# 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 1nb8A 353 2.70e-48 d.3.1.9 80385 1nseA 444 3.31e-03 1nseA d.174.1.1 42534 1d0cA 444 3.49e-03 d.174.1.1 64769 1d1vA 444 3.52e-03 1nseA d.174.1.1 59101 1hleA 345 3.90e-03 1ovaA e.1.1.1 42618 1ed5A 444 5.16e-03 1nseA d.174.1.1 42530 5nseA 444 6.44e-03 d.174.1.1 74644 1ogwA 76 3.73e-02 d.15.1.1 87001 1d3zA 76 3.82e-02 1ubi d.15.1.1 37592 1ubq 76 4.14e-02 1ubi d.15.1.1 37585 1ubi 76 4.23e-02 1ubi d.15.1.1 37584 1gvhA 396 9.00e-02 a.1.1.2 70601 b.43.4.2 70602 c.25.1.5 70603 1osa 148 1.66e-01 1cll a.39.1.5 17300 1l5wA 796 2.05e-01 c.87.1.4 73605 1exrA 148 2.63e-01 1cll a.39.1.5 17299 1mdaH 368 2.66e-01 2bbkH b.69.2.1 27637 1gnc 178 2.73e-01 1bgc a.26.1.1 16821 1clqA 903 4.42e-01 1clqA c.55.3.5 33717 e.8.1.1 43006 1ksfX 758 4.84e-01 a.174.1.1 77522 c.37.1.20 77523 c.37.1.20 77524 1ih7A 903 4.85e-01 1clqA c.55.3.5 62375 e.8.1.1 62376 1lm8B 118 5.88e-01 d.15.1.1 74033 1vcbA 118 6.20e-01 1vcbA d.15.1.1 37603 1b9rA 105 7.02e-01 1ayfA d.15.4.1 37683 1jqnA 883 7.45e-01 c.1.12.3 77159 1fiy 883 7.65e-01 1fiy c.1.12.3 29307 1ngvA 534 7.67e-01 c.111.1.2 85698 1cqxA 403 7.94e-01 1cqxA a.1.1.2 15635 b.43.4.2 25667 c.25.1.5 31562 1qb4A 883 8.93e-01 c.1.12.3 74640 1uurA 473 8.98e-01 a.47.1.1 -968 b.2.5.5 -2904 d.93.1.1 -10632 9apiA 347 9.12e-01 1ovaA e.1.1.1 42630 1kk1A 410 9.33e-01 b.43.3.1 72634 b.44.1.1 72635 c.37.1.8 72636 1iybA 208 1.05e+00 d.124.1.1 -10977 1cd9C 175 1.11e+00 1bgc a.26.1.1 16816 1b4cA 92 1.13e+00 1b4cA a.39.1.2 17169 1eg3A 261 1.20e+00 1eg3A a.39.1.7 17376 a.39.1.7 17377 b.72.1.1 27805 1hc7A 477 1.23e+00 1hc7A c.51.1.1 60938 d.68.5.1 60940 d.104.1.1 60939 1hkfA 122 1.27e+00 b.1.1.1 83553 1k6kA 143 1.33e+00 a.174.1.1 77274 1ahpA 797 1.41e+00 1a8i c.87.1.4 35544 1g87A 614 1.43e+00 a.102.1.2 83275 b.2.2.2 83276 1ts3A 194 1.45e+00 1aw7A b.40.2.2 25168 d.15.6.1 37757 1gm5A 780 1.55e+00 unknown_sccs 65298 b.40.4.9 65299 c.37.1.19 65300 c.37.1.19 65301 1sqgA 429 1.69e+00 1fnnA 389 1.72e+00 1fnnA a.4.5.11 16129 c.37.1.20 32426 1a81A 254 1.82e+00 1a81A d.93.1.1 40507 d.93.1.1 40508 1f0cA 305 1.88e+00 1c8oA e.1.1.1 42676 1om4A 422 1.98e+00 d.174.1.1 87067 1oxsC 353 2.21e+00 b.40.6.3 87519 c.37.1.12 87520 1id0A 152 2.33e+00 d.122.1.3 66111 1mtpA 323 2.52e+00 e.1.1.1 85107 1dlc 584 2.61e+00 1ciy b.18.1.3 23719 b.77.2.1 27976 f.1.3.1 43391 1oxxK 353 2.67e+00 b.40.6.3 -3969 c.37.1.12 -7187 1hjp 203 2.71e+00 1hjp a.5.1.1 16274 a.60.2.1 17947 b.40.4.2 25266 1jrrA 382 2.76e+00 e.1.1.1 63256 1nddA 76 2.86e+00 1ubi