# 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 1lam 484 8.20e-46 1lam c.50.1.1,c.56.5.3 33166,33829 1bllE 488 9.23e-46 1lam c.50.1.1,c.56.5.3 33170,33833 1lap 488 2.12e-45 1lam c.50.1.1,c.56.5.3 33171,33834 1tkjA 284 4.30e-01 1tf9A 284 4.88e-01 1xjo 284 5.44e-01 1xjo c.56.5.4 33843 1qq9A 284 6.34e-01 1xjo c.56.5.4 33841 1v71A 323 6.63e-01 1lokA 291 1.13e+00 c.56.5.4 78122 1suwA 249 1.16e+00 e.52.1.1 106027 1amp 291 1.28e+00 1amp c.56.5.4 33837 1tz9A 367 1.37e+00 c.1.15.6 107466 1x13A 401 1.74e+00 1z0sA 278 1.76e+00 1wznA 252 1.91e+00 1tl9A 339 2.36e+00 2anpA 291 2.36e+00 1rtqA 299 2.58e+00 c.56.5.4 97819 1pnkA 209 2.96e+00 1ajqA d.153.1.2 41839 1j5sA 463 2.99e+00 c.1.9.8 71580 1h1yA 228 3.06e+00 c.1.2.2 76506 1pv9A 348 3.20e+00 c.55.2.1,d.127.1.1 95157,95158 1cjcA 460 3.30e+00 1cjcA c.3.1.1,c.4.1.1 30319,30604 1bjnA 360 3.90e+00 1bjnA c.67.1.4 34469 1kxrA 339 3.95e+00 d.3.1.3 73175 1o0xA 262 4.07e+00 d.127.1.1 80755 1bjoA 360 4.07e+00 1bjnA c.67.1.4 34471 1im8A 244 4.17e+00 c.66.1.14 66212 1dpe 507 4.27e+00 1dpe c.94.1.1 35799 1ajqA 209 4.35e+00 1ajqA d.153.1.2 41840 1wa3A 205 4.74e+00 1o4vA 183 4.92e+00 c.23.8.1 86628 2frnA 278 4.93e+00 1e3aA 260 5.10e+00 1ajqA d.153.1.2 41838 1el5A 389 5.30e+00 1b3mA c.3.1.2,d.16.1.3 30369,37937 1khdA 345 5.47e+00 a.46.2.1,c.27.1.1 77400,77401 1fp3A 402 5.67e+00 1fp3A a.102.1.3 18842 1tzbA 302 5.85e+00 c.80.1.1 107470 1ai7A 209 5.93e+00 1ajqA d.153.1.2 41845 2fliA 220 6.16e+00 1x9iA 302 6.41e+00 1iloA 77 6.43e+00 c.47.1.1 66205 1b3mA 389 6.56e+00 1b3mA 1iugA 352 6.83e+00 c.67.1.3 90699 2cg4A 152 6.84e+00 1tqxA 227 6.89e+00 1kyqA 274 7.33e+00 c.2.1.11,e.37.1.1 73281,73282 1woyA 500 7.36e+00 1gm7A 209 7.65e+00 d.153.1.2 65302 1l9fA 389 7.95e+00 c.3.1.2,d.16.1.3 73716,73717 1i6wA 181 8.09e+00 1i6wA c.69.1.18 61859 1s4nA 348 8.21e+00 c.68.1.16 98501 1gk9A 260 8.44e+00 d.153.1.2 65246 1a8h 500 8.56e+00 1a8h a.27.1.1,c.26.1.1 16922,31589 1ve1A 304 8.90e+00 1vgyA 393 9.04e+00 c.56.5.4,d.58.19.1 100620,100621 1ispA 181 9.12e+00 c.69.1.18 76778 1kid 203 9.60e+00 1derA c.8.5.1 30771 1ysjA 404 9.89e+00 1ohlA 342 9.92e+00 c.1.10.3 87035 1dppA 507 1.00e+01 1dpe c.94.1.1 35800 1lxnA 99 1.05e+01 d.58.48.1 84737 1iygA 133 1.09e+01 a.118.8.1 76947 1tdj 514 1.09e+01 1tdj c.79.1.1,d.58.18.2,d.58.18.2 35297,39356,39357 1r5iD 216 1.15e+01 a.202.1.1 97091 1omrA 201 1.18e+01 a.39.1.5 93349 2fiqA 420 1.22e+01 