# List of top-scoring protein chains for t2k-100-30-alpha-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 1dnlA 199 3.86e-41 1ci0A b.45.1.1 25753 1g79A 218 4.18e-41 1ci0A b.45.1.1 25752 1nrgA 261 4.96e-35 b.45.1.1 80694 1t9mA 214 6.54e-32 1ty9A 222 2.50e-29 1ci0A 228 1.74e-28 1ci0A b.45.1.1 25750 1rfeA 162 4.16e-17 2fhqA 141 2.74e-16 2fg9A 178 7.62e-13 1vl7A 157 1.62e-11 b.45.1.1 108732 2asfA 137 1.18e-10 2aq6A 147 5.99e-10 1w9aA 147 6.00e-09 1xxoA 147 1.21e-08 2furA 209 1.52e-06 1xhnA 184 2.83e-06 2arzA 247 5.56e-06 1w3oA 216 2.31e-04 1ejeA 192 7.28e-04 1ejeA b.45.1.2 25757 1axj 122 8.09e-04 1axj b.45.1.1 25749 1flmA 122 1.78e-03 1axj b.45.1.1 25747 1m1hA 248 9.77e-03 b.114.1.1,d.58.42.1 78415,78416 1nar 290 1.01e-02 1nar c.1.8.5 28988 1r2zA 274 2.17e-02 a.156.1.2,b.113.1.1,g.39.1.8 96892,96893,96894 1l1zA 274 2.70e-02 a.156.1.2,b.113.1.1,g.39.1.8 75911,75912,75913 1ryp2 233 2.89e-02 1ryp2 2bgzA 299 6.72e-02 1wlgA 299 6.72e-02 1a7j 290 1.29e-01 1a7j c.37.1.6 31952 1y1pA 342 1.90e-01 1ujmA 342 2.19e-01 2f6kA 307 2.38e-01 1jdqA 98 2.47e-01 d.68.3.3 66559 1ye8A 178 2.66e-01 2a6sA 84 3.07e-01 1p9bA 442 4.67e-01 c.37.1.10 94385 1k68A 140 4.75e-01 c.23.1.1 90943 1g0u1 266 5.71e-01 1qp2A 70 6.56e-01 1pse b.34.4.2 24596 2evwX 166 7.94e-01 2f9dA 125 8.81e-01 1tr8A 102 9.16e-01 1yzyA 413 1.09e+00 1zt3A 80 1.12e+00 1aye 401 1.13e+00 1aye c.56.5.1,d.58.3.1 33824,39065 1vc1A 110 1.19e+00 c.13.2.1 108493 1vi7A 217 1.39e+00 d.14.1.11,d.58.11.2 100740,100741 2bgiA 272 1.42e+00 2ag5A 246 1.45e+00 1gm6A 175 1.51e+00 b.60.1.1 70272 1ollA 188 1.65e+00 b.1.1.4,b.1.1.4 93313,93314 1qyaA 307 1.74e+00 d.21.1.2,d.21.1.2 104653,104654 2f15A 96 1.84e+00 1btl 263 1.89e+00 1btl e.3.1.1 42691 1fqgA 263 1.89e+00 1btl e.3.1.1 42699 2eifA 136 1.97e+00 1bkb b.34.5.2,b.40.4.5 24607,25339 1sdjA 310 2.03e+00 d.21.1.2,d.21.1.2 98807,98808 1t00A 112 2.14e+00 1ermA 263 2.23e+00 1btl e.3.1.1 42690 1zkpA 268 2.24e+00 1wocA 103 2.41e+00 1pyaB 228 2.50e+00 1pyaB 1euhA 475 2.85e+00 1euhA c.82.1.1 35369 1gnwA 211 2.88e+00 1gnwA a.45.1.1,c.47.1.5 17727,33021 1hxn 219 3.06e+00 1hxn b.66.1.1 27529 1ygtA 111 3.54e+00 1prr 173 3.56e+00 1prs b.11.1.1,b.11.1.1 23623,23624 1qi6A 475 3.60e+00 1euhA c.82.1.1 35373 1oz9A 150 3.60e+00 d.92.1.15 93808 1d2fA 390 3.73e+00 1d2fA c.67.1.3 34411 1rm6A 769 3.76e+00 2c07A 285 4.01e+00 1npsA 88 4.18e+00 1prs b.11.1.1 23622 1m40A 263 4.23e+00 e.3.1.1 74437 1wj9A 211 4.28e+00 1b8aA 