# List of top-scoring protein chains for t2k.w0.5 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.soe.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 2hsgA 332 2.04e-42 a.35.1.5 136722 c.93.1.1 136723 2jcgA 332 2.76e-42 1jh9A 340 1.45e-39 a.35.1.5 66710 c.93.1.1 66711 1qpzA 340 1.56e-39 1qpzA a.35.1.5 17097 c.93.1.1 35673 2pugA 340 1.57e-39 1qpzA a.35.1.5 17088 c.93.1.1 35683 1qqbA 340 1.61e-39 1qpzA a.35.1.5 17099 c.93.1.1 35674 2pucA 340 1.66e-39 1qpzA a.35.1.5 17094 c.93.1.1 35684 1jfsA 340 1.93e-39 a.35.1.5 66650 c.93.1.1 66651 1jftA 340 2.04e-39 a.35.1.5 66652 c.93.1.1 66653 1vpwA 340 2.16e-39 1qpzA a.35.1.5 17087 c.93.1.1 35680 2o20A 332 2.96e-39 3ctpA 330 9.84e-37 2nzuG 280 7.05e-34 c.93.1.1 138854 2fepA 289 4.23e-33 1efaA 333 4.79e-33 1tlfA a.35.1.5 17106 c.93.1.1 35691 1jyfA 349 4.84e-33 c.93.1.1 67456 1lbiA 360 4.86e-33 1tlfA c.93.1.1 35694 1jyeA 349 5.18e-33 c.93.1.1 67455 2pe5A 330 1.15e-32 3bilA 348 1.55e-32 1dbqA 289 6.45e-32 1qpzA c.93.1.1 35666 1jhzA 289 8.13e-32 c.93.1.1 66731 3brqA 296 2.33e-30 3bblA 287 7.31e-28 3c3kA 285 2.61e-27 3clkA 290 4.15e-26 2rgyA 290 4.84e-26 2qu7A 288 4.57e-24 1tlfA 301 2.52e-23 1tlfA c.93.1.1 35687 2p9hA 269 3.91e-23 c.93.1.1 139580 3cs3A 277 9.27e-22 2iksA 293 1.56e-20 2h0aA 276 1.14e-19 2ioyA 283 2.68e-17 1bykA 255 1.26e-16 1bykA c.93.1.1 35706 2gx6A 278 1.36e-16 1dbpA 271 2.77e-16 c.93.1.1 35639 2driA 271 3.22e-16 c.93.1.1 35637 1ba2A 271 3.74e-16 2dri c.93.1.1 35640 1drjA 271 4.06e-16 c.93.1.1 35642 1drkA 271 4.72e-16 c.93.1.1 35638 2fn8A 303 2.34e-14 2fn9A 290 2.63e-14 1gudA 288 1.24e-11 c.93.1.1 83326 2bjcA 62 1.68e-11 a.35.1.5 128620 1cjgA 62 2.27e-11 1pru a.35.1.5 17112 1l1mA 62 2.85e-11 a.35.1.5 73474 1lqcA 56 1.25e-10 a.35.1.5 17109 1pruA 56 8.83e-10 a.35.1.5 17104 1lccA 51 9.87e-10 1pru a.35.1.5 17110 2qvcA 313 4.21e-09 2h3hA 313 7.26e-09 3c6qA 311 1.23e-08 1uxcA 65 6.65e-08 a.35.1.5 17119 3brsA 289 3.24e-07 2rjoA 332 5.85e-07 2ipnA 318 9.04e-07 2fvyA 309 1.07e-06 c.93.1.1 134227 2hphA 316 1.07e-06 c.93.1.1 136652 2ipmA 318 1.24e-06 2iplA 318 1.78e-06 3gbpA 307 3.18e-06 c.93.1.1 35661 1gcaA 309 3.18e-06 