# List of top-scoring protein chains for T0293.t2k-w0.5 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 1t43A 277 1.94e-21 c.66.1.30 106392 2b3tA 276 1.96e-21 1sg9A 282 4.24e-18 c.66.1.30 105526 1nv8A 284 4.24e-18 c.66.1.30 86224 1vq1A 294 4.26e-18 1dusA 194 2.05e-11 1dusA c.66.1.4 34182 1ufkA 254 1.50e-10 c.66.1.39 99340 2as0A 396 1.53e-10 1l3iA 192 1.29e-08 c.66.1.22 77676 1wxxA 382 1.57e-08 1g6q1 328 2.97e-08 1g6q2 2fytA 340 4.82e-08 1ne2A 200 6.11e-08 c.66.1.32 85586 1f3lA 321 8.76e-08 1g6q2 c.66.1.6 59630 1wznA 252 1.31e-07 1ve3A 227 1.33e-07 2esrA 177 1.68e-07 1wy7A 207 2.68e-07 2fhpA 187 3.23e-07 1jg1A 235 8.64e-07 c.66.1.7 66661 1or8A 340 1.22e-06 c.66.1.6 93451 1oriA 343 1.23e-06 c.66.1.6 87339 1orhA 353 1.71e-06 c.66.1.6 93455 1xxlA 239 1.83e-06 1nkvA 256 2.00e-06 c.66.1.21 80577 1ws6A 171 2.95e-06 1dl5A 317 3.02e-06 1dl5A c.66.1.7,d.197.1.1 64720,64721 2gh1A 301 5.33e-06 1o54A 277 6.03e-06 c.66.1.13 92482 2frnA 278 1.23e-05 1sqgA 429 1.57e-05 a.79.1.3,c.66.1.38 105912,105913 1uwvA 433 1.73e-05 b.40.4.12,c.66.1.40 100128,100129 1vl5A 260 1.84e-05 c.66.1.41 108720 1yzhA 214 2.09e-05 1xvaA 292 2.31e-05 1xvaA c.66.1.5 34183 1vbfA 231 2.38e-05 c.66.1.7 108475 1d2gA 292 2.71e-05 1xvaA c.66.1.5 34187 2admA 421 3.39e-05 2admA c.66.1.27 34238 1aqjA 421 3.41e-05 2admA c.66.1.27 34242 1g38A 393 3.53e-05 2admA c.66.1.27 60235 1r8xA 292 5.05e-05 c.66.1.5 104855 1zq9A 285 8.57e-05 1yub 245 9.39e-05 2ercA c.66.1.24 34219 1jsxA 207 9.96e-05 c.66.1.20 71846 1r74A 294 1.01e-04 c.66.1.5 104828 1m6yA 301 1.17e-04 a.60.13.1,c.66.1.23 78716,78717 1tw3A 360 1.89e-04 a.4.5.29,c.66.1.12 107373,107374 1qzzA 374 1.92e-04 a.4.5.29,c.66.1.12 96719,96720 2b2cA 314 1.94e-04 2avnA 260 2.13e-04 1y8cA 246 2.64e-04 1i9gA 280 5.78e-04 c.66.1.13 62090 1yb2A 275 7.15e-04 1jvbA 347 7.71e-04 b.35.1.2,c.2.1.1 77181,77182 1suiA 247 7.84e-04 2fpoA 202 9.65e-04 1ntoA 347 1.03e-03 b.35.1.2,c.2.1.1 92137,92138 1vlmA 219 1.13e-03 c.66.1.41 108836 2avdA 219 1.31e-03 1ri5A 298 1.36e-03 c.66.1.34 97502 1p91A 269 1.68e-03 c.66.1.33 94378 2f8lA 344 1.87e-03 2b25A 336 2.73e-03 1ixkA 315 4.39e-03 c.66.1.38 90716 1i1nA 226 4.73e-03 c.66.1.7 71102 1qamA 244 4.73e-03 2ercA c.66.1.24 34220 1o9gA 250 4.90e-03 c.66.1.29 86692 1xdzA 