# List of top-scoring protein chains for t2k-100-30-alpha 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 1dptA 117 6.76e-03 1dptA d.80.1.3 39862 1hfoA 113 8.54e-03 d.80.1.3 61006 1gyxA 76 2.56e-02 d.80.1.1 76387 9gafA 295 1.10e-01 1apyA d.153.1.5 42008 1p4kA 295 1.31e-01 d.153.1.5 87772 1hqsA 423 1.73e-01 1iso c.77.1.1 61154 1otfA 62 1.88e-01 1otfA d.80.1.1 39820 1s0yA 76 2.37e-01 d.80.1.1 -10434 1qysA 106 2.44e-01 unknown_sccs -13432 1iv3A 152 3.01e-01 d.79.5.1 76828 1ur1A 378 3.85e-01 c.1.8.3 -5311 1uvqB 198 5.65e-01 b.1.1.2 -2659 d.19.1.1 -9348 1mfiA 114 6.56e-01 1dptA d.80.1.3 39856 1k6iA 352 7.09e-01 c.2.1.2 68223 1pwhA 327 9.15e-01 c.79.1.1 -8524 1ffkI 194 9.71e-01 1ffkI d.12.1.2 37494 1k6xA 352 1.02e+00 c.2.1.2 68238 1ukkA 142 1.53e+00 d.227.1.1 -11206 1q8yA 373 1.95e+00 d.144.1.7 -11319 1jtaA 361 1.96e+00 b.80.1.1 71859 1i60A 278 1.97e+00 c.1.15.4 71118 1otgA 125 2.13e+00 1otgA d.80.1.2 39831 1pe9A 361 2.24e+00 b.80.1.1 -4765 1k4jA 230 2.25e+00 d.108.1.3 72057 1ex2A 189 2.44e+00 1ex2A c.51.4.2 33225 1mwwA 128 2.51e+00 unknown_sccs -10451 1kzfA 230 2.53e+00 d.108.1.3 73354 1npdA 288 2.66e+00 c.2.1.7 80681 c.58.1.5 80682 1owfA 99 2.79e+00 a.55.1.1 87487 1howA 373 2.79e+00 1hcl d.144.1.7 41679 1gd0A 122 2.79e+00 1dptA d.80.1.3 39834 1rypI 222 2.80e+00 d.153.1.4 41877 1mml 265 3.14e+00 1mml e.8.1.2 43015 1pieA 419 3.14e+00 d.14.1.5 -9075 unknown_sccs -10120 1i1gA 141 3.18e+00 a.4.5.32 65982 d.58.4.2 65983 1ihfA 99 3.20e+00 1huuA a.55.1.1 17893 1vi2A 300 3.44e+00 c.2.1.7 -5960 c.58.1.5 -6366 1nm1G 125 3.50e+00 d.109.1.1 80653 1d4xG 126 3.74e+00 1d0nA d.109.1.1 59109 1p5jA 372 3.86e+00 1dt6A 473 3.95e+00 1dt6A a.104.1.1 18977 1k20A 310 3.97e+00 c.107.1.1 68027 1q53A 112 4.36e+00 d.58.4.4 -9944 1j7nB 776 4.44e+00 d.92.1.14 66412 d.92.1.14 66413 d.166.1.1 66414 1nrhX 472 4.72e+00 c.2.1.5 -5944 d.162.1.2 -11511 1eluB 390 4.72e+00 1elqA c.67.1.3 34435 1i58A 189 4.74e+00 1b3qA d.122.1.3 61773 1brsD 89 4.78e+00 1ay7B c.9.1.1 30825 1elqA 390 4.81e+00 1elqA c.67.1.3 34436 1eluA 390 4.82e+00 1elqA c.67.1.3 34434 7a3hA 303 4.92e+00 7a3hA c.1.8.3 28817 