# List of top-scoring protein chains for t04-100-30-alpha-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 2b99A 156 7.78e-02 1jf8A 131 8.61e-02 c.44.1.1 66621 1z47A 355 2.00e-01 1vypX 364 2.42e-01 c.1.4.1 108905 1vyrA 364 2.49e-01 c.1.4.1 108906 1h61A 364 2.74e-01 1oyc c.1.4.1 60657 1gvoA 364 2.75e-01 c.1.4.1 76357 2abbA 364 2.82e-01 1fobA 334 3.99e-01 c.1.8.3 83255 1l2tA 235 4.75e-01 c.37.1.12 73514 1srrA 124 4.90e-01 1dz3A c.23.1.1 31110 1cr1A 296 6.30e-01 1cr1A c.37.1.11 32286 1p5jA 372 7.87e-01 c.79.1.1 104067 1yuwA 554 8.71e-01 1mb3A 124 8.91e-01 c.23.1.1 78907 2cqnA 77 8.92e-01 1yvkA 163 9.23e-01 1vp8A 201 9.69e-01 2anuA 255 1.05e+00 1c9kA 180 1.06e+00 1c9kB c.37.1.11 32363 2gqrA 237 1.25e+00 1tmy 120 1.46e+00 1dbwA c.23.1.1 31083 1eiwA 111 1.46e+00 1eiwA c.23.3.1 31130 1kay 381 1.58e+00 1ba1 c.55.1.1,c.55.1.1 33385,33386 2c31A 568 1.81e+00 1n2sA 299 1.82e+00 c.2.1.2 79857 1h49A 512 1.82e+00 c.1.8.4 83477 1bupA 386 1.83e+00 1ba1 c.55.1.1,c.55.1.1 33377,33378 1u0sY 118 1.85e+00 c.23.1.1 107566 1ofuA 320 1.89e+00 c.32.1.1,d.79.2.1 86972,86973 1e55A 512 2.10e+00 1e70M c.1.8.4 28934 1hp1A 516 2.23e+00 d.114.1.1,d.159.1.2 70976,70977 1tqmA 282 2.27e+00 a.4.5.56,d.144.1.9 107236,107237 1b0uA 262 2.41e+00 1b0uA c.37.1.12 32370 1ciy 590 2.61e+00 1ciy b.18.1.3,b.77.2.1,f.1.3.1 23720,27977,43392 2bl5A 140 2.62e+00 2f5gA 133 2.66e+00 1xx4A 261 2.71e+00 1a04A 215 2.77e+00 1a04A a.4.6.2,c.23.1.1 16234,31089 1t8tA 271 2.80e+00 c.37.1.5 106685 1u1wA 298 2.94e+00 1ne9A 335 3.11e+00 d.108.1.4,d.108.1.4 91839,91840 1k1xA 659 3.15e+00 a.8.3.2,b.30.5.8,c.6.2.2 84279,84280,84281 1q45A 391 3.28e+00 c.1.4.1 95780 1v33A 366 3.28e+00 d.264.1.1 100278 1bg4 302 3.75e+00 1taxA c.1.8.3 28806 1e19A 314 3.80e+00 1b7bA c.73.1.1 34967 1ush 550 3.84e+00 1ush d.114.1.1,d.159.1.2 40923,42079 1dik 874 3.90e+00 1dik c.1.12.2,c.8.1.1,d.142.1.5 29304,30702,41572 1ek0A 170 3.96e+00 1ctqA c.37.1.8 32076 1cnzA 363 3.96e+00 1cnzA c.77.1.1 35061 1rl2A 137 3.96e+00 1rl2A b.34.5.3,b.40.4.5 24610,25342 1n13B 113 4.02e+00 2ethA 154 4.19e+00 1y9kA 157 4.69e+00 2b61A 377 4.72e+00 1w5fA 353 4.79e+00 1kutA 230 4.98e+00 d.143.1.1 73017 1fzqA 181 5.22e+00 1hurA c.37.1.8 32060 1kblA 873 5.29e+00 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 1pm3A 78 5.38e+00 b.41.1.2 94889 2ct8A 497 5.46e+00 1nu7D 282 5.68e+00 a.8.6.1,a.8.6.1 92191,92192 1huqA 164 5.82e+00 1byuA c.37.1.8 32020 1k77A 260 5.84e+00 c.1.15.5 72096 1v02A 565 