# List of top-scoring protein chains for t2k-100-30-str2-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.soe.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 2jz5A 91 6.86e-13 1u55A 188 5.21e-02 d.278.1.1 107677 2cz8A 69 6.16e-02 2vfxA 206 1.06e+00 1fnoA 417 1.08e+00 d.58.19.1,c.56.5.4 70145,75841 1klqA 197 1.35e+00 d.135.1.1 68689 2cy7A 396 1.58e+00 2bjdA 101 1.98e+00 1vixA 420 2.11e+00 c.56.5.4,d.58.19.1 100777,100778 1gqeA 365 2.26e+00 e.38.1.1 70351 1a6zA 275 2.30e+00 1agdA b.1.1.2,d.19.1.1 20781,38280 1go4A 205 2.43e+00 d.135.1.1 70292 1skoB 130 2.53e+00 d.110.7.1 105677 1qzrA 418 3.15e+00 d.14.1.3,d.122.1.2 96659,96660 2cstA 411 3.25e+00 1ajsA c.67.1.1 34273 2gagA 965 3.34e+00 1pvgA 418 4.00e+00 d.14.1.3,d.122.1.2 95161,95162 2z0dA 357 4.13e+00 2e7vA 121 4.15e+00 1in0A 163 4.24e+00 d.58.49.1,d.58.49.1 83694,83695 3bevA 274 4.71e+00 2obdA 476 4.93e+00 2o09A 189 5.25e+00 1gydB 315 5.63e+00 b.67.2.1 70751 2imjA 166 5.79e+00 1gyhA 318 5.86e+00 b.67.2.1 70757 1kjvA 284 5.90e+00 b.1.1.2,d.19.1.1 77421,77422 1dq3A 454 6.29e+00 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1k2yX 463 6.58e+00 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 2qx2A 344 6.59e+00 1p5dX 463 6.59e+00 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 2qswA 100 7.07e+00 2omdA 154 7.09e+00 1k5nA 276 7.29e+00 b.1.1.2,d.19.1.1 77266,77267 1cg2A 393 7.44e+00 1cg2A c.56.5.4,d.58.19.1 33844,39360 2ftrA 108 7.47e+00 d.58.4.15 134077 2yx1A 336 7.53e+00 3cedA 98 7.57e+00 3cx5B 352 8.49e+00 2dtjA 178 8.57e+00 2olnA 397 9.04e+00 1icxA 155 9.50e+00 d.129.3.1 71191 1vetB 125 9.68e+00 d.110.7.1 108554 2iihA 157 1.00e+01 1tw0A 157 1.01e+01 d.129.3.1 119364 1yb3A 175 1.04e+01 d.296.1.2 122869 2gpyA 233 1.05e+01 2g6yA 217 1.06e+01 1lxdA 100 1.09e+01 1lfdA d.15.1.5 37624 1r62A 160 1.11e+01 d.122.1.3 104816 1wr2A 238 1.11e+01 2bvpA 276 1.11e+01 b.1.1.2,d.19.1.1 129291,129292 1a1mA 278 1.19e+01 1agdA b.1.1.2,d.19.1.1 20753,38266 1pjqA 457 1.22e+01 c.2.1.11,c.90.1.1,e.37.1.1 94766,94767,94768 2ek0A 90 1.23e+01 2dkhA 639 1.23e+01 2yweA 600 1.26e+01 3fruA 269 1.29e+01 1agdA b.1.1.2,d.19.1.1 20657,38150 2b7aA 293 1.33e+01 1pyaB 228 1.40e+01 1pyaB 2uuuA 584 1.44e+01 3b8mA 280 1.49e+01 1xh3A 276 1.50e+01 b.1.1.2,d.19.1.1 115287,115288 1agdA 276 1.54e+01 1agdA b.1.1.2,d.19.1.1 20741,38260 1csjA 531 1.56e+01 1quvA e.8.1.4 43120 2rjzA 147 1.56e+01 1t7vA 278 1.63e+01 b.1.1.2,d.19.1.1 112302,112303 2jyaA 106 1.67e+01 1roaA 122 1.68e+01 d.17.1.2 105024 2yxyA 115 1.70e+01 2uubJ 105 1.78e+01 d.58.15.1 139941 3b49A 211 1.82e+01 1a9eA 277 1.82e+01 1agdA b.1.1.2,d.19.1.1 20757,38268 3b4tA 262 1.83e+01 1w0dA 337 1.85e+01 c.77.1.1 114060 1r9wA 145 1.85e+01 d.89.1.2 97264 1kb9B 352 1.86e+01 d.185.1.1,d.185.1.1 77313,77314 1gx5A 536 1.87e+01 e.8.1.4 70682 1a1oA 276 1.87e+01 1agdA b.1.1.2,d.19.1.1 20751,38265 3bwaA 276 1.92e+01 1rm4A 337 1.98e+01 