# List of top-scoring protein chains for t04-100-30-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 1y8qA 346 8.30e-02 1zu0A 529 2.85e-01 1sgvA 316 3.21e-01 b.122.1.1,d.265.1.2 98858,98859 2cybA 323 5.53e-01 1xgsA 295 5.84e-01 1bn5 a.4.5.25,d.127.1.1 16216,41153 1gy8A 397 6.31e-01 c.2.1.2 83376 1h7mA 102 6.61e-01 d.79.3.1 83485 1jg5A 83 6.83e-01 d.205.1.1 66666 1w41A 101 9.04e-01 1a99A 344 9.66e-01 1pot c.94.1.1 35812 2fb0A 94 1.20e+00 1t0hB 224 1.31e+00 c.37.1.1 106208 1qo7A 394 1.39e+00 1qo7A c.69.1.11 34697 1t3lA 337 1.55e+00 b.34.2.1,c.37.1.1 106358,106359 1ldjA 760 1.75e+00 a.4.5.34,a.118.17.1,e.40.1.1 73847,73848,73849 1wj9A 211 1.80e+00 1gefA 123 1.87e+00 1gefA c.52.1.18 60465 2faoA 309 1.88e+00 1yqfA 203 1.98e+00 2gtqA 867 1.99e+00 1m2oA 768 2.08e+00 a.71.2.1,b.2.8.1,c.62.1.2,d.109.2.1,g.41.10.1 78480,78481,78482,78483,78484 1wm3A 72 2.18e+00 1xnzA 264 2.19e+00 1k2eA 156 2.20e+00 d.113.1.1 72010 1nb5I 98 2.28e+00 d.17.1.2 80381 1y60A 169 2.44e+00 1va4A 279 2.60e+00 c.69.1.12 108458 1e5dA 402 2.73e+00 1e5dA c.23.5.1,d.157.1.3 31208,42061 2ggcA 263 2.73e+00 1n9lA 109 2.81e+00 d.110.3.6 85468 1fukA 165 2.96e+00 1fukA c.37.1.19 32409 2d5cA 263 3.16e+00 1n3lA 372 3.16e+00 c.26.1.1 79966 3il8 72 3.24e+00 1tvxA d.9.1.1 37356 2bzoB 79 3.39e+00 1l7mA 211 3.51e+00 c.108.1.4 73664 2cvlA 124 3.63e+00 1g6oA 330 3.73e+00 1g6oA c.37.1.11 32430 1o0xA 262 3.79e+00 d.127.1.1 80755 2mhr 118 3.89e+00 2mhr a.24.4.1 16581 1j7nA 776 4.01e+00 d.92.1.14,d.92.1.14,d.166.1.1 66409,66410,66411 1j3mA 129 4.12e+00 d.129.7.1 103836 1wxdA 263 4.27e+00 2cy0A 263 4.31e+00 1q5yA 85 4.33e+00 d.58.18.4 95950 1c24A 263 4.45e+00 1c24A d.127.1.1 41148 1vp8A 201 4.61e+00 1tia 279 4.70e+00 3tgl c.69.1.17 34737 1vmiA 355 4.80e+00 1nrfA 262 4.81e+00 e.3.1.1 92086 1u7iA 136 4.83e+00 d.32.1.7 107724 1j97A 211 4.85e+00 1f5sA c.108.1.4 62753 1nf2A 268 4.87e+00 c.108.1.10 91849 1fjgE 162 5.04e+00 1pkp d.14.1.1,d.50.1.2 37553,38789 1qy1A 174 5.26e+00 b.60.1.1 96568 1r3eA 309 5.34e+00 b.122.1.1,d.265.1.2 96907,96908 1jzuA 157 5.46e+00 b.60.1.1 84271 1vd4A 62 5.64e+00 1f1uA 323 5.66e+00 d.32.1.3,d.32.1.3 83200,83201 1yqzA 438 5.71e+00 1e0bA 68 5.77e+00 1e0bA b.34.13.2 37476 1iukA 140 5.81e+00 c.2.1.8 83712 1fyhB 229 5.90e+00 1jrhI b.1.2.1,b.1.2.1 22055,22056 1zndA 174 5.91e+00 1j8rA 196 5.93e+00 1j8rA b.2.3.3 62745 1xt9A 212 6.00e+00 2bkrA 212 6.20e+00 1v8gA 329 6.22e+00 a.46.2.1,c.27.1.1 100505,100506 