# List of top-scoring protein chains for t04-100-40-40-str2+CB_burial_14_7-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 1o6aA 96 3.11e-01 b.139.1.1 92562 1q6uA 245 5.65e-01 d.26.1.1 95998 1wjnA 97 5.99e-01 1c1yB 77 7.82e-01 1c1yB d.15.1.5 37618 1gy7A 125 8.88e-01 d.17.4.2 70738 1ahsA 126 9.24e-01 1ahsA b.19.1.1 23794 1dvpA 220 1.03e+00 1dvpA a.118.9.2,g.50.1.1 19216,45358 1x3eA 165 1.08e+00 1pylA 97 1.10e+00 d.1.1.2 104391 1z7gA 217 1.17e+00 1mwmA 320 1.24e+00 c.55.1.1,c.55.1.1 79580,79581 2bwqA 129 1.25e+00 1ue1A 164 1.28e+00 b.40.4.3 99243 1gpc 218 1.30e+00 1gpc b.40.4.7 25393 1f53A 84 1.31e+00 1f53A b.11.1.4 23632 1aw7A 194 1.39e+00 1aw7A b.40.2.2,d.15.6.1 25164,37753 1vjqA 79 1.56e+00 k.43.1.1 100830 1bzyA 217 1.62e+00 1qk3A c.61.1.1 34071 1y1oA 203 1.62e+00 1q38A 89 1.63e+00 b.1.2.1 95663 1ogoX 574 1.69e+00 b.133.1.1,b.80.1.10 92925,92926 2a4vA 159 1.86e+00 1dwkA 156 1.95e+00 1dw9A a.35.1.4,d.72.1.1 17075,39606 1xwvA 129 2.01e+00 1dkgA 197 2.03e+00 1dkgA b.73.1.1,h.1.9.1 27812,45626 1vdxA 184 2.17e+00 1eu3A 210 2.21e+00 1an8 b.40.2.2,d.15.6.1 25206,37795 1vgjA 184 2.29e+00 1tyjA 170 2.32e+00 1vr9A 213 2.38e+00 1iz6A 138 2.43e+00 b.34.5.2,b.40.4.5 76976,76977 1o54A 277 2.49e+00 c.66.1.13 92482 1i4fB 100 2.57e+00 1agdB b.1.1.2 61689 1fw1A 216 2.64e+00 a.45.1.1,c.47.1.5 60051,60052 1g4mA 393 2.70e+00 b.1.18.11,b.1.18.11 65143,65144 1x9uA 116 2.92e+00 1k5nB 100 2.97e+00 b.1.1.2 77268 1uvqA 197 3.02e+00 b.1.1.2,d.19.1.1 100062,100063 2d0oB 125 3.08e+00 2a1kA 233 3.11e+00 1n1tA 641 3.20e+00 b.29.1.15,b.68.1.1 79821,79822 1auvA 311 3.28e+00 1auvA c.30.1.5,d.142.1.3 31723,41558 1lr7A 74 3.37e+00 g.3.11.3,g.68.1.1 84679,84680 1m4jA 142 3.50e+00 d.109.1.2 78602 1mpp 361 3.62e+00 2rmpA b.50.1.2 26856 1c8uA 285 3.63e+00 1c8uA d.38.1.3,d.38.1.3 38547,38548 1q6hA 224 3.70e+00 d.26.1.1 95975 1j6qA 136 3.74e+00 b.40.9.1 77091 2bhgA 209 3.75e+00 2gfaA 119 3.81e+00 2b3gA 123 3.84e+00 2arpF 152 3.87e+00 1zeqX 84 4.00e+00 1mjc 69 4.11e+00 1mjc b.40.4.5 25319 1cv8 174 4.11e+00 1cv8 d.3.1.1 37089 2evbA 74 4.20e+00 1eaiC 61 4.27e+00 1eaiC g.22.1.1 44894 2akaA 776 4.34e+00 3tss 194 4.47e+00 1aw7A b.40.2.2,d.15.6.1 25160,37749 1i1qB 192 4.50e+00 1qdlB c.23.16.1 61544 1d4tA 104 4.54e+00 1d4tA d.93.1.1 40537 1tlyA 278 4.79e+00 f.4.6.1 107143 1hpi 71 4.86e+00 1ckuA g.35.1.1 44995 1vhsA 175 4.90e+00 d.108.1.1 100698 1iakA 199 4.91e+00 1iakA b.1.1.2,d.19.1.1 21625,38199 2fpeA 62 4.95e+00 2b5oA 