c.2.1.3,d.81.1.1 105000,105001 1t17A 148 2.00e+01 d.129.3.6 112215 2b5eA 504 2.02e+01 c.47.1.2,c.47.1.2,c.47.1.2,c.47.1.2 127888,127889,127890,127891 1a1nA 276 2.02e+01 1agdA b.1.1.2,d.19.1.1 20755,38267 2haiA 576 2.04e+01 1b24A 188 2.08e+01 1b24A d.95.2.1,d.95.2.1 40573,40574 1ry9A 145 2.15e+01 d.198.1.1 98094 1r0pA 312 2.15e+01 d.144.1.7 96734 1yycA 174 2.20e+01 2abyA 146 2.21e+01 1ezvB 352 2.23e+01 1ezvB d.185.1.1,d.185.1.1 59543,59544 2cc6A 68 2.30e+01 d.230.2.1 130218 1ftrA 296 2.33e+01 1ftrA d.58.33.1,d.58.33.1 39485,39486 1laxA 370 2.43e+01 c.94.1.1 84576 1vs3A 249 2.44e+01 2ffsA 157 2.44e+01 d.129.3.7 133391 1omp 370 2.45e+01 4mbp 1t3lA 337 2.52e+01 b.34.2.1,c.37.1.1 106358,106359 1tz0A 114 2.54e+01 d.58.4.5 107463 2jamA 304 2.63e+01 2yy3A 91 2.65e+01 1u8sA 192 2.68e+01 d.58.18.5,d.58.18.5 107737,107738 2cw9A 194 2.74e+01 d.17.4.13 130920 1sqeA 109 2.75e+01 d.58.4.5 105908 2fjlA 150 2.78e+01 b.55.1.1 133611 1d3uA 181 2.80e+01 1ytbA d.129.1.1,d.129.1.1 41290,41291 1f08A 148 2.82e+01 1f08A d.89.1.2 59564 1kf6A 602 2.90e+01 a.7.3.1,c.3.1.4,d.168.1.1 72394,72395,72396 1zq1C 633 2.94e+01 a.182.1.2,d.74.4.1,d.128.1.5 125493,125494,125495 1lfdA 87 2.94e+01 1lfdA d.15.1.5 37622 1k8kA 418 2.95e+01 c.55.1.1,c.55.1.1 68305,68306 1r3nA 462 3.05e+01 c.56.5.4,d.58.19.1 96945,96946 1zpwX 90 3.10e+01 d.58.58.1 125478 2op5A 117 3.11e+01 2asfA 137 3.14e+01 b.45.1.1 127253 4mbp 370 3.17e+01 4mbp 1mogA 67 3.17e+01 d.230.2.1 85034 1k1gA 131 3.21e+01 d.51.1.1 68015 2ozpA 345 3.21e+01 2rerA 173 3.26e+01 2av1A 275 3.30e+01 b.1.1.2,d.19.1.1 127349,127350 1yx2A 365 3.32e+01 2qyxA 238 3.36e+01 2c61A 469 3.36e+01 2bopA 85 3.37e+01 2bopA d.58.8.1 39217 1m1sA 116 3.38e+01 b.1.11.2 84747 1p1lA 102 3.47e+01 d.58.5.2 87695 1u5rA 348 3.49e+01 d.144.1.7 113050 1w4vA 119 3.50e+01 1c7nA 399 3.50e+01 1d2fA c.67.1.3 34413 1c2pA 576 3.52e+01 1quvA e.8.1.4 43117 2g2kA 170 3.58e+01 1raxA 115 3.60e+01 1lfdA d.15.1.5 37626 2fipA 115 3.60e+01 1efuB 282 3.63e+01 1efuB d.43.1.1,a.5.2.2,d.43.1.1 38677,58975,58976 2eknA 159 3.79e+01 2aehA 369 3.80e+01 a.11.2.1,b.55.1.5,d.15.1.4 126625,126626,126627 1f45B 197 3.85e+01 1f45B a.26.1.1 59642 1hsbA 270 3.88e+01 1agdA b.1.1.2,d.19.1.1 20736,38257 3blcA 330 3.88e+01 2v8hA 474 3.89e+01 2ifsA 169 3.89e+01 1nrkA 328 3.91e+01 b.44.2.1,d.250.1.1 92089,92090 2ohdA 151 3.96e+01 2hyxA 352 4.02e+01 2z1uA 343 4.03e+01 3bs6A 280 4.05e+01 2rb9A 334 4.09e+01 1aisA 182 4.11e+01 1ytbA d.129.1.1,d.129.1.1 41288,41289 2p4pA 86 4.11e+01 2yvsA 219 4.12e+01 2dtcA 126 4.16e+01 1j4wA 174 4.35e+01 d.51.1.1,d.51.1.1 71529,71530 1pzsA 208 4.35e+01 b.1.8.1 104397 2flhA 155 4.36e+01 1pczA 191 4.38e+01 1ytbA d.129.1.1,d.129.1.1 41292,41293 1mi0A 65 4.49e+01 d.15.7.1 79135 2p0pA 126 4.49e+01 2av7A 275 4.56e+01 b.1.1.2,d.19.1.1 127359,127360 1p3dA 475 4.58e+01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1c9bB 180 