# List of top-scoring protein chains for t2k-100-30-alpha 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 1x23A 155 4.94e-41 1z2uA 150 8.90e-41 2ayvA 166 2.36e-40 1y6lA 149 3.29e-39 1jbbA 153 1.77e-36 1u9aA d.20.1.1 62842 2bepA 159 3.70e-36 1u9aA 160 3.72e-36 1u9aA d.20.1.1 38333 1jatA 155 6.10e-36 1u9aA d.20.1.1 62818 2ucz 165 7.10e-36 1u9aA d.20.1.1 38330 1yh2A 175 8.00e-36 1fzyA 149 9.00e-36 d.20.1.1 65072 2e2c 156 1.09e-35 1u9aA d.20.1.1 38336 1fxtA 149 7.49e-35 d.20.1.1 65055 1i7kA 179 2.08e-34 1u9aA d.20.1.1 61889 1zdnA 158 1.26e-33 1yh6A 179 8.61e-33 1yrvA 169 1.55e-31 1yf9A 171 4.67e-31 2awfA 172 2.73e-30 1wzvA 155 4.93e-30 2a4dA 160 1.61e-26 1j7dA 145 1.43e-25 1jatB d.20.1.1 62680 1jatB 138 3.85e-25 1jatB d.20.1.1 62819 1zuoA 186 2.05e-17 1s1qA 145 7.60e-06 d.20.1.2 98351 1kppA 145 1.16e-05 d.20.1.2 72846 1uzxA 169 2.21e-05 d.20.1.2 100238 1tgoA 773 3.52e-02 1tgoA c.55.3.5 33721 e.8.1.1 43010 1ywzA 175 6.53e-02 1qhtA 775 1.82e-01 1tgoA c.55.3.5 33722 e.8.1.1 43011 1qqcA 773 1.88e-01 1tgoA c.55.3.5 33724 e.8.1.1 43013 2ac5A 316 2.07e-01 1ukxA 137 2.16e-01 d.20.1.3 107919 2ac3A 316 2.38e-01 1ks8A 433 2.38e-01 a.102.1.2 77519 1eyvA 156 3.61e-01 1eyvA a.79.1.1 18446 2es9A 115 4.10e-01 2biiA 424 4.89e-01 1who 96 6.47e-01 1who b.7.3.1 23215 2auaA 224 6.76e-01 1bihA 395 6.79e-01 1bihA b.1.1.4 21752 b.1.1.4 21753 b.1.1.4 21754 b.1.1.4 21755 1h3oB 76 8.60e-01 a.22.1.3 76645 1jpzA 473 9.00e-01 a.104.1.1 67069 1xaoA 121 9.03e-01 1nekC 129 1.12e+00 f.21.2.2 80431 6gsvA 217 1.21e+00 1b8xA a.45.1.1 17633 c.47.1.5 32925 1winA 143 1.27e+00 1eqfA 280 1.42e+00 1eqfA a.29.2.1 16972 a.29.2.1 16973 1gaxA 862 1.50e+00 1gaxA a.2.7.3 75842 a.27.1.1 75843 b.51.1.1 26893 c.26.1.1 31595 1iynA 295 1.88e+00 a.93.1.1 90722 1srqA 341 2.13e+00 e.55.1.1 105967 1c3cA 429 2.53e+00 1c3cA a.127.1.1 19425 1kbhB 59 2.69e+00 a.153.1.1 68383 2bnxA 386 2.73e+00 1x8vA 455 2.76e+00 1d8hA 311 3.02e+00 1d8iA d.63.1.1 39544 1ccg 291 3.11e+00 1ryc a.93.1.1 18627 1bu7A 455 3.24e+00 1bu7A a.104.1.1 18937 1b2pA 119 3.41e+00 1b2pA b.78.1.1 27998 2cyp 294 3.51e+00 1ryc a.93.1.1 18600 1ryc 294 3.56e+00 1ryc a.93.1.1 18601 1vj7A 393 3.59e+00 a.211.1.1 100801 d.218.1.8 100802 2bzvA 181 3.81e+00 2bzuA 181 3.86e+00 1wloA 136 3.96e+00 1kb9F 74 4.05e+00 f.28.1.1 77321 1dseA 292 4.08e+00 1ryc a.93.1.1 59130 1kb9D 246 4.11e+00 a.3.1.3 77317 f.23.11.1 77318 1y4wA 518 4.16e+00 1mkrA 294 4.29e+00 a.93.1.1 84997 1xx1A 285 4.33e+00 1kyoD 248 4.34e+00 a.3.1.3 73254 f.23.11.1 73255 1ny9A 143 4.35e+00 a.181.1.1 