# List of top-scoring protein chains for t06-100-30-alpha-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 1lam 484 1.43e-71 1lam c.50.1.1,c.56.5.3 33166,33829 1h1yA 228 5.22e-02 c.1.2.2 76506 1tkjA 284 7.44e-02 1pn0A 665 7.82e-02 c.3.1.2,c.47.1.10,d.16.1.2 94918,94919,94920 1qq9A 284 8.15e-02 1xjo c.56.5.4 33841 1lrzA 426 8.27e-02 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 2fliA 220 2.78e-01 1tqxA 227 3.55e-01 1tqjA 230 4.11e-01 c.1.2.2 107228 1x13A 401 5.21e-01 1iloA 77 6.01e-01 c.47.1.1 66205 1nm2A 317 6.50e-01 c.19.1.1,d.58.23.1 80654,80655 1cjcA 460 9.05e-01 1cjcA c.3.1.1,c.4.1.1 30319,30604 1wcgA 464 1.05e+00 1uz5A 402 1.42e+00 b.85.6.1,b.103.1.1,c.57.1.2 100217,100218,100219 1v71A 323 1.45e+00 1ua4A 455 1.46e+00 c.72.1.3 99128 2f06A 144 1.55e+00 1xnzA 264 1.62e+00 1jztA 246 1.62e+00 c.104.1.1 63319 1gc0A 398 1.66e+00 c.67.1.3 70168 1li4A 432 1.71e+00 c.2.1.4,c.23.12.3 84616,84617 1o4tA 133 1.72e+00 b.82.1.9 86622 1g8iA 190 1.73e+00 1rec a.39.1.5 60363 1z0sA 278 1.73e+00 1g57A 217 2.02e+00 1g57A d.115.1.2 60253 1spvA 184 2.11e+00 c.50.1.2 98957 1rifA 282 2.17e+00 c.37.1.23 97507 1xd8A 289 2.27e+00 1efvB 255 2.74e+00 1efvB c.26.2.3 31634 3prn 289 3.26e+00 3prn f.4.3.1 43761 2gdzA 267 3.30e+00 1q6uA 245 3.33e+00 d.26.1.1 95998 1s5jA 847 3.70e+00 2fswA 107 3.83e+00 1wy1A 172 3.86e+00 1ulyA 192 3.93e+00 1gpjA 404 4.05e+00 a.151.1.1,c.2.1.7,d.58.39.1 65451,65452,65453 1q6hA 224 4.22e+00 d.26.1.1 95975 1v8bA 479 4.47e+00 1qusA 322 4.50e+00 1ltm d.2.1.6 36991 1kw3B 292 4.61e+00 d.32.1.3,d.32.1.3 77549,77550 1vkwA 218 4.73e+00 d.90.1.2 108695 1gqeA 365 4.81e+00 e.38.1.1 70351 2etvA 346 4.88e+00 1evsA 187 5.19e+00 1evsA a.26.1.1 16845 1p99A 295 5.48e+00 c.94.1.1 94384 1l2tA 235 5.91e+00 c.37.1.12 73514 1zjcA 418 5.94e+00 2ex4A 241 5.94e+00 1pvvA 315 6.15e+00 c.78.1.1,c.78.1.1 95190,95191 1yh1A 359 6.30e+00 1omrA 201 6.31e+00 a.39.1.5 93349 1p5zB 263 6.35e+00 c.37.1.1 87815 1x9dA 538 6.42e+00 1p7tA 731 6.60e+00 c.1.13.1 94319 1nq6A 302 6.64e+00 c.1.8.3 92046 1o0xA 262 6.71e+00 d.127.1.1 80755 1syyA 346 6.71e+00 a.25.1.2 106126 1lkdA 297 6.84e+00 d.32.1.3,d.32.1.3 78059,78060 1qxyA 252 6.89e+00 