1iicA 422 4.94e+00 1nmtA d.108.1.2 62422 d.108.1.2 62423 1l0oA 150 5.09e+00 d.122.1.3 73403 1qhtA 775 5.19e+00 1tgoA c.55.3.5 33722 e.8.1.1 43011 1h5vA 304 5.30e+00 c.1.8.3 70898 1j7nA 776 5.31e+00 d.92.1.14 66409 d.92.1.14 66410 d.166.1.1 66411 1d5mB 192 5.52e+00 1iakB b.1.1.2 21618 d.19.1.1 38192 1m0dA 138 5.57e+00 c.52.1.17 74354 1cqqA 180 5.59e+00 1cqqA b.47.1.4 26422 1yagG 125 5.67e+00 1d0nA d.109.1.1 40846 1r6wA 322 5.68e+00 c.1.11.2 -5563 d.54.1.1 -9821 1fhuA 320 6.01e+00 1fhuA c.1.11.2 29234 d.54.1.1 38878 1bam 213 6.09e+00 1bam c.52.1.3 33285 1sdoA 203 6.42e+00 unknown_sccs -7558 1kkoA 413 6.44e+00 c.1.11.2 68675 d.54.1.1 68676 1q4rA 112 6.62e+00 d.58.4.4 -9943 1pgl2 370 6.83e+00 1v7rA 186 6.90e+00 c.51.4.1 -7546 1a3h 300 7.03e+00 7a3hA c.1.8.3 28819 1gt91 357 7.23e+00 1sviA 195 7.43e+00 1ldjA 760 7.53e+00 a.4.5.34 73847 a.118.17.1 73848 e.40.1.1 73849 2ptd 298 7.74e+00 2plc c.1.18.2 29605 1fjgJ 105 8.43e+00 1fjfJ d.58.15.1 39330 1uiuA 502 8.49e+00 c.94.1.1 -8674 1m4jA 142 9.17e+00 d.109.1.2 78602 1qy1A 174 9.46e+00 b.60.1.1 -4445 1h2rL 534 9.87e+00 1h2rL e.18.1.1 43298 1rp4A 389 1.01e+01 1esgA 213 1.03e+01 1bam c.52.1.3 33286 1evlA 401 1.04e+01 1qf6A c.51.1.1 33202 d.104.1.1 40751 1ow1A 195 1.05e+01 unknown_sccs -4422 1th8A 145 1.07e+01 1iakB 185 1.08e+01 1iakB b.1.1.2 21626 d.19.1.1 38200 1p7tA 731 1.13e+01 c.1.13.1 -5600 1bmv2 374 1.13e+01 1bmv2 1ibsA 317 1.14e+01 c.61.1.2 66107 c.61.1.2 66108 1ev0A 58 1.18e+01 1ev0A d.71.1.1 39594 1jv4A 162 1.18e+01 b.60.1.1 67343 1i06A 180 1.19e+01 1mup b.60.1.1 27131 1b6rA 355 1.26e+01 1b6rA b.84.2.1 28241 c.30.1.1 31648 d.142.1.2 41493 1garA 212 1.26e+01 2gar c.65.1.1 34162 1mup 166 1.26e+01 1mup b.60.1.1 27133 3bamB 213 1.29e+01 1bam c.52.1.3 33289 1hnnA 282 1.29e+01 c.66.1.15 65895 1spvA 184 1.29e+01 c.50.1.2 -7937 1bx2B 191 1.35e+01 1iakB b.1.1.2 21610 d.19.1.1 38184 1i05A 180 1.35e+01 1mup b.60.1.1 27130 1sy6A 204 1.36e+01 1a99A 344 1.36e+01 1pot c.94.1.1 35812 1dd9A 338 1.39e+01 1dd9A e.13.1.1 43254 1kr4A 125 1.40e+01 d.58.5.2 72889 1dkrA 317 1.41e+01 1dkuA c.61.1.2 34114 c.61.1.2 34115 1a0rP 