# List of top-scoring protein chains for t04-100-30-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 2fe5A 94 2.82e-18 2fneA 117 1.44e-17 1g9oA 91 2.65e-17 1pdr b.36.1.1 60400 1qavA 90 3.52e-17 1qauA b.36.1.1 24777 1tp5A 119 3.96e-17 1be9A 119 7.81e-17 1pdr b.36.1.1 24774 2fcfA 103 8.65e-17 1n7eA 97 7.92e-16 b.36.1.1 91691 1n7fA 97 2.11e-15 b.36.1.1 91692 2h2bA 107 2.41e-15 1ihjA 98 2.96e-15 1pdr b.36.1.1 62382 1mfgA 95 6.55e-15 b.36.1.1 79043 1q3oA 109 7.08e-15 b.36.1.1 95700 1l6oA 95 9.37e-15 b.36.1.1 84534 2h3lA 103 1.56e-14 2f0aA 98 2.34e-14 1kwaA 88 5.84e-14 1kwaA b.36.1.1 24772 1nf3C 128 7.77e-14 b.36.1.1 85596 2f5yA 91 9.60e-14 1qauA 112 1.86e-13 1qauA b.36.1.1 24779 1wf7A 103 5.55e-13 1v5lA 103 3.03e-12 b.36.1.1 108378 1nteA 82 4.59e-12 b.36.1.1 86163 1r6jA 82 1.04e-11 b.36.1.1 97151 1fc6A 388 6.00e-08 1fc6A b.36.1.3,c.14.1.2 64738,64739 1lcyA 325 2.25e-07 b.36.1.4,b.47.1.1 73834,73835 1te0A 318 3.22e-07 1y8tA 324 5.41e-06 1sotA 320 3.26e-03 b.36.1.4,b.47.1.1 105852,105853 2brfA 110 2.12e-01 1yjmA 110 2.41e-01 1zn8A 180 4.07e-01 2d4pA 141 8.46e-01 2bshA 125 8.93e-01 2fe7A 166 1.00e+00 1f3z 161 1.11e+00 1gpr b.84.3.1 28273 1fxlA 167 1.22e+00 1b7fA d.58.7.1,d.58.7.1 39183,39184 1kk1A 410 1.32e+00 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 2bhoA 130 1.38e+00 1ad3A 452 1.58e+00 1ad3A c.82.1.1 35335 1yg9A 330 1.63e+00 2bw3A 534 1.73e+00 2bsjA 133 1.79e+00 1y9wA 140 2.06e+00 1r13A 148 2.09e+00 d.169.1.1,h.1.1.1 96782,96783 2gwnA 452 2.27e+00 2c5qA 240 2.38e+00 2fvgA 340 2.41e+00 1gpr 162 2.56e+00 1gpr b.84.3.1 28267 1qb7A 236 2.72e+00 1qb7A c.61.1.1 34087 1db3A 372 3.21e+00 1db3A c.2.1.2 29813 1mkmA 249 3.24e+00 a.4.5.33,d.110.2.2 79242,79243 2f4wA 187 3.43e+00 1rutX 188 3.44e+00 1xebA 150 3.57e+00 2bh8A 101 3.63e+00 1vj0A 380 3.75e+00 b.35.1.2,c.2.1.1 100786,100787 1t6t1 118 3.90e+00 1q52A 314 3.94e+00 c.14.1.3 95846 1g57A 217 4.13e+00 1g57A d.115.1.2 60253 1fdr 248 4.29e+00 1fdr b.43.4.2,c.25.1.1 25653,31543 1cliA 345 4.47e+00 1cliA d.79.4.1,d.139.1.1 39816,41459 1vc3B 97 4.48e+00 2bsyA 278 4.85e+00 1bo4A 168 5.11e+00 1bo4A d.108.1.1 40798 1a62 130 5.27e+00 1a62 a.140.3.1,b.40.4.5 64708,64709 1yvcA 70 5.53e+00 