# List of top-scoring protein chains for t2k-100-30-alpha 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 1nfjA 89 1.06e-18 1h0xA 100 7.97e-18 d.68.6.1 76451 1nh9A 87 2.12e-17 1udvA 89 9.26e-09 1olsB 342 7.18e-01 1j5xA 342 8.85e-01 c.80.1.1 71591 1v1rB 342 9.63e-01 1vhwA 253 1.01e+00 1dtwB 342 1.13e+00 1qs0B c.36.1.7 31828 c.48.1.2 33102 1ra9 159 2.11e+00 1vdrA c.71.1.1 34820 2bby 69 2.16e+00 2bby a.4.5.15 16148 1bby 69 2.30e+00 2bby a.4.5.15 16149 1aky 221 2.45e+00 1zin c.37.1.1 31896 g.41.2.1 45197 6dfr 159 2.46e+00 1vdrA c.71.1.1 34874 1px5A 349 2.81e+00 2pia 321 3.10e+00 2pia b.43.4.2 25663 c.25.1.2 31553 d.15.4.2 37704 1bpyA 335 3.60e+00 1bpyA a.60.6.1 17980 a.60.12.1 75819 d.218.1.2 75820 1draA 159 3.77e+00 1vdrA c.71.1.1 34831 1jmkC 230 3.88e+00 c.69.1.22 71747 1noyA 388 3.95e+00 1clqA c.55.3.5 33713 1o2dA 371 4.18e+00 e.22.1.2 86591 1pch 88 4.27e+00 1ptf d.94.1.1 40564 1ml8A 134 4.39e+00 d.227.1.2 85013 1o0uA 429 4.39e+00 c.118.1.1 80743 1a3c 181 4.56e+00 1a3c c.61.1.1 34095 1qgdA 662 4.79e+00 c.36.1.6 88367 c.36.1.10 88368 c.48.1.1 88369 1rpl 251 5.12e+00 1bpyA a.60.12.1 75933 d.218.1.2 75934 1k5dC 386 5.57e+00 c.10.1.2 68170 1s5dA 240 5.63e+00 1fbaA 361 5.65e+00 1fbaA c.1.10.1 29120 1hq3B 126 5.99e+00 1aoiD a.22.1.1 16444 1yrgA 385 6.05e+00 1yrgA c.10.1.2 30854 1fnmA 691 6.21e+00 1dar b.43.3.1 25709 c.37.1.8 32144 d.14.1.1 37546 d.58.11.1 39302 d.58.11.1 39303 1cm7A 363 6.24e+00 1cnzA c.77.1.1 35063 1j5rA 371 6.34e+00 1bpb 248 6.45e+00 1bpyA a.60.12.1 75811 d.218.1.2 75812 1ozjA 144 6.58e+00 1mhdA 132 6.76e+00 1mhdA d.164.1.1 42175 1ou0A 207 6.84e+00 1seiA 130 7.02e+00 1seiA d.140.1.1 41463 1iatA 557 7.04e+00 1dqrA c.80.1.2 62123 1r7aA 504 7.34e+00 1cnzA 363 7.49e+00 1cnzA c.77.1.1 35061 1jykA 254 7.52e+00 c.68.1.13 67458 1cf2O 337 7.52e+00 1b7gO c.2.1.3 29994 d.81.1.1 39909 1h0cA 392 7.79e+00 c.67.1.3 83424 1nijA 318 7.82e+00 c.37.1.10 85741 d.237.1.1 85742 1nom 248 7.99e+00 1bpyA a.60.12.1 75929 d.218.1.2 75930 1ltsA 185 8.01e+00 1lt3A d.166.1.1 42229 1ik6A 369 8.09e+00 c.36.1.7 66174 c.48.1.2 66175 1pedA 351 8.38e+00 1pedA b.35.1.2 24753 c.2.1.1 29769 1dz4A 414 8.59e+00 1phd a.104.1.1 18903 1k6iA 352 8.72e+00 c.2.1.2 68223 1tmy 120 8.91e+00 1dbwA c.23.1.1 31083 1k6xA 352 9.00e+00 c.2.1.2 68238 1kevA 351 9.10e+00 1pedA b.35.1.2 24749 c.2.1.1 29765 1q8rA 120 9.29e+00 1mh1 186 9.58e+00 1eesA c.37.1.8 