# List of top-scoring protein chains for t2k-100-30-o_notor2-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 1nxmA 197 2.51e-02 b.82.1.1 86385 2awaA 390 1.67e+00 2al1A 436 1.82e+00 1apa 266 1.90e+00 1qi7A d.165.1.1 42205 2al2A 436 2.00e+00 1llnA 262 2.21e+00 d.165.1.1 84625 1fa8A 135 2.24e+00 1qipA d.32.1.1 38486 2oneA 436 2.29e+00 4enl c.1.11.1,d.54.1.1 29203,38847 1f9zA 135 2.35e+00 1qipA d.32.1.1 38484 1oneA 436 2.36e+00 4enl c.1.11.1,d.54.1.1 29200,38844 1ww9A 392 2.39e+00 1tqzA 133 2.45e+00 1lxdA 100 2.88e+00 1lfdA d.15.1.5 37624 2grrA 161 3.19e+00 4enl 436 3.44e+00 4enl c.1.11.1,d.54.1.1 29202,38846 1u9aA 160 3.66e+00 1u9aA d.20.1.1 38333 1umzA 278 3.67e+00 b.29.1.2 99639 1wwrA 171 3.98e+00 1q8bA 105 4.04e+00 d.58.4.6 96201 1a3s 160 4.15e+00 1u9aA d.20.1.1 38335 2rgf 97 4.21e+00 1lfdA d.15.1.5 37627 1eur 365 4.22e+00 1eut b.68.1.1 27607 1gyfA 62 4.35e+00 1gyfA d.76.1.1 39749 1yh6A 179 4.42e+00 1prq 125 4.84e+00 3nul d.110.1.1 40883 1ps2 60 5.44e+00 2pspA g.16.1.1 44746 1raxA 115 5.72e+00 1lfdA d.15.1.5 37626 1acf 125 5.80e+00 3nul d.110.1.1 40882 2as0A 396 6.03e+00 1yprA 125 6.04e+00 3nul d.110.1.1 40888 1lfdA 87 6.13e+00 1lfdA d.15.1.5 37622 1o97C 264 6.15e+00 c.26.2.3 81232 1dkxA 219 6.43e+00 1dkzA a.8.4.1,b.130.1.1 90339,90340 1pk6A 133 6.64e+00 b.22.1.1 94801 1eo1A 124 6.76e+00 1eo1A c.55.5.1 33739 1qipA 183 7.03e+00 1qipA d.32.1.1 38470 1w8oA 601 7.11e+00 2a38A 194 7.31e+00 1ej1A 190 7.32e+00 1ejhA d.86.1.1 40144 1ld4A 264 7.65e+00 i.6.1.1 77886 1xfsA 178 7.88e+00 d.129.3.5 109589 1wcqA 601 7.93e+00 1han 297 8.30e+00 1han d.32.1.3,d.32.1.3 38506,38507 1svpA 161 8.30e+00 1svpA b.47.1.3 26384 1eut 605 9.61e+00 1eut b.1.18.2,b.18.1.1,b.68.1.1 21891,23712,27609 1gvmA 136 9.63e+00 b.109.1.1 70612 1lkdA 297 9.71e+00 d.32.1.3,d.32.1.3 78059,78060 1nszA 347 9.79e+00 b.30.5.4 80724 1lgtA 297 9.86e+00 d.32.1.3,d.32.1.3 77956,77957 1xygD 359 1.02e+01 1h1iB 350 1.02e+01 b.82.1.5 76470 1fxzA 476 1.05e+01 b.82.1.2,b.82.1.2 65059,65060 1khdA 345 1.08e+01 a.46.2.1,c.27.1.1 77400,77401 1a0k 131 1.09e+01 3nul d.110.1.1 40892 1zboA 210 1.11e+01 1p5zB 263 1.11e+01 c.37.1.1 87815 1euu 605 1.13e+01 1eut b.1.18.2,b.18.1.1,b.68.1.1 21892,23713,27610 1h1iD 350 1.13e+01 b.82.1.5 76472 1mmuA 347 1.16e+01 b.30.5.4 79303 1syxB 86 1.17e+01 1acz 108 1.17e+01 1kum b.3.1.1 22524 1juhA 350 1.20e+01 b.82.1.5 71884 1dkzA 219 1.21e+01 1dkzA a.8.4.1,b.130.1.1 90345,90346 1jtdB 273 1.23e+01 b.69.5.2 