# List of top-scoring protein chains for t2k-100-30-bys-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 1jpaA 312 2.40e-42 d.144.1.7 67011 1opjA 293 7.32e-42 d.144.1.7 87230 1ir3A 306 2.47e-41 1fmk d.144.1.7 41702 1irk 306 5.34e-41 1fmk d.144.1.7 41703 1t46A 313 6.06e-41 d.144.1.7 106397 1lufA 343 8.49e-41 d.144.1.7 78223 1p4oA 322 2.13e-40 d.144.1.7 87775 1qpcA 279 2.34e-40 1fgkA d.144.1.7 41685 1fmk 452 3.08e-40 1fmk b.34.2.1,d.93.1.1,d.144.1.7 24511,40436,41690 1fgkA 310 3.10e-40 1fgkA d.144.1.7 41693 3lck 271 4.57e-40 1fmk d.144.1.7 41686 1r0pA 312 9.11e-40 d.144.1.7 96734 1jqhA 308 1.16e-39 d.144.1.7 71793 1fvrA 327 2.72e-39 d.144.1.7 60047 1mp8A 281 2.63e-38 d.144.1.7 91384 2b7aA 293 2.71e-37 1u59A 287 2.96e-37 d.144.1.7 107681 1ywnA 316 3.79e-37 1u46A 291 1.04e-36 d.144.1.7 107656 1xbbA 291 1.13e-36 1mq4A 272 1.80e-35 d.144.1.7 91391 1yhvA 297 4.22e-35 2evaA 307 5.78e-35 1f3mC 297 1.92e-34 1hcl d.144.1.7 41677 2bdwA 362 2.53e-34 2bfxA 284 4.76e-34 2f57A 317 5.51e-34 1gz8A 299 6.86e-34 d.144.1.7 83405 1xjdA 345 7.43e-34 1e1xA 299 8.81e-34 1hcl d.144.1.7 59157 1jvpP 298 9.45e-34 d.144.1.7 67371 1hcl 298 1.53e-33 1hcl d.144.1.7 41593 1phk 298 6.43e-33 1cdkA d.144.1.7 41635 1o6lA 337 6.85e-33 d.144.1.7 81092 2c30A 321 8.13e-33 1cmkE 350 1.04e-32 1cdkA d.144.1.7 41623 1jksA 294 1.20e-32 d.144.1.7 71710 1q8uA 350 3.29e-32 d.144.1.7 96230 1ia8A 289 3.54e-32 1ia8A d.144.1.7 62112 1uu3A 310 4.14e-32 d.144.1.7 99999 1xh9A 350 4.90e-32 1zrzA 364 5.28e-32 1cdkA 350 5.37e-32 1cdkA d.144.1.7 41620 1h1wA 289 6.08e-32 d.144.1.7 83460 2eueA 279 7.83e-32 1s9jA 341 9.36e-32 1p4fA 293 1.02e-31 d.144.1.7 104063 1apmE 350 1.98e-31 1cdkA d.144.1.7 41628 1blxA 326 2.40e-31 1hcl d.144.1.7 41596 2b9hA 353 2.50e-31 1tvoA 368 3.30e-31 3erk 364 3.62e-31 1hcl d.144.1.7 41654 1vzoA 355 6.87e-31 d.144.1.7 108971 1kobA 387 7.21e-31 1tkiA d.144.1.7 41640 1rdqE 350 9.84e-31 d.144.1.7 97314 2bvaA 292 1.22e-30 1o6yA 299 1.91e-30 d.144.1.7 81106 1pmnA 364 2.94e-30 d.144.1.7 94907 1pme 380 3.11e-30 1hcl d.144.1.7 41653 1t4hA 290 3.63e-30 d.144.1.7 106420 1zy4A 303 4.72e-30 1omwA 689 1.05e-29 a.91.1.1,b.55.1.1,d.144.1.7 87086,87087,87088 1wbsA 360 1.57e-29 1r3cA 366 1.64e-29 d.144.1.7 96906 2a19B 284 