d.127.1.1 96565 1suwA 249 6.94e+00 e.52.1.1 106027 1oxwA 373 6.95e+00 c.19.1.3 87539 1m48A 133 6.98e+00 a.26.1.2 74443 1wrvA 308 7.00e+00 1xxaA 78 7.14e+00 1xxaA d.74.2.1 39700 1ve1A 304 7.60e+00 1r2jA 366 7.75e+00 a.29.3.1,e.6.1.1 96869,96870 1oaoC 729 7.80e+00 e.26.1.3 86746 1n46A 258 8.03e+00 a.123.1.1 85315 1x79A 98 8.69e+00 1n0wA 243 8.70e+00 c.37.1.11 79772 1h8eA 510 8.95e+00 1skyB a.69.1.1,b.49.1.1,c.37.1.11 60738,60739,60740 1fqtA 112 9.02e+00 1fqtA b.33.1.1 24441 1jcfA 344 9.25e+00 c.55.1.1,c.55.1.1 62878,62879 1cp2A 269 1.02e+01 1cp2A c.37.1.10 32269 1j24A 143 1.05e+01 c.52.1.20 84008 1i4fA 275 1.06e+01 1agdA b.1.1.2,d.19.1.1 61687,61688 2eu9A 355 1.08e+01 1wyxA 69 1.08e+01 1x6mA 196 1.09e+01 2ck3A 510 1.13e+01 1vhuA 211 1.17e+01 c.50.1.2 100703 1jysA 242 1.17e+01 c.56.2.1 77216 1squA 155 1.18e+01 d.252.1.1 98971 1f4pA 147 1.21e+01 5nul c.23.5.1 59651 1zq6A 359 1.21e+01 1cg2A 393 1.26e+01 1cg2A c.56.5.4,d.58.19.1 33844,39360 1w68A 390 1.27e+01 a.25.1.2 109216 1dpe 507 1.27e+01 1dpe c.94.1.1 35799 1nfp 228 1.28e+01 1nfp c.1.16.2 29555 1kyhA 276 1.29e+01 c.72.1.4 73222 1cxyA 90 1.33e+01 1cyo d.120.1.1 41085 2bjvA 265 1.33e+01 3daaA 277 1.34e+01 1daaA e.17.1.1 43272 1gk9A 260 1.36e+01 d.153.1.2 65246 1pieA 419 1.36e+01 d.14.1.5,d.58.26.7 94706,94707 1h5wA 309 1.37e+01 e.27.1.1 65635 1o20A 427 1.37e+01 c.82.1.1 86556 1pvtA 238 1.38e+01 c.74.1.1 95189 1tqhA 247 1.38e+01 c.69.1.29 107225 1jmvA 141 1.39e+01 c.26.2.4 66897 1rtqA 299 1.39e+01 c.56.5.4 97819 1qcsA 211 1.41e+01 1qcsA b.52.2.3,d.31.1.1 26927,38461 1vl4A 447 1.45e+01 d.283.1.1 108718 2c07A 285 1.47e+01 1fvpA 231 1.48e+01 1nfp c.1.16.2 29556 1utiA 58 1.49e+01 b.34.2.1 99962 2fh5A 185 1.54e+01 1wmhB 86 1.57e+01 1utyA 187 1.59e+01 b.147.1.1 108036 1in4A 334 1.64e+01 1hqcA a.4.5.11,c.37.1.20 62597,62598 1i1rB 181 1.66e+01 1i1rB a.26.1.1 61548 1khdA 345 1.69e+01 a.46.2.1,c.27.1.1 77400,77401 1pt6A 213 1.70e+01 c.62.1.1 95091 2frnA 278 1.74e+01 1fm0E 150 1.79e+01 1fmaE d.41.5.1 38629 1ihgA 370 1.82e+01 2cpl a.118.8.1,b.62.1.1 62380,62381 1vctA 205 1.83e+01 1iwmA 186 1.84e+01 b.125.1.2 83758 1s98A 107 1.84e+01 b.124.1.1 105377 1rt8A 513 1.86e+01 