c.93.1.1 35659 1jx6A 342 5.12e-03 c.93.1.1 67406 2hj9A 339 5.12e-03 c.93.1.1 136538 1zhhA 344 5.12e-03 c.93.1.1 125095 8abpA 306 1.19e-02 c.93.1.1 35647 1abeA 306 1.22e-02 c.93.1.1 35648 1bapA 306 1.40e-02 c.93.1.1 35654 2fqxA 318 2.46e-02 6pfkA 319 3.41e-02 3pfk c.89.1.1 35583 3d02A 303 4.42e-02 4pfkA 319 4.57e-02 c.89.1.1 35582 1mtoA 319 4.60e-02 c.89.1.1 79458 1pfkA 320 3.94e-01 3pfk c.89.1.1 35575 2pfkA 320 3.94e-01 3pfk c.89.1.1 35577 1tjyA 316 4.63e-01 c.93.1.1 107062 1tybE 319 8.22e-01 2ts1 c.26.1.1 31569 3c2xA 171 8.65e-01 2gmgA 105 1.02e+00 1rvv1 154 1.06e+00 1rvv1 1tyaE 319 1.07e+00 2ts1 c.26.1.1 31570 2rasA 212 1.21e+00 1w9hA 427 1.21e+00 c.55.3.10 120785 1d1gA 168 1.41e+00 1d1gA c.71.1.1 34889 1yt8A 539 1.56e+00 c.46.1.2 123996 c.46.1.2 123997 c.46.1.2 123998 c.46.1.2 123999 2pfrA 294 1.58e+00 2jj7A 186 1.60e+00 2fx0A 201 1.69e+00 a.4.1.9 134269 a.121.1.1 134270 2p5tA 158 1.75e+00 1tydE 319 1.84e+00 2ts1 c.26.1.1 31567 4ts1A 319 2.25e+00 2ts1 c.26.1.1 31565 2ts1A 419 2.42e+00 c.26.1.1 31564 2pqtA 295 2.78e+00 1tycA 319 2.82e+00 c.26.1.1 31568 1cqjB 385 2.87e+00 2scuB c.23.4.1 31143 d.142.1.4 41564 2nu8B 388 2.90e+00 2scuB 388 2.90e+00 2scuB c.23.4.1 31141 d.142.1.4 41562 1jllB 388 2.91e+00 c.23.4.1 66853 d.142.1.4 66854 1yckA 175 2.93e+00 d.118.1.1 122968 1uedA 406 3.24e+00 a.104.1.1 99256 2qwtA 196 3.28e+00 2of7A 260 3.43e+00 2yy8A 201 3.79e+00 1xtqA 177 3.88e+00 c.37.1.8 122297 2ictA 94 3.92e+00 2rekA 199 4.42e+00 1ewkA 490 4.48e+00 1ewkA c.93.1.1 35712 2z1aA 552 4.64e+00 1k7jA 206 4.69e+00 d.115.1.1 72103 1mf7A 194 4.70e+00 c.62.1.1 84937 1wb0A 445 4.72e+00 c.1.8.5 120825 d.26.3.1 120826 1iv3A 152 4.87e+00 d.79.5.1 76828 2ijaA 295 4.89e+00 1o1zA 234 4.98e+00 c.1.18.3 86555 1lbqA 362 5.07e+00 c.92.1.1 77877 1kk9A 221 5.16e+00 d.115.1.1 77432 1na5A 197 5.18e+00 c.62.1.1 85483 1idn1 189 6.02e+00 1ido 1rkdA 309 6.29e+00 c.72.1.1 34928 2cf2E 226 6.33e+00 i.26.1.1 130363 1jlmA 192 6.37e+00 c.62.1.1 34140 1idoA 189 6.46e+00 c.62.1.1 34139 1n9zA 192 6.53e+00 c.62.1.1 85478 3b7hA 78 6.94e+00 1m1uA 195 7.04e+00 c.62.1.1 74421 2hqbA 296 7.25e+00 3bwdD 182 7.31e+00 1dosA 