# 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 1h2kA 349 1.12e-19 b.82.2.6 76572 1mzeA 351 1.76e-19 b.82.2.6 79694 1plzA 189 1.61e-04 b.82.1.7 88160 1qxrA 189 1.68e-04 2arcB 164 4.91e-04 2arcA b.82.4.1 28149 2aacA 177 6.38e-04 2arcA b.82.4.1 28150 2arcA 164 6.80e-04 2arcA b.82.4.1 28148 1fi2A 201 7.20e-04 1fi2A b.82.1.2 59845 1j58A 385 8.34e-04 b.82.1.2 71531 2cavA 445 2.42e-03 1dgwA b.82.1.2 28094 b.82.1.2 28095 1cauB 184 4.69e-03 1caxB b.82.1.2 28103 1cawB 184 8.34e-03 1caxB b.82.1.2 28113 1od5A 492 8.74e-03 b.82.1.2 86832 b.82.1.2 86833 1caxB 184 1.13e-02 1caxB b.82.1.2 28105 1qwrA 319 4.24e-02 1lr5A 163 6.04e-02 b.82.1.2 74215 1o4tA 133 7.91e-02 b.82.1.9 86622 1ofnA 205 1.68e-01 1oi6A 205 1.98e-01 1e5rA 290 2.15e-01 1e5rA b.82.2.4 59276 1dgwA 178 2.63e-01 1dgwA b.82.1.2 28090 1dgrC 178 2.68e-01 1dgwA b.82.1.2 28100 1nxmA 197 3.12e-01 b.82.1.1 86385 1fxzA 476 3.22e-01 b.82.1.2 65059 b.82.1.2 65060 1dar 691 4.65e-01 1dar b.43.3.1 25707 c.37.1.8 32142 d.14.1.1 37547 d.58.11.1 39300 1oaoA 674 5.20e-01 e.26.1.2 86744 1o5nA 126 5.73e-01 1vj2A 126 5.73e-01 1cauA 181 5.89e-01 1dgwA b.82.1.2 28102 2phlA 397 6.06e-01 1dgwA b.82.1.2 28082 b.82.1.2 28083 1rl2A 137 7.28e-01 1rl2A b.34.5.3 24610 b.40.4.5 25342 2ts1 419 8.18e-01 2ts1 c.26.1.1 31564 1o5uA 101 8.82e-01 1tfaA 329 9.31e-01 1nnt c.94.1.2 35880 1mrzA 293 9.49e-01 1h1iC 350 1.02e+00 b.82.1.5 76471 1h1iB 350 1.07e+00 b.82.1.5 76470 1h1iD 350 1.11e+00 b.82.1.5 76472 1fnmA 691 1.14e+00 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 1juhA 350 1.24e+00 b.82.1.5 71884 4ts1A 319 1.26e+00 2ts1 c.26.1.1 31565 1dgrM 93 1.36e+00 1caxB b.82.1.2 28101 1iejA 332 1.36e+00 1nnt c.94.1.2 62328 1nftA 329 1.39e+00 1nnt c.94.1.2 35881 1dgrW 93 1.42e+00 1caxB 1nnt 328 1.42e+00 1nnt c.94.1.2 35884 1ds1A 324 1.56e+00 1drtA b.82.2.2 28127 1dgwY 93 1.75e+00 1caxB 1lgpA 116 1.98e+00 b.26.1.2 73890 2cb5A 453 2.14e+00 3gcb d.3.1.1 37035 1jcfA 344 2.35e+00 c.55.1.1 62878 c.55.1.1 62879 1drtA 324 2.42e+00 1drtA b.82.2.2 28130 1dryA 324 2.44e+00 1drtA b.82.2.2 28128 1rm8A 169 2.50e+00 1jceA 344 2.94e+00 c.55.1.1 62876 c.55.1.1 62877 1pbuA 162 