# 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 1ycdA 243 6.80e-02 1v7rA 186 7.30e-02 c.51.4.1 100482 1k7kA 221 9.52e-02 c.51.4.1 72104 1lfpA 249 1.15e-01 e.39.1.1 73885 2ci1A 275 1.35e-01 2f1kA 279 2.30e-01 1regX 122 2.95e-01 1regX d.58.27.1 39406 1m93B 245 3.03e-01 1wnaA 131 5.89e-01 1iro 54 6.09e-01 1rb9 g.41.5.1 45223 1uanA 227 6.97e-01 c.134.1.1 99135 2g03A 194 9.82e-01 1dd9A 338 1.07e+00 1dd9A e.13.1.1 43254 1yr1A 119 1.29e+00 1l3iA 192 1.38e+00 c.66.1.22 77676 1wdyA 285 1.40e+00 1t3gA 159 1.49e+00 1ik9A 213 1.53e+00 b.59.1.1,h.1.11.1 66176,66177 1g61A 228 1.82e+00 1g61A d.126.1.1 41126 1cy5A 97 1.83e+00 1cy5A a.77.1.3 18430 2cwxA 430 1.94e+00 1wy7A 207 2.04e+00 2c1xA 456 2.14e+00 2b9eA 303 2.15e+00 1q0rA 298 2.33e+00 c.69.1.28 95508 1eokA 290 2.39e+00 1eokA c.1.8.5 28991 1lw7A 365 2.61e+00 c.26.1.3,c.37.1.1 74295,74296 1yk4A 52 2.71e+00 1n40A 396 2.87e+00 a.104.1.1 79977 2b3yA 888 2.99e+00 2au3A 407 3.04e+00 2c2aA 258 3.11e+00 1sdjA 310 3.18e+00 d.21.1.2,d.21.1.2 98807,98808 1n4qB 377 3.30e+00 a.102.4.3 91636 1rm8A 169 3.32e+00 d.92.1.11 97660 1i24A 404 3.41e+00 c.2.1.2 83663 1rdg 53 3.42e+00 1rb9 g.41.5.1 45221 2d69A 430 3.46e+00 1brfA 53 3.59e+00 1rb9 g.41.5.1 45236 1p4oA 322 3.72e+00 d.144.1.7 87775 1wwjA 105 4.01e+00 1cpo 299 4.07e+00 1cpo a.39.3.1,a.39.3.1 17390,17391 1m3sA 186 4.37e+00 c.80.1.3 78573 1lj5A 379 4.38e+00 e.1.1.1 73928 1pufB 73 4.51e+00 a.4.1.1 95132 1nn5A 215 4.68e+00 c.37.1.1 85892 1v3vA 333 4.74e+00 b.35.1.2,c.2.1.1 108345,108346 1qzzA 374 5.18e+00 a.4.5.29,c.66.1.12 96719,96720 1ufyA 122 5.24e+00 d.79.1.2 88489 1ne9A 335 5.36e+00 d.108.1.4,d.108.1.4 91839,91840 1w2wB 191 5.68e+00 1nzaA 103 5.92e+00 d.58.5.2 86444 1utaA 81 6.11e+00 d.58.52.1 108029 1heiA 451 6.23e+00 1heiA c.37.1.14,c.37.1.14 32463,32464 1od6A 160 6.40e+00 c.26.1.3 86836 1dzkA 157 6.40e+00 1obpA b.60.1.1 27096 1nrzA 164 6.49e+00 c.38.1.1 86131 1unlD 208 6.59e+00 2eutA 294 6.60e+00 1j4aA 333 6.79e+00 c.2.1.4,c.23.12.1 71502,71503 1zejA 293 6.84e+00 1wiwA 290 6.89e+00 1kq6A 141 7.05e+00 d.189.1.1 91020 2a33A 215 7.19e+00 1i8nA 126 7.35e+00 1i8nA g.10.1.2 61976 1hc7A 477 7.36e+00 1hc7A c.51.1.1,d.104.1.1,d.68.5.1 60938,60939,60940 1wwzA 159 7.39e+00 1qksA 567 7.40e+00 1qksA a.3.1.2,b.70.2.1 15951,27710 2ah5A 210 7.44e+00 1vraA 208 7.50e+00 2fwtA 125 7.52e+00 2csoA 127 7.52e+00 1rb9 53 7.58e+00 1rb9 g.41.5.1 45214 1bsg 266 7.80e+00 1btl e.3.1.1 42729 