# List of top-scoring protein chains for t04-100-40-40-str2+CB_burial_14_7-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 1zoyC 140 1.03e-01 1u7kA 131 3.74e-01 1n00A 321 4.30e-01 a.65.1.1 85241 1fseA 74 4.67e-01 1fseA a.4.6.2 60000 2fj6A 82 8.67e-01 1uyrA 737 9.00e-01 c.14.1.4,c.14.1.4 100188,100189 1exrA 148 9.17e-01 1cll a.39.1.5 17299 2h88C 140 9.54e-01 2a2pA 129 9.58e-01 1zg2A 107 1.22e+00 1z5bA 469 1.27e+00 1xppA 115 1.42e+00 1rqlA 267 1.57e+00 c.108.1.3 97750 1a17 166 1.71e+00 1a17 a.118.8.1 19206 1nrjA 158 1.85e+00 d.110.4.4 86124 1v64A 108 1.86e+00 a.21.1.1 108392 1swvA 267 1.86e+00 1wgxA 73 1.97e+00 2fbwC 141 2.09e+00 1zfpE 98 2.11e+00 1griA d.93.1.1 40465 1xteA 154 2.26e+00 1fezA 256 2.40e+00 1fezA c.108.1.3 43343 1xiuA 230 2.42e+00 2d7vA 162 2.58e+00 1yirA 408 2.60e+00 1pzlA 237 2.78e+00 a.123.1.1 104393 1tn4 159 2.99e+00 1ncx a.39.1.5 17248 1wxcB 134 3.12e+00 1sx7A 164 3.13e+00 1swyA 164 3.20e+00 1p36A 164 3.23e+00 d.2.1.3 93978 1uujA 88 3.27e+00 a.221.1.1 108046 2bpsA 81 3.35e+00 1yvhA 329 3.77e+00 2a3qA 170 3.90e+00 1lkkA 105 4.09e+00 1lckA d.93.1.1 40412 1ywmA 200 4.17e+00 1lvfA 110 4.27e+00 a.47.2.1 74280 1jl5A 454 4.34e+00 c.10.2.6 66830 1lw9A 164 4.39e+00 d.2.1.3 84727 1xtnA 120 4.42e+00 1td6A 306 4.79e+00 1jyoE 105 4.81e+00 d.184.1.2 67487 1kq6A 141 5.48e+00 d.189.1.1 91020 2gupA 292 5.73e+00 1w33A 181 5.79e+00 1q48A 134 5.83e+00 d.224.1.2 95783 1gs9A 165 5.86e+00 a.24.1.1 83313 1nfvA 179 5.99e+00 a.25.1.1 85642 1x9zA 188 6.08e+00 1yfuA 174 6.23e+00 1xdfA 157 6.54e+00 1xc3A 302 6.67e+00 1ywfA 296 6.87e+00 1r1qA 100 6.91e+00 d.93.1.1 104763 1h2kA 349 7.28e+00 b.82.2.6 76572 1x7yA 400 7.38e+00 2c5rA 67 7.41e+00 1olsA 400 7.41e+00 c.36.1.11 93331 2bfdA 400 7.67e+00 1xa3A 437 7.71e+00 1zo0A 126 7.89e+00 1ebmA 317 7.95e+00 1ebmA a.96.1.3,d.129.1.2 18751,41300 2f3yA 148 7.97e+00 2g0uA 92 7.99e+00 1k8tA 510 8.15e+00 e.41.1.1 68316 1k28A 584 8.21e+00 b.40.8.1,b.108.1.2,d.2.1.3 68049,68050,68051 2ahqA 76 8.22e+00 2g7uA 257 8.28e+00 1tkeA 224 8.32e+00 2cu1A 103 8.40e+00 1yz8P 68 8.47e+00 1whxA 111 8.47e+00 1ywlA 96 8.51e+00 1sjiA 350 9.32e+00 1ddf 127 9.36e+00 1ddf a.77.1.2 18423 1wmhA 89 9.39e+00 1lre 81 9.62e+00 1lre a.13.1.1 16376 1zd9A 188 9.64e+00 1m9xC 146 1.01e+01 a.73.1.1 84907 2f9dA 125 1.03e+01 1go4A 205 1.07e+01 d.135.1.1 70292 1ov2A 99 1.08e+01 a.13.1.1 93580 1b72B 87 1.08e+01 