# List of top-scoring protein chains for T0336.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 1bk5A 422 2.78e-28 1bk5A a.118.1.1 19130 1bk6A 422 2.80e-28 1bk5A a.118.1.1 19133 1ee4A 423 2.81e-28 1ee4A a.118.1.1 19128 1ee5A 424 2.81e-28 1ee4A a.118.1.1 19132 1un0A 443 2.85e-28 a.118.1.1 99641 2c1tA 454 2.86e-28 1wa5B 530 2.90e-28 2c1mA 424 5.57e-28 1y2aC 428 5.58e-28 1ialA 453 5.58e-28 1bk5A a.118.1.1 19116 1pjmB 460 5.64e-28 a.118.1.1 94764 1q1sC 466 5.65e-28 a.118.1.1 95606 1b3uA 588 1.03e-15 1b3uA a.118.1.2 19135 2bptA 861 1.16e-14 1m5nS 485 3.80e-14 a.118.1.1 78653 1qbkB 890 2.29e-13 1qbkB a.118.1.1 19127 1ibrB 462 2.32e-13 1qgrA a.118.1.1 19120 1qgrA 876 4.81e-13 1qgrA a.118.1.1 19119 1uklA 876 5.53e-13 a.118.1.1 99493 1gcjA 460 1.87e-12 1qgrA a.118.1.1 19125 1f59A 442 2.24e-12 1qgrA a.118.1.1 19123 1w63B 584 2.87e-11 i.23.1.1 109193 1gw5B 591 1.16e-10 a.118.1.10 70630 1u6gC 1230 3.82e-10 1oyzA 280 1.02e-09 a.118.1.16 93775 1te4A 131 1.05e-09 a.118.1.16 106794 1g3jA 532 8.21e-08 3bct a.118.1.1 19114 1qz7A 533 8.23e-08 a.118.1.1 96618 1jdhA 529 8.24e-08 a.118.1.1 66549 1t08A 519 8.26e-08 1lujA 514 8.26e-08 a.118.1.1 78225 3bct 470 8.28e-08 3bct a.118.1.1 19112 2bct 516 8.28e-08 3bct a.118.1.1 19113 1jpwA 540 8.29e-08 a.118.1.1 67059 1i7wA 538 8.33e-08 3bct a.118.1.1 61909 1lrv 244 2.50e-07 1lrv a.118.1.5 19146 1xm9A 457 1.16e-06 1w63A 618 3.10e-05 i.23.1.1 109192 1gw5A 621 3.92e-05 a.118.1.10 70629 1xqsA 280 6.44e-04 1xqrA 296 6.54e-04 1lshA 1056 5.40e-03 a.118.4.1,f.7.1.1,f.7.1.1 74242,74243,74244 1upkA 341 2.74e-02 a.118.1.15 99758 2d1yA 256 7.43e-01 1dliA 402 8.05e-01 1dliA a.100.1.4,c.2.1.6,c.26.3.1 18809,30213,31622 1dljA 402 1.08e+00 1dliA a.100.1.4,c.2.1.6,c.26.3.1 18808,30212,31621 1a06 332 1.14e+00 1tkiA d.144.1.7 41634 1vdyA 140 1.50e+00 1z3yA 238 2.46e+00 1z3xA 238 2.47e+00 1m3gA 145 2.98e+00 c.45.1.1 84783 2fflA 756 3.51e+00 1hu3A 260 3.74e+00 1hu3A a.118.1.14 19137 1o5xA 248 4.00e+00 c.1.1.1 92528 1ztmA 490 4.03e+00 1zp2A 235 4.24e+00 1rlzA 369 4.65e+00 c.31.1.1 104989 1dhs 361 4.65e+00 1dhs c.31.1.1 31727 1oi7A 288 5.01e+00 c.2.1.8,c.23.4.1 87049,87050 1wgkA 114 5.02e+00 1pt2A 447 5.11e+00 b.67.2.2 95086 1xo3A 101 5.17e+00 1nwmX 142 5.45e+00 a.7.8.1 86301 1oxzA 186 5.57e+00 a.7.8.1 87542 1oygA 447 5.74e+00 b.67.2.2 93726 