# List of top-scoring protein chains for t04-100-30-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 1.86e-01 2gaeA 346 2.61e-01 2c3mA 1231 3.91e-01 1b0pA 1231 4.01e-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 1kekA 1231 5.48e-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 1cjbA 231 1.59e+00 1qk3A c.61.1.1 34079 1zd0A 150 1.91e+00 1vjhA 122 2.47e+00 d.129.3.1 100811 1ryp2 233 2.85e+00 1ryp2 1g2rA 100 3.45e+00 1g2rA d.192.1.1 60231 1n9lA 109 4.04e+00 d.110.3.6 85468 1rypJ 204 4.23e+00 d.153.1.4 41878 1vqvA 306 5.46e+00 1wmhB 86 5.57e+00 1g0uL 241 5.77e+00 d.153.1.4 41894 1yueA 427 5.88e+00 2akaB 299 7.03e+00 1sq9A 397 7.48e+00 b.69.4.1 105889 1wmhA 89 7.88e+00 1ryp1 222 8.36e+00 1ryp1 1bmv1 198 8.37e+00 1bmv1 1b9mA 265 8.76e+00 1b9mA a.4.5.8,b.40.6.2,b.40.6.2 16118,58938,58939 2napA 723 8.93e+00 2napA b.52.2.2,c.81.1.1 26926,35334 1quqA 129 9.15e+00 1quqA b.40.4.3 25303 1v25A 541 9.58e+00 e.23.1.1 108275 1a8d 452 9.87e+00 1a8d b.29.1.6,b.42.4.2 24262,25607 1pgl1 185 1.03e+01 1s5uA 138 1.09e+01 d.38.1.1 98573 1ahsA 126 1.13e+01 1ahsA b.19.1.1 23794 2ghsA 326 1.14e+01 1cv2A 296 1.17e+01 1bn6A c.69.1.8 34680 1rhfA 182 1.28e+01 b.1.1.1,b.1.1.4 97469,97470 1vemA 516 1.34e+01 1mj5A 302 1.37e+01 c.69.1.8 91285 1w3uA 362 1.38e+01 1kolA 398 1.44e+01 b.35.1.2,c.2.1.1 77474,77475 2fdbM 164 1.51e+01 1tc6A 236 1.55e+01 d.122.1.1 106756 3cox 507 1.59e+01 1b8sA c.3.1.2,d.16.1.1 30332,37863 1aohA 147 1.59e+01 1aohA b.2.2.2 22401 1qy5A 269 1.64e+01 d.122.1.1 96573 1s9jA 341 1.64e+01 2gokA 429 1.67e+01 1vd2A 89 1.69e+01 d.15.2.2 108517 8dfr 189 1.76e+01 1aoeA c.71.1.1 34895 1xm8A 254 1.78e+01 1o54A 277 1.87e+01 c.66.1.13 92482 1rocA 155 1.89e+01 b.1.22.1 97673 2c0rA 362 1.91e+01 1oebA 62 1.94e+01 b.34.2.1 86909 1ef1A 294 1.95e+01 1ef1A a.11.2.1,b.55.1.5,d.15.1.4 16368,27003,37611 1g7oA 215 1.99e+01 1g7oA a.45.1.1,c.47.1.5 60332,60333 2fa1A 160 2.05e+01 1l1jA 239 2.09e+01 b.47.1.1 84516 1cqyA 99 2.22e+01 1b9zA b.3.1.1 22527 1h9sA 140 2.30e+01 1b9mA b.40.6.2,b.40.6.2 60843,60844 1zh5A 195 2.35e+01 1utiA 58 2.36e+01 b.34.2.1 99962 1ov3A 138 2.39e+01 b.34.2.1,b.34.2.1 87451,87452 1a34A 159 2.39e+01 1a34A b.121.7.1 23286 1cz4A 185 2.43e+01 1cz4A b.52.2.3,d.31.1.1 26934,38468 1lokA 291 2.48e+01 c.56.5.4 78122 1qreA 247 2.50e+01 1qreA b.81.1.5 