1yqhA 109 1.23e+01 1uayA 242 1.29e+01 c.2.1.2 88390 1o58A 303 1.30e+01 c.79.1.1 92491 1h7nA 342 1.31e+01 1b4kA c.1.10.3 60726 1p99A 295 1.31e+01 c.94.1.1 94384 1phk 298 1.31e+01 1cdkA d.144.1.7 41635 1ylvA 342 1.36e+01 1b4kA c.1.10.3 29180 1z7wA 322 1.38e+01 1fohA 664 1.40e+01 1fohA c.3.1.2,c.47.1.10,d.16.1.2 30381,33078,37900 1vlwA 217 1.41e+01 c.1.10.1 108868 2cy7A 396 1.48e+01 1w5qA 337 1.48e+01 1pn0A 665 1.49e+01 c.3.1.2,c.47.1.10,d.16.1.2 94918,94919,94920 1oj7A 408 1.52e+01 e.22.1.2 103971 1qusA 322 1.58e+01 1ltm d.2.1.6 36991 1ks2A 219 1.59e+01 c.124.1.4,d.58.40.1 72908,72909 1b3uA 588 1.62e+01 1b3uA a.118.1.2 19135 1rpxA 230 1.65e+01 1rpxA c.1.2.2 28536 1ltm 320 1.66e+01 1ltm d.2.1.6 36992 1xcrA 316 1.69e+01 1z7yA 322 1.71e+01 1vp8A 201 1.76e+01 1yz7A 188 1.78e+01 1tlfA 301 1.78e+01 1tlfA c.93.1.1 35687 1vheA 373 1.79e+01 b.49.3.1,c.56.5.4 100669,100670 1hjrA 158 1.81e+01 1hjrA c.55.3.6 33727 1zbtA 371 1.89e+01 1f5xA 208 1.90e+01 1f5xA a.87.1.1 18516 1lngA 87 1.90e+01 d.201.1.1 74045 1ad1A 266 1.92e+01 1aj2 c.1.21.1 29668 1rec 201 1.92e+01 1rec a.39.1.5 17326 1j9eA 147 1.92e+01 c.23.5.1 62756 1dxy 333 1.96e+01 1dxy c.2.1.4,c.23.12.1 30094,31354 1vljA 407 1.96e+01 e.22.1.2 108832 2fvgA 340 1.97e+01 1pwhA 327 1.98e+01 c.79.1.1 95224 2bylA 439 1.99e+01 1tqjA 230 2.02e+01 c.1.2.2 107228 1fc4A 401 2.08e+01 1bs0A c.67.1.4 59760 1ys1X 320 2.08e+01 1wv2A 265 2.13e+01 1axn 323 2.14e+01 1avc a.65.1.1 18149 1e5eA 404 2.23e+01 1ibjA c.67.1.3 59265 1ebdA 455 2.25e+01 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30577,30578,40210 1wdyA 285 2.26e+01 1gd9A 389 2.27e+01 c.67.1.1 60454 1vk9A 151 2.32e+01 c.139.1.1 108640 1ky9B 448 2.33e+01 b.36.1.4,b.36.1.4,b.47.1.1 73200,73201,73202 1g5pA 289 2.33e+01 1cp2A c.37.1.10 32253 1j03A 102 2.47e+01 d.120.1.2 90733 1nv8A 284 2.53e+01 c.66.1.30 86224 1vloA 381 2.57e+01 b.44.2.1,d.250.1.1 108838,108839 1wlsA 328 2.64e+01 1qxyA 252 2.64e+01 d.127.1.1 96565 1ve5A 311 2.69e+01 193l 129 2.70e+01 3lzt d.2.1.2 36247 1o4sA 389 2.73e+01 c.67.1.1 86620 1wdvA 152 2.74e+01 1u4nA 310 2.76e+01 1azl 147 2.77e+01 5nul c.23.5.1 31154 1a2yC 129 2.77e+01 3lzt d.2.1.2 36305 1bncA 449 2.80e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28236,31643,41488 1vr6A 350 2.81e+01 1akt 147 2.83e+01 5nul c.23.5.1 31157 1dv2A 452 2.86e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28238,31645,41490 1tvjA 166 2.88e+01 