# List of top-scoring protein chains for t2k-100-30-n_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 1qw9A 502 7.97e-01 b.71.1.2,c.1.8.3 96466,96467 1ei6A 406 8.07e-01 c.76.1.4 90443 1ejeA 192 1.04e+00 1ejeA b.45.1.2 25757 1xvwA 160 1.33e+00 1db3A 372 1.53e+00 1db3A c.2.1.2 29813 1fwrA 213 1.54e+00 1fwrA c.1.10.1 29164 1ww9A 392 1.56e+00 1gteA 1025 1.69e+00 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70440,70441,70442,70443,70444 1gteD 1025 1.83e+00 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70455,70456,70457,70458,70459 1h7wB 1025 1.83e+00 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15684,28629,30325,30610,39008 1h7wD 1025 1.95e+00 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15686,28631,30327,30612,39010 1h7wA 1025 2.01e+00 1h7wA a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15683,28628,30324,30609,39007 1b0aA 288 2.11e+00 1a4iA c.2.1.7,c.58.1.2 30286,33934 1ve3A 227 2.53e+00 2aioA 269 2.83e+00 1tml 286 3.38e+00 1tml c.6.1.1 30656 1o66A 275 3.40e+00 c.1.12.8 92547 1s31A 273 3.62e+00 1ecfA 504 4.06e+00 1ecfB c.61.1.1,d.153.1.1 34053,41820 1kxrA 339 4.33e+00 d.3.1.3 73175 1s2kA 206 4.51e+00 b.29.1.20 98389 1gt91 357 4.72e+00 1yadA 221 4.92e+00 1omp 370 4.99e+00 4mbp c.94.1.1 35778 1dgrC 178 5.61e+00 1dgwA b.82.1.2 28100 2bnfB 241 5.92e+00 1f0iA 504 6.04e+00 1f0iA d.136.1.2,d.136.1.2 59566,59567 1sxgA 280 6.04e+00 1tvoA 368 6.05e+00 1h7xB 1025 6.18e+00 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15688,28633,30329,30614,39012 1e7uA 961 6.28e+00 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 1ig3A 263 6.29e+00 1ig3A b.82.6.1,c.100.1.1 62358,62359 1c3oC 1073 6.29e+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 18563,31492,31683,31684,41528,41529 1h7xA 1025 6.34e+00 1h7wA a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15687,28632,30328,30613,39011 1jixA 351 6.50e+00 1c3jA c.87.1.1 63081 1iciA 256 6.51e+00 1iciA c.31.1.5 62266 1fwcC 567 6.72e+00 1ubpC b.92.1.1,c.1.9.2 28410,29032 1ht6A 405 6.74e+00 b.71.1.1,c.1.8.1 83629,83630 2cvhA 220 6.96e+00 1iruK 201 7.01e+00 d.153.1.4 71362 3erk 364 7.25e+00 1hcl d.144.1.7 41654 1hf2A 210 7.40e+00 1hf2A b.80.3.1,c.102.1.1 60992,60993 1ktaA 365 7.45e+00 e.17.1.1 77533 1edzA 320 7.64e+00 1ee9A c.2.1.7,c.58.1.2 30287,33935 1kqfB 294 7.76e+00 d.58.1.5,f.23.22.1 75900,75901 1drtA 324 7.83e+00 1drtA b.82.2.2 28130 1l2uA 245 8.08e+00 c.1.2.3 73516 1yzyA 413 8.32e+00 1jg7A 351 8.40e+00 1c3jA c.87.1.1 