# List of top-scoring protein chains for t2k-100-30-alpha 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 1ftrA 296 9.69e-02 1ftrA d.58.33.1 39485 d.58.33.1 39486 1ap8 213 2.24e-01 1ap8 d.86.1.1 40151 1vixA 420 3.31e-01 c.56.5.4 -7866 d.58.19.1 -10090 1q8bA 105 3.99e-01 unknown_sccs -9958 1nfp 228 6.25e-01 1nfp c.1.16.2 29555 1m5sA 297 7.26e-01 d.58.33.1 74511 d.58.33.1 74512 1rlr 761 8.56e-01 1rlr a.98.1.1 18753 c.7.1.2 30679 1hi9A 274 8.80e-01 1hi9A c.99.1.1 61063 1hfc 169 1.41e+00 1hfc d.92.1.11 40335 1fnoA 417 1.41e+00 c.56.5.4 75841 d.58.19.1 70145 1souA 194 1.81e+00 1d2eA 397 2.02e+00 1efcA b.43.3.1 25701 b.44.1.1 25741 c.37.1.8 32136 1e8gA 560 2.26e+00 1qltA d.58.32.1 39455 d.145.1.1 41718 1ffkS 70 2.28e+00 1ffkS a.2.2.1 15692 1qf6A 642 2.28e+00 1qf6A c.51.1.1 33210 d.15.10.1 39551 d.67.1.1 39562 d.104.1.1 40759 1s72V 71 2.73e+00 1i5gA 144 2.98e+00 1ewxA c.47.1.10 61784 1itzA 675 3.08e+00 c.36.1.6 76798 c.36.1.10 76797 c.48.1.1 76799 1fc4A 401 3.14e+00 1bs0A c.67.1.4 59760 1w1kA 560 3.14e+00 1jj2U 70 3.29e+00 1ffkS a.2.2.1 63106 1uj2A 252 3.30e+00 c.37.1.6 -7061 1kvdB 77 3.92e+00 1kveB 1udmA 149 4.11e+00 1q5yA 85 4.37e+00 unknown_sccs -10081 1es5A 262 4.56e+00 1skf e.3.1.1 42679 1i39A 225 4.59e+00 1ekeA c.55.3.1 61585 1esiA 262 4.68e+00 1skf e.3.1.1 42682 1w0bA 102 4.82e+00 1p65A 73 4.94e+00 unknown_sccs -10331 1kveB 77 5.06e+00 1kveB 1ris 101 5.16e+00 1ris d.58.14.1 39314 1vaoA 560 5.17e+00 1qltA d.58.32.1 39461 d.145.1.1 41724 1f2tB 148 6.01e+00 1f2tB 1sk4A 163 6.21e+00 1o6jA 150 6.26e+00 c.47.1.10 81089 1esgA 213 6.40e+00 1bam c.52.1.3 33286 1qnxA 209 6.65e+00 1qnxA d.111.1.1 40914 1skf 262 6.77e+00 1skf e.3.1.1 42684 1kw4A 89 6.89e+00 a.60.1.2 73077 1i8jA 323 7.04e+00 1b4kA c.1.10.3 61968 1louA 101 7.09e+00 1ris d.58.14.1 39323 1s2xA 206 7.11e+00 1b4eA 323 7.26e+00 1b4kA c.1.10.3 29186 1tk9A 188 7.29e+00 1jmxA 494 7.47e+00 a.3.1.7 66901 a.3.1.7 66902 b.1.18.14 66903 b.1.18.14 66904 b.61.4.1 66905 1hj8A 222 7.72e+00 b.47.1.2 65844 1l6sA 323 7.93e+00 c.1.10.3 73627 1umsA 174 8.15e+00 1hfc d.92.1.11 40368 1cqmA 101 8.30e+00 1ris d.58.14.1 39321 1l3iA 192 8.32e+00 c.66.1.22 77676 1b57A 358 8.58e+00 1dosA c.1.10.2 29177 2tbs 222 8.66e+00 5ptp b.47.1.2 26009 1es2A 262 9.04e+00 1skf e.3.1.1 42680 1o12A 376 