# 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 1nb8A 353 6.39e-48 d.3.1.9 80385 1hleA 345 3.61e-02 1ovaA e.1.1.1 42618 1ubi 76 9.31e-02 1ubi d.15.1.1 37584 1ubq 76 1.12e-01 1ubi d.15.1.1 37585 1ogwA 76 1.22e-01 d.15.1.1 87001 1d0cA 444 1.24e-01 d.174.1.1 64769 1nseA 444 1.26e-01 1nseA d.174.1.1 42534 1ed5A 444 1.26e-01 1nseA d.174.1.1 42530 1d1vA 444 1.34e-01 1nseA d.174.1.1 59101 1ksfX 758 1.80e-01 a.174.1.1 77522 c.37.1.20 77523 c.37.1.20 77524 5nseA 444 1.86e-01 d.174.1.1 74644 1k6kA 143 1.90e-01 a.174.1.1 77274 1gm5A 780 2.02e-01 unknown_sccs 65298 b.40.4.9 65299 c.37.1.19 65300 c.37.1.19 65301 2cas 548 2.39e-01 2cas b.121.5.2 23376 1d3zA 76 2.69e-01 1ubi d.15.1.1 37592 1c8gA 548 3.61e-01 2cas b.121.5.2 23380 1mdaH 368 3.83e-01 2bbkH b.69.2.1 27637 1exrA 148 4.04e-01 1cll a.39.1.5 17299 1osa 148 4.38e-01 1cll a.39.1.5 17300 1mjhA 162 5.01e-01 1mjhA c.26.2.4 31639 1hkfA 122 5.34e-01 b.1.1.1 83553 1lm8B 118 5.37e-01 d.15.1.1 74033 1vcbA 118 5.80e-01 1vcbA d.15.1.1 37603 1ng7A 60 6.67e-01 a.178.1.1 85671 1eg3A 261 7.34e-01 1eg3A a.39.1.7 17376 a.39.1.7 17377 b.72.1.1 27805 1sqgA 429 8.81e-01 1rdg 53 9.57e-01 1rb9 g.41.5.1 45221 1gnc 178 1.05e+00 1bgc a.26.1.1 16821 1a0p 290 1.11e+00 1a0p a.60.9.1 18105 d.163.1.1 42165 1l1oC 181 1.19e+00 b.40.4.3 73480 1hgxA 183 1.34e+00 1tc1A c.61.1.1 34027 1cd9C 175 1.36e+00 1bgc a.26.1.1 16816 1as4A 341 1.42e+00 1sek e.1.1.1 42623 1qb4A 883 1.57e+00 c.1.12.3 74640 4dpvZ 584 1.63e+00 2cas b.121.5.2 23377 1jqnA 883 1.68e+00 c.1.12.3 77159 1alvA 173 1.74e+00 1alvA a.39.1.8 17370 9apiA 347 1.84e+00 1ovaA e.1.1.1 42630 1bq8A 54 2.05e+00 1rb9 g.41.5.1 45237 1fiy 883 2.22e+00 1fiy c.1.12.3 29307 1ipiA 123 2.52e+00 c.52.1.18 66255 1bq9A 54 2.66e+00 1rb9 g.41.5.1 45238 1fvuB 125 2.82e+00 1ixxB d.169.1.1 42346 1brfA 53 2.91e+00 1rb9 g.41.5.1 45236 1hc7A 477 3.03e+00 1hc7A c.51.1.1 60938 d.68.5.1 60940 d.104.1.1 60939 1ih7A 903 3.04e+00 1clqA c.55.3.5 62375 e.8.1.1 62376 1vh4A 435 3.20e+00 unknown_sccs -4794 1qhhA 167 3.23e+00 1pjr c.37.1.19 32393 1kfuS 184 3.28e+00 a.39.1.8 68574 1a28A 256 3.35e+00 1a28A a.123.1.1 19290 1mjhB 162 3.70e+00 1mjhA c.26.2.4 31640 1qf8A 182 3.80e+00 1qf8A g.41.4.1 45212 1top 162 3.99e+00 1ncx a.39.1.5 17223 1fnnA 389 4.13e+00 1fnnA a.4.5.11 16129 c.37.1.20 32426 1r9dA 787 4.41e+00 1ncx 162 4.50e+00 1ncx a.39.1.5 17222 1itbB 315 