# List of top-scoring protein chains for t2k-100-30-bys-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 2bcoA 350 4.14e-34 1yw4A 341 9.65e-32 1qmuA 380 4.72e-06 1qmuA b.3.2.1,c.56.5.1 22534,33827 1h8lA 380 5.34e-06 b.3.2.1,c.56.5.1 65737,65738 1yp5A 58 1.64e-01 3hmgA 328 3.27e-01 1hgeA b.19.1.2 23825 1ekrA 161 4.18e-01 1ekrA d.58.21.1 39380 1hgeA 328 6.06e-01 1hgeA b.19.1.2 23816 2c1cA 312 6.13e-01 1vm8A 534 8.74e-01 1jv1A 505 9.08e-01 c.68.1.5 71892 1az9 457 9.28e-01 1az9 c.55.2.1,d.127.1.1 33547,41164 1jqgA 433 9.59e-01 c.56.5.1,d.58.3.1 71791,71792 1f7wA 144 1.33e+00 1f46A d.129.4.1 59679 1ycsB 239 1.52e+00 1ycsB d.211.1.1,b.34.2.1 19155,24553 1ruwA 69 1.55e+00 1a16 440 1.60e+00 1az9 c.55.2.1,d.127.1.1 33548,41165 2viuA 328 1.61e+00 1hgeA b.19.1.2 23797 2bo9A 308 1.83e+00 1wl9A 440 2.10e+00 1f47B 144 2.42e+00 1f46A d.129.4.1 59645 2bwvA 440 2.89e+00 1csp 67 4.00e+00 1mjc b.40.4.5 25321 1ag8A 499 4.42e+00 1bpwA c.82.1.1 35341 1xhkA 187 4.60e+00 1ummA 172 4.73e+00 a.3.1.1 107958 2aqjA 538 4.85e+00 2c8sA 172 4.90e+00 1t2wA 145 5.18e+00 b.100.1.1 106289 1f46A 140 5.62e+00 1f46A d.129.4.1 59643 1aye 401 5.78e+00 1aye c.56.5.1,d.58.3.1 33824,39065 1cz1A 394 5.91e+00 1cz1A c.1.8.3 28839 2conA 79 6.28e+00 1vhuA 211 6.31e+00 c.50.1.2 100703 1aw7A 194 6.34e+00 1aw7A b.40.2.2,d.15.6.1 25164,37753 2f9cA 334 6.50e+00 1b9dA 163 6.71e+00 1b9dA c.55.3.2 33649 1jhfA 202 7.12e+00 a.4.5.2,b.87.1.1 63057,63058 1eqcA 394 7.57e+00 1cz1A c.1.8.3 28811 1ki9A 192 7.68e+00 c.37.1.1 84404 1rc6A 261 7.83e+00 b.82.1.11 97287 1fngA 192 8.03e+00 1iakA b.1.1.2,d.19.1.1 59904,59905 1m2rA 327 8.11e+00 d.144.1.7 84760 1xd5A 112 8.22e+00 1rtfB 252 8.66e+00 5ptp 1bqg 451 8.77e+00 1bqg c.1.11.2,d.54.1.1 29217,38861 1k77A 260 9.01e+00 c.1.15.5 72096 1x7vA 99 9.08e+00 d.58.4.11 109501 1ieaA 192 9.23e+00 1iakA b.1.1.2,d.19.1.1 21631,38205 1wkrA 340 9.43e+00 b.50.1.2 109395 2aliA 158 9.54e+00 1hjzA 192 9.74e+00 c.50.1.2 83520 1fneA 192 1.08e+01 1iakA b.1.1.2,d.19.1.1 59896,59897 1a6o 332 1.14e+01 1a6o 1yqfA 203 1.17e+01 1nmoA 247 1.17e+01 c.135.1.1 91980 1te5A 257 1.19e+01 d.153.1.1 106795 2er7E 330 1.24e+01 2er7E b.50.1.2 26779 1u14A 172 1.25e+01 c.51.4.3 107579 2c5qA 240 1.30e+01 1o4tA 133 1.36e+01 b.82.1.9 86622 8dfr 189 1.43e+01 1aoeA c.71.1.1 