# List of top-scoring protein chains for T0295.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 1zq9A 285 5.16e-36 1qyrA 252 8.87e-33 c.66.1.24 104657 1qamA 244 3.80e-24 2ercA c.66.1.24 34220 1yub 245 3.29e-23 2ercA c.66.1.24 34219 1jg1A 235 7.96e-15 c.66.1.7 66661 1ve3A 227 7.89e-13 1vbfA 231 2.45e-12 c.66.1.7 108475 1dl5A 317 3.15e-12 1dl5A c.66.1.7,d.197.1.1 64720,64721 1uwvA 433 9.29e-11 b.40.4.12,c.66.1.40 100128,100129 1xxlA 239 1.67e-10 1t43A 277 1.80e-10 c.66.1.30 106392 2b3tA 276 1.82e-10 1wznA 252 2.47e-10 1l3iA 192 2.67e-10 c.66.1.22 77676 1dusA 194 2.99e-10 1dusA c.66.1.4 34182 1vl5A 260 1.15e-09 c.66.1.41 108720 1i1nA 226 2.31e-09 c.66.1.7 71102 1sg9A 282 3.75e-09 c.66.1.30 105526 1nv8A 284 3.76e-09 c.66.1.30 86224 1vq1A 294 3.80e-09 1ufkA 254 4.44e-09 c.66.1.39 99340 1g6q1 328 1.39e-08 1g6q2 1wy7A 207 2.22e-08 1i9gA 280 4.55e-08 c.66.1.13 62090 2fytA 340 8.90e-08 1r18A 227 1.23e-07 c.66.1.7 96800 2as0A 396 1.39e-07 1y8cA 246 2.24e-07 2gh1A 301 2.46e-07 1f3lA 321 2.48e-07 1g6q2 c.66.1.6 59630 2avnA 260 2.58e-07 1yb2A 275 3.80e-07 1r8xA 292 1.50e-06 c.66.1.5 104855 1g38A 393 1.76e-06 2admA c.66.1.27 60235 1aqjA 421 1.76e-06 2admA c.66.1.27 34242 2admA 421 1.76e-06 2admA c.66.1.27 34238 1d2gA 292 1.81e-06 1xvaA c.66.1.5 34187 1xvaA 292 1.84e-06 1xvaA c.66.1.5 34183 1r74A 294 1.87e-06 c.66.1.5 104828 2b25A 336 2.33e-06 1o54A 277 2.80e-06 c.66.1.13 92482 1nkvA 256 2.85e-06 c.66.1.21 80577 1ne2A 200 2.95e-06 c.66.1.32 85586 1m6yA 301 3.59e-06 a.60.13.1,c.66.1.23 78716,78717 1tw3A 360 4.42e-06 a.4.5.29,c.66.1.12 107373,107374 1wxxA 382 9.79e-06 1or8A 340 1.19e-05 c.66.1.6 93451 1oriA 343 1.19e-05 c.66.1.6 87339 1orhA 353 1.32e-05 c.66.1.6 93455 1kpgA 287 1.55e-05 c.66.1.18 68735 2fk8A 318 2.36e-05 2b2cA 314 2.87e-05 1p91A 269 3.40e-05 c.66.1.33 94378 1im8A 244 4.65e-05 c.66.1.14 66212 2frnA 278 4.97e-05 2ex4A 241 5.73e-05 1tpyA 287 5.98e-05 1i4wA 353 9.95e-05 c.66.1.24 66028 1xtpA 254 1.10e-04 1vlmA 219 1.43e-04 c.66.1.41 108836 1sqgA 429 1.45e-04 a.79.1.3,c.66.1.38 105912,105913 1ixkA 315 2.05e-04 c.66.1.38 90716 1ri5A 298 2.07e-04 c.66.1.34 97502 1l1eA 287 2.64e-04 c.66.1.18 73454 2b9eA 303 2.88e-04 1mjfA 281 2.94e-04 c.66.1.17 79198 2fpoA 202 4.59e-04 1kpiA 302 4.68e-04 c.66.1.18 68743 1qzzA 374 4.96e-04 a.4.5.29,c.66.1.12 96719,96720 1zdzA 302 6.14e-04 2esrA 177 6.77e-04 1iy9A 275 7.42e-04 c.66.1.17 76943 1jsxA 207 8.90e-04 c.66.1.20 71846 2fhpA 187 9.09e-04 1wg8A 285 1.16e-03 1yzhA 214 1.73e-03 1h1dA 221 3.86e-03 c.66.1.1 83452 1uirA 314 5.44e-03 c.66.1.17 