# 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 5.21e-02 1jf8A 131 1.11e-01 c.44.1.1 66621 1z47A 355 1.63e-01 1l2tA 235 1.73e-01 c.37.1.12 73514 1vypX 364 2.88e-01 c.1.4.1 108905 1vyrA 364 2.96e-01 c.1.4.1 108906 1h61A 364 3.15e-01 1oyc c.1.4.1 60657 1gvoA 364 3.20e-01 c.1.4.1 76357 2abbA 364 3.28e-01 1srrA 124 4.37e-01 1dz3A c.23.1.1 31110 1cr1A 296 4.51e-01 1cr1A c.37.1.11 32286 1fobA 334 5.61e-01 c.1.8.3 83255 1yuwA 554 5.90e-01 1yvkA 163 6.75e-01 1mb3A 124 7.65e-01 c.23.1.1 78907 1p5jA 372 8.13e-01 c.79.1.1 104067 1vp8A 201 9.14e-01 1woqA 267 1.00e+00 c.55.1.10,c.55.1.10 109462,109463 2gqrA 237 1.04e+00 1c9kA 180 1.05e+00 1c9kB c.37.1.11 32363 2anuA 255 1.07e+00 2c31A 568 1.15e+00 1kay 381 1.18e+00 1ba1 c.55.1.1,c.55.1.1 33385,33386 1n2sA 299 1.25e+00 c.2.1.2 79857 2cqnA 77 1.25e+00 1ofuA 320 1.36e+00 c.32.1.1,d.79.2.1 86972,86973 1bupA 386 1.41e+00 1ba1 c.55.1.1,c.55.1.1 33377,33378 1tmy 120 1.53e+00 1dbwA c.23.1.1 31083 1b0uA 262 1.57e+00 1b0uA c.37.1.12 32370 2ct8A 497 1.92e+00 1u0sY 118 1.95e+00 c.23.1.1 107566 1eiwA 111 2.03e+00 1eiwA c.23.3.1 31130 2awaA 390 2.06e+00 1tqmA 282 2.39e+00 a.4.5.56,d.144.1.9 107236,107237 1hp1A 516 2.47e+00 d.114.1.1,d.159.1.2 70976,70977 1bg4 302 2.53e+00 1taxA c.1.8.3 28806 1h49A 512 2.69e+00 c.1.8.4 83477 1u1wA 298 2.82e+00 2f5gA 133 2.84e+00 1a04A 215 2.92e+00 1a04A a.4.6.2,c.23.1.1 16234,31089 2reb 352 3.08e+00 2reb c.37.1.11,d.48.1.1 32282,38767 1w5fA 353 3.10e+00 1e55A 512 3.13e+00 1e70M c.1.8.4 28934 1y9kA 157 3.26e+00 1e19A 314 3.41e+00 1b7bA c.73.1.1 34967 2bl5A 140 3.42e+00 1ciy 590 3.44e+00 1ciy b.18.1.3,b.77.2.1,f.1.3.1 23720,27977,43392 1t8tA 271 3.61e+00 c.37.1.5 106685 1cnzA 363 3.66e+00 1cnzA c.77.1.1 35061 1h8gA 95 3.69e+00 b.109.1.1 65735 1m6iA 493 3.70e+00 c.3.1.5,c.3.1.5,d.87.1.1 74533,74534,74535 1q45A 391 3.83e+00 c.1.4.1 95780 1kutA 230 3.85e+00 d.143.1.1 73017 1dik 874 3.89e+00 1dik c.1.12.2,c.8.1.1,d.142.1.5 29304,30702,41572 1ne9A 335 3.97e+00 d.108.1.4,d.108.1.4 91839,91840 1i39A 225 4.05e+00 1ekeA c.55.3.1 61585 1k1xA 659 4.07e+00 a.8.3.2,b.30.5.8,c.6.2.2 84279,84280,84281 1ush 550 4.11e+00 1ush d.114.1.1,d.159.1.2 40923,42079 1ek0A 170 4.26e+00 1ctqA c.37.1.8 32076 1v33A 366 4.45e+00 d.264.1.1 100278 2f5tX 233 4.64e+00 1a48 306 4.68e+00 1a48 d.143.1.1 41590 1wleA 501 4.72e+00 2ethA 154 4.73e+00 1xx4A 261 4.74e+00 1n13B 113 4.85e+00 1k77A 260 4.95e+00 c.1.15.5 72096 1ypfA 336 5.00e+00 