28066 1tqyB 415 2.53e+01 c.95.1.1,c.95.1.1 107247,107248 1uheA 97 2.55e+01 1dzfA 215 2.58e+01 1dzfA c.52.3.1,d.78.1.1 33344,39753 1xseA 295 2.61e+01 1kbvA 327 2.72e+01 b.6.1.3,b.6.1.3 68395,68396 1qhqA 140 2.77e+01 1qhqA b.6.1.1 63326 1ixh 321 2.77e+01 1ixh c.94.1.1 35761 1itcA 516 2.88e+01 b.3.1.1,c.1.8.1 83705,83706 2cwzA 141 3.00e+01 1cfzA 162 3.03e+01 1cfzA c.56.1.1 33754 2anpA 291 3.06e+01 2bkdN 134 3.06e+01 1c4xA 285 3.11e+01 1c4xA c.69.1.10 34684 2pth 193 3.19e+01 2pth c.56.3.1 33793 1rypL 212 3.31e+01 d.153.1.4 41880 2dpmA 284 3.38e+01 2dpmA c.66.1.28 34246 1umuA 116 3.39e+01 1umuA b.87.1.1 28382 1j26A 112 3.42e+01 d.50.4.1 103823 2fuqA 747 3.49e+01 1dnlA 199 3.74e+01 1ci0A b.45.1.1 25753 3pcgM 238 3.74e+01 3pchM b.3.6.1 22742 1b8aA 438 3.75e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1imjA 210 3.78e+01 c.69.1.23 71246 1g291 372 3.79e+01 1g291 1ng2A 193 3.83e+01 b.34.2.1,b.34.2.1 85660,85661 1p3wA 404 3.86e+01 c.67.1.3 87752 2asfA 137 3.96e+01 1v3yA 192 3.97e+01 1pb7A 292 4.00e+01 c.94.1.1 88025 2c3gA 98 4.01e+01 1z2mA 155 4.01e+01 1lf7A 182 4.07e+01 b.60.1.1 73878 1h5zA 455 4.07e+01 a.104.1.1 90622 1bvoA 175 4.10e+01 1a3qA b.2.5.3 22457 1zsyA 357 4.10e+01 1ro7A 259 4.13e+01 c.130.1.1 97667 1nulA 152 4.15e+01 1nulA c.61.1.1 34011 2ezvA 269 4.20e+01 1rdo1 113 4.26e+01 1rtm1 1amp 291 4.29e+01 1amp c.56.5.4 33837 1aonO 97 4.30e+01 b.35.1.1 24642 2amlA 373 4.38e+01 1t0yA 122 4.47e+01 d.15.1.1 99066 2auhB 59 4.51e+01 1kmvA 186 4.53e+01 c.71.1.1 72757 1m2tA 254 4.55e+01 d.165.1.1 84761 2a50A 73 4.58e+01 1v8aA 265 4.66e+01 c.72.1.2 100494 1l3iA 192 4.73e+01 c.66.1.22 77676 1vclA 432 4.77e+01 b.42.2.1,b.42.2.1,d.281.1.1 108498,108499,108500 1rdj1 113 4.77e+01 1rtm1 1yzsA 121 4.80e+01 1d2fA 390 4.88e+01 1d2fA c.67.1.3 34411 1fsgA 233 4.88e+01 1qk3A c.61.1.1 34029 1e3jA 352 4.90e+01 1e3jA b.35.1.2,c.2.1.1 24765,29781 1npoA 95 4.95e+01 1npoA b.9.1.1 23270 1mrj 247 4.97e+01 1mrj d.165.1.1 42177 1id2A 106 5.24e+01 1aac b.6.1.1 62288 1g79A 218 5.24e+01 1ci0A b.45.1.1 25752 1o5zA 442 5.43e+01 c.59.1.2,c.72.2.2 92530,92531 1t2wA 145 5.47e+01 b.100.1.1 106289 1uirA 314 5.48e+01 c.66.1.17 99429 1jk4A 89 5.50e+01 b.9.1.1 77130 1vdmA 153 5.56e+01 1dytA 133 5.62e+01 7rsa d.5.1.1 37288 1x8vA 455 5.73e+01 1aw8B 91 5.77e+01 1aw8B 1oe8A 211 