d.15.1.1 37599 1nijA 318 2.95e+00 c.37.1.10 85741 d.237.1.1 85742 1dixA 208 2.97e+00 1bk7A d.124.1.1 41122 1as4A 341 3.16e+00 1sek e.1.1.1 42623 1f83A 425 3.17e+00 1f82A d.92.1.7 40306 1bt0A 76 3.48e+00 1ubi d.15.1.1 37607 1nddD 76 3.87e+00 1ubi d.15.1.1 37602 1sva1 361 3.87e+00 1vpsA 1n62A 166 3.95e+00 a.56.1.1 80090 d.15.4.2 80091 1avsA 90 4.02e+00 1cll a.39.1.5 17226 2cblA 305 4.17e+00 2cblA a.39.1.7 17380 a.48.1.1 17774 d.93.1.1 40528 1mi1A 414 4.22e+00 a.169.1.1 79137 b.55.1.6 79138 1qj2A 166 4.36e+00 1qj2A 1h3nA 878 4.39e+00 a.27.1.1 76641 b.51.1.1 76642 c.26.1.1 76643 1dbhA 354 4.90e+00 1awe a.87.1.1 18514 b.55.1.1 26967 1f82A 424 5.01e+00 1f82A d.92.1.7 40307 1uhgA 385 5.21e+00 e.1.1.1 88491 1jnyA 435 5.25e+00 b.43.3.1 66982 b.44.1.1 66983 c.37.1.8 66984 1c8gA 548 5.33e+00 2cas b.121.5.2 23380 1ovaA 386 5.34e+00 1ovaA e.1.1.1 42619 2cas 548 5.35e+00 2cas b.121.5.2 23376 1bgeB 175 5.53e+00 1bgc a.26.1.1 16824 3nodB 423 5.57e+00 1nseA d.174.1.1 42513 1qwyA 291 5.62e+00 unknown_sccs -5023 1h09A 338 6.04e+00 b.109.1.1 83420 c.1.8.8 83421 1qxfA 66 6.19e+00 g.41.8.4 -12822 1pa7A 130 6.37e+00 a.40.1.1 -896 1szqA 483 6.52e+00 unknown_sccs -11791 1foeA 377 6.99e+00 1foeA a.87.1.1 18517 b.55.1.1 26969 1b47A 304 7.15e+00 2cblA a.39.1.7 17381 a.48.1.1 17775 d.93.1.1 40529 1lla 628 7.29e+00 1lla a.85.1.1 18485 a.86.1.1 18496 b.1.18.3 21861 1rdg 53 8.12e+00 1rb9 g.41.5.1 45221 1o1fC 147 8.14e+00 i.15.1.1 80997 1k4nA 192 8.38e+00 d.32.1.5 72059 1ktaA 365 8.72e+00 e.17.1.1 77533 1vh4A 435 9.15e+00 unknown_sccs -4794 1pb6A 212 9.18e+00 a.4.1.9 88017 a.121.1.1 88018 1jjoC 261 9.43e+00 1v3eA 431 1.00e+01 b.68.1.1 -4584 1kfuS 184 1.04e+01 a.39.1.8 68574 1nvhA 66 1.05e+01 1r6fA 310 1.06e+01 unknown_sccs -11804 1ltlA 279 1.08e+01 b.40.4.11 84701 1a7cA 379 1.11e+01 1sek e.1.1.1 42660 1ekfA 365 1.14e+01 1ekfA e.17.1.1 59445 1cc1L 498 1.16e+01 1h2rL e.18.1.1 43301 1q1aA 289 1.17e+01 c.31.1.5 -6781 1b5pA 385 1.24e+01 c.67.1.1 -8133 1bq8A 54 1.25e+01 1rb9 g.41.5.1 45237 1bq9A 54 1.25e+01 1rb9 g.41.5.1 45238 1qxyA 252 1.25e+01 d.127.1.1 -10993 1kt8A 365 1.26e+01 e.17.1.1 77531 1s9pA 227 1.26e+01 1cuk 203 1.27e+01 1hjp a.5.1.1 16273 a.60.2.1 17946 b.40.4.2 25265 1s0uA 408 1.28e+01 b.43.3.1 -4053 b.44.1.1 -4061 c.37.1.8 -7096 1ki1B 352 1.31e+01 a.87.1.1 72497 b.55.1.1 72498 1brfA 53 1.32e+01 1rb9 g.41.5.1 45236 1i7hA 111 1.41e+01 d.15.4.1 71122 1jbuH 254 1.41e+01 5ptp b.47.1.2 62856 1onqA 283 1.43e+01 b.1.1.2 -2640 d.19.1.1 -9390 1cll 148 1.48e+01 1cll a.39.1.5 17263 1top 162 1.48e+01 