# List of top-scoring protein chains for t2k-100-30-bys 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 1ihrA 76 1.35e-17 1ihrA d.212.1.2 62392 1lr0A 129 8.46e-07 d.212.1.1 74213 1hn2A 159 2.31e-02 b.60.1.1 65890 1gt1A 159 2.33e-02 b.60.1.1 -4436 1n8jA 186 3.63e-02 c.47.1.10 85401 1f5mA 180 5.07e-02 1f5mB d.110.2.1 40895 1obpA 159 6.57e-02 1obpA b.60.1.1 27092 3cox 507 2.30e-01 1b8sA c.3.1.2 30332 d.16.1.1 37863 1tiiD 99 2.52e-01 1tiiD b.40.2.1 24965 1ospO 257 2.73e-01 1ospO b.76.1.1 27971 1f5mB 180 2.95e-01 1f5mB d.110.2.1 40896 1coy 507 3.59e-01 1b8sA c.3.1.2 30333 d.16.1.1 37864 1qb5D 99 4.34e-01 b.40.2.1 88357 1b6sA 355 5.52e-01 1b6rA b.84.2.1 28242 c.30.1.1 31649 d.142.1.2 41494 1b6rA 355 6.36e-01 1b6rA b.84.2.1 28241 c.30.1.1 31648 d.142.1.2 41493 1qmvA 197 7.45e-01 1qq2A c.47.1.10 33066 1o1zA 234 8.33e-01 c.1.18.3 86555 2pflA 759 8.41e-01 1cm5A c.7.1.1 30675 1orc 71 8.77e-01 1orc a.35.1.2 17054 1cm5A 759 1.00e+00 1cm5A c.7.1.1 30671 1h16A 759 1.00e+00 c.7.1.1 76462 1p4kA 295 1.04e+00 d.153.1.5 87772 3pflA 759 1.08e+00 1cm5A c.7.1.1 30673 5croA 66 1.41e+00 1orc a.35.1.2 17044 1qq2A 199 1.46e+00 1qq2A c.47.1.10 33064 1iow 306 1.58e+00 1iow c.30.1.2 31713 d.142.1.1 41481 1bh9B 89 1.78e+00 1bh9B a.22.1.3 16485 1quqB 121 1.96e+00 1quqB b.40.4.3 25305 1urrA 102 2.06e+00 1ub0A 258 2.27e+00 c.72.1.2 88394 1js3A 486 2.38e+00 c.67.1.6 67215 1st9A 143 2.51e+00 c.47.1.10 -7503 1mwwA 128 2.72e+00 unknown_sccs -10451 1g291 372 2.91e+00 1g291 1rh6A 55 2.97e+00 1h91A 180 3.02e+00 b.60.1.1 60805 1ri6A 343 3.19e+00 unknown_sccs -4621 1pm6A 72 3.29e+00 a.6.1.7 -386 1nx8A 273 3.31e+00 b.82.2.8 86374 1bla 155 3.45e+00 1bfg b.42.1.1 25502 1n9lA 109 3.55e+00 d.110.3.6 85468 1jj2L 194 3.57e+00 1ffkI d.12.1.2 63097 1czaN 917 3.67e+00 1qhaA c.55.1.3 33463 c.55.1.3 33464 c.55.1.3 33465 c.55.1.3 33466 1dkxA 219 3.80e+00 1dkzA unknown_sccs -446 unknown_sccs -3061 1lx8A 55 4.08e+00 a.6.1.7 84734 1b2rA 304 4.10e+00 1fnc b.43.4.2 25648 c.25.1.1 31538 1f0kA 364 4.10e+00 1f0kA c.87.1.2 35465 1qh0A 295 4.13e+00 b.43.4.2 68891 c.25.1.1 68892 1go2A 304 4.22e+00 b.43.4.2 76243 c.25.1.1 76244 1bykA 255 