# List of top-scoring protein chains for t04-100-30-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 1jtgB 165 9.13e-14 d.98.1.1 67267 2g2uB 165 9.13e-14 d.98.1.1 134541 1j7lA 264 6.28e-02 d.144.1.6 62697 1h6vA 499 1.07e-01 3grs c.3.1.5,c.3.1.5,d.87.1.1 60693,60694,60695 1ta8A 332 2.15e-01 d.142.2.2 112375 1jenA 267 2.75e-01 1jenA 2bkkA 264 2.93e-01 1wdvA 152 3.13e-01 d.116.1.1 114539 1jl0A 334 3.24e-01 1jenA d.156.1.1 63155 2fikA 287 3.75e-01 b.1.1.2,d.19.1.1 133524,133525 1knwA 425 6.90e-01 b.49.2.3,c.1.6.1 90969,90970 2r78A 117 7.59e-01 1qksA 567 8.60e-01 1qksA a.3.1.2,b.70.2.1 15951,27710 2r9zA 463 1.06e+00 1b04A 318 1.26e+00 1b04A d.142.2.2 41579 2h36X 112 1.48e+00 2iorA 235 1.61e+00 1wy2A 351 1.74e+00 1on3A 523 1.88e+00 c.14.1.4,c.14.1.4 87107,87108 2gfaA 119 1.91e+00 b.34.9.1,b.34.9.1 135089,135090 2qqrA 118 2.04e+00 2gu1A 361 2.09e+00 2akrA 285 2.21e+00 b.1.1.2,d.19.1.1 126931,126932 2b0vA 153 2.25e+00 d.113.1.1 127650 1hq0A 295 2.44e+00 1hzgA d.194.1.1 61122 1p7gA 222 2.64e+00 a.2.11.1,d.44.1.1 94223,94224 1hruA 188 2.76e+00 1hruA d.115.1.1 40926 1j7jA 178 3.27e+00 c.61.1.1 84131 1poiA 317 3.38e+00 1poiA c.124.1.2 34153 2j3mA 572 3.45e+00 1zkiA 133 3.46e+00 d.38.1.5 125199 2v6oA 596 3.51e+00 1dkiA 371 3.80e+00 1dkiA d.3.1.1 37090 2uu8A 237 4.00e+00 1nls 237 4.18e+00 1nls 2gqpA 236 4.24e+00 d.122.1.1 135513 1zghA 260 4.52e+00 b.46.1.1,c.65.1.1 125028,125029 2yvyA 278 4.64e+00 1nox 205 4.71e+00 1nox 1noxA 205 4.71e+00 d.90.1.1 40242 2j4jA 226 4.73e+00 1vkiA 181 4.75e+00 d.116.1.1 108664 1w61A 414 5.38e+00 2iskA 230 5.42e+00 1lfpA 249 5.83e+00 e.39.1.1 73885 1xxqA 161 5.92e+00 1konA 249 6.04e+00 e.39.1.1 72823 2reiA 318 6.42e+00 2g09A 297 6.42e+00 2ia1A 178 6.62e+00 2afbA 351 6.96e+00 c.72.1.1 126674 3c96A 415 7.05e+00 1fo0A 116 7.16e+00 1tvdA b.1.1.1 20610 2pebA 122 7.32e+00 1tueB 218 7.32e+00 b.91.1.1 107324 1pv9A 348 7.46e+00 c.55.2.1,d.127.1.1 95157,95158 1w7jB 151 7.80e+00 a.39.1.5 120690 2boyA 254 8.06e+00 2z2nA 299 8.10e+00 2qolA 376 8.17e+00 1fxlA 167 8.21e+00 1b7fA d.58.7.1,d.58.7.1 39183,39184 1h8dH 260 8.47e+00 5ptp 1xoyA 161 8.50e+00 b.18.1.26 115718 1j3wA 163 8.54e+00 d.110.7.1 90833 1stzA 338 8.70e+00 a.4.5.51,d.110.2.3 