# 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 1.31e-22 1yw4A 341 1.48e-21 1qmuA 380 3.61e-05 1qmuA b.3.2.1,c.56.5.1 22534,33827 1h8lA 380 3.86e-05 b.3.2.1,c.56.5.1 65737,65738 2bo9A 308 3.00e-03 1aye 401 5.19e-02 1aye c.56.5.1,d.58.3.1 33824,39065 2c1cA 312 6.95e-02 1dtdA 303 1.05e-01 1aye c.56.5.1 33823 1ag8A 499 2.63e-01 1bpwA c.82.1.1 35341 1f7wA 144 2.64e-01 1f46A d.129.4.1 59679 1jqgA 433 2.80e-01 c.56.5.1,d.58.3.1 71791,71792 1f47B 144 4.51e-01 1f46A d.129.4.1 59645 1o04A 500 8.41e-01 c.82.1.1 86508 1f46A 140 1.14e+00 1f46A d.129.4.1 59643 2aqjA 538 1.60e+00 1yme 309 1.61e+00 1aye c.56.5.1 33804 1bavA 309 1.61e+00 1aye c.56.5.1 33806 1x74A 360 1.62e+00 1m4lA 307 1.66e+00 c.56.5.1 78604 1b9dA 163 1.80e+00 1b9dA c.55.3.2 33649 2ctb 307 1.96e+00 1aye c.56.5.1 33803 1vp4A 425 2.04e+00 1kwmA 402 2.07e+00 c.56.5.1,d.58.3.1 73079,73080 1akq 147 2.35e+00 5nul c.23.5.1 31159 2ctc 307 2.38e+00 1aye c.56.5.1 33802 2conA 79 2.42e+00 1azl 147 2.65e+00 5nul c.23.5.1 31154 1j9eA 147 2.68e+00 c.23.5.1 62756 1akr 147 2.71e+00 1rcf c.23.5.1 31152 1akt 147 2.79e+00 5nul c.23.5.1 31157 1bu5A 147 2.82e+00 5nul c.23.5.1 31155 1akw 147 2.86e+00 5nul c.23.5.1 31153 1d6mA 653 3.47e+00 1d6mA e.10.1.1 43248 1gntA 553 3.90e+00 e.26.1.1 70290 1jvbA 347 4.11e+00 b.35.1.2,c.2.1.1 77181,77182 1t2aA 375 4.13e+00 c.2.1.2 99078 1xwyA 264 4.43e+00 1nmoA 247 4.61e+00 c.135.1.1 91980 2fx2 147 4.75e+00 1rcf c.23.5.1 31158 1rpnA 335 4.80e+00 c.2.1.2 97708 1oglA 283 4.86e+00 a.204.1.1 92922 1lam 484 5.02e+00 1lam c.50.1.1,c.56.5.3 33166,33829 1e2uA 553 5.14e+00 1e1dA e.26.1.1 43362 1i24A 404 5.39e+00 c.2.1.2 83663 1e1dA 553 5.75e+00 1e1dA e.26.1.1 43363 1a8y 367 5.79e+00 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 1ex2A 189 5.88e+00 1ex2A c.51.4.2 33225 1rq2A 382 6.06e+00 c.32.1.1,d.79.2.1 105048,105049 1f4pA 147 6.19e+00 5nul c.23.5.1 59651 1im4A 221 6.49e+00 e.8.1.7 62581 1d8yA 605 6.75e+00 1xwl c.55.3.5,e.8.1.1 33684,42977 1hdcA 253 7.23e+00 1e6wA c.2.1.2 29862 1hyvA 166 7.39e+00 1b9dA c.55.3.2 61424 2d1yA 256 7.43e+00 1xhkA 187 7.49e+00 1m2rA 327 8.11e+00 d.144.1.7 84760 1ki9A 192 8.20e+00 c.37.1.1 84404 1gnxA 479 8.29e+00 c.1.8.4 76241 1db3A 372 8.40e+00 1db3A c.2.1.2 29813 1tkeA 224 8.49e+00 1b37B 472 8.79e+00 1b37B c.3.1.2,d.16.1.5 30390,37954 1lap 488 9.07e+00 1lam c.50.1.1,c.56.5.3 33171,33834 1xa3A 437 9.35e+00 2kfnA 605 9.68e+00 1xwl c.55.3.5,e.8.1.1 33682,42975 1hxhA 253 9.80e+00 c.2.1.2 