# 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 1jpaA 312 1.26e-65 d.144.1.7 67011 1ir3A 306 4.12e-64 1fmk d.144.1.7 41702 1opjA 293 1.05e-63 d.144.1.7 87230 1p4oA 322 1.36e-63 d.144.1.7 87775 1t46A 313 4.43e-63 d.144.1.7 106397 1fgkA 310 6.17e-62 1fgkA d.144.1.7 41693 1qpcA 279 1.37e-60 1fgkA d.144.1.7 41685 1r0pA 312 9.49e-59 d.144.1.7 96734 1u59A 287 1.18e-57 d.144.1.7 107681 1mp8A 281 3.85e-57 d.144.1.7 91384 1fvrA 327 7.75e-57 d.144.1.7 60047 1xbbA 291 9.42e-57 1u46A 291 3.28e-56 d.144.1.7 107656 1ywnA 316 5.24e-56 2b7aA 293 9.13e-55 2evaA 307 1.83e-44 2f57A 317 3.09e-39 1mq4A 272 4.38e-39 d.144.1.7 91391 1yhvA 297 4.97e-38 2bfxA 284 8.79e-37 1t4hA 290 1.51e-36 d.144.1.7 106420 1f3mC 297 3.12e-36 1hcl d.144.1.7 41677 2c30A 321 3.42e-36 1xjdA 345 3.91e-36 2bdwA 362 3.52e-34 1jksA 294 5.29e-34 d.144.1.7 71710 1o6lA 337 7.00e-34 d.144.1.7 81092 1xh9A 350 2.55e-33 1apmE 350 3.52e-33 1cdkA d.144.1.7 41628 1o6yA 299 4.80e-33 d.144.1.7 81106 1s9jA 341 5.01e-33 1ia8A 289 6.10e-33 1ia8A d.144.1.7 62112 1h1wA 289 6.70e-33 d.144.1.7 83460 1rdqE 350 1.45e-32 d.144.1.7 97314 1gz8A 299 1.88e-32 d.144.1.7 83405 1hcl 298 2.19e-32 1hcl d.144.1.7 41593 1py5A 326 2.71e-32 d.144.1.7 104389 1uu3A 310 2.74e-32 d.144.1.7 99999 1phk 298 5.70e-32 1cdkA d.144.1.7 41635 1vjyA 303 9.10e-32 d.144.1.7 108633 2a19B 284 1.04e-31 1p4fA 293 4.26e-31 d.144.1.7 104063 1zrzA 364 6.07e-31 1vzoA 355 9.29e-31 d.144.1.7 108971 1zy4A 303 1.95e-30 1blxA 326 3.24e-30 1hcl d.144.1.7 41596 2bvaA 292 3.72e-30 1tkiA 321 3.77e-30 1tkiA d.144.1.7 41638 1omwA 689 1.59e-29 a.91.1.1,b.55.1.1,d.144.1.7 87086,87087,87088 1tvoA 368 2.82e-29 2eueA 279 6.85e-29 1xwsA 313 7.51e-29 1x8bA 289 7.79e-29 3erk 364 1.38e-28 1hcl d.144.1.7 41654 1pme 380 2.31e-28 1hcl d.144.1.7 41653 2bikB 313 4.51e-28 1pmnA 364 5.98e-27 d.144.1.7 94907 2b9hA 353 1.29e-26 1zzlA 351 2.63e-26 1wbsA 360 3.95e-26 1r3cA 366 4.06e-26 d.144.1.7 96906 2gfsA 372 7.49e-26 1ymiA 334 1.36e-25 1j1bA 420 4.76e-25 d.144.1.7 90758 1ckiA 317 5.09e-25 1csn d.144.1.7 41660 1ywrA 360 5.20e-25 1zz2A 360 7.08e-25 2ac5A 316 7.77e-25 2ac3A 316 8.35e-25 1z57A 339 3.04e-24 1om1A 332 1.31e-23 d.144.1.7 93347 1csn 298 1.54e-23 1csn d.144.1.7 41664 2eu9A 355 2.67e-23 1m2rA 327 3.68e-23 d.144.1.7 84760 1howA 373 1.32e-20 1hcl d.144.1.7 41679 1q8yA 373 2.27e-20 d.144.1.7 96234 1wbpA 397 2.29e-20 1tqmA 282 3.86e-08 a.4.5.56,d.144.1.9 107236,107237 1zarA 282 