# 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 1m3jA 471 7.47e-01 f.9.1.1 -12372 1h4rA 314 1.02e+00 a.11.2.1 65616 b.55.1.5 65617 d.15.1.4 65618 1m3iA 471 1.12e+00 f.9.1.1 -12374 1rypH 205 1.42e+00 d.153.1.4 41876 1mngA 203 2.34e+00 1avmA a.2.11.1 15776 d.44.1.1 38701 1as4A 341 3.13e+00 1sek e.1.1.1 42623 1dgwA 178 3.82e+00 1dgwA b.82.1.2 28090 1jj2B 337 4.28e+00 1ffkB b.43.3.2 63086 1s72B 338 4.29e+00 1pfo 500 4.98e+00 1pfo f.9.1.1 43826 1jofA 365 5.02e+00 b.69.10.1 71775 1t0yA 122 5.42e+00 d.15.1.1 -9151 1s14A 194 5.49e+00 d.122.1.2 -10973 1h8eG 272 5.64e+00 1e79G c.49.2.1 60756 1ud9A 245 5.68e+00 1b63A 333 5.74e+00 1b63A d.14.1.3 37566 d.122.1.2 41107 1ip9A 85 5.78e+00 1ip9A d.15.2.2 62638 1j1tA 233 6.22e+00 unknown_sccs -3462 1vybA 238 6.90e+00 1plr 258 7.17e+00 1plq d.131.1.2 41390 d.131.1.2 41391 1iz5A 249 7.49e+00 d.131.1.2 83834 d.131.1.2 83835 1pyaB 228 7.54e+00 1pyaB 1g7sA 594 7.56e+00 1g7rA b.43.3.1 25712 b.43.3.1 25713 c.20.1.1 31032 c.37.1.8 32147 1ugmA 125 7.58e+00 1plq 258 8.17e+00 1plq d.131.1.2 41388 d.131.1.2 41389 1poiB 260 8.18e+00 1poiB unknown_sccs 34155 1m4jA 142 8.19e+00 d.109.1.2 78602 1cr5A 189 8.35e+00 1cr5A b.52.2.3 26931 d.31.1.1 38465 1ky9A 448 8.79e+00 b.36.1.4 73198 b.47.1.1 73199 1nmtA 392 9.12e+00 1nmtA d.108.1.2 40823 d.108.1.2 40824 1dgrC 178 9.18e+00 1dgwA b.82.1.2 28100 1us8A 147 9.26e+00 c.37.1.12 -7194 1ex2A 189 9.98e+00 1ex2A c.51.4.2 33225 1nijA 318 1.02e+01 c.37.1.10 85741 d.237.1.1 85742 1g7tA 594 1.05e+01 1g7rA b.43.3.1 25714 b.43.3.1 25715 c.20.1.1 31033 c.37.1.8 32148 1ibvB 229 1.05e+01 1cof 143 1.05e+01 1cof d.109.1.2 40860 1mejA 223 1.06e+01 c.65.1.1 79029 1amuA 563 1.10e+01 1amuA e.23.1.1 43351 1nr0A 611 1.11e+01 b.69.4.1 86078 b.69.4.1 86079 2cavA 445 1.22e+01 1dgwA b.82.1.2 28094 b.82.1.2 28095 1oeyJ 107 1.24e+01 d.15.2.2 -9168 1jkxA 212 1.31e+01 c.65.1.1 66813 1hpcA 131 1.35e+01 1htp b.84.1.1 28221 1lshA 1056 1.36e+01 a.118.4.1 74242 f.7.1.1 74243 f.7.1.1 74244 1g7rA 594 1.41e+01 1g7rA b.43.3.1 25716 b.43.3.1 25717 c.20.1.1 31034 c.37.1.8 32149 1cauA 181 1.44e+01 1dgwA b.82.1.2 28102 1thx 115 1.55e+01 