# List of top-scoring protein chains for t04-100-30-alpha-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 1o0sA 605 6.26e-01 c.2.1.7,c.58.1.3 86540,86541 1que 303 1.24e+00 1fnc b.43.4.2,c.25.1.1 25647,31537 1rtfB 252 1.31e+00 5ptp 2bsaA 303 1.37e+00 1ocxA 182 1.40e+00 b.81.1.3 86814 1sxvA 172 1.43e+00 1fjrA 195 1.45e+00 1fjrA b.102.1.1 59855 1fnd 314 1.53e+00 1fnc b.43.4.2,c.25.1.1 25626,31516 1fnc 314 1.59e+00 1fnc b.43.4.2,c.25.1.1 25627,31517 1ex7A 186 1.59e+00 1gky c.37.1.1 59537 1bx1A 314 1.72e+00 1fnc b.43.4.2,c.25.1.1 25629,31519 1go2A 304 1.81e+00 b.43.4.2,c.25.1.1 76243,76244 1gky 187 1.83e+00 1gky c.37.1.1 31839 2a9dA 372 2.08e+00 1ogiA 303 2.22e+00 b.43.4.2,c.25.1.1 92914,92915 1w34A 304 2.29e+00 1mwwA 128 2.36e+00 d.80.1.4 91483 2b5oA 402 2.38e+00 1soxA 466 2.55e+00 1soxA b.1.18.6,d.120.1.1,d.176.1.1 21947,41090,42563 1tu1A 148 3.09e+00 d.107.1.3 107316 1ly1A 181 3.25e+00 c.37.1.1 74334 1aokB 122 3.29e+00 1poa a.133.1.2 19561 1s31A 273 3.31e+00 1dy9A 187 3.81e+00 1jxpA b.47.1.3 26400 2f1lA 187 3.85e+00 1dbhA 354 4.44e+00 1awe a.87.1.1,b.55.1.1 18514,26967 1jltB 122 4.47e+00 a.133.1.2 66868 1dkzA 219 4.64e+00 1dkzA a.8.4.1,b.130.1.1 90345,90346 1uch 230 4.73e+00 1uch d.3.1.6 37129 1ltqA 301 4.94e+00 c.108.1.9,c.37.1.1 78208,78209 1xd3A 230 5.16e+00 1dp4A 435 5.23e+00 1dp4A c.93.1.1 35710 1bb9 115 5.29e+00 1bb9 b.34.2.1 24554 1c8zA 265 5.96e+00 1c8zA d.23.1.1 38375 2cyeA 133 6.49e+00 1b65A 375 6.51e+00 1b65A d.154.1.1 42020 2b6nA 278 6.54e+00 1aym3 238 7.53e+00 1aym3 1ryoA 327 8.17e+00 c.94.1.2 98108 1y4wA 518 8.66e+00 1h59B 54 8.75e+00 g.3.9.1 70881 2axyA 73 8.83e+00 1zj8A 566 8.91e+00 1a8e 329 9.14e+00 1cb6A c.94.1.2 35888 1ifrA 121 9.24e+00 b.1.16.1 71203 1vj2A 126 9.31e+00 b.82.1.10 100796 1xl3C 92 9.77e+00 2fimA 276 9.87e+00 3sil 379 1.03e+01 3sil b.68.1.1 27542 1mwmA 320 1.04e+01 c.55.1.1,c.55.1.1 79580,79581 2cz2A 223 1.08e+01 1j1bA 420 1.11e+01 d.144.1.7 90758 1xkzA 255 1.12e+01 1x9gA 200 1.13e+01 c.33.1.3 109527 1gw0A 559 1.13e+01 b.6.1.3,b.6.1.3,b.6.1.3 70623,70624,70625 1gcqC 70 1.17e+01 1gcpA b.34.2.1 60436 1e79H 146 1.22e+01 1e79H a.2.10.1,b.93.1.1 15721,28438 2bpsA 81 1.25e+01 1ywnA 316 1.26e+01 1j3wA 163 1.29e+01 d.110.7.1 90833 1s4iA 175 1.30e+01 2b18A 164 1.32e+01 1vk0A 206 1.33e+01 c.55.3.5 100839 1nqeA 594 1.38e+01 f.4.3.3 86027 1i19A 561 1.39e+01 1i19A d.58.32.3,d.145.1.1 61522,61523 1jxcA 68 1.40e+01 g.3.7.5 77201 1sskA 158 1.44e+01 b.148.1.1 105986 1rlw 126 1.50e+01 1rlw b.7.1.1 23177 2b1xA 470 1.51e+01 2aw5A 