# List of top-scoring protein chains for t2k-100-30-str2-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 2bkqA 212 6.61e-02 2bkrA 212 8.53e-02 1euvA 221 1.01e-01 1euvA d.3.1.7 37133 1xt9A 212 1.20e-01 1fhuA 320 2.47e-01 1fhuA c.1.11.2,d.54.1.1 29234,38878 1r6wA 322 3.45e-01 c.1.11.2,d.54.1.1 97165,97166 1fhvA 323 6.59e-01 1fhuA c.1.11.2,d.54.1.1 29235,38879 2b49A 287 8.54e-01 1uwzA 136 1.59e+00 c.97.1.1 108081 1hzgA 295 1.65e+00 1hzgA d.194.1.1 61436 1wnaA 131 1.84e+00 1wbpA 397 1.88e+00 1hq0A 295 1.92e+00 1hzgA d.194.1.1 61122 1nfiA 301 3.07e+00 1a3qA b.1.18.1,b.2.5.3 21942,22455 1nfiC 301 3.19e+00 b.1.18.1,b.2.5.3 21943,22456 2ap1A 327 3.37e+00 1vicA 262 3.64e+00 c.68.1.13 100756 1fchA 368 3.83e+00 1fchA a.118.8.1 19212 1pgs 314 3.84e+00 1pgs b.121.1.1,b.121.1.1 23653,23654 1k2eA 156 3.90e+00 d.113.1.1 72010 1k26A 156 4.01e+00 d.113.1.1 72003 1jrkA 156 4.08e+00 d.113.1.1 71827 1jtkA 136 4.14e+00 c.97.1.1 71862 3cla 213 4.36e+00 3cla c.43.1.1 32610 1q8yA 373 4.52e+00 d.144.1.7 96234 1p90A 145 4.56e+00 c.55.5.2 94377 1dc1A 323 4.57e+00 1dc1A c.52.1.11 33321 1mpxA 615 4.70e+00 b.18.1.13,c.69.1.21 85041,85042 2dg5B 190 4.90e+00 1wsrA 375 5.41e+00 2gx9A 129 6.02e+00 1howA 373 6.26e+00 1hcl d.144.1.7 41679 1poiB 260 6.35e+00 1poiB c.124.1.3 34155 1zrzA 364 6.79e+00 2adzA 178 7.12e+00 2az4A 429 7.12e+00 1u6dX 308 7.24e+00 1zgkA 308 7.54e+00 1y74A 57 7.96e+00 1qhtA 775 8.48e+00 1tgoA c.55.3.5,e.8.1.1 33722,43011 1n8fA 350 8.70e+00 c.1.10.4 85397 1ih7A 903 9.12e+00 1clqA c.55.3.5,e.8.1.1 62375,62376 1udxA 416 9.75e+00 b.117.1.1,c.37.1.8,d.242.1.1 99228,99229,99230 1rjdA 334 9.80e+00 c.66.1.37 97558 1bh6A 274 1.02e+01 1gci c.41.1.1 32487 1xs0A 136 1.04e+01 1ufhA 180 1.09e+01 d.108.1.1 88485 1hnoA 280 1.17e+01 1hnoA c.14.1.3 61095 3nul 130 1.25e+01 3nul d.110.1.1 40891 1iv0A 98 1.28e+01 c.55.3.8 90706 1wa3A 205 1.28e+01 1ayoA 130 1.29e+01 1ayoA b.2.4.1 22431 1z6nA 167 1.29e+01 1hnuA 280 1.30e+01 1hnoA c.14.1.3 61096 1pbyB 337 1.34e+01 b.69.2.2 94422 1s01 283 1.35e+01 1gci c.41.1.1 32511 1sup 275 1.36e+01 1gci c.41.1.1 32510 1zdrA 164 1.36e+01 1ak9 275 1.36e+01 1gci c.41.1.1 32517 1a2q 275 1.37e+01 1gci c.41.1.1 32512 1iknA 286 1.38e+01 1a3qA b.1.18.1,b.2.5.3 21936,22449 1aqn 275 1.39e+01 1gci c.41.1.1 32514 1bksA 268 1.39e+01 2tysA c.1.2.4 28585 