# List of top-scoring protein chains for t04-100-30-stride-ebghtl-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.soe.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 2plsA 86 4.41e-17 2oaiA 94 1.09e-16 2p13A 90 2.88e-16 2o1rA 81 3.29e-16 2pliA 91 7.07e-16 2nqwA 93 1.27e-15 2p4pA 86 1.31e-15 2r2zA 93 2.15e-15 2rk5A 87 7.98e-13 2p3hA 101 3.57e-11 1c0pA 363 3.61e-01 1an9A c.4.1.2,d.16.1.3 30647,37934 2pp6A 102 3.97e-01 1ifc 132 5.25e-01 1ifcA 132 5.25e-01 b.60.1.2 27173 1icmA 131 5.40e-01 b.60.1.2 27174 2anrA 178 5.91e-01 2ehsA 77 1.06e+00 1jb7B 260 1.46e+00 1otcB b.40.4.3 62839 2amwA 83 2.01e+00 1i8dA 213 2.45e+00 b.43.4.3,b.43.4.3 61953,61954 2b49A 287 2.52e+00 1o3yA 166 2.66e+00 c.37.1.8 86618 2gcuA 245 2.85e+00 2hy1A 280 3.16e+00 1kzlA 208 3.16e+00 b.43.4.3,b.43.4.3 77635,77636 1nofA 383 3.31e+00 b.71.1.2,c.1.8.3 92020,92021 2g2kA 170 3.48e+00 1vr9A 213 3.50e+00 d.37.1.1,d.37.1.1 120446,120447 1vmeA 410 3.50e+00 c.23.5.1,d.157.1.3 108893,108894 1uptA 171 3.53e+00 c.37.1.8 99767 1a9xB 379 3.95e+00 1c3oB c.8.3.1,c.23.16.1 30732,31409 1st9A 143 4.09e+00 c.47.1.10 98987 1wh2A 78 4.10e+00 d.76.1.1 114630 2a5dA 175 4.14e+00 c.37.1.8 126172 1c30B 382 4.21e+00 c.8.3.1,c.23.16.1 30736,31413 2f9sA 151 4.22e+00 c.47.1.10 133168 1l1nA 183 4.40e+00 b.47.1.4 73476 2nrlA 147 4.41e+00 1udxA 416 4.52e+00 b.117.1.1,c.37.1.8,d.242.1.1 99228,99229,99230 1tmxA 293 4.56e+00 1b8aA 438 5.04e+00 1b8aA b.40.4.1,d.104.1.1 25244,40765 1z06A 189 5.13e+00 c.37.1.8 124301 2r0yA 311 5.36e+00 1r8sA 164 5.58e+00 c.37.1.8 97247 2aorA 223 6.22e+00 1sjiA 350 6.38e+00 1aisA 182 6.99e+00 1ytbA d.129.1.1,d.129.1.1 41288,41289 2rb7A 364 7.04e+00 1zcbA 362 7.46e+00 a.66.1.1,c.37.1.8 124901,124902 2z14A 133 7.65e+00 1r4aA 165 8.22e+00 c.37.1.8 96986 1eyqA 222 8.52e+00 1eypA d.36.1.1 38534 1gycA 499 8.73e+00 b.6.1.3,b.6.1.3,b.6.1.3 70748,70749,70750 2i6gA 199 9.01e+00 c.66.1.44 137096 2p18A 311 9.11e+00 2uuuA 584 9.20e+00 2fmlA 273 9.50e+00 a.4.5.68,d.113.1.6 133778,133779 1zfjA 491 9.74e+00 1ak5 c.1.5.1,d.37.1.1,d.37.1.1 28638,38540,38541 1smlA 269 1.03e+01 1smlA d.157.1.1 42053 2aioA 269 1.03e+01 d.157.1.1 126829 1hskA 326 1.07e+01 2mbr d.145.1.2,d.146.1.1 