9.05e+00 b.92.1.5 80758 c.1.9.10 80759 1o20A 427 9.12e+00 c.82.1.1 86556 1hurA 180 9.19e+00 1hurA c.37.1.8 32052 1lldA 319 9.36e+00 3ldh c.2.1.5 30177 d.162.1.1 42144 1kjwA 295 9.42e+00 b.34.2.1 68643 c.37.1.1 68644 1uzbA 516 9.57e+00 c.82.1.1 -8552 1iq8A 582 9.82e+00 b.122.1.1 83074 c.1.20.1 71270 d.17.6.1 83075 1kutA 230 9.82e+00 d.143.1.1 73017 1j2iA 166 1.00e+01 1o3yA 166 1.00e+01 c.37.1.8 86618 1he1A 135 1.02e+01 1he1A a.24.11.1 16641 1ee8A 266 1.04e+01 1ee8A a.156.1.2 75823 b.113.1.1 75824 g.39.1.8 75825 1jx2B 315 1.04e+01 c.37.1.8 67404 1huuA 90 1.05e+01 1huuA a.55.1.1 17897 1q4rA 112 1.06e+01 d.58.4.4 -9943 1k1gA 131 1.06e+01 d.51.1.1 68015 1j1hA 144 1.09e+01 b.111.1.1 77056 1ml4A 308 1.09e+01 c.78.1.1 79255 c.78.1.1 79256 1kao 167 1.09e+01 1ctqA c.37.1.8 32014 1qs2A 401 1.10e+01 1qs1A d.166.1.1 42268 d.166.1.1 42269 1j27A 102 1.13e+01 unknown_sccs -10116 1e1dA 553 1.18e+01 1e1dA e.26.1.1 43363 1b8zA 90 1.19e+01 1huuA a.55.1.1 17902 1lf6A 684 1.22e+01 a.102.1.5 77918 b.30.5.5 77919 1qltA 560 1.24e+01 1qltA d.58.32.1 39457 d.145.1.1 41720 1r8sA 164 1.25e+01 c.37.1.8 -7082 1oc2A 348 1.28e+01 c.2.1.2 -5753 1edqA 540 1.30e+01 1ctn b.1.18.2 21873 c.1.8.5 29002 d.26.3.1 38436 1k9tA 540 1.32e+01 b.1.18.2 77298 c.1.8.5 77299 d.26.3.1 77300 1nksA 194 1.34e+01 1nksA c.37.1.1 31886 1s0yB 71 1.40e+01 d.80.1.1 -10442 1ois 223 1.42e+01 1a36A e.15.1.1 43267 1f7lA 121 1.46e+01 1f7lA d.150.1.2 59666 1pf5A 131 1.47e+01 d.79.1.1 -10368 1eonA 245 1.49e+01 1rvaA c.52.1.2 33238 1qs1A 462 1.54e+01 1qs1A d.166.1.1 42260 d.166.1.1 42261 1nx8A 273 1.54e+01 b.82.2.8 86374 1jxmA 301 1.57e+01 b.34.2.1 67420 c.37.1.1 67421 1p27B 106 1.59e+01 d.58.7.1 -10020 1v8dA 235 1.61e+01 1fukA 165 1.62e+01 1fukA c.37.1.19 32409 1b24A 188 1.64e+01 1b24A d.95.2.1 40573 d.95.2.1 40574 1e2uA 553 1.66e+01 1e1dA e.26.1.1 43362 1oe4A 247 1.66e+01 c.18.1.3 86895 1ctn 540 1.68e+01 1ctn b.1.18.2 21876 c.1.8.5 29005 d.26.3.1 38439 1krhA 338 1.70e+01 b.43.4.2 72891 c.25.1.2 72892 d.15.4.2 72893 1bxsA 501 1.71e+01 1bpwA c.82.1.1 35357 1hl6A 165 1.74e+01 d.58.7.1 83609 1kepA 348 1.74e+01 c.2.1.2 68536 1qc7A 101 1.76e+01 1qc7A a.118.14.1 18456 1ae1A 273 1.84e+01 1bdb c.2.1.2 29943 1dgqA 188 1.84e+01 1ido c.62.1.1 34131 1es4A 262 1.84e+01 1skf e.3.1.1 42683 1sesA 421 