# List of top-scoring protein chains for t2k-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 1ykiA 217 6.12e-01 1dfaA 454 6.12e-01 1vdeA b.86.1.2,d.95.2.2,d.95.2.2 28375,40575,40576 1eluB 390 6.40e-01 1elqA c.67.1.3 34435 1elqA 390 8.05e-01 1elqA c.67.1.3 34436 1vdeA 454 8.33e-01 1vdeA b.86.1.2,d.95.2.2,d.95.2.2 28378,40581,40582 1icrA 217 8.41e-01 1vfrA d.90.1.1 62274 1eluA 390 9.16e-01 1elqA c.67.1.3 34434 1yyaA 250 1.02e+00 1zq1A 438 1.73e+00 1yt3A 375 1.74e+00 1ve3A 227 1.77e+00 1x11A 172 1.92e+00 1x11A b.55.1.2 26985 1j5sA 463 2.39e+00 c.1.9.8 71580 1i0lA 221 2.76e+00 c.61.1.1 71096 1k4nA 192 3.25e+00 d.32.1.5 72059 1necA 216 3.35e+00 1vfrA d.90.1.1 40249 1tx4B 178 4.63e+00 1ctqA c.37.1.8 32045 1yb2A 275 4.85e+00 1qh0A 295 5.14e+00 b.43.4.2,c.25.1.1 68891,68892 1ewkA 490 5.21e+00 1ewkA c.93.1.1 35712 1ihgA 370 5.33e+00 2cpl a.118.8.1,b.62.1.1 62380,62381 1umkA 275 5.67e+00 1kmqA 184 5.80e+00 c.37.1.8 84412 1jb0D 138 5.98e+00 1jb0D d.187.1.1 62823 1tc1A 220 6.06e+00 1tc1A c.61.1.1 34083 1o5hA 214 6.09e+00 a.191.1.1 92497 1esgA 213 6.09e+00 1bam c.52.1.3 33286 1vk8A 106 6.88e+00 d.58.48.1 108636 1v1aA 309 6.90e+00 c.72.1.1 100249 1lxjA 104 6.98e+00 d.58.48.1 84736 1aqcA 172 7.17e+00 1x11A b.55.1.2 26983 1r5lA 262 7.43e+00 a.5.3.1,c.13.1.1 97099,97100 2bv5A 282 7.62e+00 1zelA 298 7.87e+00 1a8p 258 7.90e+00 1fdr b.43.4.2,c.25.1.1 25654,31544 1aoxA 203 7.92e+00 1aoxA c.62.1.1 34151 1treA 255 7.94e+00 1amk c.1.1.1 28505 1qaxA 428 8.14e+00 1qaxA d.58.20.1,d.179.1.1 39376,42597 1w34A 304 8.19e+00 1r31A 428 8.26e+00 d.58.20.1,d.179.1.1 96897,96898 1qayA 428 9.04e+00 1qaxA d.58.20.1,d.179.1.1 39378,42599 2c2hA 192 9.08e+00 1c2pA 576 9.15e+00 1quvA e.8.1.4 43117 1bam 213 9.16e+00 1bam c.52.1.3 33285 2fh7A 595 9.21e+00 1i7pA 274 9.84e+00 b.43.4.2,c.25.1.1 66048,66049 2bijA 305 9.90e+00 1mh1 186 1.08e+01 1eesA c.37.1.8 32002 1que 303 1.10e+01 1fnc b.43.4.2,c.25.1.1 25647,31537 1rm4A 337 1.12e+01 c.2.1.3,d.81.1.1 105000,105001 2b5oA 402 1.13e+01 1b2rA 304 1.14e+01 1fnc b.43.4.2,c.25.1.1 25648,31538 1ro7A 259 1.18e+01 c.130.1.1 97667 1jvwA 167 1.30e+01 d.26.1.1 71907 2apqA 139 1.35e+01 1b43A 340 1.35e+01 1a76 a.60.7.1,c.120.1.2 18092,33362 2bo4A 397 1.38e+01 1zmdA 474 1.41e+01 1guzA 310 1.46e+01 c.2.1.5,d.162.1.1 65586,65587 1whxA 111 1.50e+01 2fbhA 146 1.54e+01 1nxiA 132 1.55e+01 d.58.47.1 86381 1as0 353 1.60e+01 1cipA a.66.1.1,c.37.1.8 18212,32095 1gtdA 85 1.61e+01 d.284.1.1 76344 2acvA 463 1.61e+01 1fnc 314 1.62e+01 1fnc b.43.4.2,c.25.1.1 25627,31517 