# List of top-scoring protein chains for t06-100-30-str2-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 2fneA 117 2.65e-17 2fe5A 94 3.03e-17 2fcfA 103 5.47e-17 1qavA 90 1.29e-16 1qauA b.36.1.1 24777 1g9oA 91 1.51e-16 1pdr b.36.1.1 60400 1tp5A 119 3.11e-16 2h2bA 107 7.42e-16 1q3oA 109 1.07e-15 b.36.1.1 95700 1n7eA 97 2.94e-15 b.36.1.1 91691 1n7fA 97 1.29e-14 b.36.1.1 91692 1ihjA 98 1.79e-14 1pdr b.36.1.1 62382 1kwaA 88 1.90e-14 1kwaA b.36.1.1 24772 1nf3C 128 3.51e-14 b.36.1.1 85596 2f0aA 98 4.50e-14 2f5yA 91 7.26e-14 2h3lA 103 7.57e-14 1qauA 112 7.63e-14 1qauA b.36.1.1 24779 1mfgA 95 8.63e-14 b.36.1.1 79043 1wf7A 103 2.44e-13 1r6jA 82 9.30e-13 b.36.1.1 97151 1fc6A 388 1.61e-09 1fc6A b.36.1.3,c.14.1.2 64738,64739 1lcyA 325 9.37e-08 b.36.1.4,b.47.1.1 73834,73835 1te0A 318 1.26e-07 1y8tA 324 2.85e-06 1zn8A 180 1.47e-01 1kk1A 410 6.59e-01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 2d4pA 141 8.70e-01 1fxlA 167 1.17e+00 1b7fA d.58.7.1,d.58.7.1 39183,39184 1xebA 150 1.23e+00 1h3gA 601 1.30e+00 b.1.18.2,b.71.1.1,c.1.8.1 90594,90595,90596 1vqqA 646 1.37e+00 1jmuB 666 1.39e+00 1k32A 1045 1.46e+00 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 68068,68069,68070,68071 2bsjA 133 1.60e+00 1mkmA 249 1.86e+00 a.4.5.33,d.110.2.2 79242,79243 1vj0A 380 1.87e+00 b.35.1.2,c.2.1.1 100786,100787 2bsyA 278 1.91e+00 2bhoA 130 1.91e+00 1se8A 301 2.10e+00 b.40.4.3 105448 1o6dA 163 2.14e+00 c.116.1.3 92567 2c5qA 240 2.35e+00 2brfA 110 2.40e+00 1qb7A 236 2.56e+00 1qb7A c.61.1.1 34087 1t6t1 118 2.58e+00 2a19A 175 2.61e+00 2bh8A 101 2.69e+00 1hh1A 143 2.83e+00 1gefA c.52.1.18 61036 1yvcA 70 2.89e+00 1y9wA 140 3.34e+00 1avaC 181 3.35e+00 1avaC b.42.4.1 25604 1x3mA 415 4.30e+00 1g57A 217 4.36e+00 1g57A d.115.1.2 60253 2fa1A 160 4.47e+00 1bx4A 345 4.70e+00 1bx4A c.72.1.1 34935 1fr3A 67 4.78e+00 1fr3A b.40.6.1 25436 1ugmA 125 5.07e+00 d.15.1.3 107827 2gwnA 452 5.12e+00 1yloA 348 5.32e+00 1vkmA 297 5.72e+00 c.138.1.1 108670 2cu5A 129 7.22e+00 1ti6A 875 7.57e+00 b.52.2.2,c.81.1.1 106974,106975 1y791 680 7.80e+00 1g8aA 227 8.07e+00 c.66.1.3 90506 2aefA 234 8.21e+00 1p2hA 571 8.32e+00 a.138.1.3,c.3.1.4,d.168.1.1 93930,93931,93932 1yqfA 203 8.90e+00 