# List of top-scoring protein chains for t2k-100-30-near-backbone-11-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 1xngA 268 3.27e-06 1gpmA 525 1.16e-05 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 1wy5A 317 3.70e-05 1vl2A 421 7.69e-05 c.26.2.1,d.210.1.1 108708,108709 2d13A 227 7.02e-04 1ni5A 433 9.57e-04 c.26.2.5,d.229.1.1 80533,80534 1ru8A 232 1.21e-03 c.26.2.1 97849 1korA 400 1.90e-03 c.26.2.1,d.210.1.1 72824,72825 1k92A 455 8.04e-03 c.26.2.1,d.210.1.1 68325,68326 1ct9A 553 8.30e-03 1ct9A c.26.2.1,d.153.1.1 31616,41834 1jgtA 513 8.57e-03 c.26.2.1,d.153.1.1 66684,66685 1m1zA 513 1.16e-02 c.26.2.1,d.153.1.1 78457,78458 1q15A 503 2.25e-02 c.26.2.1,d.153.1.1 95538,95539 2nsyA 271 2.78e-02 2nsyA c.26.2.1 31612 1kqpA 271 3.93e-02 c.26.2.1 72883 1nsyA 271 4.78e-02 2nsyA c.26.2.1 31614 1ih8A 271 5.04e-02 2nsyA c.26.2.1 62377 1o89A 345 9.12e-02 b.35.1.2,c.2.1.1 92644,92645 1wxiA 275 1.02e-01 1t2aA 375 1.92e-01 c.2.1.2 99078 1wqaA 455 1.97e-01 1rpnA 335 4.48e-01 c.2.1.2 97708 7odcA 424 5.16e-01 7odcA b.49.2.3,c.1.6.1 26488,28650 1vbkA 307 7.44e-01 1xg5A 279 9.19e-01 1gosA 520 9.45e-01 c.3.1.2,d.16.1.5 65425,65426 1o5xA 248 1.24e+00 c.1.1.1 92528 1d7kA 421 1.29e+00 7odcA b.49.2.3,c.1.6.1 26486,28648 1lyxA 248 1.31e+00 c.1.1.1 78304 1db3A 372 1.61e+00 1db3A c.2.1.2 29813 1yq7A 374 1.72e+00 1yv5A 374 1.81e+00 1qv9A 283 1.94e+00 c.127.1.1 96356 1ojaA 520 1.96e+00 c.3.1.2,d.16.1.5 93096,93097 2blnA 305 1.97e+00 1uetA 437 2.14e+00 a.160.1.3,d.218.1.7,d.58.16.2 99272,99273,99274 1vr6A 350 2.14e+00 1s3eA 520 2.29e+00 c.3.1.2,d.16.1.5 98426,98427 1tksA 204 2.43e+00 d.115.1.2 107114 2f94F 350 2.56e+00 1jztA 246 2.59e+00 c.104.1.1 63319 1delA 241 2.63e+00 1dekA c.37.1.1 31844 1dekA 241 2.67e+00 1dekA c.37.1.1 31842 1n82A 331 2.76e+00 c.1.8.3 91703 1treA 255 2.92e+00 1amk c.1.1.1 28505 1vjzA 341 3.01e+00 c.1.8.3 100838 1zcoA 262 3.20e+00 1c0pA 363 3.54e+00 1an9A c.4.1.2,d.16.1.3 30647,37934 1q8fA 313 3.76e+00 c.70.1.1 96203 1w5fA 353 3.97e+00 1rzmA 338 4.06e+00 c.1.10.4 105137 1r89A 437 4.35e+00 a.160.1.3,d.218.1.7,d.58.16.2 97221,97222,97223 1rxxA 421 4.56e+00 d.126.1.4 98061 1uayA 242 5.14e+00 c.2.1.2 88390 1vbuA 328 5.62e+00 1mgtA 174 5.64e+00 1mgtA a.4.2.1,c.55.7.1 16078,33753 1ecpA 238 5.80e+00 1ecpA c.56.2.1 33775 1neyA 247 6.05e+00 c.1.1.1 80449 1vqtA 213 6.08e+00 1xdwA 331 6.20e+00 1xmpA 170 6.25e+00 2adr 60 6.29e+00 2adr g.37.1.1,g.37.1.1 45030,45031 1n7hA 381 6.42e+00 c.2.1.2 