1.84e+01 1sesA a.2.7.1 15710 d.104.1.1 40710 1jqlB 140 1.87e+01 c.37.1.20 63234 1gntA 553 1.90e+01 e.26.1.1 70290 1f7tA 122 2.01e+01 1f7lA d.150.1.2 59667 1cfr 285 2.01e+01 1cfr c.52.1.7 33312 1n5uA 585 2.01e+01 a.126.1.1 85339 a.126.1.1 85340 a.126.1.1 85341 1afi 72 2.04e+01 1aw0 d.58.17.1 39339 1q53A 112 2.05e+01 d.58.4.4 -9944 1jqjC 343 2.06e+01 a.80.1.1 67097 c.37.1.20 67098 1r89A 437 2.06e+01 unknown_sccs -1147 unknown_sccs -9801 unknown_sccs -10061 1mli 96 2.07e+01 1mli d.58.4.1 39070 1dljA 402 2.10e+01 1dliA a.100.1.4 18808 c.2.1.6 30212 c.26.3.1 31621 1pbyA 489 2.12e+01 a.3.1.7 -178 a.3.1.7 -179 b.1.18.14 -2762 b.1.18.14 -2763 b.61.4.1 -4528 1j5pA 253 2.12e+01 c.2.1.3 83092 d.81.1.3 71577 1ry9A 145 2.16e+01 d.198.1.1 -9020 1rvaA 244 2.16e+01 1rvaA c.52.1.2 33240 1pyoA 167 2.27e+01 c.17.1.1 -7932 1m2dA 110 2.27e+01 c.47.1.11 78476 1q3kA 259 2.27e+01 unknown_sccs -6335 1mg7A 417 2.28e+01 d.14.1.6 84954 d.58.26.6 84955 1hyhA 309 2.29e+01 1hyhA c.2.1.5 30150 d.162.1.1 42117 1oo0B 110 2.30e+01 d.58.7.1 87183 1lkvX 232 2.37e+01 a.118.14.1 73980 1r2zA 274 2.41e+01 a.156.1.2 -370 b.113.1.1 -5094 g.39.1.8 -12748 1a8rA 221 2.51e+01 1a8rA d.96.1.1 40587 1nmeA 146 2.52e+01 c.17.1.1 85874 1gc5A 467 2.53e+01 1gc5A c.72.1.3 60429 1vknA 351 2.54e+01 1hueA 90 2.59e+01 1huuA a.55.1.1 17900 1auwA 468 2.59e+01 1auwA a.127.1.1 19416 1qu9A 128 2.59e+01 1qu9A d.79.1.1 39755 1qu9C 128 2.59e+01 1qu9A d.79.1.1 39757 1m4tA 392 2.60e+01 c.95.1.1 78617 c.95.1.1 78618 1nzaA 103 2.65e+01 d.58.5.2 86444 1nf8A 207 2.72e+01 unknown_sccs 85630 1ck7A 631 2.73e+01 1ck7A a.20.1.2 58969 b.66.1.1 27538 d.92.1.11 58970 g.14.1.2 44674 g.14.1.2 44675 g.14.1.2 44676 1ac5 483 2.75e+01 1ac5 c.69.1.5 34653 1io2A 213 2.75e+01 1ekeA c.55.3.1 62612 1nf9A 207 2.78e+01 unknown_sccs 85631 1ha2A 585 2.78e+01 1bj5 a.126.1.1 60866 a.126.1.1 60867 a.126.1.1 60868 1mai 131 2.79e+01 1mai b.55.1.1 26951 1sx5A 244 2.80e+01 c.52.1.2 -7551 7timA 247 2.82e+01 1amk c.1.1.1 28457 1j6wA 175 2.84e+01 1j98A d.185.1.2 62663 1jjuA 489 2.86e+01 a.3.1.7 66774 a.3.1.7 66775 b.1.18.14 66776 b.1.18.14 66777 b.61.4.1 66778 1iqrA 420 2.88e+01 a.99.1.1 66275 c.28.1.1 66276 1n82A 331 2.89e+01 c.1.8.3 -5306 1lfaA 187 2.90e+01 1ido c.62.1.1 34122 1io1A 398 2.91e+01 1io1A e.32.1.1 62611 1ud0A 113 