34895 1im4A 221 1.43e+01 e.8.1.7 62581 1yj7A 171 1.43e+01 1nykA 165 1.47e+01 b.33.1.1 86408 1xovA 326 1.47e+01 1om1A 332 1.49e+01 d.144.1.7 93347 1nuuA 252 1.50e+01 c.26.1.3 86209 1ihnA 113 1.57e+01 1ihnA c.103.1.1 62388 1nstA 325 1.58e+01 1nstA c.37.1.5 31951 2f9nA 245 1.58e+01 1dtdA 303 1.70e+01 1aye c.56.5.1 33823 1m1nB 522 1.75e+01 c.92.2.3 78418 1uj0A 62 1.77e+01 b.34.2.1 99449 1o04A 500 1.78e+01 c.82.1.1 86508 1x0vA 354 1.79e+01 1qxrA 189 1.80e+01 b.82.1.7 96552 1lp4A 332 1.82e+01 d.144.1.7 74170 2ajrA 331 1.87e+01 1b5l 172 1.87e+01 1b5l a.26.1.3 16900 1vj0A 380 1.88e+01 b.35.1.2,c.2.1.1 100786,100787 1ijaA 148 1.89e+01 1ijaA b.100.1.1 62484 1ex2A 189 1.91e+01 1ex2A c.51.4.2 33225 1oewA 329 1.97e+01 b.50.1.2 86924 1hyvA 166 2.08e+01 1b9dA c.55.3.2 61424 1sefA 274 2.08e+01 b.82.1.11 105452 1pv9A 348 2.10e+01 c.55.2.1,d.127.1.1 95157,95158 1c0aA 585 2.10e+01 1c0aA b.40.4.1,d.74.4.1,d.104.1.1 25246,39731,40767 1vmfA 145 2.11e+01 1bia 321 2.13e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1vjlA 164 2.13e+01 d.257.1.1 100822 1x82A 190 2.13e+01 2fflA 756 2.15e+01 1iqaA 160 2.15e+01 b.22.1.1 71274 2fpeA 62 2.16e+01 1df7A 159 2.17e+01 3dfr c.71.1.1 34885 5er2E 330 2.20e+01 2er7E b.50.1.2 26783 1lpuA 332 2.22e+01 d.144.1.7 74177 1uyjA 296 2.28e+01 f.8.1.2 108143 1a0lA 244 2.28e+01 5ptp b.47.1.2 26286 1d5yA 292 2.29e+01 1d5yA a.4.1.8,a.4.1.8,d.60.1.2 16055,16056,39532 1iawA 317 2.30e+01 c.52.1.9 62126 1bdb 277 2.30e+01 1bdb c.2.1.2 29874 2cxaA 256 2.35e+01 1gkuB 1054 2.35e+01 c.37.1.16,c.37.1.16,e.10.1.1 65257,65258,65259 1sx5A 244 2.40e+01 c.52.1.2 99023 1epnE 330 2.40e+01 2er7E b.50.1.2 26780 1ltoA 245 2.42e+01 b.47.1.2 84707 1hv2A 99 2.42e+01 d.42.1.1 61287 3ullA 132 2.45e+01 3ullA b.40.4.3 25282 1bavA 309 2.48e+01 1aye c.56.5.1 33806 1irxA 523 2.49e+01 a.97.1.2,c.26.1.1 71378,71379 1u6zA 513 2.52e+01 1occG 84 2.52e+01 2occG f.23.2.1 43562 1qhtA 775 2.53e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1vp4A 425 2.62e+01 1f35A 162 2.67e+01 1f35A b.94.1.1 59628 1rsy 152 2.67e+01 1rsy b.7.1.2 23192 1d6mA 653 2.69e+01 1d6mA e.10.1.1 43248 1c9oA 66 2.79e+01 1mjc b.40.4.5 25325 1derA 547 2.79e+01 1derA 1xfjA 261 2.79e+01 d.194.1.2 109585 1kmvA 186 2.81e+01 c.71.1.1 72757 1wyuB 474 2.82e+01 1i07A 60 2.83e+01 