4.28e+00 1bykA c.93.1.1 35706 2dln 306 4.35e+00 1iow c.30.1.2 31715 d.142.1.1 41483 1mnmA 100 4.37e+00 1mnmA d.88.1.1 40232 1mqoA 227 4.42e+00 1kebA 108 4.59e+00 c.47.1.1 77341 1udsA 255 4.60e+00 d.14.1.4 -9055 d.101.1.1 -10745 1m1hA 248 4.60e+00 b.114.1.1 78415 d.58.42.1 78416 1k4iA 233 4.61e+00 d.115.1.2 72056 1p32C 209 4.79e+00 1p32A d.25.1.1 38381 1gp1A 198 4.80e+00 1gp1A c.47.1.10 33059 1a99A 344 4.90e+00 1pot c.94.1.1 35812 2fgf 146 5.21e+00 1bfg b.42.1.1 25487 1qhaA 917 5.26e+00 1qhaA c.55.1.3 33467 c.55.1.3 33468 c.55.1.3 33469 c.55.1.3 33470 1k2yX 463 5.27e+00 c.84.1.1 68063 c.84.1.1 68064 c.84.1.1 68065 d.129.2.1 68066 1h3gA 601 5.28e+00 b.1.18.2 -2725 b.71.1.1 -4653 c.1.8.1 -5277 1lgtA 297 5.34e+00 d.32.1.3 77956 d.32.1.3 77957 1g1kA 143 5.36e+00 1aohA b.2.2.2 22404 1que 303 5.54e+00 1fnc b.43.4.2 25647 c.25.1.1 31537 1hi9A 274 5.55e+00 1hi9A c.99.1.1 61063 1gw5M 435 5.61e+00 b.2.7.1 70631 d.110.4.2 70632 1uc2A 481 5.75e+00 unknown_sccs -11725 1dgkN 917 5.85e+00 1qhaA c.55.1.3 33487 c.55.1.3 33488 c.55.1.3 33489 c.55.1.3 33490 1oj4A 283 5.91e+00 d.14.1.5 -9088 d.58.26.5 -10133 1h6gA 256 6.08e+00 1h6gA a.24.9.1 60669 a.24.9.1 60670 1pvmA 184 6.16e+00 d.37.1.1 -9612 d.37.1.1 -9613 unknown_sccs -12799 1fecA 490 6.30e+00 3grs c.3.1.5 30489 c.3.1.5 30490 d.87.1.1 40176 1nt0A 286 6.33e+00 b.23.1.1 86143 b.23.1.1 86144 g.3.11.1 86145 1p5dX 463 6.39e+00 c.84.1.1 -8554 c.84.1.1 -8555 c.84.1.1 -8556 d.129.2.1 -11029 1ogiA 303 6.51e+00 b.43.4.2 -4042 c.25.1.1 -6587 1bfg 146 6.51e+00 1bfg b.42.1.1 25485 1n6zA 105 6.78e+00 unknown_sccs 85369 1i4uA 181 6.98e+00 b.60.1.1 61732 4fgf 146 7.02e+00 1bfg b.42.1.1 25486 1ecl 597 7.36e+00 1ecl e.10.1.1 43238 1fchA 368 7.41e+00 1fchA a.118.8.1 19212 1o0xA 262 7.52e+00 d.127.1.1 80755 1qauA 112 7.53e+00 1qauA b.36.1.1 24779 1kk9A 221 7.83e+00 d.115.1.1 77432 1copD 66 8.26e+00 1orc a.35.1.2 17058 1vk8A 106 8.29e+00 1g5cA 170 8.32e+00 1g5cA c.53.2.1 60264 2trxA 108 8.41e+00 1thx c.47.1.1 32719 1pj5A 830 8.56e+00 unknown_sccs -4066 c.3.1.2 -6031 d.16.1.5 -9251 unknown_sccs -10171 1hbq 183 8.89e+00 1aqb b.60.1.1 27078 2bc2B 227 9.09e+00 1a7tA