1qr7A 350 1.39e+01 1qr7A c.1.10.4 29191 1u5tC 202 1.40e+01 a.4.5.54,a.4.5.54 107688,107689 2fm8A 135 1.40e+01 1vlwA 217 1.40e+01 c.1.10.1 108868 1ah2 269 1.44e+01 1gci c.41.1.1 32542 1pu5A 164 1.44e+01 b.95.1.1 104310 1a0k 131 1.48e+01 3nul d.110.1.1 40892 1gg1A 350 1.50e+01 1qr7A c.1.10.4 29187 1lw6E 281 1.53e+01 c.41.1.1 74293 1t7pA 698 1.55e+01 1t7pA c.55.3.5,e.8.1.1 33712,43005 1ii6A 368 1.56e+01 1bg2 c.37.1.9 62413 1ia9A 280 1.58e+01 1ia9A d.144.1.5 62113 1to2E 281 1.60e+01 2tysA 268 1.60e+01 2tysA c.1.2.4 28572 1gci 269 1.61e+01 1gci c.41.1.1 32503 1a5v 162 1.63e+01 1cxqA c.55.3.2 33629 1x9mA 698 1.64e+01 1vljA 407 1.64e+01 e.22.1.2 108832 1bqcA 302 1.65e+01 1bqcA c.1.8.3 28831 1jx4A 352 1.69e+01 d.240.1.1,e.8.1.7 90378,90379 1vsd 152 1.69e+01 1cxqA c.55.3.2 33625 2g8yA 385 1.69e+01 1gc5A 467 1.71e+01 1gc5A c.72.1.3 60429 1g13A 162 1.71e+01 1g13A b.95.1.1 60194 1pysB 785 1.77e+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 1tuoA 464 1.77e+01 1vl4A 447 1.78e+01 d.283.1.1 108718 2eu9A 355 1.80e+01 2cn3A 737 1.84e+01 1dkgD 383 1.85e+01 1ba1 c.55.1.1,c.55.1.1 33427,33428 2f7tA 227 1.86e+01 1avt 274 1.88e+01 1gci c.41.1.1 32488 1r5jA 337 1.91e+01 c.77.1.5 97097 1qopA 268 1.95e+01 2tysA c.1.2.4 28570 1uheA 97 1.96e+01 1jjuB 337 1.97e+01 b.69.2.2 66779 1zclA 180 2.03e+01 1on0A 158 2.05e+01 d.108.1.1 87095 1o2dA 371 2.06e+01 e.22.1.2 86591 1mkp 144 2.10e+01 1vhrA c.45.1.1 32654 1cxqA 162 2.13e+01 1cxqA c.55.3.2 33621 1ltzA 297 2.15e+01 d.178.1.1 74254 1kfcA 268 2.21e+01 c.1.2.4 77371 1qqcA 773 2.28e+01 1tgoA c.55.3.5,e.8.1.1 33724,43013 1xviA 275 2.28e+01 1yu6A 275 2.31e+01 1spuB 727 2.33e+01 1oacA b.30.2.1,d.17.2.1,d.17.2.1,d.82.1.1 24399,38025,38026,40012 2cvbA 188 2.36e+01 1bv8A 138 2.40e+01 1ayoA b.2.4.1 22430 1tgoA 773 2.41e+01 1tgoA c.55.3.5,e.8.1.1 33721,43010 2f7fA 494 2.47e+01 1zo0A 126 2.52e+01 1u7zA 226 2.52e+01 1qdlA 422 2.55e+01 1qdlA d.161.1.1 42088 1tfr 305 2.57e+01 1tfr a.60.7.1,c.120.1.2 18081,33351 1h32A 261 2.59e+01 a.3.1.8,a.3.1.8 76618,76619 1asu 162 2.61e+01 1cxqA c.55.3.2 33626 1cseE 274 2.62e+01 1gci c.41.1.1 32481 1rch 155 2.63e+01 2rn2 c.55.3.1 33570 1nozA 388 2.66e+01 1clqA c.55.3.5 33715 1ofuX 119 2.73e+01 c.37.1.22 86976 1qqtA 551 2.85e+01 1qqtA a.27.1.1,c.26.1.1,g.41.1.1 16923,31590,45175 1r0rE 274 2.87e+01 