1lx7A 253 6.36e+00 c.56.2.1 74329 1f1zA 273 6.46e+00 1f1zA a.4.5.27,c.52.1.16 16081,33334 1j1uA 306 6.51e+00 c.26.1.1 83980 2bkqA 212 6.72e+00 1jv4A 162 6.74e+00 b.60.1.1 67343 1wvfA 520 6.90e+00 1ml4A 308 6.98e+00 c.78.1.1,c.78.1.1 79255,79256 1v7rA 186 6.98e+00 c.51.4.1 100482 1yzbA 182 7.27e+00 1ockA 412 7.39e+00 c.117.1.1 86802 1mjhA 162 7.42e+00 1mjhA c.26.2.4 31639 1tqhA 247 7.47e+00 c.69.1.29 107225 1i05A 180 7.48e+00 1mup b.60.1.1 27130 2fi0A 81 7.50e+00 1bkpA 278 7.94e+00 1bkpA d.117.1.1 41029 2fhzA 109 7.95e+00 1l5jA 865 8.06e+00 a.118.15.1,c.8.2.1,c.83.1.1 73592,73593,73594 1xwyA 264 8.15e+00 1w6uA 302 8.22e+00 1u6pA 56 8.45e+00 1gmlA 178 8.46e+00 c.8.5.2 70273 1f1xA 322 8.47e+00 d.32.1.3,d.32.1.3 83208,83209 1pfkA 320 8.90e+00 3pfk c.89.1.1 35575 1ww8A 439 9.10e+00 2gupA 292 9.20e+00 1jj2T 66 9.21e+00 1ffkR g.39.1.6 63105 1s72U 66 9.21e+00 g.39.1.6 105340 2b8tA 223 9.24e+00 2ew8A 249 9.29e+00 1sauA 115 9.31e+00 1yzhA 214 9.35e+00 1rxyA 253 9.36e+00 c.56.2.1 98065 1nbwA 607 9.38e+00 c.8.6.1,c.55.1.6,c.55.1.6 80393,80394,80395 2an3A 289 9.44e+00 2ctoA 93 9.48e+00 1fe0A 68 9.49e+00 1cc8A d.58.17.1 39345 1ubi 76 9.50e+00 1ubi d.15.1.1 37584 1vchA 175 9.60e+00 1ufkA 254 9.62e+00 c.66.1.39 99340 1mup 166 9.64e+00 1mup b.60.1.1 27133 1r1dA 247 9.79e+00 c.69.1.29 96813 1t0fA 276 9.80e+00 1mkiA 330 9.98e+00 e.3.1.2 84994 1ignA 246 1.03e+01 1ignA a.4.1.6,a.4.1.6 16048,16049 1o22A 170 1.05e+01 d.238.1.1 86557 1oz9A 150 1.06e+01 d.92.1.15 93808 1qysA 106 1.06e+01 k.41.1.1 96603 2fulA 178 1.07e+01 1y81A 138 1.08e+01 1vqoU 66 1.08e+01 1nbfD 76 1.09e+01 d.15.1.1 80390 1t6aA 126 1.12e+01 d.129.8.1 106555 1vpqA 273 1.15e+01 1u5mA 73 1.17e+01 1z08A 170 1.18e+01 1xa1A 255 1.20e+01 e.3.1.1 109529 2d1pA 140 1.22e+01 1i6wA 181 1.23e+01 1i6wA c.69.1.18 61859 1rypL 212 1.24e+01 d.153.1.4 41880 1ogwA 76 1.24e+01 d.15.1.1 87001 1xmrA 243 1.25e+01 1dzkA 157 1.25e+01 1obpA b.60.1.1 27096 1whi 122 1.26e+01 1whi b.39.1.1 24810 1othA 321 1.27e+01 1othA c.78.1.1,c.78.1.1 35260,35261 1yj1A 76 1.27e+01 1fezA 256 1.28e+01 1fezA c.108.1.3 43343 1nzjA 298 1.29e+01 c.26.1.1 92377 1okjA 251 1.30e+01 c.55.1.9,c.55.1.9 103998,103999 1a3aA 148 1.32e+01 1a3aA d.112.1.1 40917 1v6tA 255 1.33e+01 1hnnA 282 1.34e+01 c.66.1.15 65895 1l1qA 186 1.35e+01 c.61.1.1 77653 1srb 21 1.38e+01 j.28.1.1 46201 1ek1A 554 1.38e+01 1cr6B c.69.1.11,c.108.1.2 34685,43335 2frnA 278 1.39e+01 1v4pA 157 1.40e+01 1wzcA 249 