# List of top-scoring protein chains for t2k-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 1ir3A 306 1.21e-59 1fmk d.144.1.7 41702 1opjA 293 6.63e-59 d.144.1.7 87230 1lufA 343 1.52e-58 d.144.1.7 78223 1t46A 313 3.53e-58 d.144.1.7 106397 1jpaA 312 4.23e-58 d.144.1.7 67011 1fgkA 310 5.01e-58 1fgkA d.144.1.7 41693 1p4oA 322 8.75e-58 d.144.1.7 87775 1irk 306 1.77e-57 1fmk d.144.1.7 41703 1qpcA 279 3.45e-57 1fgkA d.144.1.7 41685 3lck 271 6.50e-57 1fmk d.144.1.7 41686 1jqhA 308 5.65e-56 d.144.1.7 71793 1r0pA 312 1.35e-55 d.144.1.7 96734 1fmk 452 4.62e-55 1fmk b.34.2.1,d.93.1.1,d.144.1.7 24511,40436,41690 2b7aA 293 2.61e-54 1u59A 287 3.73e-54 d.144.1.7 107681 1fvrA 327 5.12e-54 d.144.1.7 60047 1ywnA 316 9.40e-54 1mp8A 281 2.14e-53 d.144.1.7 91384 1xbbA 291 5.39e-53 1mq4A 272 9.04e-52 d.144.1.7 91391 1u46A 291 1.98e-51 d.144.1.7 107656 2bfxA 284 4.53e-51 1yhvA 297 7.12e-51 2f57A 317 7.71e-51 2evaA 307 4.30e-50 2bdwA 362 4.80e-50 1gz8A 299 5.29e-50 d.144.1.7 83405 1hcl 298 7.87e-50 1hcl d.144.1.7 41593 1xjdA 345 1.40e-49 1e1xA 299 3.19e-49 1hcl d.144.1.7 59157 1jksA 294 4.44e-49 d.144.1.7 71710 1o6lA 337 6.49e-49 d.144.1.7 81092 1phk 298 7.47e-49 1cdkA d.144.1.7 41635 1jvpP 298 7.47e-49 d.144.1.7 67371 1ia8A 289 2.79e-48 1ia8A d.144.1.7 62112 2c30A 321 3.68e-48 1kobA 387 1.71e-47 1tkiA d.144.1.7 41640 1q8uA 350 2.16e-47 d.144.1.7 96230 1f3mC 297 2.18e-47 1hcl d.144.1.7 41677 1h1wA 289 2.88e-47 d.144.1.7 83460 1cmkE 350 4.84e-47 1cdkA d.144.1.7 41623 1cdkA 350 5.53e-47 1cdkA d.144.1.7 41620 1xh9A 350 8.23e-47 1apmE 350 1.10e-46 1cdkA d.144.1.7 41628 1uu3A 310 1.13e-46 d.144.1.7 99999 1p4fA 293 1.78e-46 d.144.1.7 104063 1s9jA 341 1.26e-45 1t4hA 290 1.92e-45 d.144.1.7 106420 1zrzA 364 2.15e-45 1rdqE 350 2.95e-45 d.144.1.7 97314 1blxA 326 9.55e-45 1hcl d.144.1.7 41596 1o6yA 299 1.01e-44 d.144.1.7 81106 1tvoA 368 1.24e-44 2b9hA 353 1.71e-44 3erk 364 2.12e-44 1hcl d.144.1.7 41654 1vzoA 355 2.54e-44 d.144.1.7 108971 1tkiA 321 3.70e-44 1tkiA d.144.1.7 41638 1pme 380 1.99e-43 1hcl d.144.1.7 41653 1zy4A 303 3.89e-43 2eueA 279 9.33e-43 1omwA 689 1.82e-42 a.91.1.1,b.55.1.1,d.144.1.7 87086,87087,87088 2a19B 284 3.21e-42 1q41A 424 3.32e-42 d.144.1.7 95774 1pmnA 364 4.38e-42 d.144.1.7 94907 1r3cA 366 4.88e-42 d.144.1.7 96906 1wbsA 360 1.01e-41 1xwsA 313 1.96e-41 1j1bA 420 3.12e-41 d.144.1.7 90758 2gfsA 372 4.02e-41 1zzlA 351 4.50e-41 2bikB 313 4.60e-41 1ywrA 360 5.30e-41 2bvaA 292 