# List of top-scoring protein chains for t04-100-40-40-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 1t9bA 677 1.74e-02 1h65A 270 1.73e-01 c.37.1.8 65640 1b8oA 284 2.37e-01 1b8oA c.56.2.1 33762 1a6q 382 3.66e-01 1a6q a.159.1.1,d.219.1.1 75801,75802 1jvnA 555 3.82e-01 c.1.2.1,c.23.16.1 67355,67356 1ox6A 555 4.04e-01 c.1.2.1,c.23.16.1 87505,87506 1vljA 407 6.49e-01 e.22.1.2 108832 2bbhA 269 6.94e-01 1tqjA 230 7.41e-01 c.1.2.2 107228 1nt4A 391 7.79e-01 c.60.1.2 92102 1ccwB 483 8.49e-01 1cb7B c.1.19.2 29646 1sviA 195 9.57e-01 c.37.1.8 106048 2bcoA 350 1.06e+00 1to6A 371 1.21e+00 c.141.1.1 107170 2b8wA 328 1.25e+00 1w1wA 430 1.29e+00 2akaB 299 1.60e+00 1dv1A 449 1.78e+00 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28234,31641,41486 1ohlA 342 1.78e+00 c.1.10.3 87035 1v6tA 255 1.78e+00 1zczA 464 1.91e+00 1l0wA 580 2.55e+00 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 2cunA 410 3.01e+00 1r6xA 395 3.07e+00 b.122.1.3,c.26.1.5 97167,97168 1rfmA 344 3.19e+00 c.122.1.1 97385 1ejeA 192 3.36e+00 1ejeA b.45.1.2 25757 1oe4A 247 3.37e+00 c.18.1.3 86895 2fgeA 995 3.67e+00 1jx2B 315 3.70e+00 c.37.1.8 67404 1kk1A 410 3.73e+00 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1l7aA 318 3.90e+00 c.69.1.25 77772 2b3yA 888 4.12e+00 1z0sA 278 4.28e+00 1kp8A 547 4.30e+00 a.129.1.1,c.8.5.1,d.56.1.1 84414,84415,84416 1vdc 333 4.43e+00 1trb c.3.1.5,c.3.1.5 30545,30546 1sy7A 715 4.46e+00 1o66A 275 4.49e+00 c.1.12.8 92547 1ha3A 405 4.51e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 1g6hA 257 4.57e+00 1gajA c.37.1.12 60318 1ynpA 317 4.57e+00 1q6cA 495 4.72e+00 c.1.8.1 95970 2bsxA 253 4.78e+00 1v3hA 495 4.81e+00 c.1.8.1 108303 1u1hA 765 4.95e+00 c.1.22.2,c.1.22.2 107580,107581 1q1gA 276 5.06e+00 c.56.2.1 95574 1f74A 293 5.11e+00 1nal3 c.1.10.1 29079 1wf3A 301 5.26e+00 1h7nA 342 5.30e+00 1b4kA c.1.10.3 60726 1suwA 249 5.45e+00 e.52.1.1 106027 1qmyA 167 5.47e+00 1qmyA d.3.1.2 37094 1vknA 351 5.49e+00 c.2.1.3,d.81.1.1 108676,108677 2b4rO 345 5.61e+00 1wlsA 328 5.66e+00 1om0A 274 5.74e+00 c.1.8.5 87058 1innA 166 5.74e+00 1j98A d.185.1.2 62608 1a7tA 232 5.96e+00 1a7tA d.157.1.1 42041 1k1xA 659 6.02e+00 a.8.3.2,b.30.5.8,c.6.2.2 84279,84280,84281 1e9rA 437 6.13e+00 c.37.1.11 64827 1ko3A 230 6.15e+00 d.157.1.1 90974 2bv5A 282 6.20e+00 2fliA 220 6.22e+00 1j6oA 268 6.39e+00 c.1.9.12 77088 1vhwA 253 6.42e+00 c.56.2.1 100706 1tfzA 424 6.55e+00 d.32.1.3,d.32.1.3 106886,106887 1rpxA 230 