c.41.1.1 96735 1x6oA 174 2.95e+01 b.34.5.2,b.40.4.5 109493,109494 1h0hA 977 2.97e+01 b.52.2.2,c.81.1.1 76435,76436 2a7kA 250 2.97e+01 2fpmA 322 2.99e+01 1vlaA 150 2.99e+01 d.227.1.2 108735 1t0iA 191 3.00e+01 c.23.5.4 106209 1yw5A 177 3.07e+01 1m1hA 248 3.13e+01 b.114.1.1,d.58.42.1 78415,78416 1hqz1 141 3.13e+01 2kinA 238 3.15e+01 1bg2 c.37.1.9 32190 2fpnA 216 3.16e+01 1d6zA 727 3.16e+01 1oacA b.30.2.1,d.17.2.1,d.17.2.1,d.82.1.1 24394,38015,38016,40007 1hqz9 141 3.17e+01 1q52A 314 3.17e+01 c.14.1.3 95846 1f4lA 551 3.26e+01 1qqtA a.27.1.1,c.26.1.1,g.41.1.1 59648,59649,59650 1pfvA 551 3.26e+01 a.27.1.1,c.26.1.1,g.41.1.1 94660,94661,94662 2fvx 138 3.27e+01 5nul c.23.5.1 31200 1u9cA 224 3.29e+01 3nll 138 3.30e+01 5nul c.23.5.1 31206 5nul 138 3.31e+01 5nul c.23.5.1 31191 1qb5D 99 3.35e+01 b.40.2.1 88357 1tiiD 99 3.35e+01 1tiiD b.40.2.1 24965 1p8xA 344 3.38e+01 d.109.1.1,d.109.1.1,d.109.1.1 94365,94366,94367 1rybA 212 3.45e+01 c.56.3.1 98098 1hywA 68 3.47e+01 1hywA d.186.1.1 61425 1knvA 293 3.53e+01 c.52.1.7 68707 1n8nA 212 3.55e+01 c.108.1.12 91706 1qfjA 232 3.61e+01 1qfjA b.43.4.2,c.25.1.1 25655,31545 2fox 138 3.61e+01 5nul c.23.5.1 31197 1pjhA 280 3.64e+01 c.14.1.3 94761 2b7aA 293 3.68e+01 1o1yA 239 3.68e+01 c.23.16.1 86554 1vpqA 273 3.69e+01 1eo1A 124 3.70e+01 1eo1A c.55.5.1 33739 1tp9A 162 3.71e+01 1aroL 151 3.72e+01 1lba d.118.1.1 41063 1ec7A 446 3.77e+01 1bqg c.1.11.2,d.54.1.1 29218,38862 2iadB 205 3.86e+01 1iakB b.1.1.2,d.19.1.1 21640,38214 1x88A 359 3.90e+01 2ajrA 331 3.92e+01 1noyA 388 3.94e+01 1clqA c.55.3.5 33713 1ad1A 266 3.98e+01 1aj2 c.1.21.1 29668 1svdM 110 3.99e+01 1jm1A 204 4.01e+01 b.33.1.1 71745 1sqhA 312 4.05e+01 d.108.1.5 98966 1q18A 332 4.06e+01 c.55.1.7,c.55.1.7 104470,104471 1f37A 110 4.07e+01 1f37A c.47.1.11 33088 2h1tA 188 4.12e+01 1jdfA 447 4.14e+01 c.1.11.2,d.54.1.1 62897,62898 1gpl 432 4.17e+01 1gpl b.12.1.2,c.69.1.19 23645,34793 1o4sA 389 4.20e+01 c.67.1.1 86620 1lba 146 4.26e+01 1lba d.118.1.1 41062 1xb4A 202 4.28e+01 1hh1A 143 4.31e+01 1gefA c.52.1.18 61036 1q0bA 367 4.35e+01 c.37.1.9 95502 1j5pA 253 4.49e+01 d.81.1.3,c.2.1.3 71577,83092 1oxkB 134 4.52e+01 c.23.1.1 93691 1ad4A 266 4.59e+01 1aj2 c.1.21.1 29670 1vraB 215 4.62e+01 1g0uG 252 4.68e+01 d.153.1.4 41952 2fn0A 437 4.69e+01 1y88A 199 4.70e+01 1sg4A 260 