76725 1yj7A 171 9.85e+00 1i7dA 659 9.88e+00 1d6mA e.10.1.1 61886 1xk7A 408 1.01e+01 1b5qA 472 1.02e+01 1b37B c.3.1.2,d.16.1.5 30404,37968 6cpa 307 1.06e+01 1aye c.56.5.1 33816 2f02A 323 1.09e+01 1xfjA 261 1.10e+01 d.194.1.2 109585 1bde 35 1.13e+01 1bde j.11.1.1 46142 2awdA 323 1.13e+01 1qo2A 241 1.13e+01 1qo2A c.1.2.1 28533 2ajrA 331 1.21e+01 2cybA 323 1.21e+01 1xq6A 253 1.22e+01 1z5rA 306 1.23e+01 1a6o 332 1.24e+01 1a6o 1ihnA 113 1.26e+01 1ihnA c.103.1.1 62388 1dbxA 158 1.27e+01 1dbuA d.116.1.1 40928 1wg8A 285 1.29e+01 1kdgA 546 1.30e+01 c.3.1.2,d.16.1.1 77337,77338 1gmxA 108 1.34e+01 c.46.1.3 65355 1c3oE 1073 1.44e+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 1om1A 332 1.45e+01 d.144.1.7 93347 1nstA 325 1.47e+01 1nstA c.37.1.5 31951 1g94A 448 1.48e+01 b.71.1.1,c.1.8.1 65169,65170 1wpgA 994 1.49e+01 1b37A 472 1.49e+01 1b37B c.3.1.2,d.16.1.5 30389,37953 1lp4A 332 1.50e+01 d.144.1.7 74170 2evaA 307 1.51e+01 1keeE 1073 1.52e+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 1v7cA 351 1.52e+01 c.79.1.1 100446 1su4A 994 1.56e+01 b.82.7.1,c.108.1.7,d.220.1.1,f.33.1.1 98993,98994,98995,98996 1bllE 488 1.57e+01 1lam c.50.1.1,c.56.5.3 33170,33833 1rkiA 102 1.61e+01 1klnA 605 1.62e+01 1xwl c.55.3.5,e.8.1.1 33693,42986 1h6kZ 98 1.67e+01 d.58.7.1 60686 1rliA 184 1.80e+01 c.23.5.6 97647 1tyyA 339 1.80e+01 1p9bA 442 1.80e+01 c.37.1.10 94385 1bl3A 160 1.81e+01 1b9dA c.55.3.2 33655 1jdbB 1073 1.85e+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 1h3fA 432 1.86e+01 c.26.1.1,d.66.1.4 76631,76632 2hsdA 253 1.90e+01 1e6wA c.2.1.2 29866 1dsj 28 1.95e+01 j.11.1.1 46139 1f0kA 364 1.97e+01 1f0kA c.87.1.2 35465 1wzcA 249 1.98e+01 1djxB 624 2.01e+01 1djxB a.39.1.7,b.7.1.1,c.1.18.1 17343,23160,29588 1x59A 73 2.01e+01 1nhp 447 2.03e+01 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30549,30550,40196 1cy9A 264 2.03e+01 1ecl e.10.1.1 43236 1kfd 605 2.07e+01 1xwl c.55.3.5,e.8.1.1 33694,42987 1s95A 333 2.12e+01 d.159.1.3 105375 1gnlA 544 2.13e+01 e.26.1.1 70287 1cs0A 1073 2.13e+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 1qhtA 775 2.17e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1ynuA 473 2.19e+01 1cz1A 394 2.21e+01 1cz1A c.1.8.3 28839 2b81A 323 2.22e+01 1qatB 622 2.23e+01 1djxB a.39.1.7,b.7.1.1,c.1.18.1 17355,23172,29600 1y8qB 640 2.25e+01 1c3oA 1073 2.25e+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 1lbd 282 2.25e+01 1lbd a.123.1.1 19279 1cs0C 1073 