# List of top-scoring protein chains for t06-100-30-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 1ok0A 74 3.60e-02 b.5.1.1 93191 1zn8A 180 3.74e-02 2fhxA 246 5.61e-02 2c78A 405 8.00e-02 1yhfA 115 8.77e-02 1y7rA 133 9.77e-02 1oaqL 120 1.05e-01 b.1.1.1 92708 2fs2A 151 2.85e-01 1tu7A 208 4.10e-01 1x8hA 228 4.13e-01 1yb3A 175 4.44e-01 1kk1A 410 4.65e-01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1uldA 150 5.60e-01 b.29.1.3 99545 1f39A 101 5.85e-01 1umuA b.87.1.1 28386 1ifrA 121 5.96e-01 b.1.16.1 71203 1o9yA 84 6.38e-01 b.139.1.1 92692 1q2yA 140 6.43e-01 d.108.1.1 95655 1h8eD 482 7.73e-01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 60747,60748,60749 2ck3D 482 9.41e-01 1nqeA 594 9.53e-01 f.4.3.3 86027 2gpzA 111 9.64e-01 1cd9B 215 9.94e-01 1cto b.1.2.1,b.1.2.1 22041,22042 1b25A 619 1.03e+00 1b25A a.110.1.1,d.152.1.1 19044,41796 1suwA 249 1.10e+00 e.52.1.1 106027 1plc 99 1.14e+00 1plc b.6.1.1 22846 1avyA 74 1.34e+00 1avyB h.1.17.1 45656 2d7nA 93 1.42e+00 1j1bA 420 1.42e+00 d.144.1.7 90758 1qcsA 211 1.70e+00 1qcsA b.52.2.3,d.31.1.1 26927,38461 1wruA 379 1.73e+00 1v3eA 431 1.75e+00 b.68.1.1 100287 1j7xA 302 1.89e+00 c.14.1.2 66425 1hnjA 317 1.89e+00 1hn9A c.95.1.2,c.95.1.2 35969,35970 2gqrA 237 1.96e+00 1z8gA 372 2.09e+00 2rhe 114 2.20e+00 8fabA b.1.1.1 20523 1te5A 257 2.36e+00 d.153.1.1 106795 1vckA 115 2.38e+00 1z0sA 278 2.63e+00 1fs0E 138 2.80e+00 1aqt a.2.10.1,b.93.1.1 59997,59998 1oalA 151 3.09e+00 b.1.8.1 86739 1c7gA 456 3.21e+00 c.67.1.2 90415 1yhpA 212 3.28e+00 1ptmA 329 3.29e+00 c.77.1.3 95104 1qyaA 307 3.32e+00 d.21.1.2,d.21.1.2 104653,104654 1kte 105 3.35e+00 1kte c.47.1.1 32771 1vjqA 79 3.49e+00 k.43.1.1 100830 1xfcA 384 3.61e+00 1ed7A 45 3.77e+00 1ed7A b.72.2.1 27809 1vk3A 615 3.77e+00 d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 100846,100847,100848,100849 1lo6A 223 3.80e+00 b.47.1.2 74143 1hpcA 131 3.95e+00 1htp b.84.1.1 28221 1yukA 103 4.04e+00 1g3kA 174 4.51e+00 1nedA d.153.1.4 41989 1v1hA 103 4.60e+00 b.83.1.1,h.1.17.1 108243,108244 1j48A 110 5.02e+00 b.1.7.1 84112 1wh0A 134 5.02e+00 1czfA 362 5.03e+00 1czfA b.80.1.3 28031 2as0A 396 5.27e+00 2fl4A 149 5.41e+00 1o0sA 605 5.44e+00 c.2.1.7,c.58.1.3 86540,86541 1v70A 105 5.61e+00 1x8gA 227 5.78e+00 1cq3A 233 6.02e+00 1cq3A b.27.1.1 23923 1w2tA 432 6.45e+00 2mcm 112 6.69e+00 2mcm b.1.7.1 22207 1fdr 248 7.01e+00 