# List of top-scoring protein chains for t2k-100-30-dssp-ebghstl 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 1kqnA 279 1.67e-30 c.26.1.3 77492 1kkuA 279 2.24e-30 c.26.1.3 72661 1nuuA 252 1.60e-28 1kamA 194 2.32e-26 c.26.1.3 72254 1k4mA 213 4.42e-25 c.26.1.3 77258 1b6tA 159 4.36e-15 1b6tA c.26.1.3 31600 1qjcA 158 5.85e-15 1b6tA c.26.1.3 63328 1od6A 160 5.97e-15 1f9aA 168 1.63e-10 1f9aA c.26.1.3 31602 1ej2A 181 1.64e-08 1f9aA c.26.1.3 59414 1hybA 181 1.85e-07 1f9aA c.26.1.3 61399 1cozA 129 9.65e-05 1cozA c.26.1.2 31598 1g8fA 511 1.22e-03 1g8fA b.58.1.2 60348 c.26.1.5 60349 c.37.1.15 60350 1mrzA 293 2.58e-03 1jhdA 396 7.23e-03 b.58.1.2 66712 c.26.1.5 66713 1eqjA 511 5.01e-02 1ejjA c.105.1.1 59495 c.76.1.3 59496 1d2fA 390 5.15e-02 1d2fA c.67.1.3 34411 1ejjA 511 5.92e-02 1ejjA c.105.1.1 59422 c.76.1.3 59423 1o98A 511 1.00e-01 1o0uA 429 4.51e-01 c.118.1.1 80743 1be1 137 5.32e-01 1be1 c.23.6.1 31237 1fkx 349 8.43e-01 1a4mA c.1.9.1 29018 1hl2A 297 8.73e-01 1a4mA 349 8.76e-01 1a4mA c.1.9.1 29014 1jilA 420 1.03e+00 c.26.1.1 66745 1add 349 1.15e+00 1a4mA c.1.9.1 29020 1d3yA 301 1.25e+00 1d3yA e.12.1.1 43252 1fdyA 297 1.42e+00 1nal3 c.1.10.1 29071 1h0cA 392 1.49e+00 1hnjA 317 1.50e+00 1hn9A c.95.1.1 35969 c.95.1.1 35970 1nal1 297 1.56e+00 1nal3 1fsz 372 1.58e+00 1fsz c.32.1.1 31750 d.79.2.1 39802 1bzyA 217 1.64e+00 1qk3A c.61.1.1 34071 1hn9A 317 1.68e+00 1hn9A c.95.1.1 35977 c.95.1.1 35978 1o0yA 260 1.76e+00 c.1.10.1 80756 1hv8A 367 2.19e+00 1hv8A c.37.1.19 32405 c.37.1.19 32406 1dliA 402 2.19e+00 1dliA a.100.1.4 18809 c.2.1.6 30213 c.26.3.1 31622 1jr1A 514 2.25e+00 c.1.5.1 63241 d.37.1.1 63242 d.37.1.1 63243 1dljA 402 2.36e+00 1dliA a.100.1.4 18808 c.2.1.6 30212 c.26.3.1 31621 3csuA 310 2.40e+00 3csuA c.78.1.1 35094 c.78.1.1 35095 1nal3 297 2.65e+00 1nal3 1gajA 257 3.03e+00 1gajA c.37.1.12 60416 1hxs3 237 3.15e+00 1bksA 268 3.27e+00 2tysA c.1.2.4 28585 1oxxK 353 3.39e+00 1oxsC 353 3.45e+00 1im2A 444 3.47e+00 1do0A c.37.1.20 62564 1eblA 317 3.66e+00 1hn9A c.95.1.1 35973 c.95.1.1 35974 1hg3A 225 3.70e+00 1hg3A c.1.1.1 61025 1d4oA 184 4.05e+00 1d4oA c.31.1.4 31748 1f74A 293 4.22e+00 1nal3 c.1.10.1 29079 1qamA 244 4.43e+00 2ercA c.66.1.9 34220 1gewA 356 4.53e+00 1gewA c.67.1.1 