61241,61242 1ywsA 82 1.12e+01 g.41.17.1 124163 3cfuA 159 1.20e+01 2f7vA 369 1.22e+01 1tk1A 260 1.24e+01 d.248.1.1 107066 1tvgA 153 1.32e+01 b.18.1.9 112683 1yvcA 70 1.42e+01 b.40.4.12 124094 1wv2A 265 1.46e+01 c.1.31.1 114910 3bwvA 180 1.47e+01 1rewC 135 1.50e+01 g.7.1.3 97336 2yvyA 278 1.51e+01 2bv5A 282 1.51e+01 2ehjA 208 1.51e+01 2zbwA 335 1.51e+01 1nt4A 391 1.54e+01 c.60.1.2 92102 2zivB 351 1.56e+01 1t8kA 77 1.56e+01 a.28.1.1 106666 2btiA 63 1.56e+01 1offA 97 1.56e+01 d.15.4.1 86947 1uliA 460 1.58e+01 b.33.1.2,d.129.3.3 107921,107922 2v40A 459 1.65e+01 1yb2A 275 1.67e+01 c.66.1.13 122868 2ohdA 151 1.67e+01 1lv7A 257 1.72e+01 c.37.1.20 78232 2b1xA 470 1.76e+01 b.33.1.2,d.129.3.3 127675,127676 1vpzA 73 1.77e+01 b.151.1.1 113998 1svsA 353 1.80e+01 c.37.1.8 106051 1jqgA 433 1.83e+01 c.56.5.1,d.58.3.1 71791,71792 1qhoA 686 1.84e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21844,22513,27751,28738 2qt6A 498 1.86e+01 1tocR 120 1.87e+01 1tocR g.8.1.2,g.8.1.2 44558,44559 2pia 321 1.90e+01 2pia 2piaA 321 1.90e+01 b.43.4.2,c.25.1.2,d.15.4.2 25663,31553,37704 2h62C 129 1.91e+01 g.7.1.3 136179 1b5pA 385 1.92e+01 c.67.1.1 90403 2cx6A 90 1.94e+01 c.9.1.1 130981 1frrA 95 1.98e+01 1awd d.15.4.1 37674 1xcbA 211 1.99e+01 a.4.5.38,c.2.1.12 109552,109553 2g7bA 137 2.00e+01 1ve1A 304 2.07e+01 c.79.1.1 120007 1p6pA 125 2.07e+01 b.60.1.2 87839 1hfuA 503 2.11e+01 b.6.1.3,b.6.1.3,b.6.1.3 65827,65828,65829 1hlgA 371 2.12e+01 1hlgA c.69.1.6 34656 1nh8A 304 2.12e+01 c.94.1.1,d.58.5.3 80507,80508 1hk8A 605 2.16e+01 c.7.1.3 83540 1erjA 393 2.27e+01 1erjA b.69.4.1 27660 1jztA 246 2.27e+01 c.104.1.1 63319 1ok7A 366 2.41e+01 d.131.1.1,d.131.1.1,d.131.1.1 103992,103993,103994 1a65A 504 2.43e+01 1a65A b.6.1.3,b.6.1.3,b.6.1.3 23148,23149,23150 1azo 232 2.48e+01 1azo 1azoA 232 2.48e+01 c.52.1.14 33329 1rx0A 393 2.51e+01 a.29.3.1,e.6.1.1 98007,98008 1f6bA 198 2.51e+01 c.37.1.8 64986 1cnt1 187 2.54e+01 1cnt3 1vqzA 341 2.55e+01 d.224.1.3,d.104.1.3 120426,120427 2bijA 305 2.62e+01 1o20A 427 2.64e+01 c.82.1.1 86556 1iweA 457 2.70e+01 c.37.1.10 71486 2e6mA 208 2.74e+01 2ibpA 409 2.75e+01 2bbhA 269 2.76e+01 d.328.1.1 128266 1a8y 367 2.85e+01 1a8y 1a8yA 