# 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 4.16e-03 1xubA 298 9.06e-03 1t6kA 278 1.08e-02 1w61A 414 6.88e-02 1xttA 216 1.14e-01 2gkeA 274 1.19e-01 1tm0A 350 1.29e-01 d.21.1.3 107147 1gqzA 274 1.40e-01 d.21.1.1,d.21.1.1 83311,83312 1gqyA 475 2.53e-01 c.5.1.1,c.59.1.1,c.72.2.1 83305,83306,83307 1o0pA 104 4.08e-01 d.58.7.1 86535 1p3dA 475 4.58e-01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1qx4A 274 6.52e-01 b.43.4.2,c.25.1.1 104624,104625 1pj5A 830 7.31e-01 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 1bwzA 274 8.28e-01 1bwzA d.21.1.1,d.21.1.1 38337,38338 1gv3A 248 1.31e+00 a.2.11.1,d.44.1.1 70585,70586 1dp4A 435 1.53e+00 1dp4A c.93.1.1 35710 1mngA 203 1.62e+00 1avmA a.2.11.1,d.44.1.1 15776,38701 2b3nA 159 1.83e+00 2aioA 269 1.86e+00 1vdkA 466 1.90e+00 a.127.1.1 100561 2azpA 318 2.15e+00 1c0aA 585 2.20e+00 1c0aA b.40.4.1,d.74.4.1,d.104.1.1 25246,39731,40767 1sr8A 298 2.22e+00 e.54.1.1 105959 1d0iA 156 3.33e+00 2dhqA c.23.13.1 31383 1umkA 275 3.91e+00 1nnsA 326 4.22e+00 c.88.1.1 85910 1mxmA 254 4.46e+00 b.38.1.3,d.58.43.1,f.34.1.1 79647,79648,79649 1gtzA 156 4.71e+00 c.23.13.1 70539 3tdt 274 4.83e+00 3tdt b.81.1.2 28053 1a8rA 221 5.17e+00 1a8rA d.96.1.1 40587 1smlA 269 5.42e+00 1smlA d.157.1.1 42053 1h0bA 256 5.51e+00 b.29.1.11 83422 2cw8A 537 5.54e+00 1y9wA 140 5.69e+00 1oe4A 247 5.96e+00 c.18.1.3 86895 1vl2A 421 6.26e+00 c.26.2.1,d.210.1.1 108708,108709 1nnxA 109 6.51e+00 b.40.10.1 92013 1ygs 234 6.59e+00 1ygs b.26.1.1 23907 2gjgA 248 7.33e+00 1ym5A 300 8.02e+00 1jc9A 269 8.11e+00 d.171.1.1 66490 1josA 128 8.15e+00 d.52.7.1 84191 2eiaB 206 9.48e+00 1eia a.28.3.1,a.73.1.1 16950,18330 2bw8A 227 1.02e+01 1a9cA 221 1.09e+01 1a8rA d.96.1.1 40602 1vh5A 148 1.12e+01 d.38.1.5 100642 1eia 207 1.12e+01 1eia a.28.3.1,a.73.1.1 16951,18331 1sdjA 310 1.21e+01 d.21.1.2,d.21.1.2 98807,98808 1ba1 386 1.22e+01 1ba1 c.55.1.1,c.55.1.1 33387,33388 1q15A 503 1.25e+01 c.26.2.1,d.153.1.1 95538,95539 1i7pA 274 1.28e+01 b.43.4.2,c.25.1.1 66048,66049 1tafB 70 1.30e+01 1tafB a.22.1.3 16482 1vljA 407 1.30e+01 e.22.1.2 108832 1alu 186 1.30e+01 1alu a.26.1.1 16826 1evhA 112 1.31e+01 1evhA b.55.1.4 26997 1bupA 386 1.35e+01 1ba1 c.55.1.1,c.55.1.1 33377,33378 