# List of top-scoring protein chains for t2k-100-30-bys-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 1vjkA 98 3.56e-04 d.15.3.1 108631 1rwsA 77 4.69e-03 d.15.3.2 97991 1oqqA 106 1.70e-02 d.15.4.1 93422 1put 106 3.18e-02 1ayfA d.15.4.1 37680 1frrA 95 3.49e-02 1awd d.15.4.1 37674 1fmaD 81 4.20e-02 1fmaD d.15.3.1 37643 1fm0D 81 4.48e-02 1fmaD d.15.3.1 37642 1xlqA 106 1.04e-01 1jenA 267 1.63e-01 1jenA 1uwmA 106 1.85e-01 1e9mA 106 1.87e-01 1ayfA d.15.4.1 59397 1jl0A 334 1.99e-01 1jenA d.156.1.1 63155 1ryjA 70 2.82e-01 d.15.3.2 98104 2bb6A 414 3.46e-01 1f0zA 66 3.67e-01 1f0zA d.15.3.2 37644 1qorA 327 5.55e-01 1qorA b.35.1.2,c.2.1.1 24766,29782 2f4pA 147 6.12e-01 1frd 98 9.36e-01 1awd d.15.4.1 37648 1ra6A 461 1.00e+00 e.8.1.4 104879 1k07A 263 1.06e+00 d.157.1.1 77218 1zud2 66 1.33e+00 1i7hA 111 1.41e+00 d.15.4.1 71122 1zpuA 534 1.46e+00 2cu3A 64 1.49e+00 1rdr 461 1.72e+00 1rdr e.8.1.4 43116 1awd 94 1.86e+00 1awd d.15.4.1 37673 1doi 128 2.00e+00 1awd d.15.4.1 37676 1zu0A 529 2.14e+00 1l5pA 93 2.30e+00 d.15.4.1 73598 1r5lA 262 2.31e+00 a.5.3.1,c.13.1.1 97099,97100 1rfkA 98 2.31e+00 2g1lA 104 2.63e+00 1offA 97 3.10e+00 d.15.4.1 86947 1f1uA 323 3.33e+00 d.32.1.3,d.32.1.3 83200,83201 1omzA 293 3.59e+00 c.68.1.15 87093 1qt9A 98 3.90e+00 1awd d.15.4.1 37647 1czpA 98 3.94e+00 1awd d.15.4.1 37645 1e0zA 128 4.14e+00 1awd d.15.4.1 59153 1nw1A 429 4.16e+00 d.144.1.8 86286 1dmhA 311 4.16e+00 1dmhA b.3.6.1 22633 1woqA 267 4.54e+00 c.55.1.10,c.55.1.10 109462,109463 1f1xA 322 4.74e+00 d.32.1.3,d.32.1.3 83208,83209 2bwfA 77 4.90e+00 1pvmA 184 5.54e+00 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1wwkA 307 6.85e+00 2al3A 90 7.11e+00 1l2hA 153 7.21e+00 b.42.1.2 77655 2bpsA 81 7.36e+00 1r3eA 309 7.63e+00 b.122.1.1,d.265.1.2 96907,96908 1s0uA 408 7.89e+00 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 1a70 97 8.02e+00 1awd d.15.4.1 37678 1cxyA 90 8.64e+00 1cyo d.120.1.1 41085 1kqfC 217 8.65e+00 f.21.1.1 72874 2cfeA 162 8.71e+00 1vf7A 369 9.27e+00 f.46.1.1 108557 1f76A 336 9.73e+00 c.1.4.1 76160 1o5oA 221 9.84e+00 c.61.1.1 92509 1h9sA 140 9.99e+00 1b9mA b.40.6.2,b.40.6.2 60843,60844 1gpr 162 1.03e+01 1gpr b.84.3.1 28267 1guaB 81 1.06e+01 1c1yB d.15.1.5 37619 1xdyA 298 1.11e+01 1wruA 379 1.12e+01 2aj2A 208 1.17e+01 2fcr 173 1.21e+01 1rcf c.23.5.1 31151 2azwA 148 1.24e+01 1xc3A 302 1.29e+01 2a4hA 126 