# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7-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 1hn9A 317 7.07e-01 1hn9A c.95.1.2,c.95.1.2 35977,35978 1vm8A 534 7.20e-01 1tjyA 316 9.51e-01 c.93.1.1 107062 1u7nA 336 1.01e+00 c.77.1.4 107726 1jv1A 505 1.13e+00 c.68.1.5 71892 1r9dA 787 1.53e+00 c.7.1.1 104865 1tedA 393 1.59e+00 c.95.1.2 106807 1ldg 316 2.88e+00 1ceqA c.2.1.5,d.162.1.1 30165,42132 1pzgA 331 3.75e+00 c.2.1.5,d.162.1.1 95425,95426 1t2dA 322 3.80e+00 c.2.1.5,d.162.1.1 99084,99085 1z90A 469 3.96e+00 1r5jA 337 4.50e+00 c.77.1.5 97097 1hnjA 317 5.47e+00 1hn9A c.95.1.2,c.95.1.2 35969,35970 1ceqA 316 5.57e+00 1ceqA c.2.1.5,d.162.1.1 30163,42130 1kr5A 226 5.68e+00 c.66.1.7 68847 1kaeA 434 6.14e+00 c.82.1.2 72247 1jbwA 428 6.30e+00 c.59.1.2,c.72.2.2 62860,62861 1fhdA 312 6.36e+00 1taxA c.1.8.3 28915 1eblA 317 6.99e+00 1hn9A c.95.1.2,c.95.1.2 35973,35974 1od8A 313 7.60e+00 c.1.8.3 86838 1rypI 222 7.67e+00 d.153.1.4 41877 1k6wA 426 8.11e+00 b.92.1.2,c.1.9.5 68236,68237 1li5A 461 8.13e+00 a.27.1.1,c.26.1.1 73912,73913 1zowA 313 8.14e+00 1pswA 348 8.64e+00 c.87.1.7 88287 1eblB 317 8.77e+00 1hn9A c.95.1.2,c.95.1.2 35975,35976 1v0lA 313 9.07e+00 c.1.8.3 108207 1h8eD 482 9.47e+00 1skyE a.69.1.1,b.49.1.1,c.37.1.11 60747,60748,60749 2bvyA 475 1.03e+01 1jmxB 349 1.03e+01 b.69.2.2 66906 1ra0A 430 1.04e+01 1k75A 434 1.06e+01 c.82.1.2 68253 1j79A 347 1.06e+01 1j79A c.1.9.4 62675 1e0wA 313 1.09e+01 1taxA c.1.8.3 59150 1wzaA 488 1.10e+01 1i1nA 226 1.10e+01 c.66.1.7 71102 2dorA 311 1.11e+01 2dorA c.1.4.1 28593 1p1mA 406 1.15e+01 b.92.1.4,c.1.9.9 87696,87697 1w0mA 226 1.24e+01 c.1.1.1 109027 1zxxA 319 1.31e+01 2dkaA 544 1.32e+01 1fh9A 312 1.43e+01 1taxA c.1.8.3 28913 1xr4A 509 1.44e+01 4pfk 319 1.45e+01 3pfk c.89.1.1 35582 3pfk 319 1.47e+01 3pfk c.89.1.1 35581 1w32A 348 1.48e+01 1pbyB 337 1.53e+01 b.69.2.2 94422 2g39A 497 1.56e+01 1jjuB 337 1.60e+01 b.69.2.2 66779 1wq3A 322 1.64e+01 1frb 315 1.67e+01 1frb c.1.7.1 28665 1i88A 389 1.70e+01 c.95.1.2,c.95.1.2 66070,66071 1clxA 347 1.70e+01 1taxA c.1.8.3 28899 1hjsA 332 1.72e+01 c.1.8.3 83492 1kewA 361 1.79e+01 c.2.1.2 68544 2bi0A 337 1.80e+01 1ryp2 233 1.80e+01 1ryp2 1abbA 828 1.86e+01 1a8i c.87.1.4 35536 1vjoA 393 1.88e+01 c.67.1.3 100827 1dorA 311 1.97e+01 2dorA c.1.4.1 28595 1vmiA 355 2.01e+01 1w5tA 