# List of top-scoring protein chains for t2k.100-30-str 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.soe.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 1bnzA 64 7.90e-02 1azpA b.34.13.1 37468 1xyiA 66 2.85e-01 1tdhA 364 2.96e-01 a.156.1.2 106772 b.113.1.1 106773 g.39.1.8 106774 2o9uX 97 3.78e-01 d.17.1.1 138960 2q8oA 136 4.06e-01 1bf4A 63 4.13e-01 1azpA b.34.13.1 37461 2fxqA 264 4.25e-01 1suuA 312 4.65e-01 b.68.10.1 99006 1azpA 66 4.75e-01 1azpA b.34.13.1 37467 3d2lA 243 7.97e-01 2breA 219 8.27e-01 d.122.1.1 128994 1c8cA 64 9.03e-01 1azpA b.34.13.1 59084 1pfo 500 9.84e-01 1pfo 1pfoA 500 9.84e-01 f.9.1.1 43826 2rb6A 61 1.02e+00 2iwxA 214 1.22e+00 d.122.1.1 137758 2prdA 174 1.28e+00 b.40.5.1 25435 2q1mA 130 1.42e+00 2ft6A 124 1.44e+00 3b93A 133 1.57e+00 1nb8A 353 1.60e+00 d.3.1.9 80385 2b0vA 153 1.63e+00 d.113.1.1 127650 3bjuA 521 1.63e+00 1cc3A 130 1.92e+00 1nwpA b.6.1.1 23008 2f7tA 227 1.92e+00 1molA 94 2.16e+00 1molA d.17.1.1 37988 2v0uA 146 2.17e+00 1iscA 192 2.34e+00 1avmA a.2.11.1 15733 d.44.1.1 38726 1s3rA 535 2.35e+00 3cloA 258 2.37e+00 2ra2A 64 2.63e+00 2p9rA 102 2.64e+00 2hesX 330 2.65e+00 2uubL 135 3.03e+00 b.40.4.5 139943 2cw9A 194 3.30e+00 d.17.4.13 130920 2uurA 245 3.43e+00 1zxzA 197 3.54e+00 1z3qA 200 3.73e+00 2pd8A 149 3.79e+00 2vqiA 515 3.89e+00 2gu9A 113 3.98e+00 1azrA 128 4.11e+00 1nwpA b.6.1.1 22983 1o7iA 119 4.13e+00 b.40.4.3 86642 1e2wA 251 4.16e+00 1hcz b.2.6.1 22466 b.84.2.2 28252 1jzgA 128 4.21e+00 b.6.1.1 67855 1wpxB 220 4.43e+00 1ag0A 129 4.74e+00 1nwpA b.6.1.1 23001 2nybA 192 4.79e+00 a.2.11.1 138804 d.44.1.1 138805 2zcwA 202 4.85e+00 2cohA 202 4.85e+00 a.4.5.4 130677 b.82.3.2 130678 2glfA 450 5.06e+00 1jq4A 98 5.18e+00 d.15.4.2 67083 3bjsA 428 5.28e+00 2v72A 143 5.39e+00 2pdrA 149 5.65e+00 2ealA 148 5.78e+00 3b77A 193 5.82e+00 1dt9A 437 5.93e+00 1dt9A c.55.4.2 33738 d.79.3.2 39815 d.91.1.1 40257 2jc7A 244 6.01e+00 1oxsC 353 6.36e+00 b.40.6.3 87519 c.37.1.12 87520 1oxxK 353 6.36e+00 b.40.6.3 93715 c.37.1.12 93716 1x9lA 149 6.53e+00 b.2.10.1 109528 1lqyA 184 6.70e+00 d.167.1.1 74212 2f2aB 483 7.00e+00 a.182.1.2 132802 d.128.1.5 132803 2h41A 95 7.18e+00 2uwiA 142 7.54e+00 2r78A 117 7.56e+00 1cruA 454 7.63e+00 1c9uA b.68.2.1 27617 2oqkA 117 8.15e+00 2d73A 738 8.35e+00 1jmcA 246 8.36e+00 1jmcA b.40.4.3 25300 b.40.4.3 25301 1ddwA 120 8.44e+00 1evhA b.55.1.4 27001 1lm8C 96 8.87e+00 d.42.1.1 74034 1fjgL 135 9.01e+00 1fjfL b.40.4.5 25346 3bb7A 321 9.10e+00 1z47A 355 9.20e+00 2p6yA 142 9.22e+00 2cxvA 219 9.39e+00 b.47.1.4 131012 1se8A 301 9.40e+00 b.40.4.3 105448 1h6lA 353 9.41e+00 b.68.3.1 