80250 1zk7A 467 6.53e+00 1f5mA 180 6.68e+00 1f5mB d.110.2.1 40895 1xm7A 195 7.17e+00 2gm3A 175 7.20e+00 2cvjA 180 7.32e+00 3timA 250 7.60e+00 1amk c.1.1.1 28483 1xa0A 328 7.63e+00 2pfkA 320 7.86e+00 3pfk c.89.1.1 35577 1pk9A 237 8.18e+00 c.56.2.1 94823 2ct8A 497 8.29e+00 1kv5A 250 8.43e+00 c.1.1.1 73052 1k2yX 463 8.46e+00 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 1tpfA 250 8.55e+00 1amk c.1.1.1 28467 1wstA 417 8.68e+00 1o5oA 221 8.82e+00 c.61.1.1 92509 1cqzA 554 8.83e+00 1cr6B c.69.1.11,c.108.1.2 34689,43339 1vjuA 309 9.05e+00 d.248.1.1 100835 1i45A 248 9.19e+00 1amk c.1.1.1 61665 1f6yA 262 9.42e+00 1f6yA c.1.21.2 29673 1vp8A 201 9.50e+00 1aw1A 256 9.66e+00 1amk c.1.1.1 28515 7timA 247 9.74e+00 1amk c.1.1.1 28457 2c0cA 362 1.03e+01 1vhtA 218 1.03e+01 c.37.1.1 100700 1ny1A 240 1.06e+01 c.6.2.3 86395 1gsoA 431 1.08e+01 1gsoA b.84.2.1,c.30.1.1,d.142.1.2 28240,31647,41492 1nmoA 247 1.08e+01 c.135.1.1 91980 1aw2A 256 1.08e+01 1amk c.1.1.1 28523 1bw0A 416 1.08e+01 1bw0A c.67.1.1 34385 2d5cA 263 1.12e+01 1zx1A 231 1.13e+01 2tpsA 227 1.13e+01 2tpsA c.1.3.1 28591 1p5dX 463 1.14e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 2bzsA 236 1.18e+01 1sg0A 230 1.20e+01 2b8nA 429 1.23e+01 1coy 507 1.25e+01 1b8sA c.3.1.2,d.16.1.1 30333,37864 1f5mB 180 1.26e+01 1f5mB d.110.2.1 40896 1qwgA 251 1.27e+01 c.1.27.1 96473 1pfkA 320 1.28e+01 3pfk c.89.1.1 35575 1uumA 372 1.28e+01 c.1.4.1 100010 3cox 507 1.29e+01 1b8sA c.3.1.2,d.16.1.1 30332,37863 1o0uA 429 1.29e+01 c.118.1.1 80743 1jmvA 141 1.30e+01 c.26.2.4 66897 1qczA 169 1.30e+01 1qczA c.23.8.1 31276 1l1zA 274 1.31e+01 a.156.1.2,b.113.1.1,g.39.1.8 75911,75912,75913 1q1lA 401 1.32e+01 d.258.1.1 95591 1j79A 347 1.32e+01 1j79A c.1.9.4 62675 1k9sA 237 1.34e+01 c.56.2.1 68359 1r2zA 274 1.37e+01 a.156.1.2,b.113.1.1,g.39.1.8 96892,96893,96894 1oi7A 288 1.42e+01 c.2.1.8,c.23.4.1 87049,87050 1ek1A 554 1.43e+01 1cr6B c.69.1.11,c.108.1.2 34685,43335 1a1vA 476 1.43e+01 1heiA c.37.1.14,c.37.1.14 32467,32468 1tt7A 330 1.43e+01 1zd3A 555 1.44e+01 1qxoA 388 1.45e+01 d.258.1.1 96539 1b9bA 255 1.47e+01 1amk c.1.1.1 28531 1jmtA 104 1.49e+01 d.58.7.3 63180 1n3bA 216 1.52e+01 c.37.1.1 79959 2a9gA 418 1.53e+01 1egiA 147 1.55e+01 1eggA d.169.1.1 42331 1tqyB 415 1.56e+01 c.95.1.1,c.95.1.1 107247,107248 1b93A 152 1.56e+01 1b93A c.24.1.2 31507 1i9sA 210 1.56e+01 1i9sA c.45.1.1 62099 1b93B 152 1.59e+01 1b93A c.24.1.2 31508 1yt8A 539 1.60e+01 1vj5A 555 1.61e+01 c.108.1.2,c.69.1.11 100799,100800 2c5aA 379 1.61e+01 1vfsA 386 1.62e+01 b.49.2.2,c.1.6.1 108584,108585 1lit 144 1.64e+01 1qddA d.169.1.1 42325 2c46A 241 1.64e+01 1cr6B 554 1.66e+01 1cr6B c.69.1.11,c.108.1.2 34688,43338 1vhwA 253 1.66e+01 c.56.2.1 100706 3bdpA 580 1.66e+01 1xwl c.55.3.5,e.8.1.1 33711,43004 1v3vA 333 1.67e+01 b.35.1.2,c.2.1.1 108345,108346 1z2aA 168 1.69e+01 1mo0A 275 1.69e+01 c.1.1.1 79329 1s4nA 348 1.69e+01 c.68.1.16 98501 2gf9A 189 1.69e+01 1ofuA 320 1.73e+01 c.32.1.1,d.79.2.1 86972,86973 1n81A 186 1.74e+01 a.185.1.1 85388 1dzkA 157 1.77e+01 1obpA b.60.1.1 27096 1wteA 272 1.79e+01 1u4bA 580 1.81e+01 c.55.3.5,e.8.1.1 107664,107665 1wxdA 263 1.81e+01 1vl1A 232 1.84e+01 c.124.1.1 108707 1a3yA 149 1.86e+01 1obpA b.60.1.1 27110 1dtyA 429 1.94e+01 1dtyA c.67.1.4 34495 2bdpA 580 1.94e+01 1xwl c.55.3.5,e.8.1.1 33709,43002 1xkqA 280 1.94e+01 1qddA 144 1.94e+01 1qddA d.169.1.1 42324 1amk 251 1.95e+01 1amk c.1.1.1 28503 1jflA 228 1.96e+01 c.78.2.1,c.78.2.1 71656,71657 1gqoM 143 1.98e+01 c.23.13.1 76307 1npyA 271 1.98e+01 c.2.1.7,c.58.1.5 85995,85996 2gmfA 127 1.98e+01 2gmfA a.26.1.2 16849 1r2rA 248 1.99e+01 c.1.1.1 96875 1y2qA 143 1.99e+01 1i24A 404 1.99e+01 c.2.1.2 83663 1pbtA 244 2.00e+01 c.124.1.1 94416 1i4nA 251 2.00e+01 c.1.2.4 71114 1j8yF 297 2.03e+01 1ng1 a.24.13.1,c.37.1.10 62747,62748 2bw0A 329 2.06e+01 1q9iA 571 2.07e+01 a.138.1.3,c.3.1.4,d.168.1.1 96273,96274,96275 1buoA 121 2.07e+01 1buoA d.42.1.1 38631 1nk4A 580 2.08e+01 c.55.3.5,e.8.1.1 91923,91924 2bnlA 136 2.09e+01 1sh0A 510 2.10e+01 e.8.1.4 98876 1eny 268 2.11e+01 1eny c.2.1.2 29910 1d3hA 367 2.11e+01 1d3gA c.1.4.1 28601 1mxtA 504 2.11e+01 c.3.1.2,d.16.1.1 79671,79672 2cy0A 263 2.14e+01 1ng1 294 2.14e+01 1ng1 a.24.13.1,c.37.1.10 16961,32272 2gl5A 410 2.15e+01 1n4kA 381 2.16e+01 a.118.22.1,b.42.6.1 79992,79993 1udb 338 2.19e+01 1xel c.2.1.2 29787 1wt9B 123 2.20e+01 1reoA 486 2.21e+01 c.3.1.2,d.16.1.5 97325,97326 1n55A 251 2.21e+01 c.1.1.1 80007 1j34B 123 2.22e+01 d.169.1.1 84049 1b8sA 504 2.22e+01 1b8sA c.3.1.2,d.16.1.1 30335,37866 1u6tA 121 2.23e+01 1dv2A 452 2.25e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28238,31645,41490 1wh5A 80 2.26e+01 1n4nA 47 2.26e+01 g.3.7.5 91620 1a9y 338 2.29e+01 1xel c.2.1.2 29789 1heiA 451 2.30e+01 1heiA c.37.1.14,c.37.1.14 32463,32464 1qy5A 269 2.31e+01 d.122.1.1 96573 1qjdA 571 2.31e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19695,30432,42315 1y0pA 571 2.33e+01 1sl4A 