6.51e-41 1zz2A 360 1.52e-40 1ymiA 334 5.16e-40 1b6cB 342 6.10e-40 1b6cB d.144.1.7 41673 1py5A 326 1.16e-39 d.144.1.7 104389 1vjyA 303 5.22e-39 d.144.1.7 108633 2ac5A 316 8.94e-39 1x8bA 289 9.29e-39 1lpuA 332 1.34e-38 d.144.1.7 74177 1om1A 332 2.58e-38 d.144.1.7 93347 1lp4A 332 4.27e-38 d.144.1.7 74170 1a6o 332 4.66e-38 1a6o 2ac3A 316 5.05e-38 1z57A 339 8.21e-38 1m2rA 327 1.42e-37 d.144.1.7 84760 2eu9A 355 1.28e-36 1jwhA 337 5.40e-34 d.144.1.7 71913 1wbpA 397 1.11e-33 1ckiA 317 1.21e-33 1csn d.144.1.7 41660 1csn 298 2.08e-31 1csn d.144.1.7 41664 1howA 373 3.32e-31 1hcl d.144.1.7 41679 1q8yA 373 4.76e-31 d.144.1.7 96234 1tqmA 282 1.13e-09 a.4.5.56,d.144.1.9 107236,107237 1zarA 282 4.84e-09 1zthA 258 3.89e-06 1nd4A 264 6.37e-06 d.144.1.6 91815 1j7lA 264 1.25e-04 d.144.1.6 62697 1j7iA 264 1.71e-03 1j7iA d.144.1.6 62694 2bkkA 264 6.69e-03 1sauA 115 5.25e-02 1nw1A 429 1.36e-01 d.144.1.8 86286 1f3iA 481 2.05e-01 1b7eA 1e8xA 961 2.08e-01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19148,23183,37631,41711 1e7uA 961 2.42e-01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 2ct9A 208 2.73e-01 1k3eA 156 2.86e-01 d.198.1.1 68103 1f2hA 169 4.04e-01 1f3vA d.58.22.1 59612 1ia9A 280 4.23e-01 1ia9A d.144.1.5 62113 1e8yA 966 5.51e-01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 2ap1A 327 6.12e-01 2a6hC 1119 6.63e-01 1muhA 481 7.70e-01 c.55.3.4 79485 1e17A 150 8.84e-01 2hfh a.4.5.14 16143 2c6yA 111 9.39e-01 1ako 268 1.15e+00 1ako d.151.1.1 41779 6paxA 133 1.25e+00 6paxA a.4.1.5,a.4.1.5 64758,64759 1ur4A 399 1.29e+00 1zbsA 291 1.43e+00 1musA 477 1.46e+00 c.55.3.4 79494 1tzpA 255 1.89e+00 d.65.1.3 107520 2bmhA 455 2.20e+00 1bu7A a.104.1.1 18941 1iw7C 1119 2.37e+00 e.29.1.1 71474 1fmaE 150 2.42e+00 1fmaE d.41.5.1 38630 1o4tA 133 2.44e+00 b.82.1.9 86622 1z7mA 344 2.49e+00 1ek1A 554 2.59e+00 1cr6B c.69.1.11,c.108.1.2 34685,43335 1s4bP 674 3.06e+00 d.92.1.5 105252 1ttwA 138 3.36e+00 d.198.1.1 107308 1ug6A 431 3.36e+00 c.1.8.4 88490 1l7jA 347 3.40e+00 b.30.5.4 73660 1wduA 245 3.43e+00 d.151.1.1 109286 1ncx 162 3.55e+00 1ncx a.39.1.5 17222 1top 162 3.71e+00 1ncx a.39.1.5 17223 1y1xA 191 3.72e+00 1l7jB 347 3.75e+00 b.30.5.4 73661 1nx8A 273 3.96e+00 b.82.2.8 86374 1ng5A 215 3.98e+00 b.100.1.1 91867 1hl8A 449 3.98e+00 b.71.1.3,c.1.8.11 90646,90647 1j27A 102 4.22e+00 d.58.50.1 90778 1cqzA 554 4.25e+00 1cr6B c.69.1.11,c.108.1.2 34689,43339 2a6mA 155 4.60e+00 2fnaA 357 4.60e+00 