# List of top-scoring protein chains for t04-100-30-str2-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 1z47A 355 6.70e-02 1fobA 334 7.42e-02 c.1.8.3 83255 1l2tA 235 7.86e-02 c.37.1.12 73514 1c9kA 180 9.14e-02 1c9kB c.37.1.11 32363 1z2lA 423 1.05e-01 1xx4A 261 1.17e-01 2b99A 156 1.18e-01 2f9zC 159 1.94e-01 1yvkA 163 2.69e-01 1vypX 364 3.02e-01 c.1.4.1 108905 1vyrA 364 3.43e-01 c.1.4.1 108906 1gvoA 364 3.45e-01 c.1.4.1 76357 1h61A 364 3.45e-01 1oyc c.1.4.1 60657 2abbA 364 3.70e-01 1sg4A 260 4.28e-01 1u1wA 298 4.50e-01 1w2xA 758 5.12e-01 c.14.1.4,c.14.1.4 109134,109135 1mb3A 124 5.68e-01 c.23.1.1 78907 1uyrA 737 6.16e-01 c.14.1.4,c.14.1.4 100188,100189 1y9kA 157 6.39e-01 1a04A 215 9.44e-01 1a04A a.4.6.2,c.23.1.1 16234,31089 1xubA 298 9.49e-01 1jf8A 131 9.84e-01 c.44.1.1 66621 1t6kA 278 1.08e+00 1ig8A 486 1.18e+00 2yhx c.55.1.3,c.55.1.3 64746,64747 1srrA 124 1.23e+00 1dz3A c.23.1.1 31110 1phk 298 1.25e+00 1cdkA d.144.1.7 41635 1b0uA 262 1.26e+00 1b0uA c.37.1.12 32370 1y10A 407 1.32e+00 1n13B 113 1.36e+00 1u9jA 358 1.65e+00 1wb4A 297 1.67e+00 1o0iA 138 2.10e+00 d.38.1.5 86532 1hp1A 516 2.23e+00 d.114.1.1,d.159.1.2 70976,70977 1k77A 260 2.23e+00 c.1.15.5 72096 2anuA 255 2.28e+00 1jmvA 141 2.38e+00 c.26.2.4 66897 1gklA 297 2.58e+00 c.69.1.2 65250 1e19A 314 2.61e+00 1b7bA c.73.1.1 34967 1ctn 540 2.62e+00 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21876,29005,38439 1u0sY 118 2.66e+00 c.23.1.1 107566 1dkiA 371 2.72e+00 1dkiA d.3.1.1 37090 1e7rA 321 2.76e+00 1bsvA c.2.1.2 29808 1tmy 120 2.85e+00 1dbwA c.23.1.1 31083 2c31A 568 2.88e+00 1e6uA 321 2.88e+00 1bsvA c.2.1.2 29805 2bllA 345 2.91e+00 1h49A 512 2.96e+00 c.1.8.4 83477 1e55A 512 3.02e+00 1e70M c.1.8.4 28934 1z41A 338 3.05e+00 1z7bA 358 3.07e+00 1qe5A 266 3.33e+00 1b8oA c.56.2.1 33784 1p5jA 372 3.34e+00 c.79.1.1 104067 1nu0A 138 3.39e+00 c.55.3.8 92165 1gheA 177 3.40e+00 d.108.1.1 76222 1j8yF 297 3.47e+00 1ng1 a.24.13.1,c.37.1.10 62747,62748 1i39A 225 3.49e+00 1ekeA c.55.3.1 61585 2ct8A 497 3.94e+00 1g291 372 3.96e+00 1g291 1ush 550 4.19e+00 1ush d.114.1.1,d.159.1.2 40923,42079 2reb 352 4.41e+00 2reb c.37.1.11,d.48.1.1 32282,38767 1edqA 540 4.49e+00 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21873,29002,38436 1vplA 256 4.59e+00 1e9lA 377 4.61e+00 1e9lA c.1.8.5,d.26.3.1 59395,59396 1w5fA 353 4.61e+00 1b4kA 337 4.67e+00 1b4kA c.1.10.3 29184 1g6hA 257 4.70e+00 1gajA c.37.1.12 60318 1nekA 588 4.75e+00 