# List of top-scoring protein chains for t06-100-40-40-str2+CB_burial_14_7-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 1y14B 171 1.45e-02 2d9rA 104 2.43e-01 2cwpA 112 2.95e-01 1zkdA 387 3.17e-01 1k3yA 221 3.44e-01 a.45.1.1,c.47.1.5 77245,77246 2h6lA 146 4.11e-01 2gfaA 119 5.77e-01 2fwkA 121 6.08e-01 1dbhA 354 7.84e-01 1awe a.87.1.1,b.55.1.1 18514,26967 2gu2A 312 8.05e-01 1fr3A 67 1.07e+00 1fr3A b.40.6.1 25436 1c9oA 66 1.14e+00 1mjc b.40.4.5 25325 1vf1A 229 1.42e+00 1yfuA 174 1.44e+00 1kq1A 77 1.50e+00 b.38.1.2 72848 1bia 321 1.59e+00 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1dj7B 75 1.82e+00 1dj7B b.34.4.3 24598 1y96B 85 1.85e+00 1o5uA 101 2.02e+00 b.82.1.8 92518 1cjwA 166 2.16e+00 1cjwA d.108.1.1 40818 1z85A 234 2.18e+00 2cu3A 64 2.23e+00 2fe7A 166 2.27e+00 1zybA 232 2.47e+00 2fb7A 95 2.83e+00 1z4eA 153 2.87e+00 1m0dA 138 3.03e+00 c.52.1.17 74354 1b8aA 438 3.23e+00 1b8aA b.40.4.1,d.104.1.1 25244,40765 1l2mA 118 3.27e+00 d.89.1.4 77657 1u1tA 82 3.29e+00 1ecsA 126 3.42e+00 1ecsA d.32.1.2 59407 1u1sA 82 3.85e+00 1wi5A 119 4.03e+00 1y9qA 192 4.26e+00 2cw9A 194 4.33e+00 1yavA 159 4.57e+00 1v7pB 128 4.70e+00 d.169.1.1 108407 1avyA 74 4.80e+00 1avyB h.1.17.1 45656 1yb3A 175 4.86e+00 1k0iA 394 5.35e+00 c.3.1.2,d.16.1.2 67942,67943 1mvfD 82 5.38e+00 b.129.1.1 85143 1ykjA 394 5.40e+00 1ne2A 200 5.73e+00 c.66.1.32 85586 2ch9A 131 5.75e+00 1vr9A 213 5.77e+00 1h9mA 145 5.83e+00 1h9jA b.40.6.2,b.40.6.2 60833,60834 1h75A 81 6.02e+00 1h75A c.47.1.1 60716 1wzoA 246 6.16e+00 1khoA 370 6.27e+00 a.124.1.1,b.12.1.3 72489,72490 1ibyA 112 6.34e+00 1ibzA b.6.1.4 62233 1lba 146 6.55e+00 1lba d.118.1.1 41062 1lvoA 302 6.99e+00 b.47.1.4 74284 1s5aA 150 7.01e+00 d.17.4.10 98525 1e4cP 215 7.41e+00 2fua c.74.1.1 34969 2gwnA 452 7.71e+00 1i24A 404 7.96e+00 c.2.1.2 83663 1rutX 188 8.00e+00 1ne9A 335 8.02e+00 d.108.1.4,d.108.1.4 91839,91840 1wraA 308 8.25e+00 1x47A 98 8.34e+00 1a7tA 232 8.41e+00 1a7tA d.157.1.1 42041 1y9wA 140 8.73e+00 2gokA 429 8.98e+00 2bpsA 81 9.19e+00 2dg5B 190 9.38e+00 1ihjA 98 9.77e+00 1pdr b.36.1.1 62382 2g3aA 152 9.93e+00 2f4pA 147 1.00e+01 1q6hA 224 1.00e+01 d.26.1.1 95975 2arcA 164 1.02e+01 2arcA b.82.4.1 28148 1a62 130 1.05e+01 1a62 a.140.3.1,b.40.4.5 64708,64709 1g2iA 166 1.06e+01 1g2iA c.23.16.2 31438 2aj6A 159 1.06e+01 1g291 372 1.06e+01 1g291 1whsB 153 1.07e+01 1whtB 1zud2 66 1.08e+01 2b95A 106 1.10e+01 1b9mA 265 1.18e+01 1b9mA a.4.5.8,b.40.6.2,b.40.6.2 16118,58938,58939 1kqqA 