5.95e+00 c.1.8.4 108194 1m8jA 181 5.96e+00 c.26.1.3 84875 1amf 233 6.05e+00 1wod c.94.1.1 35833 1zarA 282 6.10e+00 1svfB 38 6.14e+00 1svfB h.3.2.1 45764 1wod 233 6.17e+00 1wod c.94.1.1 35832 1jmvA 141 6.19e+00 c.26.2.4 66897 2f9zC 159 6.43e+00 1vk9A 151 6.45e+00 c.139.1.1 108640 1t6kA 278 6.46e+00 1mvoA 136 6.50e+00 c.23.1.1 79513 1i39A 225 6.58e+00 1ekeA c.55.3.1 61585 1g291 372 6.77e+00 1g291 1ctn 540 6.84e+00 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21876,29005,38439 1vl8A 267 6.92e+00 c.2.1.2 108733 2fiuA 99 6.96e+00 1xubA 298 7.17e+00 1mzjA 339 7.19e+00 c.95.1.2,c.95.1.2 79700,79701 1ypfA 336 7.36e+00 1rcb 129 7.40e+00 1rcb a.26.1.2 16854 1atg 231 7.43e+00 1atg c.94.1.1 35834 1s7iA 124 7.44e+00 d.58.4.9 105353 2fukA 220 7.44e+00 1k66A 149 7.50e+00 c.23.1.1 90941 1y8tA 324 7.56e+00 1r2qA 170 7.70e+00 c.37.1.8 96874 1nu0A 138 7.87e+00 c.55.3.8 92165 1s8nA 205 7.88e+00 c.23.1.1 105374 1h54A 754 8.09e+00 a.102.1.4,b.30.5.3 60634,60635 2gkeA 274 8.16e+00 1ji0A 240 8.21e+00 c.37.1.12 71665 1i60A 278 8.54e+00 c.1.15.4 71118 1gqzA 274 8.65e+00 d.21.1.1,d.21.1.1 83311,83312 1z2lA 423 8.87e+00 2bbsA 290 9.23e+00 1b6g 310 9.30e+00 1b6g c.69.1.8 34661 1g71A 347 9.48e+00 1g71A d.264.1.1 43268 1qv9A 283 1.02e+01 c.127.1.1 96356 2b0vA 153 1.04e+01 2reb 352 1.06e+01 2reb c.37.1.11,d.48.1.1 32282,38767 1qk8A 146 1.06e+01 1ewxA c.47.1.10 33061 1dkiA 371 1.11e+01 1dkiA d.3.1.1 37090 1ak5 503 1.13e+01 1ak5 c.1.5.1 28639 1meoA 209 1.14e+01 c.65.1.1 79035 1wleA 501 1.17e+01 1ej2A 181 1.21e+01 1f9aA c.26.1.3 59414 1edqA 540 1.21e+01 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21873,29002,38436 1z4eA 153 1.23e+01 1u6tA 121 1.23e+01 1ccwA 137 1.23e+01 1be1 c.23.6.1 31238 1hziA 129 1.26e+01 1rcb a.26.1.2 61449 1z5oA 242 1.27e+01 1o8xA 146 1.28e+01 c.47.1.10 86681 1oxsC 353 1.29e+01 b.40.6.3,c.37.1.12 87519,87520 1kyhA 276 1.29e+01 c.72.1.4 73222 1ede 310 1.31e+01 1b6g c.69.1.8 34662 1c3wA 222 1.31e+01 1c3wA f.13.1.1 43405 1z5nA 242 1.31e+01 1me8A 503 1.36e+01 c.1.5.1 79028 1xmiA 291 1.36e+01 2b06A 155 1.38e+01 1g7sA 594 1.39e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 2ffjA 300 1.39e+01 1jysA 242 1.41e+01 c.56.2.1 77216 1q35A 320 1.41e+01 c.94.1.1 95661 1w78A 422 1.48e+01 7odcA 424 1.52e+01 7odcA b.49.2.3,c.1.6.1 26488,28650 1oxxK 353 1.52e+01 b.40.6.3,c.37.1.12 93715,93716 2fyxA 143 1.52e+01 1g8sA 230 1.53e+01 c.66.1.3 90507 1gheA 177 1.54e+01 d.108.1.1 76222 1qb7A 236 1.55e+01 