# List of top-scoring protein chains for t2k-100-30-dssp-ebghstl-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.soe.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 1rj9A 304 1.50e-01 a.24.13.1,c.37.1.10 97553,97554 2zumA 458 4.12e-01 2pa6A 427 1.01e+00 2i2wA 212 1.13e+00 1zhaA 267 1.14e+00 1pe1A 267 1.65e+00 c.1.10.4 94591 2b0jA 358 1.68e+00 a.100.1.11,c.2.1.6 127639,127640 2ixnA 310 1.71e+00 a.268.1.1 137777 1iatA 557 1.76e+00 1dqrA c.80.1.2 62123 2akzA 439 1.78e+00 c.1.11.1,d.54.1.1 126944,126945 3ciwA 348 1.79e+00 3crvA 551 1.91e+00 2nvaA 372 2.14e+00 1i4nA 251 2.34e+00 c.1.2.4 71114 1lroA 267 2.37e+00 c.1.10.4 78161 2r3bA 310 2.40e+00 2orwA 184 2.50e+00 1iyxA 432 2.73e+00 c.1.11.1,d.54.1.1 83815,83816 2nwrA 267 2.79e+00 2a2fX 325 2.92e+00 2o7iA 592 2.94e+00 2fymA 431 3.01e+00 c.1.11.1,d.54.1.1 134379,134380 3iixA 348 3.27e+00 1fmtA 314 3.68e+00 1fmtA b.46.1.1,c.65.1.1 25758,34174 2gzaA 361 3.98e+00 1pcxA 810 4.30e+00 a.71.2.1,b.2.8.1,c.62.1.2,d.109.2.1,g.41.10.1 94497,94498,94499,94500,94501 3ckjA 329 4.31e+00 1mjgM 729 4.32e+00 e.26.1.3 79204 2hyvA 308 4.60e+00 3lerA 301 4.80e+00 1y8qA 346 4.83e+00 3dagA 358 5.13e+00 3i04M 728 5.17e+00 3ca8A 266 5.25e+00 3e0iA 267 5.39e+00 1oaoC 729 5.55e+00 e.26.1.3 86746 3f47A 358 5.68e+00 3k5wA 475 6.29e+00 1w7bA 339 6.36e+00 a.65.1.1 114317 1w6tA 444 6.45e+00 c.1.11.1,d.54.1.1 120670,120671 1o60A 292 6.52e+00 c.1.10.4 92532 1ybtA 184 7.03e+00 1zcoA 262 7.39e+00 1ab5A 125 7.43e+00 3chy c.23.1.1 31056 1vlwA 217 7.83e+00 c.1.10.1 108868 1efyA 350 8.35e+00 1a26 a.41.1.1,d.166.1.2 17413,42275 1egdA 396 8.39e+00 3mdeA a.29.3.1,e.6.1.1 16596,42857 1wa3A 205 8.42e+00 c.1.10.1 120802 3m0zA 249 8.72e+00 3bc9A 599 9.22e+00 3fsiA 255 9.28e+00 2qddA 378 9.53e+00 2gruA 368 9.60e+00 3hnpA 353 9.92e+00 2f6hX 419 1.00e+01 1o5kA 306 1.01e+01 c.1.10.1 92504 2kbiA 97 1.01e+01 1g5aA 628 1.05e+01 b.71.1.1,c.1.8.1 65152,65153 1np8A 159 1.06e+01 a.39.1.8 92022 3brjA 175 1.14e+01 a.285.1.1 155511 3fxgA 455 1.14e+01 2rcyA 262 1.15e+01 3c8tA 451 1.16e+01 2nw2B 243 1.16e+01 1g6oA 330 1.18e+01 1g6oA c.37.1.11 32430 2a11A 242 1.19e+01 1vr5A 547 1.22e+01 c.94.1.1 120437 1j5yA 187 1.26e+01 a.4.5.1,d.94.2.1 71592,71593 2o0jA 385 1.26e+01 3fvdA 378 1.27e+01 1no5A 114 1.29e+01 d.218.1.5 92014 1fl9A 161 1.30e+01 c.37.1.18 70137 1m0uA 249 1.34e+01 a.45.1.1,c.47.1.5 78359,78360 2ivyA 101 1.34e+01 d.58.58.1 