# List of top-scoring protein chains for t2k-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 1yhpA 212 6.06e-01 1nfn 191 9.33e-01 1nfn a.24.1.1 16523 1wqaA 455 1.03e+00 1w1wA 430 1.18e+00 2u1a 88 1.25e+00 2u1a d.58.7.1 39164 1qo0D 196 1.83e+00 1qo0D c.23.1.3 31125 2fbiA 142 1.85e+00 1vjeA 166 2.02e+00 d.185.1.2 100807 2lbd 267 2.27e+00 2lbd a.123.1.1 19287 1innA 166 2.58e+00 1j98A d.185.1.2 62608 1fcyA 236 2.90e+00 2lbd a.123.1.1 19282 2fcr 173 3.18e+00 1rcf c.23.5.1 31151 1ursA 402 3.36e+00 c.94.1.1 99833 1yfqA 342 3.46e+00 4lbd 267 3.53e+00 2lbd a.123.1.1 19289 1pjcA 361 5.08e+00 1sayA c.2.1.4,c.23.12.2 30101,31361 1d3uB 201 5.12e+00 1aisB a.74.1.2,a.74.1.2 18386,18387 1v8gA 329 5.25e+00 a.46.2.1,c.27.1.1 100505,100506 1zin 217 5.31e+00 1zin c.37.1.1,g.41.2.1 31915,45178 1pjbA 361 5.46e+00 1sayA c.2.1.4,c.23.12.2 30103,31363 1e9rA 437 6.27e+00 c.37.1.11 64827 3mhtA 327 6.56e+00 6mhtA c.66.1.26 34234 1ri7A 171 6.80e+00 a.4.5.32,d.58.4.2 97504,97505 1ow1A 195 6.99e+00 b.131.1.3 93625 2b0cA 206 7.00e+00 1j5kA 89 7.03e+00 d.51.1.1 71565 2c7pA 327 7.52e+00 1sayA 361 7.58e+00 1sayA c.2.1.4,c.23.12.2 30102,31362 1xn7A 78 7.61e+00 1q1hA 110 8.29e+00 a.4.5.41 95580 2cuaA 135 8.37e+00 2cuaA b.6.1.2 23039 1jmtA 104 8.42e+00 d.58.7.3 63180 1fjxA 327 8.42e+00 6mhtA c.66.1.26 34228 1x7oA 287 8.67e+00 1zip 217 8.91e+00 1zin c.37.1.1,g.41.2.1 31916,45179 1nx8A 273 9.37e+00 b.82.2.8 86374 1rzsA 61 9.45e+00 a.35.1.2 105139 2dbbA 151 1.01e+01 1fnlA 175 1.01e+01 2fcbA b.1.1.4,b.1.1.4 21783,21784 1cc1S 283 1.03e+01 2frvA e.19.1.1 43313 6mhtA 327 1.04e+01 6mhtA c.66.1.26 34226 1ouwA 152 1.04e+01 b.77.3.1 93571 2jdxA 385 1.06e+01 1jdw d.126.1.2 41139 1zsyA 357 1.11e+01 2bo4A 397 1.11e+01 1qb5D 99 1.13e+01 b.40.2.1 88357 1hyqA 263 1.22e+01 1hyqA c.37.1.10 61412 1h1nA 305 1.22e+01 c.1.8.3 70855 2bolA 314 1.23e+01 1i35A 95 1.27e+01 d.15.1.5 66017 1aisB 200 1.28e+01 1aisB a.74.1.2,a.74.1.2 18384,18385 1u4cA 349 1.28e+01 b.69.4.2 107666 1yj7A 171 1.36e+01 2cfxA 144 1.38e+01 1zpvA 91 1.49e+01 2d8dA 90 1.55e+01 1u4nA 310 1.56e+01 1ass 159 1.59e+01 1a6dA c.8.5.2 30818 1y02A 120 1.67e+01 2f5gA 133 1.74e+01 1h70A 255 1.77e+01 1h70A d.126.1.3 60711 2anuA 255 1.88e+01 2fu0A 160 1.89e+01 1szqA 483 1.93e+01 e.44.1.1 99045 1fjgP 88 1.94e+01 1emwA d.27.1.1 38444 1s96A 219 1.96e+01 c.37.1.1 98740 1fx3A 169 1.99e+01 1fx3B d.33.1.1 38524 1jdw 423 2.01e+01 1jdw d.126.1.2 41129 1k4wA 252 2.02e+01 a.123.1.1 72068 2a61A 145 2.03e+01 1a0i 348 2.04e+01 1a0i b.40.4.6,d.142.2.1 25363,41577 1dgsA 667 2.09e+01 1dgsA a.60.2.2,b.40.4.6,d.142.2.2 17963,25365,41581 1fehA 574 2.10e+01 1fehA c.96.1.1,d.15.4.2,d.58.1.5 36015,37690,38998 1w4tA 299 2.11e+01 