1akhA a.4.1.1 16001 1jyrA 96 1.11e+01 d.93.1.1 71969 1dat 174 1.12e+01 2fha a.25.1.1 16677 1uw0A 117 1.15e+01 g.39.1.12 108063 1w15A 153 1.17e+01 b.7.1.2 109041 1v1rA 400 1.20e+01 c.36.1.11 108272 1a8y 367 1.21e+01 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 1v2zA 111 1.23e+01 a.186.1.1 108300 1s62A 106 1.24e+01 1ywxA 102 1.24e+01 2fjlA 150 1.34e+01 1m5yA 408 1.36e+01 a.167.1.1,d.26.1.1,d.26.1.1 78664,78665,78666 2fa8A 105 1.36e+01 1lci 550 1.40e+01 1lci e.23.1.1 43349 1g4yR 148 1.44e+01 1cll a.39.1.5 60252 1xk7A 408 1.44e+01 1xfuA 747 1.45e+01 1xkpB 124 1.46e+01 1qgtA 149 1.48e+01 1qgtA a.62.1.1 18135 1uxtA 501 1.48e+01 c.82.1.1 108125 1yruB 74 1.50e+01 1m3qA 317 1.56e+01 a.96.1.3,d.129.1.2 91184,91185 1r5eA 115 1.58e+01 1ztpA 251 1.65e+01 1w0bA 102 1.71e+01 a.7.11.1 108985 1top 162 1.72e+01 1ncx a.39.1.5 17223 1hynP 379 1.76e+01 1hynP d.112.1.2 61408 1j5yA 187 1.76e+01 a.4.5.1,d.94.2.1 71592,71593 1auiA 521 1.79e+01 1auiA d.159.1.3 42085 1ggzA 148 1.80e+01 a.39.1.5 70176 2db9A 149 1.80e+01 1g73C 121 1.82e+01 1g3fA g.52.1.1 45375 2ajrA 331 1.82e+01 1gpuA 680 1.85e+01 c.36.1.10,c.36.1.6,c.48.1.1 65454,65455,65456 1em9A 154 1.87e+01 1d1dA a.73.1.1 18333 2ffsA 157 1.89e+01 1v4pA 157 1.92e+01 1k1fA 72 1.95e+01 a.147.1.1 68007 1jr7A 311 1.97e+01 b.82.2.3 63255 1gg3A 279 1.98e+01 1ef1A a.11.2.1,b.55.1.5,d.15.1.4 16372,27007,37615 1iapA 211 1.99e+01 a.91.1.1 62119 2gpiA 91 2.01e+01 1yx1A 264 2.04e+01 1qvbA 481 2.07e+01 1qvbA c.1.8.4 28983 1fcdA 401 2.09e+01 1fcdA c.3.1.5,c.3.1.5,d.87.1.1 30593,30594,40218 1jkvA 266 2.12e+01 a.25.1.3 71719 1nu0A 138 2.13e+01 c.55.3.8 92165 1trkA 680 2.15e+01 1trkA c.36.1.10,c.36.1.6,c.48.1.1 31803,31804,33090 1rdfA 267 2.16e+01 c.108.1.3 104884 2gp5A 349 2.19e+01 1o9iA 266 2.19e+01 a.25.1.3 92671 1qf6A 642 2.21e+01 1qf6A c.51.1.1,d.15.10.1,d.67.1.1,d.104.1.1 33210,39551,39562,40759 1wwuA 99 2.21e+01 1wf9A 107 2.29e+01 1a41 234 2.30e+01 1a41 d.163.1.2 42174 2cblA 305 2.36e+01 2cblA a.39.1.7,a.48.1.1,d.93.1.1 17380,17774,40528 1mn8A 100 2.36e+01 a.61.1.6 79318 1z21A 112 2.37e+01 2rmcA 182 2.40e+01 2cpl b.62.1.1 27491 1g9zA 152 2.47e+01 1bp7A d.95.2.1 60408 1z8uA 102 2.48e+01 2ae0X 345 2.51e+01 1pea 385 2.51e+01 1pea c.93.1.1 35662 2a10A 125 2.53e+01 1f3mA 80 2.53e+01 1f3mA j.66.1.1 46358 3nul 130 2.57e+01 3nul d.110.1.1 40891 1fzqA 181 2.61e+01 1hurA c.37.1.8 32060 1ayaA 