# List of top-scoring protein chains for t2k-100-30-bys-scores 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 1g79A 218 1.11e-24 1ci0A b.45.1.1 25752 1dnlA 199 1.38e-24 1ci0A b.45.1.1 25753 1nrgA 261 1.04e-21 b.45.1.1 80694 1t9mA 214 8.44e-19 1ci0A 228 6.66e-18 1ci0A b.45.1.1 25750 1ty9A 222 9.92e-18 1rfeA 162 1.44e-11 2fhqA 141 7.88e-11 2fg9A 178 6.11e-08 1vl7A 157 6.18e-08 b.45.1.1 108732 2aq6A 147 7.44e-07 1xxoA 147 9.04e-07 1w9aA 147 9.60e-07 2asfA 137 2.34e-06 2furA 209 8.93e-06 1xhnA 184 4.46e-05 2arzA 247 7.20e-05 1w3oA 216 8.01e-04 1ejeA 192 2.37e-02 1ejeA b.45.1.2 25757 1m1hA 248 4.39e-02 b.114.1.1,d.58.42.1 78415,78416 1flmA 122 4.59e-02 1axj b.45.1.1 25747 1axj 122 3.10e-01 1axj b.45.1.1 25749 1nar 290 5.26e-01 1nar c.1.8.5 28988 1g0u1 266 1.11e+00 1ryp2 233 1.13e+00 1ryp2 1zt3A 80 1.32e+00 2bgiA 272 1.45e+00 1ye8A 178 1.85e+00 1v0wA 506 2.12e+00 d.136.1.2,d.136.1.2 108220,108221 1btl 263 2.21e+00 1btl e.3.1.1 42691 1i24A 404 2.25e+00 c.2.1.2 83663 1ygtA 111 2.25e+00 1m40A 263 2.27e+00 e.3.1.1 74437 1f0iA 504 2.28e+00 1f0iA d.136.1.2,d.136.1.2 59566,59567 1wj9A 211 2.50e+00 2f15A 96 2.67e+00 1ermA 263 3.23e+00 1btl e.3.1.1 42690 1mkmA 249 3.29e+00 a.4.5.33,d.110.2.2 79242,79243 1wocA 103 3.52e+00 2bh8A 101 3.64e+00 2gukA 120 3.70e+00 1jdqA 98 3.90e+00 d.68.3.3 66559 1fqgA 263 3.98e+00 1btl e.3.1.1 42699 2fvvA 194 4.11e+00 1jysA 242 4.96e+00 c.56.2.1 77216 2evwX 166 5.36e+00 1vdnA 162 5.64e+00 1rypF 233 5.67e+00 1rypF d.153.1.4 41937 1tr8A 102 5.85e+00 2ag5A 246 6.01e+00 1h6fA 193 6.20e+00 b.2.5.4 70901 1bc8C 93 6.37e+00 1awcA a.4.5.21 16168 1q3iA 214 6.61e+00 d.220.1.1 104524 1v1qA 134 6.79e+00 1txyA 104 7.51e+00 1wlgA 299 7.82e+00 2bvfA 459 7.86e+00 2bgzA 299 7.97e+00 1y4tA 322 8.06e+00 1qrrA 394 8.18e+00 1qrrA c.2.1.2 29824 1z5oA 242 8.33e+00 2bwrA 401 8.40e+00 1z5nA 242 8.80e+00 1rm6A 769 9.00e+00 1qp2A 70 9.03e+00 1pse b.34.4.2 24596 2bitX 165 9.18e+00 1ecsA 126 9.32e+00 1ecsA d.32.1.2 59407 1d8yA 605 9.83e+00 1xwl c.55.3.5,e.8.1.1 33684,42977 2bduA 297 9.86e+00 2carA 196 9.92e+00 1g0uE 234 1.00e+01 d.153.1.4 41950 1wvnA 82 1.02e+01 1vqb 87 1.09e+01 1gvp b.40.4.7 25370 1gvp 87 1.09e+01 1gvp b.40.4.7 25369 1b8aA 438 1.11e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 2thiA 379 1.12e+01 2thiA c.94.1.1 35794 2f6kA 307 1.13e+01 1sdjA 310 1.13e+01 d.21.1.2,d.21.1.2 98807,98808 1an7A 136 1.16e+01 1seiA d.140.1.1 41465 2g09A 297 1.18e+01 1vpmA 