# List of top-scoring protein chains for t2k-100-30-alpha-scores 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 1gumA 222 8.07e-03 1pgtA a.45.1.1,c.47.1.5 17683,32977 1gulA 222 2.14e-02 1pgtA a.45.1.1,c.47.1.5 17675,32969 1rybA 212 5.88e-02 c.56.3.1 98098 1womA 271 1.87e-01 1v7cA 351 2.01e-01 c.79.1.1 100446 1vhmA 195 3.62e-01 d.110.2.1 100691 1u69A 163 4.50e-01 d.32.1.7 107699 1b5sA 242 5.07e-01 1eaf c.43.1.1 32626 1zemA 262 6.67e-01 1gzqA 300 8.18e-01 b.1.1.2,d.19.1.1 70818,70819 1vcdA 126 1.06e+00 1aroL 151 1.09e+00 1lba d.118.1.1 41063 1i1qA 520 1.48e+00 1qdlA d.161.1.1 61543 1k3lA 221 1.52e+00 a.45.1.1,c.47.1.5 77229,77230 1plfA 72 1.53e+00 1tvxA d.9.1.1 37373 2gaiA 633 1.73e+00 1gseA 221 1.80e+00 1pgtA a.45.1.1,c.47.1.5 17667,32961 1y74A 57 1.84e+00 1k3bA 119 2.01e+00 b.61.5.1 72016 1k3yA 221 2.22e+00 a.45.1.1,c.47.1.5 77245,77246 1lba 146 2.59e+00 1lba d.118.1.1 41062 2b33A 140 2.68e+00 1ats 386 2.98e+00 1ba1 c.55.1.1,c.55.1.1 33423,33424 2c0cA 362 3.29e+00 1phk 298 3.78e+00 1cdkA d.144.1.7 41635 1wwpA 119 4.71e+00 1b47A 304 5.29e+00 2cblA a.39.1.7,a.48.1.1,d.93.1.1 17381,17775,40529 1qxrA 189 5.55e+00 b.82.1.7 96552 1yuwA 554 5.83e+00 1ba1 386 5.85e+00 1ba1 c.55.1.1,c.55.1.1 33387,33388 1rw2A 152 5.88e+00 a.118.19.1 97961 1bupA 386 5.89e+00 1ba1 c.55.1.1,c.55.1.1 33377,33378 2f60K 64 6.30e+00 8pchA 220 6.32e+00 1cs8A 1jvnA 555 6.36e+00 c.1.2.1,c.23.16.1 67355,67356 1z6oM 191 6.43e+00 1xygD 359 6.61e+00 1hpm 386 6.71e+00 1ba1 c.55.1.1,c.55.1.1 33381,33382 1atr 386 7.05e+00 1ba1 c.55.1.1,c.55.1.1 33421,33422 1kay 381 7.14e+00 1ba1 c.55.1.1,c.55.1.1 33385,33386 1xd7A 145 7.17e+00 a.4.5.55 109566 1f3aA 222 7.25e+00 1pgtA a.45.1.1,c.47.1.5 17701,32995 1zl8A 53 7.51e+00 1kl7A 514 7.55e+00 c.79.1.1 72678 2cblA 305 7.62e+00 2cblA a.39.1.7,a.48.1.1,d.93.1.1 17380,17774,40528 1x82A 190 7.64e+00 1sdoA 203 7.68e+00 c.52.1.21 98809 1ox6A 555 7.97e+00 c.1.2.1,c.23.16.1 87505,87506 1zmbA 290 8.16e+00 1ee8A 266 8.61e+00 1ee8A a.156.1.2,b.113.1.1,g.39.1.8 75823,75824,75825 1y9lA 115 8.75e+00 1h1wA 289 8.78e+00 d.144.1.7 83460 1osdA 72 9.82e+00 d.58.17.1 104022 1z5hA 780 1.04e+01 1rypC 244 1.05e+01 1rypC d.153.1.4 41934 1jb0D 138 1.07e+01 1jb0D d.187.1.1 62823 1tf1A 198 1.07e+01 d.110.2.2 106826 1yvhA 329 1.09e+01 1ihfB 