7.18e+01 b.43.4.1,c.23.5.2,c.25.1.4 107128,107129,107130 1ew2A 513 7.23e+01 1b8jA c.76.1.1 59525 1qwoA 442 7.29e+01 c.60.1.2 104620 1cbf 285 7.30e+01 1cbf c.90.1.1 35587 1vclA 432 7.30e+01 b.42.2.1,b.42.2.1,d.281.1.1 108498,108499,108500 2f4qA 346 7.34e+01 1d3yA 301 7.37e+01 1d3yA e.12.1.1 43252 1t95A 240 7.38e+01 a.5.8.1,d.235.1.2,d.58.11.3 106705,106706,106707 1jkmB 361 7.40e+01 1jkmA c.69.1.2 34634 1ao0A 459 7.44e+01 1ecfB c.61.1.1,d.153.1.1 34049,41816 2frgP 106 7.47e+01 1x9iA 302 7.53e+01 1ws6A 171 7.60e+01 1f20A 435 7.61e+01 b.43.4.1,c.25.1.4 64932,64933 1h72C 296 7.61e+01 d.14.1.5,d.58.26.1 60712,60713 1pkoA 139 7.64e+01 b.1.1.1 88147 2h2tB 175 7.68e+01 1umkA 275 7.73e+01 821p 166 7.73e+01 1ctqA c.37.1.8 31969 2azpA 318 7.80e+01 1dbs 224 7.81e+01 1byi c.37.1.10 32209 1f2fA 104 7.83e+01 1fmk d.93.1.1 40455 1rl6A 177 7.86e+01 1rl6A d.141.1.1,d.141.1.1 41473,41474 2aysA 348 7.89e+01 1vr7A 142 7.93e+01 1qb5D 99 8.03e+01 b.40.2.1 88357 1k8kD 300 8.05e+01 d.198.2.1,d.198.2.1 68309,68310 1inlA 296 8.08e+01 c.66.1.17 66220 1aoy 78 8.15e+01 1aoy a.4.5.3 16087 1a0hA 159 8.15e+01 1a0hA b.47.1.2,g.14.1.1 26229,44655 2ervA 150 8.29e+01 1kit 757 8.35e+01 1kit b.29.1.8,b.29.1.8,b.68.1.1 24272,24273,27616 1hqcA 324 8.41e+01 1hqcA a.4.5.11,c.37.1.20 16127,32424 1fwkA 296 8.49e+01 1fwkA d.14.1.5,d.58.26.1 37576,39398 2eu8A 216 8.50e+01 1o0uA 429 8.68e+01 c.118.1.1 80743 2fhxA 246 8.69e+01 1ws0A 156 8.70e+01 1t0bA 252 8.74e+01 c.23.16.6 106199 1bxkA 355 8.77e+01 1bxkA c.2.1.2 29803 1joa 447 8.87e+01 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30563,30564,40203 1h7zA 194 8.87e+01 1qhvA b.21.1.1 60733 1i1kA 309 8.94e+01 1daaA e.17.1.1 61533 1qsoA 149 8.94e+01 1qsmA d.108.1.1 40812 1w9pA 433 8.95e+01