3.45e+00 d.58.46.1 88030 3hmgA 328 3.54e+00 1hgeA b.19.1.2 23825 1vddA 228 4.09e+00 1lxyA 409 4.14e+00 1s9rA 410 4.30e+00 1dupA 152 4.32e+00 1dupA b.85.4.1 28351 2viuA 328 4.45e+00 1hgeA b.19.1.2 23797 1ru4A 400 4.62e+00 1hgeA 328 5.29e+00 1hgeA b.19.1.2 23816 1fnc 314 5.48e+00 1fnc b.43.4.2 25627 c.25.1.1 31517 1ji8A 111 5.55e+00 d.203.1.1 66733 1smd 496 5.88e+00 1smd b.71.1.1 27768 c.1.8.1 28755 1az9 457 6.33e+00 1az9 c.55.2.1 33547 d.127.1.1 41164 1fnb 314 6.34e+00 1fnc b.43.4.2 25628 c.25.1.1 31518 1euwA 152 6.38e+00 1dupA b.85.4.1 28349 1f2rI 100 6.46e+00 1c9fA d.15.2.1 37641 1fnd 314 6.61e+00 1fnc b.43.4.2 25626 c.25.1.1 31516 1cb6A 691 6.80e+00 1cb6A c.94.1.2 35840 c.94.1.2 35841 1oltA 457 7.45e+00 1ujxA 119 7.46e+00 1a16 440 8.05e+00 1az9 c.55.2.1 33548 d.127.1.1 41165 1kyqA 274 8.13e+00 c.2.1.11 73281 e.37.1.1 73282 1dgrV 79 8.50e+00 1caxB b.82.1.2 28099 1ko3A 230 8.79e+00 1o7jA 327 8.95e+00 c.88.1.1 81140 1exmA 405 9.03e+00 1efcA b.43.3.1 25696 b.44.1.1 25736 c.37.1.8 32131 1dgwX 79 9.17e+00 1caxB b.82.1.2 28091 1kewA 361 9.30e+00 c.2.1.2 68544 1lv7A 257 9.43e+00 c.37.1.20 78232 1o6dA 163 9.60e+00 2rslA 140 9.64e+00 2rslA c.53.1.1 33345 1jsrA 327 9.66e+00 c.88.1.1 67237 1ep0A 185 9.76e+00 1dzrA b.82.1.1 28080 1n5dA 288 1.00e+01 c.2.1.2 80030 1hu4A 288 1.01e+01 1hu4A 1hg2A 289 1.01e+01 1hg5A a.118.10.1 61024 1v5lA 103 1.06e+01 1jslA 327 1.07e+01 c.88.1.1 67233 1lj2A 110 1.09e+01 h.1.13.2 73926 1ao0A 459 1.10e+01 1ecfB c.61.1.1 34049 d.153.1.1 41816 1ejhA 190 1.11e+01 1ejhA d.86.1.1 40147 1elt 236 1.23e+01 5ptp b.47.1.2 26281 1rkd 309 1.23e+01 1rkd c.72.1.1 34928 1uu1A 335 1.26e+01 1dgrN 79 1.29e+01 1caxB 1ebuA 358 1.30e+01 1ebuA c.2.1.3 30035 d.81.1.2 39950 1qg0A 308 1.30e+01 1fnc b.43.4.2 25639 c.25.1.1 31529 1pmi 440 1.32e+01 1pmi b.82.1.3 28114 2matA 264 1.33e+01 1c24A d.127.1.1 41146 1mat 264 1.33e+01 1c24A d.127.1.1 41152 1hf8A 289 1.39e+01 1hg5A a.118.10.1 19219 1r6dA 337 1.39e+01 1c24A 263 1.41e+01 1c24A d.127.1.1 41148 1st9A 143 1.44e+01 1ha3A 405 1.46e+01 1efcA b.43.3.1 60869 b.44.1.1 60870 c.37.1.8 60871 1jhdA 396 1.46e+01 b.122.1.3 66712 c.26.1.5 66713 1hqcA 