94 1.09e+01 1huuA a.55.1.1 17894 1y7tA 327 1.12e+01 1ysjA 404 1.15e+01 1bdmA 327 1.20e+01 1bmdA c.2.1.5,d.162.1.1 30137,42104 1q2zA 120 1.20e+01 a.118.19.1 95656 1vf1A 229 1.27e+01 1k75A 434 1.31e+01 c.82.1.2 68253 1onqA 283 1.32e+01 b.1.1.2,d.19.1.1 93365,93366 1bdmB 327 1.32e+01 1bmdA c.2.1.5,d.162.1.1 30138,42105 1cvjA 190 1.33e+01 1cvjB d.58.7.1,d.58.7.1 39191,39192 1kaeA 434 1.34e+01 c.82.1.2 72247 1iugA 352 1.46e+01 c.67.1.3 90699 2ae6A 166 1.48e+01 1owfB 94 1.50e+01 a.55.1.1 87488 1qh4A 380 1.52e+01 1qh4A a.83.1.1,d.128.1.2 18462,41197 1cojA 212 1.52e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1yr2A 741 1.53e+01 2awdA 323 1.53e+01 1wxxA 382 1.53e+01 1bmdA 327 1.54e+01 1bmdA c.2.1.5,d.162.1.1 30139,42106 1p6xA 334 1.56e+01 c.37.1.1 94195 1hnjA 317 1.56e+01 1hn9A c.95.1.2,c.95.1.2 35969,35970 1avv 151 1.57e+01 1efnB d.102.1.1 40703 1b9bA 255 1.58e+01 1amk c.1.1.1 28531 1k1xA 659 1.61e+01 a.8.3.2,b.30.5.8,c.6.2.2 84279,84280,84281 1hn9A 317 1.62e+01 1hn9A c.95.1.2,c.95.1.2 35977,35978 1eblB 317 1.64e+01 1hn9A c.95.1.2,c.95.1.2 35975,35976 1mw7A 240 1.65e+01 e.39.1.1 79557 1c6vX 81 1.65e+01 1ihvA b.34.7.1 24641 1ppjJ 62 1.66e+01 f.23.14.1 104266 1qlaB 239 1.70e+01 1qlaB a.1.2.1,d.15.4.2 15679,37707 1vrpA 381 1.70e+01 2bmeA 186 1.72e+01 1uunA 184 1.72e+01 f.6.1.2 100012 1wloA 136 1.74e+01 1oxjA 173 1.84e+01 a.60.1.2,a.118.1.13 87517,87518 1s3sG 127 2.00e+01 d.15.1.2 98457 1nowA 507 2.01e+01 c.1.8.6,d.92.2.1 85936,85937 1mldA 314 2.01e+01 2cmd c.2.1.5,d.162.1.1 30122,42089 1nouA 507 2.02e+01 c.1.8.6,d.92.2.1 85932,85933 1eblA 317 2.02e+01 1hn9A c.95.1.2,c.95.1.2 35973,35974 1st9A 143 2.03e+01 c.47.1.10 98987 1xn7A 78 2.13e+01 1vliA 385 2.14e+01 b.85.1.1,c.1.10.6 108830,108831 1t7lA 766 2.16e+01 2f02A 323 2.19e+01 1uu3A 310 2.20e+01 d.144.1.7 99999 2ashA 381 2.23e+01 2fd5A 180 2.23e+01 1avoA 60 2.23e+01 1avoA a.24.8.1 16619 1d7qA 143 2.25e+01 1d7qA b.40.4.5 25331 1e3dB 542 2.32e+01 1h2rL e.18.1.1 59189 1l3lA 234 2.36e+01 a.4.6.2,d.110.5.1 73541,73542 2f9sA 151 2.38e+01 1k2xA 177 2.47e+01 d.153.1.5 90929 1siiA 646 2.48e+01 b.30.2.1,d.17.2.1,d.17.2.1 105578,105579,105580 1vpkA 378 2.49e+01 1lk5A 229 2.52e+01 c.124.1.4,d.58.40.1 73960,73961 1apc 106 2.53e+01 256bA a.24.3.1 16543 2pviA 157 2.55e+01 3pviA c.52.1.6 