1.30e+01 2gaxA 135 1.32e+01 1vr6A 350 1.35e+01 1wgrA 100 1.36e+01 1qtnA 164 1.36e+01 1pauA c.17.1.1 30999 1tqxA 227 1.39e+01 1gz5A 456 1.47e+01 c.87.1.6 76406 1q2wA 308 1.54e+01 b.47.1.4 88355 1uasA 362 1.56e+01 b.71.1.1,c.1.8.1 88388,88389 1l7yA 94 1.77e+01 d.15.1.6 73676 1wstA 417 1.82e+01 1vp4A 425 1.83e+01 1ku0A 388 1.87e+01 c.69.1.18 72994 1vybA 238 1.88e+01 d.151.1.1 108897 2a5kA 307 1.92e+01 1ihfB 94 1.98e+01 1huuA a.55.1.1 17894 1b9mA 265 1.98e+01 1b9mA a.4.5.8,b.40.6.2,b.40.6.2 16118,58938,58939 1siqA 392 1.98e+01 a.29.3.1,e.6.1.1 105585,105586 1kf6B 243 2.10e+01 a.1.2.1,d.15.4.2 72397,72398 1pvc3 238 2.10e+01 1aym3 1uqtA 482 2.11e+01 c.87.1.6 99794 1qmvA 197 2.11e+01 1qq2A c.47.1.10 33066 1sfe 180 2.12e+01 1sfe a.4.2.1,c.55.7.1 16073,33748 1t6aA 126 2.13e+01 d.129.8.1 106555 1euvB 86 2.15e+01 1a5r d.15.1.1 37598 1c1yB 77 2.22e+01 1c1yB d.15.1.5 37618 1cf2O 337 2.22e+01 1b7gO c.2.1.3,d.81.1.1 29994,39909 1owfB 94 2.22e+01 a.55.1.1 87488 2bh8A 101 2.24e+01 2d42A 249 2.27e+01 1d2qA 173 2.33e+01 1d4vB b.22.1.1 23894 1uquA 482 2.33e+01 c.87.1.6 99796 1agjA 242 2.40e+01 1agjA b.47.1.1 25827 1ixmA 192 2.42e+01 1ixmA d.123.1.1 41114 4gr1 478 2.48e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30461,30462,40162 1knmA 130 2.53e+01 b.42.2.1 72781 1m93B 245 2.66e+01 1zvtA 256 2.74e+01 2f96A 224 2.76e+01 3grs 478 2.80e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30441,30442,40152 1ixmB 192 2.81e+01 1ixmA d.123.1.1 41115 1d4vB 163 2.83e+01 1d4vB b.22.1.1 23884 2i1b 153 2.87e+01 2i1b b.42.1.2 25538 2bodX 286 2.88e+01 2gptA 523 2.89e+01 1ciqA 40 2.94e+01 2sniI d.40.1.1 38576 1hdmA 201 2.96e+01 1iakA b.1.1.2,d.19.1.1 21583,38157 1ayfA 105 2.97e+01 1ayfA d.15.4.1 37684 1mpp 361 2.99e+01 2rmpA b.50.1.2 26856 1i1b 153 3.15e+01 2i1b b.42.1.2 25537 2amdA 311 3.15e+01 1q5dA 419 3.16e+01 a.104.1.1 95891 1ykdA 398 3.24e+01 1shkA 173 3.25e+01 1shkA c.37.1.2 31932 2g8lA 299 3.25e+01 2asi 360 3.25e+01 2rmpA b.50.1.2 26824 1dl5A 317 3.32e+01 1dl5A c.66.1.7,d.197.1.1 64720,64721 1fmtB 314 3.40e+01 1fmtA b.46.1.1,c.65.1.1 25759,34175 1p4oA 322 3.45e+01 d.144.1.7 87775 1p9sA 300 3.52e+01 b.47.1.4 87999 1amj 754 3.62e+01 1amj c.8.2.1,c.83.1.1 30725,35401 1ub0A 258 3.62e+01 c.72.1.2 88394 2azeB 106 3.65e+01 1snzA 344 3.78e+01 b.30.5.4 98930 1pl8A 356 3.78e+01 b.35.1.2,c.2.1.1 94878,94879 1yj1A 76 3.81e+01 