# 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 1t3gA 159 2.83e-03 2ew8A 249 7.71e-03 2ci1A 275 1.47e-02 1wmaA 276 2.16e-02 1m93B 245 7.69e-02 1x9iA 302 1.07e-01 1h1dA 221 2.56e-01 c.66.1.1 83452 2f9dA 125 3.29e-01 2b9dA 52 3.30e-01 1tqhA 247 3.69e-01 c.69.1.29 107225 1j77A 209 5.41e-01 1j77A a.132.1.2 62674 1yzxA 226 5.42e-01 1l0wA 580 6.09e-01 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 8tlnE 316 6.46e-01 1hyt d.92.1.2 59075 1xg5A 279 7.20e-01 1fe0A 68 7.77e-01 1cc8A d.58.17.1 39345 1regX 122 1.09e+00 1regX d.58.27.1 39406 2d4pA 141 1.14e+00 1zosA 230 1.25e+00 2bd0A 244 1.38e+00 2bwnA 401 1.38e+00 1iro 54 1.48e+00 1rb9 g.41.5.1 45223 1m3sA 186 1.77e+00 c.80.1.3 78573 1ht6A 405 1.77e+00 b.71.1.1,c.1.8.1 83629,83630 1v7rA 186 1.86e+00 c.51.4.1 100482 2csgA 424 1.97e+00 2f2hA 773 1.97e+00 1n40A 396 2.05e+00 a.104.1.1 79977 2ghrA 302 2.14e+00 1ja9A 274 2.15e+00 c.2.1.2 62817 12asA 330 2.29e+00 12asA d.104.1.1 40783 3bamA 213 2.38e+00 1bam c.52.1.3 33288 1ka8A 100 2.47e+00 a.4.5.20 72241 2cspA 130 2.52e+00 1msk 331 2.56e+00 1msk d.173.1.1 42495 1uvjA 664 2.59e+00 e.8.1.6 100045 1ugpA 203 2.64e+00 d.149.1.1 107831 1u5mA 73 2.70e+00 1yk4A 52 2.87e+00 1s2oA 244 2.95e+00 1v76A 96 3.09e+00 2cbzA 237 3.11e+00 1bebA 162 3.15e+00 1bebA b.60.1.1 27115 1cbf 285 3.26e+00 1cbf c.90.1.1 35587 2f06A 144 3.31e+00 1jae 471 3.37e+00 1smd b.71.1.1,c.1.8.1 27773,28760 1wdtA 665 3.39e+00 1gegA 256 3.50e+00 1ybvA c.2.1.2 29888 1y7bA 542 3.50e+00 1k7kA 221 3.58e+00 c.51.4.1 72104 1wiwA 290 3.75e+00 2c36A 285 3.79e+00 1s7kA 182 3.84e+00 2bgkA 278 3.90e+00 1udxA 416 4.05e+00 b.117.1.1,c.37.1.8,d.242.1.1 99228,99229,99230 2d83A 363 4.13e+00 1stzA 338 4.16e+00 a.4.5.51,d.110.2.3 106009,106010 1brfA 53 4.23e+00 1rb9 g.41.5.1 45236 1e4yA 214 4.35e+00 1zin c.37.1.1,g.41.2.1 31901,45181 1shwB 181 4.43e+00 b.18.1.4 105563 1ve3A 227 4.48e+00 1xdnA 277 4.50e+00 1rdg 53 4.53e+00 1rb9 g.41.5.1 45221 1pieA 419 4.65e+00 d.14.1.5,d.58.26.7 94706,94707 1yj7A 171 4.73e+00 1k87A 669 4.80e+00 a.176.1.1,c.1.23.2 77286,77287 1zymA 258 5.06e+00 1zymA a.60.10.1,c.8.1.2 18110,30705 1oz9A 150 5.07e+00 d.92.1.15 93808 1t5iA 172 5.14e+00 c.37.1.19 106450 1evhA 112 5.30e+00 1evhA b.55.1.4 26997 1rewC 135 5.46e+00 g.7.1.3 97336 1dkqA 410 5.58e+00 1dklA c.60.1.2 33998 1g26A 31 6.03e+00 1g26A g.3.16.1 44381 1bd8 156 6.06e+00 1bd8 d.211.1.1 19157 1l6wA 220 6.17e+00 c.1.10.1 73632 1v3wA 173 6.20e+00 