# List of top-scoring protein chains for t04-100-30-n_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 1h3nA 878 1.56e-01 a.27.1.1,b.51.1.1,c.26.1.1 76641,76642,76643 2a9uA 144 2.17e-01 1o7eA 276 3.78e-01 e.3.1.1 92622 1e9xA 455 4.98e-01 1ea1A a.104.1.1 18969 1hnjA 317 7.19e-01 1hn9A c.95.1.2,c.95.1.2 35969,35970 1ogsA 497 8.09e-01 b.71.1.2,c.1.8.3 86997,86998 1h5zA 455 9.79e-01 a.104.1.1 90622 8abp 306 1.17e+00 8abp c.93.1.1 35647 1ee4A 423 1.89e+00 1ee4A a.118.1.1 19128 1u2wA 122 1.94e+00 1ek9A 428 2.09e+00 1ek9A f.5.1.1 43809 1bf6A 291 2.45e+00 1pscA c.1.9.3 29065 2bcqA 335 2.53e+00 1ohlA 342 2.72e+00 c.1.10.3 87035 1el4A 195 2.77e+00 1ej3A a.39.1.5 59453 2gdzA 267 2.87e+00 1iysA 262 2.96e+00 e.3.1.1 90723 1vd5A 377 3.07e+00 a.102.1.7 108518 1db3A 372 3.13e+00 1db3A c.2.1.2 29813 1m3yA 413 3.28e+00 b.121.2.3,b.121.2.3 78579,78580 1a0p 290 3.29e+00 1a0p a.60.9.1,d.163.1.1 18105,42165 1k0fA 277 3.38e+00 c.92.2.2 71974 1d8dB 437 4.31e+00 1ft1B a.102.4.3 18866 2ct9A 208 4.61e+00 1ks8A 433 4.78e+00 a.102.1.2 77519 2gdnA 267 4.78e+00 2bvlA 543 4.81e+00 1pg4A 652 4.91e+00 e.23.1.1 88067 1qqfA 277 5.66e+00 1c3d a.102.4.4 18875 1hzoA 271 5.87e+00 e.3.1.1 71092 1zybA 232 6.08e+00 1a59 378 6.22e+00 1aj8A a.103.1.1 18902 1a9xB 379 6.27e+00 1c3oB c.8.3.1,c.23.16.1 30732,31409 2ah6A 208 6.45e+00 2fug1 438 6.82e+00 1gjjA 168 7.01e+00 a.140.1.1,a.140.1.1 83291,83292 1ih8A 271 7.14e+00 2nsyA c.26.2.1 62377 1mswD 883 7.15e+00 e.8.1.3 79427 1r5iD 216 7.27e+00 a.202.1.1 97091 1u4bA 580 7.72e+00 c.55.3.5,e.8.1.1 107664,107665 1vprA 374 7.76e+00 2cx9A 387 7.93e+00 1lfaA 187 8.19e+00 1ido c.62.1.1 34122 1upkA 341 8.21e+00 a.118.1.15 99758 1pq4A 291 8.34e+00 c.92.2.2 94995 1fpzA 212 8.51e+00 1fpzA c.45.1.1 59976 1t7rA 269 8.71e+00 a.123.1.1 106635 1fy7A 278 9.07e+00 1fy7A d.108.1.1 40817 1yozA 116 9.18e+00 1bsg 266 9.38e+00 1btl e.3.1.1 42729 1j7nA 776 9.41e+00 d.92.1.14,d.92.1.14,d.166.1.1 66409,66410,66411 1wmbA 260 9.95e+00 2gauA 232 1.01e+01 1qxyA 252 1.03e+01 d.127.1.1 96565 1e4yA 214 1.04e+01 1zin c.37.1.1,g.41.2.1 31901,45181 1yn9A 169 1.04e+01 1nthA 458 1.07e+01 c.1.25.1 80730 1amy 403 1.08e+01 1jdc b.71.1.1,c.1.8.1 27799,28786 1lk9A 448 1.08e+01 c.67.1.1 78057 1yljA 263 1.12e+01 1jpzA 473 1.15e+01 a.104.1.1 67069 2as0A 396 1.18e+01 1qxoA 388 1.18e+01 d.258.1.1 96539 1sgvA 316 1.19e+01 b.122.1.1,d.265.1.2 98858,98859 1xkyA 301 1.21e+01 1sl8A 191 1.23e+01 1auiA 521 1.23e+01 