# List of top-scoring protein chains for t2k-100-30-o_notor2-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 1y60A 169 1.61e+00 1efcA 393 2.15e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25680,25720,32113 1tx4B 178 2.27e+00 1ctqA c.37.1.8 32045 1i9sA 210 2.37e+00 1i9sA c.45.1.1 62099 1v7oA 165 2.44e+00 d.67.1.2 100480 1jr7A 311 2.50e+00 b.82.2.3 63255 2c46A 241 2.57e+00 1v4pA 157 2.57e+00 1vj0A 380 2.65e+00 b.35.1.2,c.2.1.1 100786,100787 1vfgA 390 2.74e+00 a.173.1.1,d.218.1.4 108570,108571 1s1eA 224 2.94e+00 1huqA 164 3.25e+00 1byuA c.37.1.8 32020 1w4vA 119 4.88e+00 1uvzA 119 5.27e+00 1dioA 554 5.29e+00 1dioA c.1.19.3 29656 1n6hA 170 5.99e+00 c.37.1.8 80197 2abk 211 6.09e+00 2abk a.96.1.1 18743 1oi2A 366 6.74e+00 c.119.1.2 103802 1efuA 385 7.17e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25682,25722,32115 1eljA 381 7.72e+00 4mbp c.94.1.1 35791 1tkkA 366 7.72e+00 c.1.11.2,d.54.1.1 107089,107090 1mc2A 122 7.94e+00 a.133.1.2 74622 1db1A 259 8.19e+00 1db1A a.123.1.1 19329 2clbA 188 8.24e+00 1p8xA 344 8.46e+00 d.109.1.1,d.109.1.1,d.109.1.1 94365,94366,94367 3rp2A 224 8.63e+00 1a7s b.47.1.2 26298 1kmqA 184 9.04e+00 c.37.1.8 84412 1r2qA 170 9.08e+00 c.37.1.8 96874 2c78A 405 9.15e+00 1ot8A 239 9.20e+00 d.211.1.1 93507 1nr6A 473 9.68e+00 a.104.1.1 92085 1b37A 472 9.72e+00 1b37B c.3.1.2,d.16.1.5 30389,37953 1zbsA 291 1.04e+01 1etu 394 1.12e+01 1efcA c.37.1.8 64737 1b37B 472 1.12e+01 1b37B c.3.1.2,d.16.1.5 30390,37954 1gmuA 143 1.13e+01 b.107.1.1,d.58.38.1 65335,65336 1jrkA 156 1.14e+01 d.113.1.1 71827 1ha3A 405 1.18e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 1bvoA 175 1.19e+01 1a3qA b.2.5.3 22457 1zzgA 415 1.19e+01 1atg 231 1.20e+01 1atg c.94.1.1 35834 2fh1A 344 1.25e+01 1g72A 573 1.28e+01 4aahA b.70.1.1 27680 1w9gA 104 1.29e+01 1uumA 372 1.30e+01 c.1.4.1 100010 1tk1A 260 1.33e+01 d.248.1.1 107066 1kvnA 104 1.35e+01 d.201.1.1 73066 2f8yA 223 1.36e+01 1gmwA 143 1.36e+01 b.107.1.1,d.58.38.1 65347,65348 1ylmA 144 1.42e+01 1x42A 232 1.43e+01 1z08A 170 1.44e+01 1jpmA 366 1.46e+01 c.1.11.2,d.54.1.1 67031,67032 1wv2A 265 1.48e+01 1ef1C 90 1.50e+01 1ef1C a.137.5.1 19642 1f7zA 233 1.54e+01 5ptp b.47.1.2 59681 1eexA 554 1.54e+01 1dioA c.1.19.3 29650 1aqcA 172 1.54e+01 1x11A b.55.1.2 26983 1ypqA 135 1.57e+01 1dwkA 156 1.60e+01 1dw9A a.35.1.4,d.72.1.1 17075,39606 2trxA 108 1.61e+01 1thx c.47.1.1 32719 1dw9A 156 1.62e+01 1dw9A a.35.1.4,d.72.1.1 17065,39596 1r5zA 323 1.64e+01 f.40.1.1 97135 1lxnA 99 