# List of top-scoring protein chains for t04-100-30-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 1vpdA 299 8.65e-04 1wwkA 307 1.46e-03 1uufA 369 1.98e-03 b.35.1.2,c.2.1.1 100006,100007 1pswA 348 2.00e-03 c.87.1.7 88287 1yqdA 366 2.91e-03 1xhcA 367 1.03e-02 1yrlA 491 1.13e-02 1sc6A 404 1.22e-02 2ashA 381 1.74e-02 4uagA 437 2.19e-02 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30651,33952,34955 1o6dA 163 2.63e-02 c.116.1.3 92567 1mldA 314 2.70e-02 2cmd c.2.1.5,d.162.1.1 30122,42089 1j4aA 333 3.08e-02 c.2.1.4,c.23.12.1 71502,71503 1psdA 409 3.25e-02 1psdA c.2.1.4,c.23.12.1,d.58.18.1 30097,31357,39354 1pjqA 457 3.39e-02 c.2.1.11,c.90.1.1,e.37.1.1 94766,94767,94768 1vid 221 3.90e-02 1vid c.66.1.1 34178 1lsuA 147 4.08e-02 c.2.1.9 74250 1ofuX 119 4.13e-02 c.37.1.22 86976 1txgA 335 4.38e-02 1xdwA 331 5.09e-02 1tqjA 230 5.65e-02 c.1.2.2 107228 1h1dA 221 5.70e-02 c.66.1.1 83452 1fl2A 310 6.88e-02 1hyuA c.3.1.5,c.3.1.5 59869,59870 1broA 277 7.89e-02 1brt c.69.1.12 34700 1b8oA 284 7.99e-02 1b8oA c.56.2.1 33762 1v8bA 479 8.71e-02 1bg6 359 9.24e-02 1bg6 a.100.1.5,c.2.1.6 18810,30214 1q9uA 130 9.76e-02 d.129.7.1 96314 1y81A 138 9.78e-02 1w4xA 542 1.04e-01 c.3.1.5,c.3.1.5 109171,109172 1brt 277 1.13e-01 1brt c.69.1.12 34699 1q7zA 566 1.45e-01 c.1.21.2,c.1.26.1 96090,96091 1vizA 240 1.46e-01 c.1.4.1 100784 2f1kA 279 1.60e-01 1np3A 338 1.61e-01 a.100.1.2,c.2.1.6 85946,85947 1zs7A 190 1.66e-01 2d0iA 333 1.76e-01 2cx1A 187 1.81e-01 1ezwA 349 2.22e-01 1ezwA c.1.16.3 29558 1dxy 333 2.30e-01 1dxy c.2.1.4,c.23.12.1 30094,31354 2c4nA 250 2.39e-01 1h7wA 1025 2.44e-01 1h7wA a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15683,28628,30324,30609,39007 1xwfA 431 2.69e-01 1x9gA 200 2.99e-01 c.33.1.3 109527 1ml4A 308 3.11e-01 c.78.1.1,c.78.1.1 79255,79256 1u2zA 433 3.19e-01 c.66.1.31 107626 1hyuA 521 3.22e-01 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1li4A 432 3.25e-01 c.2.1.4,c.23.12.3 84616,84617 1o94A 729 3.43e-01 c.1.4.1,c.3.1.1,c.4.1.1 81200,81201,81202 1gteA 1025 3.71e-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 1jdpA 441 4.05e-01 c.93.1.1 62906 1yxyA 234 4.10e-01 1y0eA 223 4.19e-01 2b0cA 206 4.50e-01 1qmgA 524 4.66e-01 1qmgA a.100.1.2,c.2.1.6 18785,30182 1e8yA 966 4.98e-01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 1k0iA 394 5.02e-01 c.3.1.2,d.16.1.2 67942,67943 1rcuA 195 5.34e-01 c.129.1.1 97295 2ffeA 311 5.35e-01 1gca 309 5.67e-01 1gca c.93.1.1 