# 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.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 1g9oA 91 1.25e-20 1pdr b.36.1.1 60400 2ozfA 92 9.70e-20 2i1nA 102 1.14e-19 2fe5A 94 3.03e-19 b.36.1.1 133323 2he4A 90 3.30e-19 2he2A 102 3.55e-19 2opgA 98 5.99e-19 2jikA 101 8.58e-19 2awxA 105 8.91e-19 2ocsA 88 1.31e-18 2qg1A 92 1.41e-18 2fneA 117 3.75e-18 b.36.1.1 133813 2v90A 96 3.84e-18 2fcfA 103 4.01e-18 b.36.1.1 133267 1tp5A 119 5.28e-18 b.36.1.1 119305 1n7eA 97 9.08e-18 b.36.1.1 91691 1be9A 119 9.09e-18 1pdr b.36.1.1 24774 1qavA 90 1.16e-17 1qauA b.36.1.1 24777 2jilA 97 1.51e-17 2pktA 91 3.45e-17 2q3gA 89 1.75e-16 2egoA 96 1.84e-16 2f5yA 91 2.62e-16 b.36.1.1 133015 2uzcA 88 2.68e-16 2iwoA 120 2.80e-16 2iwnA 97 3.56e-16 1ihjA 98 4.17e-16 1pdr b.36.1.1 62382 1q3oA 109 4.97e-16 b.36.1.1 95700 2pa1A 87 7.53e-16 2q9vA 90 8.94e-16 1mfgA 95 1.47e-15 b.36.1.1 79043 2h2bA 107 1.54e-15 2h3lA 103 1.82e-15 b.36.1.1 136046 1l6oA 95 2.46e-15 b.36.1.1 84534 3bpuA 88 2.64e-15 1wf7A 103 2.97e-15 b.36.1.1 114577 2gzvA 114 5.35e-15 2reyA 100 6.31e-15 2vphA 100 1.32e-14 1nf3C 128 2.64e-14 b.36.1.1 85596 1kwaA 88 3.37e-14 1kwaA b.36.1.1 24772 1qauA 112 3.46e-14 1qauA b.36.1.1 24779 1x45A 98 3.47e-14 b.36.1.1 121679 2i04A 85 4.64e-14 2f0aA 98 4.67e-14 b.36.1.1 132661 1v5lA 103 2.25e-13 b.36.1.1 108378 1r6jA 82 2.71e-13 b.36.1.1 97151 2qkvA 96 8.00e-13 2eaqA 90 8.20e-12 2rczA 81 7.81e-09 2p3wA 112 1.77e-08 1te0A 318 3.71e-07 b.36.1.4,b.47.1.1 112400,112401 1lcyA 325 4.59e-07 b.36.1.4,b.47.1.1 73834,73835 1fc6A 388 2.80e-06 1fc6A b.36.1.3,c.14.1.2 64738,64739 1y8tA 324 4.19e-05 b.36.1.4,b.47.1.1 122763,122764 2i6vA 87 4.61e-05 1fxlA 167 8.39e-03 1b7fA d.58.7.1,d.58.7.1 39183,39184 1y9wA 140 1.85e-02 d.108.1.1 122783 2j3tD 219 2.80e-02 2h7aA 110 1.59e-01 1sotA 320 3.24e-01 b.36.1.4,b.47.1.1 105852,105853 1se8A 301 3.56e-01 b.40.4.3 105448 1wjuA 100 7.46e-01 d.15.1.1 114712 1db3A 372 8.28e-01 1db3A c.2.1.2 29813 2d8aA 348 8.95e-01 1a62 130 9.36e-01 1a62 1a62A 130 9.36e-01 a.140.3.1,b.40.4.5 64708,64709 2fl4A 149 9.98e-01 d.108.1.1 133706 1r13A 148 1.18e+00 d.169.1.1,h.1.1.1 96782,96783 1k32A 1045 1.35e+00 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 68068,68069,68070,68071 2qdfA 335 1.39e+00 2nwvA 114 1.87e+00 d.326.1.1 138720 2r7hA 177 1.89e+00 2hjeA 221 1.91e+00 1vj0A 380 2.24e+00 b.35.1.2,c.2.1.1 100786,100787 1yloA 348 2.27e+00 b.49.3.1,c.56.5.4 123659,123660 1vheA 