# List of top-scoring protein chains for t2k-100-30-bys-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 1u1wA 298 4.39e-03 1xubA 298 9.39e-03 1t6kA 278 1.07e-02 1w61A 414 3.76e-02 2gkeA 274 7.44e-02 1gqzA 274 9.47e-02 d.21.1.1,d.21.1.1 83311,83312 1tm0A 350 1.29e-01 d.21.1.3 107147 1xttA 216 1.81e-01 1gqyA 475 2.75e-01 c.5.1.1,c.59.1.1,c.72.2.1 83305,83306,83307 1o0pA 104 4.55e-01 d.58.7.1 86535 1p3dA 475 4.82e-01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1bwzA 274 5.60e-01 1bwzA d.21.1.1,d.21.1.1 38337,38338 1pj5A 830 7.45e-01 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 1dp4A 435 8.45e-01 1dp4A c.93.1.1 35710 1qx4A 274 8.69e-01 b.43.4.2,c.25.1.1 104624,104625 1b9vA 390 9.30e-01 2qwc b.68.1.1 27603 2b3nA 159 1.52e+00 2aioA 269 1.53e+00 1gv3A 248 1.79e+00 a.2.11.1,d.44.1.1 70585,70586 1mngA 203 1.97e+00 1avmA a.2.11.1,d.44.1.1 15776,38701 1vdkA 466 1.98e+00 a.127.1.1 100561 1c0aA 585 2.45e+00 1c0aA b.40.4.1,d.74.4.1,d.104.1.1 25246,39731,40767 1sr8A 298 2.78e+00 e.54.1.1 105959 1h0bA 256 3.41e+00 b.29.1.11 83422 1d0iA 156 3.67e+00 2dhqA c.23.13.1 31383 1a8rA 221 3.74e+00 1a8rA d.96.1.1 40587 1nnsA 326 4.17e+00 c.88.1.1 85910 1oe4A 247 4.34e+00 c.18.1.3 86895 2gjgA 248 4.43e+00 2azpA 318 4.56e+00 1o17A 345 4.58e+00 a.46.2.1,c.27.1.1 80765,80766 1hg3A 225 4.69e+00 1hg3A c.1.1.1 61025 1smlA 269 5.02e+00 1smlA d.157.1.1 42053 3tdt 274 5.29e+00 3tdt b.81.1.2 28053 1gtzA 156 5.33e+00 c.23.13.1 70539 1umkA 275 5.46e+00 1qtfA 246 5.98e+00 1agjA b.47.1.1 25830 2bw8A 227 6.02e+00 1ygs 234 6.29e+00 1ygs b.26.1.1 23907 1mxmA 254 6.62e+00 b.38.1.3,d.58.43.1,f.34.1.1 79647,79648,79649 1y9wA 140 6.98e+00 1vl2A 421 7.35e+00 c.26.2.1,d.210.1.1 108708,108709 1josA 128 7.58e+00 d.52.7.1 84191 2cw8A 537 7.89e+00 1nscA 390 8.06e+00 2qwc b.68.1.1 27591 1a9cA 221 8.06e+00 1a8rA d.96.1.1 40602 1qwnA 1045 8.34e+00 a.8.3.1,b.30.5.6,c.6.2.1 96487,96488,96489 1ym5A 300 9.03e+00 1nnxA 109 1.04e+01 b.40.10.1 92013 2eiaB 206 1.04e+01 1eia a.28.3.1,a.73.1.1 16950,18330 1wekA 217 1.07e+01 1m0dA 138 1.07e+01 c.52.1.17 74354 1eia 207 1.22e+01 1eia a.28.3.1,a.73.1.1 16951,18331 1jc9A 269 1.22e+01 d.171.1.1 66490 1z94A 147 1.28e+01 1abbA 828 1.29e+01 1a8i c.87.1.4 35536 1q15A 503 1.31e+01 c.26.2.1,d.153.1.1 95538,95539 1alu 186 1.33e+01 1alu a.26.1.1 16826 1oo0A 