367 2.85e+01 c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 2h57A 190 2.88e+01 1tw4A 125 2.92e+01 b.60.1.2 112690 1kwsA 261 2.94e+01 c.68.1.7 73083 1t3bA 211 2.96e+01 c.47.1.9,d.17.3.1 106341,106342 3cu0A 281 3.00e+01 1f80D 81 3.01e+01 1acp a.28.1.1 59686 1hkqA 132 3.02e+01 a.4.5.10 83555 1e39A 571 3.08e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19694,30431,42314 2ge3A 170 3.09e+01 d.108.1.1 135044 1nsf 273 3.09e+01 1d2nA 2f02A 323 3.09e+01 c.72.1.1 132649 1g3qA 237 3.14e+01 1hyqA c.37.1.10 60237 2uv4A 152 3.16e+01 2qcoA 210 3.20e+01 2ctdA 96 3.28e+01 g.37.1.1,g.37.1.1 130792,130793 1zzoA 136 3.30e+01 c.47.1.10 125913 1mp9A 198 3.31e+01 d.129.1.1,d.129.1.1 91385,91386 2hrgA 496 3.32e+01 2f7lA 455 3.34e+01 3ce7A 107 3.35e+01 2qn0A 430 3.53e+01 2c1fA 234 3.57e+01 3c5xC 130 3.58e+01 1d2nA 272 3.60e+01 1d2nA c.37.1.20 32428 2i75A 320 3.60e+01 2vg9A 217 3.62e+01 1j3wA 163 3.65e+01 d.110.7.1 90833 2c1cA 312 3.68e+01 c.56.5.1 129630 2r0cA 549 3.70e+01 1v8cA 168 3.72e+01 d.15.3.1,d.129.5.1 100495,100496 2oa8A 233 3.72e+01 1u5vA 273 3.76e+01 c.1.12.5 113054 1u5hA 273 3.78e+01 c.1.12.5 113037 1frdA 98 3.79e+01 d.15.4.1 37648 1b66A 140 3.81e+01 1b66A d.96.1.2 40657 1iq0A 592 3.81e+01 a.27.1.1,c.26.1.1,d.67.2.1 66257,66258,66259 2gwdA 449 3.85e+01 1dkqA 410 3.87e+01 1dklA c.60.1.2 33998 1i19A 561 3.90e+01 1i19A d.58.32.3,d.145.1.1 61522,61523 1csh 435 3.95e+01 1csh 1cshA 435 3.95e+01 a.103.1.1 18880 1hjxA 362 4.00e+01 c.1.8.5,d.26.3.1 83512,83513 1kssA 571 4.00e+01 a.138.1.3,c.3.1.4,d.168.1.1 72928,72929,72930 1r8eA 278 4.04e+01 a.6.1.3,d.60.1.1 104843,104844 1regX 122 4.06e+01 1regX d.58.27.1 39406 1v5tA 90 4.08e+01 d.15.1.1 108385 2i71A 400 4.08e+01 1q9iA 571 4.10e+01 a.138.1.3,c.3.1.4,d.168.1.1 96273,96274,96275 1y0pA 571 4.12e+01 a.138.1.3,c.3.1.4,d.168.1.1 122507,122508,122509 1w1oA 534 4.13e+01 d.58.32.4,d.145.1.1 109071,109072 1v10A 521 4.15e+01 b.6.1.3,b.6.1.3,b.6.1.3 108224,108225,108226 1zg2A 107 4.17e+01 1iybA 208 4.18e+01 d.124.1.1 90720 1z6kA 293 4.18e+01 1u6rA 380 4.21e+01 a.83.1.1,d.128.1.2 119600,119601 1zghA 260 4.22e+01 b.46.1.1,c.65.1.1 125028,125029 1kpf 126 4.22e+01 1kpf 2qo4A 126 4.22e+01 2g95A 491 