# 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 2ghrA 302 6.88e-48 1wl8A 189 1.57e-19 1gpmA 525 2.49e-17 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 1o1yA 239 5.24e-11 c.23.16.1 86554 1qdlB 195 2.46e-10 1qdlB c.23.16.1 31437 1i7qB 193 1.58e-09 1qdlB c.23.16.1 61902 1i1qB 192 4.92e-09 1qdlB c.23.16.1 61544 1cs0B 382 1.25e-08 1c3oB c.8.3.1,c.23.16.1 30740,31417 1a9xB 379 2.56e-07 1c3oB c.8.3.1,c.23.16.1 30732,31409 1c3oB 382 5.85e-07 1c3oB c.8.3.1,c.23.16.1 30744,31421 1c30B 382 7.28e-07 c.8.3.1,c.23.16.1 30736,31413 1q7rA 219 9.52e-05 c.23.16.1 96054 1r9gA 216 1.07e-04 c.23.16.1 97258 1vcoA 550 2.42e-03 c.23.16.1,c.37.1.10 108508,108509 1gpwB 201 4.07e-03 c.23.16.1 65461 1k9vF 201 4.18e-03 c.23.16.1 68365 1l9xA 315 1.21e-02 c.23.16.1 73762 1g2iA 166 1.61e-02 1g2iA c.23.16.2 31438 2abwA 227 2.41e-02 1jvnA 555 4.99e-02 c.1.2.1,c.23.16.1 67355,67356 1ox6A 555 5.41e-02 c.1.2.1,c.23.16.1 87505,87506 1h72C 296 1.03e-01 d.14.1.5,d.58.26.1 60712,60713 1fwkA 296 1.21e-01 1fwkA d.14.1.5,d.58.26.1 37576,39398 1p5fA 189 1.87e-01 c.23.16.2 94142 2gk3A 256 3.87e-01 1tx2A 297 4.68e-01 c.1.21.1 107420 1jixA 351 4.90e-01 1c3jA c.87.1.1 63081 1pe0A 197 5.00e-01 c.23.16.2 88045 1fcqA 350 5.38e-01 c.1.8.9 65006 1c3jA 351 6.47e-01 1c3jA c.87.1.1 35459 1jg7A 351 7.82e-01 1c3jA c.87.1.1 62945 1ka9H 200 8.30e-01 c.23.16.1 77308 1iba 101 8.57e-01 1iba d.95.1.1 40567 2bgu 351 1.02e+00 1c3jA c.87.1.1 35460 1eqjA 511 1.27e+00 1ejjA c.105.1.1,c.76.1.3 59495,59496 1ejjA 511 1.29e+00 1ejjA c.105.1.1,c.76.1.3 59422,59423 2fexA 188 1.38e+00 1o98A 511 1.45e+00 c.105.1.1,c.76.1.3 86684,86685 1vhqA 232 1.46e+00 c.23.16.2 100696 2b4wA 315 1.84e+00 1n57A 291 1.96e+00 c.23.16.2 85328 1xa1A 255 2.28e+00 e.3.1.1 109529 1a9nB 96 2.45e+00 1urnA d.58.7.1 39165 2liv 344 2.57e+00 2liv c.93.1.1 35708 1c25 161 2.58e+00 1c25 c.46.1.1 32698 1n2zA 245 2.58e+00 c.92.2.2 79865 1v0wA 506 2.65e+00 d.136.1.2,d.136.1.2 108220,108221 1xkzA 255 2.74e+00 1sg4A 260 2.91e+00 2g0wA 296 3.02e+00 1be3C 379 3.02e+00 1be3C f.32.1.1,f.21.1.2 75805,75806 2lbp 346 3.09e+00 2liv c.93.1.1 35709 1ppjC 379 3.10e+00 f.32.1.1,f.21.1.2 104256,104257 1evlA 401 3.11e+00 1qf6A c.51.1.1,d.104.1.1 33202,40751 1qf6A 642 3.25e+00 1qf6A c.51.1.1,d.15.10.1,d.67.1.1,d.104.1.1 33210,39551,39562,40759 1whzA 70 3.37e+00 1ysc 421 3.38e+00 1ivyA c.69.1.5 34652 1om1A 332 3.54e+00 d.144.1.7 93347 1zq1A 438 3.56e+00 1xx4A 261 