60470 1auq 208 4.55e+00 1auq c.62.1.1 34137 1f6kA 293 4.72e+00 1nal3 c.1.10.1 29081 1erzA 303 4.75e+00 1erzA d.160.1.2 59498 2tysA 268 5.08e+00 2tysA c.1.2.4 28572 1fts 295 5.29e+00 1ng1 a.24.13.1 16968 c.37.1.10 32279 1oe4A 247 5.38e+00 16pk 415 5.43e+00 16pk c.86.1.1 35454 1eblB 317 5.56e+00 1hn9A c.95.1.1 35975 c.95.1.1 35976 3mag 307 5.57e+00 3mag c.66.1.9 34205 1h61A 364 5.58e+00 1oyc c.1.4.1 60657 1gvoA 364 5.62e+00 c.1.4.1 76357 1n16A 381 5.81e+00 a.83.1.1 79781 d.128.1.2 79782 1m33A 258 6.17e+00 c.69.1.26 78514 1ijbA 202 6.57e+00 c.62.1.1 71229 4ts1A 319 6.60e+00 2ts1 c.26.1.1 31565 1efvB 255 6.67e+00 1efvB c.26.2.3 31634 1jq5A 370 6.77e+00 e.22.1.2 67084 1bi5A 389 6.94e+00 1bi5A c.95.1.2 35985 c.95.1.2 35986 1hyuA 521 6.97e+00 1hyuA c.3.1.5 30547 c.3.1.5 30548 c.47.1.2 32779 c.47.1.2 32780 1i88A 389 6.98e+00 c.95.1.2 66070 c.95.1.2 66071 1d1gA 168 7.00e+00 1d1gA c.71.1.1 34889 1hmpA 217 7.09e+00 1qk3A c.61.1.1 34075 1fg7A 356 7.09e+00 1gewA c.67.1.1 59819 1j7iA 264 7.12e+00 1j7iA d.144.1.6 62694 1l1eA 287 7.57e+00 c.66.1.18 73454 1mldA 314 7.74e+00 2cmd c.2.1.5 30122 d.162.1.1 42089 1jqaA 370 7.98e+00 e.22.1.2 67085 1at1A 310 8.12e+00 3csuA c.78.1.1 35168 c.78.1.1 35169 1skyE 473 8.22e+00 1skyE a.69.1.1 18314 b.49.1.1 26479 c.37.1.11 32359 2ts1 419 8.28e+00 2ts1 c.26.1.1 31564 1i86A 389 8.37e+00 c.95.1.2 66068 c.95.1.2 66069 1gz0A 253 8.40e+00 c.116.1.1 76391 d.79.3.3 76392 1v39 322 8.48e+00 3mag c.66.1.9 34206 1vp9 322 8.48e+00 3mag c.66.1.9 34210 1nw3A 416 8.78e+00 1vpt 348 8.81e+00 3mag c.66.1.9 34207 1fl2A 310 8.84e+00 1hyuA c.3.1.5 59869 c.3.1.5 59870 1qk3A 233 8.95e+00 1qk3A c.61.1.1 34031 1cz3A 168 9.34e+00 1d1gA c.71.1.1 34891 1egzA 291 9.66e+00 7a3hA c.1.8.3 28828 2ercA 244 9.78e+00 2ercA c.66.1.9 34224 1i1qB 192 1.00e+01 1qdlB c.23.16.1 61544 1bw0A 416 1.01e+01 1bw0A c.67.1.1 34385 1eh9A 558 1.01e+01 1ehaA b.1.18.2 21858 b.71.1.1 27785 c.1.8.1 28772 1nbwA 607 1.03e+01 c.8.6.1 80393 c.55.1.6 80394 c.55.1.6 80395 1pfkA 320 1.04e+01 3pfk c.89.1.1 35575 1bf6A 291 1.05e+01 1pscA c.1.9.3 29065 1dekA 241 1.06e+01 1dekA c.37.1.1 31842 1qtrA 317 1.07e+01 1qtrA c.69.1.7 34660 1deaA 266 1.08e+01 1deaA c.35.1.1 31760 1kv8A 216 1.08e+01 c.1.2.3 73054 1e79A 510 1.10e+01 