1.40e+01 1rqlA 267 1.44e+01 c.108.1.3 97750 1vf8A 377 1.45e+01 1hh1A 143 1.46e+01 1gefA c.52.1.18 61036 1vhzA 198 1.47e+01 d.113.1.1 100718 1e25A 282 1.47e+01 1e25A e.3.1.1 42731 1wyuA 438 1.48e+01 1uekA 275 1.50e+01 d.14.1.5,d.58.26.5 88483,88484 2ao0A 324 1.54e+01 1fviA 297 1.54e+01 1fviA b.40.4.6,d.142.2.1 25364,41578 2fblA 153 1.55e+01 2bolA 314 1.57e+01 1jm1A 204 1.64e+01 b.33.1.1 71745 1s68A 249 1.64e+01 d.142.2.4 98591 1a9xA 1058 1.64e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18550,31479,31657,31658,41502,41503 1wod 233 1.65e+01 1wod c.94.1.1 35832 1amf 233 1.66e+01 1wod c.94.1.1 35833 2b18A 164 1.68e+01 1a05A 358 1.69e+01 1cnzA c.77.1.1 35059 1oo0B 110 1.70e+01 d.58.7.1 87183 1ksiA 642 1.70e+01 1ksiB b.30.2.1,d.17.2.1,d.17.2.1 24408,38043,38044 1aw7A 194 1.73e+01 1aw7A b.40.2.2,d.15.6.1 25164,37753 1jidA 128 1.73e+01 d.201.1.1 66735 1ispA 181 1.73e+01 c.69.1.18 76778 1xreA 217 1.75e+01 2amyA 246 1.75e+01 2b3yA 888 1.77e+01 1r31A 428 1.77e+01 d.58.20.1,d.179.1.1 96897,96898 1xocA 520 1.80e+01 1wojA 214 1.80e+01 1a6bB 40 1.80e+01 1a6bB g.40.1.1 45172 2f5gA 133 1.82e+01 1k8qA 377 1.84e+01 c.69.1.6 72177 1wurA 220 1.85e+01 1f52A 468 1.86e+01 1lgr d.15.9.1,d.128.1.1 37839,41169 2dtr 226 1.87e+01 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 16193,18399,24450 1wu7A 434 1.87e+01 2bkrB 77 1.87e+01 1vkyA 347 1.89e+01 e.53.1.1 108696 1w85I 49 1.89e+01 1z5yE 149 1.90e+01 1i6pA 220 1.91e+01 1ddzA c.53.2.1 61848 1p57A 114 1.92e+01 d.170.1.2 94125 1dgaA 375 1.93e+01 1yagA 1wcwA 261 1.95e+01 2bgcA 238 2.00e+01 1exkA 79 2.03e+01 1exkA g.54.1.1 45384 2d4pA 141 2.03e+01 1cvl 319 2.04e+01 1cvl c.69.1.18 34786 2f7fA 494 2.07e+01 1nt4A 391 2.07e+01 c.60.1.2 92102 1ubkL 534 2.09e+01 e.18.1.1 88422 2d8sA 80 2.11e+01 1swvA 267 2.11e+01 1v7oA 165 2.13e+01 d.67.1.2 100480 1hmt 132 2.14e+01 1hmt b.60.1.2 27169 2f20A 240 2.15e+01 2acy 98 2.15e+01 2acy d.58.10.1 39298 1l8bA 190 2.17e+01 d.86.1.1 73683 1q9uA 130 2.18e+01 d.129.7.1 96314 1y9kA 157 2.23e+01 1d4xA 375 2.25e+01 1yagA c.55.1.1,c.55.1.1 59107,59108 3chbD 104 2.25e+01 3chbD b.40.2.1 24970 1dj7A 117 2.26e+01 1dj7A g.36.1.1 44997 1rk8A 165 2.26e+01 d.58.7.1 97603 2fxuA 375 2.26e+01 1jnyA 435 2.27e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 2btfA 375 2.30e+01 1yagA c.55.1.1,c.55.1.1 33429,33430 1h70A 255 2.30e+01 1h70A d.126.1.3 60711 1h2rL 534 2.30e+01 1h2rL e.18.1.1 43298 1reqB 637 2.31e+01 1reqB