60687 1sczA 233 9.58e+00 c.43.1.1 98802 2i5vO 251 9.76e+00 1fnhA 271 9.86e+00 1fnhA b.1.2.1 21976 b.1.2.1 21977 b.1.2.1 21978 1gsoA 431 9.90e+00 1gsoA b.84.2.1 28240 c.30.1.1 31647 d.142.1.2 41492 1tp6A 128 9.99e+00 d.17.4.12 107184 2qcuA 501 1.00e+01 1s4uX 407 1.01e+01 b.69.4.1 112027 1vsd 152 1.02e+01 1cxqA 2rb8A 104 1.02e+01 1cxqA 162 1.02e+01 1cxqA c.55.3.2 33621 1aznA 128 1.04e+01 1nwpA b.6.1.1 23003 3cewA 125 1.06e+01 1i40A 175 1.07e+01 b.40.5.1 66024 2z1cA 75 1.09e+01 1kv9A 668 1.10e+01 a.3.1.6 73056 b.70.1.1 73057 1zupA 315 1.10e+01 c.55.3.11 125681 1dkzA 219 1.12e+01 1dkzA a.8.4.1 90345 b.130.1.1 90346 2gu3A 136 1.15e+01 1thv 207 1.17e+01 1thv 3cc6A 281 1.20e+01 1fnyA 237 1.20e+01 1led b.29.1.1 59920 2pi2E 142 1.21e+01 2blrA 206 1.22e+01 b.25.1.1 128741 1ughI 82 1.22e+01 1ugiA d.17.5.1 38133 1kwnA 207 1.22e+01 b.25.1.1 77568 1nciA 110 1.24e+01 1edhA b.1.6.1 22191 1sznA 417 1.25e+01 b.71.1.1 106162 c.1.8.1 106163 1rvkA 382 1.26e+01 c.1.11.2 97928 d.54.1.1 97929 1wgrA 100 1.27e+01 d.15.1.5 114621 1yqzA 438 1.28e+01 2j73A 103 1.30e+01 3bgaA 1010 1.34e+01 1quqB 121 1.34e+01 1quqB b.40.4.3 25305 1xvsA 126 1.34e+01 b.1.23.1 116095 1xd5A 112 1.35e+01 b.78.1.1 115155 1m6kA 251 1.35e+01 e.3.1.1 78695 2halA 212 1.35e+01 b.47.1.4 136289 1dar 691 1.36e+01 1dar 1xe1A 116 1.36e+01 b.43.3.1 109571 2oulA 241 1.40e+01 1bqg 451 1.42e+01 1bqg 2ipiA 521 1.44e+01 1yiqA 689 1.47e+01 1pcfA 66 1.48e+01 1pcfA d.18.1.1 38142 1m1sA 116 1.49e+01 b.1.11.2 84747 2aieP 203 1.50e+01 1h9sA 140 1.50e+01 1b9mA b.40.6.2 60843 b.40.6.2 60844 2vqeL 135 1.50e+01 1jnyA 435 1.51e+01 b.43.3.1 66982 b.44.1.1 66983 c.37.1.8 66984 2d6mA 159 1.52e+01 2oynA 146 1.52e+01 1dkxA 219 1.53e+01 1dkzA a.8.4.1 90339 b.130.1.1 90340 1kj1D 109 1.53e+01 b.78.1.1 68639 2oy7A 320 1.56e+01 2qngA 199 1.58e+01 2vktA 289 1.60e+01 1w9aA 147 1.60e+01 b.45.1.1 114408 1qlgA 355 1.60e+01 1qlgA b.68.3.1 27627 2ix2B 245 1.61e+01 1lm6A 215 1.62e+01 d.167.1.1 84628 2biwA 490 1.63e+01 1ddvA 111 1.67e+01 1evhA b.55.1.4 27002 1pdr 99 1.67e+01 1pdr 1e69B 322 1.68e+01 1e69B c.37.1.12 32377 1be9A 119 1.68e+01 1pdr b.36.1.1 24774 1y08A 323 1.71e+01 d.3.1.12 116280 2q7aA 152 1.71e+01 2g8cO 251 1.72e+01 2apr 325 1.72e+01 2er7E 2aprA 325 1.72e+01 b.50.1.2 26819 2v6vA 156 1.72e+01 3c2qA 345 1.73e+01 1nwwA 149 1.75e+01 d.17.4.8 86306 1y6hA 177 1.75e+01 d.167.1.1 116505 1bbxC 63 1.77e+01 1azpA b.34.13.1 37465 2v7bA 529 1.77e+01 1ywhA 313 1.79e+01 2rcfA 91 1.79e+01 1b88A 114 1.80e+01 1tcrA b.1.1.1 20608 2cc1A 262 1.80e+01 e.3.1.1 130211 1jdfA 447 1.83e+01 c.1.11.2 62897 d.54.1.1 62898 1ec7A 446 1.83e+01 