a.40.1.1 105095 1womA 271 1.86e+01 1el5A 389 1.88e+01 1b3mA c.3.1.2,d.16.1.3 30369,37937 1s28A 132 1.91e+01 d.198.1.1 105223 1yemA 179 1.98e+01 1vjvA 415 2.02e+01 d.3.1.9 108632 1m0uA 249 2.03e+01 a.45.1.1,c.47.1.5 78359,78360 1n6zA 105 2.04e+01 d.263.1.1 85369 1vjqA 79 2.06e+01 k.43.1.1 100830 1q35A 320 2.08e+01 c.94.1.1 95661 1xi1A 575 2.12e+01 1c8cA 64 2.14e+01 1azpA b.34.13.1 59084 2c1iA 431 2.14e+01 1qkmA 255 2.16e+01 3erdA a.123.1.1 19309 2eryA 172 2.22e+01 1vkfA 188 2.24e+01 c.1.29.1 108656 1krhA 338 2.24e+01 b.43.4.2,c.25.1.2,d.15.4.2 72891,72892,72893 2bbhA 269 2.26e+01 1rypH 205 2.26e+01 d.153.1.4 41876 1ks9A 291 2.28e+01 a.100.1.7,c.2.1.6 68857,68858 2d5cA 263 2.29e+01 1vclA 432 2.37e+01 b.42.2.1,b.42.2.1,d.281.1.1 108498,108499,108500 1ul7A 102 2.39e+01 d.129.6.1 99540 1x99A 145 2.39e+01 2gsq 202 2.41e+01 1pd21 a.45.1.1,c.47.1.5 17715,33009 1o08A 221 2.44e+01 c.108.1.6 86525 1vjpA 394 2.44e+01 c.2.1.3,d.81.1.3 100828,100829 1in6A 334 2.44e+01 1hqcA a.4.5.11,c.37.1.20 62601,62602 1e19A 314 2.46e+01 1b7bA c.73.1.1 34967 1vk3A 615 2.55e+01 d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 100846,100847,100848,100849 2ajrA 331 2.60e+01 1d2vC 466 2.64e+01 1mhlC 1nh1A 330 2.64e+01 e.45.1.1 91871 2bswA 146 2.64e+01 1jx4A 352 2.65e+01 d.240.1.1,e.8.1.7 90378,90379 1j4aA 333 2.68e+01 c.2.1.4,c.23.12.1 71502,71503 1qnrA 344 2.69e+01 1qnoA c.1.8.3 28834 1yeyA 444 2.72e+01 1unlD 208 2.73e+01 1r7mA 235 2.74e+01 1q2lA 939 2.75e+01 1evlA 401 2.79e+01 1qf6A c.51.1.1,d.104.1.1 33202,40751 1hqz1 141 2.83e+01 1t6cA 315 2.85e+01 c.55.1.8,c.55.1.8 106558,106559 2cxhA 217 2.86e+01 1svsA 353 2.91e+01 c.37.1.8 106051 1sviA 195 2.92e+01 c.37.1.8 106048 1b00A 127 2.94e+01 3chy c.23.1.1 31122 1wy2A 351 2.97e+01 2b3hA 329 3.04e+01 1uanA 227 3.07e+01 c.134.1.1 99135 1sbzA 197 3.09e+01 1qwoA 442 3.11e+01 c.60.1.2 104620 1wr2A 238 3.13e+01 1n8jA 186 3.14e+01 c.47.1.10 85401 2tpsA 227 3.19e+01 2tpsA c.1.3.1 28591 1ysjA 404 3.22e+01 2fd5A 180 3.26e+01 2cwxA 430 3.28e+01 1scfA 273 3.31e+01 1exzA a.26.1.2 16873 1l3iA 192 3.32e+01 c.66.1.22 77676 1ea5A 537 3.33e+01 2bce c.69.1.1 34592 1i60A 278 3.35e+01 c.1.15.4 71118 1s8nA 205 