# List of top-scoring protein chains for t2k-100-30-dssp-ehl2 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 1rxxA 421 2.60e-05 1jdw 423 2.97e-04 1jdw d.126.1.2 41129 1s9rA 410 9.83e-03 1lxyA 409 1.12e-02 1hv9A 456 8.30e-02 1fwyA b.81.1.4 28060 c.68.1.5 34518 1qjcA 158 1.56e-01 1b6tA c.26.1.3 63328 1fwyA 331 1.96e-01 1fwyA b.81.1.4 28064 c.68.1.5 34522 1fxjA 331 1.97e-01 1fwyA b.81.1.4 28062 c.68.1.5 34520 1b6tA 159 2.00e-01 1b6tA c.26.1.3 31600 1tdj 514 5.21e-01 1tdj c.79.1.1 35297 d.58.18.2 39356 d.58.18.2 39357 1ej6A 1289 7.25e-01 i.7.1.1 45967 1h70A 255 7.89e-01 1h70A d.126.1.3 60711 1bcpC 199 8.56e-01 1bcpB b.40.2.1 25121 d.169.1.2 42430 3pgk 416 8.62e-01 16pk c.86.1.1 35451 1fztA 211 9.55e-01 1qhfA c.60.1.1 60158 1q7zA 566 1.10e+00 1gqyA 475 1.34e+00 c.5.1.1 83305 c.59.1.1 83306 c.72.2.1 83307 1vhwA 253 1.53e+00 1p3dA 475 1.63e+00 c.5.1.1 87728 c.59.1.1 87729 c.72.2.1 87730 1egzA 291 1.66e+00 7a3hA c.1.8.3 28828 1fzrA 138 1.66e+00 1fzrA c.52.1.17 33336 1hqcA 324 2.12e+00 1hqcA a.4.5.11 16127 c.37.1.20 32424 1bs0A 384 2.18e+00 1bs0A c.67.1.4 34490 1o6zA 303 2.39e+00 c.2.1.5 81107 d.162.1.1 81108 1m0dA 138 2.60e+00 c.52.1.17 74354 1g61A 228 2.65e+00 1g61A d.126.1.1 41126 1rzjG 321 2.66e+00 1nnmA 652 2.70e+00 1pg4A 652 2.70e+00 e.23.1.1 88067 1hlrA 907 2.80e+00 a.56.1.1 65850 d.15.4.2 65851 d.41.1.1 65852 d.133.1.1 65853 1o8bA 219 2.83e+00 c.35.1.2 81180 d.58.40.1 81181 1q33A 292 2.94e+00 1vhrA 184 3.09e+00 1vhrA c.45.1.1 32651 1ks2A 219 3.38e+00 c.35.1.2 72908 d.58.40.1 72909 1kk9A 221 3.55e+00 d.115.1.1 77432 1msc 129 3.67e+00 1msc d.85.1.1 40039 1heiA 451 3.72e+00 1heiA c.37.1.14 32463 c.37.1.14 32464 1gd9A 389 3.88e+00 c.67.1.1 60454 8ohm 435 4.02e+00 1heiA c.37.1.14 32469 c.37.1.14 32470 4bcl 366 4.13e+00 4bcl b.75.1.1 27968 1g9mG 321 4.21e+00 1gc1G d.172.1.1 42492 1b6sA 355 4.26e+00 1b6rA b.84.2.1 28242 c.30.1.1 31649 d.142.1.2 41494 1ot5A 477 4.35e+00 b.18.1.20 87409 c.41.1.1 87410 1kutA 230 4.36e+00 d.143.1.1 73017 1iv8A 720 4.38e+00 b.71.1.1 76842 c.1.8.1 76843 1fbtA 190 4.40e+00 1bif c.60.1.4 34004 1gc1G 321 4.57e+00 1gc1G d.172.1.1 42493 1pbgA 468 4.68e+00 1e70M c.1.8.4 28946 1dgjA 907 4.70e+00 1alo a.56.1.1 17909 d.15.4.2 37694 d.41.1.1 38585 d.133.1.1 41415 1nipA 289 4.75e+00 1cp2A c.37.1.10 32263 1lkzA 219 4.89e+00 c.35.1.2 73991 d.58.40.1 73992 1qo0D 196 4.95e+00 1qo0D c.23.1.3 31125 1obfO 335 4.96e+00 c.2.1.3 86768 d.81.1.1 86769 1eqnA 321 5.31e+00 1dd9A e.13.1.1 43256 1qvjA 292 5.32e+00 1bif 469 5.38e+00 1bif c.37.1.7 31961 