4.73e+01 1qxoA 388 4.75e+01 d.258.1.1 96539 2aaa 484 4.75e+01 7taa b.71.1.1,c.1.8.1 27777,28764 1iyxA 432 4.79e+01 c.1.11.1,d.54.1.1 83815,83816 1zc6A 305 4.81e+01 1zxuA 217 4.86e+01 1a05A 358 4.96e+01 1cnzA c.77.1.1 35059 1m2dA 110 4.96e+01 c.47.1.11 78476 1bg2 325 4.97e+01 1bg2 c.37.1.9 32189 1rcsA 105 5.11e+01 1jhgA a.4.12.1 19025 2wsyA 268 5.13e+01 2tysA c.1.2.4 28588 1eiyB 785 5.20e+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 16305,16306,25314,39313,40782,41458 1lzlA 323 5.23e+01 c.69.1.2 78306 1u04A 771 5.23e+01 b.34.14.1,c.55.3.10 107539,107540 1khdA 345 5.29e+01 a.46.2.1,c.27.1.1 77400,77401 1ne9A 335 5.31e+01 d.108.1.4,d.108.1.4 91839,91840 1vjnA 220 5.31e+01 d.157.1.4 100825 1dkxA 219 5.36e+01 1dkzA a.8.4.1,b.130.1.1 90339,90340 1z57A 339 5.37e+01 2b82A 211 5.39e+01 1fmk 452 5.39e+01 1fmk b.34.2.1,d.93.1.1,d.144.1.7 24511,40436,41690 1fa3A 96 5.41e+01 1molA d.17.1.1 37996 1wguA 136 5.43e+01 1rmwA 212 5.44e+01 1zg2A 107 5.46e+01 1dkzA 219 5.46e+01 1dkzA a.8.4.1,b.130.1.1 90345,90346 1oacA 727 5.51e+01 1oacA b.30.2.1,d.17.2.1,d.17.2.1,d.82.1.1 24390,38007,38008,40003 1jj2B 337 5.63e+01 1ffkB b.43.3.2 63086 1s72B 338 5.63e+01 b.43.3.2 105320 1clqA 903 5.64e+01 1clqA c.55.3.5,e.8.1.1 33717,43006 1m2aA 110 5.71e+01 c.47.1.11 78472 1taq 832 5.76e+01 1taq a.60.7.1,c.120.1.2,c.55.3.5,e.8.1.1 18082,33352,33698,42991 2fuqA 747 5.78e+01 2bh9A 489 5.79e+01 1lnsA 763 5.84e+01 a.40.2.1,b.18.1.13,c.69.1.21 78101,78102,78103 2al2A 436 5.87e+01 1yzbA 182 5.91e+01 2b5iC 199 5.91e+01 1nnwA 252 5.92e+01 d.159.1.5 80674 1qhiA 366 5.95e+01 1qhiA c.37.1.1 31860 2aplA 157 5.95e+01 1o17A 345 5.97e+01 a.46.2.1,c.27.1.1 80765,80766 1aj2 282 6.00e+01 1aj2 c.1.21.1 29665 1jhgA 101 6.02e+01 1jhgA a.4.12.1 19009 1ctt 294 6.05e+01 1ctt c.97.1.1,c.97.1.1 36022,36023 1rypA 243 6.11e+01 1pmaA d.153.1.4 41932 1wmdA 434 6.20e+01 b.18.1.20,c.41.1.1 109408,109409 2al1A 436 6.24e+01 1yaxA 153 6.24e+01 2bu3A 254 6.26e+01 1e2tA 284 6.28e+01 1e2tA d.3.1.5 37121 1u9tA 354 6.28e+01 1ko3A 230 6.31e+01 d.157.1.1 90974 2agaA 190 6.36e+01 1rpyA 114 6.38e+01 d.93.1.1 97718 1kimA 366 6.38e+01 1qhiA c.37.1.1 31864 1vqoB 338 6.40e+01 1z3iX 644 6.41e+01 2cygA 312 6.43e+01 1e2kA 331 6.48e+01 1qhiA c.37.1.1 31854 1xd5A 112 6.49e+01 2g6bA 180 6.50e+01 1x3mA 415 6.54e+01 1hrhA 136 