# 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 1ibvB 229 2.66e-01 1pyaB 228 3.48e-01 1pyaB 1szwA 379 5.13e-01 unknown_sccs -10164 1vheA 373 5.15e-01 unknown_sccs -4280 c.56.5.4 -7890 1s0uA 408 6.09e-01 b.43.3.1 -4053 b.44.1.1 -4061 c.37.1.8 -7096 1jeyA 609 7.55e-01 1jeqA unknown_sccs -4426 unknown_sccs -7990 1jeqA 609 1.15e+00 1jeqA a.140.2.1 64748 unknown_sccs -4427 unknown_sccs -7991 1cqmA 101 1.19e+00 1ris d.58.14.1 39321 1o6zA 303 1.56e+00 c.2.1.5 81107 d.162.1.1 81108 1ris 101 1.72e+00 1ris d.58.14.1 39314 1vhoA 346 1.76e+00 unknown_sccs -4283 c.56.5.4 -7893 1lqtA 456 2.03e+00 c.3.1.1 74198 c.4.1.1 74199 1i40A 175 2.13e+00 b.40.5.1 66024 1nb9A 147 2.55e+00 b.43.5.1 85515 1bj8 109 2.65e+00 1bquA b.1.2.1 22070 1louA 101 2.86e+00 1ris d.58.14.1 39323 1ii6A 368 3.36e+00 1bg2 c.37.1.9 62413 1lwdA 413 3.39e+00 c.77.1.1 78265 1c8zA 265 3.82e+00 1c8zA d.23.1.1 38375 2prd 174 4.40e+00 2prd b.40.5.1 25435 1rz2A 254 4.51e+00 1e0tA 470 4.85e+00 1a49A b.58.1.1 27064 c.1.12.1 29292 c.49.1.1 33146 1jrmA 104 4.95e+00 d.206.1.1 67136 1dyr 206 5.04e+00 1aoeA c.71.1.1 34916 1jjgA 102 5.48e+00 b.40.4.5 71696 1pysB 785 5.68e+00 1pysB a.6.1.1 16299 a.6.1.1 16300 b.40.4.4 25311 d.58.13.1 39310 d.104.1.1 40779 d.138.1.1 41455 1si7A 369 6.14e+00 unknown_sccs -10163 1iqpA 327 6.18e+00 a.80.1.1 62649 c.37.1.20 62650 1e4fT 419 6.63e+00 1e4fT c.55.1.1 33453 c.55.1.1 33454 1hnuA 280 6.72e+00 1hnoA c.14.1.3 61096 1giqA 413 6.77e+00 d.166.1.1 76224 d.166.1.1 76225 1q0bA 367 7.34e+00 c.37.1.9 -7105 1ltlA 279 7.64e+00 b.40.4.11 84701 1udxA 416 7.83e+00 b.117.1.1 -3546 c.37.1.8 -7101 unknown_sccs -9009 1mvlA 209 8.85e+00 c.34.1.1 85146 1bquA 215 9.02e+00 1bquA b.1.2.1 22066 b.1.2.1 22067 1eza 259 9.18e+00 1zymA a.60.10.1 18113 c.8.1.2 30708 1hnoA 280 9.42e+00 1hnoA c.14.1.3 61095 1hdkA 141 9.55e+00 b.29.1.3 65807 1vixA 420 1.02e+01 c.56.5.4 -7866 d.58.19.1 -10090 1tdj 514 1.06e+01 1tdj c.79.1.1 35297 d.58.18.2 39356 d.58.18.2 39357 1kmvA 186 1.06e+01 c.71.1.1 72757 1c8pA 102 1.07e+01 1c8pA b.1.2.1 22040 1b9lA 120 1.09e+01 1b9lA d.96.1.3 40665 1lcl 142 1.14e+01 1lcl b.29.1.3 24216 1fnoA 417 1.16e+01 c.56.5.4 75841 d.58.19.1 70145 1g86A 142 1.19e+01 b.29.1.3 70161 1ts3A 194 1.23e+01 1aw7A b.40.2.2 25168 d.15.6.1 37757 1nfiC 301 1.24e+01 b.1.18.1 21943 b.2.5.3 22456 1f9vA 347 1.29e+01 1bg2 c.37.1.9 59745 1ng5A 215 1.35e+01 b.100.1.1 -4541 1ci3M 249 1.42e+01 1hcz b.2.6.1 22480 b.84.2.2 28266 1cr5A 189 1.43e+01 1cr5A b.52.2.3 26931 d.31.1.1 38465 1pqnA 127 1.44e+01 c.47.1.8 -7479 1obwA 175 1.44e+01 2prd b.40.5.1 25416 1ipwA 175 1.45e+01 2prd b.40.5.1 25427 1guzA 310 1.52e+01 c.2.1.5 65586 d.162.1.1 65587 1gm6A 175 1.56e+01 b.60.1.1 70272 1lkzA 219 1.56e+01 unknown_sccs 73991 d.58.40.1 73992 1svy 114 1.60e+01 1svy d.109.1.1 40831 3tss 194 1.62e+01 1aw7A b.40.2.2 25160 d.15.6.1 37749 1gmwA 143 1.67e+01 b.107.1.1 65347 d.58.38.1 65348 1k8wA 327 1.68e+01 b.122.1.1 83094 unknown_sccs -10143 1fgyA 127 1.71e+01 1faoA b.55.1.1 26976 1fbnA 230 1.72e+01 1fbnA c.66.1.3 34181 1r0kA 388 1.80e+01 1i50A 1733 1.82e+01 e.29.1.2 61754 1isiA 265 1.83e+01 e.4.1.1 