99429 1ws6A 171 6.37e-03 1pryA 227 7.23e-03 c.66.1.3 95063 1nw3A 416 8.30e-03 c.66.1.31 86288 1jvbA 347 8.74e-03 b.35.1.2,c.2.1.1 77181,77182 1ntoA 347 9.17e-03 b.35.1.2,c.2.1.1 92137,92138 1g60A 260 9.27e-03 c.66.1.11 70151 1g8aA 227 9.44e-03 c.66.1.3 90506 1nt2A 210 4.42e-02 c.66.1.3 86149 1xj5A 334 5.15e-02 1xseA 295 5.24e-02 1u2zA 433 6.09e-02 c.66.1.31 107626 1ej0A 180 6.51e-02 1ej0A c.66.1.2 34179 1zkdA 387 7.48e-02 1g8sA 230 7.83e-02 c.66.1.3 90507 1nw8A 319 9.72e-02 c.66.1.11 86292 1eg2A 319 1.01e-01 1eg2A c.66.1.11 34249 1qe5A 266 1.41e-01 1b8oA c.56.2.1 33784 1lssA 140 1.45e-01 c.2.1.9 74246 1rjwA 339 1.53e-01 b.35.1.2,c.2.1.1 97582,97583 1xdzA 240 1.62e-01 1inlA 296 1.87e-01 c.66.1.17 66220 1lluA 342 1.99e-01 b.35.1.2,c.2.1.1 91064,91065 1ej6A 1289 2.01e-01 i.7.1.1 45967 1r6aA 295 2.21e-01 c.66.1.25 104817 1l9kA 305 2.38e-01 c.66.1.25 84569 2f8lA 344 2.62e-01 1g55A 343 2.73e-01 1g55A c.66.1.26 34247 1ionA 243 4.58e-01 c.37.1.10 62633 2g1uA 155 6.26e-01 1o9gA 250 6.30e-01 c.66.1.29 86692 1o9hA 250 6.38e-01 c.66.1.29 86693 1fp2A 352 9.64e-01 1fpxA a.4.5.29,c.66.1.12 59941,59942 1khhA 198 9.73e-01 c.66.1.16 68615 1p1cA 199 9.76e-01 c.66.1.16 87669 1xclA 235 1.03e+00 2a4kA 263 1.04e+00 2avdA 219 1.05e+00 1lsuA 147 1.11e+00 c.2.1.9 74250 1ulsA 245 1.15e+00 1uufA 369 1.20e+00 b.35.1.2,c.2.1.1 100006,100007 2bgkA 278 1.26e+00 2ag5A 246 1.28e+00 1jqeA 292 1.36e+00 c.66.1.19 71789 1g91A 77 1.40e+00 1b3aA d.9.1.1 60389 1bg6 359 1.48e+00 1bg6 a.100.1.5,c.2.1.6 18810,30214 1u3tA 374 1.54e+00 1yb1A 272 1.67e+00 2aotA 292 1.92e+00 1fjgM 126 1.93e+00 1fjfM a.156.1.1 16293 1i94M 125 1.94e+00 1fjfM a.156.1.1 62004 1pjzA 203 1.96e+00 c.66.1.36 94794 1e3jA 352 2.10e+00 1e3jA b.35.1.2,c.2.1.1 24765,29781 1u3uA 374 2.10e+00 1hdyA 374 2.10e+00 2ohxA b.35.1.2,c.2.1.1 24723,29739 1hdzA 374 2.13e+00 2ohxA b.35.1.2,c.2.1.1 24725,29741 1cydA 244 2.22e+00 1cydA c.2.1.2 29825 1htbA 374 2.28e+00 2ohxA b.35.1.2,c.2.1.1 24715,29731 1zx0A 236 2.39e+00 1e4fT 419 2.44e+00 1e4fT c.55.1.1,c.55.1.1 33453,33454 1e6bA 221 3.09e+00 1e6bA a.45.1.1,c.47.1.5 59294,59295 1kevA 351 3.21e+00 1pedA b.35.1.2,c.2.1.1 24749,29765 2belA 283 3.26e+00 1jbqA 435 3.49e+00 1oasA c.79.1.1 62850 1m54A 363 3.64e+00 c.79.1.1 74463 1t3wA 148 3.67e+00 1sb8A 352 3.78e+00 c.2.1.2 105410 1suiA 247 3.87e+00 1c4zD 154 3.92e+00 1u9aA d.20.1.1 38331 1j32A 388 3.92e+00 c.67.1.1 77067 1xu9A 286 3.93e+00 1y9aA 360 4.23e+00 1u3wA 374 4.37e+00 1y5mA 276 4.46e+00 1fmcA 255 4.73e+00 1cydA c.2.1.2 29856 2br4A 236 4.76e+00 1z78A 215 