4.23e+01 1ve0A 134 4.24e+01 1xm8A 254 4.26e+01 d.157.1.2 115475 2i1aA 148 4.26e+01 1zc0A 309 4.26e+01 1wcv1 257 4.34e+01 2dt5A 211 4.36e+01 a.4.5.38,c.2.1.12 131708,131709 1kpfA 125 4.37e+01 d.13.1.1 37507 2dxqA 150 4.40e+01 1kshA 186 4.41e+01 c.37.1.8 72914 1tp6A 128 4.42e+01 d.17.4.12 107184 1dkmA 410 4.44e+01 1dklA c.60.1.2 34000 1p2hA 571 4.50e+01 a.138.1.3,c.3.1.4,d.168.1.1 93930,93931,93932 2gj8A 172 4.53e+01 c.37.1.8 135270 1ybyA 215 4.56e+01 2cu6A 103 4.65e+01 d.52.8.2 130803 1w7lA 422 4.67e+01 c.67.1.1 109226 2j0fA 482 4.73e+01 1tzjA 338 4.76e+01 c.79.1.1 112868 1cqqA 180 4.77e+01 1cqqA b.47.1.4 26422 3d33A 108 4.78e+01 2yxbA 161 4.79e+01 2eifA 136 4.83e+01 1bkb b.34.5.2,b.40.4.5 24607,25339 2agaA 190 4.88e+01 1jyoA 130 4.92e+01 d.198.1.1 67483 1vqqA 646 4.93e+01 d.17.4.5,d.175.1.1,e.3.1.1 114009,114010,114011 1urjA 1136 5.02e+01 e.58.1.1 113410 1wu4A 396 5.02e+01 a.102.1.2 121272 2f9hA 129 5.06e+01 b.161.1.1 133162 1zj6A 187 5.09e+01 c.37.1.8 125145 2dxnA 274 5.15e+01 1f37A 110 5.25e+01 1f37A c.47.1.11 33088 2dg5B 190 5.28e+01 2z1uA 343 5.30e+01 1gt6A 269 5.31e+01 c.69.1.17 76342 1eg9A 449 5.32e+01 1ndoA b.33.1.2,d.129.3.3 24443,41322 2fl7A 232 5.33e+01 1vh4A 435 5.34e+01 b.80.6.1 100640 1o7nA 449 5.35e+01 b.33.1.2,d.129.3.3 81162,81163 1rfkA 98 5.37e+01 1xfxO 149 5.42e+01 a.39.1.5 121955 2z15A 130 5.43e+01 2inpL 89 5.46e+01 2p6hA 134 5.48e+01 1a4mA 349 5.55e+01 1a4mA c.1.9.1 29014 1fonA 240 5.57e+01 5ptp b.47.1.2 26231 2pa8L 92 5.58e+01 1k3tA 359 5.59e+01 c.2.1.3,d.81.1.1 72022,72023 1kpeA 126 5.61e+01 1kpf d.13.1.1 37508 1ionA 243 5.62e+01 c.37.1.10 62633 1w5rA 278 5.69e+01 d.3.1.5 120643 1q02A 52 5.71e+01 a.5.2.1 95490 2g6bA 180 5.74e+01 c.37.1.8 134701 1czpA 98 5.76e+01 1awd d.15.4.1 37645 1awdA 94 5.84e+01 d.15.4.1 37673 2irpA 208 5.85e+01 1ryiA 382 5.89e+01 c.3.1.2,d.16.1.3 118813,118814 2b3gA 123 5.91e+01 b.40.4.3 127786 1ujkA 147 5.97e+01 a.118.9.2 99457 1qw2A 102 5.99e+01 d.249.1.1 96456 1sq5A 308 6.01e+01 c.37.1.6 105882 2mspA 126 6.02e+01 1mspA b.1.11.2 22335 2gyqA 175 6.02e+01 a.25.1.4 135863 1zirA 173 6.04e+01 b.11.1.1,b.11.1.1 125126,125127 1mspA 126 6.05e+01 1mspA b.1.11.2 22333 2b6hA 192 6.11e+01 