373 2.74e+00 b.49.3.1,c.56.5.4 100669,100670 2r1iA 172 2.81e+00 2oqbA 117 2.91e+00 1h2kA 349 2.97e+00 b.82.2.6 76572 2rcfA 91 3.07e+00 1vhxA 150 3.26e+00 c.55.3.8 100712 1ti6A 875 3.38e+00 b.52.2.2,c.81.1.1 106974,106975 2eixA 243 3.41e+00 1uheA 97 3.65e+00 2dpkA 152 3.89e+00 b.1.27.1 131616 1id0A 152 3.92e+00 d.122.1.3 66111 1um0A 365 4.20e+00 d.258.1.1 107942 1xebA 150 4.27e+00 d.108.1.1 115219 2c5qA 240 4.30e+00 1yqbA 100 4.30e+00 d.15.1.1 123876 1uc2A 481 4.37e+00 d.261.1.1 99161 2f1lA 187 4.44e+00 b.41.1.4,b.43.3.4 132780,132781 2bkfA 87 4.45e+00 d.15.2.2 128699 2hd3A 103 4.53e+00 2dmcA 116 4.59e+00 b.1.18.10 131572 1tllA 688 4.71e+00 b.43.4.1,c.23.5.2,c.25.1.4 107128,107129,107130 1zhhB 242 4.74e+00 2o38A 120 4.77e+00 1zhvA 134 4.80e+00 d.58.18.8,d.58.18.8 125109,125110 1p5vB 147 5.32e+00 b.2.3.2 87814 2otuA 115 5.46e+00 1x6oA 174 5.58e+00 b.34.5.2,b.40.4.5 109493,109494 2d4pA 141 5.69e+00 1yb3A 175 5.73e+00 d.296.1.2 122869 1prtF 98 5.81e+00 1prtF b.40.2.1 25140 2j01Q 141 5.81e+00 2it2A 200 5.86e+00 2iayA 114 5.92e+00 2pfiA 164 5.94e+00 2joyA 96 6.02e+00 1vc3B 97 6.10e+00 2r98A 456 6.10e+00 1hh1A 143 6.12e+00 1gefA c.52.1.18 61036 1luzA 88 6.22e+00 b.40.4.5 74271 2aexA 346 6.24e+00 2cf5A 357 6.29e+00 2e85A 159 6.29e+00 2j3wA 142 6.75e+00 d.110.4.3 137981 1o8bA 219 6.81e+00 c.124.1.4,d.58.40.1 81180,81181 1vzoA 355 6.85e+00 d.144.1.7 108971 1bx4A 345 6.88e+00 1bx4A c.72.1.1 34935 2cfmA 561 6.91e+00 1y7rA 133 6.92e+00 d.108.1.1 122716 1yphC 131 6.96e+00 2f9hA 129 7.07e+00 b.161.1.1 133162 2p4gA 270 7.14e+00 1ha1 184 7.25e+00 1ha1 1c9oA 66 7.87e+00 1mjc b.40.4.5 25325 1xk5A 204 7.94e+00 2ix0A 663 7.96e+00 2qguA 211 8.26e+00 1ucyH 150 8.38e+00 1ucyH 2id0A 644 8.46e+00 2fxqA 264 8.48e+00 1sjwA 144 8.56e+00 d.17.4.9 98899 1f20A 435 8.63e+00 b.43.4.1,c.25.1.4 64932,64933 2b3rA 134 8.76e+00 1qwjA 229 9.07e+00 c.68.1.13 96478 2a6tA 271 9.20e+00 a.242.1.1,d.113.1.7 126309,126310 3b93A 133 9.21e+00 2fe7A 166 9.24e+00 d.108.1.1 133325 1wjnA 97 9.26e+00 d.15.1.1 114703 1rlhA 173 9.63e+00 d.256.1.1 97646 2ix2B 245 9.70e+00 1whi 122 9.86e+00 1whi 1whiA 122 9.86e+00 b.39.1.1 24810 2qv6A 268 1.03e+01 1v1qA 134 1.04e+01 b.40.4.3 113490 1sdjA 310 1.04e+01 d.21.1.2,d.21.1.2 98807,98808 1d4xG 126 1.06e+01 1d0nA d.109.1.1 59109 2chdA 142 1.13e+01 1t44G 147 1.14e+01 d.109.1.1 106395 3cnwA 148 1.18e+01 1x67A 146 1.19e+01 2drvA 200 1.23e+01 1nm1G 125 1.27e+01 d.109.1.1 80653 1smxA 