# List of top-scoring protein chains for t2k-100-30-alpha 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 1ca1 370 1.01e+00 1ca1 a.124.1.1 19340 b.12.1.3 23648 1ehkC 33 1.28e+00 1ehkC f.23.9.1 43626 1q8iA 783 1.30e+00 c.55.3.5 -7635 e.8.1.1 -11885 1dd3A 128 1.42e+00 1dd3C a.108.1.1 19031 d.45.1.1 38760 1fzkA 274 1.43e+00 1agdA b.1.1.2 60149 d.19.1.1 60150 2cblA 305 1.52e+00 2cblA a.39.1.7 17380 a.48.1.1 17774 d.93.1.1 40528 1b47A 304 2.05e+00 2cblA a.39.1.7 17381 a.48.1.1 17775 d.93.1.1 40529 1agdA 276 2.14e+00 1agdA b.1.1.2 20741 d.19.1.1 38260 1g7pA 274 2.61e+00 b.1.1.2 70153 d.19.1.1 70154 1fzoA 274 2.75e+00 1agdA b.1.1.2 60155 d.19.1.1 60156 1nozA 388 2.81e+00 1clqA c.55.3.5 33715 1lvwA 295 2.87e+00 c.68.1.6 84723 1k5nA 276 2.92e+00 b.1.1.2 77266 d.19.1.1 77267 1g1eB 89 2.94e+00 1g1eB a.59.1.1 17931 2occJ 59 3.11e+00 2occJ f.23.4.1 43524 1trkA 680 3.28e+00 1trkA c.36.1.6 31804 c.36.1.10 31803 c.48.1.1 33090 1dtoA 221 3.37e+00 1dtoA b.91.1.1 28405 1lk2A 274 3.42e+00 b.1.1.2 -2610 d.19.1.1 -9365 1kpuA 274 3.45e+00 b.1.1.2 84456 d.19.1.1 84457 1hkhA 279 3.53e+00 c.69.1.12 -8342 1e3dB 542 3.75e+00 1h2rL e.18.1.1 59189 1keyA 235 3.90e+00 a.118.16.1 72389 1s9aA 257 3.92e+00 1d3uB 201 3.96e+00 1aisB a.74.1.2 18386 a.74.1.2 18387 1gpb 842 4.28e+00 1a8i c.87.1.4 35478 1noyA 388 4.29e+00 1clqA c.55.3.5 33713 1gpuA 680 4.64e+00 c.36.1.6 65455 c.36.1.10 65454 c.48.1.1 65456 1ekeA 230 4.90e+00 1ekeA c.55.3.1 33572 1tkaA 678 4.91e+00 1trkA c.36.1.6 31816 c.36.1.10 31815 c.48.1.1 33096 1pq1A 196 5.15e+00 f.1.4.1 -12055 1v54J 59 5.33e+00 f.23.4.1 -12112 1elkA 157 5.36e+00 1dvpA a.118.9.2 19217 1c8kA 842 5.67e+00 1a8i c.87.1.4 35491 1pvyA 227 5.75e+00 d.115.1.2 -10937 1aj8A 371 6.19e+00 1aj8A a.103.1.1 18900 1snnA 227 6.51e+00 1a8i 842 6.60e+00 1a8i c.87.1.4 35490 1h5uA 842 6.62e+00 1a8i c.87.1.4 60655 1hsbA 270 6.86e+00 1agdA b.1.1.2 20736 d.19.1.1 38257 1g8iA 190 7.44e+00 1rec a.39.1.5 60363 1b25A 619 7.63e+00 1b25A a.110.1.1 19044 d.152.1.1 41796 1kv9A 668 7.64e+00 a.3.1.6 73056 b.70.1.1 73057 1duzA 275 7.96e+00 1agdA b.1.1.2 20670 d.19.1.1 38224 1e0cA 271 7.98e+00 1e0cA c.46.1.2 32717 c.46.1.2 32718 1ba1 386 7.98e+00 1ba1 c.55.1.1 33387 c.55.1.1 33388 1pxtB 390 8.42e+00 1afwA c.95.1.1 35906 c.95.1.1 35907 1m1hA 248 8.50e+00 b.114.1.1 78415 d.58.42.1 78416 1ithA 141 8.78e+00 1ithA a.1.1.2 15623 3blm 257 8.86e+00 1btl e.3.1.1 42709 1rh5A 436 8.98e+00 unknown_sccs -12298 1i4fA 275 9.00e+00 1agdA b.1.1.2 61687 d.19.1.1 61688 1h38B 883 9.32e+00 e.8.1.3 76626 1f47B 144 1.00e+01 1f46A d.129.4.1 59645 1r6xA 395 1.04e+01 b.122.1.3 -5125 c.26.1.5 -6620 1afwA 393 1.04e+01 1afwA c.95.1.1 35900 c.95.1.1 35901 1pufA 77 1.05e+01 a.4.1.1 -191 1foeA 377 1.05e+01 1foeA a.87.1.1 18517 