# List of top-scoring protein chains for t2k-100-30-stride-ebghtl 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 1a4mA 349 1.09e-01 1a4mA c.1.9.1 29014 1hg3A 225 1.52e-01 1hg3A c.1.1.1 61025 1cqzA 554 1.78e-01 1cr6B c.108.1.2 43339 c.69.1.11 34689 1add 349 2.43e-01 1a4mA c.1.9.1 29020 1gpjA 404 2.45e-01 a.151.1.1 65451 c.2.1.10 65452 d.58.39.1 65453 1jsbA 73 3.73e-01 d.15.3.2 67223 1i1dA 161 4.21e-01 1i21A d.108.1.1 61526 1hgeA 328 4.91e-01 1hgeA b.19.1.2 23816 1ja9A 274 4.94e-01 c.2.1.2 62817 1j8mF 297 5.49e-01 1ng1 a.24.13.1 62742 c.37.1.10 62743 1ldg 316 5.64e-01 1ceqA c.2.1.5 30165 d.162.1.1 42132 1i21A 159 5.70e-01 1i21A d.108.1.1 61549 2viuA 328 5.82e-01 1hgeA b.19.1.2 23797 1dik 874 7.58e-01 1dik c.1.12.2 29304 c.8.1.1 30702 d.142.1.5 41572 1i12A 160 8.04e-01 1i21A d.108.1.1 61515 3hmgA 328 8.86e-01 1hgeA b.19.1.2 23825 1byrA 155 9.43e-01 1byrA d.136.1.1 41450 1ekjB 221 9.56e-01 1ekjB c.53.2.1 33365 1jpnA 296 9.88e-01 a.24.13.1 67039 c.37.1.10 67040 1bw9A 356 1.35e+00 1bw9A c.2.1.7 30274 c.58.1.1 33922 1ceqA 316 1.39e+00 1ceqA c.2.1.5 30163 d.162.1.1 42130 1jhdA 396 1.47e+00 b.58.1.2 66712 c.26.1.5 66713 1kvs 338 1.48e+00 1xel c.2.1.2 29799 1xel 338 1.48e+00 1xel c.2.1.2 29786 1udc 338 1.49e+00 1xel c.2.1.2 29785 1bvp1 349 1.49e+00 1bvp1 2udpA 338 1.49e+00 1xel c.2.1.2 29791 1udb 338 1.59e+00 1xel c.2.1.2 29787 1ekjA 221 1.67e+00 1ekjB c.53.2.1 33364 2ng1 293 1.76e+00 1ng1 a.24.13.1 16962 c.37.1.10 32273 1efpB 252 1.77e+00 1efvB c.29.1.1 31636 1pfkA 320 1.96e+00 3pfk c.89.1.1 35575 2pfkA 320 2.01e+00 3pfk c.89.1.1 35577 16pk 415 2.26e+00 16pk c.86.1.1 35454 1spa 396 2.29e+00 1ajsA c.67.1.1 34291 1kblA 873 2.34e+00 c.1.12.2 68384 c.8.1.1 68385 d.142.1.5 68386 1eo1A 124 2.39e+00 1eo1A c.55.5.1 33739 1in4A 334 2.41e+00 1hqcA a.4.5.11 62597 c.37.1.13 62598 1c1dA 355 2.49e+00 1bw9A c.2.1.7 30270 c.58.1.1 33918 1b25A 619 2.58e+00 1b25A a.110.1.1 19044 d.152.1.1 41796 1hqcA 324 2.59e+00 1hqcA a.4.5.11 16127 c.37.1.13 32424 1yacA 208 2.95e+00 1yacA c.33.1.2 31757 1ek1A 554 3.00e+00 1cr6B c.108.1.2 43335 c.69.1.11 34685 3minC 491 3.15e+00 1qguA c.92.2.3 35607 2minA 491 3.20e+00 1qguA c.92.2.3 35609 1onrA 316 3.22e+00 1onrA c.1.10.1 29169 1g5cA 170 3.41e+00 1g5cA c.53.2.1 60264 1g4uS 383 3.60e+00 