86401 1ezvD 245 4.52e+00 1be3D a.3.1.3 59546 f.23.11.1 59547 1ds4A 292 4.56e+00 1ryc a.93.1.1 59129 1zbyA 294 4.90e+00 1z53A 294 4.95e+00 1jdrA 294 5.21e+00 1ryc a.93.1.1 62908 1cdy 178 5.24e+00 1cdy b.1.1.1 19719 b.1.1.3 21658 1vfaB 116 5.30e+00 1gc1H b.1.1.1 19929 1d8iA 311 5.40e+00 1d8iA d.63.1.1 39541 1ffyA 917 5.55e+00 1qu2A a.27.1.1 16926 b.51.1.1 26891 c.26.1.1 31593 1qu2A 917 5.55e+00 1qu2A a.27.1.1 16925 b.51.1.1 26890 c.26.1.1 31592 1nu5A 370 5.68e+00 c.1.11.2 92183 d.54.1.1 92184 1i8kB 124 5.82e+00 b.1.1.1 71131 2b1yA 104 6.16e+00 1s5jA 847 6.19e+00 1f6fB 210 6.21e+00 1axiB b.1.2.1 22033 b.1.2.1 22034 1h5zA 455 6.44e+00 a.104.1.1 90622 1bp3B 211 6.48e+00 1axiB b.1.2.1 22031 b.1.2.1 22032 2bmhA 455 6.51e+00 1bu7A a.104.1.1 18941 1g7jB 116 6.67e+00 1f3rB b.1.1.1 19933 1a2yB 116 6.78e+00 1gc1H b.1.1.1 19927 1go3E 187 7.32e+00 b.40.4.5 83054 d.230.1.1 83055 1uu1A 335 7.40e+00 c.67.1.1 99993 1g9mC 185 7.41e+00 1cdy b.1.1.1 19721 b.1.1.3 21660 1otkA 249 7.44e+00 a.25.1.2 93521 1u13A 455 7.87e+00 a.104.1.1 107578 1htrB 329 8.04e+00 1smrA 1vhzA 198 8.04e+00 d.113.1.1 100718 1ezvH 74 8.12e+00 1be3H f.28.1.1 59552 1z2cB 383 8.38e+00 1h3fA 432 9.53e+00 c.26.1.1 76631 d.66.1.4 76632 1rtwA 220 9.71e+00 a.132.1.3 97823 1kkjA 419 9.80e+00 c.67.1.4 72647 1chrA 370 9.87e+00 1mucA c.1.11.2 29252 d.54.1.1 38896 1lvmA 229 1.00e+01 b.47.1.3 78243 1itkA 731 1.06e+01 a.93.1.3 71417 a.93.1.3 71418 1fm2A 169 1.06e+01 1fm2A d.153.1.2 59877 1o5oA 221 1.07e+01 c.61.1.1 92509 1iapA 211 1.09e+01 a.91.1.1 62119 1kl1A 419 1.10e+01 c.67.1.4 72663 1xszA 356 1.10e+01 1qnrA 344 1.15e+01 1qnoA c.1.8.3 28834 1jk0A 419 1.15e+01 a.25.1.2 63142 1fg7A 356 1.16e+01 1gewA c.67.1.1 59819 2a4nA 182 1.18e+01 1v54A 514 1.20e+01 f.24.1.1 100321 1ykhA 108 1.22e+01 1b87A 181 1.23e+01 1b87A d.108.1.1 40797 1ezfA 340 1.24e+01 1ezfA a.128.1.2 19440 3cd4 182 1.25e+01 1cdy b.1.1.1 19720 b.1.1.3 21659 1keyA 235 1.26e+01 a.118.16.1 72389 1j0tA 78 1.26e+01 a.163.1.1 77051 1td6A 306 1.27e+01 1ibrB 462 1.28e+01 1qgrA a.118.1.1 19120 1eal 127 1.29e+01 1hmt b.60.1.2 27227 1w4xA 542 1.29e+01 c.3.1.5 109171 c.3.1.5 109172 2bnfB 241 1.31e+01 1ea1A 455 1.34e+01 1ea1A a.104.1.1 18970 2bneA 241 1.35e+01 1rt8A 513 1.40e+01 a.40.1.1 105095 1qnoA 344 1.40e+01 1qnoA c.1.8.3 28838 1j1jA 240 1.42e+01 a.118.16.1 90762 1im2A 444 1.45e+01 1do0A c.37.1.20 62564 1c1kA 217 1.47e+01 1c1kA a.120.1.1 19239 1snrA 341 1.48e+01 b.6.1.3 105823 b.6.1.3 105824 1bd3A 243 1.50e+01 1bd3A c.61.1.1 34098 1fdlH 218 1.53e+01 1igtB b.1.1.1 