5.06e+00 1jqbA 351 5.14e+00 b.35.1.2,c.2.1.1 77151,77152 1za4A 251 5.17e+00 2erfA 209 5.22e+00 2bm8A 236 5.26e+00 1pr9A 244 5.49e+00 c.2.1.2 95060 1piwA 360 5.75e+00 b.35.1.2,c.2.1.1 104156,104157 1zx8A 136 6.01e+00 1pl8A 356 6.59e+00 b.35.1.2,c.2.1.1 94878,94879 1ab5A 125 6.60e+00 3chy c.23.1.1 31056 1qo8A 566 7.74e+00 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19696,30433,42316 1zejA 293 7.99e+00 1g3qA 237 8.22e+00 1hyqA c.37.1.10 60237 2tunA 157 8.83e+00 2tnfA b.22.1.1 23874 1zcjA 463 9.10e+00 1a71A 374 9.38e+00 2ohxA b.35.1.2,c.2.1.1 24673,29689 1axgA 374 9.40e+00 2ohxA b.35.1.2,c.2.1.1 24691,29707 1bby 69 9.44e+00 2bby a.4.5.15 16149 2fbqA 235 1.03e+01 1ng6A 148 1.05e+01 a.182.1.1 85670 1w33A 181 1.07e+01 1ktnA 250 1.07e+01 c.1.10.1 72988 1p1xA 260 1.12e+01 c.1.10.1 104060 1jcjA 260 1.13e+01 c.1.10.1 66499 1kyzA 365 1.14e+01 a.4.5.29,c.66.1.12 73312,73313 1qv6A 374 1.22e+01 b.35.1.2,c.2.1.1 96348,96349 1ab6A 125 1.23e+01 3chy c.23.1.1 31054 1gvnB 287 1.33e+01 c.37.1.21 76354 2cqdA 116 1.41e+01 2chy 128 1.43e+01 3chy c.23.1.1 31081 2cwcA 303 1.49e+01 1zdmA 129 1.55e+01 1z5bA 469 1.60e+01 1ee2A 373 1.62e+01 2ohxA b.35.1.2,c.2.1.1 24663,29679 1mu5A 471 1.62e+01 a.156.1.3,d.14.1.3,d.122.1.2 79472,79473,79474 1mx0A 472 1.63e+01 a.156.1.3,d.14.1.3,d.122.1.2 79618,79619,79620 1ydeA 270 1.63e+01 1ae1A 273 1.66e+01 1bdb c.2.1.2 29943 1s1hM 132 1.66e+01 i.1.1.1 105165 1w25A 459 1.68e+01 1ehc 128 1.71e+01 3chy c.23.1.1 31053 1z7eA 660 1.74e+01 1z74A 358 1.74e+01 1u9jA 358 1.74e+01 1z75A 358 1.74e+01 1z7bA 358 1.75e+01 2bllA 345 1.76e+01 1u8tA 128 1.79e+01 1ihjA 98 1.82e+01 1pdr b.36.1.1 62382 1itzA 675 1.87e+01 c.36.1.10,c.36.1.6,c.48.1.1 76797,76798,76799 1mo7A 213 1.88e+01 d.220.1.1 85028 1nytA 271 1.89e+01 c.2.1.7,c.58.1.5 86417,86418 2bzgA 232 1.98e+01 1fl2A 310 2.02e+01 1hyuA c.3.1.5,c.3.1.5 59869,59870 1zvuA 716 2.03e+01 1x3pA 54 2.04e+01 1c4wA 128 2.04e+01 3chy c.23.1.1 31046 1mgoA 374 2.05e+01 b.35.1.2,c.2.1.1 79094,79095 1axeA 374 2.05e+01 2ohxA b.35.1.2,c.2.1.1 24681,29697 1heuA 374 2.05e+01 2ohxA b.35.1.2,c.2.1.1 60979,60980 1v0bA 288 2.05e+01 d.144.1.7 100241 1oaoA 674 2.11e+01 e.26.1.2 86744 1m6eX 359 2.11e+01 c.66.1.35 91188 1a1s 314 2.11e+01 1othA c.78.1.1,c.78.1.1 35258,35259 1pvvA 315 2.12e+01 c.78.1.1,c.78.1.1 95190,95191 2c0cA 362 2.16e+01 2az5A 148 2.17e+01 1p1tA 104 2.21e+01 d.58.7.1 93899 1m6hA 373 2.25e+01 b.35.1.2,c.2.1.1 74529,74530 1mc5A 374 2.25e+01 b.35.1.2,c.2.1.1 84929,84930 1tnfA 157 2.26e+01 2tnfA b.22.1.1 23871 1ju9A 374 2.33e+01 