# List of top-scoring protein chains for t2k-100-30-dssp-ebghstl-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 2bcoA 350 8.82e-35 1yw4A 341 7.97e-32 1h8lA 380 1.22e-06 b.3.2.1,c.56.5.1 65737,65738 1qmuA 380 3.44e-06 1qmuA b.3.2.1,c.56.5.1 22534,33827 1jqgA 433 1.91e-03 c.56.5.1,d.58.3.1 71791,71792 2c1cA 312 3.00e-02 2bo9A 308 3.70e-02 1aye 401 1.24e-01 1aye c.56.5.1,d.58.3.1 33824,39065 1xovA 326 1.26e-01 1yme 309 1.31e-01 1aye c.56.5.1 33804 1jv1A 505 1.47e-01 c.68.1.5 71892 1m4lA 307 1.52e-01 c.56.5.1 78604 2ctb 307 1.60e-01 1aye c.56.5.1 33803 1d0nA 729 2.30e-01 1d0nA d.109.1.1,d.109.1.1,d.109.1.1,d.109.1.1,d.109.1.1,d.109.1.1 40834,40835,40836,40837,40838,40839 2ctc 307 2.33e-01 1aye c.56.5.1 33802 1dtdA 303 2.73e-01 1aye c.56.5.1 33823 6cpa 307 2.74e-01 1aye c.56.5.1 33816 1bavA 309 2.75e-01 1aye c.56.5.1 33806 1z5rA 306 2.77e-01 1cz1A 394 3.31e-01 1cz1A c.1.8.3 28839 1kwmA 402 3.31e-01 c.56.5.1,d.58.3.1 73079,73080 1eqcA 394 3.50e-01 1cz1A c.1.8.3 28811 1vm8A 534 4.25e-01 1hh2P 344 5.51e-01 b.40.4.5,d.52.3.1,d.52.3.1,d.202.1.1 65835,65836,65837,65838 1o0wA 252 8.13e-01 a.149.1.1,d.50.1.1 80751,80752 1pkm 530 1.40e+00 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27051,29254,33108 1csp 67 1.84e+00 1mjc b.40.4.5 25321 1h4pA 408 2.79e+00 c.1.8.3 90617 1lqtA 456 3.86e+00 c.3.1.1,c.4.1.1 74198,74199 1pkn 530 3.91e+00 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27042,29271,33125 1jwqA 179 4.14e+00 c.56.5.6 90921 1c9oA 66 4.32e+00 1mjc b.40.4.5 25325 1qm4A 396 4.61e+00 1mxb d.130.1.1,d.130.1.1,d.130.1.1 41350,41351,41352 1a6o 332 4.96e+00 1a6o 1fp3A 402 5.01e+00 1fp3A a.102.1.3 18842 1jsmA 325 5.18e+00 b.19.1.2 63264 1lpuA 332 5.46e+00 d.144.1.7 74177 3hmgA 328 5.99e+00 1hgeA b.19.1.2 23825 1t2wA 145 6.37e+00 b.100.1.1 106289 2b25A 336 6.46e+00 1om1A 332 6.62e+00 d.144.1.7 93347 1s0uA 408 6.67e+00 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 1lp4A 332 6.67e+00 d.144.1.7 74170 1m2rA 327 6.68e+00 d.144.1.7 84760 1uyjA 296 6.77e+00 f.8.1.2 108143 1uanA 227 6.93e+00 c.134.1.1 99135 1yqfA 203 6.93e+00 1z9hA 290 7.11e+00 2fokA 579 7.37e+00 2fokA a.4.5.12,a.4.5.12,a.4.5.12,c.52.1.12 16131,16132,16133,33323 1x7vA 99 9.51e+00 d.58.4.11 109501 1laxA 370 9.53e+00 c.94.1.1 84576 1a49A 530 9.66e+00 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27026,29255,33109 1ekrA 161 9.80e+00 