2.29e+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 1t0bA 252 2.30e+01 c.23.16.6 106199 1gn0A 108 2.30e+01 c.46.1.3 65358 1kl7A 514 2.30e+01 c.79.1.1 72678 1f20A 435 2.31e+01 b.43.4.1,c.25.1.4 64932,64933 1nhs 447 2.32e+01 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30555,30556,40199 1keeG 1073 2.37e+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 1bdb 277 2.39e+01 1bdb c.2.1.2 29874 1rwrA 301 2.41e+01 b.80.1.11 97990 1wolA 122 2.43e+01 1keeC 1073 2.43e+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 1vig 71 2.46e+01 1vih d.51.1.1 38806 1eqcA 394 2.51e+01 1cz1A c.1.8.3 28811 1nxqA 251 2.51e+01 c.2.1.2 86388 1g0cA 364 2.59e+01 7a3hA c.1.8.3 60165 1k0dA 260 2.59e+01 a.45.1.1,c.47.1.5 67930,67931 1m6yA 301 2.64e+01 a.60.13.1,c.66.1.23 78716,78717 2av5A 120 2.72e+01 1g01A 364 2.74e+01 7a3hA c.1.8.3 60161 1fgkA 310 2.75e+01 1fgkA d.144.1.7 41693 1qf6A 642 2.76e+01 1qf6A c.51.1.1,d.15.10.1,d.67.1.1,d.104.1.1 33210,39551,39562,40759 1dusA 194 2.79e+01 1dusA c.66.1.4 34182 1itzA 675 2.80e+01 c.36.1.10,c.36.1.6,c.48.1.1 76797,76798,76799 1pv1A 299 2.84e+01 1v8fA 276 2.87e+01 c.26.1.4 100503 1ktjA 129 2.91e+01 b.1.18.7 72974 1vqvA 306 2.93e+01 1bxrA 1073 2.97e+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 18570,31499,31697,31698,41542,41543 2gl5A 410 3.03e+01 1c3oG 1073 3.05e+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 18565,31494,31687,31688,41532,41533 1djnA 729 3.07e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28612,30313,30598 1zk4A 251 3.08e+01 1ceo 343 3.09e+01 1ceo c.1.8.3 28808 1keeA 1073 3.11e+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 1qjcA 158 3.13e+01 1b6tA c.26.1.3 63328 1aqm 453 3.19e+01 1smd b.71.1.1,c.1.8.1 27717,28704 1pyfA 312 3.25e+01 c.1.7.1 95334 1qrrA 394 3.25e+01 1qrrA c.2.1.2 29824 1h1nA 305 3.27e+01 c.1.8.3 70855 1n7hA 381 3.28e+01 c.2.1.2 80250 2vil 126 3.30e+01 2vil d.109.1.1 40830 1lpuA 332 3.31e+01 d.144.1.7 74177 1wyuB 474 3.32e+01 1eexB 224 3.33e+01 1dioB c.51.3.1 33213 1wznA 252 3.33e+01 1q5yA 85 3.38e+01 d.58.18.4 95950 1lqpA 135 3.40e+01 d.32.1.2 78151 1djqA 729 3.42e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28614,30315,30600 2aj7A 163 3.52e+01 1rijA 25 3.53e+01 k.32.1.1 104951 1ydhA 216 3.62e+01 1r0mA 375 3.63e+01 c.1.11.2,d.54.1.1 104747,104748 1wurA 220 3.66e+01 1vgwA 231 3.69e+01 c.68.1.13 100612 1f6yA 262 3.78e+01 1f6yA c.1.21.2 29673 1qasA 622 3.86e+01 1djxB a.39.1.7,b.7.1.1,c.1.18.1 