# List of top-scoring protein chains for t04-100-30-str2-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 2igd 61 1.25e-14 2igd 2igdA 61 1.25e-14 d.15.7.1 37821 2qmtA 56 1.29e-14 2gi9A 56 1.44e-14 2on8A 56 6.97e-13 2go8A 122 5.58e-02 2uubJ 105 1.07e-01 d.58.15.1 139941 1ufmA 84 4.74e-01 a.4.5.47 107816 2hfnA 153 4.78e-01 1dekA 241 9.01e-01 1dekA c.37.1.1 31842 2b7eA 59 1.02e+00 1j98A 157 1.02e+00 1j98A d.185.1.2 62755 1bkjA 240 1.43e+00 1bkjA d.90.1.1 40243 1ri7A 171 1.55e+00 a.4.5.32,d.58.4.2 97504,97505 3cjsA 60 1.94e+00 2nuhA 118 2.07e+00 3c6fA 153 2.12e+00 1u1iA 392 2.28e+00 c.2.1.3,d.81.1.3 107582,107583 2cyyA 151 2.32e+00 a.4.5.32,d.58.4.2 131028,131029 1fjgJ 105 2.97e+00 1fjfJ d.58.15.1 39330 2bjoA 136 3.30e+00 1iznB 277 3.35e+00 e.43.1.2 83848 1c0eA 157 3.52e+00 1dg9A c.44.1.1 32638 2r01A 210 3.87e+00 4ubpA 101 4.20e+00 1ubpA d.8.1.1 37352 3bm1A 183 4.38e+00 2irfG 113 5.32e+00 2irfG a.4.5.23 16185 2qtwA 124 5.83e+00 1ne2A 200 6.25e+00 c.66.1.32 85586 2pmwA 126 6.30e+00 3bcwA 123 8.00e+00 2pbzA 320 8.04e+00 1nslA 184 8.34e+00 d.108.1.1 86137 1ysjA 404 9.27e+00 c.56.5.4,d.58.19.1 123975,123976 1uilA 113 9.47e+00 d.50.1.1 113255 1x0pA 143 9.56e+00 d.58.10.2 121552 2nxcA 254 9.60e+00 c.66.1.39 138739 1otvA 259 9.60e+00 a.132.1.4 93526 1dg9A 157 9.71e+00 1dg9A c.44.1.1 32637 1v5iB 76 1.02e+01 3bdiA 207 1.04e+01 2ifxA 114 1.07e+01 1f06A 320 1.07e+01 1dapA c.2.1.3,d.81.1.3 59556,59557 1ftrA 296 1.11e+01 1ftrA d.58.33.1,d.58.33.1 39485,39486 1x2mA 64 1.11e+01 a.4.1.1 121645 1s3iA 310 1.12e+01 b.46.1.1,c.65.1.1 98435,98436 1lfwA 470 1.18e+01 c.56.5.4,d.58.19.1 77942,77943 1tuvA 114 1.20e+01 d.58.4.11 112665 1ufyA 122 1.22e+01 d.79.1.2 88489 2cpcA 113 1.28e+01 1co6A 107 1.29e+01 1ycc a.3.1.1 15894 1jaeA 471 1.35e+01 b.71.1.1,c.1.8.1 27773,28760 2jamA 304 1.35e+01 1txoA 237 1.38e+01 d.219.1.1 112781 2cksA 306 1.41e+01 2bw0A 329 1.43e+01 b.46.1.1,c.65.1.1 129303,129304 1q2lA 939 1.47e+01 d.185.1.1,d.185.1.1,d.185.1.1,d.185.1.1 118731,118732,118733,118734 2cwdA 161 1.56e+01 1y96B 85 1.63e+01 1phkA 298 1.65e+01 d.144.1.7 41635 1y0zA 330 1.68e+01 b.82.2.8 116317 2fyxA 143 1.69e+01 d.58.57.1 134411 2nnnA 140 1.76e+01 1sw2A 275 1.77e+01 c.94.1.1 106064 1sw5A 275 1.79e+01 c.94.1.1 106069 2cm1A 260 1.84e+01 1r6yA 115 1.87e+01 d.58.4.11 111711 1zthA 258 1.89e+01 2pn6A 150 1.92e+01 1gs5A 258 1.96e+01 c.73.1.2 70395 2hlvA 160 1.98e+01 1xwwA 157 2.07e+01 2e7xA 150 2.12e+01 2nyiA 195 2.12e+01 3bs9A 87 2.16e+01 1konA 249 2.16e+01 e.39.1.1 72823 2f4mA 295 2.32e+01 2qyxA 238 2.32e+01 2raqA 97 2.39e+01 1dqzA 280 