c.60.1.4 34003 1dpgA 485 5.73e+00 1dpgA c.2.1.3 30074 d.81.1.5 39989 1ivd 388 5.81e+00 2qwc b.68.1.1 27568 1gdeA 389 6.08e+00 c.67.1.1 60456 1qgvA 142 6.25e+00 1qgvA c.47.1.8 33056 1hkcA 917 6.48e+00 1qhaA c.55.1.3 33475 c.55.1.3 33476 c.55.1.3 33477 c.55.1.3 33478 1r64A 481 6.49e+00 1ijgA 309 6.66e+00 1fouA e.27.1.1 62493 2dpg 485 6.82e+00 1dpgA c.2.1.3 30076 d.81.1.5 39991 1ji8A 111 6.84e+00 d.203.1.1 66733 1hkbA 917 7.05e+00 1qhaA c.55.1.3 33479 c.55.1.3 33480 c.55.1.3 33481 c.55.1.3 33482 1k7jA 206 7.20e+00 d.115.1.1 72103 1e19A 314 7.35e+00 1b7bA c.73.1.1 34967 1pk9A 237 7.46e+00 1ecpA 238 8.07e+00 1ecpA c.56.2.1 33775 1hdoA 206 8.12e+00 1he2A c.2.1.2 60965 1hrnA 337 8.12e+00 1smrA b.50.1.2 26869 1ad1A 266 8.15e+00 1aj2 c.1.21.1 29668 1nnlA 225 8.40e+00 c.108.1.4 85906 1b7fA 168 8.42e+00 1b7fA d.58.7.1 39169 d.58.7.1 39170 1f6dA 376 8.87e+00 1f6dA c.87.1.3 35467 1uu1A 335 8.98e+00 1fp6A 289 9.10e+00 1cp2A c.37.1.10 32243 1914 232 9.30e+00 1914 d.49.1.1 83028 d.49.1.1 83029 1vgvA 384 9.45e+00 1bg6 359 9.69e+00 1bg6 a.100.1.5 18810 c.2.1.6 30214 7at1B 154 9.70e+00 8atcB d.58.2.1 39053 g.41.7.1 45305 1k9sA 237 9.86e+00 c.56.2.1 68359 1fc4A 401 9.91e+00 1bs0A c.67.1.4 59760 2bifA 469 1.02e+01 1bif c.37.1.7 31963 c.60.1.4 34009 1mzhA 225 1.03e+01 c.1.10.1 79698 1f3rB 257 1.07e+01 1f3rB b.1.1.1 20417 b.1.1.1 20416 3bifA 468 1.07e+01 1bif c.37.1.7 31962 c.60.1.4 34008 1ivg 388 1.08e+01 2qwc b.68.1.1 27578 8atcB 154 1.11e+01 8atcB d.58.2.1 39027 g.41.7.1 45279 1qp8A 303 1.13e+01 1qp8A c.2.1.4 30092 c.23.12.1 31352 1n7hA 381 1.14e+01 c.2.1.2 80250 1dqaC 467 1.15e+01 1dqaA d.58.20.1 39366 d.179.1.1 42587 1dqaA 467 1.15e+01 1dqaA d.58.20.1 39364 d.179.1.1 42585 1qhaA 917 1.16e+01 1qhaA c.55.1.3 33467 c.55.1.3 33468 c.55.1.3 33469 c.55.1.3 33470 1q77A 138 1.21e+01 1pz1A 333 1.25e+01 1hw8A 467 1.26e+01 1dqaA d.58.20.1 61298 d.179.1.1 61299 1kzhA 555 1.34e+01 c.89.1.1 73361 1jr3E 334 1.34e+01 a.80.1.1 63253 c.37.1.20 63254 1e58A 249 1.37e+01 1qhfA c.60.1.1 59262 1b6rA 355 1.38e+01 1b6rA b.84.2.1 28241 c.30.1.1 31648 d.142.1.2 41493 1dd9A 338 1.42e+01 1dd9A e.13.1.1 43254 1n99A 166 1.42e+01 b.36.1.1 85459 b.36.1.1 85460 1j7iA 264 1.48e+01 1j7iA d.144.1.6 62694 1cf9A 753 1.50e+01 1cf9A c.23.16.3 31441 e.5.1.1 42815 1czaN 917 1.52e+01 1qhaA c.55.1.3 33463 c.55.1.3 33464 c.55.1.3 33465 c.55.1.3 33466 1i5gA 144 1.62e+01 1ewxA c.47.1.10 61784 1riqA 465 1.65e+01 1swuA 127 1.65e+01 1swuA b.61.1.1 27230 1o60A 292 1.68e+01 1dkuA 317 1.71e+01 1dkuA c.61.1.2 34118 c.61.1.2 34119 