17340,23157,29585 1aj4 161 4.04e+01 1ncx a.39.1.5 17244 1yfnA 118 4.06e+01 1jztA 246 4.08e+01 c.104.1.1 63319 1xhcA 367 4.09e+01 1h2vZ 156 4.09e+01 d.58.7.1 76595 1dbuA 158 4.15e+01 1dbuA d.116.1.1 40930 1o0pA 104 4.16e+01 d.58.7.1 86535 1vkwA 218 4.17e+01 d.90.1.2 108695 1f24A 402 4.18e+01 1rom a.104.1.1 18953 1jfbA 404 4.24e+01 a.104.1.1 66624 1gqeA 365 4.29e+01 e.38.1.1 70351 1obr 326 4.30e+01 1aye c.56.5.2 33828 1kjnA 157 4.32e+01 c.115.1.1 72614 1s3eA 520 4.33e+01 c.3.1.2,d.16.1.5 98426,98427 2bi7A 384 4.35e+01 1c3oC 1073 4.39e+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 1cmnA 402 4.43e+01 1rom a.104.1.1 18958 2d4qA 257 4.46e+01 1se7A 83 4.46e+01 1j1uA 306 4.50e+01 c.26.1.1 83980 1nkiA 135 4.50e+01 d.32.1.2 91941 1g6wA 261 4.52e+01 1hqoA a.45.1.1,c.47.1.5 17751,33045 1rom 403 4.57e+01 1rom a.104.1.1 18963 2vik 126 4.61e+01 2vil d.109.1.1 40829 1b6tA 159 4.63e+01 1b6tA c.26.1.3 31600 1nonA 179 4.71e+01 c.61.1.1 103868 2f6hX 419 4.71e+01 1m4jA 142 4.75e+01 d.109.1.2 78602 16pk 415 4.82e+01 16pk c.86.1.1 35454 1qcxA 359 4.84e+01 1qcxA b.80.1.2 28028 1o94A 729 4.86e+01 c.1.4.1,c.3.1.1,c.4.1.1 81200,81201,81202 1zy7A 403 4.93e+01 1iqcA 308 4.99e+01 a.3.1.5,a.3.1.5 66266,66267 2c46A 241 5.02e+01 1joa 447 5.03e+01 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30563,30564,40203 1dbwA 126 5.06e+01 1dbwA c.23.1.1 31095 1a9xA 1058 5.06e+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 18550,31479,31657,31658,41502,41503 1ub9A 100 5.15e+01 a.4.5.28 99159 1cjcA 460 5.15e+01 1cjcA c.3.1.1,c.4.1.1 30319,30604 1u13A 455 5.17e+01 a.104.1.1 107578 1ou8A 111 5.17e+01 b.136.1.1 93543 1mjc 69 5.17e+01 1mjc b.40.4.5 25319 1q1rA 431 5.19e+01 c.3.1.5,c.3.1.5,d.87.1.1 95600,95601,95602 2c3zA 222 5.27e+01 2axpA 173 5.32e+01 1i9sA 210 5.39e+01 1i9sA c.45.1.1 62099 1jclA 260 5.48e+01 c.1.10.1 66501 2al6A 375 5.51e+01 1uzmA 247 5.54e+01 1ox8A 107 5.55e+01 b.136.1.1 93671 1p1xA 260 5.57e+01 c.1.10.1 104060 1vmfA 145 5.58e+01 1al3 324 5.65e+01 1al3 c.94.1.1 35835 1uch 230 5.68e+01 1uch d.3.1.6 37129 1pmi 440 5.71e+01 1pmi b.82.1.3 28114 1ojaA 520 5.74e+01 c.3.1.2,d.16.1.5 93096,93097 1nffA 260 5.79e+01 c.2.1.2 80457 1dcjA 81 5.79e+01 1dcjA d.68.3.3 59115 1pjcA 361 5.85e+01 1sayA c.2.1.4,c.23.12.2 30101,31361 1pjbA 361 5.87e+01 1sayA c.2.1.4,c.23.12.2 30103,31363 1yqeA 282 5.88e+01 1c3kA 147 5.93e+01 1jotA b.77.3.1 27984 1sayA 361 6.07e+01 1sayA c.2.1.4,c.23.12.2 30102,31362 1fliA 98 