# 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 2gkeA 274 4.37e-06 1w61A 414 5.26e-06 1gqzA 274 6.47e-06 d.21.1.1,d.21.1.1 83311,83312 1bwzA 274 4.85e-05 1bwzA d.21.1.1,d.21.1.1 38337,38338 1u1wA 298 1.02e-02 1xubA 298 1.87e-02 1t6kA 278 1.98e-02 1l1nA 183 2.60e-02 b.47.1.4 73476 1tm0A 350 4.57e-02 d.21.1.3 107147 1z94A 147 7.72e-02 1b9vA 390 2.14e-01 2qwc b.68.1.1 27603 1xttA 216 3.68e-01 2calA 154 4.11e-01 1e30A 155 5.12e-01 1rcy b.6.1.1 23016 1gqyA 475 5.51e-01 c.5.1.1,c.59.1.1,c.72.2.1 83305,83306,83307 1a8z 153 6.61e-01 1rcy b.6.1.1 23020 1sdjA 310 6.68e-01 d.21.1.2,d.21.1.2 98807,98808 1qyaA 307 6.95e-01 d.21.1.2,d.21.1.2 104653,104654 2bw0A 329 8.94e-01 1o0pA 104 1.01e+00 d.58.7.1 86535 1p3dA 475 1.03e+00 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1rcy 151 1.12e+00 1rcy b.6.1.1 23018 1a3z 155 1.52e+00 1rcy b.6.1.1 23019 1pj5A 830 1.73e+00 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 1nscA 390 1.86e+00 2qwc b.68.1.1 27591 1sr8A 298 1.92e+00 e.54.1.1 105959 2f6uA 234 2.18e+00 2fclA 169 2.19e+00 1h0bA 256 2.30e+00 b.29.1.11 83422 1ats 386 2.37e+00 1ba1 c.55.1.1,c.55.1.1 33423,33424 1vdkA 466 2.57e+00 a.127.1.1 100561 1vhzA 198 2.64e+00 d.113.1.1 100718 2g6yA 217 2.79e+00 1mkeA 152 2.89e+00 b.55.1.4 79231 1vrmA 325 3.43e+00 2bw8A 227 3.56e+00 1rec 201 3.62e+00 1rec a.39.1.5 17326 1qtfA 246 3.66e+00 1agjA b.47.1.1 25830 1orrA 347 3.71e+00 c.2.1.2 93460 1mngA 203 3.98e+00 1avmA a.2.11.1,d.44.1.1 15776,38701 1d0iA 156 4.00e+00 2dhqA c.23.13.1 31383 1dp4A 435 4.05e+00 1dp4A c.93.1.1 35710 1omrA 201 4.21e+00 a.39.1.5 93349 1bqsA 209 4.29e+00 1bqsA b.1.1.4,b.1.1.4 21704,21705 1ym5A 300 4.39e+00 1hpm 386 4.93e+00 1ba1 c.55.1.1,c.55.1.1 33381,33382 1j5qA 437 5.01e+00 b.121.2.3,b.121.2.3 77084,77085 1bupA 386 5.17e+00 1ba1 c.55.1.1,c.55.1.1 33377,33378 1atr 386 5.42e+00 1ba1 c.55.1.1,c.55.1.1 33421,33422 2sli 679 5.49e+00 2sli b.29.1.9,b.68.1.1 24274,27611 1ba1 386 5.56e+00 1ba1 c.55.1.1,c.55.1.1 33387,33388 4sli 679 5.57e+00 2sli b.29.1.9,b.68.1.1 24275,27612 1kay 381 5.79e+00 1ba1 c.55.1.1,c.55.1.1 33385,33386 1c0aA 585 5.94e+00 1c0aA b.40.4.1,d.74.4.1,d.104.1.1 25246,39731,40767 1gtzA 156 5.96e+00 c.23.13.1 70539 1gv3A 248 6.22e+00 a.2.11.1,d.44.1.1 70585,70586 1a8rA 221 6.41e+00 1a8rA d.96.1.1 40587 2ewrA 170 6.77e+00 1b0vA 106 7.15e+00 1a6l d.58.1.2 38982 1o17A 345 7.44e+00 a.46.2.1,c.27.1.1 80765,80766 1i1iP 681 7.66e+00 1i1iP d.92.1.5 40297 1oe4A 247 7.83e+00 c.18.1.3 