# List of top-scoring protein chains for t2k-100-30-stride-ebghtl-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.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 1g9oA 91 1.17e-18 1pdr b.36.1.1 60400 1i92A 91 2.74e-18 1pdr b.36.1.1 61990 2ozfA 92 5.46e-18 2ocsA 88 9.43e-18 2he4A 90 1.06e-17 2he2A 102 4.07e-17 1tp5A 119 7.32e-17 b.36.1.1 119305 1be9A 119 7.55e-17 1pdr b.36.1.1 24774 2jikA 101 1.55e-16 2i1nA 102 1.64e-16 1pdr 99 3.18e-16 1pdr 2opgA 98 3.40e-16 2fe5A 94 4.63e-16 b.36.1.1 133323 2fcfA 103 6.71e-16 b.36.1.1 133267 2qg1A 92 7.16e-16 2awxA 105 8.19e-16 2jilA 97 1.41e-15 2pktA 91 1.76e-15 2fneA 117 3.48e-15 b.36.1.1 133813 1q3oA 109 7.02e-15 b.36.1.1 95700 2uzcA 88 1.85e-14 2iwnA 97 1.86e-14 2egoA 96 2.18e-14 1n7eA 97 3.93e-14 b.36.1.1 91691 1qavA 90 5.12e-14 1qauA b.36.1.1 24777 2f5yA 91 5.48e-14 b.36.1.1 133015 2pa1A 87 8.11e-14 1qavB 115 1.26e-13 1qauA b.36.1.1 24780 1wf7A 103 1.75e-13 b.36.1.1 114577 1b8qA 127 2.11e-13 1qauA b.36.1.1 24781 1qauA 112 3.17e-13 1qauA b.36.1.1 24779 1ihjA 98 4.71e-13 1pdr b.36.1.1 62382 2q3gA 89 6.33e-13 2h3lA 103 7.25e-13 b.36.1.1 136046 2i04A 85 8.59e-13 2f0aA 98 9.09e-13 b.36.1.1 132661 1l6oA 95 1.27e-12 b.36.1.1 84534 2q9vA 90 1.34e-12 1m5zA 91 1.34e-12 b.36.1.1 78676 1mfgA 95 1.40e-12 b.36.1.1 79043 2iwoA 120 2.26e-12 2reyA 100 2.26e-12 1x45A 98 2.41e-12 b.36.1.1 121679 2h2bA 107 3.49e-12 1v5lA 103 3.57e-12 b.36.1.1 108378 1nf3C 128 4.60e-12 b.36.1.1 85596 2gzvA 114 9.75e-12 2eaqA 90 1.14e-11 1kwaA 88 1.40e-11 1kwaA b.36.1.1 24772 1fc6A 388 1.66e-11 1fc6A b.36.1.3,c.14.1.2 64738,64739 2vphA 100 2.56e-11 3bpuA 88 4.01e-11 2rczA 81 1.25e-10 2qkvA 96 1.45e-10 1r6jA 82 2.01e-10 b.36.1.1 97151 1lcyA 325 7.50e-09 b.36.1.4,b.47.1.1 73834,73835 2p3wA 112 1.22e-08 1te0A 318 1.39e-07 b.36.1.4,b.47.1.1 112400,112401 1y8tA 324 1.55e-06 b.36.1.4,b.47.1.1 122763,122764 1sotA 320 1.55e-05 b.36.1.4,b.47.1.1 105852,105853 1ky9A 448 1.37e-04 b.36.1.4,b.47.1.1 73198,73199 2i6vA 87 1.06e-03 2dy0A 190 1.27e-02 2ps1A 226 4.13e-02 1zn8A 180 5.78e-02 c.61.1.1 125376 1ao0A 459 9.36e-02 1ecfB c.61.1.1,d.153.1.1 34049,41816 2j3tD 219 1.57e-01 1db3A 372 1.61e-01 1db3A c.2.1.2 29813 1bx4A 345 2.64e-01 1bx4A c.72.1.1 34935 2bonA 332 