1aojA b.34.2.1 61477 1ly2A 130 2.87e+01 g.18.1.1,g.18.1.1 74335,74336 1ooeA 236 2.90e+01 c.2.1.2 87196 1qo2A 241 2.91e+01 1qo2A c.1.2.1 28533 1f3lA 321 2.99e+01 1g6q2 c.66.1.6 59630 1s55A 156 3.00e+01 1yoxA 250 3.03e+01 1jvbA 347 3.09e+01 b.35.1.2,c.2.1.1 77181,77182 2occG 84 3.13e+01 2occG f.23.2.1 43522 2cvlA 124 3.21e+01 1hxhA 253 3.24e+01 c.2.1.2 76725 1a5iA 265 3.27e+01 5ptp b.47.1.2 26331 1gr5A 547 3.38e+01 i.16.1.1 65478 1gvuA 329 3.39e+01 b.50.1.2 70619 1vpdA 299 3.39e+01 1qwiA 143 3.41e+01 d.227.1.1 96474 1ymmA 191 3.43e+01 1ghqB 134 3.46e+01 1ghqB g.18.1.1,g.18.1.1 60522,60523 1bl3A 160 3.50e+01 1b9dA c.55.3.2 33655 1v7cA 351 3.51e+01 c.79.1.1 100446 1b06A 210 3.56e+01 1avmA a.2.11.1,d.44.1.1 15740,38737 1roaA 122 3.71e+01 d.17.1.2 105024 1jobA 162 3.73e+01 1f35A b.94.1.1 63207 1tf5A 844 3.79e+01 a.162.1.1,a.172.1.1,c.37.1.19,c.37.1.19 106834,106835,106836,106837 1v54G 85 3.85e+01 f.23.2.1 100328 1pmi 440 3.91e+01 1pmi b.82.1.3 28114 1ev7A 317 3.91e+01 1ev7B c.52.1.9 33315 1h4pA 408 3.96e+01 c.1.8.3 90617 1yme 309 4.09e+01 1aye c.56.5.1 33804 1hdcA 253 4.12e+01 1e6wA c.2.1.2 29862 1vi4A 174 4.12e+01 c.8.7.1 100731 1ykfA 352 4.23e+01 1pedA b.35.1.2,c.2.1.1 24757,29773 1es4A 262 4.23e+01 1skf e.3.1.1 42683 1jcjA 260 4.24e+01 c.1.10.1 66499 2f02A 323 4.26e+01 2minB 522 4.31e+01 1qguB c.92.2.3 35610 1t2aA 375 4.41e+01 c.2.1.2 99078 1earA 147 4.43e+01 b.107.1.1,d.58.38.1 64875,64876 1u1zA 168 4.43e+01 d.38.1.6 107602 2rveA 244 4.44e+01 1rvaA c.52.1.2 33283 1gqeA 365 4.48e+01 e.38.1.1 70351 1o89A 345 4.48e+01 b.35.1.2,c.2.1.1 92644,92645 1mg2D 155 4.49e+01 a.3.1.1 79062 1jsmA 325 4.54e+01 b.19.1.2 63264 1p1xA 260 4.54e+01 c.1.10.1 104060 1eexB 224 4.55e+01 1dioB c.51.3.1 33213 1rijA 25 4.56e+01 k.32.1.1 104951 1j9lA 247 4.58e+01 c.106.1.1 62762 1xwyA 264 4.60e+01 1yphE 97 4.66e+01 1b97A 244 4.70e+01 1rvaA c.52.1.2 33252 1jclA 260 4.71e+01 c.1.10.1 66501 1dp4A 435 4.72e+01 1dp4A c.93.1.1 35710 1g31A 111 4.76e+01 1g31A b.35.1.1 24656 1l4dB 122 4.80e+01 d.15.5.1 77684 1hd7A 318 4.82e+01 1bix d.151.1.1 41780 1m4lA 307 4.84e+01 c.56.5.1 78604 2d1yA 256 4.90e+01 1p9yA 121 4.94e+01 d.241.2.1 94402 1a49A 530 4.94e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27026,29255,33109 1dcjA 81 4.95e+01 1dcjA d.68.3.3 