402 4.99e+00 1ykwA 435 5.01e+00 2c26A 260 5.17e+00 1bcpD 110 5.21e+00 1bcpD b.40.2.1 25132 1u2xA 474 5.24e+00 c.72.1.3 107622 1yfnA 118 5.28e+00 1el6A 219 5.33e+00 1el6B d.182.1.1 42606 1v5vA 401 5.77e+00 1yu4A 381 5.78e+00 1apmE 350 5.83e+00 1cdkA d.144.1.7 41628 1o0wA 252 5.88e+00 a.149.1.1,d.50.1.1 80751,80752 1o7iA 119 5.97e+00 b.40.4.3 86642 1wj9A 211 6.00e+00 1n27A 96 6.06e+00 b.34.9.2 91549 1t0qC 86 6.20e+00 d.15.12.1 106222 1n2aA 201 6.25e+00 a.45.1.1,c.47.1.5 91553,91554 1cf1A 404 6.30e+00 1cf1A b.1.18.11,b.1.18.11 21907,21908 1m2rA 327 6.36e+00 d.144.1.7 84760 1gcqC 70 6.43e+00 1gcpA b.34.2.1 60436 1ieaA 192 6.64e+00 1iakA b.1.1.2,d.19.1.1 21631,38205 1bia 321 6.68e+00 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1dg6A 191 6.69e+00 1d4vB b.22.1.1 23883 1wy7A 207 6.96e+00 1b0uA 262 7.00e+00 1b0uA c.37.1.12 32370 1uyrA 737 7.24e+00 c.14.1.4,c.14.1.4 100188,100189 1t6lA 290 7.30e+00 d.131.1.2,d.131.1.2 106574,106575 2c4xA 260 7.34e+00 1k2eA 156 7.52e+00 d.113.1.1 72010 1pyaB 228 7.64e+00 1pyaB 1zlmA 58 7.72e+00 2aheA 267 7.72e+00 1iqaA 160 7.72e+00 b.22.1.1 71274 1is3A 135 7.73e+00 b.29.1.3 76773 1sluA 142 8.11e+00 1sluA b.16.1.1 23685 1n7oA 721 8.21e+00 a.102.3.2,b.24.1.1,b.30.5.2 80259,80260,80261 1yu3A 381 8.27e+00 1uowA 159 8.36e+00 b.7.1.2 107975 1vqoU 66 8.37e+00 1zt7A 276 8.48e+00 2b29A 123 8.51e+00 1bkb 136 8.52e+00 1bkb b.34.5.2,b.40.4.5 24609,25341 1yg9A 330 8.55e+00 2cvdA 198 8.60e+00 1vqoS 85 8.61e+00 1dfaA 454 8.68e+00 1vdeA b.86.1.2,d.95.2.2,d.95.2.2 28375,40575,40576 2bcoA 350 8.98e+00 1ze3D 125 9.08e+00 1iyhA 198 9.13e+00 a.45.1.1,c.47.1.5 83790,83791 1fsgA 233 9.19e+00 1qk3A c.61.1.1 34029 1khcA 147 9.30e+00 b.34.9.2 68608 2c1iA 431 9.32e+00 1wbpA 397 9.33e+00 1mgrA 99 9.43e+00 d.1.1.2 79106 1tjxA 159 9.44e+00 1vjlA 164 9.46e+00 d.257.1.1 100822 1txqA 93 9.48e+00 1go2A 304 9.57e+00 b.43.4.2,c.25.1.1 76243,76244 2f0aA 98 9.80e+00 2cw5A 255 9.85e+00 1w2xA 758 9.86e+00 c.14.1.4,c.14.1.4 109134,109135 2mcm 112 9.96e+00 2mcm b.1.7.1 22207 1xovA 326 1.00e+01 1wruA 379 1.00e+01 1a0fA 201 1.03e+01 1a0fA a.45.1.1,c.47.1.5 17737,33031 1z47A 355 1.05e+01 1yqfA 203 1.09e+01 4dpvZ 584 1.10e+01 2cas b.121.5.2 23377 1dkuA 317 1.11e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 2cvbA 188 1.13e+01 1yu1A 381 1.14e+01 1fjgL 135 1.15e+01 1fjfL b.40.4.5 25346 1yu0A 381 1.15e+01 2bsaA 303 1.15e+01 1yruA 364 1.17e+01 1hdmB 193 1.18e+01 1hdmB b.1.1.2,d.19.1.1 21584,38158 