1omrA 201 4.73e+00 a.39.1.5 93349 2fug5 207 4.76e+00 1b24A 188 4.81e+00 1b24A d.95.2.1,d.95.2.1 40573,40574 1tr0A 108 4.87e+00 d.58.4.4 107261 1f3vA 179 4.90e+00 1f3vA d.58.22.1 39382 1mmuA 347 5.15e+00 b.30.5.4 79303 1eq6A 189 5.30e+00 1eq6A d.107.1.1 40796 1jplA 171 5.56e+00 a.118.9.2 67027 1amuA 563 5.90e+00 1amuA e.23.1.1 43351 1st0A 337 5.91e+00 d.13.1.3,d.246.1.1 98979,98980 1twfK 120 6.04e+00 1l2tA 235 6.06e+00 c.37.1.12 73514 2bzlA 325 6.07e+00 1svdA 473 6.10e+00 1quqA 129 6.31e+00 1quqA b.40.4.3 25303 1nu0A 138 6.32e+00 c.55.3.8 92165 1o9gA 250 6.46e+00 c.66.1.29 86692 1twdA 256 6.49e+00 c.1.30.1 107397 1nszA 347 6.66e+00 b.30.5.4 80724 1fm0E 150 6.86e+00 1fmaE d.41.5.1 38629 1mt6A 280 6.99e+00 b.76.2.1,b.85.7.1 79446,79447 1wmiA 90 7.04e+00 1v2dA 381 7.05e+00 c.67.1.1 108281 1efuB 282 7.10e+00 1efuB d.43.1.1,a.5.2.2,d.43.1.1 38677,58975,58976 1a8y 367 7.16e+00 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 1ojqA 212 7.46e+00 d.166.1.1 93146 1w0dA 337 7.48e+00 1wmiB 67 7.53e+00 1usyA 275 7.53e+00 1c4xA 285 7.58e+00 1c4xA c.69.1.10 34684 1gwiA 411 7.84e+00 a.104.1.1 76364 1aj4 161 7.88e+00 1ncx a.39.1.5 17244 1cliA 345 7.89e+00 1cliA d.79.4.1,d.139.1.1 39816,41459 1rzhH 260 7.93e+00 b.41.1.1,f.23.10.1 98162,98163 1yptA 305 8.23e+00 1ytw c.45.1.2 32686 1cr6B 554 8.24e+00 1cr6B c.69.1.11,c.108.1.2 34688,43338 1t2bA 397 8.31e+00 2b06A 155 8.31e+00 1yal 218 8.38e+00 1cs8A d.3.1.1 37025 1iufA 144 8.43e+00 a.4.1.7,a.4.1.7 71439,71440 1hjrA 158 8.53e+00 1hjrA c.55.3.6 33727 1yh2A 175 8.71e+00 1u2cA 246 8.72e+00 b.1.6.2,d.272.1.1 107610,107611 1p1mA 406 8.83e+00 b.92.1.4,c.1.9.9 87696,87697 1dzkA 157 9.12e+00 1obpA b.60.1.1 27096 1i50K 120 9.30e+00 d.74.3.2 61765 1x0pA 143 9.53e+00 1dun 134 9.72e+00 1dun b.85.4.1 28371 1a3yA 149 1.01e+01 1obpA b.60.1.1 27110 1tw6A 133 1.03e+01 1qpbA 563 1.10e+01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31739,31781,31782 1ffk1 177 1.12e+01 1ffk1 2awdA 323 1.14e+01 1kqfA 1015 1.14e+01 b.52.2.2,c.81.1.1 72871,72872 1ovnA 248 1.15e+01 a.71.1.1,c.47.1.7 93602,93603 1e32A 458 1.18e+01 1e32A b.52.2.3,c.37.1.20,d.31.1.1 59183,59184,59185 1vqoE 178 1.18e+01 1sfxA 109 1.20e+01 a.4.5.50 105505 2f5xA 312 1.22e+01 2f02A 323 1.22e+01 1o7eA 276 1.23e+01 e.3.1.1 92622 1or0B 528 1.23e+01 1txqA 93 1.24e+01 2b4yA 271 1.26e+01 1xdfA 157 1.28e+01 1unqA 125 1.29e+01 b.55.1.1 107968 2gnxA 365 1.33e+01 1vk8A 106 1.35e+01 d.58.48.1 108636 