67265 1jmcA 246 1.23e+01 1jmcA b.40.4.3,b.40.4.3 25300,25301 1yhfA 115 1.26e+01 1ug6A 431 1.27e+01 c.1.8.4 88490 1uisA 231 1.29e+01 d.22.1.1 99431 2b7yA 182 1.31e+01 1a2pA 110 1.31e+01 1b20A d.1.1.2 36140 1brhA 110 1.32e+01 1b20A d.1.1.2 36151 1b2sA 110 1.33e+01 1b20A d.1.1.2 36213 1l8bA 190 1.36e+01 d.86.1.1 73683 1mal 421 1.36e+01 2mprA f.4.3.2 43784 1hcxA 127 1.37e+01 b.109.1.1 65800 1h8gA 95 1.38e+01 b.109.1.1 65735 1af6A 421 1.39e+01 2mprA f.4.3.2 43772 1a81A 254 1.40e+01 1a81A d.93.1.1,d.93.1.1 40507,40508 2gaxA 135 1.41e+01 1a90 108 1.41e+01 1cewI d.17.1.2 38001 1d6aB 262 1.43e+01 1qi7A d.165.1.1 42198 1m98A 317 1.45e+01 a.175.1.1,d.17.4.6 78866,78867 1ark 60 1.46e+01 1bb9 b.34.2.1 24473 2fqpA 97 1.49e+01 1baoA 110 1.50e+01 1b20A d.1.1.2 36187 1kum 108 1.50e+01 1kum b.3.1.1 22525 1s5aA 150 1.50e+01 d.17.4.10 98525 1vquA 374 1.51e+01 1b3sA 110 1.51e+01 1b20A d.1.1.2 36229 1qz8A 113 1.51e+01 b.140.1.1 96619 1bngA 110 1.51e+01 1b20A d.1.1.2 36184 1o0xA 262 1.52e+01 d.127.1.1 80755 2fymA 431 1.52e+01 2c4bA 143 1.54e+01 1gy7A 125 1.55e+01 d.17.4.2 70738 1banA 110 1.57e+01 1b20A d.1.1.2 36197 1zn6A 227 1.58e+01 1q67A 231 1.58e+01 b.55.1.7 95960 1d7yA 408 1.61e+01 1d7yA c.3.1.5,c.3.1.5,d.87.1.1 30565,30566,40204 1h1iC 350 1.61e+01 b.82.1.5 76471 1q8fA 313 1.61e+01 c.70.1.1 96203 1y71A 130 1.63e+01 2fa8A 105 1.64e+01 1vkdA 338 1.65e+01 b.67.2.4 108644 1qv1A 195 1.67e+01 a.39.1.5 96347 1b2zA 110 1.70e+01 1b20A d.1.1.2 36216 1brnL 110 1.71e+01 1b20A d.1.1.2 36143 1ak2 233 1.72e+01 1zin c.37.1.1,g.41.2.1 31894,45195 1ggxA 223 1.74e+01 1ggxA d.22.1.1 38367 1gbg 214 1.83e+01 1axkA b.29.1.2 24171 3nul 130 1.86e+01 3nul d.110.1.1 40891 1o5uA 101 1.89e+01 b.82.1.8 92518 1ne8A 117 1.90e+01 b.34.6.2 80424 2fhfA 1083 1.92e+01 2fp8A 322 1.95e+01 1voqa 90 1.95e+01 1zgoA 223 1.96e+01 1u6dX 308 2.00e+01 1ewqA 765 2.01e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19069,32383,33740,39743 1jatA 155 2.01e+01 1u9aA d.20.1.1 62818 1el4A 195 2.01e+01 1ej3A a.39.1.5 59453 2d93A 134 2.01e+01 1zn8A 180 2.04e+01 1cjtA 217 2.05e+01 1azsA d.58.29.1 39419 1n3gA 113 2.06e+01 d.204.1.1 79962 1b20A 110 2.07e+01 1b20A d.1.1.2 36207 1l4sA 112 2.11e+01 d.204.1.1 77693 1kdgA 546 2.13e+01 c.3.1.2,d.16.1.1 77337,77338 1vqoQ 96 2.14e+01 2ffsA 157 2.18e+01 1jf0A 195 2.19e+01 1ej3A a.39.1.5 62926 1nnxA 109 2.22e+01 b.40.10.1 92013 1vmjA 151 2.24e+01 2gupA 292 2.34e+01 2ayh 214 2.40e+01 1axkA b.29.1.2 24172 