2adcA 229 5.62e+00 1hh1A 143 5.67e+00 1gefA c.52.1.18 61036 1ugmA 125 5.74e+00 d.15.1.3 107827 1vkmA 297 5.86e+00 c.138.1.1 108670 1yloA 348 5.88e+00 1x3mA 415 5.96e+00 1un8A 552 6.35e+00 c.119.1.2,a.208.1.1 103806,99661 1uheA 97 7.17e+00 1hvyA 288 7.24e+00 1bkpA d.117.1.1 41049 2f9dA 125 7.49e+00 1se8A 301 7.71e+00 b.40.4.3 105448 1jnyA 435 7.96e+00 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1o6dA 163 8.17e+00 c.116.1.3 92567 1p42A 270 8.20e+00 d.14.1.7,d.14.1.7 87754,87755 1a79A 171 8.48e+00 1a79A c.52.2.1,d.75.1.1 33340,39739 2agcA 162 8.67e+00 1h3gA 601 8.79e+00 b.1.18.2,b.71.1.1,c.1.8.1 90594,90595,90596 1sdjA 310 9.35e+00 d.21.1.2,d.21.1.2 98807,98808 1o63A 219 9.64e+00 c.94.1.1 92540 2polA 366 9.65e+00 2polA d.131.1.1,d.131.1.1,d.131.1.1 41356,41357,41358 1vheA 373 9.70e+00 b.49.3.1,c.56.5.4 100669,100670 2avtA 378 9.78e+00 1xewX 182 1.02e+01 1ltlA 279 1.04e+01 b.40.4.11 84701 1xnzA 264 1.09e+01 2ggcA 263 1.10e+01 2g8oA 264 1.10e+01 1c24A 263 1.11e+01 1c24A d.127.1.1 41148 1a8vA 121 1.13e+01 1a62 a.140.3.1,b.40.4.5 64712,64713 2g8mA 264 1.14e+01 1evfA 264 1.16e+01 1bkpA d.117.1.1 40932 1y0gA 191 1.17e+01 1uc2A 481 1.18e+01 d.261.1.1 99161 1qqqA 264 1.19e+01 1bkpA d.117.1.1 40931 1g8aA 227 1.19e+01 c.66.1.3 90506 1ok7A 366 1.20e+01 d.131.1.1,d.131.1.1,d.131.1.1 103992,103993,103994 1rxxA 421 1.23e+01 d.126.1.4 98061 1yezA 68 1.29e+01 1w94A 156 1.30e+01 1cq3A 233 1.32e+01 1cq3A b.27.1.1 23923 1tllA 688 1.38e+01 b.43.4.1,c.23.5.2,c.25.1.4 107128,107129,107130 3fib 249 1.38e+01 3fib d.171.1.1 42455 2fl4A 149 1.38e+01 2awaA 390 1.38e+01 1hzdA 272 1.39e+01 c.14.1.3 65969 1cauB 184 1.45e+01 1caxB b.82.1.2 28103 1fr3A 67 1.46e+01 1fr3A b.40.6.1 25436 1p7tA 731 1.47e+01 c.1.13.1 94319 1ypvA 313 1.48e+01 1wpgA 994 1.49e+01 1ym5A 300 1.50e+01 2fibA 269 1.52e+01 3fib d.171.1.1 42457 1g2qA 187 1.54e+01 c.61.1.1 65117 1lnzA 342 1.56e+01 b.117.1.1,c.37.1.8 78112,78113 1y791 680 1.56e+01 2affA 120 1.56e+01 1ujxA 119 1.57e+01 b.26.1.2 99473 2c0cA 362 1.58e+01 2bs3A 656 1.58e+01 1qyaA 307 1.59e+01 d.21.1.2,d.21.1.2 104653,104654 2b3hA 329 1.62e+01 1q5xA 161 1.62e+01 c.8.7.1 95947 1s0uA 408 1.64e+01 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 