# List of top-scoring protein chains for t2k-100-30-near-backbone-11 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 1ho1A 242 1.65e-03 1ho1A c.1.24.1 61097 1m5wA 243 6.15e-03 c.1.24.1 84836 1ezwA 349 1.46e-02 1ezwA c.1.16.3 29558 1czyA 168 3.71e-02 1d0aB b.8.1.1 23220 h.1.2.1 45427 1czyC 168 6.51e-02 1d0aB b.8.1.1 23222 h.1.2.1 45429 1mumA 295 7.06e-02 c.1.12.7 85108 1d0aB 168 1.17e-01 1d0aB b.8.1.1 23224 h.1.2.1 45431 1ca4A 168 1.20e-01 1d0aB b.8.1.1 23238 h.1.2.1 45445 1iktA 120 1.66e-01 d.106.1.1 66188 1ca9A 192 1.77e-01 1d0aB b.8.1.1 23244 h.1.2.1 45451 1p32A 209 2.39e-01 1p32A d.25.1.1 38379 1tljA 213 2.40e-01 1b5tA 275 2.71e-01 1b5tA c.1.23.1 29676 1qwgA 251 4.29e-01 unknown_sccs -5678 1di6A 195 4.41e-01 1di6A c.57.1.1 33863 1edt 271 5.52e-01 2ebn c.1.8.5 28993 1ojqA 212 6.16e-01 d.166.1.1 -11568 1oa8A 133 6.75e-01 unknown_sccs -5142 1hyqA 263 7.19e-01 1hyqA c.37.1.10 61412 1p32C 209 7.68e-01 1p32A d.25.1.1 38381 1mvfD 82 7.89e-01 b.129.1.1 85143 1rhcA 330 7.90e-01 c.1.16.3 -5606 1vi9A 299 8.16e-01 c.72.1.5 -8393 1esmA 316 9.85e-01 1esmA c.37.1.6 31953 1g291 372 1.02e+00 1g291 1s6cA 183 1.13e+00 a.39.1.5 -858 1g94A 448 1.13e+00 b.71.1.1 65169 c.1.8.1 65170 1f1xA 322 1.20e+00 d.32.1.3 83208 d.32.1.3 83209 1pqzA 238 1.31e+00 1v93A 296 1.36e+00 c.1.23.1 -5654 1fc4A 401 1.73e+00 1bs0A c.67.1.4 59760 1cjaA 342 1.75e+00 1cjaA d.144.1.3 41708 1mxgA 435 1.76e+00 b.71.1.1 85193 c.1.8.1 85194 1f07A 321 1.79e+00 1ezwA c.1.16.3 59560 1pk5A 248 1.85e+00 a.123.1.1 88139 1aqm 453 1.86e+00 1smd b.71.1.1 27717 c.1.8.1 28704 1umdB 324 1.97e+00 c.36.1.7 -6929 c.48.1.2 -7539 1o5kA 306 2.23e+00 c.1.10.1 -5482 1gvnB 287 2.48e+00 c.37.1.21 76354 1qndA 123 2.50e+00 1qndA d.106.1.1 40794 1hw5A 210 2.57e+00 2cgpA a.4.5.4 16098 b.82.3.2 28137 1ub4C 85 2.60e+00 b.129.1.1 88401 1auiB 169 2.77e+00 1auiB a.39.1.5 17325 1gtxA 472 2.95e+00 1gtxA 1ta3A 274 3.24e+00 3nodB 423 3.25e+00 1nseA d.174.1.1 42513 1kutA 230 3.29e+00 d.143.1.1 73017 1m6jA 261 3.43e+00 c.1.1.1 78693 1cec 343 3.47e+00 1ceo c.1.8.3 28809 1l2tA 235 3.50e+00 c.37.1.12 73514 1k9uA 78 3.52e+00 a.39.1.10 84348 1ohvA 472 3.55e+00 c.67.1.4 -8181 1lkyA 77 3.55e+00 a.60.1.1 73985 1nq6A 302 3.57e+00 c.1.8.3 -5332 1g8iA 190 3.64e+00 1rec a.39.1.5 60363 1a79A 171 3.64e+00 1a79A c.52.2.1 33340 d.75.1.1 39739 1jhsA 188 3.76e+00 d.107.1.1 84172 1n7kA 234 4.22e+00 c.1.10.1 85374 1mo0A 275 4.28e+00 c.1.1.1 79329 1pkoA 139 4.57e+00 b.1.1.1 88147 1jljA 189 4.60e+00 c.57.1.1 63169 1o8uA 257 4.62e+00 c.14.1.3 81194 2dvh 79 4.80e+00 1c53 a.3.1.1 15803 1f1uA 323 