6.67e+00 1rpxA c.1.2.2 28536 1f5nA 592 6.80e+00 1dg3A a.114.1.1,c.37.1.8 19077,32152 2cbzA 237 6.80e+00 1w8sA 263 6.91e+00 1q2lA 939 7.03e+00 1zjcA 418 7.05e+00 1aj2 282 7.05e+00 1aj2 c.1.21.1 29665 1trb 320 7.06e+00 1trb c.3.1.5,c.3.1.5 30529,30530 1qf6A 642 7.29e+00 1qf6A c.51.1.1,d.15.10.1,d.67.1.1,d.104.1.1 33210,39551,39562,40759 1ojxA 263 7.44e+00 c.1.10.1 93164 1vqwA 457 7.74e+00 1l6sA 323 7.90e+00 c.1.10.3 73627 1vjeA 166 7.93e+00 d.185.1.2 100807 1xwyA 264 7.98e+00 2f4lA 297 7.98e+00 1qlpA 394 8.06e+00 1ovaA e.1.1.1 42628 2f5gA 133 8.13e+00 1ua4A 455 8.40e+00 c.72.1.3 99128 7odcA 424 8.44e+00 7odcA b.49.2.3,c.1.6.1 26488,28650 1aisB 200 8.53e+00 1aisB a.74.1.2,a.74.1.2 18384,18385 1u9iA 519 8.59e+00 1hr6A 475 8.60e+00 1hr6A d.185.1.1,d.185.1.1 61164,61165 1lx7A 253 8.63e+00 c.56.2.1 74329 1ypxA 375 8.70e+00 1dssG 333 8.90e+00 1dssG c.2.1.3,d.81.1.1 30022,39937 1exmA 405 8.92e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 3grs 478 8.94e+00 3grs c.3.1.5,c.3.1.5,d.87.1.1 30441,30442,40152 1q7zA 566 8.96e+00 c.1.21.2,c.1.26.1 96090,96091 1ta3A 274 9.00e+00 c.1.8.5 106731 1dp4A 435 9.31e+00 1dp4A c.93.1.1 35710 2b3oA 532 9.34e+00 1qe5A 266 9.35e+00 1b8oA c.56.2.1 33784 1sk4A 163 9.59e+00 d.118.1.1 105664 1nwaA 203 9.76e+00 d.58.28.1 86295 1rvkA 382 9.90e+00 c.1.11.2,d.54.1.1 97928,97929 1x9iA 302 9.92e+00 2asbA 251 1.00e+01 1wdpA 495 1.01e+01 1rzrA 332 1.03e+01 1evlA 401 1.03e+01 1qf6A c.51.1.1,d.104.1.1 33202,40751 1tcvA 287 1.05e+01 1iirA 415 1.05e+01 1iirA c.87.1.5 62453 2bs9A 503 1.07e+01 1zzmA 259 1.08e+01 1pjcA 361 1.08e+01 1sayA c.2.1.4,c.23.12.2 30101,31361 1jubA 311 1.09e+01 c.1.4.1 90908 1vypX 364 1.12e+01 c.1.4.1 108905 1hl2A 297 1.14e+01 c.1.10.1 83581 1dkmA 410 1.14e+01 1dklA c.60.1.2 34000 1mjfA 281 1.15e+01 c.66.1.17 79198 1dkqA 410 1.16e+01 1dklA c.60.1.2 33998 1pjqA 457 1.24e+01 c.2.1.11,c.90.1.1,e.37.1.1 94766,94767,94768 1w3iA 293 1.24e+01 c.1.10.1 109152 1nrjB 218 1.25e+01 c.37.1.8 86125 1wchA 315 1.25e+01 1tzbA 302 1.28e+01 c.80.1.1 107470 1d8cA 723 1.29e+01 1d8cA c.1.13.1 29325 1rpa 342 1.31e+01 1cviA c.60.1.2 33983 1k0rA 366 1.31e+01 b.40.4.5,d.52.3.1,d.52.3.1,d.202.1.1 67961,67962,67963,67964 2fiqA 420 1.33e+01 1ji0A 240 1.36e+01 c.37.1.12 71665 1q74A 303 1.37e+01 c.134.1.1 96019 1ad3A 452 1.37e+01 1ad3A c.82.1.1 35335 1agjA 242 1.37e+01 1agjA b.47.1.1 25827 1t5iA 172 1.37e+01 c.37.1.19 106450 2dorA 311 1.38e+01 2dorA c.1.4.1 28593 1xkrA 206 