# List of top-scoring protein chains for t2k-100-30-str2 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 1mzeA 351 1.14e-16 b.82.2.6 79694 1h2kA 349 1.83e-16 b.82.2.6 76572 1j58A 385 8.87e-04 b.82.1.2 71531 1fi2A 201 1.15e-03 1fi2A b.82.1.2 59845 1cawB 184 1.39e-03 1caxB b.82.1.2 28113 2arcA 164 2.08e-03 2arcA b.82.4.1 28148 2aacA 177 2.22e-03 2arcA b.82.4.1 28150 2arcB 164 2.25e-03 2arcA b.82.4.1 28149 2cavA 445 3.66e-03 1dgwA b.82.1.2 28094 b.82.1.2 28095 1cauB 184 3.99e-03 1caxB b.82.1.2 28103 1caxB 184 1.02e-02 1caxB b.82.1.2 28105 1qxrA 189 1.50e-02 1plzA 189 1.65e-02 b.82.1.7 88160 1od5A 492 2.71e-02 b.82.1.2 86832 b.82.1.2 86833 1fxzA 476 7.56e-02 b.82.1.2 65059 b.82.1.2 65060 1nxmA 197 8.62e-02 b.82.1.1 86385 1ofnA 205 1.38e-01 1e5rA 290 1.57e-01 1e5rA b.82.2.4 59276 1oi6A 205 1.59e-01 1lr5A 163 2.20e-01 b.82.1.2 74215 2phlA 397 2.23e-01 1dgwA b.82.1.2 28082 b.82.1.2 28083 1qwrA 319 2.65e-01 1mrzA 293 3.30e-01 1pbuA 162 5.63e-01 d.58.46.1 88030 1dgrM 93 6.34e-01 1caxB b.82.1.2 28101 1dgrW 93 6.43e-01 1caxB 1o4tA 133 7.61e-01 b.82.1.9 86622 1fnmA 691 8.44e-01 1dar b.43.3.1 25709 c.37.1.8 32144 d.14.1.1 37546 d.58.11.1 39302 d.58.11.1 39303 1dgwY 93 1.28e+00 1caxB 1nnt 328 1.29e+00 1nnt c.94.1.2 35884 1tfaA 329 1.47e+00 1nnt c.94.1.2 35880 1iejA 332 1.57e+00 1nnt c.94.1.2 62328 1nftA 329 1.66e+00 1nnt c.94.1.2 35881 1dgrC 178 1.76e+00 1dgwA b.82.1.2 28100 1rl2A 137 2.29e+00 1rl2A b.34.5.3 24610 b.40.4.5 25342 1dgwA 178 2.31e+00 1dgwA b.82.1.2 28090 1q15A 503 2.46e+00 1cauA 181 2.51e+00 1dgwA b.82.1.2 28102 1dar 691 2.72e+00 1dar b.43.3.1 25707 c.37.1.8 32142 d.14.1.1 37547 d.58.11.1 39300 1h1iC 350 3.07e+00 b.82.1.5 76471 1h1iD 350 3.75e+00 b.82.1.5 76472 1juhA 350 3.82e+00 b.82.1.5 71884 1h1iB 350 3.90e+00 b.82.1.5 76470 1ft9A 222 4.18e+00 1ft9A a.4.5.4 16107 b.82.3.1 28131 1ep0A 185 5.55e+00 1dzrA b.82.1.1 28080 1a16 440 7.03e+00 1az9 c.55.2.1 33548 d.127.1.1 41165 1az9 457 7.12e+00 1az9 c.55.2.1 33547 d.127.1.1 41164 1n62C 288 7.12e+00 d.87.2.1 80094 d.145.1.3 80095 1hqsA 423 7.57e+00 1iso c.77.1.1 61154 1dctA 324 8.06e+00 6mhtA c.66.1.26 34244 1agx 331 8.06e+00 4pgaA c.88.1.1 35564 1smd 496 8.41e+00 1smd b.71.1.1 27768 c.1.8.1 28755 4ts1A 319 8.76e+00 2ts1 c.26.1.1 31565 1elt 236 8.87e+00 5ptp b.47.1.2 26281 3hmgA 328 9.11e+00 1hgeA b.19.1.2 23825 1jslA 327 9.50e+00 c.88.1.1 67233 1jsrA 327 9.52e+00 c.88.1.1 67237 1dupA 152 9.54e+00 1dupA b.85.4.1 28351 1euwA 152 9.54e+00 1dupA b.85.4.1 28349 1umdB 324 9.77e+00 2viuA 328 9.80e+00 1hgeA b.19.1.2 23797 1hgeA 328 1.00e+01 1hgeA b.19.1.2 23816 1i4wA 353 1.03e+01 c.66.1.24 66028 1o7jA 327 1.05e+01 c.88.1.1 81140 1g55A 343 1.08e+01 1g55A c.66.1.26 34247 