139 1.21e+01 a.4.3.1 72885 1doi 128 1.23e+01 1awd d.15.4.1 37676 1ex7A 186 1.24e+01 1gky c.37.1.1 59537 1bxvA 91 1.28e+01 1aac b.6.1.1 22875 1ss4A 153 1.30e+01 d.32.1.6 105976 1d3bA 75 1.33e+01 1d3bA b.38.1.1 24798 1dqzA 280 1.34e+01 1dqyA c.69.1.3 34638 1f35A 162 1.34e+01 1f35A b.94.1.1 59628 2azeB 106 1.34e+01 1ri9A 102 1.37e+01 b.34.2.1 97506 1te0A 318 1.40e+01 1x6mA 196 1.41e+01 1go3E 187 1.41e+01 b.40.4.5,d.230.1.1 83054,83055 1q6uA 245 1.47e+01 d.26.1.1 95998 1squA 155 1.50e+01 d.252.1.1 98971 1vkkA 154 1.50e+01 d.109.1.2 108669 1qwrA 319 1.50e+01 b.82.1.3 96491 1k3bA 119 1.51e+01 b.61.5.1 72016 1qqrA 138 1.51e+01 1bmlC d.15.5.1 37721 2d93A 134 1.55e+01 1zt3A 80 1.55e+01 1zx8A 136 1.56e+01 1uyrA 737 1.58e+01 c.14.1.4,c.14.1.4 100188,100189 1j1lA 290 1.58e+01 b.82.1.12 90766 1vie 62 1.59e+01 1vie b.34.4.1 24592 1fxxA 482 1.62e+01 1fxxA c.55.3.5 33726 1vkbA 161 1.65e+01 d.269.1.1 108643 1p4kA 295 1.82e+01 d.153.1.5 87772 1widA 130 1.85e+01 1y8xB 98 1.92e+01 1owfB 94 1.95e+01 a.55.1.1 87488 2bpa1 426 1.96e+01 2bpa1 1kwiA 101 1.98e+01 d.17.1.3 77564 1orc 71 2.03e+01 1orc a.35.1.2 17054 2gjgA 248 2.03e+01 1ew0A 130 2.03e+01 1drmA d.110.3.2 40905 1txdA 385 2.04e+01 a.87.1.1,b.55.1.1 107422,107423 1jv1A 505 2.05e+01 c.68.1.5 71892 2bayA 61 2.05e+01 1xxqA 161 2.05e+01 1s98A 107 2.09e+01 b.124.1.1 105377 2gzvA 114 2.12e+01 1qavA 90 2.12e+01 1qauA b.36.1.1 24777 1lkoA 191 2.13e+01 a.25.1.1,g.41.5.1 78063,78064 1s4iA 175 2.14e+01 1zvtA 256 2.15e+01 2bcgG 453 2.16e+01 1vk1A 242 2.17e+01 d.268.1.2 108634 1g6gA 127 2.18e+01 1g6gA b.26.1.2 23916 1u3eM 174 2.24e+01 d.4.1.3,d.285.1.1 107640,107641 1tyjA 170 2.24e+01 1fl0A 171 2.26e+01 1eujA b.40.4.4 25315 1kzlA 208 2.27e+01 b.43.4.3,b.43.4.3 77635,77636 1pbjA 125 2.28e+01 d.37.1.1,d.37.1.1 94414,94415 1vr0A 247 2.31e+01 1zd7A 159 2.32e+01 1d02A 202 2.35e+01 1d02A c.52.1.8 33313 1mgqA 83 2.39e+01 b.38.1.1 79099 1gky 187 2.39e+01 1gky c.37.1.1 31839 1cdcA 99 2.40e+01 1cdcA b.1.1.1 19746 2fcfA 103 2.41e+01 1l1qA 186 2.42e+01 c.61.1.1 77653 1fwxA 595 2.45e+01 b.6.1.4,b.69.3.1 60069,60070 1c3mA 147 2.48e+01 1jotA b.77.3.1 27983 1qznA 173 2.50e+01 b.2.2.2 104669 1i78A 297 2.52e+01 f.4.4.1 66046 2arhA 203 2.55e+01 1ca1 370 2.56e+01 1ca1 a.124.1.1,b.12.1.3 19340,23648 1d5tA 433 2.59e+01 1gnd c.3.1.3,d.16.1.6 30422,37986 1adt 356 2.66e+01 1anv a.54.1.1,g.51.1.1,g.51.1.1 17887,45362,45368 2bwnA 401 2.68e+01 1rgxA 114 2.83e+01 g.77.1.1 104932 1vheA 373 2.91e+01 b.49.3.1,c.56.5.4 