# List of top-scoring protein chains for t2k-100-30-n_sep-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 1rtfB 252 5.07e-02 5ptp 1ly1A 181 4.63e-01 c.37.1.1 74334 1tu1A 148 5.11e-01 d.107.1.3 107316 1o0sA 605 6.11e-01 c.2.1.7,c.58.1.3 86540,86541 1f5mB 180 7.21e-01 1f5mB d.110.2.1 40896 1f5mA 180 7.64e-01 1f5mB d.110.2.1 40895 1ltqA 301 8.63e-01 c.108.1.9,c.37.1.1 78208,78209 2bsaA 303 8.83e-01 1rwiA 270 9.23e-01 b.68.9.1 97987 1w34A 304 9.40e-01 1go2A 304 1.01e+00 b.43.4.2,c.25.1.1 76243,76244 1que 303 1.02e+00 1fnc b.43.4.2,c.25.1.1 25647,31537 1d8hA 311 1.03e+00 1d8iA d.63.1.1 39544 2b5oA 402 1.07e+00 1qg0A 308 1.07e+00 1fnc b.43.4.2,c.25.1.1 25639,31529 1d8iA 311 1.07e+00 1d8iA d.63.1.1 39541 1b2rA 304 1.11e+00 1fnc b.43.4.2,c.25.1.1 25648,31538 1dim 381 1.12e+00 3sil b.68.1.1 27544 1ex7A 186 1.16e+00 1gky c.37.1.1 59537 2sil 381 1.17e+00 3sil b.68.1.1 27543 3sil 379 1.32e+00 3sil b.68.1.1 27542 1c8zA 265 1.52e+00 1c8zA d.23.1.1 38375 1xd3A 230 1.62e+00 1gky 187 1.64e+00 1gky c.37.1.1 31839 1ogiA 303 1.67e+00 b.43.4.2,c.25.1.1 92914,92915 2gj8A 172 1.78e+00 1fjrA 195 1.79e+00 1fjrA b.102.1.1 59855 1uch 230 1.82e+00 1uch d.3.1.6 37129 2a90A 240 1.91e+00 1qh0A 295 1.95e+00 b.43.4.2,c.25.1.1 68891,68892 2b18A 164 1.96e+00 1xkzA 255 2.11e+00 1xhbA 472 2.20e+00 3proC 166 2.35e+00 3proC d.52.1.1,d.52.1.1 38812,38813 1vk0A 206 2.36e+00 c.55.3.5 100839 1dixA 208 2.40e+00 1bk7A d.124.1.1 41122 1vl2A 421 2.49e+00 c.26.2.1,d.210.1.1 108708,108709 3proD 166 2.51e+00 3proC d.52.1.1,d.52.1.1 38814,38815 2eifA 136 2.59e+00 1bkb b.34.5.2,b.40.4.5 24607,25339 1ggxA 223 2.59e+00 1ggxA d.22.1.1 38367 2bmwA 304 2.60e+00 1e19A 314 2.63e+00 1b7bA c.73.1.1 34967 1xa1A 255 2.70e+00 e.3.1.1 109529 1bx1A 314 2.77e+00 1fnc b.43.4.2,c.25.1.1 25629,31519 1fnb 314 2.82e+00 1fnc b.43.4.2,c.25.1.1 25628,31518 1n6eA 1071 2.88e+00 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 80149,80150,80151,80152 1ifrA 121 2.91e+00 b.1.16.1 71203 1b4aA 149 3.19e+00 1b4aA a.4.5.3,d.74.2.1 16088,39721 1zgoA 223 3.71e+00 1xl3C 92 3.77e+00 1fnd 314 3.86e+00 1fnc b.43.4.2,c.25.1.1 25626,31516 1qhlA 227 4.15e+00 1qhlA c.37.1.12 32382 1bcg 77 4.19e+00 1aho g.3.7.1 44130 1mwwA 128 4.33e+00 d.80.1.4 91483 1bb9 115 4.34e+00 1bb9 b.34.2.1 24554 1ogsA 497 4.35e+00 b.71.1.2,c.1.8.3 86997,86998 1fnc 314 4.42e+00 1fnc b.43.4.2,c.25.1.1 25627,31517 1pms 136 4.81e+00 1awe b.55.1.1 26966 1s31A 273 5.07e+00 1yn4A 99 5.18e+00 