d.157.1.1 42032 1o0uA 429 9.44e+00 c.118.1.1 80743 1pru 56 9.73e+00 1pru a.35.1.5 17104 2bc2A 227 9.82e+00 1a7tA d.157.1.1 42031 6pfkA 319 9.83e+00 3pfk c.89.1.1 35583 1k7jA 206 1.01e+01 d.115.1.1 72103 1erzA 303 1.03e+01 1erzA d.160.1.2 59498 2matA 264 1.06e+01 1c24A d.127.1.1 41146 1vlbA 907 1.06e+01 1iufA 144 1.07e+01 a.4.1.7 71439 a.4.1.7 71440 1rkuA 206 1.07e+01 unknown_sccs -6823 1lkdA 297 1.08e+01 d.32.1.3 78059 d.32.1.3 78060 4matA 278 1.09e+01 1c24A d.127.1.1 41150 1c24A 263 1.12e+01 1c24A d.127.1.1 41148 1hlrA 907 1.13e+01 a.56.1.1 65850 d.15.4.2 65851 d.41.1.1 65852 d.133.1.1 65853 1aohA 147 1.14e+01 1aohA b.2.2.2 22401 1dgsA 667 1.14e+01 1dgsA a.60.2.2 17963 b.40.4.6 25365 d.142.2.2 41581 1p32A 209 1.18e+01 1p32A d.25.1.1 38379 1hymB 24 1.21e+01 1aqb 183 1.22e+01 1aqb b.60.1.1 27084 1kjvA 284 1.24e+01 b.1.1.2 77421 d.19.1.1 77422 1uf5A 303 1.24e+01 1dkzA 219 1.25e+01 1dkzA unknown_sccs -445 unknown_sccs -3060 1f89A 291 1.26e+01 d.160.1.1 64988 1qksA 567 1.28e+01 1qksA a.3.1.2 15951 b.70.2.1 27710 1vc4A 254 1.28e+01 c.1.2.4 -5172 1s7hA 200 1.30e+01 1a79A 171 1.35e+01 1a79A c.52.2.1 33340 d.75.1.1 39739 1kk1A 410 1.35e+01 b.43.3.1 72634 b.44.1.1 72635 c.37.1.8 72636 1m40A 263 1.38e+01 e.3.1.1 74437 1crzA 403 1.38e+01 1crzA b.68.4.1 27629 c.51.2.1 33211 1aoqA 567 1.39e+01 1qksA a.3.1.2 15934 b.70.2.1 27692 1xgsA 295 1.40e+01 1bn5 a.4.5.25 16216 d.127.1.1 41153 1o59A 355 1.42e+01 unknown_sccs -3132 unknown_sccs -3133 1btl 263 1.43e+01 1btl e.3.1.1 42691 1vicA 262 1.45e+01 c.68.1.13 -8252 1e8uA 454 1.45e+01 1e8tA b.68.1.1 59389 1nmtA 392 1.47e+01 1nmtA d.108.1.2 40823 d.108.1.2 40824 1p9vA 310 1.47e+01 1sdjA 310 1.47e+01 d.21.1.2 -9420 d.21.1.2 -9421 1od2A 805 1.47e+01 c.14.1.4 86821 c.14.1.4 86822 1gv3A 248 1.48e+01 a.2.11.1 70585 d.44.1.1 70586 2scuB 388 1.49e+01 2scuB c.23.4.1 31141 d.142.1.4 41562 1gakA 141 1.52e+01 1gakA a.19.1.1 16415 1qftA 175 1.54e+01 1qftA b.60.1.1 27151 1pmmA 466 1.55e+01 c.67.1.6 -8159 1sglA 209 1.55e+01 1hbp 183 1.56e+01 1aqb b.60.1.1 27079 1aohB 147 1.56e+01 1aohA b.2.2.2 22402 1fjgJ 105 1.58e+01 1fjfJ d.58.15.1 39330 1f3yA 165 1.62e+01 