# List of top-scoring protein chains for t2k-100-30-bys-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 2ae0X 345 3.45e-01 2c3mA 1231 3.51e-01 1b0pA 1231 3.69e-01 c.36.1.8,c.36.1.12,c.48.1.3,c.64.1.1,d.58.1.5 31831,31832,33104,34157,39003 2gaeA 346 4.86e-01 1kekA 1231 4.94e-01 c.36.1.8,c.36.1.12,c.48.1.3,c.64.1.1,d.58.1.5 68524,68525,68526,68527,68528 1hxmA 229 1.42e+00 1hxmA b.1.1.1,b.1.1.2 61367,61368 1cjbA 231 2.80e+00 1qk3A c.61.1.1 34079 1zd0A 150 3.29e+00 1vjhA 122 3.98e+00 d.129.3.1 100811 1n9lA 109 4.08e+00 d.110.3.6 85468 1rypJ 204 4.29e+00 d.153.1.4 41878 1ryp2 233 4.83e+00 1ryp2 2akaB 299 6.83e+00 2ghsA 326 6.99e+00 1rhfA 182 7.60e+00 b.1.1.1,b.1.1.4 97469,97470 1sq9A 397 8.40e+00 b.69.4.1 105889 1yueA 427 9.47e+00 1vqvA 306 1.00e+01 1g2rA 100 1.02e+01 1g2rA d.192.1.1 60231 1g0uI 205 1.08e+01 d.153.1.4 41891 1g0u1 266 1.11e+01 1xm8A 254 1.13e+01 1quqA 129 1.23e+01 1quqA b.40.4.3 25303 2bkdN 134 1.25e+01 1eikA 77 1.39e+01 1eikA d.78.1.1 39751 1g0uL 241 1.41e+01 d.153.1.4 41894 3cox 507 1.47e+01 1b8sA c.3.1.2,d.16.1.1 30332,37863 1wmhA 89 1.50e+01 1cv2A 296 1.54e+01 1bn6A c.69.1.8 34680 2napA 723 1.58e+01 2napA b.52.2.2,c.81.1.1 26926,35334 1o54A 277 1.63e+01 c.66.1.13 92482 1s5uA 138 1.67e+01 d.38.1.1 98573 1uheA 97 1.68e+01 1w3uA 362 1.72e+01 1umuB 116 1.82e+01 1umuA b.87.1.1 28383 1iz7A 295 1.82e+01 c.69.1.8 76982 2gokA 429 1.89e+01 1pbp 321 1.92e+01 1ixh c.94.1.1 35768 1mj5A 302 1.92e+01 c.69.1.8 91285 1coy 507 1.95e+01 1b8sA c.3.1.2,d.16.1.1 30333,37864 1lokA 291 2.00e+01 c.56.5.4 78122 1ryp1 222 2.00e+01 1ryp1 1b9mA 265 2.07e+01 1b9mA a.4.5.8,b.40.6.2,b.40.6.2 16118,58938,58939 1bt4A 362 2.09e+01 1bjnA c.67.1.4 34468 1n99A 166 2.15e+01 b.36.1.1,b.36.1.1 85459,85460 1wmhB 86 2.16e+01 1bmv1 198 2.17e+01 1bmv1 1a8d 452 2.19e+01 1a8d b.29.1.6,b.42.4.2 24262,25607 2c0rA 362 2.27e+01 1ov3A 138 2.28e+01 b.34.2.1,b.34.2.1 87451,87452 1pgl1 185 2.29e+01 1kbvA 327 2.34e+01 b.6.1.3,b.6.1.3 68395,68396 1v25A 541 2.40e+01 e.23.1.1 108275 2fdbM 164 2.42e+01 2anpA 291 2.43e+01 1aohA 147 2.47e+01 1aohA b.2.2.2 22401 1k42A 168 2.51e+01 b.18.1.14 72032 1ahsA 126 2.53e+01 1ahsA b.19.1.1 23794 1l1jA 239 2.62e+01 b.47.1.1 84516 1tc6A 236 2.67e+01 d.122.1.1 106756 1a40 321 2.75e+01 1ixh c.94.1.1 35767 2pth 193 2.79e+01 2pth c.56.3.1 33793 1oebA 62 2.85e+01 b.34.2.1 86909 1aohB 147 2.98e+01 1aohA b.2.2.2 22402 1qhqA 140 3.03e+01 1qhqA b.6.1.1 63326 1vd2A 89 3.07e+01 d.15.2.2 108517 1cfzA 162 3.07e+01 1cfzA c.56.1.1 33754 1jjhA 86 3.08e+01 2bopA d.58.8.1 63119 1qy5A 269 3.08e+01 d.122.1.1 96573 1ixh 321 3.11e+01 1ixh c.94.1.1 35761 