1auiA d.159.1.3 42085 1ghpA 258 1.26e+01 1btl e.3.1.1 60520 1kqpA 271 1.26e+01 c.26.2.1 72883 1bjt 793 1.27e+01 1bjt e.11.1.1 43249 1pmzA 86 1.27e+01 a.39.1.10 104195 1bgvA 449 1.29e+01 1k89 c.2.1.7,c.58.1.1 30217,33865 1mun 225 1.29e+01 1mun a.96.1.2 18744 1vgmA 378 1.29e+01 1siqA 392 1.30e+01 a.29.3.1,e.6.1.1 105585,105586 1k77A 260 1.34e+01 c.1.15.5 72096 1t3cA 421 1.36e+01 d.92.1.7 106343 1yarA 233 1.36e+01 1gc5A 467 1.45e+01 1gc5A c.72.1.3 60429 1e5eA 404 1.50e+01 1ibjA c.67.1.3 59265 1iruK 201 1.50e+01 d.153.1.4 71362 1tuhA 156 1.51e+01 d.17.4.11 107345 4xis 387 1.59e+01 4xis c.1.15.3 29421 1gmjA 84 1.60e+01 h.4.8.1 65310 3xis 387 1.60e+01 4xis c.1.15.3 29423 1rgeA 96 1.63e+01 1rgeA d.1.1.2 36028 1nd6A 354 1.65e+01 c.60.1.2 80407 1r6vA 671 1.66e+01 1n0uA 842 1.67e+01 b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1,d.58.11.1 79757,79758,79759,79760,79761 1qorA 327 1.67e+01 1qorA b.35.1.2,c.2.1.1 24766,29782 2ax9A 256 1.68e+01 1fs5A 266 1.70e+01 c.124.1.1 65044 1kblA 873 1.72e+01 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 1uouA 474 1.73e+01 a.46.2.1,c.27.1.1,d.41.3.1 99706,99707,99708 1v58A 241 1.79e+01 c.47.1.9,d.17.3.1 108371,108372 1ydnA 295 1.81e+01 1k94A 165 1.85e+01 a.39.1.8 68333 1qksA 567 1.89e+01 1qksA a.3.1.2,b.70.2.1 15951,27710 1y1nA 291 1.92e+01 1ztcA 221 1.92e+01 1rlmB 271 1.94e+01 2cwyA 94 1.95e+01 2ceyA 306 1.96e+01 2ashA 381 2.03e+01 1eg5A 384 2.05e+01 1ecxA c.67.1.3 34429 2cwxA 430 2.09e+01 1pn0A 665 2.10e+01 c.3.1.2,c.47.1.10,d.16.1.2 94918,94919,94920 1ois 223 2.16e+01 1a36A e.15.1.1 43267 1hrdA 449 2.25e+01 1k89 c.2.1.7,c.58.1.1 30219,33867 2ccmA 191 2.29e+01 1zsqA 528 2.33e+01 1e3mA 800 2.33e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19075,32389,33746,39747 1vb3A 428 2.38e+01 1n82A 331 2.41e+01 c.1.8.3 91703 1t56A 216 2.43e+01 a.4.1.9,a.121.1.1 106428,106429 1wyuB 474 2.45e+01 2gn4A 344 2.51e+01 1f5nA 592 2.54e+01 1dg3A a.114.1.1,c.37.1.8 19077,32152 1e8yA 966 2.54e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 1h5uA 842 2.59e+01 1a8i c.87.1.4 60655 2h58A 330 2.62e+01 1yucA 255 2.62e+01 1fgs 428 2.65e+01 1fgs c.59.1.2,c.72.2.2 33959,34962 1x1nA 524 2.66e+01 1wkcA 184 2.68e+01 1lla 628 2.70e+01 1lla a.85.1.1,a.86.1.1,b.1.18.3 18485,18496,21861 1pjr 724 2.70e+01 1pjr c.37.1.19,c.37.1.19 32391,32392 1zvdA 380 2.73e+01 1clc 639 2.73e+01 1clc a.102.1.2,b.1.18.2 18835,21872 1p5dX 463 