1g4uS a.24.11.1 16643 c.45.1.2 32691 1qisA 396 3.62e+00 1ajsA c.67.1.1 34284 1tmy 120 3.69e+00 1dbwA c.23.1.1 31083 1jdqA 98 3.82e+00 d.68.3.2 66559 1gpmA 525 3.85e+00 1gpmA c.23.16.1 31405 c.26.2.1 31608 d.52.2.1 38826 2bpa1 426 3.88e+00 2bpa1 1jp4A 308 4.10e+00 1jp4A e.7.1.1 63223 1ewkA 490 4.11e+00 1ewkA c.93.1.1 35712 1ars 396 4.12e+00 1ajsA c.67.1.1 34287 1thfD 253 4.30e+00 1thfD c.1.2.1 28535 1gcoA 261 4.31e+00 1ybvA c.2.1.2 29884 1lqvA 193 4.32e+00 2hrvA 142 4.53e+00 2hrvA b.47.1.4 26429 1ybvA 283 4.64e+00 1ybvA c.2.1.2 29948 1art 396 4.77e+00 1ajsA c.67.1.1 34285 1psdA 409 5.18e+00 1psdA c.2.1.4 30097 c.23.12.1 31357 d.58.18.1 39354 1ptvA 321 5.18e+00 1pty c.45.1.2 32665 6pfkA 319 5.30e+00 3pfk c.89.1.1 35583 1pjcA 361 5.31e+00 1sayA c.2.1.4 30101 c.23.12.2 31361 1g0oA 283 5.31e+00 1ybvA c.2.1.2 60181 1eq2A 310 5.51e+00 1eq2A c.2.1.2 29814 1ng1 294 5.57e+00 1ng1 a.24.13.1 16961 c.37.1.10 32272 1qdlB 195 5.68e+00 1qdlB c.23.16.1 31437 1lbvA 252 5.78e+00 1gdhA 320 5.78e+00 1gdhA c.2.1.4 30095 c.23.12.1 31355 2hnp 321 5.80e+00 1pty c.45.1.2 32678 1ahxA 396 5.85e+00 1ajsA c.67.1.1 34293 1dcjA 81 5.85e+00 1dcjA d.68.3.1 59115 1sayA 361 5.86e+00 1sayA c.2.1.4 30102 c.23.12.2 31362 1pjbA 361 5.89e+00 1sayA c.2.1.4 30103 c.23.12.2 31363 1f74A 293 5.91e+00 1nal3 c.1.10.1 29079 1iloA 77 6.31e+00 c.47.1.1 66205 1hs6A 611 6.32e+00 1hs6A a.118.1.7 61233 b.98.1.1 61234 d.92.1.13 61235 1qklA 127 6.39e+00 1qklA d.78.1.2 39754 2nadA 393 6.62e+00 2nadA c.2.1.4 30090 c.23.12.1 31350 1eemA 241 6.65e+00 1eemA a.45.1.1 17717 c.47.1.5 33011 4pfk 319 6.74e+00 3pfk c.89.1.1 35582 1pszA 303 6.82e+00 1toaA c.92.2.2 35600 1ek6A 348 6.87e+00 1xel c.2.1.2 29800 2nacA 393 7.22e+00 2nadA c.2.1.4 30088 c.23.12.1 31348 1jpdX 324 7.23e+00 c.1.11.2 67014 d.54.1.1 67015 1lam 484 7.46e+00 1lam c.50.1.1 33166 c.56.5.3 33829 1jj2A 239 7.70e+00 1rl2A b.34.5.3 63084 b.40.4.5 63085 1eeoA 321 7.99e+00 1pty c.45.1.2 32655 1pty 321 8.09e+00 1pty c.45.1.2 32656 1ipaA 274 8.17e+00 1lap 488 8.36e+00 1lam c.50.1.1 33171 c.56.5.3 33834 1memA 215 8.66e+00 1cs8A d.3.1.1 37069 1a7j 290 8.96e+00 1a7j c.37.1.6 31952 1qrrA 394 8.97e+00 1qrrA c.2.1.2 29824 1qh8A 478 9.08e+00 1qguA c.92.2.3 35633 1qpzA 340 9.12e+00 1qpzA a.35.1.5 17097 c.93.1.1 35673 