3.38e+01 c.23.1.1 105374 1gs5A 258 3.47e+01 c.73.1.2 70395 1lfwA 470 3.49e+01 c.56.5.4,d.58.19.1 77942,77943 1u2kA 309 3.49e+01 1w9hA 427 3.53e+01 1g291 372 3.53e+01 1g291 1jjtA 228 3.55e+01 1a7tA d.157.1.1 63139 1eu3A 210 3.56e+01 1an8 b.40.2.2,d.15.6.1 25206,37795 1t9hA 307 3.59e+01 1yf2A 425 3.60e+01 1yqyA 523 3.71e+01 1l8nA 679 3.73e+01 c.1.8.10,d.92.2.2 84564,84565 1zjrA 211 3.75e+01 2rslA 140 3.78e+01 2rslA c.53.1.1 33345 1h5uA 842 3.80e+01 1a8i c.87.1.4 60655 2apjA 260 3.82e+01 1cipA 353 3.86e+01 1cipA a.66.1.1,c.37.1.8 18210,32093 1wq3A 322 3.88e+01 2g1uA 155 3.92e+01 1uhvA 500 3.93e+01 b.71.1.2,c.1.8.3 99402,99403 1hm6A 346 3.95e+01 1avc a.65.1.1 18147 1mslA 109 3.95e+01 1mslA f.16.1.1 43660 1xppA 115 3.97e+01 2ashA 381 3.97e+01 2fsqA 243 4.00e+01 1ki1B 352 4.06e+01 a.87.1.1,b.55.1.1 72497,72498 1musA 477 4.12e+01 c.55.3.4 79494 1yqdA 366 4.15e+01 1augA 215 4.15e+01 1a2zA c.56.4.1 33798 2b0aA 186 4.24e+01 2ilk 160 4.27e+01 2ilk a.26.1.3 16885 1a41 234 4.32e+01 1a41 d.163.1.2 42174 1to6A 371 4.33e+01 c.141.1.1 107170 2exnA 136 4.33e+01 1zzmA 259 4.36e+01 1nfvA 179 4.43e+01 a.25.1.1 85642 1g73A 162 4.48e+01 1fewA a.7.4.1 16332 1kq3A 376 4.53e+01 e.22.1.2 68790 1nnwA 252 4.54e+01 d.159.1.5 80674 1tbaA 67 4.56e+01 1tbaA a.15.1.1 16380 2gh1A 301 4.58e+01 1td6A 306 4.59e+01 1dbiA 280 4.60e+01 1gci c.41.1.1 32543 1iyeA 309 4.62e+01 e.17.1.1 83786 1kbvA 327 4.64e+01 b.6.1.3,b.6.1.3 68395,68396 2cxnA 557 4.66e+01 1o4vA 183 4.68e+01 c.23.8.1 86628 1u0fA 564 4.69e+01 1xqoA 256 4.69e+01 1vmaA 306 4.70e+01 a.24.13.1,c.37.1.10 108887,108888 1ru3A 732 4.74e+01 e.26.1.3 97835 1pjvA 32 4.79e+01 g.3.7.2 94792 1o97C 264 4.79e+01 c.26.2.3 81232 1m6sA 347 4.81e+01 c.67.1.1 78701 1ymiA 334 4.83e+01 2b4lA 268 4.84e+01 2fiqA 420 4.86e+01 1n7kA 234 4.88e+01 c.1.10.1 85374 1ja1A 622 4.94e+01 1amoA b.43.4.1,c.23.5.2,c.25.1.4 62803,62804,62805 1g8pA 350 4.97e+01 1g8pA c.37.1.20 60376 1ash 150 4.98e+01 1ash a.1.1.2 15622 1tm9A 137 4.99e+01 a.225.1.1 107150 2ew0A 192 5.03e+01 1x9iA 302 5.07e+01 1s6cA 183 5.07e+01 a.39.1.5 98594 1h05A 146 5.08e+01 c.23.13.1 76433 1hh1A 143 5.14e+01 1gefA c.52.1.18 61036 1sd4A 126 5.16e+01 a.4.5.39 