b.55.1.1 26969 1hl8A 449 1.07e+01 unknown_sccs -4690 unknown_sccs -5361 1ll7A 392 1.10e+01 c.1.8.5 78085 d.26.3.1 78086 1brwA 433 1.11e+01 1brwA a.46.2.1 17764 c.27.1.1 31628 d.41.3.1 38626 1kay 381 1.12e+01 1ba1 c.55.1.1 33385 c.55.1.1 33386 1f46A 140 1.13e+01 1f46A d.129.4.1 59643 1mun 225 1.15e+01 1mun a.96.1.2 18744 1lci 550 1.17e+01 1lci e.23.1.1 43349 1jggA 60 1.18e+01 2hddA a.4.1.1 62950 1hl9A 449 1.18e+01 unknown_sccs -4694 unknown_sccs -5365 1ax4A 467 1.19e+01 1ax4A c.67.1.2 34391 1h38C 883 1.22e+01 e.8.1.3 76627 1aisB 200 1.23e+01 1aisB a.74.1.2 18384 a.74.1.2 18385 1pioA 257 1.27e+01 1btl e.3.1.1 42719 1bxsA 501 1.28e+01 1bpwA c.82.1.1 35357 1d3hA 367 1.28e+01 1d3gA c.1.4.1 28601 1alq 266 1.31e+01 1btl e.3.1.1 42707 1o08A 221 1.31e+01 c.108.1.6 86525 1g8fA 511 1.35e+01 1g8fA b.122.1.3 60348 c.26.1.5 60349 c.37.1.15 60350 1pprM 312 1.35e+01 1pprM a.131.1.1 19502 a.131.1.1 19503 1dguA 183 1.35e+01 1dguA a.39.1.5 17333 1ctf 74 1.45e+01 1ctf d.45.1.1 38759 1dk8A 147 1.47e+01 1agrE a.91.1.1 18548 1i50A 1733 1.49e+01 e.29.1.2 61754 1d2kA 392 1.49e+01 1d2kA c.1.8.5 29008 d.26.3.1 38442 1bupA 386 1.51e+01 1ba1 c.55.1.1 33377 c.55.1.1 33378 1bxlA 181 1.52e+01 1maz f.1.4.1 43396 1ei9A 279 1.55e+01 1ei9A c.69.1.13 34713 1k4wA 252 1.59e+01 a.123.1.1 72068 1h38D 883 1.60e+01 e.8.1.3 76628 1lvfA 110 1.60e+01 a.47.2.1 74280 1r4pA 297 1.63e+01 d.165.1.2 -11560 1v54C 261 1.65e+01 f.25.1.1 -12239 1j7gA 144 1.67e+01 c.110.1.1 84130 1fcdA 401 1.67e+01 1fcdA c.3.1.5 30593 c.3.1.5 30594 d.87.1.1 40218 1fl1A 230 1.70e+01 1at3A b.57.1.1 27023 1n9bA 265 1.75e+01 e.3.1.1 85463 1nq7A 244 1.75e+01 a.123.1.1 -1682 1bgf 124 1.87e+01 1bgf a.90.1.1 18537 1lvhA 221 1.87e+01 c.108.1.6 74282 1ccwB 483 1.87e+01 1cb7B c.1.19.2 29646 1rxqA 178 1.88e+01 1pq1B 33 1.89e+01 1d3gA 367 1.90e+01 1d3gA c.1.4.1 28600 1dat 174 1.90e+01 2fha a.25.1.1 16677 1muyA 225 1.93e+01 1mun a.96.1.2 18745 1lit 144 1.95e+01 1qddA d.169.1.1 42325 1bbhA 131 1.95e+01 1bbhA a.24.3.2 16546 1g4yR 148 1.96e+01 1cll a.39.1.5 60252 1j1jA 240 2.05e+01 a.118.16.1 -1637 1jmuB 666 2.07e+01 1dw0A 112 2.08e+01 1dw0A a.3.1.1 15911 1bjaA 95 2.08e+01 1bjaA a.4.5.9 16122 1mbxC 106 2.08e+01 d.45.1.2 78929 4blmA 265 2.09e+01 1btl e.3.1.1 42721 487dH 224 2.10e+01 1ad2 i.1.1.2 45835 1t0gA 109 2.11e+01 unknown_sccs -10955 1o6yA 299 2.12e+01 d.144.1.7 81106 1ad2 228 2.13e+01 1ad2 e.24.1.1 43353 2occC 261 2.13e+01 1ocrC f.25.1.1 43520 1rwsA 77 2.14e+01 d.15.3.2 -9182 1o69A 394 2.15e+01 c.67.1.4 -8209 1e5eA 404 2.17e+01 1ibjA c.67.1.3 59265 1k5dC 386 2.17e+01 c.10.1.2 68170 1ee8A 266 2.21e+01 1ee8A a.156.1.2 75823 b.113.1.1 75824 g.39.1.8 75825 1g7dA 106 2.21e+01 1g7dA a.71.1.1 18318 1b7bA 310 2.22e+01 1b7bA c.73.1.1 34963 1uumA 372 