# List of top-scoring protein chains for t2k-100-30-dssp-ebghstl-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 1xngA 268 3.73e-01 1dq3A 454 9.91e-01 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1eal 127 1.01e+00 1hmt b.60.1.2 27227 1k3iA 656 1.90e+00 b.1.18.2,b.18.1.1,b.69.1.1 68113,68114,68115 1nezG 128 2.33e+00 b.1.1.1 85592 2cokA 113 2.34e+00 1goh 639 2.64e+00 1gof b.1.18.2,b.18.1.1,b.69.1.1 21809,23711,27633 1gof 639 2.66e+00 1gof b.1.18.2,b.18.1.1,b.69.1.1 21807,23709,27631 1b3mA 389 2.73e+00 1b3mA 1rzfL 213 3.00e+00 b.1.1.1,b.1.1.2 98152,98153 1rsy 152 3.01e+00 1rsy b.7.1.2 23192 2a9mL 110 3.02e+00 1theB 260 3.46e+00 1theB d.3.1.1 37057 1ekgA 127 3.57e+00 1dlxA d.82.2.1 40021 1theA 260 3.73e+00 1theB d.3.1.1 37056 1l9fA 389 3.74e+00 c.3.1.2,d.16.1.3 73716,73717 1el5A 389 3.76e+00 1b3mA c.3.1.2,d.16.1.3 30369,37937 1f89A 291 4.29e+00 d.160.1.1 64988 1jmmA 377 4.56e+00 b.30.6.1 71749 1iloA 77 4.83e+00 c.47.1.1 66205 2gxfA 142 5.49e+00 1qmeA 702 5.81e+00 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37487,37488,42560,42769 1i8nA 126 6.55e+00 1i8nA g.10.1.2 61976 1bynA 128 6.79e+00 1rsy b.7.1.2 23193 1bqhG 129 6.94e+00 1cd8 b.1.1.1 19715 1k0eA 453 7.36e+00 d.161.1.1 67938 1k2yX 463 8.72e+00 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 1dgrC 178 8.85e+00 1dgwA b.82.1.2 28100 1p5dX 463 9.03e+00 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1dgwA 178 9.25e+00 1dgwA b.82.1.2 28090 1v8hA 107 9.57e+00 1llwA 1520 9.89e+00 b.80.4.1,c.1.4.1,d.153.1.1 74017,74018,74019 1sb2A 133 1.02e+01 1k0gA 453 1.02e+01 d.161.1.1 67940 1xzoA 174 1.04e+01 2bu3A 254 1.10e+01 2a7yA 83 1.15e+01 1ll8A 114 1.18e+01 d.110.3.5 78089 1gmyA 261 1.19e+01 d.3.1.1 76236 1kppA 145 1.28e+01 d.20.1.2 72846 1xcbA 211 1.31e+01 a.4.5.38,c.2.1.12 109552,109553 1csbB 205 1.41e+01 1theB 1ly7A 121 1.46e+01 d.82.2.1 74339 1gpmA 525 1.47e+01 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 1aoiB 87 1.48e+01 1aoiB a.22.1.1 16470 1a12A 413 1.50e+01 1a12A b.69.5.1 27663 1qtfA 246 1.51e+01 1agjA b.47.1.1 25830 1qsgA 265 1.52e+01 1eny c.2.1.2 29935 1dgmA 363 1.53e+01 1bx4A c.72.1.1 34936 1c14A 262 1.55e+01 1eny c.2.1.2 29927 2pcdA 200 1.57e+01 3pchA b.3.6.1 22665 1o0wA 252 1.57e+01 a.149.1.1,d.50.1.1 80751,80752 1mvfA 135 1.58e+01 b.1.1.1 85141 1y89A 238 1.59e+01 1cauA 181 1.65e+01 1dgwA b.82.1.2 28102 1wy2A 351 1.67e+01 1ofdA 1520 1.69e+01 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 1tmcA 175 1.69e+01 1agdA d.19.1.1 38258 3pcnA 200 1.73e+01 3pchA b.3.6.1 22725 1lvwA 295 1.75e+01 c.68.1.6 84723 1asu 162 1.78e+01 1cxqA c.55.3.2 33626 3pchA 200 1.79e+01 3pchA b.3.6.1 22653 1cxqA 162 1.79e+01 1cxqA c.55.3.2 33621 