4.81e+00 d.32.1.3 83200 d.32.1.3 83201 1gky 187 4.81e+00 1gky c.37.1.1 31839 1rj9A 304 4.83e+00 a.24.13.1 -631 c.37.1.10 -7129 1fjcA 96 4.85e+00 1fjcA d.58.7.1 39212 6pfkA 319 4.89e+00 3pfk c.89.1.1 35583 1eq6A 189 5.05e+00 1eq6A d.107.1.1 40796 1rfa 79 5.13e+00 1c1yB d.15.1.5 37620 1ex7A 186 5.23e+00 1gky c.37.1.1 59537 1ihcA 188 5.35e+00 1di6A c.57.1.1 62379 1cnv 299 5.39e+00 1cnv c.1.8.5 28989 1dvh 79 5.53e+00 1c53 a.3.1.1 15802 1fjeB 175 5.63e+00 1fj7A d.58.7.1 39210 d.58.7.1 39211 1pysA 350 5.68e+00 1pysA d.104.1.1 40775 2cgpA 210 5.70e+00 2cgpA a.4.5.4 16102 b.82.3.2 28141 1lrzA 426 5.82e+00 a.2.7.4 78167 d.108.1.4 78168 d.108.1.4 78169 1b7yA 350 6.01e+00 1pysA d.104.1.1 40776 1c96A 753 6.08e+00 1amj c.8.2.1 30727 c.83.1.1 35403 4pfk 319 6.16e+00 3pfk c.89.1.1 35582 1eokA 290 6.17e+00 1eokA c.1.8.5 28991 8rucA 475 6.25e+00 1burA c.1.14.1 29339 d.58.9.1 39245 2pii 112 6.29e+00 2pii d.58.5.1 39071 3pfk 319 6.54e+00 3pfk c.89.1.1 35581 1a53 247 6.57e+00 1a53 c.1.2.4 28564 1kblA 873 6.57e+00 c.1.12.2 68384 c.8.1.1 68385 d.142.1.5 68386 1pbuA 162 6.58e+00 d.58.46.1 88030 1szoA 257 6.78e+00 1jb1A 205 6.80e+00 1jb1A c.91.1.2 62832 1ji7A 89 7.06e+00 a.60.1.1 71682 1om0A 274 7.08e+00 c.1.8.5 87058 1g8eA 116 7.13e+00 1g8eA a.145.1.1 60346 1g55A 343 7.33e+00 1g55A c.66.1.26 34247 1k7wA 468 7.49e+00 a.127.1.1 72130 1b77A 228 7.76e+00 1b77A d.131.1.2 41362 d.131.1.2 41363 1igs 248 7.82e+00 1a53 c.1.2.4 28565 1pgx 83 7.85e+00 2igd d.15.7.1 37823 1iyxA 432 8.41e+00 c.1.11.1 83815 d.54.1.1 83816 1dcnD 436 8.51e+00 1auwA a.127.1.1 19423 1je6A 275 9.11e+00 b.1.1.2 71638 d.19.1.1 71639 1n82A 331 9.22e+00 c.1.8.3 -5306 1cr1A 296 9.73e+00 1cr1A c.37.1.11 32286 1h6kX 97 9.80e+00 d.58.7.1 60684 1ceo 343 9.83e+00 1ceo c.1.8.3 28808 1avaA 403 9.97e+00 1jdc b.71.1.1 27797 c.1.8.1 28784 1igd 61 1.04e+01 2igd d.15.7.1 37822 7acn 754 1.04e+01 1amj c.8.2.1 30717 c.83.1.1 35393 2igd 61 1.06e+01 2igd d.15.7.1 37821 1rkd 309 1.08e+01 1rkd c.72.1.1 34928 1h6kZ 98 1.08e+01 d.58.7.1 60686 1vh5A 148 1.08e+01 d.38.1.5 -9677 1eal 127 1.08e+01 1hmt b.60.1.2 27227 1guaB 81 1.09e+01 1c1yB d.15.1.5 37619 1dik 874 1.15e+01 1dik c.1.12.2 29304 c.8.1.1 30702 d.142.1.5 41572 1pil 112 1.16e+01 2pii d.58.5.1 39072 6acn 754 1.18e+01 1amj c.8.2.1 30721 c.83.1.1 35397 1pfvA 551 1.18e+01 a.27.1.1 -727 c.26.1.1 -6603 g.41.1.1 -12765 2lefA 86 1.21e+01 2lefA a.21.1.1 16433 1f4lA 551 1.24e+01 1qqtA a.27.1.1 59648 c.26.1.1 59649 g.41.1.1 59650 1dysA 348 1.26e+01 1bvwA c.6.1.1 30669 1dcnA 424 1.27e+01 1auwA a.127.1.1 19420 1j5rA 371 1.27e+01 