1nafA 158 6.07e+00 a.7.8.1 85487 1o3xA 140 6.41e+00 a.7.8.1 86617 1ytlA 174 6.53e+00 1t0aA 159 7.33e+00 2b6cA 220 8.06e+00 1ys4A 354 8.80e+00 1z5hA 780 8.88e+00 1azwA 313 1.03e+01 1qtrA c.69.1.7 34658 1khoA 370 1.04e+01 a.124.1.1,b.12.1.3 72489,72490 1iy9A 275 1.10e+01 c.66.1.17 76943 1o69A 394 1.13e+01 c.67.1.4 92560 1nnwA 252 1.14e+01 d.159.1.5 80674 1th0A 226 1.18e+01 d.3.1.7 106903 2gqrA 237 1.22e+01 1yhwA 297 1.26e+01 1yhvA 297 1.31e+01 1g0cA 364 1.33e+01 7a3hA c.1.8.3 60165 2c1dB 137 1.34e+01 1ua4A 455 1.38e+01 c.72.1.3 99128 2essA 248 1.41e+01 1wkyA 464 1.55e+01 1of9A 77 1.57e+01 a.64.1.4 92821 1ho8A 480 1.62e+01 1ho8A a.118.1.9 61107 2gdqA 382 1.69e+01 1j1vA 94 1.74e+01 a.4.12.2 83981 1utcA 363 1.74e+01 a.118.1.4,b.69.6.1 99914,99915 1c9lA 357 1.81e+01 1bpoA a.118.1.4,b.69.6.1 19139,27666 1c9iA 359 1.83e+01 1bpoA a.118.1.4,b.69.6.1 19141,27668 1n7hA 381 1.87e+01 c.2.1.2 80250 1ea9C 583 2.03e+01 b.1.18.2,b.71.1.1,c.1.8.1 70087,70088,70089 1bpoA 494 2.03e+01 1bpoA a.118.1.4,b.69.6.1 19143,27670 1pmi 440 2.15e+01 1pmi b.82.1.3 28114 1ltlA 279 2.17e+01 b.40.4.11 84701 1vqzA 341 2.17e+01 1dvpA 220 2.21e+01 1dvpA a.118.9.2,g.50.1.1 19216,45358 2pfkC 320 2.23e+01 3pfk c.89.1.1 35579 1pfkA 320 2.23e+01 3pfk c.89.1.1 35575 1ggzA 148 2.24e+01 a.39.1.5 70176 1q14A 361 2.27e+01 c.31.1.5 95537 1ab5A 125 2.32e+01 3chy c.23.1.1 31056 1z3aA 168 2.49e+01 1mj1A 405 2.57e+01 i.1.1.1 79175 1jx4A 352 2.64e+01 d.240.1.1,e.8.1.7 90378,90379 2bq3A 358 2.65e+01 2asdA 360 2.67e+01 1zvcA 189 2.73e+01 1vgaA 248 2.74e+01 1ygyA 529 2.76e+01 1m53A 570 2.87e+01 b.71.1.1,c.1.8.1 84805,84806 2esnA 310 2.91e+01 1zp6A 191 2.93e+01 1pe9A 361 2.97e+01 b.80.1.1 94595 2au3A 407 3.06e+01 1ghhA 81 3.08e+01 1ghhA d.57.1.1 38940 1kyqA 274 3.10e+01 c.2.1.11,e.37.1.1 73281,73282 1u9dA 122 3.19e+01 d.80.1.5 107749 1rm6B 324 3.19e+01 1uarA 285 3.32e+01 c.46.1.2,c.46.1.2 107762,107763 1tp4A 97 3.40e+01 a.189.1.1 107183 1mo0A 275 3.46e+01 c.1.1.1 79329 2fbqA 235 3.49e+01 1pqvD 221 3.53e+01 i.8.1.1 95031 1qmbA 326 3.71e+01 1ovaA e.1.1.1 42633 1kgnA 329 3.73e+01 a.25.1.2 68584 1u8tA 128 3.80e+01 1ehc 128 3.80e+01 3chy c.23.1.1 31053 1uasA 362 3.80e+01 b.71.1.1,c.1.8.1 88388,88389 1wa5C 960 3.96e+01 1z3hA 968 3.97e+01 2b8qA 142 4.31e+01 1z8kA 193 4.35e+01 2b8pA 157 4.41e+01 1cn3A 283 4.53e+01 