438 4.35e+00 1b8aA b.40.4.1,d.104.1.1 25244,40765 1mkmA 249 4.38e+00 a.4.5.33,d.110.2.2 79242,79243 2f2tA 161 4.45e+00 2czrA 226 4.60e+00 1ibvB 229 4.73e+00 1eu3A 210 4.83e+00 1an8 b.40.2.2,d.15.6.1 25206,37795 1d02A 202 4.96e+00 1d02A c.52.1.8 33313 1ha1 184 5.06e+00 1ha1 d.58.7.1,d.58.7.1 39147,39148 2abqA 306 5.07e+00 2c60A 111 5.11e+00 1h7zA 194 5.12e+00 1qhvA b.21.1.1 60733 1wcdJ 441 5.22e+00 1pjjA 271 5.34e+00 a.156.1.2,b.113.1.1,g.39.1.8 104164,104165,104166 1cauB 184 5.44e+00 1caxB b.82.1.2 28103 1ut7A 171 5.49e+00 b.143.1.1 99906 1ctqA 166 5.57e+00 1ctqA c.37.1.8 31965 1b97A 244 5.65e+00 1rvaA c.52.1.2 33252 1f0iA 504 5.76e+00 1f0iA d.136.1.2,d.136.1.2 59566,59567 1eonA 245 5.83e+00 1rvaA c.52.1.2 33238 1gmlA 178 5.96e+00 c.8.5.2 70273 1r0vA 305 6.03e+00 c.52.2.1,c.52.2.1,d.75.1.1 96742,96743,96744 2u2fA 85 6.03e+00 2u2fA d.58.7.1 39167 1b04A 318 6.44e+00 1b04A d.142.2.2 41579 1pytA 94 6.45e+00 1pytA d.58.3.1 39064 1d2iA 223 6.45e+00 1d2iA c.52.1.5 33297 1sx5A 244 6.46e+00 c.52.1.2 99023 1dfmA 223 6.47e+00 1d2iA c.52.1.5 33295 1rvaA 244 6.49e+00 1rvaA c.52.1.2 33240 1agp 166 6.49e+00 1ctqA c.37.1.8 31985 1wnhA 225 6.59e+00 1b94A 244 6.61e+00 1rvaA c.52.1.2 33250 2a0kA 161 6.68e+00 1q3iA 214 6.89e+00 d.220.1.1 104524 1td5A 202 6.94e+00 d.110.2.2 106767 2ghrA 302 6.95e+00 1tdzA 272 7.13e+00 a.156.1.2,b.113.1.1,g.39.1.8 106787,106788,106789 1nnjA 271 7.19e+00 a.156.1.2,b.113.1.1,g.39.1.8 80669,80670,80671 2axoA 270 7.38e+00 1b6tA 159 7.40e+00 1b6tA c.26.1.3 31600 1ywyA 74 7.43e+00 1ibcA 194 7.66e+00 1pauA c.17.1.1 30997 1l3kA 196 7.66e+00 d.58.7.1,d.58.7.1 73539,73540 1j58A 385 7.73e+00 b.82.1.2 71531 1e5pA 151 8.00e+00 1bj7 b.60.1.1 59272 2ddrA 306 8.03e+00 1kb0A 677 8.06e+00 a.3.1.6,b.70.1.1 68378,68379 1v1qA 134 8.27e+00 2f62A 161 8.36e+00 1h3fA 432 8.43e+00 c.26.1.1,d.66.1.4 76631,76632 1sbyA 254 8.61e+00 2bh8A 101 8.66e+00 1vpkA 378 8.72e+00 1v0wA 506 8.85e+00 d.136.1.2,d.136.1.2 108220,108221 1b96A 244 9.06e+00 1rvaA c.52.1.2 33268 1pauA 147 9.13e+00 1pauA c.17.1.1 30994 1j5kA 89 9.37e+00 d.51.1.1 71565 1id0A 152 9.42e+00 d.122.1.3 66111 1bssA 244 9.85e+00 1rvaA c.52.1.2 33256 2c3nA 247 1.02e+01 1nmeA 146 1.02e+01 c.17.1.1 85874 2bvfA 459 1.02e+01 1b16A 254 1.02e+01 1b16A c.2.1.2 29875 1h6fA 193 1.03e+01 b.2.5.4 70901 2azpA 318 1.03e+01 2bwrA 401 1.03e+01 1y4tA 322 1.04e+01 1v6fA 151 1.04e+01 d.109.1.2 108395 1pvtA 238 1.05e+01 c.74.1.1 95189 1b7yA 350 1.08e+01 