19961 b.1.1.2 21021 1yjsA 419 1.53e+01 1fo8A 343 1.55e+01 1foaA c.68.1.10 59927 1xo1A 291 1.56e+01 1exnA a.60.7.1 18086 c.120.1.2 33356 1gewA 356 1.56e+01 1gewA c.67.1.1 60470 2occA 514 1.57e+01 2occA f.24.1.1 43518 1t7sA 137 1.57e+01 a.7.7.1 106636 1ornA 226 1.58e+01 a.96.1.1 87342 1lm8V 160 1.59e+01 b.3.3.1 74035 1isaA 192 1.59e+01 1avmA a.2.11.1 15731 d.44.1.1 38724 1fjgB 256 1.59e+01 1fjfB c.23.15.1 31400 1jpmA 366 1.59e+01 c.1.11.2 67031 d.54.1.1 67032 1fm4A 159 1.60e+01 1bv1 d.129.3.1 76186 1fo9A 348 1.61e+01 1foaA c.68.1.10 59928 1iscA 192 1.63e+01 1avmA a.2.11.1 15733 d.44.1.1 38726 1n71A 180 1.63e+01 d.108.1.1 85370 1vljA 407 1.64e+01 e.22.1.2 108832 1um0A 365 1.65e+01 d.258.1.1 107942 2c1dA 264 1.68e+01 1cdi 179 1.71e+01 1cdy b.1.1.1 19727 b.1.1.3 21666 1xkrA 206 1.72e+01 1zgsA 447 1.72e+01 1tkkA 366 1.74e+01 c.1.11.2 107089 d.54.1.1 107090 1wgzA 510 1.75e+01 1q8bA 105 1.76e+01 d.58.4.6 96201 1ev0A 58 1.78e+01 1ev0A d.71.1.1 39594 1senA 164 1.82e+01 c.47.1.1 105465 1qfhA 212 1.83e+01 1qfhA b.1.18.10 21893 b.1.18.10 21894 1bw0A 416 1.86e+01 1bw0A c.67.1.1 34385 1y60A 169 1.87e+01 1oivA 191 1.87e+01 c.37.1.8 93076 1mla 309 1.88e+01 1mla c.19.1.1 31031 d.58.23.1 39383 1u08A 386 1.88e+01 c.67.1.1 107543 1u1jA 765 1.91e+01 c.1.22.2 107590 c.1.22.2 107591 2aq4A 434 1.92e+01 1oxsC 353 1.93e+01 b.40.6.3 87519 c.37.1.12 87520 1cd9C 175 1.96e+01 1bgc a.26.1.1 16816 1bea 127 1.97e+01 1bea a.52.1.2 17826 1qkrA 188 1.97e+01 1qkrA a.24.9.1 16628 1bfa 134 1.99e+01 1bea a.52.1.2 17827 1mqsA 671 2.00e+01 e.25.1.1 79414 1j9qA 341 2.00e+01 1nif b.6.1.3 62765 b.6.1.3 62766 1v9sA 208 2.05e+01 1q8cA 151 2.07e+01 a.79.1.2 96202 1ldjA 760 2.08e+01 a.4.5.34 73847 a.118.17.1 73848 e.40.1.1 73849 1c4kA 730 2.09e+01 1ordA c.23.1.4 31273 c.67.1.5 34502 d.125.1.1 41123 1kewA 361 2.09e+01 c.2.1.2 68544 1ut8A 291 2.09e+01 a.60.7.1 99908 c.120.1.2 99909 1oxxK 353 2.10e+01 b.40.6.3 93715 c.37.1.12 93716 1mxrA 375 2.10e+01 a.25.1.2 85197 1uxtA 501 2.11e+01 c.82.1.1 108125 1br0A 120 2.16e+01 a.47.2.1 17772 1e9xA 455 2.19e+01 1ea1A a.104.1.1 18969 1exnB 290 2.19e+01 1exnA a.60.7.1 18089 c.120.1.2 33359 1oixA 191 2.19e+01 1bs0A 384 2.22e+01 1bs0A c.67.1.4 34490 1tqgA 105 2.22e+01 a.24.10.3 107224 1foaA 348 2.27e+01 1foaA c.68.1.10 59929 1deeG 54 2.29e+01 1fc2C a.8.1.1 16343 1vb5A 276 2.35e+01 1j7vR 214 2.35e+01 b.1.2.1 62705 b.1.2.1 62706 1i0lA 221 2.38e+01 c.61.1.1 71096 1xp3A 307 2.43e+01 2ar9A 278 2.46e+01 1et7A 341 2.52e+01 1nif b.6.1.3 23070 b.6.1.3 23071 2a5jA 191 2.56e+01 2bwnA 