# 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 1dnlA 199 1.86e-19 1ci0A b.45.1.1 25753 1g79A 218 2.90e-19 1ci0A b.45.1.1 25752 1nrgA 261 2.51e-18 b.45.1.1 80694 2fhqA 141 7.50e-16 1rfeA 162 1.02e-15 1ty9A 222 1.57e-15 2fg9A 178 2.78e-13 1vl7A 157 5.75e-13 b.45.1.1 108732 2asfA 137 1.67e-12 2aq6A 147 6.32e-12 1w9aA 147 1.15e-11 2arzA 247 3.93e-11 2furA 209 3.48e-10 1w3oA 216 6.61e-09 1xhnA 184 4.60e-08 1flmA 122 1.24e-07 1axj b.45.1.1 25747 1ejeA 192 7.13e-04 1ejeA b.45.1.2 25757 2bgiA 272 1.39e-01 1ko3A 230 3.42e-01 d.157.1.1 90974 1q6uA 245 3.48e-01 d.26.1.1 95998 1s2wA 295 5.99e-01 c.1.12.7 98407 1q6hA 224 6.41e-01 d.26.1.1 95975 1zzkA 82 8.83e-01 1goiA 499 9.65e-01 b.72.2.1,c.1.8.5,d.26.3.1 65413,65414,65415 2fgtA 417 1.06e+00 1m40A 263 1.12e+00 e.3.1.1 74437 1x88A 359 1.28e+00 1b25A 619 1.33e+00 1b25A a.110.1.1,d.152.1.1 19044,41796 1lrzA 426 1.36e+00 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 1i24A 404 1.72e+00 c.2.1.2 83663 1zd7A 159 2.22e+00 1ukuA 102 2.28e+00 d.58.5.2 99533 1tr8A 102 2.29e+00 1me4A 215 2.30e+00 d.3.1.1 79023 1v0wA 506 2.53e+00 d.136.1.2,d.136.1.2 108220,108221 1al3 324 2.76e+00 1al3 c.94.1.1 35835 1snzA 344 3.04e+00 b.30.5.4 98930 1ww7A 160 3.12e+00 1uirA 314 3.35e+00 c.66.1.17 99429 1kr4A 125 3.38e+00 d.58.5.2 72889 1n9lA 109 3.42e+00 d.110.3.6 85468 1iejA 332 3.52e+00 1nnt c.94.1.2 62328 2abqA 306 3.91e+00 2etjA 250 3.99e+00 1gvp 87 4.06e+00 1gvp b.40.4.7 25369 1yzsA 121 4.12e+00 1oxxK 353 4.14e+00 b.40.6.3,c.37.1.12 93715,93716 1i0rA 169 4.17e+00 1i0rA b.45.1.2 61489 1uzmA 247 4.47e+00 2f15A 96 4.58e+00 2f4iA 197 5.07e+00 1jfuA 186 5.26e+00 c.47.1.10 62940 1ta3A 274 5.58e+00 c.1.8.5 106731 2cw5A 255 5.61e+00 1a8d 452 5.74e+00 1a8d b.29.1.6,b.42.4.2 24262,25607 1zkkA 167 6.11e+00 1zvkA 358 6.16e+00 1z0nA 96 6.27e+00 1qsmA 152 6.32e+00 1qsmA d.108.1.1 40808 2gp4A 628 6.38e+00 1wsrA 375 6.45e+00 1qx4A 274 6.48e+00 b.43.4.2,c.25.1.1 104624,104625 1sdjA 310 6.84e+00 d.21.1.2,d.21.1.2 98807,98808 1wbiA 129 6.87e+00 2ag5A 246 7.09e+00 1y0yA 353 7.52e+00 1vpjA 192 7.70e+00 1a2zA 220 7.85e+00 1a2zA c.56.4.1 33794 2gukA 120 8.04e+00 1ne9A 335 8.47e+00 d.108.1.4,d.108.1.4 91839,91840 2bwqA 129 8.63e+00 1jjtA 228 8.79e+00 1a7tA d.157.1.1 63139 1k8kD 300 9.88e+00 d.198.2.1,d.198.2.1 68309,68310 1pvtA 238 1.00e+01 c.74.1.1 95189 1rz3A 201 1.01e+01 c.37.1.6 98132 1q5xA 161 1.01e+01 c.8.7.1 95947 2gibA 103 1.04e+01 1u69A 163 1.07e+01 d.32.1.7 107699 1rkqA 282 1.09e+01 c.108.1.10 97621 4fiv 113 