96 1.29e+01 b.40.4.5 105772 2fvgA 340 1.30e+01 b.49.3.1,c.56.5.4 134201,134202 1xrsB 262 1.32e+01 c.23.6.1,d.230.4.1 115884,115885 2vbuA 136 1.32e+01 1stmA 157 1.32e+01 1stmA b.121.7.1 23281 2cwaA 263 1.33e+01 1p4fA 293 1.33e+01 d.144.1.7 104063 1f8fA 371 1.34e+01 b.35.1.2,c.2.1.1 83246,83247 2dafA 118 1.35e+01 1rsy 152 1.36e+01 1rsy 1rsyA 152 1.36e+01 b.7.1.2 23192 2aefA 234 1.36e+01 1t0yA 122 1.36e+01 d.15.1.1 99066 2glwA 92 1.36e+01 2qsqA 111 1.36e+01 2uyzB 79 1.37e+01 d.15.1.1 140039 1qyaA 307 1.40e+01 d.21.1.2,d.21.1.2 104653,104654 1a8vA 121 1.42e+01 1a62 a.140.3.1,b.40.4.5 64712,64713 2cu1A 103 1.45e+01 d.15.2.2 130802 2g3aA 152 1.46e+01 d.108.1.1 134557 2nyiA 195 1.48e+01 2r2qA 110 1.48e+01 1qorA 327 1.49e+01 1qorA b.35.1.2,c.2.1.1 24766,29782 2bsjA 133 1.51e+01 2z0dB 125 1.51e+01 d.15.1.3 140096 2cw5A 255 1.53e+01 3bciA 186 1.54e+01 1fdr 248 1.54e+01 1fdr 1fdrA 248 1.54e+01 b.43.4.2,c.25.1.1 25653,31543 1kzlA 208 1.55e+01 b.43.4.3,b.43.4.3 77635,77636 2dpyA 438 1.55e+01 1viuA 203 1.58e+01 d.113.1.1 100771 1e7uA 961 1.62e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 1j5uA 136 1.64e+01 d.208.1.1 71584 2ohwA 133 1.67e+01 1z9lA 128 1.69e+01 2v03A 303 1.72e+01 1nepA 130 1.72e+01 b.1.18.7 80440 3cgxA 242 1.72e+01 2fywA 267 1.74e+01 c.135.1.1 134408 2bshA 125 1.74e+01 2epgA 487 1.76e+01 1y96A 86 1.76e+01 2nvmA 126 1.78e+01 d.326.1.1 138631 2pa2A 151 1.78e+01 2euiA 153 1.80e+01 d.108.1.1 132387 2oynA 146 1.82e+01 2yzqA 282 1.84e+01 2o0tA 467 1.84e+01 2bhoA 130 1.85e+01 1fxrA 64 1.85e+01 1fxd d.58.1.4 38993 1l3kA 196 1.87e+01 d.58.7.1,d.58.7.1 73539,73540 2nptB 100 1.89e+01 d.15.2.2 138449 1widA 130 1.95e+01 b.142.1.2 114667 1r26A 125 1.97e+01 c.47.1.1 96847 1mq7A 154 1.99e+01 b.85.4.1 79404 1n3jA 119 2.00e+01 b.85.7.2 79963 1ppjB 439 2.00e+01 d.185.1.1,d.185.1.1 104254,104255 1k3eA 156 2.01e+01 d.198.1.1 68103 2pn0A 141 2.02e+01 1ev5A 264 2.03e+01 1bkpA d.117.1.1 40935 1l0bA 229 2.03e+01 c.15.1.3,c.15.1.3 73391,73392 1a79A 171 2.03e+01 1a79A c.52.2.1,d.75.1.1 33340,39739 2z1cA 75 2.04e+01 1jhsA 188 2.08e+01 d.107.1.1 84172 2bw3A 534 2.10e+01 a.270.1.1,c.55.3.12 129317,129318 1ifyA 49 2.11e+01 a.5.2.1 71207 1mb3A 124 2.11e+01 c.23.1.1 78907 1hvyA 288 2.14e+01 1bkpA d.117.1.1 41049 2nn6H 308 2.15e+01 2c60A 111 2.19e+01 d.15.2.2 129966 1m4zA 238 2.19e+01 b.34.12.1 78630 3bpdA 100 2.22e+01 1t9fA 187 2.22e+01 b.42.6.1 106710 2j58A 359 2.26e+01 1qfjA 232 2.26e+01 