3.57e+00 1z15A 344 3.62e+00 1lp4A 332 3.63e+00 d.144.1.7 74170 1a6o 332 3.72e+00 1a6o 1qcrC 378 3.77e+00 1be3C f.32.1.1,f.21.1.2 75931,75932 1m2rA 327 4.07e+00 d.144.1.7 84760 1fjhB 257 4.07e+00 1fjhB c.2.1.2 29871 1xv5A 401 4.10e+00 1lpuA 332 4.27e+00 d.144.1.7 74177 2agdA 287 4.54e+00 2fy7A 287 4.67e+00 1usgA 346 5.00e+00 c.93.1.1 99864 1ecfB 504 5.57e+00 1ecfB c.61.1.1,d.153.1.1 34054,41821 1ecfA 504 5.74e+00 1ecfB c.61.1.1,d.153.1.1 34053,41820 1e19A 314 5.79e+00 1b7bA c.73.1.1 34967 1uanA 227 6.00e+00 c.134.1.1 99135 1lbqA 362 6.03e+00 c.92.1.1 77877 9ldtA 332 6.06e+00 3ldh c.2.1.5,d.162.1.1 30154,42121 2gokA 429 6.12e+00 1i0lA 221 6.19e+00 c.61.1.1 71096 1apyA 162 6.44e+00 1apyA d.153.1.5 42004 1kmdA 117 6.85e+00 d.189.1.1 72744 1scfA 273 7.18e+00 1exzA a.26.1.2 16873 1njrA 284 7.26e+00 c.50.1.2 103858 2a5lA 200 7.28e+00 1cb0A 283 7.41e+00 1cb0A c.56.2.1 33790 2f1lA 187 7.90e+00 2c4wA 176 8.33e+00 1tc1A 220 8.49e+00 1tc1A c.61.1.1 34083 1vzsA 76 8.52e+00 f.45.1.1 108972 1o51A 114 9.25e+00 d.58.5.4 92480 6ldh 330 9.26e+00 3ldh c.2.1.5,d.162.1.1 30161,42128 2ajrA 331 9.26e+00 1xqwA 293 9.44e+00 1mtzA 293 9.98e+00 c.69.1.7 79467 1wnfA 328 1.04e+01 1ldm 329 1.04e+01 3ldh c.2.1.5,d.162.1.1 30160,42127 1t0bA 252 1.07e+01 c.23.16.6 106199 1uk8A 282 1.07e+01 c.69.1.10 107907 1tljA 213 1.12e+01 d.282.1.1 107126 1pwhA 327 1.18e+01 c.79.1.1 95224 1yh3A 256 1.18e+01 1yacA 208 1.19e+01 1yacA c.33.1.3 31757 1t9bA 677 1.20e+01 1wlsA 328 1.21e+01 3ldh 330 1.24e+01 3ldh i.12.1.1 46015 1fjhA 257 1.24e+01 1fjhB c.2.1.2 29870 1f0iA 504 1.27e+01 1f0iA d.136.1.2,d.136.1.2 59566,59567 1cpy 421 1.29e+01 1ivyA c.69.1.5 34651 1yucA 255 1.30e+01 1nf5B 286 1.31e+01 c.68.1.2 80454 1nmmB 286 1.32e+01 c.68.1.2 80662 1kzhA 555 1.33e+01 c.89.1.1 73361 1ihjA 98 1.34e+01 1pdr b.36.1.1 62382 1gp1A 198 1.35e+01 1gp1A c.47.1.10 33059 1iupA 282 1.38e+01 c.69.1.10 76815 2gjlA 328 1.40e+01 1yroB 286 1.41e+01 1kgdA 180 1.42e+01 c.37.1.1 68582 1pztA 286 1.43e+01 c.68.1.2 95470 1vcdA 126 1.45e+01 1vk5A 157 1.53e+01 a.220.1.1 108635 1x7oA 287 1.57e+01 1kgsA 225 1.57e+01 a.4.6.1,c.23.1.1 68596,68597 2a2kA 175 1.63e+01 1u9cA 224 1.67e+01 9rnt 104 1.67e+01 9rnt d.1.1.4 36055 1ma3A 253 1.72e+01 c.31.1.5 78883 1exzA 141 1.77e+01 1exzA a.26.1.2 16877 1wdtA 665 1.80e+01 1wxxA 382 1.82e+01 1vr0A 247 1.85e+01 1oy1A 228 1.87e+01 c.23.16.2 87548 1rd5A 262 1.87e+01 1ymiA 334 1.94e+01 2occB 227 1.95e+01 2occB