147817 1d9eA 284 1.36e+01 1d9eA c.1.10.4 29195 1e6mA 128 1.36e+01 3chy c.23.1.1 31039 3i16A 427 1.37e+01 2aeuA 374 1.39e+01 c.67.1.8 126646 1nofA 383 1.41e+01 b.71.1.2,c.1.8.3 92020,92021 3gg9A 352 1.43e+01 1ixkA 315 1.45e+01 c.66.1.38 90716 1jbeA 128 1.46e+01 3chy c.23.1.1 62845 2ps2A 371 1.48e+01 2nuwA 288 1.54e+01 3c3yA 237 1.58e+01 1mml 265 1.58e+01 1mml 1mmlA 265 1.58e+01 e.8.1.2 43015 3a5vA 397 1.60e+01 1mvwA 840 1.75e+01 i.15.1.1 79523 1y9zA 441 1.78e+01 2ozlB 341 1.80e+01 c.36.1.7,c.48.1.2 139447,139448 2pyyA 228 1.84e+01 2v8qA 157 1.85e+01 d.129.6.2 152781 1jbaA 204 1.89e+01 1rec a.39.1.5 17330 2b9eA 303 1.89e+01 c.66.1.38 128124 2d4xA 248 1.92e+01 3b96A 587 1.93e+01 2weyA 343 1.94e+01 1n7kA 234 1.99e+01 c.1.10.1 85374 1qr7A 350 2.01e+01 1qr7A c.1.10.4 29191 3e9aA 286 2.02e+01 2okjA 504 2.03e+01 3chy 128 2.07e+01 3chy 1ab6A 125 2.08e+01 3chy c.23.1.1 31054 1u3wA 374 2.09e+01 b.35.1.2,c.2.1.1 113013,113014 1g8xA 1010 2.13e+01 1lvk k.1.1.1 46378 3m6wA 464 2.14e+01 2uxwA 607 2.18e+01 2pt7A 330 2.19e+01 c.37.1.11 149834 2sqcA 631 2.20e+01 2sqcA a.102.4.2,a.102.4.2 18854,18855 3brcA 156 2.23e+01 3fcdA 134 2.30e+01 3kl4A 433 2.31e+01 1j8yF 297 2.33e+01 1ng1 a.24.13.1,c.37.1.10 62747,62748 1vrmA 325 2.36e+01 d.96.2.1 120472 3fayA 387 2.36e+01 3ix7A 134 2.36e+01 1mxrA 375 2.39e+01 a.25.1.2 85197 3pga1 337 2.43e+01 4pgaA 1tzzA 392 2.44e+01 c.1.11.2,d.54.1.1 112896,112897 1ae9A 179 2.46e+01 1ae9A d.163.1.1 42153 1ru3A 732 2.46e+01 e.26.1.3 97835 1vq0A 302 2.52e+01 d.193.1.1,g.81.1.1 114000,114001 2v1lA 148 2.54e+01 1biqA 375 2.54e+01 1xikA a.25.1.2 16786 3igsA 232 2.57e+01 1zejA 293 2.60e+01 2ekcA 262 2.61e+01 1jv2B 692 2.63e+01 b.1.15.1,c.62.1.1,d.200.1.1,g.3.11.6,g.3.11.6 67338,67339,67340,67341,67342 3eweB 564 2.64e+01 1ml4A 308 2.65e+01 c.78.1.1,c.78.1.1 79255,79256 1uumA 372 2.65e+01 c.1.4.1 100010 1ribA 375 2.68e+01 1xikA a.25.1.2 16788 3i99A 357 2.72e+01 1u14A 172 2.72e+01 c.51.4.3 107579 1umpA 631 2.75e+01 a.102.4.2,a.102.4.2 99619,99620 1vmaA 306 2.79e+01 a.24.13.1,c.37.1.10 108887,108888 2ganA 190 2.80e+01 d.108.1.1 134889 2h5nA 133 2.80e+01 a.287.1.2 147227 2z3yA 662 2.80e+01 a.4.1.18,c.3.1.2,d.16.1.5 154024,154025,154026 1n8fA 350 2.82e+01 c.1.10.4 85397 2goyA 275 2.86e+01 2b4gA 317 2.88e+01 c.1.4.1 127829 2pl5A 366 2.91e+01 c.69.1.40 149611 1vr6A 350 2.91e+01 c.1.10.4 120439 3dlcA 219 2.98e+01 3dssB 331 