5.75e-08 1zthA 258 6.78e-04 1nd4A 264 2.22e-03 d.144.1.6 91815 1ako 268 5.94e-03 1ako d.151.1.1 41779 1jysA 242 1.04e-02 c.56.2.1 77216 1wduA 245 1.13e-02 d.151.1.1 109286 1je0A 236 1.61e-02 c.56.2.1 66581 1z5oA 242 1.90e-02 1a6f 119 4.05e-02 1a6f d.14.1.2 37564 1z5nA 242 5.57e-02 1j7lA 264 9.09e-02 d.144.1.6 62697 1b8aA 438 9.23e-02 1b8aA b.40.4.1,d.104.1.1 25244,40765 1i9zA 347 1.15e-01 1i9yA d.151.1.2 62102 2f5xA 312 1.34e-01 2bkkA 264 1.43e-01 1tvxA 75 1.49e-01 1tvxA d.9.1.1 37441 1p3dA 475 1.51e-01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1c4xA 285 2.34e-01 1c4xA c.69.1.10 34684 1vgjA 184 2.36e-01 1nw1A 429 2.49e-01 d.144.1.8 86286 1q7zA 566 2.74e-01 c.1.21.2,c.1.26.1 96090,96091 1vybA 238 2.75e-01 d.151.1.1 108897 1v58A 241 2.80e-01 c.47.1.9,d.17.3.1 108371,108372 1q52A 314 2.94e-01 c.14.1.3 95846 1u4nA 310 3.68e-01 1o6dA 163 3.80e-01 c.116.1.3 92567 1or0B 528 4.10e-01 2ptd 298 4.29e-01 2plc c.1.18.2 29605 2g0wA 296 4.50e-01 2b4yA 271 5.50e-01 1zp4A 304 5.63e-01 1jw9B 249 5.70e-01 c.111.1.1 67377 1odkA 235 5.76e-01 c.56.2.1 86863 1fm2B 520 6.04e-01 1fm2B 2if1 126 6.54e-01 2if1 d.64.1.1 39547 1tcvA 287 7.46e-01 1bn7A 294 7.49e-01 1bn6A c.69.1.8 34677 1twdA 256 7.75e-01 c.1.30.1 107397 1ecpA 238 7.88e-01 1ecpA c.56.2.1 33775 2ajrA 331 8.16e-01 2awdA 323 8.75e-01 1bm9A 122 9.34e-01 1bm9A a.4.5.7 16116 1uwvA 433 9.62e-01 b.40.4.12,c.66.1.40 100128,100129 1nowA 507 9.93e-01 c.1.8.6,d.92.2.1 85936,85937 2bzlA 325 1.02e+00 1k3sA 113 1.05e+00 d.198.1.1 68120 2f02A 323 1.08e+00 1rxyA 253 1.09e+00 c.56.2.1 98065 2booA 247 1.12e+00 1z7mA 344 1.12e+00 1j1iA 296 1.25e+00 c.69.1.10 83977 1sauA 115 1.30e+00 1k9sA 237 1.32e+00 c.56.2.1 68359 1usyA 275 1.39e+00 1o9gA 250 1.47e+00 c.66.1.29 86692 2ae5B 528 1.48e+00 2ghpA 292 1.58e+00 1gvoA 364 1.62e+00 c.1.4.1 76357 1y2qA 143 1.63e+00 1w5qA 337 1.64e+00 1va4A 279 1.67e+00 c.69.1.12 108458 2gk9A 426 1.67e+00 1hq3A 129 1.72e+00 1aoiC a.22.1.1 16434 1ji8A 111 1.74e+00 d.203.1.1 66733 1h1nA 305 1.75e+00 c.1.8.3 70855 1t64A 377 1.79e+00 c.42.1.2 106543 2comA 124 1.92e+00 1yqtA 538 2.00e+00 1k3eA 156 2.08e+00 d.198.1.1 68103 1fp1D 372 2.09e+00 1fpqA a.4.5.29,c.66.1.12 59939,59940 2ddrA 306 2.10e+00 2d1sA 548 2.30e+00 1vdxA 184 2.30e+00 1bo1A 416 2.34e+00 1bo1A d.143.1.2 41591 1yixA 265 2.42e+00 1frb 315 2.48e+00 1frb c.1.7.1 28665 1tzyA 129 2.51e+00 a.22.1.1 107530 1ad1A 266 2.58e+00 1aj2 c.1.21.1 29668 1hqz1 141 