59115 1bb9 115 5.00e+01 1bb9 b.34.2.1 24554 1lbd 282 5.00e+01 1lbd a.123.1.1 19279 2ahuA 531 5.01e+01 1zsyA 357 5.02e+01 1aijH 260 5.04e+01 6prcH b.41.1.1,f.23.10.1 25466,43463 1amoA 615 5.05e+01 1amoA b.43.4.1,c.23.5.2,c.25.1.4 25669,31210,31557 1mjc 69 5.08e+01 1mjc b.40.4.5 25319 2ctb 307 5.13e+01 1aye c.56.5.1 33803 1jsdA 319 5.20e+01 b.19.1.2 63258 1fo4A 1332 5.24e+01 a.56.1.1,d.15.4.2,d.41.1.1,d.87.2.1,d.133.1.1,d.145.1.3 17910,37695,38586,40227,41416,41758 1kwmA 402 5.24e+01 c.56.5.1,d.58.3.1 73079,73080 1ev7B 317 5.27e+01 1ev7B c.52.1.9 33316 1jdfA 447 5.32e+01 c.1.11.2,d.54.1.1 62897,62898 1qcsA 211 5.35e+01 1qcsA b.52.2.3,d.31.1.1 26927,38461 1yb3A 175 5.41e+01 1kp8A 547 5.44e+01 a.129.1.1,c.8.5.1,d.56.1.1 84414,84415,84416 2fikA 287 5.48e+01 1p5vB 147 5.54e+01 b.2.3.2 87814 1nt4A 391 5.55e+01 c.60.1.2 92102 1hdr 244 5.55e+01 1dhr c.2.1.2 29837 1pyfA 312 5.59e+01 c.1.7.1 95334 3tss 194 5.65e+01 1aw7A b.40.2.2,d.15.6.1 25160,37749 1ov3A 138 5.65e+01 b.34.2.1,b.34.2.1 87451,87452 1kdgA 546 5.65e+01 c.3.1.2,d.16.1.1 77337,77338 1vig 71 5.71e+01 1vih d.51.1.1 38806 1hxmD 242 5.73e+01 b.1.1.1,b.1.1.2 61373,61374 1rwrA 301 5.73e+01 b.80.1.11 97990 2ctc 307 5.77e+01 1aye c.56.5.1 33802 1ecfB 504 5.79e+01 1ecfB c.61.1.1,d.153.1.1 34054,41821 1afqC 96 5.81e+01 5ptp 1ab9C 97 5.83e+01 5ptp 1gg6C 97 5.86e+01 5ptp 1vcaA 202 5.87e+01 1vcaA b.1.1.3,b.1.1.4 21649,21685 1j9jA 247 5.89e+01 c.106.1.1 62758 1v97A 1332 5.99e+01 a.56.1.1,d.15.4.2,d.41.1.1,d.87.2.1,d.133.1.1,d.145.1.3 108436,108437,108438,108439,108440,108441 1b07A 59 6.01e+01 1ckaA b.34.2.1 24461 3minB 522 6.02e+01 1qguB c.92.2.3 35606 1lab 80 6.09e+01 1ghj b.84.1.1 28226 2awdA 323 6.10e+01 2cgaA 245 6.16e+01 5ptp b.47.1.2 26028 1dg9A 157 6.20e+01 1dg9A c.44.1.1 32637 1gdhA 320 6.24e+01 1gdhA c.2.1.4,c.23.12.1 30095,31355 2ahmA 88 6.25e+01 1vqwA 457 6.27e+01 1wpnA 188 6.31e+01 1ipwA 175 6.32e+01 2prd b.40.5.1 25427 2mhr 118 6.40e+01 2mhr a.24.4.1 16581 2b5eA 504 6.50e+01 1diaA 306 6.57e+01 1a4iA c.2.1.7,c.58.1.2 30280,33928 1e32A 458 6.60e+01 1e32A b.52.2.3,c.37.1.20,d.31.1.1 59183,59184,59185 1hm9A 468 6.61e+01 b.81.1.4,c.68.1.5 65866,65867 1bix 287 6.63e+01 1bix d.151.1.1 41781 1pf5A 131 6.66e+01 d.79.1.1 94604 1td6A 306 6.70e+01 1u02A 239 6.71e+01 c.108.1.15 