# List of top-scoring protein chains for t2k-100-30-str 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 1b65A 375 2.72e-02 1b65A d.154.1.1 42020 1ezvD 245 1.45e-01 1be3D a.3.1.3 59546 f.2.1.8 59547 1am7A 158 2.63e-01 1am7A d.2.1.4 36981 1qnrA 344 4.03e-01 1qnoA c.1.8.3 28834 1qqfA 277 4.67e-01 1c3d a.102.4.4 18875 1byqA 228 5.32e-01 1yer d.122.1.1 41100 1qnoA 344 5.57e-01 1qnoA c.1.8.3 28838 1pjcA 361 7.03e-01 1sayA c.2.1.4 30101 c.23.12.2 31361 1sayA 361 9.41e-01 1sayA c.2.1.4 30102 c.23.12.2 31362 1fnuA 221 1.06e+00 3seb b.40.2.2 25212 d.15.6.1 37801 1yer 228 1.08e+00 1yer d.122.1.1 41101 1ccr 112 1.16e+00 1ycc a.3.1.1 15877 1irw 108 1.27e+00 1ycc a.3.1.1 15855 1pjbA 361 1.37e+00 1sayA c.2.1.4 30103 c.23.12.2 31363 5cytR 104 1.41e+00 1ycc a.3.1.1 15878 1ycc 108 1.92e+00 1ycc a.3.1.1 15834 1ndh 272 2.46e+00 1ndh b.43.4.2 25662 c.25.1.1 31552 1ytc 112 2.57e+00 1ycc a.3.1.1 15835 1jevA 517 3.09e+00 1jevA c.94.1.1 35720 1i7pA 274 3.14e+00 b.43.4.2 66048 c.25.1.1 66049 1jetA 517 3.33e+00 1jevA c.94.1.1 35718 2olbA 517 3.38e+00 1jevA c.94.1.1 35721 1e32A 458 5.22e+00 1e32A b.52.2.3 59183 c.37.1.13 59184 d.31.1.1 59185 1g2nA 264 5.66e+00 1lbd a.123.1.1 60227 1g73C 121 5.80e+00 1g3fA g.52.1.1 45375 1pmy 123 6.20e+00 1bqk b.6.1.1 22888 1d5mC 239 6.51e+00 3seb b.40.2.2 25185 d.15.6.1 37774 1h2aS 317 7.36e+00 2frvA e.19.1.1 43311 1cfyA 143 7.42e+00 1cof d.109.1.2 40858 1gai 472 7.97e+00 1ayx a.102.1.1 18819 1glm 470 8.18e+00 1ayx a.102.1.1 18821 1kwhA 492 8.34e+00 c.94.1.1 68876 1g3fA 117 8.36e+00 1g3fA g.52.1.1 45378 1hcxA 127 9.06e+00 b.109.1.1 65800 1hylA 230 9.07e+00 5ptp b.47.1.2 26076 2hlcA 230 9.44e+00 5ptp b.47.1.2 26074 1c3d 294 9.64e+00 1c3d a.102.4.4 18874 1f9mA 112 9.71e+00 1erv c.47.1.1 32736 1hc7A 477 1.06e+01 1hc7A c.51.1.1 60938 d.104.1.1 60939 g.56.1.1 60940 1d2zA 108 1.07e+01 1d2zA a.77.1.1 18437 1gp6A 356 1.07e+01 b.82.2.1 65441 1aj8A 371 1.08e+01 1aj8A a.103.1.1 18900 1faaA 124 1.10e+01 1erv c.47.1.1 32738 1m4vA 204 1.12e+01 1a3gA 308 1.21e+01 1daaA e.17.1.1 43286 1pls 113 1.22e+01 1pls b.55.1.1 26965 1gp4A 356 1.22e+01 b.82.2.1 65439 1cof 143 1.24e+01 1cof d.109.1.2 40860 1kp9B 287 1.24e+01 c.66.1.18 68734 1doi 128 1.27e+01 1awd d.15.4.1 37676 1bbl 51 1.29e+01 1bbl a.9.1.1 16356 1i1kA 309 1.31e+01 1daaA e.17.1.1 61533 1bal 51 1.32e+01 1bbl a.9.1.1 16357 1cne 270 1.33e+01 1ndh b.43.4.2 25661 c.25.1.1 31551 1bmr 68 1.37e+01 1aho g.3.7.1 44144 