101 2.66e+01 1qadA d.93.1.1 40460 1t3uA 104 2.67e+01 d.244.1.1 99120 1vpbA 451 2.68e+01 2bnkA 67 2.69e+01 1kao 167 2.70e+01 1ctqA c.37.1.8 32014 1mu5A 471 2.73e+01 a.156.1.3,d.14.1.3,d.122.1.2 79472,79473,79474 1fjgM 126 2.74e+01 1fjfM a.156.1.1 16293 1d4tA 104 2.82e+01 1d4tA d.93.1.1 40537 1t17A 148 2.85e+01 1zyeA 220 2.89e+01 1t9iA 163 2.91e+01 1g4yB 101 2.92e+01 1g4yB f.15.1.1 60251 1wdcC 156 2.95e+01 1wdcC a.39.1.5 17317 1w2wA 211 3.04e+01 c.124.1.5 109130 1k3eA 156 3.04e+01 d.198.1.1 68103 1v98A 140 3.05e+01 1yhlA 362 3.07e+01 1ip9A 85 3.07e+01 1ip9A d.15.2.2 62638 1gwiA 411 3.09e+01 a.104.1.1 76364 2ciaA 102 3.13e+01 1fu1A 203 3.14e+01 1fu1B b.59.1.1,h.1.11.1 27076,45630 1z2mA 155 3.18e+01 2aa4A 289 3.21e+01 1w9cA 321 3.23e+01 2a61A 145 3.24e+01 1kz7A 353 3.34e+01 a.87.1.1,b.55.1.1 73333,73334 119l 164 3.34e+01 1l92 d.2.1.3 36622 1szoA 257 3.36e+01 c.14.1.3 106164 2gaeA 346 3.37e+01 2et1A 201 3.43e+01 1s5jA 847 3.43e+01 1rktA 205 3.46e+01 a.4.1.9,a.121.1.1 97623,97624 1wi0A 113 3.48e+01 1vd2A 89 3.50e+01 d.15.2.2 108517 1rloA 271 3.50e+01 1yg2A 179 3.51e+01 1qm9A 198 3.54e+01 1qm9A d.58.7.1,d.58.7.1 39207,39208 2hddA 61 3.58e+01 2hddA a.4.1.1 15971 1zsoA 164 3.63e+01 2glzA 153 3.68e+01 1vkjA 285 3.73e+01 c.37.1.5 108666 1s9pA 227 3.75e+01 a.123.1.1 105384 1w1hA 151 3.76e+01 1josA 128 3.76e+01 d.52.7.1 84191 1wqgA 185 3.80e+01 1q15A 503 3.81e+01 c.26.2.1,d.153.1.1 95538,95539 1y6xA 93 3.88e+01 1fjgP 88 3.89e+01 1emwA d.27.1.1 38444 1tw0A 157 3.92e+01 1q02A 52 3.92e+01 a.5.2.1 95490 1eyzA 392 3.97e+01 1ez1A b.84.2.1,c.30.1.1,d.142.1.2 28246,31653,41498 1amuA 563 3.98e+01 1amuA e.23.1.1 43351 2afdA 88 3.99e+01 1fa0A 537 4.01e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39335,75837,75838 1jf3A 147 4.03e+01 a.1.1.2 71642 1uj8A 77 4.04e+01 1r8sA 164 4.07e+01 c.37.1.8 97247 2fi9A 128 4.07e+01 1u69A 163 4.11e+01 d.32.1.7 107699 1x74A 360 4.11e+01 1xxlA 239 4.13e+01 2b7kA 200 4.19e+01 1hs7A 97 4.20e+01 1hs7A a.47.2.1 61236 1kr4A 125 4.21e+01 d.58.5.2 72889 1mdbA 539 4.22e+01 e.23.1.1 79008 1j1vA 94 4.23e+01 a.4.12.2 83981 1ub1A 133 4.23e+01 d.10.1.3 99140 1xttA 216 4.26e+01 1fi2A 201 4.29e+01 1fi2A b.82.1.2 59845 1k99A 99 4.35e+01 a.21.1.1 68341 1guxA 218 4.38e+01 1guxA a.74.1.3 18388 1b68A 191 4.38e+01 1nfn a.24.1.1 59076 1u9aA 160 4.39e+01 1u9aA d.20.1.1 38333 1rfmA 344 4.41e+01 c.122.1.1 97385 1wad 