# List of top-scoring protein chains for t04-100-30-str2-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 6.33e-05 1xubA 298 7.12e-05 2gkeA 274 3.32e-04 1gqzA 274 3.98e-04 d.21.1.1,d.21.1.1 83311,83312 1t6kA 278 6.17e-04 1tm0A 350 8.44e-04 d.21.1.3 107147 1bwzA 274 2.33e-03 1bwzA d.21.1.1,d.21.1.1 38337,38338 1w61A 414 2.46e-03 1ym5A 300 1.63e-02 1o17A 345 1.45e-01 a.46.2.1,c.27.1.1 80765,80766 1dkmA 410 1.51e-01 1dklA c.60.1.2 34000 1dkqA 410 1.64e-01 1dklA c.60.1.2 33998 1wc3A 219 4.16e-01 1xtqA 177 6.27e-01 1sdjA 310 8.40e-01 d.21.1.2,d.21.1.2 98807,98808 1tx4B 178 9.21e-01 1ctqA c.37.1.8 32045 1bupA 386 1.05e+00 1ba1 c.55.1.1,c.55.1.1 33377,33378 1kay 381 1.11e+00 1ba1 c.55.1.1,c.55.1.1 33385,33386 2b6eA 146 1.52e+00 1o0iA 138 1.83e+00 d.38.1.5 86532 1p3dA 475 1.86e+00 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1u0kA 288 1.86e+00 d.21.1.2,d.21.1.2 107547,107548 1d0iA 156 2.02e+00 2dhqA c.23.13.1 31383 1ycoA 279 2.14e+00 2acfA 182 2.17e+00 2azpA 318 2.31e+00 1vh5A 148 2.44e+00 d.38.1.5 100642 1hzdA 272 2.58e+00 c.14.1.3 65969 1ubkL 534 2.60e+00 e.18.1.1 88422 1h2rL 534 2.61e+00 1h2rL e.18.1.1 43298 1wuiL 534 2.64e+00 1sr8A 298 2.76e+00 e.54.1.1 105959 1vdkA 466 3.39e+00 a.127.1.1 100561 1oe4A 247 3.71e+00 c.18.1.3 86895 1o0pA 104 3.98e+00 d.58.7.1 86535 1z5hA 780 4.03e+00 2bw8A 227 4.13e+00 1s7jA 262 4.46e+00 d.21.1.2 98647 1dazC 99 5.07e+00 1hvc b.50.1.1 26501 1gtzA 156 5.36e+00 c.23.13.1 70539 1yqfA 203 5.88e+00 1lp8A 254 6.36e+00 d.165.1.1 91082 1dmhA 311 6.40e+00 1dmhA b.3.6.1 22633 1yuwA 554 6.63e+00 1h0bA 256 6.72e+00 b.29.1.11 83422 1n2eA 300 6.73e+00 c.26.1.4 85268 1nt4A 391 6.74e+00 c.60.1.2 92102 1rl0A 255 7.42e+00 2a84A 300 7.60e+00 1u9yA 284 7.67e+00 1zhhB 242 8.60e+00 1wtaA 275 8.68e+00 1iznB 277 8.70e+00 e.43.1.2 83848 1rsy 152 9.31e+00 1rsy b.7.1.2 23192 1q15A 503 1.03e+01 c.26.2.1,d.153.1.1 95538,95539 2cxcA 144 1.08e+01 2cx7A 130 1.09e+01 1vqzA 341 1.12e+01 2fvhA 120 1.15e+01 1o8bA 219 1.19e+01 c.124.1.4,d.58.40.1 81180,81181 1psuA 140 1.19e+01 d.38.1.5 88285 2fs2A 151 1.29e+01 2f23A 156 1.32e+01 1srqA 341 1.33e+01 e.55.1.1 105967 1ogsA 497 1.37e+01 b.71.1.2,c.1.8.3 86997,86998 1e3pA 757 1.39e+01 1e3hA a.4.9.1,b.40.4.5,d.14.1.4,d.14.1.4,d.52.3.1,d.101.1.1,d.101.1.1 16258,25328,37574,37575,38811,40697,40698 1mxmA 254 1.39e+01 b.38.1.3,d.58.43.1,f.34.1.1 79647,79648,79649 1w77A 228 1.41e+01 1dp4A 435 1.43e+01 1dp4A c.93.1.1 35710 1q87A 221 1.45e+01 