1urrA 102 2.41e+01 d.58.10.1 107998 1kn0A 212 2.41e+01 d.50.1.3 77444 1jf2A 195 2.44e+01 1ej3A a.39.1.5 62930 1ts9A 102 2.46e+01 1zq4A 693 2.47e+01 1l6oA 95 2.48e+01 b.36.1.1 84534 2pia 321 2.48e+01 2pia b.43.4.2,c.25.1.2,d.15.4.2 25663,31553,37704 1w1kA 560 2.51e+01 d.58.32.1,d.145.1.1 109059,109060 1zt3A 80 2.53e+01 1vplA 256 2.54e+01 1ipcA 217 2.57e+01 d.86.1.1 71257 1vavA 222 2.57e+01 b.29.1.18 108472 1rnbA 110 2.58e+01 1b20A d.1.1.2 36196 2aysA 348 2.59e+01 1jsg 114 2.68e+01 1a1x b.63.1.1 27513 2ck3D 482 2.68e+01 1o12A 376 2.75e+01 b.92.1.5,c.1.9.10 80758,80759 1bh5A 183 2.76e+01 1qipA d.32.1.1 38476 1a67 108 2.76e+01 1cewI d.17.1.2 38000 1h3iA 293 2.79e+01 b.76.2.1,b.85.7.1 76635,76636 1ri6A 343 2.81e+01 b.69.11.1 97503 1b21A 110 2.81e+01 1b20A d.1.1.2 36219 2b6dA 345 2.84e+01 1h8eD 482 2.91e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 60747,60748,60749 2bepA 159 2.92e+01 1e8gA 560 2.93e+01 1qltA d.58.32.1,d.145.1.1 39455,41718 1csyA 112 2.94e+01 1lckA d.93.1.1 40519 2ltnA 181 2.99e+01 1led b.29.1.1 24024 1mt6A 280 3.02e+01 b.76.2.1,b.85.7.1 79446,79447 1jbbA 153 3.06e+01 1u9aA d.20.1.1 62842 1l7jA 347 3.12e+01 b.30.5.4 73660 1vr3A 191 3.13e+01 1bxsA 501 3.14e+01 1bpwA c.82.1.1 35357 1ym0A 238 3.19e+01 1ue1A 164 3.27e+01 b.40.4.3 99243 1r3cA 366 3.29e+01 d.144.1.7 96906 1a7cA 379 3.30e+01 1sek e.1.1.1 42660 1nkxA 348 3.32e+01 c.94.1.2 91943 1fzvA 132 3.34e+01 1vpfA g.17.1.1 60159 1rzhH 260 3.35e+01 b.41.1.1,f.23.10.1 98162,98163 1qltA 560 3.39e+01 1qltA d.58.32.1,d.145.1.1 39457,41720 2ahjA 206 3.44e+01 2ahjA d.149.1.1 41772 1dgrN 79 3.45e+01 1caxB 1jv1A 505 3.45e+01 c.68.1.5 71892 1culA 217 3.47e+01 1azsA d.58.29.1 39417 1n7zA 334 3.50e+01 b.127.1.1 85380 1okjA 251 3.50e+01 c.55.1.9,c.55.1.9 103998,103999 1qu5A 182 3.52e+01 1qu5A b.26.1.2 23922 1ejhA 190 3.57e+01 1ejhA d.86.1.1 40147 1e79D 482 3.63e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 18272,26437,32317 1fyeA 229 3.65e+01 1fyeA c.23.16.4 31477 1lcyA 325 3.69e+01 b.36.1.4,b.47.1.1 73834,73835 1lenA 181 3.69e+01 1led b.29.1.1 24032 2bwnA 401 3.70e+01 1gikA 261 3.77e+01 d.165.1.1 90513 1dx5I 118 3.80e+01 1dx5I g.3.11.1,g.3.11.1,g.3.11.1 44302,44303,44304 1i3zA 103 3.81e+01 d.93.1.1 83667 1azsA 220 3.85e+01 1azsA d.58.29.1 39416 1gwmA 153 3.86e+01 b.18.1.19 83348 1tq5A 242 3.87e+01 2cz1A 206 3.89e+01 2ahjC 206 3.91e+01 2ahjA d.149.1.1 41773 1jj2P 95 3.94e+01 1ffkN b.34.5.1 63101 1xrtA 467 3.99e+01 