33302 1be3J 62 2.63e+01 1be3J f.23.14.1 43671 1eijA 80 2.64e+01 1eijA a.5.6.1 16298 2ddrA 306 2.65e+01 1ftt 68 2.68e+01 2hddA a.4.1.1 15997 2f6mA 65 2.72e+01 3pviA 157 2.75e+01 3pviA c.52.1.6 33300 1pvuA 154 2.75e+01 3pviA c.52.1.6 33306 1rktA 205 2.80e+01 a.4.1.9,a.121.1.1 97623,97624 1pa1A 310 2.82e+01 c.45.1.2 94404 1cdzA 96 2.85e+01 1cdzA c.15.1.1 30925 1g5aA 628 2.87e+01 b.71.1.1,c.1.8.1 65152,65153 1jruA 89 2.92e+01 1jruA d.15.1.2 63257 1x3cA 73 2.96e+01 1omwA 689 3.01e+01 a.91.1.1,b.55.1.1,d.144.1.7 87086,87087,87088 1e1hA 287 3.02e+01 d.92.1.7 83167 1b7yB 785 3.08e+01 1pysB a.6.1.1,a.6.1.1,b.40.4.4,d.58.13.1,d.104.1.1,d.138.1.1 16301,16302,25312,39311,40780,41456 1t3uA 104 3.12e+01 d.244.1.1 99120 2aw5A 541 3.16e+01 1ivwA 638 3.16e+01 b.30.2.1,d.17.2.1,d.17.2.1 71456,71457,71458 1rjoA 646 3.17e+01 1bccJ 62 3.17e+01 1be3J f.23.14.1 43703 1u2wA 122 3.20e+01 1g7fA 298 3.21e+01 1pty c.45.1.2 60330 1hjzA 192 3.22e+01 c.50.1.2 83520 1ksqA 75 3.23e+01 g.23.1.1 91026 1ujrA 110 3.27e+01 1w6gA 646 3.27e+01 2f71A 298 3.30e+01 1avqA 228 3.30e+01 1avqA c.52.1.13 33326 1f5qB 252 3.33e+01 1f5qB a.74.1.1,a.74.1.1 18362,18363 1df7A 159 3.34e+01 3dfr c.71.1.1 34885 1lj2A 110 3.35e+01 h.1.13.2 73926 2mysB 166 3.40e+01 1wdcB a.39.1.5 17308 2blkA 122 3.42e+01 1zwxA 301 3.48e+01 1i42A 89 3.49e+01 1jruA d.15.1.2 61651 1u20A 212 3.50e+01 1zi8A 236 3.53e+01 1eyuA 157 3.56e+01 3pviA c.52.1.6 33304 1xw8A 252 3.59e+01 1tffA 234 3.60e+01 d.3.1.11 106854 1ytfD 121 3.61e+01 1ytfD a.32.1.1,b.56.1.1 16998,27011 1v6tA 255 3.64e+01 2nef 136 3.64e+01 1efnB d.102.1.1 40704 1hxkA 1015 3.66e+01 a.8.3.1,b.30.5.6,c.6.2.1 83070,83071,83072 1htyA 1015 3.66e+01 a.8.3.1,b.30.5.6,c.6.2.1 83064,83065,83066 1aax 321 3.75e+01 1pty c.45.1.2 32657 1avu 181 3.75e+01 1wba b.42.4.1 25603 1ihvA 52 3.75e+01 1ihvA b.34.7.1 24629 1knvA 293 3.77e+01 c.52.1.7 68707 1dl5A 317 3.82e+01 1dl5A c.66.1.7,d.197.1.1 64720,64721 1hwwA 1015 3.82e+01 a.8.3.1,b.30.5.6,c.6.2.1 83067,83068,83069 1b1cA 181 3.82e+01 1amoA c.23.5.2 31212 1n13B 113 3.85e+01 1vhuA 211 3.93e+01 c.50.1.2 100703 1om2A 95 3.94e+01 1om2A a.23.4.1 16520 1z9lA 128 4.07e+01 2hnp 321 4.10e+01 1pty c.45.1.2 32678 1e58A 249 4.11e+01 1qhfA c.60.1.1 59262 1yq5A 144 4.18e+01 1yoaA 159 4.22e+01 1a5y 330 4.24e+01 1pty