106009,106010 2c60A 111 9.22e+00 d.15.2.2 129966 3bmzA 199 9.42e+00 1c3pA 375 9.47e+00 1c3pA c.42.1.2 32606 1ucrA 78 9.65e+00 a.4.5.45 99188 1suuA 312 9.69e+00 b.68.10.1 99006 1h65A 270 9.79e+00 c.37.1.8 65640 1gqvA 135 9.88e+00 d.5.1.1 70376 2pvfA 334 9.93e+00 3b2tA 311 1.10e+01 2atfA 200 1.10e+01 b.82.1.19 127290 2b5hA 200 1.10e+01 b.82.1.19 127894 1pixA 587 1.14e+01 c.14.1.4,c.14.1.4 118578,118579 2fug7 129 1.16e+01 1bywA 110 1.19e+01 1bywA d.110.3.6 40912 1gg1A 350 1.20e+01 1qr7A c.1.10.4 29187 1n8fA 350 1.23e+01 c.1.10.4 85397 1i1nA 226 1.25e+01 c.66.1.7 71102 2ff7A 247 1.26e+01 c.37.1.12 133377 2r6fA 972 1.27e+01 1ogpA 393 1.31e+01 b.1.18.6,d.176.1.1 92927,92928 1qqhA 144 1.32e+01 1dtoA b.91.1.1 28404 2bduA 297 1.32e+01 2pmkA 243 1.33e+01 1vqoT 120 1.38e+01 b.34.5.1 120381 2b9wA 424 1.38e+01 1hfuA 503 1.39e+01 b.6.1.3,b.6.1.3,b.6.1.3 65827,65828,65829 1h7sA 365 1.48e+01 d.14.1.3,d.122.1.2 65705,65706 2r01A 210 1.48e+01 2amyA 246 1.65e+01 c.108.1.10 127026 1txkA 498 1.66e+01 b.1.18.2,b.30.5.9 107425,107426 2z1aA 552 1.70e+01 1jj2S 119 1.71e+01 1ffkQ b.34.5.1 63104 1lam 484 1.73e+01 1lam 1lamA 484 1.73e+01 c.50.1.1,c.56.5.3 33166,33829 1grx 85 1.73e+01 1kte 1g0oA 283 1.78e+01 1ybvA c.2.1.2 60181 2qe8A 343 1.80e+01 2retB 175 1.81e+01 1u0kA 288 1.86e+01 d.21.1.2,d.21.1.2 107547,107548 1m7xA 617 1.88e+01 b.1.18.2,b.71.1.1,c.1.8.1 78749,78750,78751 2va8A 715 1.92e+01 2bpa2 175 2.00e+01 2bpa2 3bemA 218 2.00e+01 1n9lA 109 2.03e+01 d.110.3.6 85468 2dekA 265 2.12e+01 c.90.1.1 131430 2p9wA 334 2.13e+01 1v5rA 97 2.13e+01 d.82.4.1 119854 1gweA 503 2.20e+01 e.5.1.1 70667 2fhqA 141 2.20e+01 b.45.1.1 133497 1hbzA 498 2.22e+01 1cf9A e.5.1.1 60937 2ai4A 119 2.28e+01 b.6.1.7 126816 2a6zA 222 2.29e+01 b.29.1.13 126319 1u6lA 149 2.30e+01 d.32.1.7 113067 2c5uA 375 2.34e+01 2azwA 148 2.34e+01 d.113.1.1 127615 1yoxA 250 2.35e+01 b.82.5.2 123789 2bf6A 449 2.43e+01 2ie7A 318 2.43e+01 a.65.1.1 137293 1e1oA 504 2.48e+01 1lylA b.40.4.1,d.104.1.1 25258,40714 1w1kA 560 2.50e+01 d.58.32.1,d.145.1.1 109059,109060 1d3bA 75 2.55e+01 1d3bA b.38.1.1 24798 2g5xA 234 2.56e+01 3biaX 116 2.58e+01 1vkpA 383 2.59e+01 d.126.1.6 108686 2ip2A 334 2.63e+01 2gysA 419 2.67e+01 b.1.2.1,b.1.2.1,b.1.2.1,b.1.2.1 