# List of top-scoring protein chains for t2k-100-30-near-backbone-11-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 1hsbB 99 9.65e-01 1agdB b.1.1.2 20737 1kjvB 100 1.00e+00 b.1.1.2 77423 1ao7B 100 1.02e+00 1agdB b.1.1.2 20697 1duzB 100 1.04e+00 1agdB b.1.1.2 20671 1agdB 99 1.12e+00 1agdB b.1.1.2 20742 1fzkB 99 1.15e+00 1agdB b.1.1.2 60151 1i4fB 100 1.21e+00 1agdB b.1.1.2 61689 1g7pB 99 1.37e+00 b.1.1.2 70155 1knvA 293 1.40e+00 c.52.1.7 68707 1jnjA 100 1.41e+00 b.1.1.2 66955 1dx8A 70 1.44e+00 1rb9 g.41.5.1 45243 1k5nB 100 1.53e+00 b.1.1.2 77268 1fzoB 99 1.54e+00 1agdB b.1.1.2 60157 1kpuB 99 1.65e+00 b.1.1.2 84458 1mhcB 99 1.77e+00 1agdB b.1.1.2 20832 1lk2B 99 1.92e+00 b.1.1.2 91058 1v4eA 299 2.44e+00 a.128.1.1 100296 1rlyA 60 3.07e+00 g.41.3.1 104988 1bx2B 191 3.18e+00 1iakB b.1.1.2,d.19.1.1 21610,38184 1w9yA 319 3.55e+00 1v87A 114 3.58e+00 g.44.1.1 108422 1aqdB 198 3.94e+00 1iakB b.1.1.2,d.19.1.1 21586,38160 1d5mB 192 4.09e+00 1iakB b.1.1.2,d.19.1.1 21618,38192 1ieaB 228 4.15e+00 1iakB b.1.1.2,d.19.1.1 21632,38206 1dl6A 58 4.20e+00 1dl6A g.41.3.1 45207 2af8 86 4.76e+00 2af8 a.28.1.1 16933 1q1aA 289 4.83e+00 c.31.1.5 95561 1dlhB 188 4.91e+00 1iakB b.1.1.2,d.19.1.1 21598,38172 2a14A 263 5.40e+00 1a6aB 187 5.41e+00 1iakB b.1.1.2,d.19.1.1 21616,38190 1jk8B 190 5.56e+00 1iakB b.1.1.2,d.19.1.1 63147,63148 1bob 320 5.62e+00 1bob d.108.1.1 40816 1im4A 221 5.63e+00 e.8.1.7 62581 1j7xA 302 6.26e+00 c.14.1.2 66425 1uvqB 198 6.43e+00 b.1.1.2,d.19.1.1 100064,100065 1knzA 164 6.43e+00 e.34.1.1 68709 1sr2A 116 6.56e+00 1dk5A 322 7.54e+00 1dk5A a.65.1.1 18192 1reqA 727 7.85e+00 1reqA c.1.19.1,c.23.6.1 29620,31247 1eswA 500 8.25e+00 1cwyA c.1.8.1 59500 1jigA 146 8.60e+00 a.25.1.1 71685 1v2bA 177 9.07e+00 d.107.1.2 108279 1dv2A 452 1.05e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28238,31645,41490 1cwyA 500 1.08e+01 1cwyA c.1.8.1 28789 5reqA 727 1.09e+01 1reqA c.1.19.1,c.23.6.1 29632,31259 1u5kA 244 1.19e+01 1aa6 715 1.27e+01 2napA b.52.2.2,c.81.1.1 26916,35324 1bor 56 1.29e+01 1bor g.44.1.1 45324 1z6nA 167 1.30e+01 7reqA 727 1.32e+01 1reqA c.1.19.1,c.23.6.1 29616,31243 1gtvA 214 1.37e+01 c.37.1.1 70537 1xreA 217 1.40e+01 1zglB 192 1.40e+01 2fztA 79 1.42e+01 1zlqA 502 1.44e+01 1qzzA 374 1.49e+01 a.4.5.29,c.66.1.12 96719,96720 2g42A 79 1.60e+01 1uiuA 502 1.63e+01 c.94.1.1 99434 1ymmB 198 1.76e+01 1bncA 449 1.76e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28236,31643,41488 2a8yA 270 1.77e+01 1xocA 520 1.80e+01 1y1pA 342 1.96e+01 1vr5A 547 1.97e+01 1yk4A 52 2.01e+01 1iro 54 2.02e+01 1rb9 g.41.5.1 45223 1fdo 715 2.03e+01 2napA b.52.2.2,c.81.1.1 26917,35325 1fdi 715 2.07e+01 2napA b.52.2.2,c.81.1.1 26918,35326 1rw1A 114 2.10e+01 2carA 196 2.11e+01 1f6rA 123 2.20e+01 3lzt d.2.1.2 36606 2axwA 134 2.26e+01 1ujmA 342 2.28e+01 1ede 310 2.29e+01 1b6g c.69.1.8 34662 1vmjA 151 2.33e+01 1yua 122 2.33e+01 1yua g.41.3.3,g.41.3.3 