1g5cA 170 1.36e+01 1g5cA c.53.2.1 60264 1abbA 828 1.38e+01 1a8i c.87.1.4 35536 1rsy 152 1.40e+01 1rsy b.7.1.2 23192 2tdt 274 1.41e+01 3tdt b.81.1.2 28054 1kay 381 1.48e+01 1ba1 c.55.1.1,c.55.1.1 33385,33386 1tdtA 259 1.52e+01 3tdt b.81.1.2 28055 1ui7A 638 1.53e+01 b.30.2.1,d.17.2.1,d.17.2.1 99413,99414,99415 1hpm 386 1.60e+01 1ba1 c.55.1.1,c.55.1.1 33381,33382 1rzhM 307 1.61e+01 f.26.1.1 98165 1siiA 646 1.61e+01 b.30.2.1,d.17.2.1,d.17.2.1 105578,105579,105580 1aijM 307 1.63e+01 6prcM f.26.1.1 43462 1qjtA 99 1.64e+01 1eh2 a.39.1.6 17335 1a8i 842 1.64e+01 1a8i c.87.1.4 35490 1w6gA 646 1.67e+01 1oo0A 147 1.68e+01 d.232.1.1 87182 1rjoA 646 1.73e+01 1f3uA 118 1.76e+01 1f3uA b.65.1.1 27521 1wudA 89 1.80e+01 1f2rI 100 1.80e+01 1c9fA d.15.2.1 37641 1wekA 217 1.83e+01 1k66A 149 1.92e+01 c.23.1.1 90941 1eueA 86 1.92e+01 1cyo d.120.1.1 59504 1aijL 281 1.94e+01 6prcL f.26.1.1 43461 2fr2A 172 1.99e+01 1w9sA 142 2.01e+01 1e1oA 504 2.02e+01 1lylA b.40.4.1,d.104.1.1 25258,40714 1awd 94 2.04e+01 1awd d.15.4.1 37673 1atr 386 2.04e+01 1ba1 c.55.1.1,c.55.1.1 33421,33422 1kvdA 63 2.05e+01 1kveA d.70.1.2 39592 1kveA 63 2.05e+01 1kveA d.70.1.2 39590 1prxA 224 2.07e+01 1prxA c.47.1.10 33076 2d0oA 610 2.19e+01 1sziA 247 2.20e+01 a.24.23.1 106159 2c4xA 260 2.23e+01 1s1qA 145 2.31e+01 d.20.1.2 98351 1ru0A 105 2.37e+01 1h5uA 842 2.39e+01 1a8i c.87.1.4 60655 1iscA 192 2.42e+01 1avmA a.2.11.1,d.44.1.1 15733,38726 1nksA 194 2.53e+01 1nksA c.37.1.1 31886 1c8kA 842 2.54e+01 1a8i c.87.1.4 35491 1c0nA 406 2.59e+01 1c0nA c.67.1.3 34433 1kgqA 274 2.60e+01 b.81.1.2 72447 1ih7A 903 2.66e+01 1clqA c.55.3.5,e.8.1.1 62375,62376 1yqfA 203 2.66e+01 1rxr 83 2.68e+01 2nllB g.39.1.2 45114 1aijS 301 2.69e+01 6prcM f.26.1.1 43465 1ogsA 497 2.74e+01 b.71.1.2,c.1.8.3 86997,86998 1ztdA 133 2.75e+01 1aipE 405 2.77e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25699,25739,32134 2b6eA 146 2.77e+01 1r44A 202 2.85e+01 d.65.1.4 104787 1jf9A 408 2.86e+01 1c0nA c.67.1.3 62931 1ygaA 342 2.89e+01 1vhzA 198 2.89e+01 d.113.1.1 100718 1avk 638 2.89e+01 1a2vA b.30.2.1,d.17.2.1,d.17.2.1 24410,38047,38048 1dkqA 410 3.01e+01 1dklA c.60.1.2 33998 1fxzA 476 3.03e+01 b.82.1.2,b.82.1.2 65059,65060 1q1rA 431 3.04e+01 