# List of top-scoring protein chains for t2k-100-30-near-backbone-11-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 3.32e-19 1yw4A 341 3.58e-17 1qmuA 380 7.68e-04 1qmuA b.3.2.1,c.56.5.1 22534,33827 1h8lA 380 8.03e-04 b.3.2.1,c.56.5.1 65737,65738 2bo9A 308 1.38e-03 2c1cA 312 5.31e-02 1aye 401 5.49e-02 1aye c.56.5.1,d.58.3.1 33824,39065 1dtdA 303 6.92e-02 1aye c.56.5.1 33823 1jqgA 433 2.79e-01 c.56.5.1,d.58.3.1 71791,71792 1m4lA 307 8.32e-01 c.56.5.1 78604 1yme 309 1.02e+00 1aye c.56.5.1 33804 2ctb 307 1.05e+00 1aye c.56.5.1 33803 2ctc 307 1.10e+00 1aye c.56.5.1 33802 1kwmA 402 2.73e+00 c.56.5.1,d.58.3.1 73079,73080 1bavA 309 3.04e+00 1aye c.56.5.1 33806 6cpa 307 3.19e+00 1aye c.56.5.1 33816 1po5A 476 3.47e+00 a.104.1.1 94963 1gnxA 479 3.64e+00 c.1.8.4 76241 2aqjA 538 4.47e+00 1vpbA 451 4.58e+00 1nonA 179 5.28e+00 c.61.1.1 103868 1xznA 179 6.84e+00 2adcA 229 6.95e+00 1z5rA 306 7.62e+00 1ttuA 477 8.08e+00 b.1.18.1,b.2.5.8,b.42.7.1 107305,107306,107307 1wcgA 464 9.29e+00 1gxmA 332 1.09e+01 a.102.5.1 76371 1a3c 181 1.20e+01 1a3c c.61.1.1 34095 2gl5A 410 1.27e+01 1v8fA 276 1.29e+01 c.26.1.4 100503 1l3iA 192 1.31e+01 c.66.1.22 77676 1t2aA 375 1.36e+01 c.2.1.2 99078 1zhrA 238 1.36e+01 1xx9A 238 1.41e+01 1zhpA 238 1.58e+01 1zhmA 238 1.68e+01 1ki9A 192 1.68e+01 c.37.1.1 84404 1d6mA 653 1.72e+01 1d6mA e.10.1.1 43248 1mjc 69 1.78e+01 1mjc b.40.4.5 25319 1rc9A 221 1.79e+01 1i7dA 659 2.23e+01 1d6mA e.10.1.1 61886 1jvbA 347 2.25e+01 b.35.1.2,c.2.1.1 77181,77182 1w61A 414 2.28e+01 1i24A 404 2.36e+01 c.2.1.2 83663 2a35A 215 2.37e+01 3mefA 69 2.37e+01 1mjc b.40.4.5 25320 1f47B 144 2.42e+01 1f46A d.129.4.1 59645 1eqcA 394 2.43e+01 1cz1A c.1.8.3 28811 2bsfA 176 2.62e+01 1cz1A 394 2.67e+01 1cz1A c.1.8.3 28839 1c3oE 1073 2.71e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18564,31493,31685,31686,41530,41531 1wphA 201 2.79e+01 1n7hA 381 2.80e+01 c.2.1.2 80250 1midA 91 2.81e+01 a.52.1.1 91280 1gehA 444 2.83e+01 c.1.14.1,d.58.9.1 65181,65182 1w30A 201 2.83e+01 1lu9A 287 2.83e+01 c.2.1.7,c.58.1.4 78210,78211 1wovA 250 2.84e+01 2fi1A 190 2.85e+01 1x59A 73 3.02e+01 1cy9A 264 3.07e+01 1ecl e.10.1.1 43236 1hdoA 206 3.14e+01 1he2A c.2.1.2 60965 1b37B 472 3.17e+01 1b37B c.3.1.2,d.16.1.5 30390,37954 1b37A 472 3.19e+01 1b37B c.3.1.2,d.16.1.5 30389,37953 1tsm 316 3.32e+01 1bkpA d.117.1.1 41024 1qm9A 198 3.38e+01 1qm9A d.58.7.1,d.58.7.1 39207,39208 1he2A 206 3.39e+01 1he2A c.2.1.2 60966 1xruA 282 3.40e+01 1rfeA 162 3.52e+01 2conA 79 3.54e+01 1cs0A 1073 3.55e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18558,31487,31673,31674,41518,41519 1keeA 1073 3.55e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 68492,68493,68494,68495,68496,68497 2cq2A 114 3.58e+01 1b5qA 472 3.60e+01 1b37B c.3.1.2,d.16.1.5 30404,37968 1lmzA 187 3.61e+01 a.96.1.4 74037 1f46A 140 3.67e+01 1f46A d.129.4.1 59643 1joa 447 3.81e+01 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30563,30564,40203 1wyuB 474 3.89e+01 1xhcA 367 3.98e+01 1cs0C 1073 4.05e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18559,31488,31675,31676,41520,41521 1c3oA 1073 4.09e+01 1c3oA a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18562,31491,31681,31682,41526,41527 1bxrA 1073 