a.7.3.1,c.3.1.4,d.168.1.1 80426,80427,80428 1w5qA 337 4.79e+00 2b6eA 146 4.94e+00 1ru8A 232 4.95e+00 c.26.2.1 97849 1vr5A 547 5.05e+00 2ftxB 64 5.08e+00 1ivyA 452 5.12e+00 1ivyA c.69.1.5 34654 2f5gA 133 5.16e+00 1w44A 331 5.18e+00 1hkkA 364 5.38e+00 c.1.8.5,d.26.3.1 90634,90635 1wb0A 445 5.59e+00 1cr1A 296 5.62e+00 1cr1A c.37.1.11 32286 1xwiA 322 6.00e+00 2ae2A 260 6.02e+00 1bdb c.2.1.2 29945 2az4A 429 6.49e+00 1vf8A 377 6.50e+00 1j8mF 297 6.62e+00 1ng1 a.24.13.1,c.37.1.10 62742,62743 1bqcA 302 6.65e+00 1bqcA c.1.8.3 28831 1n2sA 299 6.76e+00 c.2.1.2 79857 1pm3A 78 6.89e+00 b.41.1.2 94889 7a3hA 303 7.15e+00 7a3hA c.1.8.3 28817 1g0hA 252 7.23e+00 1dk4A e.7.1.1 60171 1z3eA 132 7.24e+00 2bbsA 290 7.31e+00 2c34A 116 7.61e+00 1jksA 294 7.70e+00 d.144.1.7 71710 1f1zA 273 7.74e+00 1f1zA a.4.5.27,c.52.1.16 16081,33334 1t0fA 276 7.75e+00 1eiwA 111 7.99e+00 1eiwA c.23.3.1 31130 1ekeA 230 8.00e+00 1ekeA c.55.3.1 33572 1g0cA 364 8.20e+00 7a3hA c.1.8.3 60165 1z4eA 153 8.53e+00 2gqrA 237 8.72e+00 1ji0A 240 8.82e+00 c.37.1.12 71665 2fyxA 143 8.92e+00 1hh1A 143 9.06e+00 1gefA c.52.1.18 61036 1ciy 590 9.13e+00 1ciy b.18.1.3,b.77.2.1,f.1.3.1 23720,27977,43392 7odcA 424 9.33e+00 7odcA b.49.2.3,c.1.6.1 26488,28650 2azpA 318 9.33e+00 1c3wA 222 9.39e+00 1c3wA f.13.1.1 43405 2fukA 220 9.40e+00 1xmiA 291 9.49e+00 2ethA 154 9.58e+00 1s8nA 205 9.67e+00 c.23.1.1 105374 1g7fA 298 9.68e+00 1pty c.45.1.2 60330 1w5nA 337 9.70e+00 1hjsA 332 9.81e+00 c.1.8.3 83492 2aa4A 289 9.86e+00 1gzgA 337 9.98e+00 c.1.10.3 70805 1pkoA 139 1.01e+01 b.1.1.1 88147 1ne9A 335 1.06e+01 d.108.1.4,d.108.1.4 91839,91840 2ffcA 353 1.08e+01 1u94A 356 1.08e+01 c.37.1.11,d.48.1.1 107743,107744 1qvbA 481 1.09e+01 1qvbA c.1.8.4 28983 1jykA 254 1.12e+01 c.68.1.13 67458 1w78A 422 1.12e+01 1ezm 301 1.16e+01 1hyt d.92.1.2 58980 1cnzA 363 1.19e+01 1cnzA c.77.1.1 35061 2f71A 298 1.20e+01 1meoA 209 1.20e+01 c.65.1.1 79035 1vk9A 151 1.21e+01 c.139.1.1 108640 1yavA 159 1.22e+01 1zmtA 254 1.22e+01 1auk 489 1.23e+01 1auk c.76.1.2 35030 2f4nA 273 1.25e+01 2ai4A 119 1.28e+01 1f28A 297 1.31e+01 1bkpA d.117.1.1 59608 1m3uA 264 1.31e+01 c.1.12.8 84784 1pwxA 254 1.32e+01 c.2.1.2 95262 1orrA 347 1.33e+01 c.2.1.2 93460 1zarA 282 1.34e+01 2gkeA 274 1.35e+01 1wab 232 1.36e+01 1wab c.23.10.3 31341 1ac5 483 1.36e+01 1ac5 c.69.1.5 34653 2fexA 188 1.41e+01 1pwhA 327 1.42e+01 c.79.1.1 95224 1jlnA 297 1.44e+01 1pty c.45.1.2 63172 1vetA 124 1.45e+01 d.110.7.1 