1who 96 3.20e+01 1who b.7.3.1 23215 1amp 291 3.25e+01 1amp c.56.5.4 33837 1lf7A 182 3.28e+01 b.60.1.1 73878 1rocA 155 3.30e+01 b.1.22.1 97673 8dfr 189 3.36e+01 1aoeA c.71.1.1 34895 2cwzA 141 3.41e+01 2fa1A 160 3.43e+01 2amlA 373 3.48e+01 5bcaA 516 3.57e+01 1b9zA b.3.1.1,c.1.8.1 22529,28799 1utiA 58 3.57e+01 b.34.2.1 99962 1rdo1 113 3.69e+01 1rtm1 1ng2A 193 3.82e+01 b.34.2.1,b.34.2.1 85660,85661 1ef1A 294 3.85e+01 1ef1A a.11.2.1,b.55.1.5,d.15.1.4 16368,27003,37611 1a34A 159 3.89e+01 1a34A b.121.7.1 23286 1c4xA 285 3.91e+01 1c4xA c.69.1.10 34684 1s9jA 341 3.92e+01 2a50A 73 3.95e+01 1delA 241 4.00e+01 1dekA c.37.1.1 31844 1vemA 516 4.00e+01 1b9zA 516 4.01e+01 1b9zA b.3.1.1,c.1.8.1 22528,28798 1rdj1 113 4.03e+01 1rtm1 1rtqA 299 4.14e+01 c.56.5.4 97819 1v3yA 192 4.19e+01 1c3qA 272 4.27e+01 1c3qA c.72.1.2 34948 1kolA 398 4.32e+01 b.35.1.2,c.2.1.1 77474,77475 1dekA 241 4.45e+01 1dekA c.37.1.1 31842 1nfjA 89 4.50e+01 d.68.6.1 91866 1ay9A 108 4.51e+01 1umuA b.87.1.1 28384 1bv4A 118 4.55e+01 1rtm1 d.169.1.1 42380 1h5zA 455 4.69e+01 a.104.1.1 90622 1bvoA 175 4.72e+01 1a3qA b.2.5.3 22457 1dzfA 215 4.85e+01 1dzfA c.52.3.1,d.78.1.1 33344,39753 1v3wA 173 4.86e+01 b.81.1.5 100291 1p3wA 404 4.86e+01 c.67.1.3 87752 1b8aA 438 4.88e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1h9sA 140 4.98e+01 1b9mA b.40.6.2,b.40.6.2 60843,60844 1h0xA 100 5.01e+01 d.68.6.1 76451 1njkA 156 5.09e+01 d.38.1.1 85818 1vclA 432 5.11e+01 b.42.2.1,b.42.2.1,d.281.1.1 108498,108499,108500 1ekqA 272 5.13e+01 1c3qA c.72.1.2 34941 2ch4A 320 5.16e+01 1wdxA 69 5.18e+01 2fuqA 747 5.19e+01 1r8nA 185 5.29e+01 b.42.4.1 104851 8cho 125 5.32e+01 1opy d.17.4.3 38108 2dpmA 284 5.41e+01 2dpmA c.66.1.28 34246 1imjA 210 5.41e+01 c.69.1.23 71246 1aonO 97 5.41e+01 b.35.1.1 24642 1zh5A 195 5.42e+01 1dnlA 199 5.44e+01 1ci0A b.45.1.1 25753 1cz4A 185 5.56e+01 1cz4A b.52.2.3,d.31.1.1 26934,38468 1sqrA 95 5.58e+01 1j26A 112 5.66e+01 d.50.4.1 103823 1g7oA 215 5.68e+01 1g7oA a.45.1.1,c.47.1.5 60332,60333 1qgdA 662 5.70e+01 c.36.1.6,c.36.1.10,c.48.1.1 88367,88368,88369 1q6oA 216 5.75e+01 c.1.2.3 95986 1v8aA 265 5.80e+01 c.72.1.2 100494 1fsgA 233 5.81e+01 1qk3A c.61.1.1 34029 1pvdA 537 5.86e+01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31737,31777,31778 1d0hA 469 5.86e+01 1a8d b.29.1.6,b.42.4.2 24265,25610 1npoA 95 5.89e+01 1npoA b.9.1.1 23270 1t0yA 122 5.91e+01 d.15.1.1 99066 2c1cA 312 5.93e+01 1izoA 417 5.97e+01 a.104.1.1 83851 1g2qA 187 6.04e+01 c.61.1.1 65117 1l3iA 192 6.06e+01 c.66.1.22 77676 1qreA 247 6.08e+01 1qreA b.81.1.5 28066 1cqyA 99 6.14e+01 1b9zA b.3.1.1 22527 1cr1A 296 