# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7-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.soe.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 1e54A 332 1.35e-18 1e54A f.4.3.1 59258 2fgqX 332 3.24e-18 f.4.3.1 133439 1hxxA 340 4.62e-16 2omf f.4.3.1 61385 2omf 340 5.17e-16 2omf 2j1nA 346 9.55e-16 2por 301 1.64e-06 2por 2porA 301 1.64e-06 f.4.3.1 43759 1prn 289 1.12e-05 3prn 3prn 289 1.48e-05 3prn 3prnA 289 1.48e-05 f.4.3.1 43761 2o4vA 411 1.85e-05 1a0tP 413 9.09e-03 1a0tP f.4.3.2 43794 2iwvA 281 1.47e-01 1t16A 427 1.51e-01 f.4.3.4 106242 1p4tA 155 1.86e-01 f.4.1.1 87779 2odjA 428 4.70e-01 2mprA 421 7.93e-01 2mprA f.4.3.2 43788 1qfgA 725 1.04e+00 1by5A f.4.3.3 43803 1f60A 458 1.13e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 1h54A 754 1.46e+00 a.102.1.4,b.30.5.3 60634,60635 1ux6A 350 1.54e+00 b.29.1.16,g.75.1.1 100145,100146 1by5A 714 2.26e+00 1by5A f.4.3.3 43800 1mkfA 382 2.75e+00 b.116.1.1 79232 1ei5A 520 3.05e+00 1ei5A b.61.3.1,b.61.3.1,e.3.1.1 27418,27419,42772 1jnyA 435 3.15e+00 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 2fcpA 723 3.51e+00 1by5A f.4.3.3 43802 1af6A 421 4.29e+00 2mprA f.4.3.2 43772 1i78A 297 4.39e+00 f.4.4.1 66046 1s0uA 408 4.41e+00 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 1qd6C 240 4.65e+00 1qd5A 2jqyA 280 4.69e+00 2hkdA 320 4.78e+00 1qd5A 275 4.81e+00 1qd5A f.4.2.1 43748 1phm 310 4.83e+00 1phm 1qj8A 148 4.95e+00 1qj8A f.4.1.1 43744 1yo8A 634 5.12e+00 3bk5A 237 5.22e+00 2c9jA 223 5.28e+00 1hn0A 1021 5.47e+00 a.102.3.2,b.18.1.17,b.24.1.1,b.30.5.2 83616,83617,83618,83619 1yi9A 309 5.67e+00 b.121.1.2,b.121.1.2 123276,123277 1h1aA 191 5.98e+00 b.29.1.11 83450 1kmoA 774 6.06e+00 f.4.3.3 72753 2dd7A 216 6.17e+00 1pvxA 194 6.26e+00 1axkA b.29.1.11 24341 2e26A 725 6.45e+00 1k8kC 372 6.87e+00 b.69.4.1 68308 1jv2A 957 6.99e+00 b.1.15.1,b.1.15.1,b.1.15.1,b.69.8.1 67334,67335,67336,67337 1rhi3 236 7.68e+00 1aym3 1ynaA 194 7.80e+00 b.29.1.11 24335 2icrA 237 8.17e+00 1sdwA 314 8.23e+00 b.121.1.2,b.121.1.2 98810,98811 1qjpA 171 8.46e+00 1bxwA f.4.1.1 43742 1w99A 558 8.86e+00 2axtO 247 9.51e+00 1fx5A 242 9.67e+00 1led b.29.1.1 24135 1ux2A 212 9.70e+00 b.96.1.1 100132 2f1cX 286 1.01e+01 1ggxA 223 1.04e+01 1ggxA d.22.1.1 38367 1uv6A 210 1.07e+01 b.96.1.1 100030 1f1sA 814 1.10e+01 a.102.3.2,b.1.18.2,b.24.1.1,b.30.5.2 64928,64929,64930,64931 1opoA 348 1.19e+01 b.121.4.7 87240 2dddA 225 1.21e+01 1xnkA 196 1.26e+01 b.29.1.11 122195 2bcmA 165 1.28e+01 2a46A 238 1.29e+01 1so7A 382 1.30e+01 b.68.1.1 112106 2aqmA 154 1.33e+01 2f1vA 197 1.36e+01 2phlA 397 1.37e+01 1dgwA b.82.1.2,b.82.1.2 28082,28083 2dfbA 190 1.38e+01 b.29.1.11 131470 1jrrA 382 1.40e+01 e.1.1.1 63256 1zgoA 223 1.42e+01 2oy7A 320 1.42e+01 2c4xA 260 1.42e+01 1i9bA 217 1.45e+01 1i9bA b.96.1.1 62084 1n67A 359 1.47e+01 b.2.3.4,b.2.3.4 85354,85355 1vq0A 302 1.54e+01 d.193.1.1,g.81.1.1 114000,114001 1yewA 382 