1cq3A 233 8.92e+00 1cq3A b.27.1.1 23923 1jnyA 435 8.94e+00 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1uc2A 481 9.15e+00 d.261.1.1 99161 2fxqA 264 9.44e+00 2fe7A 166 9.47e+00 1rutX 188 9.58e+00 1kv7A 488 9.89e+00 b.6.1.3,b.6.1.3,b.6.1.3 68873,68874,68875 1a62 130 1.01e+01 1a62 a.140.3.1,b.40.4.5 64708,64709 1yy6A 155 1.09e+01 1g2qA 187 1.12e+01 c.61.1.1 65117 1eexA 554 1.15e+01 1dioA c.1.19.3 29650 2bs3A 656 1.18e+01 1tif 78 1.22e+01 1tif d.15.8.1 37836 1vhxA 150 1.24e+01 c.55.3.8 100712 1bdfA 235 1.25e+01 1bdfA d.74.3.1,d.181.1.1 39727,42602 1htrB 329 1.36e+01 1smrA 1uzvA 114 1.38e+01 1yg9A 330 1.45e+01 1yllA 200 1.47e+01 2f4wA 187 1.48e+01 1vc3B 97 1.49e+01 1koe 172 1.54e+01 1koe d.169.1.5 42448 1yhfA 115 1.57e+01 2d8aA 348 1.62e+01 1w99A 558 1.65e+01 1yqyA 523 1.66e+01 2bw3A 534 1.70e+01 2fojA 155 1.70e+01 1whi 122 1.71e+01 1whi b.39.1.1 24810 1o6aA 96 1.77e+01 b.139.1.1 92562 1to2I 64 1.82e+01 1r62A 160 1.82e+01 d.122.1.3 104816 1v8yA 170 1.92e+01 1uheA 97 1.92e+01 1fjrA 195 1.94e+01 1fjrA b.102.1.1 59855 1gvhA 396 1.95e+01 a.1.1.2,b.43.4.2,c.25.1.5 70601,70602,70603 1zh5A 195 1.95e+01 1wvhA 134 1.97e+01 1f20A 435 1.98e+01 b.43.4.1,c.25.1.4 64932,64933 2fvgA 340 2.01e+01 1p0fA 373 2.01e+01 b.35.1.2,c.2.1.1 87642,87643 1w94A 156 2.01e+01 1sfp 114 2.06e+01 1sfp b.23.1.1 23895 1zn6A 227 2.06e+01 1g7sA 594 2.10e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 2avtA 378 2.12e+01 1trb 320 2.15e+01 1trb c.3.1.5,c.3.1.5 30529,30530 2fhqA 141 2.27e+01 1p7tA 731 2.27e+01 c.1.13.1 94319 1fdr 248 2.27e+01 1fdr b.43.4.2,c.25.1.1 25653,31543 1xdnA 277 2.28e+01 1zhhB 242 2.31e+01 1cliA 345 2.31e+01 1cliA d.79.4.1,d.139.1.1 39816,41459 1ym5A 300 2.34e+01 1i1wA 303 2.35e+01 c.1.8.3 76732 1s98A 107 2.35e+01 b.124.1.1 105377 1vkcA 158 2.37e+01 1kw4A 89 2.39e+01 a.60.1.2 73077 1h72C 296 2.40e+01 d.14.1.5,d.58.26.1 60712,60713 1r31A 428 2.45e+01 d.58.20.1,d.179.1.1 96897,96898 1tvgA 153 2.46e+01 2abwA 227 2.47e+01 1o50A 157 2.51e+01 d.37.1.1,d.37.1.1 92478,92479 1q52A 314 2.53e+01 c.14.1.3 95846 1qzzA 374 2.55e+01 a.4.5.29,c.66.1.12 96719,96720 1h2bA 359 2.59e+01 b.35.1.2,c.2.1.1 90543,90544 1s29A 92 2.60e+01 a.4.5.46 98373 2gdjA 264 2.61e+01 