1rtqA 299 7.88e+00 c.56.5.4 97819 1zwyA 185 8.12e+00 1r29A 127 8.14e+00 d.42.1.1 96856 1r5tA 142 8.53e+00 c.97.1.1 104812 1sheA 103 8.97e+00 d.274.1.1 105551 1x0vA 354 9.03e+00 1jg1A 235 9.10e+00 c.66.1.7 66661 1qlpA 394 9.15e+00 1ovaA e.1.1.1 42628 1q2lA 939 9.70e+00 1gmxA 108 1.01e+01 c.46.1.3 65355 1otjA 283 1.02e+01 b.82.2.5 93517 1qv1A 195 1.03e+01 a.39.1.5 96347 1u7pA 164 1.03e+01 2b81A 323 1.04e+01 1ss9A 311 1.08e+01 c.68.1.4 105978 2asbA 251 1.12e+01 1u7iA 136 1.13e+01 d.32.1.7 107724 1b6rA 355 1.13e+01 1b6rA b.84.2.1,c.30.1.1,d.142.1.2 28241,31648,41493 1cewI 108 1.16e+01 1cewI d.17.1.2 37999 1x9iA 302 1.17e+01 1o9gA 250 1.18e+01 c.66.1.29 86692 1udxA 416 1.18e+01 b.117.1.1,c.37.1.8,d.242.1.1 99228,99229,99230 1xzpB 150 1.19e+01 1kr4A 125 1.21e+01 d.58.5.2 72889 1ztpA 251 1.22e+01 1txgA 335 1.23e+01 1vmaA 306 1.23e+01 a.24.13.1,c.37.1.10 108887,108888 1ey4A 149 1.25e+01 1snc b.40.1.1 24815 1ob8A 135 1.27e+01 1iapA 211 1.29e+01 a.91.1.1 62119 1wd7A 261 1.31e+01 1ne2A 200 1.32e+01 c.66.1.32 85586 6rxn 46 1.36e+01 1rb9 g.41.5.1 45222 1t0iA 191 1.36e+01 c.23.5.4 106209 2b61A 377 1.37e+01 1nu0A 138 1.38e+01 c.55.3.8 92165 1js1X 324 1.40e+01 c.78.1.1,c.78.1.1 71834,71835 1wrjA 156 1.42e+01 2g0dA 409 1.43e+01 1buoA 121 1.44e+01 1buoA d.42.1.1 38631 1qs1A 462 1.45e+01 1qs1A d.166.1.1,d.166.1.1 42260,42261 2ghpA 292 1.45e+01 1a3aA 148 1.46e+01 1a3aA d.112.1.1 40917 1qmhA 347 1.47e+01 1qmhA c.47.2.1,d.68.2.1 33082,39568 1c7sA 858 1.47e+01 1qba b.1.18.2,b.2.2.3,c.1.8.6,d.92.2.1 21812,22408,29011,40410 1lriA 98 1.48e+01 a.134.1.1 74223 1iirA 415 1.49e+01 1iirA c.87.1.5 62453 2d83A 363 1.50e+01 1ryaA 160 1.52e+01 d.113.1.5 105122 1zvkA 358 1.52e+01 1t4nA 94 1.52e+01 d.50.1.1 106424 1odoA 408 1.54e+01 a.104.1.1 92783 1t0fA 276 1.55e+01 1o57A 291 1.56e+01 a.4.5.40,c.61.1.1 92483,92484 1lrzA 426 1.56e+01 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 1budA 197 1.57e+01 1atlA d.92.1.9 40328 2fi1A 190 1.57e+01 1wmaA 276 1.57e+01 1s7zA 117 1.57e+01 a.159.3.1 98715 1qr0A 228 1.59e+01 1qr0A d.150.1.1,d.150.1.1 59038,59039 2g40A 224 1.61e+01 1tr9A 341 1.61e+01 1nv8A 284 1.61e+01 c.66.1.30 86224 1l8bA 190 1.62e+01 d.86.1.1 73683 1u5mA 73 1.63e+01 1bgk 37 1.64e+01 1bgk g.19.1.1 44875 2a2pA 129 1.64e+01 1z7xW 461 1.66e+01 2aq5A 402 1.67e+01 2bycA 137 1.67e+01 2fq3A 104 1.68e+01 2aibA 98 1.69e+01 1tc5A 194 1.73e+01 c.110.1.1 106752 1lvaA 258 1.74e+01 