c.3.1.5,c.3.1.5,d.87.1.1 95600,95601,95602 1kkcA 221 3.08e+01 a.2.11.1,d.44.1.1 68660,68661 2airB 153 3.09e+01 2a8yA 270 3.10e+01 1whzA 70 3.15e+01 1sltB 134 3.15e+01 1c1lA b.29.1.3 24187 1gpb 842 3.16e+01 1a8i c.87.1.4 35478 1dkmA 410 3.19e+01 1dklA c.60.1.2 34000 1f08A 148 3.19e+01 1f08A d.89.1.2 59564 1m5yA 408 3.21e+01 a.167.1.1,d.26.1.1,d.26.1.1 78664,78665,78666 1mpyA 307 3.22e+01 1mpyA d.32.1.3,d.32.1.3 38508,38509 1ntn 72 3.25e+01 3ebx g.7.1.1 44414 1lylA 504 3.29e+01 1lylA b.40.4.1,d.104.1.1 25261,40717 1ualA 274 3.35e+01 c.116.1.4 88383 1ui8A 638 3.37e+01 b.30.2.1,d.17.2.1,d.17.2.1 99419,99420,99421 1gz2A 142 3.38e+01 d.169.1.1 83392 1mkiA 330 3.40e+01 e.3.1.2 84994 1lox 662 3.51e+01 1lox a.119.1.2,b.12.1.1 19238,23638 1hxmD 242 3.54e+01 b.1.1.1,b.1.1.2 61373,61374 2a35A 215 3.55e+01 1iznB 277 3.56e+01 e.43.1.2 83848 2aliA 158 3.56e+01 1bdo 80 3.66e+01 1bdo b.84.1.1 28214 1dklA 410 3.68e+01 1dklA c.60.1.2 33996 1ycoA 279 3.76e+01 1y791 680 3.81e+01 2gsq 202 3.82e+01 1pd21 a.45.1.1,c.47.1.5 17715,33009 1pg4A 652 3.84e+01 e.23.1.1 88067 1o8bA 219 3.87e+01 c.124.1.4,d.58.40.1 81180,81181 1isaA 192 3.90e+01 1avmA a.2.11.1,d.44.1.1 15731,38724 2acfA 182 3.92e+01 1z94A 147 3.94e+01 1rzhL 281 4.06e+01 f.26.1.1 98164 1aipA 405 4.08e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25697,25737,32132 2pgi 445 4.09e+01 2pgi c.80.1.2 35308 1b0zA 445 4.09e+01 2pgi c.80.1.2 35309 1w8oA 601 4.09e+01 1o0iA 138 4.13e+01 d.38.1.5 86532 1lkzA 219 4.13e+01 c.124.1.4,d.58.40.1 73991,73992 3uagA 437 4.14e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30652,33953,34956 1g5aA 628 4.17e+01 b.71.1.1,c.1.8.1 65152,65153 2cxcA 144 4.18e+01 1xtzA 264 4.19e+01 1b26A 416 4.20e+01 1hwyA c.2.1.7,c.58.1.1 30232,33880 1h8cA 82 4.21e+01 1h8cA d.15.1.2 37608 2f4nA 273 4.27e+01 1xm0A 147 4.28e+01 1ks2A 219 4.29e+01 c.124.1.4,d.58.40.1 72908,72909 1rypE 242 4.30e+01 1rypE d.153.1.4 41936 1wriA 93 4.34e+01 1awpA 92 4.36e+01 1cyo d.120.1.1 41071 1iwmA 186 4.39e+01 b.125.1.2 83758 1pzsA 208 4.45e+01 b.1.8.1 104397 2c26A 260 4.45e+01 1wstA 417 4.50e+01 1wcqA 601 4.55e+01 2gfgA 193 4.56e+01 2d4qA 257 4.63e+01 1zoyC 140 4.65e+01 4tmkA 213 4.65e+01 5tmpA c.37.1.1 31930 1o17A 345 4.66e+01 