# List of top-scoring protein chains for t04-80-60-80-str2+near-backbone-11-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 2gkeA 274 5.59e-03 1w61A 414 7.37e-03 1gqzA 274 3.50e-02 d.21.1.1,d.21.1.1 83311,83312 1ym5A 300 6.53e-02 1bwzA 274 6.91e-02 1bwzA d.21.1.1,d.21.1.1 38337,38338 1qyaA 307 1.05e-01 d.21.1.2,d.21.1.2 104653,104654 1sdjA 310 1.65e-01 d.21.1.2,d.21.1.2 98807,98808 1xubA 298 2.73e-01 1u1wA 298 3.54e-01 1lm4A 194 5.15e-01 d.167.1.1 84626 1ohfA 644 6.30e-01 b.121.4.8 93014 2azpA 318 6.36e-01 1t6kA 278 6.39e-01 1s7jA 262 7.80e-01 d.21.1.2 98647 1tm0A 350 9.00e-01 d.21.1.3 107147 1usyA 275 1.18e+00 1dceA 567 2.02e+00 1dceA a.118.6.1,b.7.4.1,c.10.2.2 19191,23218,30867 1bs4A 168 2.54e+00 1bs4A d.167.1.1 42287 2exrA 524 2.72e+00 2cmd 312 3.24e+00 2cmd c.2.1.5,d.162.1.1 30135,42102 1xeoA 168 4.03e+00 2aneA 125 4.12e+00 1imbA 277 4.17e+00 1imbA e.7.1.1 42957 1sznA 417 4.27e+00 b.71.1.1,c.1.8.1 106162,106163 1mldA 314 4.28e+00 2cmd c.2.1.5,d.162.1.1 30122,42089 1ci3M 249 4.36e+00 1hcz b.2.6.1,b.84.2.2 22480,28266 1feuA 206 4.46e+00 1feuA b.53.1.1 59801 1f60A 458 4.66e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 2hhmA 276 4.80e+00 1imbA e.7.1.1 42955 2napA 723 4.89e+00 2napA b.52.2.2,c.81.1.1 26926,35334 2fsjA 346 4.91e+00 1s14A 194 4.92e+00 d.122.1.2 98329 1dhkB 223 5.14e+00 1led b.29.1.1 24157 2bjiA 277 6.57e+00 1kdgA 546 6.70e+00 c.3.1.2,d.16.1.1 77337,77338 1woqA 267 6.80e+00 c.55.1.10,c.55.1.10 109462,109463 1umgA 362 7.04e+00 d.280.1.1 107956 1a02N 301 7.15e+00 1a02N b.1.18.1,b.2.5.3 21923,22440 1p4uA 153 7.50e+00 b.1.10.2 87780 1g291 372 7.75e+00 1g291 1e2wA 251 7.77e+00 1hcz b.2.6.1,b.84.2.2 22466,28252 2a7bA 120 9.28e+00 2b5rC 165 9.55e+00 1ca1 370 9.89e+00 1ca1 a.124.1.1,b.12.1.3 19340,23648 1nc5A 373 1.02e+01 a.102.1.6 85548 1nezG 128 1.04e+01 b.1.1.1 85592 2sicI 107 1.10e+01 3ssi d.84.1.1 40031 1prxA 224 1.11e+01 1prxA c.47.1.10 33076 1v25A 541 1.12e+01 e.23.1.1 108275 2cr4A 126 1.21e+01 1gyvA 120 1.26e+01 b.1.10.2 70790 2ew2A 316 1.29e+01 1xe0A 114 1.29e+01 1u0kA 288 1.33e+01 d.21.1.2,d.21.1.2 107547,107548 1w4tA 299 1.38e+01 1iu1A 146 1.42e+01 b.1.10.2 71428 1gweA 503 1.43e+01 e.5.1.1 70667 1ciy 590 1.43e+01 1ciy b.18.1.3,b.77.2.1,f.1.3.1 23720,27977,43392 1y0yA 353 1.45e+01 2fb5A 205 1.47e+01 2a84A 300 1.50e+01 1g0hA 252 1.52e+01 