b.81.1.5 100291 1skz 119 6.23e+00 1skz g.3.15.1,g.3.15.1 44366,44367 1eokA 290 6.27e+00 1eokA c.1.8.5 28991 1xaoA 121 6.28e+00 2dexX 671 6.30e+00 2erfA 209 6.31e+00 2bepA 159 6.40e+00 1o8xA 146 6.52e+00 c.47.1.10 86681 2cw5A 255 6.57e+00 1vjqA 79 6.58e+00 k.43.1.1 100830 1yxmA 303 6.93e+00 1edt 271 7.09e+00 2ebn c.1.8.5 28993 1uzmA 247 7.23e+00 6rxn 46 7.31e+00 1rb9 g.41.5.1 45222 1dkmA 410 7.45e+00 1dklA c.60.1.2 34000 1zemA 262 7.53e+00 1ne9A 335 7.81e+00 d.108.1.4,d.108.1.4 91839,91840 1edqA 540 8.01e+00 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21873,29002,38436 1xc3A 302 8.24e+00 1rgxA 114 8.36e+00 g.77.1.1 104932 1shfA 59 8.71e+00 1bbzA b.34.2.1 24462 1vjyA 303 8.79e+00 d.144.1.7 108633 1yovA 537 8.83e+00 1r1a1 287 9.01e+00 1aym1 1yqeA 282 9.02e+00 1lssA 140 9.06e+00 c.2.1.9 74246 1wd7A 261 9.35e+00 1ufyA 122 9.36e+00 d.79.1.2 88489 1zwyA 185 9.38e+00 1f0lA 535 9.51e+00 1ddt b.2.1.1,d.166.1.1,f.1.2.1 22377,42239,43382 1s9uA 207 9.56e+00 a.184.1.1 105390 1odkA 235 9.58e+00 c.56.2.1 86863 1id0A 152 9.87e+00 d.122.1.3 66111 1xqaA 113 9.88e+00 1ogaD 215 1.01e+01 b.1.1.1,b.1.1.2 86990,86991 1ofcX 304 1.04e+01 a.4.1.3,a.4.1.13,a.187.1.1 92826,92827,92828 1vqoV 71 1.05e+01 1ro7A 259 1.06e+01 c.130.1.1 97667 1wcwA 261 1.06e+01 1jixA 351 1.07e+01 1c3jA c.87.1.1 63081 1rb9 53 1.08e+01 1rb9 g.41.5.1 45214 1gcqA 61 1.08e+01 1ckaA b.34.2.1 60434 1csh 435 1.09e+01 1csh a.103.1.1 18880 1t1gA 364 1.11e+01 c.41.1.2 106246 1kq6A 141 1.11e+01 d.189.1.1 91020 1ash 150 1.13e+01 1ash a.1.1.2 15622 1gntA 553 1.13e+01 e.26.1.1 70290 1qwyA 291 1.15e+01 b.84.3.2 96509 1xqoA 256 1.16e+01 2aa1A 144 1.17e+01 1gycA 499 1.17e+01 b.6.1.3,b.6.1.3,b.6.1.3 70748,70749,70750 1xodA 118 1.18e+01 1zdrA 164 1.18e+01 1izoA 417 1.21e+01 a.104.1.1 83851 1irdB 146 1.21e+01 a.1.1.2 66287 1sc3A 178 1.25e+01 c.17.1.1 105416 2bi7A 384 1.28e+01 2fliA 220 1.29e+01 1q9uA 130 1.30e+01 d.129.7.1 96314 1wwjA 105 1.31e+01 1g61A 228 1.33e+01 1g61A d.126.1.1 41126 1uw4A 91 1.33e+01 d.58.7.4 100071 1z90A 469 1.33e+01 1wqwA 235 1.34e+01 1qopB 396 1.35e+01 2tysB c.79.1.1 35270 1lt8A 406 1.35e+01 c.1.26.1 78186 1nzaA 103 1.35e+01 d.58.5.2 86444 1tt7A 330 1.40e+01 1oo0A 147 1.40e+01 d.232.1.1 87182 1t7rA 269 1.41e+01 a.123.1.1 106635 1i5gA 144 1.42e+01 1ewxA c.47.1.10 61784 1t71A 281 1.44e+01 1vr6A 350 1.49e+01 1w6uA 302 1.50e+01 1bm8 99 1.51e+01 1bm8 d.34.1.1 38528 1vsrA 136 1.52e+01 1vsrA c.52.1.15 33332 