# List of top-scoring protein chains for t2k-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 1nxiA 132 6.10e-01 d.58.47.1 86381 1lxjA 104 2.15e+00 d.58.48.1 84736 1v37A 177 2.91e+00 2fyxA 143 3.07e+00 2c2hA 192 4.03e+00 1yyaA 250 4.27e+00 1aoxA 203 4.94e+00 1aoxA c.62.1.1 34151 1tx4B 178 6.33e+00 1ctqA c.37.1.8 32045 1kmqA 184 7.38e+00 c.37.1.8 84412 1a9xB 379 7.47e+00 1c3oB c.8.3.1,c.23.16.1 30732,31409 1cs0B 382 7.54e+00 1c3oB c.8.3.1,c.23.16.1 30740,31417 2aq4A 434 7.74e+00 1c3oB 382 8.05e+00 1c3oB c.8.3.1,c.23.16.1 30744,31421 1c30B 382 8.19e+00 c.8.3.1,c.23.16.1 30736,31413 1j5sA 463 8.39e+00 c.1.9.8 71580 1treA 255 8.90e+00 1amk c.1.1.1 28505 1b7aA 186 9.38e+00 1a44 b.17.1.1 23705 1zq1A 438 9.48e+00 1a8p 258 1.11e+01 1fdr b.43.4.2,c.25.1.1 25654,31544 2apqA 139 1.16e+01 1ro7A 259 1.20e+01 c.130.1.1 97667 1e9lA 377 1.22e+01 1e9lA c.1.8.5,d.26.3.1 59395,59396 1zwwA 256 1.24e+01 1v7pC 200 1.29e+01 c.62.1.1 108408 1v8gA 329 1.31e+01 a.46.2.1,c.27.1.1 100505,100506 1a27 289 1.32e+01 1fds c.2.1.2 29839 1x11A 172 1.37e+01 1x11A b.55.1.2 26985 1hkkA 364 1.41e+01 c.1.8.5,d.26.3.1 90634,90635 1lxnA 99 1.47e+01 d.58.48.1 84737 1fds 327 1.49e+01 1fds c.2.1.2 29838 1jtvA 327 1.53e+01 c.2.1.2 84230 1dzaA 129 1.53e+01 7rsa d.5.1.1 37275 1i5rA 327 1.57e+01 c.2.1.2 83668 1fdt 327 1.61e+01 1fds c.2.1.2 29841 1aqjA 421 1.69e+01 2admA c.66.1.27 34242 1vf8A 377 1.72e+01 1a44 185 1.77e+01 1a44 b.17.1.1 23704 1ihgA 370 1.79e+01 2cpl a.118.8.1,b.62.1.1 62380,62381 2admA 421 1.83e+01 2admA c.66.1.27 34238 1qd1A 325 1.84e+01 1qd1A d.58.34.1,d.58.34.1 39493,39494 1ek4A 418 1.84e+01 1dd8A c.95.1.1,c.95.1.1 59436,59437 1zd9A 188 2.04e+01 1yacA 208 2.10e+01 1yacA c.33.1.3 31757 1c2pA 576 2.21e+01 1quvA e.8.1.4 43117 1dd8A 406 2.23e+01 1dd8A c.95.1.1,c.95.1.1 35932,35933 7rsa 124 2.24e+01 7rsa d.5.1.1 37165 1rnd 124 2.25e+01 7rsa d.5.1.1 37178 1xccA 220 2.25e+01 2bywA 418 2.28e+01 2f1fA 164 2.29e+01 1txoA 237 2.32e+01 1dy5A 124 2.33e+01 7rsa d.5.1.1 37163 1o5hA 214 2.34e+01 a.191.1.1 92497 1a5q 124 2.36e+01 7rsa d.5.1.1 37258 2bbdA 350 2.39e+01 2bl0C 142 2.43e+01 1aqcA 172 2.43e+01 1x11A b.55.1.2 26983 1uj2A 252 2.50e+01 c.37.1.6 99452 1ksiA 642 2.50e+01 1ksiB b.30.2.1,d.17.2.1,d.17.2.1 24408,38043,38044 