2bl0C 142 1.68e+01 1v54A 514 1.71e+01 f.24.1.1 100321 1b4bA 71 1.71e+01 1b4aA d.74.2.1 39718 2occA 514 1.72e+01 2occA f.24.1.1 43518 1ogiA 303 1.76e+01 b.43.4.2,c.25.1.1 92914,92915 1fnd 314 1.81e+01 1fnc b.43.4.2,c.25.1.1 25626,31516 2f2lA 167 1.83e+01 1jztA 246 1.84e+01 c.104.1.1 63319 1fnb 314 1.87e+01 1fnc b.43.4.2,c.25.1.1 25628,31518 1a1s 314 1.88e+01 1othA c.78.1.1,c.78.1.1 35258,35259 1vf8A 377 1.88e+01 1yb5A 351 1.94e+01 2bsaA 303 1.99e+01 1svsA 353 1.99e+01 c.37.1.8 106051 1eq6A 189 2.01e+01 1eq6A d.107.1.1 40796 1cipA 353 2.06e+01 1cipA a.66.1.1,c.37.1.8 18210,32093 2bjvA 265 2.09e+01 1dcjA 81 2.10e+01 1dcjA d.68.3.3 59115 1zd9A 188 2.10e+01 1e9lA 377 2.14e+01 1e9lA c.1.8.5,d.26.3.1 59395,59396 1aqjA 421 2.16e+01 2admA c.66.1.27 34242 1jb9A 316 2.21e+01 1fnc b.43.4.2,c.25.1.1 62840,62841 1tqyB 415 2.23e+01 c.95.1.1,c.95.1.1 107247,107248 1ub0A 258 2.24e+01 c.72.1.2 88394 1x6fA 88 2.33e+01 1azsC 388 2.35e+01 1cipA a.66.1.1,c.37.1.8 18203,32086 1zxoA 291 2.37e+01 1bx1A 314 2.40e+01 1fnc b.43.4.2,c.25.1.1 25629,31519 1xxcA 78 2.41e+01 1xxaA d.74.2.1 39712 1jhsA 188 2.45e+01 d.107.1.1 84172 2f1fA 164 2.56e+01 1wpoA 256 2.59e+01 1lay b.57.1.1 27012 1go2A 304 2.67e+01 b.43.4.2,c.25.1.1 76243,76244 1obfO 335 2.71e+01 c.2.1.3,d.81.1.1 86768,86769 1l0bA 229 2.93e+01 c.15.1.3,c.15.1.3 73391,73392 1ogsA 497 2.99e+01 b.71.1.2,c.1.8.3 86997,86998 1s5lT 32 3.00e+01 2axtT 32 3.10e+01 1xccA 220 3.11e+01 1vddA 228 3.11e+01 e.49.1.1 108519 1zwwA 256 3.13e+01 2fsxA 148 3.13e+01 2a4aA 281 3.17e+01 2azpA 318 3.21e+01 1e1xA 299 3.22e+01 1hcl d.144.1.7 59157 1b4aA 149 3.28e+01 1b4aA a.4.5.3,d.74.2.1 16088,39721 1pvvA 315 3.28e+01 c.78.1.1,c.78.1.1 95190,95191 1t4aA 84 3.36e+01 d.284.1.1 106404 1ze3D 125 3.36e+01 1vj7A 393 3.40e+01 a.211.1.1,d.218.1.8 100801,100802 1twjA 84 3.43e+01 d.284.1.1 107407 2b3wA 168 3.46e+01 2bo9A 308 3.47e+01 1qpxA 218 3.56e+01 1qpxA b.1.11.1,b.7.2.1 22318,23200 2kinB 100 3.68e+01 3kinB 1b04A 318 3.76e+01 1b04A d.142.2.2 41579 1xahA 354 3.86e+01 1kdxA 81 3.87e+01 1kdxA a.12.1.1 16375 1z08A 170 3.88e+01 1hruA 188 3.92e+01 1hruA d.115.1.1 40926 1ka2A 499 3.94e+01 d.92.1.5 77305 1aokA 122 3.98e+01 1poa a.133.1.2 19560 1tadA 324 4.03e+01 1cipA a.66.1.1,c.37.1.8 18194,32077 1jeoA 180 4.11e+01 c.80.1.3 66611 1ojrA 274 4.11e+01 c.74.1.1 93147 1qx4A 274 4.20e+01 b.43.4.2,c.25.1.1 104624,104625 1wv9A 94 4.21e+01 1uarA 285 4.26e+01 c.46.1.2,c.46.1.2 107762,107763 2a0mA 316 4.34e+01 7rsa 124 4.35e+01 7rsa d.5.1.1 37165 1sb0A 87 4.41e+01 a.12.1.1 