1v8fA 276 5.18e+00 c.26.1.4 100503 1b9wA 89 5.98e+00 1b9wA g.3.11.4,g.3.11.4 44334,44335 1jp4A 308 6.45e+00 1jp4A e.7.1.1 63223 1a5iA 265 6.45e+00 5ptp b.47.1.2 26331 1k32A 1045 6.73e+00 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 68068,68069,68070,68071 2snv 151 6.83e+00 1svpA b.47.1.3 26394 1x82A 190 6.94e+00 1b6rA 355 6.99e+00 1b6rA b.84.2.1,c.30.1.1,d.142.1.2 28241,31648,41493 1qxrA 189 7.19e+00 b.82.1.7 96552 1b6sA 355 7.45e+00 1b6rA b.84.2.1,c.30.1.1,d.142.1.2 28242,31649,41494 1a9y 338 7.46e+00 1xel c.2.1.2 29789 1kzfA 230 7.50e+00 d.108.1.3 73354 1ryp1 222 7.57e+00 1ryp1 1jxcA 68 7.60e+00 g.3.7.5 77201 2a9dA 372 7.90e+00 1a9z 338 7.93e+00 1xel c.2.1.2 29795 1j7xA 302 8.15e+00 c.14.1.2 66425 1udb 338 8.18e+00 1xel c.2.1.2 29787 1a8e 329 8.46e+00 1cb6A c.94.1.2 35888 1xel 338 8.46e+00 1xel c.2.1.2 29786 2ajrA 331 8.80e+00 1svpA 161 8.87e+00 1svpA b.47.1.3 26384 1ocxA 182 8.92e+00 b.81.1.3 86814 1j3wA 163 9.07e+00 d.110.7.1 90833 1qbiA 454 9.10e+00 1c9uA b.68.2.1 27619 1e79H 146 9.23e+00 1e79H a.2.10.1,b.93.1.1 15721,28438 2udpA 338 9.26e+00 1xel c.2.1.2 29791 1d3kA 329 9.29e+00 1nnt c.94.1.2 35889 1qhbA 596 9.31e+00 1qhbA a.111.1.2 19055 1iybA 208 9.39e+00 d.124.1.1 90720 1k4jA 230 9.47e+00 d.108.1.3 72057 1ryoA 327 9.49e+00 c.94.1.2 98108 1cruA 454 9.49e+00 1c9uA b.68.2.1 27617 1fadA 99 9.70e+00 1fadA a.77.1.2 18428 2fp7B 172 9.76e+00 1qy1A 174 1.04e+01 b.60.1.1 96568 1zndA 174 1.04e+01 1dy9A 187 1.04e+01 1jxpA b.47.1.3 26400 2bh8A 101 1.05e+01 1aj6 219 1.05e+01 1aj6 d.122.1.2 41106 1a80 277 1.05e+01 1frb c.1.7.1 28700 1udc 338 1.06e+01 1xel c.2.1.2 29785 1c9uA 454 1.07e+01 1c9uA b.68.2.1 27623 1hw6A 278 1.08e+01 1frb c.1.7.1 61296 1soxA 466 1.09e+01 1soxA b.1.18.6,d.120.1.1,d.176.1.1 21947,41090,42563 1e4eA 343 1.10e+01 1iow c.30.1.2,d.142.1.1 59221,59222 1kvs 338 1.11e+01 1xel c.2.1.2 29799 1jv4A 162 1.13e+01 b.60.1.1 67343 1ynmA 247 1.14e+01 2fkcA 247 1.15e+01 1df3A 162 1.17e+01 1mup b.60.1.1 27134 1vd3A 217 1.17e+01 1smeA 329 1.17e+01 1smrA b.50.1.2 26885 1pgjA 478 1.18e+01 2pgd a.100.1.1,c.2.1.6 18783,30195 1g55A 343 1.18e+01 1g55A c.66.1.26 34247 1psuA 140 1.19e+01 d.38.1.5 88285 2agyA 361 1.20e+01 1h8eH 146 1.20e+01 1e79H b.93.1.1 60757 2a2lA 145 1.21e+01 1lw6E 281 1.22e+01 c.41.1.1 74293 2fs2A 151 1.23e+01 1jqfA 334 1.24e+01 c.94.1.2 67086 1i05A 180 1.24e+01 1mup b.60.1.1 27130 1gppA 237 1.24e+01 b.86.1.2 76262 1lrwA 600 1.28e+01 b.70.1.1 91111 1xw2A 405 