3.92e-01 1gph1 465 5.25e-01 1ecfB 1aiqA 264 6.75e-01 1bkpA d.117.1.1 40967 2g8oA 264 7.43e-01 d.117.1.1 134779 1qqqA 264 7.63e-01 1bkpA d.117.1.1 40931 1axwA 265 7.68e-01 1bkpA d.117.1.1 40938 1evfA 264 7.87e-01 1bkpA d.117.1.1 40932 2g8mA 264 8.34e-01 1jalA 363 9.80e-01 c.37.1.8,d.15.10.2 84138,84139 2ywvA 244 1.03e+00 2ogxB 270 1.15e+00 1hvyA 288 1.22e+00 1bkpA d.117.1.1 41049 1ev5A 264 1.35e+00 1bkpA d.117.1.1 40935 1vpqA 273 1.46e+00 c.1.32.1 113974 2tscA 264 1.65e+00 1bkpA d.117.1.1 40952 1zm8A 259 1.75e+00 2gwnA 452 2.00e+00 1ypvA 313 2.04e+00 2p5iA 288 2.14e+00 1a9xA 1058 2.16e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18550,31479,31657,31658,41502,41503 1x3mA 415 2.25e+00 c.55.1.2,c.55.1.2 121664,121665 2hjgA 436 2.33e+00 1fwkA 296 2.47e+00 1fwkA d.14.1.5,d.58.26.1 37576,39398 2e1zA 415 2.82e+00 2z0dB 125 3.01e+00 d.15.1.3 140096 1ti6A 875 3.39e+00 b.52.2.2,c.81.1.1 106974,106975 1t6t1 118 3.68e+00 1cs0A 1073 3.75e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18558,31487,31673,31674,41518,41519 1uc2A 481 3.81e+00 d.261.1.1 99161 1zq9A 285 4.05e+00 c.66.1.24 125505 1opr 213 4.23e+00 1opr 1p99A 295 4.25e+00 c.94.1.1 94384 1qb7A 236 4.46e+00 1qb7A c.61.1.1 34087 2yv1A 294 4.52e+00 1wlsA 328 4.71e+00 1kw4A 89 4.77e+00 a.60.1.2 73077 1h1dA 221 4.80e+00 c.66.1.1 83452 1xebA 150 4.97e+00 d.108.1.1 115219 1r13A 148 5.08e+00 d.169.1.1,h.1.1.1 96782,96783 1yb2A 275 5.10e+00 c.66.1.13 122868 1c3oA 1073 5.21e+00 1c3oA a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18562,31491,31681,31682,41526,41527 3bs5B 80 5.31e+00 1y0yA 353 5.59e+00 b.49.3.1,c.56.5.4 122514,122515 1fxrA 64 5.70e+00 1fxd d.58.1.4 38993 1oroA 213 6.29e+00 1opr c.61.1.1 34093 2iyeA 263 6.48e+00 1xfoA 357 6.64e+00 b.49.3.1,c.56.5.4 115265,115266 1zsyA 357 7.14e+00 2v03A 303 7.28e+00 3bkxA 275 7.30e+00 1fr3A 67 7.38e+00 1fr3A b.40.6.1 25436 2fa1A 160 7.77e+00 d.190.1.2 133182 1h3gA 601 7.78e+00 b.1.18.2,b.71.1.1,c.1.8.1 90594,90595,90596 2bw3A 534 7.80e+00 a.270.1.1,c.55.3.12 129317,129318 1h72C 296 8.10e+00 d.14.1.5,d.58.26.1 60712,60713 2pfuA 99 8.67e+00 2pkpA 170 9.10e+00 1skyB 502 9.54e+00 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18313,26478,32358 1g2qA 187 9.70e+00 