86895 1qcnA 421 7.85e+00 1qcnA b.34.8.1,d.177.1.1 59017,59018 1ci3M 249 8.23e+00 1hcz b.2.6.1,b.84.2.2 22480,28266 1wekA 217 9.00e+00 1v58A 241 9.10e+00 c.47.1.9,d.17.3.1 108371,108372 1dmhA 311 9.49e+00 1dmhA b.3.6.1 22633 1fd2 106 9.56e+00 1a6l d.58.1.2 38962 1k3bB 164 9.65e+00 d.3.1.1 72015 1qwnA 1045 9.67e+00 a.8.3.1,b.30.5.6,c.6.2.1 96487,96488,96489 1hg3A 225 9.82e+00 1hg3A c.1.1.1 61025 1ut9A 609 1.01e+01 a.102.1.2,b.1.18.2 99912,99913 1b0tA 106 1.01e+01 1a6l d.58.1.2 38965 1mxmA 254 1.03e+01 b.38.1.3,d.58.43.1,f.34.1.1 79647,79648,79649 1m3yA 413 1.03e+01 b.121.2.3,b.121.2.3 78579,78580 1y0gA 191 1.06e+01 1a6l 106 1.10e+01 1a6l d.58.1.2 38966 1qqjA 419 1.11e+01 1qcnA b.34.8.1,d.177.1.1 59034,59035 2cw8A 537 1.12e+01 2b3nA 159 1.16e+01 1vljA 407 1.18e+01 e.22.1.2 108832 1fdd 106 1.24e+01 1a6l d.58.1.2 38960 7fd1A 106 1.27e+01 1a6l d.58.1.2 38953 1a9cA 221 1.31e+01 1a8rA d.96.1.1 40602 1cwvA 492 1.36e+01 1cwvA b.1.14.1,b.1.14.1,b.1.14.1,b.1.14.1,d.169.1.3 22373,22374,22375,22376,42442 2cr4A 126 1.42e+01 1zynA 202 1.44e+01 1zo2A 129 1.45e+01 1wbpA 397 1.62e+01 2b59B 172 1.70e+01 1josA 128 1.75e+01 d.52.7.1 84191 1qx4A 274 1.78e+01 b.43.4.2,c.25.1.1 104624,104625 1wosA 364 1.81e+01 b.44.2.1,d.250.1.1 109468,109469 2aioA 269 1.85e+01 1lm6A 215 1.88e+01 d.167.1.1 84628 1js8A 394 1.88e+01 a.86.1.1,b.112.1.1 67219,67220 1l5jA 865 1.90e+01 a.118.15.1,c.8.2.1,c.83.1.1 73592,73593,73594 1oc2A 348 1.91e+01 c.2.1.2 92765 2fr2A 172 1.95e+01 1hyuA 521 1.97e+01 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1xo1A 291 1.98e+01 1exnA a.60.7.1,c.120.1.2 18086,33356 2ckiA 262 2.08e+01 1r7lA 110 2.09e+01 d.277.1.1 104837 1kepA 348 2.09e+01 c.2.1.2 68536 1nnsA 326 2.11e+01 c.88.1.1 85910 1oa4A 222 2.17e+01 b.29.1.11 86731 2a8yA 270 2.18e+01 1s1qA 145 2.21e+01 d.20.1.2 98351 1ygs 234 2.26e+01 1ygs b.26.1.1 23907 2gjgA 248 2.28e+01 1ux8A 132 2.29e+01 1q15A 503 2.29e+01 c.26.2.1,d.153.1.1 95538,95539 1ogsA 497 2.38e+01 b.71.1.2,c.1.8.3 86997,86998 1vl2A 421 2.44e+01 c.26.2.1,d.210.1.1 108708,108709 2bsaA 303 2.47e+01 1w34A 304 2.48e+01 1y43A 39 2.50e+01 1tafB 70 2.50e+01 1tafB a.22.1.3 16482 1htyA 1015 2.53e+01 a.8.3.1,b.30.5.6,c.6.2.1 83064,83065,83066 1ogiA 303 2.63e+01 b.43.4.2,c.25.1.1 92914,92915 1exnA 290 2.65e+01 1exnA a.60.7.1,c.120.1.2 18088,33358 1cur 155 2.75e+01 1rcy b.6.1.1 23021 1xtqA 177 2.75e+01 1mqoA 227 2.78e+01 d.157.1.1 103846 1wudA 89 2.80e+01 1jjiA 311 2.81e+01 c.69.1.2 66766 1sv6A 