1fdr b.43.4.2,c.25.1.1 25653,31543 1hic 51 7.14e+00 4htcI g.3.15.2 44371 1xdnA 277 7.23e+00 1e8pA 46 7.35e+00 g.55.1.1 59385 1vk6A 269 7.38e+00 d.113.1.4,d.113.1.4 100851,100852 1fqtA 112 7.44e+00 1fqtA b.33.1.1 24441 1gvp 87 7.74e+00 1gvp b.40.4.7 25369 2brfA 110 7.98e+00 1c01A 76 7.98e+00 1c01A b.11.1.5 23633 2bolA 314 8.11e+00 1m2xA 223 9.20e+00 d.157.1.1 84764 1ryiA 382 1.05e+01 1y7mA 164 1.05e+01 1rzfL 213 1.06e+01 b.1.1.1,b.1.1.2 98152,98153 1ve6A 582 1.09e+01 7ahlA 293 1.13e+01 7ahlA f.6.1.1 43812 1zkkA 167 1.14e+01 2f91B 35 1.15e+01 1sqwA 188 1.19e+01 1qmvA 197 1.28e+01 1qq2A c.47.1.10 33066 1pfiA 46 1.31e+01 1pfiA h.1.4.1 45558 2ch4A 320 1.36e+01 1aiw 62 1.44e+01 1aiw b.72.2.1 27808 1vavA 222 1.44e+01 b.29.1.18 108472 1vziA 126 1.46e+01 b.1.13.1,g.41.5.2 108967,108968 1t2bA 397 1.49e+01 1pjcA 361 1.56e+01 1sayA c.2.1.4,c.23.12.2 30101,31361 1v5rA 97 1.57e+01 1pne 140 1.57e+01 1pne d.110.1.1 40866 1kapP 479 1.59e+01 1sat b.80.7.1,d.92.1.6 28012,40298 1m9xC 146 1.61e+01 a.73.1.1 84907 1ag6 99 1.62e+01 1plc b.6.1.1 22857 1vljA 407 1.65e+01 e.22.1.2 108832 1fecA 490 1.67e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30489,30490,40176 1ukgA 252 1.67e+01 b.29.1.1 99489 1pzgA 331 1.69e+01 c.2.1.5,d.162.1.1 95425,95426 1ygtA 111 1.71e+01 2gcfA 73 1.71e+01 1zuoA 186 1.73e+01 1pz4A 116 1.74e+01 d.106.1.1 95400 1t95A 240 1.79e+01 a.5.8.1,d.235.1.2,d.58.11.3 106705,106706,106707 1ut7A 171 1.83e+01 b.143.1.1 99906 1cvrA 435 1.87e+01 1cvrA b.1.18.12,c.17.1.2 21949,31006 2g0qA 173 1.88e+01 2bs3A 656 1.93e+01 1jjtA 228 1.94e+01 1a7tA d.157.1.1 63139 2c2aA 258 1.95e+01 2c60A 111 1.97e+01 1zo0A 126 2.01e+01 2fazA 78 2.04e+01 1mla 309 2.05e+01 1mla c.19.1.1,d.58.23.1 31031,39383 1lf7A 182 2.09e+01 b.60.1.1 73878 1k5nA 276 2.14e+01 b.1.1.2,d.19.1.1 77266,77267 1vqoE 178 2.15e+01 3tss 194 2.17e+01 1aw7A b.40.2.2,d.15.6.1 25160,37749 1sddA 306 2.28e+01 b.6.1.3,b.6.1.3 105431,105432 1xe1A 116 2.29e+01 b.43.3.1 109571 1j05A 111 2.30e+01 b.1.1.1 90735 1sg6A 393 2.32e+01 e.22.1.1 105522 1j2gA 319 2.33e+01 d.96.1.4,d.96.1.4,d.96.1.4,d.96.1.4,d.96.1.4 103824,103825,103826,103827,103828 1qj8A 148 2.37e+01 1qj8A f.4.1.1 43744 2dd8S 202 2.37e+01 1jhfA 202 2.38e+01 a.4.5.2,b.87.1.1 63057,63058 1bg6 359 2.39e+01 1bg6 a.100.1.5,c.2.1.6 18810,30214 1m1zA 513 2.42e+01 c.26.2.1,d.153.1.1 78457,78458 1uaiA 224 