# List of top-scoring protein chains for t04-100-30-o_notor2-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 1ly1A 181 2.29e-01 c.37.1.1 74334 1g55A 343 6.06e-01 1g55A c.66.1.26 34247 1d8hA 311 6.79e-01 1d8iA d.63.1.1 39544 1rtfB 252 7.81e-01 5ptp 1ltqA 301 7.85e-01 c.108.1.9,c.37.1.1 78208,78209 1fjrA 195 8.41e-01 1fjrA b.102.1.1 59855 1bx1A 314 8.89e-01 1fnc b.43.4.2,c.25.1.1 25629,31519 2b5oA 402 8.90e-01 1fnd 314 9.33e-01 1fnc b.43.4.2,c.25.1.1 25626,31516 2cjtA 131 9.37e-01 1o0sA 605 9.98e-01 c.2.1.7,c.58.1.3 86540,86541 1fnc 314 1.01e+00 1fnc b.43.4.2,c.25.1.1 25627,31517 1aokB 122 1.48e+00 1poa a.133.1.2 19561 1ifrA 121 1.65e+00 b.1.16.1 71203 1ppjB 439 1.75e+00 d.185.1.1,d.185.1.1 104254,104255 1mrzA 293 1.89e+00 b.43.5.1,c.26.1.3 91452,91453 1f5mA 180 1.96e+00 1f5mB d.110.2.1 40895 2b18A 164 2.20e+00 1om4A 422 2.28e+00 d.174.1.1 87067 1rwiA 270 2.52e+00 b.68.9.1 97987 1rliA 184 2.66e+00 c.23.5.6 97647 1xa1A 255 2.88e+00 e.3.1.1 109529 1mmvB 419 3.12e+00 d.174.1.1 91318 1aym3 238 3.12e+00 1aym3 1tu1A 148 3.22e+00 d.107.1.3 107316 1b65A 375 3.25e+00 1b65A d.154.1.1 42020 1xkzA 255 3.27e+00 2bsaA 303 3.44e+00 1vj2A 126 3.48e+00 b.82.1.10 100796 1go2A 304 3.54e+00 b.43.4.2,c.25.1.1 76243,76244 1que 303 3.76e+00 1fnc b.43.4.2,c.25.1.1 25647,31537 1bb9 115 4.26e+00 1bb9 b.34.2.1 24554 1jltB 122 4.27e+00 a.133.1.2 66868 1ogiA 303 4.47e+00 b.43.4.2,c.25.1.1 92914,92915 2cyeA 133 4.49e+00 2bmwA 304 4.98e+00 1l0lB 439 5.17e+00 d.185.1.1,d.185.1.1 84484,84485 1dixA 208 5.19e+00 1bk7A d.124.1.1 41122 1b9wA 89 5.37e+00 1b9wA g.3.11.4,g.3.11.4 44334,44335 2ff4A 388 5.39e+00 1ryoA 327 5.72e+00 c.94.1.2 98108 1g73C 121 5.73e+00 1g3fA g.52.1.1 45375 1w34A 304 5.80e+00 1m7vA 363 6.25e+00 d.174.1.1 78748 1k7kA 221 6.29e+00 c.51.4.1 72104 1y8oB 128 6.33e+00 1uch 230 6.70e+00 1uch d.3.1.6 37129 1e5mA 416 6.73e+00 1dd8A c.95.1.1,c.95.1.1 58973,58974 1yemA 179 6.97e+00 1zgoA 223 7.18e+00 1vr3A 191 7.67e+00 1twuA 139 7.89e+00 d.32.1.8 107413 1a8e 329 7.94e+00 1cb6A c.94.1.2 35888 2esnA 310 8.08e+00 1sxvA 172 8.15e+00 1e19A 314 8.19e+00 1b7bA c.73.1.1 34967 3proC 166 8.30e+00 3proC d.52.1.1,d.52.1.1 38812,38813 1gw0A 559 8.53e+00 b.6.1.3,b.6.1.3,b.6.1.3 70623,70624,70625 1g0hA 252 8.87e+00 1dk4A e.7.1.1 60171 1mwwA 128 9.18e+00 d.80.1.4 91483 1dbhA 354 9.20e+00 1awe a.87.1.1,b.55.1.1 