541 1.51e+01 1xa1A 255 1.52e+01 e.3.1.1 109529 1kdj 102 1.54e+01 1plc b.6.1.1 22864 1w85A 368 1.55e+01 2bkqA 212 1.59e+01 1o4tA 133 1.59e+01 b.82.1.9 86622 2eifA 136 1.61e+01 1bkb b.34.5.2,b.40.4.5 24607,25339 1y43B 173 1.61e+01 1j1lA 290 1.64e+01 b.82.1.12 90766 1gppA 237 1.64e+01 b.86.1.2 76262 1cjxA 357 1.65e+01 1cjxA d.32.1.3,d.32.1.3 38516,38517 1t46A 313 1.67e+01 d.144.1.7 106397 1v8fA 276 1.67e+01 c.26.1.4 100503 1x0vA 354 1.67e+01 1za7A 165 1.71e+01 1sbzA 197 1.74e+01 1g8aA 227 1.75e+01 c.66.1.3 90506 1pyaB 228 1.81e+01 1pyaB 1dmhA 311 1.81e+01 1dmhA b.3.6.1 22633 1tqnA 486 1.85e+01 a.104.1.1 107238 2f1rA 171 1.85e+01 1xel 338 1.91e+01 1xel c.2.1.2 29786 1k6wA 426 1.94e+01 b.92.1.2,c.1.9.5 68236,68237 1udc 338 1.95e+01 1xel c.2.1.2 29785 1po5A 476 1.97e+01 a.104.1.1 94963 1bs0A 384 1.98e+01 1bs0A c.67.1.4 34490 1ixcA 294 2.01e+01 a.4.5.37,c.94.1.1 83764,83765 1gdvA 85 2.01e+01 1ctj a.3.1.1 60458 1pvc3 238 2.02e+01 1aym3 1ra0A 430 2.03e+01 1g55A 343 2.04e+01 1g55A c.66.1.26 34247 1fuiA 591 2.05e+01 1fuiA b.43.2.1,c.85.1.1 25674,35444 1m0wA 491 2.09e+01 c.30.1.4,d.142.1.6 78363,78364 1xg8A 111 2.10e+01 1h8eH 146 2.17e+01 1e79H b.93.1.1 60757 1y8oB 128 2.18e+01 1q9jA 422 2.23e+01 c.43.1.2,c.43.1.2 104590,104591 1rjiA 31 2.24e+01 g.3.7.2 97568 1qxrA 189 2.24e+01 b.82.1.7 96552 1s21A 206 2.25e+01 d.166.1.4 105222 1rq2A 382 2.29e+01 c.32.1.1,d.79.2.1 105048,105049 1to2E 281 2.29e+01 2blkA 122 2.30e+01 1ujnA 348 2.30e+01 e.22.1.1 99460 1t61A 229 2.31e+01 d.169.1.6,d.169.1.6 106529,106530 1e19A 314 2.34e+01 1b7bA c.73.1.1 34967 1sup 275 2.44e+01 1gci c.41.1.1 32510 1rliA 184 2.45e+01 c.23.5.6 97647 1cruA 454 2.48e+01 1c9uA b.68.2.1 27617 1fjgB 256 2.49e+01 1fjfB c.23.15.1 31400 1jxpA 186 2.52e+01 1jxpA b.47.1.3 26402 1fsu 492 2.56e+01 1auk c.76.1.2 35032 1g6oA 330 2.59e+01 1g6oA c.37.1.11 32430 1txvB 440 2.66e+01 1g0hA 252 2.67e+01 1dk4A e.7.1.1 60171 1r6wA 322 2.68e+01 c.1.11.2,d.54.1.1 97165,97166 2fmlA 273 2.71e+01 1ze3D 125 2.77e+01 2aegA 268 2.87e+01 1ebfA 358 2.89e+01 1ebuA c.2.1.3,d.81.1.2 30033,39948 2avtA 378 2.92e+01 1dm9A 133 2.94e+01 1dm9A d.66.1.3 39560 1h4rA 314 2.96e+01 a.11.2.1,b.55.1.5,d.15.1.4 65616,65617,65618 1lf2A 331 2.98e+01 b.50.1.2 77914 1lw6E 281 3.02e+01 c.41.1.1 74293 1rybA 212 3.03e+01 c.56.3.1 98098 2c0nA 203 3.07e+01 1gg3A 279 3.11e+01 1ef1A a.11.2.1,b.55.1.5,d.15.1.4 16372,27007,37615 1shyB 551 3.14e+01 b.69.12.1,g.16.2.1 105565,105566 1w25A 459 3.15e+01 1yemA 179 3.17e+01 1sesA 421 3.18e+01 1sesA a.2.7.1,d.104.1.1 