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 2bz1A 196 1.74e+01 1zymA 258 1.75e+01 1zymA a.60.10.1,c.8.1.2 18110,30705 2cujA 108 1.75e+01 1lt8A 406 1.75e+01 c.1.26.1 78186 1ga8A 311 1.76e+01 1ga8A c.68.1.4 34516 1xmxA 385 1.78e+01 1u0kA 288 1.79e+01 d.21.1.2,d.21.1.2 107547,107548 1b24A 188 1.80e+01 1b24A d.95.2.1,d.95.2.1 40573,40574 1n46A 258 1.81e+01 a.123.1.1 85315 1jnrA 643 1.86e+01 a.7.3.1,c.3.1.4,d.168.1.1 66966,66967,66968 2dexX 671 1.86e+01 1r55A 214 1.87e+01 1t15A 214 1.87e+01 c.15.1.3,c.15.1.3 99067,99068 1i4uA 181 1.89e+01 b.60.1.1 61732 2aa1A 144 1.89e+01 1id0A 152 1.95e+01 d.122.1.3 66111 1y7lA 316 1.95e+01 2d4pA 141 1.95e+01 1t77A 414 1.97e+01 1dfmA 223 1.98e+01 1d2iA c.52.1.5 33295 2sqcA 631 1.99e+01 2sqcA a.102.4.2,a.102.4.2 18854,18855 2fliA 220 2.02e+01 1n8yC 608 2.02e+01 c.10.2.5,c.10.2.5,g.3.9.1,g.3.9.1 80314,80315,80316,80317 1e5dA 402 2.04e+01 1e5dA c.23.5.1,d.157.1.3 31208,42061 1vchA 175 2.06e+01 2carA 196 2.07e+01 1auoA 218 2.08e+01 1auoA c.69.1.14 34716 2gk4A 232 2.11e+01 1vhxA 150 2.13e+01 c.55.3.8 100712 1yj7A 171 2.14e+01 1qyaA 307 2.14e+01 d.21.1.2,d.21.1.2 104653,104654 1r9kA 172 2.14e+01 a.168.1.1 104869 1rfeA 162 2.14e+01 1r1tA 122 2.16e+01 a.4.5.5 104769 2fjbA 643 2.17e+01 1gxrA 337 2.17e+01 b.69.4.1 70722 1yb2A 275 2.18e+01 1o26A 232 2.18e+01 d.207.1.1 86566 1dptA 117 2.19e+01 1dptA d.80.1.3 39862 16vpA 366 2.20e+01 16vpA d.180.1.1 42601 1xw3A 110 2.21e+01 1x89A 178 2.21e+01 1v76A 96 2.22e+01 1sgwA 214 2.23e+01 c.37.1.12 105541 1im8A 244 2.24e+01 c.66.1.14 66212 2a65A 519 2.25e+01 1atlA 202 2.29e+01 1atlA d.92.1.9 40322 1y7bA 542 2.31e+01 1ruwA 69 2.31e+01 1wf3A 301 2.32e+01 1nlnA 204 2.34e+01 d.3.1.7 91962 1z90A 469 2.39e+01 1pa4A 116 2.41e+01 d.52.7.1 94409 1xkzA 255 2.41e+01 830cA 168 2.44e+01 1ck7A d.92.1.11 40400 1mtpA 323 2.45e+01 e.1.1.1 85107 1rifA 282 2.45e+01 c.37.1.23 97507 2bwnA 401 2.46e+01 1qjcA 158 2.46e+01 1b6tA c.26.1.3 63328 1e5mA 416 2.46e+01 1dd8A c.95.1.1,c.95.1.1 58973,58974 1shfA 59 2.49e+01 1bbzA b.34.2.1 24462 1mwwA 128 2.50e+01 d.80.1.4 91483 1u7nA 336 2.50e+01 c.77.1.4 107726 1hdoA 206 2.51e+01 1he2A c.2.1.2 60965 2bb6A 414 2.54e+01 1evlA 401 2.57e+01 1qf6A c.51.1.1,d.104.1.1 33202,40751 2bd0A 244 2.59e+01 1w53A 84 2.62e+01 a.186.1.2 109175 1gtkA 313 2.65e+01 c.94.1.1,d.50.2.1 76346,76347 1o54A 277 2.67e+01 c.66.1.13 92482 1lc5A 364 2.68e+01 c.67.1.1 73827 1r45A 204 2.69e+01 1wdeA 294 2.71e+01 1rq2A 