2bt6A 108 3.83e+01 2shkA 173 3.84e+01 1shkA c.37.1.2 31934 1f4qA 165 3.84e+01 1alvA a.39.1.8 17360 1q2lA 939 3.86e+01 1pg4A 652 3.86e+01 e.23.1.1 88067 1hmvA 560 3.87e+01 1rthA c.55.3.1,e.8.1.2 33587,43046 4tsvA 150 3.89e+01 2tnfA b.22.1.1 23860 1v4aA 440 4.11e+01 a.24.16.4,d.218.1.9 108350,108351 2h1tA 188 4.16e+01 2apoA 357 4.21e+01 1cqa 133 4.23e+01 3nul d.110.1.1 40890 1ktgA 138 4.24e+01 d.113.1.1 72972 2es7A 142 4.27e+01 1k8wA 327 4.27e+01 b.122.1.1,d.265.1.2 83094,90388 1gsmA 210 4.30e+01 b.1.1.4,b.1.1.4 65535,65536 1ktbA 405 4.32e+01 b.71.1.1,c.1.8.1 72960,72961 1o54A 277 4.32e+01 c.66.1.13 92482 2fcfA 103 4.33e+01 1ir3A 306 4.35e+01 1fmk d.144.1.7 41702 1bpyA 335 4.37e+01 1bpyA a.60.6.1,a.60.12.1,d.218.1.2 17980,75819,75820 2d7nA 93 4.40e+01 1k94A 165 4.42e+01 a.39.1.8 68333 1wm3A 72 4.46e+01 2fug1 438 4.55e+01 1eokA 290 4.56e+01 1eokA c.1.8.5 28991 1d02A 202 4.61e+01 1d02A c.52.1.8 33313 1fbaA 361 4.67e+01 1fbaA c.1.10.1 29120 1ubeA 349 4.70e+01 c.37.1.11,d.48.1.1 88412,88413 6acn 754 4.83e+01 1amj c.8.2.1,c.83.1.1 30721,35397 1vioA 243 4.83e+01 d.265.1.3,d.66.1.5 100762,100763 1ubi 76 4.88e+01 1ubi d.15.1.1 37584 1dg6A 191 4.94e+01 1d4vB b.22.1.1 23883 2ohxA 374 4.95e+01 2ohxA b.35.1.2,c.2.1.1 24669,29685 1zn8A 180 4.95e+01 1jb3A 131 4.96e+01 1jc7A b.40.3.2 62833 1jsdA 319 5.02e+01 b.19.1.2 63258 1twfK 120 5.07e+01 2as0A 396 5.12e+01 1egpA 45 5.16e+01 1egpA d.40.1.1 38561 1d3zA 76 5.23e+01 1ubi d.15.1.1 37592 487dH 224 5.25e+01 1ad2 i.1.1.2 45835 1ad2 228 5.29e+01 1ad2 e.24.1.1 43353 2gupA 292 5.30e+01 1cnzA 363 5.33e+01 1cnzA c.77.1.1 35061 1fvrA 327 5.37e+01 d.144.1.7 60047 1iwgA 1053 5.41e+01 d.58.44.1,d.58.44.1,d.58.44.1,d.58.44.1,d.225.1.1,d.225.1.1,f.35.1.1,f.35.1.1 76874,76875,76876,76877,76878,76879,76880,76881 1df9A 191 5.43e+01 1befA b.47.1.3 26420 1vhzA 198 5.44e+01 d.113.1.1 100718 1mqdA 261 5.44e+01 c.94.1.1 85049 1v76A 96 5.45e+01 1cm7A 363 5.47e+01 1cnzA c.77.1.1 35063 2c5lC 117 5.51e+01 1ghhA 81 5.56e+01 1ghhA d.57.1.1 38940 1wjnA 97 5.58e+01 1i50K 120 5.60e+01 d.74.3.2 61765 1t0qC 86 5.62e+01 d.15.12.1 106222 1htrP 43 5.69e+01 1htrP b.50.1.2 26852 1gcqC 70 5.70e+01 1gcpA b.34.2.1 60436 1x3zB 72 5.71e+01 1m5eA 263 5.72e+01 c.94.1.1 78642 1befA 181 5.80e+01 1befA b.47.1.3 26419 1lfdA 87 5.81e+01 1lfdA d.15.1.5 37622 2rmpA 361 5.87e+01 2rmpA b.50.1.2 26825 1pgs 314 5.89e+01 