1yu2A 381 1.19e+01 1se8A 301 1.22e+01 b.40.4.3 105448 2b0vA 153 1.23e+01 1yrtA 364 1.26e+01 1ounA 127 1.26e+01 1ounA d.17.4.2 38090 1kjvB 100 1.27e+01 b.1.1.2 77423 1pk6C 129 1.29e+01 b.22.1.1 94803 1y8oB 128 1.30e+01 1ki0A 253 1.31e+01 g.14.1.1,g.14.1.1,g.14.1.1 72493,72494,72495 1br9 194 1.32e+01 1br9 b.40.3.1 25235 1qd9A 124 1.33e+01 1qu9A d.79.1.1 39758 1fzoB 99 1.37e+01 1agdB b.1.1.2 60157 1mo9A 523 1.37e+01 c.3.1.5,c.3.1.5,d.87.1.1 79341,79342,79343 1xqbA 247 1.38e+01 1x1mA 107 1.38e+01 2bfxA 284 1.39e+01 1c5yB 253 1.41e+01 5ptp 1v52A 133 1.43e+01 1om1A 332 1.43e+01 d.144.1.7 93347 1jj2R 84 1.43e+01 1ffkP d.12.1.1 63103 1yb3A 175 1.44e+01 1nlqA 108 1.44e+01 b.121.3.1 85853 2fytA 340 1.44e+01 1rdqE 350 1.45e+01 d.144.1.7 97314 1tdhA 364 1.45e+01 a.156.1.2,b.113.1.1,g.39.1.8 106772,106773,106774 2gf6A 135 1.46e+01 1s3rA 535 1.48e+01 1s72S 85 1.49e+01 d.12.1.1 105338 1vc3B 97 1.52e+01 1v88A 130 1.52e+01 b.55.1.1 108423 1gy6A 127 1.52e+01 d.17.4.2 70736 1xn5A 146 1.53e+01 1a78A 134 1.55e+01 1c1lA b.29.1.3 24212 1a8q 274 1.56e+01 1brt c.69.1.12 34702 1sz7A 200 1.57e+01 1w34A 304 1.58e+01 1w9iA 770 1.64e+01 1zn6A 227 1.65e+01 1je6A 275 1.66e+01 b.1.1.2,d.19.1.1 71638,71639 1uovA 159 1.67e+01 b.7.1.2 107974 1wh0A 134 1.68e+01 1tx4B 178 1.68e+01 1ctqA c.37.1.8 32045 1oxsC 353 1.68e+01 b.40.6.3,c.37.1.12 87519,87520 1lniA 96 1.69e+01 d.1.1.2 74046 1ktjA 129 1.71e+01 b.1.18.7 72974 1s55A 156 1.74e+01 1oxxK 353 1.76e+01 b.40.6.3,c.37.1.12 93715,93716 1wsrA 375 1.77e+01 2dg5A 366 1.77e+01 1j79A 347 1.81e+01 1j79A c.1.9.4 62675 1qavA 90 1.81e+01 1qauA b.36.1.1 24777 1sfp 114 1.83e+01 1sfp b.23.1.1 23895 1zx8A 136 1.83e+01 1kcmA 270 1.83e+01 d.129.3.4 72300 1o0pA 104 1.83e+01 d.58.7.1 86535 1r9hA 135 1.84e+01 d.26.1.1 97260 1shxA 138 1.85e+01 1f3lA 321 1.86e+01 1g6q2 c.66.1.6 59630 1ki1B 352 1.86e+01 a.87.1.1,b.55.1.1 72497,72498 1lxiA 139 1.88e+01 g.17.1.2 84735 1c9oA 66 1.92e+01 1mjc b.40.4.5 25325 2ak5A 64 1.94e+01 2aneA 125 1.94e+01 1x2kA 68 1.95e+01 2djkA 133 1.98e+01 1fzkB 99 1.99e+01 1agdB b.1.1.2 60151 1ogiA 303 2.00e+01 b.43.4.2,c.25.1.1 92914,92915 1rutX 188 2.01e+01 1bxvA 91 2.04e+01 1aac b.6.1.1 22875 1wwzA 159 2.09e+01 1ymiA 334 2.09e+01 1v70A 105 2.10e+01 2al3A 90 2.13e+01 1cm9A 74 2.14e+01 1b3aA d.9.1.1 37405 1bx1A 314 2.14e+01 1fnc b.43.4.2,c.25.1.1 25629,31519 1mq4A 272 2.15e+01 d.144.1.7 91391 1lk2B 99 2.16e+01 b.1.1.2 91058 1uw4A 91 2.21e+01 d.58.7.4 100071 1vyoA 