4.51e+00 1itbB b.1.1.4 21720 b.1.1.4 21721 b.1.1.4 21722 1f0cA 305 4.56e+00 1c8oA e.1.1.1 42676 1hjp 203 4.64e+00 1hjp a.5.1.1 16274 a.60.2.1 17947 b.40.4.2 25266 1uurA 473 4.81e+00 a.47.1.1 -968 b.2.5.5 -2904 d.93.1.1 -10632 1dx8A 70 4.84e+00 1rb9 g.41.5.1 45243 1exzA 141 5.14e+00 1exzA a.26.1.2 16877 1sr7A 259 5.29e+00 1rzfH 235 5.33e+00 b.1.1.1 -2188 b.1.1.2 -2453 1gefA 123 5.35e+00 1gefA c.52.1.18 60465 1s6cA 183 5.60e+00 a.39.1.5 -858 1clqA 903 5.66e+00 1clqA c.55.3.5 33717 e.8.1.1 43006 1fipA 98 5.68e+00 1fipA unknown_sccs 18980 1meyC 87 5.81e+00 2gliA k.12.1.1 46430 1ekfA 365 5.82e+00 1ekfA e.17.1.1 59445 1avsA 90 5.89e+00 1cll a.39.1.5 17226 1kz7A 353 6.33e+00 a.87.1.1 73333 b.55.1.1 73334 1f4kA 122 6.88e+00 1bm9A a.4.5.7 59646 1j55A 95 7.12e+00 a.39.1.2 77078 6rxn 46 7.15e+00 1rb9 g.41.5.1 45222 1bgeB 175 7.27e+00 1bgc a.26.1.1 16824 1dabA 539 7.37e+00 1dabA b.80.1.7 28049 1nvhA 66 7.43e+00 1cknA 330 7.58e+00 1ckmA b.40.4.6 25360 d.142.2.3 41587 1ckmA 330 7.79e+00 1ckmA b.40.4.6 25358 d.142.2.3 41585 1s6tA 285 8.16e+00 c.37.1.5 -7040 1vkjA 285 8.16e+00 1kt8A 365 8.32e+00 e.17.1.1 77531 1onqA 283 8.38e+00 b.1.1.2 -2640 d.19.1.1 -9390 1jmtA 104 8.76e+00 d.58.7.3 63180 1nddA 76 8.83e+00 1ubi d.15.1.1 37599 1ktaA 365 8.99e+00 e.17.1.1 77533 1qlpA 394 9.01e+00 1ovaA e.1.1.1 42628 1jjoC 261 9.07e+00 1qxfA 66 9.36e+00 g.41.8.4 -12822 1uf2C 421 9.68e+00 unknown_sccs -1522 b.19.1.1 -3155 1sviA 195 9.75e+00 1pa7A 130 9.89e+00 a.40.1.1 -896 1jf2A 195 1.03e+01 1ej3A a.39.1.5 62930 1nijA 318 1.05e+01 c.37.1.10 85741 d.237.1.1 85742 1b4cA 92 1.09e+01 1b4cA a.39.1.2 17169 3fisA 98 1.10e+01 1fipA unknown_sccs 18994 1cmiA 85 1.12e+01 1cmiA d.39.1.1 38551 1f4qA 165 1.12e+01 1alvA a.39.1.8 17360 1ggzA 148 1.12e+01 a.39.1.5 70176 1rb9 53 1.16e+01 1rb9 g.41.5.1 45214 1qz8A 113 1.16e+01 unknown_sccs -4264 1r89A 437 1.16e+01 unknown_sccs -1147 unknown_sccs -9801 unknown_sccs -10061 1g2fC 90 1.17e+01 k.12.1.1 60222 1id0A 152 1.18e+01 d.122.1.3 66111 1pb6A 212 1.18e+01 a.4.1.9 88017 a.121.1.1 88018 1uc2A 481 1.18e+01 unknown_sccs -11725 1nddD 76 1.19e+01 1ubi d.15.1.1 37602 1i37A 260 1.19e+01 1a28A a.123.1.1 61583 1ovaA 386 1.19e+01 1ovaA e.1.1.1 42619 1jeyB 565 1.21e+01 1jeqB unknown_sccs -4431 unknown_sccs -7995 1cuk 203 1.22e+01 1hjp a.5.1.1 16273 a.60.2.1 17946 b.40.4.2 25265 2f5bH 235 1.24e+01 b.1.1.1 