135865,135866,135867,135868 2oajA 902 2.67e+01 2z6rA 265 2.72e+01 2q3uA 383 2.73e+01 d.126.1.6 139809 3c4aA 381 2.78e+01 2ouxA 286 2.79e+01 1es6A 296 2.83e+01 1es6A b.31.1.1,b.31.1.1 83048,83049 2f7tA 227 2.88e+01 2brxA 244 2.89e+01 c.73.1.3 129028 2p90A 319 2.94e+01 1p3jA 217 2.97e+01 c.37.1.1,g.41.2.1 94022,94023 1cojA 212 2.99e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 2pqvA 154 3.08e+01 1mzbA 136 3.09e+01 a.4.5.42 91497 1a8rA 221 3.09e+01 1a8rA d.96.1.1 40587 2eq8C 40 3.10e+01 2j04B 524 3.14e+01 1eu3A 210 3.17e+01 1an8 b.40.2.2,d.15.6.1 25206,37795 1pea 385 3.17e+01 1pea 1peaA 385 3.17e+01 c.93.1.1 35662 1lylA 504 3.27e+01 1lylA b.40.4.1,d.104.1.1 25261,40717 2ch4A 320 3.28e+01 b.40.7.1,d.122.1.3 130447,130448 1vz0A 230 3.29e+01 a.4.14.1,d.268.1.1 108929,108930 2ghsA 326 3.33e+01 b.68.6.1 135209 1zh8A 340 3.39e+01 c.2.1.3,d.81.1.5 125077,125078 1f42A 306 3.40e+01 1f42A b.1.1.4,b.1.2.1,b.1.2.1 59636,59637,59638 2cz9A 350 3.42e+01 2choA 716 3.55e+01 a.246.1.1,c.1.8.10,d.92.2.3 130479,130480,130481 2dejA 350 3.56e+01 1bolA 222 3.56e+01 1bolA d.124.1.1 41120 1gotB 340 3.61e+01 1tbgA b.69.4.1 27648 2bbvA 363 3.61e+01 2bbvA b.121.4.4 23323 1r6jA 82 3.62e+01 b.36.1.1 97151 1sfp 114 3.64e+01 1sfp 1sfpA 114 3.64e+01 b.23.1.1 23895 2a4xA 138 3.69e+01 d.32.1.2 126166 1gt6A 269 3.74e+01 c.69.1.17 76342 1tu5A 746 3.79e+01 2ebbA 101 3.84e+01 1tk1A 260 3.88e+01 d.248.1.1 107066 2a2cA 478 3.89e+01 1y56A 493 3.91e+01 1uohA 226 3.92e+01 d.211.1.1 99690 1a41 234 3.93e+01 1a41 1a41A 234 3.93e+01 d.163.1.2 42174 1xr4A 509 3.95e+01 c.124.1.2,c.124.1.2 115860,115861 1prxA 224 4.00e+01 1prxA c.47.1.10 33076 2vokA 188 4.04e+01 1a65A 504 4.05e+01 1a65A b.6.1.3,b.6.1.3,b.6.1.3 23148,23149,23150 2q6kA 283 4.07e+01 1xwvA 129 4.08e+01 b.1.18.7 116134 1vr5A 547 4.08e+01 c.94.1.1 120437 1keyA 235 4.10e+01 a.118.16.1 72389 1pwaA 162 4.14e+01 b.42.1.1 95211 1o54A 277 4.16e+01 c.66.1.13 92482 2gopA 347 4.17e+01 1a9xA 1058 4.19e+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 2nxbA 123 4.21e+01 3bioA 304 4.31e+01 1hlgA 371 4.42e+01 1hlgA c.69.1.6 34656 1oe8A 211 4.42e+01 a.45.1.1,c.47.1.5 86905,86906 1rzmA 338 4.50e+01 c.1.10.4 105137 1u59A 287 