# List of top-scoring protein chains for t2k-100-30-near-backbone-11-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 2.86e-40 1wl8A 189 2.01e-17 1gpmA 525 5.69e-16 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 1o1yA 239 1.05e-09 c.23.16.1 86554 1qdlB 195 7.96e-08 1qdlB c.23.16.1 31437 1i7qB 193 9.11e-08 1qdlB c.23.16.1 61902 1i1qB 192 1.52e-07 1qdlB c.23.16.1 61544 1cs0B 382 5.44e-07 1c3oB c.8.3.1,c.23.16.1 30740,31417 1a9xB 379 5.21e-06 1c3oB c.8.3.1,c.23.16.1 30732,31409 1c3oB 382 1.54e-05 1c3oB c.8.3.1,c.23.16.1 30744,31421 1c30B 382 1.86e-05 c.8.3.1,c.23.16.1 30736,31413 1q7rA 219 9.09e-05 c.23.16.1 96054 1r9gA 216 2.52e-04 c.23.16.1 97258 1g2iA 166 4.31e-04 1g2iA c.23.16.2 31438 1vcoA 550 6.18e-03 c.23.16.1,c.37.1.10 108508,108509 1oy1A 228 7.85e-02 c.23.16.2 87548 1vhqA 232 8.39e-02 c.23.16.2 100696 1h72C 296 8.93e-02 d.14.1.5,d.58.26.1 60712,60713 1fwkA 296 9.58e-02 1fwkA d.14.1.5,d.58.26.1 37576,39398 1p5fA 189 9.59e-02 c.23.16.2 94142 1pe0A 197 1.44e-01 c.23.16.2 88045 1ka9H 200 1.90e-01 c.23.16.1 77308 1k9vF 201 1.90e-01 c.23.16.1 68365 2b4wA 315 1.98e-01 1n57A 291 2.62e-01 c.23.16.2 85328 2fexA 188 2.95e-01 1ox6A 555 3.01e-01 c.1.2.1,c.23.16.1 87505,87506 1gpwB 201 3.71e-01 c.23.16.1 65461 1jvnA 555 5.21e-01 c.1.2.1,c.23.16.1 67355,67356 1jixA 351 5.96e-01 1c3jA c.87.1.1 63081 1jg7A 351 7.90e-01 1c3jA c.87.1.1 62945 1u9cA 224 8.47e-01 1c3jA 351 8.81e-01 1c3jA c.87.1.1 35459 2bgu 351 9.85e-01 1c3jA c.87.1.1 35460 1qcrC 378 1.51e+00 1be3C f.32.1.1,f.21.1.2 75931,75932 1xqwA 293 1.61e+00 1ykfA 352 2.02e+00 1pedA b.35.1.2,c.2.1.1 24757,29773 1kcmA 270 2.43e+00 d.129.3.4 72300 1mtzA 293 2.43e+00 c.69.1.7 79467 1fcqA 350 2.72e+00 c.1.8.9 65006 2a6sA 84 3.03e+00 2c4wA 176 3.05e+00 2abwA 227 3.11e+00 1uk8A 282 3.26e+00 c.69.1.10 107907 1iupA 282 3.64e+00 c.69.1.10 76815 1zq1A 438 3.80e+00 1cnv 299 4.33e+00 1cnv c.1.8.5 28989 1n2zA 245 4.94e+00 c.92.2.2 79865 1l9xA 315 5.18e+00 c.23.16.1 73762 2acvA 463 5.28e+00 1yacA 208 5.67e+00 1yacA c.33.1.3 31757 1s5aA 150 5.68e+00 d.17.4.10 98525 1ovlA 271 6.90e+00 a.123.1.1 87455 1vcdA 126 7.02e+00 1ppjC 379 7.56e+00 f.32.1.1,f.21.1.2 104256,104257 1gp1A 198 8.02e+00 1gp1A c.47.1.10 33059 1x3mA 415 8.66e+00 1d3hA 367 8.77e+00 1d3gA c.1.4.1 28601 1sg4A 260 9.29e+00 1be3C 379 9.47e+00 1be3C f.32.1.1,f.21.1.2 75805,75806 1fvzA 271 9.65e+00 1fvzA 1vemA 516 9.66e+00 1df7A 159 9.72e+00 3dfr c.71.1.1 34885 1rd5A 262 9.72e+00 5bcaA 516 1.03e+01 1b9zA b.3.1.1,c.1.8.1 22529,28799 1d3gA 367 