# List of top-scoring protein chains for t04-100-30-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 2f6sA 201 1.24e-19 2g03A 194 1.49e-19 1sxjE 354 1.82e-01 a.80.1.1,c.37.1.20 106089,106090 1z2nX 324 3.78e-01 2gh1A 301 3.90e-01 1uqtA 482 5.02e-01 c.87.1.6 99794 1knyA 253 1.05e+00 1knyA a.24.16.1,d.218.1.1 75896,75897 1u00A 227 1.22e+00 1exrA 148 1.34e+00 1cll a.39.1.5 17299 1nh1A 330 1.72e+00 e.45.1.1 91871 1d5rA 324 2.18e+00 1d5rA b.7.1.1,c.45.1.1 23181,32697 1ggzA 148 2.22e+00 a.39.1.5 70176 1t1gA 364 2.42e+00 c.41.1.2 106246 1g8lA 411 2.69e+00 1g8lA b.85.6.1,b.103.1.1,c.57.1.2 60365,60366,60367 1mc2A 122 2.70e+00 a.133.1.2 74622 1gt91 357 2.95e+00 1mxrA 375 3.03e+00 a.25.1.2 85197 2astA 159 3.09e+00 1yi8A 351 3.41e+00 2au3A 407 3.45e+00 1w33A 181 3.60e+00 1cm5A 759 3.77e+00 1cm5A c.7.1.1 30671 1di1A 300 3.84e+00 1di1A a.128.1.4 19446 1xikA 375 4.48e+00 1xikA a.25.1.2 16784 1d0vA 356 4.51e+00 1d0vA c.39.1.1 32476 1nj4A 363 4.53e+00 b.105.1.1,e.3.1.1 80545,80546 1l5oA 356 4.53e+00 c.39.1.1 77711 1m5yA 408 4.71e+00 a.167.1.1,d.26.1.1,d.26.1.1 78664,78665,78666 1y1xA 191 4.78e+00 1wy9A 147 4.88e+00 2bzlA 325 5.12e+00 1h16A 759 5.23e+00 c.7.1.1 76462 2b3oA 532 5.32e+00 1ywfA 296 5.42e+00 2b7kA 200 5.85e+00 1f5nA 592 5.85e+00 1dg3A a.114.1.1,c.37.1.8 19077,32152 1m0uA 249 6.00e+00 a.45.1.1,c.47.1.5 78359,78360 1xfxO 149 6.04e+00 1x0vA 354 6.13e+00 1tq4A 413 6.71e+00 c.37.1.8 107201 1u0mA 382 6.87e+00 c.95.1.2,c.95.1.2 107557,107558 2fiyA 309 6.93e+00 1ppjD 241 7.14e+00 a.3.1.3,f.23.11.1 104258,104259 1q4mA 221 8.35e+00 a.132.1.3 95805 1pdo 135 8.66e+00 1pdo c.54.1.1 33376 1gadO 330 9.05e+00 1dssG c.2.1.3,d.81.1.1 29950,39865 1cr1A 296 9.05e+00 1cr1A c.37.1.11 32286 1u46A 291 9.11e+00 d.144.1.7 107656 1bli 483 9.54e+00 1bli b.71.1.1,c.1.8.1 27715,28702 2cwcA 303 9.93e+00 1m0kA 262 1.00e+01 f.13.1.1 78344 1vlgA 176 1.01e+01 a.25.1.1 108816 2a14A 263 1.02e+01 1gegA 256 1.11e+01 1ybvA c.2.1.2 29888 2f3yA 148 1.13e+01 1u8xX 472 1.16e+01 c.2.1.5,d.162.1.2 107741,107742 2gfoA 396 1.18e+01 1uzbA 516 1.19e+01 c.82.1.1 100220 1nd7A 374 1.20e+01 d.148.1.1 91817 1in6A 334 1.22e+01 1hqcA a.4.5.11,c.37.1.20 62601,62602 1t5hX 504 1.22e+01 e.23.1.1 106449 1w7bA 339 1.25e+01 1kid 203 1.30e+01 1derA c.8.5.1 30771 1kay 381 1.31e+01 1ba1 c.55.1.1,c.55.1.1 33385,33386 1l1lA 739 1.31e+01 c.7.1.4 73470 1bmtA 246 1.34e+01 1bmtA a.46.1.1,c.23.6.1 17757,31235 1ux8A 132 1.36e+01 2bjkA 516 1.39e+01 2f2gA 221 