35659 1o4sA 389 5.70e-01 c.67.1.1 86620 2anuA 255 5.74e-01 1cb0A 283 5.76e-01 1cb0A c.56.2.1 33790 1b8gA 429 5.79e-01 1b8gA c.67.1.4 34499 1f8rA 498 5.92e-01 1f8rA c.3.1.2,d.16.1.5 30410,37974 2bi7A 384 5.92e-01 2cdcA 366 6.21e-01 1yc5A 246 6.29e-01 7aatA 401 6.32e-01 1ajsA c.67.1.1 34250 1p1jA 533 6.37e-01 c.2.1.3,d.81.1.3 87687,87688 1lssA 140 6.40e-01 c.2.1.9 74246 1rpxA 230 6.41e-01 1rpxA c.1.2.2 28536 1j79A 347 6.59e-01 1j79A c.1.9.4 62675 1hkhA 279 6.60e-01 c.69.1.12 90628 1y8aA 332 7.18e-01 1yqzA 438 7.28e-01 1t0hB 224 7.57e-01 c.37.1.1 106208 1vrbA 342 7.81e-01 1gdhA 320 8.15e-01 1gdhA c.2.1.4,c.23.12.1 30095,31355 1vdc 333 8.50e-01 1trb c.3.1.5,c.3.1.5 30545,30546 1wbhA 214 8.61e-01 2c0aA 214 8.61e-01 1lst 239 8.80e-01 1lst c.94.1.1 35755 1djnA 729 8.98e-01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28612,30313,30598 1f06A 320 9.04e-01 1dapA c.2.1.3,d.81.1.3 59556,59557 1qisA 396 9.12e-01 1ajsA c.67.1.1 34284 2b4yA 271 9.37e-01 2g76A 335 9.56e-01 1m7yA 435 9.80e-01 c.67.1.4 78761 1tp9A 162 9.81e-01 5nul 138 9.93e-01 5nul c.23.5.1 31191 1pbe 394 1.00e+00 1pbe c.3.1.2,d.16.1.2 30338,37869 1euaA 213 1.02e+00 1fwrA c.1.10.1 29155 1reoA 486 1.08e+00 c.3.1.2,d.16.1.5 97325,97326 1ykjA 394 1.09e+00 1quqB 121 1.09e+00 1quqB b.40.4.3 25305 1t3lA 337 1.09e+00 b.34.2.1,c.37.1.1 106358,106359 2ga9A 297 1.11e+00 1guzA 310 1.14e+00 c.2.1.5,d.162.1.1 65586,65587 1m2kA 249 1.14e+00 c.31.1.5 84754 1ad3A 452 1.16e+00 1ad3A c.82.1.1 35335 1y9aA 360 1.18e+00 1pud 386 1.18e+00 1pud c.1.20.1 29658 2b9wA 424 1.20e+00 1i2aA 219 1.22e+00 e.24.1.1 90660 1cbf 285 1.24e+00 1cbf c.90.1.1 35587 1djqA 729 1.28e+00 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28614,30315,30600 1z5yE 149 1.35e+00 1f37A 110 1.37e+00 1f37A c.47.1.11 33088 3mag 307 1.38e+00 3mag c.66.1.25 34205 1e3jA 352 1.45e+00 1e3jA b.35.1.2,c.2.1.1 24765,29781 1j5pA 253 1.50e+00 d.81.1.3,c.2.1.3 71577,83092 1b7yB 785 1.53e+00 1pysB a.6.1.1,a.6.1.1,b.40.4.4,d.58.13.1,d.104.1.1,d.138.1.1 16301,16302,25312,39311,40780,41456 1n3bA 216 1.56e+00 c.37.1.1 79959 1ars 396 1.61e+00 1ajsA c.67.1.1 34287 2ajrA 331 1.67e+00 2f1rA 171 1.68e+00 1o04A 500 1.74e+00 c.82.1.1 86508 1vmeA 410 1.75e+00 c.23.5.1,d.157.1.3 108893,108894 1e7uA 961 1.78e+00 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 1vjrA 271 1.80e+00 c.108.1.14 100832 1v25A 541 1.80e+00 e.23.1.1 108275 1evyA 366 1.82e+00 1evyA a.100.1.6,c.2.1.6 18811,30215 1y7pA 223 