98789 1hcl 298 4.44e+01 1hcl d.144.1.7 41593 3kinB 117 4.47e+01 3kinB 1vg8A 207 4.55e+01 c.37.1.8 108606 2admA 421 4.55e+01 2admA c.66.1.27 34238 1az5 99 4.58e+01 1hvc b.50.1.1 26747 1v5vA 401 4.60e+01 1gt7A 274 4.63e+01 c.74.1.1 70398 1qg0A 308 4.70e+01 1fnc b.43.4.2,c.25.1.1 25639,31529 1xxbA 78 4.74e+01 1xxaA d.74.2.1 39706 2cw8A 537 4.81e+01 1m1fA 110 4.82e+01 b.34.6.2 78401 1mc2A 122 4.92e+01 a.133.1.2 74622 1l3iA 192 4.95e+01 c.66.1.22 77676 1xxaA 78 5.04e+01 1xxaA d.74.2.1 39700 1opjA 293 5.04e+01 d.144.1.7 87230 1dujA 187 5.14e+01 1dujA d.135.1.1 41449 1z98A 281 5.18e+01 1cfpA 92 5.22e+01 1b4cA a.39.1.2 17172 1edoA 244 5.23e+01 1ybvA c.2.1.2 29896 1fqtA 112 5.28e+01 1fqtA b.33.1.1 24441 1go4A 205 5.29e+01 d.135.1.1 70292 1a98A 152 5.29e+01 1nulA c.61.1.1 34021 3bamB 213 5.33e+01 1bam c.52.1.3 33289 1a5q 124 5.34e+01 7rsa d.5.1.1 37258 1w8xM 83 5.35e+01 1c25 161 5.38e+01 1c25 c.46.1.1 32698 1gz8A 299 5.47e+01 d.144.1.7 83405 2gd1O 334 5.47e+01 1dssG c.2.1.3,d.81.1.1 29978,39893 1v9nA 360 5.55e+01 1mbxC 106 5.57e+01 d.45.1.2 78929 1tx4A 198 5.58e+01 1tx4A a.116.1.1 19098 1ctdA 36 5.62e+01 1ctdA a.39.1.5 17230 1b93B 152 5.62e+01 1b93A c.24.1.2 31508 1b1cA 181 5.65e+01 1amoA c.23.5.2 31212 1x8mA 288 5.70e+01 b.82.1.13 109516 1f60B 94 5.73e+01 1b64 d.58.12.1 39307 1s7iA 124 5.73e+01 d.58.4.9 105353 1g7cB 94 5.75e+01 1b64 d.58.12.1 39308 1a76 326 5.78e+01 1a76 a.60.7.1,c.120.1.2 18091,33361 1eesA 178 5.90e+01 1eesA c.37.1.8 32073 1ywmA 200 5.92e+01 1a9xB 379 5.98e+01 1c3oB c.8.3.1,c.23.16.1 30732,31409 1h75A 81 6.05e+01 1h75A c.47.1.1 60716 1e79A 510 6.08e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18269,26434,32314 3bamA 213 6.08e+01 1bam c.52.1.3 33288 1b93A 152 6.11e+01 1b93A c.24.1.2 31507 1ooeA 236 6.18e+01 c.2.1.2 87196 1vplA 256 6.20e+01 1f2vA 219 6.21e+01 1f2vA c.23.17.1 59627 1wn2A 121 6.31e+01 1ldm 329 6.38e+01 3ldh c.2.1.5,d.162.1.1 30160,42127 1jltA 122 6.40e+01 a.133.1.2 66867 1attA 421 6.40e+01 1ovaA e.1.1.1 42638 1gmuA 143 6.44e+01 b.107.1.1,d.58.38.1 65335,65336 1i76A 163 6.62e+01 1hfc d.92.1.11 61877 2a9kA 187 6.63e+01 1fdpA 235 6.64e+01 5ptp b.47.1.2 26322 1wab 232 6.73e+01 1wab c.23.10.3 31341 1upaA 573 6.76e+01 c.31.1.3,c.36.1.5,c.36.1.9 99714,99715,99716 1fztA 211 6.77e+01 1qhfA c.60.1.1 60158 1odkA 235 6.78e+01 c.56.2.1 86863 1q32A 544 6.81e+01 d.136.1.3,d.136.1.3 104507,104508 1gd1O 334 6.81e+01 1dssG c.2.1.3,d.81.1.1 29962,39877 1a6q 382 6.86e+01 1a6q a.159.1.1,d.219.1.1 75801,75802 2ceyA 306 6.88e+01 1gadO 330 6.89e+01 