1bqg c.1.11.2 29218 d.54.1.1 38862 2gk6A 624 1.83e+01 2vbuA 136 1.90e+01 1v3yA 192 1.91e+01 d.167.1.1 113508 1rqwA 207 1.91e+01 b.25.1.1 97781 2e7dA 131 1.92e+01 2avwA 311 1.93e+01 2he2A 102 1.93e+01 1cvrA 435 1.94e+01 1cvrA b.1.18.12 21949 c.17.1.2 31006 2cgpA 210 1.96e+01 2cgpA a.4.5.4 16102 b.82.3.2 28141 2vgdA 218 1.97e+01 2pil 159 2.00e+01 2pil 1c96A 753 2.02e+01 1amj c.8.2.1 30727 c.83.1.1 35403 1gv3A 248 2.02e+01 a.2.11.1 70585 d.44.1.1 70586 1s31A 273 2.03e+01 1fm2B 520 2.05e+01 1fm2B 2pooA 355 2.09e+01 1qlgA b.68.3.1 27626 1w6tA 444 2.10e+01 c.1.11.1 120670 d.54.1.1 120671 1x6zA 123 2.11e+01 d.24.1.1 121763 2h6oA 470 2.11e+01 2au7A 175 2.12e+01 1c8zA 265 2.16e+01 1c8zA d.23.1.1 38375 1v5vA 401 2.16e+01 b.44.2.1 113539 d.250.1.1 113540 1nx8A 273 2.18e+01 b.82.2.8 86374 1vpmA 169 2.19e+01 d.38.1.1 113967 2ae5B 528 2.23e+01 1pkp 150 2.24e+01 1pkp 1lla 628 2.26e+01 1lla 1llaA 628 2.26e+01 a.85.1.1 18485 a.86.1.1 18496 b.1.18.3 21861 2cu9A 161 2.28e+01 1ugiA 84 2.31e+01 1ugiA d.17.5.1 38125 2oqhA 385 2.32e+01 1soxA 466 2.33e+01 1soxA b.1.18.6 21947 d.120.1.1 41090 d.176.1.1 42563 2jn0A 61 2.33e+01 1qw9A 502 2.33e+01 b.71.1.2 96466 c.1.8.3 96467 1xe0A 114 2.34e+01 b.121.3.1 115197 3bduA 62 2.35e+01 1aerA 205 2.38e+01 1aerA d.166.1.1 42249 3b3qE 197 2.40e+01 3c5pA 197 2.41e+01 2gdqA 382 2.42e+01 c.1.11.2 135020 d.54.1.1 135021 2oklA 185 2.43e+01 2v6oA 596 2.49e+01 1s55A 156 2.49e+01 b.22.1.1 118865 1jenA 267 2.50e+01 1jenA 1epfA 191 2.51e+01 2ncm b.1.1.4 21694 b.1.1.4 21695 1svpA 161 2.51e+01 1svpA b.47.1.3 26384 35c8H 217 2.52e+01 8fabA b.1.1.1 20297 b.1.1.2 21289 1ybyA 215 2.53e+01 2fnjC 96 2.53e+01 d.42.1.1 133820 1j6qA 136 2.54e+01 b.40.9.1 77091 2fdoA 94 2.55e+01 d.337.1.1 133314 1kb0A 677 2.55e+01 a.3.1.6 68378 b.70.1.1 68379 1fepA 724 2.58e+01 1fepA f.4.3.3 43808 1udiI 83 2.59e+01 1ugiA d.17.5.1 38124 2z4tA 514 2.60e+01 2a9dA 372 2.61e+01 b.1.18.6 126431 d.176.1.1 126432 1dzoA 123 2.62e+01 1dzoA d.24.1.1 38378 1ten 90 2.64e+01 1ten 1tenA 90 2.64e+01 b.1.2.1 21990 1yfsA 465 2.64e+01 a.203.1.1 123088 d.104.1.1 123089 3cpxA 321 2.66e+01 2frqA 225 2.68e+01 d.3.1.1 133999 1vqoA 240 2.72e+01 b.34.5.3 120361 b.40.4.5 120362 1am2 199 2.74e+01 1am2 1am2A 199 2.74e+01 b.86.1.2 28381 1dhkB 223 2.74e+01 1led b.29.1.1 24157 1a8d 452 2.76e+01 1a8d 1a8dA 452 2.76e+01 b.29.1.6 24262 b.42.4.2 25607 2covD 104 2.77e+01 1n9bA 265 2.78e+01 e.3.1.1 85463 3bpuA 88 2.79e+01 1g60A 260 2.80e+01 c.66.1.11 70151 2e5yA 133 2.83e+01 2qf7A 1165 2.86e+01 1noyA 388 2.86e+01 1clqA c.55.3.5 33713 1jdpA 441 2.88e+01 c.93.1.1 62906 1p6pA 125 2.88e+01 