3.02e+01 a.102.4.3 157841 2ch0A 133 3.05e+01 3eehA 125 3.07e+01 1gg1A 350 3.07e+01 1qr7A c.1.10.4 29187 4pgaA 337 3.08e+01 4pgaA c.88.1.1 35565 3glrA 285 3.10e+01 2i53A 258 3.11e+01 a.74.1.1,a.74.1.1 147505,147506 2kavA 129 3.14e+01 3gjwA 350 3.16e+01 1j9aA 184 3.20e+01 c.55.3.5 84135 2nnnA 140 3.23e+01 1cnv 299 3.24e+01 1cnv 1cnvA 299 3.24e+01 c.1.8.5 28989 1jx2B 315 3.24e+01 c.37.1.8 67404 2z15A 130 3.25e+01 d.370.1.1 153921 1y1xA 191 3.29e+01 a.39.1.8 116374 1dofA 403 3.30e+01 1c3cA a.127.1.1 19429 2gp4A 628 3.32e+01 c.8.2.2,d.334.1.1 135448,135449 3e9vA 120 3.34e+01 d.370.1.1 158072 2d13A 227 3.35e+01 c.26.2.1 131121 2e12A 101 3.43e+01 1mxsA 225 3.45e+01 c.1.10.1 91494 3eypA 469 3.51e+01 1xngA 268 3.52e+01 c.26.2.1 122186 1v9mA 323 3.55e+01 f.40.1.1 100543 2z43A 324 3.60e+01 2qltA 275 3.64e+01 3l0gA 300 3.67e+01 1phnB 172 3.67e+01 1qgwC a.1.1.3 15642 1iciA 256 3.70e+01 1iciA c.31.1.5 62266 1sd4A 126 3.74e+01 a.4.5.39 105428 1j24A 143 3.75e+01 c.52.1.20 84008 1xikA 375 3.80e+01 1xikA a.25.1.2 16784 2zvfA 171 3.81e+01 3a9zA 432 3.81e+01 1zu4A 320 3.81e+01 1b68A 191 3.85e+01 1nfn a.24.1.1 59076 2d1hA 109 3.87e+01 a.4.5.50 131125 2ef0A 301 3.90e+01 2ovyA 362 3.91e+01 1xvlA 321 3.98e+01 c.92.2.2 122380 1f2hA 169 3.98e+01 1f3vA d.58.22.1 59612 2i62A 265 3.99e+01 3kyjB 145 4.06e+01 1u2zA 433 4.09e+01 c.66.1.31 107626 1hrkA 359 4.09e+01 1hrkA c.92.1.1 61228 3bb7A 321 4.11e+01 1jbkA 195 4.12e+01 c.37.1.20 71631 1f75A 249 4.20e+01 1f75A c.101.1.1 59662 1kpgA 287 4.20e+01 c.66.1.18 68735 3mddA 385 4.28e+01 3mdeA a.29.3.1,e.6.1.1 16592,42853 2ihyA 279 4.34e+01 2nyvA 222 4.36e+01 3cc8A 230 4.39e+01 2as0A 396 4.45e+01 b.122.1.9,c.66.1.51 127227,127228 2aamA 309 4.53e+01 c.1.8.15 126489 1d3gA 367 4.60e+01 1d3gA c.1.4.1 28600 1wmmA 145 4.62e+01 b.122.1.8 121049 2pa2A 151 4.63e+01 d.41.4.1 149337 3c9uA 342 4.69e+01 d.79.4.1,d.139.1.1 156144,156145 2pceA 386 4.69e+01 3gwfA 540 4.71e+01 3fhlA 362 4.78e+01 3f44A 220 4.78e+01 1m1jA 491 4.80e+01 h.1.8.1 74369 1vb5A 276 4.85e+01 c.124.1.5 113604 1wxqA 397 4.89e+01 c.37.1.8,d.15.10.2 121406,121407 2vm6A 150 4.90e+01 1sq5A 308 4.94e+01 c.37.1.6 105882 2hd9A 145 4.97e+01 b.122.1.8 147268 1l1sA 113 4.98e+01 c.114.1.1 73484 3g8rA 350 4.98e+01 1vqvA 306 4.98e+01 d.79.4.1,d.139.1.1 114024,114025 2r7gA 347 4.99e+01 a.74.1.3,a.74.1.3 151637,151638 1qfjA 232 5.01e+01 1qfjA b.43.4.2,c.25.1.1 25655,31545 