# 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 1d2eA 397 1.66e-02 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25701,25741,32136 1hoe 74 1.57e-01 1hoe b.5.1.1 22833 1yhfA 115 1.84e-01 1uebA 184 2.06e-01 b.34.5.2,b.40.4.5,b.40.4.5 107782,107783,107784 1ok0A 74 2.30e-01 b.5.1.1 93191 2c78A 405 3.46e-01 1ha3A 405 3.67e-01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 1z6bA 154 5.04e-01 2fhxA 246 6.58e-01 2fs2A 151 8.83e-01 1psuA 140 8.95e-01 d.38.1.5 88285 1exmA 405 9.07e-01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 1m2xA 223 1.19e+00 d.157.1.1 84764 1yhpA 212 1.20e+00 1x8hA 228 1.52e+00 1dq3A 454 1.75e+00 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1ifrA 121 1.75e+00 b.1.16.1 71203 1oaqL 120 1.78e+00 b.1.1.1 92708 2gpzA 111 2.07e+00 1oalA 151 3.12e+00 b.1.8.1 86739 2d4qA 257 3.36e+00 2brcA 214 3.66e+00 1cd8 114 4.01e+00 1cd8 b.1.1.1 19714 1kk1A 410 4.02e+00 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 2breA 219 4.22e+00 2d7nA 93 4.78e+00 2cw8A 537 4.88e+00 1neu 124 4.97e+00 1neu b.1.1.1 19704 1jjeA 222 5.61e+00 1a7tA d.157.1.1 63117 1wh0A 134 5.94e+00 2bwrA 401 6.01e+00 1yaiA 151 6.18e+00 1yaiA b.1.8.1 22289 1ah6 220 6.20e+00 1yer d.122.1.1 41094 1yb3A 175 6.39e+00 1v6fA 151 6.54e+00 d.109.1.2 108395 1zkiA 133 6.87e+00 1a6wL 109 6.91e+00 1mfa b.1.1.1 20252 1quqB 121 7.04e+00 1quqB b.40.4.3 25305 1khbA 625 7.15e+00 c.91.1.1,c.109.1.1 68606,68607 1z9lA 128 7.18e+00 1pkoA 139 7.30e+00 b.1.1.1 88147 2mspA 126 7.30e+00 1mspA b.1.11.2 22335 1zn8A 180 8.83e+00 1dyoA 160 9.61e+00 1dyoA b.18.1.7 23771 1suwA 249 9.74e+00 e.52.1.1 106027 1u1zA 168 1.03e+01 d.38.1.6 107602 1x8mA 288 1.10e+01 b.82.1.13 109516 1vk3A 615 1.11e+01 d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 100846,100847,100848,100849 1nqeA 594 1.14e+01 f.4.3.3 86027 1mspA 126 1.18e+01 1mspA b.1.11.2 22333 1vzyA 291 1.19e+01 2g1lA 104 1.22e+01 1fs0E 138 1.24e+01 1aqt a.2.10.1,b.93.1.1 59997,59998 2alaA 391 1.28e+01 1z0sA 278 1.30e+01 1e8pA 46 1.31e+01 g.55.1.1 59385 1qpxA 218 1.37e+01 1qpxA b.1.11.1,b.7.2.1 22318,23200 1g1kA 143 1.39e+01 1aohA b.2.2.2 22404 1yukB 120 1.41e+01 1uaiA 224 1.41e+01 b.29.1.18 107761 1tu7A 208 1.45e+01 2aw2A 120 1.45e+01 1c01A 76 1.50e+01 1c01A b.11.1.5 23633 1ts9A 102 1.50e+01 1zkkA 167 1.52e+01 1h8eD 482 1.54e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 60747,60748,60749 2bjqA 345 1.56e+01 1xe1A 116 1.59e+01 b.43.3.1 109571 1jjtA 228 1.61e+01 1a7tA