1ru8A 232 1.85e+01 c.26.2.1 97849 1ebdC 41 1.87e+01 1ebdC a.9.1.1 16355 1aoiF 87 1.87e+01 1aoiB a.22.1.1 16471 2a2pA 129 1.87e+01 2cavA 445 1.88e+01 1dgwA b.82.1.2,b.82.1.2 28094,28095 1wu7A 434 1.89e+01 1z5yE 149 1.92e+01 1vsd 152 1.92e+01 1cxqA c.55.3.2 33625 1a5v 162 1.92e+01 1cxqA c.55.3.2 33629 1s68A 249 1.97e+01 d.142.2.4 98591 1lfo 128 1.99e+01 1hmt b.60.1.2 27223 1tif 78 2.08e+01 1tif d.15.8.1 37836 1in0A 163 2.11e+01 d.58.49.1,d.58.49.1 83694,83695 1hm2A 700 2.13e+01 1cb8A a.102.3.2,b.24.1.1,b.30.5.2 61083,61084,61085 1hq3D 103 2.18e+01 1aoiB a.22.1.1 16464 1tzyD 103 2.18e+01 a.22.1.1 107533 2absA 383 2.19e+01 1id3B 102 2.21e+01 a.22.1.1 66113 1jj2S 119 2.23e+01 1ffkQ b.34.5.1 63104 1s72T 120 2.23e+01 b.34.5.1 105339 1vqoT 120 2.25e+01 1b3aA 67 2.25e+01 1b3aA d.9.1.1 37410 1jmxB 349 2.29e+01 b.69.2.2 66906 1kx5B 102 2.29e+01 a.22.1.1 77594 1eqtA 68 2.30e+01 1b3aA d.9.1.1 37412 2alp 198 2.35e+01 1qq4A b.47.1.1 25772 1ssxA 198 2.40e+01 b.47.1.1 98978 1qg6A 261 2.40e+01 1eny c.2.1.2 29919 1ass 159 2.48e+01 1a6dA c.8.5.2 30818 1ffkQ 119 2.48e+01 1ffkQ b.34.5.1 24605 1vj0A 380 2.52e+01 b.35.1.2,c.2.1.1 100786,100787 1nykA 165 2.56e+01 b.33.1.1 86408 1u2fA 90 2.57e+01 1u2fA d.58.7.1 39168 1p0hA 318 2.58e+01 d.108.1.1 93866 1r26A 125 2.59e+01 c.47.1.1 96847 1vcbB 112 2.61e+01 1vcbB d.42.1.1 38633 1z5bA 469 2.64e+01 1kl9A 182 2.69e+01 b.40.4.5 72681 1zvyA 136 2.74e+01 1yezA 68 2.74e+01 2bvpA 276 2.90e+01 1gkuB 1054 2.92e+01 c.37.1.16,c.37.1.16,e.10.1.1 65257,65258,65259 1cb8A 678 2.96e+01 1cb8A a.102.3.2,b.24.1.1,b.30.5.2 18849,23898,24422 1xfpA 142 2.97e+01 b.1.1.1 109587 1qsoA 149 2.98e+01 1qsmA d.108.1.1 40812 1xh3A 276 3.03e+01 1m4vA 204 3.06e+01 b.40.2.2,d.15.6.1 74459,74460 1hsbA 270 3.07e+01 1agdA b.1.1.2,d.19.1.1 20736,38257 1gheA 177 3.11e+01 d.108.1.1 76222 1brlB 324 3.12e+01 1lucA c.1.16.1 29554 1qydA 313 3.14e+01 c.2.1.2 96583 1a1oA 276 3.15e+01 1agdA b.1.1.2,d.19.1.1 20751,38265 1y9wA 140 3.20e+01 1vlmA 219 3.21e+01 c.66.1.41 108836 2g76A 335 3.24e+01 1aorA 605 3.28e+01 1b25A a.110.1.1,d.152.1.1 19042,41794 1wy5A 317 3.30e+01 7catA 506 3.35e+01 1cf9A e.5.1.1 42781 1wiwA 290 3.35e+01 1a1mA 278 3.38e+01 1agdA b.1.1.2,d.19.1.1 20753,38266 2azwA 148 3.46e+01 1qw1A 121 3.51e+01 1a1nA 276 3.57e+01 1agdA b.1.1.2,d.19.1.1 20755,38267 1asx 159 3.62e+01 1a6dA c.8.5.2 30821 1jm1A 204 3.64e+01 b.33.1.1 71745 1upiA 225 3.67e+01 b.82.1.1 99757 1vkiA 181 3.68e+01 d.116.1.1 108664 1w85I 49 3.68e+01 2ew2A 316 3.69e+01 1cojA 212 3.78e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1qtnA 164 3.79e+01 1pauA c.17.1.1 30999 1wosA 364 3.79e+01 b.44.2.1,d.250.1.1 109468,109469 1qq4A 198 3.80e+01 1qq4A b.47.1.1 25768 