d.113.1.1 59635 1ca1 370 1.63e+01 1ca1 a.124.1.1 19340 b.12.1.3 23648 1n7eA 97 1.64e+01 b.36.1.1 -3745 1tiqA 180 1.68e+01 1cc1L 498 1.71e+01 1h2rL e.18.1.1 43301 1fqgA 263 1.73e+01 1btl e.3.1.1 42699 1bw8A 321 1.75e+01 1bw8A b.2.7.1 22482 1iba 101 1.75e+01 1iba d.95.1.1 40567 1usrA 454 1.76e+01 b.68.1.1 -4569 1dlfL 113 1.76e+01 8fabA b.1.1.1 20382 1gvmA 136 1.76e+01 b.109.1.1 70612 1mat 264 1.77e+01 1c24A d.127.1.1 41152 1ojjA 402 1.77e+01 b.29.1.10 -3473 1h7zA 194 1.80e+01 1qhvA b.21.1.1 60733 1olzA 663 1.80e+01 b.1.1.4 -2678 unknown_sccs -4626 unknown_sccs -12590 1kngA 156 1.81e+01 c.47.1.10 72777 1exqA 154 1.82e+01 1b9dA c.55.3.2 33646 1cs8A 316 1.88e+01 1cs8A d.3.1.1 37065 1ecsA 126 1.89e+01 1ecsA d.32.1.2 59407 1i9zA 347 1.92e+01 1i9yA d.151.1.2 62102 1uu1A 335 1.94e+01 c.67.1.1 -8146 1v2yA 105 1.94e+01 d.15.1.1 -9148 1g8jA 825 1.95e+01 1g8jA b.52.2.2 26924 c.81.1.1 35332 1thx 115 1.96e+01 1thx c.47.1.1 32732 1flrL 219 1.97e+01 8fabA b.1.1.1 19904 b.1.1.2 20998 1ffkF 157 1.97e+01 1ffkF d.41.4.1 38628 1aps 98 1.99e+01 2acy d.58.10.1 39299 1kt6A 183 1.99e+01 b.60.1.1 84466 1pil 112 1.99e+01 2pii d.58.5.1 39072 1p0zA 131 2.05e+01 unknown_sccs -10853 1ctt 294 2.07e+01 1ctt c.97.1.1 36022 c.97.1.1 36023 1jd5A 124 2.07e+01 g.52.1.1 66544 1op4A 159 2.09e+01 b.1.6.1 -2794 1k1xA 659 2.09e+01 a.8.3.2 84279 b.30.5.8 84280 c.6.2.2 84281 1q48A 134 2.11e+01 unknown_sccs -9776 1hyxL 216 2.12e+01 8fabA b.1.1.1 20166 b.1.1.2 21190 1rbp 182 2.13e+01 1aqb b.60.1.1 27085 1s1qA 145 2.14e+01 d.20.1.2 -9405 1mogA 67 2.16e+01 d.230.2.1 85034 1qe5A 266 2.16e+01 1b8oA c.56.2.1 33784 1psuA 140 2.17e+01 d.38.1.5 88285 2cblA 305 2.19e+01 2cblA a.39.1.7 17380 a.48.1.1 17774 d.93.1.1 40528 1s71A 316 2.23e+01 1sgvA 316 2.23e+01 b.122.1.1 -5120 unknown_sccs -10148 1ou8A 111 2.24e+01 unknown_sccs -3799 1q72L 218 2.25e+01 b.1.1.1 -2071 b.1.1.2 -2347 1ermA 263 2.31e+01 1btl e.3.1.1 42690 3ladA 476 2.34e+01 1lvl c.3.1.5 30573 c.3.1.5 30574 d.87.1.1 40208 1p5tA 127 2.36e+01 b.55.1.2 -4368 1ns5A 155 2.39e+01 c.116.1.3 80705 1pytA 94 2.40e+01 1pytA d.58.3.1 39064 1esgA 213 2.40e+01 1bam c.52.1.3 33286 1bam 213 