1.65e+01 d.58.48.1 84737 2c5qA 240 1.66e+01 2c07A 285 1.67e+01 1uohA 226 1.69e+01 d.211.1.1 99690 1je5A 206 1.77e+01 1je5A b.40.4.7 62909 2dhqA 146 1.79e+01 2dhqA c.23.13.1 31382 1avc 673 1.81e+01 1avc a.65.1.1,a.65.1.1 18178,18179 1yyhA 253 1.81e+01 1wz7A 111 1.82e+01 3nodB 423 1.83e+01 1nseA d.174.1.1 42513 1s6cA 183 1.84e+01 a.39.1.5 98594 1sumB 235 1.87e+01 a.7.12.1 106025 1b5qA 472 1.93e+01 1b37B c.3.1.2,d.16.1.5 30404,37968 1e58A 249 1.93e+01 1qhfA c.60.1.1 59262 4aahA 571 2.05e+01 4aahA b.70.1.1 27678 1f93A 104 2.07e+01 1dcpA d.74.1.1 39688 1kebA 108 2.08e+01 c.47.1.1 77341 1g8jB 133 2.11e+01 1g8jB b.33.1.1 24439 1sqhA 312 2.12e+01 d.108.1.5 98966 2bbeA 108 2.20e+01 2b0mA 393 2.21e+01 1xw5A 217 2.22e+01 1szwA 379 2.23e+01 d.265.1.4 99047 1lkxA 697 2.25e+01 c.37.1.9 73981 2iu4A 336 2.27e+01 1go4E 100 2.30e+01 h.1.22.1 70296 2azqA 311 2.31e+01 1f8rA 498 2.34e+01 1f8rA c.3.1.2,d.16.1.5 30410,37974 1ceqA 316 2.40e+01 1ceqA c.2.1.5,d.162.1.1 30163,42130 1sauA 115 2.40e+01 1xzoA 174 2.44e+01 1gmlA 178 2.44e+01 c.8.5.2 70273 1n6bA 473 2.46e+01 a.104.1.1 85359 2b18A 164 2.47e+01 1u2eA 289 2.48e+01 2sas 185 2.49e+01 2sas a.39.1.5 17258 1k89 449 2.51e+01 1k89 c.2.1.7,c.58.1.1 30218,33866 2c4wA 176 2.52e+01 1si7A 369 2.52e+01 d.265.1.4 98883 2cohA 202 2.52e+01 1xxsA 122 2.55e+01 1h7cA 108 2.62e+01 a.7.5.1 70914 2ad6A 571 2.64e+01 1d3gA 367 2.66e+01 1d3gA c.1.4.1 28600 2a1xA 308 2.74e+01 1d3hA 367 2.75e+01 1d3gA c.1.4.1 28601 1knt 58 2.78e+01 1bpi g.8.1.1 44538 1pty 321 2.79e+01 1pty c.45.1.2 32656 2d9bA 109 2.83e+01 1bgvA 449 2.84e+01 1k89 c.2.1.7,c.58.1.1 30217,33865 1y4lA 121 2.85e+01 2a5vA 213 2.86e+01 1rh9A 373 2.86e+01 1th8A 145 2.88e+01 d.122.1.3 106908 1eyuA 157 2.91e+01 3pviA c.52.1.6 33304 1dt6A 473 2.92e+01 1dt6A a.104.1.1 18977 1up8A 598 2.94e+01 a.111.1.2 99710 1i7hA 111 2.95e+01 d.15.4.1 71122 1jysA 242 2.99e+01 c.56.2.1 77216 1kthA 58 3.01e+01 g.8.1.1 68863 2knt 58 3.01e+01 1bpi g.8.1.1 44537 1s8iA 121 3.03e+01 a.133.1.2 98735 1v9mA 323 3.05e+01 f.40.1.1 100543 1ptvA 321 3.10e+01 1pty c.45.1.2 32665 2gk9A 426 3.10e+01 1l6rA 227 3.12e+01 c.108.1.10 77768 1h3iA 293 3.15e+01 b.76.2.1,b.85.7.1 76635,76636 2fi1A 190 3.16e+01 1w6sA 599 3.24e+01 1f45B 197 3.25e+01 1f45B a.26.1.1 59642 2c4jA 218 3.29e+01 1k82A 268 3.31e+01 a.156.1.2,b.113.1.1,g.39.1.8 75866,75867,75868 1ppa 121 3.35e+01 1poa a.133.1.2 19550 1eeoA 321 3.38e+01 1pty c.45.1.2 32655 2drwA 363 3.43e+01 1n1cA 217 3.43e+01 a.184.1.1 85254 1uayA 242 