# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7-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 1qs1A 462 1.36e-01 1qs1A d.166.1.1 42260 d.166.1.1 42261 1yge 839 2.16e-01 1yge a.119.1.1 19234 b.12.1.1 23634 1qs2A 401 2.59e-01 1qs1A d.166.1.1 42268 d.166.1.1 42269 1f8nA 839 2.97e-01 1yge a.119.1.1 59703 b.12.1.1 59704 1fgqA 839 6.00e-01 1yge a.119.1.1 59826 b.12.1.1 59827 1lnh 857 8.93e-01 1yge a.119.1.1 19237 b.12.1.1 23637 1i8dA 213 1.00e+00 b.43.4.3 61953 b.43.4.3 61954 1jeqB 565 1.00e+00 1jeqB unknown_sccs -4432 unknown_sccs -7996 1khiA 176 1.03e+00 b.34.5.2 77408 b.40.4.5 77409 1vjuA 309 1.23e+00 unknown_sccs -9594 1dg3A 592 1.32e+00 1dg3A a.114.1.1 19078 c.37.1.8 32153 1f13A 731 1.39e+00 1f13A b.1.18.9 21877 b.1.5.1 22163 b.1.5.1 22164 d.3.1.4 37107 1jeyB 565 1.47e+00 1jeqB unknown_sccs -4431 unknown_sccs -7995 1ex0A 731 1.57e+00 b.1.18.9 -2754 b.1.5.1 -2778 b.1.5.1 -2779 d.3.1.4 -8889 1ggtB 731 1.73e+00 1f13A b.1.18.9 21882 b.1.5.1 22173 b.1.5.1 22174 d.3.1.4 37112 1k28D 391 1.75e+00 b.106.1.1 68052 b.106.1.1 68053 1giqA 413 2.38e+00 d.166.1.1 76224 d.166.1.1 76225 1gt1A 159 2.41e+00 b.60.1.1 -4436 1vybA 238 2.65e+00 1hn2A 159 2.72e+00 b.60.1.1 65890 1evuA 731 2.77e+00 1f13A b.1.18.9 21883 b.1.5.1 22175 b.1.5.1 22176 d.3.1.4 37113 1kzlA 208 2.92e+00 b.43.4.3 77635 b.43.4.3 77636 1uw6A 211 3.01e+00 b.96.1.1 -3077 1c0pA 363 3.01e+00 1an9A c.4.1.2 30647 d.16.1.3 37934 1rovA 857 3.04e+00 a.119.1.1 -1656 b.12.1.1 -3034 1f5nA 592 3.16e+00 1dg3A a.114.1.1 19077 c.37.1.8 32152 1obpA 159 3.18e+00 1obpA b.60.1.1 27092 1ac5 483 3.41e+00 1ac5 c.69.1.5 34653 1rybA 212 4.12e+00 c.56.3.1 -7858 1rz1A 161 4.14e+00 b.45.1.2 -4088 1iz6A 138 4.53e+00 b.34.5.2 76976 b.40.4.5 76977 1pzdA 322 4.82e+00 unknown_sccs -2848 unknown_sccs -10778 1udxA 416 4.96e+00 b.117.1.1 -3546 c.37.1.8 -7101 unknown_sccs -9009 1r4xA 275 5.01e+00 unknown_sccs -2846 unknown_sccs -10776 1szwA 379 5.08e+00 unknown_sccs -10164 1aisA 182 5.52e+00 1ytbA d.129.1.1 41288 d.129.1.1 41289 1lkxA 697 5.85e+00 c.37.1.9 73981 1i9bA 217 5.95e+00 1i9bA b.96.1.1 62084 1bkb 136 6.19e+00 1bkb b.34.5.2 24609 b.40.4.5 25341 1vj1A 363 6.44e+00 b.35.1.2 -3728 c.2.1.1 -5752 1mp9A 198 7.16e+00 a.74.1.2 -1127 a.74.1.2 -1128 1mwmA 320 8.12e+00 c.55.1.1 79580 c.55.1.1 79581 1dqqA 214 9.00e+00 8fabA b.1.1.1 20420 b.1.1.2 21390 1si7A 369 9.09e+00 unknown_sccs -10163 1eagA 342 9.36e+00 1eagA b.50.1.2 