a.46.2.1,c.27.1.1 80765,80766 2aneA 125 4.67e+01 1wosA 364 4.69e+01 b.44.2.1,d.250.1.1 109468,109469 1b0jA 754 4.74e+01 1amj c.8.2.1,c.83.1.1 30719,35395 1hekA 131 4.76e+01 a.61.1.5 65818 2f1kA 279 4.76e+01 1bx2B 191 4.84e+01 1iakB b.1.1.2,d.19.1.1 21610,38184 1b3bA 415 4.88e+01 1hwyA c.2.1.7,c.58.1.1 30244,33892 1clqA 903 4.96e+01 1clqA c.55.3.5,e.8.1.1 33717,43006 1avbA 226 4.97e+01 1led b.29.1.1 24158 1ksyA 154 5.00e+01 d.89.1.2 72948 1slaA 134 5.03e+01 1c1lA b.29.1.3 24196 1q3iA 214 5.05e+01 d.220.1.1 104524 1efuA 385 5.08e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25682,25722,32115 1wznA 252 5.14e+01 1hg2A 289 5.14e+01 1hg5A a.7.8.2,a.118.9.3 90358,90359 1hf8A 289 5.14e+01 1hg5A a.7.8.2,a.118.9.3 90354,90355 1tkeA 224 5.15e+01 1ffkE 119 5.20e+01 1ffkE d.79.3.1 39812 1hg5A 289 5.23e+01 1hg5A a.7.8.2,a.118.9.3 90360,90361 2a13A 166 5.25e+01 1rcy 151 5.29e+01 1rcy b.6.1.1 23018 1r5eA 115 5.41e+01 1pyoA 167 5.48e+01 c.17.1.1 95370 1lvl 458 5.50e+01 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30567,30568,40205 1wtaA 275 5.52e+01 1dszB 85 5.56e+01 2nllB g.39.1.2 45108 1ijyA 130 5.58e+01 1ijxA a.141.1.1 62517 2lhb 149 5.68e+01 2fal a.1.1.2 15597 1x6vA 630 5.74e+01 1uwkA 557 5.78e+01 e.51.1.1 108065 1ftrA 296 5.91e+01 1ftrA d.58.33.1,d.58.33.1 39485,39486 1dim 381 5.91e+01 3sil b.68.1.1 27544 1ivwA 638 5.92e+01 b.30.2.1,d.17.2.1,d.17.2.1 71456,71457,71458 1xtqA 177 5.93e+01 1eumA 165 5.94e+01 1eumA a.25.1.1 59507 1p5zB 263 5.96e+01 c.37.1.1 87815 1bkjA 240 5.98e+01 1bkjA d.90.1.1 40243 4sli 679 6.07e+01 2sli b.29.1.9,b.68.1.1 24275,27612 1e30A 155 6.12e+01 1rcy b.6.1.1 23016 1z0nA 96 6.14e+01 1z0mA 96 6.16e+01 2govA 195 6.17e+01 1tw9A 206 6.17e+01 a.45.1.1,c.47.1.5 107381,107382 2aaa 484 6.18e+01 7taa b.71.1.1,c.1.8.1 27777,28764 1u9yA 284 6.22e+01 1q0pA 223 6.30e+01 c.62.1.1 95507 2fkbA 180 6.31e+01 1v7oA 165 6.32e+01 d.67.1.2 100480 1j5eK 129 6.37e+01 c.55.4.1 71554 1kskA 234 6.52e+01 d.66.1.5,d.265.1.3 72920,90389 1a6x 87 6.56e+01 1bdo b.84.1.1 28215 1q5zA 177 6.57e+01 a.196.1.1 95954 1ryc 294 6.57e+01 1ryc a.93.1.1 18601 1hg8A 349 6.61e+01 b.80.1.3 65830 1izmA 184 6.74e+01 a.199.1.1 90725 1jb9A 316 6.83e+01 1fnc b.43.4.2,c.25.1.1 