# List of top-scoring protein chains for t2k-100-30-stride-ebghtl-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 1mkmA 249 9.11e-32 a.4.5.33,d.110.2.2 79242,79243 1yspA 181 8.94e-31 1td5A 202 2.11e-29 d.110.2.2 106767 2o99A 182 4.01e-28 d.110.2.2 138952 1tf1A 198 5.04e-28 d.110.2.2 106826 2ia2A 265 3.31e-27 2g7uA 257 9.71e-26 1ysqA 193 1.93e-25 3bjnA 165 3.48e-22 2o0yA 260 4.31e-22 1mc0A 368 3.31e-04 d.110.2.1,d.110.2.1 78937,78938 1ykdA 398 2.21e-02 1f5mA 180 7.12e-01 1f5mB d.110.2.1 40895 2aexA 346 8.17e-01 2gx5A 170 9.07e-01 1v5iB 76 9.75e-01 1itpA 77 9.93e-01 d.58.3.2 66371 2oqrA 230 9.99e-01 2pb2A 420 1.00e+00 2b18A 164 1.19e+00 2o28A 184 1.27e+00 2uv0E 175 1.29e+00 1yw5A 177 1.60e+00 2bjoA 136 1.78e+00 1q7lA 198 2.29e+00 c.56.5.4 96044 2qfmA 364 2.33e+00 3c6kA 381 2.34e+00 2f5gA 133 2.39e+00 d.58.57.1 132991 3c19A 186 2.57e+00 2cpmA 94 2.68e+00 3caxA 369 2.83e+00 2qybA 181 3.34e+00 1t9mA 214 4.18e+00 b.45.1.1 112364 1hbxA 92 4.57e+00 1mnmA d.88.1.1 60930 1r7mA 235 4.63e+00 d.95.2.1,d.95.2.1 111713,111714 1dgmA 363 4.68e+00 1bx4A c.72.1.1 34936 2debA 653 4.83e+00 2dgdA 223 5.02e+00 2fgoA 82 5.40e+00 1vr4A 103 5.41e+00 d.230.5.1 120432 2absA 383 5.47e+00 c.72.1.1 126534 2qdfA 335 5.57e+00 1mx3A 347 5.61e+00 c.2.1.4,c.23.12.1 79638,79639 2q81A 119 5.64e+00 2okjA 504 6.70e+00 1qwgA 251 6.74e+00 c.1.27.1 96473 3c0wA 235 6.94e+00 2v0uA 146 7.18e+00 1yvkA 163 7.22e+00 d.108.1.1 124101 1l2tA 235 7.46e+00 c.37.1.12 73514 1t70A 255 7.50e+00 d.159.1.9 112275 1fb6A 105 7.54e+00 1thx c.47.1.1 32739 2qr6A 393 7.90e+00 2icyA 469 8.35e+00 b.81.1.4,c.68.1.5 137257,137258 1p0zA 131 8.41e+00 d.110.6.1 93882 1lml 478 8.47e+00 1lml 1lmlA 478 8.47e+00 d.92.1.3 40295 2vjvA 159 8.52e+00 1id0A 152 8.72e+00 d.122.1.3 66111 1hyeA 313 8.76e+00 2cmd c.2.1.5,d.162.1.1 61400,61401 1mnmA 100 8.82e+00 1mnmA d.88.1.1 40232 2qvpA 275 9.55e+00 2vfjA 366 9.57e+00 1xtmA 175 9.77e+00 2pn0A 141 1.03e+01 1f2tB 148 1.03e+01 1f2tB 1b64 91 1.04e+01 1b64 1xtlA 175 1.05e+01 1jqgA 433 1.06e+01 c.56.5.1,d.58.3.1 71791,71792 1pc6A 146 1.11e+01 d.262.1.1 94430 3ctpA 330 1.15e+01 1g8yA 279 1.18e+01 1g8yA c.37.1.11 32302 1p4kA 295 1.19e+01 d.153.1.5 87772 1lpjA 133 1.19e+01 b.60.1.2 78123 2ou6A 190 1.19e+01 2yvyA 278 1.25e+01 2mysB 166 1.25e+01 1wdcB a.39.1.5 17308 2nx9A 464 1.25e+01 1z90A 469 1.26e+01 b.81.1.4,c.68.1.5 124732,124733 1n9lA 109 1.29e+01 d.110.3.6 85468 2c1cA 312 