1.84e+00 1xa0A 328 1.85e+00 2gbp 309 1.86e+00 1gca c.93.1.1 35657 1tt0A 623 1.88e+00 1tqgA 105 1.89e+00 a.24.10.3 107224 1a53 247 1.89e+00 1a53 c.1.2.4 28564 1wzuA 300 1.90e+00 2avnA 260 1.90e+00 1twyA 290 1.96e+00 2b34A 199 1.96e+00 1dxeA 256 2.01e+00 1dxeA c.1.12.5 29310 1e5dA 402 2.01e+00 1e5dA c.23.5.1,d.157.1.3 31208,42061 1j8fA 323 2.01e+00 1j8fA c.31.1.5 62738 1vhtA 218 2.05e+00 c.37.1.1 100700 1ynuA 473 2.06e+00 1hd2A 161 2.07e+00 c.47.1.10 60962 2tmdA 729 2.09e+00 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28616,30317,30602 1nthA 458 2.14e+00 c.1.25.1 80730 1pzgA 331 2.16e+00 c.2.1.5,d.162.1.1 95425,95426 1js1X 324 2.20e+00 c.78.1.1,c.78.1.1 71834,71835 1ejbA 168 2.20e+00 1rvv1 c.16.1.1 59417 1kv8A 216 2.24e+00 c.1.2.3 73054 1pjcA 361 2.25e+00 1sayA c.2.1.4,c.23.12.2 30101,31361 1xkqA 280 2.30e+00 1iibA 106 2.34e+00 1iibA c.44.2.1 32648 1rvgA 305 2.38e+00 c.1.10.2 97920 1s4qA 228 2.38e+00 c.37.1.1 98507 1ve3A 227 2.39e+00 1vp9 322 2.41e+00 3mag c.66.1.25 34210 2cunA 410 2.41e+00 1h4xA 117 2.43e+00 1auz c.13.2.1 60626 1zhaA 267 2.54e+00 2ffjA 300 2.66e+00 1ma3A 253 2.68e+00 c.31.1.5 78883 2ccmA 191 2.70e+00 1ddgA 374 2.71e+00 1amoA b.43.4.1,c.25.1.4 25671,31559 1vpt 348 2.71e+00 3mag c.66.1.25 34207 1igs 248 2.73e+00 1a53 c.1.2.4 28565 1r5yA 386 2.73e+00 c.1.20.1 97134 1d4fA 431 2.77e+00 1b3rA c.2.1.4,c.23.12.3 30110,31370 1y80A 210 2.80e+00 3csuA 310 2.85e+00 3csuA c.78.1.1,c.78.1.1 35094,35095 1q6oA 216 2.94e+00 c.1.2.3 95986 1l8bA 190 2.97e+00 d.86.1.1 73683 1q1gA 276 3.05e+00 c.56.2.1 95574 1m2dA 110 3.08e+00 c.47.1.11 78476 1v39 322 3.10e+00 3mag c.66.1.25 34206 1z8fA 228 3.22e+00 2bb2 181 3.22e+00 2bb2 b.11.1.1,b.11.1.1 23604,23605 1tzlA 622 3.27e+00 1ps9A 671 3.38e+00 c.1.4.1,c.3.1.1,c.4.1.1 95076,95077,95078 1u0tA 307 3.47e+00 e.52.1.1 107567 1pxgA 382 3.59e+00 c.1.20.1 95287 1geeA 261 3.61e+00 c.2.1.2 90509 1vh7A 265 3.63e+00 c.1.2.1 100646 1gc0A 398 3.67e+00 c.67.1.3 70168 1y89A 238 3.73e+00 1qpoA 284 3.75e+00 1qpoA c.1.17.1,d.41.2.1 29561,38597 1q1rA 431 3.78e+00 c.3.1.5,c.3.1.5,d.87.1.1 95600,95601,95602 1kx5B 102 3.78e+00 a.22.1.1 77594 1w8sA 263 3.81e+00 1gcoA 261 3.83e+00 1ybvA c.2.1.2 29884 1t8xA 267 3.84e+00 1h2rS 267 3.89e+00 2frvA e.19.1.1 43310 2ahrA 259 4.03e+00 1jeoA 180 4.03e+00 c.80.1.3 66611 1lc5A 364 4.05e+00 c.67.1.1 73827 2g8lA 299 4.05e+00 1ju3A 583 4.10e+00 b.18.1.13,c.69.1.21 67300,67301 1wiwA 290 4.19e+00 1qj4A 257 4.24e+00 1qj4A