c.45.1.2 32673 1qwnA 1045 4.24e+01 a.8.3.1,b.30.5.6,c.6.2.1 96487,96488,96489 1jogA 146 4.25e+01 a.24.16.2 77142 1avk 638 4.29e+01 1a2vA b.30.2.1,d.17.2.1,d.17.2.1 24410,38047,38048 1wb4A 297 4.33e+01 2hddA 61 4.36e+01 2hddA a.4.1.1 15971 1gw5S 142 4.46e+01 d.110.4.2 70633 1x6vA 630 4.47e+01 1r8gA 372 4.54e+01 d.128.1.3 104845 2fbyA 205 4.54e+01 1ryp2 233 4.56e+01 1ryp2 1fnmA 691 4.58e+01 1dar b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1,d.58.11.1 25709,32144,37546,39302,39303 1qgmA 30 4.62e+01 g.3.16.1 44380 1z84A 351 4.64e+01 1cyo 93 4.65e+01 1cyo d.120.1.1 41065 1n4kA 381 4.72e+01 a.118.22.1,b.42.6.1 79992,79993 1gwmA 153 4.73e+01 b.18.1.19 83348 1rp4A 389 4.79e+01 a.227.1.1 105027 1pysB 785 4.79e+01 1pysB a.6.1.1,a.6.1.1,b.40.4.4,d.58.13.1,d.104.1.1,d.138.1.1 16299,16300,25311,39310,40779,41455 1eeoA 321 4.80e+01 1pty c.45.1.2 32655 1iseA 185 4.85e+01 d.67.3.1 90691 1efnB 152 4.88e+01 1efnB d.102.1.1 40699 1pty 321 4.89e+01 1pty c.45.1.2 32656 1tvxB 75 4.91e+01 1tvxA d.9.1.1 37442 1su0B 159 4.95e+01 d.224.1.2 106015 1gklA 297 4.95e+01 c.69.1.2 65250 1wgbA 159 4.97e+01 1yw5A 177 5.01e+01 1v5dA 386 5.06e+01 1fjlA 81 5.07e+01 2hddA a.4.1.1 16017 1ozjA 144 5.16e+01 d.164.1.1 93846 1ptvA 321 5.18e+01 1pty c.45.1.2 32665 1akz 223 5.22e+01 3eugA c.18.1.1 31007 1liaA 164 5.26e+01 1cpcA a.1.1.3 15661 1wucA 250 5.27e+01 1v9yA 167 5.29e+01 d.110.3.2 108454 2au3A 407 5.30e+01 1k5dB 201 5.34e+01 b.55.1.3 68169 256bA 106 5.36e+01 256bA a.24.3.1 16539 1clvI 32 5.39e+01 1qfdA g.3.2.1 44075 2cs7A 55 5.42e+01 1hd2A 161 5.55e+01 c.47.1.10 60962 2a74C 343 5.66e+01 1nh2D 121 5.70e+01 a.32.1.1,b.56.1.1 91876,91877 1cf4B 44 5.73e+01 1cf4B 1go4E 100 5.75e+01 h.1.22.1 70296 1fntc 245 5.81e+01 1gkkA 297 5.81e+01 c.69.1.2 65248 1sxrA 183 5.83e+01 d.118.1.1 106101 1avwB 171 5.86e+01 1wba b.42.4.1 25599 1ui8A 638 5.86e+01 b.30.2.1,d.17.2.1,d.17.2.1 99419,99420,99421 1ituA 369 5.90e+01 c.1.9.7 71423 1tuwA 109 5.93e+01 d.58.4.8 107346 1lmeA 176 5.93e+01 d.167.1.1 84629 1qzgA 187 5.95e+01 b.40.4.3 96643 1wzoA 246 6.04e+01 1mkp 144 6.08e+01 1vhrA c.45.1.1 32654 1fo0B 112 6.12e+01 1kb5B b.1.1.1 20631 1v7lA 163 6.15e+01 1jqpA 438 6.16e+01 b.61.5.1,d.3.1.1 77162,77163 1eal 127 6.16e+01 1hmt b.60.1.2 27227 1bno 87 6.18e+01 1bpyA a.60.6.1 18079 