15710,40710 1x82A 190 3.22e+01 1eljA 381 3.22e+01 4mbp c.94.1.1 35791 1fgxA 288 3.26e+01 1fgxA c.68.1.2 34508 1cl8A 276 3.28e+01 1ckqA c.52.1.1 33230 1wd6A 123 3.28e+01 1ru0A 105 3.37e+01 1wddS 128 3.38e+01 1cp2A 269 3.39e+01 1cp2A c.37.1.10 32269 1yzfA 195 3.43e+01 1fxoA 293 3.50e+01 1g0rA c.68.1.6 34524 1ov3A 138 3.54e+01 b.34.2.1,b.34.2.1 87451,87452 1wlpB 138 3.59e+01 1rwrA 301 3.64e+01 b.80.1.11 97990 1kte 105 3.64e+01 1kte c.47.1.1 32771 1afwA 393 3.67e+01 1afwA c.95.1.1,c.95.1.1 35900,35901 1b9wA 89 3.68e+01 1b9wA g.3.11.4,g.3.11.4 44334,44335 1ik9A 213 3.69e+01 b.59.1.1,h.1.11.1 66176,66177 2ffcA 353 3.76e+01 1o0iA 138 3.80e+01 d.38.1.5 86532 1dixA 208 3.83e+01 1bk7A d.124.1.1 41122 1d8hA 311 3.85e+01 1d8iA d.63.1.1 39544 3proC 166 3.86e+01 3proC d.52.1.1,d.52.1.1 38812,38813 1wi9A 72 3.89e+01 1wloA 136 3.95e+01 1xaoA 121 3.99e+01 1ufkA 254 4.03e+01 c.66.1.39 99340 1hg4A 279 4.07e+01 1lbd a.123.1.1 19333 1bdyA 123 4.10e+01 1bdyA b.7.1.1 23190 1yn4A 99 4.12e+01 1opd 85 4.14e+01 1ptf d.94.1.1 40560 2d4rA 147 4.17e+01 1fjgE 162 4.20e+01 1pkp d.14.1.1,d.50.1.2 37553,38789 1mv3A 213 4.22e+01 b.34.2.1 91468 1yroB 286 4.27e+01 1nmmB 286 4.28e+01 c.68.1.2 80662 1uj0A 62 4.30e+01 b.34.2.1 99449 1vlmA 219 4.32e+01 c.66.1.41 108836 1vpqA 273 4.34e+01 2afwA 329 4.34e+01 1dosA 358 4.36e+01 1dosA c.1.10.2 29175 1f5mA 180 4.37e+01 1f5mB d.110.2.1 40895 1a4iA 301 4.38e+01 1a4iA c.2.1.7,c.58.1.2 30278,33926 1sqeA 109 4.39e+01 d.58.4.5 105908 1twuA 139 4.45e+01 d.32.1.8 107413 1pfzA 380 4.46e+01 1smrA b.50.1.2 26881 1fadA 99 4.46e+01 1fadA a.77.1.2 18428 1zbmA 280 4.50e+01 1kbvA 327 4.53e+01 b.6.1.3,b.6.1.3 68395,68396 1jv4A 162 4.53e+01 b.60.1.1 67343 1w96A 554 4.55e+01 1g2nA 264 4.55e+01 1lbd a.123.1.1 60227 1v93A 296 4.57e+01 c.1.23.1 100532 1k7kA 221 4.62e+01 c.51.4.1 72104 1kv9A 668 4.65e+01 a.3.1.6,b.70.1.1 73056,73057 2g9iA 249 4.74e+01 3tdt 274 4.74e+01 3tdt b.81.1.2 28053 1zxuA 217 4.78e+01 1wr3A 36 4.78e+01 1hleA 345 4.80e+01 1ovaA e.1.1.1 42618 1gs5A 258 4.90e+01 c.73.1.2 70395 1nnvA 110 4.93e+01 d.17.7.1 92012 1i05A 180 4.93e+01 1mup b.60.1.1 27130 1pgjA 478 4.93e+01 2pgd a.100.1.1,c.2.1.6 18783,30195 1li1A 229 4.96e+01 d.169.1.6,d.169.1.6 73898,73899 1w2lA 99 4.97e+01 1ru4A 400 4.97e+01 b.80.1.9 97836 1gxrA 337 5.03e+01 b.69.4.1 70722 2a0fA 310 5.03e+01 1pg6A 243 5.05e+01 b.82.5.2 94673 1o59A 355 5.05e+01 b.18.1.22,b.18.1.22 92495,92496 2czdA 208 5.05e+01 1f39A 101 5.08e+01 1umuA b.87.1.1 28386 1bjwA 382 5.12e+01 1bjwA c.67.1.1 34349 1xtlA 175 5.22e+01 