1iv3A 152 1.55e+01 d.79.5.1 76828 1zvkA 358 1.56e+01 1d2fA 390 1.56e+01 1d2fA c.67.1.3 34411 1vjeA 166 1.56e+01 d.185.1.2 100807 1j2jB 45 1.58e+01 a.7.8.1 84017 1td6A 306 1.58e+01 1uanA 227 1.61e+01 c.134.1.1 99135 1gxrA 337 1.62e+01 b.69.4.1 70722 1goiA 499 1.63e+01 b.72.2.1,c.1.8.5,d.26.3.1 65413,65414,65415 1i8kA 107 1.68e+01 b.1.1.1 71130 1pufB 73 1.69e+01 a.4.1.1 95132 1rvkA 382 1.72e+01 c.1.11.2,d.54.1.1 97928,97929 1qlpA 394 1.72e+01 1ovaA e.1.1.1 42628 1j5uA 136 1.76e+01 d.208.1.1 71584 1wq3A 322 1.76e+01 1kr4A 125 1.78e+01 d.58.5.2 72889 1ysjA 404 1.85e+01 1dl0A 37 1.87e+01 1dl0A g.3.6.2 44112 1gqiA 708 1.87e+01 c.1.8.10,d.92.2.2 76279,76280 1ocsA 162 1.87e+01 d.189.1.1 92776 1yr1A 119 1.90e+01 1bbzA 58 1.91e+01 1bbzA b.34.2.1 24477 1yw4A 341 1.92e+01 1nu0A 138 1.93e+01 c.55.3.8 92165 1vjoA 393 1.94e+01 c.67.1.3 100827 1r7lA 110 1.96e+01 d.277.1.1 104837 1c93A 265 1.97e+01 2ebn c.1.8.5 28998 1cjcA 460 1.97e+01 1cjcA c.3.1.1,c.4.1.1 30319,30604 1h4vB 421 1.98e+01 1adjA c.51.1.1,d.104.1.1 60624,60625 1vggA 161 2.01e+01 1n2eA 300 2.01e+01 c.26.1.4 85268 1qh8B 519 2.01e+01 1qguB c.92.2.3 35634 1nox 205 2.03e+01 1nox d.90.1.1 40242 1vqoX 92 2.05e+01 2f0aA 98 2.05e+01 1gj7B 253 2.07e+01 1zo0A 126 2.12e+01 1j5pA 253 2.13e+01 d.81.1.3,c.2.1.3 71577,83092 1dhn 121 2.16e+01 1dhn d.96.1.3 40663 1xouB 95 2.17e+01 1fcyA 236 2.18e+01 2lbd a.123.1.1 19282 1bsg 266 2.18e+01 1btl e.3.1.1 42729 1epwA 1290 2.19e+01 b.29.1.6,b.42.4.2,d.92.1.7,h.4.2.1 24269,25614,40305,45785 2a84A 300 2.20e+01 1n4qB 377 2.21e+01 a.102.4.3 91636 2aq5A 402 2.21e+01 1lm8C 96 2.22e+01 d.42.1.1 74034 1o4vA 183 2.25e+01 c.23.8.1 86628 1yuzA 202 2.25e+01 2cwxA 430 2.30e+01 1qv1A 195 2.31e+01 a.39.1.5 96347 1ufzA 83 2.33e+01 a.5.9.1 107821 1vhxA 150 2.34e+01 c.55.3.8 100712 2f8lA 344 2.35e+01 1tqzA 133 2.35e+01 1k0mA 241 2.37e+01 a.45.1.1,c.47.1.5 67949,67950 1pgvA 197 2.37e+01 c.10.1.1 88073 1ospO 257 2.38e+01 1ospO b.76.1.1 27971 1l8aA 886 2.39e+01 c.36.1.10,c.36.1.6,c.48.1.1 73677,73678,73679 2d5xB 146 2.40e+01 1mixA 206 2.41e+01 a.11.2.1,b.55.1.5 79166,79167 1nrzA 164 2.41e+01 c.38.1.1 86131 1d2vA 104 2.44e+01 1d2vA a.93.1.2 18697 1wchA 315 2.46e+01 1s5aA 150 2.46e+01 d.17.4.10 98525 1ts9A 102 2.47e+01 1yeyA 444 2.49e+01 1lj5A 379 2.51e+01 e.1.1.1 73928 1q7zA 566 2.51e+01 c.1.21.2,c.1.26.1 96090,96091 1nulA 152 2.51e+01 1nulA c.61.1.1 34011 3seb 238 2.54e+01 3seb b.40.2.2,d.15.6.1 25184,37773 