324 1.50e+01 1hqcA a.4.5.11 16127 c.37.1.20 32424 1hg5A 289 1.51e+01 1hg5A a.118.10.1 19221 1div 149 1.54e+01 1div d.99.1.1 40692 d.100.1.1 40693 1in6A 334 1.55e+01 1hqcA a.4.5.11 62601 c.37.1.20 62602 1o04A 500 1.59e+01 c.82.1.1 86508 1pex 207 1.61e+01 1gen b.66.1.1 27540 1ns5A 155 1.62e+01 c.116.1.3 80705 1dzrA 183 1.65e+01 1dzrA b.82.1.1 28076 1dfoA 417 1.71e+01 1bj4A c.67.1.4 34480 1avoA 60 1.71e+01 1avoA a.24.8.1 16619 1n82A 331 1.76e+01 1hf2A 210 1.77e+01 1hf2A b.80.3.1 60992 c.102.1.1 60993 1pauA 147 1.78e+01 1pauA c.17.1.1 30994 1id2A 106 1.78e+01 1aac b.6.1.1 62288 1ni9A 338 1.83e+01 e.7.1.2 85739 1ka6A 128 1.84e+01 d.93.1.1 68370 1hqsA 423 1.84e+01 1iso c.77.1.1 61154 1h6fA 193 1.85e+01 b.2.5.4 70901 1dtgA 334 1.87e+01 1nnt c.94.1.2 35896 4matA 278 1.88e+01 1c24A d.127.1.1 41150 1agx 331 1.94e+01 4pgaA c.88.1.1 35564 1b3eA 330 1.99e+01 1nnt c.94.1.2 35897 1nmeA 146 1.99e+01 c.17.1.1 85874 1aipE 405 2.04e+01 1efcA b.43.3.1 25699 b.44.1.1 25739 c.37.1.8 32134 1i9bA 217 2.07e+01 1i9bA b.96.1.1 62084 1c3cA 429 2.11e+01 1c3cA a.127.1.1 19425 1a8e 329 2.14e+01 1cb6A c.94.1.2 35888 2gmfA 127 2.14e+01 2gmfA a.26.1.2 16849 1qwgA 251 2.20e+01 1djxA 624 2.21e+01 1djxB a.39.1.7 17342 b.7.1.1 23159 c.1.18.1 29587 1hvc 203 2.23e+01 1hvc b.50.1.1 26614 1jqfA 334 2.24e+01 c.94.1.2 67086 1ej1A 190 2.30e+01 1ejhA d.86.1.1 40144 1pmy 123 2.33e+01 1bqk b.6.1.1 22888 1uw6A 211 2.38e+01 1avgI 142 2.40e+01 1avgI b.60.1.3 27229 1b7bA 310 2.40e+01 1b7bA c.73.1.1 34963 1lct 333 2.40e+01 1cb6A c.94.1.2 35836 1kp0A 402 2.45e+01 c.55.2.1 72834 d.127.1.1 72835 1iz0A 302 2.46e+01 b.35.1.2 83821 c.2.1.1 83822 1gx3A 284 2.49e+01 d.3.1.5 70678 1bqk 124 2.52e+01 1bqk b.6.1.1 22889 1ebfA 358 2.52e+01 1ebuA c.2.1.3 30033 d.81.1.2 39948 1i50F 155 2.54e+01 d.78.1.2 61760 1iupA 282 2.55e+01 c.69.1.10 76815 1b7yA 350 2.61e+01 1pysA d.104.1.1 40776 1fgxA 288 2.63e+01 1fgxA c.68.1.2 34508 1hrnA 337 2.68e+01 1smrA b.50.1.2 26869 1ryoA 327 2.71e+01 1b77A 228 2.72e+01 1b77A d.131.1.2 41362 d.131.1.2 41363 1pgvA 197 2.80e+01 c.10.1.1 88073 1innA 166 2.81e+01 1j98A d.185.1.2 62608 1skyB 502 2.82e+01 1skyB a.69.1.1 