4.10e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18570,31499,31697,31698,41542,41543 1iygA 133 4.20e+01 a.118.8.1 76947 1jz8A 1023 4.24e+01 b.1.4.1,b.1.4.1,b.18.1.5,b.30.5.1,c.1.8.3 67830,67831,67832,67833,67834 1jwqA 179 4.28e+01 c.56.5.6 90921 1rwzA 245 4.34e+01 d.131.1.2,d.131.1.2 98005,98006 1uypA 432 4.37e+01 b.29.1.19,b.67.2.3 100176,100177 1jdbB 1073 4.42e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18574,31503,31705,31706,41550,41551 1obr 326 4.50e+01 1aye c.56.5.2 33828 1keeE 1073 4.58e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 68508,68509,68510,68511,68512,68513 1bh9A 45 4.66e+01 1bh9A a.22.1.3 16483 1zy9A 564 4.66e+01 1eswA 500 4.72e+01 1cwyA c.1.8.1 59500 1c3oG 1073 4.97e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18565,31494,31687,31688,41532,41533 1fp3A 402 5.03e+01 1fp3A a.102.1.3 18842 1jigA 146 5.08e+01 a.25.1.1 71685 1p9bA 442 5.19e+01 c.37.1.10 94385 1cwyA 500 5.30e+01 1cwyA c.1.8.1 28789 1cjcA 460 5.34e+01 1cjcA c.3.1.1,c.4.1.1 30319,30604 1c3oC 1073 5.40e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18563,31492,31683,31684,41528,41529 1lox 662 5.48e+01 1lox a.119.1.2,b.12.1.1 19238,23638 1rpnA 335 5.55e+01 c.2.1.2 97708 1eybA 471 5.56e+01 1ey2A b.82.1.4 28115 2d13A 227 5.70e+01 1keeC 1073 5.70e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 68500,68501,68502,68503,68504,68505 1ihnA 113 5.71e+01 1ihnA c.103.1.1 62388 1kl7A 514 5.83e+01 c.79.1.1 72678 1jfxA 217 5.87e+01 c.1.8.8 62943 1yemA 179 5.91e+01 1oakA 196 5.98e+01 1auq c.62.1.1 34138 2ashA 381 6.09e+01 1auq 208 6.15e+01 1auq c.62.1.1 34137 1keeG 1073 6.17e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 68516,68517,68518,68519,68520,68521 1fwxA 595 6.28e+01 b.6.1.4,b.69.3.1 60069,60070 1db3A 372 6.29e+01 1db3A c.2.1.2 29813 1dp0A 1023 6.32e+01 b.1.4.1,b.1.4.1,b.18.1.5,b.30.5.1,c.1.8.3 22073,22074,23722,24346,28845 1a8y 367 6.47e+01 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 1bglA 1023 6.56e+01 1bglA b.1.4.1,b.1.4.1,b.18.1.5,b.30.5.1,c.1.8.3 22097,22098,23734,24358,28857 1w2tA 432 6.65e+01 1g2rA 100 6.65e+01 1g2rA d.192.1.1 60231 2admA 421 6.70e+01 2admA c.66.1.27 34238 1h8aC 128 6.78e+01 a.4.1.3,a.4.1.3 65731,65732 1f8rA 498 6.86e+01 1f8rA c.3.1.2,d.16.1.5 30410,37974 2tmp 127 6.90e+01 1br9 b.40.3.1 25236 1xovA 326 7.01e+01 1g99A 408 7.04e+01 1g99A c.55.1.2,c.55.1.2 33457,33458 2aegA 268 7.07e+01 1rqpA 299 7.30e+01 b.141.1.1,c.132.1.1 97754,97755 1nznA 126 7.32e+01 a.118.8.1 92382 1qrrA 394 7.37e+01 1qrrA c.2.1.2 29824 1j8yF 297 7.62e+01 1ng1 a.24.13.1,c.37.1.10 62747,62748 1wj7A 104 7.72e+01 2b4yA 271 7.73e+01 1za0A 275 7.76e+01 1nhp 447 7.86e+01 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30549,30550,40196 1luaA 287 7.96e+01 c.2.1.7,c.58.1.4 78216,78217 2hsdA 253 8.00e+01 1e6wA c.2.1.2 29866 1dfx 125 8.03e+01 1dfx b.1.13.1,g.41.5.2 22367,45255 1mvoA 136 8.18e+01 c.23.1.1 79513 1nhs 447 8.23e+01 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30555,30556,40199 1vgwA 231 8.25e+01 c.68.1.13 100612 1wurA 220 8.26e+01 1hdcA 253 8.29e+01 1e6wA c.2.1.2 29862 1ei1A 391 8.56e+01 1aj6 d.14.1.3,d.122.1.2 37570,41104 1fjjA 159 8.62e+01 1fjjA b.17.1.2 59852 1im4A 221 8.74e+01 e.8.1.7 62581