1.40e+01 1v33A 366 1.43e+01 d.264.1.1 100278 1o2dA 371 1.44e+01 e.22.1.2 86591 1y0vH 146 1.49e+01 1z21A 112 1.51e+01 1p1jA 533 1.53e+01 c.2.1.3,d.81.1.3 87687,87688 1swxA 209 1.57e+01 a.224.1.1 106075 1aop 497 1.57e+01 2aop d.58.36.1,d.58.36.1,d.134.1.1,d.134.1.1 39501,39502,41425,41426 1c24A 263 1.66e+01 1c24A d.127.1.1 41148 4pfk 319 1.67e+01 3pfk c.89.1.1 35582 1srqA 341 1.67e+01 e.55.1.1 105967 1z6gA 218 1.71e+01 1uxtA 501 1.72e+01 c.82.1.1 108125 1xnzA 264 1.73e+01 1ve0A 134 1.73e+01 1na3A 91 1.74e+01 k.38.1.1 85481 1rcwA 231 1.76e+01 a.132.1.4 97299 1uh5A 329 1.77e+01 c.2.1.2 107840 2gauA 232 1.90e+01 1ww9A 392 1.91e+01 1aru 344 1.92e+01 1arv a.93.1.1 18589 1e8cA 498 1.99e+01 c.98.1.1,c.59.1.1,c.72.2.1 59377,59378,59379 1lycA 343 2.01e+01 a.93.1.1 74344 1qbkB 890 2.03e+01 1qbkB a.118.1.1 19127 1qhtA 775 2.04e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1n35A 1267 2.06e+01 e.8.1.4 79935 1ezvD 245 2.13e+01 1be3D a.3.1.3,f.23.11.1 59546,59547 1g99A 408 2.14e+01 1g99A c.55.1.2,c.55.1.2 33457,33458 1jrrA 382 2.16e+01 e.1.1.1 63256 1txdA 385 2.19e+01 a.87.1.1,b.55.1.1 107422,107423 1ej2A 181 2.19e+01 1f9aA c.26.1.3 59414 1bupA 386 2.22e+01 1ba1 c.55.1.1,c.55.1.1 33377,33378 1yuwA 554 2.23e+01 1tag 324 2.28e+01 1cipA a.66.1.1,c.37.1.8 18197,32080 1ex7A 186 2.29e+01 1gky c.37.1.1 59537 1euvA 221 2.32e+01 1euvA d.3.1.7 37133 1ow4A 129 2.33e+01 a.39.2.1 93628 1kb9D 246 2.33e+01 a.3.1.3,f.23.11.1 77317,77318 1gky 187 2.33e+01 1gky c.37.1.1 31839 1tadA 324 2.34e+01 1cipA a.66.1.1,c.37.1.8 18194,32077 1jltB 122 2.37e+01 a.133.1.2 66868 1m0wA 491 2.47e+01 c.30.1.4,d.142.1.6 78363,78364 1tqmA 282 2.49e+01 a.4.5.56,d.144.1.9 107236,107237 1h3fA 432 2.51e+01 c.26.1.1,d.66.1.4 76631,76632 1t5oA 351 2.51e+01 c.124.1.5 106459 1zarA 282 2.51e+01 2af4C 333 2.52e+01 1fp2A 352 2.54e+01 1fpxA a.4.5.29,c.66.1.12 59941,59942 1v7bA 185 2.56e+01 1lvaA 258 2.59e+01 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 2g3aA 152 2.60e+01 1u2kA 309 2.61e+01 1uocA 289 2.62e+01 c.55.3.9 99686 1dw0A 112 2.63e+01 1dw0A a.3.1.1 15911 1vbuA 328 2.64e+01 1gjwA 637 2.65e+01 b.71.1.1,c.1.8.1 60582,60583 1yyvA 131 2.66e+01 2g5cA 281 2.67e+01 1m8jA 181 2.69e+01 c.26.1.3 84875 2abqA 306 2.72e+01 1wu4A 396 2.73e+01 1paqA 189 2.79e+01 a.118.1.14 94413 1tueA 212 2.81e+01 c.37.1.20 107323 1wusA 180 2.82e+01 1i5pA 633 2.83e+01 1i5pA b.18.1.3,b.77.2.1,f.1.3.1 61817,61818,61819 1p0iA 529 2.84e+01 c.69.1.1 93867 1r5yA 386 