# 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 2f22A 144 2.01e-09 1rxqA 178 1.21e-03 a.213.1.1 105118 2b0tA 738 2.20e-01 1ekeA 230 5.44e-01 1ekeA c.55.3.1 33572 1l3pA 102 1.43e+00 a.24.17.1 84520 1r71A 178 1.64e+00 a.4.14.1 104823 2bb6A 414 1.74e+00 1iw7C 1119 2.25e+00 e.29.1.1 71474 1itwA 741 2.90e+00 c.77.1.2 76793 1ku2A 241 2.99e+00 a.4.13.1,a.177.1.1 83096,83097 3ladA 476 3.15e+00 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30573,30574,40208 1exzA 141 3.30e+00 1exzA a.26.1.2 16877 2a6hC 1119 3.44e+00 1h2aL 567 3.57e+00 1h2rL e.18.1.1 43299 1ui5A 215 3.82e+00 a.4.1.9,a.121.1.1 107856,107857 1nw3A 416 4.25e+00 c.66.1.31 86288 1h2rL 534 4.68e+00 1h2rL e.18.1.1 43298 2a65A 519 4.85e+00 1itf 165 5.38e+00 1b5l a.26.1.3 16899 1sqgA 429 5.50e+00 a.79.1.3,c.66.1.38 105912,105913 1i6kA 328 5.62e+00 c.26.1.1 66040 1xg1A 67 5.92e+00 1b8aA 438 5.93e+00 1b8aA b.40.4.1,d.104.1.1 25244,40765 1ahxA 396 6.36e+00 1ajsA c.67.1.1 34293 1i6lA 328 6.78e+00 c.26.1.1 66041 1io2A 213 6.93e+00 1ekeA c.55.3.1 62612 1fp3A 402 7.51e+00 1fp3A a.102.1.3 18842 1d2rB 326 7.54e+00 1d2rB c.26.1.1 31573 1zroA 602 7.61e+00 2c3nA 247 7.62e+00 2cmwA 310 7.71e+00 1d2fA 390 7.73e+00 1d2fA c.67.1.3 34411 3bdpA 580 8.90e+00 1xwl c.55.3.5,e.8.1.1 33711,43004 1d2rA 326 9.79e+00 1d2rB c.26.1.1 31572 1z6oM 191 9.93e+00 2f1sA 186 1.05e+01 1ariA 396 1.07e+01 1ajsA c.67.1.1 34331 1l3eB 101 1.07e+01 g.53.1.1 73536 1ubkL 534 1.10e+01 e.18.1.1 88422 1asg 396 1.10e+01 1ajsA c.67.1.1 34335 1arhA 396 1.14e+01 1ajsA c.67.1.1 34321 1au1A 166 1.14e+01 1ifa a.26.1.3 16889 2f7fA 494 1.16e+01 2ae5B 528 1.17e+01 1xahA 354 1.20e+01 1ajqA 209 1.21e+01 1ajqA d.153.1.2 41840 1t77A 414 1.22e+01 1nk4A 580 1.23e+01 c.55.3.5,e.8.1.1 91923,91924 1wuiL 534 1.34e+01 6gsvA 217 1.35e+01 1b8xA a.45.1.1,c.47.1.5 17633,32925 1qisA 396 1.39e+01 1ajsA c.67.1.1 34284 1fm2B 520 1.43e+01 1fm2B 1wxiA 275 1.47e+01 1aiaA 396 1.47e+01 1ajsA c.67.1.1 34306 1vj7A 393 1.50e+01 a.211.1.1,d.218.1.8 100801,100802 2bdpA 580 1.52e+01 1xwl c.55.3.5,e.8.1.1 33709,43002 1xkgA 312 1.60e+01 1xwl 580 1.65e+01 1xwl c.55.3.5,e.8.1.1 33708,43001 2bzlA 325 1.65e+01 2fh5A 185 1.72e+01 1or0B 528 1.72e+01 1tazA 365 1.73e+01 a.211.1.2 106734 1k6kA 143 1.87e+01 a.174.1.1 77274 1rmi 160 1.94e+01 1ifa a.26.1.3 16891 1l3sA 580 2.06e+01 c.55.3.5,e.8.1.1 84521,84522 2bbrA 195 2.11e+01 2a5yA 204 2.12e+01 1l6nA 289 2.14e+01 a.61.1.1,a.73.1.1 73624,73625 1ymmB 198 2.14e+01 2abk 211 2.15e+01 2abk a.96.1.1 18743 1pmnA 364 2.22e+01 d.144.1.7 94907 