88506 b.1.1.2 88507 1s9pA 227 1.28e+01 1mzbA 136 1.29e+01 unknown_sccs -266 1b5pA 385 1.30e+01 c.67.1.1 -8133 8rxnA 52 1.32e+01 1rb9 g.41.5.1 45215 1f0jA 377 1.33e+01 1f0jA a.125.1.1 19346 1jwhC 215 1.34e+01 g.41.4.1 71915 1b06A 210 1.37e+01 1avmA a.2.11.1 15740 d.44.1.1 38737 1kk1A 410 1.38e+01 b.43.3.1 72634 b.44.1.1 72635 c.37.1.8 72636 1o13A 136 1.38e+01 c.55.5.1 80762 1mijA 152 1.38e+01 a.4.1.1 79150 2ifeA 100 1.41e+01 1tig d.68.1.1 39567 1fc6A 388 1.43e+01 1fc6A b.36.1.3 64738 c.14.1.2 64739 1iml 76 1.44e+01 1iml g.39.1.3 45145 g.39.1.3 45146 1k94A 165 1.45e+01 a.39.1.8 68333 1bjwA 382 1.51e+01 1bjwA c.67.1.1 34349 1bksB 397 1.52e+01 2tysB c.79.1.1 35285 1szqA 483 1.57e+01 unknown_sccs -11791 1dp7P 76 1.57e+01 1dp7P a.4.5.20 16159 1zbdB 134 1.58e+01 1zbdB g.50.1.1 45359 1dt6A 473 1.58e+01 1dt6A a.104.1.1 18977 1nc8 29 1.59e+01 g.40.1.1 45170 1zac 90 1.59e+01 1ncx a.39.1.5 17236 1pl8A 356 1.60e+01 b.35.1.2 -3716 c.2.1.1 -5740 1uetA 437 1.61e+01 unknown_sccs -1144 unknown_sccs -9798 unknown_sccs -10058 1n1jA 93 1.63e+01 a.22.1.3 79813 1e5pA 151 1.63e+01 1bj7 b.60.1.1 59272 1fpzA 212 1.74e+01 1fpzA c.45.1.1 59976 1aw7A 194 1.74e+01 1aw7A b.40.2.2 25164 d.15.6.1 37753 3rnt 104 1.78e+01 9rnt d.1.1.4 36069 1h3gA 601 1.78e+01 b.1.18.2 -2725 b.71.1.1 -4653 c.1.8.1 -5277 1iro 54 1.80e+01 1rb9 g.41.5.1 45223 1s72Z 73 1.83e+01 1jrrA 382 1.86e+01 e.1.1.1 63256 1xypA 190 1.88e+01 1axkA b.29.1.11 24327 1enxA 190 1.90e+01 1axkA b.29.1.11 24325 1j1vA 94 1.91e+01 a.4.12.2 83981 1r8sE 203 1.95e+01 a.118.3.1 -1579 1vapA 123 2.01e+01 1poa a.133.1.2 19548 1bgp 309 2.01e+01 1bgp a.93.1.1 18690 1jeqB 565 2.02e+01 1jeqB unknown_sccs -4432 unknown_sccs -7996 1ohuA 175 2.02e+01 f.1.4.1 -12058 1oniA 137 2.02e+01 d.79.1.1 87144 1gvmA 136 2.06e+01 b.109.1.1 70612 1pv5A 264 2.06e+01 unknown_sccs -10182 1pft 50 2.07e+01 1pft g.41.3.1 45206 1g8lA 411 2.09e+01 1g8lA b.85.6.1 60365 b.103.1.1 60366 c.57.1.2 60367 9rnt 104 2.10e+01 9rnt d.1.1.4 36055 1n6bA 473 2.11e+01 a.104.1.1 85359 1e6fA 143 2.12e+01 1e6fA b.64.1.1 59304 1ithA 141 2.21e+01 1ithA a.1.1.2 15623 1o5zA 442 2.21e+01 c.59.1.2 -7939 c.72.2.2 -8418 1nr6A 473 2.21e+01 a.104.1.1 -1464 1uhgA 385 2.22e+01 e.1.1.1 88491 1sh0A 510 2.24e+01 e.8.1.4 -11949 1gp0A 143 2.26e+01 b.64.1.1 70300 1i0vA 104 2.34e+01 9rnt d.1.1.4 36054 1dvh 79 2.38e+01 1c53 a.3.1.1 15802 1h09A 