26826 1lr0A 129 9.40e+00 d.212.1.1 74213 1oxsC 353 9.53e+00 b.40.6.3 87519 c.37.1.12 87520 1nwwA 149 1.02e+01 d.17.4.8 86306 1j71A 334 1.06e+01 1eagA b.50.1.2 62669 1olsA 400 1.07e+01 c.36.1.11 -6959 1cof 143 1.08e+01 1cof d.109.1.2 40860 1gguA 731 1.13e+01 1f13A b.1.18.9 21885 b.1.5.1 22179 b.1.5.1 22180 d.3.1.4 37115 1mjuL 219 1.13e+01 b.1.1.1 -2083 b.1.1.2 -2360 1vpt 348 1.14e+01 3mag c.66.1.25 34207 1bjmA 216 1.16e+01 8fabA b.1.1.1 20524 b.1.1.2 21460 1j0hA 588 1.18e+01 b.1.18.2 77027 b.71.1.1 77028 c.1.8.1 77029 1thv 207 1.21e+01 1thv b.25.1.1 23904 1qrkA 731 1.22e+01 1f13A b.1.18.9 21889 b.1.5.1 22187 b.1.5.1 22188 d.3.1.4 37119 1mexL 213 1.26e+01 b.1.1.1 -2124 b.1.1.2 -2352 1vhoA 346 1.28e+01 unknown_sccs -4283 c.56.5.4 -7893 1vjlA 164 1.36e+01 unknown_sccs -11117 1oe9A 795 1.36e+01 b.34.3.1 -3581 c.37.1.9 -7103 1ospL 214 1.37e+01 32c2A b.1.1.1 20116 b.1.1.2 21146 1rqwA 207 1.37e+01 b.25.1.1 -3313 1oxxK 353 1.38e+01 b.40.6.3 -3969 c.37.1.12 -7187 1dlfH 124 1.45e+01 1igtB b.1.1.1 20383 1se8A 301 1.46e+01 1b7fA 168 1.47e+01 1b7fA d.58.7.1 39169 d.58.7.1 39170 1bob 320 1.48e+01 1bob d.108.1.1 40816 1o5yA 193 1.49e+01 1tetL 216 1.49e+01 32c2A b.1.1.1 19902 b.1.1.2 20996 1thw 207 1.54e+01 1thv b.25.1.1 23903 1hcz 252 1.55e+01 1hcz b.2.6.1 22464 b.84.2.2 28250 1i0sA 169 1.55e+01 1i0rA b.45.1.2 61491 1ipwA 175 1.55e+01 2prd b.40.5.1 25427 1v74A 107 1.58e+01 unknown_sccs -9319 1e6oL 212 1.63e+01 32c2A b.1.1.1 20494 b.1.1.2 21452 3sil 379 1.64e+01 3sil b.68.1.1 27542 2sil 381 1.67e+01 3sil b.68.1.1 27543 3mag 307 1.67e+01 3mag c.66.1.25 34205 1kqfB 294 1.73e+01 d.58.1.5 75900 f.23.22.1 75901 1v39 322 1.75e+01 3mag c.66.1.25 34206 1jixA 351 1.76e+01 1c3jA c.87.1.1 63081 1gy7A 125 1.77e+01 d.17.4.2 70738 1vp9 322 1.88e+01 3mag c.66.1.25 34210 1a3lL 217 1.91e+01 8fabA b.1.1.1 20240 b.1.1.2 21252 1gc1H 229 1.93e+01 1gc1H b.1.1.1 20265 b.1.1.2 21265 2prd 174 1.94e+01 2prd b.40.5.1 25435 1jg7A 351 1.95e+01 1c3jA c.87.1.1 62945 1i0rA 169 1.99e+01 1i0rA b.45.1.2 61489 2pcfB 250 1.99e+01 1hcz i.4.1.1 45911 1c5cL 214 2.01e+01 32c2A b.1.1.1 20474 b.1.1.2 21438 1orvA 728 2.04e+01 b.70.3.1 87354 c.69.1.24 87355 1nrgA 261 2.15e+01 b.45.1.1 80694 1sjyA 159 2.20e+01 d.113.1.1 -10908 1mlbA 214 2.23e+01 8fabA b.1.1.1 20050 b.1.1.2 21092 1n1tA 641 2.28e+01 b.29.1.15 79821 b.68.1.1 79822 1lox 662 2.29e+01 1lox a.119.1.2 19238 b.12.1.1 23638 1kwnA 207 2.32e+01 