# List of top-scoring protein chains for t2k-100-30-dssp-ehl2-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 1ofgA 381 4.12e-38 1ofgA c.2.1.3,d.81.1.5 30064,39979 1h6dA 433 5.64e-38 c.2.1.3,d.81.1.5 65656,65657 1ydwA 362 6.51e-30 1tltA 319 3.62e-26 c.2.1.3,d.81.1.5 107135,107136 1xeaA 323 6.61e-24 c.2.1.3,d.81.1.5 109572,109573 1lc0A 294 2.61e-18 c.2.1.3,d.81.1.4 73823,73824 1gcuA 295 2.66e-18 1gcuA c.2.1.3,d.81.1.4 30063,39978 1b7gO 340 2.74e-05 1b7gO c.2.1.3,d.81.1.1 29992,39907 1cf2O 337 2.87e-05 1b7gO c.2.1.3,d.81.1.1 29994,39909 1arzC 273 8.40e-05 1drw c.2.1.3,d.81.1.3 30061,39976 1drw 273 1.97e-04 1drw c.2.1.3,d.81.1.3 30057,39972 1ff9A 450 1.98e-04 1ff9A c.2.1.3,d.81.1.2 30039,39954 2czcA 334 2.73e-04 2gd1O 334 4.19e-04 1dssG c.2.1.3,d.81.1.1 29978,39893 1ys4A 354 4.30e-04 1gd1O 334 5.11e-04 1dssG c.2.1.3,d.81.1.1 29962,39877 2ahrA 259 6.48e-04 1dih 273 7.97e-04 1drw c.2.1.3,d.81.1.3 30056,39971 1ldnA 316 9.38e-04 1hyhA c.2.1.5,d.162.1.1 30166,42133 1nvmB 312 9.43e-04 c.2.1.3,d.81.1.1 86251,86252 1gadO 330 2.18e-03 1dssG c.2.1.3,d.81.1.1 29950,39865 1vpdA 299 4.55e-03 2g5cA 281 5.73e-03 1y81A 138 6.37e-03 1obbA 480 8.15e-03 c.2.1.5,d.162.1.2 86760,86761 1np3A 338 1.32e-02 a.100.1.2,c.2.1.6 85946,85947 1bg6 359 1.71e-02 1bg6 a.100.1.5,c.2.1.6 18810,30214 2c82A 413 1.75e-02 1nytA 271 2.58e-02 c.2.1.7,c.58.1.5 86417,86418 1vm6A 228 2.59e-02 c.2.1.3,d.81.1.3 108876,108877 1wwkA 307 3.12e-02 3dapA 320 3.81e-02 1dapA c.2.1.3,d.81.1.3 30051,39966 1dapA 320 3.90e-02 1dapA c.2.1.3,d.81.1.3 30053,39968 1obfO 335 4.11e-02 c.2.1.3,d.81.1.1 86768,86769 1rm4A 337 4.22e-02 c.2.1.3,d.81.1.1 105000,105001 1f06A 320 4.23e-02 1dapA c.2.1.3,d.81.1.3 59556,59557 2f1kA 279 4.34e-02 1gpjA 404 5.17e-02 a.151.1.1,c.2.1.7,d.58.39.1 65451,65452,65453 1yrlA 491 5.40e-02 1vknA 351 5.74e-02 c.2.1.3,d.81.1.1 108676,108677 1yqdA 366 5.94e-02 2b4rO 345 6.86e-02 1a5z 319 7.48e-02 1ceqA c.2.1.5,d.162.1.1 30181,42148 1lldA 319 7.53e-02 3ldh c.2.1.5,d.162.1.1 30177,42144 1u8fO 335 7.68e-02 2gv8A 447 8.12e-02 1j4aA 333 8.58e-02 c.2.1.4,c.23.12.1 71502,71503 1b74A 254 8.69e-02 1b74A c.78.2.1,c.78.2.1 35264,35265 1xgkA 352 9.91e-02 1vqwA 457 1.03e-01 1i36A 264 1.19e-01 a.100.1.8,c.2.1.6 71108,71109 2h78A 302 1.27e-01 1pgjA 478 1.33e-01 2pgd a.100.1.1,c.2.1.6 18783,30195 2cy0A 263 1.80e-01 1wxdA 263 1.94e-01 2gn4A 344 2.07e-01 2d0iA 333 2.13e-01 2d5cA 263 2.16e-01 1yqgA 263 2.46e-01 1pzgA 331 2.52e-01 c.2.1.5,d.162.1.1 