105428 1lngA 87 5.19e+01 d.201.1.1 74045 1qnaA 200 5.23e+01 1ytbA d.129.1.1,d.129.1.1 41226,41227 1xwvA 129 5.26e+01 1php 394 5.27e+01 16pk c.86.1.1 35452 1fvuA 133 5.31e+01 1ixxB d.169.1.1 42345 1ub0A 258 5.33e+01 c.72.1.2 88394 1jm1A 204 5.33e+01 b.33.1.1 71745 1zlqA 502 5.36e+01 1wj2A 78 5.36e+01 1ufbA 127 5.38e+01 a.24.16.3 99331 1g2bA 62 5.39e+01 1tud b.34.2.1 24488 1yd0A 96 5.44e+01 2fk8A 318 5.47e+01 1rqbA 539 5.50e+01 a.5.7.2,c.1.10.5 105057,105058 2arcA 164 5.51e+01 2arcA b.82.4.1 28148 1xl7A 612 5.56e+01 1m0dA 138 5.57e+01 c.52.1.17 74354 2gauA 232 5.61e+01 2mcm 112 5.69e+01 2mcm b.1.7.1 22207 1wznA 252 5.71e+01 1w23A 360 5.73e+01 1i4mA 108 5.77e+01 d.6.1.1 66025 1ry9A 145 5.79e+01 d.198.1.1 98094 1zxtA 76 5.79e+01 1euvA 221 5.85e+01 1euvA d.3.1.7 37133 1wl8A 189 5.88e+01 1ct9A 553 5.96e+01 1ct9A c.26.2.1,d.153.1.1 31616,41834 2anuA 255 5.97e+01 1x67A 146 5.98e+01 2b8eA 273 5.99e+01 1w0mA 226 5.99e+01 c.1.1.1 109027 1h65A 270 6.03e+01 c.37.1.8 65640 2bgkA 278 6.18e+01 1cyx 205 6.18e+01 1cyx b.6.1.2 23023 1ec7A 446 6.20e+01 1bqg c.1.11.2,d.54.1.1 29218,38862 1wdyA 285 6.20e+01 1h2eA 207 6.36e+01 c.60.1.1 70857 1cnv 299 6.43e+01 1cnv c.1.8.5 28989 1za0A 275 6.43e+01 1xo0A 324 6.45e+01 1hhnA 101 6.47e+01 1hhnA b.104.1.1 61043 1twfB 1224 6.51e+01 1sbxA 106 6.57e+01 a.6.1.4 105414 1xteA 154 6.60e+01 1qwzA 235 6.60e+01 b.100.1.1 96510 1sfsA 240 6.61e+01 c.1.8.8 98846 1uf5A 303 6.63e+01 d.160.1.2 107808 2d69A 430 6.71e+01 1ufaA 520 6.71e+01 a.8.3.3,c.6.2.4 99329,99330 1vhwA 253 6.73e+01 c.56.2.1 100706 1ustA 93 6.83e+01 a.4.5.13 99884 1nv8A 284 6.87e+01 c.66.1.30 86224 2fflA 756 6.91e+01 1dkuA 317 6.93e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 1mo9A 523 6.93e+01 c.3.1.5,c.3.1.5,d.87.1.1 79341,79342,79343 1smbA 154 6.94e+01 d.111.1.1 105756 1l1lA 739 7.00e+01 c.7.1.4 73470 1pa4A 116 7.02e+01 d.52.7.1 94409 1uxjA 309 7.02e+01 c.2.1.5,d.162.1.1 108112,108113 1vjlA 164 7.05e+01 d.257.1.1 100822 1ytvA 366 7.07e+01 1bea 127 7.13e+01 1bea a.52.1.2 17826 1ay7B 89 7.15e+01 1ay7B c.9.1.1 30836 2pii 112 7.16e+01 2pii d.58.5.1 39071 1vmeA 410 7.18e+01 c.23.5.1,d.157.1.3 108893,108894 1u04A 771 7.21e+01 