1j6pA 418 1.38e+01 b.92.1.4,c.1.9.9 77089,77090 1jobA 162 1.38e+01 1f35A b.94.1.1 63207 1n4oA 276 1.39e+01 e.3.1.1 91621 1k3sA 113 1.41e+01 d.198.1.1 68120 1b5pA 385 1.42e+01 c.67.1.1 90403 1h10A 125 1.43e+01 b.55.1.1 83446 1icxA 155 1.43e+01 d.129.3.1 71191 1ile 821 1.44e+01 1ile a.27.1.1,b.51.1.1,c.26.1.1 16924,26889,31591 1b4aA 149 1.48e+01 1b4aA a.4.5.3,d.74.2.1 16088,39721 1vybA 238 1.50e+01 d.151.1.1 108897 1vgjA 184 1.50e+01 1oshA 232 1.50e+01 a.123.1.1 93496 1kq8A 100 1.50e+01 a.4.5.14 68797 1t98A 287 1.52e+01 1zmbA 290 1.53e+01 1wg8A 285 1.54e+01 1f7dA 136 1.54e+01 1dun b.85.4.1 28353 2cwxA 430 1.54e+01 2fq3A 104 1.57e+01 1xeqA 103 1.57e+01 1gk8A 475 1.58e+01 c.1.14.1,d.58.9.1 65234,65235 1whzA 70 1.59e+01 1s72E 178 1.61e+01 d.141.1.1,d.141.1.1 105323,105324 1jj2L 194 1.64e+01 1ffkI d.12.1.2 63097 1dqnA 230 1.65e+01 1dqnA c.61.1.1 34067 2axpA 173 1.65e+01 1fxkC 133 1.66e+01 1fxkC a.2.5.1 15702 1f1zA 273 1.68e+01 1f1zA a.4.5.27,c.52.1.16 16081,33334 2a19A 175 1.68e+01 1q4rA 112 1.68e+01 d.58.4.4 95823 1x9zA 188 1.69e+01 1cot 129 1.69e+01 1ycc a.3.1.1 15899 1uj8A 77 1.69e+01 1c8zA 265 1.70e+01 1c8zA d.23.1.1 38375 1gpjA 404 1.70e+01 a.151.1.1,c.2.1.7,d.58.39.1 65451,65452,65453 2comA 124 1.70e+01 2bh4X 134 1.75e+01 1qs1A 462 1.76e+01 1qs1A d.166.1.1,d.166.1.1 42260,42261 1u35C 120 1.76e+01 1b4bA 71 1.76e+01 1b4aA d.74.2.1 39718 1tw0A 157 1.78e+01 1bjwA 382 1.78e+01 1bjwA c.67.1.1 34349 1p9oA 313 1.80e+01 c.72.3.1 94397 2fa1A 160 1.83e+01 1fm2B 520 1.83e+01 1fm2B 1g8iA 190 1.85e+01 1rec a.39.1.5 60363 1t0fA 276 1.87e+01 1u7gA 385 1.87e+01 f.44.1.1 107723 1m6pA 152 1.88e+01 1m6pA b.64.1.1 27519 1jscA 630 1.88e+01 c.31.1.3,c.36.1.5,c.36.1.9 67224,67225,67226 1io2A 213 1.91e+01 1ekeA c.55.3.1 62612 1huxA 270 1.94e+01 1huxA c.55.1.5 61278 1ccr 112 1.95e+01 1ycc a.3.1.1 15877 2cb2A 318 1.95e+01 1o4sA 389 1.95e+01 c.67.1.1 86620 1hl9A 449 1.96e+01 b.71.1.3,c.1.8.11 90650,90651 1gw5S 142 2.00e+01 d.110.4.2 70633 1dutA 133 2.01e+01 1dun b.85.4.1 28355 1fnoA 417 2.02e+01 d.58.19.1,c.56.5.4 70145,75841 1k78A 149 2.02e+01 a.4.1.5,a.4.1.5 68255,68256 1jj2E 177 2.05e+01 1ffk1 d.141.1.1,d.141.1.1 63089,63090 1jj7A 260 2.06e+01 c.37.1.12 63114 1ygmA 118 2.07e+01 1yqtA 538 2.08e+01 1tfe 145 2.08e+01 1tfe d.43.1.1 38680 1daqA 71 2.09e+01 1daqA a.139.1.1 59113 1itpA 77 2.09e+01 d.58.3.2 66371 1jysA 242 2.10e+01 c.56.2.1 77216 1sqeA 109 2.14e+01 d.58.4.5 105908 1mvcA 240 