c.37.1.8 127994 2om6A 235 6.12e+01 1aerA 205 6.15e+01 1aerA d.166.1.1 42249 1l0iA 78 6.22e+01 a.28.1.1 77643 1jb0A 755 6.23e+01 1jb0A f.29.1.1 62820 1gu7A 364 6.27e+01 b.35.1.2,c.2.1.1 83321,83322 1r4wA 226 6.30e+01 c.47.1.13 97050 1ng4A 390 6.33e+01 c.3.1.2,d.16.1.3 85666,85667 1hs6A 611 6.34e+01 1hs6A a.118.1.7,b.98.1.1,d.92.1.13 61233,61234,61235 2fztA 79 6.36e+01 a.46.3.1 134476 2vj8A 611 6.37e+01 3bzcA 785 6.42e+01 2b3oA 532 6.45e+01 2r6gG 296 6.48e+01 2vdxA 373 6.48e+01 1ucdA 190 6.54e+01 d.124.1.1 107767 2oauA 306 6.57e+01 b.38.1.3,d.58.43.1,f.34.1.1 138978,138979,138980 1vlwA 217 6.60e+01 c.1.10.1 108868 2ew0A 192 6.73e+01 d.310.1.1 132445 1bjwA 382 6.73e+01 1bjwA c.67.1.1 34349 2h3bA 494 6.82e+01 1kqwA 134 6.83e+01 b.60.1.2 72887 2fgtA 417 6.84e+01 1m2oA 768 6.85e+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 2polA 366 6.87e+01 2polA d.131.1.1,d.131.1.1,d.131.1.1 41356,41357,41358 2rkuA 294 6.89e+01 2afdA 88 6.90e+01 2owbA 335 6.97e+01 3bfmA 235 7.03e+01 1xruA 282 7.04e+01 b.82.1.13 122262 1div 149 7.05e+01 1div 2i0kA 561 7.06e+01 1zkoA 136 7.17e+01 1twiA 434 7.20e+01 b.49.2.3,c.1.6.1 107399,107400 1sxrA 183 7.22e+01 d.118.1.1 106101 1gypA 358 7.23e+01 1dssG c.2.1.3,d.81.1.1 30004,39919 1mkyA 439 7.24e+01 c.37.1.8,c.37.1.8,d.52.5.1 79250,79251,79252 2nxwA 565 7.24e+01 1dsxA 87 7.31e+01 1t1dA d.42.1.2 38644 1a70A 97 7.34e+01 d.15.4.1 37678 1tufA 434 7.34e+01 b.49.2.3,c.1.6.1 107335,107336 2d13A 227 7.36e+01 c.26.2.1 131121 1dmhA 311 7.42e+01 1dmhA b.3.6.1 22633 1k8qA 377 7.42e+01 c.69.1.6 72177 2dxeA 160 7.43e+01 d.58.6.1 131870 2bekA 257 7.43e+01 2cwkA 160 7.45e+01 d.58.6.1 130925 2essA 248 7.47e+01 d.38.1.8,d.38.1.8 132346,132347 2z3xA 63 7.52e+01 1rfyA 102 7.54e+01 a.2.13.1 111798 2g23A 612 7.57e+01 1kqfB 294 7.59e+01 d.58.1.5,f.23.22.1 75900,75901 2f40A 96 7.59e+01 i.11.1.1 132903 2b8eA 273 7.61e+01 c.108.1.7,d.220.1.1 128068,128069 2ih8A 559 7.63e+01 b.6.1.3,b.6.1.3,b.6.1.3 137407,137408,137409 1nwwA 149 7.68e+01 d.17.4.8 86306 1sgvA 316 7.75e+01 b.122.1.1,d.265.1.2 98858,98859 1txnA 328 7.82e+01 d.248.1.1 112779 1mr3F 181 7.84e+01 c.37.1.8 79422 3choA 610 7.88e+01 1cjaA 342 7.90e+01 1cjaA d.144.1.3 41708