45210,45211 1orjA 130 2.39e+01 a.24.19.1 93456 1g3uA 214 2.44e+01 c.37.1.1 65132 1meyC 87 2.55e+01 2gliA k.12.1.1 46430 2g7sA 194 2.60e+01 1yfoA 302 2.67e+01 2shpA c.45.1.2 32681 1b4pA 217 2.75e+01 a.45.1.1,c.47.1.5 83158,83159 3pvaA 335 2.75e+01 3pvaA d.153.1.3 41854 5rxn 54 2.76e+01 1rb9 g.41.5.1 45225 1stzA 338 2.78e+01 a.4.5.51,d.110.2.3 106009,106010 1tv9A 335 2.80e+01 2pvaA 345 2.81e+01 3pvaA d.153.1.3 41850 1rpl 251 2.82e+01 1bpyA a.60.12.1,d.218.1.2 75933,75934 1pft 50 2.88e+01 1pft g.41.3.1 45206 1bmg 98 2.90e+01 1agdB b.1.1.2 20667 1q5nA 454 2.91e+01 a.127.1.1 95901 1ed1A 135 2.93e+01 1hiwA a.61.1.1 18130 1vls 146 2.94e+01 1vls a.24.2.1 16532 1axiA 191 2.95e+01 1huw a.26.1.1 16832 1qs2A 401 2.99e+01 1qs1A d.166.1.1,d.166.1.1 42268,42269 1jwyB 315 3.04e+01 c.37.1.8 67401 1f00I 282 3.13e+01 1f00I b.1.14.1,b.1.14.1,d.169.1.3 22368,22369,42439 1jb0A 755 3.17e+01 1jb0A f.29.1.1 62820 1t77A 414 3.20e+01 1q1lA 401 3.24e+01 d.258.1.1 95591 1taq 832 3.24e+01 1taq a.60.7.1,c.120.1.2,c.55.3.5,e.8.1.1 18082,33352,33698,42991 1b2jA 54 3.25e+01 1rb9 g.41.5.1 45231 1v54F 98 3.25e+01 g.41.5.3 100327 1n40A 396 3.26e+01 a.104.1.1 79977 4rxn 54 3.28e+01 1rb9 g.41.5.1 45226 1lh1 153 3.30e+01 2gdm a.1.1.2 15222 2aawA 222 3.31e+01 1nom 248 3.40e+01 1bpyA a.60.12.1,d.218.1.2 75929,75930 1jpnA 296 3.41e+01 a.24.13.1,c.37.1.10 67039,67040 1kzfA 230 3.51e+01 d.108.1.3 73354 2occF 98 3.51e+01 2occF g.41.5.3 45256 1keyA 235 3.53e+01 a.118.16.1 72389 1f62A 51 3.53e+01 1f62A g.50.1.2 45360 2lh2 153 3.53e+01 2gdm a.1.1.2 15220 1n9dA 199 3.57e+01 a.26.1.1 85464 1wcrA 103 3.65e+01 2gdm 153 3.68e+01 2gdm a.1.1.2 15212 1jqlB 140 3.73e+01 c.37.1.20 63234 1bpb 248 3.73e+01 1bpyA a.60.12.1,d.218.1.2 75811,75812 1wyuA 438 3.74e+01 2g8mA 264 3.80e+01 1b6g 310 3.82e+01 1b6g c.69.1.8 34661 1cvjA 190 3.85e+01 1cvjB d.58.7.1,d.58.7.1 39191,39192 2g8oA 264 3.87e+01 1dfoA 417 3.93e+01 1bj4A c.67.1.4 34480 2g8yA 385 4.22e+01 1af8 86 4.23e+01 2af8 a.28.1.1 16932 1dv1A 449 4.24e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28234,31641,41486 1e8oA 85 4.26e+01 1914 d.49.1.1 38773 1vckA 115 4.26e+01 1g8sA 230 4.27e+01 c.66.1.3 90507 1k4jA 230 4.31e+01 d.108.1.3 72057 1gdj 153 4.32e+01 2gdm a.1.1.2 15213 1eudB 396 4.35e+01 2scuB c.23.4.1,d.142.1.4 31150,41571 1pydA 556 4.36e+01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31735,31773,31774 1fkqA 124 4.41e+01 3lzt d.2.1.2 36601 1k0fA 277 4.41e+01 c.92.2.2 71974 1ffh 294 4.47e+01 1ng1 a.24.13.1,c.37.1.10 16960,32271 1jx2B 315 4.47e+01 c.37.1.8 67404 2tscA 264 4.50e+01 1bkpA d.117.1.1 40952 8rxnA 52 4.53e+01 1rb9 g.41.5.1 45215 1bpyA 335 4.57e+01 1bpyA a.60.6.1,a.60.12.1,d.218.1.2 17980,75819,75820 1axwA 265 4.57e+01 1bkpA d.117.1.1 40938 1toaA 313 4.60e+01 1toaA c.92.2.2 35598 1qs1A 462 4.77e+01 1qs1A d.166.1.1,d.166.1.1 42260,42261 1fbnA 230 4.77e+01 1fbnA c.66.1.3 34181 1bncB 449 