1pgs b.121.1.1,b.121.1.1 23653,23654 1txqA 93 5.90e+01 1m5dA 263 5.92e+01 c.94.1.1 78641 1mqiA 263 6.01e+01 c.94.1.1 91398 2c36A 285 6.06e+01 1gr2A 279 6.07e+01 1gr2A c.94.1.1 35825 1nbfD 76 6.07e+01 d.15.1.1 80390 1ftkA 279 6.08e+01 1gr2A c.94.1.1 35819 2ah5A 210 6.09e+01 2b0vA 153 6.10e+01 1vmiA 355 6.11e+01 1l7aA 318 6.15e+01 c.69.1.25 77772 2sniI 83 6.21e+01 2sniI d.40.1.1 38573 1irsA 112 6.27e+01 1qqgA b.55.1.2 26991 1b9rA 105 6.29e+01 1ayfA d.15.4.1 37683 1hcz 252 6.30e+01 1hcz b.2.6.1,b.84.2.2 22464,28250 2fexA 188 6.31e+01 173l 164 6.37e+01 1l92 d.2.1.3 36728 1p3qQ 54 6.39e+01 a.5.2.4 87748 1tmxA 293 6.44e+01 1o4sA 389 6.49e+01 c.67.1.1 86620 1wkaA 147 6.51e+01 1yfbA 59 6.55e+01 1jzuA 157 6.59e+01 b.60.1.1 84271 1k1zA 78 6.70e+01 b.34.2.1 68026 1aw0 72 6.85e+01 1aw0 d.58.17.1 39342 2a4vA 159 6.88e+01 2u1a 88 6.90e+01 2u1a d.58.7.1 39164 1onrA 316 7.06e+01 1onrA c.1.10.1 29169 1tml 286 7.09e+01 1tml c.6.1.1 30656 1kk1A 410 7.14e+01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1i2oA 316 7.21e+01 1onrA c.1.10.1 61574 1coaI 64 7.25e+01 2sniI d.40.1.1 38574 1kt9A 138 7.25e+01 d.113.1.1 72959 1jc7A 131 7.33e+01 1jc7A b.40.3.2 62873 1qq2A 199 7.33e+01 1qq2A c.47.1.10 33064 1gxuA 91 7.44e+01 d.58.10.1 76378 2h2bA 107 7.51e+01 1tfuA 157 7.52e+01 c.26.1.3 106859 1f0cA 305 7.56e+01 1c8oA e.1.1.1 42676 2hmiA 558 7.58e+01 1rthA c.55.3.1,e.8.1.2 33604,43106 1j0aA 325 7.62e+01 c.79.1.1 83871 1mn3A 54 7.74e+01 a.5.2.4 85024 2fv1A 377 7.76e+01 1vkyA 347 7.80e+01 e.53.1.1 108696 1xe1A 116 7.85e+01 b.43.3.1 109571 1oi2A 366 7.87e+01 c.119.1.2 103802 1xkpA 246 7.91e+01 1g19A 350 8.01e+01 2reb c.37.1.11,d.48.1.1 32284,38770 2fmpA 335 8.04e+01 2fsqA 243 8.06e+01 1pk1B 89 8.15e+01 1ryaA 160 8.17e+01 d.113.1.5 105122 1nh9A 87 8.18e+01 d.68.6.1 91878 1n3jA 119 8.25e+01 b.85.7.2 79963 1vd5A 377 8.25e+01 a.102.1.7 108518 1c8oA 300 8.27e+01 1c8oA e.1.1.1 42677 1otgA 125 8.43e+01 1otgA d.80.1.2 39831 1j3mA 129 8.46e+01 d.129.7.1 103836 1ejbA 168 8.50e+01 1rvv1 c.16.1.1 59417 1pb7A 292 8.52e+01 c.94.1.1 88025 1yzhA 214 8.65e+01 1rx0A 393 8.69e+01 a.29.3.1,e.6.1.1 98007,98008 1e6eB 128 8.72e+01 1ayfA d.15.4.1 59300 1qrvA 73 8.74e+01 1cktA a.21.1.1 16425 1h8eA 510 8.75e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 60738,60739,60740 1zyeA 220 8.81e+01 21bi 153 8.85e+01 2i1b b.42.1.2 25542 2ab0A 205 8.88e+01