6.21e+01 1cr1A c.37.1.11 32286 2booA 247 6.22e+01 1cr0A 296 6.25e+01 1cr1A c.37.1.11 32287 1shsA 147 6.25e+01 1shsA b.15.1.1 23675 1g291 372 6.26e+01 1g291 1ggtB 731 6.27e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21882,22173,22174,37112 1a54A 321 6.34e+01 1ixh c.94.1.1 35763 1z2mA 155 6.38e+01 1ky9B 448 6.44e+01 b.36.1.4,b.36.1.4,b.47.1.1 73200,73201,73202 1pydA 556 6.48e+01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31735,31773,31774 1rwsA 77 6.49e+01 d.15.3.2 97991 1tg0A 68 6.57e+01 1x8vA 455 6.60e+01 2auhB 59 6.64e+01 2ezvA 269 6.66e+01 1tqyB 415 6.68e+01 c.95.1.1,c.95.1.1 107247,107248 1kv8A 216 6.74e+01 c.1.2.3 73054 2c3gA 98 6.74e+01 1e9xA 455 6.91e+01 1ea1A a.104.1.1 18969 1tlgA 125 6.94e+01 1byfA d.169.1.1 42421 3seb 238 7.02e+01 3seb b.40.2.2,d.15.6.1 25184,37773 1gupA 348 7.07e+01 1guqA d.13.1.2,d.13.1.2 37534,37535 1atg 231 7.09e+01 1atg c.94.1.1 35834 1xyfA 436 7.20e+01 1taxA b.42.2.1,c.1.8.3 25577,28909 1g79A 218 7.22e+01 1ci0A b.45.1.1 25752 1ahc 246 7.24e+01 1mrj d.165.1.1 42184 1ocvA 125 7.25e+01 d.17.4.3 86810 1dcs 311 7.28e+01 1dcs b.82.2.1 28124 1pt1A 143 7.29e+01 b.52.2.1 95084 1ok8A 394 7.34e+01 b.1.18.4,f.10.1.1 93236,93237 1b34A 119 7.36e+01 1d3bA b.38.1.1 24796 1qpbA 563 7.46e+01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31739,31781,31782 2bkyA 97 7.47e+01 1y2tA 142 7.52e+01 1umuA 116 7.55e+01 1umuA b.87.1.1 28382 1asu 162 7.55e+01 1cxqA c.55.3.2 33626 3pchM 238 7.59e+01 3pchM b.3.6.1 22748 1bdmB 327 7.61e+01 1bmdA c.2.1.5,d.162.1.1 30138,42105 2pcdM 238 7.69e+01 3pchM b.3.6.1 22760 1aw8B 91 7.69e+01 1aw8B 1zboA 210 7.69e+01 1aw8E 91 7.69e+01 1aw8B 1cnuA 137 7.74e+01 1cof d.109.1.2 40862 1v1qA 134 7.75e+01 1i6wA 181 7.76e+01 1i6wA c.69.1.18 61859 1o5zA 442 7.78e+01 c.59.1.2,c.72.2.2 92530,92531 1nfa 178 7.83e+01 1a02N b.2.5.3 22442 1u13A 455 7.90e+01 a.104.1.1 107578 1qjvA 342 8.00e+01 1qjvA b.80.1.5 28035 1zsyA 357 8.01e+01 1zoiA 276 8.05e+01 1rypL 212 8.09e+01 d.153.1.4 41880 1ckmA 330 8.13e+01 1ckmA b.40.4.6,d.142.2.3 25358,41585 1xseA 295 8.15e+01 1vdwA 254 8.17e+01 e.7.1.1 100569 1bn7A 294 8.23e+01 1bn6A c.69.1.8 34677 1byfA 125 8.26e+01 1byfA d.169.1.1 42419 1jk4A 89 8.26e+01 b.9.1.1 77130 2f6rA 281 8.28e+01 2gw6A 123 8.35e+01 3pcgM 238 8.41e+01 3pchM b.3.6.1 22742 1xtmA 175 8.58e+01 1nulA 152 8.68e+01 1nulA c.61.1.1 34011 1itcA 516 8.68e+01 b.3.1.1,c.1.8.1 83705,83706 1d2fA 390 8.69e+01 1d2fA c.67.1.3 34411 1cqwA 295 8.75e+01 1b6g c.69.1.8 34679 1bn6A 294 8.79e+01 1bn6A c.69.1.8 34678 1k3bA 119 8.86e+01 b.61.5.1 72016 1h0cA 392 8.96e+01 c.67.1.3 83424 1s4iA 175 8.98e+01