338 2.42e+01 b.109.1.1 83420 c.1.8.8 83421 1izcA 339 2.45e+01 c.1.12.5 83838 1iv8A 720 2.45e+01 b.71.1.1 76842 c.1.8.1 76843 1bf8 205 2.46e+01 1qpxA b.1.11.1 22332 b.7.2.1 23214 1v9kA 228 2.47e+01 1huuA 90 2.50e+01 1huuA a.55.1.1 17897 1gy6A 127 2.50e+01 d.17.4.2 70736 1op3H 225 2.51e+01 b.1.1.1 87208 b.1.1.2 87209 1oxsC 353 2.53e+01 b.40.6.3 87519 c.37.1.12 87520 1tfi 50 2.58e+01 1tfi g.41.3.1 45204 1d8dA 377 2.60e+01 1ft1A a.118.6.1 19185 1mho 88 2.60e+01 1b4cA a.39.1.2 17171 1f3cA 89 2.65e+01 1cmiA d.39.1.1 38557 1hcxA 127 2.65e+01 b.109.1.1 65800 1mtpA 323 2.69e+01 e.1.1.1 85107 1lwyA 324 2.74e+01 a.96.1.3 78285 d.129.1.2 78286 1b47A 304 2.76e+01 2cblA a.39.1.7 17381 a.48.1.1 17775 d.93.1.1 40529 1nzjA 298 2.81e+01 c.26.1.1 -6600 1cll 148 2.81e+01 1cll a.39.1.5 17263 1k8uA 90 2.85e+01 a.39.1.2 72181 1s96A 219 2.89e+01 c.37.1.1 -6972 1g87A 614 2.89e+01 a.102.1.2 83275 b.2.2.2 83276 3cln 148 2.90e+01 1cll a.39.1.5 17286 8fabB 224 2.92e+01 1igtB b.1.1.1 19773 b.1.1.2 20883 1p3jA 217 2.92e+01 c.37.1.1 -6996 g.41.2.1 -12769 1qbqA 333 3.02e+01 1ft1A a.118.6.1 19187 1m3qA 317 3.02e+01 a.96.1.3 -1288 d.129.1.2 -11006 1mugA 168 3.05e+01 1mugA c.18.1.2 31030 1far 52 3.07e+01 1far g.49.1.1 45351 1q1aA 289 3.10e+01 c.31.1.5 -6781 1el4A 195 3.14e+01 1ej3A a.39.1.5 59453 1jb2A 127 3.17e+01 d.17.4.2 71624 1owfA 99 3.20e+01 a.55.1.1 87487 1h1aA 191 3.21e+01 b.29.1.11 83450 1gc1H 229 3.23e+01 1gc1H b.1.1.1 20265 b.1.1.2 21265 1b5eA 246 3.25e+01 1b5eA d.117.1.1 41056 1jfkA 134 3.25e+01 a.39.1.5 66639 2cblA 305 3.28e+01 2cblA a.39.1.7 17380 a.48.1.1 17774 d.93.1.1 40528 1hmcA 148 3.35e+01 1hmcB a.26.1.2 16867 1c0aA 585 3.40e+01 1c0aA b.40.4.1 25246 d.74.4.1 39731 d.104.1.1 40767 1vjnA 220 3.42e+01 unknown_sccs -11458 1qyp 57 3.43e+01 1qyp g.41.3.1 45205 1bx4A 345 3.45e+01 1bx4A c.72.1.1 34935 1jlnA 297 3.48e+01 1pty c.45.1.2 63172 1hmcB 148 3.49e+01 1hmcB a.26.1.2 16868 1jcrA 377 3.49e+01 a.118.6.1 66506 1psrA 100 3.50e+01 1psrA a.39.1.2 17180 1bm9A 122 3.56e+01 1bm9A a.4.5.7 16116 1eo1A 124 3.57e+01 1eo1A c.55.5.1 33739 1ihfA 99 3.57e+01 1huuA a.55.1.1 17893 1vdrA 162 3.61e+01 1vdrA c.71.1.1 34893 1bt0A 76 3.62e+01 1ubi d.15.1.1 37607 1h4lD 147 3.63e+01 a.74.1.1 70873 2tysB 397 3.68e+01 2tysB c.79.1.1 35272 1vavA 222 3.71e+01 1f83A 425 3.92e+01 1f82A d.92.1.7 40306 1dvkA 173 3.98e+01 1dvkA a.72.1.1 18319