1i50A 1733 2.24e+01 e.29.1.2 61754 2a6cA 83 2.28e+01 1le6A 123 2.31e+01 a.133.1.2 73862 2afdA 88 2.32e+01 1ujwB 135 2.33e+01 h.4.9.1 99472 1art 396 2.35e+01 1ajsA c.67.1.1 34285 1us6A 102 2.36e+01 a.2.13.1 107999 1gk1B 522 2.38e+01 1jbkA 195 2.41e+01 c.37.1.20 71631 2fug1 438 2.41e+01 3lck 271 2.41e+01 1fmk d.144.1.7 41686 1ufaA 520 2.48e+01 a.8.3.3,c.6.2.4 99329,99330 1pnkA 209 2.48e+01 1ajqA d.153.1.2 41839 1rm8A 169 2.50e+01 d.92.1.11 97660 1nz6A 101 2.52e+01 a.2.3.1 86441 1r2rA 248 2.53e+01 c.1.1.1 96875 1amk 251 2.60e+01 1amk c.1.1.1 28503 1f07A 321 2.62e+01 1ezwA c.1.16.3 59560 1qh0A 295 2.63e+01 b.43.4.2,c.25.1.1 68891,68892 1twfA 1733 2.64e+01 1z8oA 404 2.65e+01 1xdpA 687 2.68e+01 1xrsA 516 2.70e+01 1que 303 2.70e+01 1fnc b.43.4.2,c.25.1.1 25647,31537 1syyA 346 2.77e+01 a.25.1.2 106126 1qpcA 279 2.78e+01 1fgkA d.144.1.7 41685 1lrv 244 2.78e+01 1lrv a.118.1.5 19146 1tpfA 250 2.83e+01 1amk c.1.1.1 28467 2bsaA 303 2.85e+01 1ars 396 2.85e+01 1ajsA c.67.1.1 34287 1qgiA 259 2.88e+01 1qgiA d.2.1.7 37001 1n55A 251 2.89e+01 c.1.1.1 80007 1w34A 304 2.92e+01 1b2rA 304 2.93e+01 1fnc b.43.4.2,c.25.1.1 25648,31538 1ew6B 137 2.96e+01 1ewaA a.1.1.2 15638 1tns 76 2.98e+01 1qpmA a.6.1.7 16228 1gthB 1025 3.00e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70488,70489,70490,70491,70492 1w0uA 55 3.03e+01 1vnc 609 3.05e+01 1vns a.111.1.3 19065 1lrrA 131 3.08e+01 d.228.1.1 78165 1ckiA 317 3.08e+01 1csn d.144.1.7 41660 1vns 609 3.12e+01 1vns a.111.1.3 19061 1xrjA 261 3.25e+01 1go2A 304 3.26e+01 b.43.4.2,c.25.1.1 76243,76244 2amlA 373 3.29e+01 1gteA 1025 3.37e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70440,70441,70442,70443,70444 1ithA 141 3.40e+01 1ithA a.1.1.2 15623 1wu3I 161 3.41e+01 1gteD 1025 3.42e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70455,70456,70457,70458,70459 1q7sA 117 3.44e+01 c.131.1.1 96055 1tu7A 208 3.51e+01 2gfoA 396 3.57e+01 1qjaA 245 3.60e+01 1qjaA a.118.7.1 19204 1aw2A 256 3.63e+01 1amk c.1.1.1 28523 1tfb 208 3.69e+01 1tfb a.74.1.2,a.74.1.2 18382,18383 1qyrA 252 3.80e+01 c.66.1.24 104657 1x4tA 92 3.81e+01 1u4bA 580 3.83e+01 c.55.3.5,e.8.1.1 107664,107665 2bh4X 134 3.85e+01 1bco 327 3.86e+01 1bco b.48.1.1,c.55.3.3 26431,33676 1gt8B 1025 3.88e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70423,70424,70425,70426,70427 1zhxA 438 3.90e+01 1frvB 536 3.94e+01 1h2rL e.18.1.1 43296 1gk9A 260 4.03e+01 d.153.1.2 65246 1vd5A 377 4.05e+01 a.102.1.7 108518 1ew6A 137 4.06e+01 1ewaA a.1.1.2 15637 1ewaA 137 4.06e+01 1ewaA a.1.1.2 