1vkfA 188 2.12e+01 c.1.29.1 108656 1vl6A 388 2.13e+01 c.2.1.7,c.58.1.3 108724,108725 1ozhA 566 2.14e+01 c.31.1.3,c.36.1.5,c.36.1.9 93833,93834,93835 1wi9A 72 2.17e+01 1ub9A 100 2.19e+01 a.4.5.28 99159 1zu4A 320 2.21e+01 1hw1A 239 2.25e+01 1e2xA a.4.5.6,a.78.1.1 16111,18441 1ehkB 168 2.25e+01 2cuaA b.6.1.2,f.17.2.1 23041,43625 1e8cA 498 2.26e+01 c.98.1.1,c.59.1.1,c.72.2.1 59377,59378,59379 1o7qA 289 2.31e+01 c.68.1.9 92626 1aszB 490 2.38e+01 1b8aA b.40.4.1,d.104.1.1 25241,40762 1y89A 238 2.42e+01 1lvaA 258 2.44e+01 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 1eiwA 111 2.45e+01 1eiwA c.23.3.1 31130 1v7pC 200 2.46e+01 c.62.1.1 108408 1tl0D 103 2.46e+01 1cipA 353 2.49e+01 1cipA a.66.1.1,c.37.1.8 18210,32093 2fliA 220 2.64e+01 1u8sA 192 2.64e+01 d.58.18.5,d.58.18.5 107737,107738 1g3qA 237 2.65e+01 1hyqA c.37.1.10 60237 1wr8A 231 2.66e+01 1e2xA 243 2.68e+01 1e2xA a.4.5.6,a.78.1.1 16113,18443 1rom 403 2.72e+01 1rom a.104.1.1 18963 1a73A 163 2.75e+01 1a73A d.4.1.3 37145 1k2fA 190 2.77e+01 b.8.1.2 68054 1lr0A 129 2.77e+01 d.212.1.1 74213 1jkoC 52 2.79e+01 a.4.1.2 66809 1n83A 270 2.79e+01 a.123.1.1 80276 2cxcA 144 2.80e+01 2wsyA 268 2.81e+01 2tysA c.1.2.4 28588 1ble 163 2.83e+01 1ble c.38.1.1 32475 1s0uA 408 2.89e+01 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 2liv 344 2.90e+01 2liv c.93.1.1 35708 1nq7A 244 2.90e+01 a.123.1.1 92047 2bl1A 172 2.98e+01 1b8bA 605 2.98e+01 1b8bA 2b3nA 159 3.01e+01 1cmnA 402 3.02e+01 1rom a.104.1.1 18958 1fsz 372 3.04e+01 1fsz c.32.1.1,d.79.2.1 31750,39802 1ro5A 201 3.05e+01 d.108.1.3 105023 1omzA 293 3.07e+01 c.68.1.15 87093 1aoxA 203 3.08e+01 1aoxA c.62.1.1 34151 1sep 261 3.09e+01 1oaa c.2.1.2 29830 1yvoA 172 3.11e+01 1ysrA 150 3.12e+01 1l9mA 692 3.14e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 73732,73733,73734,73735 1ykfA 352 3.35e+01 1pedA b.35.1.2,c.2.1.1 24757,29773 1oz9A 150 3.38e+01 d.92.1.15 93808 1i8tA 367 3.39e+01 c.4.1.3,d.16.1.7 66094,66095 1lea 84 3.43e+01 1lea a.4.5.2 16085 1evxA 162 3.44e+01 1a73A d.4.1.3 37149 1ypfA 336 3.48e+01 1svsA 353 3.50e+01 c.37.1.8 106051 1k4vA 289 3.52e+01 c.68.1.9 72066 2c9aA 259 3.54e+01 2ff4A 388 3.54e+01 1gx4A 289 3.55e+01 c.68.1.9 83362 1q0uA 219 3.57e+01 c.37.1.19 95512 1a6dA 545 3.60e+01 1a6dA a.129.1.2,c.8.5.2,d.56.1.2 19488,30819,38936 1oaa 259 3.62e+01 1oaa c.2.1.2 29829 1oc2A 348 3.62e+01 c.2.1.2 92765 1gegA 256 3.64e+01 1ybvA c.2.1.2 29888 1ydgA 211 3.64e+01 2gjgA 248 3.68e+01 1bfd 528 3.78e+01 1bfd c.31.1.3,c.36.1.5,c.36.1.9 31745,31801,31802 1zkdA 387 3.80e+01 1q7zA 566 3.93e+01 c.1.21.2,c.1.26.1 96090,96091 1jhfA 202 3.93e+01 a.4.5.2,b.87.1.1 63057,63058 1exmA 405 