1dk4A e.7.1.1 60171 1vpkA 378 1.53e+01 1suwA 249 1.54e+01 e.52.1.1 106027 1sz2A 332 1.54e+01 1hbzA 498 1.54e+01 1cf9A e.5.1.1 60937 1iq4A 179 1.55e+01 1iq4A d.77.1.1 62641 1ig0A 319 1.55e+01 1ig0A b.82.6.1,c.100.1.1 62354,62355 1cr1A 296 1.61e+01 1cr1A c.37.1.11 32286 2ar1A 172 1.62e+01 1tt0A 623 1.64e+01 1xfoA 357 1.68e+01 1qciA 262 1.75e+01 1qi7A d.165.1.1 42201 1urjA 1136 1.78e+01 2a6zA 222 1.78e+01 1vdwA 254 1.78e+01 e.7.1.1 100569 1jmsA 381 1.88e+01 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 2erfA 209 1.91e+01 1fsoA 139 1.91e+01 1rhoA b.1.18.8 60007 2amhA 207 1.94e+01 1led 243 1.96e+01 1led b.29.1.1 24039 1lj5A 379 1.98e+01 e.1.1.1 73928 1d2oA 187 2.00e+01 1d2oA b.3.5.1,b.3.5.1 22625,22626 1vjkA 98 2.01e+01 d.15.3.1 108631 1my7A 114 2.02e+01 b.1.18.1 79675 1vkwA 218 2.08e+01 d.90.1.2 108695 1f6fB 210 2.09e+01 1axiB b.1.2.1,b.1.2.1 22033,22034 1mkfA 382 2.19e+01 b.116.1.1 79232 1sr8A 298 2.21e+01 e.54.1.1 105959 1h9oA 112 2.22e+01 1qadA d.93.1.1 60837 1bu8A 452 2.22e+01 1gpl b.12.1.2,c.69.1.19 23647,34795 1x82A 190 2.23e+01 1kskA 234 2.24e+01 d.66.1.5,d.265.1.3 72920,90389 1usrA 454 2.27e+01 b.68.1.1 99881 1s1dA 331 2.27e+01 b.67.3.1 98344 2axcA 264 2.28e+01 1uteA 313 2.30e+01 1uteA d.159.1.1 42078 1dyqA 234 2.32e+01 3seb b.40.2.2,d.15.6.1 59140,59141 1cruA 454 2.36e+01 1c9uA b.68.2.1 27617 1h2wA 710 2.36e+01 b.69.7.1,c.69.1.4 76596,76597 1cd9B 215 2.40e+01 1cto b.1.2.1,b.1.2.1 22041,22042 1siqA 392 2.44e+01 a.29.3.1,e.6.1.1 105585,105586 1rdo1 113 2.47e+01 1rtm1 1zc1A 208 2.51e+01 2msbA 115 2.58e+01 1rtm1 d.169.1.1 42355 1hfs 160 2.58e+01 1hfc d.92.1.11 40370 1ev7A 317 2.61e+01 1ev7B c.52.1.9 33315 1g2aA 168 2.63e+01 d.167.1.1 65109 1i76A 163 2.67e+01 1hfc d.92.1.11 61877 1havA 217 2.70e+01 1havA b.47.1.4 26423 1zpuA 534 2.72e+01 1noa 113 2.72e+01 2mcm b.1.7.1 22208 1qexA 288 2.76e+01 1qexA b.32.1.1 24425 1bkzA 135 2.84e+01 1a3k b.29.1.3 24202 1p7hL 286 2.86e+01 b.1.18.1,b.2.5.3 94271,94272 1axiB 236 2.90e+01 1axiB b.1.2.1,b.1.2.1 21997,21998 1rec 201 2.90e+01 1rec a.39.1.5 17326 1zc6A 305 2.93e+01 1vkpA 383 3.00e+01 d.126.1.6 108686 2cxvA 219 3.01e+01 1wb9A 800 3.02e+01 1jkxA 212 3.03e+01 c.65.1.1 66813 1rdj1 113 3.04e+01 1rtm1 1q18A 332 3.15e+01 c.55.1.7,c.55.1.7 104470,104471 1wkbA 810 3.15e+01 1wpuA 147 3.19e+01 1wmqA 147 3.19e+01 1fsz 372 3.20e+01 