1ncx a.39.1.5 17223 1r8sE 203 1.48e+01 a.118.3.1 -1579 1jlnA 297 1.48e+01 1pty c.45.1.2 63172 1bgp 309 1.54e+01 1bgp a.93.1.1 18690 1oygA 447 1.55e+01 unknown_sccs -4549 1mijA 152 1.59e+01 a.4.1.1 79150 1ncx 162 1.59e+01 1ncx a.39.1.5 17222 1q2wA 308 1.62e+01 b.47.1.4 88355 4dpvZ 584 1.63e+01 2cas b.121.5.2 23377 1j8uA 325 1.65e+01 d.178.1.1 71611 1c8oA 300 1.66e+01 1c8oA e.1.1.1 42677 1sh0A 510 1.66e+01 e.8.1.4 -11949 1knaA 69 1.71e+01 b.34.13.2 72771 2pia 321 1.73e+01 2pia b.43.4.2 25663 c.25.1.2 31553 d.15.4.2 37704 1ngkA 128 1.75e+01 a.1.1.1 85673 1bgc 174 1.76e+01 1bgc a.26.1.1 16822 1f2eA 201 1.79e+01 1a0fA a.45.1.1 17745 c.47.1.5 33039 1cii 602 1.80e+01 1cii f.1.1.1 43381 h.4.3.1 45787 1jf2A 195 1.80e+01 1ej3A a.39.1.5 62930 1k9uA 78 1.81e+01 a.39.1.10 84348 1ipiA 123 1.90e+01 c.52.1.18 66255 1lkoA 191 1.93e+01 a.25.1.1 78063 g.41.5.1 78064 1qubA 319 1.94e+01 1qubA g.18.1.1 44863 g.18.1.1 44864 g.18.1.1 44865 g.18.1.1 44866 g.18.1.1 44867 1qlpA 394 1.95e+01 1ovaA e.1.1.1 42628 1mjhB 162 1.96e+01 1mjhA c.26.2.4 31640 1gc1H 229 1.98e+01 1gc1H b.1.1.1 20265 b.1.1.2 21265 1mho 88 2.00e+01 1b4cA a.39.1.2 17171 1fpzA 212 2.01e+01 1fpzA c.45.1.1 59976 1bjwA 382 2.02e+01 1bjwA c.67.1.1 34349 1qhhA 167 2.04e+01 1pjr c.37.1.19 32393 1ggzA 148 2.04e+01 a.39.1.5 70176 1ryt 190 2.07e+01 1ryt a.25.1.1 16646 g.41.5.1 45245 1vjoA 393 2.07e+01 c.67.1.3 -8173 1gefA 123 2.10e+01 1gefA c.52.1.18 60465 1dvbA 191 2.17e+01 1ryt a.25.1.1 16645 g.41.5.1 45244 2masA 314 2.18e+01 2masA c.70.1.1 34810 1b71A 191 2.18e+01 1ryt a.25.1.1 16647 g.41.5.1 45246 1khvA 516 2.21e+01 e.8.1.4 68627 1bmlC 362 2.22e+01 1bmlC d.15.5.1 37729 d.15.5.1 37730 d.15.5.1 37731 1fzaB 328 2.23e+01 3fib d.171.1.1 42480 h.1.8.1 45621 1ift 263 2.23e+01 1mrj d.165.1.1 42211 1a0p 290 2.25e+01 1a0p a.60.9.1 18105 d.163.1.1 42165 1a8h 500 2.25e+01 1a8h a.27.1.1 16922 c.26.1.1 31589 1eijA 80 2.30e+01 1eijA a.5.6.1 16298 1jr7A 311 2.31e+01 b.82.2.3 63255 1k07A 263 2.33e+01 d.157.1.1 77218 1mg7A 417 2.34e+01 d.14.1.6 84954 d.58.26.6 84955 1aca 86 2.35e+01 1aca a.11.1.1 16367 1hmcB 148 2.36e+01 1hmcB a.26.1.2 16868 1bf5A 545 2.36e+01 1bg1A a.47.1.1 17766 b.2.5.5 22460 d.93.1.1 40526 1j55A 95 2.37e+01 a.39.1.2 77078 1euvB 86 2.40e+01 1a5r d.15.1.1 37598 1aw7A 194 2.40e+01 1aw7A b.40.2.2 25164 d.15.6.1 37753 1k28D 391 2.40e+01 b.106.1.1 68052 b.106.1.1 68053 3cln 148 2.42e+01 1cll a.39.1.5 17286 2hgsA 474 2.45e+01 2hgsA c.30.1.4 31722 d.142.1.6 75997 1fjgQ 105 2.46e+01 1fjfQ b.40.4.5 25352 1sjwA 144 2.46e+01 