1ckmA 330 1.72e+01 1ckmA b.40.4.6 25358 d.142.2.3 41585 1he2A 206 1.74e+01 1he2A c.2.1.2 60966 1nngA 153 1.75e+01 1g6sA 427 1.76e+01 1eps d.68.2.2 39584 1d09B 153 1.82e+01 8atcB d.58.2.1 39015 g.41.7.1 45267 1hd2A 161 1.83e+01 c.47.1.10 60962 1mopA 300 1.83e+01 c.26.1.4 85035 1n2eA 300 1.83e+01 c.26.1.4 85268 1f74A 293 1.86e+01 1nal3 c.1.10.1 29079 1euvA 221 1.91e+01 1euvA d.3.1.7 37133 1dljA 402 1.92e+01 1dliA a.100.1.4 18808 c.2.1.6 30212 c.26.3.1 31621 1azo 232 1.92e+01 1azo c.52.1.14 33329 1fcdA 401 1.93e+01 1fcdA c.3.1.5 30593 c.3.1.5 30594 d.87.1.1 40218 1ng4A 390 1.95e+01 c.3.1.2 85666 d.16.1.3 85667 2ms2A 129 1.95e+01 1msc d.85.1.1 40049 1s14A 194 1.97e+01 1h09A 338 1.98e+01 b.109.1.1 83420 c.1.8.8 83421 1jubA 311 2.01e+01 2trxA 108 2.02e+01 1thx c.47.1.1 32719 1qr7A 350 2.03e+01 1qr7A c.1.10.4 29191 1ufhA 180 2.07e+01 d.108.1.1 88485 1ktbA 405 2.07e+01 b.71.1.1 72960 c.1.8.1 72961 1ctn 540 2.07e+01 1ctn b.1.18.2 21876 c.1.8.5 29005 d.26.3.1 38439 1eemA 241 2.08e+01 1eemA a.45.1.1 17717 c.47.1.5 33011 1cvjB 190 2.08e+01 1cvjB d.58.7.1 39193 d.58.7.1 39194 1ddeA 338 2.08e+01 1dd9A e.13.1.1 43255 1ag9A 175 2.09e+01 1rcf c.23.5.1 31178 1id0A 152 2.13e+01 d.122.1.3 66111 1cv2A 296 2.13e+01 1bn6A c.69.1.8 34680 1iz7A 295 2.14e+01 c.69.1.8 76982 1dliA 402 2.15e+01 1dliA a.100.1.4 18809 c.2.1.6 30213 c.26.3.1 31622 1gceA 364 2.19e+01 1gceA e.3.1.1 42738 1f6kA 293 2.19e+01 1nal3 c.1.10.1 29081 1dgkN 917 2.20e+01 1qhaA c.55.1.3 33487 c.55.1.3 33488 c.55.1.3 33489 c.55.1.3 33490 1hxs3 237 2.20e+01 1by2 119 2.27e+01 1by2 d.170.1.1 42452 3sxlA 184 2.30e+01 1b7fA d.58.7.1 39173 d.58.7.1 39174 1dorA 311 2.37e+01 2dorA c.1.4.1 28595 1vhxA 150 2.40e+01 1d6jA 211 2.41e+01 1d6jA c.37.1.4 31940 4uagA 437 2.42e+01 4uagA c.5.1.1 30651 c.59.1.1 33952 c.72.2.1 34955 1prtF 98 2.43e+01 1prtF b.40.2.1 25140 1b1cA 181 2.44e+01 1amoA c.23.5.2 31212 1k30A 368 2.46e+01 c.112.1.1 68067 1uag 437 2.47e+01 4uagA c.5.1.1 30653 c.59.1.1 33954 c.72.2.1 34957 1fxlA 167 2.54e+01 1b7fA d.58.7.1 39183 d.58.7.1 39184 1pvc3 238 2.54e+01 1aym3 1ogdA 131 2.55e+01 1aj0 282 2.55e+01 1aj2 c.1.21.1 29667 1rf6A 427 2.55e+01 1v4sA 455 2.56e+01 1diiC 80 2.57e+01 1diiC a.3.1.1 15925 1fqvA 336 2.62e+01 1fqvA a.158.1.1 19254 c.10.1.3 30856 3pbgA 468 2.63e+01 1e70M c.1.8.4 28951 1p80A 753 2.65e+01 1a5t 334 2.66e+01 1a5t a.80.1.1 18450 c.37.1.20 32423 1eza 259 2.66e+01 1zymA a.60.10.1 18113 c.8.1.2 30708 1qlwA 328 2.67e+01 1qlwA c.69.1.15 34722 1od6A 160 2.72e+01 c.26.1.3 86836 1luqA 127 2.73e+01 