401 2.61e+01 1t7lA 766 2.65e+01 2abk 211 2.67e+01 2abk a.96.1.1 18743 1m98A 317 2.70e+01 a.175.1.1 78866 d.17.4.6 78867 1iomA 377 2.72e+01 a.103.1.1 83698 1pszA 303 2.74e+01 1toaA c.92.2.2 35600 1e1aA 314 2.76e+01 1e1aA b.68.6.1 59155 1ha2A 585 2.77e+01 1bj5 a.126.1.1 60866 a.126.1.1 60867 a.126.1.1 60868 1pufB 73 2.78e+01 a.4.1.1 95132 1b72B 87 2.79e+01 1akhA a.4.1.1 16001 1lqsR 214 2.80e+01 b.1.2.1 74194 b.1.2.1 74195 1or0A 160 2.81e+01 d.153.1.2 93445 1w9hA 427 2.82e+01 1qgrA 876 2.91e+01 1qgrA a.118.1.1 19119 1xauA 122 2.94e+01 1n5uA 585 2.96e+01 a.126.1.1 85339 a.126.1.1 85340 a.126.1.1 85341 1exnA 290 3.00e+01 1exnA a.60.7.1 18088 c.120.1.2 33358 1h6qA 168 3.00e+01 1h6qA b.88.1.2 60692 1lqbC 162 3.01e+01 b.3.3.1 74186 1tc1A 220 3.01e+01 1tc1A c.61.1.1 34083 1bg1A 722 3.02e+01 1bg1A a.47.1.1 17767 b.2.5.5 22461 d.93.1.1 40527 1o4tA 133 3.05e+01 b.82.1.9 86622 1dh3A 55 3.05e+01 1a02J h.1.3.1 45546 1sxjE 354 3.05e+01 a.80.1.1 106089 c.37.1.20 106090 1m41A 380 3.06e+01 c.1.16.4 78595 1humA 69 3.08e+01 1b3aA d.9.1.1 37397 1wpaA 114 3.09e+01 1xsrA 168 3.13e+01 2d2eA 250 3.14e+01 1as8A 343 3.17e+01 1nif b.6.1.3 23074 b.6.1.3 23075 1t4hA 290 3.17e+01 d.144.1.7 106420 1w2wB 191 3.17e+01 1v63A 101 3.17e+01 a.21.1.1 108391 1r3sA 367 3.19e+01 c.1.22.1 96963 1biqA 375 3.19e+01 1xikA a.25.1.2 16786 1dypA 271 3.20e+01 1dypA b.29.1.2 24185 1iruK 201 3.21e+01 d.153.1.4 71362 1iq0A 592 3.22e+01 a.27.1.1 66257 c.26.1.1 66258 d.67.2.1 66259 1nt0A 286 3.24e+01 b.23.1.1 86143 b.23.1.1 86144 g.3.11.1 86145 1l4uA 176 3.32e+01 c.37.1.2 73568 2bxkA 585 3.35e+01 1dd5A 185 3.40e+01 1dd5A d.67.3.1 39564 1ksr 100 3.40e+01 1qfhA b.1.18.10 21897 1rcd 173 3.42e+01 2fha a.25.1.1 16687 1v0aA 178 3.46e+01 1djtA 64 3.47e+01 1aho g.3.7.1 44132 1uroA 367 3.48e+01 1uroA c.1.22.1 29675 1hjxA 362 3.48e+01 c.1.8.5 83512 d.26.3.1 83513 1ir6A 424 3.50e+01 c.107.1.2 71342 1ej8A 140 3.58e+01 1qupA b.1.8.1 22300 1imvA 398 3.58e+01 e.1.1.1 62591 1vi0A 206 3.66e+01 a.4.1.9 100720 a.121.1.1 100721 1mwvA 714 3.67e+01 a.93.1.3 85161 a.93.1.3 85162 1fo5A 85 3.72e+01 1fo5A c.47.1.1 59922 1rj1A 151 3.72e+01 a.29.6.1 97526 1i5nA 146 3.75e+01 1i5nA a.24.10.3 61805 1j5vA 351 3.83e+01 c.72.1.1 71585 1ospH 218 3.85e+01 1igtB b.1.1.1 20117 b.1.1.2 21147 2bi7A 384 3.86e+01 1k6kA 143 3.90e+01 a.174.1.1 77274 6acn 754 3.96e+01 1amj c.8.2.1 30721 c.83.1.1 35397 1gtkA 313 3.96e+01 c.94.1.1 76346 d.50.2.1 76347 1qupA 222 3.98e+01 1qupA b.1.8.1 22301 d.58.17.1 39352 1dvpA 220 3.99e+01 1dvpA a.118.9.2 19216 g.50.1.1 45358