c.69.1.20 34796 1fxqA 267 4.25e+00 1d9eA c.1.10.4 60108 1uwkA 557 4.26e+00 e.51.1.1 108065 1qvcA 145 4.27e+00 3ullA b.40.4.3 25284 1gsoA 431 4.35e+00 1gsoA b.84.2.1,c.30.1.1,d.142.1.2 28240,31647,41492 2bfwA 200 4.35e+00 1g4wR 383 4.39e+00 1g4uS a.24.11.1,c.45.1.2 16644,32692 2c3zA 222 4.41e+00 1l3iA 192 4.47e+00 c.66.1.22 77676 1o13A 136 4.50e+00 c.55.5.1 80762 1gadO 330 4.51e+00 1dssG c.2.1.3,d.81.1.1 29950,39865 1rq2A 382 4.55e+00 c.32.1.1,d.79.2.1 105048,105049 1zmdA 474 4.66e+00 1e3dA 266 4.70e+00 2frvA e.19.1.1 59188 1id1A 153 4.83e+00 1id1A c.2.1.9 62286 1dljA 402 4.94e+00 1dliA a.100.1.4,c.2.1.6,c.26.3.1 18808,30212,31621 1u7pA 164 4.96e+00 1tzyD 103 4.98e+00 a.22.1.1 107533 1trb 320 5.00e+00 1trb c.3.1.5,c.3.1.5 30529,30530 1jysA 242 5.02e+00 c.56.2.1 77216 1zq1A 438 5.06e+00 1ej0A 180 5.17e+00 1ej0A c.66.1.2 34179 1xi3A 215 5.29e+00 c.1.3.1 109601 1xklA 273 5.29e+00 1t0bA 252 5.34e+00 c.23.16.6 106199 1vm6A 228 5.35e+00 c.2.1.3,d.81.1.3 108876,108877 1ej1A 190 5.36e+00 1ejhA d.86.1.1 40144 1zbsA 291 5.38e+00 1wi9A 72 5.44e+00 2b4aA 138 5.47e+00 1ubkS 267 5.49e+00 e.19.1.1 88423 1ac5 483 5.53e+00 1ac5 c.69.1.5 34653 1a8vA 121 5.54e+00 1a62 a.140.3.1,b.40.4.5 64712,64713 1o12A 376 5.65e+00 b.92.1.5,c.1.9.10 80758,80759 1kyqA 274 5.67e+00 c.2.1.11,e.37.1.1 73281,73282 3ladA 476 5.73e+00 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30573,30574,40208 1mv8A 436 5.74e+00 a.100.1.4,c.2.1.6,c.26.3.1 85128,85129,85130 2bg5A 324 5.85e+00 1qv9A 283 6.06e+00 c.127.1.1 96356 1kte 105 6.06e+00 1kte c.47.1.1 32771 1gtmA 419 6.09e+00 1hwyA c.2.1.7,c.58.1.1 30223,33871 1hq3D 103 6.12e+00 1aoiB a.22.1.1 16464 2aefA 234 6.19e+00 1wj9A 211 6.20e+00 1zq6A 359 6.27e+00 1vm7A 311 6.32e+00 c.72.1.1 108884 1edzA 320 6.34e+00 1ee9A c.2.1.7,c.58.1.2 30287,33935 1fwsA 267 6.39e+00 1d9eA c.1.10.4 60063 1x42A 232 6.47e+00 1ww8A 439 6.52e+00 2coeA 120 6.59e+00 1th0A 226 6.61e+00 d.3.1.7 106903 1vimA 200 6.61e+00 c.80.1.3 100758 1lt8A 406 6.68e+00 c.1.26.1 78186 1dhs 344 6.71e+00 1dhs c.31.1.1 31727 4pgaA 337 6.71e+00 4pgaA c.88.1.1 35565 1o9rA 162 6.71e+00 a.25.1.1 86706 2bkyA 97 6.74e+00 1fa8A 135 6.75e+00 1qipA d.32.1.1 38486 1dyqA 234 6.76e+00 3seb b.40.2.2,d.15.6.1 59140,59141 1vkmA 297 6.84e+00 c.138.1.1 108670 1ecpA 238 6.97e+00 1ecpA c.56.2.1 33775 1jcxA 267 7.10e+00 c.1.10.4 66510 2a4nA 182 7.12e+00 1k9sA 237 7.15e+00 c.56.2.1 68359 1f9zA 135 7.16e+00 1qipA d.32.1.1 38484 1vjnA 220 