1.73e-29 1zzlA 351 3.44e-29 1zz2A 360 8.85e-29 2gfsA 372 9.88e-29 1ywrA 360 1.80e-28 2ac3A 316 2.73e-28 1xwsA 313 4.80e-28 1q41A 424 5.82e-28 d.144.1.7 95774 1j1bA 420 5.94e-28 d.144.1.7 90758 1tkiA 321 6.55e-28 1tkiA d.144.1.7 41638 2bikB 313 7.90e-28 2ac5A 316 1.35e-27 1ymiA 334 4.51e-27 1b6cB 342 5.50e-27 1b6cB d.144.1.7 41673 1vjyA 303 1.18e-26 d.144.1.7 108633 1py5A 326 1.67e-26 d.144.1.7 104389 1a6o 332 7.42e-26 1a6o 1lpuA 332 1.32e-25 d.144.1.7 74177 1z57A 339 1.51e-25 1lp4A 332 1.62e-25 d.144.1.7 74170 1x8bA 289 1.71e-25 1om1A 332 1.91e-25 d.144.1.7 93347 1m2rA 327 2.53e-25 d.144.1.7 84760 1jwhA 337 2.59e-25 d.144.1.7 71913 2eu9A 355 3.12e-24 1howA 373 7.76e-24 1hcl d.144.1.7 41679 1q8yA 373 1.82e-23 d.144.1.7 96234 1wbpA 397 2.04e-22 1ckiA 317 2.03e-21 1csn d.144.1.7 41660 1csn 298 7.84e-18 1csn d.144.1.7 41664 1zarA 282 4.36e-07 1tqmA 282 6.26e-07 a.4.5.56,d.144.1.9 107236,107237 1nd4A 264 1.03e-01 d.144.1.6 91815 1nw1A 429 6.84e-01 d.144.1.8 86286 1e7uA 961 9.38e-01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 1j7lA 264 9.77e-01 d.144.1.6 62697 1g6aA 271 1.01e+00 1btl e.3.1.1 42704 2ct9A 208 1.03e+00 1zthA 258 1.16e+00 2bkkA 264 1.42e+00 1jb3A 131 1.90e+00 1jc7A b.40.3.2 62833 1rybA 212 1.94e+00 c.56.3.1 98098 1e8yA 966 1.96e+00 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 1jc7A 131 1.97e+00 1jc7A b.40.3.2 62873 1fqgA 263 2.31e+00 1btl e.3.1.1 42699 1j7iA 264 2.39e+00 1j7iA d.144.1.6 62694 1e8xA 961 2.44e+00 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19148,23183,37631,41711 1btl 263 3.33e+00 1btl e.3.1.1 42691 1bsg 266 3.71e+00 1btl e.3.1.1 42729 1hzoA 271 4.45e+00 e.3.1.1 71092 1gz2A 142 4.54e+00 d.169.1.1 83392 1b35B 255 4.64e+00 1b35B b.121.4.1 23334 1e17A 150 4.66e+00 2hfh a.4.5.14 16143 1ermA 263 4.87e+00 1btl e.3.1.1 42690 1fxkC 133 5.28e+00 1fxkC a.2.5.1 15702 1yixA 265 5.52e+00 1c4xA 285 5.55e+00 1c4xA c.69.1.10 34684 1xdfA 157 6.71e+00 1m40A 263 6.86e+00 e.3.1.1 74437 2bfwA 200 6.89e+00 1jl2A 156 7.20e+00 c.55.3.1 66822 1vixA 420 7.67e+00 c.56.5.4,d.58.19.1 100777,100778 1iysA 262 7.88e+00 e.3.1.1 90723 1gvjA 146 7.95e+00 a.4.5.21 90525 2gdnA 267 8.08e+00 2be4A 272 8.16e+00 1vheA 373 8.20e+00 b.49.3.1,c.56.5.4 100669,100670 1hqcA 