240 5.47e-03 1im8A 244 5.56e-03 c.66.1.14 66212 1o9hA 250 5.98e-03 c.66.1.29 86693 1kpiA 302 8.75e-03 c.66.1.18 68743 1h1dA 221 9.27e-03 c.66.1.1 83452 1tpyA 287 1.05e-02 1l1eA 287 1.09e-02 c.66.1.18 73454 1kpgA 287 1.16e-02 c.66.1.18 68735 2ex4A 241 1.48e-02 1zdzA 302 1.54e-02 1uirA 314 1.67e-02 c.66.1.17 99429 1mjfA 281 1.79e-02 c.66.1.17 79198 1r18A 227 2.11e-02 c.66.1.7 96800 2fk8A 318 3.21e-02 1xtpA 254 3.23e-02 1xj5A 334 9.05e-02 1nw8A 319 1.25e-01 c.66.1.11 86292 1eg2A 319 1.31e-01 1eg2A c.66.1.11 34249 1iy9A 275 2.33e-01 c.66.1.17 76943 1jqeA 292 2.53e-01 c.66.1.19 71789 2aotA 292 3.15e-01 1nw3A 416 4.69e-01 c.66.1.31 86288 1g55A 343 6.30e-01 1g55A c.66.1.26 34247 1h2bA 359 6.65e-01 b.35.1.2,c.2.1.1 90543,90544 1g60A 260 7.86e-01 c.66.1.11 70151 1bc5A 269 8.04e-01 1af7 a.58.1.1,c.66.1.8 17929,34204 1y9kA 157 8.05e-01 1af7 274 8.09e-01 1af7 a.58.1.1,c.66.1.8 17928,34203 1fp2A 352 9.63e-01 1fpxA a.4.5.29,c.66.1.12 59941,59942 1zcjA 463 9.81e-01 1u2zA 433 1.05e+00 c.66.1.31 107626 1zemA 262 1.26e+00 1nytA 271 1.87e+00 c.2.1.7,c.58.1.5 86417,86418 1ej6A 1289 1.96e+00 i.7.1.1 45967 1lluA 342 2.04e+00 b.35.1.2,c.2.1.1 91064,91065 1rjdA 334 2.11e+00 c.66.1.37 97558 1inlA 296 2.54e+00 c.66.1.17 66220 1b3rA 431 2.56e+00 1b3rA c.2.1.4,c.23.12.3 30106,31366 1xwfA 431 2.56e+00 2ar0A 541 2.62e+00 1p1cA 199 2.68e+00 c.66.1.16 87669 1khhA 198 2.70e+00 c.66.1.16 68615 1zx0A 236 2.72e+00 1xclA 235 2.86e+00 1o0yA 260 3.43e+00 c.1.10.1 80756 1pl8A 356 3.53e+00 b.35.1.2,c.2.1.1 94878,94879 1booA 323 3.87e+00 1booA c.66.1.11 34248 2dpmA 284 4.06e+00 2dpmA c.66.1.28 34246 1g3kA 174 4.11e+00 1nedA d.153.1.4 41989 2a14A 263 5.16e+00 1woqA 267 5.43e+00 c.55.1.10,c.55.1.10 109462,109463 1d0vA 356 5.54e+00 1d0vA c.39.1.1 32476 1a7aA 432 5.54e+00 1b3rA c.2.1.4,c.23.12.3 30104,31364 1li4A 432 5.54e+00 c.2.1.4,c.23.12.3 84616,84617 2fb7A 95 5.68e+00 1q0sA 259 6.13e+00 c.66.1.28 95509 1k7hA 476 7.20e+00 c.76.1.1 72101 1wj9A 211 7.21e+00 1bg6 359 7.35e+00 1bg6 a.100.1.5,c.2.1.6 18810,30214 1yfjA 259 7.38e+00 1yf3A 259 7.43e+00 1fmcA 255 7.62e+00 1cydA c.2.1.2 29856 2b9eA 303 8.16e+00 1ej0A 180 8.24e+00 1ej0A c.66.1.2 34179 1yvkA 163 8.27e+00 1dabA 539 8.34e+00 1dabA b.80.1.7 28049 1s4nA 348 8.81e+00 c.68.1.16 