# 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 1gumA 222 1.26e-04 1pgtA a.45.1.1 17683 c.47.1.5 32977 1pd21 199 1.49e-04 1pd21 1gulA 222 2.21e-04 1pgtA a.45.1.1 17675 c.47.1.5 32969 1iyhA 198 2.34e-04 a.45.1.1 83790 c.47.1.5 83791 1oktA 211 3.90e-03 a.45.1.1 -942 c.47.1.5 -7467 6gsvA 217 5.80e-03 1b8xA a.45.1.1 17633 c.47.1.5 32925 1f3aA 222 7.91e-03 1pgtA a.45.1.1 17701 c.47.1.5 32995 1b4pA 217 1.60e-02 a.45.1.1 83158 c.47.1.5 83159 2gsq 202 1.80e-02 1pd21 a.45.1.1 17715 c.47.1.5 33009 1pgtA 210 3.92e-02 1pgtA a.45.1.1 17515 c.47.1.5 32809 1oe8A 211 4.71e-02 a.45.1.1 86905 c.47.1.5 86906 1k3yA 221 5.61e-02 a.45.1.1 77245 c.47.1.5 77246 1k3lA 221 5.82e-02 a.45.1.1 77229 c.47.1.5 77230 1b8xA 280 7.41e-02 1b8xA a.45.1.1 17739 c.47.1.5 33033 1gseA 221 1.28e-01 1pgtA a.45.1.1 17667 c.47.1.5 32961 1dugA 234 1.34e-01 1b8xA a.45.1.1 17718 c.47.1.5 33012 1ezfA 340 1.62e-01 1ezfA a.128.1.2 19440 1l2lA 457 4.23e-01 c.72.1.3 77656 1r2rA 248 5.85e-01 c.1.1.1 -5147 1m0uA 249 9.04e-01 a.45.1.1 78359 c.47.1.5 78360 1kzhA 555 1.05e+00 c.89.1.1 73361 1ky9A 448 1.61e+00 b.36.1.4 73198 b.47.1.1 73199 1o6zA 303 1.68e+00 c.2.1.5 81107 d.162.1.1 81108 1fpxA 352 2.67e+00 1fpxA a.4.5.29 59950 c.66.1.12 59951 1amk 251 3.43e+00 1amk c.1.1.1 28503 1gnd 447 3.52e+00 1gnd c.3.1.3 30423 d.16.1.6 37987 1ky9B 448 3.61e+00 b.36.1.4 73200 b.36.1.4 73201 b.47.1.1 73202 1fp2A 352 3.69e+00 1fpxA a.4.5.29 59941 c.66.1.12 59942 1nhyA 219 3.70e+00 a.45.1.1 80520 c.47.1.5 80521 1qz9A 416 3.73e+00 c.67.1.3 -8180 1f47B 144 3.80e+00 1f46A d.129.4.1 59645 1uf2A 1019 4.24e+00 unknown_sccs -12036 1i19A 561 4.30e+00 1i19A d.58.32.3 61522 d.145.1.1 61523 1f46A 140 4.36e+00 1f46A d.129.4.1 59643 1f7wA 144 4.39e+00 1f46A d.129.4.1 59679 1n55A 251 4.53e+00 c.1.1.1 80007 1d5tA 433 4.67e+00 1gnd c.3.1.3 30422 d.16.1.6 37986 1eu8A 409 4.77e+00 1eu8A c.94.1.1 59502 1e6bA 221 4.85e+00 1e6bA a.45.1.1 59294 c.47.1.5 59295 1bo1A 416 5.13e+00 1bo1A d.143.1.2 41591 1e9gA 286 5.31e+00 1wgjA b.40.5.1 59393 1wgjA 286 5.37e+00 1wgjA b.40.5.1 25397 1e9gB 286 5.48e+00 1wgjA b.40.5.1 59394 8prkA 287 5.92e+00 1wgjA b.40.5.1 25395 