# 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.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 1qzzA 374 4.17e-01 a.4.5.29,c.66.1.12 96719,96720 1neeA 138 7.01e-01 d.241.1.1,g.59.1.1 91841,91842 1v87A 114 7.45e-01 g.44.1.1 108422 1dx8A 70 7.96e-01 1rb9 g.41.5.1 45243 1weoA 93 1.34e+00 1qs2A 401 1.51e+00 1qs1A d.166.1.1,d.166.1.1 42268,42269 1u5kA 244 1.61e+00 2fokA 579 1.95e+00 2fokA a.4.5.12,a.4.5.12,a.4.5.12,c.52.1.12 16131,16132,16133,33323 1yk4A 52 2.29e+00 1k4jA 230 2.87e+00 d.108.1.3 72057 1kzfA 230 2.89e+00 d.108.1.3 73354 1bob 320 3.07e+00 1bob d.108.1.1 40816 1dl6A 58 3.50e+00 1dl6A g.41.3.1 45207 1rlyA 60 3.50e+00 g.41.3.1 104988 1jjrA 151 3.61e+00 a.140.2.1 66772 2aa1B 146 3.82e+00 1xreA 217 4.02e+00 1b2jA 54 5.30e+00 1rb9 g.41.5.1 45231 1pft 50 5.35e+00 1pft g.41.3.1 45206 1vq0A 302 5.36e+00 1iro 54 5.45e+00 1rb9 g.41.5.1 45223 1qs1A 462 5.62e+00 1qs1A d.166.1.1,d.166.1.1 42260,42261 2f4mA 295 5.93e+00 1aa6 715 6.20e+00 2napA b.52.2.2,c.81.1.1 26916,35324 1m4zA 238 6.43e+00 b.34.12.1 78630 2b5eA 504 7.22e+00 1fdi 715 7.23e+00 2napA b.52.2.2,c.81.1.1 26918,35326 1wgxA 73 7.86e+00 1ii2A 524 8.30e+00 c.91.1.1,c.109.1.1 66146,66147 4rxn 54 8.33e+00 1rb9 g.41.5.1 45226 5rxn 54 8.33e+00 1rb9 g.41.5.1 45225 1ykhA 108 9.11e+00 1kv9A 668 1.02e+01 a.3.1.6,b.70.1.1 73056,73057 1meyC 87 1.14e+01 2gliA k.12.1.1 46430 1j7xA 302 1.17e+01 c.14.1.2 66425 1iyxA 432 1.18e+01 c.1.11.1,d.54.1.1 83815,83816 1uz3A 102 1.26e+01 1cpcA 162 1.27e+01 1cpcA a.1.1.3 15643 1a6aB 187 1.34e+01 1iakB b.1.1.2,d.19.1.1 21616,38190 2fztA 79 1.35e+01 1rb9 53 1.36e+01 1rb9 g.41.5.1 45214 8rxnA 52 1.36e+01 1rb9 g.41.5.1 45215 1utuA 108 1.42e+01 1rdg 53 1.47e+01 1rb9 g.41.5.1 45221 1l2qA 458 1.49e+01 c.1.25.1 73510 1fdo 715 1.49e+01 2napA b.52.2.2,c.81.1.1 26917,35325 1nthA 458 1.50e+01 c.1.25.1 80730 1q7lB 88 1.51e+01 1yf3A 259 1.55e+01 1a8q 274 1.56e+01 1brt c.69.1.12 34702 2a8eA 220 1.70e+01 1bq9A 54 1.73e+01 1rb9 g.41.5.1 45238 1yhvA 297 1.76e+01 2a14A 263 1.76e+01 2g42A 79 1.77e+01 1q0sA 259 1.78e+01 c.66.1.28 95509 1bq8A 54 1.78e+01 1rb9 g.41.5.1 45237 1brfA 53 1.81e+01 1rb9 g.41.5.1 45236 1d8bA 81 1.83e+01 1d8bA a.60.8.1 18094 1p3jA 217 1.89e+01 c.37.1.1,g.41.2.1 94022,94023 1oqcA 125 1.93e+01 a.24.15.1 87264 1a8h 500 1.95e+01 1a8h a.27.1.1,c.26.1.1 16922,31589 1rh2F 165 1.96e+01 1rh2F a.26.1.3 16898 1w85A 368 1.98e+01 1bx2B 191 1.98e+01 1iakB b.1.1.2,d.19.1.1 21610,38184 