2.14e+01 a.123.1.1 79499 1ks9A 291 2.14e+01 a.100.1.7,c.2.1.6 68857,68858 1fxrA 64 2.15e+01 1fxd d.58.1.4 38993 1jpzA 473 2.15e+01 a.104.1.1 67069 1t6cA 315 2.17e+01 c.55.1.8,c.55.1.8 106558,106559 2bycA 137 2.17e+01 1mvwC 147 2.20e+01 i.15.1.1 79525 1o1fC 147 2.20e+01 i.15.1.1 80997 1hdhA 536 2.20e+01 c.76.1.2 65805 1adeA 431 2.22e+01 1adeA c.37.1.10 32213 1jhsA 188 2.22e+01 d.107.1.1 84172 1auiB 169 2.23e+01 1auiB a.39.1.5 17325 1f93A 104 2.23e+01 1dcpA d.74.1.1 39688 1zzpA 130 2.25e+01 1v5iB 76 2.28e+01 1ykwA 435 2.28e+01 1ytw 306 2.31e+01 1ytw c.45.1.2 32689 1l7aA 318 2.35e+01 c.69.1.25 77772 1e3dA 266 2.35e+01 2frvA e.19.1.1 59188 1cor 82 2.35e+01 451c a.3.1.1 15903 1uetA 437 2.39e+01 a.160.1.3,d.218.1.7,d.58.16.2 99272,99273,99274 1pbgA 468 2.39e+01 1e70M c.1.8.4 28946 2ebn 289 2.46e+01 2ebn c.1.8.5 28990 1woqA 267 2.47e+01 c.55.1.10,c.55.1.10 109462,109463 1gdeA 389 2.48e+01 c.67.1.1 60456 1jsxA 207 2.50e+01 c.66.1.20 71846 3tdt 274 2.53e+01 3tdt b.81.1.2 28053 2gwxA 267 2.57e+01 2prgA a.123.1.1 19323 1w66A 232 2.57e+01 1ytn 306 2.62e+01 1ytw c.45.1.2 32688 1lyvA 306 2.65e+01 c.45.1.2 74348 2tdt 274 2.65e+01 3tdt b.81.1.2 28054 1ddf 127 2.70e+01 1ddf a.77.1.2 18423 1sd4A 126 2.71e+01 a.4.5.39 105428 1kgqA 274 2.73e+01 b.81.1.2 72447 2erbA 125 2.74e+01 1dcpA 104 2.76e+01 1dcpA d.74.1.1 39672 1mroC 247 2.77e+01 1mroC d.58.31.1 39437 1fsz 372 2.78e+01 1fsz c.32.1.1,d.79.2.1 31750,39802 2bodX 286 2.80e+01 1e8cA 498 2.82e+01 c.98.1.1,c.59.1.1,c.72.2.1 59377,59378,59379 1yvcA 70 2.84e+01 1okrA 123 2.84e+01 a.4.5.39 93269 2b49A 287 2.85e+01 1q53A 112 2.85e+01 d.58.4.4 95858 1gd9A 389 2.87e+01 c.67.1.1 60454 1a04A 215 2.88e+01 1a04A a.4.6.2,c.23.1.1 16234,31089 1wxrA 1048 2.89e+01 1rec 201 2.89e+01 1rec a.39.1.5 17326 1i4sA 147 2.92e+01 a.149.1.1 66026 2aa4A 289 2.94e+01 1yemA 179 2.96e+01 1o51A 114 2.97e+01 d.58.5.4 92480 1o6aA 96 2.97e+01 b.139.1.1 92562 1i8tA 367 2.99e+01 c.4.1.3,d.16.1.7 66094,66095 2a9kA 187 3.03e+01 1jfzA 154 3.04e+01 a.149.1.1 66655 1aijH 260 3.04e+01 6prcH b.41.1.1,f.23.10.1 25466,43463 1u53A 196 3.04e+01 2bcfA 276 3.04e+01 1uarA 285 3.05e+01 c.46.1.2,c.46.1.2 107762,107763 1regX 122 3.06e+01 1regX d.58.27.1 39406 1o9yA 84 3.08e+01 b.139.1.1 92692 2awgA 118 3.12e+01 1z85A 234 3.20e+01 1xkpC 143 3.21e+01 1cpo 299 3.22e+01 1cpo a.39.3.1,a.39.3.1 17390,17391 1yts 278 3.23e+01 1ytw c.45.1.2 32690 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