95425,95426 1b73A 254 2.59e-01 1b74A c.78.2.1,c.78.2.1 35266,35267 1zcjA 463 2.71e-01 1oi7A 288 2.95e-01 c.2.1.8,c.23.4.1 87049,87050 2dldA 337 3.02e-01 1dxy c.2.1.4,c.23.12.1 30099,31359 1ebuA 358 3.03e-01 1ebuA c.2.1.3,d.81.1.2 30035,39950 1k3tA 359 3.30e-01 c.2.1.3,d.81.1.1 72022,72023 2ez3A 302 3.31e-01 1o60A 292 3.67e-01 c.1.10.4 92532 1jayA 212 3.69e-01 c.2.1.6 66478 1jaxA 212 3.69e-01 c.2.1.6 66476 1k0fA 277 3.77e-01 c.92.2.2 71974 1lsuA 147 4.25e-01 c.2.1.9 74250 1gsoA 431 4.46e-01 1gsoA b.84.2.1,c.30.1.1,d.142.1.2 28240,31647,41492 1fmtA 314 4.57e-01 1fmtA b.46.1.1,c.65.1.1 25758,34174 2pgd 482 4.71e-01 2pgd a.100.1.1,c.2.1.6 18778,30190 1hyeA 313 4.99e-01 2cmd c.2.1.5,d.162.1.1 61400,61401 1z82A 335 5.02e-01 1p77A 272 5.11e-01 c.2.1.7,c.58.1.5 94214,94215 1ebfA 358 5.40e-01 1ebuA c.2.1.3,d.81.1.2 30033,39948 1hyhA 309 5.70e-01 1hyhA c.2.1.5,d.162.1.1 30150,42117 1toaA 313 5.84e-01 1toaA c.92.2.2 35598 1q0qA 406 6.48e-01 a.69.3.1,c.2.1.3,d.81.1.3 104464,104465,104466 1u8xX 472 6.82e-01 c.2.1.5,d.162.1.2 107741,107742 1vllA 334 7.88e-01 c.2.1.13 108834 1fmtB 314 8.32e-01 1fmtA b.46.1.1,c.65.1.1 25759,34175 1mldA 314 8.52e-01 2cmd c.2.1.5,d.162.1.1 30122,42089 1jvsA 400 8.68e-01 a.69.3.1,c.2.1.3,d.81.1.3 77187,77188,77189 1dpgA 485 8.80e-01 1dpgA c.2.1.3,d.81.1.5 30074,39989 2ew2A 316 9.04e-01 1cydA 244 9.10e-01 1cydA c.2.1.2 29825 1dik 874 9.18e-01 1dik c.1.12.2,c.8.1.1,d.142.1.5 29304,30702,41572 1uufA 369 9.28e-01 b.35.1.2,c.2.1.1 100006,100007 1a2oA 349 9.42e-01 1chd c.23.1.1,c.40.1.1 31120,32479 1omoA 322 9.82e-01 c.2.1.13 104017 1kf6A 602 1.09e+00 a.7.3.1,c.3.1.4,d.168.1.1 72394,72395,72396 1k5hA 398 1.09e+00 a.69.3.1,c.2.1.3,d.81.1.3 68192,68193,68194 1gypA 358 1.11e+00 1dssG c.2.1.3,d.81.1.1 30004,39919 1dxy 333 1.16e+00 1dxy c.2.1.4,c.23.12.1 30094,31354 1up7A 417 1.17e+00 2cmd 312 1.19e+00 2cmd c.2.1.5,d.162.1.1 30135,42102 1evyA 366 1.19e+00 1evyA a.100.1.6,c.2.1.6 18811,30215 1mv8A 436 1.19e+00 a.100.1.4,c.2.1.6,c.26.3.1 85128,85129,85130 1xygD 359 1.31e+00 1qydA 313 1.32e+00 c.2.1.2 96583 1k6iA 352 1.38e+00 c.2.1.2 68223 1x7dA 350 1.48e+00 1qp8A 303 1.51e+00 1qp8A c.2.1.4,c.23.12.1 30092,31352 1x1eA 239 1.51e+00 1up6A 416 1.54e+00 c.2.1.5,d.162.1.2 107976,107977 1j5pA 253 1.83e+00 d.81.1.3,c.2.1.3 71577,83092 1o54A 277 1.92e+00 c.66.1.13 92482 1zdzA 302 1.95e+00 1k6xA 352 1.97e+00 c.2.1.2 68238 1dliA 402 1.97e+00 1dliA a.100.1.4,c.2.1.6,c.26.3.1 18809,30213,31622 