71394 1i50F 155 1.83e+01 d.78.1.2 61760 1ry9A 145 1.84e+01 d.198.1.1 -9020 1f15A 218 1.86e+01 1f15B b.121.4.5 23320 1kk1A 410 1.87e+01 b.43.3.1 72634 b.44.1.1 72635 c.37.1.8 72636 1e20A 209 1.91e+01 1e20A c.34.1.1 31759 1j6wA 175 1.93e+01 1j98A d.185.1.2 62663 1nfiA 301 2.04e+01 1a3qA b.1.18.1 21942 b.2.5.3 22455 1o8bA 219 2.08e+01 unknown_sccs 81180 d.58.40.1 81181 1v2bA 177 2.09e+01 1mrzA 293 2.09e+01 b.43.5.1 -4048 c.26.1.3 -6616 1l5aA 436 2.10e+01 c.43.1.2 75923 c.43.1.2 75924 1cfyA 143 2.11e+01 1cof d.109.1.2 40858 1g8sA 230 2.15e+01 c.66.1.3 -8047 1edg 380 2.16e+01 1edg c.1.8.3 28807 1eiyB 785 2.22e+01 1pysB a.6.1.1 16305 a.6.1.1 16306 b.40.4.4 25314 d.58.13.1 39313 d.104.1.1 40782 d.138.1.1 41458 1lvoA 302 2.23e+01 b.47.1.4 74284 1tvdA 116 2.31e+01 1tvdA b.1.1.1 20650 1dkgD 383 2.34e+01 1ba1 c.55.1.1 33427 c.55.1.1 33428 1kcmA 270 2.39e+01 d.129.3.4 72300 1ks2A 219 2.41e+01 unknown_sccs 72908 d.58.40.1 72909 1cklA 126 2.45e+01 1cklB g.18.1.1 44851 g.18.1.1 44852 1aw7A 194 2.45e+01 1aw7A b.40.2.2 25164 d.15.6.1 37753 1aizA 129 2.47e+01 1nwpA b.6.1.1 22903 1gl4B 98 2.47e+01 b.1.1.4 65288 2if1 126 2.51e+01 2if1 d.64.1.1 39547 1jkeA 145 2.52e+01 c.110.1.1 66791 1tdhA 364 2.56e+01 1q92A 197 2.63e+01 c.108.1.8 -6819 1mh9A 197 2.67e+01 c.108.1.8 79118 1f7dA 136 2.68e+01 1dun b.85.4.1 28353 1b7yB 785 2.75e+01 1pysB a.6.1.1 16301 a.6.1.1 16302 b.40.4.4 25312 d.58.13.1 39311 d.104.1.1 40780 d.138.1.1 41456 1cklB 126 2.81e+01 1cklB g.18.1.1 44853 g.18.1.1 44854 1bp3B 211 2.88e+01 1axiB b.1.2.1 22031 b.1.2.1 22032 1n0lA 224 2.88e+01 b.1.11.1 79744 b.7.2.1 79745 1n9pA 207 2.88e+01 b.1.18.16 80343 1p4dA 330 2.90e+01 unknown_sccs -10522 1bam 213 2.92e+01 1bam c.52.1.3 33285 1i1qA 520 3.00e+01 1qdlA d.161.1.1 61543 1e42A 258 3.02e+01 1e42A b.1.10.1 22316 d.105.1.1 40792 1kq6A 141 3.04e+01 d.189.1.1 -9926 1efcA 393 3.10e+01 1efcA b.43.3.1 25680 b.44.1.1 25720 c.37.1.8 32113 1pkn 530 3.10e+01 1a49A b.58.1.1 27042 c.1.12.1 29271 c.49.1.1 33125 1r12A 258 3.12e+01 e.4.1.1 -11807 1p9uA 302 3.13e+01 b.47.1.4 88001 1an9A 340 3.18e+01 1an9A c.4.1.2 30617 d.16.1.3 37904 1tfr 305 3.24e+01 1tfr a.60.7.1 18081 c.120.1.2 33351 1a8rA 221 3.28e+01 1a8rA d.96.1.1 40587 1bftA 101 3.29e+01 1a3qA b.1.18.1 21934 1nb8A 353 3.29e+01 d.3.1.9 80385 1jlm 192 3.34e+01 1ido c.62.1.1 34140 1hv8A 367 3.35e+01 1hv8A c.37.1.19 32405 c.37.1.19 32406 1aszB 490 3.42e+01 1b8aA b.40.4.1 25241 d.104.1.1 40762 1cof 143 3.44e+01 1cof d.109.1.2 40860 1bjt 793 3.45e+01 1bjt e.11.1.1 43249 1h6yA 170 3.46e+01 b.18.1.7 70904 1j9lA 247 3.46e+01 c.106.1.1 62762 1ih7A 903 3.48e+01 1clqA c.55.3.5 62375 e.8.1.1 62376 1igwA 434 3.51e+01 c.1.12.7 62370 1quqA 129 3.53e+01 1quqA b.40.4.3 25303 1sluA 142 3.55e+01 1sluA b.16.1.1 23685 1bxkA 355 3.57e+01 1bxkA c.2.1.2 29803 1gmuA 143 3.59e+01 b.107.1.1 65335 d.58.38.1 65336 1q4rA 112 3.60e+01 d.58.4.4 -9943 1rthA 560 3.64e+01 1rthA c.55.3.1 33576 e.8.1.2 43028 1mjgM 729 3.66e+01 e.26.1.3 79204 1l1eA 287 3.73e+01 c.66.1.18 73454 1eq2A 310 3.76e+01 1eq2A c.2.1.2 29814 1j9jA 247 3.82e+01 c.106.1.1 62758 1q7eA 428 3.94e+01 c.123.1.1 -8768