1ekrA d.58.21.1 39380 2occB 227 1.01e+01 2occB b.6.1.2,f.17.2.1 23027,43519 1ijaA 148 1.08e+01 1ijaA b.100.1.1 62484 1brwA 433 1.10e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1cy9A 264 1.10e+01 1ecl e.10.1.1 43236 1sltB 134 1.12e+01 1c1lA b.29.1.3 24187 1yloA 348 1.17e+01 1v54B 227 1.19e+01 b.6.1.2,f.17.2.1 100322,100323 2g50A 530 1.20e+01 2f9cA 334 1.21e+01 1f1sA 814 1.28e+01 a.102.3.2,b.1.18.2,b.24.1.1,b.30.5.2 64928,64929,64930,64931 1h7eA 245 1.33e+01 c.68.1.13 60717 1yp5A 58 1.34e+01 1qrdA 273 1.39e+01 1d4aA c.23.5.3 31217 1sx5A 244 1.43e+01 c.52.1.2 99023 1hlcA 129 1.45e+01 1c1lA b.29.1.3 24208 2ac5A 316 1.46e+01 1kbqA 273 1.49e+01 c.23.5.3 68391 1xjdA 345 1.50e+01 1ezoA 370 1.53e+01 4mbp c.94.1.1 59539 1ywnA 316 1.54e+01 1jvbA 347 1.64e+01 b.35.1.2,c.2.1.1 77181,77182 1hgeA 328 1.68e+01 1hgeA b.19.1.2 23816 2viuA 328 1.68e+01 1hgeA b.19.1.2 23797 1sltA 134 1.69e+01 1c1lA b.29.1.3 24186 1qd1A 325 1.74e+01 1qd1A d.58.34.1,d.58.34.1 39493,39494 1xx1A 285 1.75e+01 1nt4A 391 1.75e+01 c.60.1.2 92102 1mfgA 95 1.75e+01 b.36.1.1 79043 1ruwA 69 1.78e+01 1j7nB 776 1.81e+01 d.92.1.14,d.92.1.14,d.166.1.1 66412,66413,66414 1bl3A 160 1.82e+01 1b9dA c.55.3.2 33655 2a5hA 416 1.85e+01 1f35A 162 1.86e+01 1f35A b.94.1.1 59628 2aujD 309 1.87e+01 1z1zA 131 1.89e+01 1r6lA 239 1.92e+01 d.14.1.4,d.101.1.1 97153,97154 1d4aA 273 1.96e+01 1d4aA c.23.5.3 31219 1obr 326 2.02e+01 1aye c.56.5.2 33828 1vnc 609 2.03e+01 1vns a.111.1.3 19065 1c0aA 585 2.04e+01 1c0aA b.40.4.1,d.74.4.1,d.104.1.1 25246,39731,40767 1jobA 162 2.04e+01 1f35A b.94.1.1 63207 1is3A 135 2.04e+01 b.29.1.3 76773 1w36B 1180 2.05e+01 1gsoA 431 2.10e+01 1gsoA b.84.2.1,c.30.1.1,d.142.1.2 28240,31647,41492 1nuuA 252 2.16e+01 c.26.1.3 86209 2aqjA 538 2.18e+01 1mjc 69 2.19e+01 1mjc b.40.4.5 25319 1b97A 244 2.22e+01 1rvaA c.52.1.2 33252 1f7wA 144 2.22e+01 1f46A d.129.4.1 59679 1qyaA 307 2.26e+01 d.21.1.2,d.21.1.2 104653,104654 1jhfA 202 2.29e+01 a.4.5.2,b.87.1.1 63057,63058 1fokA 568 2.32e+01 2fokA a.4.5.12,a.4.5.12,a.4.5.12,c.52.1.12 16137,16138,16139,33325 1pg6A 243 2.33e+01 b.82.5.2 94673 1x47A 98 2.33e+01 1ki9A 192 2.36e+01 c.37.1.1 84404 1sdjA 310 2.40e+01 d.21.1.2,d.21.1.2 98807,98808 1yvvA 336 2.41e+01 1hjzA 192 2.42e+01 c.50.1.2 83520 1jcjA 260 2.47e+01 c.1.10.1 66499 1vhuA 211 2.54e+01 c.50.1.2 100703 1bynA 128 2.54e+01 1rsy b.7.1.2 23193 1d3uA 181 