# 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 1hfoA 113 1.45e-03 d.80.1.3 61006 1gyxA 76 1.02e-02 d.80.1.1 76387 1dptA 117 1.61e-02 1dptA d.80.1.3 39862 1mfiA 114 1.07e-01 1dptA d.80.1.3 39856 9gafA 295 1.52e-01 1apyA d.153.1.5 42008 1p4kA 295 1.53e-01 d.153.1.5 87772 1ur1A 378 3.64e-01 c.1.8.3 -5311 1s0yA 76 4.64e-01 d.80.1.1 -10434 1adjA 421 5.05e-01 1adjA c.51.1.1 33188 d.104.1.1 40737 1h4vB 421 5.82e-01 1adjA c.51.1.1 60624 d.104.1.1 60625 1otfA 62 7.07e-01 1otfA d.80.1.1 39820 1q4rA 112 8.35e-01 d.58.4.4 -9943 1otgA 125 9.70e-01 1otgA d.80.1.2 39831 1gd0A 122 1.07e+00 1dptA d.80.1.3 39834 1ffkI 194 1.12e+00 1ffkI d.12.1.2 37494 1ow1A 195 1.41e+00 unknown_sccs -4422 1mwwA 128 1.41e+00 unknown_sccs -10451 1m0dA 138 1.49e+00 c.52.1.17 74354 1esgA 213 1.94e+00 1bam c.52.1.3 33286 1cqqA 180 2.27e+00 1cqqA b.47.1.4 26422 1k20A 310 2.39e+00 c.107.1.1 68027 1k6xA 352 2.45e+00 c.2.1.2 68238 1b3qA 379 2.49e+00 1b3qA a.30.2.1 16993 b.40.7.1 25454 d.122.1.3 41112 1k6iA 352 2.49e+00 c.2.1.2 68223 1j7nA 776 2.94e+00 d.92.1.14 66409 d.92.1.14 66410 d.166.1.1 66411 1j7nB 776 2.96e+00 d.92.1.14 66412 d.92.1.14 66413 d.166.1.1 66414 1bam 213 3.09e+00 1bam c.52.1.3 33285 1ihfA 99 3.34e+00 1huuA a.55.1.1 17893 3bamB 213 3.40e+00 1bam c.52.1.3 33289 1qj5A 429 3.72e+00 1dtyA c.67.1.4 34493 1owfA 99 3.81e+00 a.55.1.1 87487 1mml 265 3.87e+00 1mml e.8.1.2 43015 1fjgJ 105 4.21e+00 1fjfJ d.58.15.1 39330 1dtyA 429 4.22e+00 1dtyA c.67.1.4 34495 1f2tB 148 4.28e+00 1f2tB 2ptd 298 4.32e+00 2plc c.1.18.2 29605 3bamA 213 4.40e+00 1bam c.52.1.3 33288 1k2yX 463 4.40e+00 c.84.1.1 68063 c.84.1.1 68064 c.84.1.1 68065 d.129.2.1 68066 1i58A 189 4.41e+00 1b3qA d.122.1.3 61773 1lylA 504 4.75e+00 1lylA b.40.4.1 25261 d.104.1.1 40717 1q53A 112 4.88e+00 d.58.4.4 -9944 1ukkA 142 5.21e+00 d.227.1.1 -11206 1pwhA 327 5.22e+00 c.79.1.1 -8524 1r3nA 462 5.73e+00 c.56.5.4 -7872 d.58.19.1 -10096 1evlA 401 6.16e+00 1qf6A c.51.1.1 33202 d.104.1.1 40751 1vknA 351 6.24e+00 1exnB 290 6.77e+00 1exnA a.60.7.1 18089 c.120.1.2 33359 1vixA 420 6.81e+00 c.56.5.4 -7866 d.58.19.1 -10090 1i1gA 141 6.98e+00 a.4.5.32 65982 d.58.4.2 65983 1e1oA 504 7.03e+00 1lylA b.40.4.1 25258 d.104.1.1 40714 1rp4A 389 7.31e+00 1fzrA 138 7.33e+00 1fzrA c.52.1.17 33336 1j3mA 129 7.34e+00 1d4xG 126 7.94e+00 1d0nA d.109.1.1 59109 1iz5A 249 7.94e+00 d.131.1.2 83834 d.131.1.2 83835 1s0aA 429 8.03e+00 c.67.1.4 -8201 1e9iA 431 8.07e+00 c.1.11.1 64818 d.54.1.1 64819 1jznA 135 8.13e+00 d.169.1.1 84262 1josA 128 8.93e+00 d.52.7.1 84191 1m5sA 297 9.07e+00 d.58.33.1 74511 d.58.33.1 74512 1p1lA 102 9.07e+00 d.58.5.2 87695 1yagG 125 9.39e+00 1d0nA d.109.1.1 40846 1nm1G 125 9.39e+00 d.109.1.1 80653 1p5dX 463 9.59e+00 c.84.1.1 -8554 c.84.1.1 -8555 c.84.1.1 -8556 d.129.2.1 -11029 1fnoA 417 9.66e+00 c.56.5.4 75841 d.58.19.1 70145 1i74A 309 9.70e+00 1i74A c.107.1.1 61867 2chsA 127 9.76e+00 2chsA d.79.1.2 39764 1k8wA 327 9.80e+00 b.122.1.1 83094 unknown_sccs -10143 2e2c 156 9.81e+00 1u9aA d.20.1.1 38336 1grvB 182 9.91e+00 c.61.1.1 76322 1fzyA 149 1.00e+01 d.20.1.1 65072 1azsB 212 1.02e+01 1azsA d.58.29.1 39423 1dbfA 127 1.04e+01 2chsA d.79.1.2 39761 1i1qA 520 1.04e+01 1qdlA d.161.1.1 61543 1kmnD 424 1.05e+01 1adjA c.51.1.1 33185 d.104.1.1 40734 1k4jA 230 1.05e+01 d.108.1.3 72057 1sdoA 203 1.06e+01 unknown_sccs -7558 1ukuA 102 1.13e+01 d.58.5.2 -9992 1faeA 629 1.16e+01 1fce a.102.1.2 18837 1lshB 319 1.17e+01 f.7.1.1 74245 1iicA 422 1.19e+01 1nmtA d.108.1.2 62422 d.108.1.2 62423 1dkuA 317 1.19e+01 1dkuA c.61.1.2 34118 c.61.1.2 34119 1g9gA 629 1.26e+01 a.102.1.2 83279 1efuB 282 1.27e+01 1efuB a.5.2.2 58975 d.43.1.1 58976 d.43.1.1 38677 1uw4A 91 1.27e+01 unknown_sccs -10038 1kr4A 125 1.30e+01 d.58.5.2 72889 1k8kD 300 1.31e+01 d.198.2.1 68309 d.198.2.1 68310 1qq2A 199 1.35e+01 1qq2A c.47.1.10 33064 1nrjA 158 1.35e+01 d.110.4.4 86124 1dmuA 299 1.36e+01 1dmuA c.52.1.4 33294 1dkrA 317 1.38e+01 1dkuA c.61.1.2 34114 c.61.1.2 34115 1a99A 344 1.39e+01 1pot c.94.1.1 35812 1gd8A 118 1.39e+01 d.188.1.1 60445 1kzfA 230 1.41e+01 d.108.1.3 73354 1v8dA 235 1.43e+01 1ab8A 220 1.46e+01 1azsA d.58.29.1 39414 1j27A 102 1.47e+01 unknown_sccs -10116 1j6uA 469 1.49e+01 c.5.1.1 77094 c.59.1.1 77095 c.72.2.1 77096 1fce 629 1.52e+01 1fce a.102.1.2 18836 1rpl 251 1.58e+01 1bpyA a.60.12.1 75933 d.218.1.2 75934 1svq 114 1.63e+01 1svy d.109.1.1 40832 1q8yA 373 1.68e+01 d.144.1.7 -11319 1phk 298 1.71e+01 1cdkA d.144.1.7 41635 1kmmA 424 1.73e+01 1adjA c.51.1.1 33174 d.104.1.1 40723 1f3vA 179 1.77e+01 1f3vA d.58.22.1 39382 1acf 125 1.77e+01 3nul d.110.1.1 40882 1fxlA 167 1.78e+01 1b7fA d.58.7.1 39183 d.58.7.1 39184 1eceA 358 1.79e+01 1eceA c.1.8.3 28813 1jj2L 194 1.81e+01 1ffkI d.12.1.2 63097 1p5vA 235 1.84e+01 b.1.11.1 87812 b.7.2.1 87813 1iyhA 198 1.85e+01 a.45.1.1 83790 c.47.1.5 83791 1elqA 390 1.86e+01 1elqA c.67.1.3 34436 1c0dA 358 1.87e+01 1eceA c.1.8.3 28815 1eluB 390 1.88e+01 1elqA c.67.1.3 34435 1eluA 390 1.88e+01 1elqA c.67.1.3 34434 1m4jA 142 1.89e+01 d.109.1.2 78602 1pbgA 468 1.91e+01 1e70M c.1.8.4 28946 1i60A 278 1.97e+01 c.1.15.4 71118 1atiA 505 2.00e+01 1atiA c.51.1.1 33196 d.104.1.1 40745 1ex2A 189 2.01e+01 1ex2A c.51.4.2 33225 1iv3A 152 2.05e+01 d.79.5.1 76828 1itwA 741 2.06e+01 c.77.1.2 76793 1je6A 275 2.08e+01 b.1.1.2 71638 d.19.1.1 71639 1howA 373 2.09e+01 1hcl d.144.1.7 41679 1mjc 69 2.12e+01 1mjc b.40.4.5 25319 1rypD 241 2.13e+01 1rypD d.153.1.4 41935 1qqrA 138 2.13e+01 1bmlC