1lgpA 116 3.87e+01 b.26.1.2 73890 1p04A 198 3.92e+01 1qq4A b.47.1.1 25805 3pcgA 200 3.92e+01 3pchA b.3.6.1 22647 1lucB 324 3.95e+01 1lucA c.1.16.1 29548 1ky9A 448 3.95e+01 b.36.1.4,b.47.1.1 73198,73199 1oeyA 83 4.01e+01 d.15.2.2 92800 1nycA 111 4.09e+01 b.61.2.2 92336 1cd0A 111 4.14e+01 8fabA b.1.1.1 20559 1ws0A 156 4.21e+01 2cbp 96 4.22e+01 2cbp b.6.1.1 22895 1lb2B 84 4.26e+01 a.60.3.1 77871 2c0zA 216 4.28e+01 1svpA 161 4.34e+01 1svpA b.47.1.3 26384 1ky9B 448 4.35e+01 b.36.1.4,b.36.1.4,b.47.1.1 73200,73201,73202 1obdA 306 4.42e+01 d.143.1.1 86767 1qsmA 152 4.45e+01 1qsmA d.108.1.1 40808 2c27A 315 4.46e+01 1egxA 115 4.46e+01 1evhA b.55.1.4 27000 1j8mF 297 4.52e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 1mfgA 95 4.58e+01 b.36.1.1 79043 1zmaA 118 4.59e+01 1j8yF 297 4.66e+01 1ng1 a.24.13.1,c.37.1.10 62747,62748 1hh2P 344 4.72e+01 b.40.4.5,d.52.3.1,d.52.3.1,d.202.1.1 65835,65836,65837,65838 1lufA 343 4.74e+01 d.144.1.7 78223 1i3uA 127 4.80e+01 1gc1H b.1.1.1 61636 2pdd 43 4.82e+01 1ebdC a.9.1.1 16358 2g6fX 59 4.85e+01 1zt1A 277 4.90e+01 1wlyA 333 4.93e+01 1lcyA 325 4.93e+01 b.36.1.4,b.47.1.1 73834,73835 1io1A 398 5.03e+01 1io1A e.32.1.1 62611 1l1nA 183 5.04e+01 b.47.1.4 73476 1wvfA 520 5.04e+01 1uvzA 119 5.05e+01 1gya 105 5.14e+01 1qa9A b.1.1.1 19745 1knlA 130 5.14e+01 b.42.2.1 72780 1knmA 130 5.15e+01 b.42.2.1 72781 1hgxA 183 5.16e+01 1tc1A c.61.1.1 34027 1adqH 225 5.30e+01 1igtB b.1.1.1,b.1.1.2 20273,21273 1kbaA 66 5.32e+01 3ebx g.7.1.1 44431 1idsA 207 5.34e+01 1avmA a.2.11.1,d.44.1.1 15722,38730 1scmB 145 5.35e+01 1wdcB a.39.1.5 17304 1kpeA 126 5.40e+01 1kpf d.13.1.1 37508 1ld4A 264 5.44e+01 i.6.1.1 77886 1b4jL 214 5.44e+01 8fabA b.1.1.1,b.1.1.2 20308,21300 2av5A 120 5.49e+01 2gfaA 119 5.67e+01 1w4vA 119 5.68e+01 1ab6A 125 5.78e+01 3chy c.23.1.1 31054 2g5dA 422 5.80e+01 1fvuB 125 5.82e+01 1ixxB d.169.1.1 42346 1po5A 476 5.84e+01 a.104.1.1 94963 1b2pA 119 5.88e+01 1b2pA b.78.1.1 27998 1pvyA 227 5.89e+01 d.115.1.2 95195 1zt7A 276 5.89e+01 1qwdA 177 5.90e+01 b.60.1.1 96471 1p1mA 406 5.91e+01 b.92.1.4,c.1.9.9 87696,87697 1bb8 71 5.94e+01 2bb8 d.10.1.1 37478 1pmzA 86 5.95e+01 a.39.1.10 104195 2fyxA 143 5.96e+01 1x0pA 143 5.97e+01 1k32A 1045 5.98e+01 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 68068,68069,68070,68071 1nbwB 117 6.01e+01 c.51.3.2 80396 2ak5A 64 6.07e+01 2av7A 275 6.11e+01 1nlnA 204 6.11e+01 d.3.1.7 91962 1chmA 401 6.12e+01 1chmA c.55.2.1,d.127.1.1 33545,41142 1i4fA 275 6.13e+01 1agdA b.1.1.2,d.19.1.1 61687,61688 2a19A 175 6.19e+01 1x74A 360 6.20e+01 1ounA 127 6.28e+01 1ounA d.17.4.2 38090 1u24A 337 6.37e+01 1duzA 275 6.38e+01 1agdA b.1.1.2,d.19.1.1 20670,38224 1ni5A 433 6.41e+01 