245 1.43e+01 1b9yC c.47.1.6 33054 1p8xA 344 1.44e+01 d.109.1.1 -10813 d.109.1.1 -10814 d.109.1.1 -10815 1jkxA 212 1.44e+01 c.65.1.1 66813 1ubkL 534 1.44e+01 e.18.1.1 88422 1i74A 309 1.45e+01 1i74A c.107.1.1 61867 1konA 249 1.46e+01 e.39.1.1 72823 1jgtA 513 1.46e+01 c.26.2.1 66684 d.153.1.1 66685 1d0nA 729 1.46e+01 1d0nA d.109.1.1 40834 d.109.1.1 40835 d.109.1.1 40836 d.109.1.1 40837 d.109.1.1 40838 d.109.1.1 40839 1b6sA 355 1.47e+01 1b6rA b.84.2.1 28242 c.30.1.1 31649 d.142.1.2 41494 1tx4B 178 1.48e+01 1ctqA c.37.1.8 32045 1b3qA 379 1.49e+01 1b3qA a.30.2.1 16993 b.40.7.1 25454 d.122.1.3 41112 2vik 126 1.52e+01 2vil d.109.1.1 40829 1nkxA 348 1.56e+01 c.94.1.2 -8704 2iadB 205 1.60e+01 1iakB b.1.1.2 21640 d.19.1.1 38214 1fce 629 1.61e+01 1fce a.102.1.2 18836 1iuhA 198 1.63e+01 d.61.1.2 83711 1dlhB 188 1.64e+01 1iakB b.1.1.2 21598 d.19.1.1 38172 1r2rA 248 1.64e+01 c.1.1.1 -5147 1bolA 222 1.68e+01 1bolA d.124.1.1 41120 1o0wA 252 1.69e+01 a.149.1.1 80751 d.50.1.1 80752 9apiA 347 1.70e+01 1ovaA e.1.1.1 42630 1bzyA 217 1.70e+01 1qk3A c.61.1.1 34071 1btkA 169 1.71e+01 1btkA b.55.1.1 26959 2cb5A 453 1.75e+01 3gcb d.3.1.1 37035 1e8gA 560 1.76e+01 1qltA d.58.32.1 39455 d.145.1.1 41718 1ii7A 333 1.78e+01 1ii7A d.159.1.4 62415 1g8aA 227 1.85e+01 c.66.1.3 -8049 1f9vA 347 1.91e+01 1bg2 c.37.1.9 59745 1btkB 169 1.91e+01 1btkA b.55.1.1 26960 1pf5A 131 1.93e+01 d.79.1.1 -10368 1qumA 285 1.94e+01 1qumA c.1.15.1 29393 1o4tA 133 1.96e+01 b.82.1.9 86622 1tph1 247 1.99e+01 1amk 1mijA 152 2.01e+01 a.4.1.1 79150 1qqrA 138 2.02e+01 1bmlC d.15.5.1 37721 2vil 126 2.03e+01 2vil d.109.1.1 40830 1ukuA 102 2.03e+01 d.58.5.2 -9992 1kyhA 276 2.04e+01 c.72.1.4 73222 1lswA 131 2.05e+01 d.110.3.2 78181 1is1A 185 2.07e+01 d.67.3.1 83704 1q25A 432 2.08e+01 1st9A 143 2.09e+01 c.47.1.10 -7503 1fiuA 286 2.10e+01 1fiuA c.52.1.10 33317 1jbbA 153 2.13e+01 1u9aA d.20.1.1 62842 1v93A 296 2.17e+01 c.1.23.1 -5654 1qtwA 285 2.21e+01 1qumA c.1.15.1 29392 3bamA 213 2.24e+01 1bam c.52.1.3 33288 1naqA 112 2.24e+01 d.58.5.2 -9984 1qltA 560 2.25e+01 1qltA d.58.32.1 39457 d.145.1.1 41720 1pi4A 358 2.30e+01 