2gasA 307 2.01e+00 1dljA 402 2.06e+00 1dliA a.100.1.4,c.2.1.6,c.26.3.1 18808,30212,31621 1d9eA 284 2.18e+00 1d9eA c.1.10.4 29195 1pkn 530 2.19e+00 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27042,29271,33125 1vl8A 267 2.27e+00 c.2.1.2 108733 1xdwA 331 2.50e+00 2dpg 485 2.50e+00 1dpgA c.2.1.3,d.81.1.5 30076,39991 1b3bA 415 2.54e+00 1hwyA c.2.1.7,c.58.1.1 30244,33892 1gtmA 419 2.60e+00 1hwyA c.2.1.7,c.58.1.1 30223,33871 1b26A 416 2.64e+00 1hwyA c.2.1.7,c.58.1.1 30232,33880 1zejA 293 2.65e+00 1kblA 873 2.70e+00 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 1y9aA 360 2.75e+00 2cvzA 289 2.99e+00 2ajrA 331 3.19e+00 1r0kA 388 3.26e+00 a.69.3.1,c.2.1.3,d.81.1.3 104723,104724,104725 1crwG 333 3.30e+00 1dssG c.2.1.3,d.81.1.1 30026,39941 1gr0A 367 3.52e+00 c.2.1.3,d.81.1.3 70379,70380 1dssG 333 3.73e+00 1dssG c.2.1.3,d.81.1.1 30022,39937 2bh9A 489 3.93e+00 1l3iA 192 4.04e+00 c.66.1.22 77676 1lw7A 365 4.14e+00 c.26.1.3,c.37.1.1 74295,74296 1ceqA 316 4.18e+00 1ceqA c.2.1.5,d.162.1.1 30163,42130 1ykfA 352 4.32e+00 1pedA b.35.1.2,c.2.1.1 24757,29773 1qycA 308 4.36e+00 c.2.1.2 96581 1sayA 361 4.59e+00 1sayA c.2.1.4,c.23.12.2 30102,31362 1zowA 313 4.64e+00 2dbqA 334 4.99e+00 1fxqA 267 5.87e+00 1d9eA c.1.10.4 60108 1pe1A 267 6.00e+00 c.1.10.4 94591 1kevA 351 6.22e+00 1pedA b.35.1.2,c.2.1.1 24749,29765 1jcxA 267 6.31e+00 c.1.10.4 66510 1lroA 267 6.31e+00 c.1.10.4 78161 1fxpA 267 6.47e+00 1d9eA c.1.10.4 60106 1skyE 473 6.49e+00 1skyE a.69.1.1,b.49.1.1,c.37.1.11 18314,26479,32359 1mx3A 347 6.60e+00 c.2.1.4,c.23.12.1 79638,79639 1guzA 310 6.69e+00 c.2.1.5,d.162.1.1 65586,65587 1pedA 351 6.77e+00 1pedA b.35.1.2,c.2.1.1 24753,29769 1jqbA 351 6.77e+00 b.35.1.2,c.2.1.1 77151,77152 1lu9A 287 6.85e+00 c.2.1.7,c.58.1.4 78210,78211 1o0yA 260 6.96e+00 c.1.10.1 80756 1npyA 271 6.96e+00 c.2.1.7,c.58.1.5 85995,85996 1luaA 287 6.97e+00 c.2.1.7,c.58.1.4 78216,78217 2g50A 530 6.98e+00 1t2dA 322 7.06e+00 c.2.1.5,d.162.1.1 99084,99085 1a49A 530 7.25e+00 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27026,29255,33109 1fwsA 267 7.34e+00 1d9eA c.1.10.4 60063 1ldg 316 7.49e+00 1ceqA c.2.1.5,d.162.1.1 30165,42132 1pjcA 361 7.62e+00 1sayA c.2.1.4,c.23.12.2 30101,31361 1vjtA 483 7.70e+00 c.2.1.5,d.162.1.2 100833,100834 1inlA 296 7.73e+00 c.66.1.17 66220 2ampA 304 8.24e+00 1itwA 741 8.49e+00 c.77.1.2 76793 1lvoA 302 8.69e+00 b.47.1.4 74284 1t8xA 267 8.73e+00 1g0oA 283 8.91e+00 1ybvA c.2.1.2 60181 1tmy 120 9.01e+00 