32002 1yrgB 385 9.67e+00 1yrgA c.10.1.2 30855 1pbn 289 1.11e+01 1b8oA c.56.2.1 33771 1k4nA 192 1.15e+01 d.32.1.5 72059 1h8eG 272 1.15e+01 1e79G c.49.2.1 60756 1b8oA 284 1.17e+01 1b8oA c.56.2.1 33762 1phd 414 1.17e+01 1phd a.104.1.1 18913 1v61A 132 1.26e+01 1krhA 338 1.27e+01 b.43.4.2 72891 c.25.1.2 72892 d.15.4.2 72893 1sphA 88 1.27e+01 1ptf d.94.1.1 40544 1p42A 270 1.30e+01 d.14.1.7 87754 d.14.1.7 87755 2frvA 264 1.35e+01 2frvA e.19.1.1 43303 1e58A 249 1.36e+01 1qhfA c.60.1.1 59262 3pnp 289 1.38e+01 1b8oA c.56.2.1 33763 1bn7A 294 1.42e+01 1bn6A c.69.1.8 34677 1luaA 287 1.47e+01 c.2.1.7 78216 c.58.1.4 78217 1gy8A 397 1.47e+01 c.2.1.2 83376 1lu9A 287 1.48e+01 c.2.1.7 78210 c.58.1.4 78211 3pgm 241 1.51e+01 1qhfA c.60.1.1 33982 1f4pA 147 1.53e+01 5nul c.23.5.1 59651 1e3tA 203 1.54e+01 1d4oA c.31.1.4 31749 2bnh 457 1.55e+01 1a4yA c.10.1.1 30850 1bu5A 147 1.57e+01 5nul c.23.5.1 31155 1kppA 145 1.59e+01 d.20.1.2 72846 1dckA 126 1.63e+01 1dbwA c.23.1.1 31097 1oi7A 288 1.69e+01 c.2.1.8 87049 c.23.4.1 87050 1cb6A 691 1.70e+01 1cb6A c.94.1.2 35840 c.94.1.2 35841 1gpuA 680 1.70e+01 c.36.1.6 65455 c.36.1.10 65454 c.48.1.1 65456 1v54E 109 1.71e+01 1trkA 680 1.74e+01 1trkA c.36.1.6 31804 c.36.1.10 31803 c.48.1.1 33090 1skyB 502 1.74e+01 1skyB a.69.1.1 18313 b.49.1.1 26478 c.37.1.11 32358 5cpp 414 1.75e+01 1phd a.104.1.1 18935 1kx5D 125 1.76e+01 a.22.1.1 77596 1o65A 246 1.78e+01 1dnlA 199 1.79e+01 1ci0A b.45.1.1 25753 1phb 414 1.80e+01 1phd a.104.1.1 18906 1rypD 241 1.84e+01 1rypD d.153.1.4 41935 1h4vB 421 1.88e+01 1adjA c.51.1.1 60624 d.104.1.1 60625 2hfh 109 1.91e+01 2hfh a.4.5.14 16145 1qmqA 414 1.91e+01 1phd a.104.1.1 18907 1gikA 261 1.95e+01 1kexA 155 1.95e+01 b.18.1.2 77350 1lct 333 1.96e+01 1cb6A c.94.1.2 35836 2occE 109 1.98e+01 2occE a.118.11.1 19224 1b7eA 420 1.99e+01 1b7eA c.55.3.4 33680 1qgoA 264 2.00e+01 1qgoA c.92.1.2 35596 1bn6A 294 2.00e+01 1bn6A c.69.1.8 34678 1tkaA 678 2.06e+01 1trkA c.36.1.6 31816 c.36.1.10 31815 c.48.1.1 33096 1pyoB 105 2.06e+01 1uaqA 158 2.08e+01 c.97.1.2 88386 1phg 414 2.09e+01 1phd a.104.1.1 18910 1rztA 331 2.16e+01 1j1qA 261 2.17e+01 1aoeA 192 2.18e+01 1aoeA c.71.1.1 34923 1dar 691 2.20e+01 1dar b.43.3.1 25707 c.37.1.8 32142 d.14.1.1 37547 d.58.11.1 39300 1nr3A 122 2.20e+01 d.236.1.1 86092 1eokA 290 2.21e+01 1eokA c.1.8.5 28991 1mgtA 174 2.28e+01 1mgtA a.4.2.1 16078 c.55.7.1 33753 