18514,26967 2cz2A 223 9.42e+00 1ocxA 182 9.57e+00 b.81.1.3 86814 1qxrA 189 9.60e+00 b.82.1.7 96552 1ggxA 223 9.82e+00 1ggxA d.22.1.1 38367 1i58A 189 9.87e+00 1b3qA d.122.1.3 61773 1pvc3 238 1.03e+01 1aym3 1v8fA 276 1.05e+01 c.26.1.4 100503 1xd3A 230 1.06e+01 1fadA 99 1.08e+01 1fadA a.77.1.2 18428 2fmlA 273 1.09e+01 2biiA 424 1.10e+01 1x82A 190 1.13e+01 1x99A 145 1.19e+01 1naqA 112 1.20e+01 d.58.5.2 91761 1rg9A 383 1.22e+01 d.130.1.1,d.130.1.1,d.130.1.1 97427,97428,97429 1vl2A 421 1.25e+01 c.26.2.1,d.210.1.1 108708,108709 1bdb 277 1.27e+01 1bdb c.2.1.2 29874 1kao 167 1.27e+01 1ctqA c.37.1.8 32014 3sil 379 1.28e+01 3sil b.68.1.1 27542 2eifA 136 1.29e+01 1bkb b.34.5.2,b.40.4.5 24607,25339 2a90A 240 1.32e+01 1jd5A 124 1.34e+01 g.52.1.1 66544 1ebfA 358 1.36e+01 1ebuA c.2.1.3,d.81.1.2 30033,39948 1kdj 102 1.37e+01 1plc b.6.1.1 22864 1h59B 54 1.40e+01 g.3.9.1 70881 1ohpA 125 1.41e+01 2b1xA 470 1.43e+01 1pyaB 228 1.43e+01 1pyaB 1ywnA 316 1.48e+01 1dbxA 158 1.53e+01 1dbuA d.116.1.1 40928 1dmhA 311 1.56e+01 1dmhA b.3.6.1 22633 1gppA 237 1.59e+01 b.86.1.2 76262 1odfA 290 1.60e+01 c.37.1.6 92782 1g8aA 227 1.64e+01 c.66.1.3 90506 1umwA 237 1.66e+01 d.223.1.2,d.223.1.2 99631,99632 1c3hA 137 1.68e+01 b.22.1.1 90405 1tuaA 191 1.69e+01 d.51.1.1,d.51.1.1 107321,107322 2avtA 378 1.69e+01 1i19A 561 1.71e+01 1i19A d.58.32.3,d.145.1.1 61522,61523 2aw5A 541 1.72e+01 2hf9A 226 1.75e+01 1j7xA 302 1.76e+01 c.14.1.2 66425 1ocvA 125 1.77e+01 d.17.4.3 86810 1vj0A 380 1.79e+01 b.35.1.2,c.2.1.1 100786,100787 2bwqA 129 1.79e+01 1qorA 327 1.81e+01 1qorA b.35.1.2,c.2.1.1 24766,29782 1o0iA 138 1.82e+01 d.38.1.5 86532 1kv9A 668 1.84e+01 a.3.1.6,b.70.1.1 73056,73057 2ch4A 320 1.87e+01 1t8sA 484 1.89e+01 c.56.2.1 106679 2gj8A 172 1.91e+01 1tvdA 116 1.93e+01 1tvdA b.1.1.1 20650 1eaqA 140 1.98e+01 b.2.5.6 76144 2g8yA 385 2.00e+01 1t46A 313 2.05e+01 d.144.1.7 106397 1k4tA 592 2.08e+01 a.2.8.1,d.163.1.2,e.15.1.1 77263,77264,77265 1b8aA 438 2.09e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1eljA 381 2.09e+01 4mbp c.94.1.1 35791 2ausB 60 2.14e+01 1yn4A 99 2.15e+01 1g2nA 264 2.16e+01 1lbd a.123.1.1 60227 2czvC 120 2.17e+01 1iybA 208 2.17e+01 d.124.1.1 90720 1dy9A 187 2.20e+01 1jxpA b.47.1.3 26400 1in0A 163 2.20e+01 d.58.49.1,d.58.49.1 83694,83695 1i05A 180 2.24e+01 1mup b.60.1.1 27130 1b6rA 355 2.24e+01 1b6rA