4.79e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28237,31644,41489 2etvA 346 4.79e+01 1oj4A 283 4.80e+01 d.14.1.5,d.58.26.5 93083,93084 2djkA 133 4.88e+01 2cokA 113 5.00e+01 1aosA 464 5.02e+01 1auwA a.127.1.1 19414 1tys 265 5.03e+01 1bkpA d.117.1.1 40937 1u69A 163 5.03e+01 d.32.1.7 107699 1aiqA 264 5.11e+01 1bkpA d.117.1.1 40967 1rdg 53 5.13e+01 1rb9 g.41.5.1 45221 1hl9A 449 5.14e+01 b.71.1.3,c.1.8.11 90650,90651 1pu6A 218 5.20e+01 a.96.1.5 95123 2ligA 164 5.29e+01 1vls a.24.2.1 16530 1i1gA 141 5.31e+01 a.4.5.32,d.58.4.2 65982,65983 1z90A 469 5.34e+01 1b4bA 71 5.40e+01 1b4aA d.74.2.1 39718 2aa1B 146 5.41e+01 1hl8A 449 5.44e+01 b.71.1.3,c.1.8.11 90646,90647 1rb9 53 5.50e+01 1rb9 g.41.5.1 45214 1a6l 106 5.53e+01 1a6l d.58.1.2 38966 1ls1A 295 5.53e+01 a.24.13.1,c.37.1.10 78170,78171 1evfA 264 5.63e+01 1bkpA d.117.1.1 40932 1ddt 535 5.63e+01 1ddt b.2.1.1,d.166.1.1,f.1.2.1 22379,42241,43384 1cx4A 305 5.68e+01 b.82.3.2,b.82.3.2 59099,59100 2awpA 198 5.73e+01 1wozA 177 5.74e+01 1xg2B 153 5.78e+01 1eucB 396 5.93e+01 2scuB c.23.4.1,d.142.1.4 31149,41570 1bi5A 389 5.95e+01 1bi5A c.95.1.2,c.95.1.2 35985,35986 2fq3A 104 5.98e+01 2ng1 293 6.14e+01 1ng1 a.24.13.1,c.37.1.10 16962,32273 1ylmA 144 6.15e+01 1dfx 125 6.22e+01 1dfx b.1.13.1,g.41.5.2 22367,45255 1lq7A 67 6.34e+01 k.9.1.1 74183 1zkeA 83 6.49e+01 2comA 124 6.52e+01 1lvaA 258 6.57e+01 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 1wwiA 148 6.61e+01 2ap1A 327 6.78e+01 1uz5A 402 6.89e+01 b.85.6.1,b.103.1.1,c.57.1.2 100217,100218,100219 1jwwA 80 6.95e+01 d.58.17.1 71919 2fmpA 335 6.96e+01 1bq8A 54 6.98e+01 1rb9 g.41.5.1 45237 1gzqA 300 7.06e+01 b.1.1.2,d.19.1.1 70818,70819 1z5lA 285 7.09e+01 1nu5A 370 7.23e+01 c.1.11.2,d.54.1.1 92183,92184 1jjrA 151 7.25e+01 a.140.2.1 66772 1adoA 363 7.29e+01 1fbaA c.1.10.1 29124 1rkuA 206 7.36e+01 c.108.1.11 97627 1d8bA 81 7.48e+01 1d8bA a.60.8.1 18094 1atzB 189 7.52e+01 1atzA c.62.1.1 34133 1wijA 140 7.70e+01 1bq9A 54 7.73e+01 1rb9 g.41.5.1 45238 1y13A 181 7.74e+01 1rljA 139 7.80e+01 c.23.5.7 104983 2fikA 287 7.86e+01 1xkrA 206 7.91e+01 1vp6A 138 7.95e+01 1xg9A 260 7.96e+01 2a0b 125 7.96e+01 2a0b a.24.10.1 16630 1l6uA 128 8.01e+01 d.15.4.1 73630 1n2aA 201 8.01e+01 a.45.1.1,c.47.1.5 91553,91554 1wer 334 8.01e+01 1wer a.116.1.2 19108 1ng1 294 8.05e+01 1ng1 a.24.13.1,c.37.1.10 16961,32272 1iakB 185 8.20e+01 1iakB b.1.1.2,d.19.1.1 21626,38200 1sziA 247 8.36e+01 a.24.23.1 106159 1exnB 290 8.46e+01 1exnA a.60.7.1,c.120.1.2 18089,33359 1rh2F 165 8.47e+01 1rh2F a.26.1.3 16898 1h98A 78 8.50e+01 d.58.1.2 65743 1yukB 120 8.55e+01 1k7yA 577 8.56e+01 a.46.1.1,c.23.6.1,d.173.1.1 68272,68273,68274 1xuvA 178 8.63e+01 1hu3A 260 8.69e+01 1hu3A a.118.1.14 19137 2bg5A 324 8.80e+01 1v6zA 228 8.85e+01 1gpmA 525 8.85e+01 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 1a1d 146 8.92e+01 1a1d b.40.4.8 25394 1li5B 461 8.96e+01 a.27.1.1,c.26.1.1 73914,73915