358 7.63e+00 1dosA c.1.10.2 29175 2oljA 263 7.65e+00 1gynA 358 7.79e+00 c.1.10.2 83385 2id3A 225 8.11e+00 a.4.1.9 137261 a.121.1.1 137262 1iv1A 152 8.45e+00 d.79.5.1 76816 1sgmA 191 8.95e+00 a.4.1.9 105537 a.121.1.1 105538 1omoA 322 9.04e+00 c.2.1.13 104017 1vllA 334 9.28e+00 c.2.1.13 108834 1wzaA 488 9.35e+00 b.71.1.1 121489 c.1.8.1 121490 1lkvX 232 9.38e+00 a.118.14.1 73980 3bjbA 207 9.80e+00 2vptA 215 9.93e+00 2ocbA 180 9.98e+00 2dzdA 461 9.98e+00 3cwrA 208 1.00e+01 2dzpA 248 1.06e+01 2dzwA 248 1.06e+01 1geqA 248 1.06e+01 2tysA c.1.2.4 28589 2g7uA 257 1.16e+01 1mc3A 296 1.17e+01 c.68.1.6 78943 2ehhA 294 1.18e+01 2dzvA 248 1.19e+01 2dzxA 248 1.21e+01 1surA 215 1.22e+01 c.26.2.2 31620 2gy9B 236 1.22e+01 2yxgA 289 1.23e+01 2b0jA 358 1.25e+01 a.100.1.11 127639 c.2.1.6 127640 2qalB 240 1.26e+01 1vs5B 241 1.27e+01 2o8vA 252 1.31e+01 1hkmA 365 1.32e+01 c.1.8.5 90636 d.26.3.1 90637 1lg2A 365 1.32e+01 c.1.8.5 77950 d.26.3.1 77951 1guvA 366 1.32e+01 c.1.8.5 83333 d.26.3.1 83334 1jilA 420 1.33e+01 c.26.1.1 66745 2uygA 149 1.33e+01 2ebyA 113 1.33e+01 1hkkA 364 1.34e+01 c.1.8.5 90634 d.26.3.1 90635 2np5A 203 1.45e+01 a.4.1.9 138424 a.121.1.1 138425 1mq8B 177 1.46e+01 c.62.1.1 79407 1mjnA 179 1.47e+01 c.62.1.1 79210 1wcxA 261 1.48e+01 2dt9A 167 1.48e+01 1urhA 280 1.48e+01 c.46.1.2 99829 c.46.1.2 99830 1yzlA 179 1.50e+01 c.37.1.8 124282 2gilA 162 1.53e+01 1cl1A 395 1.55e+01 1cl2A c.67.1.3 34395 1cl2A 395 1.55e+01 1cl2A c.67.1.3 34397 1o98A 511 1.55e+01 c.105.1.1 86684 c.76.1.3 86685 1ejjA 511 1.55e+01 1ejjA c.105.1.1 59422 c.76.1.3 59423 2fq6A 415 1.55e+01 c.67.1.3 133939 2dzsA 248 1.56e+01 2dfvA 347 1.57e+01 2d8aA 348 1.57e+01 1o99A 511 1.57e+01 c.105.1.1 81235 c.76.1.3 81236 2hypA 280 1.58e+01 2acvA 463 1.58e+01 2fp4B 395 1.58e+01 c.23.4.1 133897 d.142.1.4 133898 2e09A 248 1.58e+01 2acwA 465 1.58e+01 1eudB 396 1.58e+01 2scuB c.23.4.1 31150 d.142.1.4 41571 1cm0A 168 1.59e+01 1yghA d.108.1.1 40800 1ezuA 142 1.59e+01 1sluA b.16.1.1 23695 1zuaX 317 1.61e+01 2c4kA 370 1.62e+01 c.61.1.2 129824 c.61.1.2 129825 2i14A 395 1.64e+01 c.1.17.1 136966 d.41.2.1 136967 1wmsA 177 1.64e+01 c.37.1.8 109414 