1.38e+01 1wnfA 328 1.40e+01 1cqxA 403 1.40e+01 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 1xuuA 349 1.40e+01 1y0eA 223 1.42e+01 1kid 203 1.44e+01 1derA c.8.5.1 30771 1g2oA 268 1.44e+01 1b8oA c.56.2.1 60228 1qh3A 260 1.50e+01 1qh5A d.157.1.2 42059 2fw2A 260 1.52e+01 1vz6A 393 1.55e+01 d.154.1.2 108949 1yqtA 538 1.55e+01 1aszB 490 1.56e+01 1b8aA b.40.4.1,d.104.1.1 25241,40762 1jilA 420 1.56e+01 c.26.1.1 66745 1thtA 305 1.57e+01 1thtA c.69.1.13 34711 1w6tA 444 1.58e+01 2bijA 305 1.60e+01 2gu2A 312 1.61e+01 1k9sA 237 1.62e+01 c.56.2.1 68359 1w78A 422 1.69e+01 1oj7A 408 1.69e+01 e.22.1.2 103971 1kjqA 391 1.69e+01 b.84.2.1,c.30.1.1,d.142.1.2 72616,72617,72618 1t7lA 766 1.70e+01 1xccA 220 1.71e+01 1qmeA 702 1.72e+01 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37487,37488,42560,42769 1knwA 425 1.74e+01 b.49.2.3,c.1.6.1 90969,90970 1nal1 297 1.76e+01 1nal3 1kafA 108 1.77e+01 d.199.1.1 68372 1t0hB 224 1.77e+01 c.37.1.1 106208 1kicA 339 1.79e+01 c.70.1.1 72510 1vyrA 364 1.80e+01 c.1.4.1 108906 1zkpA 268 1.81e+01 1e5eA 404 1.81e+01 1ibjA c.67.1.3 59265 1zvkA 358 1.82e+01 1wtaA 275 1.83e+01 2bfgA 503 1.83e+01 2bgzA 299 1.85e+01 1vjuA 309 1.86e+01 d.248.1.1 100835 1yyvA 131 1.87e+01 1yacA 208 1.89e+01 1yacA c.33.1.3 31757 2f57A 317 1.89e+01 1ryiA 382 1.90e+01 1avqA 228 1.93e+01 1avqA c.52.1.13 33326 1h1yA 228 1.94e+01 c.1.2.2 76506 1ecpA 238 1.94e+01 1ecpA c.56.2.1 33775 1vr1H 261 1.95e+01 5ptp 1qo7A 394 1.96e+01 1qo7A c.69.1.11 34697 1vliA 385 1.99e+01 b.85.1.1,c.1.10.6 108830,108831 1blxA 326 2.00e+01 1hcl d.144.1.7 41596 1eny 268 2.01e+01 1eny c.2.1.2 29910 1xn7A 78 2.01e+01 1ub3A 220 2.01e+01 c.1.10.1 88395 1uslA 170 2.02e+01 c.121.1.1 99871 1b5qA 472 2.03e+01 1b37B c.3.1.2,d.16.1.5 30404,37968 1kdoA 227 2.04e+01 c.37.1.1 68478 1h8dH 260 2.06e+01 5ptp 1u1jA 765 2.06e+01 c.1.22.2,c.1.22.2 107590,107591 2abbA 364 2.09e+01 1dorA 311 2.09e+01 2dorA c.1.4.1 28595 1geqA 248 2.13e+01 2tysA c.1.2.4 28589 1egaA 301 2.14e+01 1egaA c.37.1.8,d.52.3.1 32150,38836 1ng4A 390 2.15e+01 c.3.1.2,d.16.1.3 85666,85667 1lwdA 413 2.15e+01 c.77.1.1 78265 1orvA 728 2.16e+01 b.70.3.1,c.69.1.24 87354,87355 1r0wA 286 2.19e+01 c.37.1.12 96754 1iyxA 432 2.20e+01 c.1.11.1,d.54.1.1 83815,83816 1wu7A 434 2.22e+01 2bryA 497 2.24e+01 1zjjA 263 2.25e+01 1tbd 134 2.26e+01 2tbd d.89.1.1 40240 1wcuA 153 2.26e+01 1dq3A 454 2.27e+01 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 2bklA 695 2.32e+01 1ka9H 