1.13e+01 1fmb b.50.1.1 26762 1r45A 204 1.23e+01 1tuhA 156 1.24e+01 d.17.4.11 107345 1vkkA 154 1.32e+01 d.109.1.2 108669 1pg4A 652 1.34e+01 e.23.1.1 88067 1gt1A 159 1.35e+01 b.60.1.1 90515 2c1lA 358 1.40e+01 2c07A 285 1.40e+01 1yrbA 262 1.45e+01 1oa4A 222 1.48e+01 b.29.1.11 86731 1vpmA 169 1.50e+01 2dg5B 190 1.51e+01 1wocA 103 1.52e+01 1ux6A 350 1.53e+01 b.29.1.16,g.75.1.1 100145,100146 2fp8A 322 1.54e+01 1bj7 156 1.54e+01 1bj7 b.60.1.1 27113 1sjyA 159 1.56e+01 d.113.1.1 98900 2cfxA 144 1.56e+01 2be4A 272 1.56e+01 1vqoE 178 1.57e+01 2rslA 140 1.58e+01 2rslA c.53.1.1 33345 1z4rA 168 1.60e+01 1ukgA 252 1.61e+01 b.29.1.1 99489 1vkbA 161 1.62e+01 d.269.1.1 108643 2bvfA 459 1.62e+01 1k55A 246 1.65e+01 e.3.1.1 68156 2mcm 112 1.74e+01 2mcm b.1.7.1 22207 1qwdA 177 1.76e+01 b.60.1.1 96471 1kuuA 202 1.76e+01 d.153.2.1 73019 1pbyA 489 1.77e+01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 94417,94418,94419,94420,94421 1g0oA 283 1.78e+01 1ybvA c.2.1.2 60181 2ftrA 108 1.79e+01 1t5iA 172 1.80e+01 c.37.1.19 106450 2a1vA 144 1.88e+01 2bi7A 384 1.91e+01 1zx4A 192 1.92e+01 1ub9A 100 1.97e+01 a.4.5.28 99159 2bwrA 401 1.99e+01 2arpA 116 2.00e+01 2f46A 156 2.07e+01 2axoA 270 2.08e+01 1vi6A 208 2.11e+01 c.23.15.1 100736 1qmyA 167 2.11e+01 1qmyA d.3.1.2 37094 1b8aA 438 2.18e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1v6tA 255 2.20e+01 1txuA 273 2.23e+01 a.222.1.1 107439 1cruA 454 2.30e+01 1c9uA b.68.2.1 27617 1twfK 120 2.31e+01 1r53A 382 2.32e+01 d.258.1.1 97063 1f60A 458 2.45e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 1m7vA 363 2.45e+01 d.174.1.1 78748 1vi4A 174 2.46e+01 c.8.7.1 100731 1so7A 382 2.50e+01 2czrA 226 2.54e+01 1eluA 390 2.56e+01 1elqA c.67.1.3 34434 2g9zA 348 2.61e+01 1dbfA 127 2.63e+01 2chsA d.79.1.2 39761 1e8cA 498 2.64e+01 c.98.1.1,c.59.1.1,c.72.2.1 59377,59378,59379 1pii 452 2.64e+01 1pii c.1.2.4,c.1.2.4 28559,28563 1kk1A 410 2.69e+01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1aoeA 192 2.71e+01 1aoeA c.71.1.1 34923 1bywA 110 2.72e+01 1bywA d.110.3.6 40912 1xfkA 336 2.74e+01 1qyaA 307 2.74e+01 d.21.1.2,d.21.1.2 104653,104654 1wlgA 299 2.76e+01 1wq3A 322 2.77e+01 1xw3A 110 2.78e+01 2gkeA 274 2.81e+01 1t1gA 364 2.86e+01 c.41.1.2 106246 1dzkA 157 2.87e+01 1obpA b.60.1.1 27096 1z5sD 83 2.88e+01 1o54A 277 2.89e+01 c.66.1.13 92482 1o4sA 389 2.92e+01 c.67.1.1 86620 1zfjA 491 2.95e+01 1ak5 c.1.5.1,d.37.1.1,d.37.1.1 28638,38540,38541 1xvxA 312 2.95e+01 1w66A 232 2.95e+01 1xf1A 926 2.99e+01 2df7A 458 