1binA 143 6.22e+01 2gdm a.1.1.2 15231 1wk2A 121 6.22e+01 1din 236 6.23e+01 1din c.69.1.9 34682 1vd3A 217 6.27e+01 2csgA 424 6.29e+01 1y08A 323 6.37e+01 1mrj 247 6.48e+01 1mrj d.165.1.1 42177 1llmC 88 6.50e+01 g.37.1.1,g.37.1.1 91059,91060 2fsqA 243 6.50e+01 1y3nA 490 6.60e+01 1mnmA 100 6.62e+01 1mnmA d.88.1.1 40232 1g0u1 266 6.68e+01 1xrkA 124 6.71e+01 1qc7A 101 6.78e+01 1qc7A a.118.14.1 18456 2hqi 72 6.93e+01 1aw0 d.58.17.1 39340 1ek9A 428 6.96e+01 1ek9A f.5.1.1 43809 1avbA 226 6.99e+01 1led b.29.1.1 24158 1iqyA 638 7.02e+01 b.30.2.1,d.17.2.1,d.17.2.1 76763,76764,76765 2tmkA 216 7.02e+01 3tmkA c.37.1.1 31928 1v32A 101 7.04e+01 a.42.1.1 100277 2ethA 154 7.05e+01 1ui7A 638 7.06e+01 b.30.2.1,d.17.2.1,d.17.2.1 99413,99414,99415 2mltA 27 7.10e+01 j.19.1.1 46171 1wkvA 389 7.11e+01 3tmkA 216 7.27e+01 3tmkA c.37.1.1 31920 1qh8A 478 7.28e+01 1qguA c.92.2.3 35633 1afi 72 7.47e+01 1aw0 d.58.17.1 39339 2bx2L 517 7.53e+01 1kq6A 141 7.57e+01 d.189.1.1 91020 1fmk 452 7.59e+01 1fmk b.34.2.1,d.93.1.1,d.144.1.7 24511,40436,41690 1qguA 478 7.67e+01 1qguA c.92.2.3 35625 1m1nA 491 7.67e+01 c.92.2.3 78417 1wyuB 474 7.68e+01 1g6uA 48 7.68e+01 1g6uA k.9.1.1 46425 1qryA 80 7.70e+01 2hddA a.4.1.1 16016 1nqbA 256 7.72e+01 1mfa b.1.1.1,b.1.1.1 20042,20043 1rgxA 114 7.84e+01 g.77.1.1 104932 1mnaA 298 7.86e+01 c.69.1.22 79322 5nseA 444 7.88e+01 d.174.1.1 74644 1gcvA 140 7.89e+01 1cg5B a.1.1.2 15410 2b3nA 159 7.89e+01 1ustA 93 7.95e+01 a.4.5.13 99884 1wgzA 510 7.96e+01 1m7vA 363 8.03e+01 d.174.1.1 78748 1x4rA 99 8.09e+01 2f9lA 199 8.16e+01 1nseA 444 8.29e+01 1nseA d.174.1.1 42534 1b8dA 164 8.30e+01 1cpcA a.1.1.3 15665 1tu7A 208 8.41e+01 1lkvX 232 8.41e+01 a.118.14.1 73980 1d1vA 444 8.41e+01 1nseA d.174.1.1 59101 1bix 287 8.44e+01 1bix d.151.1.1 41781 1fqvA 336 8.52e+01 1fqvA a.158.1.1,c.10.1.3 19254,30856 1d0cA 444 8.54e+01 d.174.1.1 64769 1pd21 199 8.56e+01 1pd21 1gdvA 85 8.59e+01 1ctj a.3.1.1 60458 2f8mA 244 8.59e+01 1e85A 127 8.64e+01 1bbhA a.24.3.2 16549 1xmbA 418 8.66e+01 2a5jA 191 8.73e+01 1ed5A 444 8.80e+01 1nseA d.174.1.1 42530 1wt4A 73 8.84e+01 1kezA 300 8.84e+01 c.69.1.22 68546 1wmiB 67 8.85e+01 1pv1A 299 8.87e+01 1w8kA 447 8.92e+01 1yz8P 68 8.96e+01 1t35A 191 8.97e+01 c.129.1.1 99108 1t8sA 484 8.99e+01 c.56.2.1 106679 2b18A 164 9.00e+01