1thx c.47.1.1 32732 1cfyA 143 1.58e+01 1cof d.109.1.2 40858 1f7sA 139 1.64e+01 1cof d.109.1.2 40857 1kzkA 99 1.64e+01 b.50.1.1 73371 1dcuA 357 1.65e+01 1frpA e.7.1.1 42943 1huxA 270 1.71e+01 1huxA c.55.1.5 61278 1b35C 282 1.71e+01 1b35C 1rg9A 383 1.72e+01 d.130.1.1 -11057 d.130.1.1 -11058 d.130.1.1 -11059 1htp 131 1.73e+01 1htp b.84.1.1 28220 1onqA 283 1.74e+01 b.1.1.2 -2640 d.19.1.1 -9390 1sefA 274 1.80e+01 1oeyA 83 1.87e+01 d.15.2.2 -9162 1go3E 187 1.88e+01 b.40.4.5 83054 d.230.1.1 83055 2gar 212 1.89e+01 2gar c.65.1.1 34161 1p0hA 318 1.90e+01 d.108.1.1 -10802 1rpuA 172 1.90e+01 unknown_sccs -10738 1qzgA 187 1.93e+01 b.40.4.3 -3920 1ci8A 392 1.97e+01 e.3.1.1 64765 1auiA 521 1.99e+01 1auiA d.159.1.3 42085 1lu4A 136 2.01e+01 c.47.1.10 -7509 1r62A 160 2.03e+01 1aj6 219 2.05e+01 1aj6 d.122.1.2 41106 1ge8A 249 2.06e+01 1plq d.131.1.2 41398 d.131.1.2 41399 1m93B 245 2.07e+01 1f52A 468 2.07e+01 1lgr d.15.9.1 37839 d.128.1.1 41169 1bmlC 362 2.08e+01 1bmlC d.15.5.1 37729 d.15.5.1 37730 d.15.5.1 37731 1unnC 115 2.10e+01 unknown_sccs -10216 1cy9A 264 2.13e+01 1ecl e.10.1.1 43236 1ci9A 392 2.14e+01 e.3.1.1 64767 1obpA 159 2.15e+01 1obpA b.60.1.1 27092 1al0G 175 2.17e+01 2bpa2 b.121.5.1 23275 1nstA 325 2.17e+01 1nstA c.37.1.5 31951 1vk9A 151 2.22e+01 1gnhA 206 2.23e+01 1sacA b.29.1.5 24252 1ih7A 903 2.26e+01 1clqA c.55.3.5 62375 e.8.1.1 62376 1hqz1 141 2.30e+01 1skoA 143 2.35e+01 1ef1A 294 2.35e+01 1ef1A a.11.2.1 16368 b.55.1.5 27003 d.15.1.4 37611 1ix9A 205 2.36e+01 a.2.11.1 76899 d.44.1.1 76900 1qy5A 269 2.37e+01 d.122.1.1 -10958 2glsA 470 2.40e+01 1lgr d.15.9.1 37851 d.128.1.1 41181 1d5nA 205 2.42e+01 1avmA a.2.11.1 15762 d.44.1.1 38687 2lgsA 468 2.47e+01 1lgr d.15.9.1 37838 d.128.1.1 41168 1s6tA 285 2.49e+01 c.37.1.5 -7040 1vkjA 285 2.49e+01 1rypI 222 2.52e+01 d.153.1.4 41877 1giqA 413 2.53e+01 d.166.1.1 76224 d.166.1.1 76225 1lgr 468 2.62e+01 1lgr d.15.9.1 37837 d.128.1.1 41167 1j7dA 145 2.69e+01 1jatB d.20.1.1 62680 2sak 121 2.70e+01 2sak d.15.5.1 37711 2bpa2 175 2.72e+01 2bpa2 1s2kA 206 2.76e+01 unknown_sccs -3494 1qasA 622 2.78e+01 1djxB a.39.1.7 17340 b.7.1.1 23157 