112 4.47e+01 3cyr a.138.1.1 19658 1eo1A 124 4.51e+01 1eo1A c.55.5.1 33739 1a8o 70 4.52e+01 1a8o a.28.3.1 16953 1xawA 140 4.56e+01 1g7dA 106 4.65e+01 1g7dA a.71.1.1 18318 2ci9A 102 4.66e+01 1q52A 314 4.77e+01 c.14.1.3 95846 1qj4A 257 4.78e+01 1qj4A c.69.1.20 34796 2aegA 268 4.80e+01 1pysA 350 4.81e+01 1pysA d.104.1.1 40775 1xn9A 101 4.84e+01 1s96A 219 4.89e+01 c.37.1.1 98740 1jd1A 129 4.92e+01 1qu9A d.79.1.1 62890 1srqA 341 4.96e+01 e.55.1.1 105967 1ahxA 396 5.00e+01 1ajsA c.67.1.1 34293 1qx2A 76 5.01e+01 a.39.1.1 104622 1n3gA 113 5.06e+01 d.204.1.1 79962 2f4mA 295 5.09e+01 1z6oM 191 5.11e+01 2abqA 306 5.15e+01 1e2fA 215 5.21e+01 3tmkA c.37.1.1 59164 1oapA 109 5.23e+01 d.79.7.1 92706 1mvwC 147 5.23e+01 i.15.1.1 79525 1tz0A 114 5.23e+01 d.58.4.5 107463 1ukxA 137 5.24e+01 d.20.1.3 107919 1xn5A 146 5.26e+01 1yz4A 160 5.34e+01 1ez0A 510 5.47e+01 1eyyA c.82.1.1 35385 1y8tA 324 5.51e+01 1yasA 257 5.52e+01 1qj4A c.69.1.20 34801 2d1uA 104 5.54e+01 1jggA 60 5.55e+01 2hddA a.4.1.1 62950 2bwfA 77 5.59e+01 1j2mA 99 5.65e+01 a.165.1.1 84018 1zbsA 291 5.68e+01 1iznA 286 5.68e+01 e.43.1.1 83847 1omiA 248 5.75e+01 b.82.3.3,a.4.5.4 87079,87080 1yqbA 100 5.75e+01 1u5dA 108 5.78e+01 1i50J 70 5.83e+01 a.4.11.1 61764 2cu6A 103 5.85e+01 1wwhA 119 5.85e+01 1uwdA 103 5.86e+01 1ovnA 248 5.89e+01 a.71.1.1,c.47.1.7 93602,93603 2bycA 137 5.91e+01 2hbg 147 5.95e+01 2hbg a.1.1.2 15014 1hlgA 371 5.98e+01 1hlgA c.69.1.6 34656 1iseA 185 6.01e+01 d.67.3.1 90691 1woqA 267 6.02e+01 c.55.1.10,c.55.1.10 109462,109463 1o5oA 221 6.04e+01 c.61.1.1 92509 1shbA 104 6.04e+01 1fmk d.93.1.1 40425 1s4kA 120 6.05e+01 a.35.1.6 105254 2an9A 207 6.06e+01 1uzeA 589 6.07e+01 d.92.1.5 108174 1t4nA 94 6.14e+01 d.50.1.1 106424 1pufB 73 6.14e+01 a.4.1.1 95132 1nkpB 83 6.16e+01 a.38.1.1 80574 1t5hX 504 6.17e+01 e.23.1.1 106449 1fcyA 236 6.22e+01 2lbd a.123.1.1 19282 1v7oA 165 6.22e+01 d.67.1.2 100480 1o8uA 257 6.22e+01 c.14.1.3 81194 1q2hA 69 6.23e+01 a.34.4.1 104498 1fjlA 81 6.28e+01 2hddA a.4.1.1 16017 1pzxA 289 6.30e+01 c.119.1.1 95484 1y0vH 146 6.42e+01 1o86A 589 6.43e+01 d.92.1.5 81177 1ii7A 333 6.45e+01 1ii7A d.159.1.4 62415 2f4qA 346 6.46e+01 1sfkA 76 6.48e+01 a.190.1.1 105488 1p4kA 295 6.51e+01 d.153.1.5 87772 2fggA 101 6.52e+01 1nstA 325 6.53e+01 1nstA c.37.1.5 31951 1nekA 588 6.54e+01 a.7.3.1,c.3.1.4,d.168.1.1 80426,80427,80428 1mijA 152 6.54e+01 a.4.1.1 