# 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 2fs2A 151 2.36e-21 1psuA 140 2.76e-21 d.38.1.5 88285 1wluA 136 2.11e-18 1j1yA 136 2.20e-18 d.38.1.5 90776 1zkiA 133 8.84e-18 1o0iA 138 1.67e-14 d.38.1.5 86532 2b6eA 146 2.24e-14 1yliA 153 1.33e-13 1ixlA 131 3.48e-13 d.38.1.5 90717 1vpmA 169 6.32e-13 1vh5A 148 6.71e-13 d.38.1.5 100642 1q4uA 151 1.39e-12 d.38.1.5 95828 2gvhA 288 7.74e-12 2cyeA 133 3.74e-07 1sh8A 154 4.78e-07 d.38.1.5 105549 1njkA 156 2.06e-06 d.38.1.1 85818 1yocA 147 3.72e-06 1s5uA 138 7.16e-06 d.38.1.1 98573 2b3nA 159 7.45e-06 1z54A 132 7.59e-05 2cwzA 141 1.75e-04 1t82A 155 3.17e-04 d.38.1.5 106639 2av9A 147 3.69e-04 1c8uA 285 4.39e-04 1c8uA d.38.1.3,d.38.1.3 38547,38548 1u1zA 168 5.36e-04 d.38.1.6 107602 1iq6A 134 1.99e-03 d.38.1.4 76755 2gf6A 135 8.63e-03 1z6bA 154 2.04e-02 1tbuA 118 5.28e-02 1lo7A 141 8.94e-02 d.38.1.1 74144 2essA 248 1.96e-01 1prtF 98 2.51e-01 1prtF b.40.2.1 25140 1bvqA 141 3.54e-01 1bvqA d.38.1.1 38542 2bi0A 337 4.01e-01 1l0wA 580 4.04e-01 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1zo2A 129 7.09e-01 1tf4A 605 7.60e-01 1tf4A a.102.1.2,b.2.2.2 18827,22393 1y9qA 192 1.71e+00 1pn2A 280 1.75e+00 d.38.1.4,d.38.1.4 94930,94931 1yycA 174 2.28e+00 1xrtA 467 2.29e+00 1jjyA 636 2.72e+00 1jjyA 1su8A 636 2.80e+00 e.26.1.2 98999 1c0aA 585 3.35e+00 1c0aA b.40.4.1,d.74.4.1,d.104.1.1 25246,39731,40767 1g87A 614 3.39e+00 a.102.1.2,b.2.2.2 83275,83276 1fts 295 4.27e+00 1ng1 a.24.13.1,c.37.1.10 16968,32279 1fm0D 81 4.58e+00 1fmaD d.15.3.1 37642 1vzyA 291 4.86e+00 2b59A 187 5.01e+00 1sotA 320 6.00e+00 b.36.1.4,b.47.1.1 105852,105853 1fmaD 81 6.16e+00 1fmaD d.15.3.1 37643 1o9yA 84 6.57e+00 b.139.1.1 92692 1q7fA 286 7.20e+00 b.68.9.1 96036 2as9A 210 8.12e+00 2conA 79 8.42e+00 1ny4A 82 9.00e+00 b.40.4.5 92316 1se8A 301 9.06e+00 b.40.4.3 105448 1ayyA 151 9.40e+00 1apyA d.153.1.5 42016 1bhgA 613 9.94e+00 1bhgA b.1.4.1,b.18.1.5,c.1.8.3 22161,23766,28889 2fivA 116 1.00e+01 1fmb b.50.1.1 26766 1h5uA 842 1.04e+01 1a8i c.87.1.4 60655 2bm3A 166 1.12e+01 1ltlA 279 1.15e+01 b.40.4.11 84701 1tupA 219 1.17e+01 1tupA b.2.5.2 22434 1ycsA 199 1.30e+01 1tupA b.2.5.2 22433 1bkzA 135 