169 1.19e+01 3thiA 371 1.24e+01 2thiA c.94.1.1 35792 1qyaA 307 1.27e+01 d.21.1.2,d.21.1.2 104653,104654 1ujmA 342 1.29e+01 1di2A 69 1.29e+01 1di2A d.50.1.1 38780 1rz3A 201 1.31e+01 c.37.1.6 98132 1zd7A 159 1.32e+01 2abqA 306 1.32e+01 1pysA 350 1.33e+01 1pysA d.104.1.1 40775 1pbyA 489 1.33e+01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 94417,94418,94419,94420,94421 1zx5A 300 1.35e+01 1ag8A 499 1.38e+01 1bpwA c.82.1.1 35341 1z4rA 168 1.40e+01 1y1pA 342 1.42e+01 1c8uA 285 1.47e+01 1c8uA d.38.1.3,d.38.1.3 38547,38548 2ddrA 306 1.47e+01 1vkkA 154 1.53e+01 d.109.1.2 108669 1b7yA 350 1.53e+01 1pysA d.104.1.1 40776 2a6sA 84 1.55e+01 6hir 65 1.64e+01 4htcI g.3.15.2 44375 1qfjA 232 1.68e+01 1qfjA b.43.4.2,c.25.1.1 25655,31545 1z82A 335 1.72e+01 2gfsA 372 1.73e+01 1o04A 500 1.76e+01 c.82.1.1 86508 1ukgA 252 1.76e+01 b.29.1.1 99489 1ewjA 126 1.81e+01 1ecsA d.32.1.2 59526 1n9lA 109 1.82e+01 d.110.3.6 85468 1pauA 147 1.86e+01 1pauA c.17.1.1 30994 1tvjA 166 1.93e+01 1j4wA 174 1.98e+01 d.51.1.1,d.51.1.1 71529,71530 2a74A 643 1.98e+01 2fcjA 119 2.04e+01 1wd6A 123 2.10e+01 1gxuA 91 2.11e+01 d.58.10.1 76378 1mo7A 213 2.14e+01 d.220.1.1 85028 1q15A 503 2.16e+01 c.26.2.1,d.153.1.1 95538,95539 1k68A 140 2.19e+01 c.23.1.1 90943 2b5oA 402 2.19e+01 1si6X 282 2.31e+01 1td5A 202 2.31e+01 d.110.2.2 106767 1nmeA 146 2.34e+01 c.17.1.1 85874 1so7A 382 2.41e+01 2fp8A 322 2.46e+01 1jjuA 489 2.48e+01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 66774,66775,66776,66777,66778 2bcgG 453 2.55e+01 1amuA 563 2.60e+01 1amuA e.23.1.1 43351 1ukvG 453 2.61e+01 c.3.1.3,c.3.1.3,d.16.1.6 107915,107916,107917 1ut7A 171 2.67e+01 b.143.1.1 99906 1ibcA 194 2.81e+01 1pauA c.17.1.1 30997 1pse 69 2.83e+01 1pse b.34.4.2 24595 2bwqA 129 2.85e+01 1a4iB 301 2.88e+01 1a4iA c.2.1.7,c.58.1.2 30279,33927 1h7zA 194 2.94e+01 1qhvA b.21.1.1 60733 1t77A 414 3.00e+01 2axoA 270 3.02e+01 1b04A 318 3.05e+01 1b04A d.142.2.2 41579 1gmlA 178 3.06e+01 c.8.5.2 70273 1ap8 213 3.11e+01 1ap8 d.86.1.1 40151 2etjA 250 3.17e+01 1jr7A 311 3.17e+01 b.82.2.3 63255 1hic 51 3.20e+01 4htcI g.3.15.2 44371 1a7j 290 3.20e+01 1a7j c.37.1.6 31952 1wnyA 186 3.21e+01 1j5kA 89 3.32e+01 d.51.1.1 71565 1v6fA 151 3.32e+01 d.109.1.2 108395 1qauA 112 3.33e+01 1qauA b.36.1.1 24779 1wk8A 194 3.41e+01 1pvmA 184 3.46e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1zfjA 491 3.56e+01 1ak5 c.1.5.1,d.37.1.1,d.37.1.1 28638,38540,38541 2f4iA 197 