6.12e+01 1awcA a.4.5.21 16160 1g5cA 170 6.16e+01 1g5cA c.53.2.1 60264 1jcjA 260 6.17e+01 c.1.10.1 66499 1c3mA 147 6.21e+01 1jotA b.77.3.1 27983 1w61A 414 6.23e+01 1u1iA 392 6.25e+01 c.2.1.3,d.81.1.3 107582,107583 1dkuA 317 6.30e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 1gmjA 84 6.32e+01 h.4.8.1 65310 1vavA 222 6.42e+01 b.29.1.18 108472 1ubpB 122 6.45e+01 1ubpB b.85.3.1 28346 2cbf 234 6.46e+01 1cbf c.90.1.1 35588 2ahxA 617 6.53e+01 1o77D 146 6.60e+01 c.23.2.1 81128 2f15A 96 6.61e+01 1wr8A 231 6.79e+01 1dxy 333 6.81e+01 1dxy c.2.1.4,c.23.12.1 30094,31354 1hqoA 258 6.82e+01 1hqoA a.45.1.1,c.47.1.5 17749,33043 1a3c 181 6.83e+01 1a3c c.61.1.1 34095 1v71A 323 6.84e+01 1khtA 192 6.90e+01 c.37.1.1 84401 1gosA 520 6.94e+01 c.3.1.2,d.16.1.5 65425,65426 1ofwA 296 6.94e+01 a.138.1.1 92850 1ji0A 240 7.06e+01 c.37.1.12 71665 1vkjA 285 7.14e+01 c.37.1.5 108666 1cec 343 7.16e+01 1ceo c.1.8.3 28809 1eulA 994 7.20e+01 1eulA 1dkrA 317 7.24e+01 1dkuA c.61.1.2,c.61.1.2 34114,34115 1nrzA 164 7.30e+01 c.38.1.1 86131 1xfsA 178 7.33e+01 d.129.3.5 109589 1x8vA 455 7.35e+01 1ngkA 128 7.36e+01 a.1.1.1 85673 1frvA 264 7.41e+01 2frvA e.19.1.1 43308 1j9iA 68 7.42e+01 a.6.1.5 71619 1mi3A 322 7.52e+01 c.1.7.1 91274 1bjt 793 7.54e+01 1bjt e.11.1.1 43249 1jbeA 128 7.58e+01 3chy c.23.1.1 62845 1y81A 138 7.61e+01 2fi1A 190 7.76e+01 2au3A 407 7.78e+01 2tmdA 729 7.82e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28616,30317,30602 2arkA 188 7.92e+01 1xznA 179 7.94e+01 2ab0A 205 7.95e+01 1gkuB 1054 8.03e+01 c.37.1.16,c.37.1.16,e.10.1.1 65257,65258,65259 2a35A 215 8.09e+01 1txnA 328 8.10e+01 1ux8A 132 8.11e+01 1w78A 422 8.18e+01 1x1rA 178 8.24e+01 1b97A 244 8.31e+01 1rvaA c.52.1.2 33252 1xovA 326 8.33e+01 1tluA 130 8.41e+01 d.156.1.2 107139 1h5zA 455 8.43e+01 a.104.1.1 90622 1j99A 293 8.48e+01 c.37.1.5 71618 1w30A 201 8.49e+01 1szqA 483 8.49e+01 e.44.1.1 99045 1ats 386 8.52e+01 1ba1 c.55.1.1,c.55.1.1 33423,33424 1q7eA 428 8.53e+01 c.123.1.1 96035 1o8rA 94 8.56e+01 d.234.1.1 86677 4ubpB 126 8.65e+01 1ubpB b.85.3.1 28345 1ecl 597 8.69e+01 1ecl e.10.1.1 43238 1dckA 126 8.70e+01 1dbwA c.23.1.1 31097 1wd5A 208 8.77e+01 1wnaA 131 8.80e+01 1vnc 609 8.80e+01 1vns a.111.1.3 19065 1uwvA 433 8.88e+01 b.40.4.12,c.66.1.40 100128,100129 1o1zA 234 8.94e+01 c.1.18.3 86555 1oq9A 363 8.95e+01 a.25.1.2 87257 1q53A 112 8.96e+01 d.58.4.4 95858 1hm6A 346 8.97e+01 1avc a.65.1.1 18147 1nytA 271 9.00e+01 c.2.1.7,c.58.1.5 86417,86418