1qfjA b.43.4.2,c.25.1.1 25655,31545 2ovsA 118 2.27e+01 1qstA 160 2.28e+01 1yghA d.108.1.1 40804 3bo5A 290 2.29e+01 1fl0A 171 2.33e+01 1eujA b.40.4.4 25315 1sixA 174 2.34e+01 b.85.4.1 98892 1eo6A 117 2.34e+01 1eo6A d.15.1.3 37609 2d9bA 109 2.36e+01 1pqhA 143 2.42e+01 b.52.2.1 95017 1e3jA 352 2.43e+01 1e3jA b.35.1.2,c.2.1.1 24765,29781 1y9kA 157 2.43e+01 d.108.1.1 122779 2zbvA 263 2.44e+01 1evfA 264 2.46e+01 1bkpA d.117.1.1 40932 1gnuA 117 2.47e+01 d.15.1.3 65403 1fmtA 314 2.47e+01 1fmtA b.46.1.1,c.65.1.1 25758,34174 1l7bA 92 2.48e+01 c.15.1.2 91053 1wxaA 116 2.50e+01 d.15.1.5 121395 1g8aA 227 2.50e+01 c.66.1.3 90506 1mjc 69 2.53e+01 1mjc 1mjcA 69 2.53e+01 b.40.4.5 25319 1x65A 89 2.58e+01 1ex2A 189 2.58e+01 1ex2A c.51.4.2 33225 1ryjA 70 2.62e+01 d.15.3.2 98104 2eihA 343 2.62e+01 2hb5A 164 2.65e+01 1ema 236 2.71e+01 1ema 1nd4A 264 2.73e+01 d.144.1.6 91815 1xfoA 357 2.73e+01 b.49.3.1,c.56.5.4 115265,115266 1f00I 282 2.76e+01 1f00I b.1.14.1,b.1.14.1,d.169.1.3 22368,22369,42439 1txyA 104 2.78e+01 b.40.4.3 112791 1jmuB 666 2.78e+01 3c3mA 138 2.79e+01 1z7gA 217 2.81e+01 c.61.1.1 124624 1l1dA 152 2.83e+01 b.88.1.3 73452 1ionA 243 2.83e+01 c.37.1.10 62633 1cliA 345 2.87e+01 1cliA d.79.4.1,d.139.1.1 39816,41459 1ut7A 171 2.89e+01 b.143.1.1 99906 1cyx 205 2.89e+01 1cyx 1cyxA 205 2.89e+01 b.6.1.2 23023 1cd8 114 2.94e+01 1cd8 2bwfA 77 2.95e+01 d.15.1.1 129363 1bkb 136 2.96e+01 1bkb 1bkbA 136 2.96e+01 b.34.5.2,b.40.4.5 24609,25341 2c3gA 98 2.96e+01 1mk0A 97 2.97e+01 d.226.1.1 79216 1eo1A 124 2.97e+01 1eo1A c.55.5.1 33739 1gsmA 210 2.98e+01 b.1.1.4,b.1.1.4 65535,65536 2oqrA 230 2.99e+01 2mspA 126 3.04e+01 1mspA b.1.11.2 22335 2g8mA 264 3.04e+01 1xewX 182 3.04e+01 c.37.1.12 115235 2i1qA 322 3.05e+01 a.60.4.1,c.37.1.11 136984,136985 2qa1A 500 3.08e+01 1uw0A 117 3.10e+01 g.39.1.12 108063 2awkA 228 3.12e+01 1v70A 105 3.14e+01 b.82.1.9 113555 1h4gA 207 3.15e+01 b.29.1.11 70863 2z5wA 136 3.15e+01 1cq3A 233 3.16e+01 1cq3A b.27.1.1 23923 2f1wA 158 3.19e+01 1wwtA 88 3.22e+01 2oq2A 261 3.23e+01 1xa0A 328 3.26e+01 b.35.1.2,c.2.1.1 115021,115022 1zsyA 357 3.26e+01 1wvhA 134 3.29e+01 b.55.1.2 121341 2jsxA 95 3.30e+01 2btuA 346 3.32e+01 2fmpA 335 3.33e+01 a.60.6.1,a.60.12.1,d.218.1.2 133786,133787,133788 1dunA 134 3.34e+01 b.85.4.1 28371 1rxwA 336 3.35e+01 a.60.7.1,c.120.1.2 98059,98060 2ganA 190 3.37e+01 d.108.1.1 134889 1kw4A 89 3.37e+01 a.60.1.2 73077 2e7vA 121 3.38e+01 2fl7A 232 3.40e+01 