98501 1jbqA 435 8.84e+00 1oasA c.79.1.1 62850 1wg8A 285 9.56e+00 1nt2A 210 9.82e+00 c.66.1.3 86149 1m54A 363 9.84e+00 c.79.1.1 74463 1a71A 374 1.06e+01 2ohxA b.35.1.2,c.2.1.1 24673,29689 1ul5A 88 1.07e+01 g.72.1.1 99539 1axgA 374 1.08e+01 2ohxA b.35.1.2,c.2.1.1 24691,29707 1zejA 293 1.11e+01 2ew2A 316 1.18e+01 1x9nA 688 1.21e+01 1rjwA 339 1.22e+01 b.35.1.2,c.2.1.1 97582,97583 2aedA 181 1.23e+01 1u3tA 374 1.25e+01 1f8fA 371 1.26e+01 b.35.1.2,c.2.1.1 83246,83247 1b0uA 262 1.27e+01 1b0uA c.37.1.12 32370 1z0fA 179 1.30e+01 1d4fA 431 1.31e+01 1b3rA c.2.1.4,c.23.12.3 30110,31370 1m03A 512 1.32e+01 c.1.8.6,d.92.2.1 78322,78323 1p5vA 235 1.37e+01 b.1.11.1,b.7.2.1 87812,87813 1m04A 512 1.37e+01 c.1.8.6,d.92.2.1 78324,78325 1jakA 512 1.39e+01 c.1.8.6,d.92.2.1 66472,66473 2jxrA 329 1.39e+01 1smrA b.50.1.2 26831 1e0jA 289 1.40e+01 1cr1A c.37.1.11 32290 2bgkA 278 1.40e+01 1cr1A 296 1.41e+01 1cr1A c.37.1.11 32286 1dpjA 329 1.46e+01 1smrA b.50.1.2 26828 1shqA 478 1.50e+01 c.76.1.1 105560 1znqO 338 1.51e+01 1u8fO 335 1.53e+01 1lssA 140 1.54e+01 c.2.1.9 74246 1bdfA 235 1.55e+01 1bdfA d.74.3.1,d.181.1.1 39727,42602 1w25A 459 1.75e+01 2azjA 289 1.80e+01 2c4wA 176 1.82e+01 2azkA 289 1.99e+01 1zx3A 122 2.02e+01 1g0vA 329 2.06e+01 1smrA b.50.1.2 60189 1qv6A 374 2.06e+01 b.35.1.2,c.2.1.1 96348,96349 1b9bA 255 2.14e+01 1amk c.1.1.1 28531 1hdyA 374 2.15e+01 2ohxA b.35.1.2,c.2.1.1 24723,29739 1u3uA 374 2.16e+01 1htbA 374 2.16e+01 2ohxA b.35.1.2,c.2.1.1 24715,29731 1qo8A 566 2.31e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19696,30433,42316 1reoA 486 2.39e+01 c.3.1.2,d.16.1.5 97325,97326 1wvbA 322 2.48e+01 2aebA 322 2.48e+01 1l5oA 356 2.56e+01 c.39.1.1 77711 1q57A 503 2.60e+01 c.37.1.11,e.13.1.2 95867,95868 1axeA 374 2.61e+01 2ohxA b.35.1.2,c.2.1.1 24681,29697 1heuA 374 2.65e+01 2ohxA b.35.1.2,c.2.1.1 60979,60980 1n8kA 374 2.65e+01 b.35.1.2,c.2.1.1 80298,80299 1ju9A 374 2.68e+01 b.35.1.2,c.2.1.1 63293,63294 1jxsA 98 2.71e+01 a.4.5.14 84254 1mgoA 374 2.72e+01 b.35.1.2,c.2.1.1 79094,79095 1jl3A 139 2.74e+01 c.44.1.1 66826 2acxA 576 2.80e+01 2c6yA 111 2.80e+01 1qlhA 374 2.82e+01 2ohxA b.35.1.2,c.2.1.1 24685,29701 1ee2A 373 2.83e+01 2ohxA b.35.1.2,c.2.1.1 24663,29679 1xdwA 331 2.85e+01 1a1s 314 2.88e+01 1othA