b.84.2.1,c.30.1.1,d.142.1.2 28241,31648,41493 1dm9A 133 2.24e+01 1dm9A d.66.1.3 39560 1kutA 230 2.28e+01 d.143.1.1 73017 2axyA 73 2.29e+01 1bkjA 240 2.29e+01 1bkjA d.90.1.1 40243 1bw0A 416 2.32e+01 1bw0A c.67.1.1 34385 1xaoA 121 2.34e+01 1t5yA 190 2.35e+01 b.122.1.1,d.17.6.3 106495,106496 2cwsA 237 2.38e+01 1xwtA 405 2.39e+01 2h3bA 494 2.46e+01 1w2lA 99 2.46e+01 2gm5A 139 2.47e+01 1fgxA 288 2.48e+01 1fgxA c.68.1.2 34508 2blkA 122 2.54e+01 1y5eA 169 2.57e+01 1hw6A 278 2.59e+01 1frb c.1.7.1 61296 1s3zA 165 2.66e+01 d.108.1.1 105250 1jv4A 162 2.66e+01 b.60.1.1 67343 1avbA 226 2.69e+01 1led b.29.1.1 24158 1to2E 281 2.69e+01 1w85A 368 2.72e+01 1ryp2 233 2.74e+01 1ryp2 1jae 471 2.76e+01 1smd b.71.1.1,c.1.8.1 27773,28760 1xw2A 405 2.77e+01 1i06A 180 2.85e+01 1mup b.60.1.1 27131 1h12A 405 2.87e+01 a.102.1.2 83447 1zndA 174 2.93e+01 2bvfA 459 2.94e+01 1qy1A 174 2.94e+01 b.60.1.1 96568 1gdvA 85 2.96e+01 1ctj a.3.1.1 60458 1eazA 125 2.97e+01 b.55.1.1 70113 1tmxA 293 3.01e+01 1i2mA 216 3.05e+01 1byuA c.37.1.8 61568 1fdr 248 3.08e+01 1fdr b.43.4.2,c.25.1.1 25653,31543 1res 43 3.11e+01 1ret a.4.1.2 16023 1j1lA 290 3.20e+01 b.82.1.12 90766 1wjxA 122 3.27e+01 1yfsA 465 3.27e+01 1x6mA 196 3.31e+01 1cl8A 276 3.32e+01 1ckqA c.52.1.1 33230 1lkkA 105 3.33e+01 1lckA d.93.1.1 40412 1y6hA 177 3.34e+01 2a9dA 372 3.35e+01 1sup 275 3.38e+01 1gci c.41.1.1 32510 2olbA 517 3.42e+01 1jevA c.94.1.1 35721 1soxA 466 3.49e+01 1soxA b.1.18.6,d.120.1.1,d.176.1.1 21947,41090,42563 1jxcA 68 3.51e+01 g.3.7.5 77201 1lw6E 281 3.57e+01 c.41.1.1 74293 1bs0A 384 3.61e+01 1bs0A c.67.1.4 34490 1o59A 355 3.62e+01 b.18.1.22,b.18.1.22 92495,92496 1yqfA 203 3.64e+01 1uekA 275 3.69e+01 d.14.1.5,d.58.26.5 88483,88484 1utcA 363 3.71e+01 a.118.1.4,b.69.6.1 99914,99915 1gky 187 3.86e+01 1gky c.37.1.1 31839 1jetA 517 3.89e+01 1jevA c.94.1.1 35718 1k6wA 426 3.90e+01 b.92.1.2,c.1.9.5 68236,68237 1zq4A 693 3.91e+01 1y60A 169 3.95e+01 2b6eA 146 3.96e+01 1vd5A 377 4.00e+01 a.102.1.7 108518 1owfA 99 4.00e+01 a.55.1.1 87487 1xzoA 174 4.09e+01 1ax0 239 4.11e+01 1led b.29.1.1 24042 1c8zA 265 4.13e+01 1c8zA d.23.1.1 38375 1sqwA 188 4.17e+01 1kte 105 4.17e+01 1kte c.47.1.1 32771 1mwmA 320 4.19e+01 c.55.1.1,c.55.1.1 79580,79581 2gs8A 317 4.23e+01 1g4mA 393 4.28e+01 b.1.18.11,b.1.18.11 65143,65144 1xneA 113 4.30e+01 2d0oA 610 4.34e+01 1gp6A 