# List of top-scoring protein chains for t2k-100-30-o_sep-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 1l2tA 235 1.77e-01 c.37.1.12 73514 1jf8A 131 3.16e-01 c.44.1.1 66621 2awaA 390 3.52e-01 2ct8A 497 3.58e-01 1z47A 355 3.94e-01 2b99A 156 4.14e-01 1q7zA 566 4.29e-01 c.1.21.2,c.1.26.1 96090,96091 1m5tA 124 4.87e-01 c.23.1.1 78660 1jfvA 131 4.89e-01 c.44.1.1 66654 1ush 550 5.85e-01 1ush d.114.1.1,d.159.1.2 40923,42079 1mb3A 124 5.91e-01 c.23.1.1 78907 1hp1A 516 6.98e-01 d.114.1.1,d.159.1.2 70976,70977 1m6iA 493 8.02e-01 c.3.1.5,c.3.1.5,d.87.1.1 74533,74534,74535 1jmvA 141 8.40e-01 c.26.2.4 66897 1gv4A 528 9.48e-01 c.3.1.5,c.3.1.5,d.87.1.1 70589,70590,70591 1eal 127 1.01e+00 1hmt b.60.1.2 27227 1a6dA 545 1.19e+00 1a6dA a.129.1.2,c.8.5.2,d.56.1.2 19488,30819,38936 1woqA 267 1.20e+00 c.55.1.10,c.55.1.10 109462,109463 1h61A 364 1.49e+00 1oyc c.1.4.1 60657 1fobA 334 1.50e+00 c.1.8.3 83255 1c9kB 180 1.59e+00 1c9kB c.37.1.11 32364 1hpm 386 1.60e+00 1ba1 c.55.1.1,c.55.1.1 33381,33382 1gvoA 364 1.63e+00 c.1.4.1 76357 1ek0A 170 1.65e+00 1ctqA c.37.1.8 32076 1ba1 386 1.68e+00 1ba1 c.55.1.1,c.55.1.1 33387,33388 1vp8A 201 1.73e+00 1c9kA 180 1.75e+00 1c9kB c.37.1.11 32363 2reb 352 1.75e+00 2reb c.37.1.11,d.48.1.1 32282,38767 1lt8A 406 1.83e+00 c.1.26.1 78186 2gqrA 237 1.83e+00 1a04A 215 1.87e+00 1a04A a.4.6.2,c.23.1.1 16234,31089 1tmy 120 1.88e+00 1dbwA c.23.1.1 31083 1h6zA 913 1.89e+00 c.1.12.2,c.8.1.1,d.142.1.5 70906,70907,70908 1kn0A 212 1.96e+00 d.50.1.3 77444 1vyrA 364 1.99e+00 c.1.4.1 108906 1k77A 260 2.00e+00 c.1.15.5 72096 1cnzA 363 2.04e+00 1cnzA c.77.1.1 35061 1a6dB 543 2.05e+00 1a6dA a.129.1.2,c.8.5.2,d.56.1.2 19489,30820,38937 1b0uA 262 2.11e+00 1b0uA c.37.1.12 32370 1vypX 364 2.12e+00 c.1.4.1 108905 1atr 386 2.12e+00 1ba1 c.55.1.1,c.55.1.1 33421,33422 1yuwA 554 2.20e+00 1f9zA 135 2.26e+00 1qipA d.32.1.1 38484 1bupA 386 2.27e+00 1ba1 c.55.1.1,c.55.1.1 33377,33378 1e19A 314 2.31e+00 1b7bA c.73.1.1 34967 1kay 381 2.32e+00 1ba1 c.55.1.1,c.55.1.1 33385,33386 2c31A 568 2.38e+00 1ats 386 2.42e+00 1ba1 c.55.1.1,c.55.1.1 33423,33424 1i39A 225 2.49e+00 1ekeA c.55.3.1 61585 2abbA 364 2.58e+00 1mzjA 339 2.63e+00 c.95.1.2,c.95.1.2 79700,79701 1h3fA 432 2.70e+00 c.26.1.1,d.66.1.4 76631,76632 1pm3A 78 2.82e+00 b.41.1.2 94889 1pvdA 537 2.87e+00 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31737,31777,31778 1pea 385 3.04e+00 1pea c.93.1.1 35662 1u0sY 118 3.06e+00 c.23.1.1 107566 1u94A 356 3.06e+00 