1vizA 240 1.29e+01 c.1.4.1 -5212 1v2dA 381 1.30e+01 1juk 248 1.30e+01 1a53 c.1.2.4 28567 1dmtA 696 1.30e+01 1dmtA d.92.1.4 40296 1v4eA 299 1.31e+01 a.128.1.1 -1781 1nf9A 207 1.31e+01 unknown_sccs 85631 1s2wA 295 1.33e+01 c.1.12.7 -5577 1e5kA 201 1.37e+01 1fr9A c.68.1.8 34578 1n3kA 130 1.37e+01 a.77.1.4 79965 1o7jA 327 1.38e+01 c.88.1.1 81140 1g0oA 283 1.40e+01 1ybvA c.2.1.2 60181 1ybvA 283 1.41e+01 1ybvA c.2.1.2 29948 1a0cA 438 1.41e+01 1a0cA c.1.15.3 29529 1o08A 221 1.43e+01 c.108.1.6 86525 1moq 368 1.43e+01 1moq c.80.1.1 35302 1jpmA 366 1.44e+01 c.1.11.2 67031 d.54.1.1 67032 1r5zA 323 1.46e+01 unknown_sccs -12289 1cktA 71 1.47e+01 1cktA a.21.1.1 16417 1su4A 994 1.50e+01 b.82.7.1 -4927 c.108.1.7 -6854 d.220.1.1 -11668 f.33.1.1 -12333 1jsrA 327 1.50e+01 c.88.1.1 67237 1qqtA 551 1.56e+01 1qqtA a.27.1.1 16923 c.26.1.1 31590 g.41.1.1 45175 1ub3A 220 1.57e+01 c.1.10.1 88395 1mejA 223 1.58e+01 c.65.1.1 79029 1cr0A 296 1.59e+01 1cr1A c.37.1.11 32287 1dcoA 104 1.59e+01 1dcpA d.74.1.1 39680 1cb7B 483 1.61e+01 1cb7B c.1.19.2 29648 1aab 83 1.61e+01 1cktA a.21.1.1 16420 1fr9A 194 1.63e+01 1fr9A c.68.1.8 34579 1o2dA 371 1.64e+01 e.22.1.2 86591 1geqA 248 1.67e+01 2tysA c.1.2.4 28589 8acn 754 1.69e+01 1amj c.8.2.1 30724 c.83.1.1 35400 1jslA 327 1.70e+01 c.88.1.1 67233 1g7vA 284 1.72e+01 1d9eA c.1.10.4 60335 1jx6A 342 1.74e+01 c.93.1.1 67406 1ccwB 483 1.75e+01 1cb7B c.1.19.2 29646 1fr2A 86 1.76e+01 a.28.2.1 83256 1nf8A 207 1.79e+01 unknown_sccs 85630 1exrA 148 1.79e+01 1cll a.39.1.5 17299 1eulA 994 1.81e+01 1eulA 1amj 754 1.83e+01 1amj c.8.2.1 30725 c.83.1.1 35401 1e3sA 261 1.88e+01 1e6wA c.2.1.2 59201 1lwjA 441 1.88e+01 b.71.1.1 74303 c.1.8.1 74304 1m41A 380 1.89e+01 c.1.16.4 78595 1gqnA 252 1.92e+01 c.1.10.1 -5494 1hh1A 143 1.95e+01 1gefA c.52.1.18 61036 1qfeA 252 2.00e+01 1qfeA c.1.10.1 29167 1riqA 465 2.02e+01 unknown_sccs -1295 d.104.1.1 -10769 1j6rA 214 2.04e+01 d.173.1.2 71598 1jndA 420 2.05e+01 c.1.8.5 71757 d.26.3.1 71758 1q7fA 286 2.09e+01 unknown_sccs -4599 1qzpA 68 2.11e+01 a.14.1.1 -460 1b0jA 754 2.12e+01 1amj c.8.2.1 30719 c.83.1.1 35395 1v9mA 323 2.14e+01 unknown_sccs -12292 1s3zA 165 2.24e+01 1j31A 262 2.24e+01 d.160.1.2 -11473 1q1hA 110 2.27e+01 unknown_sccs -262 1nkpB 83 2.29e+01 a.38.1.1 80574 2ae2A 260 2.36e+01 1bdb c.2.1.2 29945 1c1yB 77 2.40e+01 1c1yB d.15.1.5 37618 1psdA 409 2.41e+01 1psdA c.2.1.4 30097 c.23.12.1 31357 d.58.18.1 39354 1oj4A 283 2.42e+01 d.14.1.5 -9088 d.58.26.5 -10133 1ozjA 144 2.49e+01 d.164.1.1 -11537 1cll 148 2.51e+01 1cll a.39.1.5 17263 1pymA 295 2.51e+01 