3prn 289 2.93e+01 3prn f.4.3.1 43761 2gbp 309 2.96e+01 1gca c.93.1.1 35657 5lyz 129 2.98e+01 3lzt d.2.1.2 36289 1vixA 420 2.99e+01 c.56.5.4,d.58.19.1 100777,100778 1o0uA 429 3.02e+01 c.118.1.1 80743 2a0iA 330 3.02e+01 1s6yA 450 3.03e+01 c.2.1.5,d.162.1.2 105314,105315 1rzmA 338 3.06e+01 c.1.10.4 105137 2bz1A 196 3.11e+01 1scfA 273 3.12e+01 1exzA a.26.1.2 16873 1kp8A 547 3.13e+01 a.129.1.1,c.8.5.1,d.56.1.1 84414,84415,84416 1f4pA 147 3.18e+01 5nul c.23.5.1 59651 1yvrA 538 3.20e+01 1vplA 256 3.21e+01 8prn 289 3.24e+01 3prn f.4.3.1 43767 1vhwA 253 3.24e+01 c.56.2.1 100706 3lzt 129 3.28e+01 3lzt d.2.1.2 36245 1tahB 318 3.34e+01 1cvl c.69.1.18 34774 1akr 147 3.41e+01 1rcf c.23.5.1 31152 2aat 396 3.45e+01 1ajsA c.67.1.1 34348 1akq 147 3.49e+01 5nul c.23.5.1 31159 1prn 289 3.51e+01 3prn f.4.3.1 43762 1zosA 230 3.51e+01 1bg7 176 3.51e+01 2fha a.25.1.1 16686 2dhqA 146 3.59e+01 2dhqA c.23.13.1 31382 1cg2A 393 3.59e+01 1cg2A c.56.5.4,d.58.19.1 33844,39360 1m7yA 435 3.62e+01 c.67.1.4 78761 1dtyA 429 3.64e+01 1dtyA c.67.1.4 34495 1wo8A 126 3.66e+01 2flsA 132 3.73e+01 2at9 247 3.75e+01 1c3wA f.13.1.1 43427 1akw 147 3.76e+01 5nul c.23.5.1 31153 1aii 323 3.78e+01 1avc a.65.1.1 18150 2b8nA 429 3.78e+01 1kczA 413 3.81e+01 c.1.11.2,d.54.1.1 68451,68452 1ad4A 266 3.82e+01 1aj2 c.1.21.1 29670 1vjpA 394 3.86e+01 c.2.1.3,d.81.1.3 100828,100829 3sdhA 146 3.90e+01 3sdhA a.1.1.2 14984 1tahA 318 3.90e+01 1cvl c.69.1.18 34775 1b8gA 429 3.93e+01 1b8gA c.67.1.4 34499 1fxxA 482 3.98e+01 1fxxA c.55.3.5 33726 1h05A 146 4.00e+01 c.23.13.1 76433 1bncB 449 4.03e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28237,31644,41489 1td2A 287 4.08e+01 c.72.1.5 106765 1bh3 289 4.11e+01 3prn f.4.3.1 43766 1wl8A 189 4.13e+01 1gdeA 389 4.13e+01 c.67.1.1 60456 2fx2 147 4.16e+01 1rcf c.23.5.1 31158 1xhkA 187 4.26e+01 1xd8A 289 4.28e+01 1whvA 100 4.29e+01 2asbA 251 4.35e+01 1jmvA 141 4.37e+01 c.26.2.4 66897 1tm9A 137 4.39e+01 a.225.1.1 107150 1vpt 348 4.40e+01 3mag c.66.1.25 34207 1jse 129 4.43e+01 3lzt d.2.1.2 36387 1nm2A 317 4.51e+01 c.19.1.1,d.58.23.1 80654,80655 1in0A 163 4.51e+01 d.58.49.1,d.58.49.1 83694,83695 1bu5A 147 4.52e+01 5nul c.23.5.1 31155 1o4tA 133 4.53e+01 b.82.1.9 86622 1j4aA 333 4.59e+01 c.2.1.4,c.23.12.1 71502,71503 1tf5A 844 4.64e+01 a.162.1.1,a.172.1.1,c.37.1.19,c.37.1.19 106834,106835,106836,106837 1lkzA 219 4.68e+01 c.124.1.4,d.58.40.1 73991,73992 1ks8A 