3.95e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 1kepA 348 3.95e+01 c.2.1.2 68536 1s7hA 200 4.00e+01 d.58.48.2 105349 1r6vA 671 4.05e+01 1eu8A 409 4.07e+01 1eu8A c.94.1.1 59502 1q6zA 528 4.14e+01 1hmy 327 4.28e+01 6mhtA c.66.1.26 34229 1t71A 281 4.34e+01 1wleA 501 4.34e+01 1jfbA 404 4.34e+01 a.104.1.1 66624 1sg4A 260 4.36e+01 1f24A 402 4.38e+01 1rom a.104.1.1 18953 1tin 69 4.41e+01 2sniI d.40.1.1 38580 1vq2A 193 4.42e+01 1f1zA 273 4.42e+01 1f1zA a.4.5.27,c.52.1.16 16081,33334 2ag9A 164 4.49e+01 1t0fA 276 4.59e+01 1tiiD 99 4.61e+01 1tiiD b.40.2.1 24965 2fckA 181 4.64e+01 1xx6A 191 4.66e+01 1wzlA 585 4.68e+01 1buoA 121 4.69e+01 1buoA d.42.1.1 38631 1wxiA 275 4.74e+01 1k4mA 213 4.80e+01 c.26.1.3 77258 1tc5A 194 4.82e+01 c.110.1.1 106752 1ymiA 334 4.83e+01 1k3eA 156 4.87e+01 d.198.1.1 68103 2ag4A 164 4.88e+01 2ch8A 201 4.90e+01 2d00A 109 4.93e+01 2an9A 207 4.96e+01 2f9sA 151 5.00e+01 1gveA 327 5.00e+01 c.1.7.1 70597 1chuA 540 5.16e+01 1chuA a.7.3.1,c.3.1.4,d.168.1.1 16325,30424,42307 1ha3A 405 5.17e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 1xmxA 385 5.20e+01 2evaA 307 5.20e+01 4enl 436 5.32e+01 4enl c.1.11.1,d.54.1.1 29202,38846 1ar1A 558 5.33e+01 2occA f.24.1.1 43618 1bd3A 243 5.34e+01 1bd3A c.61.1.1 34098 1i1kA 309 5.34e+01 1daaA e.17.1.1 61533 1xhbA 472 5.36e+01 1yd9A 193 5.43e+01 1s7kA 182 5.43e+01 1oboA 169 5.44e+01 c.23.5.1 86776 1nal3 297 5.59e+01 1nal3 1g8oA 310 5.61e+01 1g8oA c.68.1.9 60375 1lfo 128 5.72e+01 1hmt b.60.1.2 27223 1nkiA 135 5.81e+01 d.32.1.2 91941 1ckeA 227 5.83e+01 1ckeA c.37.1.1 31846 1jflA 228 5.85e+01 c.78.2.1,c.78.2.1 71656,71657 1kyhA 276 5.95e+01 c.72.1.4 73222 1wnlA 235 6.00e+01 1wn5A 130 6.04e+01 1klo 162 6.05e+01 1klo g.3.11.2,g.3.11.2,g.3.11.2 44326,44327,44328 1peqA 714 6.21e+01 a.98.1.1,c.7.1.2 104131,104132 2ae2A 260 6.24e+01 1bdb c.2.1.2 29945 1v7wA 807 6.31e+01 a.102.1.4,b.30.5.3 108411,108412 1jdfA 447 6.32e+01 c.1.11.2,d.54.1.1 62897,62898 1s99A 200 6.33e+01 1vpjA 192 6.39e+01 1z83A 196 6.45e+01 1vbuA 328 6.45e+01 1srvA 145 6.46e+01 1derA c.8.5.1 30817 1ipiA 123 6.47e+01 c.52.1.18 66255 1fx3B 169 6.53e+01 1fx3B d.33.1.1 38525 1pu5A 164 6.55e+01 b.95.1.1 104310 1yacA 208 6.62e+01 1yacA c.33.1.3 31757 1yal 218 6.64e+01 1cs8A d.3.1.1 37025 1gfsA 321 6.72e+01 c.2.1.2 29811 1sdsA 117 6.73e+01 d.79.3.1 105439 1j3bA 529 6.73e+01 c.91.1.1,c.109.1.1 77071,77072 1rgyA 360 6.77e+01 e.3.1.1 97456 1gtvA 214 6.78e+01 c.37.1.1 70537 2fuvA 549 6.82e+01 1qwgA 251 6.84e+01 c.1.27.1 96473 1o6dA 163 6.85e+01 c.116.1.3 92567 1t95A 240 6.86e+01 a.5.8.1,d.235.1.2,d.58.11.3 106705,106706,106707 1ecfA 504 6.94e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 1xcrA 316 6.95e+01 1pot 325 6.95e+01 