2b61A 377 5.05e+00 1kblA 873 5.34e+00 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 1pk6A 133 5.35e+00 b.22.1.1 94801 1z90A 469 5.59e+00 1g291 372 5.63e+00 1g291 1qv9A 283 5.64e+00 c.127.1.1 96356 1mvoA 136 5.82e+00 c.23.1.1 79513 1juhA 350 5.84e+00 b.82.1.5 71884 1jmvA 141 6.12e+00 c.26.2.4 66897 1wod 233 6.20e+00 1wod c.94.1.1 35832 1amf 233 6.21e+00 1wod c.94.1.1 35833 1g7sA 594 6.32e+00 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 1nu7D 282 6.36e+00 a.8.6.1,a.8.6.1 92191,92192 1zarA 282 6.43e+00 1k66A 149 6.47e+00 c.23.1.1 90941 1obdA 306 6.51e+00 d.143.1.1 86767 1svfB 38 6.61e+00 1svfB h.3.2.1 45764 1ji0A 240 6.66e+00 c.37.1.12 71665 1v04A 355 6.69e+00 b.68.6.2 100240 1huqA 164 6.70e+00 1byuA c.37.1.8 32020 1pm3A 78 6.76e+00 b.41.1.2 94889 1xubA 298 6.85e+00 1i60A 278 6.86e+00 c.1.15.4 71118 1t6kA 278 6.99e+00 1vk9A 151 7.14e+00 c.139.1.1 108640 1nu0A 138 7.28e+00 c.55.3.8 92165 1rcb 129 7.28e+00 1rcb a.26.1.2 16854 1u6tA 121 7.34e+00 1m8jA 181 7.36e+00 c.26.1.3 84875 2fiuA 99 7.38e+00 1d7yA 408 7.40e+00 1d7yA c.3.1.5,c.3.1.5,d.87.1.1 30565,30566,40204 1oxsC 353 7.42e+00 b.40.6.3,c.37.1.12 87519,87520 1atg 231 7.53e+00 1atg c.94.1.1 35834 1mzjA 339 7.60e+00 c.95.1.2,c.95.1.2 79700,79701 1v02A 565 7.67e+00 c.1.8.4 108194 1lt8A 406 8.10e+00 c.1.26.1 78186 1vr3A 191 8.17e+00 1nxmA 197 8.36e+00 b.82.1.1 86385 1vl8A 267 8.65e+00 c.2.1.2 108733 1oxxK 353 8.77e+00 b.40.6.3,c.37.1.12 93715,93716 1s8nA 205 8.83e+00 c.23.1.1 105374 1s7iA 124 8.90e+00 d.58.4.9 105353 2avtA 378 8.96e+00 1yymG 313 8.97e+00 1z4eA 153 9.04e+00 2b06A 155 9.14e+00 2b0vA 153 9.22e+00 1r2qA 170 9.29e+00 c.37.1.8 96874 1y8tA 324 9.71e+00 1fzqA 181 9.71e+00 1hurA c.37.1.8 32060 1qipA 183 9.81e+00 1qipA d.32.1.1 38470 1ctn 540 1.06e+01 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21876,29005,38439 1yd7A 395 1.08e+01 1qk8A 146 1.11e+01 1ewxA c.47.1.10 33061 1z2lA 423 1.13e+01 1n0wA 243 1.13e+01 c.37.1.11 79772 1wryA 121 1.14e+01 1g71A 347 1.16e+01 1g71A d.264.1.1 43268 1qb7A 236 1.17e+01 1qb7A c.61.1.1 34087 1pea 385 1.18e+01 1pea c.93.1.1 35662 2gkeA 274 1.21e+01 1vplA 256 1.23e+01 1gqzA 274 1.24e+01 d.21.1.1,d.21.1.1 83311,83312 1n82A 331 1.24e+01 c.1.8.3 91703 1w78A 422 1.25e+01 1hziA 129 1.25e+01 1rcb a.26.1.2 61449 2bbsA 290 1.25e+01 1qc7A 101 1.26e+01 1qc7A a.118.14.1 18456 1ccwA 137 1.26e+01 1be1 c.23.6.1 31238 1h54A 754 1.27e+01 a.102.1.4,b.30.5.3 60634,60635 2czdA 