2.91e+01 unknown_sccs -450 1bzsA 165 2.98e+01 1hfc d.92.1.11 40348 1nj4A 363 3.04e+01 b.105.1.1 80545 e.3.1.1 80546 1i9gA 280 3.04e+01 c.66.1.13 62090 1bj5 585 3.04e+01 1bj5 a.126.1.1 19369 a.126.1.1 19370 a.126.1.1 19371 1nzoA 363 3.06e+01 b.105.1.1 -2933 e.3.1.1 -11784 1egwA 77 3.08e+01 1mnmA d.88.1.1 40234 1uuqA 440 3.09e+01 c.1.8.3 -5321 1jd1A 129 3.09e+01 1qu9A d.79.1.1 62890 1dliA 402 3.09e+01 1dliA a.100.1.4 18809 c.2.1.6 30213 c.26.3.1 31622 2ezl 99 3.11e+01 2ezk a.4.1.2 16026 1jmtA 104 3.14e+01 d.58.7.3 63180 1at3A 247 3.14e+01 1at3A b.57.1.1 27021 1jysA 242 3.17e+01 c.56.2.1 77216 1f75A 249 3.21e+01 1f75A c.101.1.1 59662 1gnlA 544 3.21e+01 e.26.1.1 70287 2rspB 124 3.27e+01 2rspB b.50.1.1 26772 1sedA 117 3.29e+01 1hy7A 173 3.30e+01 d.92.1.11 65957 2ezk 99 3.32e+01 2ezk a.4.1.2 16027 1pl8A 356 3.34e+01 b.35.1.2 -3716 c.2.1.1 -5740 1b0pA 1231 3.36e+01 c.36.1.8 31831 c.36.1.12 31832 c.48.1.3 33104 c.64.1.1 34157 d.58.1.5 39003 1o5zA 442 3.40e+01 c.59.1.2 -7939 c.72.2.2 -8418 2chsA 127 3.41e+01 2chsA d.79.1.2 39764 1mjnA 179 3.49e+01 c.62.1.1 79210 1by9 81 3.51e+01 2bopA d.58.8.1 39223 1m2aA 110 3.54e+01 c.47.1.11 78472 1em2A 229 3.54e+01 1em2A d.129.3.2 41321 1h8vA 218 3.55e+01 2nlrA b.29.1.11 60795 1mkyA 439 3.55e+01 c.37.1.8 79250 c.37.1.8 79251 d.52.5.1 79252 1gehA 444 3.55e+01 c.1.14.1 65181 d.58.9.1 65182 1ffkC 246 3.57e+01 1ffkC c.22.1.1 31037 1v7zA 260 3.60e+01 unknown_sccs -6353 1gw5S 142 3.61e+01 d.110.4.2 70633 1rypB 250 3.61e+01 1rypB d.153.1.4 41933 1nc5A 373 3.63e+01 a.102.1.6 85548 1msk 331 3.68e+01 1msk d.173.1.1 42495 1pz1A 333 3.68e+01 c.1.7.1 -5255 1hzdA 272 3.72e+01 c.14.1.3 65969 1un7A 400 3.73e+01 b.92.1.5 -5077 c.1.9.10 -5429 1nykA 165 3.75e+01 b.33.1.1 86408 1bglA 1023 3.77e+01 1bglA b.1.4.1 22097 b.1.4.1 22098 b.18.1.5 23734 b.30.5.1 24358 c.1.8.3 28857 1uu1A 335 3.80e+01 c.67.1.1 -8146 1jj2C 246 3.82e+01 1ffkC c.22.1.1 63087 1m2bA 110 3.83e+01 c.47.1.11 78474 1p1lA 102 3.83e+01 d.58.5.2 87695 1s72C 246 3.84e+01 1sk7A 198 3.84e+01 1oa2A 218 3.87e+01 b.29.1.11 86721 1l1zA 274 3.90e+01 a.156.1.2 75911 b.113.1.1 75912 g.39.1.8 75913 1i76A 163 3.91e+01 1hfc d.92.1.11 61877 1k99A 99 3.95e+01 a.21.1.1 68341 1jr3D 343 3.99e+01 a.80.1.1 63251 c.37.1.20 63252 1cxvA 164 4.00e+01 1ck7A d.92.1.11 40404