147 1.37e+01 d.232.1.1 87182 1sdjA 310 1.41e+01 d.21.1.2,d.21.1.2 98807,98808 1tafB 70 1.42e+01 1tafB a.22.1.3 16482 1xtqA 177 1.42e+01 1i7pA 274 1.50e+01 b.43.4.2,c.25.1.1 66048,66049 1r44A 202 1.52e+01 d.65.1.4 104787 1ui7A 638 1.55e+01 b.30.2.1,d.17.2.1,d.17.2.1 99413,99414,99415 1c0nA 406 1.56e+01 1c0nA c.67.1.3 34433 1ba1 386 1.58e+01 1ba1 c.55.1.1,c.55.1.1 33387,33388 2tdt 274 1.61e+01 3tdt b.81.1.2 28054 1a8i 842 1.64e+01 1a8i c.87.1.4 35490 1aijM 307 1.64e+01 6prcM f.26.1.1 43462 1rzhM 307 1.65e+01 f.26.1.1 98165 1qjtA 99 1.65e+01 1eh2 a.39.1.6 17335 1rsy 152 1.69e+01 1rsy b.7.1.2 23192 1evhA 112 1.70e+01 1evhA b.55.1.4 26997 1siiA 646 1.71e+01 b.30.2.1,d.17.2.1,d.17.2.1 105578,105579,105580 1g5cA 170 1.71e+01 1g5cA c.53.2.1 60264 1vljA 407 1.75e+01 e.22.1.2 108832 1bupA 386 1.77e+01 1ba1 c.55.1.1,c.55.1.1 33377,33378 1w6gA 646 1.77e+01 1dmhA 311 1.78e+01 1dmhA b.3.6.1 22633 1rjoA 646 1.79e+01 1vh5A 148 1.79e+01 d.38.1.5 100642 1tdtA 259 1.84e+01 3tdt b.81.1.2 28055 1kay 381 1.85e+01 1ba1 c.55.1.1,c.55.1.1 33385,33386 1nksA 194 1.86e+01 1nksA c.37.1.1 31886 1f2rI 100 1.90e+01 1c9fA d.15.2.1 37641 1jf9A 408 1.96e+01 1c0nA c.67.1.3 62931 1fxzA 476 2.00e+01 b.82.1.2,b.82.1.2 65059,65060 1yqfA 203 2.01e+01 1htyA 1015 2.02e+01 a.8.3.1,b.30.5.6,c.6.2.1 83064,83065,83066 1hpm 386 2.03e+01 1ba1 c.55.1.1,c.55.1.1 33381,33382 1w9sA 142 2.04e+01 1zzcA 198 2.07e+01 1wudA 89 2.07e+01 1gmuA 143 2.07e+01 b.107.1.1,d.58.38.1 65335,65336 1z54A 132 2.08e+01 1s1qA 145 2.10e+01 d.20.1.2 98351 1wosA 364 2.17e+01 b.44.2.1,d.250.1.1 109468,109469 1eueA 86 2.17e+01 1cyo d.120.1.1 59504 1h9dB 134 2.19e+01 2jhbA b.54.1.1 60822 1k66A 149 2.19e+01 c.23.1.1 90941 1ru0A 105 2.21e+01 1rcy 151 2.24e+01 1rcy b.6.1.1 23018 1f3uA 118 2.29e+01 1f3uA b.65.1.1 27521 1zm0A 114 2.30e+01 1e1oA 504 2.32e+01 1lylA b.40.4.1,d.104.1.1 25258,40714 1atr 386 2.35e+01 1ba1 c.55.1.1,c.55.1.1 33421,33422 1prxA 224 2.37e+01 1prxA c.47.1.10 33076 2fr2A 172 2.40e+01 1awd 94 2.43e+01 1awd d.15.4.1 37673 1aijL 281 2.45e+01 6prcL f.26.1.1 43461 1c8kA 842 2.49e+01 1a8i c.87.1.4 35491 1h5uA 842 2.51e+01 1a8i c.87.1.4 60655 1kvdA 63 2.51e+01 1kveA d.70.1.2 39592 1kveA 63 2.51e+01 1kveA d.70.1.2 39590 1sziA 247 2.52e+01 a.24.23.1 106159 1hwwA 1015 2.53e+01 a.8.3.1,b.30.5.6,c.6.2.1 83067,83068,83069 