2.40e+01 1bam c.52.1.3 33285 1lvwA 295 2.40e+01 c.68.1.6 84723 1umsA 174 2.40e+01 1hfc d.92.1.11 40368 1hkbA 917 2.43e+01 1qhaA c.55.1.3 33479 c.55.1.3 33480 c.55.1.3 33481 c.55.1.3 33482 1j6qA 136 2.43e+01 b.40.9.1 77091 1c0pA 363 2.44e+01 1an9A c.4.1.2 30647 d.16.1.3 37934 1gu7A 364 2.47e+01 b.35.1.2 83321 c.2.1.1 83322 1e25A 282 2.52e+01 1e25A e.3.1.1 42731 1an7A 136 2.52e+01 1seiA d.140.1.1 41465 1dwmA 70 2.55e+01 1hymA d.40.1.1 38583 9gafA 295 2.58e+01 1apyA d.153.1.5 42008 1bpr 191 2.59e+01 1dkzA unknown_sccs 43319 1bxxA 285 2.59e+01 1bw8A b.2.7.1 22483 1ffkI 194 2.60e+01 1ffkI d.12.1.2 37494 1mt6A 280 2.61e+01 b.76.2.1 79446 b.85.7.1 79447 1uzbA 516 2.62e+01 c.82.1.1 -8552 1oa8A 133 2.64e+01 unknown_sccs -5142 1e8tA 454 2.66e+01 1e8tA b.68.1.1 59387 1pjcA 361 2.66e+01 1sayA c.2.1.4 30101 c.23.12.2 31361 1e5pA 151 2.67e+01 1bj7 b.60.1.1 59272 1mexL 213 2.69e+01 b.1.1.1 -2124 b.1.1.2 -2352 1hlgA 371 2.72e+01 1hlgA c.69.1.6 34656 1aogA 485 2.73e+01 3grs c.3.1.5 30517 c.3.1.5 30518 d.87.1.1 40190 1m4iA 181 2.73e+01 d.108.1.1 74457 1fp3A 402 2.80e+01 1fp3A a.102.1.3 18842 1mek 120 2.83e+01 1erv c.47.1.2 32775 1tf1A 198 2.86e+01 1agdA 276 2.87e+01 1agdA b.1.1.2 20741 d.19.1.1 38260 1hdmA 201 2.88e+01 1iakA b.1.1.2 21583 d.19.1.1 38157 1gsoA 431 2.88e+01 1gsoA b.84.2.1 28240 c.30.1.1 31647 d.142.1.2 41492 1g6zA 70 2.91e+01 1g6zA b.34.13.2 60321 1aym1 285 2.91e+01 1aym1 1qwdA 177 2.93e+01 b.60.1.1 -4455 1g6gA 127 2.93e+01 1g6gA b.26.1.2 23916 1mkaA 171 2.94e+01 1mkaA d.38.1.2 38543 1vjtA 483 2.96e+01 c.2.1.5 -5941 d.162.1.2 -11508 1tetL 216 2.99e+01 32c2A b.1.1.1 19902 b.1.1.2 20996 1ctn 540 3.03e+01 1ctn b.1.18.2 21876 c.1.8.5 29005 d.26.3.1 38439 1fztA 211 3.07e+01 1qhfA c.60.1.1 60158 1n67A 359 3.09e+01 b.2.3.4 85354 b.2.3.4 85355 1svpA 161 3.10e+01 1svpA b.47.1.3 26384 1dnlA 199 3.11e+01 1ci0A b.45.1.1 25753 1g8kA 825 3.11e+01 1g8jA b.52.2.2 26920 c.81.1.1 35328 1iazA 179 3.14e+01 1iazA b.97.1.1 62131 1iuhA 198 3.18e+01 d.61.1.2 83711 1avmA 201 3.18e+01 1avmA a.2.11.1 15782 d.44.1.1 38745 1nu0A 138 3.18e+01 unknown_sccs -7658 1rurL 217 3.19e+01 b.1.1.1 -2094 b.1.1.2 -2389 