e.47.1.1 96192 2b3nA 159 1.46e+01 1zcjA 463 1.48e+01 1ixlA 131 1.50e+01 d.38.1.5 90717 1uz5A 402 1.52e+01 b.85.6.1,b.103.1.1,c.57.1.2 100217,100218,100219 1yloA 348 1.52e+01 1o70A 324 1.69e+01 b.118.1.1,b.118.1.1 81115,81116 1y791 680 1.70e+01 2g6yA 217 1.71e+01 1pjcA 361 1.82e+01 1sayA c.2.1.4,c.23.12.2 30101,31361 2a6aA 218 1.82e+01 2gtqA 867 1.86e+01 1m0wA 491 1.90e+01 c.30.1.4,d.142.1.6 78363,78364 1p7gA 222 1.98e+01 a.2.11.1,d.44.1.1 94223,94224 1tueB 218 2.04e+01 b.91.1.1 107324 1pfsA 78 2.12e+01 1pfsA b.40.4.7 25391 1yghA 164 2.21e+01 1yghA d.108.1.1 40802 1pzsA 208 2.21e+01 b.1.8.1 104397 1cc1L 498 2.26e+01 1h2rL e.18.1.1 43301 1ntvA 152 2.30e+01 b.55.1.2 86168 1h9dB 134 2.31e+01 2jhbA b.54.1.1 60822 1wdkC 390 2.33e+01 c.95.1.1,c.95.1.1 109258,109259 1z54A 132 2.35e+01 1zvpA 133 2.37e+01 1nnhA 294 2.39e+01 d.104.1.1 92005 1rzuA 485 2.42e+01 c.87.1.8 105140 1qwiA 143 2.42e+01 d.227.1.1 96474 1jcfA 344 2.53e+01 c.55.1.1,c.55.1.1 62878,62879 2nlrA 234 2.53e+01 2nlrA b.29.1.11 24344 1zkiA 133 2.63e+01 1difA 99 2.67e+01 1fmb b.50.1.1 26503 1qm4A 396 2.75e+01 1mxb d.130.1.1,d.130.1.1,d.130.1.1 41350,41351,41352 1lo7A 141 2.78e+01 d.38.1.1 74144 1jc9A 269 2.84e+01 d.171.1.1 66490 1mtpA 323 2.87e+01 e.1.1.1 85107 1kmqA 184 2.89e+01 c.37.1.8 84412 1gkmA 509 2.92e+01 a.127.1.2 70228 1kkcA 221 2.92e+01 a.2.11.1,d.44.1.1 68660,68661 1ru0A 105 2.93e+01 1tafB 70 2.97e+01 1tafB a.22.1.3 16482 2dgkA 452 3.09e+01 2aneA 125 3.12e+01 1l0wA 580 3.15e+01 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1qyaA 307 3.16e+01 d.21.1.2,d.21.1.2 104653,104654 1v8hA 107 3.18e+01 4uagA 437 3.18e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30651,33952,34955 1m2oA 768 3.18e+01 a.71.2.1,b.2.8.1,c.62.1.2,d.109.2.1,g.41.10.1 78480,78481,78482,78483,78484 1f08A 148 3.24e+01 1f08A d.89.1.2 59564 1k2yX 463 3.25e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 2bvbA 137 3.27e+01 1cl8A 276 3.28e+01 1ckqA c.52.1.1 33230 1r44A 202 3.30e+01 d.65.1.4 104787 1i1nA 226 3.30e+01 c.66.1.7 71102 1g7sA 594 3.35e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 1xizA 159 3.35e+01 1ab8A 220 3.37e+01 1azsA d.58.29.1 39414 2a8yA 270 3.39e+01 2aioA 269 3.42e+01 1pmmA 466 3.42e+01 c.67.1.6 94901 1p5dX 463 3.43e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1br9 194 3.46e+01 1br9 b.40.3.1 25235 2b5wA 357 3.52e+01 1nziA 159 3.57e+01 b.23.1.1,g.3.11.1 86449,86450 1lr0A 129 3.61e+01 d.212.1.1 74213 