c.1.19.1,c.23.6.1 29621,31248 1gnkA 112 2.31e+01 2pii d.58.5.1 39073 1o13A 136 2.32e+01 c.55.5.1 80762 1xuuA 349 2.33e+01 1d0cA 444 2.34e+01 d.174.1.1 64769 1qz5A 375 2.34e+01 c.55.1.1,c.55.1.1 96614,96615 1v25A 541 2.34e+01 e.23.1.1 108275 1nv8A 284 2.34e+01 c.66.1.30 86224 1ju3A 583 2.35e+01 b.18.1.13,c.69.1.21 67300,67301 1jfrA 262 2.36e+01 1jfrA c.69.1.16 34724 1wv9A 94 2.36e+01 1zejA 293 2.36e+01 1wuaA 375 2.39e+01 1wosA 364 2.42e+01 b.44.2.1,d.250.1.1 109468,109469 1np6A 174 2.43e+01 c.37.1.10 85954 1l7dA 384 2.44e+01 c.2.1.4,c.23.12.2 77774,77775 1wd7A 261 2.45e+01 1tit 98 2.49e+01 1tit b.1.1.4 21716 1i06A 180 2.51e+01 1mup b.60.1.1 27131 1p4fA 293 2.52e+01 d.144.1.7 104063 2cwkA 160 2.52e+01 1f8gA 384 2.52e+01 1sayA c.2.1.4,c.23.12.2 59695,59696 1cs0A 1073 2.53e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18558,31487,31673,31674,41518,41519 1kkoA 413 2.53e+01 c.1.11.2,d.54.1.1 68675,68676 1om4A 422 2.55e+01 d.174.1.1 87067 1mmvB 419 2.58e+01 d.174.1.1 91318 1dl5A 317 2.58e+01 1dl5A c.66.1.7,d.197.1.1 64720,64721 1jnrB 150 2.59e+01 d.58.1.5 66969 2a14A 263 2.61e+01 1rdfA 267 2.64e+01 c.108.1.3 104884 2pfkA 320 2.68e+01 3pfk c.89.1.1 35577 1b24A 188 2.70e+01 1b24A d.95.2.1,d.95.2.1 40573,40574 1zowA 313 2.75e+01 1bt0A 76 2.80e+01 1ubi d.15.1.1 37607 1obbA 480 2.82e+01 c.2.1.5,d.162.1.2 86760,86761 1opjA 293 2.82e+01 d.144.1.7 87230 2a9sA 171 2.83e+01 1zljA 78 2.84e+01 1bmdA 327 2.84e+01 1bmdA c.2.1.5,d.162.1.1 30139,42106 2c1iA 431 2.86e+01 1ihoA 283 2.87e+01 1ihoA c.26.1.4 62390 1mzbA 136 2.88e+01 a.4.5.42 91497 1o4wA 147 2.88e+01 c.120.1.1 86629 1dumA 23 2.90e+01 j.4.1.1 59136 2c1gA 431 2.91e+01 1oivA 191 2.93e+01 c.37.1.8 93076 3seb 238 2.93e+01 3seb b.40.2.2,d.15.6.1 25184,37773 2glfA 450 2.93e+01 1xb4A 202 2.94e+01 1omiA 248 2.96e+01 b.82.3.3,a.4.5.4 87079,87080 1yzyA 413 2.97e+01 2ajrA 331 2.98e+01 1nddA 76 2.99e+01 1ubi d.15.1.1 37599 2b9eA 303 3.01e+01 1y7tA 327 3.02e+01 1ooeA 236 3.03e+01 c.2.1.2 87196 1mwyA 73 3.06e+01 d.58.17.1 79616 1u8zA 168 3.08e+01 1iyxA 432 3.09e+01 c.1.11.1,d.54.1.1 83815,83816 1t4hA 290 3.10e+01 d.144.1.7 106420 1h75A 81 3.10e+01 1h75A c.47.1.1 60716 1innA 166 3.12e+01 1j98A d.185.1.2 62608 1wuiL 534 3.13e+01 1bdmA 327 3.14e+01 1bmdA c.2.1.5,d.162.1.1 30137,42104 2c31A 568 3.16e+01 1k8wA 327 3.17e+01 b.122.1.1,d.265.1.2 83094,90388 1ey4A 149 3.20e+01 1snc b.40.1.1 24815 1oahA 519 3.20e+01 a.138.1.3 86736 1n13B 113 