1k7yA 577 2.07e+01 a.46.1.1,c.23.6.1,d.173.1.1 68272,68273,68274 1woyA 500 2.07e+01 1ffh 294 2.08e+01 1ng1 a.24.13.1,c.37.1.10 16960,32271 1adoA 363 2.14e+01 1fbaA c.1.10.1 29124 1jeqA 609 2.16e+01 1jeqA a.140.2.1,b.131.1.1,c.62.1.3 64748,90366,90367 2basA 431 2.18e+01 1zip 217 2.21e+01 1zin c.37.1.1,g.41.2.1 31916,45179 2ng1 293 2.21e+01 1ng1 a.24.13.1,c.37.1.10 16962,32273 2fflA 756 2.23e+01 1vhtA 218 2.29e+01 c.37.1.1 100700 1glv 303 2.30e+01 1gsa c.30.1.3,d.142.1.1 31721,41480 1msk 331 2.30e+01 1msk d.173.1.1 42495 1vp6A 138 2.31e+01 1vqqA 646 2.32e+01 1mwsA 646 2.34e+01 d.17.4.5,d.175.1.1,e.3.1.1 79592,79593,79594 1bncA 449 2.35e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28236,31643,41488 1zin 217 2.43e+01 1zin c.37.1.1,g.41.2.1 31915,45178 1gx1A 160 2.47e+01 d.79.5.1 70675 1lnsA 763 2.50e+01 a.40.2.1,b.18.1.13,c.69.1.21 78101,78102,78103 1b13A 54 2.52e+01 1rb9 g.41.5.1 45227 1dv1A 449 2.54e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28234,31641,41486 1wdjA 187 2.54e+01 1ezjA 115 2.71e+01 1ezjA h.1.14.1 45638 1hs6A 611 2.72e+01 1hs6A a.118.1.7,b.98.1.1,d.92.1.13 61233,61234,61235 1alu 186 2.83e+01 1alu a.26.1.1 16826 2czcA 334 2.87e+01 1aqdB 198 2.90e+01 1iakB b.1.1.2,d.19.1.1 21586,38160 2a2pA 129 2.92e+01 2b8wA 328 2.98e+01 1ash 150 2.99e+01 1ash a.1.1.2 15622 1dlhB 188 2.99e+01 1iakB b.1.1.2,d.19.1.1 21598,38172 1rdqE 350 3.00e+01 d.144.1.7 97314 1cvjB 190 3.09e+01 1cvjB d.58.7.1,d.58.7.1 39193,39194 1i4fB 100 3.09e+01 1agdB b.1.1.2 61689 1k5nB 100 3.09e+01 b.1.1.2 77268 1mwrA 646 3.10e+01 d.17.4.5,d.175.1.1,e.3.1.1 79586,79587,79588 1d5mB 192 3.11e+01 1iakB b.1.1.2,d.19.1.1 21618,38192 1cojA 212 3.14e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1zkeA 83 3.15e+01 1fqyA 269 3.19e+01 1fqyA f.19.1.1 43649 1mp1A 111 3.21e+01 a.188.1.1 91382 1sgwA 214 3.21e+01 c.37.1.12 105541 1jr8A 117 3.26e+01 a.24.15.1 67115 1g2fC 90 3.43e+01 k.12.1.1 60222 1fbaA 361 3.44e+01 1fbaA c.1.10.1 29120 1v6zA 228 3.45e+01 1j3mA 129 3.46e+01 d.129.7.1 103836 1d5nA 205 3.49e+01 1avmA a.2.11.1,d.44.1.1 15762,38687 1bncB 449 3.50e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28237,31644,41489 1ft9A 222 3.51e+01 1ft9A a.4.5.4,b.82.3.1 16107,28131 1pieA 419 3.52e+01 d.14.1.5,d.58.26.7 94706,94707 1ls1A 295 3.56e+01 a.24.13.1,c.37.1.10 78170,78171 1hsbB 99 3.59e+01 1agdB b.1.1.2 20737 1ee8A 266 3.65e+01 1ee8A a.156.1.2,b.113.1.1,g.39.1.8 75823,75824,75825 1h2bA 