269 2.84e+01 d.177.1.1 106043 1m0dA 138 2.84e+01 c.52.1.17 74354 1yqfA 203 2.85e+01 1uwkA 557 2.88e+01 e.51.1.1 108065 1y9wA 140 2.89e+01 1jc9A 269 2.94e+01 d.171.1.1 66490 2dcyA 185 2.97e+01 1npyA 271 3.00e+01 c.2.1.7,c.58.1.5 85995,85996 1lj5A 379 3.00e+01 e.1.1.1 73928 1qbeA 132 3.02e+01 1qbeA d.85.1.1 40138 1y1nA 291 3.02e+01 2fomB 185 3.02e+01 2beiA 170 3.04e+01 1jc7A 131 3.11e+01 1jc7A b.40.3.2 62873 1r44A 202 3.17e+01 d.65.1.4 104787 1e1oA 504 3.23e+01 1lylA b.40.4.1,d.104.1.1 25258,40714 1x6zA 123 3.24e+01 1hwwA 1015 3.26e+01 a.8.3.1,b.30.5.6,c.6.2.1 83067,83068,83069 1f2rI 100 3.28e+01 1c9fA d.15.2.1 37641 1gmiA 136 3.28e+01 b.7.1.1 65309 1rzhM 307 3.31e+01 f.26.1.1 98165 1que 303 3.36e+01 1fnc b.43.4.2,c.25.1.1 25647,31537 1dlwA 116 3.37e+01 1dlyA a.1.1.1 14982 1w6sA 599 3.39e+01 1aijM 307 3.40e+01 6prcM f.26.1.1 43462 1u2hA 99 3.45e+01 1hxkA 1015 3.52e+01 a.8.3.1,b.30.5.6,c.6.2.1 83070,83071,83072 1abbA 828 3.52e+01 1a8i c.87.1.4 35536 1b2rA 304 3.55e+01 1fnc b.43.4.2,c.25.1.1 25648,31538 1alu 186 3.59e+01 1alu a.26.1.1 16826 1go2A 304 3.59e+01 b.43.4.2,c.25.1.1 76243,76244 2hrvA 142 3.61e+01 2hrvA b.47.1.4 26429 1lkzA 219 3.62e+01 c.124.1.4,d.58.40.1 73991,73992 1x99A 145 3.64e+01 1k66A 149 3.65e+01 c.23.1.1 90941 2a35A 215 3.66e+01 1pzsA 208 3.67e+01 b.1.8.1 104397 1a65A 504 3.72e+01 1a65A b.6.1.3,b.6.1.3,b.6.1.3 23148,23149,23150 1rzl 91 3.73e+01 1rzl a.52.1.1 17817 1nksA 194 3.76e+01 1nksA c.37.1.1 31886 1ui7A 638 3.78e+01 b.30.2.1,d.17.2.1,d.17.2.1 99413,99414,99415 1ut8A 291 3.84e+01 a.60.7.1,c.120.1.2 99908,99909 1uctA 218 3.85e+01 b.1.1.4,b.1.1.4 88467,88468 1ks2A 219 3.86e+01 c.124.1.4,d.58.40.1 72908,72909 1umkA 275 3.99e+01 1y791 680 3.99e+01 2eiaB 206 4.01e+01 1eia a.28.3.1,a.73.1.1 16950,18330 1gpiA 431 4.17e+01 b.29.1.10 65450 1qi9A 556 4.20e+01 1qhbA a.111.1.2 19053 2eifA 136 4.27e+01 1bkb b.34.5.2,b.40.4.5 24607,25339 1b26A 416 4.29e+01 1hwyA c.2.1.7,c.58.1.1 30232,33880 1fxzA 476 4.30e+01 b.82.1.2,b.82.1.2 65059,65060 1wkvA 389 4.33e+01 1siiA 646 4.33e+01 b.30.2.1,d.17.2.1,d.17.2.1 105578,105579,105580 1azdA 237 4.34e+01 1nls b.29.1.1 24020 1yuwA 554 4.37e+01 1smlA 269 4.37e+01 1smlA d.157.1.1 42053 1rjoA 646 4.37e+01 1gsmA 210 4.46e+01 b.1.1.4,b.1.1.4 65535,65536 1f3uA 118 4.47e+01 1f3uA b.65.1.1 27521 1u84A 90 4.47e+01 1w6gA 646 4.48e+01 1lylA 504 4.49e+01 1lylA b.40.4.1,d.104.1.1 25261,40717 1oo0A 147 4.50e+01 d.232.1.1 87182 1a8i 842 4.50e+01 1a8i c.87.1.4 