208 1.28e+01 1meoA 209 1.28e+01 c.65.1.1 79035 1b6g 310 1.29e+01 1b6g c.69.1.8 34661 1o70A 324 1.31e+01 b.118.1.1,b.118.1.1 81115,81116 1s0aA 429 1.32e+01 c.67.1.4 98263 1qj5A 429 1.33e+01 1dtyA c.67.1.4 34493 1c3wA 222 1.33e+01 1c3wA f.13.1.1 43405 1o8xA 146 1.34e+01 c.47.1.10 86681 2ffjA 300 1.37e+01 1lcyA 325 1.38e+01 b.36.1.4,b.47.1.1 73834,73835 1q35A 320 1.39e+01 c.94.1.1 95661 1g8sA 230 1.40e+01 c.66.1.3 90507 2fp8A 322 1.41e+01 1zr6A 503 1.41e+01 1qxyA 252 1.42e+01 d.127.1.1 96565 1ej2A 181 1.42e+01 1f9aA c.26.1.3 59414 2bnjA 303 1.42e+01 1kyhA 276 1.43e+01 c.72.1.4 73222 1fbnA 230 1.45e+01 1fbnA c.66.1.3 34181 1ta3B 303 1.45e+01 c.1.8.3 106732 1z5oA 242 1.46e+01 2fyxA 143 1.48e+01 7odcA 424 1.49e+01 7odcA b.49.2.3,c.1.6.1 26488,28650 1q8fA 313 1.50e+01 c.70.1.1 96203 1wosA 364 1.54e+01 b.44.2.1,d.250.1.1 109468,109469 2ajrA 331 1.56e+01 1pwhA 327 1.57e+01 c.79.1.1 95224 1o22A 170 1.58e+01 d.238.1.1 86557 1jysA 242 1.58e+01 c.56.2.1 77216 1itwA 741 1.60e+01 c.77.1.2 76793 1wb0A 445 1.63e+01 1z5nA 242 1.63e+01 1exqA 154 1.64e+01 1b9dA c.55.3.2 33646 1me8A 503 1.65e+01 c.1.5.1 79028 1cseE 274 1.65e+01 1gci c.41.1.1 32481 2d48A 129 1.66e+01 1ekqA 272 1.67e+01 1c3qA c.72.1.2 34941 1ede 310 1.70e+01 1b6g c.69.1.8 34662 1mzhA 225 1.75e+01 c.1.10.1 79698 1xmiA 291 1.77e+01 1g6hA 257 1.77e+01 1gajA c.37.1.12 60318 1e7rA 321 1.78e+01 1bsvA c.2.1.2 29808 1ufoA 238 1.79e+01 c.69.1.27 99344 1i1wA 303 1.81e+01 c.1.8.3 76732 1qhtA 775 1.82e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1k4zA 159 1.82e+01 b.80.5.1 72070 2cbiA 594 1.82e+01 1edqA 540 1.82e+01 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21873,29002,38436 1shsA 147 1.83e+01 1shsA b.15.1.1 23675 1u2eA 289 1.85e+01 2fbiA 142 1.86e+01 1ve1A 304 1.88e+01 1y9uA 323 1.88e+01 2azpA 318 1.90e+01 1y10A 407 1.92e+01 1qwgA 251 1.92e+01 c.1.27.1 96473 1wywA 230 1.93e+01 1vf8A 377 1.93e+01 1gheA 177 1.94e+01 d.108.1.1 76222 1ko7A 314 1.95e+01 c.98.2.1,c.91.1.2 72797,72798 1yu6A 275 1.97e+01 1ra0A 430 2.04e+01 2a84A 300 2.04e+01 1u94A 356 2.05e+01 c.37.1.11,d.48.1.1 107743,107744 1eo1A 124 2.05e+01 1eo1A c.55.5.1 33739 1qd1A 325 2.06e+01 1qd1A d.58.34.1,d.58.34.1 39493,39494 1dkiA 371 2.06e+01 1dkiA d.3.1.1 37090 1omp 370 2.06e+01 4mbp c.94.1.1 35778 1c96A 753 2.10e+01 1amj c.8.2.1,c.83.1.1 30727,35403 1r0rE 274 2.18e+01 c.41.1.1 96735 1ti6B 274 2.18e+01 b.3.5.1,d.58.1.5 106976,106977 1ivyA 452 2.19e+01 1ivyA