1yqfA 203 1.71e+01 1qlaA 656 1.72e+01 1qlaA a.7.3.1,c.3.1.4,d.168.1.1 16328,30427,42310 1ikpA 613 1.74e+01 b.29.1.7,d.166.1.1,f.1.5.1 66182,66183,66184 1whi 122 1.77e+01 1whi b.39.1.1 24810 1nm1G 125 1.85e+01 d.109.1.1 80653 1xdnA 277 1.89e+01 1mmiA 366 1.94e+01 d.131.1.1,d.131.1.1,d.131.1.1 91309,91310,91311 1nulA 152 1.96e+01 1nulA c.61.1.1 34011 1d4xG 126 1.99e+01 1d0nA d.109.1.1 59109 2aefA 234 2.00e+01 1euwA 152 2.00e+01 1dupA b.85.4.1 28349 1q2yA 140 2.02e+01 d.108.1.1 95655 1t44G 147 2.03e+01 d.109.1.1 106395 1dy9A 187 2.11e+01 1jxpA b.47.1.3 26400 1c9oA 66 2.11e+01 1mjc b.40.4.5 25325 1koe 172 2.12e+01 1koe d.169.1.5 42448 1g7sA 594 2.13e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 1k32A 1045 2.18e+01 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 68068,68069,68070,68071 2d8aA 348 2.18e+01 2fb5A 205 2.20e+01 1o50A 157 2.21e+01 d.37.1.1,d.37.1.1 92478,92479 1oq1A 223 2.21e+01 b.29.1.17 93408 1dg6A 191 2.24e+01 1d4vB b.22.1.1 23883 1hw7A 255 2.28e+01 1i7fA d.193.1.1 61297 1xfoA 357 2.38e+01 1bx4A 345 2.39e+01 1bx4A c.72.1.1 34935 2a19A 175 2.41e+01 1fxrA 64 2.45e+01 1fxd d.58.1.4 38993 1xs1A 193 2.48e+01 2cy2A 174 2.56e+01 2cu5A 129 2.63e+01 2f51A 118 2.65e+01 1fm0E 150 2.71e+01 1fmaE d.41.5.1 38629 1jmuB 666 2.71e+01 1vraB 215 2.72e+01 1d8cA 723 2.73e+01 1d8cA c.1.13.1 29325 1qzzA 374 2.76e+01 a.4.5.29,c.66.1.12 96719,96720 1f20A 435 2.77e+01 b.43.4.1,c.25.1.4 64932,64933 1y0yA 353 2.79e+01 1w30A 201 2.79e+01 1fy7A 278 2.90e+01 1fy7A d.108.1.1 40817 2cxaA 256 2.92e+01 1h30A 422 2.96e+01 b.29.1.4,b.29.1.4 76604,76605 1r0vA 305 3.02e+01 c.52.2.1,c.52.2.1,d.75.1.1 96742,96743,96744 1lw6I 64 3.07e+01 d.40.1.1 74294 1ttwA 138 3.10e+01 d.198.1.1 107308 1td5A 202 3.12e+01 d.110.2.2 106767 1bywA 110 3.15e+01 1bywA d.110.3.6 40912 1r26A 125 3.16e+01 c.47.1.1 96847 1wwzA 159 3.16e+01 1tiqA 180 3.20e+01 d.108.1.1 107010 1kolA 398 3.23e+01 b.35.1.2,c.2.1.1 77474,77475 1mo1A 87 3.23e+01 d.94.1.1 91363 1z4eA 153 3.30e+01 1aac 105 3.30e+01 1aac b.6.1.1 22838 1bxaA 105 3.31e+01 1aac b.6.1.1 22839 1y07A 128 3.31e+01 1y0bA 197 3.35e+01 1uadC 99 3.40e+01 b.1.18.18 88379 1vkcA 158 3.41e+01 1jxpA 186 