108553 2aefA 234 1.45e+01 1m7xA 617 1.46e+01 b.1.18.2,b.71.1.1,c.1.8.1 78749,78750,78751 1u24A 337 1.46e+01 1iy8A 267 1.46e+01 c.2.1.2 83774 1vjoA 393 1.46e+01 c.67.1.3 100827 2av4A 162 1.50e+01 1r0wA 286 1.51e+01 c.37.1.12 96754 1h6zA 913 1.52e+01 c.1.12.2,c.8.1.1,d.142.1.5 70906,70907,70908 1pa1A 310 1.55e+01 c.45.1.2 94404 1es9A 232 1.56e+01 1wab c.23.10.3 31340 1oxsC 353 1.56e+01 b.40.6.3,c.37.1.12 87519,87520 1a0i 348 1.57e+01 1a0i b.40.4.6,d.142.2.1 25363,41577 1n2eA 300 1.59e+01 c.26.1.4 85268 1b35B 255 1.61e+01 1b35B b.121.4.1 23334 1szoA 257 1.62e+01 c.14.1.3 106164 1q74A 303 1.62e+01 c.134.1.1 96019 1n0wA 243 1.62e+01 c.37.1.11 79772 1oxxK 353 1.63e+01 b.40.6.3,c.37.1.12 93715,93716 1dbiA 280 1.64e+01 1gci c.41.1.1 32543 2ac2A 309 1.67e+01 1fzqA 181 1.68e+01 1hurA c.37.1.8 32060 1mvoA 136 1.68e+01 c.23.1.1 79513 1o8uA 257 1.71e+01 c.14.1.3 81194 1bg4 302 1.72e+01 1taxA c.1.8.3 28806 1lam 484 1.72e+01 1lam c.50.1.1,c.56.5.3 33166,33829 1u4gA 301 1.74e+01 d.92.1.2 107670 1r8gA 372 1.75e+01 d.128.1.3 104845 1r94A 118 1.75e+01 b.124.1.1 97251 1tqmA 282 1.77e+01 a.4.5.56,d.144.1.9 107236,107237 2ap1A 327 1.79e+01 1c0pA 363 1.79e+01 1an9A c.4.1.2,d.16.1.3 30647,37934 1zmoA 244 1.80e+01 2b0mA 393 1.81e+01 2b49A 287 1.81e+01 1o70A 324 1.81e+01 b.118.1.1,b.118.1.1 81115,81116 1vl8A 267 1.82e+01 c.2.1.2 108733 1on0A 158 1.85e+01 d.108.1.1 87095 1xbbA 291 1.85e+01 1gmlA 178 1.86e+01 c.8.5.2 70273 1lwjA 441 1.86e+01 b.71.1.1,c.1.8.1 74303,74304 1zy9A 564 1.87e+01 1vpqA 273 1.88e+01 1h3fA 432 1.91e+01 c.26.1.1,d.66.1.4 76631,76632 1u04A 771 1.92e+01 b.34.14.1,c.55.3.10 107539,107540 1vp8A 201 1.97e+01 1u2eA 289 1.97e+01 1mzjA 339 1.98e+01 c.95.1.2,c.95.1.2 79700,79701 1yu6A 275 2.00e+01 1iazA 179 2.03e+01 1iazA b.97.1.1 62131 1nxuA 333 2.07e+01 c.122.1.1 86389 2ac4A 309 2.10e+01 2czdA 208 2.10e+01 1v5eA 590 2.15e+01 1r0rE 274 2.15e+01 c.41.1.1 96735 1ptvA 321 2.16e+01 1pty c.45.1.2 32665 2a84A 300 2.16e+01 1i60A 278 2.16e+01 c.1.15.4 71118 1ma3A 253 2.16e+01 c.31.1.5 78883 1z5nA 242 2.17e+01 1m8jA 181 2.17e+01 c.26.1.3 84875 1z5oA 242 2.19e+01 2eueA 279 2.21e+01 2bhuA 602 2.23e+01 1vfvA 366 2.26e+01 c.37.1.9 108592 1wbsA 360 2.28e+01 1ei6A 406 2.28e+01 c.76.1.4 90443 2a67A 167 2.33e+01 1nu7D 282 2.33e+01 a.8.6.1,a.8.6.1 92191,92192 1qo2A 241 2.34e+01 1qo2A c.1.2.1 28533 1k1eA 180 2.35e+01 c.108.1.5 67995 1cseE 274 2.35e+01 1gci c.41.1.1 32481 1ye8A 178 2.38e+01 1yuwA 