d.15.5.1 37721 1uvqB 198 2.14e+01 b.1.1.2 -2659 d.19.1.1 -9348 1g63A 181 2.15e+01 1g5qA c.34.1.1 60299 1nrhX 472 2.19e+01 c.2.1.5 -5944 d.162.1.2 -11511 1pjzA 203 2.22e+01 unknown_sccs -8075 1ibsA 317 2.22e+01 c.61.1.2 66107 c.61.1.2 66108 1b6sA 355 2.26e+01 1b6rA b.84.2.1 28242 c.30.1.1 31649 d.142.1.2 41494 1bpb 248 2.32e+01 1bpyA a.60.12.1 75811 d.218.1.2 75812 1s72M 194 2.40e+01 1fxtA 149 2.41e+01 d.20.1.1 65055 1h5vA 304 2.43e+01 c.1.8.3 70898 1ifqA 138 2.45e+01 1ifqA d.110.4.1 62350 1gm5A 780 2.49e+01 unknown_sccs 65298 b.40.4.9 65299 c.37.1.19 65300 c.37.1.19 65301 1gefA 123 2.49e+01 1gefA c.52.1.18 60465 1clxA 347 2.49e+01 1taxA c.1.8.3 28899 1ub9A 100 2.54e+01 a.4.5.28 -231 1s71A 316 2.56e+01 1sgvA 316 2.56e+01 b.122.1.1 -5120 unknown_sccs -10148 2cb5A 453 2.57e+01 3gcb d.3.1.1 37035 1prq 125 2.57e+01 3nul d.110.1.1 40883 2vil 126 2.58e+01 2vil d.109.1.1 40830 1jyoA 130 2.69e+01 d.198.1.1 67483 3xis 387 2.69e+01 4xis c.1.15.3 29423 2vik 126 2.70e+01 2vil d.109.1.1 40829 1eljA 381 2.77e+01 4mbp c.94.1.1 35791 1npeA 267 2.78e+01 b.68.5.1 -4588 1hmpA 217 2.82e+01 1qk3A c.61.1.1 34075 1c8bA 371 2.86e+01 1c8bA c.56.1.2 59082 1konA 249 2.90e+01 e.39.1.1 72823 1ut8A 291 2.92e+01 a.60.7.1 -1036 c.120.1.2 -6675 1gt91 357 2.93e+01 1sviA 195 2.97e+01 1qmvA 197 2.99e+01 1qq2A c.47.1.10 33066 1brwA 433 3.05e+01 1brwA a.46.2.1 17764 c.27.1.1 31628 d.41.3.1 38626 1m0wA 491 3.06e+01 c.30.1.4 78363 d.142.1.6 78364 1gnxA 479 3.07e+01 c.1.8.4 76241 1b7fA 168 3.16e+01 1b7fA d.58.7.1 39169 d.58.7.1 39170 1dapA 320 3.18e+01 1dapA c.2.1.3 30053 d.81.1.3 39968 1ihnA 113 3.19e+01 1ihnA c.103.1.1 62388 1atiB 505 3.19e+01 1atiA c.51.1.1 33197 d.104.1.1 40746 1vk4A 298 3.20e+01 c.72.1.1 -8414 1o0wA 252 3.21e+01 a.149.1.1 80751 d.50.1.1 80752 1c9oA 66 3.37e+01 1mjc b.40.4.5 25325 1exnA 290 3.43e+01 1exnA a.60.7.1 18088 c.120.1.2 33358 1jhsA 188 3.44e+01 d.107.1.1 84172 1aisA 182 3.45e+01 1ytbA d.129.1.1 41288 d.129.1.1 41289 1bix 287 3.52e+01 1bix d.151.1.1 41781 1l9gA 192 3.54e+01 c.18.1.2 84568 4enl 436 3.55e+01 4enl c.1.11.1 29202 d.54.1.1 38846 1qf6A 642 3.56e+01 1qf6A c.51.1.1 33210 d.15.10.1 39551 d.67.1.1 39562 d.104.1.1 40759 1uouA 474 3.59e+01 a.46.2.1 -951 c.27.1.1 -6642 d.41.3.1 -9715 1ftrA 296 3.61e+01 1ftrA d.58.33.1 39485 d.58.33.1 39486 1molA 94 3.65e+01 1molA d.17.1.1 37988 1lq9A 112 3.73e+01 d.58.4.3 78129 1ako 268 3.78e+01 1ako d.151.1.1 41779 1b7yA 350 3.79e+01 1pysA d.104.1.1 40776 1nvmB 312 3.82e+01 c.2.1.3 86251 d.81.1.1 86252 1rypI 222 3.82e+01 d.153.1.4 41877 1mijA 152 3.84e+01 a.4.1.1 79150 3pbgA 468 3.85e+01 1e70M c.1.8.4 28951 1oneA 436 3.88e+01 4enl c.1.11.1 29200 d.54.1.1 38844 1qhtA 775 3.96e+01 1tgoA c.55.3.5 33722 e.8.1.1 43011