324 8.70e+00 1hqcA a.4.5.11,c.37.1.20 16127,32424 1fm0E 150 8.96e+00 1fmaE d.41.5.1 38629 1mdyA 68 9.39e+00 1mdyA a.38.1.1 17132 1yljA 263 9.60e+00 1kr4A 125 1.03e+01 d.58.5.2 72889 1fmaE 150 1.04e+01 1fmaE d.41.5.1 38630 1zbfA 142 1.07e+01 1o51A 114 1.10e+01 d.58.5.4 92480 1txqA 93 1.21e+01 1wu4A 396 1.23e+01 1sfxA 109 1.26e+01 a.4.5.50 105505 1i2sA 282 1.32e+01 e.3.1.1 71104 1uebA 184 1.35e+01 b.34.5.2,b.40.4.5,b.40.4.5 107782,107783,107784 1g8iA 190 1.41e+01 1rec a.39.1.5 60363 1a5mC 566 1.42e+01 1ubpC b.92.1.1,c.1.9.2 28423,29045 1ohtA 215 1.43e+01 d.118.1.1 87036 2eifA 136 1.47e+01 1bkb b.34.5.2,b.40.4.5 24607,25339 1rxwA 336 1.48e+01 a.60.7.1,c.120.1.2 98059,98060 2fjbA 643 1.50e+01 1r2qA 170 1.50e+01 c.37.1.8 96874 1qjpA 171 1.54e+01 1bxwA f.4.1.1 43742 1nthA 458 1.55e+01 c.1.25.1 80730 1fnoA 417 1.65e+01 d.58.19.1,c.56.5.4 70145,75841 1l2qA 458 1.71e+01 c.1.25.1 73510 1fs5A 266 1.73e+01 c.124.1.1 65044 1a5kC 566 1.74e+01 1ubpC b.92.1.1,c.1.9.2 28425,29047 1n6hA 170 1.75e+01 c.37.1.8 80197 1ekfA 365 1.76e+01 1ekfA e.17.1.1 59445 1bza 262 1.79e+01 1btl e.3.1.1 42701 1iyoA 262 1.83e+01 e.3.1.1 76970 1f2hA 169 1.85e+01 1f3vA d.58.22.1 59612 1wk2A 121 1.87e+01 1u7iA 136 1.88e+01 d.32.1.7 107724 1j6oA 268 1.91e+01 c.1.9.12 77088 1pm4A 119 2.02e+01 b.135.1.1 94891 2aw5A 541 2.06e+01 1a3qA 285 2.06e+01 1a3qA b.1.18.1,b.2.5.3 21932,22447 1ukuA 102 2.17e+01 d.58.5.2 99533 2fbyA 205 2.19e+01 1fsfA 266 2.29e+01 c.124.1.1 65047 1qr6A 584 2.33e+01 1qr6A c.2.1.7,c.58.1.3 30293,33941 1bxwA 172 2.37e+01 1bxwA f.4.1.1 43743 1zcbA 362 2.39e+01 3tgl 269 2.41e+01 3tgl c.69.1.17 34733 2fyxA 143 2.44e+01 1fgyA 127 2.45e+01 1faoA b.55.1.1 26976 1deaA 266 2.47e+01 1deaA c.124.1.1 31760 1o6dA 163 2.50e+01 c.116.1.3 92567 2exrA 524 2.53e+01 1wmwA 330 2.64e+01 1nxuA 333 2.66e+01 c.122.1.1 86389 1usmA 80 2.69e+01 d.74.1.1 99876 1so7A 382 2.70e+01 1e0gA 48 2.74e+01 1e01A d.7.1.1 37325 2c6yA 111 2.74e+01 2coeA 120 2.77e+01 1oxcA 114 2.79e+01 b.115.1.1 93683 1psrA 100 2.83e+01 1psrA a.39.1.2 17180 1gztA 115 2.87e+01 b.115.1.1 76428 1ktaA 365 3.01e+01 e.17.1.1 77533 1bn8A 420 3.02e+01 1pcl b.80.1.1 28022 2rn2 155 3.03e+01 2rn2 c.55.3.1 33551 1gw5S 142 3.06e+01 d.110.4.2 70633 2bspA 420 3.16e+01 