1.54e+01 2rh7A 239 1.62e+01 2arrA 382 1.72e+01 2qn6A 414 1.73e+01 2otnA 308 1.79e+01 1snzA 344 1.80e+01 b.30.5.4 98930 1olzA 663 1.83e+01 b.1.1.4,b.69.12.1,g.16.2.1 93341,93342,93343 1ospO 257 1.83e+01 1ospO b.76.1.1 27971 1pvc1 301 1.87e+01 1pov1 2vadA 223 1.87e+01 2ismA 352 1.91e+01 1g0dA 695 1.93e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 60166,60167,60168,60169 1qnxA 209 1.96e+01 1qnxA d.111.1.1 40914 1k32A 1045 1.97e+01 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 68068,68069,68070,68071 1a5iA 265 1.98e+01 5ptp b.47.1.2 26331 2bf6A 449 2.00e+01 3cjyA 259 2.04e+01 1po0A 751 2.09e+01 f.4.3.3 94960 3b9cA 144 2.10e+01 1w61A 414 2.17e+01 1kk1A 410 2.17e+01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1xssA 225 2.17e+01 1ne9A 335 2.18e+01 d.108.1.4,d.108.1.4 91839,91840 1c3hA 137 2.28e+01 b.22.1.1 90405 1ajoA 214 2.28e+01 1axkA b.29.1.2 24179 1uw6A 211 2.31e+01 b.96.1.1 100079 2oggA 152 2.37e+01 1uwvA 433 2.38e+01 b.40.4.12,c.66.1.40 100128,100129 1gl4A 285 2.46e+01 d.22.1.2,g.3.11.5 65286,65287 1cb8A 678 2.47e+01 1cb8A a.102.3.2,b.24.1.1,b.30.5.2 18849,23898,24422 1c3mA 147 2.49e+01 1jotA b.77.3.1 27983 1al21 302 2.61e+01 1pov1 1n6eA 1071 2.61e+01 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 80149,80150,80151,80152 2oitA 434 2.63e+01 2ib5A 233 2.69e+01 1h2wA 710 2.69e+01 b.69.7.1,c.69.1.4 76596,76597 2a73B 991 2.72e+01 1f0lA 535 2.76e+01 1ddt b.2.1.1,d.166.1.1,f.1.2.1 22377,42239,43382 1xnaA 183 2.80e+01 1xnaA b.18.1.8 23773 1m26A 133 2.84e+01 1qfmA 710 2.88e+01 1qfmA b.69.7.1,c.69.1.4 27673,34641 1cov3 238 2.94e+01 1aym3 1lrwA 600 2.96e+01 b.70.1.1 91111 1ar61 302 2.99e+01 1pov1 2hyxA 352 3.02e+01 1xmzA 241 3.08e+01 1hxs1 302 3.09e+01 2i6qA 517 3.10e+01 1o6gA 710 3.19e+01 b.69.7.1,c.69.1.4 81087,81088 1usyA 275 3.21e+01 d.104.1.1 113422 2i3oA 516 3.23e+01 d.153.1.6 137027 1zuxA 224 3.25e+01 2p0wA 324 3.26e+01 1ar71 302 3.29e+01 1pov1 2q86B 254 3.35e+01 1h2xA 710 3.37e+01 b.69.7.1,c.69.1.4 76598,76599 1e8nA 710 3.46e+01 1qfmA b.69.7.1,c.69.1.4 27675,34643 1q40B 219 3.53e+01 d.17.4.2 95771 1hx6A 394 3.59e+01 1cjdA b.121.2.1,b.121.2.1 58995,58996 2i51A 195 3.66e+01 2zaiA 497 3.71e+01 2q5iA 691 3.77e+01 1d8hA 311 3.86e+01 1d8iA d.63.1.1 39544 1pov1 302 3.89e+01 1pov1 2cxaA 256 3.93e+01 d.108.1.6 130993 2bfgA 503 3.96e+01 b.71.1.2,c.1.8.3 128423,128424 2p52A 196 4.08e+01 2hbtA 247 4.12e+01 1hr6B 443 4.17e+01 1be3A d.185.1.1,d.185.1.1 61166,61167 1i31A 314 4.18e+01 1bw8A b.2.7.1 22481 2hdiA 639 4.22e+01 1q8iA 783 4.26e+01 c.55.3.5,e.8.1.1 96208,96209 2rb8A 104 4.32e+01 1ugxA 133 4.32e+01 2ejoA 223 4.34e+01 1lj5A 379 4.35e+01 e.1.1.1 73928 1m9sA 605 4.36e+01 b.1.18.15,b.34.11.1,b.34.11.1,b.34.11.1,c.10.2.1 78874,78875,78876,78877,78878 2v74B 346 4.37e+01 2ehzA 302 4.43e+01 1r0uA 148 4.43e+01 b.60.1.5 96741 1gcyA 527 4.44e+01 1jdc b.71.1.1,c.1.8.1 27788,28775 2dduA 387 4.47e+01 1k1xA 659 