4.54e+01 d.144.1.7 107681 1sv6A 269 4.54e+01 d.177.1.1 106043 1cs0A 1073 4.57e+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 2ab5A 269 4.58e+01 1lvwA 295 4.58e+01 c.68.1.6 84723 1o59A 355 4.59e+01 b.18.1.22,b.18.1.22 92495,92496 1msk 331 4.60e+01 1msk 1mskA 331 4.60e+01 d.173.1.1 42495 2j5aA 110 4.62e+01 1bsmA 201 4.63e+01 1avmA a.2.11.1,d.44.1.1 15780,38743 2ns2A 242 4.73e+01 2olnA 397 4.84e+01 1whbA 157 4.89e+01 c.46.1.4 114639 3bgyA 237 4.92e+01 2joyA 96 4.93e+01 1wgoA 123 4.97e+01 b.1.3.1 114618 1rwsA 77 4.98e+01 d.15.3.2 97991 1gp6A 356 4.98e+01 b.82.2.1 65441 1r9cA 139 5.01e+01 d.32.1.2 97255 1i60A 278 5.09e+01 c.1.15.4 71118 1p22A 435 5.12e+01 a.158.1.1,b.69.4.1 87715,87716 2gwfA 157 5.12e+01 c.46.1.4 135802 1gpiA 431 5.13e+01 b.29.1.10 65450 1vr6A 350 5.14e+01 c.1.10.4 120439 2eu8A 216 5.21e+01 2gu3A 136 5.24e+01 1ecfA 504 5.27e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 1vrmA 325 5.29e+01 d.96.2.1 120472 2f9dA 125 5.33e+01 d.58.7.1 133159 1qdlA 422 5.44e+01 1qdlA d.161.1.1 42088 1e0cA 271 5.47e+01 1e0cA c.46.1.2,c.46.1.2 32717,32718 1txnA 328 5.48e+01 d.248.1.1 112779 2z0tA 109 5.48e+01 1ka1A 357 5.50e+01 e.7.1.1 68369 1h80A 464 5.56e+01 b.80.1.8 65714 1j1jA 240 5.57e+01 a.118.16.1 90762 1pl4A 198 5.57e+01 a.2.11.1,d.44.1.1 94854,94855 1t5hX 504 5.66e+01 e.23.1.1 106449 1vzyA 291 5.66e+01 d.193.1.1,g.81.1.1 114042,114043 1kllA 130 5.68e+01 d.32.1.2 72720 2odiA 238 5.68e+01 1qfoA 119 5.76e+01 1qfoA b.1.1.1 19708 2acaA 189 5.80e+01 d.63.1.2 126545 1wzcA 249 5.82e+01 c.108.1.10 121491 1xewX 182 5.83e+01 c.37.1.12 115235 1vjnA 220 5.86e+01 d.157.1.4 100825 2ouaA 188 5.86e+01 1jetA 517 5.87e+01 1jevA c.94.1.1 35718 1yduA 170 5.88e+01 b.162.1.1 123003 1avmA 201 5.92e+01 1avmA a.2.11.1,d.44.1.1 15782,38745 1wd5A 208 5.92e+01 c.61.1.1 114524 2r2dA 276 5.94e+01 2dxaA 166 5.98e+01 1xxgA 233 6.01e+01 1n0nA 199 6.03e+01 a.2.11.1,d.44.1.1 79750,79751 1rqlA 267 6.05e+01 c.108.1.3 97750 1r9jA 673 6.05e+01 c.36.1.6,c.36.1.10,c.48.1.1 111722,111723,111724 1szhA 161 6.06e+01 a.226.1.1 106157 1jpaA 312 6.09e+01 d.144.1.7 67011 1qloA 34 6.11e+01 1qloA j.35.1.1 46281 2gwdA 449 6.13e+01 1mjc 69 6.15e+01 1mjc 1mjcA 69 6.15e+01 b.40.4.5 25319 1mr3F 