2.90e+01 c.1.20.1 97134 1t46A 313 2.93e+01 d.144.1.7 106397 1c3wA 222 3.00e+01 1c3wA f.13.1.1 43405 1ulyA 192 3.08e+01 1kdj 102 3.12e+01 1plc b.6.1.1 22864 1u24A 337 3.13e+01 1qhlA 227 3.17e+01 1qhlA c.37.1.12 32382 1aokB 122 3.19e+01 1poa a.133.1.2 19561 2a10A 125 3.19e+01 1ah7 245 3.23e+01 1ah7 a.124.1.1 19339 1sbyA 254 3.25e+01 1vflA 356 3.26e+01 1j98A 157 3.27e+01 1j98A d.185.1.2 62755 1t01A 255 3.31e+01 a.24.9.1,a.24.9.1 106188,106189 1wa5C 960 3.33e+01 2fk8A 318 3.36e+01 1td6A 306 3.38e+01 1wcgA 464 3.38e+01 1bm9A 122 3.39e+01 1bm9A a.4.5.7 16116 1w6vA 141 3.40e+01 1wbeA 209 3.42e+01 1r2rA 248 3.43e+01 c.1.1.1 96875 1b5pA 385 3.44e+01 c.67.1.1 90403 1ylmA 144 3.45e+01 1x0lA 333 3.48e+01 1e0bA 68 3.48e+01 1e0bA b.34.13.2 37476 1p0hA 318 3.49e+01 d.108.1.1 93866 1dboA 506 3.49e+01 1dbgA b.80.1.4 28034 1jchA 551 3.50e+01 b.101.1.1,b.110.1.1,h.4.9.1 66491,66492,66493 1dbgA 506 3.52e+01 1dbgA b.80.1.4 28033 1wp1A 474 3.55e+01 1buoA 121 3.62e+01 1buoA d.42.1.1 38631 2cu1A 103 3.63e+01 1v61A 132 3.64e+01 b.55.1.1 108389 1g71A 347 3.64e+01 1g71A d.264.1.1 43268 1hqsA 423 3.68e+01 1iso c.77.1.1 61154 1pfkA 320 3.69e+01 3pfk c.89.1.1 35575 1n62A 166 3.75e+01 a.56.1.1,d.15.4.2 80090,80091 1kn1A 160 3.76e+01 a.1.1.3 77455 2ng1 293 3.79e+01 1ng1 a.24.13.1,c.37.1.10 16962,32273 1zbqA 327 3.80e+01 2arrA 382 3.80e+01 1hf8A 289 3.87e+01 1hg5A a.7.8.2,a.118.9.3 90354,90355 1au1A 166 3.89e+01 1ifa a.26.1.3 16889 1tk1A 260 3.90e+01 d.248.1.1 107066 1vj7A 393 3.92e+01 a.211.1.1,d.218.1.8 100801,100802 1ca1 370 3.93e+01 1ca1 a.124.1.1,b.12.1.3 19340,23648 1y8qB 640 3.95e+01 1b16A 254 3.96e+01 1b16A c.2.1.2 29875 2g39A 497 4.00e+01 1nepA 130 4.04e+01 b.1.18.7 80440 1t8qA 336 4.04e+01 c.1.18.3 106669 1su8A 636 4.06e+01 e.26.1.2 98999 1qwiA 143 4.14e+01 d.227.1.1 96474 2c27A 315 4.18e+01 2pfkA 320 4.20e+01 3pfk c.89.1.1 35577 1j09A 468 4.21e+01 a.97.1.1,c.26.1.1 77025,77026 2ac7A 235 4.26e+01 1lehA 364 4.28e+01 1bw9A c.2.1.7,c.58.1.1 30268,33916 1k04A 162 4.29e+01 a.24.14.1 67904 1dvoA 152 4.29e+01 1dvoA a.136.1.1 19623 1jjyA 636 4.29e+01 1jjyA 1tbxA 99 4.30e+01 a.4.5.48 106748 1w7lA 422 4.31e+01 c.67.1.1 109226 1no1A 126 4.36e+01 a.179.1.1 85913 1rtwA 220 4.38e+01 a.132.1.3 97823 1vkcA 158 4.38e+01 2exrA 524 4.42e+01 1ytzT 107 4.46e+01 1bjwA 382 4.48e+01 1bjwA c.67.1.1 34349 2ggcA 263 4.49e+01 1k6dA 220 4.51e+01 c.124.1.2 72082 2ftrA 108 4.54e+01 1ydyA 356 4.55e+01 1yruB 74 4.56e+01 2b3yA 888 4.60e+01 