1vl2A 421 5.23e+01 c.26.2.1,d.210.1.1 108708,108709 1c3jA 351 5.23e+01 1c3jA c.87.1.1 35459 1iwmA 186 5.25e+01 b.125.1.2 83758 2a5jA 191 5.37e+01 2prd 174 5.39e+01 2prd b.40.5.1 25435 1vm6A 228 5.41e+01 c.2.1.3,d.81.1.3 108876,108877 1u1zA 168 5.42e+01 d.38.1.6 107602 1tvdA 116 5.44e+01 1tvdA b.1.1.1 20650 2rslA 140 5.44e+01 2rslA c.53.1.1 33345 2bshA 125 5.47e+01 1qy1A 174 5.49e+01 b.60.1.1 96568 1aq0A 306 5.52e+01 1aq0A c.1.8.3 28842 1tuaA 191 5.54e+01 d.51.1.1,d.51.1.1 107321,107322 1k0wA 231 5.55e+01 c.74.1.1 77220 1s2kA 206 5.57e+01 b.29.1.20 98389 1wqwA 235 5.58e+01 1wcqA 601 5.59e+01 1y5eA 169 5.65e+01 1rwiA 270 5.67e+01 b.68.9.1 97987 1sr4C 166 5.72e+01 b.42.2.1 105950 1qr6A 584 5.73e+01 1qr6A c.2.1.7,c.58.1.3 30293,33941 1ycdA 243 5.75e+01 2a6sA 84 5.78e+01 1go3F 107 5.81e+01 a.60.8.2 65407 2aw2B 108 5.82e+01 1mc0A 368 5.82e+01 d.110.2.1,d.110.2.1 78937,78938 1kaeA 434 5.87e+01 c.82.1.2 72247 1d2eA 397 5.91e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25701,25741,32136 1g99A 408 5.93e+01 1g99A c.55.1.2,c.55.1.2 33457,33458 1bowA 159 5.96e+01 1bowA d.60.1.1 39528 1o7dE 126 6.06e+01 1svb 395 6.06e+01 1svb b.1.18.4,f.10.1.1 21814,43827 1yqfA 203 6.08e+01 1ha3A 405 6.09e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 2b5lC 222 6.12e+01 1e5eA 404 6.15e+01 1ibjA c.67.1.3 59265 1w8oA 601 6.18e+01 1y0zA 330 6.21e+01 1gvp 87 6.23e+01 1gvp b.40.4.7 25369 1ryqA 69 6.25e+01 g.41.9.3 105126 1kao 167 6.28e+01 1ctqA c.37.1.8 32014 1blxA 326 6.28e+01 1hcl d.144.1.7 41596 1ng2A 193 6.29e+01 b.34.2.1,b.34.2.1 85660,85661 1vqb 87 6.30e+01 1gvp b.40.4.7 25370 1m40A 263 6.30e+01 e.3.1.1 74437 2bjuA 453 6.35e+01 1vd5A 377 6.41e+01 a.102.1.7 108518 2bopA 85 6.42e+01 2bopA d.58.8.1 39217 1ta9A 450 6.43e+01 1ra9 159 6.43e+01 1vdrA c.71.1.1 34820 1wnlA 235 6.43e+01 1lktA 104 6.44e+01 1lktA b.90.1.1 28398 1b5pA 385 6.46e+01 c.67.1.1 90403 1t8sA 484 6.46e+01 c.56.2.1 106679 1ogdA 131 6.47e+01 c.133.1.1 92893 2f62A 161 6.53e+01 1v3vA 333 6.55e+01 b.35.1.2,c.2.1.1 108345,108346 1eerB 227 6.57e+01 1eerB b.1.2.1,b.1.2.1 22011,22012 1xtmA 175 6.59e+01 1jeyA 609 6.62e+01 1jeqA b.131.1.1,c.62.1.3 90370,90371 1fw1A 216 6.62e+01 a.45.1.1,c.47.1.5 60051,60052 1rgzA 363 6.62e+01 e.3.1.1 97457 1tzaA 134 6.66e+01 b.1.23.1 107468 2mev1 277 6.66e+01 2mev1 1tp9A 162 6.67e+01 1zndA 174 6.68e+01 2cc3A 150 6.69e+01 1khiA 176 6.77e+01 b.34.5.2,b.40.4.5 77408,77409 1b35A 260 6.77e+01 1b35A b.121.4.1 23333 1ignA 246 6.77e+01 1ignA a.4.1.6,a.4.1.6 16048,16049 1zt2B 212 