# 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 2i51A 195 1.15e-37 1t9mA 214 3.21e-14 1ty9A 222 1.11e-12 1nrgA 261 1.78e-10 b.45.1.1 80694 1dnlA 199 9.43e-10 1ci0A b.45.1.1 25753 1g79A 218 1.14e-09 1ci0A b.45.1.1 25752 2a2jA 246 1.81e-07 1ci0A 228 3.03e-07 1ci0A b.45.1.1 25750 2i02A 148 1.23e-04 2aq6A 147 2.02e-03 1rfeA 162 2.77e-03 1w9aA 147 4.25e-03 1xxoA 147 5.19e-03 2fhqA 141 7.56e-03 2asfA 137 1.85e-02 1egxA 115 7.35e-02 1evhA b.55.1.4 27000 2hhzA 150 3.30e-01 1d8iA 311 3.84e-01 1d8iA d.63.1.1 39541 1d8hA 311 4.71e-01 1d8iA d.63.1.1 39544 1i7qA 519 1.18e+00 1qdlA d.161.1.1 61901 2b29A 123 1.39e+00 1e1hA 287 1.69e+00 d.92.1.7 83167 2htdA 140 1.78e+00 2dafA 118 1.85e+00 2hq7A 146 1.87e+00 1vkxA 273 2.05e+00 1a3qA b.1.18.1 21941 b.2.5.3 22454 1llwA 1520 2.21e+00 b.80.4.1 74017 c.1.4.1 74018 d.153.1.1 74019 2ucz 165 2.72e+00 1u9aA d.20.1.1 38330 1z02A 446 2.89e+00 1qu0A 191 2.92e+00 1dykA b.29.1.4 24225 2iutA 574 3.02e+00 2dfkA 402 3.18e+00 1q67A 231 3.20e+00 b.55.1.7 95960 1ayzA 169 3.46e+00 1u9aA d.20.1.1 38326 1zdnA 158 3.68e+00 1tqnA 486 3.88e+00 a.104.1.1 107238 2bfdA 400 4.19e+00 1olsA 400 4.25e+00 c.36.1.11 93331 1qtsA 247 4.39e+00 1qtsA b.1.10.1 22313 d.105.1.1 40789 1c4zD 154 4.46e+00 1u9aA d.20.1.1 38331 1rypK 198 4.56e+00 d.153.1.4 41879 1x7yA 400 4.68e+00 1otcA 495 4.76e+00 1otcA b.40.4.3 25307 b.40.4.3 25308 b.40.4.3 25309 1jbbA 153 5.06e+00 1u9aA d.20.1.1 62842 1kyfA 247 5.15e+00 b.1.10.1 73220 d.105.1.1 73221 1b9kA 238 5.57e+00 1qtsA b.1.10.1 22315 d.105.1.1 40791 1fl0A 171 5.61e+00 1eujA b.40.4.4 25315 2gvaA 87 5.89e+00 1gvp b.40.4.7 25389 2av1A 275 5.90e+00 3thiA 371 6.16e+00 2thiA c.94.1.1 35792 1z9tA 255 6.18e+00 1jlnA 297 6.39e+00 1pty c.45.1.2 63172 1tmcA 175 6.40e+00 1agdA d.19.1.1 38258 1avbA 226 6.54e+00 1led b.29.1.1 24158 2av7A 275 6.60e+00 1jatA 155 6.69e+00 1u9aA d.20.1.1 62818 1dykA 394 6.69e+00 1dykA b.29.1.4 24223 b.29.1.4 24224 1u4cA 349 6.84e+00 b.69.4.2 107666 1duzA 275 6.97e+00 1agdA b.1.1.2 20670 d.19.1.1 38224 1v1rA 400 7.07e+00 c.36.1.11 108272 1i4fA 275 7.15e+00 1agdA b.1.1.2 61687 d.19.1.1 61688 1eujA 166 7.38e+00 1eujA b.40.4.4 25316 2awfA 172 7.82e+00 2ac1A 541 7.99e+00 1jb7A 495 8.15e+00 1otcA b.40.4.3 62836 b.40.4.3 62837 b.40.4.3 62838 1o5uA 101 8.39e+00 b.82.1.8 92518 1gywA 128 8.54e+00 b.1.10.2 70791 