1vpsA b.121.6.1 23346 1vpsA 289 4.60e+01 1vpsA b.121.6.1 23336 2agqA 341 4.67e+01 2af6A 258 4.72e+01 1zvwA 378 4.77e+01 2bpqA 373 4.80e+01 1ty9A 222 4.82e+01 3sqcA 631 4.89e+01 2sqcA a.102.4.2,a.102.4.2 18860,18861 1o20A 427 5.00e+01 c.82.1.1 86556 1zelA 298 5.10e+01 1eqnA 321 5.16e+01 1dd9A e.13.1.1 43256 1c6s 87 5.17e+01 1ctj a.3.1.1 15806 1otkA 249 5.19e+01 a.25.1.2 93521 1ku9A 152 5.20e+01 a.4.5.36 77544 1gl2D 65 5.21e+01 h.1.15.1 65281 1umpA 631 5.24e+01 a.102.4.2,a.102.4.2 99619,99620 1p16A 395 5.34e+01 b.40.4.6,d.142.2.3 87661,87662 1xk8A 147 5.34e+01 1av1A 201 5.36e+01 1av1A h.5.1.1 45796 1dd9A 338 5.37e+01 1dd9A e.13.1.1 43254 1p88A 216 5.40e+01 1ezxA 335 5.49e+01 1ovaA e.1.1.1 42629 1hw5A 210 5.55e+01 2cgpA a.4.5.4,b.82.3.2 16098,28137 2bckA 294 5.61e+01 1d5sA 334 5.64e+01 e.1.1.1 42635 1wy7A 207 5.64e+01 1c2yA 156 5.68e+01 1rvv1 c.16.1.1 30972 1ab6A 125 5.70e+01 3chy c.23.1.1 31054 1jtaA 361 5.71e+01 b.80.1.1 71859 2sqcA 631 5.74e+01 2sqcA a.102.4.2,a.102.4.2 18854,18855 1x5bA 163 5.78e+01 1wdcB 156 5.90e+01 1wdcB a.39.1.5 17302 1eohA 209 5.91e+01 1pgtA a.45.1.1,c.47.1.5 17574,32868 1bg7 176 6.02e+01 2fha a.25.1.1 16686 2bnmA 198 6.06e+01 1d8yA 605 6.15e+01 1xwl c.55.3.5,e.8.1.1 33684,42977 1oscA 126 6.19e+01 d.58.5.2 93490 7apiA 347 6.22e+01 1ovaA e.1.1.1 42631 1nkwH 174 6.24e+01 i.1.1.2 80593 2a01A 243 6.26e+01 1eft 405 6.27e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25688,25728,32123 1b23P 405 6.28e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25689,25729,32124 1m5xA 170 6.47e+01 d.95.2.1 84844 1bvyF 191 6.50e+01 1bvyF c.23.5.1 31207 1kbnA 209 6.53e+01 a.45.1.1,c.47.1.5 90947,90948 1p1jA 533 6.60e+01 c.2.1.3,d.81.1.3 87687,87688 2a1rA 430 6.69e+01 2dg5A 366 6.80e+01 2bvaA 292 6.84e+01 1pbyC 79 6.87e+01 a.137.9.1 94423 1qlpA 394 6.89e+01 1ovaA e.1.1.1 42628 1sidA 383 6.95e+01 1vpsA b.121.6.1 23351 2cdzA 303 6.99e+01 1q36A 427 7.04e+01 d.68.2.2 95662 1vkhA 273 7.08e+01 c.69.1.32 108662 1g6sA 427 7.10e+01 1eps d.68.2.2 39584 2fnuA 375 7.14e+01 1hkxA 147 7.15e+01 d.17.4.7 83567 1klzA 247 7.15e+01 c.1.2.3 72731 1md4A 209 7.32e+01 a.45.1.1,c.47.1.5 74632,74633 1eps 427 7.34e+01 1eps d.68.2.2 39586 1k1sA 354 7.45e+01 d.240.1.1,e.8.1.7 90386,90387 1ei3A 491 7.46e+01 i.9.1.1 46001 1p4bH 124 7.47e+01 b.1.1.1 94098 1eogA 208 