unknown_sccs -9296 1huuA 90 2.46e+01 1huuA a.55.1.1 17897 1vk6A 269 2.52e+01 unknown_sccs -10923 unknown_sccs -10924 1ht9A 76 2.56e+01 4icb a.39.1.1 61252 1nzjA 298 2.58e+01 c.26.1.1 -6600 1jmtA 104 2.65e+01 d.58.7.3 63180 1iml 76 2.70e+01 1iml g.39.1.3 45145 g.39.1.3 45146 1s6cA 183 2.72e+01 a.39.1.5 -858 1ig3A 263 2.75e+01 1ig3A b.82.6.1 62358 c.100.1.1 62359 1lfdA 87 2.75e+01 1lfdA d.15.1.5 37622 1gp0A 143 2.80e+01 b.64.1.1 70300 1sek 378 2.85e+01 1sek e.1.1.1 42675 2ng1 293 2.88e+01 1ng1 a.24.13.1 16962 c.37.1.10 32273 1mp8A 281 2.91e+01 d.144.1.7 -11361 1v9kA 228 2.95e+01 1hmcA 148 2.99e+01 1hmcB a.26.1.2 16867 1rypK 198 3.03e+01 d.153.1.4 41879 1rtxA 123 3.09e+01 a.1.1.1 -3 1alvA 173 3.10e+01 1alvA a.39.1.8 17370 1gaxA 862 3.11e+01 1gaxA a.2.7.3 75842 a.27.1.1 75843 b.51.1.1 26893 c.26.1.1 31595 1uetA 437 3.17e+01 unknown_sccs -1144 unknown_sccs -9798 unknown_sccs -10058 1op0A 234 3.18e+01 1ysc 421 3.19e+01 1ivyA c.69.1.5 34652 1n0xH 230 3.22e+01 b.1.1.1 -2201 b.1.1.2 -2473 1el4A 195 3.24e+01 1ej3A a.39.1.5 59453 1qwkA 317 3.26e+01 c.1.7.1 -5237 1nrfA 262 3.26e+01 e.3.1.1 -11780 1mlvA 444 3.28e+01 a.166.1.1 79283 b.85.7.3 79284 1uctA 218 3.30e+01 b.1.1.4 88467 b.1.1.4 88468 1kmiZ 214 3.31e+01 h.4.11.1 72752 1fvuB 125 3.33e+01 1ixxB d.169.1.1 42346 1paqA 189 3.33e+01 unknown_sccs -1557 3bct 457 3.34e+01 3bct a.118.1.1 19112 2f5bH 235 3.38e+01 b.1.1.1 88506 b.1.1.2 88507 1rzfH 235 3.39e+01 b.1.1.1 -2188 b.1.1.2 -2453 2arcB 164 3.41e+01 2arcA b.82.4.1 28149 1fc6A 388 3.41e+01 1fc6A b.36.1.3 64738 c.14.1.2 64739 1ospO 257 3.42e+01 1ospO b.76.1.1 27971 1l1oC 181 3.46e+01 b.40.4.3 73480 1e6fA 143 3.47e+01 1e6fA b.64.1.1 59304 1ohuA 175 3.47e+01 f.1.4.1 -12058 1cmiA 85 3.50e+01 1cmiA d.39.1.1 38551 1jofA 365 3.55e+01 b.69.10.1 71775 1hb6A 86 3.59e+01 a.11.1.1 70959 1v54C 261 3.69e+01 f.25.1.1 -12239 1hgxA 183 3.71e+01 1tc1A c.61.1.1 34027 1nd7A 374 3.71e+01 d.148.1.1 -11394 4pah 308 3.72e+01 4pah d.178.1.1 42576 1jeyB 565 3.73e+01 1jeqB unknown_sccs -4431 unknown_sccs -7995 1qf8A 182 3.75e+01 1qf8A g.41.4.1 45212 1pah 308 3.81e+01 4pah d.178.1.1 42578 1ig5A 75 3.85e+01 4icb a.39.1.1 62363 2dvh 79 3.86e+01 1c53 a.3.1.1 15803 1jfkA 134 3.86e+01 a.39.1.5 66639 1a5r 103 3.88e+01 1a5r d.15.1.1 37597 1ihfA 99 3.89e+01 1huuA a.55.1.1 17893 8kme2 259 3.94e+01 1ucyE 1ha1 184 3.96e+01 1ha1 d.58.7.1 39147 d.58.7.1 39148 1lt3A 240 3.97e+01 1lt3A d.166.1.1 42230 1n1jA 93 3.99e+01 a.22.1.3 79813 1dipA 78 3.99e+01 1dipA h.1.12.1 45632 1mjhA 162 4.00e+01 1mjhA c.26.2.4 31639