3.59e+01 1sx5A 244 3.61e+01 c.52.1.2 99023 1udzA 182 3.62e+01 b.51.1.1 99239 2f9dA 125 3.64e+01 1yruB 74 3.66e+01 1ezvD 245 3.67e+01 1be3D a.3.1.3,f.23.11.1 59546,59547 1ntfA 282 3.67e+01 d.151.1.2 92104 2ebn 289 3.71e+01 2ebn c.1.8.5 28990 1vclA 432 3.72e+01 b.42.2.1,b.42.2.1,d.281.1.1 108498,108499,108500 1j5eK 129 3.72e+01 c.55.4.1 71554 1tmxA 293 3.77e+01 1t00A 112 3.78e+01 1e7rA 321 3.78e+01 1bsvA c.2.1.2 29808 1bwsA 321 3.81e+01 1bsvA c.2.1.2 29812 1n3oA 252 3.82e+01 b.29.1.1 79967 1dzkA 157 3.82e+01 1obpA b.60.1.1 27096 1aow 309 3.85e+01 1avc a.65.1.1 18152 1e6uA 321 3.95e+01 1bsvA c.2.1.2 29805 1ae2 87 4.00e+01 1gvp b.40.4.7 25382 1atr 386 4.03e+01 1ba1 c.55.1.1,c.55.1.1 33421,33422 1uv4A 293 4.08e+01 2airB 153 4.12e+01 1wq3A 322 4.13e+01 1f2tB 148 4.14e+01 1f2tB 1xbfA 140 4.14e+01 d.273.1.1 109538 1wdjA 187 4.15e+01 2c07A 285 4.17e+01 1bkb 136 4.24e+01 1bkb b.34.5.2,b.40.4.5 24609,25341 1qwdA 177 4.24e+01 b.60.1.1 96471 1iycA 36 4.25e+01 g.31.1.2 83782 1bxsA 501 4.31e+01 1bpwA c.82.1.1 35357 1ywqA 200 4.42e+01 1ta8A 332 4.44e+01 2hts 88 4.45e+01 2hts a.4.5.22 16174 2fe7A 166 4.49e+01 1yw5A 177 4.56e+01 1ba1 386 4.61e+01 1ba1 c.55.1.1,c.55.1.1 33387,33388 1mjc 69 4.65e+01 1mjc b.40.4.5 25319 1bywA 110 4.66e+01 1bywA d.110.3.6 40912 1k1zA 78 4.67e+01 b.34.2.1 68026 1agp 166 4.67e+01 1ctqA c.37.1.8 31985 1wb9A 800 4.67e+01 1cl1A 395 4.71e+01 1cl2A c.67.1.3 34395 1f3uA 118 4.72e+01 1f3uA b.65.1.1 27521 1w6tA 444 4.73e+01 1xdfA 157 4.81e+01 2c1cA 312 4.83e+01 1dgmA 363 4.83e+01 1bx4A c.72.1.1 34936 1qmyA 167 4.84e+01 1qmyA d.3.1.2 37094 1ibvB 229 4.88e+01 1i3cA 149 5.00e+01 c.23.1.1 71112 2bltA 361 5.01e+01 1gceA e.3.1.1 42739 1a8p 258 5.04e+01 1fdr b.43.4.2,c.25.1.1 25654,31544 1k89 449 5.06e+01 1k89 c.2.1.7,c.58.1.1 30218,33866 1p5tA 127 5.07e+01 b.55.1.2 94148 2ckiA 262 5.09e+01 1smoA 119 5.13e+01 b.1.1.1 105764 1b96A 244 5.14e+01 1rvaA c.52.1.2 33268 1rvaA 244 5.17e+01 1rvaA c.52.1.2 33240 1eonA 245 5.18e+01 1rvaA c.52.1.2 33238 1b94A 244 5.18e+01 1rvaA c.52.1.2 33250 1iqrA 420 5.18e+01 a.99.1.1,c.28.1.1 66275,66276 1jv2B 692 5.19e+01 b.1.15.1,c.62.1.1,d.200.1.1,g.3.11.6,g.3.11.6 67338,67339,67340,67341,67342 1y42X 392 5.24e+01 3mefA 69 5.26e+01 1mjc b.40.4.5 25320 1klnA 605 5.26e+01 1xwl c.55.3.5,e.8.1.1 33693,42986 1b97A 244 5.29e+01 1rvaA c.52.1.2 33252 1bssA 244 5.30e+01 1rvaA c.52.1.2 33256 1kay 381 5.30e+01 1ba1 c.55.1.1,c.55.1.1 33385,33386 2a2lA 145 