2.43e+01 b.29.1.18 107761 1nkgA 508 2.44e+01 b.3.1.2,b.18.1.25,b.30.5.10 103859,103860,103861 1uypA 432 2.47e+01 b.29.1.19,b.67.2.3 100176,100177 2fb1A 226 2.49e+01 1yemA 179 2.49e+01 1dkuA 317 2.50e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 1i78A 297 2.51e+01 f.4.4.1 66046 1dyoA 160 2.52e+01 1dyoA b.18.1.7 23771 1m3wA 32 2.52e+01 k.8.1.1 78575 1muwA 386 2.54e+01 c.1.15.3 79495 1fm0D 81 2.55e+01 1fmaD d.15.3.1 37642 1zq9A 285 2.57e+01 1jyoA 130 2.62e+01 d.198.1.1 67483 2a8jA 420 2.65e+01 1bdo 80 2.65e+01 1bdo b.84.1.1 28214 1z6bA 154 2.66e+01 2f4pA 147 2.68e+01 1vfvA 366 2.68e+01 c.37.1.9 108592 1bhi 38 2.75e+01 1bhi g.37.1.1 45052 1yx0A 159 2.76e+01 1wloA 136 2.78e+01 2c2nA 339 2.84e+01 1m8aA 70 2.89e+01 d.9.1.1 74579 1snzA 344 2.96e+01 b.30.5.4 98930 1z9lA 128 2.98e+01 1uacL 107 2.99e+01 b.1.1.1 99133 1ww7A 160 3.02e+01 1uwfA 158 3.04e+01 2bivA 243 3.08e+01 1pdkB 157 3.10e+01 1pdkB b.2.3.2 22427 1gsmA 210 3.12e+01 b.1.1.4,b.1.1.4 65535,65536 2d4qA 257 3.14e+01 1a78A 134 3.15e+01 1c1lA b.29.1.3 24212 1bkf 107 3.17e+01 1fkj d.26.1.1 38382 1vjw 60 3.19e+01 1fxd d.58.1.4 38991 1gvzA 237 3.20e+01 b.47.1.2 76360 1i58A 189 3.25e+01 1b3qA d.122.1.3 61773 2avtA 378 3.28e+01 2cw8A 537 3.28e+01 1gr3A 160 3.31e+01 b.22.1.1 65476 1h9oA 112 3.33e+01 1qadA d.93.1.1 60837 1yfqA 342 3.41e+01 1bquA 215 3.58e+01 1bquA b.1.2.1,b.1.2.1 22066,22067 1ux6A 350 3.61e+01 b.29.1.16,g.75.1.1 100145,100146 1gt1A 159 3.75e+01 b.60.1.1 90515 1pg6A 243 3.77e+01 b.82.5.2 94673 1ix9A 205 3.79e+01 a.2.11.1,d.44.1.1 76899,76900 2eifA 136 3.79e+01 1bkb b.34.5.2,b.40.4.5 24607,25339 1c0pA 363 3.81e+01 1an9A c.4.1.2,d.16.1.3 30647,37934 2ar1A 172 3.86e+01 8fabA 212 3.88e+01 8fabA b.1.1.1,b.1.1.2 19772,20882 1gv9A 260 3.93e+01 b.29.1.13 70596 1lqvA 193 3.93e+01 d.19.1.1 74206 1hf2A 210 4.02e+01 1hf2A b.80.3.1,c.102.1.1 60992,60993 1mveA 243 4.09e+01 b.29.1.2 85140 1bb9 115 4.21e+01 1bb9 b.34.2.1 24554 1fljA 260 4.21e+01 2cba b.74.1.1 27954 1kb0A 677 4.22e+01 a.3.1.6,b.70.1.1 68378,68379 3prn 289 4.25e+01 3prn f.4.3.1 43761 2brcA 214 4.25e+01 1npsA 88 4.27e+01 1prs b.11.1.1 23622 1uc2A 481 4.35e+01 d.261.1.1 99161 2aeeA 211 4.38e+01 2cwsA 237 4.39e+01 2aqaA 63 4.41e+01 1vr8A 142 4.45e+01 1ta3A 274 4.47e+01 c.1.8.5 106731 1uwvA 433 4.47e+01 b.40.4.12,c.66.1.40 100128,100129 1upqA 123 4.48e+01 1w8oA 601 4.50e+01 1e0tA 470 