2pbxA 203 1.66e+01 2h0vA 338 1.67e+01 1y3tA 337 1.70e+01 b.82.1.5 122600 1s8fA 177 1.70e+01 c.37.1.8 105370 3bbpA 211 1.74e+01 2jfbA 164 1.79e+01 2iaiA 230 1.80e+01 1wcwA 261 1.81e+01 1wd7A 261 1.81e+01 c.113.1.1 114526 2v9dA 343 1.83e+01 1o0sA 605 1.84e+01 c.2.1.7 86540 c.58.1.3 86541 2guhA 214 1.85e+01 1pjzA 203 1.86e+01 c.66.1.36 94794 1q7lA 198 1.88e+01 c.56.5.4 96044 3bhqA 211 1.89e+01 2hjgA 436 1.93e+01 1q1yA 191 1.94e+01 d.167.1.1 104480 1mq9A 180 1.97e+01 c.62.1.1 79411 2icaA 183 1.99e+01 c.62.1.1 137236 1rd4A 191 1.99e+01 c.62.1.1 97304 1lfaA 187 2.00e+01 1ido c.62.1.1 34122 1vfoA 585 2.03e+01 b.1.18.2 120048 b.71.1.1 120049 c.1.8.1 120050 2d2oA 585 2.04e+01 b.1.18.2 131176 b.71.1.1 131177 c.1.8.1 131178 1pgjA 478 2.08e+01 2pgd a.100.1.1 18783 c.2.1.6 30195 1wzkA 585 2.12e+01 b.1.18.2 121507 b.71.1.1 121508 c.1.8.1 121509 1j0eA 341 2.12e+01 c.79.1.1 83906 1wzmA 585 2.13e+01 b.1.18.2 121519 b.71.1.1 121520 c.1.8.1 121521 1ji2A 585 2.13e+01 b.1.18.2 71672 b.71.1.1 71673 c.1.8.1 71674 1bvzA 585 2.13e+01 1bvzA b.1.18.2 21856 b.71.1.1 27783 c.1.8.1 28770 1g1yA 585 2.16e+01 1bvzA b.1.18.2 60210 b.71.1.1 60211 c.1.8.1 60212 2ffqA 171 2.18e+01 1ruoA 209 2.19e+01 2cgpA a.4.5.4 16105 b.82.3.2 28144 2uxuA 210 2.21e+01 1jf6A 585 2.25e+01 b.1.18.2 71650 b.71.1.1 71651 c.1.8.1 71652 1wzlA 585 2.25e+01 b.1.18.2 121513 b.71.1.1 121514 c.1.8.1 121515 2ntyC 180 2.27e+01 1b0uA 262 2.28e+01 1b0uA c.37.1.12 32370 2bdqA 224 2.29e+01 1w9yA 319 2.31e+01 b.82.2.1 120801 1zgzA 122 2.32e+01 c.23.1.1 125065 1f2dA 341 2.33e+01 1f2dA c.79.1.1 35298 1jf5A 585 2.34e+01 b.1.18.2 71644 b.71.1.1 71645 c.1.8.1 71646 1j0dA 341 2.41e+01 c.79.1.1 83902 1xfoA 357 2.41e+01 b.49.3.1 115265 c.56.5.4 115266 1up7A 417 2.41e+01 c.2.1.5 113374 d.162.1.2 113375 2ifyA 508 2.43e+01 1y0yA 353 2.55e+01 b.49.3.1 122514 c.56.5.4 122515 1up6A 416 2.55e+01 c.2.1.5 107976 d.162.1.2 107977 2dztA 248 2.56e+01 2hafA 211 2.59e+01 d.310.1.1 136286 2aj2A 208 2.60e+01 d.310.1.1 126840 1ukhA 369 2.61e+01 d.144.1.7 107913 1c3rA 375 2.61e+01 1c3pA c.42.1.2 32607 1c3pA 375 2.62e+01 1c3pA c.42.1.2 32606 1vkhA 273 2.62e+01 c.69.1.32 