b.34.14.1,c.55.3.10 107539,107540 1fgyA 127 7.26e+01 1faoA b.55.1.1 26976 1hs6A 611 7.26e+01 1hs6A a.118.1.7,b.98.1.1,d.92.1.13 61233,61234,61235 1y60A 169 7.30e+01 1y10A 407 7.30e+01 1oheA 348 7.39e+01 c.45.1.1,c.45.1.1 87013,87014 2g7lA 243 7.39e+01 1ydiA 263 7.39e+01 1ppjG 81 7.41e+01 f.23.13.1 104263 1vkyA 347 7.42e+01 e.53.1.1 108696 1ep3B 262 7.43e+01 1ep2B b.43.4.2,c.25.1.3 25664,31554 1vicA 262 7.45e+01 c.68.1.13 100756 1ohvA 472 7.46e+01 c.67.1.4 93031 1m5iA 125 7.46e+01 h.4.13.1 78648 1zb9A 143 7.47e+01 1m1nB 522 7.50e+01 c.92.2.3 78418 1xvaA 292 7.50e+01 1xvaA c.66.1.5 34183 1wqgA 185 7.56e+01 1yqfA 203 7.56e+01 2aaxA 275 7.57e+01 1j09A 468 7.65e+01 a.97.1.1,c.26.1.1 77025,77026 1vkcA 158 7.67e+01 1yzyA 413 7.71e+01 1atzA 189 7.77e+01 1atzA c.62.1.1 34132 1hw7A 255 7.79e+01 1i7fA d.193.1.1 61297 1wjgA 137 7.89e+01 1y80A 210 7.91e+01 1nf3A 195 7.92e+01 c.37.1.8 85594 2a1fA 247 7.95e+01 1pu1A 94 7.99e+01 d.266.1.1 104307 1wkbA 810 8.01e+01 1ywnA 316 8.01e+01 2bi7A 384 8.06e+01 1y51A 88 8.15e+01 1ohlA 342 8.18e+01 c.1.10.3 87035 1neiA 60 8.18e+01 d.253.1.1 91843 1l8bA 190 8.19e+01 d.86.1.1 73683 1vljA 407 8.20e+01 e.22.1.2 108832 1twfC 318 8.23e+01 2azwA 148 8.25e+01 1n1fA 159 8.25e+01 a.26.1.3 79803 1tksA 204 8.26e+01 d.115.1.2 107114 1sznA 417 8.26e+01 b.71.1.1,c.1.8.1 106162,106163 1ky3A 182 8.27e+01 c.37.1.8 73193 1vp8A 201 8.27e+01 2bvlA 543 8.29e+01 1xqwA 293 8.31e+01 2ajtA 500 8.35e+01 1f1gA 154 8.37e+01 b.1.8.1 76153 1vr6A 350 8.38e+01 1bn7A 294 8.40e+01 1bn6A c.69.1.8 34677 1wrrA 301 8.45e+01 2gi3A 476 8.48e+01 2ag4A 164 8.50e+01 1uvqA 197 8.52e+01 b.1.1.2,d.19.1.1 100062,100063 2d13A 227 8.55e+01 1tzyD 103 8.57e+01 a.22.1.1 107533 1wmsA 177 8.58e+01 c.37.1.8 109414 1azsA 220 8.60e+01 1azsA d.58.29.1 39416 1sqsA 242 8.64e+01 c.23.5.5 98968 1othA 321 8.65e+01 1othA c.78.1.1,c.78.1.1 35260,35261 2avdA 219 8.67e+01 2b8nA 429 8.73e+01 1k3sA 113 8.79e+01 d.198.1.1 68120 1bif 469 8.80e+01 1bif c.37.1.7,c.60.1.4 31961,34003 1v1dA 31 8.80e+01 1lm8C 96 8.80e+01 d.42.1.1 74034 1zthA 258 8.84e+01 1k5nA 276 8.87e+01 b.1.1.2,d.19.1.1 77266,77267 2bu3A 254 8.89e+01 1yz7A 188 8.90e+01 2a6cA 83 8.93e+01