2.99e+01 1ftrA 296 3.00e+01 1ftrA d.58.33.1,d.58.33.1 39485,39486 1p35A 299 3.03e+01 1p35A b.28.1.1 23925 1nnvA 110 3.03e+01 d.17.7.1 92012 1l7mA 211 3.04e+01 c.108.1.4 73664 1kllA 130 3.11e+01 d.32.1.2 72720 1odkA 235 3.11e+01 c.56.2.1 86863 1agqA 135 3.21e+01 1agqA g.17.1.2 44789 1wy2A 351 3.23e+01 1v0aA 178 3.23e+01 1zk4A 251 3.26e+01 1vmjA 151 3.29e+01 1vdnA 162 3.30e+01 2b0jA 358 3.33e+01 2g1uA 155 3.40e+01 1j4aA 333 3.43e+01 c.2.1.4,c.23.12.1 71502,71503 2ganA 190 3.45e+01 2ae2A 260 3.46e+01 1bdb c.2.1.2 29945 2fo3A 125 3.51e+01 1mtzA 293 3.51e+01 c.69.1.7 79467 1o3yA 166 3.52e+01 c.37.1.8 86618 1pz7A 204 3.55e+01 b.29.1.4 95405 1y08A 323 3.56e+01 1vmeA 410 3.57e+01 c.23.5.1,d.157.1.3 108893,108894 1m0wA 491 3.57e+01 c.30.1.4,d.142.1.6 78363,78364 1r8sA 164 3.58e+01 c.37.1.8 97247 2fe7A 166 3.58e+01 1vi2A 300 3.62e+01 c.2.1.7,c.58.1.5 100726,100727 1ojrA 274 3.63e+01 c.74.1.1 93147 1sbyA 254 3.63e+01 2fswA 107 3.65e+01 2ddrA 306 3.67e+01 1tqnA 486 3.68e+01 a.104.1.1 107238 2cveA 191 3.71e+01 1h2eA 207 3.75e+01 c.60.1.1 70857 1v5vA 401 3.78e+01 1b7yA 350 3.80e+01 1pysA d.104.1.1 40776 1vlyA 338 3.84e+01 b.44.2.1,d.250.1.1 108871,108872 1obbA 480 3.86e+01 c.2.1.5,d.162.1.2 86760,86761 1cfzA 162 3.87e+01 1cfzA c.56.1.1 33754 1lm8V 160 3.88e+01 b.3.3.1 74035 1iy8A 267 3.88e+01 c.2.1.2 83774 1b9hA 388 3.90e+01 1b9hA c.67.1.4 34488 1o97D 320 3.91e+01 c.26.2.3,c.31.1.2 81233,81234 1h1nA 305 3.93e+01 c.1.8.3 70855 1gheA 177 3.98e+01 d.108.1.1 76222 1g5tA 196 4.00e+01 1g5rA c.37.1.11 32366 2gb7A 305 4.04e+01 1iqrA 420 4.06e+01 a.99.1.1,c.28.1.1 66275,66276 1xteA 154 4.08e+01 1wznA 252 4.09e+01 1vljA 407 4.09e+01 e.22.1.2 108832 1agjA 242 4.10e+01 1agjA b.47.1.1 25827 1v4aA 440 4.11e+01 a.24.16.4,d.218.1.9 108350,108351 1exqA 154 4.11e+01 1b9dA c.55.3.2 33646 1wj9A 211 4.11e+01 1gqzA 274 4.26e+01 d.21.1.1,d.21.1.1 83311,83312 1v7pB 128 4.30e+01 d.169.1.1 108407 1sqgA 429 4.33e+01 a.79.1.3,c.66.1.38 105912,105913 1cr5A 189 4.34e+01 1cr5A b.52.2.3,d.31.1.1 26931,38465 2azpA 318 4.35e+01 2av5A 120 4.35e+01 1gvjA 146 4.35e+01 a.4.5.21 90525 2fcjA 119 4.36e+01 1m6yA 301 4.37e+01 a.60.13.1,c.66.1.23 78716,78717 1mqoA 227 4.40e+01 d.157.1.1 103846 1otjA 283 4.50e+01 b.82.2.5 93517 1t3qA 168 4.59e+01 a.56.1.1,d.15.4.2 106367,106368 1j58A 385 4.59e+01 b.82.1.2 71531 1ox0A 430 4.65e+01 c.95.1.1,c.95.1.1 87495,87496 3pviA 157 4.70e+01 3pviA c.52.1.6 33300 1sqeA 109 4.80e+01 d.58.4.5 105908 1jrrA 382 4.82e+01 e.1.1.1 63256 1qauA 112 4.83e+01 