1.29e+01 1h12A 405 1.30e+01 a.102.1.2 83447 1xwtA 405 1.31e+01 2axyA 73 1.31e+01 1dbuA 158 1.36e+01 1dbuA d.116.1.1 40930 1pyaB 228 1.37e+01 1pyaB 1tqyB 415 1.37e+01 c.95.1.1,c.95.1.1 107247,107248 2cz2A 223 1.40e+01 1m0wA 491 1.40e+01 c.30.1.4,d.142.1.6 78363,78364 1xqiA 195 1.42e+01 1i06A 180 1.43e+01 1mup b.60.1.1 27131 1rliA 184 1.44e+01 c.23.5.6 97647 2he7A 283 1.47e+01 1a2q 275 1.47e+01 1gci c.41.1.1 32512 1f3aA 222 1.48e+01 1pgtA a.45.1.1,c.47.1.5 17701,32995 1ri6A 343 1.49e+01 b.69.11.1 97503 1crkA 380 1.49e+01 1qh4A a.83.1.1,d.128.1.2 18458,41193 1gdvA 85 1.51e+01 1ctj a.3.1.1 60458 1ywnA 316 1.52e+01 1v04A 355 1.53e+01 b.68.6.2 100240 1bjwA 382 1.53e+01 1bjwA c.67.1.1 34349 2f1lA 187 1.58e+01 1pvmA 184 1.60e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1i58A 189 1.61e+01 1b3qA d.122.1.3 61773 1lcjA 109 1.62e+01 1qadA d.93.1.1 40414 1ak9 275 1.63e+01 1gci c.41.1.1 32517 1fu1B 203 1.63e+01 1fu1B b.59.1.1,h.1.11.1 27077,45631 1np1A 184 1.67e+01 1np1A b.60.1.1 27155 1h59B 54 1.69e+01 g.3.9.1 70881 1gs5A 258 1.71e+01 c.73.1.2 70395 1xtlA 175 1.71e+01 1n1cA 217 1.71e+01 a.184.1.1 85254 1bihA 395 1.73e+01 1bihA b.1.1.4,b.1.1.4,b.1.1.4,b.1.1.4 21752,21753,21754,21755 1xneA 113 1.76e+01 1u04A 771 1.77e+01 b.34.14.1,c.55.3.10 107539,107540 1ogqA 313 1.77e+01 c.10.2.8 86996 1xtmA 175 1.80e+01 1to2E 281 1.84e+01 1utcA 363 1.85e+01 a.118.1.4,b.69.6.1 99914,99915 1ik9A 213 1.86e+01 b.59.1.1,h.1.11.1 66176,66177 1xdpA 687 1.86e+01 1sup 275 1.87e+01 1gci c.41.1.1 32510 1f1uA 323 1.88e+01 d.32.1.3,d.32.1.3 83200,83201 1awe 130 1.93e+01 1awe b.55.1.1 26968 2faoA 309 1.94e+01 1njhA 119 1.96e+01 b.128.1.1 85787 1fu1A 203 1.96e+01 1fu1B b.59.1.1,h.1.11.1 27076,45630 1ebuA 358 1.97e+01 1ebuA c.2.1.3,d.81.1.2 30035,39950 1o59A 355 1.98e+01 b.18.1.22,b.18.1.22 92495,92496 1ghr 306 2.00e+01 1aq0A c.1.8.3 28844 1aoqA 567 2.00e+01 1qksA a.3.1.2,b.70.2.1 15934,27692 1iazA 179 2.02e+01 1iazA b.97.1.1 62131 3nodB 423 2.03e+01 1nseA d.174.1.1 42513 1ddvA 111 2.04e+01 1evhA b.55.1.4 27002 1b3eA 330 2.04e+01 1nnt c.94.1.2 35897 1aqn 275 2.05e+01 1gci c.41.1.1 32514 2asfA 137 2.07e+01 1hg4A 279 2.08e+01 1lbd a.123.1.1 19333 1q7fA 286 2.11e+01 b.68.9.1 96036 1mwmA 320 2.14e+01 c.55.1.1,c.55.1.1 79580,79581 2blkA 122 2.14e+01 2cvdA 198 2.15e+01 1aym3 238 2.17e+01 1aym3 1lfo 128 2.18e+01 1hmt b.60.1.2 27223 1aokB 122 2.20e+01 1poa a.133.1.2 19561 1zyeA 220 2.22e+01 1tvdA 116 2.25e+01 1tvdA b.1.1.1 