1gmwA 143 2.56e+01 b.107.1.1,d.58.38.1 65347,65348 1gmiA 136 2.59e+01 b.7.1.1 65309 2h0bA 184 2.63e+01 1dkqA 410 2.63e+01 1dklA c.60.1.2 33998 2a8yA 270 2.64e+01 1ih7A 903 2.71e+01 1clqA c.55.3.5,e.8.1.1 62375,62376 1bdo 80 2.71e+01 1bdo b.84.1.1 28214 2a35A 215 2.71e+01 1aijS 301 2.74e+01 6prcM f.26.1.1 43465 1rxr 83 2.75e+01 2nllB g.39.1.2 45114 1hxkA 1015 2.79e+01 a.8.3.1,b.30.5.6,c.6.2.1 83070,83071,83072 1dkmA 410 2.80e+01 1dklA c.60.1.2 34000 1ygaA 342 2.89e+01 1e30A 155 2.90e+01 1rcy b.6.1.1 23016 2calA 154 2.92e+01 1ztdA 133 2.93e+01 1gz2A 142 2.94e+01 d.169.1.1 83392 1avk 638 2.97e+01 1a2vA b.30.2.1,d.17.2.1,d.17.2.1 24410,38047,38048 1kgqA 274 2.98e+01 b.81.1.2 72447 1gpb 842 3.01e+01 1a8i c.87.1.4 35478 1ycoA 279 3.12e+01 1w0hA 204 3.13e+01 1ualA 274 3.15e+01 c.116.1.4 88383 1fzrA 138 3.16e+01 1fzrA c.52.1.17 33336 1b26A 416 3.23e+01 1hwyA c.2.1.7,c.58.1.1 30232,33880 1a3z 155 3.28e+01 1rcy b.6.1.1 23019 1m5yA 408 3.31e+01 a.167.1.1,d.26.1.1,d.26.1.1 78664,78665,78666 2airB 153 3.32e+01 1dklA 410 3.32e+01 1dklA c.60.1.2 33996 1lkzA 219 3.36e+01 c.124.1.4,d.58.40.1 73991,73992 2d93A 134 3.43e+01 1kkcA 221 3.45e+01 a.2.11.1,d.44.1.1 68660,68661 1g5aA 628 3.45e+01 b.71.1.1,c.1.8.1 65152,65153 1mkiA 330 3.45e+01 e.3.1.2 84994 2b6eA 146 3.49e+01 1aipE 405 3.50e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25699,25739,32134 1o8bA 219 3.51e+01 c.124.1.4,d.58.40.1 81180,81181 1q1rA 431 3.54e+01 c.3.1.5,c.3.1.5,d.87.1.1 95600,95601,95602 2d0oA 610 3.54e+01 1ks2A 219 3.55e+01 c.124.1.4,d.58.40.1 72908,72909 1wstA 417 3.55e+01 1f08A 148 3.64e+01 1f08A d.89.1.2 59564 1lox 662 3.65e+01 1lox a.119.1.2,b.12.1.1 19238,23638 1ui8A 638 3.67e+01 b.30.2.1,d.17.2.1,d.17.2.1 99419,99420,99421 2d4qA 257 3.71e+01 1y791 680 3.72e+01 1mpyA 307 3.73e+01 1mpyA d.32.1.3,d.32.1.3 38508,38509 1lylA 504 3.79e+01 1lylA b.40.4.1,d.104.1.1 25261,40717 1qipA 183 3.83e+01 1qipA d.32.1.1 38470 1whzA 70 3.97e+01 1b3bA 415 3.98e+01 1hwyA c.2.1.7,c.58.1.1 30244,33892 1iscA 192 4.09e+01 1avmA a.2.11.1,d.44.1.1 15733,38726 1ogsA 497 4.11e+01 b.71.1.2,c.1.8.3 86997,86998 1iznB 277 4.11e+01 e.43.1.2 83848 1vhzA 198 4.14e+01 d.113.1.1 100718 1x6vA 630 4.18e+01 2gsq 202 4.19e+01 1pd21 a.45.1.1,c.47.1.5 17715,33009 2aliA 158 4.21e+01 1a8z 153 4.30e+01 1rcy b.6.1.1 23020 2acfA 