6.77e+01 1dq3A 454 6.79e+01 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1bj7 156 6.84e+01 1bj7 b.60.1.1 27113 1amx 180 6.85e+01 1amx b.2.3.1 22410 1ermA 263 6.86e+01 1btl e.3.1.1 42690 1k5cA 335 6.90e+01 b.80.1.3 72076 1mnnA 340 6.92e+01 b.2.5.7 79324 1lkkA 105 6.94e+01 1lckA d.93.1.1 40412 2bsjA 133 6.96e+01 1lst 239 6.97e+01 1lst c.94.1.1 35755 1wgkA 114 6.98e+01 1y60A 169 6.98e+01 1mrzA 293 6.98e+01 b.43.5.1,c.26.1.3 91452,91453 1uliA 460 7.01e+01 b.33.1.2,d.129.3.3 107921,107922 1ll7A 392 7.02e+01 c.1.8.5,d.26.3.1 78085,78086 1binB 143 7.04e+01 2gdm a.1.1.2 15232 1ppt 36 7.06e+01 1ppt j.6.1.1 46089 1b8aA 438 7.08e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 2bhvA 246 7.10e+01 1r9jA 673 7.11e+01 2bkyA 97 7.12e+01 2a0kA 161 7.16e+01 2f2tA 161 7.19e+01 1fmb 104 7.22e+01 1fmb b.50.1.1 26777 1b34B 118 7.23e+01 1b34B b.38.1.1 24797 1xcbA 211 7.23e+01 a.4.5.38,c.2.1.12 109552,109553 3csuA 310 7.27e+01 3csuA c.78.1.1,c.78.1.1 35094,35095 2gdnA 267 7.29e+01 1xgkA 352 7.33e+01 1a05A 358 7.34e+01 1cnzA c.77.1.1 35059 1ztuA 341 7.34e+01 1xr4A 509 7.35e+01 1oxwA 373 7.35e+01 c.19.1.3 87539 2arkA 188 7.36e+01 1i58A 189 7.38e+01 1b3qA d.122.1.3 61773 1v8yA 170 7.39e+01 1d2kA 392 7.41e+01 1d2kA c.1.8.5,d.26.3.1 29008,38442 1uqxA 113 7.49e+01 b.115.1.1 99801 1fu1A 203 7.49e+01 1fu1B b.59.1.1,h.1.11.1 27076,45630 2biiA 424 7.50e+01 2bf9A 36 7.55e+01 2a4nA 182 7.56e+01 1orc 71 7.57e+01 1orc a.35.1.2 17054 1zxkA 98 7.59e+01 1ymzA 43 7.60e+01 1fzqA 181 7.65e+01 1hurA c.37.1.8 32060 1oaqL 120 7.68e+01 b.1.1.1 92708 1zyeA 220 7.68e+01 1ti6B 274 7.70e+01 b.3.5.1,d.58.1.5 106976,106977 1s7jA 262 7.79e+01 d.21.1.2 98647 1wdvA 152 7.80e+01 1ggxA 223 7.81e+01 1ggxA d.22.1.1 38367 1mmvB 419 7.88e+01 d.174.1.1 91318 1e4cP 215 7.91e+01 2fua c.74.1.1 34969 2b6eA 146 7.96e+01 2amyA 246 8.09e+01 1je0A 236 8.09e+01 c.56.2.1 66581 1k6xA 352 8.11e+01 c.2.1.2 68238 1uteA 313 8.34e+01 1uteA d.159.1.1 42078 1t33A 224 8.40e+01 a.4.1.9,a.121.1.1 106295,106296 2bh8A 101 8.41e+01 1btl 263 8.43e+01 1btl e.3.1.1 42691 1bvoA 175 8.50e+01 1a3qA b.2.5.3 22457 2f7tA 227 8.52e+01 1a32 88 8.55e+01 1a32 a.16.1.2 16384 1zgoA 223 8.60e+01 1zbpA 273 8.68e+01 2chhA 114 8.71e+01 1vyyA 113 8.71e+01 1wfuA 120 8.72e+01 1s5pA 235 8.72e+01 c.31.1.5 98569 2a9gA 418 8.73e+01 2f6rA 281 8.81e+01 1u6rA 380 8.82e+01 1lx7A 253 8.86e+01 c.56.2.1 74329 4dfrA 159 8.86e+01 1vdrA c.71.1.1 34822 1xo3A 101 8.88e+01 1jixA 351 8.88e+01 1c3jA c.87.1.1 63081 1om4A 422 8.90e+01 d.174.1.1 87067 2fp7B 172 8.94e+01