1gc5A 467 6.20e+00 1gc5A c.72.1.3 60429 8prkB 287 6.28e+00 1wgjA b.40.5.1 25396 1rt8A 513 6.30e+00 1k2yX 463 6.40e+00 c.84.1.1 68063 c.84.1.1 68064 c.84.1.1 68065 d.129.2.1 68066 1jdlA 121 6.42e+00 a.3.1.1 66557 1bp3A 191 6.95e+00 1huw a.26.1.1 16838 1augA 215 7.30e+00 1a2zA c.56.4.1 33798 1l0lK 56 7.54e+00 f.23.15.1 84497 1p5dX 463 7.60e+00 c.84.1.1 -8554 c.84.1.1 -8555 c.84.1.1 -8556 d.129.2.1 -11029 1eh2 106 8.26e+00 1eh2 a.39.1.6 17339 1kid 203 8.39e+00 1derA c.8.5.1 30771 3nul 130 8.59e+00 3nul d.110.1.1 40891 1broA 277 8.80e+00 1brt c.69.1.12 34700 1fxxA 482 9.26e+00 1fxxA c.55.3.5 33726 1eb7A 323 9.72e+00 1eb7A a.3.1.5 59404 a.3.1.5 59405 1ua4A 455 1.00e+01 c.72.1.3 -8416 1brt 277 1.03e+01 1brt c.69.1.12 34699 1q9iA 571 1.03e+01 a.138.1.3 -2051 c.3.1.4 -6041 d.168.1.1 -11607 1im5A 180 1.09e+01 unknown_sccs 66211 1a0k 131 1.33e+01 3nul d.110.1.1 40892 1p9bA 442 1.40e+01 c.37.1.10 -7115 1kssA 571 1.51e+01 a.138.1.3 72928 c.3.1.4 72929 d.168.1.1 72930 1aw9 216 1.52e+01 1gnwA a.45.1.1 17736 c.47.1.5 33030 1iu8A 206 1.54e+01 c.56.4.1 71436 1ql3A 99 1.55e+01 1ycc a.3.1.1 15822 1qmvA 197 1.57e+01 1qq2A c.47.1.10 33066 1poiB 260 1.58e+01 1poiB unknown_sccs 34155 1hm9A 468 1.61e+01 b.81.1.4 65866 c.68.1.5 65867 1g7nA 131 1.63e+01 b.60.1.2 83274 1l8aA 886 1.74e+01 c.36.1.6 73678 c.36.1.10 73677 c.48.1.1 73679 1aijL 281 1.77e+01 6prcL f.26.1.1 43461 1q6oA 216 1.78e+01 c.1.2.3 -5162 1ksfX 758 1.81e+01 a.174.1.1 77522 c.37.1.20 77523 c.37.1.20 77524 1e39A 571 1.82e+01 1qjdA a.138.1.3 19694 c.3.1.4 30431 d.168.1.1 42314 1ozhA 566 1.82e+01 c.31.1.3 -6737 c.36.1.5 -6895 c.36.1.9 -6935 1lj1A 571 1.85e+01 a.138.1.3 78023 c.3.1.4 78024 d.168.1.1 78025 1pyp 285 1.86e+01 1wgjA b.40.5.1 25409 1v7zA 260 1.87e+01 unknown_sccs -6353 1rzhL 281 1.88e+01 f.26.1.1 -12215 1jkmB 361 1.91e+01 1jkmA c.69.1.2 34634 1n82A 331 1.91e+01 c.1.8.3 -5306 1m64A 571 1.93e+01 a.138.1.3 78683 c.3.1.4 78684 d.168.1.1 78685 1h72C 296 1.96e+01 d.14.1.5 60712 d.58.26.1 60713 1f9aA 168 1.96e+01 1f9aA c.26.1.3 31602 1d7kA 421 2.05e+01 7odcA b.49.2.3 26486 c.1.6.1 28648 1do0A 442 2.12e+01 1do0A c.37.1.20 32432 1cot 129 