1.06e+01 1d3gA c.1.4.1 28600 2b0mA 393 1.14e+01 1kzhA 555 1.16e+01 c.89.1.1 73361 1xx4A 261 1.17e+01 1c25 161 1.18e+01 1c25 c.46.1.1 32698 1tjyA 316 1.18e+01 c.93.1.1 107062 1egzA 291 1.21e+01 7a3hA c.1.8.3 28828 1lhpA 312 1.25e+01 c.72.1.5 77960 1z08A 170 1.31e+01 1vi4A 174 1.32e+01 c.8.7.1 100731 1ea3A 164 1.32e+01 1aa7A a.95.1.1 59398 1uf3A 228 1.32e+01 d.159.1.6 99317 1rm6A 769 1.36e+01 1l0oC 243 1.36e+01 a.4.13.2 73405 1itcA 516 1.48e+01 b.3.1.1,c.1.8.1 83705,83706 1aa7A 158 1.48e+01 1aa7A a.95.1.1 18741 1ulyA 192 1.50e+01 1j75A 67 1.51e+01 a.4.5.19 62673 1w0mA 226 1.52e+01 c.1.1.1 109027 1wnfA 328 1.53e+01 1cksA 79 1.54e+01 1puc d.97.1.1 40683 1qkmA 255 1.58e+01 3erdA a.123.1.1 19309 1tsm 316 1.63e+01 1bkpA d.117.1.1 41024 1bksA 268 1.64e+01 2tysA c.1.2.4 28585 1nbaA 264 1.64e+01 1nbaA c.33.1.3 31753 1m6jA 261 1.65e+01 c.1.1.1 78693 1jsrA 327 1.71e+01 c.88.1.1 67237 1jr2A 286 1.73e+01 c.113.1.1 67111 1mo0A 275 1.79e+01 c.1.1.1 79329 1ag9A 175 1.82e+01 1rcf c.23.5.1 31178 1jslA 327 1.82e+01 c.88.1.1 67233 1q5xA 161 1.83e+01 c.8.7.1 95947 1evlA 401 1.90e+01 1qf6A c.51.1.1,d.104.1.1 33202,40751 1kgsA 225 1.93e+01 a.4.6.1,c.23.1.1 68596,68597 1kfcA 268 1.94e+01 c.1.2.4 77371 1v71A 323 1.95e+01 1wlsA 328 1.97e+01 1eiwA 111 1.99e+01 1eiwA c.23.3.1 31130 1o7jA 327 2.00e+01 c.88.1.1 81140 1xvwA 160 2.02e+01 1hd2A 161 2.02e+01 c.47.1.10 60962 1qopA 268 2.06e+01 2tysA c.1.2.4 28570 1b9zA 516 2.10e+01 1b9zA b.3.1.1,c.1.8.1 22528,28798 1yp2A 451 2.13e+01 2ab0A 205 2.23e+01 1vzsA 76 2.29e+01 f.45.1.1 108972 1d2nA 272 2.29e+01 1d2nA c.37.1.20 32428 2aj6A 159 2.31e+01 1j97A 211 2.32e+01 1f5sA c.108.1.4 62753 1b4aA 149 2.36e+01 1b4aA a.4.5.3,d.74.2.1 16088,39721 1vp2A 208 2.38e+01 1twdA 256 2.40e+01 c.1.30.1 107397 2f8aA 208 2.41e+01 1tx2A 297 2.48e+01 c.1.21.1 107420 1tvnA 293 2.52e+01 7timA 247 2.53e+01 1amk c.1.1.1 28457 2liv 344 2.53e+01 2liv c.93.1.1 35708 2ab5A 269 2.79e+01 1xwyA 264 2.83e+01 2aeuA 374 2.92e+01 1ozhA 566 2.94e+01 c.31.1.3,c.36.1.5,c.36.1.9 93833,93834,93835 1zosA 230 2.94e+01 2cs7A 55 2.97e+01 1xv5A 401 2.98e+01 1z15A 344 3.13e+01 1ea0A 1479 3.16e+01 b.80.4.1,c.1.4.1,d.153.1.1 64854,64855,64856 1ymqA 261 3.21e+01 1krhA 338 3.24e+01 b.43.4.2,c.25.1.2,d.15.4.2 72891,72892,72893 1iba 101 3.26e+01 1iba d.95.1.1 40567 1uumA 372 3.27e+01 c.1.4.1 100010 1nsf 273 3.35e+01 1d2nA c.37.1.20 32429 1neyA 247 3.44e+01 c.1.1.1 80449 1php 394 3.46e+01 16pk c.86.1.1 35452 1epuA 591 3.51e+01 1dn1A e.25.1.1 43358 2aamA 309 3.51e+01 2gk3A 256 