1pysA d.104.1.1 40776 1xtmA 175 1.09e+01 1qjcA 158 1.12e+01 1b6tA c.26.1.3 63328 1z4xA 532 1.12e+01 1yixA 265 1.12e+01 1a4uA 254 1.14e+01 1b16A c.2.1.2 29878 1prs 173 1.18e+01 1prs b.11.1.1,b.11.1.1 23625,23626 1aba 87 1.19e+01 1aba c.47.1.1 32760 1gr0A 367 1.21e+01 c.2.1.3,d.81.1.3 70379,70380 1bc8C 93 1.21e+01 1awcA a.4.5.21 16168 1vj1A 363 1.24e+01 b.35.1.2,c.2.1.1 100794,100795 1i3cA 149 1.26e+01 c.23.1.1 71112 1e7rA 321 1.27e+01 1bsvA c.2.1.2 29808 1aazA 87 1.28e+01 1aba c.47.1.1 32761 1zatA 250 1.28e+01 1cp3A 277 1.31e+01 1pauA c.17.1.1 30992 1ta8A 332 1.33e+01 1wq3A 322 1.34e+01 1z4vA 532 1.34e+01 1wi6A 88 1.36e+01 1fmcA 255 1.37e+01 1cydA c.2.1.2 29856 2ahuA 531 1.38e+01 1suuA 312 1.38e+01 b.68.10.1 99006 1ukgA 252 1.45e+01 b.29.1.1 99489 1pse 69 1.49e+01 1pse b.34.4.2 24595 1jyoE 105 1.52e+01 d.184.1.2 67487 1v5xA 203 1.57e+01 c.1.2.4 100377 2bitX 165 1.57e+01 1e6uA 321 1.57e+01 1bsvA c.2.1.2 29805 1iweA 457 1.57e+01 c.37.1.10 71486 1iz6A 138 1.59e+01 b.34.5.2,b.40.4.5 76976,76977 2cfxA 144 1.59e+01 1txyA 104 1.60e+01 1pe1A 267 1.64e+01 c.1.10.4 94591 1fwsA 267 1.64e+01 1d9eA c.1.10.4 60063 1b34B 118 1.64e+01 1b34B b.38.1.1 24797 1zzkA 82 1.65e+01 1h4rA 314 1.67e+01 a.11.2.1,b.55.1.5,d.15.1.4 65616,65617,65618 1sacA 204 1.68e+01 1sacA b.29.1.5 24237 1cl1A 395 1.69e+01 1cl2A c.67.1.3 34395 1i35A 95 1.69e+01 d.15.1.5 66017 2g09A 297 1.70e+01 1d2dA 59 1.73e+01 1r1bA a.16.1.3 16397 1rz3A 201 1.73e+01 c.37.1.6 98132 1qrrA 394 1.74e+01 1qrrA c.2.1.2 29824 1n9lA 109 1.78e+01 d.110.3.6 85468 3hsf 92 1.79e+01 2hts a.4.5.22 16182 1c8uA 285 1.80e+01 1c8uA d.38.1.3,d.38.1.3 38547,38548 1cl2A 395 1.82e+01 1cl2A c.67.1.3 34397 1fxpA 267 1.83e+01 1d9eA c.1.10.4 60106 5p21 166 1.83e+01 1ctqA c.37.1.8 31966 1ualA 274 1.86e+01 c.116.1.4 88383 1h8mA 140 1.87e+01 1h8mA d.110.4.1 60782 1jq4A 98 1.89e+01 d.15.4.2 67083 1ywxA 102 1.91e+01 1jcxA 267 1.92e+01 c.1.10.4 66510 1r1bA 59 1.93e+01 1r1bA a.16.1.3 16396 1fxqA 267 1.96e+01 1d9eA c.1.10.4 60108 1amuA 563 1.98e+01 1amuA e.23.1.1 43351 1zx5A 300 1.98e+01 1lroA 267 1.98e+01 c.1.10.4 78161 1al3 324 1.99e+01 1al3 c.94.1.1 35835 1j57A 143 2.00e+01 d.221.1.1 77079 1bax 94 2.01e+01 1bax a.61.1.3 18133 1zhaA 267 2.01e+01 1qwdA 177 2.02e+01 b.60.1.1 96471 1t8hA 277 2.03e+01 d.194.1.2 106664 1caxB 184 2.03e+01 1caxB b.82.1.2 28105 1sxvA 172 2.12e+01 1jysA 242 2.12e+01 c.56.2.1 77216 1t8xA 267 2.12e+01 2carA 196 2.13e+01 1uf2C 421 2.14e+01 