3.50e+01 c.2.1.2 88390 1aax 321 3.50e+01 1pty c.45.1.2 32657 1xc1A 309 3.51e+01 c.94.1.1 109543 1ym3A 215 3.52e+01 1pa1A 310 3.52e+01 c.45.1.2 94404 1t00A 112 3.54e+01 1ulyA 192 3.57e+01 1nd7A 374 3.58e+01 d.148.1.1 91817 2d83A 363 3.61e+01 1hdcA 253 3.67e+01 1e6wA c.2.1.2 29862 1yz4A 160 3.67e+01 1uuyA 167 3.68e+01 c.57.1.1 108059 1ldg 316 3.68e+01 1ceqA c.2.1.5,d.162.1.1 30165,42132 1ie9A 259 3.71e+01 1db1A a.123.1.1 62318 1y0yA 353 3.71e+01 1aup 449 3.76e+01 1k89 c.2.1.7,c.58.1.1 30222,33870 1mrp 309 3.76e+01 1mrp c.94.1.1 35796 2bcgY 206 3.76e+01 1anb 223 3.77e+01 5ptp b.47.1.2 25998 1nffA 260 3.78e+01 c.2.1.2 80457 1anc 223 3.83e+01 5ptp b.47.1.2 25982 1icpA 376 3.84e+01 1oyc c.1.4.1 62270 1qlaB 239 3.84e+01 1qlaB a.1.2.1,d.15.4.2 15679,37707 1hrdA 449 3.86e+01 1k89 c.2.1.7,c.58.1.1 30219,33867 1fzqA 181 3.95e+01 1hurA c.37.1.8 32060 2f71A 298 3.95e+01 1h05A 146 3.95e+01 c.23.13.1 76433 1g8kB 133 3.96e+01 1g8jB b.33.1.1 24435 1k8bA 52 4.00e+01 d.241.1.1 72171 2cglA 489 4.10e+01 1o7tA 309 4.14e+01 c.94.1.1 86645 1ihbA 162 4.15e+01 1bd8 d.211.1.1 19161 1reoA 486 4.17e+01 c.3.1.2,d.16.1.5 97325,97326 2ffqA 171 4.17e+01 1nnfA 309 4.18e+01 c.94.1.1 85903 1rsgA 516 4.18e+01 2aqlA 173 4.27e+01 1jltA 122 4.28e+01 a.133.1.2 66867 1kvkA 395 4.30e+01 d.14.1.5,d.58.26.3 73060,73061 2akaA 776 4.35e+01 1y791 680 4.45e+01 2anxA 146 4.59e+01 1jigA 146 4.59e+01 a.25.1.1 71685 1jr1A 514 4.66e+01 c.1.5.1,d.37.1.1,d.37.1.1 63241,63242,63243 1mho 88 4.68e+01 1b4cA a.39.1.2 17171 1rtxA 123 4.70e+01 a.1.1.1 97827 1yqfA 203 4.74e+01 2fztA 79 4.77e+01 1keaA 221 4.79e+01 a.96.1.2 68491 1xfoA 357 4.80e+01 1vq3A 94 4.81e+01 1hm6A 346 4.83e+01 1avc a.65.1.1 18147 2fcr 173 4.88e+01 1rcf c.23.5.1 31151 1nt2A 210 4.88e+01 c.66.1.3 86149 1ovnA 248 4.89e+01 a.71.1.1,c.47.1.7 93602,93603 1t2dA 322 4.93e+01 c.2.1.5,d.162.1.1 99084,99085 2aefA 234 4.97e+01 2sivB 36 5.02e+01 2sivB 1t1vA 93 5.06e+01 c.47.1.14 106278 2vsgA 358 5.08e+01 2vsgA h.4.1.1 45780 1pyoB 105 5.10e+01 1qhbA 596 5.10e+01 1qhbA a.111.1.2 19055 1jrmA 104 5.29e+01 d.206.1.1 67136 1uok 558 5.30e+01 1uok b.71.1.1,c.1.8.1 27801,28788 2cj4A 150 5.36e+01 1x1iA 752 5.37e+01 2bbhA 269 5.38e+01 1exmA 405 5.42e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 1g8fA 511 5.48e+01 1g8fA b.122.1.3,c.26.1.5,c.37.1.15 60348,60349,60350 1z5nA 242 5.49e+01 1vfqA 143 5.51e+01 2bz6H 254 5.52e+01 1biqA 375 5.52e+01 1xikA a.25.1.2 16786 1q35A 320 5.53e+01 c.94.1.1 95661 1huvA 380 5.57e+01 c.1.4.1 