d.157.1.1 63139 2bz6H 254 1.63e+01 2f4lA 297 1.68e+01 1ut7A 171 1.68e+01 b.143.1.1 99906 1x8gA 227 1.69e+01 1u3oA 82 1.71e+01 2fimA 276 1.72e+01 1ukgA 252 1.78e+01 b.29.1.1 99489 1kliH 254 1.80e+01 b.47.1.2 77435 1e79D 482 1.80e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 18272,26437,32317 2ck3D 482 1.81e+01 1umhA 184 1.83e+01 b.18.1.21 99605 1cqxA 403 1.84e+01 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 1iq6A 134 1.87e+01 d.38.1.4 76755 1mfa 247 1.88e+01 1mfa b.1.1.1,b.1.1.1 19888,19889 1danH 254 1.93e+01 5ptp b.47.1.2 26292 1cv8 174 1.93e+01 1cv8 d.3.1.1 37089 1zkpA 268 1.95e+01 1ca1 370 2.09e+01 1ca1 a.124.1.1,b.12.1.3 19340,23648 1uurA 473 2.12e+01 a.47.1.1,b.2.5.5,d.93.1.1 100016,100017,100018 1fvuB 125 2.19e+01 1ixxB d.169.1.1 42346 1ofdA 1520 2.20e+01 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 1vkkA 154 2.25e+01 d.109.1.2 108669 1xauA 122 2.32e+01 1o4tA 133 2.34e+01 b.82.1.9 86622 1lo6A 223 2.35e+01 b.47.1.2 74143 1aohA 147 2.43e+01 1aohA b.2.2.2 22401 2bgoA 140 2.48e+01 1wruA 379 2.50e+01 1njkA 156 2.53e+01 d.38.1.1 85818 1earA 147 2.62e+01 b.107.1.1,d.58.38.1 64875,64876 1ok8A 394 2.71e+01 b.1.18.4,f.10.1.1 93236,93237 1cid 177 2.72e+01 1cid b.1.1.1,b.1.1.3 19740,21679 1owxA 121 2.76e+01 d.58.7.1 87494 2d1eA 248 2.81e+01 1n3oA 252 2.82e+01 b.29.1.1 79967 2fcbA 173 2.82e+01 2fcbA b.1.1.4,b.1.1.4 21781,21782 1fr3A 67 2.89e+01 1fr3A b.40.6.1 25436 1ji6A 589 2.97e+01 b.18.1.3,b.77.2.1,f.1.3.1 63066,63067,63068 1q87A 221 3.01e+01 e.47.1.1 96192 1z4xA 532 3.06e+01 1z4vA 532 3.13e+01 1j7xA 302 3.13e+01 c.14.1.2 66425 1ogsA 497 3.19e+01 b.71.1.2,c.1.8.3 86997,86998 1z8gA 372 3.24e+01 1qznA 173 3.24e+01 b.2.2.2 104669 1tbuA 118 3.28e+01 1bk0 331 3.45e+01 1bk0 b.82.2.1 28118 1sltA 134 3.50e+01 1c1lA b.29.1.3 24186 1q7sA 117 3.53e+01 c.131.1.1 96055 1g38A 393 3.66e+01 2admA c.66.1.27 60235 1jeyA 609 3.72e+01 1jeqA b.131.1.1,c.62.1.3 90370,90371 1yruA 364 3.81e+01 1m8aA 70 3.82e+01 d.9.1.1 74579 2b3nA 159 3.82e+01 1jmtA 104 3.84e+01 d.58.7.3 63180 1odmA 331 3.85e+01 b.82.2.1 86875 1h54A 754 3.86e+01 a.102.1.4,b.30.5.3 60634,60635 1go7P 462 3.96e+01 b.80.7.1,d.92.1.6 76245,76246 1k7iA 479 4.00e+01 b.80.7.1,d.92.1.6 77281,77282 1qfgA 725 4.03e+01 1by5A f.4.3.3 43803 1ylnA 252 4.12e+01 1q9jA 422 4.15e+01 c.43.1.2,c.43.1.2 104590,104591 1mla 309 4.16e+01 1mla c.19.1.1,d.58.23.1 31031,39383 1kb0A 677 4.17e+01 a.3.1.6,b.70.1.1 68378,68379 2crvA 120 4.19e+01 1vfvA 366 4.20e+01 