1.31e+01 c.56.5.1 129630 2j6vA 301 1.31e+01 1yexA 186 1.33e+01 c.47.1.10 123021 1vkpA 383 1.34e+01 d.126.1.6 108686 1icxA 155 1.38e+01 d.129.3.1 71191 1wubA 178 1.39e+01 b.61.6.1 114891 2q3uA 383 1.39e+01 d.126.1.6 139809 1tluA 130 1.41e+01 d.156.1.2 107139 1vr7A 142 1.42e+01 d.156.1.2 120443 1qxhA 167 1.47e+01 c.47.1.10 96528 1lc0A 294 1.48e+01 c.2.1.3,d.81.1.4 73823,73824 3rubS 123 1.49e+01 1rboC d.73.1.1 39616 1nlfA 279 1.53e+01 c.37.1.11 85850 2gjlA 328 1.54e+01 1gx1A 160 1.54e+01 d.79.5.1 70675 2atrA 138 1.55e+01 d.108.1.1 127305 9gafA 295 1.57e+01 1apyA d.153.1.5 42008 3cblA 377 1.58e+01 1spvA 184 1.60e+01 c.50.1.2 98957 1e3mA 800 1.65e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19075,32389,33746,39747 2hx1A 284 1.66e+01 1bavA 309 1.68e+01 1aye c.56.5.1 33806 1y791 680 1.70e+01 1wb9A 800 1.75e+01 a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 120833,120834,120835,120836 1s4iA 175 1.76e+01 1rkuA 206 1.76e+01 c.108.1.11 97627 1jr3A 373 1.77e+01 a.80.1.1,c.37.1.20 63245,63246 2e85A 159 1.85e+01 2h4tA 626 1.87e+01 1vjyA 303 1.90e+01 d.144.1.7 108633 1louA 101 1.92e+01 1ris d.58.14.1 39323 2b06A 155 1.94e+01 d.113.1.1 127624 1liiA 363 2.00e+01 c.72.1.1 73921 2ae6A 166 2.00e+01 d.108.1.1 126600 2nq2C 253 2.01e+01 2g39A 497 2.02e+01 c.124.1.2,c.124.1.2 134553,134554 1vi9A 299 2.03e+01 c.72.1.5 100750 1bjwA 382 2.07e+01 1bjwA c.67.1.1 34349 2vdjA 301 2.08e+01 2ghrA 302 2.10e+01 c.23.16.8 135208 1vliA 385 2.12e+01 b.85.1.1,c.1.10.6 108830,108831 1u1sA 82 2.12e+01 b.38.1.2 119451 2iwtA 125 2.12e+01 1hk9A 74 2.15e+01 b.38.1.2 83541 2dy1A 665 2.15e+01 2hjeA 221 2.18e+01 1ns5A 155 2.21e+01 c.116.1.3 80705 1adeA 431 2.25e+01 1adeA c.37.1.10 32213 1j31A 262 2.26e+01 d.160.1.2 90808 2h5nA 133 2.26e+01 2nwhA 317 2.27e+01 1bw9A 356 2.31e+01 1bw9A c.2.1.7,c.58.1.1 30274,33922 1rhcA 330 2.31e+01 c.1.16.3 97468 1bs2A 607 2.35e+01 1bs2A a.27.1.1,c.26.1.1,d.67.2.1 16930,31597,39563 1qf5A 431 2.37e+01 1adeA c.37.1.10 32212 1vcdA 126 2.37e+01 d.113.1.1 119970 1u9tA 354 2.39e+01 e.62.1.1 119651 1svdM 110 2.39e+01 d.73.1.1 119059 2vgdA 218 2.40e+01 2z8xA 617 2.48e+01 1u55A 188 2.53e+01 d.278.1.1 107677 2p2sA 336 2.54e+01 1yljA 263 2.55e+01 1vlwA 217 2.57e+01 c.1.10.1 108868 1wa3A 205 2.59e+01 c.1.10.1 120802 1poiA 317 2.60e+01 1poiA c.124.1.2 34153 2fcoA 200 2.62e+01 2p74A 263 2.65e+01 2trxA 108 2.65e+01 1thx c.47.1.1 32719 1uwzA 136 2.67e+01 