15639 1ogiA 303 4.08e+01 b.43.4.2,c.25.1.1 92914,92915 1toaA 313 4.08e+01 1toaA c.92.2.2 35598 1w6tA 444 4.08e+01 1k8kE 178 4.16e+01 a.148.1.1 68311 1yirA 408 4.21e+01 1e3dB 542 4.23e+01 1h2rL e.18.1.1 59189 1pioA 257 4.23e+01 1btl e.3.1.1 42719 1gthC 1025 4.25e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70493,70494,70495,70496,70497 1spa 396 4.29e+01 1ajsA c.67.1.1 34291 1h7wD 1025 4.31e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15686,28631,30327,30612,39010 1lt3A 240 4.32e+01 1lt3A d.166.1.1 42230 1ytaA 180 4.35e+01 1irxA 523 4.36e+01 a.97.1.2,c.26.1.1 71378,71379 1ai7A 209 4.40e+01 1ajqA d.153.1.2 41845 2bdeA 470 4.42e+01 1kepA 348 4.44e+01 c.2.1.2 68536 1lt4A 247 4.45e+01 1lt3A d.166.1.1 42231 1tn6A 382 4.50e+01 2c2qA 199 4.51e+01 1adjA 421 4.55e+01 1adjA c.51.1.1,d.104.1.1 33188,40737 1sjdA 368 4.62e+01 c.1.11.2,d.54.1.1 105632,105633 3timA 250 4.63e+01 1amk c.1.1.1 28483 1fmk 452 4.65e+01 1fmk b.34.2.1,d.93.1.1,d.144.1.7 24511,40436,41690 1d5mB 192 4.71e+01 1iakB b.1.1.2,d.19.1.1 21618,38192 1fc3A 120 4.74e+01 1fc3A a.4.6.3 16237 1mu5A 471 4.76e+01 a.156.1.3,d.14.1.3,d.122.1.2 79472,79473,79474 1f7cA 231 4.84e+01 1f7cA a.116.1.1 19107 1z5hA 780 4.88e+01 2frvB 536 4.90e+01 1h2rL e.18.1.1 43291 2bmwA 304 4.92e+01 1gt8D 1025 5.04e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70433,70434,70435,70436,70437 1j5xA 342 5.09e+01 c.80.1.1 71591 1dk8A 147 5.09e+01 1agrE a.91.1.1 18548 1biqA 375 5.10e+01 1xikA a.25.1.2 16786 1ft1A 377 5.19e+01 1ft1A a.118.6.1 19186 1lvl 458 5.22e+01 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30567,30568,40205 1xo0A 324 5.23e+01 2e2aA 105 5.28e+01 a.7.2.1 88499 1oc2A 348 5.30e+01 c.2.1.2 92765 1ahr 146 5.39e+01 1cll a.39.1.5 17287 1ppjH 78 5.47e+01 f.28.1.1 104264 5eat 548 5.48e+01 5eat a.102.4.1,a.128.1.3 18853,19445 2essA 248 5.51e+01 2h1rA 299 5.60e+01 2adr 60 5.63e+01 2adr g.37.1.1,g.37.1.1 45030,45031 1irl 133 5.64e+01 3inkC a.26.1.2 16883 1gm7A 209 5.64e+01 d.153.1.2 65302 1mznA 240 5.73e+01 a.123.1.1 79704 1dq3A 454 5.82e+01 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 2c2pA 199 5.87e+01 1rfyA 102 5.88e+01 1bx2B 191 5.90e+01 1iakB b.1.1.2,d.19.1.1 21610,38184 1ghpA 258 5.94e+01 1btl e.3.1.1 60520 1aw1A 256 5.98e+01 1amk c.1.1.1 28515 1alq 266 6.02e+01 1btl e.3.1.1 42707 2fv1A 377 6.20e+01 1e3aA 260 6.25e+01 1ajqA d.153.1.2 41838 1iyxA 432 6.32e+01 c.1.11.1,d.54.1.1 83815,83816 1br0A 120 6.60e+01 a.47.2.1 17772 1bu6O 501 6.61e+01 1glcG c.55.1.4,c.55.1.4 33499,33500 1tueB 