2ayvA 166 8.54e+00 1x1fA 149 8.68e+00 2extA 77 8.70e+00 2bcjB 340 8.78e+00 2fg9A 178 9.28e+00 1ywnA 316 9.54e+00 1tbgA 340 9.87e+00 1tbgA b.69.4.1 27649 1e3aB 560 9.91e+00 1ajqB 1wapA 75 1.03e+01 1wapA b.82.5.1 28153 1pnkB 557 1.04e+01 1ajqB 7ceiB 206 1.04e+01 1bxiB d.4.1.1 37134 1ajqB 557 1.04e+01 1ajqB 7ahlA 293 1.07e+01 7ahlA f.6.1.1 43812 1pysA 350 1.08e+01 1pysA d.104.1.1 40775 1gtfA 74 1.08e+01 b.82.5.1 70460 2thiA 379 1.10e+01 2thiA c.94.1.1 35794 1ofdA 1520 1.14e+01 b.80.4.1 86935 c.1.4.1 86936 d.153.1.1 86937 1a0rB 340 1.16e+01 1tbgA b.69.4.1 27658 1gk9B 557 1.17e+01 1gm9B 557 1.18e+01 1gkfB 557 1.20e+01 1waaA 93 1.20e+01 1gm7B 557 1.20e+01 1ae3 86 1.21e+01 1gvp b.40.4.7 25381 1hsbA 270 1.25e+01 1agdA b.1.1.2 20736 d.19.1.1 38257 1qawF 74 1.26e+01 1wapA b.82.5.1 28202 2hq9A 149 1.31e+01 1gbg 214 1.36e+01 1axkA b.29.1.2 24171 2f15A 96 1.37e+01 1vqb 87 1.41e+01 1gvp b.40.4.7 25370 1gvp 87 1.41e+01 1gvp b.40.4.7 25369 1agdA 276 1.41e+01 1agdA b.1.1.2 20741 d.19.1.1 38260 1gotB 340 1.45e+01 1tbgA b.69.4.1 27648 1sacA 204 1.46e+01 1sacA b.29.1.5 24237 2bvpA 276 1.46e+01 2mtaC 147 1.48e+01 2mtaC a.3.1.1 15908 1j8uA 325 1.52e+01 d.178.1.1 71611 2gp5A 349 1.54e+01 1kb0A 677 1.57e+01 a.3.1.6 68378 b.70.1.1 68379 2cdpA 160 1.58e+01 1gv4A 528 1.59e+01 c.3.1.5 70589 c.3.1.5 70590 d.87.1.1 70591 1m1hA 248 1.60e+01 b.114.1.1 78415 d.58.42.1 78416 1mg2D 155 1.63e+01 a.3.1.1 79062 1z2uA 150 1.69e+01 1pah 308 1.70e+01 4pah d.178.1.1 42578 2cr4A 126 1.74e+01 1ksgB 152 1.75e+01 b.1.18.8 72913 2b5lC 222 1.77e+01 1a65A 504 1.80e+01 1a65A b.6.1.3 23148 b.6.1.3 23149 b.6.1.3 23150 1xh3A 276 1.82e+01 1mlwA 301 1.83e+01 d.178.1.1 79289 1yh2A 175 1.83e+01 1hfuA 503 1.85e+01 b.6.1.3 65827 b.6.1.3 65828 b.6.1.3 65829 1rypJ 204 1.88e+01 d.153.1.4 41878 1aol 228 1.93e+01 1aol b.20.1.1 23840 1w3oA 216 1.97e+01 1b7yA 350 1.97e+01 1pysA d.104.1.1 40776 1g0uI 205 1.99e+01 d.153.1.4 41891 1kshB 152 2.04e+01 b.1.18.8 72915 1oo0A 147 2.06e+01 d.232.1.1 87182 1if1A 113 2.08e+01 2irfG a.4.5.23 16183 1a1nA 276 2.09e+01 1agdA b.1.1.2 20755 d.19.1.1 38267 1k5nA 276 2.11e+01 b.1.1.2 77266 d.19.1.1 77267 1ww7A 160 2.14e+01 1toh 343 2.22e+01 4pah d.178.1.1 42573 1uk8A 282 2.23e+01 c.69.1.10 107907 2f82A 450 2.24e+01 1a1oA 276 2.24e+01 1agdA b.1.1.2 20751 d.19.1.1 38265 1z5bA 469 2.24e+01 