c.61.1.1 65117 1oi7A 288 9.82e+00 c.2.1.8,c.23.4.1 87049,87050 1fsgA 233 1.13e+01 1qk3A c.61.1.1 34029 1u4nA 310 1.17e+01 c.69.1.2 113021 2oqrA 230 1.20e+01 1fxlA 167 1.22e+01 1b7fA d.58.7.1,d.58.7.1 39183,39184 2cc0A 195 1.25e+01 c.6.2.3 130209 2dyoA 297 1.28e+01 1mo1A 87 1.28e+01 d.94.1.1 91363 1vc3B 97 1.31e+01 2og1A 286 1.35e+01 1vkmA 297 1.36e+01 c.138.1.1 108670 1ecfA 504 1.43e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 2pe3A 354 1.45e+01 1ecfB 504 1.45e+01 1ecfB c.61.1.1,d.153.1.1 34054,41821 2iayA 114 1.46e+01 1befA 181 1.50e+01 1befA b.47.1.3 26419 2p1zA 180 1.51e+01 1se8A 301 1.54e+01 b.40.4.3 105448 1g57A 217 1.55e+01 1g57A d.115.1.2 60253 2fvgA 340 1.55e+01 b.49.3.1,c.56.5.4 134201,134202 1dioA 554 1.60e+01 1dioA c.1.19.3 29656 1eexA 554 1.60e+01 1dioA c.1.19.3 29650 2dykA 161 1.67e+01 2a9oA 120 1.75e+01 c.23.1.1 126444 1gjjA 168 1.82e+01 a.140.1.1,a.140.1.1 83291,83292 1bu6O 501 1.83e+01 1glcG c.55.1.4,c.55.1.4 33499,33500 1xv5A 401 1.84e+01 2hb5A 164 1.87e+01 2pn0A 141 1.91e+01 1vid 221 1.92e+01 1vid 1qwjA 229 1.97e+01 c.68.1.13 96478 2yysA 286 2.00e+01 1vheA 373 2.00e+01 b.49.3.1,c.56.5.4 100669,100670 1dgsA 667 2.01e+01 1dgsA a.60.2.2,b.40.4.6,d.142.2.2 17963,25365,41581 2rhwA 283 2.04e+01 2e85A 159 2.09e+01 2vbuA 136 2.09e+01 2r6fA 972 2.11e+01 1vybA 238 2.12e+01 d.151.1.1 108897 1r2jA 366 2.17e+01 a.29.3.1,e.6.1.1 96869,96870 2puhA 286 2.19e+01 1xx6A 191 2.20e+01 c.37.1.24,g.39.1.14 116139,116140 2btuA 346 2.20e+01 1lh0A 213 2.21e+01 c.61.1.1 73896 1iezA 217 2.22e+01 d.115.1.2 66129 2pujA 286 2.22e+01 1w30A 201 2.23e+01 c.61.1.1 114118 2fp7B 172 2.35e+01 b.47.1.3 133899 2pnkA 428 2.38e+01 2qeeA 437 2.40e+01 3sxlA 184 2.41e+01 1b7fA d.58.7.1,d.58.7.1 39173,39174 2oq2A 261 2.43e+01 1dl5A 317 2.48e+01 1dl5A c.66.1.7,d.197.1.1 64720,64721 1xocA 520 2.54e+01 c.94.1.1 122201 1uheA 97 2.70e+01 1cliA 345 2.74e+01 1cliA d.79.4.1,d.139.1.1 39816,41459 2o62A 270 2.84e+01 2if6A 186 2.86e+01 1o8bA 219 2.87e+01 c.124.1.4,d.58.40.1 81180,81181 1l1qA 186 2.89e+01 c.61.1.1 77653 2bh8A 101 3.04e+01 2oynA 146 3.05e+01 1i0hA 205 3.07e+01 1avmA a.2.11.1,d.44.1.1 15760,38685 1ix9A 205 3.07e+01 a.2.11.1,d.44.1.1 76899,76900 1fdr 248 3.13e+01 1fdr 1fdrA 248 3.13e+01 