e.3.1.1 -11774 1tig 94 2.30e+01 1tig d.68.1.1 39566 1w1kA 560 2.31e+01 1dctA 324 2.33e+01 6mhtA c.66.1.26 34244 1je6A 275 2.34e+01 b.1.1.2 71638 d.19.1.1 71639 1ig8A 486 2.37e+01 2yhx c.55.1.3 64746 c.55.1.3 64747 1f2tB 148 2.37e+01 1f2tB 1i6lA 328 2.38e+01 c.26.1.1 66041 1i6kA 328 2.39e+01 c.26.1.1 66040 1h5qA 265 2.40e+01 1cydA c.2.1.2 60643 1gefA 123 2.41e+01 1gefA c.52.1.18 60465 1kvlA 358 2.41e+01 e.3.1.1 73062 2chsA 127 2.42e+01 2chsA d.79.1.2 39764 1mo0A 275 2.42e+01 c.1.1.1 79329 1nz0A 118 2.43e+01 d.14.1.2 86433 1tml 286 2.43e+01 1tml c.6.1.1 30656 1fzrA 138 2.43e+01 1fzrA c.52.1.17 33336 1iyhA 198 2.45e+01 a.45.1.1 83790 c.47.1.5 83791 1fzyA 149 2.46e+01 d.20.1.1 65072 1bif 469 2.46e+01 1bif c.37.1.7 31961 c.60.1.4 34003 1g9gA 629 2.47e+01 a.102.1.2 83279 1jdfA 447 2.50e+01 c.1.11.2 62897 d.54.1.1 62898 1grvB 182 2.50e+01 c.61.1.1 76322 1tgoA 773 2.51e+01 1tgoA c.55.3.5 33721 e.8.1.1 43010 1faeA 629 2.52e+01 1fce a.102.1.2 18837 1h2aL 567 2.53e+01 1h2rL e.18.1.1 43299 1dbfA 127 2.55e+01 2chsA d.79.1.2 39761 1fr1A 361 2.57e+01 1gceA e.3.1.1 42734 1bg2 325 2.60e+01 1bg2 c.37.1.9 32189 1cnuA 137 2.61e+01 1cof d.109.1.2 40862 1eljA 381 2.63e+01 4mbp c.94.1.1 35791 1vaoA 560 2.63e+01 1qltA d.58.32.1 39461 d.145.1.1 41724 1hjzA 192 2.66e+01 c.50.1.2 83520 1nvmB 312 2.68e+01 c.2.1.3 86251 d.81.1.1 86252 1azsB 212 2.68e+01 1azsA d.58.29.1 39423 1l0gA 358 2.69e+01 e.3.1.1 73400 1j6pA 418 2.70e+01 b.92.1.4 77089 c.1.9.9 77090 1ffkP 84 2.73e+01 1ffkP d.12.1.1 37493 1r8hA 87 2.74e+01 d.58.8.1 -10041 1pjr 724 2.74e+01 1pjr c.37.1.19 32391 c.37.1.19 32392 2gar 212 2.77e+01 2gar c.65.1.1 34161 1jx2B 315 2.78e+01 c.37.1.8 67404 7aatA 401 2.79e+01 1ajsA c.67.1.1 34250 1fxtA 149 2.81e+01 d.20.1.1 65055 1ay7B 89 2.83e+01 1ay7B c.9.1.1 30836 1fsyA 358 2.88e+01 1gceA e.3.1.1 60016 2bltA 361 2.90e+01 1gceA e.3.1.1 42739 1n0wA 243 3.03e+01 c.37.1.11 79772 1f3cA 89 3.03e+01 1cmiA d.39.1.1 38557 1hmpA 217 3.05e+01 1qk3A c.61.1.1 34075 1atiB 505 3.05e+01 1atiA c.51.1.1 33197 d.104.1.1 40746 1mc2A 122 3.11e+01 a.133.1.2 74622 1atiA 505 3.12e+01 1atiA c.51.1.1 33196 