3i4kA 383 5.02e+01 1dcuA 357 5.04e+01 1frpA e.7.1.1 42943 2r91A 286 5.07e+01 2x4dA 271 5.07e+01 2dyuA 334 5.12e+01 2elcA 329 5.21e+01 a.46.2.1,c.27.1.1 146897,146898 2ftrA 108 5.22e+01 d.58.4.15 134077 2nvoA 535 5.22e+01 1p4kA 295 5.22e+01 d.153.1.5 87772 1r85A 379 5.27e+01 c.1.8.3 104839 2ebfX 746 5.30e+01 a.296.1.1,c.150.1.2,d.3.1.17 146766,146767,146768 3gb5A 259 5.32e+01 2r1iA 172 5.37e+01 1dfaA 454 5.37e+01 1vdeA b.86.1.2,d.95.2.2,d.95.2.2 28375,40575,40576 1w3iA 293 5.38e+01 c.1.10.1 109152 3inpA 246 5.38e+01 2cy2A 174 5.38e+01 d.108.1.1 131016 1phkA 298 5.44e+01 d.144.1.7 41635 1wpbA 172 5.47e+01 a.233.1.1 114783 3g8dA 444 5.48e+01 1vkyA 347 5.49e+01 e.53.1.1 108696 1wybA 392 5.53e+01 e.3.1.1 145837 1rqbA 539 5.55e+01 a.5.7.2,c.1.10.5 105057,105058 2ev0A 142 5.56e+01 a.4.5.24,a.76.1.1 132413,132414 9gafA 295 5.58e+01 1apyA d.153.1.5 42008 3mdeA 385 5.60e+01 3mdeA a.29.3.1,e.6.1.1 16594,42855 2glfA 450 5.63e+01 1nxhA 126 5.63e+01 a.200.1.1 92300 1dceB 331 5.68e+01 1dceB a.102.4.3 18872 3gzdA 440 5.70e+01 1ytaA 180 5.72e+01 c.55.3.5 124002 2b4uA 335 5.78e+01 3l1bA 233 5.80e+01 1ixmA 192 5.83e+01 1ixmA d.123.1.1 41114 2gqpA 236 5.83e+01 d.122.1.1 135513 1pjhA 280 5.85e+01 c.14.1.3 94761 1yydA 357 5.85e+01 a.93.1.1 124212 3bjsA 428 5.87e+01 1aj5A 173 5.88e+01 1alvA a.39.1.8 17367 2bzbA 62 5.88e+01 a.30.7.1 129556 2a8yA 270 5.91e+01 1v8fA 276 5.95e+01 c.26.1.4 100503 1bz4A 144 5.96e+01 1nfn a.24.1.1 16521 3l05A 359 5.97e+01 1bzsA 165 5.97e+01 1hfc d.92.1.11 40348 1uzeA 589 6.01e+01 d.92.1.5 108174 1ufvA 276 6.04e+01 c.26.1.4 88487 1u24A 337 6.05e+01 c.45.1.4 112968 1i76A 163 6.09e+01 1hfc d.92.1.11 61877 2nutB 753 6.11e+01 1othA 321 6.11e+01 1othA c.78.1.1,c.78.1.1 35260,35261 1on2A 142 6.13e+01 a.4.5.24,a.76.1.1 87103,87104 3lm7A 249 6.14e+01 2zdrA 349 6.23e+01 b.85.1.1,c.1.10.6 154398,154399 2qg3A 208 6.24e+01 3dojA 310 6.24e+01 1x13A 401 6.33e+01 2apxA 112 6.37e+01 1y4oA 104 6.46e+01 d.110.7.1 145901 1bu2A 229 6.48e+01 1bu2A a.74.1.1,a.74.1.1 18360,18361 2wadA 680 6.48e+01 1al3 324 6.56e+01 1al3 1al3A 324 6.56e+01 c.94.1.1 35835 1oj7A 408 6.56e+01 e.22.1.2 103971 1dcoA 104 6.59e+01 1dcpA d.74.1.1 39680 2fcr 173 6.60e+01 1rcf 2fcrA 173 6.60e+01 c.23.5.1 31151 1ff9A 450 6.62e+01 1ff9A c.2.1.3,d.81.1.2 30039,39954 1aunA 208 6.66e+01 b.25.1.1 23900 1wycA 392 6.66e+01 e.3.1.1 145838 3evnA 329 6.68e+01 1d1dA 262 6.69e+01 