359 3.70e+01 b.35.1.2,c.2.1.1 90543,90544 1ieaB 228 3.70e+01 1iakB b.1.1.2,d.19.1.1 21632,38206 1kb0A 677 3.71e+01 a.3.1.6,b.70.1.1 68378,68379 2cc0A 195 3.71e+01 1usuA 260 3.73e+01 d.14.1.8 99885 1ald 363 3.76e+01 1fbaA c.1.10.1 29100 1mz4A 137 3.77e+01 a.3.1.1 91496 1z41A 338 3.79e+01 1agdB 99 3.80e+01 1agdB b.1.1.2 20742 1i0hA 205 3.83e+01 1avmA a.2.11.1,d.44.1.1 15760,38685 1ix9A 205 3.83e+01 a.2.11.1,d.44.1.1 76899,76900 1fpqA 372 3.84e+01 1fpqA a.4.5.29,c.66.1.12 59947,59948 1zaiA 363 3.88e+01 1fp0A 88 3.88e+01 1fp0A g.50.1.2 45361 1nnhA 294 4.01e+01 d.104.1.1 92005 1dsvA 31 4.07e+01 1dsvA g.40.1.1 45174 1f62A 51 4.07e+01 1f62A g.50.1.2 45360 1h5wA 309 4.12e+01 e.27.1.1 65635 1q8uA 350 4.13e+01 d.144.1.7 96230 1wphA 201 4.14e+01 1duzB 100 4.14e+01 1agdB b.1.1.2 20671 1nm2A 317 4.26e+01 c.19.1.1,d.58.23.1 80654,80655 1ub4A 110 4.28e+01 b.34.6.2 88399 1lv7A 257 4.31e+01 c.37.1.20 78232 1jdlA 121 4.36e+01 a.3.1.1 66557 1far 52 4.37e+01 1far g.49.1.1 45351 1iznB 277 4.43e+01 e.43.1.2 83848 2avnA 260 4.48e+01 1bgeB 175 4.57e+01 1bgc a.26.1.1 16824 1yxmA 303 4.62e+01 1fokA 568 4.66e+01 2fokA a.4.5.12,a.4.5.12,a.4.5.12,c.52.1.12 16137,16138,16139,33325 2d69A 430 4.82e+01 1cdkA 350 4.84e+01 1cdkA d.144.1.7 41620 1l1oC 181 4.87e+01 b.40.4.3 73480 1jqlB 140 4.88e+01 c.37.1.20 63234 1nal3 297 5.05e+01 1nal3 1l7vC 249 5.09e+01 c.37.1.12 73674 2cwxA 430 5.11e+01 1bor 56 5.24e+01 1bor g.44.1.1 45324 1n40A 396 5.27e+01 a.104.1.1 79977 1fp1D 372 5.33e+01 1fpqA a.4.5.29,c.66.1.12 59939,59940 1ufbA 127 5.35e+01 a.24.16.3 99331 2ex4A 241 5.37e+01 1p3qQ 54 5.42e+01 a.5.2.4 87748 1nal1 297 5.45e+01 1nal3 1uesA 191 5.52e+01 a.2.11.1,d.44.1.1 107798,107799 1faq 52 5.55e+01 1far g.49.1.1 45352 1ng1 294 5.59e+01 1ng1 a.24.13.1,c.37.1.10 16961,32272 1ed1A 135 5.60e+01 1hiwA a.61.1.1 18130 1spgB 147 5.61e+01 1cg5B a.1.1.2 15588 1xh9A 350 5.70e+01 1apxA 249 5.72e+01 1ryc a.93.1.1 18669 1ornA 226 5.73e+01 a.96.1.1 87342 2gsaA 432 5.83e+01 2gsaA c.67.1.4 34446 1ao7B 100 5.84e+01 1agdB b.1.1.2 20697 1jpnA 296 5.86e+01 a.24.13.1,c.37.1.10 67039,67040 1enwA 114 5.98e+01 1enwA a.5.4.1 16291 1rmd 116 5.99e+01 1rmd g.37.1.1,g.44.1.1 45025,45322 1fz1C 389 6.03e+01 1mtyB a.25.1.2 16746 1nrjA 158 6.04e+01 d.110.4.4 86124 1apmE 350 6.07e+01 1cdkA d.144.1.7 41628 1u7eB 154 6.15e+01 1cx4A 305 6.20e+01 b.82.3.2,b.82.3.2 59099,59100 1vr5A 547 6.20e+01 1n9lA 109 6.44e+01 d.110.3.6 85468 1ap6A 198 6.46e+01 