433 4.68e+01 a.102.1.2 77519 1vl4A 447 4.69e+01 d.283.1.1 108718 1u7nA 336 4.77e+01 c.77.1.4 107726 1gc0A 398 4.79e+01 c.67.1.3 70168 1ckiA 317 4.84e+01 1csn d.144.1.7 41660 2fauA 341 4.84e+01 1ul7A 102 4.88e+01 d.129.6.1 99540 1rpjA 288 4.90e+01 2dri c.93.1.1 35656 2b0jA 358 4.92e+01 1npdA 288 4.95e+01 c.2.1.7,c.58.1.5 80681,80682 2fz0A 149 4.97e+01 1mdwA 328 4.98e+01 d.3.1.3 84934 1at6 129 4.98e+01 3lzt d.2.1.2 36333 1xmpA 170 4.99e+01 2g9iA 249 5.00e+01 1c24A 263 5.02e+01 1c24A d.127.1.1 41148 1vk3A 615 5.04e+01 d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 100846,100847,100848,100849 1qrrA 394 5.05e+01 1qrrA c.2.1.2 29824 1o6dA 163 5.06e+01 c.116.1.3 92567 1nipA 289 5.09e+01 1cp2A c.37.1.10 32263 1derA 547 5.11e+01 1derA 1s0aA 429 5.11e+01 c.67.1.4 98263 1eia 207 5.20e+01 1eia a.28.3.1,a.73.1.1 16951,18331 1wyuB 474 5.26e+01 2matA 264 5.29e+01 1c24A d.127.1.1 41146 1xnzA 264 5.30e+01 1fp6A 289 5.35e+01 1cp2A c.37.1.10 32243 1oxxK 353 5.38e+01 b.40.6.3,c.37.1.12 93715,93716 2bnlA 136 5.39e+01 1qj5A 429 5.44e+01 1dtyA c.67.1.4 34493 1zxzA 197 5.44e+01 1g8iA 190 5.46e+01 1rec a.39.1.5 60363 1hybA 181 5.52e+01 1f9aA c.26.1.3 61399 2fh5A 185 5.56e+01 1rznA 205 5.56e+01 1ris 101 5.57e+01 1ris d.58.14.1 39314 1wjgA 137 5.66e+01 1wy2A 351 5.71e+01 1hcv 117 5.71e+01 1igtB b.1.1.1 20514 1efm 393 5.81e+01 1efcA c.37.1.8 64732 1efaA 333 5.89e+01 1tlfA a.35.1.5,c.93.1.1 17106,35691 1cp2A 269 5.90e+01 1cp2A c.37.1.10 32269 1cvl 319 5.91e+01 1cvl c.69.1.18 34786 1zvtA 256 5.98e+01 1vkkA 154 6.04e+01 d.109.1.2 108669 1trb 320 6.05e+01 1trb c.3.1.5,c.3.1.5 30529,30530 1hw1A 239 6.09e+01 1e2xA a.4.5.6,a.78.1.1 16111,18441 1fr2A 86 6.14e+01 a.28.2.1 83256 1jyeA 349 6.15e+01 c.93.1.1 67455 1u0tA 307 6.23e+01 e.52.1.1 107567 2cfxA 144 6.25e+01 2dri 271 6.28e+01 2dri c.93.1.1 35637 1aw5 326 6.28e+01 1b4kA c.1.10.3 29181 2dldA 337 6.29e+01 1dxy c.2.1.4,c.23.12.1 30099,31359 1vp9 322 6.30e+01 3mag c.66.1.25 34210 1y3jA 77 6.36e+01 1bsg 266 6.38e+01 1btl e.3.1.1 42729 1bt3A 345 6.40e+01 1bt3A a.86.1.2 18507 1vi9A 299 6.48e+01 c.72.1.5 100750 1iz1A 294 6.48e+01 a.4.5.37,c.94.1.1 83823,83824 1txvB 440 6.50e+01 1b5tA 275 6.56e+01 1b5tA c.1.23.1 29676 1yozA 116 6.72e+01 1afvL 217 6.79e+01 32c2A b.1.1.1,b.1.1.2 20130,21160 1tde 316 6.86e+01 1trb c.3.1.5,c.3.1.5 30531,30532 1nnwA 252 6.86e+01 d.159.1.5 80674 1amoA 615 6.89e+01 1amoA b.43.4.1,c.23.5.2,c.25.1.4 