# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7-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 1tsp 559 3.79e-01 1tyv b.80.1.6 28044 1d0hA 469 4.36e-01 1a8d b.29.1.6 24265 b.42.4.2 25610 1i8nA 126 5.54e-01 1i8nA g.10.1.2 61976 1n9eA 787 5.61e-01 b.30.2.1 -3529 d.17.2.1 -9278 d.17.2.1 -9279 1tyv 542 5.76e-01 1tyv b.80.1.6 28038 1a8d 452 5.96e-01 1a8d b.29.1.6 24262 b.42.4.2 25607 1k28A 584 5.98e-01 b.40.8.1 68049 b.108.1.2 68050 d.2.1.3 68051 1tyu 543 5.99e-01 1tyv b.80.1.6 28037 1qq1A 559 6.08e-01 1tyv b.80.1.6 28041 1qa1A 554 6.47e-01 1tyv b.80.1.6 28047 1hw5A 210 6.65e-01 2cgpA a.4.5.4 16098 b.82.3.2 28137 1kzyC 259 8.41e-01 c.15.1.4 73383 c.15.1.4 73384 1k2xA 177 8.70e-01 d.153.1.5 -11450 1gaxA 862 1.26e+00 1gaxA a.2.7.3 75842 a.27.1.1 75843 b.51.1.1 26893 c.26.1.1 31595 1diwA 441 1.59e+00 1a8d b.29.1.6 24264 b.42.4.2 25609 1qubA 319 1.90e+00 1qubA g.18.1.1 44863 g.18.1.1 44864 g.18.1.1 44865 g.18.1.1 44866 g.18.1.1 44867 1tie 172 2.44e+00 1wba b.42.4.1 25592 1b12A 248 2.70e+00 1b12A b.87.1.2 28388 1mn4A 282 2.78e+00 b.2.5.7 79313 1g5aA 628 3.04e+00 b.71.1.1 65152 c.1.8.1 65153 1ffkB 338 3.22e+00 1ffkB b.43.3.2 25719 1a0rP 245 3.60e+00 1b9yC c.47.1.6 33054 1h7nA 342 4.95e+00 1b4kA c.1.10.3 60726 2cgpA 210 4.97e+00 2cgpA a.4.5.4 16102 b.82.3.2 28141 1gmnA 183 5.31e+00 g.10.1.1 65315 g.14.1.1 65316 1omiA 248 5.49e+00 a.4.5.4 87079 b.82.3.3 87080 1lcyA 325 5.79e+00 b.36.1.4 73834 b.47.1.1 73835 1m1hA 248 5.79e+00 b.114.1.1 78415 d.58.42.1 78416 1ylvA 342 5.80e+00 1b4kA c.1.10.3 29180 1dt6A 473 6.18e+00 1dt6A a.104.1.1 18977 1cleA 534 6.28e+00 1thg c.69.1.17 34771 1pbiA 72 6.40e+00 1pi2 g.3.13.1 44346 1ep3B 262 6.43e+00 1ep2B b.43.4.2 25664 c.25.1.3 31554 1t4hA 290 6.56e+00 1fhvA 323 6.75e+00 1fhuA c.1.11.2 29235 d.54.1.1 38879 1h5wA 309 6.90e+00 e.27.1.1 65635 1ih7A 903 7.17e+00 1clqA c.55.3.5 62375 e.8.1.1 62376 1guqA 348 7.47e+00 1guqA d.13.1.2 37522 d.13.1.2 37523 1bhtA 176 7.49e+00 1bhtA g.10.1.1 44603 g.14.1.1 44663 1m1cA 680 7.78e+00 e.42.1.1 78395 1spa 396 7.90e+00 1ajsA c.67.1.1 34291 1hh2P 344 8.01e+00 b.40.4.5 65835 d.52.3.1 65836 d.52.3.1 65837 d.202.1.1 65838 1llfA 534 8.21e+00 c.69.1.17 78094 2hgf 97 8.65e+00 1bhtA g.10.1.1 44607 1dt9A 437 8.85e+00 1dt9A c.55.4.2 33738 d.79.3.2 39815 d.91.1.1 40257 1k7hA 476 8.90e+00 c.76.1.1 72101 1ohlA 342 8.97e+00 c.1.10.3 87035 1ars 396 9.34e+00 1ajsA c.67.1.1 34287 1yua 122 9.35e+00 1yua g.41.3.3 45210 g.41.3.3 45211 1hxpA 348 9.82e+00 