2.61e+00 1rie 129 2.62e+00 1rie b.33.1.1 24427 1st0A 337 2.64e+00 d.13.1.3,d.246.1.1 98979,98980 1vhwA 253 2.65e+00 c.56.2.1 100706 1k07A 263 2.65e+00 d.157.1.1 77218 1qnrA 344 2.65e+00 1qnoA c.1.8.3 28834 2gdzA 267 2.70e+00 1zwxA 301 2.74e+00 1ppjE 196 2.88e+00 b.33.1.1,f.23.12.1 104260,104261 2ae2A 260 2.89e+00 1bdb c.2.1.2 29945 1iow 306 2.90e+00 1iow c.30.1.2,d.142.1.1 31713,41481 1g0sA 209 2.92e+00 1g0sA d.113.1.1 60187 1zosA 230 2.94e+00 1wm1A 317 3.04e+00 c.69.1.7 109405 1ry6A 360 3.06e+00 c.37.1.9 98090 1svb 395 3.32e+00 1svb b.1.18.4,f.10.1.1 21814,43827 2fnaA 357 3.43e+00 1vypX 364 3.46e+00 c.1.4.1 108905 2b49A 287 3.56e+00 1r77A 103 3.70e+00 2b5eA 504 3.73e+00 1b5tA 275 3.76e+00 1b5tA c.1.23.1 29676 1g6oA 330 3.79e+00 1g6oA c.37.1.11 32430 1gvhA 396 3.90e+00 a.1.1.2,b.43.4.2,c.25.1.5 70601,70602,70603 1yal 218 4.19e+00 1cs8A d.3.1.1 37025 1qtrA 317 4.23e+00 1qtrA c.69.1.7 34660 1h7nA 342 4.32e+00 1b4kA c.1.10.3 60726 1uouA 474 4.46e+00 a.46.2.1,c.27.1.1,d.41.3.1 99706,99707,99708 1h61A 364 4.50e+00 1oyc c.1.4.1 60657 1xpxA 163 4.51e+00 1e5pA 151 4.58e+00 1bj7 b.60.1.1 59272 1lx7A 253 4.61e+00 c.56.2.1 74329 1ytw 306 4.86e+00 1ytw c.45.1.2 32689 2fjlA 150 4.91e+00 1f3iA 481 4.94e+00 1b7eA 1q48A 134 4.97e+00 d.224.1.2 95783 7ahlA 293 5.00e+00 7ahlA f.6.1.1 43812 2bneA 241 5.03e+00 2bryA 497 5.07e+00 1at3A 247 5.19e+00 1at3A b.57.1.1 27021 2irfG 113 5.23e+00 2irfG a.4.5.23 16185 1t1dA 100 5.36e+00 1t1dA d.42.1.2 38637 1gzgA 337 5.42e+00 c.1.10.3 70805 1earA 147 5.54e+00 b.107.1.1,d.58.38.1 64875,64876 1qg7A 67 5.56e+00 1a15A d.9.1.1 37449 1din 236 5.68e+00 1din c.69.1.9 34682 1ehiA 377 5.87e+00 1iow c.30.1.2,d.142.1.1 31716,41484 1u7kA 131 6.01e+00 1ohlA 342 6.06e+00 c.1.10.3 87035 1hdhA 536 6.13e+00 c.76.1.2 65805 2bnfB 241 6.28e+00 1s1eA 224 6.34e+00 1w5nA 337 6.64e+00 1tx2A 297 6.71e+00 c.1.21.1 107420 2a5lA 200 6.74e+00 1lyvA 306 7.07e+00 c.45.1.2 74348 1b8oA 284 7.36e+00 1b8oA c.56.2.1 33762 1oz9A 150 7.42e+00 d.92.1.15 93808 1top 162 7.45e+00 1ncx a.39.1.5 17223 1q1gA 276 7.46e+00 c.56.2.1 95574 1x31D 99 7.61e+00 1e3dA 266 7.63e+00 2frvA e.19.1.1 59188 1pb1A 416 7.63e+00 c.77.1.1 88014 1uozA 315 7.72e+00 1k77A 260 7.88e+00 c.1.15.5 72096 1dsxA 87 7.91e+00 1t1dA d.42.1.2 38644 1twiA 434 7.91e+00 b.49.2.3,c.1.6.1 107399,107400 1lt8A 406 8.03e+00 c.1.26.1 78186 1vyrA 364 8.18e+00 c.1.4.1 108906 1zmtA 254 8.30e+00 1e5xA 486 8.34e+00 c.79.1.1 59283 