181 6.16e+01 c.37.1.8 79422 1swvA 267 6.19e+01 c.108.1.3 112134 1oi6A 205 6.20e+01 b.82.1.1 103940 1tib 269 6.28e+01 3tgl 1tibA 269 6.28e+01 c.69.1.17 34738 1u04A 771 6.32e+01 b.34.14.1,c.55.3.10 107539,107540 1vjfA 180 6.32e+01 d.116.1.1 100809 1dlcA 584 6.38e+01 b.18.1.3,b.77.2.1,f.1.3.1 23719,27976,43391 1tuaA 191 6.40e+01 d.51.1.1,d.51.1.1 107321,107322 1wjxA 122 6.41e+01 b.111.1.1 114716 2dy0A 190 6.47e+01 2qxfA 482 6.52e+01 1i58A 189 6.56e+01 1b3qA d.122.1.3 61773 2pkfA 334 6.58e+01 1dv1A 449 6.59e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28234,31641,41486 1f89A 291 6.60e+01 d.160.1.1 64988 1qgxA 357 6.63e+01 1qgxA e.7.1.1 42973 2eqaA 352 6.65e+01 2gx5A 170 6.66e+01 1ykiA 217 6.69e+01 d.90.1.1 123520 1x3zA 335 6.75e+01 d.3.1.4 121673 2gc7A 386 6.75e+01 b.69.2.1 134954 1m6iA 493 6.80e+01 c.3.1.5,c.3.1.5,d.87.1.1 74533,74534,74535 2dpfA 115 6.85e+01 1ywnA 316 6.91e+01 d.144.1.7 124161 2o7iA 592 6.92e+01 1gq6A 313 6.93e+01 c.42.1.1 70341 1r75A 141 6.97e+01 b.134.1.1 97189 1ofzA 312 6.97e+01 b.68.8.1 86978 2ipxA 233 6.98e+01 1yb3A 175 7.00e+01 d.296.1.2 122869 2i9dA 217 7.01e+01 1q0sA 259 7.04e+01 c.66.1.28 95509 1ekfA 365 7.08e+01 1ekfA e.17.1.1 59445 1fxxA 482 7.13e+01 1fxxA c.55.3.5 33726 1qy5A 269 7.19e+01 d.122.1.1 96573 2hf0A 316 7.20e+01 2jw5A 106 7.21e+01 1w96A 554 7.24e+01 b.84.2.1,c.30.1.1,d.142.1.2 114397,114398,114399 1xv5A 401 7.26e+01 2oqeA 660 7.28e+01 b.30.2.1,d.17.2.1,d.17.2.1 139222,139223,139224 1vkmA 297 7.36e+01 c.138.1.1 108670 1ubkL 534 7.41e+01 e.18.1.1 88422 3cq9A 227 7.43e+01 1uebA 184 7.45e+01 b.34.5.2,b.40.4.5,b.40.4.5 107782,107783,107784 2bcjB 340 7.47e+01 b.69.4.1 128289 1tuhA 156 7.47e+01 d.17.4.11 107345 1kolA 398 7.52e+01 b.35.1.2,c.2.1.1 77474,77475 1wuiL 534 7.53e+01 e.18.1.1 121289 1fjrA 195 7.64e+01 1fjrA b.102.1.1 59855 1lmb3 92 7.73e+01 1lmb3 1whtB 153 7.73e+01 1whtB 2hsiA 282 7.80e+01 1qnaA 200 7.82e+01 1ytbA d.129.1.1,d.129.1.1 41226,41227 1vhqA 232 7.83e+01 c.23.16.2 100696 1h2rL 534 7.84e+01 1h2rL e.18.1.1 43298 1v30A 124 7.89e+01 d.269.1.1 113496 1oqcA 125 7.91e+01 a.24.15.1 87264 2j69A 695 7.92e+01 2aexA 346 7.93e+01 2bh0A 208 7.93e+01 1fmb 104 7.96e+01 1fmb 1fmbA 104 7.96e+01 b.50.1.1 26777