c.37.1.9 108592 1xypA 190 4.20e+01 1axkA b.29.1.11 24327 1lfo 128 4.21e+01 1hmt b.60.1.2 27223 1pov1 302 4.34e+01 1pov1 1ym5A 300 4.38e+01 1bx1A 314 4.40e+01 1fnc b.43.4.2,c.25.1.1 25629,31519 1x0tA 120 4.42e+01 1zhxA 438 4.45e+01 1t6cA 315 4.47e+01 c.55.1.8,c.55.1.8 106558,106559 1x4rA 99 4.47e+01 1ax0 239 4.48e+01 1led b.29.1.1 24042 1h6qA 168 4.56e+01 1h6qA b.88.1.2 60692 1uvqA 197 4.63e+01 b.1.1.2,d.19.1.1 100062,100063 1hxs1 302 4.63e+01 1mkaA 171 4.65e+01 1mkaA d.38.1.2 38543 1s12A 94 4.72e+01 1uylA 236 4.73e+01 d.122.1.1 108147 1rypL 212 4.75e+01 d.153.1.4 41880 1yrtA 364 4.81e+01 2carA 196 4.81e+01 1dkuA 317 4.84e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 1ztxE 108 4.85e+01 1xo8A 151 4.87e+01 1xx0A 127 4.92e+01 1byqA 228 4.94e+01 1yer d.122.1.1 41100 2av9A 147 4.99e+01 2bw2A 140 5.01e+01 1fnd 314 5.08e+01 1fnc b.43.4.2,c.25.1.1 25626,31516 1p57B 255 5.10e+01 b.47.1.2 94126 1hl9A 449 5.18e+01 b.71.1.3,c.1.8.11 90650,90651 1wnhA 225 5.19e+01 1t77A 414 5.22e+01 1n0lA 224 5.24e+01 b.1.11.1,b.7.2.1 79744,79745 2c5qA 240 5.25e+01 1vb0A 61 5.27e+01 1gv9A 260 5.32e+01 b.29.1.13 70596 1xfcA 384 5.37e+01 1yy5B 513 5.39e+01 1sacA 204 5.45e+01 1sacA b.29.1.5 24237 1tlyA 278 5.56e+01 f.4.6.1 107143 1euoA 180 5.62e+01 1np1A b.60.1.1 27163 4ubpA 101 5.68e+01 1ubpA d.8.1.1 37352 1g3kA 174 5.69e+01 1nedA d.153.1.4 41989 1wzaA 488 5.71e+01 1w0pA 781 5.71e+01 b.29.1.8,b.29.1.8,b.68.1.1 109038,109039,109040 1qmhA 347 5.81e+01 1qmhA c.47.2.1,d.68.2.1 33082,39568 1pk6B 132 5.85e+01 b.22.1.1 94802 1onjA 61 5.86e+01 g.7.1.1 93358 1obpA 159 5.91e+01 1obpA b.60.1.1 27092 2fblA 153 5.92e+01 1kte 105 5.95e+01 1kte c.47.1.1 32771 1hn2A 159 5.96e+01 b.60.1.1 65890 1gt1A 159 5.96e+01 b.60.1.1 90515 2sfa 191 6.00e+01 1qq4A b.47.1.1 25815 1s5jA 847 6.05e+01 2f9cA 334 6.05e+01 1tltA 319 6.09e+01 c.2.1.3,d.81.1.5 107135,107136 1kcqA 104 6.09e+01 d.109.1.1 68449 1o7iA 119 6.11e+01 b.40.4.3 86642 1wbiA 129 6.12e+01 1o97C 264 6.12e+01 c.26.2.3 81232 1y55X 126 6.12e+01 1gpc 218 6.15e+01 1gpc b.40.4.7 25393 1v88A 130 6.20e+01 b.55.1.1 108423 1ixmA 192 6.29e+01 1ixmA d.123.1.1 41114 1o9yA 84 6.30e+01 b.139.1.1 92692 1ff4A 65 6.31e+01 g.7.1.1 83251 1khoA 370 6.33e+01 a.124.1.1,b.12.1.3 72489,72490 2cvhA 220 6.41e+01 1i8aA 189 6.42e+01 1i82A b.1.9.2 61951 1z47A 355 6.45e+01 1gzwA 134 6.52e+01 b.29.1.3 90535 1pzgA 331 6.54e+01 c.2.1.5,d.162.1.1 95425,95426 1c0pA 363 6.57e+01 1an9A c.4.1.2,d.16.1.3 30647,37934 1p9bA 442 