1dbwA c.23.1.1 31083 1zhaA 267 9.10e+00 1p9uA 302 9.15e+00 b.47.1.4 88001 1u0sY 118 9.31e+00 c.23.1.1 107566 1lqtA 456 9.80e+00 c.3.1.1,c.4.1.1 74198,74199 2bbsA 290 9.85e+00 1ee8A 266 1.01e+01 1ee8A a.156.1.2,b.113.1.1,g.39.1.8 75823,75824,75825 1xcbA 211 1.08e+01 a.4.5.38,c.2.1.12 109552,109553 1i16 130 1.08e+01 1i16 b.36.1.2 24787 1w9hA 427 1.09e+01 1vp8A 201 1.12e+01 2fafA 608 1.12e+01 1v4vA 376 1.13e+01 c.87.1.3 100313 1pjbA 361 1.14e+01 1sayA c.2.1.4,c.23.12.2 30103,31363 1zq1C 633 1.14e+01 1twfB 1224 1.14e+01 1xmiA 291 1.16e+01 3pgm 241 1.16e+01 1qhfA c.60.1.1 33982 2tscA 264 1.18e+01 1bkpA d.117.1.1 40952 1ybvA 283 1.21e+01 1ybvA c.2.1.2 29948 1khbA 625 1.21e+01 c.91.1.1,c.109.1.1 68606,68607 1ltqA 301 1.23e+01 c.108.1.9,c.37.1.1 78208,78209 1yxmA 303 1.25e+01 1qh3A 260 1.28e+01 1qh5A d.157.1.2 42059 1gehA 444 1.29e+01 c.1.14.1,d.58.9.1 65181,65182 1uxjA 309 1.31e+01 c.2.1.5,d.162.1.1 108112,108113 1gy8A 397 1.33e+01 c.2.1.2 83376 1qh5A 260 1.35e+01 1qh5A d.157.1.2 42057 1pkm 530 1.35e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27051,29254,33108 1r0wA 286 1.36e+01 c.37.1.12 96754 2udpA 338 1.36e+01 1xel c.2.1.2 29791 2d00A 109 1.38e+01 1z7aA 308 1.40e+01 1vrbA 342 1.42e+01 1jq3A 296 1.42e+01 c.66.1.17 67079 1wkbA 810 1.42e+01 1s3iA 310 1.42e+01 b.46.1.1,c.65.1.1 98435,98436 1rpjA 288 1.44e+01 2dri c.93.1.1 35656 1f74A 293 1.45e+01 1nal3 c.1.10.1 29079 1wcv1 257 1.46e+01 1bw0A 416 1.46e+01 1bw0A c.67.1.1 34385 1gudA 288 1.52e+01 c.93.1.1 83326 1vjoA 393 1.53e+01 c.67.1.3 100827 1ur5A 309 1.56e+01 c.2.1.5,d.162.1.1 99807,99808 1pdz 434 1.57e+01 4enl c.1.11.1,d.54.1.1 29215,38859 1wzaA 488 1.58e+01 1kvs 338 1.62e+01 1xel c.2.1.2 29799 1pq4A 291 1.65e+01 c.92.2.2 94995 1vjpA 394 1.72e+01 c.2.1.3,d.81.1.3 100828,100829 1xfcA 384 1.73e+01 1o5iA 249 1.79e+01 c.2.1.2 92499 2f5tX 233 1.79e+01 1fhoA 119 1.79e+01 1fhoA b.55.1.1 26982 1qz8A 113 1.80e+01 b.140.1.1 96619 2gptA 523 1.80e+01 16pk 415 1.81e+01 16pk c.86.1.1 35454 2cdcA 366 1.82e+01 1fdyA 297 1.82e+01 1nal3 c.1.10.1 29071 2d13A 227 1.90e+01 3uagA 437 1.90e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30652,33953,34956 1who 96 1.90e+01 1who b.7.3.1 23215 1ahxA 396 1.91e+01 1ajsA c.67.1.1 34293 2g76A 335 1.91e+01 1cpy 421 1.97e+01 1ivyA c.69.1.5 34651 1ps9A 671 1.98e+01 c.1.4.1,c.3.1.1,c.4.1.1 95076,95077,95078 2av4A 162 1.98e+01 2c3mA 1231 2.01e+01 1tqxA 227 2.03e+01 1yiyA 429 2.05e+01 1dckA 126 2.08e+01 1dbwA c.23.1.1 