62945 1ws6A 171 8.47e+00 1c3oG 1073 8.64e+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 18565,31494,31687,31688,41532,41533 1smlA 269 8.85e+00 1smlA d.157.1.1 42053 2bsxA 253 9.06e+00 1m2kA 249 9.14e+00 c.31.1.5 84754 1klnA 605 9.27e+00 1xwl c.55.3.5,e.8.1.1 33693,42986 1pn0A 665 9.36e+00 c.3.1.2,c.47.1.10,d.16.1.2 94918,94919,94920 2a1hA 365 9.45e+00 1ju2A 536 9.63e+00 c.3.1.2,d.16.1.1 77169,77170 1d4fA 431 9.73e+00 1b3rA c.2.1.4,c.23.12.3 30110,31370 2c0hA 353 9.74e+00 1iq6A 134 9.92e+00 d.38.1.4 76755 1lxtA 561 9.97e+00 3pmgA c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 35432,35433,35434,41309 2ch4A 320 1.02e+01 1tluA 130 1.02e+01 d.156.1.2 107139 1wqaA 455 1.03e+01 1euaA 213 1.06e+01 1fwrA c.1.10.1 29155 2fhxA 246 1.07e+01 1h7xC 1025 1.09e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15689,28634,30330,30615,39013 2f4nA 273 1.09e+01 1bhjA 292 1.13e+01 1xvaA c.66.1.5 34189 1vkhA 273 1.17e+01 c.69.1.32 108662 1fgkA 310 1.22e+01 1fgkA d.144.1.7 41693 1j9yA 385 1.25e+01 1j9yA c.1.8.3 62791 1dryA 324 1.25e+01 1drtA b.82.2.2 28128 1elyA 449 1.25e+01 1b8jA c.76.1.1 35028 2bodX 286 1.27e+01 2bgu 351 1.32e+01 1c3jA c.87.1.1 35460 2bfwA 200 1.32e+01 1miqA 375 1.33e+01 b.50.1.2 79151 1zvkA 358 1.34e+01 2c2xA 281 1.35e+01 1p57B 255 1.35e+01 b.47.1.2 94126 2fp4B 395 1.36e+01 1vr7A 142 1.40e+01 1kfwA 435 1.42e+01 c.1.8.5,d.26.3.1 77376,77377 1t5oA 351 1.43e+01 c.124.1.5 106459 2bv9A 290 1.43e+01 1u1hA 765 1.45e+01 c.1.22.2,c.1.22.2 107580,107581 1ibsA 317 1.45e+01 c.61.1.2,c.61.1.2 66107,66108 1l1lA 739 1.46e+01 c.7.1.4 73470 2arhA 203 1.47e+01 1ivnA 190 1.49e+01 c.23.10.5 83719 1cb7B 483 1.51e+01 1cb7B c.1.19.2 29648 1nqkA 381 1.51e+01 c.1.16.4 92050 1jpzA 473 1.52e+01 a.104.1.1 67069 1va6A 518 1.54e+01 1bw0A 416 1.55e+01 1bw0A c.67.1.1 34385 1uohA 226 1.57e+01 d.211.1.1 99690 1c8zA 265 1.57e+01 1c8zA d.23.1.1 38375 1keeG 1073 1.57e+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 1rlmB 271 1.58e+01 1fc6A 388 1.59e+01 1fc6A b.36.1.3,c.14.1.2 64738,64739 1w0dA 337 1.59e+01 1vpbA 451 1.64e+01 1af6A 421 1.69e+01 2mprA f.4.3.2 43772 1byi 224 1.71e+01 1byi c.37.1.10 32199 1gthB 1025 1.73e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70488,70489,70490,70491,70492 1ejrC 567 1.75e+01 1ubpC b.92.1.1,c.1.9.2 28420,29042 1dmr 823 1.78e+01 1dmr b.52.2.2,c.81.1.1 26904,35312 1qusA 322 1.78e+01 1ltm d.2.1.6 36991 1ido 192 1.79e+01 1ido c.62.1.1 34139 1qs8A 329 1.81e+01 1smrA b.50.1.2 26887 