c.37.1.11,d.48.1.1 107743,107744 1xx4A 261 3.13e+00 1h8gA 95 3.14e+00 b.109.1.1 65735 1ekeA 230 3.24e+00 1ekeA c.55.3.1 33572 1fa8A 135 3.26e+00 1qipA d.32.1.1 38486 2cqnA 77 3.30e+00 1cm7A 363 3.31e+00 1cnzA c.77.1.1 35063 1mvoA 136 3.44e+00 c.23.1.1 79513 1io2A 213 3.55e+00 1ekeA c.55.3.1 62612 1pfkA 320 3.58e+00 3pfk c.89.1.1 35575 1cbuA 180 3.63e+00 1c9kB c.37.1.11 32360 2ftxB 64 3.82e+00 7odcA 424 3.88e+00 7odcA b.49.2.3,c.1.6.1 26488,28650 1vr3A 191 3.90e+00 1obdA 306 3.92e+00 d.143.1.1 86767 1u1wA 298 3.94e+00 1u6dX 308 4.03e+00 1yvkA 163 4.09e+00 1qhdA 398 4.21e+00 1qhdA a.115.1.2,b.19.1.1 63324,63325 1ifc 132 4.27e+00 b.60.1.2 27173 1gegA 256 4.30e+00 1ybvA c.2.1.2 29888 1sg4A 260 4.32e+00 1tqzA 133 4.47e+00 1rvgA 305 4.49e+00 c.1.10.2 97920 1pydA 556 4.49e+00 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31735,31773,31774 1w78A 422 4.55e+00 2fsp 124 4.62e+00 1dz3A c.23.1.1 31119 1e4eA 343 4.67e+00 1iow c.30.1.2,d.142.1.1 59221,59222 1hcxA 127 4.68e+00 b.109.1.1 65800 1p5jA 372 4.70e+00 c.79.1.1 104067 1k66A 149 4.75e+00 c.23.1.1 90941 1n6hA 170 4.78e+00 c.37.1.8 80197 1csyA 112 4.90e+00 1lckA d.93.1.1 40519 1gvmA 136 4.95e+00 b.109.1.1 70612 1lfkA 398 5.02e+00 a.104.1.1 77926 1c4rA 182 5.06e+00 1c4rA b.29.1.4 24229 1xubA 298 5.17e+00 1kagA 173 5.18e+00 c.37.1.2 72249 1u4gA 301 5.18e+00 d.92.1.2 107670 1a48 306 5.22e+00 1a48 d.143.1.1 41590 1ig3A 263 5.40e+00 1ig3A b.82.6.1,c.100.1.1 62358,62359 1yprA 125 5.43e+00 3nul d.110.1.1 40888 1srrA 124 5.50e+00 1dz3A c.23.1.1 31110 1qipA 183 5.52e+00 1qipA d.32.1.1 38470 1qv9A 283 5.57e+00 c.127.1.1 96356 1z2lA 423 5.60e+00 1t6kA 278 5.60e+00 1wleA 501 5.60e+00 1ko7A 314 5.64e+00 c.98.2.1,c.91.1.2 72797,72798 2f5tX 233 5.64e+00 3ladA 476 5.66e+00 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30573,30574,40208 2axyA 73 5.71e+00 1f28A 297 5.77e+00 1bkpA d.117.1.1 59608 1f1zA 273 5.83e+00 1f1zA a.4.5.27,c.52.1.16 16081,33334 1vrmA 325 5.84e+00 1y10A 407 5.90e+00 1qvbA 481 6.01e+00 1qvbA c.1.8.4 28983 1gadO 330 6.06e+00 1dssG c.2.1.3,d.81.1.1 29950,39865 1wlsA 328 6.06e+00 1jtdB 273 6.11e+00 b.69.5.2 67265 1v04A 355 6.24e+00 b.68.6.2 100240 2cnqA 306 6.37e+00 1b25A 619 6.38e+00 1b25A a.110.1.1,d.152.1.1 19044,41796 1hybA 181 6.44e+00 1f9aA c.26.1.3 61399 1a81A 254 6.59e+00 1a81A d.93.1.1,d.93.1.1 40507,40508 1y9kA 157 6.72e+00 2h4vA 320 6.92e+00 2avtA 378 7.02e+00 1gheA 177 7.07e+00 d.108.1.1 76222 1e9lA 377 7.14e+00 1e9lA