1dssG c.2.1.3,d.81.1.1 29950,39865 1v8gA 329 6.91e+01 a.46.2.1,c.27.1.1 100505,100506 1dzaA 129 6.93e+01 7rsa d.5.1.1 37275 1qppA 218 6.96e+01 1qpxA b.1.11.1,b.7.2.1 22320,23202 1jvpP 298 6.97e+01 d.144.1.7 67371 2ga9A 297 7.02e+01 1v7pC 200 7.05e+01 c.62.1.1 108408 2bcoA 350 7.07e+01 1hfc 169 7.11e+01 1hfc d.92.1.11 40335 1y8tA 324 7.14e+01 1b9bA 255 7.22e+01 1amk c.1.1.1 28531 1mdbA 539 7.23e+01 e.23.1.1 79008 1c3oB 382 7.30e+01 1c3oB c.8.3.1,c.23.16.1 30744,31421 3fib 249 7.31e+01 3fib d.171.1.1 42455 1n27A 96 7.37e+01 b.34.9.2 91549 1g60A 260 7.38e+01 c.66.1.11 70151 1vpi 122 7.44e+01 1poa a.133.1.2 19559 1h91A 180 7.46e+01 b.60.1.1 60805 2ewrA 170 7.50e+01 1avmA 201 7.50e+01 1avmA a.2.11.1,d.44.1.1 15782,38745 1nf3A 195 7.54e+01 c.37.1.8 85594 1iqpA 327 7.56e+01 a.80.1.1,c.37.1.20 62649,62650 1ge9A 184 7.57e+01 1dd5A d.67.3.1 60463 1a85A 158 7.60e+01 1hfc d.92.1.11 40355 1omhA 293 7.63e+01 d.89.1.5 93348 1y4lA 121 7.63e+01 1i4uA 181 7.68e+01 b.60.1.1 61732 1ogaD 215 7.71e+01 b.1.1.1,b.1.1.2 86990,86991 1um8A 376 7.73e+01 c.37.1.20 99580 1rgqC 22 7.80e+01 1i7nA 309 7.90e+01 c.30.1.5,d.142.1.3 83681,83682 1g38A 393 7.95e+01 2admA c.66.1.27 60235 1udsA 255 7.97e+01 d.14.1.4,d.101.1.1 99219,99220 1e5pA 151 8.02e+01 1bj7 b.60.1.1 59272 1es9A 232 8.14e+01 1wab c.23.10.3 31340 1r6oC 106 8.14e+01 1p32C 209 8.18e+01 1p32A d.25.1.1 38381 1cs0B 382 8.21e+01 1c3oB c.8.3.1,c.23.16.1 30740,31417 1mgpA 313 8.21e+01 c.119.1.1 79098 1bzsA 165 8.21e+01 1hfc d.92.1.11 40348 1r8hA 87 8.24e+01 d.58.8.1 97233 1klqA 197 8.24e+01 d.135.1.1 68689 1am4D 177 8.26e+01 1ctqA c.37.1.8 32068 1lxnA 99 8.27e+01 d.58.48.1 84737 1h8eA 510 8.35e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 60738,60739,60740 1v71A 323 8.44e+01 1c30B 382 8.46e+01 c.8.3.1,c.23.16.1 30736,31413 1mwyA 73 8.55e+01 d.58.17.1 79616 1iqvA 218 8.55e+01 1rss a.75.1.1 62661 1k77A 260 8.57e+01 c.1.15.5 72096 1t0hB 224 8.58e+01 c.37.1.1 106208 1aq3A 129 8.63e+01 1msc d.85.1.1 40079 1trkA 680 8.64e+01 1trkA c.36.1.10,c.36.1.6,c.48.1.1 31803,31804,33090 1idsA 207 8.66e+01 1avmA a.2.11.1,d.44.1.1 15722,38730 1ck7A 631 8.76e+01 1ck7A b.66.1.1,g.14.1.2,g.14.1.2,g.14.1.2,a.20.1.2,d.92.1.11 27538,44674,44675,44676,58969,58970 1j55A 95 8.79e+01 a.39.1.2 77078 1b4cA 92 8.83e+01 1b4cA a.39.1.2 17169 1a1vA 476 8.88e+01 1heiA c.37.1.14,c.37.1.14 32467,32468 2fn4A 181 8.89e+01 1t3lA 337 8.89e+01 b.34.2.1,c.37.1.1 106358,106359 1k6iA 352 8.91e+01 c.2.1.2 68223 1o26A 232 8.94e+01 d.207.1.1 86566 2gjsA 176 8.96e+01