1umkA 275 2.24e+01 1spjA 238 2.28e+01 1evhA 112 2.28e+01 1evhA b.55.1.4 26997 1bunB 61 2.29e+01 1bpi g.8.1.1 44552 1gmnA 183 2.29e+01 g.10.1.1 65315 g.14.1.1 65316 4pah 308 2.36e+01 4pah d.178.1.1 42576 2b3gA 123 2.42e+01 1fvzA 271 2.47e+01 1fvzA 1iu1A 146 2.48e+01 b.1.10.2 71428 1bhtA 176 2.53e+01 1bhtA g.10.1.1 44603 g.14.1.1 44663 1rewA 114 2.53e+01 g.17.1.2 97334 1yfqA 342 2.56e+01 1iruK 201 2.59e+01 d.153.1.4 71362 1a1mA 278 2.61e+01 1agdA b.1.1.2 20753 d.19.1.1 38266 1dmwA 307 2.61e+01 4pah d.178.1.1 42580 2a74A 643 2.63e+01 1mu5A 471 2.69e+01 a.156.1.3 79472 d.14.1.3 79473 d.122.1.2 79474 1xd3A 230 2.72e+01 1iupA 282 2.74e+01 c.69.1.10 76815 2a7bA 120 2.76e+01 1o59A 355 2.78e+01 b.18.1.22 92495 b.18.1.22 92496 1x23A 155 2.79e+01 1msk 331 2.87e+01 1msk d.173.1.1 42495 1r1hA 696 2.89e+01 d.92.1.4 104756 1crzA 403 2.90e+01 1crzA b.68.4.1 27629 c.51.2.1 33211 2c2pA 199 2.90e+01 1z5yE 149 2.91e+01 1xewX 182 2.91e+01 1ndh 272 2.97e+01 1ndh b.43.4.2 25662 c.25.1.1 31552 2bc4B 211 2.97e+01 1vm6A 228 3.07e+01 c.2.1.3 108876 d.81.1.3 108877 1a81A 254 3.08e+01 1a81A d.93.1.1 40507 d.93.1.1 40508 2c2qA 199 3.11e+01 1e7uA 961 3.14e+01 1e8xA a.118.1.6 19147 b.7.1.1 23182 d.15.1.5 37630 d.144.1.4 41710 1guqA 348 3.15e+01 1guqA d.13.1.2 37522 d.13.1.2 37523 1gpmA 525 3.18e+01 1gpmA c.23.16.1 31405 c.26.2.1 31608 d.52.2.1 38826 1k6wA 426 3.24e+01 b.92.1.2 68236 c.1.9.5 68237 1nuyA 337 3.25e+01 e.7.1.1 86213 1rypB 250 3.31e+01 1rypB d.153.1.4 41933 1p4uA 153 3.34e+01 b.1.10.2 87780 1f1uA 323 3.35e+01 d.32.1.3 83200 d.32.1.3 83201 1gupA 348 3.35e+01 1guqA d.13.1.2 37534 d.13.1.2 37535 1qfoA 119 3.45e+01 1qfoA b.1.1.1 19708 2gw6A 123 3.46e+01 1fn9A 365 3.46e+01 1fn9A d.196.1.1 59894 2hkjA 469 3.50e+01 1v4sA 455 3.50e+01 c.55.1.3 100309 c.55.1.3 100310 1n1tA 641 3.51e+01 b.29.1.15 79821 b.68.1.1 79822 2gpjA 252 3.60e+01 1ts9A 102 3.60e+01 1e43A 483 3.61e+01 1bli b.71.1.1 59217 c.1.8.1 59218 1vprA 374 3.62e+01 1a2vA 655 3.65e+01 1a2vA b.30.2.1 24416 d.17.2.1 38059 d.17.2.1 38060 2bi7A 384 3.69e+01 1o65A 246 3.71e+01 b.58.1.2 92544 2fujA 137 3.72e+01 2h00A 254 3.73e+01 1f83A 425 3.73e+01 1f82A d.92.1.7 40306 1k8kA 418 3.76e+01 c.55.1.1 68305 c.55.1.1 68306 1wu4A 396 3.76e+01 1u69A 163 3.81e+01 d.32.1.7 107699 1l1zA 274 3.88e+01 a.156.1.2 75911 b.113.1.1 75912 g.39.1.8 75913