1d1dA a.28.3.1,a.73.1.1 16958,18335 2ousA 331 6.72e+01 1csh 435 6.73e+01 1csh 1cshA 435 6.73e+01 a.103.1.1 18880 3frkA 373 6.74e+01 3b40A 417 6.74e+01 1ncx 162 6.75e+01 1ncx 2pt0A 340 6.76e+01 c.45.1.4 149832 3glcA 295 6.79e+01 2ob0A 170 6.79e+01 2b4pA 334 6.80e+01 3kvnA 632 6.84e+01 3h12A 397 6.85e+01 1i5pA 633 6.86e+01 1i5pA b.18.1.3,b.77.2.1,f.1.3.1 61817,61818,61819 1qopA 268 6.88e+01 2tysA c.1.2.4 28570 1m6eX 359 6.91e+01 c.66.1.35 91188 2wolA 562 6.92e+01 3bmxA 642 6.93e+01 1s94A 180 6.99e+01 a.47.2.1 98738 1r44A 202 7.05e+01 d.65.1.4 104787 3k8lA 669 7.05e+01 2qdxA 257 7.05e+01 1a8pA 258 7.06e+01 b.43.4.2,c.25.1.1 25654,31544 2pvpA 367 7.06e+01 3l04A 359 7.06e+01 3it4B 205 7.08e+01 1dqrA 557 7.09e+01 1dqrA c.80.1.2 35305 1esmA 316 7.10e+01 1esmA c.37.1.6 31953 1vdeA 454 7.10e+01 1vdeA b.86.1.2,d.95.2.2,d.95.2.2 28378,40581,40582 1pea 385 7.11e+01 1pea 1peaA 385 7.11e+01 c.93.1.1 35662 3h87C 73 7.13e+01 3hhdA 965 7.13e+01 1brwA 433 7.13e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 2x2zA 456 7.14e+01 1av8A 340 7.19e+01 1xikA a.25.1.2 16796 1u5uA 374 7.19e+01 e.5.1.2 113052 1aroP 883 7.21e+01 1cezA e.8.1.3 43112 2e8iA 392 7.21e+01 1gs9A 165 7.21e+01 a.24.1.1 83313 1zymA 258 7.22e+01 1zymA a.60.10.1,c.8.1.2 18110,30705 2aaoA 166 7.25e+01 8atcA 310 7.26e+01 3csuA c.78.1.1,c.78.1.1 35132,35133 1xrsA 516 7.26e+01 c.1.19.4 115883 1zclA 180 7.26e+01 1q0sA 259 7.33e+01 c.66.1.28 95509 3hoaA 509 7.35e+01 3cwwA 990 7.36e+01 1xuuA 349 7.40e+01 b.85.1.1,c.1.10.6 116067,116068 3hm2A 178 7.42e+01 3fv9A 386 7.44e+01 1d1gA 168 7.50e+01 1d1gA c.71.1.1 34889 1snyA 267 7.52e+01 c.2.1.2 105833 1bg4A 302 7.54e+01 c.1.8.3 28806 3d6kA 422 7.55e+01 3e4aA 1019 7.57e+01 2dcfA 392 7.61e+01 e.3.1.1 146485 3igoA 486 7.63e+01 2rc5A 314 7.66e+01 1dowA 205 7.66e+01 1dovA a.24.9.1 16626 1u5pA 216 7.68e+01 a.7.1.1,a.7.1.1 113046,113047 2g47A 990 7.70e+01 1ec7A 446 7.70e+01 1bqg c.1.11.2,d.54.1.1 29218,38862 1ekeA 230 7.73e+01 1ekeA c.55.3.1 33572 1j98A 157 7.77e+01 1j98A d.185.1.2 62755 1mhsA 920 7.84e+01 i.18.1.1 79130 1w6kA 732 7.87e+01 a.102.4.2,a.102.4.2 114271,114272 2i7aA 174 7.88e+01 2vf7A 842 7.89e+01 3kczA 368 7.93e+01 2pefA 373 7.93e+01 1ijhA 504 7.94e+01 c.3.1.2,d.16.1.1 66161,66162 3i1hA 161 7.94e+01 2fk8A 318 7.95e+01 c.66.1.18 133648 3l06A 359 7.96e+01 3lvuA 258 7.97e+01 1bucA 383 7.98e+01 3mdeA a.29.3.1,e.6.1.1 16590,42851