c.97.1.1 108081 1jtkA 136 2.67e+01 c.97.1.1 71862 1py5A 326 2.71e+01 d.144.1.7 104389 1erv 105 2.75e+01 1erv 1xuuA 349 2.77e+01 b.85.1.1,c.1.10.6 116067,116068 1jfuA 186 2.79e+01 c.47.1.10 62940 1vefA 395 2.80e+01 c.67.1.4 120018 1s2oA 244 2.80e+01 c.108.1.10 118846 1gcuA 295 2.81e+01 1gcuA c.2.1.3,d.81.1.4 30063,39978 1r13A 148 2.86e+01 d.169.1.1,h.1.1.1 96782,96783 2v2gA 233 2.98e+01 2a1hA 365 3.01e+01 e.17.1.1 125997 1v33A 366 3.08e+01 d.264.1.1 100278 1ir21 140 3.09e+01 2a6mA 155 3.11e+01 d.58.57.1 126287 1w7bA 339 3.13e+01 a.65.1.1 114317 1r5jA 337 3.14e+01 c.77.1.5 97097 1qjtA 99 3.16e+01 1eh2 a.39.1.6 17335 1lqwA 183 3.24e+01 d.167.1.1 74210 1twdA 256 3.24e+01 c.1.30.1 107397 2j5aA 110 3.25e+01 1q2lA 939 3.27e+01 d.185.1.1,d.185.1.1,d.185.1.1,d.185.1.1 118731,118732,118733,118734 2a2lA 145 3.32e+01 d.110.9.1 126035 2pbqA 178 3.37e+01 1mvwB 145 3.40e+01 i.15.1.1 79524 2pc1A 201 3.44e+01 1zhhB 242 3.46e+01 2hgcA 102 3.46e+01 1w44A 331 3.51e+01 c.37.1.11 114147 1pz7A 204 3.52e+01 b.29.1.4 95405 1lmhA 184 3.54e+01 d.167.1.1 74036 1qfcA 306 3.60e+01 1uteA d.159.1.1 42077 1aiu 105 3.60e+01 1erv 1l1lA 739 3.60e+01 c.7.1.4 73470 1kq1A 77 3.61e+01 b.38.1.2 72848 1td2A 287 3.61e+01 c.72.1.5 106765 1sgjA 284 3.66e+01 c.1.12.5 105535 1k6kA 143 3.69e+01 a.174.1.1 77274 2oo6A 409 3.71e+01 2q02A 272 3.71e+01 1zgdA 312 3.73e+01 1ris 101 3.73e+01 1ris 1n0wA 243 3.75e+01 c.37.1.11 79772 2c5uA 375 3.77e+01 2azwA 148 3.78e+01 d.113.1.1 127615 1b34A 119 3.83e+01 1d3bA b.38.1.1 24796 2r6uA 148 3.87e+01 1zkjA 359 3.87e+01 2hq2A 354 3.87e+01 e.62.1.1 136656 1o65A 246 3.92e+01 b.58.1.2 92544 1o5zA 442 3.95e+01 c.59.1.2,c.72.2.2 92530,92531 1u7bA 261 3.96e+01 d.131.1.2,d.131.1.2 113083,113084 1y1oA 203 3.99e+01 c.52.1.28 116345 1gk8I 140 3.99e+01 d.73.1.1 65242 2adoA 196 4.01e+01 1cqmA 101 4.03e+01 1ris d.58.14.1 39321 2q2gA 180 4.03e+01 2etxA 209 4.05e+01 1frpA 335 4.13e+01 1frpA e.7.1.1 42875 1p3y1 194 4.14e+01 2rhmA 193 4.17e+01 2ifqA 105 4.19e+01 c.47.1.1 137343 1y96B 85 4.20e+01 8rucI 123 4.22e+01 1rboC d.73.1.1 39629 2vluA 122 4.23e+01 2j0pA 345 4.25e+01 e.62.1.1 137903 1c1dA 355 4.33e+01 1bw9A c.2.1.7,c.58.1.1 30270,33918 1we0A 187 4.34e+01 c.47.1.10 120930 2oajA 902 4.38e+01 1g71A 347 4.38e+01 1g71A d.264.1.1 43268 2gaeA 346 4.42e+01 1sedA 117 4.46e+01 a.219.1.1 105449 1u04A 771 4.49e+01 b.34.14.1,c.55.3.10 107539,107540 2o6pA 161 4.53e+01 1qwjA 229 