# List of top-scoring protein chains for t04-100-40-40-str2+CB_burial_14_7-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 1guqA 348 9.03e-48 1guqA d.13.1.2 37522 d.13.1.2 37523 1kpeA 126 6.81e-15 1kpf d.13.1.1 37508 1kpf 126 4.75e-14 1kpf d.13.1.1 37507 1fit 147 1.43e-13 1fit d.13.1.1 37499 2fhi 147 1.18e-12 1fit d.13.1.1 37505 1st0A 337 5.28e-04 1azsB 212 2.84e-02 1azsA d.58.29.1 39423 1bzyA 217 5.22e-02 1qk3A c.61.1.1 34071 1qh4A 380 6.10e-02 1qh4A a.83.1.1 18462 d.128.1.2 41197 1i19A 561 1.03e-01 1i19A d.58.32.3 61522 d.145.1.1 61523 1ptmA 329 1.09e-01 1qz9A 416 1.58e-01 1e8gA 560 1.93e-01 1qltA d.58.32.1 39455 d.145.1.1 41718 1ab8A 220 2.30e-01 1azsA d.58.29.1 39414 1cjbA 231 2.79e-01 1qk3A c.61.1.1 34079 1lldA 319 4.19e-01 3ldh c.2.1.5 30177 d.162.1.1 42144 1sr9A 644 4.20e-01 1k3eA 156 4.26e-01 d.198.1.1 68103 1hyeA 313 4.33e-01 2cmd c.2.1.5 61400 d.162.1.1 61401 1m15A 357 4.64e-01 a.83.1.1 78368 d.128.1.2 78369 1jl0A 334 4.77e-01 1jenA d.156.1.1 63155 1fsgA 233 5.17e-01 1qk3A c.61.1.1 34029 1bg0 356 7.08e-01 1qh4A a.83.1.1 18476 d.128.1.2 41211 1hr6A 475 8.06e-01 1hr6A d.185.1.1 61164 d.185.1.1 61165 1a0cA 438 8.31e-01 1a0cA c.1.15.3 29529 1d1vA 444 8.38e-01 1nseA d.174.1.1 59101 1m55A 197 8.50e-01 d.89.1.3 74469 1d0cA 444 1.14e+00 d.174.1.1 64769 1fukA 165 1.16e+00 1fukA c.37.1.19 32409 1ithA 141 1.27e+00 1ithA a.1.1.2 15623 1d5tA 433 1.29e+00 1gnd c.3.1.3 30422 d.16.1.6 37986 1aisA 182 1.32e+00 1ytbA d.129.1.1 41288 d.129.1.1 41289 1jmsA 381 1.56e+00 a.60.6.1 66889 a.60.12.1 75862 d.218.1.2 75863 1f3vA 179 1.63e+00 1f3vA d.58.22.1 39382 1azsA 220 1.71e+00 1azsA d.58.29.1 39416 1om4A 422 1.73e+00 d.174.1.1 87067 1pvgA 418 1.81e+00 1jndA 420 1.82e+00 c.1.8.5 71757 d.26.3.1 71758 1iy8A 267 1.88e+00 c.2.1.2 83774 1eg9A 449 1.89e+00 1ndoA b.33.1.2 24443 d.129.3.3 41322 1ed5A 444 1.95e+00 1nseA d.174.1.1 42530 1hdhA 536 1.98e+00 c.76.1.2 65805 1phk 298 2.01e+00 1cdkA d.144.1.7 41635 1o5xA 248 2.01e+00 1o7nA 449 2.02e+00 b.33.1.2 81162 d.129.3.3 81163 1dozA 309 2.10e+00 1ak1 c.92.1.1 35592 1cfr 285 2.21e+00 1cfr c.52.1.7 33312 1eu8A 409 2.22e+00 1eu8A c.94.1.1 59502 1iuqA 367 2.43e+00 1bpyA 335 2.50e+00 1bpyA a.60.6.1 17980 a.60.12.1 75819 d.218.1.2 75820 1ut0A 190 2.53e+00 1d7oA 297 2.64e+00 1enp c.2.1.2 29907 1rztA 331 2.73e+00 1ny1A 240 2.77e+00 c.6.2.3 86395 1nnwA 252 