3.52e+01 1dbwA 126 3.52e+01 1dbwA c.23.1.1 31095 6pfkA 319 3.55e+01 3pfk c.89.1.1 35583 1whzA 70 3.64e+01 1kzfA 230 3.66e+01 d.108.1.3 73354 1k26A 156 3.73e+01 d.113.1.1 72003 1l7mA 211 3.77e+01 c.108.1.4 73664 1yucA 255 3.78e+01 2tysA 268 3.79e+01 2tysA c.1.2.4 28572 2a0jA 149 3.87e+01 4pgaA 337 3.90e+01 4pgaA c.88.1.1 35565 1ae6L 219 3.91e+01 8fabA b.1.1.1,b.1.1.2 20210,21222 1ei6A 406 3.95e+01 c.76.1.4 90443 1o4vA 183 4.06e+01 c.23.8.1 86628 1z6aA 500 4.08e+01 1geqA 248 4.10e+01 2tysA c.1.2.4 28589 1ppn 212 4.14e+01 1cs8A d.3.1.1 37004 1e1dA 553 4.14e+01 1e1dA e.26.1.1 43363 1g5hA 454 4.18e+01 1g5hA c.51.1.1,d.104.1.1 60270,60271 1dckA 126 4.20e+01 1dbwA c.23.1.1 31097 2cb2A 318 4.22e+01 1ybhA 590 4.28e+01 1f5sA 211 4.39e+01 1f5sA c.108.1.4 59656 3pga1 337 4.40e+01 4pgaA 1a6dB 543 4.53e+01 1a6dA a.129.1.2,c.8.5.2,d.56.1.2 19489,30820,38937 2dubE 261 4.55e+01 1nzyA c.14.1.3 30916 9ldtA 332 4.56e+01 3ldh c.2.1.5,d.162.1.1 30154,42121 1dx8A 70 4.60e+01 1rb9 g.41.5.1 45243 1tfzA 424 4.64e+01 d.32.1.3,d.32.1.3 106886,106887 1njrA 284 4.67e+01 c.50.1.2 103858 1i45A 248 4.74e+01 1amk c.1.1.1 61665 1gntA 553 4.78e+01 e.26.1.1 70290 1ypxA 375 4.84e+01 1din 236 4.86e+01 1din c.69.1.9 34682 1khqA 212 4.89e+01 d.3.1.1 90964 1qf6A 642 4.93e+01 1qf6A c.51.1.1,d.15.10.1,d.67.1.1,d.104.1.1 33210,39551,39562,40759 1apyA 162 4.97e+01 1apyA d.153.1.5 42004 1vzoA 355 4.98e+01 d.144.1.7 108971 1b2jA 54 5.01e+01 1rb9 g.41.5.1 45231 1ejjA 511 5.04e+01 1ejjA c.105.1.1,c.76.1.3 59422,59423 1usgA 346 5.05e+01 c.93.1.1 99864 1r1dA 247 5.10e+01 c.69.1.29 96813 1pk5A 248 5.10e+01 a.123.1.1 88139 2cw6A 298 5.13e+01 1k1xA 659 5.15e+01 a.8.3.2,b.30.5.8,c.6.2.2 84279,84280,84281 1z0jA 170 5.16e+01 1q72L 218 5.17e+01 b.1.1.1,b.1.1.2 96016,96017 9pap 212 5.20e+01 1cs8A d.3.1.1 37006 2d0iA 333 5.28e+01 1pud 386 5.31e+01 1pud c.1.20.1 29658 1eqjA 511 5.32e+01 1ejjA c.105.1.1,c.76.1.3 59495,59496 1wdtA 665 5.36e+01 1k2eA 156 5.38e+01 d.113.1.1 72010 1zxxA 319 5.38e+01 4pfk 319 5.40e+01 3pfk c.89.1.1 35582 1sbzA 197 5.51e+01 1jajA 174 5.54e+01 d.218.1.2 66471 1b2oA 54 5.59e+01 1rb9 g.41.5.1 45233 1vjzA 341 5.59e+01 c.1.8.3 100838 2bl9A 238 5.60e+01 1e2uA 553 5.62e+01 1e1dA e.26.1.1 43362 1ku1A 230 5.71e+01 a.118.3.1 72996 2cioA 212 5.78e+01 1wcuA 153 5.84e+01 1f3eA 386 5.86e+01 1pud c.1.20.1 29661 1ft1B 437 5.92e+01 1ft1B a.102.4.3 18867 1d5wC 126 5.95e+01 1dbwA c.23.1.1 31101 1f6kA 293 5.95e+01 1nal3 c.1.10.1 29081 1xwwA 157 5.98e+01 1om1A 332 5.98e+01 d.144.1.7 93347 1d2mA 