4.49e+01 a.8.3.2,b.30.5.8,c.6.2.2 84279,84280,84281 1xxqA 161 4.50e+01 1diwA 441 4.58e+01 1a8d b.29.1.6,b.42.4.2 24264,25609 2qxlA 658 4.59e+01 1c4rA 182 4.60e+01 1c4rA b.29.1.4 24229 2ie2A 222 4.61e+01 3b3qE 197 4.67e+01 2gw3A 225 4.74e+01 2bolA 314 4.80e+01 1yt5A 258 4.83e+01 2cu9A 161 4.84e+01 2gagA 965 4.90e+01 3cc1A 433 4.91e+01 1xnb 185 5.03e+01 1axkA 1uldA 150 5.04e+01 b.29.1.3 99545 2h5oA 234 5.08e+01 1em2A 229 5.13e+01 1em2A d.129.3.2 41321 1h4uA 265 5.22e+01 1h4uA d.22.1.2,g.3.11.5 60622,60623 1h0bA 256 5.25e+01 b.29.1.11 83422 1gjwA 637 5.26e+01 b.71.1.1,c.1.8.1 60582,60583 1zi0A 307 5.26e+01 2re9A 181 5.42e+01 2g8cO 251 5.47e+01 1a78A 134 5.51e+01 1c1lA b.29.1.3 24212 2i5vO 251 5.52e+01 2hzmB 317 5.53e+01 1suuA 312 5.53e+01 b.68.10.1 99006 1jssA 224 5.55e+01 d.129.3.2 71844 1jdc 429 5.58e+01 1jdc 1jdcA 429 5.58e+01 b.71.1.1,c.1.8.1 27789,28776 1sy6A 204 5.59e+01 b.1.1.4,b.1.1.4 106111,106112 2b3nA 159 5.67e+01 d.38.1.4 127792 2b3rA 134 5.68e+01 2ahoA 414 5.70e+01 b.43.3.1,b.44.1.1,c.37.1.8 126767,126768,126769 1t8hA 277 5.78e+01 d.194.1.2 106664 2amdA 311 5.79e+01 2fs2A 151 5.83e+01 d.38.1.5 134003 1q2wA 308 5.99e+01 b.47.1.4 88355 2v7bA 529 6.00e+01 1p2zA 968 6.03e+01 b.121.2.2,b.121.2.2 93962,93963 1u8xX 472 6.05e+01 c.2.1.5,d.162.1.2 107741,107742 2qt6A 498 6.09e+01 2a50B 168 6.10e+01 1th8A 145 6.12e+01 d.122.1.3 106908 1p30A 952 6.13e+01 b.121.2.2,b.121.2.2 93964,93965 2yzjA 169 6.16e+01 1uhvA 500 6.18e+01 b.71.1.2,c.1.8.3 99402,99403 1jovA 270 6.22e+01 b.30.5.7 84192 2odpA 509 6.24e+01 1oa4A 222 6.24e+01 b.29.1.11 86731 1psuA 140 6.27e+01 d.38.1.5 88285 2z1pA 348 6.28e+01 1a8d 452 6.30e+01 1a8d 1a8dA 452 6.30e+01 b.29.1.6,b.42.4.2 24262,25607 2p4mA 219 6.32e+01 2g19A 244 6.33e+01 1atiA 505 6.36e+01 1atiA c.51.1.1,d.104.1.1 33196,40745 1x8qA 184 6.45e+01 b.60.1.1 114966 1ji6A 589 6.56e+01 b.18.1.3,b.77.2.1,f.1.3.1 63066,63067,63068 2gw4B 162 6.57e+01 1b76A 442 6.60e+01 1atiA c.51.1.1,d.104.1.1 33198,40747 2o8lA 274 6.66e+01 b.47.1.1 138932 1uok 558 6.76e+01 1uok 1uokA 558 6.76e+01 b.71.1.1,c.1.8.1 27801,28788 2hpwA 233 6.76e+01 1b9cA 236 6.84e+01 1ema d.22.1.1 38358 1gc1H 229 6.88e+01 1gc1H b.1.1.1,b.1.1.2 20265,21265 1of5A 221 6.95e+01 d.17.4.2 86933 2be1A 339 6.98e+01 2g82A 331 7.05e+01 c.2.1.3,d.81.1.1 134746,134747 3bodA 178 7.07e+01 2oseA 234 7.07e+01 2biwA 490 7.13e+01 1musA 477 7.15e+01 c.55.3.4 79494 2ak4E 245 7.17e+01 1bkzA 135 7.17e+01 1a3k b.29.1.3 24202 2bbhA 269 7.19e+01 d.328.1.1 128266 2bazA 142 7.30e+01 1qznA 173 7.37e+01 b.2.2.2 104669 2in5A 207 7.39e+01 2ds3A 761 7.39e+01 1bcpD 110 7.42e+01 1bcpD b.40.2.1 25132 1nr0A 611 7.43e+01 b.69.4.1,b.69.4.1 86078,86079 2qdrA 303 7.54e+01 1y7wA 291 7.59e+01 1pczA 191 7.66e+01 1ytbA d.129.1.1,d.129.1.1 41292,41293 2o4uX 334 7.85e+01 1bw8A 321 7.85e+01 1bw8A b.2.7.1 22482 1pvc3 238 7.90e+01 1aym3 1c0pA 363 7.98e+01 1an9A c.4.1.2,d.16.1.3 30647,37934