100669,100670 1lcyA 325 2.91e+01 b.36.1.4,b.47.1.1 73834,73835 1q9uA 130 2.94e+01 d.129.7.1 96314 1fbr 93 2.98e+01 1fbr g.27.1.1,g.27.1.1 44948,44949 1fmb 104 3.05e+01 1fmb b.50.1.1 26777 1mqoA 227 3.08e+01 d.157.1.1 103846 1lvmA 229 3.09e+01 b.47.1.3 78243 1kk1A 410 3.09e+01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1wruA 379 3.12e+01 1bjt 793 3.12e+01 1bjt e.11.1.1 43249 2gn4A 344 3.14e+01 1p90A 145 3.17e+01 c.55.5.2 94377 1dfuP 94 3.20e+01 1dfuP b.53.1.1 26936 1vjuA 309 3.23e+01 d.248.1.1 100835 1rijA 25 3.25e+01 k.32.1.1 104951 1dnlA 199 3.25e+01 1ci0A b.45.1.1 25753 1i6pA 220 3.25e+01 1ddzA c.53.2.1 61848 1sdjA 310 3.26e+01 d.21.1.2,d.21.1.2 98807,98808 1xeeA 91 3.27e+01 1yrrA 382 3.27e+01 1j5wA 298 3.32e+01 d.104.1.1 71589 1v9kA 228 3.37e+01 d.265.1.3 108449 1wocA 103 3.39e+01 1ixmA 192 3.43e+01 1ixmA d.123.1.1 41114 1zv9A 172 3.43e+01 2csoA 127 3.47e+01 1qreA 247 3.48e+01 1qreA b.81.1.5 28066 2b0aA 186 3.49e+01 1r29A 127 3.49e+01 d.42.1.1 96856 1b4pA 217 3.52e+01 a.45.1.1,c.47.1.5 83158,83159 1faoA 126 3.54e+01 1faoA b.55.1.1 26974 1xy7A 166 3.54e+01 1on0A 158 3.58e+01 d.108.1.1 87095 1js8A 394 3.59e+01 a.86.1.1,b.112.1.1 67219,67220 2b8mA 117 3.65e+01 1a9xB 379 3.67e+01 1c3oB c.8.3.1,c.23.16.1 30732,31409 1krhA 338 3.68e+01 b.43.4.2,c.25.1.2,d.15.4.2 72891,72892,72893 1i3jA 116 3.75e+01 1i3jA d.285.1.1 61594 1ou8A 111 3.81e+01 b.136.1.1 93543 4tsvA 150 3.86e+01 2tnfA b.22.1.1 23860 1mg4A 113 3.87e+01 d.15.11.1 84953 1h2kA 349 3.90e+01 b.82.2.6 76572 1i7kA 179 3.92e+01 1u9aA d.20.1.1 61889 1wcuA 153 3.95e+01 1z2uA 150 3.95e+01 1qw2A 102 3.99e+01 d.249.1.1 96456 2beiA 170 4.03e+01 1ntvA 152 4.04e+01 b.55.1.2 86168 1kafA 108 4.12e+01 d.199.1.1 68372 1f9zA 135 4.13e+01 1qipA d.32.1.1 38484 1p7tA 731 4.18e+01 c.1.13.1 94319 1m5q1 130 4.20e+01 2ge3A 170 4.21e+01 1dhn 121 4.22e+01 1dhn d.96.1.3 40663 1sv6A 269 4.27e+01 d.177.1.1 106043 2azeA 155 4.27e+01 1pz4A 116 4.28e+01 d.106.1.1 95400 1o91A 178 4.29e+01 b.22.1.1 92656 1jpzA 473 4.29e+01 a.104.1.1 67069 1nz0A 118 4.31e+01 d.14.1.2 86433 1h6hA 143 4.34e+01 d.189.1.1 65681 2cqsA 842 4.37e+01 2et1A 201 4.40e+01 1y12A 165 4.47e+01 1vjnA 220 4.51e+01 d.157.1.4 100825 1xm8A 254 4.53e+01 1vk0A 206 4.54e+01 c.55.3.5 100839 1ht6A 405 4.57e+01 b.71.1.1,c.1.8.1 83629,83630 3kvt 115 4.59e+01 1t1dA d.42.1.2 38642 1unqA 125 4.59e+01 b.55.1.1 107968 1ugpB 226 4.62e+01 b.34.4.4 107832 1k8qA 377 4.69e+01 c.69.1.6 72177 1np7A 489 4.70e+01 