1ufoA 238 1.13e+01 1oltA 457 1.17e+01 1shwA 138 1.21e+01 1ifqA 138 1.22e+01 1ifqA d.110.4.1 62350 1qj2C 285 1.23e+01 1qj2C 1btu 240 1.23e+01 5ptp b.47.1.2 26241 1gvkB 240 1.24e+01 b.47.1.2 70610 1iz0A 302 1.30e+01 b.35.1.2 83821 c.2.1.1 83822 1qnjA 240 1.36e+01 5ptp b.47.1.2 26238 1gnuA 117 1.37e+01 d.15.1.3 65403 1gskA 513 1.53e+01 b.6.1.3 83314 b.6.1.3 83315 b.6.1.3 83316 1o5uA 101 1.54e+01 1fnc 314 1.57e+01 1fnc b.43.4.2 25627 c.25.1.1 31517 1fnd 314 1.60e+01 1fnc b.43.4.2 25626 c.25.1.1 31516 1qg0A 308 1.63e+01 1fnc b.43.4.2 25639 c.25.1.1 31529 1o6dA 163 1.66e+01 1hx0A 496 1.74e+01 b.71.1.1 61346 c.1.8.1 61347 1dgwX 79 1.88e+01 1caxB b.82.1.2 28091 1fnb 314 1.89e+01 1fnc b.43.4.2 25628 c.25.1.1 31518 2ts1 419 1.92e+01 2ts1 c.26.1.1 31564 1gpr 162 2.06e+01 1gpr b.84.3.1 28267 1behA 187 2.17e+01 1a44 b.17.1.1 23700 16pk 415 2.20e+01 16pk c.86.1.1 35454 1dryA 324 2.23e+01 1drtA b.82.2.2 28128 1dzrA 183 2.25e+01 1dzrA b.82.1.1 28076 1nnlA 225 2.26e+01 c.108.1.4 85906 1ds1A 324 2.28e+01 1drtA b.82.2.2 28127 1dfoA 417 2.31e+01 1bj4A c.67.1.4 34480 1nkgA 508 2.33e+01 1d3hA 367 2.37e+01 1d3gA c.1.4.1 28601 1ivnA 190 2.41e+01 c.23.10.5 83719 1cb6A 691 2.41e+01 1cb6A c.94.1.2 35840 c.94.1.2 35841 1drtA 324 2.46e+01 1drtA b.82.2.2 28130 1jtkA 136 2.49e+01 c.97.1.1 71862 1ji8A 111 2.55e+01 d.203.1.1 66733 1jqfA 334 2.57e+01 c.94.1.2 67086 1ptf 88 2.57e+01 1ptf d.94.1.1 40549 2bosA 68 2.62e+01 2bosA b.40.2.1 25025 1kmqA 184 2.64e+01 c.37.1.8 84412 1uumA 372 2.65e+01 1rm8A 169 2.66e+01 1a8e 329 2.68e+01 1cb6A c.94.1.2 35888 1uw6A 211 2.71e+01 1hfx 123 2.80e+01 3lzt d.2.1.2 36600 1in6A 334 2.86e+01 1hqcA a.4.5.11 62601 c.37.1.20 62602 1erjA 393 3.05e+01 1erjA b.69.4.1 27660 1spuB 727 3.07e+01 1oacA b.30.2.1 24399 d.17.2.1 38025 d.17.2.1 38026 d.82.1.1 40012 1ryoA 327 3.15e+01 1vhoA 346 3.20e+01 1e5eA 404 3.21e+01 1ibjA c.67.1.3 59265 1pmy 123 3.23e+01 1bqk b.6.1.1 22888 1pv5A 264 3.24e+01 1dgrN 79 3.24e+01 1caxB 1d3kA 329 3.31e+01 1nnt c.94.1.2 35889 1ns5A 155 3.33e+01 c.116.1.3 80705 1bqk 124 3.47e+01 1bqk b.6.1.1 22889 1lqtA 456 3.47e+01 c.3.1.1 74198 c.4.1.1 74199 1k8kC 372 3.55e+01 b.69.4.1 68308 1i7oA 429 3.56e+01 1i7oA d.177.1.1 61893 d.177.1.1 61894 1dgrV 79 3.56e+01 1caxB b.82.1.2 28099 1uwzA 136 3.66e+01 1avaA 403 3.69e+01 1jdc b.71.1.1 27797 c.1.8.1 28784 1mkyA 439 3.71e+01 c.37.1.8 79250 c.37.1.8 79251 d.52.5.1 79252 1ijgA 309 3.79e+01 1fouA e.27.1.1 62493 1r29A 127 3.81e+01 4pgaA 337 3.84e+01 4pgaA c.88.1.1 35565 1o1yA 239 3.90e+01 c.23.16.1 86554 1gttA 429 3.93e+01 d.177.1.1 70529 d.177.1.1 70530 3pga1 337 3.97e+01 4pgaA 1a44 185 3.98e+01 1a44 b.17.1.1 23704 2pvaA 345 3.99e+01 3pvaA d.153.1.3 41850 1r4pB 70 4.00e+01