1nf3A 195 2.64e+01 c.37.1.8 85594 1b93A 152 2.69e+01 1b93A c.24.1.2 31507 1ksiB 642 2.72e+01 1ksiB b.30.2.1,d.17.2.1,d.17.2.1 24409,38045,38046 1b93B 152 2.72e+01 1b93A c.24.1.2 31508 1qy6A 274 2.85e+01 b.47.1.1 96574 2a9kA 187 2.88e+01 1behA 187 2.94e+01 1a44 b.17.1.1 23700 1u8zA 168 3.11e+01 2gjlA 328 3.11e+01 2fn4A 181 3.11e+01 4ts1A 319 3.15e+01 2ts1 c.26.1.1 31565 1dp7P 76 3.28e+01 1dp7P a.4.5.20 16159 1bqk 124 3.32e+01 1bqk b.6.1.1 22889 1yt3A 375 3.34e+01 1gz8A 299 3.38e+01 d.144.1.7 83405 1lfpA 249 3.41e+01 e.39.1.1 73885 1hcl 298 3.44e+01 1hcl d.144.1.7 41593 1e1xA 299 3.47e+01 1hcl d.144.1.7 59157 1vlaA 150 3.59e+01 d.227.1.2 108735 1j3bA 529 3.64e+01 c.91.1.1,c.109.1.1 77071,77072 2axyA 73 3.66e+01 1jvpP 298 3.70e+01 d.144.1.7 67371 1q0qA 406 3.73e+01 a.69.3.1,c.2.1.3,d.81.1.3 104464,104465,104466 1a4rA 191 3.73e+01 1ctqA c.37.1.8 32063 1w25A 459 3.76e+01 2ts1 419 3.77e+01 2ts1 c.26.1.1 31564 1t4aA 84 3.81e+01 d.284.1.1 106404 1a5p 124 3.85e+01 7rsa d.5.1.1 37201 1elqA 390 3.90e+01 1elqA c.67.1.3 34436 1eluB 390 3.90e+01 1elqA c.67.1.3 34435 1eluA 390 3.92e+01 1elqA c.67.1.3 34434 1mh1 186 3.95e+01 1eesA c.37.1.8 32002 1rr9A 200 3.99e+01 d.14.1.10 97783 1ddgA 374 4.09e+01 1amoA b.43.4.1,c.25.1.4 25671,31559 2bjvA 265 4.11e+01 1xahA 354 4.14e+01 1jilA 420 4.33e+01 c.26.1.1 66745 1svy 114 4.42e+01 1svy d.109.1.1 40831 1fviA 297 4.46e+01 1fviA b.40.4.6,d.142.2.1 25364,41578 1xrjA 261 4.47e+01 1tqyB 415 4.53e+01 c.95.1.1,c.95.1.1 107247,107248 1y51A 88 4.61e+01 1kbpA 432 4.62e+01 4kbpA b.1.12.1,d.159.1.1 22349,42068 2cveA 191 4.65e+01 1rljA 139 4.91e+01 c.23.5.7 104983 1twjA 84 5.05e+01 d.284.1.1 107407 1j3aA 142 5.06e+01 c.21.1.1 77070 1r5rA 119 5.06e+01 a.39.2.1 97104 2eryA 172 5.07e+01 1ve3A 227 5.11e+01 1k4mA 213 5.20e+01 c.26.1.3 77258 2ayvA 166 5.23e+01 2atvA 196 5.30e+01 1ltqA 301 5.36e+01 c.108.1.9,c.37.1.1 78208,78209 1jvsA 400 5.49e+01 a.69.3.1,c.2.1.3,d.81.1.3 77187,77188,77189 1lam 484 5.58e+01 1lam c.50.1.1,c.56.5.3 33166,33829 1lqtA 456 5.67e+01 c.3.1.1,c.4.1.1 74198,74199 1zjrA 211 5.68e+01 1uqvA 85 5.71e+01 a.60.1.2 99798 1g38A 393 5.72e+01 2admA c.66.1.27 60235 1wm1A 317 5.74e+01 c.69.1.7 109405 1k87A 669 5.82e+01 a.176.1.1,c.1.23.2 77286,77287 1gtdA 85 