1pymA c.1.12.7 29308 1d8jA 81 2.53e+01 1d8jA a.4.5.18 16153 3tgl 269 2.54e+01 3tgl c.69.1.17 34733 8abp 306 2.57e+01 8abp c.93.1.1 35647 1vjgA 218 2.60e+01 unknown_sccs -6447 1l9wA 252 2.78e+01 c.1.10.1 84570 1xyzA 347 2.82e+01 1taxA c.1.8.3 28804 1eejA 216 2.84e+01 1eejA c.47.1.9 33057 d.17.3.1 38071 1bg8A 89 2.85e+01 1bg8A a.57.1.1 17925 1rpxA 230 2.90e+01 1rpxA c.1.2.2 28536 1pguA 615 2.92e+01 b.69.4.1 88069 b.69.4.1 88070 1lc5A 364 2.94e+01 c.67.1.1 73827 1fs0G 230 2.94e+01 1fs0G c.49.2.1 59999 1osa 148 2.96e+01 1cll a.39.1.5 17300 1fnoA 417 2.97e+01 c.56.5.4 75841 d.58.19.1 70145 1daaA 282 2.98e+01 1daaA e.17.1.1 43270 1m46A 148 2.99e+01 a.39.1.5 78599 1f7sA 139 2.99e+01 1cof d.109.1.2 40857 1i27A 73 3.00e+01 1i27A a.4.5.30 61555 1jsbA 73 3.01e+01 1m4mA 140 3.04e+01 g.52.1.1 78605 1hy0A 466 3.05e+01 1auwA a.127.1.1 61392 1nmeA 146 3.05e+01 c.17.1.1 85874 1jj7A 260 3.08e+01 c.37.1.12 63114 1rerA 391 3.09e+01 b.1.18.4 -2740 f.10.1.1 -12385 1pwxA 254 3.10e+01 c.2.1.2 -5858 2pvaA 345 3.11e+01 3pvaA d.153.1.3 41850 1ur3M 319 3.12e+01 c.1.7.1 -5248 1n5dA 288 3.14e+01 c.2.1.2 80030 1ry6A 360 3.17e+01 c.37.1.9 -7111 1rv3A 483 3.21e+01 1nnsA 326 3.21e+01 c.88.1.1 85910 2ercA 244 3.21e+01 2ercA c.66.1.24 34224 1emvA 86 3.22e+01 1cei a.28.2.1 16944 1ur1A 378 3.23e+01 c.1.8.3 -5311 1mdc 133 3.32e+01 1hmt b.60.1.2 27198 1qamA 244 3.34e+01 2ercA c.66.1.24 34220 1hu4A 288 3.35e+01 1hu4A 1og6A 298 3.38e+01 c.1.7.1 86984 2cxbA 124 3.41e+01 1ycc a.3.1.1 15891 1fh9A 312 3.42e+01 1taxA c.1.8.3 28913 1jd5A 124 3.43e+01 g.52.1.1 66544 1axn 323 3.45e+01 1avc a.65.1.1 18149 1meoA 209 3.46e+01 c.65.1.1 79035 1f3lA 321 3.52e+01 1g6q2 c.66.1.6 59630 1jhdA 396 3.54e+01 b.122.1.3 66712 c.26.1.5 66713 1unkA 87 3.55e+01 1cei a.28.2.1 16935 1c44A 123 3.57e+01 1qndA d.106.1.1 40795 1jaxA 212 3.57e+01 c.2.1.6 66476 1nqkA 381 3.58e+01 c.1.16.4 -5607 1ri6A 343 3.59e+01 unknown_sccs -4621 1cxqA 162 3.60e+01 1cxqA c.55.3.2 33621 1qkfA 92 3.62e+01 1qkfA d.28.1.1 38456 1kamA 194 3.62e+01 c.26.1.3 72254 1ko9A 345 3.65e+01 a.96.1.3 68717 d.129.1.2 68718 1xxaA 78 3.66e+01 1xxaA d.74.2.1 39700 1mswD 883 3.69e+01 e.8.1.3 79427 1agx 331 3.71e+01 4pgaA c.88.1.1 35564 1d9eA 284 3.79e+01 1d9eA c.1.10.4 29195 1f3hA 142 3.80e+01 1f3hA g.52.1.1 45381 1kdoA 227 3.81e+01 c.37.1.1 68478 1cf2O 337 3.81e+01 1b7gO c.2.1.3 29994 d.81.1.1 39909 3rubS 123 3.87e+01 1rboC d.73.1.1 39616 1k0dA 260 3.90e+01 a.45.1.1 67930 c.47.1.5 67931 1fmcA 255 3.91e+01 1cydA c.2.1.2 29856 1cei 94 3.95e+01 1cei a.28.2.1 16939 2cmkA 227 3.97e+01 1ckeA c.37.1.1 31847