1tufA 434 8.34e+00 b.49.2.3,c.1.6.1 107335,107336 2aamA 309 8.48e+00 1k5dB 201 8.54e+00 b.55.1.3 68169 1e7uA 961 8.55e+00 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 1ybdA 239 8.95e+00 1jihA 531 8.97e+00 d.240.1.1,e.8.1.7 90374,90375 1a68 95 8.97e+00 1t1dA d.42.1.2 38639 1yzyA 413 9.06e+00 1b4kA 337 9.07e+00 1b4kA c.1.10.3 29184 1xjjA 644 9.25e+00 1k4mA 213 9.27e+00 c.26.1.3 77258 1ghpA 258 9.32e+00 1btl e.3.1.1 60520 1a88A 275 9.34e+00 1brt c.69.1.12 34707 1b6rA 355 9.44e+00 1b6rA b.84.2.1,c.30.1.1,d.142.1.2 28241,31648,41493 1vkkA 154 9.55e+00 d.109.1.2 108669 1w2yA 229 9.62e+00 a.204.1.1 109140 1iso 416 9.67e+00 1iso c.77.1.1 35065 1l7aA 318 9.71e+00 c.69.1.25 77772 1lehA 364 9.83e+00 1bw9A c.2.1.7,c.58.1.1 30268,33916 1m5yA 408 9.87e+00 a.167.1.1,d.26.1.1,d.26.1.1 78664,78665,78666 2abbA 364 9.90e+00 2bnmA 198 9.95e+00 1cl8A 276 9.96e+00 1ckqA c.52.1.1 33230 2cb2A 318 9.99e+00 1vlmA 219 9.99e+00 c.66.1.41 108836 2cygA 312 1.02e+01 1jjfA 268 1.03e+01 c.69.1.2 66765 1e17A 150 1.03e+01 2hfh a.4.5.14 16143 2gmqA 118 1.04e+01 1nnsA 326 1.04e+01 c.88.1.1 85910 1a8q 274 1.05e+01 1brt c.69.1.12 34702 1jhdA 396 1.05e+01 b.122.1.3,c.26.1.5 66712,66713 2cxxA 190 1.06e+01 1ifqA 138 1.06e+01 1ifqA d.110.4.1 62350 2c0hA 353 1.07e+01 1dzkA 157 1.07e+01 1obpA b.60.1.1 27096 1xp3A 307 1.07e+01 2ao0A 324 1.10e+01 1womA 271 1.10e+01 1idrA 136 1.11e+01 1dlyA a.1.1.1 62301 2d2eA 250 1.17e+01 1y1oA 203 1.17e+01 1aszB 490 1.18e+01 1b8aA b.40.4.1,d.104.1.1 25241,40762 1smlA 269 1.18e+01 1smlA d.157.1.1 42053 1mvwC 147 1.19e+01 i.15.1.1 79525 3il8 72 1.20e+01 1tvxA d.9.1.1 37356 1yp1A 202 1.20e+01 2aioA 269 1.22e+01 1atiA 505 1.23e+01 1atiA c.51.1.1,d.104.1.1 33196,40745 1p49A 562 1.26e+01 c.76.1.2 94089 1ia9A 280 1.27e+01 1ia9A d.144.1.5 62113 1f66C 128 1.27e+01 1aoiC a.22.1.1 16442 1whtA 256 1.28e+01 1ivyA c.69.1.5 34646 1on3A 523 1.30e+01 c.14.1.4,c.14.1.4 87107,87108 1fm0E 150 1.31e+01 1fmaE d.41.5.1 38629 1yljA 263 1.31e+01 2bswA 146 1.32e+01 1tw0A 157 1.32e+01 1vhsA 175 1.32e+01 d.108.1.1 100698 2fq3A 104 1.33e+01 2bklA 695 1.34e+01 1to3A 304 1.34e+01 c.1.10.1 107161 1tib 269 1.34e+01 3tgl c.69.1.17 34738 1o7zA 77 1.34e+01 d.9.1.1 86660 1whsA 255 1.35e+01 1ivyA c.69.1.5 34649 1l5oA 356 1.39e+01 c.39.1.1 77711 1kwgA 645 1.39e+01 b.71.1.1,c.1.8.1,c.23.16.5 77561,77562,77563 1nx8A 273 1.42e+01 b.82.2.8 86374 2f46A 156 1.42e+01 1a8y 367 1.43e+01 