128 2.22e+01 1ti6B 274 2.24e+01 b.3.5.1,d.58.1.5 106976,106977 1ozjA 144 2.28e+01 d.164.1.1 93846 1vkkA 154 2.28e+01 d.109.1.2 108669 1u4nA 310 2.33e+01 1k28D 391 2.34e+01 b.106.1.1,b.106.1.1 68052,68053 1vp6A 138 2.35e+01 1vcdA 126 2.35e+01 2aqjA 538 2.36e+01 1x9iA 302 2.36e+01 1jwiB 125 2.37e+01 d.169.1.1 67384 1w2lA 99 2.38e+01 1gj7B 253 2.40e+01 1gd8A 118 2.40e+01 d.188.1.1 60445 1tzbA 302 2.45e+01 c.80.1.1 107470 8prn 289 2.46e+01 3prn f.4.3.1 43767 1v6fA 151 2.46e+01 d.109.1.2 108395 1yhfA 115 2.48e+01 1y7xA 113 2.48e+01 1st9A 143 2.50e+01 c.47.1.10 98987 1nrgA 261 2.53e+01 b.45.1.1 80694 1u9yA 284 2.53e+01 2crvA 120 2.63e+01 1yrkA 126 2.65e+01 1tzaA 134 2.66e+01 b.1.23.1 107468 1d7qA 143 2.67e+01 1d7qA b.40.4.5 25331 1zotA 358 2.67e+01 1koe 172 2.67e+01 1koe d.169.1.5 42448 1i2aA 219 2.68e+01 e.24.1.1 90660 1j0hA 588 2.75e+01 b.1.18.2,b.71.1.1,c.1.8.1 77027,77028,77029 1xwsA 313 2.76e+01 1vavA 222 2.77e+01 b.29.1.18 108472 1vqoD 177 2.78e+01 1bdo 80 2.79e+01 1bdo b.84.1.1 28214 4pgaA 337 2.79e+01 4pgaA c.88.1.1 35565 2fikA 287 2.81e+01 1eguA 731 2.81e+01 1eguA a.102.3.2,b.24.1.1,b.30.5.2 18850,23899,24423 1x3lA 440 2.81e+01 1m4zA 238 2.83e+01 b.34.12.1 78630 1ltlA 279 2.85e+01 b.40.4.11 84701 1i7nA 309 2.86e+01 c.30.1.5,d.142.1.3 83681,83682 1mgqA 83 2.92e+01 b.38.1.1 79099 1fnc 314 2.93e+01 1fnc b.43.4.2,c.25.1.1 25627,31517 1fnd 314 2.93e+01 1fnc b.43.4.2,c.25.1.1 25626,31516 1tbuA 118 2.94e+01 1ae7 119 2.94e+01 1poa a.133.1.2 19553 1v3vA 333 2.96e+01 b.35.1.2,c.2.1.1 108345,108346 1rdg 53 2.99e+01 1rb9 g.41.5.1 45221 1u1zA 168 3.00e+01 d.38.1.6 107602 1xh9A 350 3.01e+01 1que 303 3.02e+01 1fnc b.43.4.2,c.25.1.1 25647,31537 1jj2T 66 3.04e+01 1ffkR g.39.1.6 63105 1s72U 66 3.04e+01 g.39.1.6 105340 1gtzA 156 3.04e+01 c.23.13.1 70539 1e87A 118 3.04e+01 1b6e d.169.1.1 42327 1fvuA 133 3.05e+01 1ixxB d.169.1.1 42345 1va0A 239 3.08e+01 1brwA 433 3.09e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1im3D 95 3.12e+01 1im3D b.1.18.5 62568 1f2eA 201 3.13e+01 1a0fA a.45.1.1,c.47.1.5 17745,33039 2c3gA 98 3.21e+01 1g94A 448 3.21e+01 b.71.1.1,c.1.8.1 65169,65170 2akrA 285 3.22e+01 1o20A 427 3.23e+01 c.82.1.1 86556 1n9eA 787 3.25e+01 b.30.2.1,d.17.2.1,d.17.2.1 91708,91709,91710 1te5A 257 3.25e+01 d.153.1.1 106795 1uscA 178 3.27e+01 b.45.1.2 99860 1trb 320 3.29e+01 1trb c.3.1.5,c.3.1.5 30529,30530 2f9sA 151 3.30e+01 1of5B 184 3.32e+01 d.17.4.2 86934 1mo7A 213 3.33e+01 d.220.1.1 85028 