b.35.1.2,c.2.1.1 63293,63294 1n8kA 374 2.36e+01 b.35.1.2,c.2.1.1 80298,80299 2cg5A 319 2.37e+01 1f8fA 371 2.39e+01 b.35.1.2,c.2.1.1 83246,83247 1v3vA 333 2.41e+01 b.35.1.2,c.2.1.1 108345,108346 1z73A 358 2.44e+01 1qlhA 374 2.46e+01 2ohxA b.35.1.2,c.2.1.1 24685,29701 2c43A 323 2.47e+01 1a8mA 157 2.48e+01 2tnfA b.22.1.1 23868 4tsvA 150 2.48e+01 2tnfA b.22.1.1 23860 1zsvA 349 2.56e+01 2gb3A 409 2.59e+01 1ob3A 288 2.61e+01 d.144.1.7 92747 1v0oA 288 2.68e+01 d.144.1.7 100243 2g5cA 281 2.72e+01 1vjtA 483 2.73e+01 c.2.1.5,d.162.1.2 100833,100834 1tkeA 224 2.76e+01 3kinB 117 2.76e+01 3kinB 1e6lA 127 2.80e+01 3chy c.23.1.1 59307 2cpjA 99 2.81e+01 1k2wA 256 2.81e+01 c.2.1.2 90927 1gegA 256 3.03e+01 1ybvA c.2.1.2 29888 2chf 128 3.04e+01 3chy c.23.1.1 31079 1wcv1 257 3.04e+01 1y0kA 209 3.14e+01 1e6mA 128 3.17e+01 3chy c.23.1.1 31039 2fmnA 304 3.18e+01 2c7rA 327 3.21e+01 1wu6A 396 3.25e+01 1kmiY 129 3.28e+01 c.23.1.1 72751 1ldkA 396 3.28e+01 a.118.17.1 73851 1b5tA 275 3.53e+01 1b5tA c.1.23.1 29676 1bg3A 918 3.57e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33491,33492,33493,33494 1svuA 327 3.72e+01 c.66.1.26 106052 1nhp 447 3.73e+01 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30549,30550,40196 1nhs 447 3.73e+01 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30555,30556,40199 1npx 447 3.73e+01 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30557,30558,40200 1nhr 447 3.74e+01 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30553,30554,40198 1zp3A 304 3.77e+01 1zp4A 304 3.77e+01 2c7pA 327 3.77e+01 1nhq 447 3.80e+01 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30551,30552,40197 1h2bA 359 3.80e+01 b.35.1.2,c.2.1.1 90543,90544 1fjhA 257 3.84e+01 1fjhB c.2.1.2 29870 2fkfA 462 3.85e+01 1p5dX 463 3.85e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1k2yX 463 3.90e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 1jcfA 344 3.91e+01 c.55.1.1,c.55.1.1 62878,62879 2bk6A 156 3.91e+01 2fkmX 462 3.94e+01 1eysL 280 3.95e+01 6prcL f.26.1.1 43515 1h2iA 209 3.99e+01 d.50.1.3 76550 2kinB 100 4.08e+01 3kinB 1u1iA 392 4.12e+01 c.2.1.3,d.81.1.3 107582,107583 1d4zA 128 4.12e+01 3chy c.23.1.1 31047 2fyxA 143 4.20e+01 1kn0A 212 4.22e+01 d.50.1.3 77444 1eazA 125 4.25e+01 b.55.1.1 70113 1reoA 486 4.31e+01 c.3.1.2,d.16.1.5 97325,97326 2bjyA 156 4.31e+01 1awcA 110 4.32e+01 1awcA a.4.5.21 16167 1jbeA 128 4.35e+01 3chy c.23.1.1 62845 1zkqA 517 4.42e+01 1qf6A 642 4.43e+01 1qf6A c.51.1.1,d.15.10.1,d.67.1.1,d.104.1.1 33210,39551,39562,40759 1mihA 129 4.53e+01 c.23.1.1 84975 