a.115.1.3,b.19.1.1 99291,99292 1jlwA 219 2.14e+01 a.45.1.1,c.47.1.5 71741,71742 1s2wA 295 2.15e+01 c.1.12.7 98407 2fcjA 119 2.15e+01 1y42X 392 2.16e+01 1fxlA 167 2.16e+01 1b7fA d.58.7.1,d.58.7.1 39183,39184 1gnhA 206 2.16e+01 1sacA b.29.1.5 24252 1gxuA 91 2.16e+01 d.58.10.1 76378 1fvaA 217 2.18e+01 1fvaA d.58.28.1 39409 1j4wA 174 2.20e+01 d.51.1.1,d.51.1.1 71529,71530 1a1aA 107 2.20e+01 1fmk d.93.1.1 40449 1adeA 431 2.20e+01 1adeA c.37.1.10 32213 1i24A 404 2.24e+01 c.2.1.2 83663 3mefA 69 2.26e+01 1mjc b.40.4.5 25320 2fp8A 322 2.26e+01 2b5hA 200 2.28e+01 1bbpA 173 2.29e+01 1bbpA b.60.1.1 27147 1pvmA 184 2.30e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1vqb 87 2.31e+01 1gvp b.40.4.7 25370 1sl4A 155 2.31e+01 d.169.1.1 105710 2achB 40 2.33e+01 1as4B 1bwsA 321 2.35e+01 1bsvA c.2.1.2 29812 1vj0A 380 2.36e+01 b.35.1.2,c.2.1.1 100786,100787 1f2tB 148 2.39e+01 1f2tB 1oqkA 97 2.43e+01 b.137.1.1 93419 1scjB 71 2.46e+01 1scjB d.58.3.2 39069 2azeA 155 2.49e+01 1rhfA 182 2.50e+01 b.1.1.1,b.1.1.4 97469,97470 1ecfA 504 2.51e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 1ba1 386 2.56e+01 1ba1 c.55.1.1,c.55.1.1 33387,33388 1d8hA 311 2.57e+01 1d8iA d.63.1.1 39544 1wvnA 82 2.58e+01 1n3oA 252 2.59e+01 b.29.1.1 79967 1qfjA 232 2.59e+01 1qfjA b.43.4.2,c.25.1.1 25655,31545 1j1uA 306 2.64e+01 c.26.1.1 83980 1rwrA 301 2.65e+01 b.80.1.11 97990 1ep3B 262 2.66e+01 1ep2B b.43.4.2,c.25.1.3 25664,31554 1vbvA 105 2.66e+01 1c7sA 858 2.66e+01 1qba b.1.18.2,b.2.2.3,c.1.8.6,d.92.2.1 21812,22408,29011,40410 1d8yA 605 2.67e+01 1xwl c.55.3.5,e.8.1.1 33684,42977 1tidB 119 2.67e+01 c.13.2.1 107000 1a6dB 543 2.69e+01 1a6dA a.129.1.2,c.8.5.2,d.56.1.2 19489,30820,38937 1wdjA 187 2.69e+01 1ak7 174 2.73e+01 1cof d.109.1.2 40864 1h5yA 253 2.74e+01 c.1.2.1 65638 1p5tA 127 2.74e+01 b.55.1.2 94148 1fvgA 199 2.75e+01 1fvaA d.58.28.1 39408 1bsvA 321 2.75e+01 1bsvA c.2.1.2 29809 1i1iP 681 2.75e+01 1i1iP d.92.1.5 40297 1a4iA 301 2.76e+01 1a4iA c.2.1.7,c.58.1.2 30278,33926 1e8gA 560 2.77e+01 1qltA d.58.32.1,d.145.1.1 39455,41718 1w2xA 758 2.77e+01 c.14.1.4,c.14.1.4 109134,109135 1rocA 155 2.80e+01 b.1.22.1 97673 1ntfA 282 2.81e+01 d.151.1.2 92104 1uyrA 737 2.83e+01 c.14.1.4,c.14.1.4 100188,100189 1hkvA 453 2.84e+01 b.49.2.3,c.1.6.1 83559,83560 2f4qA 346 2.86e+01 3htsB 102 2.86e+01 2hts a.4.5.22 16175 2bayA 61 2.87e+01 1yruB 74 2.89e+01 1k1zA 78 2.90e+01 b.34.2.1 68026 821p 166 2.90e+01 1ctqA c.37.1.8 31969 1spbP 