b.6.1.2,f.17.2.1 23027,43519 1vc1A 110 1.95e+01 c.13.2.1 108493 1a6dB 543 1.96e+01 1a6dA a.129.1.2,c.8.5.2,d.56.1.2 19489,30820,38937 3rnt 104 2.00e+01 9rnt d.1.1.4 36069 1no5A 114 2.07e+01 d.218.1.5 92014 1iznA 286 2.08e+01 e.43.1.1 83847 1xxqA 161 2.10e+01 1juvA 193 2.11e+01 c.71.1.1 90912 1pk5A 248 2.18e+01 a.123.1.1 88139 1w0mA 226 2.20e+01 c.1.1.1 109027 1yj7A 171 2.20e+01 1egzA 291 2.21e+01 7a3hA c.1.8.3 28828 1i0vA 104 2.22e+01 9rnt d.1.1.4 36054 1v54B 227 2.26e+01 b.6.1.2,f.17.2.1 100322,100323 2wsyA 268 2.26e+01 2tysA c.1.2.4 28588 1lldA 319 2.28e+01 3ldh c.2.1.5,d.162.1.1 30177,42144 1xygD 359 2.28e+01 2bayA 61 2.36e+01 1nbaA 264 2.41e+01 1nbaA c.33.1.3 31753 1kplA 473 2.42e+01 f.20.1.1 68782 1u7gA 385 2.45e+01 f.44.1.1 107723 1avu 181 2.45e+01 1wba b.42.4.1 25603 2a84A 300 2.47e+01 1ad1A 266 2.49e+01 1aj2 c.1.21.1 29668 1d2mA 665 2.52e+01 1d2mA c.37.1.19,c.37.1.19 32417,32418 1vzwA 244 2.52e+01 1icpA 376 2.63e+01 1oyc c.1.4.1 62270 1ymkA 175 2.64e+01 2a4vA 159 2.66e+01 1j8mF 297 2.67e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 2tysA 268 2.81e+01 2tysA c.1.2.4 28572 1p2fA 220 2.88e+01 a.4.6.1,c.23.1.1 87720,87721 1bksA 268 2.89e+01 2tysA c.1.2.4 28585 1o8uA 257 2.91e+01 c.14.1.3 81194 1tvnA 293 2.93e+01 1szoA 257 2.94e+01 c.14.1.3 106164 2bkaA 242 3.04e+01 1uf3A 228 3.10e+01 d.159.1.6 99317 1jsrA 327 3.15e+01 c.88.1.1 67237 1ba9 153 3.26e+01 1mfmA b.1.8.1 22272 1qopA 268 3.34e+01 2tysA c.1.2.4 28570 1jslA 327 3.42e+01 c.88.1.1 67233 2ab0A 205 3.43e+01 1nnwA 252 3.46e+01 d.159.1.5 80674 1jwhA 337 3.51e+01 d.144.1.7 71913 1nsj 205 3.53e+01 1nsj c.1.2.4 28560 1gqwA 283 3.57e+01 b.82.2.5 70377 1jcfA 344 3.58e+01 c.55.1.1,c.55.1.1 62878,62879 1o7jA 327 3.58e+01 c.88.1.1 81140 1jceA 344 3.59e+01 c.55.1.1,c.55.1.1 62876,62877 1j8wB 273 3.62e+01 1vzoA 355 3.65e+01 d.144.1.7 108971 1gwcA 230 3.74e+01 a.45.1.1,c.47.1.5 70660,70661 1fgxA 288 3.76e+01 1fgxA c.68.1.2 34508 2bjfA 329 3.79e+01 1zosA 230 3.89e+01 1qb0A 211 3.91e+01 1c25 c.46.1.1 32699 2d0iA 333 3.94e+01 2b8nA 429 3.96e+01 1aj0 282 4.07e+01 1aj2 c.1.21.1 29667 1d7oA 297 4.07e+01 1enp c.2.1.2 29907 1aj2 282 4.07e+01 1aj2 c.1.21.1 29665 2dlbA 80 4.15e+01 1mldA 314 4.27e+01 2cmd c.2.1.5,d.162.1.1 30122,42089 1enp 312 4.28e+01 1enp c.2.1.2 29906 1eno 312 4.32e+01 1enp c.2.1.2 29905 2fcr 173 4.36e+01 1rcf c.23.5.1 31151 1ur5A 309 4.48e+01 c.2.1.5,d.162.1.1 99807,99808 1j8yF 297 4.49e+01 