1qauA b.36.1.1 24779 2ew2A 316 4.83e+01 1vmaA 306 4.88e+01 a.24.13.1,c.37.1.10 108887,108888 2cxvA 219 4.90e+01 1gy8A 397 4.91e+01 c.2.1.2 83376 1vetA 124 4.92e+01 d.110.7.1 108553 1c8uA 285 4.93e+01 1c8uA d.38.1.3,d.38.1.3 38547,38548 1rocA 155 4.94e+01 b.1.22.1 97673 1q1rA 431 4.94e+01 c.3.1.5,c.3.1.5,d.87.1.1 95600,95601,95602 1ihuA 589 4.95e+01 c.37.1.10,c.37.1.10 62394,62395 1olmA 403 4.95e+01 a.5.3.1,b.132.1.1,c.13.1.1 104008,104009,104010 2bitX 165 4.96e+01 1h2bA 359 5.03e+01 b.35.1.2,c.2.1.1 90543,90544 1whi 122 5.07e+01 1whi b.39.1.1 24810 1vmhA 144 5.11e+01 1iu8A 206 5.12e+01 c.56.4.1 71436 2igd 61 5.12e+01 2igd d.15.7.1 37821 1wmhB 86 5.18e+01 1h7zA 194 5.18e+01 1qhvA b.21.1.1 60733 1uuyA 167 5.20e+01 c.57.1.1 108059 1giqA 413 5.29e+01 d.166.1.1,d.166.1.1 76224,76225 1tz9A 367 5.31e+01 c.1.15.6 107466 1aisA 182 5.32e+01 1ytbA d.129.1.1,d.129.1.1 41288,41289 1yb2A 275 5.32e+01 1vc1A 110 5.33e+01 c.13.2.1 108493 1kopA 223 5.34e+01 2cba b.74.1.1 27966 1i9gA 280 5.36e+01 c.66.1.13 62090 1m22A 503 5.39e+01 c.117.1.1 78464 1ualA 274 5.47e+01 c.116.1.4 88383 2gm6A 208 5.47e+01 1r3dA 264 5.54e+01 2fr1A 486 5.56e+01 2bhgA 209 5.57e+01 1w2iA 91 5.69e+01 d.58.10.1 109127 1e5mA 416 5.70e+01 1dd8A c.95.1.1,c.95.1.1 58973,58974 1vpkA 378 5.72e+01 1r9hA 135 5.77e+01 d.26.1.1 97260 1n5nA 180 5.78e+01 d.167.1.1 85336 1xtzA 264 5.79e+01 1z1yA 186 5.81e+01 1oz9A 150 5.85e+01 d.92.1.15 93808 1pfsA 78 5.86e+01 1pfsA b.40.4.7 25391 1e6wA 260 5.88e+01 1e6wA c.2.1.2 59326 1t71A 281 5.89e+01 2gi9A 56 5.89e+01 1ulyA 192 5.92e+01 1xc1A 309 5.92e+01 c.94.1.1 109543 1mhnA 59 5.94e+01 b.34.9.1 84964 1w8oA 601 5.97e+01 1i9zA 347 5.99e+01 1i9yA d.151.1.2 62102 1jdpA 441 6.00e+01 c.93.1.1 62906 2bneA 241 6.06e+01 2f06A 144 6.10e+01 1amuA 563 6.17e+01 1amuA e.23.1.1 43351 1k0mA 241 6.21e+01 a.45.1.1,c.47.1.5 67949,67950 1gca 309 6.22e+01 1gca c.93.1.1 35659 1rlmA 271 6.22e+01 1i19A 561 6.23e+01 1i19A d.58.32.3,d.145.1.1 61522,61523 1ywxA 102 6.24e+01 1zhvA 134 6.25e+01 1yj7A 171 6.31e+01 1wdjA 187 6.32e+01 1qksA 567 6.34e+01 1qksA a.3.1.2,b.70.2.1 15951,27710 1os8A 223 6.37e+01 b.47.1.1 93481 1sx5A 244 6.39e+01 c.52.1.2 99023 2b4yA 271 6.45e+01 1oj4A 283 6.49e+01 d.14.1.5,d.58.26.5 93083,93084 1hfoA 113 6.51e+01 d.80.1.3 61006 1h12A 405 6.51e+01 a.102.1.2 83447 1zxuA 217 6.52e+01 2bo9B 222 6.60e+01 1yemA 179 6.63e+01 1jgsA 138 6.73e+01 a.4.5.28 66683 1iwmA 186 6.79e+01 b.125.1.2 83758 1b6a 478 6.93e+01 1bn5 a.4.5.25,d.127.1.1 16223,41160 2gm5A 139 