c.69.1.5 34654 1ako 268 2.21e+01 1ako d.151.1.1 41779 1pj5A 830 2.21e+01 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 1cc1L 498 2.21e+01 1h2rL e.18.1.1 43301 1vk6A 269 2.23e+01 d.113.1.4,d.113.1.4 100851,100852 2frnA 278 2.26e+01 8acn 754 2.26e+01 1amj c.8.2.1,c.83.1.1 30724,35400 1t4hA 290 2.28e+01 d.144.1.7 106420 1uh5A 329 2.31e+01 c.2.1.2 107840 1rvgA 305 2.33e+01 c.1.10.2 97920 1xhcA 367 2.34e+01 1zgzA 122 2.36e+01 1o0iA 138 2.39e+01 d.38.1.5 86532 1xtnA 120 2.39e+01 1rl2A 137 2.42e+01 1rl2A b.34.5.3,b.40.4.5 24610,25342 1n2eA 300 2.42e+01 c.26.1.4 85268 1zh2A 121 2.46e+01 1xwiA 322 2.46e+01 1ayoA 130 2.46e+01 1ayoA b.2.4.1 22431 1gmlA 178 2.50e+01 c.8.5.2 70273 1nqjA 119 2.51e+01 b.23.2.1 86031 1nwbA 124 2.51e+01 b.124.1.1 86296 1e6uA 321 2.54e+01 1bsvA c.2.1.2 29805 1f28A 297 2.56e+01 1bkpA d.117.1.1 59608 1mrp 309 2.58e+01 1mrp c.94.1.1 35796 2ffcA 353 2.59e+01 1pqhA 143 2.61e+01 b.52.2.1 95017 1ak5 503 2.62e+01 1ak5 c.1.5.1 28639 1eqoA 158 2.64e+01 1hka 2bwnA 401 2.67e+01 1nnfA 309 2.68e+01 c.94.1.1 85903 1vqoS 85 2.69e+01 1i5gA 144 2.70e+01 1ewxA c.47.1.10 61784 1wohA 305 2.71e+01 c.42.1.1 109446 2ac4A 309 2.74e+01 1ho1A 242 2.76e+01 1ho1A c.1.24.1 61097 1pkoA 139 2.81e+01 b.1.1.1 88147 2cwxA 430 2.84e+01 1m3uA 264 2.86e+01 c.1.12.8 84784 1r31A 428 2.86e+01 d.58.20.1,d.179.1.1 96897,96898 1ytvA 366 2.87e+01 1k6wA 426 2.90e+01 b.92.1.2,c.1.9.5 68236,68237 1zymA 258 2.90e+01 1zymA a.60.10.1,c.8.1.2 18110,30705 1e9lA 377 2.91e+01 1e9lA c.1.8.5,d.26.3.1 59395,59396 1hkkA 364 2.93e+01 c.1.8.5,d.26.3.1 90634,90635 1zhhB 242 2.95e+01 1f1zA 273 2.96e+01 1f1zA a.4.5.27,c.52.1.16 16081,33334 2a1dD 329 2.96e+01 1jayA 212 2.98e+01 c.2.1.6 66478 1qvbA 481 2.98e+01 1qvbA c.1.8.4 28983 1nhkL 144 3.00e+01 1npk d.58.6.1 39142 1qg3A 195 3.01e+01 1qg3A b.1.2.1,b.1.2.1 21993,21994 1dz3A 130 3.01e+01 1dz3A c.23.1.1 31105 1s95A 333 3.05e+01 d.159.1.3 105375 1ekeA 230 3.08e+01 1ekeA c.55.3.1 33572 1ig3A 263 3.09e+01 1ig3A b.82.6.1,c.100.1.1 62358,62359 1aozA 552 3.11e+01 1aozA b.6.1.3,b.6.1.3,b.6.1.3 23124,23125,23126 1k2eA 156 3.11e+01 d.113.1.1 72010 1z7wA 322 3.11e+01 2gclA 261 3.15e+01 1ltzA 297 3.18e+01 d.178.1.1 74254 1zckA 154 3.18e+01 2fexA 188 3.19e+01 1ursA 402 3.20e+01 c.94.1.1 99833 1pmi 440 3.21e+01 1pmi b.82.1.3 28114 1xfcA 384 3.22e+01 1qsmA 152 3.23e+01 1qsmA d.108.1.1 40808 1wd5A 208 3.23e+01 2bbkL 125 3.25e+01 2bbkL g.21.1.1 44882 1p9yA 121 3.27e+01 