2.14e+01 1ycc a.3.1.1 15899 1jhb 106 2.14e+01 1kte c.47.1.1 32772 1ltqA 301 2.18e+01 c.108.1.9 78208 c.37.1.1 78209 1fwcA 100 2.20e+01 1ubpA d.8.1.1 37331 1kay 381 2.25e+01 1ba1 c.55.1.1 33385 c.55.1.1 33386 1qciA 262 2.26e+01 1qi7A d.165.1.1 42201 1lehA 364 2.27e+01 1bw9A c.2.1.7 30268 c.58.1.1 33916 1izoA 417 2.28e+01 a.104.1.1 83851 2kauA 100 2.32e+01 1ubpA d.8.1.1 37335 1t5yA 190 2.33e+01 1nofA 383 2.34e+01 b.71.1.2 -4668 c.1.8.3 -5339 1kf6C 130 2.36e+01 f.21.2.2 72399 1qjdA 571 2.37e+01 1qjdA a.138.1.3 19695 c.3.1.4 30432 d.168.1.1 42315 1fnoA 417 2.37e+01 c.56.5.4 75841 d.58.19.1 70145 1uocA 289 2.45e+01 unknown_sccs -7671 1d6aB 262 2.53e+01 1qi7A d.165.1.1 42198 1k7kA 221 2.55e+01 c.51.4.1 72104 1bx4A 345 2.58e+01 1bx4A c.72.1.1 34935 1vc4A 254 2.61e+01 c.1.2.4 -5172 1f0jA 377 2.62e+01 1f0jA a.125.1.1 19346 1g61A 228 2.65e+01 1g61A d.126.1.1 41126 1kv8A 216 2.69e+01 c.1.2.3 73054 1bupA 386 2.76e+01 1ba1 c.55.1.1 33377 c.55.1.1 33378 1qumA 285 2.80e+01 1qumA c.1.15.1 29393 1h1nA 305 2.85e+01 c.1.8.3 70855 1j1qA 261 2.90e+01 d.165.1.1 -11546 1ejxA 100 2.92e+01 d.8.1.1 83182 1fwkA 296 2.96e+01 1fwkA d.14.1.5 37576 d.58.26.1 39398 1qtwA 285 2.96e+01 1qumA c.1.15.1 29392 1jkmA 358 3.00e+01 1jkmA c.69.1.2 34633 1ba1 386 3.03e+01 1ba1 c.55.1.1 33387 c.55.1.1 33388 1kwgA 645 3.05e+01 b.71.1.1 77561 c.1.8.1 77562 c.23.16.5 77563 1qq2A 199 3.12e+01 1qq2A c.47.1.10 33064 1dcfA 136 3.13e+01 1dcfA c.23.1.2 31124 1kwkA 645 3.15e+01 b.71.1.1 77565 c.1.8.1 77566 c.23.16.5 77567 1nbaA 264 3.17e+01 1nbaA unknown_sccs 31753 1g97A 459 3.18e+01 1fwyA b.81.1.4 60394 c.68.1.5 60395 1ede 310 3.28e+01 1b6g c.69.1.8 34662 1hcc 59 3.36e+01 1hfh g.18.1.1 44820 1fjgM 126 3.37e+01 1fjfM a.156.1.1 16293 1okrA 123 3.41e+01 unknown_sccs -235 1ugpB 226 3.45e+01 1fokA 568 3.50e+01 2fokA a.4.5.12 16137 a.4.5.12 16138 a.4.5.12 16139 c.52.1.12 33325 1s72H 171 3.53e+01 1gu7A 364 3.62e+01 b.35.1.2 83321 c.2.1.1 83322 4aahA 571 3.67e+01 4aahA b.70.1.1 27678 1g72A 573 3.69e+01 4aahA b.70.1.1 27680 1ji0A 240 3.84e+01 c.37.1.12 71665 1ge9A 184 3.85e+01 1dd5A d.67.3.1 60463 1aboA 62 3.86e+01 1bbzA b.34.2.1 24474