b.60.1.2 87839 2hd5A 359 2.91e+01 1jl0A 334 2.91e+01 1jenA d.156.1.1 63155 1gwyA 175 2.96e+01 b.97.1.1 83356 1vyrA 364 2.96e+01 c.1.4.1 108906 2abbA 364 2.96e+01 c.1.4.1 126517 1vypX 364 2.99e+01 c.1.4.1 108905 2hkdA 320 3.00e+01 2ioiA 201 3.03e+01 2bkyA 97 3.03e+01 d.68.6.1 128715 1h5yA 253 3.05e+01 c.1.2.1 65638 1g6nA 210 3.06e+01 2cgpA a.4.5.4 16100 b.82.3.2 28139 2oq0A 206 3.07e+01 1azcA 129 3.12e+01 1nwpA b.6.1.1 22899 1iqaA 160 3.13e+01 b.22.1.1 71274 1i2hA 168 3.16e+01 b.55.1.4 71103 1ywrA 360 3.16e+01 2azaA 129 3.17e+01 1nwpA b.6.1.1 22901 2acoA 173 3.18e+01 1b9mA 265 3.20e+01 1b9mA a.4.5.8 16118 b.40.6.2 58938 b.40.6.2 58939 1diwA 441 3.27e+01 1a8d b.29.1.6 24264 b.42.4.2 25609 2r76A 152 3.27e+01 1ndoB 194 3.31e+01 1ndoB d.17.4.4 38121 2hi2A 158 3.32e+01 1rowA 109 3.32e+01 b.1.11.2 97676 1gk1B 522 3.33e+01 1g2rA 100 3.33e+01 1g2rA d.192.1.1 60231 1qr4A 186 3.36e+01 1qr4B b.1.2.1 21986 b.1.2.1 21987 1q6hA 224 3.36e+01 d.26.1.1 95975 2htuA 390 3.36e+01 1siqA 392 3.39e+01 a.29.3.1 105585 e.6.1.1 105586 2dfbA 190 3.41e+01 b.29.1.11 131470 2gdgA 114 3.41e+01 d.80.1.3 135015 1cqyA 99 3.42e+01 1b9zA b.3.1.1 22527 1fnmA 691 3.44e+01 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 3d3aA 612 3.45e+01 1i82A 189 3.45e+01 1i82A b.1.9.2 61937 1qfoA 119 3.52e+01 1qfoA b.1.1.1 19708 1nwpA 128 3.53e+01 1nwpA b.6.1.1 23011 1eg9B 194 3.54e+01 1ndoB d.17.4.4 38120 3bjoA 103 3.54e+01 1g3gA 164 3.56e+01 1g6gA b.26.1.2 23918 2re9A 181 3.58e+01 1i8aA 189 3.61e+01 1i82A b.1.9.2 61951 1uouA 474 3.66e+01 a.46.2.1 99706 c.27.1.1 99707 d.41.3.1 99708 2i02A 148 3.67e+01 b.45.1.1 136936 2arzA 247 3.69e+01 b.45.1.1 127225 3cjxA 165 3.69e+01 1dmaA 214 3.70e+01 1aerA d.166.1.1 42251 1byqA 228 3.70e+01 1yer d.122.1.1 41100 2p9bA 458 3.71e+01 1qr4B 186 3.74e+01 1qr4B b.1.2.1 21988 b.1.2.1 21989 2p19A 149 3.78e+01 2c9oA 456 3.79e+01 1mpyA 307 3.81e+01 1mpyA d.32.1.3 38508 d.32.1.3 38509 1iyxA 432 3.82e+01 c.1.11.1 83815 d.54.1.1 83816 1bd2D 204 3.83e+01 1tcrA b.1.1.1 20622 b.1.1.2 21557 1b56A 135 3.84e+01 b.60.1.2 27183 2gfaA 119 3.86e+01 b.34.9.1 135089 b.34.9.1 135090 1havA 217 3.88e+01 1havA b.47.1.4 26423 1o7kA 131 3.89e+01 d.189.1.1 81144 2ywvA 244 3.91e+01 2fvgA 340 3.92e+01 b.49.3.1 134201 c.56.5.4 134202 1fwxA 595 3.92e+01 b.6.1.4 60069 b.69.3.1 60070 1okgA 373 3.94e+01 c.46.1.2 93250 c.46.1.2 93251 d.26.1.3 93252 2f4nA 273 3.95e+01 2bh0A 208 3.98e+01 1a7cA 379 3.98e+01 1sek e.1.1.1 42660 1qwdA 177 3.99e+01 b.60.1.1 96471 1b9zA 516 3.99e+01 1b9zA b.3.1.1 22528 c.1.8.1 28798 1vemA 516 3.99e+01 b.3.1.1 120021 c.1.8.1 120022 2qqrA 118 3.99e+01