1fggA 261 1.38e+01 1fggA c.68.1.7 34576 1nfa 178 1.57e+01 1a02N b.2.5.1 22442 1f3uB 171 1.57e+01 1f3uB b.65.1.1 27525 1acf 125 1.59e+01 3nul d.110.1.1 40882 1bqcA 302 1.61e+01 1bqcA c.1.8.3 28831 1hqz1 141 1.65e+01 1ayyA 151 1.67e+01 1apyA d.153.1.5 42016 1b66A 140 1.71e+01 1b66A d.96.1.2 40657 1a79A 171 1.72e+01 1a79A c.52.2.1 33340 d.75.1.1 39739 1hqz9 141 1.74e+01 3seb 238 1.76e+01 3seb b.40.2.2 25184 d.15.6.1 37773 1reqD 637 1.81e+01 1reqB c.1.19.1 29623 c.23.6.1 31250 1kwsA 261 1.85e+01 1cezA 883 1.90e+01 1cezA e.8.1.3 43110 1qlnA 883 2.00e+01 1cezA e.8.1.3 43111 1ggwA 140 2.00e+01 1ggwA a.39.1.5 60490 1jljA 189 2.05e+01 c.57.1.1 63169 1prxA 224 2.05e+01 1prxA c.47.1.10 33076 1ihcA 188 2.09e+01 1di6A c.57.1.1 62379 1ayfA 105 2.10e+01 1ayfA d.15.4.1 37684 1h8gA 95 2.15e+01 b.109.1.1 65735 1gtqA 140 2.15e+01 1b66A d.96.1.2 40661 1bkpA 278 2.20e+01 1bkpA d.117.1.1 41029 1iibA 106 2.21e+01 1iibA c.44.2.1 32648 1fshA 105 2.28e+01 1fshA a.4.5.31 60006 1ckv 141 2.30e+01 1ckv d.137.1.1 41452 1reqB 637 2.39e+01 1reqB c.1.19.1 29621 c.23.6.1 31248 1ayfB 105 2.43e+01 1ayfA d.15.4.1 37685 1ia9A 280 2.56e+01 1ia9A d.144.1.5 62113 1co6A 107 2.63e+01 1ycc a.3.1.1 15894 2bbkL 125 2.69e+01 2bbkL g.21.1.1 44882 1ayx 492 2.71e+01 1ayx a.102.1.1 18825 1rypJ 204 2.71e+01 d.153.1.4 41878 1j9yA 385 2.76e+01 1j9yA c.1.8.3 62791 1gj7B 253 2.78e+01 1fvgA 199 2.80e+01 1fvaA d.58.28.1 39408 1mmsA 140 2.81e+01 1mmsA a.4.7.1 16247 d.47.1.1 38766 2trcP 217 2.88e+01 1b9yC c.47.1.6 33051 1irqA 71 2.92e+01 a.43.1.2 66297 487dL 133 2.95e+01 1mmsA i.1.1.2 45839 1hzoA 271 2.96e+01 1fb6A 105 3.06e+01 1thx c.47.1.1 32739 1bzg 34 3.07e+01 1bzg j.15.1.1 46166 1jceA 344 3.13e+01 c.55.1.1 62876 c.55.1.1 62877 1a6q 382 3.24e+01 1a6q d.158.1.1 42063 1b6sA 355 3.30e+01 1b6rA b.84.2.1 28242 c.30.1.1 31649 d.142.1.2 41494 1tubA 440 3.31e+01 1tubA c.32.1.1 31751 d.79.2.1 39803 1dlfH 124 3.33e+01 1igtB b.1.1.1 20383 1ft9A 222 3.42e+01 1ft9A a.4.5.4 16107 b.82.3.1 28131 1fvaA 217 3.47e+01 1fvaA d.58.28.1 39409 1bqk 124 3.49e+01 1bqk b.6.1.1 22889 1jj2W 91 3.51e+01 1ffkU d.29.1.1 63108 1nsf 273 3.61e+01 1d2nA c.37.1.13 32429 1chmA 401 3.63e+01 1chmA c.55.2.1 33545 d.127.1.1 41142 1ncs 47 3.63e+01 1ncs g.37.1.1 45040 1l5jA 865 3.66e+01 1d2nA 272 3.71e+01 1d2nA c.37.1.13 32428 5ptp 223 3.73e+01 5ptp b.47.1.2 25831 1i86A 389 3.76e+01 c.95.1.2 66068 c.95.1.2 66069 1jcfA 344 3.82e+01 c.55.1.1 62878 c.55.1.1 62879