182 4.34e+01 1rzhL 281 4.38e+01 f.26.1.1 98164 1wznA 252 4.39e+01 2gfgA 193 4.39e+01 1pg4A 652 4.42e+01 e.23.1.1 88067 1zoyC 140 4.43e+01 1ii6A 368 4.44e+01 1bg2 c.37.1.9 62413 1hekA 131 4.44e+01 a.61.1.5 65818 3uagA 437 4.45e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30652,33953,34956 2cxcA 144 4.51e+01 1bx2B 191 4.58e+01 1iakB b.1.1.2,d.19.1.1 21610,38184 1clqA 903 4.63e+01 1clqA c.55.3.5,e.8.1.1 33717,43006 4tmkA 213 4.67e+01 5tmpA c.37.1.1 31930 1wtaA 275 4.74e+01 2pgi 445 4.78e+01 2pgi c.80.1.2 35308 1b0zA 445 4.78e+01 2pgi c.80.1.2 35309 1ijyA 130 4.80e+01 1ijxA a.141.1.1 62517 1awpA 92 4.81e+01 1cyo d.120.1.1 41071 1b0jA 754 4.82e+01 1amj c.8.2.1,c.83.1.1 30719,35395 1qwkA 317 4.82e+01 c.1.7.1 96482 1qfgA 725 4.82e+01 1by5A f.4.3.3 43803 1sltB 134 4.88e+01 1c1lA b.29.1.3 24187 1wriA 93 4.92e+01 1ffkE 119 4.94e+01 1ffkE d.79.3.1 39812 2bh9A 489 5.02e+01 2f4nA 273 5.10e+01 1tkeA 224 5.15e+01 1aipA 405 5.16e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25697,25737,32132 2lhb 149 5.20e+01 2fal a.1.1.2 15597 1hxmD 242 5.23e+01 b.1.1.1,b.1.1.2 61373,61374 1btmA 252 5.25e+01 1amk c.1.1.1 28513 2f1kA 279 5.25e+01 2aneA 125 5.28e+01 1avbA 226 5.28e+01 1led b.29.1.1 24158 2aaa 484 5.29e+01 7taa b.71.1.1,c.1.8.1 27777,28764 1eumA 165 5.34e+01 1eumA a.25.1.1 59507 1zwxA 301 5.46e+01 1ksyA 154 5.54e+01 d.89.1.2 72948 2govA 195 5.55e+01 1r5eA 115 5.64e+01 1o0iA 138 5.65e+01 d.38.1.5 86532 1xtzA 264 5.67e+01 1dszB 85 5.68e+01 2nllB g.39.1.2 45108 1ynfA 458 5.71e+01 1eexA 554 5.74e+01 1dioA c.1.19.3 29650 1a6x 87 5.76e+01 1bdo b.84.1.1 28215 1fi8A 228 5.79e+01 5ptp b.47.1.2 26374 1pzsA 208 5.84e+01 b.1.8.1 104397 1h8cA 82 5.92e+01 1h8cA d.15.1.2 37608 2dbbA 151 6.11e+01 1xm0A 147 6.11e+01 2a13A 166 6.13e+01 1hg2A 289 6.16e+01 1hg5A a.7.8.2,a.118.9.3 90358,90359 1uwkA 557 6.17e+01 e.51.1.1 108065 1hf8A 289 6.18e+01 1hg5A a.7.8.2,a.118.9.3 90354,90355 1izmA 184 6.28e+01 a.199.1.1 90725 1hg5A 289 6.28e+01 1hg5A a.7.8.2,a.118.9.3 90360,90361 1iwmA 186 6.37e+01 b.125.1.2 83758 1ivwA 638 6.40e+01 b.30.2.1,d.17.2.1,d.17.2.1 71456,71457,71458 1cjsA 219 6.42e+01 1cjsA e.24.1.1 43354 1lvl 458 6.48e+01 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30567,30568,40205 1q0pA 223 6.52e+01 c.62.1.1 95507 1p5zB 263 6.54e+01 c.37.1.1 87815 2bnmA 198 