1guqA d.13.1.2 37530 d.13.1.2 37531 1bynA 128 1.02e+01 1rsy b.7.1.2 23193 7catA 506 1.03e+01 1cf9A e.5.1.1 42781 1v04A 355 1.08e+01 unknown_sccs -4592 1jofA 365 1.12e+01 b.69.10.1 71775 1har 216 1.13e+01 1rthA e.8.1.2 43025 1o12A 376 1.15e+01 b.92.1.5 80758 c.1.9.10 80759 1mxgA 435 1.17e+01 b.71.1.1 85193 c.1.8.1 85194 1jhdA 396 1.17e+01 b.122.1.3 66712 c.26.1.5 66713 1m9sA 605 1.18e+01 b.1.18.15 78874 b.34.11.1 78875 b.34.11.1 78876 b.34.11.1 78877 c.10.2.1 78878 1ubpC 570 1.19e+01 1ubpC b.92.1.1 28432 c.1.9.2 29054 1ep2B 261 1.22e+01 1ep2B b.43.4.2 25666 c.25.1.3 31556 1ffkQ 119 1.25e+01 1ffkQ b.34.5.1 24605 1ub4A 110 1.26e+01 b.34.6.2 88399 1nd6A 354 1.28e+01 c.60.1.2 80407 1olzA 663 1.30e+01 b.1.1.4 -2678 unknown_sccs -4626 unknown_sccs -12590 1gupA 348 1.32e+01 1guqA d.13.1.2 37534 d.13.1.2 37535 1vdeA 454 1.33e+01 1vdeA b.86.1.2 28378 d.95.2.2 40581 d.95.2.2 40582 1crl 534 1.34e+01 1thg c.69.1.17 34765 1pkn 530 1.34e+01 1a49A b.58.1.1 27042 c.1.12.1 29271 c.49.1.1 33125 1s8fA 177 1.37e+01 1dghB 498 1.38e+01 1cf9A e.5.1.1 42791 1pguA 615 1.40e+01 b.69.4.1 88069 b.69.4.1 88070 1qwlA 505 1.40e+01 e.5.1.1 -11823 1mpyA 307 1.44e+01 1mpyA d.32.1.3 38508 d.32.1.3 38509 1t3cA 421 1.49e+01 1rsy 152 1.50e+01 1rsy b.7.1.2 23192 1ie7C 570 1.50e+01 1ubpC b.92.1.1 62315 c.1.9.2 62316 1qe3A 489 1.51e+01 2bce c.69.1.1 34630 1mq7A 154 1.52e+01 b.85.4.1 79404 1puc 105 1.52e+01 1puc d.97.1.1 40675 1mhnA 59 1.63e+01 b.34.9.1 84964 1r4kA 169 1.63e+01 unknown_sccs -3625 1jm4B 118 1.67e+01 a.29.2.1 71746 1ogoX 574 1.72e+01 unknown_sccs -3237 unknown_sccs -4783 4ubpC 570 1.74e+01 1ubpC b.92.1.1 28431 c.1.9.2 29053 1hrnA 337 1.80e+01 1smrA b.50.1.2 26869 1m0zA 290 1.82e+01 c.10.2.7 74359 1a48 306 1.85e+01 1a48 d.143.1.1 41590 1zfjA 491 1.89e+01 1ak5 c.1.5.1 28638 d.37.1.1 38540 d.37.1.1 38541 1go3E 187 1.89e+01 b.40.4.5 83054 d.230.1.1 83055 1o7fA 469 1.89e+01 a.4.5.31 81131 b.82.3.2 81132 b.82.3.2 81133 1m6uA 272 1.90e+01 b.2.5.7 78706 1jj2B 337 1.94e+01 1ffkB b.43.3.2 63086 1t5yA 190 1.95e+01 1fjmA 330 1.97e+01 1auiA d.159.1.3 42082 1acc 735 1.99e+01 1acc f.11.1.1 43828 1s5lB 510 2.05e+01 1xsm 390 2.14e+01 1xsm a.25.1.2 16804 1jv1A 505 2.17e+01 c.68.1.5 71892 1s72B 338 2.17e+01 1lpuA 332 2.20e+01 d.144.1.7 74177 1ewiA 114 2.20e+01 1ewiA b.40.4.3 25302 2hhmA 276 2.21e+01 1imbA e.7.1.1 42955 1clqA 903 2.22e+01 1clqA c.55.3.5 33717 e.8.1.1 43006 1kn9A 249 2.23e+01 b.87.1.2 68699 1b9yC 246 2.27e+01 1b9yC c.47.1.6 33052 1kaeA 