554 2.41e+01 1dozA 309 2.43e+01 1ak1 c.92.1.1 35592 1s7iA 124 2.45e+01 d.58.4.9 105353 1m0wA 491 2.49e+01 c.30.1.4,d.142.1.6 78363,78364 1zhvA 134 2.50e+01 2cy5A 140 2.53e+01 1bu6O 501 2.58e+01 1glcG c.55.1.4,c.55.1.4 33499,33500 1izcA 339 2.58e+01 c.1.12.5 83838 1kv8A 216 2.62e+01 c.1.2.3 73054 1yd9A 193 2.62e+01 1q6oA 216 2.63e+01 c.1.2.3 95986 1v9wA 130 2.66e+01 c.47.1.16 108453 2d13A 227 2.67e+01 2sak 121 2.73e+01 2sak d.15.5.1 37711 1eo1A 124 2.73e+01 1eo1A c.55.5.1 33739 2b61A 377 2.74e+01 1bl3A 160 2.75e+01 1b9dA c.55.3.2 33655 1jx7A 117 2.76e+01 c.114.1.1 77195 1qv9A 283 2.76e+01 c.127.1.1 96356 1ydwA 362 2.77e+01 1lv7A 257 2.77e+01 c.37.1.20 78232 1he7A 126 2.79e+01 1wwcA b.1.1.4 60970 2fhxA 246 2.80e+01 2ge3A 170 2.83e+01 1p4fA 293 2.83e+01 d.144.1.7 104063 1gqzA 274 2.84e+01 d.21.1.1,d.21.1.1 83311,83312 1rvgA 305 2.88e+01 c.1.10.2 97920 1augA 215 2.88e+01 1a2zA c.56.4.1 33798 2gtrA 261 2.90e+01 1nhkL 144 2.92e+01 1npk d.58.6.1 39142 1eqjA 511 2.92e+01 1ejjA c.105.1.1,c.76.1.3 59495,59496 1me8A 503 2.92e+01 c.1.5.1 79028 2a6aA 218 2.93e+01 1v02A 565 2.95e+01 c.1.8.4 108194 1ek0A 170 2.97e+01 1ctqA c.37.1.8 32076 1x8hA 228 2.99e+01 2axyA 73 3.01e+01 1io2A 213 3.02e+01 1ekeA c.55.3.1 62612 2ey4C 82 3.02e+01 1gtmA 419 3.05e+01 1hwyA c.2.1.7,c.58.1.1 30223,33871 1i6iA 366 3.05e+01 1bg2 c.37.1.9 61844 2bkfA 87 3.05e+01 1x8gA 227 3.06e+01 1o98A 511 3.06e+01 c.105.1.1,c.76.1.3 86684,86685 2b7oA 464 3.07e+01 1t9bA 677 3.07e+01 1s57A 153 3.08e+01 1vmoA 163 3.09e+01 1vmoA b.77.1.1 27974 1xewX 182 3.10e+01 1qd1A 325 3.10e+01 1qd1A d.58.34.1,d.58.34.1 39493,39494 1r3cA 366 3.12e+01 d.144.1.7 96906 1t46A 313 3.14e+01 d.144.1.7 106397 1b74A 254 3.22e+01 1b74A c.78.2.1,c.78.2.1 35264,35265 1hzdA 272 3.23e+01 c.14.1.3 65969 1ywrA 360 3.25e+01 1qhtA 775 3.29e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1vhxA 150 3.30e+01 c.55.3.8 100712 1jndA 420 3.31e+01 c.1.8.5,d.26.3.1 71757,71758 1ayoA 130 3.31e+01 1ayoA b.2.4.1 22431 2bdwA 362 3.31e+01 1uh5A 329 3.32e+01 c.2.1.2 107840 1qwgA 251 3.32e+01 c.1.27.1 96473 1f9aA 168 3.32e+01 1f9aA c.26.1.3 31602 1jysA 242 3.32e+01 c.56.2.1 77216 2fm8A 135 3.33e+01 1skoA 143 3.34e+01 d.110.7.1 105676 2cw5A 255 3.34e+01 1j7nA 776 3.34e+01 d.92.1.14,d.92.1.14,d.166.1.1 66409,66410,66411 1bwzA 274 3.40e+01 1bwzA d.21.1.1,d.21.1.1 38337,38338 1pcxA 810 3.42e+01 a.71.2.1,b.2.8.1,c.62.1.2,d.109.2.1,g.41.10.1 94497,94498,94499,94500,94501 