6.66e+01 c.37.1.10 94385 1v70A 105 6.66e+01 1zs7A 190 6.67e+01 1yz1A 174 6.69e+01 1iarB 207 6.69e+01 1iarB b.1.2.1,b.1.2.1 22037,22038 1gvp 87 6.71e+01 1gvp b.40.4.7 25369 1vqb 87 6.71e+01 1gvp b.40.4.7 25370 1914 232 6.72e+01 1914 d.49.1.1,d.49.1.1 83028,83029 1c96A 753 6.75e+01 1amj c.8.2.1,c.83.1.1 30727,35403 1x71A 178 6.77e+01 1quqA 129 6.80e+01 1quqA b.40.4.3 25303 1c8cA 64 6.84e+01 1azpA b.34.13.1 59084 1zpuA 534 6.85e+01 1tvxA 75 6.87e+01 1tvxA d.9.1.1 37441 1t82A 155 6.96e+01 d.38.1.5 106639 1eajA 126 7.00e+01 1f5wA b.1.1.1 59401 1mvuB 121 7.04e+01 b.1.1.1 91475 1nszA 347 7.11e+01 b.30.5.4 80724 2bjfA 329 7.12e+01 1x89A 178 7.22e+01 1hnjA 317 7.24e+01 1hn9A c.95.1.2,c.95.1.2 35969,35970 1gkpA 458 7.25e+01 b.92.1.3,c.1.9.6 70231,70232 2c9wA 169 7.26e+01 1fnc 314 7.26e+01 1fnc b.43.4.2,c.25.1.1 25627,31517 1zotA 358 7.50e+01 2bjhA 260 7.50e+01 1e9pA 151 7.52e+01 1mfmA b.1.8.1 22215 1n12A 138 7.60e+01 b.2.3.2 79779 1xniA 118 7.62e+01 1pvc1 301 7.63e+01 1pov1 1jl2A 156 7.67e+01 c.55.3.1 66822 1zo0A 126 7.70e+01 1vhzA 198 7.70e+01 d.113.1.1 100718 1qqhA 144 7.70e+01 1dtoA b.91.1.1 28404 1y7rA 133 7.78e+01 1gxuA 91 7.86e+01 d.58.10.1 76378 1tit 98 7.87e+01 1tit b.1.1.4 21716 1cf9A 753 7.87e+01 1cf9A c.23.16.3,e.5.1.1 31441,42815 1aisA 182 7.93e+01 1ytbA d.129.1.1,d.129.1.1 41288,41289 1wwcA 118 7.94e+01 1wwcA b.1.1.4 21778 1mjc 69 8.11e+01 1mjc b.40.4.5 25319 1s0uA 408 8.12e+01 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 2f4nA 273 8.12e+01 1sb2A 133 8.13e+01 1ejxA 100 8.14e+01 d.8.1.1 83182 1j05B 121 8.16e+01 b.1.1.1 90736 1fjgL 135 8.17e+01 1fjfL b.40.4.5 25346 1xdnA 277 8.21e+01 1r9fA 136 8.26e+01 d.255.1.1 97257 8acn 754 8.27e+01 1amj c.8.2.1,c.83.1.1 30724,35400 1y4oA 104 8.28e+01 1mqoA 227 8.33e+01 d.157.1.1 103846 1rsgA 516 8.37e+01 1g7sA 594 8.38e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 1cq3A 233 8.42e+01 1cq3A b.27.1.1 23923 1eaqA 140 8.45e+01 b.2.5.6 76144 1v10A 521 8.45e+01 b.6.1.3,b.6.1.3,b.6.1.3 108224,108225,108226 1pz4A 116 8.45e+01 d.106.1.1 95400 2cx1A 187 8.48e+01 1z54A 132 8.50e+01 1ixlA 131 8.56e+01 d.38.1.5 90717 1e8cA 498 8.69e+01 c.98.1.1,c.59.1.1,c.72.2.1 59377,59378,59379 1f60A 458 8.76e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 2bm3A 166 8.76e+01 1mpp 361 8.78e+01 2rmpA b.50.1.2 26856 1yloA 348 8.83e+01 1nekA 588 8.83e+01 a.7.3.1,c.3.1.4,d.168.1.1 80426,80427,80428 1w97L 246 8.87e+01 1wj9A 211 8.88e+01 1osyA 115 8.91e+01 b.1.21.1 93502