1fsz c.32.1.1,d.79.2.1 31750,39802 1rqpA 299 3.22e+01 b.141.1.1,c.132.1.1 97754,97755 1xfjA 261 3.24e+01 d.194.1.2 109585 1qxrA 189 3.29e+01 b.82.1.7 96552 1v7zA 260 3.30e+01 c.125.1.1 100488 1rtm1 149 3.32e+01 1rtm1 1lbvA 252 3.35e+01 e.7.1.1 73813 1p80A 753 3.35e+01 c.23.16.3,e.5.1.1 94337,94338 1aerA 205 3.39e+01 1aerA d.166.1.1 42249 1tzlA 622 3.42e+01 1kmtA 141 3.48e+01 b.1.18.8 77442 1ri5A 298 3.48e+01 c.66.1.34 97502 1ws0A 156 3.48e+01 2glzA 153 3.49e+01 1n5nA 180 3.49e+01 d.167.1.1 85336 1z0sA 278 3.54e+01 1cby 259 3.54e+01 1cby d.103.1.1 40705 2gq1A 332 3.57e+01 1ut9A 609 3.59e+01 a.102.1.2,b.1.18.2 99912,99913 1x71A 178 3.60e+01 2fgtA 417 3.63e+01 1x1nA 524 3.63e+01 1omrA 201 3.69e+01 a.39.1.5 93349 1ewqA 765 3.70e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19069,32383,33740,39743 1cv8 174 3.74e+01 1cv8 d.3.1.1 37089 1bpyA 335 3.83e+01 1bpyA a.60.6.1,a.60.12.1,d.218.1.2 17980,75819,75820 1l0qA 391 3.85e+01 b.1.3.1,b.69.2.3 77644,77645 1vq0A 302 3.86e+01 1y93A 159 3.90e+01 1w1hA 151 3.93e+01 1z4vA 532 3.96e+01 1crzA 403 4.00e+01 1crzA b.68.4.1,c.51.2.1 27629,33211 2ex4A 241 4.12e+01 1vr1H 261 4.12e+01 5ptp 1khoA 370 4.18e+01 a.124.1.1,b.12.1.3 72489,72490 1tyyA 339 4.21e+01 1lcl 142 4.30e+01 1lcl b.29.1.3 24216 2a9kB 223 4.30e+01 1z4xA 532 4.41e+01 1pvgA 418 4.46e+01 d.14.1.3,d.122.1.2 95161,95162 1gxrA 337 4.49e+01 b.69.4.1 70722 1tg7A 971 4.51e+01 1wy7A 207 4.52e+01 1m93B 245 4.61e+01 1sqrA 95 4.63e+01 1oygA 447 4.75e+01 b.67.2.2 93726 1jzgA 128 4.76e+01 b.6.1.1 67855 1tg0A 68 4.76e+01 1rc6A 261 4.88e+01 b.82.1.11 97287 1t0qC 86 4.96e+01 d.15.12.1 106222 1cf9A 753 4.99e+01 1cf9A c.23.16.3,e.5.1.1 31441,42815 1mixA 206 5.00e+01 a.11.2.1,b.55.1.5 79166,79167 1p42A 270 5.04e+01 d.14.1.7,d.14.1.7 87754,87755 1epfA 191 5.06e+01 2ncm b.1.1.4,b.1.1.4 21694,21695 2g1lA 104 5.06e+01 1qmyA 167 5.07e+01 1qmyA d.3.1.2 37094 1n9pA 207 5.10e+01 b.1.18.16 80343 1ewkA 490 5.10e+01 1ewkA c.93.1.1 35712 1gzcA 239 5.12e+01 b.29.1.1 70803 1garA 212 5.13e+01 2gar c.65.1.1 34162 1g7sA 594 5.15e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 2akaB 299 5.22e+01 1nlnA 204 5.29e+01 d.3.1.7 91962 2bjdA 101 5.29e+01 2fiyA 309 5.30e+01 1h7wA 1025 5.38e+01 1h7wA a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15683,28628,30324,30609,39007 3grs 478 