b.43.4.2,c.25.1.1 25653,31543 1d5nA 205 3.13e+01 1avmA a.2.11.1,d.44.1.1 15762,38687 1h8eA 510 3.19e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 60738,60739,60740 2hm7A 310 3.19e+01 1sw5A 275 3.20e+01 c.94.1.1 106069 1vhoA 346 3.22e+01 b.49.3.1,c.56.5.4 100694,100695 1pii 452 3.29e+01 1pii 1piiA 452 3.29e+01 c.1.2.4,c.1.2.4 28559,28563 2z1cA 75 3.32e+01 2i2wA 212 3.32e+01 2fiwA 172 3.35e+01 d.108.1.1 133539 1ialA 453 3.37e+01 1bk5A a.118.1.1 19116 1zrnA 232 3.38e+01 c.108.1.1 43323 2dkzA 84 3.40e+01 2himA 358 3.42e+01 2qm0A 275 3.52e+01 1sw2A 275 3.57e+01 c.94.1.1 106064 1mkmA 249 3.60e+01 a.4.5.33,d.110.2.2 79242,79243 1dekA 241 3.61e+01 1dekA c.37.1.1 31842 1a8y 367 3.67e+01 1a8y 1a8yA 367 3.67e+01 c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 2b4aA 138 3.90e+01 c.23.1.1 127817 1ah1 129 3.92e+01 1ah1 2it2A 200 3.92e+01 1wspA 84 4.01e+01 1uzcA 71 4.02e+01 a.159.2.1 100222 1st0A 337 4.04e+01 d.13.1.3,d.246.1.1 98979,98980 1l7yA 94 4.07e+01 d.15.1.6 73676 1e2wA 251 4.07e+01 1hcz b.2.6.1,b.84.2.2 22466,28252 1qu9A 128 4.08e+01 1qu9A d.79.1.1 39755 2p5xA 230 4.08e+01 1kyaA 499 4.18e+01 b.6.1.3,b.6.1.3,b.6.1.3 73203,73204,73205 2jdiA 510 4.20e+01 1a8uA 277 4.20e+01 1brt c.69.1.12 34703 2ddhA 661 4.27e+01 a.29.3.2,a.29.3.2,e.6.1.2 131394,131395,131396 1ueoA 63 4.30e+01 j.107.1.1 99269 2ahqA 76 4.31e+01 2yy3A 91 4.40e+01 1scuA 288 4.41e+01 2scuA c.2.1.8,c.23.4.1 30307,31135 1efvA 315 4.47e+01 1efvA c.26.2.3,c.31.1.2 31633,31728 2j01Q 141 4.50e+01 2scuA 288 4.51e+01 2scuA c.2.1.8,c.23.4.1 30303,31131 2f7fA 494 4.57e+01 c.1.17.1,d.41.2.1 133088,133089 2ckiA 262 4.59e+01 1txvB 440 4.60e+01 b.1.15.1,c.62.1.1,g.16.2.1 112784,112785,112786 1q7rA 219 4.60e+01 c.23.16.1 96054 1w78A 422 4.67e+01 2rfiA 285 4.67e+01 3bciA 186 4.71e+01 2jsoA 88 4.77e+01 1y0bA 197 4.81e+01 c.61.1.1 122476 1xhbA 472 4.82e+01 b.42.2.1,c.68.1.17 115290,115291 1y5eA 169 4.94e+01 c.57.1.1 122632 2igqA 285 5.00e+01 1i6pA 220 5.01e+01 1ddzA c.53.2.1 61848 1yloA 348 5.14e+01 b.49.3.1,c.56.5.4 123659,123660 2epgA 487 5.17e+01 2drvA 200 5.20e+01 1broA 277 5.35e+01 1brt c.69.1.12 34700 2az4A 429 5.45e+01 d.157.1.10 127597 1earA 147 5.50e+01 b.107.1.1,d.58.38.1 64875,64876 2i1mA 333 5.61e+01 