1pot c.94.1.1 35807 1ihcA 188 7.00e+01 1di6A c.57.1.1 62379 2cviA 83 7.01e+01 1tdj 514 7.05e+01 1tdj c.79.1.1,d.58.18.2,d.58.18.2 35297,39356,39357 1gefA 123 7.15e+01 1gefA c.52.1.18 60465 1yghA 164 7.21e+01 1yghA d.108.1.1 40802 2cb2A 318 7.21e+01 1or3A 165 7.23e+01 1nfn a.24.1.1 16522 1rzjG 321 7.27e+01 d.172.1.1 98200 1yrgA 385 7.33e+01 1yrgA c.10.1.2 30854 1uedA 406 7.33e+01 a.104.1.1 99256 1yyvA 131 7.36e+01 1lb3A 182 7.37e+01 a.25.1.1 77873 1eft 405 7.40e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25688,25728,32123 1xfcA 384 7.40e+01 1b6rA 355 7.41e+01 1b6rA b.84.2.1,c.30.1.1,d.142.1.2 28241,31648,41493 1ojxA 263 7.47e+01 c.1.10.1 93164 2ca6A 386 7.48e+01 1yjmA 110 7.49e+01 1f2tB 148 7.55e+01 1f2tB 1mit 69 7.60e+01 1hymA d.40.1.1 38582 1geqA 248 7.61e+01 2tysA c.1.2.4 28589 1fipA 98 7.62e+01 1fipA a.4.1.12 18980 1qc5A 192 7.66e+01 1aoxA c.62.1.1 34147 1wvqA 167 7.72e+01 1bwsA 321 7.72e+01 1bsvA c.2.1.2 29812 1z15A 344 7.73e+01 1hymA 45 7.77e+01 1hymA d.40.1.1 38581 1lqpA 135 7.83e+01 d.32.1.2 78151 1pj5A 830 7.84e+01 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 1asx 159 7.89e+01 1a6dA c.8.5.2 30821 1pt6A 213 7.90e+01 c.62.1.1 95091 2cmkA 227 8.00e+01 1ckeA c.37.1.1 31847 1po5A 476 8.03e+01 a.104.1.1 94963 2fiyA 309 8.08e+01 2c78A 405 8.10e+01 1xzoA 174 8.16e+01 1l2iA 261 8.16e+01 a.123.1.1 73503 2ffuA 501 8.17e+01 1wzaA 488 8.18e+01 1jljA 189 8.21e+01 c.57.1.1 63169 1ku3A 73 8.23e+01 a.4.13.2 73000 1b34A 119 8.23e+01 1d3bA b.38.1.1 24796 2b0jA 358 8.26e+01 1b7bA 310 8.28e+01 1b7bA c.73.1.1 34963 1fdyA 297 8.29e+01 1nal3 c.1.10.1 29071 1kyfA 247 8.32e+01 b.1.10.1,d.105.1.1 73220,73221 2faoA 309 8.33e+01 1j0dA 341 8.38e+01 c.79.1.1 83902 1o7nA 449 8.40e+01 b.33.1.2,d.129.3.3 81162,81163 1tph1 247 8.41e+01 1amk 1qdlB 195 8.41e+01 1qdlB c.23.16.1 31437 1fo9A 348 8.45e+01 1foaA c.68.1.10 59928 1fhdA 312 8.45e+01 1taxA c.1.8.3 28915 1yp2A 451 8.49e+01 1bsvA 321 8.50e+01 1bsvA c.2.1.2 29809 1a3gA 308 8.50e+01 1daaA e.17.1.1 43286 1f08A 148 8.52e+01 1f08A d.89.1.2 59564 2as9A 210 8.53e+01 1e6uA 321 8.56e+01 1bsvA c.2.1.2 29805 1om1A 332 8.56e+01 d.144.1.7 93347 2al2A 436 8.69e+01 1eg9A 449 8.71e+01 1ndoA b.33.1.2,d.129.3.3 24443,41322 1iyeA 309 8.76e+01 e.17.1.1 83786 1p9qC 256 8.77e+01 a.5.8.1,d.235.1.2,d.58.11.3 104093,104094,104095 1bxsA 501 8.77e+01 1bpwA c.82.1.1 35357 1pswA 348 8.84e+01 c.87.1.7 88287 1id1A 153 8.84e+01 1id1A c.2.1.9 62286 3erdA 261 8.88e+01 3erdA a.123.1.1 19293 1pixA 587 8.90e+01 c.14.1.4 94708 1hy5A 136 8.97e+01 a.24.11.1 65955 1aq6A 253 8.97e+01 1qq5A c.108.1.1 43331 1pk6C 129 8.98e+01 b.22.1.1 94803 1xt5A 135 8.99e+01 1foaA 348 9.00e+01 1foaA c.68.1.10 59929