a.99.1.1,c.28.1.1 80677,80678 1idaA 99 4.70e+01 1fmb b.50.1.1 26715 1ud9A 245 4.70e+01 d.131.1.2,d.131.1.2 107768,107769 1d7uA 433 4.70e+01 2dkb c.67.1.4 34439 1yphE 97 4.71e+01 1h8eA 510 4.74e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 60738,60739,60740 1z90A 469 4.77e+01 1ms9A 648 4.79e+01 b.29.1.15,b.68.1.1 85088,85089 1vjlA 164 4.84e+01 d.257.1.1 100822 1yzsA 121 4.86e+01 1zeqX 84 4.87e+01 1n0qA 93 4.87e+01 k.37.1.1 79754 1sffA 426 4.89e+01 c.67.1.4 105482 1c30B 382 4.91e+01 c.8.3.1,c.23.16.1 30736,31413 1rowA 109 4.93e+01 b.1.11.2 97676 1oz9A 150 4.94e+01 d.92.1.15 93808 1zkjA 359 4.98e+01 1vq2A 193 4.98e+01 1olmA 403 5.03e+01 a.5.3.1,b.132.1.1,c.13.1.1 104008,104009,104010 2ck3A 510 5.10e+01 1s68A 249 5.12e+01 d.142.2.4 98591 1mw9X 592 5.12e+01 e.10.1.1 91480 1eaqA 140 5.15e+01 b.2.5.6 76144 1ugxA 133 5.18e+01 1v54B 227 5.18e+01 b.6.1.2,f.17.2.1 100322,100323 1dy9A 187 5.27e+01 1jxpA b.47.1.3 26400 1hw5A 210 5.29e+01 2cgpA a.4.5.4,b.82.3.2 16098,28137 1vefA 395 5.29e+01 1paz 123 5.32e+01 1bqk b.6.1.1 22878 1umkA 275 5.34e+01 1lgpA 116 5.38e+01 b.26.1.2 73890 1x0oA 119 5.38e+01 1yvcA 70 5.40e+01 1utyA 187 5.40e+01 b.147.1.1 108036 1o50A 157 5.44e+01 d.37.1.1,d.37.1.1 92478,92479 4ubpB 126 5.45e+01 1ubpB b.85.3.1 28345 1drw 273 5.50e+01 1drw c.2.1.3,d.81.1.3 30057,39972 1ljoA 77 5.50e+01 b.38.1.1 73941 1y0yA 353 5.54e+01 1pmi 440 5.58e+01 1pmi b.82.1.3 28114 1wckA 220 5.60e+01 1qfhA 212 5.63e+01 1qfhA b.1.18.10,b.1.18.10 21893,21894 1pueE 89 5.64e+01 1awcA a.4.5.21 16165 1my7A 114 5.65e+01 b.1.18.1 79675 1zkpA 268 5.68e+01 2bnmA 198 5.68e+01 1bouA 139 5.70e+01 1bouA a.88.1.1 18521 1rtqA 299 5.87e+01 c.56.5.4 97819 1wt9B 123 5.87e+01 1c52 131 5.89e+01 1c52 a.3.1.1 15810 1vc3B 97 5.90e+01 1s0yA 76 5.93e+01 d.80.1.1 98314 1w2xA 758 5.94e+01 c.14.1.4,c.14.1.4 109134,109135 1tuhA 156 5.95e+01 d.17.4.11 107345 2brfA 110 6.00e+01 1vp6A 138 6.13e+01 1u69A 163 6.14e+01 d.32.1.7 107699 1fjgL 135 6.17e+01 1fjfL b.40.4.5 25346 1gtfA 74 6.18e+01 b.82.5.1 70460 4ubpC 570 6.20e+01 1ubpC b.92.1.1,c.1.9.2 28431,29053 1xj4A 119 6.20e+01 2bgiA 272 6.35e+01 1xtmA 175 6.36e+01 2g0cA 76 6.40e+01 1acc 735 6.41e+01 1acc f.11.1.1 43828 2a97A 439 6.45e+01 1rvgA 305 6.46e+01 c.1.10.2 97920 1gutA 68 6.48e+01 b.40.6.1 65576 1d3bB 91 6.54e+01 1d3bB b.38.1.1 24804 5nul 138 6.54e+01 5nul c.23.5.1 31191 2frgP 106 6.55e+01 1nykA 165 6.56e+01 b.33.1.1 86408 1ag6 99 6.59e+01 1plc b.6.1.1 22857 1uacH 114 6.63e+01 b.1.1.1 99132 1cqxA 