5.31e+01 1aquA 297 5.35e+01 1aquA c.37.1.5 31942 1gp1A 198 5.36e+01 1gp1A c.47.1.10 33059 1kv0A 66 5.37e+01 g.3.7.1 91040 1m2vB 926 5.38e+01 a.71.2.1,b.2.8.1,c.62.1.2,d.109.2.1,g.41.10.1 78497,78498,78499,78500,78501 1zzkA 82 5.39e+01 2b0jA 358 5.40e+01 1vlyA 338 5.40e+01 b.44.2.1,d.250.1.1 108871,108872 1ln1A 214 5.41e+01 d.129.3.2 74038 1dbwA 126 5.43e+01 1dbwA c.23.1.1 31095 2b3hA 329 5.43e+01 1nrkA 328 5.47e+01 b.44.2.1,d.250.1.1 92089,92090 1bsvA 321 5.52e+01 1bsvA c.2.1.2 29809 1ae3 86 5.57e+01 1gvp b.40.4.7 25381 1gfsA 321 5.61e+01 c.2.1.2 29811 1p9bA 442 5.67e+01 c.37.1.10 94385 1cl2A 395 5.69e+01 1cl2A c.67.1.3 34397 1kb9D 246 5.70e+01 a.3.1.3,f.23.11.1 77317,77318 1dckA 126 5.71e+01 1dbwA c.23.1.1 31097 1txnA 328 5.72e+01 1diaA 306 5.74e+01 1a4iA c.2.1.7,c.58.1.2 30280,33928 2ay1A 394 5.75e+01 1ajsA c.67.1.1 34357 1oqkA 97 5.75e+01 b.137.1.1 93419 1b8dA 164 5.75e+01 1cpcA a.1.1.3 15665 1e3mA 800 5.80e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19075,32389,33746,39747 1vljA 407 5.83e+01 e.22.1.2 108832 3htsB 102 5.83e+01 2hts a.4.5.22 16175 1of8A 370 5.83e+01 c.1.10.4 92819 1hpm 386 5.88e+01 1ba1 c.55.1.1,c.55.1.1 33381,33382 1gceA 364 5.91e+01 1gceA e.3.1.1 42738 1rwiA 270 5.92e+01 b.68.9.1 97987 1bupA 386 5.95e+01 1ba1 c.55.1.1,c.55.1.1 33377,33378 1y21A 282 5.97e+01 5p21 166 5.97e+01 1ctqA c.37.1.8 31966 1cz3A 168 5.97e+01 1d1gA c.71.1.1 34891 1bgvA 449 5.97e+01 1k89 c.2.1.7,c.58.1.1 30217,33865 1d5wC 126 5.98e+01 1dbwA c.23.1.1 31101 1nh9A 87 6.05e+01 d.68.6.1 91878 1xtmA 175 6.11e+01 1w66A 232 6.13e+01 1wcdJ 441 6.18e+01 1g8kB 133 6.19e+01 1g8jB b.33.1.1 24435 2pil 159 6.22e+01 2pil d.24.1.1 38376 1omiA 248 6.24e+01 b.82.3.3,a.4.5.4 87079,87080 1l3kA 196 6.26e+01 d.58.7.1,d.58.7.1 73539,73540 3hsf 92 6.31e+01 2hts a.4.5.22 16182 2cfeA 162 6.31e+01 821p 166 6.38e+01 1ctqA c.37.1.8 31969 1lroA 267 6.41e+01 c.1.10.4 78161 1x88A 359 6.48e+01 1fjgK 129 6.51e+01 1fjfK c.55.4.1 33733 1obbA 480 6.51e+01 c.2.1.5,d.162.1.2 86760,86761 1z0pA 84 6.52e+01 1prr 173 6.56e+01 1prs b.11.1.1,b.11.1.1 23623,23624 1vmhA 144 6.58e+01 1t8xA 267 6.59e+01 1oz9A 150 6.61e+01 d.92.1.15 93808 1eu3A 210 6.61e+01 1an8 b.40.2.2,d.15.6.1 25206,37795 1hrdA 449 6.70e+01 1k89 c.2.1.7,c.58.1.1 30219,33867 1e5pA 151 6.77e+01 1bj7 b.60.1.1 59272 3rnt 104 6.83e+01 9rnt d.1.1.4 36069 1ann 318 6.86e+01 1avc a.65.1.1 18151 1eagA 342 6.87e+01 1eagA b.50.1.2 26826 1rzfL 213 6.90e+01 