2.41e+01 1dqyA c.69.1.3 34638 1usgA 346 2.46e+01 c.93.1.1 99864 2fvhA 120 2.49e+01 1pjvA 32 2.49e+01 g.3.7.2 94792 3bpdA 100 2.50e+01 2p4hX 322 2.53e+01 2fe3A 145 2.54e+01 1t77A 414 2.54e+01 a.169.1.1,b.55.1.6 112290,112291 1vkwA 218 2.65e+01 d.90.1.2 108695 1wubA 178 2.72e+01 b.61.6.1 114891 3cjnA 162 2.76e+01 1edzA 320 2.77e+01 1ee9A c.2.1.7,c.58.1.2 30287,33935 1aocA 175 2.77e+01 1aocA g.17.1.5 44817 1s0pA 176 2.85e+01 a.192.1.1 98300 2v72A 143 2.85e+01 2bs2B 241 2.90e+01 a.1.2.1,d.15.4.2 129033,129034 1zy9A 564 2.93e+01 b.30.5.11,c.1.8.13 125813,125814 2bycA 137 2.94e+01 d.58.10.2 129476 2ad6B 69 2.95e+01 a.137.2.1 126569 1xxaA 78 2.98e+01 1xxaA d.74.2.1 39700 1ni9A 338 2.98e+01 e.7.1.2 85739 3cnuA 116 3.01e+01 1uzcA 71 3.14e+01 a.159.2.1 100222 1gr0A 367 3.15e+01 c.2.1.3,d.81.1.3 70379,70380 2cb2A 318 3.18e+01 d.58.4.17 130174 2jsxA 95 3.30e+01 1twyA 290 3.33e+01 c.94.1.1 112767 2o1mA 258 3.33e+01 2q4aA 330 3.34e+01 b.82.2.8 139839 1u2xA 474 3.34e+01 c.72.1.3 107622 1lqvC 33 3.35e+01 g.32.1.1 74208 2fb0A 94 3.49e+01 1rgxA 114 3.51e+01 g.77.1.1 104932 1wj6A 101 3.54e+01 d.15.2.2 114693 3bv0A 437 3.58e+01 1jksA 294 3.62e+01 d.144.1.7 71710 2onfA 140 3.69e+01 2j0wA 449 3.70e+01 c.73.1.3,d.58.18.10,d.58.18.10 137923,137924,137925 1ow1A 195 3.71e+01 b.131.1.3 93625 1w5dA 462 3.74e+01 e.3.1.3 120642 1o1zA 234 3.74e+01 c.1.18.3 86555 2j44A 217 3.76e+01 1r6oC 106 3.78e+01 d.45.1.2 118738 1tluA 130 3.82e+01 d.156.1.2 107139 2azpA 318 3.82e+01 2dqlA 115 3.88e+01 1gsjA 258 3.91e+01 c.73.1.2 70397 1fseA 74 3.92e+01 1fseA a.4.6.2 60000 1ydlA 79 3.98e+01 d.295.1.1 123001 2ceyA 306 3.99e+01 2j0fA 482 4.01e+01 2pa2A 151 4.02e+01 1uouA 474 4.11e+01 a.46.2.1,c.27.1.1,d.41.3.1 99706,99707,99708 1p99A 295 4.17e+01 c.94.1.1 94384 2f4lA 297 4.19e+01 b.23.3.1 132927 1mwqA 101 4.20e+01 d.58.4.7 91481 1xwsA 313 4.22e+01 d.144.1.7 116133 1vrmA 325 4.23e+01 d.96.2.1 120472 2cmxA 118 4.26e+01 2vqcA 118 4.26e+01 1ucrA 78 4.27e+01 a.4.5.45 99188 1y8cA 246 4.28e+01 c.66.1.43 116563 2oogA 287 4.30e+01 2b95A 106 4.30e+01 1iatA 557 4.30e+01 1dqrA c.80.1.2 62123 2cibA 455 4.31e+01 1gx5A 536 4.37e+01 e.8.1.4 70682 1vr7A 142 4.47e+01 d.156.1.2 120443 1n2fA 142 4.50e+01 d.227.1.1 79853 2bikB 313 4.54e+01 2fk9A 157 4.55e+01 2iyeA 263 4.57e+01 2uuuA 584 4.62e+01 3bf7A 255 4.66e+01 1vr4A 103 4.66e+01 d.230.5.1 120432 1ukuA 102 4.72e+01 d.58.5.2 99533 2hz5A 106 4.76e+01 2sqcA 631 4.77e+01 2sqcA a.102.4.2,a.102.4.2 18854,18855 2uxyA 341 4.79e+01 2oy9A 98 4.87e+01 1g97A 459 4.87e+01 1fwyA b.81.1.4,c.68.1.5 60394,60395 1hm9A 468 4.92e+01 