1skyB a.69.1.1 18269 b.49.1.1 26434 c.37.1.11 32314 1ltqA 301 1.15e+01 c.108.1.9 78208 c.37.1.1 78209 1oakA 196 1.15e+01 1auq c.62.1.1 34138 1pdz 434 1.15e+01 4enl c.1.11.1 29215 d.54.1.1 38859 1o7fA 469 1.17e+01 a.4.5.31 81131 b.82.3.2 81132 b.82.3.2 81133 1gw1A 376 1.17e+01 c.1.8.3 76361 1qfjA 232 1.20e+01 1qfjA b.43.4.2 25655 c.25.1.1 31545 1ccwA 137 1.20e+01 1be1 c.23.6.1 31238 1qopA 268 1.21e+01 2tysA c.1.2.4 28570 1j8yF 297 1.25e+01 1ng1 a.24.13.1 62747 c.37.1.10 62748 1e79D 482 1.26e+01 1skyE a.69.1.1 18272 b.49.1.1 26437 c.37.1.11 32317 1ml4A 308 1.30e+01 c.78.1.1 79255 c.78.1.1 79256 1eluB 390 1.37e+01 1elqA c.67.1.3 34435 1g41A 444 1.40e+01 1do0A c.37.1.20 32450 1fzqA 181 1.43e+01 1hurA c.37.1.8 32060 2pfkA 320 1.46e+01 3pfk c.89.1.1 35577 1nulA 152 1.49e+01 1nulA c.61.1.1 34011 1qk4A 233 1.52e+01 1qk3A c.61.1.1 34037 1ekxA 311 1.55e+01 3csuA c.78.1.1 35088 c.78.1.1 35089 3minB 522 1.56e+01 1qguB c.92.2.3 35606 1gd9A 389 1.57e+01 c.67.1.1 60454 1fnsA 196 1.58e+01 1auq c.62.1.1 34136 2tmdA 729 1.58e+01 2tmdA c.1.4.1 28616 c.3.1.1 30317 c.4.1.1 30602 1bu6O 501 1.59e+01 1glcG c.55.1.4 33499 c.55.1.4 33500 1eluA 390 1.59e+01 1elqA c.67.1.3 34434 1elqA 390 1.60e+01 1elqA c.67.1.3 34436 1n2eA 300 1.61e+01 1mopA 300 1.61e+01 1pswA 348 1.64e+01 1m1nB 522 1.67e+01 c.92.2.3 78418 1nw2A 105 1.67e+01 1kzhA 555 1.67e+01 c.89.1.1 73361 1delA 241 1.68e+01 1dekA c.37.1.1 31844 1bn6A 294 1.72e+01 1bn6A c.69.1.8 34678 1pysB 785 1.72e+01 1pysB a.6.1.1 16299 a.6.1.1 16300 b.40.4.4 25311 d.58.13.1 39310 d.104.1.1 40779 d.138.1.1 41455 1g55A 343 1.75e+01 1g55A c.66.1.10 34247 1ej0A 180 1.75e+01 1ej0A c.66.1.2 34179 1ehaA 558 1.76e+01 1ehaA b.1.18.2 21859 b.71.1.1 27786 c.1.8.1 28773 1qh4A 380 1.81e+01 1qh4A a.83.1.1 18462 d.128.1.2 41197 1fsgA 233 1.83e+01 1qk3A c.61.1.1 34029 1h3fA 432 1.83e+01 c.26.1.1 76631 d.66.1.4 76632 1khvA 516 1.83e+01 e.8.1.4 68627 1fsfA 266 1.84e+01 c.35.1.1 65047 1b7yB 785 1.84e+01 1pysB a.6.1.1 16301 a.6.1.1 16302 b.40.4.4 25312 d.58.13.1 39311 d.104.1.1 40780 d.138.1.1 41456 1b0zA 445 1.85e+01 2pgi c.80.1.2 35309 2pgi 445 1.85e+01 2pgi c.80.1.2 35308 1qmpA 130 1.85e+01 1dz3A c.23.1.1 31106 1g6hA 257 1.86e+01 1gajA c.37.1.12 60318 1gdeA 389 1.86e+01 c.67.1.1 