b.1.1.1,b.1.1.2 98152,98153 1dttA 560 6.92e+01 1rthA c.55.3.1,e.8.1.2 33611,43088 1fxpA 267 6.94e+01 1d9eA c.1.10.4 60106 1qr7A 350 6.94e+01 1qr7A c.1.10.4 29191 4pep 326 6.96e+01 1smrA b.50.1.2 26843 1vr4A 103 6.96e+01 1s9aA 257 7.03e+01 b.3.6.1 105379 1vcbB 112 7.03e+01 1vcbB d.42.1.1 38633 1p4kA 295 7.05e+01 d.153.1.5 87772 1xsoA 150 7.16e+01 1mfmA b.1.8.1 22273 1ei6A 406 7.18e+01 c.76.1.4 90443 1ipd 345 7.24e+01 1cnzA c.77.1.1 35038 2a0jA 149 7.27e+01 2d0oA 610 7.33e+01 1ybiA 288 7.40e+01 1h3fA 432 7.40e+01 c.26.1.1,d.66.1.4 76631,76632 1onhA 364 7.41e+01 e.3.1.1 93357 1ualA 274 7.44e+01 c.116.1.4 88383 1r71A 178 7.51e+01 a.4.14.1 104823 1ptmA 329 7.51e+01 c.77.1.3 95104 1vllA 334 7.52e+01 c.2.1.13 108834 2bxxA 134 7.53e+01 1ha1 184 7.59e+01 1ha1 d.58.7.1,d.58.7.1 39147,39148 1omoA 322 7.60e+01 c.2.1.13 104017 1gskA 513 7.62e+01 b.6.1.3,b.6.1.3,b.6.1.3 83314,83315,83316 1b2rA 304 7.65e+01 1fnc b.43.4.2,c.25.1.1 25648,31538 1sb8A 352 7.66e+01 c.2.1.2 105410 1w6uA 302 7.66e+01 1aqkL 216 7.74e+01 8fabA b.1.1.1,b.1.1.2 20192,21208 1wbiA 129 7.76e+01 1cp3A 277 7.76e+01 1pauA c.17.1.1 30992 1que 303 7.77e+01 1fnc b.43.4.2,c.25.1.1 25647,31537 1cqxA 403 7.79e+01 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 1xv2A 237 7.90e+01 1x3lA 440 7.92e+01 1a3yA 149 8.02e+01 1obpA b.60.1.1 27110 1j98A 157 8.03e+01 1j98A d.185.1.2 62755 1vi6A 208 8.07e+01 c.23.15.1 100736 1hxn 219 8.11e+01 1hxn b.66.1.1 27529 1w34A 304 8.15e+01 1s2wA 295 8.16e+01 c.1.12.7 98407 1uzxA 169 8.19e+01 d.20.1.2 100238 2f8aA 208 8.26e+01 1kb0A 677 8.28e+01 a.3.1.6,b.70.1.1 68378,68379 1ihnA 113 8.30e+01 1ihnA c.103.1.1 62388 1c96A 753 8.31e+01 1amj c.8.2.1,c.83.1.1 30727,35403 2a35A 215 8.31e+01 1ogiA 303 8.33e+01 b.43.4.2,c.25.1.1 92914,92915 1duvG 333 8.34e+01 1othA c.78.1.1,c.78.1.1 35228,35229 1rl6A 177 8.37e+01 1rl6A d.141.1.1,d.141.1.1 41473,41474 2arpA 116 8.37e+01 2bsaA 303 8.41e+01 1sxvA 172 8.46e+01 1sd4A 126 8.49e+01 a.4.5.39 105428 2a4vA 159 8.51e+01 1dhn 121 8.53e+01 1dhn d.96.1.3 40663 1f6bA 198 8.54e+01 c.37.1.8 64986 1r2zA 274 8.56e+01 a.156.1.2,b.113.1.1,g.39.1.8 96892,96893,96894 2mcm 112 8.65e+01 2mcm b.1.7.1 22207 1qx4A 274 8.67e+01 b.43.4.2,c.25.1.1 104624,104625 1rp0A 284 8.70e+01 1f8yA 157 8.73e+01 1f8xA c.23.14.1 31395 1qcnA 421 8.77e+01 1qcnA b.34.8.1,d.177.1.1 59017,59018 1gm6A 175 8.82e+01 b.60.1.1 70272 1sxgA 280 8.85e+01 4enl 436 8.89e+01 4enl c.1.11.1,d.54.1.1 29202,38846