4.57e+01 c.68.1.13 96478 1kwiA 101 4.63e+01 d.17.1.3 77564 1ji7A 89 4.63e+01 a.60.1.1 71682 1b08A 158 4.64e+01 1rtm1 d.169.1.1,h.1.1.1 42416,45423 1erw 105 4.65e+01 1erv 1bueA 265 4.67e+01 1btl e.3.1.1 42727 1dkzA 219 4.72e+01 1dkzA a.8.4.1,b.130.1.1 90345,90346 2ddzA 190 4.79e+01 2ovlA 371 4.82e+01 2g2qA 124 4.82e+01 1avmA 201 4.84e+01 1avmA a.2.11.1,d.44.1.1 15782,38745 2yzhA 171 4.87e+01 2j13A 247 4.87e+01 c.6.2.3 137934 1b5pA 385 4.89e+01 c.67.1.1 90403 1zm8A 259 4.90e+01 5fbpA 335 4.91e+01 1frpA e.7.1.1 42873 1jv4A 162 4.92e+01 b.60.1.1 67343 1ty9A 222 4.92e+01 b.45.1.1 112827 1n00A 321 4.94e+01 a.65.1.1 85241 1w79A 489 5.01e+01 e.3.1.3 120680 1f1uA 323 5.02e+01 d.32.1.3,d.32.1.3 83200,83201 1twuA 139 5.04e+01 d.32.1.8 107413 2cxaA 256 5.07e+01 d.108.1.6 130993 2ho4A 259 5.09e+01 2zdrA 349 5.09e+01 1m4zA 238 5.09e+01 b.34.12.1 78630 2euiA 153 5.12e+01 d.108.1.1 132387 1uuqA 440 5.13e+01 c.1.8.3 100015 1zndA 174 5.14e+01 b.60.1.1 125380 2fe3A 145 5.21e+01 2g0bA 198 5.22e+01 1b7gO 340 5.25e+01 1b7gO c.2.1.3,d.81.1.1 29992,39907 1ko7A 314 5.29e+01 c.98.2.1,c.91.1.2 72797,72798 1i06A 180 5.30e+01 1mup b.60.1.1 27131 1iurA 88 5.33e+01 a.2.3.1 90704 2hyvA 308 5.33e+01 2hvgA 482 5.37e+01 2burB 241 5.47e+01 b.3.6.1 129228 1bg2 325 5.52e+01 1bg2 1bg2A 325 5.52e+01 c.37.1.9 32189 1ockA 412 5.58e+01 c.117.1.1 86802 2pfuA 99 5.62e+01 1yixA 265 5.63e+01 c.1.9.12 123371 1vi6A 208 5.64e+01 c.23.15.1 100736 3b6hA 498 5.69e+01 1o7eA 276 5.69e+01 e.3.1.1 92622 1zuyA 58 5.71e+01 2qgaB 465 5.72e+01 2e7uA 424 5.72e+01 1dvkA 173 5.73e+01 1dvkA a.72.1.1 18319 1w6uA 302 5.78e+01 c.2.1.2 114288 1m7yA 435 5.83e+01 c.67.1.4 78761 1p4dA 330 5.89e+01 d.89.1.5 94101 1wdjA 187 5.92e+01 c.52.1.27 114536 2reeA 224 5.92e+01 1n5dA 288 5.92e+01 c.2.1.2 80030 2o18A 340 5.93e+01 1j6wA 175 5.96e+01 1j98A d.185.1.2 62663 1jf2A 195 5.97e+01 1ej3A a.39.1.5 62930 1bsmA 201 5.98e+01 1avmA a.2.11.1,d.44.1.1 15780,38743 1uacH 114 6.02e+01 b.1.1.1 99132 2jmkA 111 6.02e+01 1k3eA 156 6.06e+01 d.198.1.1 68103 1ynuA 473 6.09e+01 c.67.1.4 123762 1qe5A 266 6.10e+01 1b8oA c.56.2.1 33784 2r00A 336 6.10e+01 1k8yB 396 6.13e+01 c.79.1.1 72184 2p4qA 497 6.17e+01 2f57A 317 6.20e+01 1ru8A 232 6.23e+01 c.26.2.1 97849 1dkxA 219 6.25e+01 1dkzA a.8.4.1,b.130.1.1 90339,90340 1f60A 458 6.28e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 1rscI 111 6.32e+01 d.73.1.1 118620 1ass 159 6.33e+01 1a6dA 1assA 