1spjA 238 4.61e+01 5rubA 490 4.63e+01 1burA c.1.14.1,d.58.9.1 29382,39288 2ccjA 205 4.66e+01 1xo5A 183 4.68e+01 1innA 166 4.68e+01 1j98A d.185.1.2 62608 1ydhA 216 4.70e+01 1vjeA 166 4.70e+01 d.185.1.2 100807 1pixA 587 4.79e+01 c.14.1.4 94708 2f6hX 419 4.82e+01 1pu1A 94 4.84e+01 d.266.1.1 104307 1z5zA 271 4.87e+01 1z63A 500 4.89e+01 1lis 136 4.90e+01 1lis a.19.1.1 16406 2lisA 136 4.90e+01 1lis a.19.1.1 16405 1y4lA 121 4.93e+01 1z6fA 363 4.94e+01 1nzoA 363 4.96e+01 b.105.1.1,e.3.1.1 92383,92384 1kxpD 458 4.98e+01 a.126.1.1,a.126.1.1,a.126.1.1 73160,73161,73162 1slqA 278 4.99e+01 f.47.1.1 105719 1k8tA 510 5.00e+01 e.41.1.1 68316 1zboA 210 5.02e+01 1v4eA 299 5.07e+01 a.128.1.1 100296 1g4yR 148 5.10e+01 1cll a.39.1.5 60252 2et1A 201 5.11e+01 2ewcA 126 5.12e+01 1h8dH 260 5.12e+01 5ptp 1fi2A 201 5.20e+01 1fi2A b.82.1.2 59845 1zy4A 303 5.22e+01 1ykjA 394 5.24e+01 2fflA 756 5.24e+01 1wvcA 259 5.26e+01 1v54G 85 5.27e+01 f.23.2.1 100328 1nxhA 126 5.29e+01 a.200.1.1 92300 1tfjA 219 5.32e+01 1p97A 114 5.36e+01 d.110.3.7 94382 1pud 386 5.37e+01 1pud c.1.20.1 29658 1in4A 334 5.38e+01 1hqcA a.4.5.11,c.37.1.20 62597,62598 1xxsA 122 5.38e+01 2f9dA 125 5.40e+01 1aisB 200 5.40e+01 1aisB a.74.1.2,a.74.1.2 18384,18385 1nfvA 179 5.47e+01 a.25.1.1 85642 2fwtA 125 5.47e+01 1j5sA 463 5.54e+01 c.1.9.8 71580 1kyqA 274 5.57e+01 c.2.1.11,e.37.1.1 73281,73282 1r7jA 95 5.61e+01 a.4.5.49 104836 1x0rA 249 5.64e+01 1aerA 205 5.66e+01 1aerA d.166.1.1 42249 1wvvA 265 5.73e+01 1zsyA 357 5.79e+01 1pxgA 382 5.80e+01 c.1.20.1 95287 1ypvA 313 5.89e+01 1zq7A 207 5.94e+01 1sb8A 352 5.98e+01 c.2.1.2 105410 1vqrA 297 6.09e+01 1w78A 422 6.11e+01 1gp8A 40 6.13e+01 2gp8A j.58.1.1 46342 1d7oA 297 6.16e+01 1enp c.2.1.2 29907 1sxvA 172 6.19e+01 1quqA 129 6.25e+01 1quqA b.40.4.3 25303 1n8vA 112 6.32e+01 a.118.21.1 85457 1zvdA 380 6.32e+01 1f75A 249 6.34e+01 1f75A c.101.1.1 59662 2c3mA 1231 6.35e+01 2f1nA 262 6.40e+01 2hgsA 474 6.41e+01 2hgsA c.30.1.4,d.142.1.6 31722,75997 1qm9A 198 6.42e+01 1qm9A d.58.7.1,d.58.7.1 39207,39208 1pm3A 78 6.42e+01 b.41.1.2 94889 1tueB 218 6.42e+01 b.91.1.1 107324 1vybA 238 6.43e+01 d.151.1.1 108897 1pbgA 468 6.45e+01 1e70M c.1.8.4 28946 1s1hM 132 6.53e+01 i.1.1.1 105165 1oo0A 147 6.56e+01 d.232.1.1 87182 1sfxA 109 6.57e+01 a.4.5.50 105505 1acf 125 6.60e+01 3nul d.110.1.1 40882 2aexA 346 6.62e+01 1ub0A 258 6.63e+01 c.72.1.2 88394 1yiiA 320 6.68e+01 1z3iX 644 6.68e+01 1owfA 99 6.69e+01 a.55.1.1 87487 1db1A 