b.81.1.4,c.68.1.5 65866,65867 1dk8A 147 4.94e+01 1agrE a.91.1.1 18548 2j5aA 110 5.06e+01 3b49A 211 5.06e+01 1bccJ 62 5.07e+01 1be3J f.23.14.1 43703 1o04A 500 5.17e+01 c.82.1.1 86508 1wi9A 72 5.24e+01 a.4.5.47 114663 2i15A 135 5.24e+01 1vdwA 254 5.26e+01 e.7.1.1 100569 1s9uA 207 5.30e+01 a.184.1.1 105390 3bfxA 296 5.31e+01 2zkqn 56 5.41e+01 1zldA 120 5.47e+01 3c19A 186 5.50e+01 2inpE 118 5.59e+01 1v9cA 218 5.66e+01 c.23.17.1 100533 3bqsA 93 5.68e+01 1zhsA 113 5.79e+01 1sw5B 275 5.81e+01 c.94.1.1 106070 1b4bA 71 5.83e+01 1b4aA d.74.2.1 39718 1vr8A 142 5.90e+01 d.312.1.1 120445 2al6A 375 5.94e+01 a.11.2.1,b.55.1.5,d.15.1.4 126966,126967,126968 1s3rA 535 5.97e+01 2gvkA 317 6.00e+01 d.58.4.14 135782 2dp9A 124 6.06e+01 b.122.1.5 131609 2p12A 176 6.11e+01 1uwmA 106 6.18e+01 d.15.4.1 119763 1u6lA 149 6.23e+01 d.32.1.7 113067 3c2eA 294 6.23e+01 1umpA 631 6.29e+01 a.102.4.2,a.102.4.2 99619,99620 1rv9A 259 6.30e+01 d.194.1.2 105105 1fusA 106 6.36e+01 d.1.1.4 36050 1wsrA 375 6.39e+01 1u9cA 224 6.39e+01 c.23.16.2 113234 1u2pA 163 6.42e+01 2r85A 334 6.43e+01 1vqzA 341 6.45e+01 d.224.1.3,d.104.1.3 120426,120427 1o22A 170 6.47e+01 d.238.1.1 86557 5hpgA 84 6.53e+01 5hpgA g.14.1.1 44642 2dchX 216 6.55e+01 2pd1A 104 6.55e+01 2dx0A 138 6.61e+01 2f6eA 127 6.63e+01 1bia 321 6.65e+01 1bia 1biaA 321 6.65e+01 a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 2gnrA 145 6.65e+01 2nsaA 170 6.75e+01 3bhyA 283 6.76e+01 1fyhA 258 6.79e+01 1d9cA a.26.1.3,a.26.1.3 16907,16908 1ezwA 349 6.79e+01 1ezwA c.1.16.3 29558 1r88A 280 6.81e+01 c.69.1.3 97219 3c0fB 91 6.86e+01 1cnzA 363 6.88e+01 1cnzA c.77.1.1 35061 2cosA 54 6.91e+01 a.5.2.1 130683 2qdqA 50 6.92e+01 2qmoA 220 7.04e+01 1brwA 433 7.05e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1ejxA 100 7.06e+01 d.8.1.1 83182 2fprA 176 7.08e+01 c.108.1.19 133919 1rr7A 129 7.11e+01 a.4.1.14 105075 1f5vA 240 7.23e+01 1bkjA d.90.1.1 40255 2v6oA 596 7.24e+01 1jpdX 324 7.26e+01 c.1.11.2,d.54.1.1 67014,67015 2r78A 117 7.26e+01 1gadO 330 7.33e+01 1dssG c.2.1.3,d.81.1.1 29950,39865 2bkfA 87 7.37e+01 d.15.2.2 128699 1qo3C 137 7.50e+01 1qo3C d.169.1.1 42350 2pi6A 361 7.54e+01 1vloA 381 7.57e+01 b.44.2.1,d.250.1.1 108838,108839 1g8mA 593 7.59e+01 1g8mA c.24.1.3,c.97.1.4 60371,60372 1ml8A 134 7.64e+01 d.227.1.2 85013 1lm5A 214 7.64e+01 d.211.2.1 74029 1tz0A 114 7.65e+01 d.58.4.5 107463 1jykA 254 7.66e+01 c.68.1.13 67458 1t3tA 1303 7.80e+01 a.5.10.1,c.23.16.1,d.284.1.2,d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 106381,106382,106383,106384,106385,106386,106387 3b50A 310 7.99e+01