b.25.1.1 77568 1n08A 163 2.33e+01 b.43.5.1 79730 1v1rA 400 2.34e+01 1b88A 114 2.34e+01 1tcrA b.1.1.1 20608 1br2A 791 2.48e+01 1lvk b.34.3.1 24558 c.37.1.9 32155 8fabB 224 2.51e+01 1igtB b.1.1.1 19773 b.1.1.2 20883 1kfiA 572 2.51e+01 c.84.1.1 68555 c.84.1.1 68556 c.84.1.1 68557 d.129.2.1 68558 1hcl 298 2.55e+01 1hcl d.144.1.7 41593 6gsvA 217 2.57e+01 1b8xA a.45.1.1 17633 c.47.1.5 32925 1f7lA 121 2.59e+01 1f7lA d.150.1.2 59666 2eifA 136 2.59e+01 1bkb b.34.5.2 24607 b.40.4.5 25339 1mz5A 638 2.70e+01 b.29.1.15 79679 b.68.1.1 79680 1jmuB 666 2.74e+01 1bix 287 2.78e+01 1bix d.151.1.1 41781 1q2wA 308 2.80e+01 b.47.1.4 88355 1dnlA 199 2.82e+01 1ci0A b.45.1.1 25753 1dim 381 2.86e+01 3sil b.68.1.1 27544 1bglA 1023 2.86e+01 1bglA b.1.4.1 22097 b.1.4.1 22098 b.18.1.5 23734 b.30.5.1 24358 c.1.8.3 28857 1c3jA 351 2.86e+01 1c3jA c.87.1.1 35459 1lckA 175 2.88e+01 1lckA b.34.2.1 24552 d.93.1.1 40421 1dghB 498 2.90e+01 1cf9A e.5.1.1 42791 1rzfH 235 2.91e+01 b.1.1.1 -2188 b.1.1.2 -2453 1nlbL 220 2.97e+01 b.1.1.1 80623 b.1.1.2 80624 3sxlA 184 3.03e+01 1b7fA d.58.7.1 39173 d.58.7.1 39174 1q9rA 219 3.03e+01 b.1.1.1 -2109 b.1.1.2 -2375 2fbjL 213 3.03e+01 8fabA b.1.1.1 19850 b.1.1.2 20954 1oi1A 221 3.05e+01 b.34.9.3 87037 b.34.9.3 87038 1cfyA 143 3.13e+01 1cof d.109.1.2 40858 1dzkA 157 3.20e+01 1obpA b.60.1.1 27096 2u2fA 85 3.22e+01 2u2fA d.58.7.1 39167 1mqkH 127 3.23e+01 b.1.1.1 85053 1ol0A 121 3.25e+01 b.1.1.1 -2311 1otcA 495 3.26e+01 1otcA b.40.4.3 25307 b.40.4.3 25308 b.40.4.3 25309 1h3nA 878 3.35e+01 a.27.1.1 76641 b.51.1.1 76642 c.26.1.1 76643 1i40A 175 3.37e+01 b.40.5.1 66024 2phlA 397 3.48e+01 1dgwA b.82.1.2 28082 b.82.1.2 28083 1jofA 365 3.48e+01 b.69.10.1 71775 1obwA 175 3.62e+01 2prd b.40.5.1 25416 1forL 210 3.64e+01 8fabA b.1.1.1 19988 b.1.1.2 21044 1t62A 166 3.65e+01 1jhsA 188 3.68e+01 d.107.1.1 84172 1b35A 260 3.70e+01 1b35A b.121.4.1 23333 1vjjA 692 3.71e+01 b.1.18.9 -2758 b.1.5.1 -2786 b.1.5.1 -2787 d.3.1.4 -8893 1ncwL 219 3.72e+01 b.1.1.1 85557 b.1.1.2 85558 1ii7A 333 3.73e+01 1ii7A d.159.1.4 62415 1g79A 218 3.77e+01 1ci0A b.45.1.1 25752 1gq6A 313 3.77e+01 c.42.1.1 70341 1te5A 257 3.79e+01 1ir3A 306 3.83e+01 1fmk d.144.1.7 41702 1hilB 220 3.85e+01 1igtB b.1.1.1 19787 b.1.1.2 20897 1a9v 129 3.85e+01 1a9v b.1.18.7 21946 1l7iL 214 3.86e+01 b.1.1.1 73658 b.1.1.2 73659 2bgu 351 3.92e+01 1c3jA c.87.1.1 35460 32c2A 217 3.97e+01 32c2A b.1.1.1 20438 b.1.1.2 21404