665 6.00e+01 1d2mA c.37.1.19,c.37.1.19 32417,32418 1b8bA 605 6.14e+01 1b8bA 3pfk 319 6.16e+01 3pfk c.89.1.1 35581 1uz5A 402 6.22e+01 b.85.6.1,b.103.1.1,c.57.1.2 100217,100218,100219 1tph1 247 6.22e+01 1amk 1o98A 511 6.29e+01 c.105.1.1,c.76.1.3 86684,86685 2b8nA 429 6.31e+01 1mjuL 219 6.55e+01 b.1.1.1,b.1.1.2 91304,91305 1y5hA 133 6.56e+01 1uv7A 110 6.57e+01 d.67.4.1 100040 1etu 394 6.60e+01 1efcA c.37.1.8 64737 1yd0A 96 6.61e+01 1o51A 114 6.65e+01 d.58.5.4 92480 1ll1 590 6.67e+01 1lla a.85.1.1,a.86.1.1,b.1.18.3 18488,18499,21864 1h67A 108 6.68e+01 a.40.1.1 65643 1ihjA 98 6.69e+01 1pdr b.36.1.1 62382 1rp0A 284 6.80e+01 2fz0A 149 6.81e+01 2lbp 346 6.88e+01 2liv c.93.1.1 35709 2blcA 238 6.91e+01 1gtkA 313 6.92e+01 c.94.1.1,d.50.2.1 76346,76347 1jf9A 408 6.92e+01 1c0nA c.67.1.3 62931 1jcrB 437 6.99e+01 a.102.4.3 66507 2ajrA 331 6.99e+01 1nxjA 183 7.08e+01 c.8.7.1 86382 1w8kA 447 7.13e+01 1zc3B 113 7.15e+01 1d8dB 437 7.22e+01 1ft1B a.102.4.3 18866 1ma3A 253 7.27e+01 c.31.1.5 78883 1bykA 255 7.28e+01 1bykA c.93.1.1 35706 1trb 320 7.32e+01 1trb c.3.1.5,c.3.1.5 30529,30530 1k4gA 386 7.32e+01 c.1.20.1 72054 1cnt1 187 7.41e+01 1cnt3 2arhA 203 7.41e+01 1gesA 450 7.43e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30473,30474,40168 1pg6A 243 7.46e+01 b.82.5.2 94673 8abp 306 7.50e+01 8abp c.93.1.1 35647 1c0eA 157 7.60e+01 1dg9A c.44.1.1 32638 1jrkA 156 7.60e+01 d.113.1.1 71827 1sxgA 280 7.61e+01 1dn1A 594 7.77e+01 1dn1A e.25.1.1 43357 1ts3A 194 7.82e+01 1aw7A b.40.2.2,d.15.6.1 25168,37757 2bkaA 242 7.84e+01 1kk8B 139 7.89e+01 a.39.1.5 77430 1deuA 277 7.90e+01 1theB d.3.1.1 37085 1yb3A 175 7.92e+01 1lldA 319 7.96e+01 3ldh c.2.1.5,d.162.1.1 30177,42144 1tde 316 8.09e+01 1trb c.3.1.5,c.3.1.5 30531,30532 1u7gA 385 8.10e+01 f.44.1.1 107723 1uiuA 502 8.17e+01 c.94.1.1 99434 2pfkA 320 8.26e+01 3pfk c.89.1.1 35577 1s14A 194 8.27e+01 d.122.1.2 98329 1lpuA 332 8.32e+01 d.144.1.7 74177 1mwwA 128 8.34e+01 d.80.1.4 91483 1ldm 329 8.41e+01 3ldh c.2.1.5,d.162.1.1 30160,42127 1jysA 242 8.42e+01 c.56.2.1 77216 1aw7A 194 8.45e+01 1aw7A b.40.2.2,d.15.6.1 25164,37753 3ldh 330 8.60e+01 3ldh i.12.1.1 46015 1yxyA 234 8.61e+01 1c0nA 406 8.62e+01 1c0nA c.67.1.3 34433 1mvoA 136 8.71e+01 c.23.1.1 79513 1aky 221 8.73e+01 1zin c.37.1.1,g.41.2.1 31896,45197 1w97L 246 8.73e+01 1cc1L 498 8.74e+01 1h2rL e.18.1.1 43301 2gokA 429 8.79e+01 2ak3A 226 8.81e+01 1zin c.37.1.1,g.41.2.1 31892,45193 1tqhA 247 8.82e+01 c.69.1.29 107225 1sbyA 254 8.85e+01 1h1yA 228 8.92e+01 c.1.2.2 76506