c.78.1.1,c.78.1.1 35258,35259 1pvvA 315 2.88e+01 c.78.1.1,c.78.1.1 95190,95191 1ton 235 2.91e+01 5ptp b.47.1.2 26307 2c4vA 167 2.92e+01 1r9lA 309 2.95e+01 c.94.1.1 97262 1jcfA 344 3.01e+01 c.55.1.1,c.55.1.1 62878,62879 1jgcA 161 3.07e+01 a.25.1.1 66673 1r6aA 295 3.15e+01 c.66.1.25 104817 1j0xO 332 3.17e+01 c.2.1.3,d.81.1.1 90750,90751 2c57A 180 3.19e+01 2chy 128 3.23e+01 3chy c.23.1.1 31081 1l9kA 305 3.23e+01 c.66.1.25 84569 1xoxA 117 3.28e+01 1e3jA 352 3.52e+01 1e3jA b.35.1.2,c.2.1.1 24765,29781 1z21A 112 3.53e+01 1zjyA 251 3.59e+01 1x13A 401 3.65e+01 1hc9B 74 3.66e+01 g.7.1.1 65787 1v8bA 479 3.70e+01 2bwnA 401 3.72e+01 1ti3A 113 3.74e+01 1mioB 458 3.89e+01 1qguB c.92.2.3 35602 1ggjA 753 3.99e+01 1cf9A c.23.16.3,e.5.1.1 31457,42831 1otsC 222 4.04e+01 b.1.1.1,b.1.1.2 87417,87418 1j34A 129 4.04e+01 d.169.1.1 84048 1kyzA 365 4.11e+01 a.4.5.29,c.66.1.12 73312,73313 1e31A 142 4.30e+01 1f3hA g.52.1.1 45379 2fbjH 220 4.30e+01 1igtB b.1.1.1,b.1.1.2 19851,20955 2abxA 74 4.31e+01 1tgxA g.7.1.1 44424 1i7bA 267 4.33e+01 1jenA 1yjdC 140 4.34e+01 1ygyA 529 4.37e+01 1jt8A 102 4.40e+01 b.40.4.5 63279 1pwkA 91 4.40e+01 d.39.1.1 95229 1ipeA 259 4.42e+01 c.2.1.2 83700 2ae2A 260 4.44e+01 1bdb c.2.1.2 29945 1x54A 434 4.49e+01 1vkaA 153 4.61e+01 a.40.1.1 108641 1v5kA 115 4.64e+01 a.40.1.1 108377 2ag5A 246 4.65e+01 1ooeA 236 4.71e+01 c.2.1.2 87196 1c7sA 858 4.73e+01 1qba b.1.18.2,b.2.2.3,c.1.8.6,d.92.2.1 21812,22408,29011,40410 1qba 858 4.74e+01 1qba b.1.18.2,b.2.2.3,c.1.8.6,d.92.2.1 21810,22406,29009,40408 1c7tA 858 4.76e+01 1qba b.1.18.2,b.2.2.3,c.1.8.6,d.92.2.1 21813,22409,29012,40411 1pwjA 89 4.78e+01 d.39.1.1 95228 1y0lB 226 4.78e+01 1yx2A 365 4.79e+01 1ftkA 279 4.80e+01 1gr2A c.94.1.1 35819 1yy3A 346 4.83e+01 1sy3A 184 4.85e+01 b.60.1.1 106110 1re6A 94 4.93e+01 d.39.1.1 97320 1hdzA 374 4.97e+01 2ohxA b.35.1.2,c.2.1.1 24725,29741 1hc9A 74 5.00e+01 g.7.1.1 65786 1mbb 342 5.03e+01 2mbr d.145.1.2,d.146.1.1 41750,41763 1h99A 224 5.07e+01 a.142.1.1,a.142.1.1 60814,60815 1pa7A 130 5.14e+01 a.40.1.1 94410 1wehA 171 5.15e+01 1ye9A 226 5.18e+01 1tlvA 221 5.24e+01 1sxwA 184 5.33e+01 b.60.1.1 106104 1gc5A 467 5.34e+01 1gc5A c.72.1.3 60429 1uxy 340 5.34e+01 2mbr d.145.1.2,d.146.1.1 41748,41761 2mbr 340 5.35e+01 2mbr