356 4.34e+01 b.82.2.1 65441 1j83A 180 4.36e+01 b.18.1.12 66430 1ex7A 186 4.41e+01 1gky c.37.1.1 59537 1v8bA 479 4.44e+01 1q9jA 422 4.45e+01 c.43.1.2,c.43.1.2 104590,104591 1fuiA 591 4.54e+01 1fuiA b.43.2.1,c.85.1.1 25674,35444 1fp2A 352 4.56e+01 1fpxA a.4.5.29,c.66.1.12 59941,59942 1jiwI 106 4.58e+01 1smpI b.61.2.1 63078 2fv1A 377 4.58e+01 1tdtA 259 4.60e+01 3tdt b.81.1.2 28055 1l0wA 580 4.63e+01 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1gzcA 239 4.65e+01 b.29.1.1 70803 2d4rA 147 4.67e+01 1ga3A 113 4.67e+01 1ga3A a.26.1.2 60411 2c52B 59 4.68e+01 2f1lA 187 4.72e+01 1xt9A 212 4.73e+01 2bkrA 212 4.74e+01 1amx 180 4.75e+01 1amx b.2.3.1 22410 1iwmA 186 4.86e+01 b.125.1.2 83758 1aohA 147 4.91e+01 1aohA b.2.2.2 22401 1x9gA 200 4.95e+01 c.33.1.3 109527 1n1cA 217 5.01e+01 a.184.1.1 85254 1ufkA 254 5.01e+01 c.66.1.39 99340 1s21A 206 5.01e+01 d.166.1.4 105222 1svy 114 5.08e+01 1svy d.109.1.1 40831 2bh8A 101 5.13e+01 1dkzA 219 5.18e+01 1dkzA a.8.4.1,b.130.1.1 90345,90346 2bj7A 138 5.24e+01 2eueA 279 5.33e+01 1ov3A 138 5.34e+01 b.34.2.1,b.34.2.1 87451,87452 2bpsA 81 5.38e+01 1xl3C 92 5.38e+01 1nmmB 286 5.39e+01 c.68.1.2 80662 1j1tA 233 5.45e+01 b.29.1.18 90771 1ae9A 179 5.57e+01 1ae9A d.163.1.1 42153 1s31A 273 5.58e+01 1miwA 404 5.59e+01 a.173.1.1,d.218.1.4 79162,79163 2bkqA 212 5.59e+01 1jb7B 260 5.63e+01 1otcB b.40.4.3 62839 2bhgA 209 5.64e+01 1ztuA 341 5.68e+01 1dcs 311 5.68e+01 1dcs b.82.2.1 28124 1ta9A 450 5.70e+01 1mjc 69 5.73e+01 1mjc b.40.4.5 25319 1emzA 21 5.78e+01 j.35.1.1 46282 1gxuA 91 5.83e+01 d.58.10.1 76378 1m40A 263 5.86e+01 e.3.1.1 74437 1q1oA 98 5.86e+01 d.15.2.2 95596 1xqiA 195 5.87e+01 1t33A 224 5.89e+01 a.4.1.9,a.121.1.1 106295,106296 1b8oA 284 5.91e+01 1b8oA c.56.2.1 33762 1gcqC 70 5.93e+01 1gcpA b.34.2.1 60436 1l0bA 229 5.93e+01 c.15.1.3,c.15.1.3 73391,73392 1trb 320 5.94e+01 1trb c.3.1.5,c.3.1.5 30529,30530 1qksA 567 5.94e+01 1qksA a.3.1.2,b.70.2.1 15951,27710 1yroB 286 5.95e+01 2he7A 283 5.97e+01 1y7rA 133 5.98e+01 1j3kA 280 5.98e+01 c.71.1.1 84070 2f1rA 171 6.00e+01 1fu1A 203 6.02e+01 1fu1B b.59.1.1,h.1.11.1 27076,45630 1k38A 254 6.09e+01 e.3.1.1 84303 1zyeA 220 6.09e+01 1vd3A 217 6.14e+01 2mev1 277 6.18e+01 2mev1 1h4rA 314 6.19e+01 a.11.2.1,b.55.1.5,d.15.1.4 65616,65617,65618 1fmb 104 6.19e+01 1fmb b.50.1.1 26777 1btl 263 6.24e+01 1btl e.3.1.1 42691 