2.78e+00 d.159.1.5 80674 1f5aA 513 2.79e+00 1fa0B a.160.1.1 75835 d.218.1.3 75836 d.58.16.1 39337 1eejA 216 2.88e+00 1eejA c.47.1.9 33057 d.17.3.1 38071 1j96A 323 3.01e+00 c.1.7.1 71616 1rypG 244 3.03e+00 d.153.1.4 41938 1iicA 422 3.23e+00 1nmtA d.108.1.2 62422 d.108.1.2 62423 1jyoA 130 3.23e+00 d.198.1.1 67483 1ur1A 378 3.40e+00 1g71A 347 3.41e+00 1g71A e.16.1.1 43268 1v33A 366 3.42e+00 1fvgA 199 3.61e+00 1fvaA d.58.28.1 39408 1n7kA 234 3.63e+00 c.1.10.1 85374 1pinA 163 3.87e+00 1pinA b.72.1.1 27802 d.26.1.1 38431 1lyxA 248 3.93e+00 c.1.1.1 78304 1o5iA 249 4.12e+00 1squA 155 4.13e+00 1ry6A 360 4.32e+00 7taa 478 4.44e+00 7taa b.71.1.1 27778 c.1.8.1 28765 1rypA 243 4.44e+00 1pmaA d.153.1.4 41932 1ia8A 289 4.46e+00 1ia8A d.144.1.7 62112 1enp 312 4.64e+00 1enp c.2.1.2 29906 1elqA 390 4.79e+00 1elqA c.67.1.3 34436 1a3c 181 4.90e+00 1a3c c.61.1.1 34095 1aszB 490 4.93e+00 1b8aA b.40.4.1 25241 d.104.1.1 40762 1b5qA 472 4.96e+00 1b37B c.3.1.2 30404 d.16.1.5 37968 1lucA 355 5.00e+00 1lucA c.1.16.1 29547 1hyhA 309 5.19e+00 1hyhA c.2.1.5 30150 d.162.1.1 42117 1nffA 260 5.26e+00 c.2.1.2 80457 1jffA 451 5.26e+00 c.32.1.1 62932 d.79.2.1 62933 1ux6A 350 5.28e+00 1k30A 368 5.42e+00 c.112.1.1 68067 1gw0A 559 5.44e+00 b.6.1.3 70623 b.6.1.3 70624 b.6.1.3 70625 1nz0A 118 6.00e+00 d.14.1.2 86433 1e1hA 287 6.12e+00 d.92.1.7 83167 1lrzA 426 6.29e+00 a.2.7.4 78167 d.108.1.4 78168 d.108.1.4 78169 1jvwA 167 6.50e+00 d.26.1.1 71907 1rypC 244 6.51e+00 1rypC d.153.1.4 41934 1f83A 425 6.65e+00 1f82A d.92.1.7 40306 1uxy 340 7.26e+00 2mbr d.145.1.2 41748 d.146.1.1 41761 2ng1 293 7.29e+00 1ng1 a.24.13.1 16962 c.37.1.10 32273 4crxA 322 7.34e+00 4crxA a.60.9.1 18095 d.163.1.1 42155 1v6fA 151 7.49e+00 1eo9A 209 7.54e+00 3pchA b.3.6.1 22731 1g9mG 321 8.07e+00 1gc1G d.172.1.1 42492 1uk5A 111 8.08e+00 1eluA 390 8.13e+00 1elqA c.67.1.3 34434 1ojqA 212 8.31e+00 1ockA 412 8.39e+00 c.117.1.1 86802 1ls1A 295 8.68e+00 a.24.13.1 78170 c.37.1.10 78171 1fnnA 389 8.82e+00 1fnnA a.4.5.11 16129 c.37.1.20 32426 1k8kA 418 9.09e+00 c.55.1.1 68305 c.55.1.1 68306 1v39 322 9.21e+00 3mag c.66.1.25 34206 1mmq 170 9.29e+00 1hfc d.92.1.11 40396 3dni 260 9.43e+00 3dni d.151.1.1 41791 1d0yA 761 9.54e+00 1lvk b.34.3.1 24581 c.37.1.9 32178 1c0pA 363 9.60e+00 1an9A c.4.1.2 30647 d.16.1.3 37934 1hn0A 1021 9.75e+00 a.102.3.2 83616 b.18.1.17 83617 