d.104.1.1 40745 1cwpA 190 3.12e+01 1cwpA b.121.4.5 23305 1ni4A 365 3.13e+01 c.36.1.7 85728 1gskA 513 3.14e+01 b.6.1.3 83314 b.6.1.3 83315 b.6.1.3 83316 1q44A 326 3.14e+01 c.37.1.5 -7037 1eqnA 321 3.18e+01 1dd9A e.13.1.1 43256 2blsA 358 3.20e+01 1gceA e.3.1.1 42747 1hxn 219 3.21e+01 1hxn b.66.1.1 27529 1v7oA 165 3.22e+01 unknown_sccs -10249 1onhA 364 3.24e+01 e.3.1.1 -11769 1an7A 136 3.26e+01 1seiA d.140.1.1 41465 1ihnA 113 3.29e+01 1ihnA c.103.1.1 62388 1qr6A 584 3.30e+01 1qr6A c.2.1.7 30293 c.58.1.3 33941 1dkuA 317 3.32e+01 1dkuA c.61.1.2 34118 c.61.1.2 34119 1rgzA 363 3.33e+01 e.3.1.1 -11771 1b37B 472 3.33e+01 1b37B c.3.1.2 30390 d.16.1.5 37954 1ckv 141 3.33e+01 1ckv d.137.1.1 41452 1id0A 152 3.38e+01 d.122.1.3 66111 2e2c 156 3.40e+01 1u9aA d.20.1.1 38336 1es7B 89 3.43e+01 1es7B g.7.1.3 44465 1df3A 162 3.43e+01 1mup b.60.1.1 27134 1goiA 499 3.44e+01 b.72.2.1 65413 c.1.8.5 65414 d.26.3.1 65415 3mefA 69 3.45e+01 1mjc b.40.4.5 25320 1i9zA 347 3.45e+01 1i9yA d.151.1.2 62102 1nrjA 158 3.48e+01 d.110.4.4 86124 1r5lA 262 3.48e+01 a.5.3.1 -360 c.13.1.1 -6215 1d2rB 326 3.54e+01 1d2rB c.26.1.1 31573 1d2rA 326 3.58e+01 1d2rB c.26.1.1 31572 1qgvA 142 3.59e+01 1qgvA c.47.1.8 33056 3pnp 289 3.61e+01 1b8oA c.56.2.1 33763 1kwaB 88 3.62e+01 1kwaA b.36.1.1 24773 1qj5A 429 3.65e+01 1dtyA c.67.1.4 34493 1ryjA 70 3.65e+01 d.15.3.2 -9179 1hcl 298 3.68e+01 1hcl d.144.1.7 41593 1ipiA 123 3.68e+01 c.52.1.18 66255 1q7hA 153 3.73e+01 b.122.1.1 -5124 unknown_sccs -9313 1qd1A 325 3.74e+01 1qd1A d.58.34.1 39493 d.58.34.1 39494 1ffkU 91 3.76e+01 1ffkU d.29.1.1 38458 1fhvA 323 3.78e+01 1fhuA c.1.11.2 29235 d.54.1.1 38879 1i37A 260 3.82e+01 1a28A a.123.1.1 61583 1p1mA 406 3.84e+01 b.92.1.4 87696 c.1.9.9 87697 1exnA 290 3.85e+01 1exnA a.60.7.1 18088 c.120.1.2 33358 1kvs 338 3.87e+01 1xel c.2.1.2 29799 1mrzA 293 3.93e+01 b.43.5.1 -4048 c.26.1.3 -6616 1mh1 186 3.95e+01 1eesA c.37.1.8 32002 1j6uA 469 3.97e+01 c.5.1.1 77094 c.59.1.1 77095 c.72.2.1 77096 1f82A 424 3.99e+01 1f82A d.92.1.7 40307 1puiA 210 3.99e+01 c.37.1.8 88292 1vi7A 217 3.99e+01 unknown_sccs -9115 unknown_sccs -10052