c.1.8.5,d.26.3.1 59395,59396 1ezm 301 7.17e+00 1hyt d.92.1.2 58980 1qc7A 101 7.23e+00 1qc7A a.118.14.1 18456 2b61A 377 7.32e+00 2fp8A 322 7.33e+00 1yavA 159 7.45e+00 1r2qA 170 7.50e+00 c.37.1.8 96874 1efvB 255 7.57e+00 1efvB c.26.2.3 31634 1mzhA 225 7.62e+00 c.1.10.1 79698 1yd7A 395 7.68e+00 2czrA 226 7.76e+00 2btzA 394 7.79e+00 1qxyA 252 7.81e+00 d.127.1.1 96565 1g6hA 257 7.92e+00 1gajA c.37.1.12 60318 1gajA 257 7.94e+00 1gajA c.37.1.12 60416 1zgkA 308 7.97e+00 2bt9A 90 8.06e+00 2czdA 208 8.35e+00 1qwgA 251 8.46e+00 c.1.27.1 96473 1ay2 159 8.57e+00 2pil d.24.1.1 38377 1a1d 146 8.64e+00 1a1d b.40.4.8 25394 1zr6A 503 8.67e+00 1huqA 164 8.68e+00 1byuA c.37.1.8 32020 2cdcA 366 8.70e+00 1g71A 347 8.76e+00 1g71A d.264.1.1 43268 1bg4 302 8.88e+00 1taxA c.1.8.3 28806 1xttA 216 9.01e+00 2pil 159 9.10e+00 2pil d.24.1.1 38376 1ltzA 297 9.23e+00 d.178.1.1 74254 1b31A 302 9.23e+00 1taxA c.1.8.3 28892 1oxxK 353 9.25e+00 b.40.6.3,c.37.1.12 93715,93716 1gmlA 178 9.26e+00 c.8.5.2 70273 1lkvX 232 9.28e+00 a.118.14.1 73980 1qmyA 167 9.48e+00 1qmyA d.3.1.2 37094 1qoiA 177 9.50e+00 2cpl b.62.1.1 27490 1e55A 512 9.54e+00 1e70M c.1.8.4 28934 1vkdA 338 9.54e+00 b.67.2.4 108644 1nsyA 271 9.76e+00 2nsyA c.26.2.1 31614 1aorA 605 9.81e+00 1b25A a.110.1.1,d.152.1.1 19042,41794 1h49A 512 9.87e+00 c.1.8.4 83477 1hc7A 477 9.88e+00 1hc7A c.51.1.1,d.104.1.1,d.68.5.1 60938,60939,60940 1d7kA 421 9.88e+00 7odcA b.49.2.3,c.1.6.1 26486,28648 1zn6A 227 9.90e+00 1vf8A 377 9.93e+00 2nsyA 271 1.00e+01 2nsyA c.26.2.1 31612 2gzxA 265 1.02e+01 2b7oA 464 1.02e+01 1kutA 230 1.03e+01 d.143.1.1 73017 1ac5 483 1.04e+01 1ac5 c.69.1.5 34653 1eur 365 1.04e+01 1eut b.68.1.1 27607 1nxmA 197 1.05e+01 b.82.1.1 86385 1b6g 310 1.06e+01 1b6g c.69.1.8 34661 1dbiA 280 1.06e+01 1gci c.41.1.1 32543 2frnA 278 1.06e+01 1ede 310 1.07e+01 1b6g c.69.1.8 34662 1acf 125 1.07e+01 3nul d.110.1.1 40882 1d7yA 408 1.08e+01 1d7yA c.3.1.5,c.3.1.5,d.87.1.1 30565,30566,40204 2g76A 335 1.09e+01 2cvjA 180 1.09e+01 1eiwA 111 1.09e+01 1eiwA c.23.3.1 31130 1gthA 1025 1.10e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70483,70484,70485,70486,70487 1ih8A 271 1.10e+01 2nsyA c.26.2.1 62377 1h5qA 265 1.11e+01 1cydA c.2.1.2 60643 1tw4A 125 1.11e+01 2ffjA 300 1.12e+01 1vl8A 267 1.12e+01 c.2.1.2 108733 2pfkA 320 1.14e+01 3pfk c.89.1.1 35577 1xhcA 367 1.17e+01 1zhhB 242 1.17e+01 1v33A 366 1.18e+01 d.264.1.1 100278 1bh5A 183 1.18e+01 1qipA d.32.1.1 38476 2azpA 318 1.18e+01 2a1dD 