5.44e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30441,30442,40152 1jk3A 158 5.46e+01 d.92.1.11 66790 1eyzA 392 5.50e+01 1ez1A b.84.2.1,c.30.1.1,d.142.1.2 28246,31653,41498 1koiA 184 5.56e+01 b.60.1.1 68725 1wmmA 145 5.56e+01 1x31D 99 5.58e+01 1kb0A 677 5.59e+01 a.3.1.6,b.70.1.1 68378,68379 1exmA 405 5.64e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 1xvaA 292 5.67e+01 1xvaA c.66.1.5 34183 1xzwA 426 5.68e+01 1gteA 1025 5.75e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70440,70441,70442,70443,70444 2freA 200 5.78e+01 1g8lA 411 5.78e+01 1g8lA b.85.6.1,b.103.1.1,c.57.1.2 60365,60366,60367 1y4hA 188 5.84e+01 2eveA 157 5.87e+01 1i7oA 429 5.88e+01 1i7oA d.177.1.1,d.177.1.1 61893,61894 2fs2A 151 5.90e+01 1vrmA 325 5.93e+01 2fvgA 340 5.99e+01 2gf6A 135 6.00e+01 1ryp2 233 6.11e+01 1ryp2 1r45A 204 6.14e+01 1xewX 182 6.15e+01 1mtpA 323 6.15e+01 e.1.1.1 85107 1zk7A 467 6.19e+01 1ko7A 314 6.19e+01 c.98.2.1,c.91.1.2 72797,72798 1fxjA 331 6.21e+01 1fwyA b.81.1.4,c.68.1.5 28062,34520 1psuA 140 6.21e+01 d.38.1.5 88285 2ft6A 124 6.22e+01 1ax0 239 6.23e+01 1led b.29.1.1 24042 2bszA 278 6.26e+01 1jp4A 308 6.26e+01 1jp4A e.7.1.1 63223 1vm6A 228 6.26e+01 c.2.1.3,d.81.1.3 108876,108877 1a0rP 245 6.28e+01 1b9yC c.47.1.6 33054 1iznB 277 6.33e+01 e.43.1.2 83848 1mmiA 366 6.33e+01 d.131.1.1,d.131.1.1,d.131.1.1 91309,91310,91311 1vemA 516 6.43e+01 1a49A 530 6.44e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27026,29255,33109 830cA 168 6.48e+01 1ck7A d.92.1.11 40400 1b12A 248 6.51e+01 1b12A b.87.1.2 28388 1gen 218 6.57e+01 1gen b.66.1.1 27536 1gttA 429 6.61e+01 d.177.1.1,d.177.1.1 70529,70530 2bgzA 299 6.63e+01 2bghA 421 6.69e+01 1y7tA 327 6.72e+01 1zceA 155 6.72e+01 1bdmA 327 6.73e+01 1bmdA c.2.1.5,d.162.1.1 30137,42104 1uc8A 280 6.73e+01 c.30.1.6,d.142.1.7 99165,99166 1gwyA 175 6.73e+01 b.97.1.1 83356 1hdkA 141 6.74e+01 b.29.1.3 65807 1zdyA 307 6.83e+01 1xknA 355 6.84e+01 1voqa 90 6.84e+01 1rq2A 382 6.85e+01 c.32.1.1,d.79.2.1 105048,105049 1w3iA 293 6.86e+01 c.1.10.1 109152 1n7zA 334 6.89e+01 b.127.1.1 85380 1vioA 243 6.89e+01 d.265.1.3,d.66.1.5 100762,100763 1udxA 416 6.91e+01 b.117.1.1,c.37.1.8,d.242.1.1 99228,99229,99230 1u6eA 335 6.92e+01 1azo 232 6.94e+01 1azo c.52.1.14 33329 2aorA 223 6.94e+01 1go7P 462 6.94e+01 b.80.7.1,d.92.1.6 76245,76246 3mddA 385 6.94e+01 3mdeA a.29.3.1,e.6.1.1 