35490 1xnb 185 4.59e+01 1axkA b.29.1.11 24308 1si7A 369 4.65e+01 d.265.1.4 98883 1ru0A 105 4.66e+01 1aijL 281 4.66e+01 6prcL f.26.1.1 43461 1ivhA 394 4.74e+01 3mdeA a.29.3.1,e.6.1.1 16608,42869 1exnB 290 4.75e+01 1exnA a.60.7.1,c.120.1.2 18089,33359 1wstA 417 4.85e+01 1eia 207 4.90e+01 1eia a.28.3.1,a.73.1.1 16951,18331 1sziA 247 4.94e+01 a.24.23.1 106159 1ufbA 127 5.02e+01 a.24.16.3 99331 1aijS 301 5.05e+01 6prcM f.26.1.1 43465 1x6vA 630 5.06e+01 1o8bA 219 5.06e+01 c.124.1.4,d.58.40.1 81180,81181 1n67A 359 5.17e+01 b.2.3.4,b.2.3.4 85354,85355 1pylA 97 5.21e+01 d.1.1.2 104391 2f4nA 273 5.23e+01 2ab5A 269 5.24e+01 1vh5A 148 5.26e+01 d.38.1.5 100642 1ooyA 481 5.29e+01 c.124.1.3,c.124.1.2 93388,93389 1awd 94 5.31e+01 1awd d.15.4.1 37673 1xxnA 185 5.34e+01 1tq5A 242 5.41e+01 1c0nA 406 5.42e+01 1c0nA c.67.1.3 34433 2asi 360 5.61e+01 2rmpA b.50.1.2 26824 1dzoA 123 5.63e+01 1dzoA d.24.1.1 38378 2airB 153 5.65e+01 1fi8A 228 5.66e+01 5ptp b.47.1.2 26374 1axkA 394 5.66e+01 1axkA b.29.1.2,b.29.1.11 24181,24315 1prxA 224 5.67e+01 1prxA c.47.1.10 33076 1wuiL 534 5.69e+01 1szwA 379 5.69e+01 d.265.1.4 99047 1jscA 630 5.70e+01 c.31.1.3,c.36.1.5,c.36.1.9 67224,67225,67226 1ygaA 342 5.72e+01 2d4qA 257 5.75e+01 2aaa 484 5.75e+01 7taa b.71.1.1,c.1.8.1 27777,28764 1gzqA 300 5.84e+01 b.1.1.2,d.19.1.1 70818,70819 1eueA 86 5.93e+01 1cyo d.120.1.1 59504 1qhkA 47 5.97e+01 1qhkA d.100.1.2 40694 1z54A 132 5.97e+01 1wtaA 275 5.99e+01 1jf9A 408 5.99e+01 1c0nA c.67.1.3 62931 1b3bA 415 6.01e+01 1hwyA c.2.1.7,c.58.1.1 30244,33892 1zoyC 140 6.08e+01 1hfuA 503 6.10e+01 b.6.1.3,b.6.1.3,b.6.1.3 65827,65828,65829 1rxr 83 6.10e+01 2nllB g.39.1.2 45114 1ihp 438 6.11e+01 1ihp c.60.1.2 33993 1yua 122 6.11e+01 1yua g.41.3.3,g.41.3.3 45210,45211 1tit 98 6.17e+01 1tit b.1.1.4 21716 1dqqB 210 6.18e+01 1igtB b.1.1.1,b.1.1.2 20421,21391 2azpA 318 6.19e+01 1iz6A 138 6.21e+01 b.34.5.2,b.40.4.5 76976,76977 1zwxA 301 6.25e+01 1aogA 485 6.28e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30517,30518,40190 1ycoA 279 6.33e+01 1ubkL 534 6.34e+01 e.18.1.1 88422 1kkcA 221 6.35e+01 a.2.11.1,d.44.1.1 68660,68661 1bdo 80 6.39e+01 1bdo b.84.1.1 28214 1dkxA 219 6.45e+01 1dkzA a.8.4.1,b.130.1.1 90339,90340 2g1uA 155 6.48e+01 1f08A 148 6.50e+01 1f08A d.89.1.2 59564 1br9 194 6.52e+01 1br9 b.40.3.1 25235 1o9lA 481 6.62e+01 c.124.1.2,c.124.1.3 81241,81242 1pg4A 652 6.66e+01 e.23.1.1 88067 1hg2A 289 6.77e+01 1hg5A a.7.8.2,a.118.9.3 90358,90359 1hf8A 289 