329 1.20e+01 1xd5A 112 1.20e+01 1qo2A 241 1.20e+01 1qo2A c.1.2.1 28533 1nu7D 282 1.21e+01 a.8.6.1,a.8.6.1 92191,92192 1pwhA 327 1.21e+01 c.79.1.1 95224 2a38A 194 1.21e+01 2bs6A 90 1.23e+01 2ethA 154 1.23e+01 1umdA 367 1.24e+01 c.36.1.11 99599 1wab 232 1.27e+01 1wab c.23.10.3 31341 1b0jA 754 1.28e+01 1amj c.8.2.1,c.83.1.1 30719,35395 1kqpA 271 1.28e+01 c.26.2.1 72883 1twfH 146 1.28e+01 1k4zA 159 1.30e+01 b.80.5.1 72070 1i50H 146 1.30e+01 b.40.4.8 61761 2bpqA 373 1.30e+01 1kblA 873 1.31e+01 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 1cr1A 296 1.32e+01 1cr1A c.37.1.11 32286 1es9A 232 1.33e+01 1wab c.23.10.3 31340 1o69A 394 1.35e+01 c.67.1.4 92560 1h7xA 1025 1.35e+01 1h7wA a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15687,28632,30328,30613,39011 1vpkA 378 1.35e+01 1jj2E 177 1.36e+01 1ffk1 d.141.1.1,d.141.1.1 63089,63090 1cr0A 296 1.38e+01 1cr1A c.37.1.11 32287 1zy9A 564 1.38e+01 1ak2 233 1.38e+01 1zin c.37.1.1,g.41.2.1 31894,45195 2f4nA 273 1.39e+01 1jjiA 311 1.40e+01 c.69.1.2 66766 1bh6A 274 1.41e+01 1gci c.41.1.1 32487 1s72E 178 1.41e+01 d.141.1.1,d.141.1.1 105323,105324 1e2tA 284 1.42e+01 1e2tA d.3.1.5 37121 2ge3A 170 1.42e+01 1h7xB 1025 1.43e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15688,28633,30329,30614,39012 1ld4A 264 1.43e+01 i.6.1.1 77886 1vk9A 151 1.44e+01 c.139.1.1 108640 1npeA 267 1.45e+01 b.68.5.1 92032 1hskA 326 1.47e+01 2mbr d.145.1.2,d.146.1.1 61241,61242 1w8oA 601 1.47e+01 1ak5 503 1.47e+01 1ak5 c.1.5.1 28639 1i2hA 168 1.47e+01 b.55.1.4 71103 1khdA 345 1.48e+01 a.46.2.1,c.27.1.1 77400,77401 2gclA 261 1.49e+01 1han 297 1.49e+01 1han d.32.1.3,d.32.1.3 38506,38507 1r0rE 274 1.49e+01 c.41.1.1 96735 1phk 298 1.50e+01 1cdkA d.144.1.7 41635 1t8tA 271 1.51e+01 c.37.1.5 106685 1sqjA 789 1.52e+01 b.69.13.1,b.69.13.1 105918,105919 1qrrA 394 1.52e+01 1qrrA c.2.1.2 29824 1h7wD 1025 1.54e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15686,28631,30327,30612,39010 2c2aA 258 1.55e+01 1h7wA 1025 1.57e+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 1h7xD 1025 1.58e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15690,28635,30331,30616,39014 1euu 605 1.59e+01 1eut b.1.18.2,b.18.1.1,b.68.1.1 21892,23713,27610 1gpiA 431 1.59e+01 b.29.1.10 65450 1lv7A 257 1.62e+01 c.37.1.20 78232 1eut 605 1.62e+01 1eut b.1.18.2,b.18.1.1,b.68.1.1 21891,23712,27609 1h7xC 1025 1.62e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15689,28634,30330,30615,39013 1h7wB 