5.85e+01 d.284.1.1 76344 1nsf 273 5.94e+01 1d2nA c.37.1.20 32429 2ae6A 166 5.95e+01 1lg2A 365 5.97e+01 c.1.8.5,d.26.3.1 77950,77951 4kbpA 432 5.97e+01 4kbpA b.1.12.1,d.159.1.1 22345,42064 2b5oA 402 5.99e+01 1zedA 484 6.00e+01 1whxA 111 6.08e+01 1i2hA 168 6.21e+01 b.55.1.4 71103 1eesA 178 6.22e+01 1eesA c.37.1.8 32073 1mi8A 158 6.29e+01 b.86.1.2 91279 1an0A 190 6.31e+01 1ctqA c.37.1.8 32066 1r31A 428 6.39e+01 d.58.20.1,d.179.1.1 96897,96898 1wq3A 322 6.72e+01 1a6q 382 6.78e+01 1a6q a.159.1.1,d.219.1.1 75801,75802 2c5qA 240 6.81e+01 1p32C 209 6.82e+01 1p32A d.25.1.1 38381 1zelA 298 6.86e+01 1t0hB 224 6.88e+01 c.37.1.1 106208 1x8dA 104 6.88e+01 1qxyA 252 7.03e+01 d.127.1.1 96565 1ew2A 513 7.07e+01 1b8jA c.76.1.1 59525 1xxbA 78 7.11e+01 1xxaA d.74.2.1 39706 1k4nA 192 7.12e+01 d.32.1.5 72059 1d2nA 272 7.13e+01 1d2nA c.37.1.20 32428 1n3oA 252 7.15e+01 b.29.1.1 79967 1ukgA 252 7.19e+01 b.29.1.1 99489 1ck7A 631 7.20e+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 1lap 488 7.25e+01 1lam c.50.1.1,c.56.5.3 33171,33834 1ogiA 303 7.40e+01 b.43.4.2,c.25.1.1 92914,92915 1dfaA 454 7.43e+01 1vdeA b.86.1.2,d.95.2.2,d.95.2.2 28375,40575,40576 1jb9A 316 7.52e+01 1fnc b.43.4.2,c.25.1.1 62840,62841 1bllE 488 7.55e+01 1lam c.50.1.1,c.56.5.3 33170,33833 1azsC 388 7.59e+01 1cipA a.66.1.1,c.37.1.8 18203,32086 1se0A 116 7.60e+01 g.52.1.1 98814 1oaoA 674 7.87e+01 e.26.1.2 86744 1led 243 7.94e+01 1led b.29.1.1 24039 1mbxC 106 7.95e+01 d.45.1.2 78929 1eziA 228 7.96e+01 1eyrA c.68.1.13 34512 1w34A 304 7.98e+01 1t15A 214 8.06e+01 c.15.1.3,c.15.1.3 99067,99068 1ytlA 174 8.15e+01 2bsaA 303 8.25e+01 1aokA 122 8.29e+01 1poa a.133.1.2 19560 1qayA 428 8.34e+01 1qaxA d.58.20.1,d.179.1.1 39378,42599 1i0lA 221 8.35e+01 c.61.1.1 71096 1b3nA 412 8.39e+01 1dd8A c.95.1.1,c.95.1.1 35966,35967 1qaxA 428 8.50e+01 1qaxA d.58.20.1,d.179.1.1 39376,42597 1vdeA 454 8.51e+01 1vdeA b.86.1.2,d.95.2.2,d.95.2.2 28378,40581,40582 1svr 114 8.54e+01 1svy d.109.1.1 40833 1bsmA 201 8.59e+01 1avmA a.2.11.1,d.44.1.1 15780,38743 1wb0A 445 8.63e+01 1s5dA 240 8.83e+01 d.166.1.1 98541 1y88A 199 8.84e+01 1go2A 304 8.91e+01 b.43.4.2,c.25.1.1 76243,76244 1b2rA 304 8.92e+01 1fnc b.43.4.2,c.25.1.1 25648,31538 1yb5A 351 8.92e+01 1x23A 155 8.98e+01