20650 1vrpA 381 2.25e+01 1qh4A 380 2.26e+01 1qh4A a.83.1.1,d.128.1.2 18462,41197 1dm9A 133 2.28e+01 1dm9A d.66.1.3 39560 1be3B 439 2.29e+01 1be3B d.185.1.1,d.185.1.1 58952,58953 1ze3D 125 2.29e+01 1i7gA 287 2.31e+01 a.123.1.1 71121 1dbxA 158 2.32e+01 1dbuA d.116.1.1 40928 2aw5A 541 2.35e+01 1fsu 492 2.36e+01 1auk c.76.1.2 35032 1ddwA 120 2.36e+01 1evhA b.55.1.4 27001 1bcpC 199 2.39e+01 1bcpB b.40.2.1,d.169.1.2 25121,42430 2avtA 378 2.44e+01 1wxxA 382 2.47e+01 1kv9A 668 2.47e+01 a.3.1.6,b.70.1.1 73056,73057 1afsA 323 2.51e+01 1frb c.1.7.1 28694 1dp4A 435 2.53e+01 1dp4A c.93.1.1 35710 2cy2A 174 2.53e+01 1kdj 102 2.53e+01 1plc b.6.1.1 22864 1ulrA 88 2.54e+01 1bj7 156 2.55e+01 1bj7 b.60.1.1 27113 1hcz 252 2.57e+01 1hcz b.2.6.1,b.84.2.2 22464,28250 1pfxC 235 2.57e+01 5ptp b.47.1.2 26353 1y7rA 133 2.58e+01 1pbjA 125 2.62e+01 d.37.1.1,d.37.1.1 94414,94415 2pcfB 250 2.62e+01 1hcz i.4.1.1 45911 1dtgA 334 2.63e+01 1nnt c.94.1.2 35896 1y4wA 518 2.64e+01 1r85A 379 2.64e+01 c.1.8.3 104839 1lkkA 105 2.64e+01 1lckA d.93.1.1 40412 1aq0A 306 2.68e+01 1aq0A c.1.8.3 28842 1qjgA 125 2.69e+01 1opy d.17.4.3 38102 1dmhA 311 2.72e+01 1dmhA b.3.6.1 22633 1pnsB 234 2.73e+01 i.1.1.1 88169 1qrzA 246 2.75e+01 5ptp b.47.1.2 26366 1mjc 69 2.79e+01 1mjc b.40.4.5 25319 1hnf 182 2.87e+01 1qa9A b.1.1.1,b.1.1.3 19741,21680 1gq2A 555 2.88e+01 c.2.1.7,c.58.1.3 70308,70309 1j5eB 256 2.93e+01 c.23.15.1 71543 1b5pA 385 2.98e+01 c.67.1.1 90403 1c5mD 255 3.00e+01 5ptp b.47.1.2 26338 1ig8A 486 3.01e+01 2yhx c.55.1.3,c.55.1.3 64746,64747 1fxoA 293 3.02e+01 1g0rA c.68.1.6 34524 1b06A 210 3.08e+01 1avmA a.2.11.1,d.44.1.1 15740,38737 1kutA 230 3.09e+01 d.143.1.1 73017 2as0A 396 3.11e+01 1diaA 306 3.16e+01 1a4iA c.2.1.7,c.58.1.2 30280,33928 1iyhA 198 3.20e+01 a.45.1.1,c.47.1.5 83790,83791 1gxuA 91 3.21e+01 d.58.10.1 76378 1n7vA 555 3.22e+01 b.126.1.1 85377 1xdfA 157 3.23e+01 1jltB 122 3.24e+01 a.133.1.2 66868 1egxA 115 3.25e+01 1evhA b.55.1.4 27000 1eo9B 241 3.28e+01 3pchM b.3.6.1 22826 1wfuA 120 3.29e+01 1a4iB 301 3.32e+01 1a4iA c.2.1.7,c.58.1.2 30279,33927 2b4wA 315 3.34e+01 1y8oB 128 3.38e+01 1u7iA 136 3.39e+01 d.32.1.7 107724 2b6eA 146 3.41e+01 1vrmA 325 3.42e+01 1bkjA 240 3.44e+01 1bkjA d.90.1.1 40243 1ld4A 264 3.45e+01 i.6.1.1 77886 1ixlA 131 3.46e+01 d.38.1.5 90717 1qksA 567 3.46e+01 1qksA a.3.1.2,b.70.2.1 15951,27710 1n99A 166 3.49e+01 b.36.1.1,b.36.1.1 85459,85460 1vhsA 175 3.50e+01 d.108.1.1 100698 2cu3A 64 3.50e+01 