6.99e+01 1uv4A 293 7.03e+01 1xtmA 175 7.04e+01 2dkaA 544 7.07e+01 1ii7A 333 7.09e+01 1ii7A d.159.1.4 62415 1rwiA 270 7.12e+01 b.68.9.1 97987 1ye8A 178 7.12e+01 2ashA 381 7.13e+01 1z9vA 121 7.16e+01 1fjgK 129 7.18e+01 1fjfK c.55.4.1 33733 2gdzA 267 7.26e+01 1vp4A 425 7.29e+01 2ffyA 358 7.34e+01 2ci1A 275 7.34e+01 1h6tA 291 7.37e+01 b.1.18.15,c.10.2.1 65686,65687 1knqA 175 7.43e+01 c.37.1.17 72786 2aebA 322 7.45e+01 1rcqA 357 7.49e+01 b.49.2.2,c.1.6.1 104882,104883 1yzxA 226 7.50e+01 1rp0A 284 7.50e+01 1rz1A 161 7.51e+01 b.45.1.2 98124 1p4kA 295 7.52e+01 d.153.1.5 87772 1mkmA 249 7.54e+01 a.4.5.33,d.110.2.2 79242,79243 1jkeA 145 7.55e+01 c.110.1.1 66791 1v9sA 208 7.56e+01 1wosA 364 7.57e+01 b.44.2.1,d.250.1.1 109468,109469 1rypA 243 7.61e+01 1pmaA d.153.1.4 41932 1pmi 440 7.61e+01 1pmi b.82.1.3 28114 1zx5A 300 7.65e+01 1jc4A 148 7.70e+01 1jc4A d.32.1.4 62863 2gdnA 267 7.71e+01 1in0A 163 7.80e+01 d.58.49.1,d.58.49.1 83694,83695 1cbf 285 7.83e+01 1cbf c.90.1.1 35587 2dlbA 80 7.91e+01 1ecfA 504 7.93e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 1kktA 511 7.96e+01 a.102.2.1 68687 1bebA 162 7.99e+01 1bebA b.60.1.1 27115 1hjrA 158 8.03e+01 1hjrA c.55.3.6 33727 1xszA 356 8.05e+01 1regX 122 8.10e+01 1regX d.58.27.1 39406 1gxuA 91 8.12e+01 d.58.10.1 76378 1on0A 158 8.13e+01 d.108.1.1 87095 1vbwA 68 8.14e+01 1ywqA 200 8.17e+01 1fmcA 255 8.18e+01 1cydA c.2.1.2 29856 1xg0A 76 8.23e+01 1yoaA 159 8.24e+01 2dpmA 284 8.25e+01 2dpmA c.66.1.28 34246 2fexA 188 8.27e+01 1a7tA 232 8.28e+01 1a7tA d.157.1.1 42041 2bbeA 108 8.30e+01 1ri6A 343 8.30e+01 b.69.11.1 97503 1y55X 126 8.30e+01 1bdmA 327 8.35e+01 1bmdA c.2.1.5,d.162.1.1 30137,42104 1grj 158 8.38e+01 1grj a.2.1.1,d.26.1.2 15691,38433 1twiA 434 8.40e+01 b.49.2.3,c.1.6.1 107399,107400 1q1oA 98 8.42e+01 d.15.2.2 95596 1th0A 226 8.49e+01 d.3.1.7 106903 2fnuA 375 8.49e+01 1sdoA 203 8.50e+01 c.52.1.21 98809 1m4lA 307 8.52e+01 c.56.5.1 78604 1xknA 355 8.52e+01 1aba 87 8.56e+01 1aba c.47.1.1 32760 2fauA 341 8.56e+01 2h1rA 299 8.58e+01 2fh1A 344 8.61e+01 2czvC 120 8.62e+01 1j71A 334 8.64e+01 1eagA b.50.1.2 62669 1ydmA 187 8.65e+01 1jv1A 505 8.67e+01 c.68.1.5 71892 1ehiA 377 8.70e+01 1iow c.30.1.2,d.142.1.1 31716,41484 1xqwA 293 8.70e+01 1qs1A 462 8.74e+01 1qs1A d.166.1.1,d.166.1.1 42260,42261 1q2lA 939 8.78e+01 1fhgA 154 8.82e+01 1tlk b.1.1.4 21706 2bjuA 453 8.82e+01 1bueA 265 8.87e+01 1btl e.3.1.1 42727 1m6dA 214 8.88e+01 d.3.1.1 84849 1htrB 329 8.90e+01 1smrA 2bswA 146 8.97e+01 2g0cA 76 8.98e+01