25669,31210,31557 1v39 322 7.07e+01 3mag c.66.1.25 34206 1l8dA 112 7.10e+01 h.4.12.1 73687 1xxbA 78 7.15e+01 1xxaA d.74.2.1 39706 2fa8A 105 7.16e+01 1tljA 213 7.17e+01 d.282.1.1 107126 2eiaB 206 7.19e+01 1eia a.28.3.1,a.73.1.1 16950,18330 1l9vA 317 7.22e+01 d.13.2.1,d.216.1.1 73760,73761 1ynuA 473 7.27e+01 1xmeA 568 7.30e+01 1yloA 348 7.31e+01 1v6fA 151 7.33e+01 d.109.1.2 108395 1gr5A 547 7.44e+01 i.16.1.1 65478 1i24A 404 7.49e+01 c.2.1.2 83663 4matA 278 7.53e+01 1c24A d.127.1.1 41150 1e2xA 243 7.66e+01 1e2xA a.4.5.6,a.78.1.1 16113,18443 1q7zA 566 7.70e+01 c.1.21.2,c.1.26.1 96090,96091 1ig0A 319 7.73e+01 1ig0A b.82.6.1,c.100.1.1 62354,62355 1a80 277 7.75e+01 1frb c.1.7.1 28700 1k4nA 192 7.75e+01 d.32.1.5 72059 1gy8A 397 7.85e+01 c.2.1.2 83376 1t6nA 220 7.85e+01 c.37.1.19 106576 1g61A 228 7.90e+01 1g61A d.126.1.1 41126 1kjlA 146 7.92e+01 2ihl 129 7.92e+01 3lzt d.2.1.2 36408 1fnoA 417 7.94e+01 d.58.19.1,c.56.5.4 70145,75841 1a5fL 220 7.96e+01 8fabA b.1.1.1,b.1.1.2 20302,21294 1xg2B 153 7.98e+01 1oxsC 353 7.99e+01 b.40.6.3,c.37.1.12 87519,87520 2g7lA 243 8.00e+01 1bebA 162 8.00e+01 1bebA b.60.1.1 27115 1vdwA 254 8.09e+01 e.7.1.1 100569 1fgqA 839 8.12e+01 1yge a.119.1.1,b.12.1.1 59826,59827 1mexL 213 8.13e+01 b.1.1.1,b.1.1.2 91259,91260 1nksA 194 8.26e+01 1nksA c.37.1.1 31886 1dv1A 449 8.34e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28234,31641,41486 1yurA 98 8.36e+01 1ky9A 448 8.38e+01 b.36.1.4,b.47.1.1 73198,73199 1xs5A 241 8.39e+01 1ivnA 190 8.43e+01 c.23.10.5 83719 1pvvA 315 8.45e+01 c.78.1.1,c.78.1.1 95190,95191 1vrmA 325 8.48e+01 1ddgA 374 8.49e+01 1amoA b.43.4.1,c.25.1.4 25671,31559 1v7cA 351 8.49e+01 c.79.1.1 100446 1ja1A 622 8.51e+01 1amoA b.43.4.1,c.23.5.2,c.25.1.4 62803,62804,62805 1e3sA 261 8.52e+01 1e6wA c.2.1.2 59201 1zh5A 195 8.52e+01 1p4dA 330 8.53e+01 d.89.1.5 94101 1syyA 346 8.54e+01 a.25.1.2 106126 1uwcA 261 8.58e+01 c.69.1.17 100101 1viaA 175 8.61e+01 c.37.1.2 100754 1yn9A 169 8.61e+01 1zy1B 197 8.62e+01 1uiuA 502 8.66e+01 c.94.1.1 99434 1ortA 335 8.78e+01 1othA c.78.1.1,c.78.1.1 35204,35205 1ztxL 212 8.81e+01 1vhoA 346 8.81e+01 b.49.3.1,c.56.5.4 100694,100695 1yge 839 8.91e+01 1yge a.119.1.1,b.12.1.1 19234,23634 1anf 370 8.93e+01 4mbp c.94.1.1 35776 1qnxA 209 8.97e+01 1qnxA d.111.1.1 40914 1f8nA 839 8.97e+01 1yge a.119.1.1,b.12.1.1 59703,59704 1avc 673 9.00e+01 1avc a.65.1.1,a.65.1.1 18178,18179