1u69A 163 2.58e+01 d.32.1.7 107699 1aie 31 2.61e+01 1aie a.53.1.1 17829 1iseA 185 2.62e+01 d.67.3.1 90691 1u7iA 136 2.63e+01 d.32.1.7 107724 1z6oM 191 2.63e+01 1zpxA 23 2.63e+01 1v5mA 136 2.64e+01 b.55.1.1 108379 1ob8A 135 2.65e+01 1qreA 247 2.67e+01 1qreA b.81.1.5 28066 1vhwA 253 2.67e+01 c.56.2.1 100706 2f5xA 312 2.67e+01 1h6pA 203 2.69e+01 a.146.1.1 60690 2c1xA 456 2.69e+01 1ukuA 102 2.71e+01 d.58.5.2 99533 1du3A 130 2.72e+01 1d4vA g.24.1.1,g.24.1.1,g.24.1.1 44927,44928,44929 1m4vA 204 2.77e+01 b.40.2.2,d.15.6.1 74459,74460 1buoA 121 2.77e+01 1buoA d.42.1.1 38631 1uuyA 167 2.78e+01 c.57.1.1 108059 1z2wA 192 2.78e+01 1kcnA 22 2.82e+01 k.30.1.2 72301 1dp4A 435 2.83e+01 1dp4A c.93.1.1 35710 1jfuA 186 2.85e+01 c.47.1.10 62940 1e5mA 416 2.85e+01 1dd8A c.95.1.1,c.95.1.1 58973,58974 1pyoA 167 2.86e+01 c.17.1.1 95370 1m7vA 363 2.86e+01 d.174.1.1 78748 2ez9A 603 2.92e+01 2d69A 430 2.95e+01 1nmoA 247 2.95e+01 c.135.1.1 91980 1xk7A 408 2.96e+01 1kwgA 645 2.96e+01 b.71.1.1,c.1.8.1,c.23.16.5 77561,77562,77563 1fukA 165 2.97e+01 1fukA c.37.1.19 32409 1j8mF 297 3.02e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 1rr7A 129 3.08e+01 a.4.1.14 105075 1ly1A 181 3.09e+01 c.37.1.1 74334 1drw 273 3.09e+01 1drw c.2.1.3,d.81.1.3 30057,39972 2sns 149 3.11e+01 1snc b.40.1.1 24860 1oh4A 179 3.13e+01 b.18.1.18 92978 1gnwA 211 3.14e+01 1gnwA a.45.1.1,c.47.1.5 17727,33021 1kgcD 206 3.16e+01 b.1.1.1,b.1.1.2 77384,77385 1xjjA 644 3.16e+01 1jr7A 311 3.17e+01 b.82.2.3 63255 1k8rB 110 3.17e+01 d.15.1.5 72180 1vrvA 101 3.18e+01 1n13B 113 3.22e+01 1gd0A 122 3.24e+01 1dptA d.80.1.3 39834 1scjB 71 3.24e+01 1scjB d.58.3.2 39069 1n3yA 198 3.25e+01 c.62.1.1 79976 1vmeA 410 3.30e+01 c.23.5.1,d.157.1.3 108893,108894 1ejdA 419 3.31e+01 1uae d.68.2.2 39576 1lzlA 323 3.35e+01 c.69.1.2 78306 1ni4B 341 3.36e+01 c.36.1.7,c.48.1.2 85729,85730 1qfjA 232 3.37e+01 1qfjA b.43.4.2,c.25.1.1 25655,31545 1i3dA 146 3.41e+01 a.1.1.2 61587 1sk4A 163 3.42e+01 d.118.1.1 105664 2cs3A 93 3.45e+01 1hc7A 477 3.45e+01 1hc7A c.51.1.1,d.104.1.1,d.68.5.1 60938,60939,60940 1muwA 386 3.50e+01 c.1.15.3 79495 1t77A 414 3.51e+01 1vcvA 226 3.51e+01 1jl5A 454 3.53e+01 c.10.2.6 66830 1iicA 422 3.55e+01 1nmtA d.108.1.2,d.108.1.2 62422,62423 1g2rA 100 3.57e+01 1g2rA d.192.1.1 60231 1t62A 166 3.57e+01 b.122.1.4 106541 1p1jA 533 3.59e+01 c.2.1.3,d.81.1.3 87687,87688 1w18A 493 3.62e+01 1vqoN 187 3.63e+01 1pea 385 3.63e+01 1pea c.93.1.1 