403 6.63e+01 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 1n9lA 109 6.64e+01 d.110.3.6 85468 2pii 112 6.64e+01 2pii d.58.5.1 39071 1vkcA 158 6.67e+01 1xf1A 926 6.67e+01 1wp5A 323 6.70e+01 1q7hA 153 6.72e+01 b.122.1.1,d.17.6.2 96042,96043 1cbf 285 6.72e+01 1cbf c.90.1.1 35587 2bv5A 282 6.73e+01 1u8bA 133 6.73e+01 1bkpA 278 6.75e+01 1bkpA d.117.1.1 41029 1kveA 63 6.81e+01 1kveA d.70.1.2 39590 2daqA 110 6.85e+01 1cr5A 189 6.85e+01 1cr5A b.52.2.3,d.31.1.1 26931,38465 1wojA 214 6.90e+01 1cfr 285 7.05e+01 1cfr c.52.1.7 33312 1uheA 97 7.05e+01 1wcv1 257 7.06e+01 1khxA 227 7.07e+01 b.26.1.1 68631 1g79A 218 7.16e+01 1ci0A b.45.1.1 25752 1eazA 125 7.18e+01 b.55.1.1 70113 1odhA 174 7.20e+01 d.239.1.1 86850 1p0zA 131 7.21e+01 d.110.6.1 93882 1j79A 347 7.31e+01 1j79A c.1.9.4 62675 1r26A 125 7.33e+01 c.47.1.1 96847 1tgxA 60 7.33e+01 1tgxA g.7.1.1 44398 1z2mA 155 7.40e+01 1y1oA 203 7.42e+01 2fl4A 149 7.46e+01 1b34B 118 7.51e+01 1b34B b.38.1.1 24797 1v54F 98 7.52e+01 g.41.5.3 100327 1ri5A 298 7.52e+01 c.66.1.34 97502 1qj4A 257 7.52e+01 1qj4A c.69.1.20 34796 2aefA 234 7.54e+01 1z47A 355 7.54e+01 2bmoB 194 7.58e+01 1rewA 114 7.60e+01 g.17.1.2 97334 2aawA 222 7.62e+01 1qd6C 240 7.63e+01 1qd5A 1hz6A 72 7.66e+01 2ptl d.15.7.1 61429 1gsmA 210 7.67e+01 b.1.1.4,b.1.1.4 65535,65536 1co4A 42 7.71e+01 1co4A g.47.1.1 45347 1f0nA 285 7.71e+01 1dqyA c.69.1.3 34636 1xc1A 309 7.72e+01 c.94.1.1 109543 1h8eH 146 7.76e+01 1e79H b.93.1.1 60757 1dpqA 20 7.77e+01 j.60.1.1 46345 1xw3A 110 7.77e+01 1e2wA 251 7.82e+01 1hcz b.2.6.1,b.84.2.2 22466,28252 1rkd 309 7.85e+01 1rkd c.72.1.1 34928 2c5aA 379 7.87e+01 1pyvA 54 7.88e+01 j.36.4.1 95376 1k55A 246 7.88e+01 e.3.1.1 68156 2fiuA 99 7.89e+01 1z4rA 168 7.90e+01 1us5A 314 7.99e+01 c.94.1.1 99856 1w70A 60 8.05e+01 1dt1A 129 8.05e+01 1c52 a.3.1.1 15811 2dgkA 452 8.11e+01 1oe1A 336 8.16e+01 b.6.1.3,b.6.1.3 86891,86892 1ywzA 175 8.19e+01 1em8B 112 8.22e+01 c.126.1.1 90458 2bj7A 138 8.24e+01 1whi 122 8.26e+01 1whi b.39.1.1 24810 1oktA 211 8.31e+01 a.45.1.1,c.47.1.5 93272,93273 2affB 44 8.43e+01 2bwfA 77 8.48e+01 1aapA 58 8.49e+01 1bpi g.8.1.1 44543 1nqzA 194 8.50e+01 d.113.1.1 86077 1bkzA 135 8.53e+01 1a3k b.29.1.3 24202 2f1fA 164 8.57e+01 1dl5A 317 8.58e+01 1dl5A c.66.1.7,d.197.1.1 64720,64721 1vjkA 98 8.70e+01 d.15.3.1 108631 1b00A 127 8.73e+01 3chy c.23.1.1 31122 1ohvA 472 8.74e+01 c.67.1.4 93031 2bxxA 134 8.74e+01 2c3gA 98 8.85e+01 1wlsA 328 8.89e+01 1m2dA 110 8.93e+01 c.47.1.11 78476