1qb7A c.61.1.1 34087 1wywA 230 1.56e+01 1fbnA 230 1.58e+01 1fbnA c.66.1.3 34181 2czdA 208 1.58e+01 1omp 370 1.59e+01 4mbp c.94.1.1 35778 1vplA 256 1.59e+01 1qg3A 195 1.62e+01 1qg3A b.1.2.1,b.1.2.1 21993,21994 1e7rA 321 1.62e+01 1bsvA c.2.1.2 29808 2ajrA 331 1.64e+01 2fbiA 142 1.64e+01 1pwhA 327 1.64e+01 c.79.1.1 95224 2d48A 129 1.66e+01 1u2eA 289 1.69e+01 1wb0A 445 1.69e+01 1yd7A 395 1.70e+01 2bnjA 303 1.73e+01 1exqA 154 1.75e+01 1b9dA c.55.3.2 33646 1itwA 741 1.75e+01 c.77.1.2 76793 1r4pB 70 1.75e+01 b.40.2.1 97026 1ekqA 272 1.75e+01 1c3qA c.72.1.2 34941 1ako 268 1.83e+01 1ako d.151.1.1 41779 1n82A 331 1.84e+01 c.1.8.3 91703 1o70A 324 1.85e+01 b.118.1.1,b.118.1.1 81115,81116 1y9uA 323 1.85e+01 1qc7A 101 1.85e+01 1qc7A a.118.14.1 18456 1pkoA 139 1.86e+01 b.1.1.1 88147 1pea 385 1.89e+01 1pea c.93.1.1 35662 1ivyA 452 1.92e+01 1ivyA c.69.1.5 34654 1ta3B 303 1.94e+01 c.1.8.3 106732 1j5pA 253 1.94e+01 d.81.1.3,c.2.1.3 71577,83092 2azpA 318 1.95e+01 1vf8A 377 1.95e+01 1ayoA 130 1.95e+01 1ayoA b.2.4.1 22431 1f28A 297 2.00e+01 1bkpA d.117.1.1 59608 1s0aA 429 2.00e+01 c.67.1.4 98263 1eqoA 158 2.02e+01 1hka 1ytvA 366 2.02e+01 1qj5A 429 2.03e+01 1dtyA c.67.1.4 34493 1i1wA 303 2.04e+01 c.1.8.3 76732 1lt8A 406 2.04e+01 c.1.26.1 78186 1vqoS 85 2.04e+01 1qd1A 325 2.05e+01 1qd1A d.58.34.1,d.58.34.1 39493,39494 1u24A 337 2.12e+01 1qwgA 251 2.13e+01 c.1.27.1 96473 1cseE 274 2.14e+01 1gci c.41.1.1 32481 1y6hA 177 2.17e+01 1pqhA 143 2.20e+01 b.52.2.1 95017 2ffcA 353 2.20e+01 1xwiA 322 2.21e+01 1k4zA 159 2.22e+01 b.80.5.1 72070 1wryA 121 2.22e+01 1t4hA 290 2.24e+01 d.144.1.7 106420 1e6uA 321 2.26e+01 1bsvA c.2.1.2 29805 1n0wA 243 2.27e+01 c.37.1.11 79772 1pj5A 830 2.28e+01 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 1f1zA 273 2.29e+01 1f1zA a.4.5.27,c.52.1.16 16081,33334 1s95A 333 2.29e+01 d.159.1.3 105375 2a1dD 329 2.30e+01 1st9A 143 2.32e+01 c.47.1.10 98987 2gclA 261 2.34e+01 2bbkL 125 2.34e+01 2bbkL g.21.1.1 44882 1qoiA 177 2.35e+01 2cpl b.62.1.1 27490 1y10A 407 2.39e+01 1ursA 402 2.43e+01 c.94.1.1 99833 1mrp 309 2.45e+01 1mrp c.94.1.1 35796 1ve1A 304 2.46e+01 4mbp 370 2.52e+01 4mbp c.94.1.1 35777 1nnfA 309 2.55e+01 c.94.1.1 85903 2axyA 73 2.55e+01 1mzhA 225 2.56e+01 c.1.10.1 79698 1f9yA 158 2.59e+01 d.58.30.1 83249 2ac4A 309 2.60e+01 2cwxA 430 2.60e+01 1yu6A 275 2.65e+01 1wohA 305 2.65e+01 c.42.1.1 109446 1ekeA 230 2.66e+01 1ekeA c.55.3.1 33572 1jj2R 84 2.69e+01 1ffkP d.12.1.1 63103 1s72S 