2.58e+01 1ytbA d.129.1.1,d.129.1.1 41290,41291 1ymiA 334 2.58e+01 1vns 609 2.63e+01 1vns a.111.1.3 19061 1j7nA 776 2.65e+01 d.92.1.14,d.92.1.14,d.166.1.1 66409,66410,66411 1rvaA 244 2.68e+01 1rvaA c.52.1.2 33240 1ecl 597 2.70e+01 1ecl e.10.1.1 43238 1v1aA 309 2.74e+01 c.72.1.1 100249 1hfoA 113 2.75e+01 d.80.1.3 61006 1gdhA 320 2.76e+01 1gdhA c.2.1.4,c.23.12.1 30095,31355 1b94A 244 2.77e+01 1rvaA c.52.1.2 33250 1ja1A 622 2.78e+01 1amoA b.43.4.1,c.23.5.2,c.25.1.4 62803,62804,62805 1wjnA 97 2.80e+01 1tltA 319 2.82e+01 c.2.1.3,d.81.1.5 107135,107136 1jh2A 99 2.84e+01 1rsy 152 2.96e+01 1rsy b.7.1.2 23192 1qbgA 272 2.97e+01 1d4aA c.23.5.3 31227 1ynmA 247 2.98e+01 1ycsB 239 3.06e+01 1ycsB d.211.1.1,b.34.2.1 19155,24553 1hyvA 166 3.07e+01 1b9dA c.55.3.2 61424 2eueA 279 3.11e+01 1l2tA 235 3.17e+01 c.37.1.12 73514 1bvp1 349 3.22e+01 1bvp1 1j9jA 247 3.25e+01 c.106.1.1 62758 1yt8A 539 3.26e+01 1slaA 134 3.27e+01 1c1lA b.29.1.3 24196 1rpxA 230 3.30e+01 1rpxA c.1.2.2 28536 1jclA 260 3.31e+01 c.1.10.1 66501 1semA 58 3.35e+01 1ckaA b.34.2.1 24544 1p1xA 260 3.43e+01 c.1.10.1 104060 1u1hA 765 3.45e+01 c.1.22.2,c.1.22.2 107580,107581 1j9lA 247 3.51e+01 c.106.1.1 62762 1tlfA 301 3.53e+01 1tlfA c.93.1.1 35687 1ummA 172 3.55e+01 a.3.1.1 107958 1f47B 144 3.61e+01 1f46A d.129.4.1 59645 1d4xG 126 3.62e+01 1d0nA d.109.1.1 59109 1n3gA 113 3.63e+01 d.204.1.1 79962 1kcqA 104 3.67e+01 d.109.1.1 68449 2axpA 173 3.73e+01 1vp4A 425 3.77e+01 1aisA 182 3.80e+01 1ytbA d.129.1.1,d.129.1.1 41288,41289 1ald 363 3.82e+01 1fbaA c.1.10.1 29100 1gpr 162 3.86e+01 1gpr b.84.3.1 28267 1wlpB 138 3.90e+01 1mh3A 421 3.91e+01 a.4.1.1,c.94.1.1 79112,79113 1pa2A 306 3.91e+01 1bgp a.93.1.1 18693 1eonA 245 3.93e+01 1rvaA c.52.1.2 33238 1pmi 440 3.94e+01 1pmi b.82.1.3 28114 1w5fA 353 4.00e+01 1gu7A 364 4.01e+01 b.35.1.2,c.2.1.1 83321,83322 2ac3A 316 4.04e+01 1u1jA 765 4.10e+01 c.1.22.2,c.1.22.2 107590,107591 1mp9A 198 4.23e+01 d.129.1.1,d.129.1.1 91385,91386 1zaiA 363 4.27e+01 1irxA 523 4.29e+01 a.97.1.2,c.26.1.1 71378,71379 1nm1G 125 4.31e+01 d.109.1.1 80653 1qr0A 228 4.37e+01 1qr0A d.150.1.1,d.150.1.1 59038,59039 1yhtA 367 4.43e+01 1aocA 175 4.43e+01 1aocA g.17.1.5 44817 1sfjA 238 4.47e+01 1a16 440 4.56e+01 1az9 c.55.2.1,d.127.1.1 33548,41165 1yr4A 237 4.60e+01 2f91A 237 4.60e+01 1adoA 363 4.61e+01 1fbaA c.1.10.1 29124 1g8lA 411 4.62e+01 1g8lA