1xknA 355 6.26e+01 1ru4A 400 6.28e+01 b.80.1.9 97836 1dp0A 1023 6.34e+01 b.1.4.1,b.1.4.1,b.18.1.5,b.30.5.1,c.1.8.3 22073,22074,23722,24346,28845 1je0A 236 6.36e+01 c.56.2.1 66581 2gu2A 312 6.38e+01 1ko3A 230 6.40e+01 d.157.1.1 90974 1jofA 365 6.42e+01 b.69.10.1 71775 1w96A 554 6.44e+01 1orc 71 6.53e+01 1orc a.35.1.2 17054 2d0iA 333 6.62e+01 1rurH 218 6.66e+01 b.1.1.1,b.1.1.2 97879,97880 1jz8A 1023 6.67e+01 b.1.4.1,b.1.4.1,b.18.1.5,b.30.5.1,c.1.8.3 67830,67831,67832,67833,67834 1svpA 161 6.68e+01 1svpA b.47.1.3 26384 1ermA 263 6.80e+01 1btl e.3.1.1 42690 1fnuA 221 6.81e+01 3seb b.40.2.2,d.15.6.1 25212,37801 1y07A 128 6.84e+01 1qs0B 338 6.88e+01 1qs0B c.36.1.7,c.48.1.2 31830,33103 1s2kA 206 6.92e+01 b.29.1.20 98389 1f5vA 240 6.95e+01 1bkjA d.90.1.1 40255 2ax3A 502 6.98e+01 1rlw 126 6.99e+01 1rlw b.7.1.1 23177 1k5nB 100 7.02e+01 b.1.1.2 77268 1zq7A 207 7.04e+01 1ogsA 497 7.04e+01 b.71.1.2,c.1.8.3 86997,86998 2frgP 106 7.05e+01 1rq2A 382 7.08e+01 c.32.1.1,d.79.2.1 105048,105049 1ze3D 125 7.11e+01 2ervA 150 7.12e+01 1gypA 358 7.19e+01 1dssG c.2.1.3,d.81.1.1 30004,39919 2bf9A 36 7.20e+01 2bycA 137 7.28e+01 1riqA 465 7.46e+01 a.203.1.1,d.104.1.1 97516,97517 1wdvA 152 7.56e+01 1dytA 133 7.59e+01 7rsa d.5.1.1 37288 1u1zA 168 7.69e+01 d.38.1.6 107602 1opd 85 7.80e+01 1ptf d.94.1.1 40560 1ik9A 213 7.83e+01 b.59.1.1,h.1.11.1 66176,66177 1gvnA 90 7.88e+01 a.8.2.1 76353 1h8eH 146 7.95e+01 1e79H b.93.1.1 60757 2bw3A 534 7.95e+01 1tjyA 316 7.97e+01 c.93.1.1 107062 1e25A 282 8.02e+01 1e25A e.3.1.1 42731 1f28A 297 8.10e+01 1bkpA d.117.1.1 59608 1cp2A 269 8.10e+01 1cp2A c.37.1.10 32269 1vapA 123 8.17e+01 1poa a.133.1.2 19548 1sbp 310 8.18e+01 1sbp c.94.1.1 35760 1pztA 286 8.19e+01 c.68.1.2 95470 1kwgA 645 8.31e+01 b.71.1.1,c.1.8.1,c.23.16.5 77561,77562,77563 2evwX 166 8.32e+01 1jyhA 157 8.34e+01 d.60.1.3 71956 1lba 146 8.38e+01 1lba d.118.1.1 41062 1rm6B 324 8.40e+01 1xtmA 175 8.42e+01 2fy7A 287 8.45e+01 2av4A 162 8.46e+01 3chbD 104 8.48e+01 3chbD b.40.2.1 24970 1jj2V 154 8.50e+01 1ffkT d.59.1.1 63107 1kktA 511 8.55e+01 a.102.2.1 68687 2frnA 278 8.57e+01 1i4fB 100 8.57e+01 1agdB b.1.1.2 61689 1whzA 70 8.64e+01 1ia8A 289 8.65e+01 1ia8A d.144.1.7 62112 1e5eA 404 8.65e+01 1ibjA c.67.1.3 59265 1gvp 87 8.66e+01 1gvp b.40.4.7 25369 1xs1A 193 8.77e+01 1ixcA 294 8.83e+01 a.4.5.37,c.94.1.1 83764,83765