c.1.18.1 29585 1st9A 143 2.78e+01 c.47.1.10 -7503 1m5q1 130 2.79e+01 1ig8A 486 2.83e+01 2yhx c.55.1.3 64746 c.55.1.3 64747 1difA 99 2.84e+01 1fmb b.50.1.1 26503 1i0hA 205 2.84e+01 1avmA a.2.11.1 15760 d.44.1.1 38685 1hxn 219 2.85e+01 1hxn b.66.1.1 27529 1i6uA 130 2.87e+01 d.140.1.1 61850 1ii7A 333 2.89e+01 1ii7A d.159.1.4 62415 1xgsA 295 2.90e+01 1bn5 a.4.5.25 16216 d.127.1.1 41153 1ig3A 263 2.98e+01 1ig3A b.82.6.1 62358 c.100.1.1 62359 1kcfA 258 3.05e+01 a.140.2.1 68434 c.55.3.7 68435 1m1cA 680 3.10e+01 e.42.1.1 78395 2pna 104 3.12e+01 1qadA d.93.1.1 40501 1jb0D 138 3.16e+01 1jb0D d.187.1.1 62823 1m2oA 768 3.19e+01 a.71.2.1 78480 b.2.8.1 78481 c.62.1.2 78482 d.109.2.1 78483 g.41.10.1 78484 2rveA 244 3.20e+01 1rvaA c.52.1.2 33283 1rwiA 270 3.21e+01 unknown_sccs -4603 1hnnA 282 3.22e+01 c.66.1.15 65895 1upiA 225 3.23e+01 b.82.1.1 -4823 1cvjA 190 3.25e+01 1cvjB d.58.7.1 39191 d.58.7.1 39192 1clc 639 3.29e+01 1clc a.102.1.2 18835 b.1.18.2 21872 1azqA 66 3.30e+01 1azpA b.34.13.1 37469 1lckA 175 3.32e+01 1lckA b.34.2.1 24552 d.93.1.1 40421 2ms2A 129 3.39e+01 1msc d.85.1.1 40049 1hleA 345 3.40e+01 1ovaA e.1.1.1 42618 1ky9B 448 3.41e+01 b.36.1.4 73200 b.36.1.4 73201 b.47.1.1 73202 1qamA 244 3.46e+01 2ercA c.66.1.24 34220 1hp1A 516 3.55e+01 d.114.1.1 70976 d.159.1.2 70977 1hh2P 344 3.57e+01 b.40.4.5 65835 d.52.3.1 65836 d.52.3.1 65837 d.202.1.1 65838 1sap 66 3.59e+01 1azpA b.34.13.1 37472 1djxA 624 3.60e+01 1djxB a.39.1.7 17342 b.7.1.1 23159 c.1.18.1 29587 1rwzA 245 3.61e+01 d.131.1.2 -11106 d.131.1.2 -11107 1azpA 66 3.65e+01 1azpA b.34.13.1 37467 1hqz9 141 3.68e+01 1e3sA 261 3.70e+01 1e6wA c.2.1.2 59201 1q1uA 144 3.73e+01 b.42.1.1 -4006 1rypK 198 3.74e+01 d.153.1.4 41879 1cnuA 137 3.75e+01 1cof d.109.1.2 40862 1q5qA 259 3.79e+01 d.153.1.4 -11433 1jhdA 396 3.80e+01 b.122.1.3 66712 c.26.1.5 66713 1ijtA 128 3.83e+01 1bfg b.42.1.1 62510 1ffkB 338 3.87e+01 1ffkB b.43.3.2 25719 1nf3C 128 3.89e+01 b.36.1.1 85596 1kpgA 287 3.94e+01 c.66.1.18 68735 1r3eA 309 3.97e+01 b.122.1.1 -5118 unknown_sccs -10146 1nrfA 262 3.98e+01 e.3.1.1 -11780 1f2tA 149 4.00e+01 1f2tA c.37.1.12 32373