412 2.16e+01 1ysrA 150 2.24e+01 1s0yA 76 2.27e+01 d.80.1.1 98314 1u0mA 382 2.30e+01 c.95.1.2,c.95.1.2 107557,107558 1e79D 482 2.39e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 18272,26437,32317 2cmd 312 2.47e+01 2cmd c.2.1.5,d.162.1.1 30135,42102 1bi5A 389 2.48e+01 1bi5A c.95.1.2,c.95.1.2 35985,35986 1dl5A 317 2.51e+01 1dl5A c.66.1.7,d.197.1.1 64720,64721 1vjzA 341 2.53e+01 c.1.8.3 100838 1af7 274 2.55e+01 1af7 a.58.1.1,c.66.1.8 17928,34203 1i86A 389 2.56e+01 c.95.1.2,c.95.1.2 66068,66069 1vb5A 276 2.56e+01 1ex1A 605 2.58e+01 1ex1A c.1.8.7,c.23.11.1 29013,31347 1vi1A 345 2.61e+01 c.77.1.4 100724 2c2aA 258 2.65e+01 1dgmA 363 2.75e+01 1bx4A c.72.1.1 34936 1guzA 310 2.78e+01 c.2.1.5,d.162.1.1 65586,65587 1c3oG 1073 2.80e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18565,31494,31687,31688,41532,41533 1pfkA 320 2.85e+01 3pfk c.89.1.1 35575 1ydhA 216 2.88e+01 1g0u1 266 2.91e+01 1fkmA 396 2.91e+01 1fkmA a.69.2.1,a.69.2.1 18315,18316 1f8yA 157 2.92e+01 1f8xA c.23.14.1 31395 1zzmA 259 2.97e+01 1a9xA 1058 2.99e+01 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 1ztpA 251 3.04e+01 1xmbA 418 3.06e+01 1zc6A 305 3.08e+01 1a8s 273 3.08e+01 1brt c.69.1.12 34710 2his 312 3.09e+01 1taxA c.1.8.3 28918 1yixA 265 3.18e+01 1bc5A 269 3.20e+01 1af7 a.58.1.1,c.66.1.8 17929,34204 1hg3A 225 3.20e+01 1hg3A c.1.1.1 61025 1wdjA 187 3.23e+01 1x38A 602 3.23e+01 2g03A 194 3.24e+01 1jg1A 235 3.30e+01 c.66.1.7 66661 1jfmA 174 3.37e+01 d.19.1.1 66640 1fcjA 322 3.40e+01 1oasA c.79.1.1 35289 1t9kA 347 3.43e+01 c.124.1.5 106721 1cs0A 1073 3.50e+01 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 1wx1A 335 3.57e+01 1b5sA 242 3.61e+01 1eaf c.43.1.1 32626 1r30A 369 3.71e+01 c.1.28.1 96895 1l8qA 324 3.72e+01 a.4.12.2,c.37.1.20 77809,77810 1q7rA 219 3.72e+01 c.23.16.1 96054 2ck3D 482 3.79e+01 1lm4A 194 3.81e+01 d.167.1.1 84626 2g8lA 299 3.88e+01 2dri 271 3.90e+01 2dri c.93.1.1 35637 1gjwA 637 3.93e+01 b.71.1.1,c.1.8.1 60582,60583 2b06A 155 3.96e+01 1o5zA 442 3.98e+01 c.59.1.2,c.72.2.2 92530,92531 1om4A 422 3.98e+01 d.174.1.1 87067 1b7bA 310 4.04e+01 1b7bA c.73.1.1 34963 1c3oC 1073 4.08e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18563,31492,31683,31684,41528,41529 1cz1A 394 4.13e+01 1cz1A c.1.8.3 28839 1s72T 120 4.19e+01 b.34.5.1 105339 1jj2S 119 4.19e+01 