382 2.71e+01 c.32.1.1,d.79.2.1 105048,105049 1h2bA 359 2.73e+01 b.35.1.2,c.2.1.1 90543,90544 1tqjA 230 2.73e+01 c.1.2.2 107228 2bi7A 384 2.74e+01 1u14A 172 2.76e+01 c.51.4.3 107579 1rv9A 259 2.77e+01 d.194.1.2 105105 2furA 209 2.78e+01 1z6mA 175 2.78e+01 1u69A 163 2.79e+01 d.32.1.7 107699 1nnfA 309 2.82e+01 c.94.1.1 85903 2gfsA 372 2.82e+01 1ojqA 212 2.84e+01 d.166.1.1 93146 1n7hA 381 2.85e+01 c.2.1.2 80250 1l1qA 186 2.86e+01 c.61.1.1 77653 1vimA 200 2.88e+01 c.80.1.3 100758 1ghpA 258 2.92e+01 1btl e.3.1.1 60520 1uxoA 192 2.97e+01 c.69.1.31 108121 1wmwA 330 3.03e+01 2abqA 306 3.06e+01 1zatA 250 3.09e+01 2aalA 131 3.10e+01 1usyA 275 3.11e+01 1kjs 74 3.12e+01 1kjs a.50.1.1 17792 1r1hA 696 3.14e+01 d.92.1.4 104756 1zo0A 126 3.16e+01 2ahrA 259 3.17e+01 1vq2A 193 3.17e+01 1h70A 255 3.19e+01 1h70A d.126.1.3 60711 1vqoX 92 3.19e+01 1gz2A 142 3.20e+01 d.169.1.1 83392 2flsA 132 3.20e+01 7taa 478 3.20e+01 7taa b.71.1.1,c.1.8.1 27778,28765 2bkkA 264 3.21e+01 1wt9B 123 3.23e+01 1t1gA 364 3.23e+01 c.41.1.2 106246 1roaA 122 3.31e+01 d.17.1.2 105024 1czfA 362 3.32e+01 1czfA b.80.1.3 28031 1f2tB 148 3.33e+01 1f2tB 1qdeA 224 3.34e+01 1qvaA c.37.1.19 32410 1i3dA 146 3.35e+01 a.1.1.2 61587 1jykA 254 3.38e+01 c.68.1.13 67458 1hfoA 113 3.40e+01 d.80.1.3 61006 1tffA 234 3.40e+01 d.3.1.11 106854 1dcfA 136 3.43e+01 1dcfA c.23.1.2 31124 1z9tA 255 3.45e+01 1dpe 507 3.46e+01 1dpe c.94.1.1 35799 1rypJ 204 3.48e+01 d.153.1.4 41878 1in0A 163 3.50e+01 d.58.49.1,d.58.49.1 83694,83695 1wd5A 208 3.51e+01 1j77A 209 3.51e+01 1j77A a.132.1.2 62674 2g6tA 306 3.53e+01 1fj2A 232 3.53e+01 1auoA c.69.1.14 34720 1ocsA 162 3.54e+01 d.189.1.1 92776 1nwaA 203 3.54e+01 d.58.28.1 86295 1udzA 182 3.55e+01 b.51.1.1 99239 1poiB 260 3.61e+01 1poiB c.124.1.3 34155 1j3mA 129 3.62e+01 d.129.7.1 103836 1x1tA 260 3.63e+01 1wcwA 261 3.64e+01 2fqpA 97 3.64e+01 1inp 400 3.69e+01 1inp e.7.1.1 42972 1ka9H 200 3.69e+01 c.23.16.1 77308 1bywA 110 3.71e+01 1bywA d.110.3.6 40912 1ywzA 175 3.71e+01 1nulA 152 3.72e+01 1nulA c.61.1.1 34011 1xovA 326 3.72e+01 2d5xA 141 3.72e+01 1fexA 59 3.74e+01 a.4.1.3 59803 1pme 380 3.75e+01 1hcl d.144.1.7 41653 1euvA 221 3.77e+01 1euvA d.3.1.7 37133 2ez9A 603 3.79e+01 1zud1 251 3.80e+01 1b0b 142 3.81e+01 2fal a.1.1.2 15010 1k3xA 262 3.83e+01 a.156.1.2,b.113.1.1,g.39.1.8 77242,77243,77244 1a8d 452 3.91e+01 1a8d b.29.1.6,b.42.4.2 24262,25607 1q44A 326 3.93e+01 c.37.1.5 95779 2a6hE 99 