3.41e+01 1jxpA b.47.1.3 26402 1yhfA 115 3.44e+01 1vhxA 150 3.47e+01 c.55.3.8 100712 1u09A 476 3.48e+01 e.8.1.4 107545 2anuA 255 3.49e+01 1zh5A 195 3.49e+01 1su4A 994 3.51e+01 b.82.7.1,c.108.1.7,d.220.1.1,f.33.1.1 98993,98994,98995,98996 1ti6A 875 3.52e+01 b.52.2.2,c.81.1.1 106974,106975 1ifyA 49 3.53e+01 a.5.2.1 71207 1ema 236 3.62e+01 1ema d.22.1.1 38339 1suuA 312 3.63e+01 b.68.10.1 99006 1t9fA 187 3.64e+01 b.42.6.1 106710 1h8eA 510 3.65e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 60738,60739,60740 1qsmA 152 3.72e+01 1qsmA d.108.1.1 40808 1e5xA 486 3.72e+01 c.79.1.1 59283 1o12A 376 3.73e+01 b.92.1.5,c.1.9.10 80758,80759 1aw8B 91 3.74e+01 1aw8B 1kssA 571 3.77e+01 a.138.1.3,c.3.1.4,d.168.1.1 72928,72929,72930 1e39A 571 3.79e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19694,30431,42314 1tzfA 259 3.79e+01 c.68.1.13 107476 1nkqA 259 3.96e+01 d.177.1.1 103862 1s1qA 145 3.98e+01 d.20.1.2 98351 1zkkA 167 4.02e+01 1to2I 64 4.03e+01 1l1qA 186 4.09e+01 c.61.1.1 77653 1s29A 92 4.10e+01 a.4.5.46 98373 1eexA 554 4.10e+01 1dioA c.1.19.3 29650 1x6oA 174 4.10e+01 b.34.5.2,b.40.4.5 109493,109494 1y0pA 571 4.14e+01 1p2hA 571 4.14e+01 a.138.1.3,c.3.1.4,d.168.1.1 93930,93931,93932 1epwA 1290 4.15e+01 b.29.1.6,b.42.4.2,d.92.1.7,h.4.2.1 24269,25614,40305,45785 1q9iA 571 4.15e+01 a.138.1.3,c.3.1.4,d.168.1.1 96273,96274,96275 1l7bA 92 4.18e+01 c.15.1.2 91053 1h9oA 112 4.20e+01 1qadA d.93.1.1 60837 1mvwB 145 4.20e+01 i.15.1.1 79524 1oalA 151 4.21e+01 b.1.8.1 86739 1sflA 238 4.22e+01 1mq7A 154 4.24e+01 b.85.4.1 79404 1iz5A 249 4.25e+01 d.131.1.2,d.131.1.2 83834,83835 1fjgQ 105 4.25e+01 1fjfQ b.40.4.5 25352 1kw4A 89 4.28e+01 a.60.1.2 73077 1eulA 994 4.30e+01 1eulA 1omyA 65 4.36e+01 g.3.7.1 93354 1od5A 492 4.41e+01 b.82.1.2,b.82.1.2 86832,86833 1r62A 160 4.44e+01 d.122.1.3 104816 1zczA 464 4.45e+01 1v5wA 343 4.52e+01 c.37.1.11 108387 1y7lA 316 4.53e+01 2gu2A 312 4.54e+01 1kmvA 186 4.55e+01 c.71.1.1 72757 1fbnA 230 4.57e+01 1fbnA c.66.1.3 34181 1eso 154 4.57e+01 1yaiA b.1.8.1 22293 1vi4A 174 4.66e+01 c.8.7.1 100731 1y7rA 133 4.67e+01 1uc7A 125 4.83e+01 c.47.1.1 99163 1a8p 258 4.85e+01 1fdr b.43.4.2,c.25.1.1 25654,31544 1rwzA 245 4.85e+01 