1.30e+01 1a3k b.29.1.3 24202 1uolA 219 1.38e+01 b.2.5.2 99695 1ygaA 342 1.44e+01 3pcgM 238 1.49e+01 3pchM b.3.6.1 22742 1ibvB 229 1.55e+01 1f3uA 118 1.55e+01 1f3uA b.65.1.1 27521 2f86B 143 1.61e+01 2aliA 158 1.68e+01 1vckA 115 1.68e+01 1pm1X 180 1.75e+01 b.60.1.1 104189 1l1nA 183 1.75e+01 b.47.1.4 73476 2bw2A 140 1.78e+01 4fiv 113 1.81e+01 1fmb b.50.1.1 26762 1ogaD 215 1.83e+01 b.1.1.1,b.1.1.2 86990,86991 1ndh 272 1.91e+01 1ndh b.43.4.2,c.25.1.1 25662,31552 1bj7 156 2.01e+01 1bj7 b.60.1.1 27113 1pyaB 228 2.03e+01 1pyaB 1tsrA 219 2.06e+01 1tupA b.2.5.2 22437 1nnxA 109 2.08e+01 b.40.10.1 92013 3pchM 238 2.09e+01 3pchM b.3.6.1 22748 2pcdM 238 2.13e+01 3pchM b.3.6.1 22760 1qyaA 307 2.14e+01 d.21.1.2,d.21.1.2 104653,104654 1h1aA 191 2.15e+01 b.29.1.11 83450 1oa8A 133 2.22e+01 b.145.1.1 92698 2tpt 440 2.30e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17759,31623,38621 1vrbA 342 2.49e+01 9gafA 295 2.58e+01 1apyA d.153.1.5 42008 1sltA 134 2.58e+01 1c1lA b.29.1.3 24186 1kzfA 230 2.60e+01 d.108.1.3 73354 3fivA 116 2.64e+01 1fmb b.50.1.1 26768 1slaA 134 2.68e+01 1c1lA b.29.1.3 24196 1bxsA 501 2.70e+01 1bpwA c.82.1.1 35357 1fivA 113 2.73e+01 1fmb b.50.1.1 26764 2brqA 97 2.73e+01 1vq0A 302 2.76e+01 1q7lA 198 2.78e+01 c.56.5.4 96044 1umkA 275 2.80e+01 1xfoA 357 2.84e+01 1y0yA 353 2.91e+01 1wgzA 510 2.92e+01 1zkpA 268 2.98e+01 1bcpF 99 3.01e+01 1prtF b.40.2.1 25142 3proC 166 3.02e+01 3proC d.52.1.1,d.52.1.1 38812,38813 2cu3A 64 3.11e+01 1p4kA 295 3.19e+01 d.153.1.5 87772 1sltB 134 3.22e+01 1c1lA b.29.1.3 24187 1p9yA 121 3.26e+01 d.241.2.1 94402 1e2tA 284 3.44e+01 1e2tA d.3.1.5 37121 1l6oA 95 3.47e+01 b.36.1.1 84534 2gr8A 99 3.57e+01 1o04A 500 3.61e+01 c.82.1.1 86508 1gzwA 134 3.65e+01 b.29.1.3 90535 1a9v 129 3.67e+01 1a9v b.1.18.7 21946 3proD 166 3.70e+01 3proC d.52.1.1,d.52.1.1 38814,38815 1mkaA 171 3.75e+01 1mkaA d.38.1.2 38543 1jjeA 222 3.78e+01 1a7tA d.157.1.1 63117 1txqA 93 3.81e+01 1xnkA 196 4.00e+01 2biqA 219 4.06e+01 1sdjA 310 4.12e+01 d.21.1.2,d.21.1.2 98807,98808 1fqtA 112 4.14e+01 1fqtA b.33.1.1 24441 1u2cA 246 4.22e+01 b.1.6.2,d.272.1.1 107610,107611 1w6nA 134 4.32e+01 1ag8A 499 4.34e+01 1bpwA