2.74e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1deeG 54 2.78e+01 1fc2C a.8.1.1 16343 1zcjA 463 2.86e+01 2c12A 439 2.86e+01 1q35A 320 2.90e+01 c.94.1.1 95661 1t94A 459 2.90e+01 d.240.1.1,e.8.1.7 106701,106702 2cchB 260 2.91e+01 1td2A 287 2.93e+01 c.72.1.5 106765 1n28A 124 2.93e+01 a.133.1.2 91550 1f0yA 302 2.93e+01 2hdhA a.100.1.3,c.2.1.6 18793,30197 1h61A 364 2.94e+01 1oyc c.1.4.1 60657 1g5gA 481 2.94e+01 f.12.1.1,h.3.2.1 65155,65156 2cvxA 888 2.94e+01 1zvkA 358 2.96e+01 1xqwA 293 2.96e+01 1qf6A 642 2.97e+01 1qf6A c.51.1.1,d.15.10.1,d.67.1.1,d.104.1.1 33210,39551,39562,40759 1w61A 414 3.02e+01 1ru8A 232 3.03e+01 c.26.2.1 97849 1ujnA 348 3.05e+01 e.22.1.1 99460 1f46A 140 3.06e+01 1f46A d.129.4.1 59643 2a4dA 160 3.07e+01 2fuvA 549 3.07e+01 1sq5A 308 3.14e+01 c.37.1.6 105882 2b5eA 504 3.14e+01 2d8dA 90 3.16e+01 1d8wA 426 3.20e+01 1de5A c.1.15.2 29394 1r03A 182 3.21e+01 a.25.1.1 104675 1xrsA 516 3.23e+01 1brmA 367 3.26e+01 1brmA c.2.1.3,d.81.1.1 30030,39945 1yt3A 375 3.31e+01 1kkhA 317 3.40e+01 d.14.1.5,d.58.26.3 72645,72646 1gvoA 364 3.40e+01 c.1.4.1 76357 1wcgA 464 3.43e+01 1v8bA 479 3.45e+01 1di1A 300 3.45e+01 1di1A a.128.1.4 19446 1g6aA 271 3.45e+01 1btl e.3.1.1 42704 1gtmA 419 3.46e+01 1hwyA c.2.1.7,c.58.1.1 30223,33871 1o7jA 327 3.46e+01 c.88.1.1 81140 1xvwA 160 3.47e+01 1k9sA 237 3.50e+01 c.56.2.1 68359 1rqbA 539 3.50e+01 a.5.7.2,c.1.10.5 105057,105058 1xsm 390 3.54e+01 1xsm a.25.1.2 16804 1p5hA 428 3.57e+01 c.123.1.1 87802 2f57A 317 3.57e+01 1x54A 434 3.62e+01 1d2zB 153 3.66e+01 1d2zB a.77.1.2 18439 1nu7D 282 3.67e+01 a.8.6.1,a.8.6.1 92191,92192 1b5l 172 3.68e+01 1b5l a.26.1.3 16900 1oq1A 223 3.69e+01 b.29.1.17 93408 2fgeA 995 3.69e+01 1jx4A 352 3.71e+01 d.240.1.1,e.8.1.7 90378,90379 1z91A 147 3.75e+01 1yz4A 160 3.76e+01 1dtoA 221 3.79e+01 1dtoA b.91.1.1 28405 1n93X 375 3.81e+01 a.206.1.1 91707 1i52A 236 3.82e+01 1i52A c.68.1.13 61767 1wa8A 99 4.00e+01 1goiA 499 4.01e+01 b.72.2.1,c.1.8.5,d.26.3.1 65413,65414,65415 1uedA 406 4.02e+01 a.104.1.1 99256 1v7pC 200 4.06e+01 c.62.1.1 108408 1ymtA 246 4.07e+01 1fpoA 171 4.07e+01 1fpoA a.2.3.1,a.23.1.1 15693,16487 1cuk 203 4.13e+01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16273,17946,25265 2sas 185 4.16e+01 2sas a.39.1.5 17258 1oyjA 231 4.16e+01 a.45.1.1,c.47.1.5 87597,87598 1xg7A 250 4.20e+01 1w9pA 433 4.25e+01 1e6pA 499 4.26e+01 1e15A b.72.2.1,c.1.8.5,d.26.3.1 59314,59315,59316 1oi7A 288 4.33e+01 c.2.1.8,c.23.4.1 87049,87050 1mtzA 