1dctA 324 2.74e+01 6mhtA c.66.1.26 34244 2dorA 311 2.74e+01 2dorA c.1.4.1 28593 1j7lA 264 2.75e+01 d.144.1.6 62697 3uagA 437 2.78e+01 4uagA c.5.1.1 30652 c.59.1.1 33953 c.72.2.1 34956 1cknA 330 2.79e+01 1ckmA b.40.4.6 25360 d.142.2.3 41587 1o6jA 150 2.84e+01 c.47.1.10 81089 1ilr1 152 2.88e+01 1irp 1m6dA 214 2.89e+01 d.3.1.1 84849 1fs0E 138 2.92e+01 1aqt a.2.10.1 59997 b.93.1.1 59998 1jbwA 428 2.92e+01 c.59.1.2 62860 c.72.2.2 62861 1auiA 521 2.99e+01 1auiA d.159.1.3 42085 1eps 427 2.99e+01 1eps d.68.2.2 39586 1bq3B 246 3.01e+01 1qhfA c.60.1.1 33979 1cw0A 155 3.01e+01 1vsrA c.52.1.15 33333 1onwA 390 3.03e+01 b.92.1.7 87172 c.1.9.13 87173 3bamB 213 3.07e+01 1bam c.52.1.3 33289 1a0cA 438 3.12e+01 1a0cA c.1.15.3 29529 1pvdA 537 3.14e+01 1zpdA c.31.1.3 31737 c.36.1.5 31777 c.36.1.9 31778 1otcB 260 3.14e+01 1otcB b.40.4.3 25310 1lngA 87 3.15e+01 d.201.1.1 74045 3bamA 213 3.17e+01 1bam c.52.1.3 33288 1psqA 163 3.18e+01 c.47.1.10 88283 1mdoA 393 3.18e+01 c.67.1.4 79013 1hxmD 242 3.21e+01 b.1.1.1 61373 b.1.1.2 61374 1yer 228 3.23e+01 1yer d.122.1.1 41101 1fh0A 221 3.23e+01 1cs8A d.3.1.1 59832 1gw9A 388 3.26e+01 c.1.15.3 70658 1mj5A 302 3.26e+01 1h3nA 878 3.27e+01 a.27.1.1 76641 b.51.1.1 76642 c.26.1.1 76643 1h5wA 309 3.31e+01 e.27.1.1 65635 1o0pA 104 3.32e+01 d.58.7.1 86535 1d3gA 367 3.32e+01 1d3gA c.1.4.1 28600 1i1qB 192 3.33e+01 1qdlB c.23.16.1 61544 2u1a 88 3.37e+01 2u1a d.58.7.1 39164 1g5pA 289 3.43e+01 1cp2A c.37.1.10 32253 1pydA 556 3.44e+01 1zpdA c.31.1.3 31735 c.36.1.5 31773 c.36.1.9 31774 1konA 249 3.48e+01 e.39.1.1 72823 1cdwA 179 3.49e+01 1ytbA d.129.1.1 41212 d.129.1.1 41213 1jeyA 609 3.52e+01 1jeqA e.31.1.1 62924 1uanA 227 3.53e+01 1v93A 296 3.53e+01 1aye 401 3.55e+01 1aye c.56.5.1 33824 d.58.3.1 39065 2scuB 388 3.59e+01 2scuB c.23.4.1 31141 d.142.1.4 41562 1bam 213 3.61e+01 1bam c.52.1.3 33285 2izhB 123 3.66e+01 1swuA b.61.1.1 27234 2izgB 123 3.66e+01 1swuA b.61.1.1 27236 1lnsA 763 3.67e+01 a.40.2.1 78101 b.18.1.13 78102 c.69.1.21 78103 1k77A 260 3.73e+01 c.1.15.5 72096 1ionA 243 3.75e+01 c.37.1.10 62633 1nw1A 429 3.77e+01 d.144.1.8 86286 1p9qC 256 3.77e+01 1ocnA 362 3.77e+01 c.6.1.1 86808 1jbkA 195 3.82e+01 c.37.1.20 71631 2xis 387 3.86e+01 4xis c.1.15.3 29427 2bvwA 362 3.87e+01 1bvwA c.6.1.1 30666 1o8xA 146 3.90e+01 c.47.1.10 86681 1rhi3 236 3.91e+01 1aym3 1tph1 247 3.91e+01 1amk 1n8fA 350 3.92e+01 c.1.10.4 85397 1cqxA 403 3.92e+01 1cqxA a.1.1.2 15635 b.43.4.2 25667 c.25.1.5 31562 1h2eA 207 3.92e+01 c.60.1.1 70857 1ovqA 138 3.96e+01 1iuqA 367 3.98e+01