6.58e+01 1rthA c.55.3.1 33577 1aj0 282 6.60e+01 1aj2 c.1.21.1 29667 1sz2A 332 6.61e+01 1kinA 366 6.64e+01 1kcqA 104 6.71e+01 d.109.1.1 68449 1a0eA 443 6.74e+01 1a0cA c.1.15.3 29537 1ua4A 455 6.81e+01 c.72.1.3 99128 1oneA 436 6.92e+01 4enl c.1.11.1,d.54.1.1 29200,38844 1gw5S 142 7.02e+01 d.110.4.2 70633 2gtrA 261 7.04e+01 1emsA 440 7.07e+01 1emsA d.13.1.1,d.160.1.1 37520,42086 1vjvA 415 7.08e+01 d.3.1.9 108632 1v72A 356 7.10e+01 1zud1 251 7.14e+01 2bc2A 227 7.15e+01 1a7tA d.157.1.1 42031 1wrjA 156 7.16e+01 1sh7A 284 7.21e+01 1j0dA 341 7.27e+01 c.79.1.1 83902 1fuxA 166 7.31e+01 1fjjA b.17.1.2 60034 1c76A 136 7.39e+01 2sak d.15.5.1 37718 2al6A 375 7.40e+01 1zxfA 155 7.43e+01 1gpmA 525 7.45e+01 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 2a1kA 233 7.46e+01 1zkrA 153 7.48e+01 1id1A 153 7.52e+01 1id1A c.2.1.9 62286 1kf6B 243 7.52e+01 a.1.2.1,d.15.4.2 72397,72398 1hd2A 161 7.64e+01 c.47.1.10 60962 1pme 380 7.65e+01 1hcl d.144.1.7 41653 1uilA 113 7.66e+01 1qaxA 428 7.76e+01 1qaxA d.58.20.1,d.179.1.1 39376,42597 2d00A 109 7.78e+01 1yh3A 256 7.79e+01 1z2mA 155 7.80e+01 1aoqA 567 7.88e+01 1qksA a.3.1.2,b.70.2.1 15934,27692 2cu1A 103 7.91e+01 2fcjA 119 7.97e+01 1mo2A 294 7.97e+01 c.69.1.22 79331 1jlwA 219 8.08e+01 a.45.1.1,c.47.1.5 71741,71742 1lvwA 295 8.09e+01 c.68.1.6 84723 2aehA 369 8.14e+01 1mqoA 227 8.14e+01 d.157.1.1 103846 2c71A 216 8.20e+01 1v6fA 151 8.22e+01 d.109.1.2 108395 1lv9A 77 8.23e+01 d.9.1.1 78233 1ep3A 311 8.23e+01 2dorA c.1.4.1 28597 1iw7C 1119 8.25e+01 e.29.1.1 71474 1i82A 189 8.34e+01 1i82A b.1.9.2 61937 1e6fA 143 8.41e+01 1e6fA b.64.1.1 59304 1uanA 227 8.41e+01 c.134.1.1 99135 2dcnA 311 8.42e+01 1fqvA 336 8.43e+01 1fqvA a.158.1.1,c.10.1.3 19254,30856 1o5kA 306 8.50e+01 c.1.10.1 92504 1i8aA 189 8.50e+01 1i82A b.1.9.2 61951 2f62A 161 8.50e+01 1w15A 153 8.52e+01 b.7.1.2 109041 1xngA 268 8.53e+01 1pne 140 8.56e+01 1pne d.110.1.1 40866 2beiA 170 8.57e+01 2a8mA 420 8.58e+01 2a8jA 420 8.69e+01 1jpc 109 8.76e+01 1b2pA b.78.1.1 27986 1f1zA 273 8.79e+01 1f1zA a.4.5.27,c.52.1.16 16081,33334 1oihA 301 8.80e+01 b.82.2.5 93051 2ki5A 366 8.85e+01 1qhiA c.37.1.1 31862 1r31A 428 8.86e+01 d.58.20.1,d.179.1.1 96897,96898 1trrA 107 8.86e+01 1jhgA a.4.12.1 19017 2ag4A 164 8.92e+01 1d3yA 301 8.96e+01 1d3yA e.12.1.1 43252 2cr9A 139 8.99e+01