1s72Q 96 4.02e+01 b.34.5.1 105336 1bpr 191 4.04e+01 1dkzA b.130.1.1 43319 1ywrA 360 4.06e+01 1ukgA 252 4.08e+01 b.29.1.1 99489 1m1fA 110 4.10e+01 b.34.6.2 78401 1ahjA 207 4.11e+01 2ahjA d.149.1.1 41774 1j1qA 261 4.12e+01 d.165.1.1 90768 1db2A 377 4.15e+01 1sek e.1.1.1 42672 2ge3A 170 4.17e+01 1u2cA 246 4.17e+01 b.1.6.2,d.272.1.1 107610,107611 1twiA 434 4.19e+01 b.49.2.3,c.1.6.1 107399,107400 1h91A 180 4.20e+01 b.60.1.1 60805 1wz4A 23 4.21e+01 1pc0A 61 4.24e+01 b.137.1.1 94426 2c7xA 436 4.25e+01 1eetB 427 4.25e+01 1rthA e.8.1.2 43079 1xbfA 140 4.34e+01 d.273.1.1 109538 1bnr 110 4.35e+01 1b20A d.1.1.2 36206 2cr9A 139 4.37e+01 6prcH 258 4.40e+01 6prcH b.41.1.1,f.23.10.1 25457,43436 2cdcA 366 4.40e+01 2avtA 378 4.40e+01 1n3oA 252 4.43e+01 b.29.1.1 79967 1j4aA 333 4.44e+01 c.2.1.4,c.23.12.1 71502,71503 1iv8A 720 4.52e+01 b.71.1.1,c.1.8.1 76842,76843 1qy6A 274 4.54e+01 b.47.1.1 96574 1ctt 294 4.54e+01 1ctt c.97.1.1,c.97.1.1 36022,36023 1d4tA 104 4.56e+01 1d4tA d.93.1.1 40537 1dgrV 79 4.58e+01 1caxB b.82.1.2 28099 1qfoA 119 4.62e+01 1qfoA b.1.1.1 19708 1gtkA 313 4.64e+01 c.94.1.1,d.50.2.1 76346,76347 1jmmA 377 4.73e+01 b.30.6.1 71749 2biqA 219 4.82e+01 1x23A 155 4.83e+01 1u69A 163 4.85e+01 d.32.1.7 107699 1ffkR 66 4.87e+01 1ffkR g.39.1.6 45152 1kxqE 120 4.96e+01 b.1.1.1 73171 1olzA 663 4.96e+01 b.1.1.4,b.69.12.1,g.16.2.1 93341,93342,93343 1y1uA 585 4.97e+01 1mz5A 638 4.97e+01 b.29.1.15,b.68.1.1 79679,79680 1vpkA 378 4.99e+01 1m4jA 142 5.04e+01 d.109.1.2 78602 1zgkA 308 5.07e+01 1eysH 259 5.09e+01 6prcH b.41.1.1,f.23.10.1 25484,43517 1fy2A 229 5.09e+01 1fyeA c.23.16.4 31478 1rypH 205 5.10e+01 d.153.1.4 41876 1nqjA 119 5.17e+01 b.23.2.1 86031 1sqjA 789 5.20e+01 b.69.13.1,b.69.13.1 105918,105919 2cy2A 174 5.22e+01 1uolA 219 5.25e+01 b.2.5.2 99695 1i4uA 181 5.28e+01 b.60.1.1 61732 1dxrH 258 5.33e+01 6prcH b.41.1.1,f.23.10.1 25456,43433 1nezG 128 5.37e+01 b.1.1.1 85592 1yovA 537 5.38e+01 1xtoA 311 5.39e+01 1vm8A 534 5.40e+01 1s4iA 175 5.43e+01 1k2fA 190 5.43e+01 b.8.1.2 68054 1pcfA 66 5.53e+01 1pcfA d.18.1.1 38142 1aijH 260 5.53e+01 6prcH b.41.1.1,f.23.10.1 25466,43463 2ac0A 200 5.56e+01 1vaoA 560 5.59e+01 1qltA d.58.32.1,d.145.1.1 39461,41724 1mvfD 82 5.65e+01 b.129.1.1 85143 1ystH 260 5.70e+01 6prcH b.41.1.1,f.23.10.1 25482,43511 1qovH 260 5.74e+01 6prcH b.41.1.1,f.23.10.1 25464,43457 1kw3B 292 5.75e+01 d.32.1.3,d.32.1.3 77549,77550 1lj5A 379 5.76e+01 e.1.1.1 73928 1h0hB 214 5.80e+01 d.58.1.5 