218 6.62e+01 b.91.1.1 107324 1e2aA 105 6.73e+01 1e2aA a.7.2.1 16322 2aat 396 6.79e+01 1ajsA c.67.1.1 34348 1rz4A 226 6.80e+01 a.4.5.53,a.118.1.18 105131,105132 1gc5A 467 6.83e+01 1gc5A c.72.1.3 60429 1ydxA 406 6.96e+01 1or7A 194 6.97e+01 a.4.13.2,a.177.1.1 87332,87333 1rypG 244 6.98e+01 d.153.1.4 41938 1r5iD 216 6.98e+01 a.202.1.1 97091 1yqgA 263 7.03e+01 2fflA 756 7.04e+01 1qy5A 269 7.05e+01 d.122.1.1 96573 1oqyA 368 7.08e+01 a.5.2.1,a.5.2.1,a.189.1.1,d.15.1.1 93439,93440,93441,93442 1z8uA 102 7.09e+01 2b4zA 104 7.13e+01 1zk7A 467 7.20e+01 1volA 204 7.32e+01 1tfb a.74.1.2,a.74.1.2 18370,18371 1h7xD 1025 7.33e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15690,28635,30331,30616,39014 1tt7A 330 7.33e+01 1g5aA 628 7.34e+01 b.71.1.1,c.1.8.1 65152,65153 1hv2A 99 7.37e+01 d.42.1.1 61287 1ulyA 192 7.38e+01 1vj5A 555 7.40e+01 c.108.1.2,c.69.1.11 100799,100800 1bmtA 246 7.41e+01 1bmtA a.46.1.1,c.23.6.1 17757,31235 1z0xA 220 7.42e+01 2breA 219 7.43e+01 1l8cA 95 7.44e+01 g.53.1.1 73685 1uf2A 1019 7.46e+01 e.28.1.2 99289 2awiA 317 7.53e+01 830cA 168 7.54e+01 1ck7A d.92.1.11 40400 1obbA 480 7.56e+01 c.2.1.5,d.162.1.2 86760,86761 1a41 234 7.65e+01 1a41 d.163.1.2 42174 1w2xA 758 7.70e+01 c.14.1.4,c.14.1.4 109134,109135 3blm 257 7.72e+01 1btl e.3.1.1 42709 1a0p 290 7.73e+01 1a0p a.60.9.1,d.163.1.1 18105,42165 1ngkA 128 7.75e+01 a.1.1.1 85673 1qqeA 292 7.77e+01 1qqeA a.118.8.1 19210 2exrA 524 7.79e+01 1aokA 122 7.80e+01 1poa a.133.1.2 19560 1t4bA 367 7.83e+01 c.2.1.3,d.81.1.1 106406,106407 1qghA 156 7.87e+01 1qghA a.25.1.1 16728 1ayl 541 7.88e+01 1ayl c.91.1.1,c.109.1.1 64718,64719 1s72N 187 7.88e+01 c.55.4.1 105333 1wcgA 464 7.93e+01 153l 185 7.98e+01 153l d.2.1.5 36984 1j3kA 280 7.99e+01 c.71.1.1 84070 1pnkB 557 8.05e+01 1ajqB 1ej2A 181 8.13e+01 1f9aA c.26.1.3 59414 1i6pA 220 8.20e+01 1ddzA c.53.2.1 61848 1nj4A 363 8.20e+01 b.105.1.1,e.3.1.1 80545,80546 1kmiZ 214 8.27e+01 h.4.11.1 72752 1vjvA 415 8.28e+01 d.3.1.9 108632 1i39A 225 8.31e+01 1ekeA c.55.3.1 61585 1io7A 368 8.34e+01 1f4tA a.104.1.1 18971 1ov2A 99 8.45e+01 a.13.1.1 93580 1a0eA 443 8.47e+01 1a0cA c.1.15.3 29537 2hbtA 247 8.49e+01 1hiwA 133 8.59e+01 1hiwA a.61.1.1 18122 1uj2A 252 8.59e+01 c.37.1.6 99452 1kqpA 271 8.66e+01 c.26.2.1 72883 1tc6A 236 8.69e+01 d.122.1.1 106756 1ax8 146 8.70e+01 1ax8 a.26.1.1 16844 1odoA 408 8.73e+01 a.104.1.1 92783 1zklA 353 8.81e+01 1gt8A 1025 8.82e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70418,70419,70420,70421,70422 2b7aA 293 8.83e+01 1x0rA 249 8.91e+01