1y0bA 197 2.64e+01 2iu4A 336 2.67e+01 1l0bA 229 2.74e+01 c.15.1.3,c.15.1.3 73391,73392 1tygB 87 2.76e+01 d.15.3.2 107455 1vie 62 2.76e+01 1vie b.34.4.1 24592 1n8kA 374 2.78e+01 b.35.1.2,c.2.1.1 80298,80299 2f51A 118 2.80e+01 1lk2B 99 2.81e+01 b.1.1.2 91058 3gcb 470 2.84e+01 3gcb d.3.1.1 37032 1ypvA 313 2.89e+01 1g6hA 257 2.92e+01 1gajA c.37.1.12 60318 1mngA 203 2.96e+01 1avmA a.2.11.1,d.44.1.1 15776,38701 1uc7A 125 2.97e+01 c.47.1.1 99163 1ikpA 613 2.99e+01 b.29.1.7,d.166.1.1,f.1.5.1 66182,66183,66184 1d4oA 184 2.99e+01 1d4oA c.31.1.4 31748 1vjyA 303 3.07e+01 d.144.1.7 108633 1g31A 111 3.09e+01 1g31A b.35.1.1 24656 1x47A 98 3.09e+01 1zsyA 357 3.10e+01 1v93A 296 3.13e+01 c.1.23.1 100532 1gutA 68 3.13e+01 b.40.6.1 65576 2f4iA 197 3.14e+01 1xtmA 175 3.16e+01 1npuA 117 3.19e+01 b.1.1.1 92038 1uwfA 158 3.22e+01 1h8eA 510 3.22e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 60738,60739,60740 1aozA 552 3.28e+01 1aozA b.6.1.3,b.6.1.3,b.6.1.3 23124,23125,23126 1zh1A 163 3.28e+01 1aop 497 3.33e+01 2aop d.58.36.1,d.58.36.1,d.134.1.1,d.134.1.1 39501,39502,41425,41426 1y07A 128 3.37e+01 2ghpA 292 3.37e+01 1cjaA 342 3.37e+01 1cjaA d.144.1.3 41708 1ta3B 303 3.39e+01 c.1.8.3 106732 1yb3A 175 3.39e+01 1iyhA 198 3.39e+01 a.45.1.1,c.47.1.5 83790,83791 1fl2A 310 3.43e+01 1hyuA c.3.1.5,c.3.1.5 59869,59870 1llnA 262 3.45e+01 d.165.1.1 84625 1mo1A 87 3.48e+01 d.94.1.1 91363 2fwhA 134 3.50e+01 1wbiA 129 3.51e+01 2f9dA 125 3.54e+01 2apr 325 3.54e+01 2er7E b.50.1.2 26819 2cvdA 198 3.55e+01 2a6tA 271 3.56e+01 1hw7A 255 3.57e+01 1i7fA d.193.1.1 61297 2a9gA 418 3.61e+01 1vplA 256 3.63e+01 1eyqA 222 3.64e+01 1eypA d.36.1.1 38534 2awkA 228 3.65e+01 1f8fA 371 3.67e+01 b.35.1.2,c.2.1.1 83246,83247 1fm0E 150 3.79e+01 1fmaE d.41.5.1 38629 1l1qA 186 3.80e+01 c.61.1.1 77653 1suuA 312 3.82e+01 b.68.10.1 99006 2g8oA 264 3.82e+01 1s4iA 175 3.88e+01 1tul 108 3.90e+01 1tul b.85.5.1 28373 1n7oA 721 3.92e+01 a.102.3.2,b.24.1.1,b.30.5.2 80259,80260,80261 2g8mA 264 3.94e+01 1h9oA 112 3.96e+01 1qadA d.93.1.1 60837 1mkkA 96 3.98e+01 g.17.1.1 79240 1u3wA 374 3.98e+01 1olmA 403 3.99e+01 a.5.3.1,b.132.1.1,c.13.1.1 104008,104009,104010 1zkpA 268 4.01e+01 1fjgQ 105 4.02e+01 1fjfQ b.40.4.5 25352 1dq3A 454 4.03e+01 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1amm 174 4.05e+01 1amm b.11.1.1,b.11.1.1 23587,23588 2anuA 255 4.06e+01 1u09A 476 4.07e+01 e.8.1.4 107545 1qb5D 99 4.08e+01 b.40.2.1 88357 1vqvA 306 4.10e+01 1rypH 205 4.21e+01 d.153.1.4 41876 2f6uA 234 4.23e+01 1nnxA 109 4.31e+01 b.40.10.1 92013 1wjuA 100 4.32e+01 1l2tA 235 4.33e+01 c.37.1.12 73514 1nziA 159 4.35e+01 b.23.1.1,g.3.11.1 86449,86450 1p42A 270 4.35e+01 d.14.1.7,d.14.1.7 87754,87755 1z85A 234 4.38e+01 1vraB 215 4.40e+01 1y55X 126 4.43e+01 2gm5A 139 4.43e+01 1q3iA 214 4.45e+01 d.220.1.1 104524 1nqjA 119 4.52e+01 b.23.2.1 86031 1qqqA 264 4.52e+01 1bkpA d.117.1.1 40931 1lvaA 258 4.53e+01 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 1l1dA 152 4.60e+01 b.88.1.3 73452 1dxrH 258 4.61e+01 6prcH b.41.1.1,f.23.10.1 25456,43433 2fpmA 322 4.62e+01 1t9fA 187 4.63e+01 b.42.6.1 106710 1rypB 250 4.64e+01 1rypB d.153.1.4 41933 1o59A 355 4.65e+01 b.18.1.22,b.18.1.22 92495,92496 1l5aA 436 4.66e+01 c.43.1.2,c.43.1.2 75923,75924 1c9oA 66 4.68e+01 1mjc b.40.4.5 25325 1wyzA 242 4.71e+01 2ceyA 306 4.74e+01 1l7aA 318 4.74e+01 c.69.1.25 77772 1ojhA 65 4.77e+01 a.214.1.1 103976 1xtoA 311 4.85e+01 1t44G 147 4.86e+01 d.109.1.1 106395 1pzxA 289 4.89e+01 c.119.1.1 95484 2ae0X 345 4.90e+01 1kmvA 186 4.90e+01 c.71.1.1 72757 1t3qB 788 4.91e+01 d.41.1.1,d.133.1.1 106369,106370 1tt7A 330 4.96e+01 2f1lA 187 4.97e+01 1j1lA 290 5.00e+01 b.82.1.12 90766 1bg4 302 5.02e+01 1taxA c.1.8.3 28806 2ckiA 262 5.11e+01 2atrA 138 5.12e+01 2ck3A 510 5.13e+01 1z96A 40 5.13e+01 1qwrA 319 5.17e+01 b.82.1.3 96491 1khiA 176 5.21e+01 b.34.5.2,b.40.4.5 77408,77409 2bhgA 209 5.26e+01 2cxaA 256 5.33e+01 1d4xG 126 5.35e+01 1d0nA d.109.1.1 59109 1qsmA 152 5.36e+01 1qsmA d.108.1.1 40808 1zdnA 158 5.43e+01 1vybA 238 5.44e+01 d.151.1.1 108897 1hgxA 183 5.47e+01 1tc1A c.61.1.1 34027 1mk4A 157 5.49e+01 d.108.1.1 84979 1zkkA 167 5.54e+01 2ahqA 76 5.69e+01 1oh4A 179 5.81e+01 b.18.1.18 92978 1j9lA 247 5.82e+01 c.106.1.1 62762 1vzyA 291 5.95e+01 2gaeA 346 6.03e+01 1u8vA 490 6.05e+01 1a2yB 116 6.06e+01 1gc1H b.1.1.1 19927 1vheA 373 6.07e+01 b.49.3.1,c.56.5.4 100669,100670 1sflA 238 6.15e+01 1rrmA 386 