155 2.33e+01 d.169.1.1 105710 1kvs 338 2.36e+01 1xel c.2.1.2 29799 1eggA 147 2.36e+01 1eggA d.169.1.1 42333 1xwl 580 2.37e+01 1xwl c.55.3.5,e.8.1.1 33708,43001 1b4vA 504 2.38e+01 1b8sA c.3.1.2,d.16.1.1 30334,37865 1n1pA 504 2.39e+01 c.3.1.2,d.16.1.1 91546,91547 1ap8 213 2.39e+01 1ap8 d.86.1.1 40151 1o2dA 371 2.40e+01 e.22.1.2 86591 1ixxB 123 2.42e+01 1ixxB d.169.1.1 42336 1lj1A 571 2.44e+01 a.138.1.3,c.3.1.4,d.168.1.1 78023,78024,78025 1jpnA 296 2.44e+01 a.24.13.1,c.37.1.10 67039,67040 1n4wA 504 2.44e+01 c.3.1.2,d.16.1.1 91676,91677 1zxxA 319 2.47e+01 1yb2A 275 2.50e+01 2ax4A 198 2.50e+01 1qrrA 394 2.55e+01 1qrrA c.2.1.2 29824 1w32A 348 2.56e+01 1wr2A 238 2.56e+01 1xwyA 264 2.57e+01 1qcrA 446 2.57e+01 1be3A d.185.1.1,d.185.1.1 59025,59026 1d3gA 367 2.58e+01 1d3gA c.1.4.1 28600 2aq8A 269 2.61e+01 1ve3A 227 2.61e+01 1mjhA 162 2.62e+01 1mjhA c.26.2.4 31639 1gqoQ 143 2.64e+01 c.23.13.1 76311 1wznA 252 2.65e+01 2ax3A 502 2.65e+01 1ihuA 589 2.67e+01 c.37.1.10,c.37.1.10 62394,62395 2b0mA 393 2.68e+01 1udc 338 2.68e+01 1xel c.2.1.2 29785 1hp4A 512 2.69e+01 1hp4A c.1.8.6,d.92.2.1 61111,61112 1xel 338 2.69e+01 1xel c.2.1.2 29786 1l3sA 580 2.70e+01 c.55.3.5,e.8.1.1 84521,84522 1e39A 571 2.71e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19694,30431,42314 1kzhA 555 2.71e+01 c.89.1.1 73361 1u11A 182 2.73e+01 c.23.8.1 107576 1a9z 338 2.73e+01 1xel c.2.1.2 29795 2cdcA 366 2.74e+01 1ijhA 504 2.74e+01 c.3.1.2,d.16.1.1 66161,66162 1kssA 571 2.75e+01 a.138.1.3,c.3.1.4,d.168.1.1 72928,72929,72930 1rc9A 221 2.75e+01 1mjhB 162 2.75e+01 1mjhA c.26.2.4 31640 1pmmA 466 2.76e+01 c.67.1.6 94901 1m64A 571 2.77e+01 a.138.1.3,c.3.1.4,d.168.1.1 78683,78684,78685 1r7lA 110 2.77e+01 d.277.1.1 104837 1j8mF 297 2.80e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 1qd1A 325 2.81e+01 1qd1A d.58.34.1,d.58.34.1 39493,39494 1ewjA 126 2.83e+01 1ecsA d.32.1.2 59526 1w24A 182 2.84e+01 1ls1A 295 2.85e+01 a.24.13.1,c.37.1.10 78170,78171 1rq2A 382 2.85e+01 c.32.1.1,d.79.2.1 105048,105049 2b43A 526 2.85e+01 1gqoL 143 2.86e+01 c.23.13.1 76306 1xhcA 367 2.86e+01 2f4iA 197 2.89e+01 1t3tA 1303 2.90e+01 a.5.10.1,c.23.16.1,d.284.1.2,d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 106381,106382,106383,106384,106385,106386,106387 1n0wA 243 2.91e+01 c.37.1.11 79772 1ynpA 317 2.92e+01 1h70A 255 2.94e+01 1h70A d.126.1.3 60711 1mioA 534 2.95e+01 1qguA c.92.2.3 35601 1csgA 127 2.95e+01 2gmfA a.26.1.2 16851 1npdA 288 2.98e+01 