b.24.1.1 83618 b.30.5.2 83619 1vj1A 363 9.81e+00 1nq6A 302 1.01e+01 2polA 366 1.04e+01 2polA d.131.1.1 41356 d.131.1.1 41357 d.131.1.1 41358 1rypB 250 1.05e+01 1rypB d.153.1.4 41933 3mag 307 1.08e+01 3mag c.66.1.25 34205 1lvk 762 1.08e+01 1lvk b.34.3.1 24576 c.37.1.9 32173 1prxA 224 1.08e+01 1prxA c.47.1.10 33076 1vp9 322 1.12e+01 3mag c.66.1.25 34210 1fy7A 278 1.13e+01 1fy7A d.108.1.1 40817 1efyA 350 1.14e+01 1a26 a.41.1.1 17413 d.166.1.2 42275 1hrkA 359 1.16e+01 1hrkA c.92.1.1 61228 1fkx 349 1.16e+01 1a4mA c.1.9.1 29018 4pfk 319 1.16e+01 3pfk c.89.1.1 35582 1gcvA 140 1.19e+01 1cg5B a.1.1.2 15410 1mbxC 106 1.21e+01 d.45.1.2 78929 1nstA 325 1.23e+01 1nstA c.37.1.5 31951 2aaa 484 1.23e+01 7taa b.71.1.1 27777 c.1.8.1 28764 1ds1A 324 1.23e+01 1drtA b.82.2.2 28127 1dekA 241 1.23e+01 1dekA c.37.1.1 31842 1o8uA 257 1.26e+01 c.14.1.3 81194 1vpt 348 1.28e+01 3mag c.66.1.25 34207 1dxrH 258 1.29e+01 6prcH b.41.1.1 25456 f.23.10.1 43433 1cydA 244 1.31e+01 1cydA c.2.1.2 29825 1mugA 168 1.31e+01 1mugA c.18.1.2 31030 1mkmA 249 1.32e+01 a.4.5.33 79242 d.110.2.2 79243 1tml 286 1.32e+01 1tml c.6.1.1 30656 1g0oA 283 1.34e+01 1ybvA c.2.1.2 60181 1knvA 293 1.34e+01 c.52.1.7 68707 1xyzA 347 1.37e+01 1taxA c.1.8.3 28804 1rzjG 321 1.39e+01 1f89A 291 1.40e+01 d.160.1.1 64988 1ayl 541 1.41e+01 1ayl c.91.1.1 64718 c.109.1.1 64719 1rkqA 282 1.41e+01 2dnjA 260 1.44e+01 3dni d.151.1.1 41790 1hfeL 421 1.49e+01 1fehA c.96.1.1 36018 d.58.1.5 39001 1ng2A 193 1.56e+01 b.34.2.1 85660 b.34.2.1 85661 1jclA 260 1.59e+01 c.1.10.1 66501 1v1rA 400 1.59e+01 1e29A 135 1.60e+01 1e29A a.3.1.1 59161 1o6zA 303 1.61e+01 c.2.1.5 81107 d.162.1.1 81108 1ow1A 195 1.62e+01 1gz6A 319 1.62e+01 c.2.1.2 76410 1us5A 314 1.62e+01 1uwvA 433 1.63e+01 1olsA 400 1.64e+01 1hbzA 498 1.64e+01 1cf9A e.5.1.1 60937 1gy8A 397 1.64e+01 c.2.1.2 83376 1oyeA 1049 1.67e+01 d.58.44.1 87587 d.58.44.1 87588 d.58.44.1 87589 d.58.44.1 87590 d.225.1.1 87591 d.225.1.1 87592 f.35.1.1 87593 f.35.1.1 87594 1k87A 669 1.68e+01 a.176.1.1 77286 c.1.23.2 77287 1b7yB 785 1.69e+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 1vkhA 273 1.69e+01 1vhh 162 1.73e+01 1vhh d.65.1.2 39550 1oi2A 366 1.74e+01 c.32.1.2 87039 d.79.2.2 87040 1iso 416 1.77e+01 1iso c.77.1.1 35065 1c96A 753 1.77e+01 1amj c.8.2.1 30727 c.83.1.1 35403 1qddA 144 1.78e+01 1qddA d.169.1.1 42324 1o8rA 