1v04A 355 1.82e+01 b.68.6.2 100240 2gw2A 198 1.85e+01 1xvaA 292 1.85e+01 1xvaA c.66.1.5 34183 1hlgA 371 1.86e+01 1hlgA c.69.1.6 34656 1x6vA 630 1.88e+01 1dt6A 473 1.94e+01 1dt6A a.104.1.1 18977 1h7xD 1025 1.94e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15690,28635,30331,30616,39014 1l6sA 323 1.96e+01 c.1.10.3 73627 1ni4A 365 1.96e+01 c.36.1.11 85728 2mprA 421 1.97e+01 2mprA f.4.3.2 43788 1k6dA 220 2.04e+01 c.124.1.2 72082 1jscA 630 2.04e+01 c.31.1.3,c.36.1.5,c.36.1.9 67224,67225,67226 1o8uA 257 2.04e+01 c.14.1.3 81194 2agkA 260 2.05e+01 1lvl 458 2.05e+01 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30567,30568,40205 1efpB 252 2.05e+01 1efvB c.26.2.3 31636 1u9iA 519 2.05e+01 1c0aA 585 2.06e+01 1c0aA b.40.4.1,d.74.4.1,d.104.1.1 25246,39731,40767 1hr6A 475 2.07e+01 1hr6A d.185.1.1,d.185.1.1 61164,61165 1uteA 313 2.08e+01 1uteA d.159.1.1 42078 1p2zA 968 2.09e+01 b.121.2.2,b.121.2.2 93962,93963 2gdzA 267 2.09e+01 1l9fA 389 2.11e+01 c.3.1.2,d.16.1.3 73716,73717 1wvcA 259 2.11e+01 1gw1A 376 2.12e+01 c.1.8.3 76361 1ot8A 239 2.14e+01 d.211.1.1 93507 1t13A 158 2.15e+01 1a0i 348 2.15e+01 1a0i b.40.4.6,d.142.2.1 25363,41577 1t1gA 364 2.18e+01 c.41.1.2 106246 1a48 306 2.20e+01 1a48 d.143.1.1 41590 2bgzA 299 2.23e+01 1wlgA 299 2.23e+01 2bfgA 503 2.26e+01 1i0sA 169 2.31e+01 1i0rA b.45.1.2 61491 1vjpA 394 2.33e+01 c.2.1.3,d.81.1.3 100828,100829 2f9sA 151 2.43e+01 1fehA 574 2.43e+01 1fehA c.96.1.1,d.15.4.2,d.58.1.5 36015,37690,38998 1ee9A 320 2.44e+01 1ee9A c.2.1.7,c.58.1.2 30288,33936 1k7qA 479 2.49e+01 b.80.7.1,d.92.1.6 77283,77284 1gthD 1025 2.54e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70498,70499,70500,70501,70502 2ab0A 205 2.56e+01 1qtrA 317 2.61e+01 1qtrA c.69.1.7 34660 1gqoB 143 2.66e+01 c.23.13.1 76296 1daaA 282 2.69e+01 1daaA e.17.1.1 43270 1qumA 285 2.69e+01 1qumA c.1.15.1 29393 1gt8D 1025 2.75e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70433,70434,70435,70436,70437 2b99A 156 2.75e+01 1v0wA 506 2.81e+01 d.136.1.2,d.136.1.2 108220,108221 1g8oA 310 2.85e+01 1g8oA c.68.1.9 60375 2afwA 329 2.87e+01 1pioA 257 2.88e+01 1btl e.3.1.1 42719 2b7kA 200 2.91e+01 2phlA 397 2.92e+01 1dgwA b.82.1.2,b.82.1.2 28082,28083 1xt5A 135 3.00e+01 1hxkA 1015 3.02e+01 a.8.3.1,b.30.5.6,c.6.2.1 83070,83071,83072 2bogX 286 3.03e+01 2bzlA 325 3.09e+01 1fxoA 293 3.09e+01 1g0rA c.68.1.6 34524 1si6X 282 3.12e+01 1kskA 234 3.15e+01 d.66.1.5,d.265.1.3 72920,90389 1cd1A 315 3.15e+01 1cd1A b.1.1.2,d.19.1.1 