2.23e+01 c.1.4.1 -5193 1rprA 63 2.26e+01 1nkd a.30.1.1 16989 1ps9A 671 2.28e+01 c.1.4.1 -5206 1pauA 147 2.31e+01 1pauA c.17.1.1 30994 1di6A 195 2.32e+01 1di6A c.57.1.1 33863 1lnwA 147 2.35e+01 a.4.5.28 78104 1yrgB 385 2.37e+01 1yrgA c.10.1.2 30855 1ocrC 261 2.39e+01 1ocrC f.25.1.1 43540 1gs5A 258 2.43e+01 c.73.1.2 70395 1tph1 247 2.49e+01 1amk 1rcsA 105 2.50e+01 1jhgA a.4.12.1 19025 1cb7B 483 2.50e+01 1cb7B c.1.19.2 29648 1qr6A 584 2.52e+01 1qr6A c.2.1.7 30293 c.58.1.3 33941 2plc 274 2.59e+01 2plc c.1.18.2 29614 1n93X 375 2.63e+01 unknown_sccs -1540 1s6cA 183 2.65e+01 a.39.1.5 -858 1m1eB 81 2.65e+01 a.161.1.1 78400 1rl4A 188 2.67e+01 d.167.1.1 -11593 1jo0A 98 2.67e+01 d.68.4.1 77140 1oivA 191 2.69e+01 c.37.1.8 -7074 2occM 46 2.70e+01 2occM f.23.7.1 43527 1ly1A 181 2.73e+01 c.37.1.1 74334 1o89A 345 2.75e+01 b.35.1.2 -3703 c.2.1.1 -5727 1a6dA 545 2.79e+01 1a6dA a.129.1.2 19488 c.8.5.2 30819 d.56.1.2 38936 1v54M 46 2.83e+01 f.23.7.1 -12124 1qddA 144 2.85e+01 1qddA d.169.1.1 42324 1nvmA 345 2.89e+01 a.5.7.1 86249 c.1.10.5 86250 1jqeA 292 2.89e+01 c.66.1.19 71789 1ptmA 329 2.91e+01 unknown_sccs -8456 1amk 251 2.93e+01 1amk c.1.1.1 28503 1k3lA 221 2.98e+01 a.45.1.1 77229 c.47.1.5 77230 1v7oA 165 2.99e+01 unknown_sccs -10249 1od2A 805 2.99e+01 c.14.1.4 86821 c.14.1.4 86822 1nmeA 146 3.05e+01 c.17.1.1 85874 1ucpA 91 3.08e+01 unknown_sccs -1193 1e9lA 377 3.09e+01 1e9lA c.1.8.5 59395 d.26.3.1 59396 1j24A 143 3.18e+01 c.52.1.20 84008 1ji1A 637 3.19e+01 b.1.18.2 71666 b.71.1.1 71667 c.1.8.1 71668 1a5j 110 3.22e+01 1a5j a.4.1.3 16043 a.4.1.3 16044 1nubA 229 3.22e+01 1sra a.39.1.3 17191 g.3.11.3 44330 unknown_sccs 44715 1e5mA 416 3.25e+01 1dd8A c.95.1.1 58973 c.95.1.1 58974 1aye 401 3.26e+01 1aye c.56.5.1 33824 d.58.3.1 39065 1mn3A 54 3.30e+01 a.5.2.4 85024 1bzpA 153 3.32e+01 1a6m a.1.1.2 15020 1il6 185 3.36e+01 1alu a.26.1.1 16827 1efpB 252 3.36e+01 1efvB c.26.2.3 31636 1b72B 87 3.44e+01 1akhA a.4.1.1 16001 1hybA 181 3.46e+01 1f9aA c.26.1.3 61399 1bsg 266 3.48e+01 1btl e.3.1.1 42729 1mbd 153 3.52e+01 1a6m a.1.1.2 15033 1c9qA 117 3.56e+01 1c9qA g.52.1.1 45377 1rpo 65 3.66e+01 1nkd a.30.1.1 16975 1jceA 344 3.69e+01 c.55.1.1 62876 c.55.1.1 62877 1a3qA 285 3.70e+01 1a3qA b.1.18.1 21932 b.2.5.3 22447 1ghpA 258 3.74e+01 1btl e.3.1.1 60520 1p65A 73 3.87e+01 unknown_sccs -10331 1pufB 73 3.87e+01 a.4.1.1 -192 1jssA 224 3.87e+01 d.129.3.2 71844 1gwiA 411 3.89e+01 a.104.1.1 76364 1aew 174 3.89e+01 2fha a.25.1.1 16676 1p3qQ 54 3.91e+01 a.5.2.4 87748 1ej2A 181 3.91e+01 1f9aA c.26.1.3 59414 1kqfB 294 3.94e+01 d.58.1.5 75900 f.23.22.1 75901 1k75A 434 3.95e+01 c.82.1.2 68253 1gr8A 412 3.96e+01 1ockA 412 3.96e+01 c.117.1.1 86802 1odoA 408 3.97e+01 a.104.1.1 -1463 1ijdB 42 3.99e+01 f.3.1.1 66156