d.131.1.2,d.131.1.2 98005,98006 1uzcA 71 4.85e+01 a.159.2.1 100222 1pzxA 289 4.89e+01 c.119.1.1 95484 1g8sA 230 4.89e+01 c.66.1.3 90507 1um0A 365 4.90e+01 d.258.1.1 107942 1kt6A 183 4.93e+01 b.60.1.1 84466 2iu4A 336 5.03e+01 2cvdA 198 5.09e+01 1ppfE 218 5.19e+01 1a7s b.47.1.2 26234 2bnjA 303 5.20e+01 1lvoA 302 5.22e+01 b.47.1.4 74284 1sfdA 105 5.23e+01 b.6.1.1 105480 1e79A 510 5.25e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18269,26434,32314 1ojhA 65 5.28e+01 a.214.1.1 103976 1ji0A 240 5.29e+01 c.37.1.12 71665 1wvcA 259 5.32e+01 2atrA 138 5.41e+01 1u0mA 382 5.43e+01 c.95.1.2,c.95.1.2 107557,107558 1llnA 262 5.43e+01 d.165.1.1 84625 2hc1A 291 5.47e+01 1v93A 296 5.48e+01 c.1.23.1 100532 2cwaA 263 5.49e+01 1pqhA 143 5.59e+01 b.52.2.1 95017 1zsyA 357 5.69e+01 1o9yA 84 5.79e+01 b.139.1.1 92692 1cskA 71 5.79e+01 1ckaA b.34.2.1 24513 1s3zA 165 5.80e+01 d.108.1.1 105250 1iyhA 198 5.85e+01 a.45.1.1,c.47.1.5 83790,83791 1i52A 236 5.91e+01 1i52A c.68.1.13 61767 2ck3A 510 5.91e+01 1htrB 329 5.91e+01 1smrA 1vplA 256 5.93e+01 1vmeA 410 5.95e+01 c.23.5.1,d.157.1.3 108893,108894 2h03A 291 5.98e+01 2cyjA 118 6.01e+01 1iieA 75 6.02e+01 1iieA a.109.1.1 19039 1w07A 659 6.06e+01 1l0bA 229 6.11e+01 c.15.1.3,c.15.1.3 73391,73392 1sw5A 275 6.17e+01 c.94.1.1 106069 1e0tA 470 6.19e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 1o91A 178 6.24e+01 b.22.1.1 92656 1wyzA 242 6.26e+01 2aaiB 262 6.30e+01 1abrB b.42.2.1,b.42.2.1 25561,25562 2a19B 284 6.31e+01 1w9gA 104 6.35e+01 1js8A 394 6.39e+01 a.86.1.1,b.112.1.1 67219,67220 1l2mA 118 6.40e+01 d.89.1.4 77657 1zh1A 163 6.41e+01 2fwhA 134 6.43e+01 1sfjA 238 6.44e+01 2bkfA 87 6.45e+01 2bh1A 250 6.52e+01 1g31A 111 6.59e+01 1g31A b.35.1.1 24656 1y43B 173 6.61e+01 1n0qA 93 6.66e+01 k.37.1.1 79754 1gtmA 419 6.70e+01 1hwyA c.2.1.7,c.58.1.1 30223,33871 1ze3H 122 6.72e+01 1q1rA 431 6.73e+01 c.3.1.5,c.3.1.5,d.87.1.1 95600,95601,95602 1t3qB 788 6.74e+01 d.41.1.1,d.133.1.1 106369,106370 1avaC 181 6.74e+01 1avaC b.42.4.1 25604 1viuA 203 6.91e+01 d.113.1.1 100771 1aqb 183 6.93e+01 1aqb b.60.1.1 27084 1j71A 334 7.00e+01 1eagA b.50.1.2 62669 2fhqA 141 7.03e+01 1qunB 279 7.04e+01 b.2.3.2,b.2.3.2 22411,22412 1lw7A 