b.85.6.1,b.103.1.1,c.57.1.2 60365,60366,60367 1kczA 413 4.70e+01 c.1.11.2,d.54.1.1 68451,68452 1a3wA 500 4.73e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27060,29288,33142 1wapA 75 4.77e+01 1wapA b.82.5.1 28153 1jnyA 435 4.77e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1tm0A 350 4.77e+01 d.21.1.3 107147 1yagG 125 4.79e+01 1d0nA d.109.1.1 40846 1b3tA 147 4.81e+01 1b3tA d.58.8.1 39228 1sefA 274 4.83e+01 b.82.1.11 105452 2ak5A 64 4.84e+01 1jsdA 319 4.85e+01 b.19.1.2 63258 1uqrA 154 4.88e+01 c.23.13.1 99779 1s5lH 66 4.90e+01 1ra6A 461 5.06e+01 e.8.1.4 104879 1hm9A 468 5.07e+01 b.81.1.4,c.68.1.5 65866,65867 1ng2A 193 5.08e+01 b.34.2.1,b.34.2.1 85660,85661 1izcA 339 5.13e+01 c.1.12.5 83838 1u02A 239 5.15e+01 c.108.1.15 107538 1dfcA 493 5.17e+01 1dfcA b.42.5.1,b.42.5.1,b.42.5.1,b.42.5.1 25616,25617,25618,25619 1l4sA 112 5.19e+01 d.204.1.1 77693 1y8qB 640 5.24e+01 1sflA 238 5.24e+01 1zdzA 302 5.29e+01 1cliA 345 5.32e+01 1cliA d.79.4.1,d.139.1.1 39816,41459 1fbaA 361 5.34e+01 1fbaA c.1.10.1 29120 2g6fX 59 5.40e+01 1mpb 370 5.41e+01 4mbp c.94.1.1 35780 1ltoA 245 5.46e+01 b.47.1.2 84707 1w9hA 427 5.48e+01 1omp 370 5.52e+01 4mbp c.94.1.1 35778 1wzcA 249 5.56e+01 2fymA 431 5.57e+01 4mbp 370 5.60e+01 4mbp c.94.1.1 35777 1bb9 115 5.70e+01 1bb9 b.34.2.1 24554 1b9dA 163 5.71e+01 1b9dA c.55.3.2 33649 1lufA 343 5.71e+01 d.144.1.7 78223 1lcyA 325 5.76e+01 b.36.1.4,b.47.1.1 73834,73835 2fpeA 62 5.77e+01 1ltlA 279 5.77e+01 b.40.4.11 84701 2axtH 66 5.79e+01 1qisA 396 5.81e+01 1ajsA c.67.1.1 34284 1ads 315 5.88e+01 1frb c.1.7.1 28671 1vajA 214 5.88e+01 1g97A 459 5.90e+01 1fwyA b.81.1.4,c.68.1.5 60394,60395 1yrgA 385 5.99e+01 1yrgA c.10.1.2 30854 2aeuA 374 6.05e+01 2c8sA 172 6.08e+01 1ariA 396 6.12e+01 1ajsA c.67.1.1 34331 1anf 370 6.21e+01 4mbp c.94.1.1 35776 1ub4A 110 6.26e+01 b.34.6.2 88399 1jbkA 195 6.31e+01 c.37.1.20 71631 1bxkA 355 6.42e+01 1bxkA c.2.1.2 29803 1e9iA 431 6.47e+01 c.1.11.1,d.54.1.1 64818,64819 3sxlA 184 6.48e+01 1b7fA d.58.7.1,d.58.7.1 39173,39174 1v10A 521 6.53e+01 b.6.1.3,b.6.1.3,b.6.1.3 108224,108225,108226 1o20A 427 6.53e+01 c.82.1.1 86556 1gw5M 435 6.54e+01 b.2.7.1,d.110.4.2 70631,70632 1kamA 194 6.76e+01 c.26.1.3 72254 1r3dA 264 6.79e+01 1vj0A 380 6.80e+01 b.35.1.2,c.2.1.1 100786,100787 2bwvA 440 6.81e+01 1az1 315 6.81e+01 1frb c.1.7.1 28677 1bg0 356 6.82e+01 1qh4A a.83.1.1,d.128.1.2 18476,41211 