18313 b.49.1.1 26478 c.37.1.11 32358 1hx0A 496 2.82e+01 b.71.1.1 61346 c.1.8.1 61347 1qatB 622 2.83e+01 1djxB a.39.1.7 17355 b.7.1.1 23172 c.1.18.1 29600 1tuc 63 2.84e+01 1tuc b.34.2.1 24492 1ytfD 121 2.85e+01 1ytfD a.32.1.1 16998 b.56.1.1 27011 1csgA 127 2.89e+01 2gmfA a.26.1.2 16851 1djxB 624 2.94e+01 1djxB a.39.1.7 17343 b.7.1.1 23160 c.1.18.1 29588 1i31A 314 2.96e+01 1bw8A b.2.7.1 22481 1lnqA 336 2.98e+01 c.2.1.9 74049 f.14.1.1 74050 1kw3B 292 3.00e+01 d.32.1.3 77549 d.32.1.3 77550 2ay1A 394 3.02e+01 1ajsA c.67.1.1 34357 1cp3A 277 3.04e+01 1pauA c.17.1.1 30992 1pvgA 418 3.05e+01 1i4nA 251 3.08e+01 c.1.2.4 71114 1tud 62 3.14e+01 1tud b.34.2.1 24489 1bxkA 355 3.16e+01 1bxkA c.2.1.2 29803 1d3kA 329 3.16e+01 1nnt c.94.1.2 35889 1in4A 334 3.17e+01 1hqcA a.4.5.11 62597 c.37.1.20 62598 1oe4A 247 3.19e+01 c.18.1.3 86895 1ko6A 187 3.25e+01 b.119.1.1 77471 1jb9A 316 3.28e+01 1fnc b.43.4.2 62840 c.25.1.1 62841 1gcqC 70 3.33e+01 1gcpA b.34.2.1 60436 1umdB 324 3.37e+01 1qvjA 292 3.37e+01 1aba 87 3.39e+01 1aba c.47.1.1 32760 1j9qA 341 3.43e+01 1nif b.6.1.3 62765 b.6.1.3 62766 1qasA 622 3.44e+01 1djxB a.39.1.7 17340 b.7.1.1 23157 c.1.18.1 29585 1khbA 625 3.45e+01 c.91.1.1 68606 c.109.1.1 68607 1bw8A 321 3.46e+01 1bw8A b.2.7.1 22482 1d6jA 211 3.46e+01 1d6jA c.37.1.4 31940 1bxxA 285 3.46e+01 1bw8A b.2.7.1 22483 1g2bA 62 3.47e+01 1tud b.34.2.1 24488 1gcpA 70 3.48e+01 1gcpA b.34.2.1 60430 1f75A 249 3.48e+01 1f75A c.101.1.1 59662 1pjqA 457 3.49e+01 1ixmB 192 3.52e+01 1ixmA d.123.1.1 41115 1bfa 134 3.60e+01 1bea a.52.1.2 17827 1jsdA 319 3.63e+01 b.19.1.2 63258 1hdcA 253 3.65e+01 1e6wA c.2.1.2 29862 1ixmA 192 3.73e+01 1ixmA d.123.1.1 41114 1jx4A 352 3.74e+01 e.8.1.5 67405 1oghA 204 3.83e+01 b.85.4.1 86994 1g59A 468 3.84e+01 a.97.1.1 60257 c.26.1.1 60258 1pztA 286 3.84e+01 1kktA 511 3.90e+01 a.102.2.1 68687 1k1zA 78 3.91e+01 b.34.2.1 68026 1h1wA 289 3.93e+01 d.144.1.7 83460 1bb9 115 3.95e+01 1bb9 b.34.2.1 24554 1mkyA 439 3.96e+01 c.37.1.8 79250 c.37.1.8 79251 d.52.5.1 79252 1bea 127 3.96e+01 1bea a.52.1.2 17826 1jj7A 260 3.98e+01 c.37.1.12 63114 1eb0A 147 4.00e+01 b.107.1.1 64890 d.58.38.1 64891