6.54e+01 1efuA 385 6.63e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25682,25722,32115 3dapA 320 6.67e+01 1dapA c.2.1.3,d.81.1.3 30051,39966 1u9yA 284 6.75e+01 1ivhA 394 6.76e+01 3mdeA a.29.3.1,e.6.1.1 16608,42869 1isaA 192 6.83e+01 1avmA a.2.11.1,d.44.1.1 15731,38724 1j5eK 129 6.96e+01 c.55.4.1 71554 1bkjA 240 7.02e+01 1bkjA d.90.1.1 40243 1bh5A 183 7.04e+01 1qipA d.32.1.1 38476 1tw9A 206 7.05e+01 a.45.1.1,c.47.1.5 107381,107382 1xhkA 187 7.25e+01 1i1iP 681 7.32e+01 1i1iP d.92.1.5 40297 1b8eA 162 7.36e+01 1bebA b.60.1.1 59077 1hg8A 349 7.37e+01 b.80.1.3 65830 1ewqA 765 7.48e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19069,32383,33740,39743 1q5zA 177 7.50e+01 a.196.1.1 95954 1rypE 242 7.56e+01 1rypE d.153.1.4 41936 1ryc 294 7.59e+01 1ryc a.93.1.1 18601 1ivnA 190 7.59e+01 c.23.10.5 83719 1evsA 187 7.60e+01 1evsA a.26.1.1 16845 1ftrA 296 7.69e+01 1ftrA d.58.33.1,d.58.33.1 39485,39486 2fkbA 180 7.71e+01 1dapA 320 7.75e+01 1dapA c.2.1.3,d.81.1.3 30053,39968 1dim 381 7.79e+01 3sil b.68.1.1 27544 1cjcA 460 7.81e+01 1cjcA c.3.1.1,c.4.1.1 30319,30604 1jl0A 334 7.92e+01 1jenA d.156.1.1 63155 1fuxA 166 7.94e+01 1fjjA b.17.1.2 60034 1dioA 554 7.95e+01 1dioA c.1.19.3 29656 1fm0E 150 8.00e+01 1fmaE d.41.5.1 38629 1vf8A 377 8.06e+01 1lo7A 141 8.06e+01 d.38.1.1 74144 1hzxA 349 8.11e+01 1f88A f.13.1.2 61466 1br9 194 8.12e+01 1br9 b.40.3.1 25235 1eulA 994 8.15e+01 1eulA 2f23A 156 8.20e+01 1e50B 134 8.21e+01 2jhbA b.54.1.1 59245 1jscA 630 8.33e+01 c.31.1.3,c.36.1.5,c.36.1.9 67224,67225,67226 1slaA 134 8.35e+01 1c1lA b.29.1.3 24196 4sli 679 8.36e+01 2sli b.29.1.9,b.68.1.1 24275,27612 1pyoA 167 8.38e+01 c.17.1.1 95370 1td2A 287 8.40e+01 c.72.1.5 106765 2ghsA 326 8.40e+01 1i2aA 219 8.51e+01 e.24.1.1 90660 6acn 754 8.57e+01 1amj c.8.2.1,c.83.1.1 30721,35397 1v9yA 167 8.61e+01 d.110.3.2 108454 1bgvA 449 8.69e+01 1k89 c.2.1.7,c.58.1.1 30217,33865 1usmA 80 8.74e+01 d.74.1.1 99876 1uag 437 8.77e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30653,33954,34957 1h2rL 534 8.80e+01 1h2rL e.18.1.1 43298 1io1A 398 8.83e+01 1io1A e.32.1.1 62611 1ixlA 131 8.86e+01 d.38.1.5 90717 1te0A 318 8.88e+01 1v98A 140 8.88e+01 1xe7A 203 8.92e+01 1amj 754 8.92e+01 1amj c.8.2.1,c.83.1.1 30725,35401 2erbA 125 8.94e+01 1fmaE 150 8.95e+01 1fmaE d.41.5.1 38630 1u3wA 374 8.95e+01