1ng1 a.24.13.1,c.37.1.10 62747,62748 1tcvA 287 4.57e+01 1mkyA 439 4.62e+01 c.37.1.8,c.37.1.8,d.52.5.1 79250,79251,79252 3pga1 337 4.64e+01 4pgaA 1b00A 127 4.65e+01 3chy c.23.1.1 31122 2cunA 410 4.73e+01 1lssA 140 4.83e+01 c.2.1.9 74246 1nzyA 269 4.85e+01 1nzyA c.14.1.3 30903 1xv2A 237 4.87e+01 1jkmB 361 4.90e+01 1jkmA c.69.1.2 34634 1muhA 481 4.98e+01 c.55.3.4 79485 1eetA 557 5.06e+01 1rthA c.55.3.1,e.8.1.2 33608,43078 1u5uA 374 5.06e+01 6pfkA 319 5.07e+01 3pfk c.89.1.1 35583 1mfmA 153 5.14e+01 1mfmA b.1.8.1 22246 4pgaA 337 5.30e+01 4pgaA c.88.1.1 35565 1kfcA 268 5.33e+01 c.1.2.4 77371 1m7jA 484 5.35e+01 b.92.1.6,b.92.1.6,c.1.9.11 78732,78733,78734 1cvsC 225 5.51e+01 1cvsC b.1.1.4,b.1.1.4 21726,21727 1tc6A 236 5.55e+01 d.122.1.1 106756 1pzgA 331 5.56e+01 c.2.1.5,d.162.1.1 95425,95426 1bpr 191 5.57e+01 1dkzA b.130.1.1 43319 1rk6A 496 5.57e+01 b.92.1.6,b.92.1.6,c.1.9.11 97599,97600,97601 2pleA 105 5.59e+01 1qadA d.93.1.1 40522 1pud 386 5.60e+01 1pud c.1.20.1 29658 1i7fA 292 5.63e+01 1i7fA d.193.1.1 61888 1bqnB 430 5.63e+01 1rthA e.8.1.2 43065 1nsf 273 5.64e+01 1d2nA c.37.1.20 32429 2bmfA 451 5.64e+01 1w8kA 447 5.66e+01 1mopA 300 5.67e+01 c.26.1.4 85035 1n2eA 300 5.67e+01 c.26.1.4 85268 1r5yA 386 5.69e+01 c.1.20.1 97134 1tqhA 247 5.70e+01 c.69.1.29 107225 1iirA 415 5.70e+01 1iirA c.87.1.5 62453 1jr2A 286 5.73e+01 c.113.1.1 67111 1twdA 256 5.80e+01 c.1.30.1 107397 1wkyA 464 5.86e+01 2gwgA 350 5.90e+01 1vemA 516 5.91e+01 1ldg 316 5.95e+01 1ceqA c.2.1.5,d.162.1.1 30165,42132 1cnv 299 5.97e+01 1cnv c.1.8.5 28989 1zxxA 319 5.97e+01 1aazA 87 6.02e+01 1aba c.47.1.1 32761 1f3eA 386 6.02e+01 1pud c.1.20.1 29661 1c4oA 664 6.06e+01 1d2mA c.37.1.19,c.37.1.19 32415,32416 1b9zA 516 6.09e+01 1b9zA b.3.1.1,c.1.8.1 22528,28798 1uxjA 309 6.14e+01 c.2.1.5,d.162.1.1 108112,108113 1k4gA 386 6.16e+01 c.1.20.1 72054 1pxgA 382 6.16e+01 c.1.20.1 95287 1e1hA 287 6.21e+01 d.92.1.7 83167 1m6jA 261 6.24e+01 c.1.1.1 78693 1aba 87 6.30e+01 1aba c.47.1.1 32760 1mp9A 198 6.34e+01 d.129.1.1,d.129.1.1 91385,91386 5bcaA 516 6.40e+01 1b9zA b.3.1.1,c.1.8.1 22529,28799 1eh9A 558 6.47e+01 1ehaA b.1.18.2,b.71.1.1,c.1.8.1 21858,27785,28772 1zd3A 555 6.49e+01 1k2eA 156 6.53e+01 d.113.1.1 72010 1e0tA 470 6.54e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 1gzqA 300 6.55e+01 b.1.1.2,d.19.1.1 70818,70819 1wq3A 322 6.57e+01 1b93B 152 6.58e+01 1b93A c.24.1.2 31508 1o0uA 429 6.62e+01 c.118.1.1 80743 