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 1xb2B 291 1.43e+01 1kid 203 1.43e+01 1derA c.8.5.1 30771 1zi8A 236 1.45e+01 1u35C 120 1.46e+01 1qfmA 710 1.48e+01 1qfmA b.69.7.1,c.69.1.4 27673,34641 1vhoA 346 1.49e+01 b.49.3.1,c.56.5.4 100694,100695 1yovA 537 1.49e+01 1lam 484 1.50e+01 1lam c.50.1.1,c.56.5.3 33166,33829 1vr8A 142 1.50e+01 1yqeA 282 1.51e+01 2bnjA 303 1.51e+01 2as0A 396 1.51e+01 1jb7A 495 1.52e+01 1otcA b.40.4.3,b.40.4.3,b.40.4.3 62836,62837,62838 1yacA 208 1.52e+01 1yacA c.33.1.3 31757 1ykwA 435 1.53e+01 1vydA 116 1.53e+01 a.3.1.1 108900 1ns5A 155 1.55e+01 c.116.1.3 80705 1fx3A 169 1.55e+01 1fx3B d.33.1.1 38524 1xn7A 78 1.57e+01 1sffA 426 1.57e+01 c.67.1.4 105482 1y7pA 223 1.59e+01 1mnaA 298 1.59e+01 c.69.1.22 79322 1sazA 381 1.61e+01 1ok8A 394 1.63e+01 b.1.18.4,f.10.1.1 93236,93237 1xq6A 253 1.65e+01 1qczA 169 1.65e+01 1qczA c.23.8.1 31276 1xk4C 113 1.66e+01 1su0B 159 1.66e+01 d.224.1.2 106015 1qw2A 102 1.66e+01 d.249.1.1 96456 1rzhH 260 1.66e+01 b.41.1.1,f.23.10.1 98162,98163 1wf3A 301 1.66e+01 1fl1A 230 1.67e+01 1at3A b.57.1.1 27023 1p1mA 406 1.67e+01 b.92.1.4,c.1.9.9 87696,87697 1if1A 113 1.69e+01 2irfG a.4.5.23 16183 1uuqA 440 1.69e+01 c.1.8.3 100015 1i1wA 303 1.70e+01 c.1.8.3 76732 1gveA 327 1.71e+01 c.1.7.1 70597 1pwxA 254 1.71e+01 c.2.1.2 95262 1of8A 370 1.72e+01 c.1.10.4 92819 1qwzA 235 1.73e+01 b.100.1.1 96510 1ads 315 1.74e+01 1frb c.1.7.1 28671 2a1fA 247 1.76e+01 1us0A 316 1.76e+01 c.1.7.1 99850 1jljA 189 1.76e+01 c.57.1.1 63169 2bbhA 269 1.77e+01 1d0vA 356 1.77e+01 1d0vA c.39.1.1 32476 1o0yA 260 1.78e+01 c.1.10.1 80756 1vheA 373 1.79e+01 b.49.3.1,c.56.5.4 100669,100670 2g6tA 306 1.80e+01 2bcfA 276 1.81e+01 1hxhA 253 1.82e+01 c.2.1.2 76725 1ekjA 221 1.83e+01 1ekjB c.53.2.1 33364 1i8jA 323 1.84e+01 1b4kA c.1.10.3 61968 1vk8A 106 1.84e+01 d.58.48.1 108636 1v8bA 479 1.84e+01 1ur3M 319 1.85e+01 c.1.7.1 99806 1j27A 102 1.85e+01 d.58.50.1 90778 1tu6A 215 1.86e+01 d.3.1.1 107318 2a6hC 1119 1.86e+01 1f1zA 273 1.87e+01 1f1zA a.4.5.27,c.52.1.16 16081,33334 2bp1A 360 1.87e+01 1yhfA 115 1.89e+01 2akaB 299 1.90e+01 1jl5A 454 1.93e+01 c.10.2.6 66830 1jwqA 179 1.94e+01 c.56.5.6 90921 1yhtA 367 1.94e+01 2myr 501 1.95e+01 1wlsA 328 1.96e+01 1wchA 315 1.97e+01 1v8dA 235 1.97e+01 c.140.1.1 108425 1yo1A 260 1.97e+01 1qamA 244 1.98e+01 2ercA c.66.1.24 34220 1tvjA 166 1.99e+01 1pyaB 228 2.00e+01 1pyaB 1tz9A 367 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