2oolA 337 3.41e+01 2hivA 621 3.44e+01 1l1oC 181 3.44e+01 b.40.4.3 73480 2uwqA 86 3.48e+01 1tv9A 335 3.54e+01 a.60.6.1,a.60.12.1,d.218.1.2 112675,112676,112677 1l1jA 239 3.57e+01 b.47.1.1 84516 1zn6A 227 3.63e+01 d.303.1.1 125373 2bkdN 134 3.63e+01 1z4rA 168 3.64e+01 d.108.1.1 124444 2igqA 285 3.66e+01 2b9eA 303 3.67e+01 c.66.1.38 128124 2qr7A 342 3.70e+01 2inwA 133 3.71e+01 d.110.8.1 137533 1qqqA 264 3.72e+01 1bkpA d.117.1.1 40931 2a19B 284 3.74e+01 1rxzA 245 3.75e+01 d.131.1.2,d.131.1.2 98067,98068 1oo0B 110 3.75e+01 d.58.7.1 87183 1yvkA 163 3.76e+01 d.108.1.1 124101 1y0yA 353 3.79e+01 b.49.3.1,c.56.5.4 122514,122515 1shsA 147 3.82e+01 1shsA b.15.1.1 23675 1ygs 234 3.84e+01 1ygs 1ygsA 234 3.84e+01 b.26.1.1 23907 2bh0A 208 3.85e+01 1nqjA 119 3.89e+01 b.23.2.1 86031 1z94A 147 3.94e+01 d.129.3.5 124740 2dyiA 162 3.95e+01 1u3wA 374 3.96e+01 b.35.1.2,c.2.1.1 113013,113014 2ikkA 173 4.00e+01 1bqbA 301 4.01e+01 1hyt d.92.1.2 58962 1sfp 114 4.04e+01 1sfp 1sfpA 114 4.04e+01 b.23.1.1 23895 2ebuA 112 4.07e+01 2ywdA 191 4.09e+01 2brfA 110 4.11e+01 b.26.1.2 128996 1qcsA 211 4.11e+01 1qcsA b.52.2.3,d.31.1.1 26927,38461 2gdjA 264 4.12e+01 c.37.1.11 135018 2gwnA 452 4.12e+01 1bo4A 168 4.18e+01 1bo4A d.108.1.1 40798 2dy0A 190 4.19e+01 1iyhA 198 4.22e+01 a.45.1.1,c.47.1.5 83790,83791 1l7yA 94 4.22e+01 d.15.1.6 73676 2cm4A 150 4.24e+01 1lluA 342 4.26e+01 b.35.1.2,c.2.1.1 91064,91065 1u0sA 86 4.28e+01 d.58.24.1 107565 1jqbA 351 4.28e+01 b.35.1.2,c.2.1.1 77151,77152 1mspA 126 4.29e+01 1mspA b.1.11.2 22333 2yyhA 139 4.30e+01 1xwwA 157 4.30e+01 3cokA 278 4.30e+01 2q1mA 130 4.33e+01 2gs8A 317 4.33e+01 1o50A 157 4.33e+01 d.37.1.1,d.37.1.1 92478,92479 2j0pA 345 4.36e+01 e.62.1.1 137903 2ejeA 114 4.36e+01 2dykA 161 4.41e+01 2jhfA 374 4.46e+01 b.35.1.2,c.2.1.1 138314,138315 1wlsA 328 4.48e+01 2ogtA 498 4.48e+01 2hq2A 354 4.52e+01 e.62.1.1 136656 2v3kA 258 4.53e+01 1h6kA 757 4.59e+01 a.118.1.14,a.118.1.14,a.118.1.14 60675,60676,60677 2cuyA 305 4.67e+01 1f7sA 139 4.69e+01 1cof d.109.1.2 40857 2v3aA 384 4.69e+01 2ij0C 118 4.70e+01 2hp4A 114 4.71e+01 1js8A 394 4.74e+01 a.86.1.1,b.112.1.1 67219,67220 1kevA 351 4.75e+01 1pedA b.35.1.2,c.2.1.1 24749,29765 2nruA 307 4.77e+01 1d3bA 75 4.77e+01 1d3bA b.38.1.1 24798 1wckA 220 4.81e+01 1m1sA 116 4.84e+01 b.1.11.2 84747 1ixkA 315 4.85e+01 c.66.1.38 90716 1tw0A 157 4.86e+01 d.129.3.1 119364 1o6dA 163 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