4pfk 319 6.63e+01 3pfk c.89.1.1 35582 1pvuA 154 6.66e+01 3pviA c.52.1.6 33306 103l 167 6.71e+01 1l92 d.2.1.3 36870 1zpuA 534 6.74e+01 1otjA 283 6.80e+01 b.82.2.5 93517 1qnxA 209 6.81e+01 1qnxA d.111.1.1 40914 2aeuA 374 6.87e+01 1u5hA 273 6.88e+01 1qv9A 283 6.88e+01 c.127.1.1 96356 1w5cB 510 6.93e+01 1zp4A 304 6.95e+01 1k1tA 99 6.96e+01 b.50.1.1 71995 1tl2A 236 6.99e+01 1tl2A b.67.1.1 27541 1jkmA 358 6.99e+01 1jkmA c.69.1.2 34633 1bjaA 95 7.08e+01 1bjaA a.4.5.9 16122 1hmvA 560 7.09e+01 1rthA c.55.3.1,e.8.1.2 33587,43046 1avwB 171 7.10e+01 1wba b.42.4.1 25599 1d2nA 272 7.14e+01 1d2nA c.37.1.20 32428 1zesA 125 7.29e+01 1o2dA 371 7.30e+01 e.22.1.2 86591 1b73A 254 7.33e+01 1b74A c.78.2.1,c.78.2.1 35266,35267 1ehaA 558 7.35e+01 1ehaA b.1.18.2,b.71.1.1,c.1.8.1 21859,27786,28773 2cdnA 201 7.36e+01 1mkzA 172 7.53e+01 c.57.1.1 84998 1j7iA 264 7.55e+01 1j7iA d.144.1.6 62694 1b93A 152 7.72e+01 1b93A c.24.1.2 31507 1bvyF 191 7.77e+01 1bvyF c.23.5.1 31207 1sbyA 254 7.77e+01 1wqaA 455 7.79e+01 1dazC 99 7.83e+01 1hvc b.50.1.1 26501 1h67A 108 7.88e+01 a.40.1.1 65643 3pfk 319 7.90e+01 3pfk c.89.1.1 35581 1umwA 237 7.91e+01 d.223.1.2,d.223.1.2 99631,99632 1a4uA 254 7.93e+01 1b16A c.2.1.2 29878 1k26A 156 7.95e+01 d.113.1.1 72003 1t62A 166 7.96e+01 b.122.1.4 106541 1r5tA 142 7.96e+01 c.97.1.1 104812 1mmoG 162 8.00e+01 1mtyG a.23.3.1 16512 1fj7A 101 8.03e+01 1fj7A d.58.7.1 39209 1jscA 630 8.03e+01 c.31.1.3,c.36.1.5,c.36.1.9 67224,67225,67226 1ad4A 266 8.04e+01 1aj2 c.1.21.1 29670 1qlyA 58 8.04e+01 1bbzA b.34.2.1 24530 1w25A 459 8.05e+01 1eswA 500 8.06e+01 1cwyA c.1.8.1 59500 1mtyG 162 8.14e+01 1mtyG a.23.3.1 16498 1sq5A 308 8.14e+01 c.37.1.6 105882 1mh1 186 8.20e+01 1eesA c.37.1.8 32002 1dm0A 287 8.21e+01 1dm0A d.165.1.2 42227 1itcA 516 8.26e+01 b.3.1.1,c.1.8.1 83705,83706 1ox0A 430 8.29e+01 c.95.1.1,c.95.1.1 87495,87496 1pc6A 146 8.31e+01 d.262.1.1 94430 2f8aA 208 8.34e+01 1b16A 254 8.35e+01 1b16A c.2.1.2 29875 1j4aA 333 8.35e+01 c.2.1.4,c.23.12.1 71502,71503 2ge3A 170 8.44e+01 1wv2A 265 8.44e+01 1a94A 99 8.53e+01 1fmb b.50.1.1 26599 1vizA 240 8.59e+01 c.1.4.1 100784 1qy5A 269 8.60e+01 d.122.1.1 96573 1jrkA 156 8.66e+01 d.113.1.1 71827 1t5iA 172 8.70e+01 c.37.1.19 106450 1eyuA 157 8.76e+01 3pviA c.52.1.6 33304 1mkp 144 8.79e+01 1vhrA c.45.1.1 32654 1d3gA 367 8.82e+01 1d3gA c.1.4.1 28600 1j27A 102 8.94e+01 d.58.50.1 90778 1b7gO 340 8.99e+01 1b7gO c.2.1.3,d.81.1.1 29992,39907