1vi6A 208 3.65e+01 c.23.15.1 100736 1lyqA 104 3.66e+01 b.1.18.17 78302 1z47A 355 3.67e+01 1qjtA 99 3.74e+01 1eh2 a.39.1.6 17335 1gmuA 143 3.75e+01 b.107.1.1,d.58.38.1 65335,65336 1i6iA 366 3.77e+01 1bg2 c.37.1.9 61844 1u7nA 336 3.78e+01 c.77.1.4 107726 1o97D 320 3.86e+01 c.26.2.3,c.31.1.2 81233,81234 1nh1A 330 3.88e+01 e.45.1.1 91871 1yliA 153 3.90e+01 2fr2A 172 3.92e+01 1j5pA 253 3.95e+01 d.81.1.3,c.2.1.3 71577,83092 2b61A 377 3.96e+01 2lhb 149 3.98e+01 2fal a.1.1.2 15597 1lkkA 105 4.03e+01 1lckA d.93.1.1 40412 1bvqA 141 4.03e+01 1bvqA d.38.1.1 38542 1qi7A 253 4.10e+01 1qi7A d.165.1.1 42210 1mqvA 125 4.11e+01 a.24.3.2 79415 1vpbA 451 4.12e+01 1xhcA 367 4.15e+01 1wnlA 235 4.17e+01 1vdxA 184 4.27e+01 1gv3A 248 4.37e+01 a.2.11.1,d.44.1.1 70585,70586 1oa4A 222 4.40e+01 b.29.1.11 86731 1nnsA 326 4.47e+01 c.88.1.1 85910 2c0zA 216 4.52e+01 1giqA 413 4.54e+01 d.166.1.1,d.166.1.1 76224,76225 1pyoA 167 4.60e+01 c.17.1.1 95370 1nbwA 607 4.61e+01 c.8.6.1,c.55.1.6,c.55.1.6 80393,80394,80395 1bia 321 4.61e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1qstA 160 4.61e+01 1yghA d.108.1.1 40804 1tdtA 259 4.68e+01 3tdt b.81.1.2 28055 1uisA 231 4.74e+01 d.22.1.1 99431 2myr 501 4.75e+01 1mngA 203 4.84e+01 1avmA a.2.11.1,d.44.1.1 15776,38701 1bywA 110 4.84e+01 1bywA d.110.3.6 40912 1kxqE 120 4.94e+01 b.1.1.1 73171 1t6cA 315 4.96e+01 c.55.1.8,c.55.1.8 106558,106559 1wmdA 434 4.98e+01 b.18.1.20,c.41.1.1 109408,109409 2aliA 158 5.01e+01 1smlA 269 5.02e+01 1smlA d.157.1.1 42053 1oj6A 151 5.04e+01 a.1.1.2 93088 1sg4A 260 5.10e+01 2fkbA 180 5.11e+01 1mw7A 240 5.15e+01 e.39.1.1 79557 1s0yB 71 5.25e+01 d.80.1.1 98315 2a15A 139 5.33e+01 1p6pA 125 5.35e+01 b.60.1.2 87839 2c7pA 327 5.43e+01 1q1rA 431 5.50e+01 c.3.1.5,c.3.1.5,d.87.1.1 95600,95601,95602 1dgfA 497 5.53e+01 1cf9A e.5.1.1 42782 1xvsA 126 5.60e+01 1wekA 217 5.64e+01 1lm6A 215 5.71e+01 d.167.1.1 84628 1k1xA 659 5.82e+01 a.8.3.2,b.30.5.8,c.6.2.2 84279,84280,84281 2etvA 346 5.86e+01 1ri5A 298 5.99e+01 c.66.1.34 97502 1xhlA 297 5.99e+01 c.2.1.2 109591 1vgjA 184 6.05e+01 1fcdA 401 6.18e+01 1fcdA c.3.1.5,c.3.1.5,d.87.1.1 30593,30594,40218 1nh0A 99 6.20e+01 b.50.1.1 91869 1ejxA 100 6.24e+01 d.8.1.1 83182 1tag 324 6.25e+01 1cipA a.66.1.1,c.37.1.8 18197,32080 1m5yA 408 6.28e+01 a.167.1.1,d.26.1.1,d.26.1.1 78664,78665,78666 2b4rO 345 6.34e+01 1h7wA 1025 6.38e+01 1h7wA a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15683,28628,30324,30609,39007 