78 2.91e+01 1scjB d.58.3.2 39068 1gfsA 321 2.91e+01 c.2.1.2 29811 1j8uA 325 2.92e+01 d.178.1.1 71611 1cawB 184 2.94e+01 1caxB b.82.1.2 28113 1tqmA 282 2.94e+01 a.4.5.56,d.144.1.9 107236,107237 1p27B 106 2.97e+01 d.58.7.1 93908 1qltA 560 2.98e+01 1qltA d.58.32.1,d.145.1.1 39457,41720 1hdmB 193 2.98e+01 1hdmB b.1.1.2,d.19.1.1 21584,38158 1c8bA 371 3.03e+01 1c8bA c.56.1.2 59082 1tvjA 166 3.15e+01 2bkfA 87 3.18e+01 1g38A 393 3.20e+01 2admA c.66.1.27 60235 1xhfA 123 3.20e+01 1w25A 459 3.20e+01 1np4A 184 3.25e+01 1np1A b.60.1.1 27166 1w1kA 560 3.28e+01 d.58.32.1,d.145.1.1 109059,109060 1igwA 434 3.30e+01 c.1.12.7 62370 1b09A 206 3.32e+01 1sacA b.29.1.5 24247 1vkkA 154 3.33e+01 d.109.1.2 108669 1d5wC 126 3.33e+01 1dbwA c.23.1.1 31101 1hpm 386 3.37e+01 1ba1 c.55.1.1,c.55.1.1 33381,33382 1ecfB 504 3.38e+01 1ecfB c.61.1.1,d.153.1.1 34054,41821 1eexB 224 3.39e+01 1dioB c.51.3.1 33213 1afqC 96 3.40e+01 5ptp 1si6X 282 3.46e+01 1y21A 282 3.47e+01 1n2aA 201 3.50e+01 a.45.1.1,c.47.1.5 91553,91554 1z5nA 242 3.50e+01 1uv4A 293 3.53e+01 1ab9C 97 3.55e+01 5ptp 2db3A 434 3.56e+01 1vaoA 560 3.56e+01 1qltA d.58.32.1,d.145.1.1 39461,41724 1b66A 140 3.57e+01 1b66A d.96.1.2 40657 1vdnA 162 3.58e+01 1as4B 37 3.60e+01 1as4B 1kay 381 3.62e+01 1ba1 c.55.1.1,c.55.1.1 33385,33386 1cqxA 403 3.64e+01 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 2atpB 115 3.65e+01 2napA 723 3.66e+01 2napA b.52.2.2,c.81.1.1 26926,35334 1jpc 109 3.67e+01 1b2pA b.78.1.1 27986 1wd6A 123 3.70e+01 1jjtA 228 3.70e+01 1a7tA d.157.1.1 63139 1wlzA 105 3.72e+01 1j1lA 290 3.72e+01 b.82.1.12 90766 2pil 159 3.72e+01 2pil d.24.1.1 38376 1jwqA 179 3.73e+01 c.56.5.6 90921 1mxgA 435 3.73e+01 b.71.1.1,c.1.8.1 85193,85194 1gmyA 261 3.74e+01 d.3.1.1 76236 1dzrA 183 3.75e+01 1dzrA b.82.1.1 28076 1wb9A 800 3.75e+01 1ts9A 102 3.75e+01 1rp0A 284 3.76e+01 1ats 386 3.79e+01 1ba1 c.55.1.1,c.55.1.1 33423,33424 1dgwX 79 3.80e+01 1caxB b.82.1.2 28091 1mtnC 97 3.81e+01 5ptp 2c4nA 250 3.81e+01 1rm4A 337 3.85e+01 c.2.1.3,d.81.1.1 105000,105001 2f4iA 197 3.87e+01 1shdA 107 3.88e+01 1fmk d.93.1.1 40440 1am2 199 3.92e+01 1am2 b.86.1.2 28381 1a8h 500 3.95e+01 1a8h a.27.1.1,c.26.1.1 16922,31589 1o6eA 235 3.95e+01 b.57.1.1 81083 1vljA 407 3.96e+01 e.22.1.2 108832 1q15A 503 3.96e+01 c.26.2.1,d.153.1.1 95538,95539 1d1gA 168 3.97e+01 1d1gA c.71.1.1 34889 1wbiA 129 3.97e+01 4pah 308 4.00e+01 4pah d.178.1.1 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