60456 1odzA 386 1.88e+01 1a98A 152 1.95e+01 1nulA c.61.1.1 34021 1glcG 501 1.95e+01 1glcG c.55.1.4 33519 c.55.1.4 33520 1c7qA 445 1.99e+01 2pgi c.80.1.2 35307 1ir6A 424 2.00e+01 c.107.1.2 71342 1mhlC 466 2.00e+01 1mhlC 1c7nA 399 2.05e+01 1d2fA c.67.1.3 34413 1h8eD 482 2.08e+01 1skyE a.69.1.1 60747 b.49.1.1 60748 c.37.1.11 60749 1k1xA 659 2.10e+01 3dapA 320 2.17e+01 1dapA c.2.1.3 30051 d.81.1.3 39966 1h6pA 203 2.18e+01 a.146.1.1 60690 1i7qB 193 2.20e+01 1qdlB c.23.16.1 61902 1fs5A 266 2.21e+01 c.35.1.1 65044 1d3vA 323 2.21e+01 1d3vA c.42.1.1 32559 1j0hA 588 2.22e+01 b.1.18.2 77027 b.71.1.1 77028 c.1.8.1 77029 2mjpA 193 2.23e+01 1b78A c.51.4.1 33223 1j9yA 385 2.23e+01 1j9yA c.1.8.3 62791 1iukA 140 2.27e+01 1qgvA 142 2.28e+01 1qgvA c.47.1.8 33056 1dpe 507 2.32e+01 1dpe c.94.1.1 35799 1b78A 193 2.34e+01 1b78A c.51.4.1 33221 1fnnA 389 2.37e+01 1fnnA a.4.5.11 16129 c.37.1.20 32426 1kq8A 100 2.38e+01 a.4.5.14 68797 1cqwA 295 2.51e+01 1b6g c.69.1.8 34679 1km4A 247 2.54e+01 c.1.2.3 72740 1wab 232 2.55e+01 1wab c.23.10.3 31341 1pymA 295 2.58e+01 1pymA c.1.12.4 29308 1djnA 729 2.62e+01 2tmdA c.1.4.1 28612 c.3.1.1 30313 c.4.1.1 30598 2wsyA 268 2.63e+01 2tysA c.1.2.4 28588 1irqA 71 2.66e+01 a.43.1.2 66297 1bn7A 294 2.66e+01 1bn6A c.69.1.8 34677 1dapA 320 2.68e+01 1dapA c.2.1.3 30053 d.81.1.3 39968 1e3sA 261 2.71e+01 1e6wA c.2.1.2 59201 1es9A 232 2.72e+01 1wab c.23.10.3 31340 1l2tA 235 2.74e+01 c.37.1.12 73514 1ysc 421 2.77e+01 1ivyA c.69.1.5 34652 1okgA 373 2.77e+01 1jx7A 117 2.81e+01 c.114.1.1 77195 1k8eA 345 2.82e+01 1o17A 345 2.82e+01 a.46.2.1 80765 c.27.1.1 80766 7aatA 401 2.83e+01 1ajsA c.67.1.1 34250 1pvc3 238 2.86e+01 1aym3 1ub3A 220 2.89e+01 2minB 522 2.90e+01 1qguB c.92.2.3 35610 1j0aA 325 2.90e+01 1de6A 426 2.91e+01 1de5A c.1.15.2 29398 1h8eA 510 2.94e+01 1skyB a.69.1.1 60738 b.49.1.1 60739 c.37.1.11 60740 1de5A 426 2.96e+01 1de5A c.1.15.2 29402 1rlaA 323 2.98e+01 1d3vA c.42.1.1 32561 1j8mF 297 3.00e+01 1ng1 a.24.13.1 62742 c.37.1.10 62743 1ogdA 131 3.00e+01 1dppA 507 3.02e+01 1dpe c.94.1.1 35800 1f61A 429 3.02e+01 1dquA c.1.12.6 29319 1lj8A 493 3.03e+01 a.100.1.9 78033 c.2.1.6 78034 1f06A 320 3.05e+01 1dapA c.2.1.3 59556 d.81.1.3 59557 1yveJ 524 3.09e+01 1qmgA a.100.1.2 