61277 1fo1A 271 5.59e+01 1fo1A c.10.2.3,d.58.7.2 30869,39213 2f4mB 61 5.62e+01 1m2dA 110 5.65e+01 c.47.1.11 78476 1epuA 591 5.67e+01 1dn1A e.25.1.1 43358 1e9mA 106 5.71e+01 1ayfA d.15.4.1 59397 1k5nA 276 5.71e+01 b.1.1.2,d.19.1.1 77266,77267 1vpi 122 5.73e+01 1poa a.133.1.2 19559 1p0hA 318 5.74e+01 d.108.1.1 93866 1g7fA 298 5.78e+01 1pty c.45.1.2 60330 2hsdA 253 5.79e+01 1e6wA c.2.1.2 29866 1cl1A 395 5.81e+01 1cl2A c.67.1.3 34395 1tzaA 134 5.81e+01 b.1.23.1 107468 1t3yA 141 5.82e+01 1l5oA 356 5.87e+01 c.39.1.1 77711 1cs1A 386 5.90e+01 1ibjA c.67.1.3 34399 4ptp 223 5.94e+01 1bd8 156 5.94e+01 1bd8 d.211.1.1 19157 1gen 218 6.07e+01 1gen b.66.1.1 27536 1cl2A 395 6.08e+01 1cl2A c.67.1.3 34397 1ek0A 170 6.16e+01 1ctqA c.37.1.8 32076 1ie5A 107 6.20e+01 b.1.1.4 62312 1ui5A 215 6.24e+01 a.4.1.9,a.121.1.1 107856,107857 1wyuB 474 6.25e+01 1khqA 212 6.26e+01 d.3.1.1 90964 1a4uA 254 6.27e+01 1b16A c.2.1.2 29878 1j98A 157 6.28e+01 1j98A d.185.1.2 62755 1z5oA 242 6.30e+01 1b04A 318 6.31e+01 1b04A d.142.2.2 41579 2fb1A 226 6.34e+01 1a6dB 543 6.35e+01 1a6dA a.129.1.2,c.8.5.2,d.56.1.2 19489,30820,38937 1wmwA 330 6.51e+01 1tqmA 282 6.52e+01 a.4.5.56,d.144.1.9 107236,107237 1axn 323 6.52e+01 1avc a.65.1.1 18149 1w32A 348 6.53e+01 1mpgA 282 6.60e+01 1mpgA a.96.1.3,d.129.1.2 18747,41296 1r6fA 310 6.61e+01 e.46.1.1 97149 1xszA 356 6.62e+01 1dcoA 104 6.65e+01 1dcpA d.74.1.1 39680 1wmbA 260 6.66e+01 1e54A 332 6.66e+01 1e54A f.4.3.1 59258 5ptp 223 6.66e+01 5ptp b.47.1.2 25831 1a5y 330 6.67e+01 1pty c.45.1.2 32673 2a5dA 175 6.71e+01 1qsaA 618 6.72e+01 1qsaA a.118.5.1,d.2.1.6 19182,36988 1u6tA 121 6.76e+01 1jq0A 84 6.78e+01 h.3.2.1 71786 2c27A 315 6.78e+01 1zarA 282 6.89e+01 1e5eA 404 6.90e+01 1ibjA c.67.1.3 59265 1vg8A 207 6.97e+01 c.37.1.8 108606 1r5iD 216 6.98e+01 a.202.1.1 97091 1k2eA 156 6.98e+01 d.113.1.1 72010 1hy5A 136 6.99e+01 a.24.11.1 65955 1amhA 223 7.04e+01 5ptp b.47.1.2 25994 1s8nA 205 7.04e+01 c.23.1.1 105374 1k26A 156 7.05e+01 d.113.1.1 72003 1xikA 375 7.05e+01 1xikA a.25.1.2 16784 1lp8A 254 7.07e+01 d.165.1.1 91082 1ba5 53 7.11e+01 1ba5 a.4.1.4 16045 1jvr 137 7.15e+01 1jvr a.61.1.2 18132 1sly 618 7.19e+01 1qsaA a.118.5.1,d.2.1.6 19184,36990 1clxA 347 7.23e+01 1taxA c.1.8.3 28899 1lnqA 336 7.24e+01 c.2.1.9,f.14.1.1 74049,74050 1puc 105 7.25e+01 1puc d.97.1.1 40675 1and 223 7.26e+01 5ptp b.47.1.2 25985 1bco 327 7.29e+01 1bco b.48.1.1,c.55.3.3 26431,33676 1pvyA 227 7.29e+01 d.115.1.2 95195 3pviA 157 7.29e+01 3pviA c.52.1.6 33300 