d.145.1.2,d.146.1.1 41749,41762 1x75A 132 5.45e+01 1rpnA 335 5.49e+01 c.2.1.2 97708 1msvA 354 5.53e+01 d.156.1.1 85094 1poiB 260 5.64e+01 1poiB c.124.1.3 34155 1rtwA 220 5.69e+01 a.132.1.3 97823 1m5dA 263 5.70e+01 c.94.1.1 78641 1f3hA 142 5.72e+01 1f3hA g.52.1.1 45381 1iwmA 186 5.76e+01 b.125.1.2 83758 1yzfA 195 5.79e+01 1sy2A 184 5.83e+01 b.60.1.1 106109 1novA 355 5.85e+01 2bbvA b.121.4.4 23326 1jl0A 334 5.89e+01 1jenA d.156.1.1 63155 1u3wA 374 5.90e+01 2a4aA 281 5.91e+01 1icpA 376 5.98e+01 1oyc c.1.4.1 62270 1gqoA 143 5.98e+01 c.23.13.1 76295 1ekbB 235 6.07e+01 5ptp b.47.1.2 26282 1gypA 358 6.10e+01 1dssG c.2.1.3,d.81.1.1 30004,39919 1i32A 360 6.13e+01 c.2.1.3,d.81.1.1 65993,65994 35c8H 217 6.31e+01 8fabA b.1.1.1,b.1.1.2 20297,21289 1x8qA 184 6.36e+01 1f39A 101 6.42e+01 1umuA b.87.1.1 28386 1sy1A 184 6.42e+01 b.60.1.1 106108 1io8A 368 6.57e+01 1f4tA a.104.1.1 62618 1sfuA 75 6.60e+01 a.4.5.19 105503 1uz6F 217 6.60e+01 b.1.1.1,b.1.1.2 108152,108153 1uz8B 212 6.62e+01 b.1.1.1,b.1.1.2 108168,108169 1jenA 267 6.63e+01 1jenA 1orrA 347 6.65e+01 c.2.1.2 93460 1vkyA 347 6.89e+01 e.53.1.1 108696 1io7A 368 6.97e+01 1f4tA a.104.1.1 18971 1kcaA 109 7.05e+01 b.87.1.1 68426 1u7pA 164 7.10e+01 1ftcA 106 7.17e+01 1a6l d.58.1.2 38974 1zc1A 208 7.18e+01 1qo2A 241 7.20e+01 1qo2A c.1.2.1 28533 1uufA 369 7.34e+01 b.35.1.2,c.2.1.1 100006,100007 1x0mA 403 7.44e+01 1h4eA 201 7.44e+01 c.68.1.8 83483 1obbA 480 7.50e+01 c.2.1.5,d.162.1.2 86760,86761 1yyfC 181 7.55e+01 1p1wA 263 7.56e+01 c.94.1.1 87713 3gpdG 334 7.57e+01 1dssG c.2.1.3,d.81.1.1 30029,39944 1rwzA 245 7.67e+01 d.131.1.2,d.131.1.2 98005,98006 1tkeA 224 7.73e+01 1ae1A 273 7.75e+01 1bdb c.2.1.2 29943 1emrA 159 7.78e+01 1lki a.26.1.1 59456 1rhwA 89 7.79e+01 d.39.1.1 97490 1pvhB 169 7.81e+01 a.26.1.1 95167 1dysA 348 7.83e+01 1bvwA c.6.1.1 30669 1bg3A 918 7.98e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33491,33492,33493,33494 1h6tA 291 8.02e+01 b.1.18.15,c.10.2.1 65686,65687 1p1oA 263 8.17e+01 c.94.1.1 87699 1w77A 228 8.22e+01 2gzqA 200 8.33e+01 2cpxA 115 8.39e+01 2anjA 263 8.45e+01 1pc5A 107 8.46e+01 d.58.1.2 94429 1f0jA 377 8.47e+01 1f0jA a.211.1.2 19346 1rorA 378 8.47e+01 1lb8A 263 8.65e+01 c.94.1.1 73800 1f5bA 106 8.68e+01 1a6l d.58.1.2 38956