107538 1il6 185 6.75e+01 1alu a.26.1.1 16827 1jt7A 146 6.76e+01 b.42.1.1 67255 1j57A 143 6.76e+01 d.221.1.1 77079 1l6sA 323 6.76e+01 c.1.10.3 73627 2fytA 340 6.76e+01 1wqwA 235 6.84e+01 2anyA 241 6.92e+01 1gcpA 70 7.00e+01 1gcpA b.34.2.1 60430 2anwA 241 7.02e+01 1ekbB 235 7.07e+01 5ptp b.47.1.2 26282 1b37B 472 7.10e+01 1b37B c.3.1.2,d.16.1.5 30390,37954 1xvaA 292 7.14e+01 1xvaA c.66.1.5 34183 1wy2A 351 7.14e+01 2bwqA 129 7.15e+01 1fp3A 402 7.20e+01 1fp3A a.102.1.3 18842 1z9lA 128 7.22e+01 1vggA 161 7.24e+01 1p1mA 406 7.26e+01 b.92.1.4,c.1.9.9 87696,87697 2fi1A 190 7.29e+01 2pfkA 320 7.30e+01 3pfk c.89.1.1 35577 1hmy 327 7.32e+01 6mhtA c.66.1.26 34229 1j6pA 418 7.33e+01 b.92.1.4,c.1.9.9 77089,77090 1h0hB 214 7.43e+01 d.58.1.5 76437 2aujD 309 7.45e+01 1m16A 146 7.51e+01 b.42.1.1 91164 1rvaA 244 7.53e+01 1rvaA c.52.1.2 33240 1el6A 219 7.54e+01 1el6B d.182.1.1 42606 1ts3A 194 7.54e+01 1aw7A b.40.2.2,d.15.6.1 25168,37757 1i7dA 659 7.56e+01 1d6mA e.10.1.1 61886 1ux8A 132 7.58e+01 1o0wA 252 7.61e+01 a.149.1.1,d.50.1.1 80751,80752 2fywA 267 7.62e+01 1zcbA 362 7.65e+01 2fp7B 172 7.66e+01 1aojA 60 7.71e+01 1aojA b.34.2.1 24555 1ow1A 195 7.71e+01 b.131.1.3 93625 1c0eA 157 7.80e+01 1dg9A c.44.1.1 32638 1fyhB 229 7.85e+01 1jrhI b.1.2.1,b.1.2.1 22055,22056 1w70A 60 7.87e+01 2c7pA 327 7.87e+01 2cs2A 134 7.90e+01 2cdpA 160 7.96e+01 2cybA 323 7.98e+01 1c3mA 147 8.00e+01 1jotA b.77.3.1 27983 1el6B 219 8.01e+01 1el6B d.182.1.1 42607 1v8fA 276 8.03e+01 c.26.1.4 100503 1p7tA 731 8.05e+01 c.1.13.1 94319 1s5lH 66 8.05e+01 1jetA 517 8.08e+01 1jevA c.94.1.1 35718 1z5rA 306 8.10e+01 2ak5A 64 8.13e+01 1gmjA 84 8.13e+01 h.4.8.1 65310 1x1mA 107 8.17e+01 1h7eA 245 8.19e+01 c.68.1.13 60717 1c3kA 147 8.23e+01 1jotA b.77.3.1 27984 1fe8A 196 8.23e+01 1atzA c.62.1.1 59783 1jevA 517 8.28e+01 1jevA c.94.1.1 35720 1elt 236 8.29e+01 5ptp b.47.1.2 26281 1x59A 73 8.33e+01 1azeA 56 8.36e+01 b.34.2.1 24536 1y8qB 640 8.41e+01 1wg8A 285 8.42e+01 2b25A 336 8.42e+01 1yqeA 282 8.47e+01 1eonA 245 8.52e+01 1rvaA c.52.1.2 33238 1d2gA 292 8.57e+01 1xvaA c.66.1.5 34187 2axtH 66 8.61e+01 1ub4A 110 8.63e+01 b.34.6.2 88399 1jwqA 179 8.68e+01 c.56.5.6 90921 1xkgA 312 8.86e+01 1fjxA 327 8.87e+01 6mhtA c.66.1.26 34228 1cliA 345 8.88e+01 1cliA d.79.4.1,d.139.1.1 39816,41459