76437 1w2lA 99 5.86e+01 1wkqA 164 5.93e+01 c.97.1.2 109393 1icfI 65 5.95e+01 1icfI g.28.1.1 44958 1um5H 217 5.97e+01 2biwA 490 6.00e+01 1k9vF 201 6.06e+01 c.23.16.1 68365 1m2tB 263 6.09e+01 b.42.2.1,b.42.2.1 84762,84763 1f6fB 210 6.10e+01 1axiB b.1.2.1,b.1.2.1 22033,22034 2db1A 118 6.14e+01 1h6hA 143 6.15e+01 d.189.1.1 65681 1vf8A 377 6.17e+01 1az9 457 6.21e+01 1az9 c.55.2.1,d.127.1.1 33547,41164 1lcjA 109 6.22e+01 1qadA d.93.1.1 40414 2cn3A 737 6.24e+01 1phm 310 6.32e+01 1phm b.121.1.2,b.121.1.2 59015,59016 1lshA 1056 6.35e+01 a.118.4.1,f.7.1.1,f.7.1.1 74242,74243,74244 1qtrA 317 6.36e+01 1qtrA c.69.1.7 34660 2cwpA 112 6.37e+01 1s6lA 212 6.41e+01 1q47A 495 6.41e+01 b.69.12.1 104532 1pxvA 183 6.42e+01 d.3.1.1 95301 1egxA 115 6.42e+01 1evhA b.55.1.4 27000 1dgwX 79 6.43e+01 1caxB b.82.1.2 28091 1a87 321 6.48e+01 1a87 f.1.1.1 43380 1zc1A 208 6.48e+01 1t0pB 86 6.53e+01 1squA 155 6.55e+01 d.252.1.1 98971 1o13A 136 6.56e+01 c.55.5.1 80762 1wriA 93 6.59e+01 1df7A 159 6.60e+01 3dfr c.71.1.1 34885 1b7aA 186 6.65e+01 1a44 b.17.1.1 23705 1y9wA 140 6.66e+01 1fjxA 327 6.67e+01 6mhtA c.66.1.26 34228 1ift 263 6.68e+01 1mrj d.165.1.1 42211 1fvuB 125 6.72e+01 1ixxB d.169.1.1 42346 1s4bP 674 6.79e+01 d.92.1.5 105252 1rreA 200 6.80e+01 d.14.1.10 97791 1kexA 155 6.81e+01 b.18.1.2 77350 1obs 267 6.83e+01 1mrj d.165.1.1 42213 1c4rA 182 6.85e+01 1c4rA b.29.1.4 24229 1qaxA 428 6.86e+01 1qaxA d.58.20.1,d.179.1.1 39376,42597 1lvmA 229 6.88e+01 b.47.1.3 78243 1ajoA 214 6.88e+01 1axkA b.29.1.2 24179 1zo2A 129 6.89e+01 1npsA 88 6.90e+01 1prs b.11.1.1 23622 1od3A 168 6.90e+01 b.18.1.10 86825 1z47A 355 6.92e+01 1e9iA 431 6.98e+01 c.1.11.1,d.54.1.1 64818,64819 1gouA 116 7.12e+01 d.1.1.2 65429 2fcr 173 7.15e+01 1rcf c.23.5.1 31151 9gafA 295 7.21e+01 1apyA d.153.1.5 42008 1gw5S 142 7.24e+01 d.110.4.2 70633 1qdlB 195 7.26e+01 1qdlB c.23.16.1 31437 1hd2A 161 7.26e+01 c.47.1.10 60962 1ac0 108 7.31e+01 1kum b.3.1.1 22526 1xeaA 323 7.38e+01 c.2.1.3,d.81.1.5 109572,109573 1an7A 136 7.40e+01 1seiA d.140.1.1 41465 1wba 175 7.41e+01 1wba b.42.4.1 25591 1gpiA 431 7.46e+01 b.29.1.10 65450 1vmfA 145 7.47e+01 1yr0A 175 7.50e+01 1rb9 53 7.54e+01 1rb9 g.41.5.1 45214 1z1zA 131 7.60e+01 2carA 196 7.61e+01 1fzkA 274 7.69e+01 1agdA b.1.1.2,d.19.1.1 60149,60150 1wvqA 167 7.75e+01 1i1qA 520 7.76e+01 1qdlA d.161.1.1 61543 1bqnA 558 7.76e+01 1rthA c.55.3.1,e.8.1.2 33599,43064 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