2hhgA 139 5.68e+01 1vraB 215 5.69e+01 1vzoA 355 5.69e+01 d.144.1.7 108971 1u5hA 273 5.70e+01 c.1.12.5 113037 2gakA 391 5.75e+01 1x92A 199 5.78e+01 c.80.1.3 114976 2bb3A 221 5.83e+01 c.90.1.1 128257 1a8vA 121 5.88e+01 1a62 a.140.3.1,b.40.4.5 64712,64713 1f28A 297 5.91e+01 1bkpA d.117.1.1 59608 2i3sB 36 5.93e+01 1t5eA 360 5.94e+01 f.46.1.1 106436 1u5vA 273 6.01e+01 c.1.12.5 113054 1cby 259 6.09e+01 1cby 1cbyA 259 6.09e+01 d.103.1.1 40705 1ybhA 590 6.11e+01 c.31.1.3,c.36.1.5,c.36.1.9 122891,122892,122893 1dpuA 99 6.13e+01 1dpuA a.4.5.16 16150 3c3mA 138 6.15e+01 3biqA 467 6.15e+01 1wfxA 186 6.22e+01 d.166.1.5 114596 1fjgK 129 6.32e+01 1fjfK c.55.4.1 33733 2qv6A 268 6.41e+01 1koe 172 6.43e+01 1koe 1koeA 172 6.43e+01 d.169.1.5 42448 2aefA 234 6.44e+01 1a62 130 6.45e+01 1a62 1a62A 130 6.45e+01 a.140.3.1,b.40.4.5 64708,64709 2jzfA 143 6.45e+01 2v76A 107 6.49e+01 1ciqA 40 6.50e+01 2sniI d.40.1.1 38576 1cmxA 236 6.52e+01 1uch d.3.1.6 37130 2r3uA 211 6.53e+01 1s29A 92 6.59e+01 a.4.5.46 98373 1ebuA 358 6.64e+01 1ebuA c.2.1.3,d.81.1.2 30035,39950 1jmcA 246 6.64e+01 1jmcA b.40.4.3,b.40.4.3 25300,25301 2q3bA 313 6.72e+01 1brt 277 6.72e+01 1brt 1brtA 277 6.72e+01 c.69.1.12 34699 1wmiA 90 6.73e+01 d.298.1.2 121045 1dzfA 215 6.80e+01 1dzfA c.52.3.1,d.78.1.1 33344,39753 2r5nA 669 6.87e+01 1qfrA 89 6.89e+01 1ptf d.94.1.1 40552 1wkvA 389 6.89e+01 c.79.1.1 120989 1nwaA 203 6.92e+01 d.58.28.1 86295 1qgdA 662 6.97e+01 c.36.1.6,c.36.1.10,c.48.1.1 88367,88368,88369 2nykA 285 6.99e+01 2p3rA 510 7.06e+01 c.55.1.4,c.55.1.4 139471,139472 2cuyA 305 7.18e+01 2j0aA 280 7.22e+01 2cduA 452 7.25e+01 1f3zA 161 7.28e+01 b.84.3.1 28273 2e0qA 104 7.29e+01 1z1dA 103 7.32e+01 a.4.5.16 124351 3b46A 447 7.32e+01 2uykA 129 7.39e+01 2ofqA 95 7.41e+01 1v7lA 163 7.43e+01 c.8.2.1 113562 3bbdA 205 7.52e+01 1l2tA 235 7.56e+01 c.37.1.12 73514 2qg3A 208 7.61e+01 1mt6A 280 7.63e+01 b.76.2.1,b.85.7.1 79446,79447 1q7gA 359 7.63e+01 c.2.1.3,d.81.1.2 96038,96039 2r8oA 669 7.68e+01 2zdiC 151 7.80e+01 2o2yA 349 7.85e+01 c.2.1.2 138894 1n6aA 259 7.88e+01 b.76.2.1,b.85.7.1 80121,80122 1nepA 130 7.88e+01 b.1.18.7 80440 1wvhA 134 7.88e+01 b.55.1.2 121341 2iacA 142 7.89e+01 3bedA 142 7.89e+01 2id0A 644 7.93e+01 2ia2A 265 7.97e+01