94 1.84e+01 d.234.1.1 86677 1nslA 184 1.85e+01 d.108.1.1 86137 1q0bA 367 1.86e+01 1jksA 294 1.87e+01 d.144.1.7 71710 1itwA 741 1.87e+01 c.77.1.2 76793 1p1xA 260 1.87e+01 1a4mA 349 1.88e+01 1a4mA c.1.9.1 29014 1dc1A 323 1.88e+01 1dc1A c.52.1.11 33321 1brmA 367 1.89e+01 1brmA c.2.1.3 30030 d.81.1.1 39945 1ush 550 1.90e+01 1ush d.114.1.1 40923 d.159.1.2 42079 1i40A 175 1.90e+01 b.40.5.1 66024 1fg7A 356 1.90e+01 1gewA c.67.1.1 59819 1nksA 194 1.93e+01 1nksA c.37.1.1 31886 1qd1A 325 1.97e+01 1qd1A d.58.34.1 39493 d.58.34.1 39494 1moq 368 1.97e+01 1moq c.80.1.1 35302 1qhfA 240 1.97e+01 1qhfA c.60.1.1 33960 1j1nA 492 1.99e+01 c.94.1.1 83978 1pn0A 665 2.00e+01 2cbp 96 2.00e+01 2cbp b.6.1.1 22895 1rypD 241 2.04e+01 1rypD d.153.1.4 41935 1g8kA 825 2.05e+01 1g8jA b.52.2.2 26920 c.81.1.1 35328 1pcxA 810 2.08e+01 1qwyA 291 2.09e+01 1gpeA 587 2.12e+01 1gpeA c.3.1.2 30387 d.16.1.1 37951 1omwA 689 2.13e+01 a.91.1.1 87086 b.55.1.1 87087 d.144.1.7 87088 1q2yA 140 2.14e+01 1h6qA 168 2.15e+01 1h6qA b.88.1.2 60692 1uspA 139 2.17e+01 1ps9A 671 2.18e+01 1pxwA 128 2.19e+01 1vhmA 195 2.19e+01 1h8dH 260 2.20e+01 5ptp 1gweA 503 2.23e+01 e.5.1.1 70667 1psdA 409 2.24e+01 1psdA c.2.1.4 30097 c.23.12.1 31357 d.58.18.1 39354 2vhbA 146 2.27e+01 2vhbA a.1.1.2 15629 1gcoA 261 2.28e+01 1ybvA c.2.1.2 29884 1gnd 447 2.29e+01 1gnd c.3.1.3 30423 d.16.1.6 37987 1ixh 321 2.31e+01 1ixh c.94.1.1 35761 1qyaA 307 2.31e+01 1az9 457 2.34e+01 1az9 c.55.2.1 33547 d.127.1.1 41164 1r1dA 247 2.36e+01 1f8vA 355 2.38e+01 2bbvA b.121.4.4 23329 1xgsA 295 2.39e+01 1bn5 a.4.5.25 16216 d.127.1.1 41153 1j1uA 306 2.39e+01 c.26.1.1 83980 1mroB 442 2.40e+01 1mroB a.89.1.1 18531 d.58.31.2 39449 1j26A 112 2.40e+01 1dxrC 336 2.43e+01 6prcC a.138.1.2 19670 1nkxA 348 2.45e+01 1i1qA 520 2.46e+01 1qdlA d.161.1.1 61543 1babA 143 2.49e+01 1abwA a.1.1.2 15235 1q52A 314 2.49e+01 1odfA 290 2.52e+01 1a7j 290 2.52e+01 1a7j c.37.1.6 31952 1o0xA 262 2.53e+01 d.127.1.1 80755 1n6zA 105 2.55e+01 d.74.5.1 85369 1mu5A 471 2.56e+01 a.156.1.3 79472 d.14.1.3 79473 d.122.1.2 79474 1fohA 664 2.58e+01 1fohA c.3.1.2 30381 c.47.1.10 33078 d.16.1.2 37900 1lvmA 229 2.60e+01 b.47.1.3 78243 1lo6A 223 2.63e+01 b.47.1.2 74143 1eulA 994 2.64e+01 1eulA b.82.7.1 75829 c.108.1.7 75830 d.220.1.1 75831 f.33.1.1 75832 1i7hA 111 2.65e+01 d.15.4.1 71122 1ee8A 266 2.65e+01 1ee8A a.156.1.2 