293 4.35e+01 c.69.1.7 79467 1nogA 177 4.36e+01 a.25.2.2 85923 1m2kA 249 4.40e+01 c.31.1.5 84754 2adcA 229 4.42e+01 1wt4A 73 4.43e+01 1om2A 95 4.46e+01 1om2A a.23.4.1 16520 1w5fA 353 4.50e+01 1bkdS 439 4.52e+01 1bkdS a.117.1.1 19111 1dciA 275 4.55e+01 1dciA c.14.1.3 30918 1zjkA 403 4.56e+01 1wm5A 208 4.58e+01 1ew4A 106 4.62e+01 1ew4A d.82.2.1 40023 1a5t 334 4.62e+01 1a5t a.80.1.1,c.37.1.20 18450,32423 1jihA 531 4.65e+01 d.240.1.1,e.8.1.7 90374,90375 1ykdA 398 4.67e+01 1xjjA 644 4.69e+01 2fnuA 375 4.70e+01 1jhgA 101 4.76e+01 1jhgA a.4.12.1 19009 2bnfB 241 4.77e+01 1hh8A 213 4.78e+01 1e96B a.118.8.1 61042 1xqoA 256 4.81e+01 2fkzA 155 4.86e+01 1zz1A 369 4.92e+01 2fk8A 318 4.95e+01 1uj6A 227 4.95e+01 c.124.1.4,d.58.40.1 107898,107899 1wa5B 530 4.98e+01 2a9gA 418 5.05e+01 1xwoA 465 5.05e+01 1u9tA 354 5.05e+01 1odoA 408 5.11e+01 a.104.1.1 92783 1dseA 292 5.13e+01 1ryc a.93.1.1 59130 1u4gA 301 5.20e+01 d.92.1.2 107670 2airB 153 5.22e+01 1orjA 130 5.27e+01 a.24.19.1 93456 1k2xB 143 5.27e+01 1wrvA 308 5.28e+01 1usuA 260 5.28e+01 d.14.1.8 99885 1tadA 324 5.29e+01 1cipA a.66.1.1,c.37.1.8 18194,32077 1xpkC 388 5.30e+01 1ktbA 405 5.33e+01 b.71.1.1,c.1.8.1 72960,72961 1top 162 5.34e+01 1ncx a.39.1.5 17223 2c3mA 1231 5.34e+01 1dlyA 164 5.40e+01 1dlyA a.1.1.1 14983 1vj0A 380 5.41e+01 b.35.1.2,c.2.1.1 100786,100787 1va6A 518 5.44e+01 1mgrA 99 5.45e+01 d.1.1.2 79106 2cw8A 537 5.45e+01 2bcfA 276 5.62e+01 1ouvA 273 5.71e+01 a.118.18.1 93570 1o66A 275 5.82e+01 c.1.12.8 92547 1rcwA 231 5.83e+01 a.132.1.4 97299 1tw9A 206 5.86e+01 a.45.1.1,c.47.1.5 107381,107382 1yc5A 246 5.89e+01 1lrv 244 5.91e+01 1lrv a.118.1.5 19146 1n4qB 377 5.93e+01 a.102.4.3 91636 1epwA 1290 6.06e+01 b.29.1.6,b.42.4.2,d.92.1.7,h.4.2.1 24269,25614,40305,45785 2ffjA 300 6.07e+01 1y08A 323 6.07e+01 2bklA 695 6.08e+01 1vr5A 547 6.12e+01 1wphA 201 6.13e+01 1ug3A 339 6.13e+01 1ni4B 341 6.14e+01 c.36.1.7,c.48.1.2 85729,85730 2a65A 519 6.16e+01 1mkrA 294 6.17e+01 a.93.1.1 84997 2bkyX 89 6.18e+01 1jbwA 428 6.20e+01 c.59.1.2,c.72.2.2 62860,62861 1z7dA 433 6.25e+01 1efdN 266 6.28e+01 1efdN c.92.2.1 35597 1nu5A 370 6.28e+01 c.1.11.2,d.54.1.1 92183,92184 1vkuA 100 6.29e+01 a.28.1.1 108690 1dm0A 287 6.31e+01 1dm0A d.165.1.2 42227 1y791 680 6.35e+01 1b0pA 1231 6.36e+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 1or7C 90 6.37e+01 a.180.1.1 87336 1l6sA 323 6.40e+01 c.1.10.3 73627 1s95A 333 6.40e+01 d.159.1.3 105375 1ihuA 589 