200 2.33e+01 c.23.16.1 77308 1ve6A 582 2.34e+01 1kqzA 273 2.35e+01 c.1.8.5 68844 2b4yA 271 2.37e+01 1c7qA 445 2.38e+01 2pgi c.80.1.2 35307 2hvm 273 2.38e+01 1cnv c.1.8.5 28985 1uxtA 501 2.39e+01 c.82.1.1 108125 1bjt 793 2.39e+01 1bjt e.11.1.1 43249 1mb3A 124 2.40e+01 c.23.1.1 78907 1o7tA 309 2.40e+01 c.94.1.1 86645 1ckeA 227 2.43e+01 1ckeA c.37.1.1 31846 1euhA 475 2.43e+01 1euhA c.82.1.1 35369 1yoeA 322 2.44e+01 2fflA 756 2.45e+01 1je0A 236 2.47e+01 c.56.2.1 66581 1xx1A 285 2.48e+01 1mml 265 2.49e+01 1mml e.8.1.2 43015 1h61A 364 2.51e+01 1oyc c.1.4.1 60657 1b6rA 355 2.53e+01 1b6rA b.84.2.1,c.30.1.1,d.142.1.2 28241,31648,41493 1rz1A 161 2.54e+01 b.45.1.2 98124 1ecfA 504 2.54e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 1t3lA 337 2.54e+01 b.34.2.1,c.37.1.1 106358,106359 2b4gA 317 2.55e+01 1vcvA 226 2.56e+01 1r6uA 437 2.59e+01 c.26.1.1 97163 1a99A 344 2.60e+01 1pot c.94.1.1 35812 1i8jA 323 2.62e+01 1b4kA c.1.10.3 61968 1q45A 391 2.62e+01 c.1.4.1 95780 1qksA 567 2.67e+01 1qksA a.3.1.2,b.70.2.1 15951,27710 1wqaA 455 2.71e+01 1s0uA 408 2.72e+01 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 2dgkA 452 2.74e+01 1vdyA 140 2.74e+01 2aq8A 269 2.74e+01 1v0wA 506 2.76e+01 d.136.1.2,d.136.1.2 108220,108221 2gv8A 447 2.76e+01 1tg6A 277 2.77e+01 1wlgA 299 2.78e+01 1hbq 183 2.80e+01 1aqb b.60.1.1 27078 1jb7B 260 2.81e+01 1otcB b.40.4.3 62839 1i1qB 192 2.81e+01 1qdlB c.23.16.1 61544 1zt2B 212 2.83e+01 1i7qB 193 2.84e+01 1qdlB c.23.16.1 61902 1sznA 417 2.87e+01 b.71.1.1,c.1.8.1 106162,106163 1f5vA 240 2.87e+01 1bkjA d.90.1.1 40255 1k6wA 426 2.88e+01 b.92.1.2,c.1.9.5 68236,68237 1qy6A 274 2.89e+01 b.47.1.1 96574 1nlnA 204 2.91e+01 d.3.1.7 91962 2bbsA 290 2.94e+01 2d0oA 610 2.95e+01 1mqoA 227 2.96e+01 d.157.1.1 103846 1y8aA 332 2.96e+01 3mddA 385 2.96e+01 3mdeA a.29.3.1,e.6.1.1 16592,42853 1xnzA 264 2.98e+01 1xknA 355 3.01e+01 1hyuA 521 3.05e+01 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1yqeA 282 3.05e+01 2ac5A 316 3.07e+01 1wzcA 249 3.09e+01 1anf 370 3.11e+01 4mbp c.94.1.1 35776 2cmuA 342 3.16e+01 1lt8A 406 3.16e+01 c.1.26.1 78186 1vb3A 428 3.16e+01 1jakA 512 3.16e+01 c.1.8.6,d.92.2.1 66472,66473 1hp5A 512 3.17e+01 1hp4A c.1.8.6,d.92.2.1 61113,61114 1at3A 247 3.19e+01 1at3A b.57.1.1 27021 1d3gA 367 3.19e+01 1d3gA c.1.4.1 28600 1elvA 333 3.19e+01 5ptp b.47.1.2,g.18.1.1 59454,59455 1t8hA 277 3.20e+01 d.194.1.2 106664 1ra0A 430 3.20e+01 1eswA 500 3.20e+01 1cwyA c.1.8.1 59500 