75823 b.113.1.1 75824 g.39.1.8 75825 1e19A 314 2.68e+01 1b7bA c.73.1.1 34967 2cuaA 135 2.69e+01 2cuaA b.6.1.2 23039 1q0sA 259 2.73e+01 1gz8A 299 2.74e+01 d.144.1.7 83405 1pb1A 416 2.78e+01 c.77.1.1 88014 1cg5B 141 2.80e+01 1cg5B a.1.1.2 15585 1n2eA 300 2.81e+01 c.26.1.4 85268 1auk 489 2.90e+01 1auk c.76.1.2 35030 1p4oA 322 2.90e+01 d.144.1.7 87775 1gzwA 134 2.94e+01 1hh1A 143 2.94e+01 1gefA c.52.1.18 61036 1sixA 174 2.95e+01 1o8bA 219 2.95e+01 c.35.1.2 81180 d.58.40.1 81181 1lfaA 187 2.96e+01 1ido c.62.1.1 34122 1vh5A 148 2.97e+01 1jj2L 194 2.97e+01 1ffkI d.12.1.2 63097 1e6yB 433 2.98e+01 1mroB a.89.1.1 18535 d.58.31.2 39453 1qs0A 407 3.01e+01 1qs0A c.36.1.11 31829 1h3fA 432 3.05e+01 c.26.1.1 76631 d.66.1.4 76632 1oihA 301 3.05e+01 1o0iA 138 3.07e+01 d.38.1.5 86532 1myt 146 3.07e+01 1a6m a.1.1.2 15207 2if1 126 3.08e+01 2if1 d.64.1.1 39547 1gtkA 313 3.09e+01 c.94.1.1 76346 d.50.2.1 76347 1hkyA 86 3.09e+01 g.10.1.3 76714 1bykA 255 3.12e+01 1bykA c.93.1.1 35706 1r4vA 171 3.13e+01 1q7bA 244 3.13e+01 1kw3B 292 3.15e+01 d.32.1.3 77549 d.32.1.3 77550 2nacA 393 3.17e+01 2nadA c.2.1.4 30088 c.23.12.1 31348 1geeA 261 3.19e+01 1frb 315 3.19e+01 1frb c.1.7.1 28665 1hcl 298 3.24e+01 1hcl d.144.1.7 41593 1nrgA 261 3.24e+01 b.45.1.1 80694 1nd4A 264 3.24e+01 1gdeA 389 3.24e+01 c.67.1.1 60456 1gheA 177 3.24e+01 d.108.1.1 76222 1pieA 419 3.26e+01 1c1dA 355 3.30e+01 1bw9A c.2.1.7 30270 c.58.1.1 33918 1cxc 124 3.33e+01 1ycc a.3.1.1 15890 1uzbA 516 3.37e+01 1byqA 228 3.39e+01 1yer d.122.1.1 41100 1s9aA 257 3.41e+01 1dkiA 371 3.42e+01 1dkiA d.3.1.1 37090 1f1zA 273 3.44e+01 1f1zA a.4.5.27 16081 c.52.1.16 33334 1qmeA 702 3.47e+01 1pmd d.11.1.1 37487 d.11.1.1 37488 d.175.1.1 42560 e.3.1.1 42769 1f7lA 121 3.51e+01 1f7lA d.150.1.2 59666 1rj9A 304 3.51e+01 1babB 146 3.54e+01 1abwA a.1.1.2 15414 1r3sA 367 3.56e+01 1gcvB 136 3.56e+01 1cg5B a.1.1.2 15589 1uroA 367 3.56e+01 1uroA c.1.22.1 29675 1e58A 249 3.62e+01 1qhfA c.60.1.1 59262 1v5sA 126 3.62e+01 1jk3A 158 3.64e+01 d.92.1.11 66790 1mldA 314 3.67e+01 2cmd c.2.1.5 30122 d.162.1.1 42089 1sdjA 310 3.70e+01 1jtvA 327 3.70e+01 c.2.1.2 84230 1ml4A 308 3.71e+01 c.78.1.1 79255 c.78.1.1 79256 1h8mA 140 3.77e+01 1h8mA d.110.4.1 60782 1fjjA 159 3.80e+01 1fjjA b.17.1.2 59852 1rreA 200 3.86e+01 2lisA 136 3.91e+01 1lis a.19.1.1 16405 2prd 174 3.92e+01 2prd b.40.5.1 25435