35662 2awpA 198 3.67e+01 1v4xA 144 3.68e+01 a.1.1.2 108363 1yzsA 121 3.72e+01 1wkcA 184 3.73e+01 1f8vA 355 3.75e+01 2bbvA b.121.4.4 23329 1wloA 136 3.76e+01 1ey4A 149 3.78e+01 1snc b.40.1.1 24815 1v6sA 390 3.82e+01 c.86.1.1 100424 1b7yB 785 3.82e+01 1pysB a.6.1.1,a.6.1.1,b.40.4.4,d.58.13.1,d.104.1.1,d.138.1.1 16301,16302,25312,39311,40780,41456 1t8kA 77 3.83e+01 a.28.1.1 106666 7taa 478 3.84e+01 7taa b.71.1.1,c.1.8.1 27778,28765 1ornA 226 3.86e+01 a.96.1.1 87342 1zn8A 180 3.86e+01 1fgkA 310 3.87e+01 1fgkA d.144.1.7 41693 1f00I 282 3.87e+01 1f00I b.1.14.1,b.1.14.1,d.169.1.3 22368,22369,42439 1ub3A 220 3.88e+01 c.1.10.1 88395 1rzuA 485 3.89e+01 c.87.1.8 105140 1pujA 282 3.92e+01 c.37.1.8 88294 1w66A 232 3.93e+01 2cbiA 594 3.96e+01 1v0wA 506 3.96e+01 d.136.1.2,d.136.1.2 108220,108221 1wnyA 186 3.97e+01 1ej2A 181 4.01e+01 1f9aA c.26.1.3 59414 1jl3A 139 4.05e+01 c.44.1.1 66826 1ud9A 245 4.05e+01 d.131.1.2,d.131.1.2 107768,107769 1irdA 141 4.08e+01 a.1.1.2 66286 2ca6A 386 4.10e+01 1zmaA 118 4.14e+01 1w2wB 191 4.18e+01 1fjnA 39 4.20e+01 1fjnA g.3.7.3 44171 1dk0A 188 4.20e+01 1b2vA d.35.1.1 38530 2culA 232 4.24e+01 1h4rA 314 4.24e+01 a.11.2.1,b.55.1.5,d.15.1.4 65616,65617,65618 1j0hA 588 4.26e+01 b.1.18.2,b.71.1.1,c.1.8.1 77027,77028,77029 1v7cA 351 4.27e+01 c.79.1.1 100446 2eifA 136 4.29e+01 1bkb b.34.5.2,b.40.4.5 24607,25339 1ls1A 295 4.31e+01 a.24.13.1,c.37.1.10 78170,78171 1x1tA 260 4.32e+01 1yhtA 367 4.33e+01 1qr0A 228 4.37e+01 1qr0A d.150.1.1,d.150.1.1 59038,59039 1tr9A 341 4.38e+01 2c07A 285 4.39e+01 1vdmA 153 4.43e+01 2aheA 267 4.44e+01 1jpyA 137 4.46e+01 g.17.1.6 67065 2b8eA 273 4.52e+01 1na3A 91 4.54e+01 k.38.1.1 85481 2d5cA 263 4.67e+01 1g24A 211 4.68e+01 1g24A d.166.1.1 42270 1m6sA 347 4.68e+01 c.67.1.1 78701 1ohzB 60 4.69e+01 a.139.1.1 93044 1ceo 343 4.75e+01 1ceo c.1.8.3 28808 2bb6A 414 4.76e+01 1fm4A 159 4.78e+01 1bv1 d.129.3.1 76186 2d5xA 141 4.79e+01 1gtkA 313 4.80e+01 c.94.1.1,d.50.2.1 76346,76347 1wkbA 810 4.81e+01 2fjbA 643 4.81e+01 1fmjA 351 4.86e+01 c.37.1.5 59879 1nv8A 284 4.90e+01 c.66.1.30 86224 3dfr 162 4.91e+01 3dfr c.71.1.1 34880 1va0A 239 4.94e+01 1z0sA 278 4.95e+01 1gmxA 108 4.97e+01 c.46.1.3 65355 2bolA 314 4.98e+01 1wmuB 146 5.00e+01 a.1.1.2 109417 1fx2A 235 5.02e+01 1fx2A d.58.29.1 39430 1wr2A 238 5.04e+01 1n81A 186 5.08e+01 a.185.1.1 85388 1ruwA 69 5.08e+01 1yf3A 259 5.10e+01 1h99A 224 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