79150 1vlpA 441 6.55e+01 d.41.2.2,d.41.2.3 108840,108841 1sfcD 87 6.59e+01 1sfcD h.1.15.1 45646 2avyM 117 6.68e+01 1t6cA 315 6.70e+01 c.55.1.8,c.55.1.8 106558,106559 1wpgA 994 6.73e+01 1shdA 107 6.76e+01 1fmk d.93.1.1 40440 1wvcA 259 6.78e+01 1euhA 475 6.83e+01 1euhA c.82.1.1 35369 1j5sA 463 6.87e+01 c.1.9.8 71580 2gf4A 100 6.89e+01 1l3pA 102 6.96e+01 a.24.17.1 84520 1ki1B 352 6.97e+01 a.87.1.1,b.55.1.1 72497,72498 2lhb 149 6.98e+01 2fal a.1.1.2 15597 1twuA 139 6.98e+01 d.32.1.8 107413 1auiB 169 7.00e+01 1auiB a.39.1.5 17325 1upqA 123 7.04e+01 2b20A 403 7.07e+01 1wm3A 72 7.10e+01 2awdA 323 7.16e+01 1qnaA 200 7.20e+01 1ytbA d.129.1.1,d.129.1.1 41226,41227 1tu3F 79 7.26e+01 1x84A 189 7.26e+01 1iirA 415 7.28e+01 1iirA c.87.1.5 62453 1o5xA 248 7.35e+01 c.1.1.1 92528 1ykhA 108 7.35e+01 1uqvA 85 7.35e+01 a.60.1.2 99798 2fu2A 102 7.43e+01 1v6tA 255 7.45e+01 2aynA 404 7.46e+01 2grrA 161 7.49e+01 1q06A 135 7.51e+01 a.6.1.3 95493 1rlmB 271 7.52e+01 1z6oA 212 7.53e+01 1vzsA 76 7.53e+01 f.45.1.1 108972 1y71A 130 7.54e+01 2bl5A 140 7.54e+01 1s1qA 145 7.55e+01 d.20.1.2 98351 2h1nA 567 7.55e+01 1xfxO 149 7.57e+01 1xbsA 149 7.58e+01 2b4jC 98 7.65e+01 1t8tA 271 7.69e+01 c.37.1.5 106685 1wpaA 114 7.72e+01 2aobA 99 7.74e+01 1xqaA 113 7.80e+01 1sjyA 159 7.80e+01 d.113.1.1 98900 1otvA 259 7.84e+01 a.132.1.4 93526 1m15A 357 7.86e+01 a.83.1.1,d.128.1.2 78368,78369 1vc1A 110 7.91e+01 c.13.2.1 108493 1s28A 132 7.92e+01 d.198.1.1 105223 1mvcA 240 7.94e+01 a.123.1.1 79499 1x3eA 165 7.95e+01 2bkfA 87 7.98e+01 1r26A 125 8.12e+01 c.47.1.1 96847 2f7fA 494 8.15e+01 1v9kA 228 8.17e+01 d.265.1.3 108449 2g7jA 124 8.17e+01 1f2rI 100 8.21e+01 1c9fA d.15.2.1 37641 2fqpA 97 8.23e+01 1h97A 147 8.24e+01 1h97A a.1.1.2 60812 1bg0 356 8.29e+01 1qh4A a.83.1.1,d.128.1.2 18476,41211 2fsrA 195 8.41e+01 2cxcA 144 8.44e+01 1tv8A 340 8.45e+01 c.1.28.3 107352 1ig5A 75 8.48e+01 4icb a.39.1.1 62363 1rlmA 271 8.48e+01 1dozA 309 8.54e+01 1ak1 c.92.1.1 35592 1r45A 204 8.55e+01 1kxoA 184 8.58e+01 b.60.1.1 84475 1r6fA 310 8.58e+01 e.46.1.1 97149 1z9eA 127 8.61e+01 1vhxA 150 8.61e+01 c.55.3.8 100712 2bl0B 145 8.65e+01 1wzvA 155 8.65e+01 1q1vA 70 8.69e+01 a.159.4.1 104479 1fxrA 64 8.70e+01 1fxd d.58.1.4 38993 2trxA 108 8.71e+01 1thx c.47.1.1 32719 2fh1A 344 8.80e+01 1qwiA 143 8.91e+01 d.227.1.1 96474 1bf2 750 8.98e+01 1bf2 b.1.18.2,b.71.1.1,c.1.8.1 21860,27787,28774