1ffkQ b.34.5.1 63104 1j6pA 418 4.21e+01 b.92.1.4,c.1.9.9 77089,77090 1wznA 252 4.34e+01 1iexA 605 4.35e+01 c.1.8.7,c.23.11.1 66127,66128 1c3oE 1073 4.38e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18564,31493,31685,31686,41530,41531 1hyhA 309 4.41e+01 1hyhA c.2.1.5,d.162.1.1 30150,42117 1g31A 111 4.42e+01 1g31A b.35.1.1 24656 1sdoA 203 4.43e+01 c.52.1.21 98809 1g8oA 310 4.43e+01 1g8oA c.68.1.9 60375 1amuA 563 4.45e+01 1amuA e.23.1.1 43351 1f8xA 157 4.45e+01 1f8xA c.23.14.1 31397 2bnjA 303 4.55e+01 1c3oA 1073 4.56e+01 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 1o6zA 303 4.58e+01 c.2.1.5,d.162.1.1 81107,81108 6pfkA 319 4.60e+01 3pfk c.89.1.1 35583 1b31A 302 4.60e+01 1taxA c.1.8.3 28892 1zjjA 263 4.70e+01 1eqcA 394 4.71e+01 1cz1A c.1.8.3 28811 1h5uA 842 4.73e+01 1a8i c.87.1.4 60655 1l4dB 122 4.75e+01 d.15.5.1 77684 1tvlA 454 4.76e+01 c.1.16.4 107366 1xg7A 250 4.79e+01 1ffkQ 119 4.81e+01 1ffkQ b.34.5.1 24605 1bxrA 1073 4.82e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18570,31499,31697,31698,41542,41543 1keeG 1073 4.85e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 68516,68517,68518,68519,68520,68521 3nodB 423 4.90e+01 1nseA d.174.1.1 42513 1vjpA 394 4.95e+01 c.2.1.3,d.81.1.3 100828,100829 1ddzA 496 4.95e+01 1ddzA c.53.2.1,c.53.2.1 33372,33373 1vqoT 120 5.00e+01 2cvzA 289 5.09e+01 1sz2A 332 5.15e+01 1bj4A 470 5.17e+01 1bj4A c.67.1.4 34479 1wkvA 389 5.20e+01 1a76 326 5.21e+01 1a76 a.60.7.1,c.120.1.2 18091,33361 1tfjA 219 5.29e+01 1r9gA 216 5.30e+01 c.23.16.1 97258 1tqyB 415 5.32e+01 c.95.1.1,c.95.1.1 107247,107248 1izcA 339 5.32e+01 c.1.12.5 83838 1r2zA 274 5.34e+01 a.156.1.2,b.113.1.1,g.39.1.8 96892,96893,96894 1eh9A 558 5.35e+01 1ehaA b.1.18.2,b.71.1.1,c.1.8.1 21858,27785,28772 1keeA 1073 5.45e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 68492,68493,68494,68495,68496,68497 1v4vA 376 5.51e+01 c.87.1.3 100313 1w96A 554 5.51e+01 1iawA 317 5.69e+01 c.52.1.9 62126 1ve5A 311 5.73e+01 2gshA 414 5.78e+01 1keeE 1073 5.79e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 68508,68509,68510,68511,68512,68513 1gjuA 637 5.81e+01 b.71.1.1,c.1.8.1 60580,60581 1obbA 480 5.86e+01 c.2.1.5,d.162.1.2 86760,86761 1eqnA 321 5.94e+01 1dd9A e.13.1.1 43256 1xyfA 436 6.00e+01 1taxA b.42.2.1,c.1.8.3 25577,28909 1keeC 1073 