c.2.1.7,c.58.1.5 80681,80682 2a2pA 129 3.02e+01 1y1uA 585 3.08e+01 1wryA 121 3.09e+01 2udpA 338 3.10e+01 1xel c.2.1.2 29791 1hp5A 512 3.10e+01 1hp4A c.1.8.6,d.92.2.1 61113,61114 1f48A 589 3.11e+01 1f48A c.37.1.10,c.37.1.10 32280,32281 1zid 268 3.13e+01 1eny c.2.1.2 29911 1bncA 449 3.13e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28236,31643,41488 1wo8A 126 3.14e+01 1e44A 85 3.20e+01 3eipA d.26.2.1 59219 1p6oA 161 3.21e+01 c.97.1.2 94185 1j6uA 469 3.21e+01 c.5.1.1,c.59.1.1,c.72.2.1 77094,77095,77096 1ffh 294 3.24e+01 1ng1 a.24.13.1,c.37.1.10 16960,32271 1rz3A 201 3.24e+01 c.37.1.6 98132 1aogA 485 3.24e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30517,30518,40190 1vljA 407 3.28e+01 e.22.1.2 108832 1twdA 256 3.28e+01 c.1.30.1 107397 1clxA 347 3.29e+01 1taxA c.1.8.3 28899 1b1cA 181 3.30e+01 1amoA c.23.5.2 31212 1ecsA 126 3.39e+01 1ecsA d.32.1.2 59407 2a7oA 112 3.41e+01 1s0pA 176 3.42e+01 a.192.1.1 98300 1uf3A 228 3.43e+01 d.159.1.6 99317 1yh3A 256 3.44e+01 1gqoF 143 3.44e+01 c.23.13.1 76300 1kq3A 376 3.45e+01 e.22.1.2 68790 1p2hA 571 3.46e+01 a.138.1.3,c.3.1.4,d.168.1.1 93930,93931,93932 1a41 234 3.47e+01 1a41 d.163.1.2 42174 1g57A 217 3.54e+01 1g57A d.115.1.2 60253 1s5jA 847 3.54e+01 1zemA 262 3.55e+01 1tph1 247 3.58e+01 1amk 1y89A 238 3.59e+01 1g3qA 237 3.59e+01 1hyqA c.37.1.10 60237 2masA 314 3.62e+01 2masA c.70.1.1 34810 1wjgA 137 3.64e+01 2c4wA 176 3.64e+01 1kao 167 3.67e+01 1ctqA c.37.1.8 32014 1rylA 167 3.68e+01 d.276.1.1 105124 1ionA 243 3.70e+01 c.37.1.10 62633 1xhlA 297 3.71e+01 c.2.1.2 109591 1d4aA 273 3.71e+01 1d4aA c.23.5.3 31219 1i60A 278 3.71e+01 c.1.15.4 71118 1ovqA 138 3.71e+01 c.55.3.8 93607 1jakA 512 3.71e+01 c.1.8.6,d.92.2.1 66472,66473 1dv1A 449 3.72e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28234,31641,41486 1yadA 221 3.73e+01 1gqoC 143 3.78e+01 c.23.13.1 76297 1yb5A 351 3.80e+01 1z15A 344 3.80e+01 1zccA 248 3.88e+01 2ng1 293 3.89e+01 1ng1 a.24.13.1,c.37.1.10 16962,32273 1gqoS 143 3.92e+01 c.23.13.1 76313 1g0xA 197 3.98e+01 1nkr b.1.1.4,b.1.1.4 21805,21806 1n3yA 198 4.10e+01 c.62.1.1 79976 1fmtB 314 4.13e+01 1fmtA b.46.1.1,c.65.1.1 25759,34175 1c9bA 207 4.14e+01 1tfb a.74.1.2,a.74.1.2 18372,18373 1ooeA 236 4.19e+01 c.2.1.2 87196 1iv0A 98 4.19e+01 c.55.3.8 90706 1bhjA 292 4.24e+01 1xvaA c.66.1.5 34189 1ia8A 289 4.26e+01 1ia8A d.144.1.7 62112 1ur1A 378 4.27e+01 c.1.8.3 99804 1yvkA 163 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