16592,42853 1ftrA 296 6.95e+01 1ftrA d.58.33.1,d.58.33.1 39485,39486 1oz2A 331 6.98e+01 b.34.9.3,b.34.9.3,b.34.9.3 93781,93782,93783 1wdxA 69 7.00e+01 1yqzA 438 7.04e+01 1uiuA 502 7.08e+01 c.94.1.1 99434 1l3iA 192 7.10e+01 c.66.1.22 77676 1hleA 345 7.10e+01 1ovaA e.1.1.1 42618 1pj5A 830 7.11e+01 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 1hfoA 113 7.19e+01 d.80.1.3 61006 1e3mA 800 7.21e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19075,32389,33746,39747 2d29A 387 7.27e+01 1v54B 227 7.30e+01 b.6.1.2,f.17.2.1 100322,100323 1fxlA 167 7.34e+01 1b7fA d.58.7.1,d.58.7.1 39183,39184 1nqzA 194 7.34e+01 d.113.1.1 86077 2g50A 530 7.39e+01 1g38A 393 7.49e+01 2admA c.66.1.27 60235 2cvhA 220 7.49e+01 1qfmA 710 7.52e+01 1qfmA b.69.7.1,c.69.1.4 27673,34641 2fcbA 173 7.57e+01 2fcbA b.1.1.4,b.1.1.4 21781,21782 1zowA 313 7.60e+01 1w24A 182 7.62e+01 1pyaB 228 7.70e+01 1pyaB 1v7rA 186 7.75e+01 c.51.4.1 100482 1hnjA 317 7.76e+01 1hn9A c.95.1.2,c.95.1.2 35969,35970 2c7hA 86 7.78e+01 2fn0A 437 7.82e+01 1l2mA 118 7.84e+01 d.89.1.4 77657 2f5tX 233 7.85e+01 2a6hD 1524 7.95e+01 1erxA 184 7.98e+01 1np1A b.60.1.1 27164 1u6zA 513 8.08e+01 1z2wA 192 8.09e+01 1ejxA 100 8.10e+01 d.8.1.1 83182 1wba 175 8.16e+01 1wba b.42.4.1 25591 1w6sA 599 8.25e+01 1gt1A 159 8.25e+01 b.60.1.1 90515 1ej1A 190 8.25e+01 1ejhA d.86.1.1 40144 1dmlA 319 8.26e+01 1dmlA d.131.1.2,d.131.1.2 41380,41381 1lmeA 176 8.27e+01 d.167.1.1 84629 1y6hA 177 8.33e+01 1w0nA 131 8.38e+01 1bmdA 327 8.39e+01 1bmdA c.2.1.5,d.162.1.1 30139,42106 1smxA 96 8.40e+01 b.40.4.5 105772 1erjA 393 8.44e+01 1erjA b.69.4.1 27660 1fukA 165 8.45e+01 1fukA c.37.1.19 32409 1j5pA 253 8.47e+01 d.81.1.3,c.2.1.3 71577,83092 1o75A 415 8.48e+01 b.1.20.1,b.1.20.1,b.120.1.1 81117,81118,81119 1v61A 132 8.49e+01 b.55.1.1 108389 1vicA 262 8.53e+01 c.68.1.13 100756 1zq9A 285 8.54e+01 1eb7A 323 8.56e+01 1eb7A a.3.1.5,a.3.1.5 59404,59405 1w1wA 430 8.67e+01 2gasA 307 8.67e+01 1yopA 83 8.69e+01 1cyx 205 8.69e+01 1cyx b.6.1.2 23023 1zboA 210 8.73e+01 1ehiA 377 8.75e+01 1iow c.30.1.2,d.142.1.1 31716,41484 1cyw 205 8.77e+01 1cyx b.6.1.2 23024 1v04A 355 8.79e+01 b.68.6.2 100240 1t5iA 172 8.79e+01 c.37.1.19 106450 1j1qA 261 8.80e+01 d.165.1.1 90768 1zckA 154 8.88e+01 1gx3A 284 8.89e+01 d.3.1.5 70678 1u2zA 433 8.90e+01 c.66.1.31 107626 2a0jA 149 8.96e+01