1ohpA 125 3.51e+01 3vub 101 3.52e+01 3vub b.34.6.1 24613 1l0lB 439 3.53e+01 d.185.1.1,d.185.1.1 84484,84485 1ehiA 377 3.53e+01 1iow c.30.1.2,d.142.1.1 31716,41484 1a4iA 301 3.54e+01 1a4iA c.2.1.7,c.58.1.2 30278,33926 1g3fA 117 3.56e+01 1g3fA g.52.1.1 45378 1l0wA 580 3.59e+01 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 2ervA 150 3.61e+01 1e58A 249 3.63e+01 1qhfA c.60.1.1 59262 1g0rA 293 3.63e+01 1g0rA c.68.1.6 34532 1orc 71 3.63e+01 1orc a.35.1.2 17054 1f1xA 322 3.66e+01 d.32.1.3,d.32.1.3 83208,83209 1lf2A 331 3.68e+01 b.50.1.2 77914 1ohuA 175 3.69e+01 f.1.4.1 93029 1yagG 125 3.71e+01 1d0nA d.109.1.1 40846 1mtpB 43 3.72e+01 1qq2A 199 3.75e+01 1qq2A c.47.1.10 33064 2hlcA 230 3.77e+01 5ptp b.47.1.2 26074 1w2lA 99 3.78e+01 1fxzA 476 3.80e+01 b.82.1.2,b.82.1.2 65059,65060 1o0iA 138 3.81e+01 d.38.1.5 86532 1fnhA 271 3.83e+01 1fnhA b.1.2.1,b.1.2.1,b.1.2.1 21976,21977,21978 1hylA 230 3.85e+01 5ptp b.47.1.2 26076 1cq3A 233 3.85e+01 1cq3A b.27.1.1 23923 1t4wA 196 3.87e+01 b.2.5.2 106427 1d2gA 292 3.88e+01 1xvaA c.66.1.5 34187 1qp8A 303 3.92e+01 1qp8A c.2.1.4,c.23.12.1 30092,31352 1u6rA 380 3.94e+01 1gywA 128 3.95e+01 b.1.10.2 70791 1q9jA 422 3.95e+01 c.43.1.2,c.43.1.2 104590,104591 1sxvA 172 3.98e+01 1gdtA 183 4.00e+01 2rslA a.4.1.2,c.53.1.1 16021,33348 1e50A 134 4.05e+01 1cmoA b.2.5.6 59244 2ch4A 320 4.06e+01 2ffcA 353 4.16e+01 1emzA 21 4.20e+01 j.35.1.1 46282 1w2xA 758 4.21e+01 c.14.1.4,c.14.1.4 109134,109135 1y07A 128 4.21e+01 1sqwA 188 4.21e+01 1p9rA 418 4.22e+01 c.37.1.11 94399 1mup 166 4.24e+01 1mup b.60.1.1 27133 1g0uL 241 4.25e+01 d.153.1.4 41894 1t8sA 484 4.26e+01 c.56.2.1 106679 8cho 125 4.27e+01 1opy d.17.4.3 38108 2bpsA 81 4.28e+01 2cjtA 131 4.29e+01 1mt6A 280 4.32e+01 b.76.2.1,b.85.7.1 79446,79447 2bbkH 355 4.32e+01 2bbkH b.69.2.1 27634 1cof 143 4.35e+01 1cof d.109.1.2 40860 1ibvB 229 4.35e+01 1t5yA 190 4.38e+01 b.122.1.1,d.17.6.3 106495,106496 1amx 180 4.38e+01 1amx b.2.3.1 22410 1opd 85 4.47e+01 1ptf d.94.1.1 40560 1h7sA 365 4.48e+01 d.14.1.3,d.122.1.2 65705,65706 1sesA 421 4.49e+01 1sesA a.2.7.1,d.104.1.1 15710,40710 1txvA 452 4.51e+01 1f39A 101 4.56e+01 1umuA b.87.1.1 28386 1ei1A 391 4.56e+01 1aj6 d.14.1.3,d.122.1.2 37570,41104 1iznA 286 4.57e+01 e.43.1.1 83847 1xg8A 111 4.57e+01 1iu1A 146 4.58e+01 b.1.10.2 71428 1yemA 179 4.59e+01 1ixcA 294 4.60e+01 a.4.5.37,c.94.1.1 83764,83765 1poh 85 4.61e+01 1ptf d.94.1.1 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