1pcl b.80.1.1 28023 1s72Q 96 3.21e+01 b.34.5.1 105336 1jj2P 95 3.26e+01 1ffkN b.34.5.1 63101 1ex2A 189 3.28e+01 1ex2A c.51.4.2 33225 1huqA 164 3.33e+01 1byuA c.37.1.8 32020 1szoA 257 3.33e+01 c.14.1.3 106164 1h99A 224 3.35e+01 a.142.1.1,a.142.1.1 60814,60815 1jysA 242 3.42e+01 c.56.2.1 77216 1f3vA 179 3.50e+01 1f3vA d.58.22.1 39382 1xioA 261 3.58e+01 1top 162 3.60e+01 1ncx a.39.1.5 17223 1uzvA 114 3.64e+01 1t4bA 367 3.69e+01 c.2.1.3,d.81.1.1 106406,106407 1ncx 162 3.70e+01 1ncx a.39.1.5 17222 1kt8A 365 3.80e+01 e.17.1.1 77531 1jnrA 643 3.83e+01 a.7.3.1,c.3.1.4,d.168.1.1 66966,66967,66968 1kcfA 258 3.85e+01 a.140.2.1,c.55.3.7 68434,68435 1ku2A 241 3.87e+01 a.4.13.1,a.177.1.1 83096,83097 1gm6A 175 3.91e+01 b.60.1.1 70272 1w19A 160 3.93e+01 2comA 124 3.96e+01 2a2fX 325 4.00e+01 1s7bA 110 4.00e+01 f.39.1.1 98634 1wekA 217 4.00e+01 1vjjA 692 4.01e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 100814,100815,100816,100817 1ar1A 558 4.07e+01 2occA f.24.1.1 43618 1zb9A 143 4.13e+01 1a3yA 149 4.13e+01 1obpA b.60.1.1 27110 1hueA 90 4.15e+01 1huuA a.55.1.1 17900 2b7oA 464 4.23e+01 1ew6B 137 4.23e+01 1ewaA a.1.1.2 15638 1egxA 115 4.29e+01 1evhA b.55.1.4 27000 1wgzA 510 4.38e+01 1jwqA 179 4.43e+01 c.56.5.6 90921 1vpjA 192 4.44e+01 1vqoQ 96 4.47e+01 1rss 151 4.50e+01 1rss a.75.1.1 18392 1e01A 48 4.51e+01 1e01A 1xksA 450 4.55e+01 1cojA 212 4.57e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 2b06A 155 4.61e+01 1dkxA 219 4.70e+01 1dkzA a.8.4.1,b.130.1.1 90339,90340 1b66A 140 4.77e+01 1b66A d.96.1.2 40657 1jp4A 308 4.82e+01 1jp4A e.7.1.1 63223 1rwiA 270 4.84e+01 b.68.9.1 97987 1je0A 236 4.84e+01 c.56.2.1 66581 1tvxA 75 4.88e+01 1tvxA d.9.1.1 37441 1f21A 155 4.89e+01 2rn2 c.55.3.1 33550 1wkuA 254 4.95e+01 1tvxB 75 4.96e+01 1tvxA d.9.1.1 37442 1dzkA 157 5.10e+01 1obpA b.60.1.1 27096 1tdhA 364 5.22e+01 a.156.1.2,b.113.1.1,g.39.1.8 106772,106773,106774 2ftrA 108 5.24e+01 1zosA 230 5.24e+01 1dsxA 87 5.31e+01 1t1dA d.42.1.2 38644 1lyvA 306 5.37e+01 c.45.1.2 74348 1i69A 219 5.38e+01 c.94.1.1 61825 1u7kA 131 5.39e+01 1wlgA 299 5.39e+01 1dkzA 219 5.44e+01 1dkzA a.8.4.1,b.130.1.1 90345,90346 1yts 278 5.64e+01 1ytw c.45.1.2 32690 1a0p 290 5.65e+01 1a0p a.60.9.1,d.163.1.1 18105,42165 1nszA 347 