2b25A 336 6.39e+01 2f2hA 773 6.52e+01 1sh8A 154 6.57e+01 d.38.1.5 105549 1sefA 274 6.63e+01 b.82.1.11 105452 1w19A 160 6.64e+01 1z6mA 175 6.71e+01 1b8fA 509 6.72e+01 1b8fA a.127.1.2 19434 1g5cA 170 6.72e+01 1g5cA c.53.2.1 60264 1wab 232 6.75e+01 1wab c.23.10.3 31341 1vjrA 271 6.92e+01 c.108.1.14 100832 1yzsA 121 6.93e+01 2msbA 115 6.93e+01 1rtm1 d.169.1.1 42355 1drw 273 7.04e+01 1drw c.2.1.3,d.81.1.3 30057,39972 1jhjA 171 7.13e+01 b.18.1.9 66714 1h05A 146 7.19e+01 c.23.13.1 76433 1jihA 531 7.24e+01 d.240.1.1,e.8.1.7 90374,90375 1r5eA 115 7.25e+01 2dbbA 151 7.27e+01 1zbqA 327 7.28e+01 1y8tA 324 7.41e+01 1tw7A 99 7.44e+01 1q79A 514 7.48e+01 a.160.1.1,d.218.1.3,d.58.16.1 104548,104549,104550 1dmmA 131 7.48e+01 1opy d.17.4.3 38114 1pysA 350 7.52e+01 1pysA d.104.1.1 40775 2gvhA 288 7.53e+01 1yzhA 214 7.54e+01 1moq 368 7.59e+01 1moq c.80.1.1 35302 2dhqA 146 7.62e+01 2dhqA c.23.13.1 31382 1dcoA 104 7.67e+01 1dcpA d.74.1.1 39680 1vliA 385 7.68e+01 b.85.1.1,c.1.10.6 108830,108831 1kc6A 257 7.79e+01 c.52.1.19 68419 1yfqA 342 7.79e+01 1v9yA 167 7.83e+01 d.110.3.2 108454 2c26A 260 7.88e+01 1lox 662 7.88e+01 1lox a.119.1.2,b.12.1.1 19238,23638 1z4rA 168 7.90e+01 1m7bA 184 7.91e+01 c.37.1.8 74572 1a9xA 1058 8.02e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18550,31479,31657,31658,41502,41503 1wcqA 601 8.04e+01 1bw0A 416 8.05e+01 1bw0A c.67.1.1 34385 1afwA 393 8.09e+01 1afwA c.95.1.1,c.95.1.1 35900,35901 1h4xA 117 8.10e+01 1auz c.13.2.1 60626 1ignA 246 8.10e+01 1ignA a.4.1.6,a.4.1.6 16048,16049 1g2bA 62 8.10e+01 1tud b.34.2.1 24488 4ubpA 101 8.13e+01 1ubpA d.8.1.1 37352 1kzkA 99 8.13e+01 b.50.1.1 73371 1nnxA 109 8.17e+01 b.40.10.1 92013 1qwkA 317 8.21e+01 c.1.7.1 96482 1th8A 145 8.21e+01 d.122.1.3 106908 1atiA 505 8.24e+01 1atiA c.51.1.1,d.104.1.1 33196,40745 1q1fA 151 8.34e+01 a.1.1.2 104476 1u7iA 136 8.40e+01 d.32.1.7 107724 1yt5A 258 8.52e+01 1g40A 244 8.60e+01 1e5gA g.18.1.1,g.18.1.1,g.18.1.1,g.18.1.1 44823,44824,44825,44826 1eg9A 449 8.62e+01 1ndoA b.33.1.2,d.129.3.3 24443,41322 1snzA 344 8.65e+01 b.30.5.4 98930 1ewqA 765 8.66e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19069,32383,33740,39743 1o7nA 449 8.70e+01 b.33.1.2,d.129.3.3 81162,81163 1g5hA 454 8.71e+01 1g5hA c.51.1.1,d.104.1.1 60270,60271 1awd 94 8.81e+01 1awd d.15.4.1 37673 1q25A 432 8.82e+01 b.64.1.1,b.64.1.1,b.64.1.1 104493,104494,104495 2fnaA 357 8.83e+01 2bjdA 101 8.84e+01 1tuhA 156 8.98e+01 d.17.4.11 107345