6.78e+01 1hg5A a.7.8.2,a.118.9.3 90354,90355 1h2rL 534 6.82e+01 1h2rL e.18.1.1 43298 1y3nA 490 6.84e+01 1mpp 361 6.84e+01 2rmpA b.50.1.2 26856 2aneA 125 6.84e+01 1c8kA 842 6.87e+01 1a8i c.87.1.4 35491 1hg5A 289 6.89e+01 1hg5A a.7.8.2,a.118.9.3 90360,90361 2bh9A 489 6.92e+01 1hyoA 421 6.96e+01 1qcnA b.34.8.1,d.177.1.1 59001,59002 1btmA 252 6.98e+01 1amk c.1.1.1 28513 1kwhA 492 7.02e+01 c.94.1.1 68876 1a7cA 379 7.10e+01 1sek e.1.1.1 42660 1y7wA 291 7.11e+01 1xtzA 264 7.16e+01 1ryaA 160 7.18e+01 d.113.1.5 105122 1f5jA 199 7.19e+01 1axkA b.29.1.11 24342 2nlrA 234 7.26e+01 2nlrA b.29.1.11 24344 1h2aL 567 7.30e+01 1h2rL e.18.1.1 43299 1hf2A 210 7.30e+01 1hf2A b.80.3.1,c.102.1.1 60992,60993 1xe7A 203 7.31e+01 1iscA 192 7.37e+01 1avmA a.2.11.1,d.44.1.1 15733,38726 2aieP 203 7.45e+01 1nnxA 109 7.47e+01 b.40.10.1 92013 1qjtA 99 7.57e+01 1eh2 a.39.1.6 17335 1zbpA 273 7.57e+01 1qcoA 423 7.57e+01 1qcnA b.34.8.1,d.177.1.1 59021,59022 2b6eA 146 7.68e+01 2fz4A 237 7.72e+01 1gpb 842 7.75e+01 1a8i c.87.1.4 35478 1f76A 336 7.75e+01 c.1.4.1 76160 1kf6B 243 7.78e+01 a.1.2.1,d.15.4.2 72397,72398 2gc9A 179 7.84e+01 1lt3A 240 7.85e+01 1lt3A d.166.1.1 42230 2gsq 202 7.87e+01 1pd21 a.45.1.1,c.47.1.5 17715,33009 1rzuA 485 7.88e+01 c.87.1.8 105140 1f00I 282 7.88e+01 1f00I b.1.14.1,b.1.14.1,d.169.1.3 22368,22369,42439 1m5yA 408 7.90e+01 a.167.1.1,d.26.1.1,d.26.1.1 78664,78665,78666 1g5aA 628 7.91e+01 b.71.1.1,c.1.8.1 65152,65153 1fh0A 221 7.92e+01 1cs8A d.3.1.1 59832 1fe0A 68 7.93e+01 1cc8A d.58.17.1 39345 1rzhL 281 7.96e+01 f.26.1.1 98164 1jhjA 171 7.97e+01 b.18.1.9 66714 3uagA 437 7.99e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30652,33953,34956 1cjsA 219 8.02e+01 1cjsA e.24.1.1 43354 1ogoX 574 8.02e+01 b.133.1.1,b.80.1.10 92925,92926 1ih7A 903 8.11e+01 1clqA c.55.3.5,e.8.1.1 62375,62376 1ynlH 219 8.12e+01 1iwmA 186 8.15e+01 b.125.1.2 83758 2f15A 96 8.16e+01 1eumA 165 8.22e+01 1eumA a.25.1.1 59507 1ii6A 368 8.27e+01 1bg2 c.37.1.9 62413 1fzrA 138 8.31e+01 1fzrA c.52.1.17 33336 1zm0A 114 8.32e+01 1ui8A 638 8.33e+01 b.30.2.1,d.17.2.1,d.17.2.1 99419,99420,99421 1h5uA 842 8.33e+01 1a8i c.87.1.4 60655 1tukA 67 8.34e+01 1ynfA 458 8.39e+01 1avk 638 8.40e+01 1a2vA b.30.2.1,d.17.2.1,d.17.2.1 24410,38047,38048 2d0oA 610 8.66e+01 1jb3A 131 8.70e+01 1jc7A b.40.3.2 62833 2govA 195 8.76e+01 1qwdA 177 8.85e+01 b.60.1.1 96471 1hekA 131 8.87e+01 a.61.1.5 65818 1eo9A 209 8.94e+01 3pchA b.3.6.1 22731 1i1nA 226 8.98e+01 c.66.1.7 71102