4.53e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 1xiwA 105 4.56e+01 1yycA 174 4.62e+01 1j5uA 136 4.62e+01 d.208.1.1 71584 1wj9A 211 4.67e+01 1vdkA 466 4.70e+01 a.127.1.1 100561 1bqsA 209 4.72e+01 1bqsA b.1.1.4,b.1.1.4 21704,21705 1k4nA 192 4.76e+01 d.32.1.5 72059 1gk9B 557 4.77e+01 1bcpB 199 4.78e+01 1bcpB b.40.2.1,d.169.1.2 25120,42429 2sqcA 631 4.79e+01 2sqcA a.102.4.2,a.102.4.2 18854,18855 1a8d 452 4.83e+01 1a8d b.29.1.6,b.42.4.2 24262,25607 1smxA 96 4.85e+01 b.40.4.5 105772 1xruA 282 4.86e+01 1cs0A 1073 4.89e+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 18558,31487,31673,31674,41518,41519 1aol 228 4.90e+01 1aol b.20.1.1 23840 2bjrA 368 5.08e+01 1f00I 282 5.08e+01 1f00I b.1.14.1,b.1.14.1,d.169.1.3 22368,22369,42439 1oxxK 353 5.14e+01 b.40.6.3,c.37.1.12 93715,93716 1pm1X 180 5.16e+01 b.60.1.1 104189 1fyeA 229 5.16e+01 1fyeA c.23.16.4 31477 2azeA 155 5.18e+01 1k07A 263 5.19e+01 d.157.1.1 77218 1t1gA 364 5.20e+01 c.41.1.2 106246 1u3wA 374 5.21e+01 1eu3A 210 5.23e+01 1an8 b.40.2.2,d.15.6.1 25206,37795 1qddA 144 5.25e+01 1qddA d.169.1.1 42324 1vkyA 347 5.31e+01 e.53.1.1 108696 1rkqA 282 5.33e+01 c.108.1.10 97621 1wbiA 129 5.34e+01 1y43A 39 5.35e+01 1dlfL 113 5.41e+01 8fabA b.1.1.1 20382 1914 232 5.58e+01 1914 d.49.1.1,d.49.1.1 83028,83029 1nddA 76 5.66e+01 1ubi d.15.1.1 37599 1fsgA 233 5.68e+01 1qk3A c.61.1.1 34029 1hkhA 279 5.70e+01 c.69.1.12 90628 1kyfA 247 5.73e+01 b.1.10.1,d.105.1.1 73220,73221 1ybdA 239 5.82e+01 4dfrA 159 5.87e+01 1vdrA c.71.1.1 34822 1yxmA 303 5.87e+01 1zlbA 122 5.88e+01 1itvA 195 5.89e+01 b.66.1.1 76791 1gxuA 91 5.89e+01 d.58.10.1 76378 1jl2A 156 5.90e+01 c.55.3.1 66822 1qwyA 291 5.97e+01 b.84.3.2 96509 1ji6A 589 6.00e+01 b.18.1.3,b.77.2.1,f.1.3.1 63066,63067,63068 1zkiA 133 6.02e+01 2fctA 313 6.07e+01 1umhA 184 6.07e+01 b.18.1.21 99605 1eajA 126 6.10e+01 1f5wA b.1.1.1 59401 1wlyA 333 6.14e+01 1vyfA 135 6.14e+01 b.60.1.2 108902 1fltX 95 6.17e+01 1fltX b.1.1.4 21765 1qy1A 174 6.17e+01 b.60.1.1 96568 1iwlA 182 6.31e+01 b.125.1.1 83757 1xniA 118 6.33e+01 1zruA 264 6.35e+01 1yk4A 52 6.38e+01 1sj1A 66 6.41e+01 d.58.1.4 105595 2azwA 148 6.42e+01 1axh 37 6.43e+01 1axh g.3.6.2 44109 2fp7B 172 6.50e+01 1cghA 224 6.53e+01 1a7s b.47.1.2 26290 1rkiA 102 6.54e+01 2cxaA 256 6.62e+01 2end 138 6.67e+01 2end a.18.1.1 16400 1w9zA 283 6.80e+01 1cjxA 357 6.82e+01 1cjxA d.32.1.3,d.32.1.3 