18790 c.2.1.6 30187 1cxpC 466 3.11e+01 1mhlC 1o1yA 239 3.16e+01 1f20A 435 3.17e+01 b.43.4.1 64932 c.25.1.4 64933 1k9vF 201 3.23e+01 c.23.16.1 68365 1ccwB 483 3.28e+01 1cb7B c.1.19.2 29646 1jk7A 323 3.28e+01 1auiA d.159.1.3 63144 1tdj 514 3.29e+01 1tdj c.79.1.1 35297 d.58.18.2 39356 d.58.18.2 39357 1cb7B 483 3.29e+01 1cb7B c.1.19.2 29648 1o1xA 155 3.34e+01 1ck7A 631 3.39e+01 1ck7A a.20.1.2 58969 b.66.1.1 27538 d.92.1.11 58970 g.14.1.2 44674 g.14.1.2 44675 g.14.1.2 44676 1ihoA 283 3.45e+01 1ihoA c.26.1.4 62390 1rpjA 288 3.45e+01 2dri c.93.1.1 35656 8dfr 189 3.47e+01 1aoeA c.71.1.1 34895 1j2iA 166 3.48e+01 1o3yA 166 3.48e+01 1ofgA 381 3.48e+01 1ofgA c.2.1.3 30064 d.81.1.5 39979 1llfA 534 3.52e+01 c.69.1.17 78094 1jclA 260 3.54e+01 c.1.10.1 66501 1ckqA 276 3.55e+01 1ckqA c.52.1.1 33229 1nsf 273 3.56e+01 1d2nA c.37.1.20 32429 1tmy 120 3.58e+01 1dbwA c.23.1.1 31083 1jcjA 260 3.59e+01 c.1.10.1 66499 1f8mA 429 3.59e+01 1dquA c.1.12.6 29315 1azwA 313 3.61e+01 1qtrA c.69.1.7 34658 1icpA 376 3.62e+01 1oyc c.1.4.1 62270 1qhoA 686 3.63e+01 1cxlA b.1.18.2 21844 b.3.1.1 22513 b.71.1.1 27751 c.1.8.1 28738 1i50C 318 3.64e+01 d.74.3.1 61756 d.181.1.1 61757 1cl8A 276 3.64e+01 1ckqA c.52.1.1 33230 1dz3A 130 3.64e+01 1dz3A c.23.1.1 31105 1cleA 534 3.66e+01 1thg c.69.1.17 34771 1qatB 622 3.70e+01 1djxB a.39.1.7 17355 b.7.1.1 23172 c.1.18.1 29600 1o94A 729 3.71e+01 c.1.4.1 81200 c.3.1.1 81201 c.4.1.1 81202 1l9wA 252 3.72e+01 1fjmA 330 3.72e+01 1auiA d.159.1.3 42082 1krhA 338 3.74e+01 b.43.4.2 72891 c.25.1.2 72892 d.15.4.2 72893 1qasA 622 3.79e+01 1djxB a.39.1.7 17340 b.7.1.1 23157 c.1.18.1 29585 1scuA 288 3.81e+01 2scuA c.2.1.8 30307 c.23.4.1 31135 1iu8A 206 3.85e+01 c.56.4.1 71436 1hs6A 611 3.87e+01 1hs6A a.118.1.7 61233 b.98.1.1 61234 d.92.1.13 61235 1efm 393 3.87e+01 1efcA c.37.1.8 64732 1aj8A 371 3.87e+01 1aj8A a.103.1.1 18900 1pbgA 468 3.90e+01 1e70M c.1.8.4 28946 1bmfA 510 3.92e+01 1skyB a.69.1.1 18281 b.49.1.1 26446 c.37.1.11 32326 1ukz 203 3.93e+01 1zin c.37.1.1 31840 1yveI 524 3.94e+01 1qmgA a.100.1.2 18789 c.2.1.6 30186 1k77A 260 3.94e+01 c.1.15.5 72096 1ahxA 396 3.94e+01 1ajsA c.67.1.1 34293 1d2nA 272 3.95e+01 1d2nA c.37.1.20 32428 1ni4B 341 3.96e+01 3adk 195 3.99e+01 1zin c.37.1.1 31885