7.48e+01 1pgtA a.45.1.1,c.47.1.5 17560,32854 1klyA 247 7.50e+01 c.1.2.3 72730 1px6A 209 7.53e+01 a.45.1.1,c.47.1.5 88333,88334 1p4iH 124 7.56e+01 b.1.1.1 94104 1sqrA 95 7.62e+01 1mi4A 427 7.66e+01 d.68.2.2 79141 1qqeA 292 7.67e+01 1qqeA a.118.8.1 19210 1gpjA 404 7.70e+01 a.151.1.1,c.2.1.7,d.58.39.1 65451,65452,65453 1ge9A 184 7.72e+01 1dd5A d.67.3.1 60463 1gp6A 356 7.75e+01 b.82.2.1 65441 1g62A 224 7.77e+01 1g61A d.126.1.1 41128 1to3A 304 7.78e+01 c.1.10.1 107161 1bwlA 399 7.84e+01 1oyc c.1.4.1 28606 1i5jA 79 7.86e+01 1i5jA j.39.1.1 61788 2f2oA 179 7.86e+01 2ffeA 311 7.87e+01 2a7sA 548 7.88e+01 2kfnA 605 7.98e+01 1xwl c.55.3.5,e.8.1.1 33682,42975 1kfd 605 7.98e+01 1xwl c.55.3.5,e.8.1.1 33694,42987 2fb1A 226 7.98e+01 1fcqA 350 8.00e+01 c.1.8.9 65006 1iznA 286 8.00e+01 e.43.1.1 83847 2b8iA 77 8.06e+01 17gsA 210 8.09e+01 1pgtA a.45.1.1,c.47.1.5 17524,32818 1dbfA 127 8.17e+01 2chsA d.79.1.2 39761 1fnjA 127 8.17e+01 2chsA d.79.1.2 39776 1e0tA 470 8.18e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 22gsA 210 8.18e+01 1pgtA a.45.1.1,c.47.1.5 17542,32836 1pkyA 470 8.18e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27068,29296,33150 1klnA 605 8.20e+01 1xwl c.55.3.5,e.8.1.1 33693,42986 2acfA 182 8.21e+01 1wa9A 368 8.22e+01 1jf3A 147 8.22e+01 a.1.1.2 71642 1zdmA 129 8.28e+01 2av5A 120 8.28e+01 1qx2A 76 8.36e+01 a.39.1.1 104622 1fnkA 127 8.48e+01 2chsA d.79.1.2 39777 1g3mA 294 8.53e+01 c.37.1.5 83268 1psi 394 8.55e+01 1ovaA e.1.1.1 42634 1iq5A 149 8.56e+01 a.39.1.5 62643 2be6A 150 8.57e+01 1mihA 129 8.57e+01 c.23.1.1 84975 1w2dA 265 8.62e+01 d.143.1.3 109121 1prwA 149 8.67e+01 a.39.1.5 95062 1eexA 554 8.69e+01 1dioA c.1.19.3 29650 1fsu 492 8.72e+01 1auk c.76.1.2 35032 2f3yA 148 8.73e+01 1y0vH 146 8.76e+01 1cdlA 147 8.77e+01 1cll a.39.1.5 17272 1e0uA 470 8.77e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27072,29300,33154 1cdmA 144 8.85e+01 1cll a.39.1.5 17270 1k93D 144 8.85e+01 a.39.1.5 68330 1grnB 203 8.87e+01 1tx4A a.116.1.1 19106 1w2fA 276 8.88e+01 d.143.1.3 109125 1fyhA 258 8.91e+01 1d9cA a.26.1.3,a.26.1.3 16907,16908 3ygsP 97 8.93e+01 3ygsP a.77.1.3 18435 1y6iA 233 8.95e+01 1qfzA 308 8.98e+01 1fnc b.43.4.2,c.25.1.1 25633,31523 1qgaA 308 8.98e+01 1fnc b.43.4.2,c.25.1.1 25637,31527 1qg0A 308 8.98e+01 1fnc b.43.4.2,c.25.1.1 25639,31529