6.05e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 68500,68501,68502,68503,68504,68505 1q18A 332 6.06e+01 c.55.1.7,c.55.1.7 104470,104471 1lldA 319 6.10e+01 3ldh c.2.1.5,d.162.1.1 30177,42144 1vbuA 328 6.13e+01 1bdg 451 6.23e+01 1qhaA c.55.1.3,c.55.1.3 33461,33462 1xyzA 347 6.28e+01 1taxA c.1.8.3 28804 1molA 94 6.33e+01 1molA d.17.1.1 37988 1i5rA 327 6.45e+01 c.2.1.2 83668 1fobA 334 6.50e+01 c.1.8.3 83255 2ar0A 541 6.52e+01 1fehA 574 6.59e+01 1fehA c.96.1.1,d.15.4.2,d.58.1.5 36015,37690,38998 2a9sA 171 6.62e+01 1ah0 316 6.71e+01 1frb c.1.7.1 28685 1ta3B 303 6.95e+01 c.1.8.3 106732 1oasA 322 7.00e+01 1oasA c.79.1.1 35293 1mmvB 419 7.09e+01 d.174.1.1 91318 1dd9A 338 7.12e+01 1dd9A e.13.1.1 43254 1gzqA 300 7.24e+01 b.1.1.2,d.19.1.1 70818,70819 1ecl 597 7.27e+01 1ecl e.10.1.1 43238 1ej6D 418 7.30e+01 i.7.1.1 45970 2pfkA 320 7.31e+01 3pfk c.89.1.1 35577 1jubA 311 7.34e+01 c.1.4.1 90908 1j33A 335 7.37e+01 c.39.1.1 77069 1wkbA 810 7.40e+01 1liiA 363 7.40e+01 c.72.1.1 73921 1wbeA 209 7.40e+01 1tux 301 7.41e+01 1taxA c.1.8.3 28907 2bg5A 324 7.51e+01 1bg4 302 7.58e+01 1taxA c.1.8.3 28806 1f6fB 210 7.63e+01 1axiB b.1.2.1,b.1.2.1 22033,22034 1tvjA 166 7.65e+01 1uaqA 158 7.74e+01 c.97.1.2 88386 2absA 383 7.77e+01 1swxA 209 7.81e+01 a.224.1.1 106075 1up7A 417 7.83e+01 1k87A 669 7.88e+01 a.176.1.1,c.1.23.2 77286,77287 1s3iA 310 7.93e+01 b.46.1.1,c.65.1.1 98435,98436 1cs0C 1073 7.94e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18559,31488,31675,31676,41520,41521 1oyzA 280 7.98e+01 a.118.1.16 93775 1iicA 422 8.00e+01 1nmtA d.108.1.2,d.108.1.2 62422,62423 1jdbB 1073 8.04e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18574,31503,31705,31706,41550,41551 1vcoA 550 8.08e+01 c.23.16.1,c.37.1.10 108508,108509 1d1vA 444 8.14e+01 1nseA d.174.1.1 59101 1k8cA 322 8.23e+01 c.1.7.1 72172 1emsA 440 8.30e+01 1emsA d.13.1.1,d.160.1.1 37520,42086 1mldA 314 8.34e+01 2cmd c.2.1.5,d.162.1.1 30122,42089 1r13A 148 8.39e+01 d.169.1.1,h.1.1.1 96782,96783 3tgl 269 8.40e+01 3tgl c.69.1.17 34733 1xfiA 367 8.46e+01 e.50.1.1 109584 2g84A 197 8.52e+01 1kzhA 555 8.57e+01 c.89.1.1 73361 2gwgA 350 8.65e+01 1va4A 279 8.66e+01 c.69.1.12 108458 1p6oA 161 8.78e+01 c.97.1.2 94185 1bgp 309 8.79e+01 1bgp a.93.1.1 18690 1lqwA 183 8.79e+01 d.167.1.1 74210 1igwA 434 8.93e+01 c.1.12.7 62370