4.58e+01 1ytbA d.129.1.1,d.129.1.1 41216,41217 1hrhA 136 4.62e+01 1rthA c.55.3.1 33577 1anf 370 4.63e+01 4mbp 1anfA 370 4.63e+01 c.94.1.1 35776 1z57A 339 4.66e+01 1xkzA 255 4.67e+01 e.3.1.1 115426 1z2lA 423 4.67e+01 c.56.5.4,d.58.19.1 124383,124384 1jjhA 86 4.74e+01 2bopA d.58.8.1 63119 1iujA 106 4.76e+01 d.58.4.5 90701 2amhA 207 4.78e+01 c.51.4.2 127019 1i4fA 275 4.79e+01 1agdA b.1.1.2,d.19.1.1 61687,61688 1i82A 189 4.96e+01 1i82A b.1.9.2 61937 1pcaA 95 5.06e+01 d.58.3.1 39063 1sr9A 644 5.07e+01 a.5.7.1,c.1.10.5,d.270.1.1 105960,105961,105962 1i8aA 189 5.09e+01 1i82A b.1.9.2 61951 1h6vA 499 5.09e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 60693,60694,60695 1tr0A 108 5.13e+01 d.58.4.4 107261 1mhxA 65 5.20e+01 d.15.7.1 79134 2hq4A 161 5.33e+01 1zwyA 185 5.40e+01 c.51.4.3 125753 2rfqA 394 5.50e+01 2hbjA 410 5.53e+01 a.60.8.4,c.55.3.5 136311,136312 1zpvA 91 5.53e+01 d.58.18.7 125475 2pbrA 195 5.53e+01 2oap1 511 5.59e+01 2h8eA 120 5.62e+01 2zfzA 79 5.62e+01 2rftA 344 5.64e+01 2b4rO 345 5.76e+01 c.2.1.3,d.81.1.1 127845,127846 3pcgM 238 5.84e+01 3pchM b.3.6.1 22742 2nvnA 122 5.88e+01 d.18.1.3 138633 1jjiA 311 5.90e+01 c.69.1.2 66766 2od4A 101 5.92e+01 1crwG 333 5.92e+01 1dssG c.2.1.3,d.81.1.1 30026,39941 2if1A 126 5.95e+01 d.64.1.1 39547 1vkwA 218 5.97e+01 d.90.1.2 108695 1dssG 333 6.07e+01 1dssG c.2.1.3,d.81.1.1 30022,39937 2dc4A 165 6.17e+01 2q8uA 336 6.18e+01 1vm6A 228 6.22e+01 d.81.1.3,c.2.1.3 108877,118631 1y4iA 398 6.34e+01 c.67.1.3 122619 2ex5A 207 6.36e+01 1dusA 194 6.37e+01 1dusA c.66.1.4 34182 1o51A 114 6.47e+01 d.58.5.4 92480 2cvjA 180 6.49e+01 2ywlA 180 6.51e+01 1j5uA 136 6.52e+01 d.208.1.1 71584 1csn 298 6.53e+01 1csn 1csnA 298 6.53e+01 d.144.1.7 41664 2sak 121 6.63e+01 2sak 2sakA 121 6.63e+01 d.15.5.1 37711 2pa8D 265 6.68e+01 1t23A 93 6.72e+01 d.247.1.1 112216 1ajsA 412 6.72e+01 1ajsA c.67.1.1 34276 2rgqA 144 6.83e+01 2g3bA 208 6.86e+01 a.4.1.9,a.121.1.1 134558,134559 1kgyA 181 6.91e+01 b.18.1.4 72449 1o6gA 710 6.91e+01 b.69.7.1,c.69.1.4 81087,81088 1zyiA 171 6.92e+01 1y7rA 133 6.93e+01 d.108.1.1 122716 1el5A 389 6.94e+01 1b3mA c.3.1.2,d.16.1.3 30369,37937 1q5yA 85 6.94e+01 d.58.18.4 95950 1yjmA 110 6.95e+01 b.26.1.2 123427 2eu9A 355 7.04e+01 2co1B 20 7.06e+01 1a0p 290 7.11e+01 1a0p 1a0pA 290 7.11e+01 a.60.9.1,d.163.1.1 18105,42165 1mh3A 421 7.11e+01 a.4.1.1,c.94.1.1 79112,79113 2axoA 270 7.14e+01 c.47.1.19 127496 1l2mA 118 7.18e+01 d.89.1.4 77657 1dujA 187 7.23e+01 1dujA d.135.1.1 41449 1gadO 330 7.23e+01 1dssG c.2.1.3,d.81.1.1 29950,39865 2g0qA 173 7.39e+01 2z1eA 342 7.40e+01 1mai 131 7.43e+01 1mai 1maiA 131 7.43e+01 b.55.1.1 26951 2al6A 375 7.47e+01 a.11.2.1,b.55.1.5,d.15.1.4 126966,126967,126968 2i39A 137 7.51e+01 1jw3A 140 7.52e+01 d.208.1.1 67373 1avwB 171 7.54e+01 1wba b.42.4.1 25599 2on8A 56 7.84e+01 1irsA 112 7.88e+01 1qqgA b.55.1.2 26991 1fjcA 96 7.98e+01 1fjcA d.58.7.1 39212