259 6.72e+01 1db1A a.123.1.1 19329 2b6eA 146 6.83e+01 1t4hA 290 6.94e+01 d.144.1.7 106420 2cmwA 310 6.95e+01 2fpoA 202 6.99e+01 1tph1 247 7.01e+01 1amk 1wmwA 330 7.03e+01 2bjvA 265 7.06e+01 1sphA 88 7.09e+01 1ptf d.94.1.1 40544 2bgxA 261 7.18e+01 2es4D 332 7.21e+01 1e3oC 160 7.23e+01 1au7A a.4.1.1,a.35.1.1 59197,59198 1k9sA 237 7.26e+01 c.56.2.1 68359 1zq9A 285 7.31e+01 2cfuA 658 7.33e+01 1o5kA 306 7.34e+01 c.1.10.1 92504 1f7uA 607 7.40e+01 1bs2A a.27.1.1,c.26.1.1,d.67.2.1 59673,59674,59675 1zwpA 121 7.46e+01 2g58A 121 7.46e+01 1sqzA 121 7.46e+01 a.133.1.2 98975 1tk4A 121 7.46e+01 a.133.1.2 107073 1z7aA 308 7.46e+01 1uk5A 111 7.48e+01 a.7.7.1 99487 1jq5A 370 7.52e+01 e.22.1.2 67084 2d1eA 248 7.58e+01 1j1iA 296 7.61e+01 c.69.1.10 83977 1fs1B 141 7.64e+01 1vcbB a.157.1.1,d.42.1.1 19252,38664 1wy7A 207 7.67e+01 1k3tA 359 7.70e+01 c.2.1.3,d.81.1.1 72022,72023 1tj9A 121 7.75e+01 a.133.1.2 107015 1u8fO 335 7.78e+01 1lam 484 7.83e+01 1lam c.50.1.1,c.56.5.3 33166,33829 2bh7A 261 7.83e+01 1o69A 394 7.84e+01 c.67.1.4 92560 2anwA 241 7.88e+01 1kvkA 395 7.88e+01 d.14.1.5,d.58.26.3 73060,73061 1j30A 144 7.91e+01 a.25.1.1 90806 2d69A 430 7.93e+01 1dp4A 435 7.95e+01 1dp4A c.93.1.1 35710 1oyeA 1049 7.96e+01 d.58.44.1,d.58.44.1,d.58.44.1,d.58.44.1,d.225.1.1,d.225.1.1,f.35.1.1,f.35.1.1 87587,87588,87589,87590,87591,87592,87593,87594 1zvzA 279 7.98e+01 1sd4A 126 8.00e+01 a.4.5.39 105428 1e8yA 966 8.06e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 1t06A 235 8.07e+01 a.118.1.17 106194 1oflA 481 8.07e+01 b.80.1.4 103934 2bbeA 108 8.11e+01 2h79A 269 8.16e+01 1enp 312 8.17e+01 1enp c.2.1.2 29906 2rmcA 182 8.20e+01 2cpl b.62.1.1 27491 1h4vB 421 8.23e+01 1adjA c.51.1.1,d.104.1.1 60624,60625 1zclA 180 8.30e+01 1eg3A 261 8.32e+01 1eg3A a.39.1.7,a.39.1.7,b.72.1.1 17376,17377,27805 1bqcA 302 8.35e+01 1bqcA c.1.8.3 28831 2cybA 323 8.35e+01 1xmaA 145 8.55e+01 1byrA 155 8.56e+01 1byrA d.136.1.1 41450 1z6oA 212 8.62e+01 1qyiA 384 8.64e+01 c.108.1.13 96595 1pv6A 417 8.65e+01 f.38.1.2 95151 1ku1A 230 8.74e+01 a.118.3.1 72996 2cwxA 430 8.79e+01 1q6uA 245 8.81e+01 d.26.1.1 95998 1b0pA 1231 8.83e+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 1z91A 147 8.83e+01 1nb9A 147 8.83e+01 b.43.5.1 85515 1ve6A 582 8.87e+01 1vplA 256 8.88e+01 1y3jA 77 8.88e+01 1efyA 350 8.90e+01 1a26 a.41.1.1,d.166.1.2 17413,42275 1j99A 293 8.92e+01 c.37.1.5 71618 1mldA 314 9.00e+01 2cmd c.2.1.5,d.162.1.1 30122,42089 2ac2A 309 9.00e+01