1qguA 478 9.15e+00 1qguA c.92.2.3 35625 2bopA 85 9.29e+00 2bopA d.58.8.1 39217 1d3gA 367 9.51e+00 1d3gA c.1.4.1 28600 1dxy 333 1.01e+01 1dxy c.2.1.4 30094 c.23.12.1 31354 1b5fA 239 1.02e+01 1smrA b.50.1.2 26836 1f5vA 240 1.03e+01 1bkjA d.90.1.1 40255 1eg7A 557 1.03e+01 1eg7A c.37.1.10 32241 1kte 105 1.06e+01 1kte c.47.1.1 32771 1bkjA 240 1.06e+01 1bkjA d.90.1.1 40243 1bdo 80 1.07e+01 1bdo b.84.1.1 28214 1k32A 1045 1.08e+01 b.36.1.3 68068 b.68.7.1 68069 b.69.9.1 68070 c.14.1.2 68071 1ik6A 369 1.10e+01 c.36.1.3 66174 c.48.1.2 66175 1d0yA 761 1.11e+01 1lvk b.34.3.1 24581 c.37.1.9 32178 1b1cA 181 1.13e+01 1amoA c.23.5.2 31212 1f4tA 368 1.15e+01 1f4tA a.104.1.1 18973 1wetA 340 1.16e+01 1qpzA a.35.1.5 17093 c.93.1.1 35670 1d3hA 367 1.16e+01 1d3gA c.1.4.1 28601 1dfcA 493 1.19e+01 1dfcA b.42.5.1 25616 b.42.5.1 25617 b.42.5.1 25618 b.42.5.1 25619 1dkrA 317 1.21e+01 1dkuA c.61.1.2 34114 c.61.1.2 34115 1dl0A 37 1.22e+01 1dl0A g.3.6.2 44112 1qr6A 584 1.25e+01 1qr6A c.2.1.7 30293 c.58.1.3 33941 1g7fA 298 1.27e+01 1pty c.45.1.2 60330 1ej0A 180 1.29e+01 1ej0A c.66.1.2 34179 2tnfA 156 1.31e+01 2tnfA b.22.1.1 23880 1io7A 368 1.33e+01 1f4tA a.104.1.1 18971 1e3mA 800 1.34e+01 1ewqA a.113.1.1 19075 c.37.1.12 32389 c.55.6.1 33746 d.75.2.1 39747 1kv8A 216 1.34e+01 1rhd 293 1.34e+01 1rhs c.46.1.2 32715 c.46.1.2 32716 1ddbA 195 1.36e+01 1ddbA f.1.4.1 43399 1qgvA 142 1.36e+01 1qgvA c.47.1.8 33056 1g4wR 383 1.37e+01 1g4uS a.24.11.1 16644 c.45.1.2 32692 1gps 47 1.37e+01 1gpt g.3.7.5 44176 1srvA 145 1.39e+01 1derA c.8.5.1 30817 1skyE 473 1.40e+01 1skyE a.69.1.1 18314 b.49.1.1 26479 c.37.1.11 32359 1b73A 254 1.40e+01 1b74A c.78.2.1 35266 c.78.2.1 35267 2at2A 300 1.43e+01 3csuA c.78.1.1 35196 c.78.1.1 35197 1tnfA 158 1.45e+01 2tnfA b.22.1.1 23871 1dbqA 289 1.50e+01 1qpzA c.93.1.1 35666 1gmxA 108 1.52e+01 c.46.1.3 65355 1b0uA 262 1.52e+01 1b0uA c.37.1.12 32370 1dkuA 317 1.53e+01 1dkuA c.61.1.2 34118 c.61.1.2 34119 1jztA 246 1.55e+01 c.104.1.1 63319 1kgsA 225 1.59e+01 a.4.6.1 68596 c.23.1.1 68597 1fiqC 763 1.59e+01 1fiqC d.41.1.1 38588 d.133.1.1 41418 1eb0A 147 1.60e+01 b.107.1.1 64890 d.58.38.1 64891 1fts 295 1.65e+01 1ng1 a.24.13.1 16968 c.37.1.10 32279 1bmtA 246 1.66e+01 1bmtA a.46.1.1 17757 c.23.6.1 31235 1i7qB 193 1.70e+01 1qdlB