1avmA a.2.11.1,d.44.1.1 15746,38705 1jraA 117 6.50e+01 a.24.15.1 67117 1dsqA 21 6.51e+01 g.40.1.1 45173 1gv3A 248 6.59e+01 a.2.11.1,d.44.1.1 70585,70586 2ahyA 110 6.70e+01 1gpmA 525 6.70e+01 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 2d2mD 145 6.81e+01 1mtyB 384 6.84e+01 1mtyB a.25.1.2 16740 1bgeA 175 6.85e+01 1bgc a.26.1.1 16823 1mmoB 384 6.87e+01 1mtyB a.25.1.2 16768 1nbwA 607 6.88e+01 c.8.6.1,c.55.1.6,c.55.1.6 80393,80394,80395 1pl4A 198 6.89e+01 a.2.11.1,d.44.1.1 94854,94855 1uj8A 77 6.92e+01 1x1fA 149 6.93e+01 2ctdA 96 7.01e+01 1fk9A 543 7.03e+01 1rthA c.55.3.1,e.8.1.2 33607,43080 1qwrA 319 7.06e+01 b.82.1.3 96491 1dk5A 322 7.11e+01 1dk5A a.65.1.1 18192 1hy0A 466 7.13e+01 1auwA a.127.1.1 61392 1zyiA 171 7.18e+01 1auwA 468 7.24e+01 1auwA a.127.1.1 19416 1abmA 198 7.26e+01 1avmA 1vfgA 390 7.27e+01 a.173.1.1,d.218.1.4 108570,108571 1umgA 362 7.28e+01 d.280.1.1 107956 1ejdA 419 7.30e+01 1uae d.68.2.2 39576 1g291 372 7.33e+01 1g291 1fuoA 467 7.41e+01 1furA a.127.1.1 19411 1sqc 631 7.44e+01 2sqcA a.102.4.2,a.102.4.2 18858,18859 1u3eM 174 7.47e+01 d.4.1.3,d.285.1.1 107640,107641 3pvaA 335 7.49e+01 3pvaA d.153.1.3 41854 6rxn 46 7.54e+01 1rb9 g.41.5.1 45222 1yua 122 7.59e+01 1yua g.41.3.3,g.41.3.3 45210,45211 1te6A 439 7.62e+01 c.1.11.1,d.54.1.1 106797,106798 1n0nA 199 7.63e+01 a.2.11.1,d.44.1.1 79750,79751 1a1iA 90 7.65e+01 1aayA g.37.1.1,g.37.1.1,g.37.1.1 44998,44999,45000 1ut9A 609 7.65e+01 a.102.1.2,b.1.18.2 99912,99913 1cxzB 86 7.71e+01 1cxzB a.2.6.1 15705 1uae 419 7.74e+01 1uae d.68.2.2 39574 1af8 86 7.75e+01 2af8 a.28.1.1 16932 1wusA 180 7.79e+01 1t3qB 788 7.88e+01 d.41.1.1,d.133.1.1 106369,106370 1m56D 51 7.88e+01 f.23.8.1 74475 1lvaA 258 8.11e+01 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 1uvqB 198 8.22e+01 b.1.1.2,d.19.1.1 100064,100065 1pls 113 8.30e+01 1pls b.55.1.1 26965 1l8aA 886 8.30e+01 c.36.1.10,c.36.1.6,c.48.1.1 73677,73678,73679 1aosA 464 8.31e+01 1auwA a.127.1.1 19414 2aat 396 8.31e+01 1ajsA c.67.1.1 34348 1n9dA 199 8.34e+01 a.26.1.1 85464 1y89A 238 8.36e+01 1mzgA 146 8.45e+01 d.224.1.1 79696 1a2n 419 8.64e+01 1uae d.68.2.2 39575 1kfiA 572 8.72e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68555,68556,68557,68558 1x6oA 174 8.77e+01 b.34.5.2,b.40.4.5 109493,109494 1uuyA 167 8.86e+01 c.57.1.1 108059 1x38A 602 8.90e+01 1vqoZ 83 8.90e+01 1kjvB 100 8.94e+01 b.1.1.2 77423 1sg7A 96 8.97e+01 1cmkE 350 9.00e+01 1cdkA d.144.1.7 41623