1h7eA 245 2.29e+01 c.68.1.13 60717 1moq 368 2.33e+01 1moq c.80.1.1 35302 1bq3B 246 2.33e+01 1qhfA c.60.1.1 33979 1d5wC 126 2.33e+01 1dbwA c.23.1.1 31101 1kamA 194 2.34e+01 c.26.1.3 72254 1j6rA 214 2.38e+01 d.173.1.2 71598 1rkuA 206 2.42e+01 1mk0A 97 2.43e+01 d.226.1.1 79216 1cqwA 295 2.44e+01 1b6g c.69.1.8 34679 1rlhA 173 2.44e+01 1i7pA 274 2.45e+01 b.43.4.2 66048 c.25.1.1 66049 1jqbA 351 2.54e+01 b.35.1.2 77151 c.2.1.1 77152 1h5qA 265 2.55e+01 1cydA c.2.1.2 60643 1oxkB 134 2.64e+01 1auoA 218 2.65e+01 1auoA c.69.1.14 34716 1fha 183 2.69e+01 2fha a.25.1.1 16675 1ctf 74 2.69e+01 1ctf d.45.1.1 38759 1p1lA 102 2.70e+01 d.58.5.2 87695 1lxnA 99 2.73e+01 d.58.48.1 84737 1qhfA 240 2.75e+01 1qhfA c.60.1.1 33960 1kveB 77 2.79e+01 1kveB 1tdj 514 2.82e+01 1tdj c.79.1.1 35297 d.58.18.2 39356 d.58.18.2 39357 1lb3A 182 2.83e+01 a.25.1.1 77873 1dqrA 557 2.94e+01 1dqrA c.80.1.2 35305 1a8o 70 2.96e+01 1a8o a.28.3.1 16953 1g1eB 89 3.00e+01 1g1eB a.59.1.1 17931 1musA 477 3.02e+01 c.55.3.4 79494 2fha 183 3.03e+01 2fha a.25.1.1 16674 1gqaA 130 3.03e+01 a.24.3.2 76275 1aurA 218 3.05e+01 1auoA c.69.1.14 34718 1kzhA 555 3.05e+01 c.89.1.1 73361 1muhA 481 3.10e+01 c.55.3.4 79485 1q44A 326 3.15e+01 1dbwA 126 3.22e+01 1dbwA c.23.1.1 31095 1kvdB 77 3.24e+01 1kveB 1nzjA 298 3.25e+01 1p6oA 161 3.28e+01 1lt3A 240 3.29e+01 1lt3A d.166.1.1 42230 2fx2 147 3.32e+01 1rcf c.23.5.1 31158 1aoiD 99 3.34e+01 1aoiD a.22.1.1 16452 1f3iA 481 3.34e+01 1b7eA 1nbuA 119 3.36e+01 1jem 87 3.39e+01 1ptf d.94.1.1 40548 1gxjA 186 3.41e+01 d.215.1.1 70707 3ldh 330 3.49e+01 3ldh i.12.1.1 46015 1pvtA 238 3.50e+01 1jvwA 167 3.50e+01 d.26.1.1 71907 1elkA 157 3.52e+01 1dvpA a.118.9.2 19217 1j9eA 147 3.53e+01 c.23.5.1 62756 1pc3A 350 3.54e+01 1nxcA 478 3.55e+01 1dtdA 303 3.60e+01 1aye c.56.5.1 33823 1a4yA 460 3.64e+01 1a4yA c.10.1.1 30852 1ceqA 316 3.71e+01 1ceqA c.2.1.5 30163 d.162.1.1 42130 1eysL 280 3.77e+01 6prcL f.26.1.1 43515 1ldg 316 3.79e+01 1ceqA c.2.1.5 30165 d.162.1.1 42132 1cz3A 168 3.87e+01 1d1gA c.71.1.1 34891 1bhjA 292 3.88e+01 1xvaA c.66.1.5 34189 1jo0A 98 3.88e+01 d.68.4.1 77140 1g79A 218 3.89e+01 1ci0A b.45.1.1 25752 1regX 122 3.90e+01 1regX d.58.27.1 39406 2lgsA 468 3.93e+01 1lgr d.15.9.1 37838 d.128.1.1 41168 1h96A 182 3.95e+01 2fha a.25.1.1 60811 1qm4A 396 3.95e+01 1mxb d.130.1.1 41350 d.130.1.1 41351 d.130.1.1 41352 1pdo 135 3.98e+01 1pdo c.54.1.1 33376