5.72e+01 b.30.5.4 80724 1mmuA 347 5.74e+01 b.30.5.4 79303 1n9bA 265 5.75e+01 e.3.1.1 85463 2a1hA 365 5.81e+01 1e54A 332 5.83e+01 1e54A f.4.3.1 59258 1bavA 309 5.84e+01 1aye c.56.5.1 33806 1pv9A 348 5.87e+01 c.55.2.1,d.127.1.1 95157,95158 1q4rA 112 5.87e+01 d.58.4.4 95823 1j6qA 136 5.88e+01 b.40.9.1 77091 1sotA 320 5.92e+01 b.36.1.4,b.47.1.1 105852,105853 2bgzA 299 5.95e+01 2c4nA 250 5.99e+01 1d3bA 75 6.01e+01 1d3bA b.38.1.1 24798 1yd0A 96 6.04e+01 2ucz 165 6.22e+01 1u9aA d.20.1.1 38330 2gnxA 365 6.30e+01 1b8aA 438 6.31e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1dtdA 303 6.38e+01 1aye c.56.5.1 33823 2erfA 209 6.41e+01 1ytw 306 6.61e+01 1ytw c.45.1.2 32689 1rzhH 260 6.76e+01 b.41.1.1,f.23.10.1 98162,98163 2ftzA 284 6.79e+01 1q53A 112 6.79e+01 d.58.4.4 95858 1l9gA 192 6.87e+01 c.18.1.2 84568 2bb6A 414 6.87e+01 1byqA 228 6.90e+01 1yer d.122.1.1 41100 1gq2A 555 6.97e+01 c.2.1.7,c.58.1.3 70308,70309 1vdxA 184 7.07e+01 1oxa 403 7.13e+01 1f4tA a.104.1.1 18965 1p1lA 102 7.19e+01 d.58.5.2 87695 2fa1A 160 7.19e+01 1gtqA 140 7.27e+01 1b66A d.96.1.2 40661 1lap 488 7.31e+01 1lam c.50.1.1,c.56.5.3 33171,33834 1w6uA 302 7.33e+01 1ntyA 311 7.33e+01 a.87.1.1,b.55.1.1 103873,103874 1z8oA 404 7.41e+01 1zp4A 304 7.58e+01 1amoA 615 7.63e+01 1amoA b.43.4.1,c.23.5.2,c.25.1.4 25669,31210,31557 1cmcA 104 7.82e+01 1cmbA a.43.1.5 17462 2fbwA 621 7.84e+01 1idk 359 7.92e+01 1qcxA b.80.1.2 28025 1c3pA 375 7.96e+01 1c3pA c.42.1.2 32606 1wy2A 351 7.97e+01 1l7jB 347 7.98e+01 b.30.5.4 73661 2b99A 156 8.00e+01 1m33A 258 8.00e+01 c.69.1.26 78514 1jipA 403 8.07e+01 a.104.1.1 66748 1uouA 474 8.15e+01 a.46.2.1,c.27.1.1,d.41.3.1 99706,99707,99708 1wn2A 121 8.17e+01 1hzdA 272 8.18e+01 c.14.1.3 65969 1va0A 239 8.19e+01 1kwmA 402 8.20e+01 c.56.5.1,d.58.3.1 73079,73080 451c 82 8.26e+01 451c a.3.1.1 15904 1a68 95 8.35e+01 1t1dA d.42.1.2 38639 351c 82 8.39e+01 451c a.3.1.1 15905 1t1dA 100 8.40e+01 1t1dA d.42.1.2 38637 1ewaA 137 8.44e+01 1ewaA a.1.1.2 15639 1ew6A 137 8.45e+01 1ewaA a.1.1.2 15637 1nvpD 108 8.48e+01 a.32.1.1,b.56.1.1 92213,92214 1zynA 202 8.49e+01 1yptA 305 8.51e+01 1ytw c.45.1.2 32686 1to3A 304 8.55e+01 c.1.10.1 107161 1t6t1 118 8.66e+01 1xhdA 173 8.74e+01 1napA 70 8.79e+01 1tvxA d.9.1.1 37445