1025 1.63e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15684,28629,30325,30610,39008 1g8lA 411 1.64e+01 1g8lA b.85.6.1,b.103.1.1,c.57.1.2 60365,60366,60367 1w8iA 156 1.64e+01 1nzjA 298 1.65e+01 c.26.1.1 92377 1wzzA 334 1.65e+01 1hh1A 143 1.65e+01 1gefA c.52.1.18 61036 1ka2A 499 1.66e+01 d.92.1.5 77305 1q6oA 216 1.67e+01 c.1.2.3 95986 2iwaA 266 1.67e+01 1t0fA 276 1.67e+01 1hkkA 364 1.70e+01 c.1.8.5,d.26.3.1 90634,90635 1vqoE 178 1.70e+01 1z41A 338 1.70e+01 1ej2A 181 1.70e+01 1f9aA c.26.1.3 59414 1yu6A 275 1.71e+01 1lkdA 297 1.71e+01 d.32.1.3,d.32.1.3 78059,78060 1h1iC 350 1.72e+01 b.82.1.5 76471 1h1iB 350 1.72e+01 b.82.1.5 76470 1qpoA 284 1.72e+01 1qpoA c.1.17.1,d.41.2.1 29561,38597 1wcqA 601 1.73e+01 1y8tA 324 1.73e+01 1lgtA 297 1.74e+01 d.32.1.3,d.32.1.3 77956,77957 1h1iD 350 1.77e+01 b.82.1.5 76472 2ac2A 309 1.77e+01 1dymA 402 1.77e+01 1celA b.29.1.10 24304 1f89A 291 1.78e+01 d.160.1.1 64988 1ep3A 311 1.79e+01 2dorA c.1.4.1 28597 2fuvA 549 1.82e+01 1wnfA 328 1.85e+01 1crwG 333 1.86e+01 1dssG c.2.1.3,d.81.1.1 30026,39941 1shsA 147 1.86e+01 1shsA b.15.1.1 23675 1avt 274 1.86e+01 1gci c.41.1.1 32488 1i1qA 520 1.87e+01 1qdlA d.161.1.1 61543 1gfsA 321 1.88e+01 c.2.1.2 29811 6pfkA 319 1.89e+01 3pfk c.89.1.1 35583 1oxsC 353 1.89e+01 b.40.6.3,c.37.1.12 87519,87520 1y8cA 246 1.89e+01 1v4vA 376 1.89e+01 c.87.1.3 100313 1itwA 741 1.93e+01 c.77.1.2 76793 1ho1A 242 1.93e+01 1ho1A c.1.24.1 61097 1s8nA 205 1.93e+01 c.23.1.1 105374 3kar 346 1.95e+01 1bg2 c.37.1.9 32198 1emsA 440 1.96e+01 1emsA d.13.1.1,d.160.1.1 37520,42086 7acn 754 1.96e+01 1amj c.8.2.1,c.83.1.1 30717,35393 1bsvA 321 1.96e+01 1bsvA c.2.1.2 29809 1i24A 404 1.97e+01 c.2.1.2 83663 3pfk 319 1.97e+01 3pfk c.89.1.1 35581 1ry6A 360 1.97e+01 c.37.1.9 98090 1ldnA 316 1.98e+01 1hyhA c.2.1.5,d.162.1.1 30166,42133 1wvhA 134 1.98e+01 1iqyA 638 1.98e+01 b.30.2.1,d.17.2.1,d.17.2.1 76763,76764,76765 2d69A 430 1.99e+01 6acn 754 2.00e+01 1amj c.8.2.1,c.83.1.1 30721,35397 1bxnA 485 2.00e+01 1burA c.1.14.1,d.58.9.1 29376,39282 2gupA 292 2.01e+01 1ojjA 402 2.02e+01 b.29.1.10 93130 1mvfD 82 2.02e+01 b.129.1.1 85143 1ne9A 335 2.03e+01 d.108.1.4,d.108.1.4 91839,91840 1ps2 60 2.03e+01 2pspA g.16.1.1 44746 1ujpA 271 2.04e+01 c.1.2.4 99462 8acn 754 2.05e+01 1amj c.8.2.1,c.83.1.1 30724,35400 3pmgA 561 2.06e+01 3pmgA c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 35408,35409,35410,41301 1od2A 805 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