31097 1vhnA 318 2.09e+01 c.1.4.1 100693 2bllA 345 2.10e+01 1zq1A 438 2.14e+01 1nal1 297 2.14e+01 1nal3 1i50B 1224 2.14e+01 e.29.1.1 61755 1kekA 1231 2.16e+01 c.36.1.8,c.36.1.12,c.48.1.3,c.64.1.1,d.58.1.5 68524,68525,68526,68527,68528 1dbwA 126 2.18e+01 1dbwA c.23.1.1 31095 2d1yA 256 2.19e+01 1x13A 401 2.19e+01 1nal3 297 2.20e+01 1nal3 2g1uA 155 2.21e+01 1w25A 459 2.22e+01 1uag 437 2.24e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30653,33954,34957 1hl2A 297 2.25e+01 c.1.10.1 83581 1fmcA 255 2.25e+01 1cydA c.2.1.2 29856 1aiqA 264 2.27e+01 1bkpA d.117.1.1 40967 1psdA 409 2.27e+01 1psdA c.2.1.4,c.23.12.1,d.58.18.1 30097,31357,39354 2bshA 125 2.30e+01 1pl8A 356 2.32e+01 b.35.1.2,c.2.1.1 94878,94879 1xel 338 2.34e+01 1xel c.2.1.2 29786 1z7bA 358 2.38e+01 1nseA 444 2.39e+01 1nseA d.174.1.1 42534 1ed5A 444 2.39e+01 1nseA d.174.1.1 42530 1udc 338 2.40e+01 1xel c.2.1.2 29785 1f6kA 293 2.40e+01 1nal3 c.1.10.1 29081 1udb 338 2.41e+01 1xel c.2.1.2 29787 1qv9A 283 2.41e+01 c.127.1.1 96356 2bgkA 278 2.41e+01 1e8yA 966 2.45e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 1ppo 216 2.46e+01 1cs8A d.3.1.1 37020 1b0pA 1231 2.47e+01 c.36.1.8,c.36.1.12,c.48.1.3,c.64.1.1,d.58.1.5 31831,31832,33104,34157,39003 1ogsA 497 2.50e+01 b.71.1.2,c.1.8.3 86997,86998 1aiaA 396 2.50e+01 1ajsA c.67.1.1 34306 2bhoA 130 2.53e+01 1vplA 256 2.57e+01 1gpmA 525 2.60e+01 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 1lssA 140 2.65e+01 c.2.1.9 74246 1a9z 338 2.67e+01 1xel c.2.1.2 29795 1j08A 226 2.67e+01 c.47.1.2,c.47.1.2 83855,83856 1a9y 338 2.67e+01 1xel c.2.1.2 29789 1wlyA 333 2.68e+01 1p9sA 300 2.70e+01 b.47.1.4 87999 1omzA 293 2.75e+01 c.68.1.15 87093 1llnA 262 2.78e+01 d.165.1.1 84625 1d0cA 444 2.79e+01 d.174.1.1 64769 1axwA 265 2.79e+01 1bkpA d.117.1.1 40938 1v71A 323 2.79e+01 1a04A 215 2.80e+01 1a04A a.4.6.2,c.23.1.1 16234,31089 1qhtA 775 2.80e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1yixA 265 2.81e+01 1v3vA 333 2.83e+01 b.35.1.2,c.2.1.1 108345,108346 2bmwA 304 2.83e+01 1ua4A 455 2.86e+01 c.72.1.3 99128 1sz6A 249 2.88e+01 1e3jA 352 2.88e+01 1e3jA b.35.1.2,c.2.1.1 24765,29781 4uagA 437 2.93e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30651,33952,34955 1jpdX 324 2.94e+01 c.1.11.2,d.54.1.1 67014,67015 1yizA 429 2.96e+01 1d1vA 444 2.98e+01 1nseA d.174.1.1 59101 1pyfA 312 2.98e+01 c.1.7.1 95334 1hw6A 278 3.00e+01 1frb c.1.7.1 61296 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