7.17e+00 d.157.1.4 100825 1ojaA 520 7.22e+00 c.3.1.2,d.16.1.5 93096,93097 2bw0A 329 7.24e+00 1cs1A 386 7.28e+00 1ibjA c.67.1.3 34399 1a4iA 301 7.29e+00 1a4iA c.2.1.7,c.58.1.2 30278,33926 1s3eA 520 7.35e+00 c.3.1.2,d.16.1.5 98426,98427 1vecA 206 7.38e+00 c.37.1.19 100575 1pj5A 830 7.41e+00 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 1qe5A 266 7.45e+00 1b8oA c.56.2.1 33784 2nacA 393 7.69e+00 2nadA c.2.1.4,c.23.12.1 30088,31348 1nhp 447 7.77e+00 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30549,30550,40196 2fr1A 486 7.77e+00 1f20A 435 7.84e+00 b.43.4.1,c.25.1.4 64932,64933 1pea 385 7.91e+00 1pea c.93.1.1 35662 1rp0A 284 7.93e+00 1ihoA 283 7.97e+00 1ihoA c.26.1.4 62390 1pfkA 320 8.05e+00 3pfk c.89.1.1 35575 1m6yA 301 8.10e+00 a.60.13.1,c.66.1.23 78716,78717 1zejA 293 8.14e+00 1rliA 184 8.26e+00 c.23.5.6 97647 1pl8A 356 8.32e+00 b.35.1.2,c.2.1.1 94878,94879 1atg 231 8.51e+00 1atg c.94.1.1 35834 1xeaA 323 8.52e+00 c.2.1.3,d.81.1.5 109572,109573 1y5eA 169 8.54e+00 1pe1A 267 8.55e+00 c.1.10.4 94591 1jflA 228 8.59e+00 c.78.2.1,c.78.2.1 71656,71657 1g2iA 166 8.60e+00 1g2iA c.23.16.2 31438 1kdgA 546 8.79e+00 c.3.1.2,d.16.1.1 77337,77338 1ns5A 155 9.01e+00 c.116.1.3 80705 1kq3A 376 9.20e+00 e.22.1.2 68790 1h2bA 359 9.23e+00 b.35.1.2,c.2.1.1 90543,90544 1vjzA 341 9.28e+00 c.1.8.3 100838 1thfD 253 9.32e+00 1thfD c.1.2.1 28535 1s3iA 310 9.36e+00 b.46.1.1,c.65.1.1 98435,98436 1m7bA 184 9.48e+00 c.37.1.8 74572 1c7nA 399 9.50e+00 1d2fA c.67.1.3 34413 1ahxA 396 9.57e+00 1ajsA c.67.1.1 34293 2f3nA 76 9.57e+00 1gesA 450 9.58e+00 3grs c.3.1.5,c.3.1.5,d.87.1.1 30473,30474,40168 2aeuA 374 9.62e+00 1t6nA 220 9.68e+00 c.37.1.19 106576 1g2oA 268 9.89e+00 1b8oA c.56.2.1 60228 2b4lA 268 1.00e+01 1tjyA 316 1.01e+01 c.93.1.1 107062 1x74A 360 1.01e+01 1b6g 310 1.02e+01 1b6g c.69.1.8 34661 2c5aA 379 1.02e+01 1tcvA 287 1.02e+01 1usgA 346 1.02e+01 c.93.1.1 99864 1kjwA 295 1.03e+01 b.34.2.1,c.37.1.1 68643,68644 1gpjA 404 1.03e+01 a.151.1.1,c.2.1.7,d.58.39.1 65451,65452,65453 1jb3A 131 1.03e+01 1jc7A b.40.3.2 62833 1npyA 271 1.05e+01 c.2.1.7,c.58.1.5 85995,85996 1xjo 284 1.06e+01 1xjo c.56.5.4 33843 1agjA 242 1.06e+01 1agjA b.47.1.1 25827 1eziA 228 1.07e+01 1eyrA c.68.1.13 34512 1huuA 90 1.07e+01 1huuA a.55.1.1 17897 1o5iA 249 1.07e+01 c.2.1.2 92499 1nqkA 381 1.08e+01 c.1.16.4 92050 1nytA 271 1.09e+01 c.2.1.7,c.58.1.5 86417,86418 2fqxA 318 1.09e+01 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