38516,38517 2cunA 410 6.84e+01 1xjcA 169 6.85e+01 1brfA 53 6.88e+01 1rb9 g.41.5.1 45236 1quqB 121 6.89e+01 1quqB b.40.4.3 25305 1u2hA 99 6.95e+01 2fblA 153 6.95e+01 1y55X 126 7.01e+01 1zvkA 358 7.03e+01 1p6oA 161 7.11e+01 c.97.1.2 94185 1uebA 184 7.12e+01 b.34.5.2,b.40.4.5,b.40.4.5 107782,107783,107784 1rm6B 324 7.13e+01 2ff4A 388 7.14e+01 1wmmA 145 7.16e+01 1rtu 114 7.20e+01 9rnt d.1.1.4 36139 1d5yA 292 7.21e+01 1d5yA a.4.1.8,a.4.1.8,d.60.1.2 16055,16056,39532 1e9pA 151 7.35e+01 1mfmA b.1.8.1 22215 1cqxA 403 7.37e+01 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 1oi7A 288 7.38e+01 c.2.1.8,c.23.4.1 87049,87050 2a90A 240 7.40e+01 1ww8A 439 7.40e+01 1musA 477 7.51e+01 c.55.3.4 79494 2gfaA 119 7.52e+01 1mk4A 157 7.54e+01 d.108.1.1 84979 1ws0A 156 7.61e+01 1o5uA 101 7.67e+01 b.82.1.8 92518 2gauA 232 7.69e+01 1f1gA 154 7.70e+01 b.1.8.1 76153 1jyhA 157 7.71e+01 d.60.1.3 71956 1l0qA 391 7.72e+01 b.1.3.1,b.69.2.3 77644,77645 1v6sA 390 7.73e+01 c.86.1.1 100424 1id0A 152 7.74e+01 d.122.1.3 66111 1ra9 159 7.77e+01 1vdrA c.71.1.1 34820 2bz6H 254 7.80e+01 1dyqA 234 7.80e+01 3seb b.40.2.2,d.15.6.1 59140,59141 1axiB 236 7.81e+01 1axiB b.1.2.1,b.1.2.1 21997,21998 1df7A 159 7.82e+01 3dfr c.71.1.1 34885 1pe9A 361 7.99e+01 b.80.1.1 94595 1fnd 314 8.05e+01 1fnc b.43.4.2,c.25.1.1 25626,31516 1q1rA 431 8.08e+01 c.3.1.5,c.3.1.5,d.87.1.1 95600,95601,95602 1o75A 415 8.10e+01 b.1.20.1,b.1.20.1,b.120.1.1 81117,81118,81119 1earA 147 8.12e+01 b.107.1.1,d.58.38.1 64875,64876 1bx1A 314 8.19e+01 1fnc b.43.4.2,c.25.1.1 25629,31519 1dq3A 454 8.25e+01 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1zndA 174 8.33e+01 1rl6A 177 8.40e+01 1rl6A d.141.1.1,d.141.1.1 41473,41474 1vkkA 154 8.42e+01 d.109.1.2 108669 1dhn 121 8.42e+01 1dhn d.96.1.3 40663 1lr5A 163 8.44e+01 b.82.1.2 74215 1h54A 754 8.46e+01 a.102.1.4,b.30.5.3 60634,60635 1ifc 132 8.53e+01 b.60.1.2 27173 1l8aA 886 8.60e+01 c.36.1.10,c.36.1.6,c.48.1.1 73677,73678,73679 2bpa2 175 8.62e+01 2bpa2 1m93B 245 8.64e+01 1i1qB 192 8.64e+01 1qdlB c.23.16.1 61544 1vixA 420 8.73e+01 c.56.5.4,d.58.19.1 100777,100778 1d3cA 686 8.79e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21827,22496,27734,28721 1tvdA 116 8.80e+01 1tvdA b.1.1.1 20650 2f0cA 191 8.82e+01 1w0pA 781 8.92e+01 b.29.1.8,b.29.1.8,b.68.1.1 109038,109039,109040 1oe1A 336 8.99e+01 b.6.1.3,b.6.1.3 86891,86892