21579,38155 1dloA 556 3.16e+01 1rthA c.55.3.1,e.8.1.2 33584,43040 1wohA 305 3.20e+01 c.42.1.1 109446 1pg4A 652 3.21e+01 e.23.1.1 88067 1u2zA 433 3.22e+01 c.66.1.31 107626 1crkA 380 3.24e+01 1qh4A a.83.1.1,d.128.1.2 18458,41193 1wbpA 397 3.25e+01 1iqcA 308 3.27e+01 a.3.1.5,a.3.1.5 66266,66267 1pgl2 370 3.31e+01 1poiA 317 3.38e+01 1poiA c.124.1.2 34153 7icd 416 3.43e+01 1iso c.77.1.1 35072 1kt8A 365 3.48e+01 e.17.1.1 77531 1pvvA 315 3.49e+01 c.78.1.1,c.78.1.1 95190,95191 1reqB 637 3.50e+01 1reqB c.1.19.1,c.23.6.1 29621,31248 1ojaA 520 3.52e+01 c.3.1.2,d.16.1.5 93096,93097 1gguA 731 3.52e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21885,22179,22180,37115 1go8P 462 3.52e+01 b.80.7.1,d.92.1.6 76247,76248 1ekbB 235 3.55e+01 5ptp b.47.1.2 26282 1jf9A 408 3.55e+01 1c0nA c.67.1.3 62931 2be1A 339 3.57e+01 1s95A 333 3.63e+01 d.159.1.3 105375 1rwhA 757 3.64e+01 a.102.3.2,b.24.1.1,b.30.5.2 97984,97985,97986 1b80A 351 3.65e+01 1arv a.93.1.1 18579 1hnjA 317 3.66e+01 1hn9A c.95.1.2,c.95.1.2 35969,35970 1gpiA 431 3.66e+01 b.29.1.10 65450 1jqbA 351 3.69e+01 b.35.1.2,c.2.1.1 77151,77152 1dtdA 303 3.70e+01 1aye c.56.5.1 33823 1ao0A 459 3.70e+01 1ecfB c.61.1.1,d.153.1.1 34049,41816 1y21A 282 3.71e+01 1pmaA 233 3.72e+01 1pmaA d.153.1.4 41918 1agjA 242 3.72e+01 1agjA b.47.1.1 25827 1ivyA 452 3.78e+01 1ivyA c.69.1.5 34654 2fimA 276 3.84e+01 1gosA 520 3.86e+01 c.3.1.2,d.16.1.5 65425,65426 1szoA 257 3.87e+01 c.14.1.3 106164 1g1sA 162 3.88e+01 d.169.1.1,g.3.11.1 65100,65101 1yarA 233 3.89e+01 1ex1A 605 3.91e+01 1ex1A c.1.8.7,c.23.11.1 29013,31347 1xhcA 367 3.94e+01 1s3eA 520 3.94e+01 c.3.1.2,d.16.1.5 98426,98427 1jovA 270 3.95e+01 b.30.5.7 84192 1qjdA 571 3.95e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19695,30432,42315 1y8tA 324 3.96e+01 1zv9A 172 3.96e+01 2fikA 287 3.99e+01 1k4vA 289 4.00e+01 c.68.1.9 72066 1dhx 967 4.01e+01 1dhx 1mtyD 512 4.04e+01 1mhyD a.25.1.2 16742 1yliA 153 4.04e+01 1kssA 571 4.05e+01 a.138.1.3,c.3.1.4,d.168.1.1 72928,72929,72930 1z7yA 322 4.13e+01 1v71A 323 4.15e+01 1kevA 351 4.19e+01 1pedA b.35.1.2,c.2.1.1 24749,29765 1e8xA 961 4.19e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19148,23183,37631,41711 1e39A 571 4.20e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19694,30431,42314 1tp9A 162 4.21e+01 2ag4A 164 4.21e+01 1ggxA 223 4.22e+01 1ggxA d.22.1.1 38367 1dgwA 178 4.23e+01 1dgwA b.82.1.2 28090 1c7sA 858 4.24e+01 1qba b.1.18.2,b.2.2.3,c.1.8.6,d.92.2.1 21812,22408,29011,40410 