434 2.30e+01 c.82.1.2 72247 1nlnA 204 2.31e+01 d.3.1.7 -8897 1fz1C 389 2.31e+01 1mtyB a.25.1.2 16746 2hmiA 558 2.31e+01 1rthA c.55.3.1 33604 e.8.1.2 43106 1ijxA 127 2.35e+01 1ijxA a.141.1.1 62511 1h0oA 390 2.35e+01 a.25.1.2 70845 2nmbA 160 2.38e+01 2nmbA b.55.1.2 26994 1c4oA 664 2.40e+01 1d2mA c.37.1.19 32415 c.37.1.19 32416 1h7sA 365 2.41e+01 d.14.1.3 65705 d.122.1.2 65706 1bkf 107 2.43e+01 1fkj d.26.1.1 38382 1imdA 277 2.48e+01 1imbA e.7.1.1 42968 1qisA 396 2.48e+01 1ajsA c.67.1.1 34284 1gsmA 210 2.52e+01 b.1.1.4 65535 b.1.1.4 65536 1tdtA 259 2.54e+01 3tdt b.81.1.2 28055 1qi9A 556 2.65e+01 1qhbA a.111.1.2 19053 1k75A 434 2.70e+01 c.82.1.2 68253 2hpaA 342 2.74e+01 1cviA c.60.1.2 33985 1q2wA 308 2.79e+01 b.47.1.4 88355 1sceA 112 2.80e+01 1puc d.97.1.1 40676 1jpmA 366 2.87e+01 c.1.11.2 67031 d.54.1.1 67032 1dhkB 223 2.90e+01 1led b.29.1.1 24157 1vh5A 148 2.91e+01 d.38.1.5 -9677 1e8bA 160 2.93e+01 1e8bA g.14.1.2 44671 g.14.1.2 44672 g.27.1.1 44951 1j34A 129 2.97e+01 d.169.1.1 84048 1eulA 994 3.03e+01 1eulA 1imbA 277 3.05e+01 1imbA e.7.1.1 42957 1ijqA 316 3.08e+01 1ijqA b.68.5.1 62506 g.3.11.1 62507 2mcm 112 3.08e+01 2mcm b.1.7.1 22207 1s4nA 348 3.15e+01 unknown_sccs -8262 2e2c 156 3.17e+01 1u9aA d.20.1.1 38336 1fzyA 149 3.19e+01 d.20.1.1 65072 1dgfA 497 3.29e+01 1cf9A e.5.1.1 42782 1ughI 82 3.29e+01 1ugiA d.17.5.1 38133 1preB 470 3.30e+01 1preA d.169.1.2 42438 f.8.1.1 43825 1sjyA 159 3.35e+01 d.113.1.1 -10908 1h8gA 95 3.36e+01 b.109.1.1 65735 1art 396 3.36e+01 1ajsA c.67.1.1 34285 1fkf 107 3.37e+01 1fkj d.26.1.1 38386 1fkj 107 3.38e+01 1fkj d.26.1.1 38384 1go4A 205 3.50e+01 d.135.1.1 70292 1q0bA 367 3.50e+01 c.37.1.9 -7105 1oz7A 131 3.54e+01 d.169.1.1 -11622 1qhlA 227 3.56e+01 1qhlA c.37.1.12 32382 1bmx 31 3.57e+01 1bmx j.47.1.1 46326 1kf6A 602 3.61e+01 a.7.3.1 72394 c.3.1.4 72395 d.168.1.1 72396 1jyhA 157 3.62e+01 d.60.1.3 71956 1m7sA 484 3.64e+01 e.5.1.1 74574 1rwzA 245 3.65e+01 d.131.1.2 -11106 d.131.1.2 -11107 1p9aG 290 3.67e+01 c.10.2.7 87990 2mnr 357 3.68e+01 2mnr c.1.11.2 29245 d.54.1.1 38889 1l3aA 228 3.70e+01 d.18.1.2 73531 1mswD 883 3.70e+01 e.8.1.3 79427 1l0oA 150 3.70e+01 d.122.1.3 73403 1bowA 159 3.76e+01 1bowA d.60.1.1 39528 1def 147 3.79e+01 1bs4A d.167.1.1 42306 1ufhA 180 3.83e+01 d.108.1.1 88485 1e88A 160 3.84e+01 g.14.1.2 44669 g.14.1.2 44670 g.27.1.1 44950 1bg2 325 3.89e+01 1bg2 c.37.1.9 32189 1ny72 369 3.92e+01 1bywA 110 3.95e+01 1bywA d.110.3.6 40912 1kgqA 274 4.00e+01 b.81.1.2 72447