1cye 129 4.55e+01 3chy c.23.1.1 31077 5chy 128 4.57e+01 3chy c.23.1.1 31050 2gbsA 145 4.70e+01 1ow1A 195 4.79e+01 b.131.1.3 93625 1sq9A 397 4.83e+01 b.69.4.1 105889 1w6uA 302 5.05e+01 1xhlA 297 5.11e+01 c.2.1.2 109591 1zsyA 357 5.14e+01 1vlzA 128 5.17e+01 3chy c.23.1.1 31048 1s4uX 407 5.20e+01 2cucA 70 5.32e+01 1cdoA 374 5.46e+01 2ohxA b.35.1.2,c.2.1.1 24747,29763 2ew2A 316 5.50e+01 1udrA 129 5.57e+01 3chy c.23.1.1 31041 6chyA 128 5.58e+01 3chy c.23.1.1 31062 2ajfA 597 5.61e+01 1v8bA 479 5.63e+01 1r42A 615 5.64e+01 d.92.1.5 96968 1nvtA 287 5.71e+01 c.2.1.7,c.58.1.5 86270,86271 1yt8A 539 5.71e+01 1wu4A 396 5.72e+01 1kolA 398 5.78e+01 b.35.1.2,c.2.1.1 77474,77475 1mw5A 187 5.82e+01 d.259.1.1 91477 1jigA 146 5.92e+01 a.25.1.1 71685 1q0sA 259 6.01e+01 c.66.1.28 95509 1k82A 268 6.08e+01 a.156.1.2,b.113.1.1,g.39.1.8 75866,75867,75868 2bj7A 138 6.11e+01 2a6aA 218 6.20e+01 1p0kA 349 6.25e+01 c.1.4.1 87648 1ldjA 760 6.40e+01 a.4.5.34,a.118.17.1,e.40.1.1 73847,73848,73849 1y7eA 458 6.50e+01 1u6gA 776 6.52e+01 1xkqA 280 6.59e+01 1p2fA 220 6.61e+01 a.4.6.1,c.23.1.1 87720,87721 1z0sA 278 6.72e+01 1qghA 156 6.75e+01 1qghA a.25.1.1 16728 1xwdC 252 6.82e+01 1x4dA 102 6.83e+01 1r2zA 274 6.87e+01 a.156.1.2,b.113.1.1,g.39.1.8 96892,96893,96894 1l1zA 274 6.88e+01 a.156.1.2,b.113.1.1,g.39.1.8 75911,75912,75913 1s6cA 183 6.99e+01 a.39.1.5 98594 2b4lA 268 7.01e+01 1fp1D 372 7.11e+01 1fpqA a.4.5.29,c.66.1.12 59939,59940 2bkcA 156 7.12e+01 1m2pA 325 7.23e+01 d.144.1.7 84758 1om1A 332 7.24e+01 d.144.1.7 93347 1m2rA 327 7.24e+01 d.144.1.7 84760 1yf3A 259 7.25e+01 1rfmA 344 7.27e+01 c.122.1.1 97385 1yfjA 259 7.34e+01 1poiA 317 7.36e+01 1poiA c.124.1.2 34153 1dl6A 58 7.73e+01 1dl6A g.41.3.1 45207 1pwhA 327 7.77e+01 c.79.1.1 95224 2b6eA 146 7.88e+01 1duxC 94 7.91e+01 1awcA a.4.5.21 16170 1tt7A 330 7.94e+01 1rlyA 60 7.97e+01 g.41.3.1 104988 1ydwA 362 8.07e+01 2bkkB 169 8.17e+01 2cxcA 144 8.18e+01 1wlqA 83 8.19e+01 h.1.28.1 109398 1vl0A 292 8.22e+01 c.2.1.2 108704 2b69A 343 8.34e+01 1o0iA 138 8.42e+01 d.38.1.5 86532 1s1eA 224 8.47e+01 1w0iA 431 8.50e+01 1zemA 262 8.55e+01 2ggmA 172 8.58e+01 1mhyB 395 8.68e+01 1mtyB a.25.1.2 16781 1vefA 395 8.70e+01 1e6kA 130 8.72e+01 3chy c.23.1.1 59306 2a2uA 181 8.73e+01 1mup b.60.1.1 27135 1snyA 267 8.73e+01 c.2.1.2 105833 1yppA 286 8.74e+01 1wgjA b.40.5.1 25407 1q35A 320 8.77e+01 c.94.1.1 95661 4uagA 437 8.88e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30651,33952,34955 1ui5A 215 8.90e+01 a.4.1.9,a.121.1.1 107856,107857 1x9uA 116 8.92e+01 1wi0A 113 8.95e+01