5.78e+01 a.45.1.1,c.47.1.5 86905,86906 1rtqA 299 5.81e+01 c.56.5.4 97819 1e9xA 455 5.97e+01 1ea1A a.104.1.1 18969 1uj0A 62 6.03e+01 b.34.2.1 99449 1njkA 156 6.03e+01 d.38.1.1 85818 1pvdA 537 6.05e+01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31737,31777,31778 1vc3B 97 6.14e+01 1dl5A 317 6.15e+01 1dl5A c.66.1.7,d.197.1.1 64720,64721 1cr1A 296 6.21e+01 1cr1A c.37.1.11 32286 1dekA 241 6.21e+01 1dekA c.37.1.1 31842 2aukA 190 6.26e+01 3seb 238 6.28e+01 3seb b.40.2.2,d.15.6.1 25184,37773 1nfjA 89 6.33e+01 d.68.6.1 91866 2ch4A 320 6.36e+01 1sqrA 95 6.40e+01 1ocvA 125 6.40e+01 d.17.4.3 86810 1v04A 355 6.40e+01 b.68.6.2 100240 1ok8A 394 6.45e+01 b.1.18.4,f.10.1.1 93236,93237 2gw6A 123 6.46e+01 1byfA 125 6.47e+01 1byfA d.169.1.1 42419 1guqA 348 6.48e+01 1guqA d.13.1.2,d.13.1.2 37522,37523 1ekqA 272 6.65e+01 1c3qA c.72.1.2 34941 1h0xA 100 6.67e+01 d.68.6.1 76451 1s4iA 175 6.74e+01 1izoA 417 6.75e+01 a.104.1.1 83851 1u13A 455 6.76e+01 a.104.1.1 107578 1kutA 230 6.77e+01 d.143.1.1 73017 1k3bA 119 6.82e+01 b.61.5.1 72016 1v3wA 173 6.85e+01 b.81.1.5 100291 1xtmA 175 6.88e+01 2b4lA 268 6.91e+01 1v9sA 208 6.92e+01 2fy6A 143 6.94e+01 2booA 247 6.96e+01 1zoiA 276 6.99e+01 1rwsA 77 7.02e+01 d.15.3.2 97991 1g2qA 187 7.03e+01 c.61.1.1 65117 1ewnA 219 7.04e+01 1bnkA b.46.1.2 25762 1je5A 206 7.08e+01 1je5A b.40.4.7 62909 1yemA 179 7.10e+01 1knmA 130 7.15e+01 b.42.2.1 72781 1qj4A 257 7.20e+01 1qj4A c.69.1.20 34796 2bitX 165 7.21e+01 1atg 231 7.21e+01 1atg c.94.1.1 35834 1v1qA 134 7.24e+01 1souA 194 7.28e+01 c.124.1.6 105858 1pqhA 143 7.41e+01 b.52.2.1 95017 1wdxA 69 7.53e+01 2gfhA 260 7.68e+01 1txkA 498 7.76e+01 b.1.18.2,b.30.5.9 107425,107426 1qgdA 662 7.77e+01 c.36.1.6,c.36.1.10,c.48.1.1 88367,88368,88369 1ounA 127 7.79e+01 1ounA d.17.4.2 38090 1uayA 242 7.83e+01 c.2.1.2 88390 1kkhA 317 7.91e+01 d.14.1.5,d.58.26.3 72645,72646 2beiA 170 8.02e+01 1ixlA 131 8.08e+01 d.38.1.5 90717 1bn7A 294 8.22e+01 1bn6A c.69.1.8 34677 1qjvA 342 8.24e+01 1qjvA b.80.1.5 28035 1x31C 206 8.28e+01 1ckmA 330 8.39e+01 1ckmA b.40.4.6,d.142.2.3 25358,41585 1a7qL 106 8.69e+01 8fabA b.1.1.1 19954 1ufkA 254 8.70e+01 c.66.1.39 99340 1idsA 207 8.78e+01 1avmA a.2.11.1,d.44.1.1 15722,38730 1y2tA 142 8.93e+01 1who 96 8.93e+01 1who b.7.3.1 23215 1nfa 178 8.98e+01 1a02N b.2.5.3 22442