6.19e+01 e.22.1.2 105081 1on0A 158 6.24e+01 d.108.1.1 87095 2cb4A 291 6.27e+01 1iieA 75 6.36e+01 1iieA a.109.1.1 19039 1j5wA 298 6.39e+01 d.104.1.1 71589 2c6cA 707 6.43e+01 2bolA 314 6.46e+01 2d9bA 109 6.47e+01 1s1dA 331 6.56e+01 b.67.3.1 98344 1n0qA 93 6.58e+01 k.37.1.1 79754 1wl4A 397 6.71e+01 1smxA 96 6.78e+01 b.40.4.5 105772 1e0tA 470 6.80e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 1e7uA 961 6.81e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 1gnuA 117 6.93e+01 d.15.1.3 65403 1gtmA 419 6.93e+01 1hwyA c.2.1.7,c.58.1.1 30223,33871 1zm8A 259 6.98e+01 1yqbA 100 7.08e+01 2fb5A 205 7.08e+01 1m65A 245 7.09e+01 c.6.3.1 84847 1y44A 320 7.14e+01 1bouA 139 7.20e+01 1bouA a.88.1.1 18521 2fl4A 149 7.22e+01 2b5gA 171 7.32e+01 1oqvA 192 7.44e+01 d.24.1.2 87320 1ex2A 189 7.44e+01 1ex2A c.51.4.2 33225 1v9yA 167 7.52e+01 d.110.3.2 108454 1z4rA 168 7.53e+01 2ai4A 119 7.58e+01 1f35A 162 7.63e+01 1f35A b.94.1.1 59628 1i8dA 213 7.74e+01 b.43.4.3,b.43.4.3 61953,61954 2aj7A 163 7.78e+01 1umzA 278 7.81e+01 b.29.1.2 99639 1earA 147 7.83e+01 b.107.1.1,d.58.38.1 64875,64876 1o8bA 219 7.89e+01 c.124.1.4,d.58.40.1 81180,81181 1gu7A 364 7.89e+01 b.35.1.2,c.2.1.1 83321,83322 1ze3H 122 7.93e+01 2cw8A 537 7.98e+01 2gshA 414 7.99e+01 1qahA 136 7.99e+01 d.79.1.1 96338 1xewX 182 7.99e+01 2cc0A 195 8.02e+01 1siqA 392 8.03e+01 a.29.3.1,e.6.1.1 105585,105586 1xtqA 177 8.06e+01 1k7iA 479 8.09e+01 b.80.7.1,d.92.1.6 77281,77282 1rypI 222 8.11e+01 d.153.1.4 41877 1n6aA 259 8.13e+01 b.76.2.1,b.85.7.1 80121,80122 1cqxA 403 8.16e+01 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 1kl9A 182 8.20e+01 b.40.4.5 72681 2btzA 394 8.20e+01 1bywA 110 8.22e+01 1bywA d.110.3.6 40912 1g2hA 61 8.23e+01 1g2hA a.4.1.12 60224 1iukA 140 8.41e+01 c.2.1.8 83712 1rxdA 159 8.41e+01 1u2cA 246 8.43e+01 b.1.6.2,d.272.1.1 107610,107611 1vpqA 273 8.56e+01 2g6fX 59 8.58e+01 1wvqA 167 8.59e+01 1xs1A 193 8.65e+01 2b3hA 329 8.70e+01 1g6sA 427 8.71e+01 1eps d.68.2.2 39584 1bu6O 501 8.82e+01 1glcG c.55.1.4,c.55.1.4 33499,33500 1xg0A 76 8.84e+01 1uylA 236 8.88e+01 d.122.1.1 108147 1wckA 220 8.93e+01 2axwA 134 8.94e+01 1iz5A 249 8.97e+01 d.131.1.2,d.131.1.2 83834,83835 2beiA 170 8.98e+01