1m0kA 262 3.49e+01 f.13.1.1 78344 2dkaA 544 3.50e+01 1kngA 156 3.50e+01 c.47.1.10 72777 1s98A 107 3.51e+01 b.124.1.1 105377 1ccwA 137 3.52e+01 1be1 c.23.6.1 31238 1jbkA 195 3.54e+01 c.37.1.20 71631 1xdyA 298 3.55e+01 1c8bA 371 3.56e+01 1c8bA c.56.1.2 59082 2a6mA 155 3.57e+01 1thm 279 3.65e+01 1gci c.41.1.1 32544 1exqA 154 3.65e+01 1b9dA c.55.3.2 33646 1ps9A 671 3.65e+01 c.1.4.1,c.3.1.1,c.4.1.1 95076,95077,95078 2b0vA 153 3.67e+01 1hyvA 166 3.71e+01 1b9dA c.55.3.2 61424 1q7zA 566 3.72e+01 c.1.21.2,c.1.26.1 96090,96091 1brwA 433 3.77e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1ualA 274 3.77e+01 c.116.1.4 88383 1ursA 402 3.78e+01 c.94.1.1 99833 1ofuA 320 3.80e+01 c.32.1.1,d.79.2.1 86972,86973 1zh2A 121 3.80e+01 1qwiA 143 3.83e+01 d.227.1.1 96474 2gshA 414 3.87e+01 1v60A 123 3.91e+01 2fiuA 99 3.92e+01 1rl2A 137 3.92e+01 1rl2A b.34.5.3,b.40.4.5 24610,25342 2c30A 321 3.93e+01 1qk8A 146 3.94e+01 1ewxA c.47.1.10 33061 1kzlA 208 3.96e+01 b.43.4.3,b.43.4.3 77635,77636 1z2iA 358 3.99e+01 1m2oA 768 4.00e+01 a.71.2.1,b.2.8.1,c.62.1.2,d.109.2.1,g.41.10.1 78480,78481,78482,78483,78484 1zz2A 360 4.01e+01 1svdA 473 4.02e+01 1mtzA 293 4.02e+01 c.69.1.7 79467 1xk7A 408 4.03e+01 1h7wA 1025 4.06e+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 1k38A 254 4.08e+01 e.3.1.1 84303 1ltzA 297 4.08e+01 d.178.1.1 74254 1wg8A 285 4.12e+01 1yvoA 172 4.15e+01 1xqwA 293 4.15e+01 1itxA 419 4.17e+01 c.1.8.5,d.26.3.1 71425,71426 1pkp 150 4.18e+01 1pkp d.14.1.1,d.50.1.2 37551,38787 1pvdA 537 4.18e+01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31737,31777,31778 1ghhA 81 4.19e+01 1ghhA d.57.1.1 38940 1n57A 291 4.21e+01 c.23.16.2 85328 1q8yA 373 4.25e+01 d.144.1.7 96234 2bo4A 397 4.30e+01 1rybA 212 4.31e+01 c.56.3.1 98098 1r4pB 70 4.33e+01 b.40.2.1 97026 1n82A 331 4.34e+01 c.1.8.3 91703 1o66A 275 4.35e+01 c.1.12.8 92547 2cmuA 342 4.37e+01 1v9nA 360 4.38e+01 1gteA 1025 4.40e+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 1ispA 181 4.40e+01 c.69.1.18 76778 1q52A 314 4.46e+01 c.14.1.3 95846 1ho1A 242 4.46e+01 1ho1A c.1.24.1 61097 1djrD 103 4.46e+01 3chbD b.40.2.1 24865 1nrfA 262 4.47e+01 e.3.1.1 92086 1kay 381 4.49e+01 1ba1 c.55.1.1,c.55.1.1 33385,33386 1p90A 145 4.53e+01 c.55.5.2 94377 1gs5A 258 4.53e+01 c.73.1.2 70395 1uuqA 440 4.61e+01 c.1.8.3 100015 2c0nA 203 4.62e+01 1xnaA 183 4.66e+01 1xnaA b.18.1.8 23773 1lnsA 763 4.69e+01 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