6.43e+01 c.37.1.10,c.37.1.10 62394,62395 1fkx 349 6.44e+01 1a4mA c.1.9.1 29018 1y6iA 233 6.45e+01 1rm6C 161 6.53e+01 1h16A 759 6.55e+01 c.7.1.1 76462 1pmmA 466 6.59e+01 c.67.1.6 94901 1bl0A 129 6.64e+01 1d5yA a.4.1.8,a.4.1.8 16053,16054 1mplA 349 6.65e+01 e.3.1.1 79387 1dowA 205 6.68e+01 1dovA a.24.9.1 16626 1k0dA 260 6.69e+01 a.45.1.1,c.47.1.5 67930,67931 1fo3A 460 6.70e+01 1dl2A a.102.2.1 18845 1nnlA 225 6.70e+01 c.108.1.4 85906 2hmzA 113 6.71e+01 2mhr a.24.4.1 16564 1ny1A 240 6.72e+01 c.6.2.3 86395 1tluA 130 6.73e+01 d.156.1.2 107139 1io2A 213 6.73e+01 1ekeA c.55.3.1 62612 1kp8A 547 6.76e+01 a.129.1.1,c.8.5.1,d.56.1.1 84414,84415,84416 1t4bA 367 6.82e+01 c.2.1.3,d.81.1.1 106406,106407 1ei1A 391 6.84e+01 1aj6 d.14.1.3,d.122.1.2 37570,41104 1mjnA 179 6.88e+01 c.62.1.1 79210 1po5A 476 6.94e+01 a.104.1.1 94963 1g9mG 321 6.94e+01 1gc1G d.172.1.1 42492 1go3F 107 6.96e+01 a.60.8.2 65407 1no1A 126 7.01e+01 a.179.1.1 85913 1ci9A 392 7.01e+01 e.3.1.1 64767 1vr7A 142 7.05e+01 1ush 550 7.15e+01 1ush d.114.1.1,d.159.1.2 40923,42079 1hp1A 516 7.19e+01 d.114.1.1,d.159.1.2 70976,70977 2cw5A 255 7.23e+01 2an3A 289 7.23e+01 1x7dA 350 7.28e+01 1htqA 477 7.29e+01 d.15.9.1,d.128.1.1 71035,71036 2gdjA 264 7.32e+01 1ll2A 333 7.33e+01 c.68.1.14 74005 1olsB 342 7.34e+01 c.36.1.7,c.48.1.2 93332,93333 1ps1A 337 7.36e+01 1ps1A a.128.1.4 19450 1t3qA 168 7.37e+01 a.56.1.1,d.15.4.2 106367,106368 1yb3A 175 7.40e+01 1vjfA 180 7.41e+01 d.116.1.1 100809 1w68A 390 7.44e+01 a.25.1.2 109216 1iugA 352 7.46e+01 c.67.1.3 90699 1xo7A 166 7.50e+01 1nd9A 49 7.53e+01 a.6.1.6 85575 3tmkA 216 7.53e+01 3tmkA c.37.1.1 31920 1b0uA 262 7.56e+01 1b0uA c.37.1.12 32370 1elwA 118 7.61e+01 1a17 a.118.8.1 19207 1k6dA 220 7.64e+01 c.124.1.2 72082 2c07A 285 7.64e+01 1udvA 89 7.68e+01 d.68.6.1 99224 2b7kA 200 7.73e+01 1j0dA 341 7.75e+01 c.79.1.1 83902 2cqsA 842 7.79e+01 1y0zA 330 7.80e+01 1bvoA 175 7.80e+01 1a3qA b.2.5.3 22457 1zynA 202 7.82e+01 1c2pA 576 7.87e+01 1quvA e.8.1.4 43117 1gl2C 65 7.90e+01 h.1.15.1 65280 1z70X 311 7.92e+01 2dbqA 334 7.92e+01 1txgA 335 7.93e+01 1gz6A 319 7.95e+01 c.2.1.2 76410 1pk5A 248 8.00e+01 a.123.1.1 88139 1bcfA 158 8.03e+01 1bcfA a.25.1.1 16648 1m7sA 484 8.12e+01 e.5.1.1 74574 1kpgA 287 8.14e+01 c.66.1.18 68735 1wwzA 159 8.15e+01 1xawA 140 8.21e+01 2hmqA 113 8.23e+01 2mhr a.24.4.1 16568 1o5oA 221 8.23e+01 c.61.1.1 92509 1qynA 153 8.38e+01 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