3.94e+01 1hh8A 213 4.00e+01 1e96B a.118.8.1 61042 2d00A 109 4.00e+01 1q9uA 130 4.06e+01 d.129.7.1 96314 1yy7A 213 4.08e+01 1h1yA 228 4.09e+01 c.1.2.2 76506 1yksA 440 4.13e+01 1djtA 64 4.15e+01 1aho g.3.7.1 44132 1otgA 125 4.19e+01 1otgA d.80.1.2 39831 1lgpA 116 4.25e+01 b.26.1.2 73890 1p4fA 293 4.25e+01 d.144.1.7 104063 2g5cA 281 4.26e+01 2end 138 4.28e+01 2end a.18.1.1 16400 2cygA 312 4.28e+01 1fe0A 68 4.30e+01 1cc8A d.58.17.1 39345 1k8kG 151 4.33e+01 a.118.13.1 68313 2f1lA 187 4.35e+01 1g5tA 196 4.35e+01 1g5rA c.37.1.11 32366 1fv5A 36 4.37e+01 1fv5A g.37.1.2 45075 1kv0A 66 4.38e+01 g.3.7.1 91040 1p35A 299 4.39e+01 1p35A b.28.1.1 23925 1du3A 130 4.39e+01 1d4vA g.24.1.1,g.24.1.1,g.24.1.1 44927,44928,44929 1s2dA 167 4.39e+01 c.23.14.1 98377 1pch 88 4.40e+01 1ptf d.94.1.1 40564 1ylhA 560 4.43e+01 1izoA 417 4.43e+01 a.104.1.1 83851 1bebA 162 4.43e+01 1bebA b.60.1.1 27115 1kufA 203 4.44e+01 d.92.1.9 73007 1o17A 345 4.48e+01 a.46.2.1,c.27.1.1 80765,80766 1rypI 222 4.49e+01 d.153.1.4 41877 1r7mA 235 4.52e+01 1jfbA 404 4.57e+01 a.104.1.1 66624 1l0wA 580 4.58e+01 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1oo0A 147 4.59e+01 d.232.1.1 87182 2bngA 149 4.62e+01 1v1aA 309 4.66e+01 c.72.1.1 100249 1xodA 118 4.68e+01 2eifA 136 4.68e+01 1bkb b.34.5.2,b.40.4.5 24607,25339 1yacA 208 4.70e+01 1yacA c.33.1.3 31757 1l8nA 679 4.71e+01 c.1.8.10,d.92.2.2 84564,84565 1j2zA 270 4.71e+01 b.81.1.1 90805 1o6lA 337 4.78e+01 d.144.1.7 81092 1uwvA 433 4.79e+01 b.40.4.12,c.66.1.40 100128,100129 2c07A 285 4.82e+01 1fcyA 236 4.82e+01 2lbd a.123.1.1 19282 1wruA 379 4.83e+01 1upkA 341 4.88e+01 a.118.1.15 99758 1oihA 301 4.89e+01 b.82.2.5 93051 1n7oA 721 4.90e+01 a.102.3.2,b.24.1.1,b.30.5.2 80259,80260,80261 1w6uA 302 4.91e+01 2c2xA 281 4.94e+01 1h4vB 421 4.94e+01 1adjA c.51.1.1,d.104.1.1 60624,60625 1w44A 331 4.98e+01 1v5iB 76 4.99e+01 1s2xA 206 4.99e+01 a.47.3.1 105229 1suwA 249 4.99e+01 e.52.1.1 106027 1yzsA 121 5.01e+01 2b0tA 738 5.03e+01 2cxkA 95 5.05e+01 1ub3A 220 5.06e+01 c.1.10.1 88395 1i5gA 144 5.06e+01 1ewxA c.47.1.10 61784 1vicA 262 5.07e+01 c.68.1.13 100756 1n81A 186 5.10e+01 a.185.1.1 85388 1u9cA 224 5.10e+01 1xi1A 575 5.10e+01 2arhA 203 5.14e+01 1j34B 123 5.14e+01 d.169.1.1 84049 1w33A 181 5.20e+01 1ps1A 337 5.22e+01 1ps1A a.128.1.4 19450 1bf5A 545 5.23e+01 1bg1A a.47.1.1,b.2.5.5,d.93.1.1 17766,22460,40526 2bywA 418 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