3.20e+01 1yovA 537 3.22e+01 2fexA 188 3.23e+01 1edn 21 3.25e+01 j.28.1.1 46197 1n8yC 608 3.26e+01 c.10.2.5,c.10.2.5,g.3.9.1,g.3.9.1 80314,80315,80316,80317 1ctqA 166 3.27e+01 1ctqA c.37.1.8 31965 1o5zA 442 3.27e+01 c.59.1.2,c.72.2.2 92530,92531 1npk 154 3.28e+01 1npk d.58.6.1 39099 1w6tA 444 3.28e+01 1xm3A 264 3.29e+01 1bn7A 294 3.35e+01 1bn6A c.69.1.8 34677 1wy5A 317 3.35e+01 4pfk 319 3.36e+01 3pfk c.89.1.1 35582 2bj7A 138 3.37e+01 1xkzA 255 3.43e+01 1djrD 103 3.43e+01 3chbD b.40.2.1 24865 1rfzA 168 3.44e+01 a.195.1.1 97411 1vl5A 260 3.44e+01 c.66.1.41 108720 1lt5D 103 3.46e+01 3chbD b.40.2.1 24875 1whzA 70 3.46e+01 1d7yA 408 3.47e+01 1d7yA c.3.1.5,c.3.1.5,d.87.1.1 30565,30566,40204 1yseA 141 3.50e+01 2fb6A 117 3.54e+01 1zmaA 118 3.59e+01 1ng7A 60 3.59e+01 a.178.1.1 85671 1louA 101 3.60e+01 1ris d.58.14.1 39323 1viuA 203 3.61e+01 d.113.1.1 100771 1brwA 433 3.63e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1fkqA 124 3.67e+01 3lzt d.2.1.2 36601 1q42A 201 3.70e+01 d.17.4.2 95776 1uiuA 502 3.71e+01 c.94.1.1 99434 1mtpB 43 3.74e+01 2bv4A 113 3.76e+01 1egiA 147 3.76e+01 1eggA d.169.1.1 42331 1sqiA 393 3.78e+01 d.32.1.3,d.32.1.3 105914,105915 1nrwA 288 3.78e+01 c.108.1.10 86128 1t6t1 118 3.78e+01 1wtjA 343 3.79e+01 1b0uA 262 3.79e+01 1b0uA c.37.1.12 32370 1vloA 381 3.80e+01 b.44.2.1,d.250.1.1 108838,108839 1zmoA 244 3.82e+01 1vk8A 106 3.83e+01 d.58.48.1 108636 1j6zA 376 3.84e+01 1yagA c.55.1.1,c.55.1.1 62667,62668 1otkA 249 3.84e+01 a.25.1.2 93521 1qwgA 251 3.85e+01 c.1.27.1 96473 1okhA 46 3.87e+01 g.13.1.1 93253 1pvvA 315 3.88e+01 c.78.1.1,c.78.1.1 95190,95191 1omp 370 3.90e+01 4mbp c.94.1.1 35778 1j5yA 187 3.90e+01 a.4.5.1,d.94.2.1 71592,71593 1q67A 231 3.93e+01 b.55.1.7 95960 3tss 194 3.94e+01 1aw7A b.40.2.2,d.15.6.1 25160,37749 1xc3A 302 3.94e+01 1pcxA 810 3.95e+01 a.71.2.1,b.2.8.1,c.62.1.2,d.109.2.1,g.41.10.1 94497,94498,94499,94500,94501 1heiA 451 3.96e+01 1heiA c.37.1.14,c.37.1.14 32463,32464 1mp9A 198 3.96e+01 d.129.1.1,d.129.1.1 91385,91386 1sgwA 214 3.97e+01 c.37.1.12 105541 1jcfA 344 3.99e+01 c.55.1.1,c.55.1.1 62878,62879 1o1xA 155 4.01e+01 c.121.1.1 86553 1ekeA 230 4.03e+01 1ekeA c.55.3.1 33572 2a9fA 398 4.05e+01 1s5aA 150 4.06e+01 d.17.4.10 98525 1cc1L 498 4.08e+01 1h2rL e.18.1.1 43301 1ktbA 405 4.09e+01 b.71.1.1,c.1.8.1 72960,72961 1u7lA 392 4.09e+01 1c7nA 399 4.11e+01 1d2fA c.67.1.3 34413 1y8tA 324 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