365 7.04e+01 c.26.1.3,c.37.1.1 74295,74296 1bb9 115 7.07e+01 1bb9 b.34.2.1 24554 1u9yA 284 7.09e+01 2a6tA 271 7.09e+01 1e9xA 455 7.15e+01 1ea1A a.104.1.1 18969 1bkzA 135 7.21e+01 1a3k b.29.1.3 24202 1olmA 403 7.23e+01 a.5.3.1,b.132.1.1,c.13.1.1 104008,104009,104010 1zhhB 242 7.25e+01 1s4iA 175 7.26e+01 1u13A 455 7.27e+01 a.104.1.1 107578 1fjrA 195 7.29e+01 1fjrA b.102.1.1 59855 1k0rA 366 7.29e+01 b.40.4.5,d.52.3.1,d.52.3.1,d.202.1.1 67961,67962,67963,67964 1klfB 279 7.36e+01 b.2.3.2,b.2.3.2 72684,72685 1k8mA 93 7.39e+01 b.84.1.1 68314 2f6uA 234 7.41e+01 1l1dA 152 7.43e+01 b.88.1.3 73452 1uh5A 329 7.44e+01 c.2.1.2 107840 1v61A 132 7.44e+01 b.55.1.1 108389 1id2A 106 7.45e+01 1aac b.6.1.1 62288 2c9wA 169 7.46e+01 1sv6A 269 7.47e+01 d.177.1.1 106043 1mjc 69 7.48e+01 1mjc b.40.4.5 25319 1y9kA 157 7.49e+01 1qsoA 149 7.51e+01 1qsmA d.108.1.1 40812 1z90A 469 7.55e+01 1lkkA 105 7.55e+01 1lckA d.93.1.1 40412 1wvqA 167 7.58e+01 1pvmA 184 7.59e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1xwsA 313 7.68e+01 1y8oB 128 7.69e+01 1x8vA 455 7.69e+01 2f6rA 281 7.72e+01 1h72C 296 7.75e+01 d.14.1.5,d.58.26.1 60712,60713 1vzoA 355 7.84e+01 d.144.1.7 108971 1z96A 40 7.89e+01 1yb3A 175 7.97e+01 2ahqA 76 8.00e+01 1shdA 107 8.03e+01 1fmk d.93.1.1 40440 1i1wA 303 8.08e+01 c.1.8.3 76732 1rypH 205 8.10e+01 d.153.1.4 41876 1eyqA 222 8.14e+01 1eypA d.36.1.1 38534 1fxkC 133 8.15e+01 1fxkC a.2.5.1 15702 1vybA 238 8.15e+01 d.151.1.1 108897 1o4rA 108 8.17e+01 d.93.1.1 92469 2cw8A 537 8.27e+01 1mlcB 218 8.29e+01 1igtB b.1.1.1,b.1.1.2 20053,21095 1o6uA 403 8.34e+01 a.5.3.1,b.132.1.1,c.13.1.1 92589,92590,92591 2ghpA 292 8.46e+01 1a58 177 8.56e+01 2cpl b.62.1.1 27495 1yp2A 451 8.62e+01 1wvhA 134 8.67e+01 1shbA 104 8.70e+01 1fmk d.93.1.1 40425 1zclA 180 8.70e+01 1ex2A 189 8.72e+01 1ex2A c.51.4.2 33225 1h5zA 455 8.78e+01 a.104.1.1 90622 1reqB 637 8.78e+01 1reqB c.1.19.1,c.23.6.1 29621,31248 1opr 213 8.79e+01 1opr c.61.1.1 34091 1kkcA 221 8.82e+01 a.2.11.1,d.44.1.1 68660,68661 1rlhA 173 8.85e+01 d.256.1.1 97646 1nqjA 119 8.91e+01 b.23.2.1 86031 1uwfA 158 8.94e+01 1vdmA 153 8.94e+01 1xx6A 191 8.95e+01 1iq8A 582 8.97e+01 c.1.20.1,b.122.1.1,d.17.6.1 71270,83074,83075