159 6.33e+01 c.8.5.2 30818 3ceaA 346 6.34e+01 2fgeA 995 6.38e+01 d.185.1.1,d.185.1.1,d.185.1.1,d.185.1.1 133430,133431,133432,133433 2rjrA 537 6.39e+01 2inpL 89 6.43e+01 2i74A 189 6.49e+01 b.18.1.29 137100 2o37A 92 6.51e+01 1awcB 153 6.52e+01 1bd8 d.211.1.1 19156 1mup 166 6.57e+01 1mup 1ylkA 172 6.58e+01 2d0iA 333 6.60e+01 1srvA 145 6.60e+01 1derA c.8.5.1 30817 2dfaA 250 6.62e+01 c.6.2.5 131469 1m4lA 307 6.67e+01 c.56.5.1 78604 2ph0A 174 6.69e+01 1qy1A 174 6.69e+01 b.60.1.1 96568 1lm4A 194 6.78e+01 d.167.1.1 84626 1qtqA 553 6.80e+01 1gtrA b.53.1.2,c.26.1.1 26940,31579 1uj2A 252 6.81e+01 c.37.1.6 99452 1lddA 74 6.88e+01 a.4.5.34 73841 2izrA 330 6.93e+01 1p32A 209 6.93e+01 1p32A d.25.1.1 38379 1zemA 262 6.94e+01 c.2.1.2 124984 2abyA 146 6.96e+01 1jyoA 130 6.97e+01 d.198.1.1 67483 2dnrA 91 6.98e+01 1xmaA 145 7.03e+01 a.4.5.61 115477 1g41A 444 7.06e+01 1do0A c.37.1.20 32450 1xvqA 175 7.06e+01 c.47.1.10 116094 1ekfA 365 7.07e+01 1ekfA e.17.1.1 59445 1cr1A 296 7.10e+01 1cr1A c.37.1.11 32286 1k3sA 113 7.10e+01 d.198.1.1 68120 1mxgA 435 7.13e+01 b.71.1.1,c.1.8.1 85193,85194 2qe6A 274 7.17e+01 2jj7A 186 7.17e+01 1kz8A 337 7.19e+01 e.7.1.1 77633 1idk 359 7.19e+01 1qcxA 1idkA 359 7.19e+01 b.80.1.2 28025 2o3fA 111 7.22e+01 1lqyA 184 7.23e+01 d.167.1.1 74212 1pq7A 224 7.25e+01 b.47.1.2 95002 1m45A 148 7.26e+01 a.39.1.5 78598 2j4oA 401 7.28e+01 2g1lA 104 7.30e+01 b.26.1.2 134520 1rblI 109 7.33e+01 d.73.1.1 118599 2gsaA 432 7.35e+01 2gsaA c.67.1.4 34446 1qxoA 388 7.37e+01 d.258.1.1 96539 2hp1A 432 7.37e+01 3cgvA 397 7.45e+01 1gefA 123 7.49e+01 1gefA c.52.1.18 60465 1ae1A 273 7.51e+01 1bdb c.2.1.2 29943 2iv2X 715 7.55e+01 b.52.2.2,c.81.1.1 137714,137715 2hehA 387 7.57e+01 2r7hA 177 7.58e+01 1mngA 203 7.59e+01 1avmA a.2.11.1,d.44.1.1 15776,38701 2awfA 172 7.59e+01 d.20.1.1 127432 1utuA 108 7.60e+01 1s28A 132 7.65e+01 d.198.1.1 105223 1xfkA 336 7.69e+01 c.42.1.1 115264 1psdA 409 7.70e+01 1psdA c.2.1.4,c.23.12.1,d.58.18.1 30097,31357,39354 1t6sA 162 7.71e+01 a.4.5.60,a.4.5.60 112271,112272 2q04A 211 7.73e+01 2eo2A 71 7.75e+01 1a62 130 7.76e+01 1a62 1a62A 130 7.76e+01 a.140.3.1,b.40.4.5 64708,64709 2g8lA 299 7.78e+01 e.50.1.1 134775 2h8eA 120 7.79e+01 1s50A 259 7.79e+01 c.94.1.1 118864 2gzsA 278 7.87e+01 1b8gA 429 7.88e+01 1b8gA c.67.1.4 34499 1rypF 233 7.88e+01 1rypF d.153.1.4 41937 2eabA 899 7.88e+01 2coiA 386 7.97e+01 2ha8A 184 7.98e+01 2d5rA 252 7.99e+01