108662 1up4A 415 2.66e+01 c.2.1.5 113358 d.162.1.2 113359 1vizA 240 2.67e+01 c.1.4.1 100784 1cs1A 386 2.71e+01 1ibjA c.67.1.3 34399 2omkA 231 2.74e+01 1lqwA 183 2.85e+01 d.167.1.1 74210 2gupA 292 2.86e+01 c.55.1.10 135744 c.55.1.10 135745 1lm4A 194 2.89e+01 d.167.1.1 84626 2c4vA 167 2.89e+01 c.23.13.1 129863 2rfgA 297 2.90e+01 2p9bA 458 2.90e+01 5pgmA 246 2.96e+01 1qhfA c.60.1.1 33962 2dzuA 248 2.97e+01 1h49A 512 2.97e+01 c.1.8.4 83477 1hqkA 154 2.98e+01 c.16.1.1 65902 1syxB 86 2.98e+01 d.76.1.1 119081 2v5jA 287 3.01e+01 2o7tA 199 3.04e+01 487dH 224 3.05e+01 1ad2 i.1.1.2 45835 3pga1 337 3.06e+01 4pgaA 1lmhA 184 3.07e+01 d.167.1.1 74036 2c57A 180 3.09e+01 c.23.13.1 129879 1zxxA 319 3.14e+01 2igpA 120 3.14e+01 2hw8A 228 3.14e+01 1zhoA 228 3.15e+01 1ad2A 228 3.15e+01 e.24.1.1 43353 1vsaA 229 3.16e+01 2janA 432 3.16e+01 1wsaA 330 3.23e+01 4pgaA c.88.1.1 35558 1qhfA 240 3.23e+01 1qhfA c.60.1.1 33960 2cevA 299 3.28e+01 1d3vA c.42.1.1 32576 1wr8A 231 3.30e+01 c.108.1.10 114836 1c3cA 429 3.30e+01 1c3cA a.127.1.1 19425 1ybhA 590 3.31e+01 c.31.1.3 122891 c.36.1.5 122892 c.36.1.9 122893 1m6jA 261 3.32e+01 c.1.1.1 78693 1c3uA 431 3.32e+01 1c3cA a.127.1.1 19427 1r22A 122 3.33e+01 a.4.5.5 104777 1z4rA 168 3.34e+01 d.108.1.1 124444 1tmhA 254 3.36e+01 1amk c.1.1.1 28507 1treA 255 3.40e+01 1amk c.1.1.1 28505 2inuA 410 3.42e+01 2q3hA 201 3.43e+01 1djpA 330 3.46e+01 4pgaA c.88.1.1 35567 4pgaA 337 3.48e+01 4pgaA c.88.1.1 35565 2j7pD 283 3.50e+01 a.24.13.1 138123 c.37.1.10 138124 2fv8A 207 3.57e+01 c.37.1.8 134199 2iylD 284 3.58e+01 a.24.13.1 137801 c.37.1.10 137802 1cgpA 205 3.59e+01 a.4.5.4 16096 b.82.3.2 28135 1o3tA 200 3.64e+01 a.4.5.4 86611 b.82.3.2 86612 2jt1A 77 3.67e+01 2c4wA 176 3.70e+01 1kutA 230 3.71e+01 d.143.1.1 73017 2i6jA 161 3.75e+01 1i5zA 209 3.77e+01 a.4.5.4 83669 b.82.3.2 83670 2j4bA 138 3.79e+01 1g6nA 210 3.80e+01 2cgpA a.4.5.4 16100 b.82.3.2 28139 2cgpA 210 3.80e+01 2cgpA a.4.5.4 16102 b.82.3.2 28141 1i6xA 209 3.81e+01 a.4.5.4 83673 b.82.3.2 83674 2a22A 215 3.83e+01 d.159.1.7 126025 2ggoA 401 3.88e+01 1kabA 136 3.95e+01 b.40.1.1 24821 1hrhA 136 3.98e+01 1rthA c.55.3.1 33577