62840,62841 1guzA 310 6.83e+01 c.2.1.5,d.162.1.1 65586,65587 1ewqA 765 6.89e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19069,32383,33740,39743 2ab5A 269 6.90e+01 1wuiL 534 6.91e+01 1b8eA 162 6.91e+01 1bebA b.60.1.1 59077 1eexA 554 6.92e+01 1dioA c.1.19.3 29650 1h2rL 534 6.98e+01 1h2rL e.18.1.1 43298 2sli 679 6.99e+01 2sli b.29.1.9,b.68.1.1 24274,27611 1dykA 394 7.04e+01 1dykA b.29.1.4,b.29.1.4 24223,24224 1ivnA 190 7.04e+01 c.23.10.5 83719 1ynfA 458 7.05e+01 1qwkA 317 7.14e+01 c.1.7.1 96482 1h2aL 567 7.18e+01 1h2rL e.18.1.1 43299 1qfhA 212 7.27e+01 1qfhA b.1.18.10,b.1.18.10 21893,21894 1lyqA 104 7.28e+01 b.1.18.17 78302 1b9vA 390 7.35e+01 2qwc b.68.1.1 27603 1xhkA 187 7.38e+01 1c7qA 445 7.38e+01 2pgi c.80.1.2 35307 1ylxA 103 7.46e+01 1hzxA 349 7.48e+01 1f88A f.13.1.2 61466 1nstA 325 7.51e+01 1nstA c.37.1.5 31951 1evsA 187 7.53e+01 1evsA a.26.1.1 16845 1fi8A 228 7.56e+01 5ptp b.47.1.2 26374 2sil 381 7.57e+01 3sil b.68.1.1 27543 1fuxA 166 7.66e+01 1fjjA b.17.1.2 60034 1usmA 80 7.86e+01 d.74.1.1 99876 1yt5A 258 7.87e+01 1ubkL 534 7.90e+01 e.18.1.1 88422 6acn 754 7.92e+01 1amj c.8.2.1,c.83.1.1 30721,35397 2cpgA 45 7.92e+01 2cpgA a.43.1.3 17455 1mqoA 227 7.98e+01 d.157.1.1 103846 2f15A 96 8.01e+01 1amj 754 8.02e+01 1amj c.8.2.1,c.83.1.1 30725,35401 1cjsA 219 8.03e+01 1cjsA e.24.1.1 43354 1aozA 552 8.04e+01 1aozA b.6.1.3,b.6.1.3,b.6.1.3 23124,23125,23126 1lo7A 141 8.11e+01 d.38.1.1 74144 1dioA 554 8.19e+01 1dioA c.1.19.3 29656 1b01A 45 8.19e+01 2cpgA a.43.1.3 17458 8acn 754 8.20e+01 1amj c.8.2.1,c.83.1.1 30724,35400 1jl0A 334 8.23e+01 1jenA d.156.1.1 63155 1yozA 116 8.23e+01 1wwtA 88 8.26e+01 1uag 437 8.28e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30653,33954,34957 1q87A 221 8.48e+01 e.47.1.1 96192 1qyaA 307 8.49e+01 d.21.1.2,d.21.1.2 104653,104654 1i1nA 226 8.49e+01 c.66.1.7 71102 1jhjA 171 8.50e+01 b.18.1.9 66714 1twuA 139 8.50e+01 d.32.1.8 107413 3sil 379 8.52e+01 3sil b.68.1.1 27542 1l9hA 349 8.54e+01 f.13.1.2 73720 1df7A 159 8.56e+01 3dfr c.71.1.1 34885 1xe7A 203 8.59e+01 1a91 79 8.65e+01 1a91 f.17.1.1 43635 1sltA 134 8.73e+01 1c1lA b.29.1.3 24186 1ycdA 243 8.78e+01 1ffkV 143 8.86e+01 1ffkV c.9.2.1 30849 1a2f 291 8.90e+01 1ryc a.93.1.1 18619