d.241.2.1 94402 1ff9A 450 3.29e+01 1ff9A c.2.1.3,d.81.1.2 30039,39954 2gk9A 426 3.34e+01 1sg4A 260 3.35e+01 1y6hA 177 3.36e+01 1ebfA 358 3.37e+01 1ebuA c.2.1.3,d.81.1.2 30033,39948 1ww8A 439 3.38e+01 1jj2R 84 3.40e+01 1ffkP d.12.1.1 63103 1s72S 85 3.41e+01 d.12.1.1 105338 1sxjE 354 3.42e+01 a.80.1.1,c.37.1.20 106089,106090 2ac2A 309 3.43e+01 2f4nA 273 3.49e+01 1f9yA 158 3.50e+01 d.58.30.1 83249 1nekA 588 3.51e+01 a.7.3.1,c.3.1.4,d.168.1.1 80426,80427,80428 1t62A 166 3.51e+01 b.122.1.4 106541 1um0A 365 3.52e+01 d.258.1.1 107942 1f9aA 168 3.53e+01 1f9aA c.26.1.3 31602 1vjpA 394 3.56e+01 c.2.1.3,d.81.1.3 100828,100829 1z41A 338 3.58e+01 1zesA 125 3.59e+01 2exnA 136 3.59e+01 1y1oA 203 3.59e+01 1nnhA 294 3.59e+01 d.104.1.1 92005 1vpqA 273 3.70e+01 1h5qA 265 3.71e+01 1cydA c.2.1.2 60643 1io2A 213 3.73e+01 1ekeA c.55.3.1 62612 1qoiA 177 3.74e+01 2cpl b.62.1.1 27490 1di0A 158 3.76e+01 1di0A c.16.1.1 30957 1u5tC 202 3.76e+01 a.4.5.54,a.4.5.54 107688,107689 1y1nA 291 3.76e+01 1ue1A 164 3.76e+01 b.40.4.3 99243 2gc9A 179 3.76e+01 1v60A 123 3.77e+01 1dbiA 280 3.85e+01 1gci c.41.1.1 32543 1t0fA 276 3.86e+01 2b6eA 146 3.87e+01 1v9nA 360 3.87e+01 2fs2A 151 3.90e+01 2axyA 73 3.91e+01 2aefA 234 3.93e+01 1ru8A 232 3.93e+01 c.26.2.1 97849 1qsoA 149 3.93e+01 1qsmA d.108.1.1 40812 1vm7A 311 3.94e+01 c.72.1.1 108884 1icxA 155 3.94e+01 d.129.3.1 71191 1wab 232 3.95e+01 1wab c.23.10.3 31341 1r4pB 70 3.96e+01 b.40.2.1 97026 1gvhA 396 3.96e+01 a.1.1.2,b.43.4.2,c.25.1.5 70601,70602,70603 1aw8B 91 3.96e+01 1aw8B 4mbp 370 3.96e+01 4mbp c.94.1.1 35777 1u9jA 358 3.99e+01 1tv8A 340 4.00e+01 c.1.28.3 107352 1v5eA 590 4.01e+01 1cv8 174 4.01e+01 1cv8 d.3.1.1 37089 1xttA 216 4.02e+01 1t7lA 766 4.04e+01 1vl6A 388 4.06e+01 c.2.1.7,c.58.1.3 108724,108725 2ey4C 82 4.07e+01 2b7oA 464 4.07e+01 1lw7A 365 4.07e+01 c.26.1.3,c.37.1.1 74295,74296 1v71A 323 4.11e+01 1st9A 143 4.12e+01 c.47.1.10 98987 1j5pA 253 4.12e+01 d.81.1.3,c.2.1.3 71577,83092 1i50H 146 4.13e+01 b.40.4.8 61761 1gc5A 467 4.14e+01 1gc5A c.72.1.3 60429 1cfr 285 4.14e+01 1cfr c.52.1.7 33312 1vcdA 126 4.18e+01 2d69A 430 4.23e+01 1djqA 729 4.24e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28614,30315,30600 1b74A 254 4.24e+01 1b74A c.78.2.1,c.78.2.1 35264,35265 1h7wA 1025 4.25e+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 1jflA 228 4.31e+01 c.78.2.1,c.78.2.1 71656,71657 2ax9A 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