c.82.1.1 35341 1vehA 92 4.34e+01 1rmg 422 4.38e+01 1rmg b.80.1.3 28029 1cskA 71 4.54e+01 1ckaA b.34.2.1 24513 1peeA 180 4.60e+01 b.60.1.1 104126 1txyA 104 4.76e+01 1ww7A 160 4.84e+01 1vdkA 466 4.91e+01 a.127.1.1 100561 1pcfA 66 4.93e+01 1pcfA d.18.1.1 38142 2fr1A 486 4.95e+01 1tzjA 338 5.06e+01 1r4vA 171 5.07e+01 a.197.1.1 97049 1y8tA 324 5.21e+01 1b8aA 438 5.24e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1wlyA 333 5.47e+01 1iezA 217 5.51e+01 d.115.1.2 66129 1sftA 388 5.82e+01 1bd0A b.49.2.2,c.1.6.1 26482,28644 1kk1A 410 5.83e+01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1jkeA 145 5.95e+01 c.110.1.1 66791 1v7rA 186 6.24e+01 c.51.4.1 100482 1yasA 257 6.26e+01 1qj4A c.69.1.20 34801 1cbs 137 6.37e+01 1hmt b.60.1.2 27201 1bd0A 388 6.42e+01 1bd0A b.49.2.2,c.1.6.1 26480,28642 1z7gA 217 6.42e+01 1zyoA 191 6.46e+01 1ihoA 283 6.49e+01 1ihoA c.26.1.4 62390 2aalA 131 6.50e+01 1ktjA 129 6.56e+01 b.1.18.7 72974 1ecfB 504 6.79e+01 1ecfB c.61.1.1,d.153.1.1 34054,41821 1g0dA 695 6.89e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 60166,60167,60168,60169 1h2aL 567 7.02e+01 1h2rL e.18.1.1 43299 1t17A 148 7.07e+01 2fg1A 158 7.26e+01 3ullA 132 7.27e+01 3ullA b.40.4.3 25282 1akjD 120 7.29e+01 1cd8 b.1.1.1 19712 2bjrA 368 7.33e+01 1nvmA 345 7.47e+01 a.5.7.1,c.1.10.5 86249,86250 1n7eA 97 7.51e+01 b.36.1.1 91691 1oe4A 247 7.52e+01 c.18.1.3 86895 1nif 340 7.65e+01 1nif b.6.1.3,b.6.1.3 23048,23049 1ihjA 98 7.69e+01 1pdr b.36.1.1 62382 1n6zA 105 7.70e+01 d.263.1.1 85369 2reb 352 7.76e+01 2reb c.37.1.11,d.48.1.1 32282,38767 1pkp 150 7.88e+01 1pkp d.14.1.1,d.50.1.2 37551,38787 1dd6A 228 7.90e+01 1a7tA d.157.1.1 42054 1yu0A 381 8.01e+01 1k51A 72 8.17e+01 d.15.7.1 68147 1cmoA 127 8.25e+01 1cmoA b.2.5.6 22462 1jegA 83 8.35e+01 b.34.2.1 66610 2f57A 317 8.37e+01 1ao0A 459 8.40e+01 1ecfB c.61.1.1,d.153.1.1 34049,41816 1qj4A 257 8.43e+01 1qj4A c.69.1.20 34796 1qx4A 274 8.55e+01 b.43.4.2,c.25.1.1 104624,104625 1vkfA 188 8.59e+01 c.1.29.1 108656 1sawA 225 8.60e+01 1vcaA 202 8.60e+01 1vcaA b.1.1.3,b.1.1.4 21649,21685 1eo9B 241 8.64e+01 3pchM b.3.6.1 22826 1x8qA 184 8.64e+01 2a15A 139 8.89e+01 1vqoE 178 8.93e+01