1ei1A 391 3.34e+01 1aj6 d.14.1.3,d.122.1.2 37570,41104 1zxuA 217 3.34e+01 1vom 762 3.36e+01 1lvk b.34.3.1,c.37.1.9 24577,32174 1v8hA 107 3.36e+01 2aukA 190 3.36e+01 1wgeA 83 3.37e+01 1ugmA 125 3.39e+01 d.15.1.3 107827 1ixh 321 3.39e+01 1ixh c.94.1.1 35761 1vazA 88 3.39e+01 d.245.1.1 100554 1wekA 217 3.44e+01 1shwA 138 3.45e+01 b.6.1.5 105562 1st0A 337 3.47e+01 d.13.1.3,d.246.1.1 98979,98980 1xxlA 239 3.48e+01 1ravA 127 3.50e+01 1swuA b.61.1.1 27409 1vq0A 302 3.50e+01 1wosA 364 3.54e+01 b.44.2.1,d.250.1.1 109468,109469 1t62A 166 3.55e+01 b.122.1.4 106541 1p1jA 533 3.56e+01 c.2.1.3,d.81.1.3 87687,87688 2cx1A 187 3.56e+01 1vkyA 347 3.58e+01 e.53.1.1 108696 1aiw 62 3.59e+01 1aiw b.72.2.1 27808 1f2tA 149 3.62e+01 1f2tA c.37.1.12 32373 1neu 124 3.64e+01 1neu b.1.1.1 19704 1inlA 296 3.65e+01 c.66.1.17 66220 1f86A 115 3.65e+01 1etb1 b.3.4.1 59689 1tygB 87 3.65e+01 d.15.3.2 107455 1iro 54 3.69e+01 1rb9 g.41.5.1 45223 1ihjA 98 3.70e+01 1pdr b.36.1.1 62382 1qfmA 710 3.70e+01 1qfmA b.69.7.1,c.69.1.4 27673,34641 1ej6B 1275 3.71e+01 i.7.1.1 45968 7taa 478 3.72e+01 7taa b.71.1.1,c.1.8.1 27778,28765 2arcA 164 3.74e+01 2arcA b.82.4.1 28148 2b5lC 222 3.76e+01 1mfgA 95 3.77e+01 b.36.1.1 79043 1ua4A 455 3.77e+01 c.72.1.3 99128 2bjuA 453 3.79e+01 1h0xA 100 3.91e+01 d.68.6.1 76451 2gdjA 264 3.97e+01 1ju3A 583 3.98e+01 b.18.1.13,c.69.1.21 67300,67301 1nepA 130 4.08e+01 b.1.18.7 80440 2f4qA 346 4.09e+01 1aqm 453 4.15e+01 1smd b.71.1.1,c.1.8.1 27717,28704 1vkbA 161 4.15e+01 d.269.1.1 108643 1pytA 94 4.15e+01 1pytA d.58.3.1 39064 1sr9A 644 4.18e+01 a.5.7.1,c.1.10.5,d.270.1.1 105960,105961,105962 1ghj 79 4.18e+01 1ghj b.84.1.1 28232 1wc9A 169 4.20e+01 1kjvA 284 4.21e+01 b.1.1.2,d.19.1.1 77421,77422 1ma3A 253 4.26e+01 c.31.1.5 78883 1ms9A 648 4.27e+01 b.29.1.15,b.68.1.1 85088,85089 1ok0A 74 4.32e+01 b.5.1.1 93191 1rds 105 4.33e+01 9rnt d.1.1.4 36236 1nddA 76 4.35e+01 1ubi d.15.1.1 37599 1zt2B 212 4.36e+01 1eyqA 222 4.38e+01 1eypA d.36.1.1 38534 2f4lA 297 4.44e+01 1d0iA 156 4.44e+01 2dhqA c.23.13.1 31383 1i4jA 110 4.46e+01 d.55.1.1 76734 2bjrA 368 4.47e+01 1za0A 275 4.49e+01 1x67A 146 4.54e+01 1ryt 190 4.55e+01 1ryt a.25.1.1,g.41.5.1 16646,45245 1z5lA 285 4.55e+01 1p65A 73 4.58e+01 d.254.1.1 94156 1i78A 297 4.60e+01 f.4.4.1 66046 2bc4B 211 4.66e+01 1bb9 115 4.70e+01 1bb9 b.34.2.1 24554 1cqxA 403 4.70e+01 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 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