1gw1A 376 3.20e+01 c.1.8.3 76361 1cqyA 99 3.22e+01 1b9zA b.3.1.1 22527 1gkfB 557 3.24e+01 1iakA 199 3.27e+01 1iakA b.1.1.2 21625 d.19.1.1 38199 1i9yA 347 3.27e+01 1i9yA d.151.1.2 62101 1ld4A 264 3.27e+01 i.6.1.1 77886 1a3yA 149 3.28e+01 1obpA b.60.1.1 27110 1lrzA 426 3.28e+01 a.2.7.4 78167 d.108.1.4 78168 d.108.1.4 78169 1hfs 160 3.29e+01 1hfc d.92.1.11 40370 1ndbA 596 3.30e+01 c.43.1.3 80411 c.43.1.3 80412 1e6oL 212 3.30e+01 32c2A b.1.1.1 20494 b.1.1.2 21452 1c5kA 439 3.33e+01 1crzA b.68.4.1 27630 c.51.2.1 33212 1iwlA 182 3.34e+01 b.125.1.1 83757 1vcbC 160 3.38e+01 1vcbC b.3.3.1 22535 1iwgA 1053 3.39e+01 d.58.44.1 76874 d.58.44.1 76875 d.58.44.1 76876 d.58.44.1 76877 d.225.1.1 76878 d.225.1.1 76879 f.35.1.1 76880 f.35.1.1 76881 1iugA 352 3.44e+01 c.67.1.3 -8176 1gm7B 557 3.48e+01 1mk0A 97 3.50e+01 d.226.1.1 79216 1pnkB 557 3.50e+01 1ajqB 1vaoA 560 3.53e+01 1qltA d.58.32.1 39461 d.145.1.1 41724 1g79A 218 3.54e+01 1ci0A b.45.1.1 25752 1forL 210 3.55e+01 8fabA b.1.1.1 19988 b.1.1.2 21044 1isaA 192 3.55e+01 1avmA a.2.11.1 15731 d.44.1.1 38724 1a8l 226 3.56e+01 1a8l c.47.1.2 32777 c.47.1.2 32778 1j08A 226 3.60e+01 c.47.1.2 83855 c.47.1.2 83856 1gk9B 557 3.61e+01 1e3aB 560 3.63e+01 1ajqB 1h8gA 95 3.64e+01 b.109.1.1 65735 1skoB 130 3.66e+01 1iscA 192 3.67e+01 1avmA a.2.11.1 15733 d.44.1.1 38726 8abp 306 3.67e+01 8abp c.93.1.1 35647 1r26A 125 3.69e+01 c.47.1.1 -7389 1nm8A 616 3.70e+01 c.43.1.3 85872 c.43.1.3 85873 1gm9B 557 3.70e+01 1k8kB 394 3.71e+01 c.55.1.1 68307 1lci 550 3.73e+01 1lci e.23.1.1 43349 2pii 112 3.76e+01 2pii d.58.5.1 39071 1mw9X 592 3.76e+01 e.10.1.1 -11986 1lngA 87 3.79e+01 d.201.1.1 74045 1udxA 416 3.79e+01 b.117.1.1 -3546 c.37.1.8 -7101 unknown_sccs -9009 1udzA 182 3.86e+01 b.51.1.1 -4307 3pfk 319 3.89e+01 3pfk c.89.1.1 35581 1e8gA 560 3.89e+01 1qltA d.58.32.1 39455 d.145.1.1 41718 8ohm 435 3.89e+01 1heiA c.37.1.14 32469 c.37.1.14 32470 1iicA 422 3.90e+01 1nmtA d.108.1.2 62422 d.108.1.2 62423 1dbtA 239 3.95e+01 1dbtA c.1.2.3 28539 1ayyA 151 3.95e+01 1apyA d.153.1.5 42016 1dqqA 214 3.96e+01 8fabA b.1.1.1 20420 b.1.1.2 21390 1dymA 402 3.99e+01 1celA b.29.1.10 24304