1j8yF 297 3.21e+01 1ng1 a.24.13.1,c.37.1.10 62747,62748 1p7tA 731 3.21e+01 c.1.13.1 94319 1wndA 495 3.23e+01 1uirA 314 3.24e+01 c.66.1.17 99429 1t8tA 271 3.26e+01 c.37.1.5 106685 1o2dA 371 3.30e+01 e.22.1.2 86591 1rm4A 337 3.30e+01 c.2.1.3,d.81.1.1 105000,105001 1vzwA 244 3.30e+01 1pvvA 315 3.31e+01 c.78.1.1,c.78.1.1 95190,95191 1xc1A 309 3.32e+01 c.94.1.1 109543 1h70A 255 3.33e+01 1h70A d.126.1.3 60711 1w85A 368 3.34e+01 1x8hA 228 3.35e+01 1xw8A 252 3.37e+01 1byb 495 3.45e+01 1byb c.1.8.1 28790 1uozA 315 3.46e+01 1nd6A 354 3.46e+01 c.60.1.2 80407 1v02A 565 3.48e+01 c.1.8.4 108194 2fm8A 135 3.48e+01 2gtrA 261 3.49e+01 2a4aA 281 3.51e+01 1u2zA 433 3.51e+01 c.66.1.31 107626 1hynP 379 3.52e+01 1hynP d.112.1.2 61408 1l6rA 227 3.53e+01 c.108.1.10 77768 1chuA 540 3.54e+01 1chuA a.7.3.1,c.3.1.4,d.168.1.1 16325,30424,42307 1l5jA 865 3.54e+01 a.118.15.1,c.8.2.1,c.83.1.1 73592,73593,73594 1wsrA 375 3.56e+01 1d3yA 301 3.57e+01 1d3yA e.12.1.1 43252 1kt6A 183 3.58e+01 b.60.1.1 84466 1mmiA 366 3.58e+01 d.131.1.1,d.131.1.1,d.131.1.1 91309,91310,91311 1gc5A 467 3.59e+01 1gc5A c.72.1.3 60429 1uwcA 261 3.61e+01 c.69.1.17 100101 1eyeA 280 3.63e+01 1aj2 c.1.21.1 29672 1n4qB 377 3.66e+01 a.102.4.3 91636 2a8yA 270 3.68e+01 2fbmA 291 3.69e+01 1icpA 376 3.69e+01 1oyc c.1.4.1 62270 1q1aA 289 3.72e+01 c.31.1.5 95561 1f0iA 504 3.72e+01 1f0iA d.136.1.2,d.136.1.2 59566,59567 1jr7A 311 3.72e+01 b.82.2.3 63255 1f2tB 148 3.76e+01 1f2tB 1d3vA 323 3.76e+01 1d3vA c.42.1.1 32559 1ok7A 366 3.76e+01 d.131.1.1,d.131.1.1,d.131.1.1 103992,103993,103994 1uuzA 137 3.77e+01 d.233.1.1 100024 1fvgA 199 3.80e+01 1fvaA d.58.28.1 39408 2ts1 419 3.82e+01 2ts1 c.26.1.1 31564 1i9zA 347 3.87e+01 1i9yA d.151.1.2 62102 1x8gA 227 3.87e+01 1jjeA 222 3.88e+01 1a7tA d.157.1.1 63117 1vm6A 228 3.92e+01 c.2.1.3,d.81.1.3 108876,108877 1ii7A 333 3.93e+01 1ii7A d.159.1.4 62415 1gvoA 364 3.95e+01 c.1.4.1 76357 1yrgA 385 3.96e+01 1yrgA c.10.1.2 30854 1lc5A 364 3.96e+01 c.67.1.1 73827 1qwgA 251 3.96e+01 c.1.27.1 96473 1xmbA 418 4.04e+01 1xgsA 295 4.06e+01 1bn5 a.4.5.25,d.127.1.1 16216,41153 1gs5A 258 4.08e+01 c.73.1.2 70395 1o8xA 146 4.10e+01 c.47.1.10 86681 1ek4A 418 4.10e+01 1dd8A c.95.1.1,c.95.1.1 59436,59437 1wl8A 189 4.11e+01 1b7gO 340 4.11e+01 1b7gO c.2.1.3,d.81.1.1 29992,39907 2ac3A 316 4.13e+01 2aebA 322 4.14e+01 1tvlA 454 4.19e+01 c.1.16.4 107366 1v93A 296 4.23e+01 c.1.23.1 100532 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