1ble 163 6.83e+01 1ble c.38.1.1 32475 1xfjA 261 6.83e+01 d.194.1.2 109585 1w5tA 412 6.85e+01 1ytvA 366 6.87e+01 1wl9A 440 6.89e+01 1jihA 531 7.02e+01 d.240.1.1,e.8.1.7 90374,90375 1e0tA 470 7.03e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 1spvA 184 7.10e+01 c.50.1.2 98957 1art 396 7.16e+01 1ajsA c.67.1.1 34285 1gca 309 7.17e+01 1gca c.93.1.1 35659 1jyeA 349 7.18e+01 c.93.1.1 67455 1f60A 458 7.25e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 1es4A 262 7.27e+01 1skf e.3.1.1 42683 1t64A 377 7.30e+01 c.42.1.2 106543 1ov3A 138 7.30e+01 b.34.2.1,b.34.2.1 87451,87452 1gpeA 587 7.30e+01 1gpeA c.3.1.2,d.16.1.1 30387,37951 1ib8A 164 7.32e+01 b.38.2.1,d.52.4.1 71168,71169 1qtnA 164 7.38e+01 1pauA c.17.1.1 30999 1yj7A 171 7.47e+01 2acr 315 7.51e+01 1frb c.1.7.1 28674 1xmbA 418 7.51e+01 1wyuB 474 7.53e+01 2fkcA 247 7.53e+01 1lw6E 281 7.57e+01 c.41.1.1 74293 1jwhA 337 7.61e+01 d.144.1.7 71913 1az9 457 7.62e+01 1az9 c.55.2.1,d.127.1.1 33547,41164 1a4iA 301 7.66e+01 1a4iA c.2.1.7,c.58.1.2 30278,33926 1wr7A 41 7.66e+01 1a7lA 389 7.68e+01 4mbp c.94.1.1 35787 1a0lA 244 7.69e+01 5ptp b.47.1.2 26286 1sup 275 7.73e+01 1gci c.41.1.1 32510 1uozA 315 7.74e+01 1qi9A 556 7.81e+01 1qhbA a.111.1.2 19053 1a4iB 301 7.86e+01 1a4iA c.2.1.7,c.58.1.2 30279,33927 1lzjA 292 7.87e+01 c.68.1.9 74352 1ne2A 200 7.88e+01 c.66.1.32 85586 1r62A 160 7.96e+01 d.122.1.3 104816 1uj0A 62 7.98e+01 b.34.2.1 99449 1u6zA 513 8.01e+01 1bqg 451 8.02e+01 1bqg c.1.11.2,d.54.1.1 29217,38861 1ghtA 105 8.10e+01 2rslA c.53.1.1 60526 2cxaA 256 8.15e+01 1onxA 390 8.17e+01 b.92.1.7,c.1.9.13 87176,87177 1wlqC 201 8.29e+01 a.4.5.52 109400 1vliA 385 8.38e+01 b.85.1.1,c.1.10.6 108830,108831 1wcgA 464 8.39e+01 1rdr 461 8.41e+01 1rdr e.8.1.4 43116 1to2E 281 8.41e+01 1o4tA 133 8.44e+01 b.82.1.9 86622 1a6aA 176 8.47e+01 1iakA b.1.1.2,d.19.1.1 21615,38189 1g5rA 196 8.48e+01 1g5rA c.37.1.11 32367 1g5tA 196 8.48e+01 1g5rA c.37.1.11 32366 1eguA 731 8.55e+01 1eguA a.102.3.2,b.24.1.1,b.30.5.2 18850,23899,24423 1v74A 107 8.58e+01 d.243.1.1 100442 1x1mA 107 8.66e+01 1cauA 181 8.73e+01 1dgwA b.82.1.2 28102 1kyqA 274 8.73e+01 c.2.1.11,e.37.1.1 73281,73282 1vhiA 142 8.76e+01 1b3tA d.58.8.1 39230 2gl5A 410 8.87e+01 1frvB 536 8.87e+01 1h2rL e.18.1.1 43296 2hsdA 253 8.92e+01 1e6wA c.2.1.2 29866 1i16 130 8.92e+01 1i16 b.36.1.2 24787 1dp4A 435 8.99e+01 1dp4A c.93.1.1 35710