85 2.69e+01 d.12.1.1 105338 1ho1A 242 2.70e+01 1ho1A c.1.24.1 61097 2fexA 188 2.71e+01 1rvgA 305 2.71e+01 c.1.10.2 97920 1ru8A 232 2.71e+01 c.26.2.1 97849 1gmlA 178 2.72e+01 c.8.5.2 70273 1ltzA 297 2.73e+01 d.178.1.1 74254 1zymA 258 2.74e+01 1zymA a.60.10.1,c.8.1.2 18110,30705 1qhtA 775 2.74e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1dz3A 130 2.76e+01 1dz3A c.23.1.1 31105 1sg4A 260 2.77e+01 1xhcA 367 2.82e+01 1e9lA 377 2.82e+01 1e9lA c.1.8.5,d.26.3.1 59395,59396 1zuhA 168 2.82e+01 1sxjE 354 2.84e+01 a.80.1.1,c.37.1.20 106089,106090 2a84A 300 2.84e+01 1vpqA 273 2.85e+01 1o22A 170 2.85e+01 d.238.1.1 86557 1h5qA 265 2.86e+01 1cydA c.2.1.2 60643 1r0rE 274 2.87e+01 c.41.1.1 96735 1zckA 154 2.87e+01 1u9jA 358 2.89e+01 1t0fA 276 2.91e+01 1ln1A 214 2.92e+01 d.129.3.2 74038 1ebfA 358 2.94e+01 1ebuA c.2.1.3,d.81.1.2 30033,39948 1nhkL 144 2.95e+01 1npk d.58.6.1 39142 1o0iA 138 2.95e+01 d.38.1.5 86532 1wosA 364 2.96e+01 b.44.2.1,d.250.1.1 109468,109469 1hkkA 364 2.98e+01 c.1.8.5,d.26.3.1 90634,90635 1jayA 212 2.98e+01 c.2.1.6 66478 2bwnA 401 2.98e+01 1r31A 428 2.99e+01 d.58.20.1,d.179.1.1 96897,96898 1uh5A 329 3.00e+01 c.2.1.2 107840 1z7wA 322 3.03e+01 1y1oA 203 3.03e+01 1w1oA 534 3.04e+01 d.58.32.4,d.145.1.1 109071,109072 1xfcA 384 3.05e+01 2ey4C 82 3.09e+01 2d13A 227 3.11e+01 1n2eA 300 3.12e+01 c.26.1.4 85268 1fmcA 255 3.14e+01 1cydA c.2.1.2 29856 1v60A 123 3.16e+01 1f9aA 168 3.19e+01 1f9aA c.26.1.3 31602 1zesA 125 3.21e+01 1t62A 166 3.28e+01 b.122.1.4 106541 1u5tC 202 3.28e+01 a.4.5.54,a.4.5.54 107688,107689 1ww8A 439 3.31e+01 2gtrA 261 3.32e+01 2gjgA 248 3.32e+01 1z3eA 132 3.34e+01 1nekA 588 3.37e+01 a.7.3.1,c.3.1.4,d.168.1.1 80426,80427,80428 2bllA 345 3.37e+01 2ac2A 309 3.37e+01 1aw8B 91 3.39e+01 1aw8B 1r0wA 286 3.40e+01 c.37.1.12 96754 1i50H 146 3.40e+01 b.40.4.8 61761 1qvbA 481 3.44e+01 1qvbA c.1.8.4 28983 1g6hA 257 3.44e+01 1gajA c.37.1.12 60318 1a48 306 3.45e+01 1a48 d.143.1.1 41590 1vm7A 311 3.48e+01 c.72.1.1 108884 2fi9A 128 3.49e+01 1anf 370 3.51e+01 4mbp c.94.1.1 35776 1lwjA 441 3.51e+01 b.71.1.1,c.1.8.1 74303,74304 1wtaA 275 3.52e+01 1zh2A 121 3.52e+01 1vjpA 394 3.53e+01 c.2.1.3,d.81.1.3 100828,100829 1q42A 201 3.57e+01 d.17.4.2 95776 1z41A 338 3.60e+01 1v71A 323 3.60e+01 1qsmA 152 3.62e+01 1qsmA d.108.1.1 40808 1twfH 146 3.63e+01 1ff9A 450 3.63e+01 1ff9A c.2.1.3,d.81.1.2 30039,39954 1v9nA 360 3.64e+01 1zgzA 122 3.70e+01 1z7bA 358 3.71e+01 2b7oA 464 3.78e+01 1djqA 729 