c.26.2.5,d.229.1.1 80533,80534 1yioA 208 6.47e+01 2ltnA 181 6.53e+01 1led b.29.1.1 24024 2awaA 390 6.56e+01 1askA 127 6.57e+01 1ounA d.17.4.2 38094 2ebn 289 6.59e+01 2ebn c.1.8.5 28990 1sgt 223 6.65e+01 5ptp b.47.1.1 25814 1kk8B 139 6.68e+01 a.39.1.5 77430 1avpA 204 6.69e+01 1avpA d.3.1.7 37132 1j83A 180 6.70e+01 b.18.1.12 66430 1v74B 87 6.72e+01 a.24.20.1 100443 1jbeA 128 6.73e+01 3chy c.23.1.1 62845 1adqL 213 6.76e+01 8fabA b.1.1.1,b.1.1.2 20272,21272 1gxuA 91 6.77e+01 d.58.10.1 76378 1eucB 396 6.77e+01 2scuB c.23.4.1,d.142.1.4 31149,41570 1eudB 396 6.84e+01 2scuB c.23.4.1,d.142.1.4 31150,41571 1wcgA 464 6.86e+01 1os8A 223 6.86e+01 b.47.1.1 93481 1s3cA 141 6.89e+01 1bymA 97 6.90e+01 1bi0 b.34.1.2 24458 1j9bA 141 6.91e+01 c.47.1.12 66459 1xer 103 6.93e+01 1xer d.58.1.3 38990 1wqsA 173 6.97e+01 1fe0A 68 6.98e+01 1cc8A d.58.17.1 39345 1g5vA 88 7.01e+01 1g5vA b.34.9.1 60292 1mylA 53 7.03e+01 1bazA a.43.1.1 17427 2av1A 275 7.06e+01 1ar0A 127 7.07e+01 1ounA d.17.4.2 38092 2bb8 71 7.09e+01 2bb8 d.10.1.1 37480 1aua 296 7.14e+01 1aua a.5.3.1,c.13.1.1 16290,30882 2ghsA 326 7.21e+01 1b69A 69 7.26e+01 2bb8 d.10.1.1 37479 1jb2A 127 7.27e+01 d.17.4.2 71624 1mhnA 59 7.29e+01 b.34.9.1 84964 1gy6A 127 7.30e+01 d.17.4.2 70736 1z3eB 73 7.30e+01 1rrmA 386 7.34e+01 e.22.1.2 105081 1kn0A 212 7.52e+01 d.50.1.3 77444 1pguA 615 7.52e+01 b.69.4.1,b.69.4.1 88069,88070 1j6pA 418 7.54e+01 b.92.1.4,c.1.9.9 77089,77090 1aw8B 91 7.54e+01 1aw8B 1eylA 186 7.55e+01 1wba b.42.4.1 25593 1uohA 226 7.55e+01 d.211.1.1 99690 1f56A 91 7.66e+01 2cbp b.6.1.1 22896 2f5tX 233 7.69e+01 1xfjA 261 7.69e+01 d.194.1.2 109585 1tuaA 191 7.69e+01 d.51.1.1,d.51.1.1 107321,107322 1p0zA 131 7.71e+01 d.110.6.1 93882 1rq6A 62 7.73e+01 2fp4B 395 7.73e+01 1xovA 326 7.76e+01 1o4sA 389 7.79e+01 c.67.1.1 86620 1tuhA 156 7.89e+01 d.17.4.11 107345 1ddgA 374 7.91e+01 1amoA b.43.4.1,c.25.1.4 25671,31559 1pqsA 77 7.94e+01 d.15.2.2 88277 1rwiA 270 8.06e+01 b.68.9.1 97987 1xauA 122 8.08e+01 1ru4A 400 8.10e+01 b.80.1.9 97836 1hlvA 131 8.13e+01 a.4.1.7,a.4.1.7 65854,65855 1kdkA 177 8.15e+01 b.29.1.4 72351 2rhe 114 8.15e+01 8fabA b.1.1.1 20523 1oaqL 120 8.15e+01 b.1.1.1 92708 1abrA 251 8.28e+01 1mrj d.165.1.1 42196 1jj2X 240 8.38e+01 1ffkV c.9.2.1 63109 1txb 73 8.38e+01 1txb g.7.1.1 44455 2czlA 272 8.48e+01 1s72Y 241 8.52e+01 c.9.2.1 105344 1vqoY 241 8.52e+01 1bjmA 216 8.59e+01 8fabA b.1.1.1,b.1.1.2 20524,21460 1mszA 86 8.66e+01 d.68.7.1 79428 1a6vL 110 8.69e+01 1mfa b.1.1.1 20256 1qk4A 233 8.71e+01 1qk3A c.61.1.1 34037 2axcA 264 8.72e+01 1snnA 227 8.75e+01 d.115.1.2 105821 1d2sA 170 8.76e+01 1d2sA b.29.1.4 24221 1t7lA 766 8.81e+01 1befA 181 8.92e+01 1befA b.47.1.3 26419 2aotA 292 8.95e+01