1oxjA 173 7.30e+01 a.60.1.2,a.118.1.13 87517,87518 1ihcA 188 7.30e+01 1di6A c.57.1.1 62379 1m7bA 184 7.32e+01 c.37.1.8 74572 1n0qA 93 7.32e+01 k.37.1.1 79754 1y02A 120 7.32e+01 1pvtA 238 7.41e+01 c.74.1.1 95189 1vgjA 184 7.43e+01 2g42A 79 7.43e+01 2aaxA 275 7.45e+01 1danH 254 7.45e+01 5ptp b.47.1.2 26292 1zxoA 291 7.49e+01 2ganA 190 7.50e+01 1b16A 254 7.50e+01 1b16A c.2.1.2 29875 1snnA 227 7.51e+01 d.115.1.2 105821 2pviA 157 7.54e+01 3pviA c.52.1.6 33302 1ejbA 168 7.54e+01 1rvv1 c.16.1.1 59417 1ocrD 147 7.59e+01 1ocrD f.23.1.1 43541 2hnp 321 7.64e+01 1pty c.45.1.2 32678 1p5zB 263 7.65e+01 c.37.1.1 87815 1hj9A 226 7.66e+01 b.47.1.2 65845 1q6zA 528 7.67e+01 1vom 762 7.69e+01 1lvk b.34.3.1,c.37.1.9 24577,32174 1ppn 212 7.74e+01 1cs8A d.3.1.1 37004 3fapB 94 7.80e+01 1nsgB a.24.7.1 16612 1v4eA 299 7.80e+01 a.128.1.1 100296 1gw5S 142 7.89e+01 d.110.4.2 70633 1bfd 528 7.90e+01 1bfd c.31.1.3,c.36.1.5,c.36.1.9 31745,31801,31802 1p4cA 380 7.90e+01 c.1.4.1 94100 1cokA 68 7.98e+01 1cokA a.60.1.2 17945 1q9uA 130 8.01e+01 d.129.7.1 96314 1txnA 328 8.05e+01 1jkoC 52 8.06e+01 a.4.1.2 66809 1sceA 112 8.06e+01 1puc d.97.1.1 40676 1m4zA 238 8.10e+01 b.34.12.1 78630 1gxyA 226 8.15e+01 d.166.1.3 76380 1ihfA 99 8.16e+01 1huuA a.55.1.1 17893 1i4fA 275 8.19e+01 1agdA b.1.1.2,d.19.1.1 61687,61688 1owfA 99 8.23e+01 a.55.1.1 87487 1vp7A 100 8.24e+01 1j0fA 100 8.28e+01 c.47.1.14 90739 1eft 405 8.29e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25688,25728,32123 1xnpA 202 8.29e+01 1r6xA 395 8.34e+01 b.122.1.3,c.26.1.5 97167,97168 2fu2A 102 8.37e+01 1lam 484 8.42e+01 1lam c.50.1.1,c.56.5.3 33166,33829 1unqA 125 8.46e+01 b.55.1.1 107968 1asx 159 8.49e+01 1a6dA c.8.5.2 30821 2erbA 125 8.49e+01 1sqc 631 8.50e+01 2sqcA a.102.4.2,a.102.4.2 18858,18859 1dpo 223 8.54e+01 5ptp b.47.1.2 25975 1h10A 125 8.56e+01 b.55.1.1 83446 1dcpA 104 8.56e+01 1dcpA d.74.1.1 39672 1ofzA 312 8.58e+01 b.68.8.1 86978 2au3A 407 8.59e+01 1ea5A 537 8.60e+01 2bce c.69.1.1 34592 3tss 194 8.61e+01 1aw7A b.40.2.2,d.15.6.1 25160,37749 2b25A 336 8.62e+01 1o8vA 134 8.66e+01 b.60.1.2 86680 2bl2A 156 8.66e+01 2fgqX 332 8.74e+01 1sbyA 254 8.75e+01 1mx4A 168 8.77e+01 d.211.1.1 79640 2db2A 119 8.80e+01 1i9aA 182 8.80e+01 1i9aA d.113.1.2 62082 1pveA 72 8.82e+01 a.189.1.1 104322 1o0xA 262 8.86e+01 d.127.1.1 80755 3proD 166 8.88e+01 3proC d.52.1.1,d.52.1.1 38814,38815 1t0qA 498 8.89e+01 a.25.1.2 106220 1zt2B 212 8.92e+01 1rl0A 255 8.92e+01 1f74A 293 8.93e+01 1nal3 c.1.10.1 29079