3.78e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28614,30315,30600 1q74A 303 3.79e+01 c.134.1.1 96019 2d1uA 104 3.80e+01 2gshA 414 3.80e+01 2d69A 430 3.81e+01 1orrA 347 3.84e+01 c.2.1.2 93460 1gc5A 467 3.85e+01 1gc5A c.72.1.3 60429 2cvhA 220 3.86e+01 1g0cA 364 3.86e+01 7a3hA c.1.8.3 60165 1r1dA 247 3.88e+01 c.69.1.29 96813 1xewX 182 3.88e+01 1pmi 440 3.94e+01 1pmi b.82.1.3 28114 1tw0A 157 3.96e+01 1zmtA 254 3.97e+01 1su0B 159 4.01e+01 d.224.1.2 106015 1jflA 228 4.06e+01 c.78.2.1,c.78.2.1 71656,71657 1wab 232 4.09e+01 1wab c.23.10.3 31341 1m3uA 264 4.11e+01 c.1.12.8 84784 1f3mC 297 4.15e+01 1hcl d.144.1.7 41677 1wvhA 134 4.15e+01 1djnA 729 4.16e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28612,30313,30598 1obdA 306 4.16e+01 d.143.1.1 86767 1lw7A 365 4.17e+01 c.26.1.3,c.37.1.1 74295,74296 1rw7A 243 4.18e+01 c.23.16.2 97963 1zhhB 242 4.24e+01 1p1jA 533 4.25e+01 c.2.1.3,d.81.1.3 87687,87688 1vl6A 388 4.26e+01 c.2.1.7,c.58.1.3 108724,108725 1u0mA 382 4.26e+01 c.95.1.2,c.95.1.2 107557,107558 1vmoA 163 4.31e+01 1vmoA b.77.1.1 27974 1a0tP 413 4.33e+01 1a0tP f.4.3.2 43794 2cb2A 318 4.35e+01 1phk 298 4.38e+01 1cdkA d.144.1.7 41635 1on2A 142 4.41e+01 a.4.5.24,a.76.1.1 87103,87104 1u94A 356 4.41e+01 c.37.1.11,d.48.1.1 107743,107744 2ax9A 256 4.42e+01 1qsoA 149 4.44e+01 1qsmA d.108.1.1 40812 1vk6A 269 4.44e+01 d.113.1.4,d.113.1.4 100851,100852 1o94A 729 4.46e+01 c.1.4.1,c.3.1.1,c.4.1.1 81200,81201,81202 1rxdA 159 4.48e+01 1itg 166 4.48e+01 1b9dA c.55.3.2 33661 1pot 325 4.49e+01 1pot c.94.1.1 35807 1f2tA 149 4.49e+01 1f2tA c.37.1.12 32373 1uyrA 737 4.49e+01 c.14.1.4,c.14.1.4 100188,100189 1b74A 254 4.50e+01 1b74A c.78.2.1,c.78.2.1 35264,35265 1ps9A 671 4.50e+01 c.1.4.1,c.3.1.1,c.4.1.1 95076,95077,95078 1y4tA 322 4.57e+01 2f9sA 151 4.58e+01 1hc7A 477 4.59e+01 1hc7A c.51.1.1,d.104.1.1,d.68.5.1 60938,60939,60940 1w9yA 319 4.64e+01 1qe5A 266 4.66e+01 1b8oA c.56.2.1 33784 1io2A 213 4.72e+01 1ekeA c.55.3.1 62612 1j7nA 776 4.77e+01 d.92.1.14,d.92.1.14,d.166.1.1 66409,66410,66411 1uehA 253 4.78e+01 c.101.1.1 99259 1xjdA 345 4.79e+01 2frnA 278 4.82e+01 1w8iA 156 4.84e+01 1wd5A 208 4.87e+01 2fhxA 246 4.90e+01 2amyA 246 4.93e+01 2cnqA 306 4.99e+01 2cy5A 140 5.02e+01 1s7jA 262 5.07e+01 d.21.1.2 98647 1hyeA 313 5.11e+01 2cmd c.2.1.5,d.162.1.1 61400,61401 1psuA 140 5.17e+01 d.38.1.5 88285 1vcdA 126 5.17e+01 1q77A 138 5.19e+01 c.26.2.4 96023 1vkmA 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