1e5uI 187 4.26e+01 1f00I b.1.14.1,d.169.1.3 22372,42441 1xfkA 336 4.28e+01 1rw7A 243 4.30e+01 c.23.16.2 97963 1aipE 405 4.35e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25699,25739,32134 1mjgM 729 4.36e+01 e.26.1.3 79204 1sq9A 397 4.38e+01 b.69.4.1 105889 1efcA 393 4.40e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25680,25720,32113 1ebuA 358 4.41e+01 1ebuA c.2.1.3,d.81.1.2 30035,39950 1n4oA 276 4.41e+01 e.3.1.1 91621 1b85A 351 4.43e+01 1arv a.93.1.1 18581 2fv7A 331 4.44e+01 1h5vA 304 4.46e+01 c.1.8.3 70898 1uf5A 303 4.46e+01 d.160.1.2 107808 1yyhA 253 4.49e+01 1lj5A 379 4.51e+01 e.1.1.1 73928 1lnqA 336 4.54e+01 c.2.1.9,f.14.1.1 74049,74050 1ntfA 282 4.56e+01 d.151.1.2 92104 1z5vA 474 4.58e+01 1wleA 501 4.64e+01 1qtwA 285 4.68e+01 1qumA c.1.15.1 29392 1dgfA 497 4.68e+01 1cf9A e.5.1.1 42782 1n7vA 555 4.69e+01 b.126.1.1 85377 1l0qA 391 4.69e+01 b.1.3.1,b.69.2.3 77644,77645 1kfuS 184 4.74e+01 a.39.1.8 68574 1ycsB 239 4.75e+01 1ycsB d.211.1.1,b.34.2.1 19155,24553 1ni4B 341 4.76e+01 c.36.1.7,c.48.1.2 85729,85730 1rypB 250 4.77e+01 1rypB d.153.1.4 41933 1bg0 356 4.87e+01 1qh4A a.83.1.1,d.128.1.2 18476,41211 1ga6A 372 4.88e+01 1ga1A c.41.1.2 32556 1v5vA 401 4.90e+01 1qazA 351 4.97e+01 1qazA a.102.3.1 18848 1dtwB 342 4.98e+01 1qs0B c.36.1.7,c.48.1.2 31828,33102 1k7iA 479 4.99e+01 b.80.7.1,d.92.1.6 77281,77282 1k0gA 453 5.00e+01 d.161.1.1 67940 1k7gA 479 5.01e+01 b.80.7.1,d.92.1.6 77279,77280 1qba 858 5.03e+01 1qba b.1.18.2,b.2.2.3,c.1.8.6,d.92.2.1 21810,22406,29009,40408 1a8q 274 5.03e+01 1brt c.69.1.12 34702 1w24A 182 5.03e+01 1itcA 516 5.04e+01 b.3.1.1,c.1.8.1 83705,83706 1a5kC 566 5.15e+01 1ubpC b.92.1.1,c.1.9.2 28425,29047 1pytC 253 5.16e+01 5ptp b.47.1.2 26233 1eudA 311 5.17e+01 2scuA c.2.1.8,c.23.4.1 30312,31140 1flzA 228 5.18e+01 3eugA c.18.1.1 31027 2cb4A 291 5.21e+01 1ltm 320 5.22e+01 1ltm d.2.1.6 36992 1st9A 143 5.22e+01 c.47.1.10 98987 1jf0A 195 5.24e+01 1ej3A a.39.1.5 62926 1m41A 380 5.26e+01 c.1.16.4 78595 1ehaA 558 5.33e+01 1ehaA b.1.18.2,b.71.1.1,c.1.8.1 21859,27786,28773 1ubeA 349 5.33e+01 c.37.1.11,d.48.1.1 88412,88413 1aop 497 5.35e+01 2aop d.58.36.1,d.58.36.1,d.134.1.1,d.134.1.1 39501,39502,41425,41426 1xr4A 509 5.40e+01 1w7jA 795 5.43e+01 2fp8A 322 5.44e+01 1sznA 417 5.45e+01 b.71.1.1,c.1.8.1 106162,106163 1eq2A 310 5.48e+01 1eq2A c.2.1.2 29814 1b26A 416 5.50e+01 1hwyA c.2.1.7,c.58.1.1 30232,33880 1v8bA 479 5.50e+01 1xdpA 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