c.23.16.1 61902 1ewqA 765 1.71e+01 1ewqA a.113.1.1 19069 c.37.1.12 32383 c.55.6.1 33740 d.75.2.1 39743 1php 394 1.71e+01 16pk c.86.1.1 35452 1jmtA 104 1.75e+01 d.58.7.3 63180 1i1qB 192 1.78e+01 1qdlB c.23.16.1 61544 2arcB 164 1.78e+01 2arcA b.82.4.1 28149 1qcxA 359 1.81e+01 1qcxA b.80.1.2 28028 1rl2A 137 1.83e+01 1rl2A b.34.5.3 24610 b.40.4.5 25342 1edoA 244 1.84e+01 1ybvA c.2.1.2 29896 3pmgA 561 1.87e+01 3pmgA c.84.1.1 35408 c.84.1.1 35409 c.84.1.1 35410 d.129.2.1 41301 1bi0 226 1.89e+01 1bi0 a.4.5.24 16202 a.76.1.1 18408 b.34.1.2 24453 1i3kA 348 1.93e+01 1xel c.2.1.2 61595 1icpA 376 1.95e+01 1oyc c.1.4.1 62270 1lxtA 561 1.96e+01 3pmgA c.84.1.1 35432 c.84.1.1 35433 c.84.1.1 35434 d.129.2.1 41309 1g57A 217 1.96e+01 1g57A d.115.1.2 60253 2arcA 164 2.00e+01 2arcA b.82.4.1 28148 1bnkA 216 2.01e+01 1bnkA b.46.1.2 25765 1gt91 357 2.04e+01 1ekgA 127 2.08e+01 1dlxA d.82.2.1 40021 1im5A 180 2.10e+01 c.33.1.2 66211 1ewnA 219 2.11e+01 1bnkA b.46.1.2 25762 1fo4A 1332 2.13e+01 a.56.1.1 17910 d.15.4.2 37695 d.41.1.1 38586 d.87.2.1 40227 d.133.1.1 41416 d.145.1.3 41758 1e5eA 404 2.18e+01 1ibjA c.67.1.3 59265 1bio 228 2.24e+01 5ptp b.47.1.2 26314 1f39A 101 2.26e+01 1umuA b.87.1.1 28386 1ddzA 496 2.28e+01 1ddzA c.53.2.1 33372 c.53.2.1 33373 2aat 396 2.30e+01 1ajsA c.67.1.1 34348 1b6rA 355 2.31e+01 1b6rA b.84.2.1 28241 c.30.1.1 31648 d.142.1.2 41493 9ldtA 332 2.32e+01 3ldh c.2.1.5 30154 d.162.1.1 42121 1eujA 166 2.35e+01 1eujA b.40.4.4 25316 1i88A 389 2.36e+01 c.95.1.2 66070 c.95.1.2 66071 1hhsA 664 2.36e+01 1hi0P e.8.1.6 61045 1opr 213 2.37e+01 1opr c.61.1.1 34091 1el5A 389 2.41e+01 1b3mA c.3.1.2 30369 d.16.1.3 37937 1aiu 105 2.44e+01 1erv c.47.1.1 32746 1alq 266 2.47e+01 1btl e.3.1.1 42707 1kewA 361 2.48e+01 c.2.1.2 68544 1f5sA 211 2.53e+01 1f5sA c.108.1.4 59656 1j97A 211 2.53e+01 1f5sA c.108.1.4 62753 1kk1A 410 2.58e+01 1lkzA 219 2.58e+01 1je3A 97 2.63e+01 1k0eA 453 2.64e+01 d.161.1.1 67938 1d2eA 397 2.64e+01 1efcA b.43.3.1 25701 b.44.1.1 25741 c.37.1.8 32136 1fvuA 133 2.67e+01 1ixxB d.169.1.1 42345 1gca 309 2.68e+01 1gca c.93.1.1 35659 1hsq 71 2.73e+01 1ckaA b.34.2.1 24551 1opy 131 2.74e+01 1opy d.17.4.3 38113 1h70A 255 2.79e+01 1h70A d.126.1.3 60711 1dhpA 292 2.80e+01 1dhpA c.1.10.1 29097 3pfk 319 2.81e+01 3pfk c.89.1.1 35581 1be3B 439 2.81e+01 1be3B d.185.1.1 58952 d.185.1.1 58953 1d9eA 284 2.82e+01 1d9eA c.1.10.4 29195 1l9fA 389 2.83e+01 1vhrA 184 2.84e+01 1vhrA c.45.1.1 32651 1ihuA 589 2.85e+01 c.37.1.10 62394 c.37.1.10 62395 1b6sA 355 2.87e+01 1b6rA b.84.2.1 28242 c.30.1.1 31649 d.142.1.2 41494 1j7xA 302 2.96e+01 c.14.1.2 66425 1ja1A 622 2.97e+01 1amoA b.43.4.1 62803 c.23.5.2 62804 c.25.1.4 62805 1rhs 296 2.99e+01 1rhs c.46.1.2 32703 c.46.1.2 32704 1gegA 256 2.99e+01 1ybvA c.2.1.2 29888 1delA 241 2.99e+01 1dekA c.37.1.1 31844 2gbp 309 3.00e+01 1gca c.93.1.1 35657 1gpt 47 3.01e+01 1gpt g.3.7.5 44175 1pymA 295 3.02e+01 1pymA c.1.12.4 29308 1xgsA 295 3.06e+01 1bn5 a.4.5.25 16216 d.127.1.1 41153 1hzpA 335 3.07e+01 1hn9A c.95.1.1 61455 c.95.1.1 61456 1bawA 105 3.07e+01 1plc b.6.1.1 22868 1ft9A 222 3.08e+01 1ft9A a.4.5.4 16107 b.82.3.1 28131 1grj 158 3.08e+01 1grj a.2.1.1 15691 d.26.1.2 38433 1f48A 589 3.22e+01 1f48A c.37.1.10 32280 c.37.1.10 32281 1qfcA 306 3.26e+01 1uteA d.159.1.1 42077 1g7vA 284 3.28e+01 1d9eA c.1.10.4 60335 1hce 118 3.32e+01 1hce b.42.5.2 25625 1jmcA 246 3.33e+01 1jmcA b.40.4.3 25300 b.40.4.3 25301 1bxkA 355 3.33e+01 1bxkA c.2.1.2 29803 1othA 321 3.33e+01 1othA c.78.1.1 35260 c.78.1.1 35261 1lylA 504 3.37e+01 1lylA b.40.4.1 25261 d.104.1.1 40717 1e5dA 402 3.39e+01 1e5dA c.23.5.1 31208 d.157.1.3 42061 7aatA 401 3.40e+01 1ajsA c.67.1.1 34250 1db3A 372 3.45e+01 1db3A c.2.1.2 29813 1ad3A 452 3.47e+01 1ad3A c.82.1.1 35335 1hrkA 359 3.50e+01 1hrkA c.92.1.1 61228 1kc0A 299 3.50e+01 1im8A 244 3.52e+01 c.66.1.14 66212 2prd 174 3.55e+01 2prd b.40.5.1 25435 1bwsA 321 3.56e+01 1bsvA c.2.1.2 29812 1iq8A 582 3.57e+01 1lh0A 213 3.57e+01 1pba 81 3.64e+01 1pytA d.58.3.1 39067 1a04A 215 3.68e+01 1a04A a.4.6.2 16234 c.23.1.1 31089 1v39 322 3.69e+01 3mag c.66.1.9 34206 1din 236 3.70e+01 1din c.69.1.9 34682 1k0gA 453 3.70e+01 d.161.1.1 67940 1hi0P 664 3.75e+01 1hi0P e.8.1.6 61051 1bykA 255 3.83e+01 1bykA c.93.1.1 35706 1e1oA 504 3.88e+01 1lylA b.40.4.1 25258 d.104.1.1 40714 1cliA 345 3.88e+01 1cliA d.79.4.1 39816 d.139.1.1 41459 1ddnA 226 3.92e+01 1bi0 a.4.5.24 16207 a.76.1.1 18413 1jwiB 125 3.95e+01 d.169.1.1 67384 4tsvA 150 3.95e+01 2tnfA b.22.1.1 23860 1sesA 421 3.96e+01 1sesA a.2.7.1 15710 d.104.1.1 40710