# List of top-scoring protein chains for t2k-100-30-dssp-ebghstl-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 1w61A 414 3.59e-09 2gkeA 274 2.66e-08 1gqzA 274 4.79e-08 d.21.1.1,d.21.1.1 83311,83312 1bwzA 274 1.07e-07 1bwzA d.21.1.1,d.21.1.1 38337,38338 1tm0A 350 5.64e-06 d.21.1.3 107147 1z94A 147 2.67e-03 1xubA 298 5.45e-03 1u1wA 298 6.44e-03 1sdjA 310 7.42e-02 d.21.1.2,d.21.1.2 98807,98808 2g6yA 217 9.08e-02 1t6kA 278 1.03e-01 1qyaA 307 2.22e-01 d.21.1.2,d.21.1.2 104653,104654 1l1nA 183 4.72e-01 b.47.1.4 73476 1ym5A 300 5.03e-01 2azpA 318 6.44e-01 1eo9A 209 1.40e+00 3pchA b.3.6.1 22731 1o0pA 104 1.55e+00 d.58.7.1 86535 1p3dA 475 1.62e+00 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1gqyA 475 1.64e+00 c.5.1.1,c.59.1.1,c.72.2.1 83305,83306,83307 1vdkA 466 2.05e+00 a.127.1.1 100561 1j6uA 469 2.44e+00 c.5.1.1,c.59.1.1,c.72.2.1 77094,77095,77096 1wc3A 219 2.87e+00 1d0iA 156 3.25e+00 2dhqA c.23.13.1 31383 1usyA 275 3.34e+00 1eft 405 3.87e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25688,25728,32123 1lshA 1056 3.99e+00 a.118.4.1,f.7.1.1,f.7.1.1 74242,74243,74244 1o17A 345 4.10e+00 a.46.2.1,c.27.1.1 80765,80766 1ab8A 220 4.38e+00 1azsA d.58.29.1 39414 1b0tA 106 4.57e+00 1a6l d.58.1.2 38965 1omrA 201 4.59e+00 a.39.1.5 93349 1ioaA 240 4.78e+00 1led b.29.1.1 24168 1h0bA 256 5.00e+00 b.29.1.11 83422 2bw8A 227 5.16e+00 1hx0A 496 5.22e+00 b.71.1.1,c.1.8.1 61346,61347 1azsB 212 5.68e+00 1azsA d.58.29.1 39423 1a6l 106 5.79e+00 1a6l d.58.1.2 38966 1gtzA 156 5.87e+00 c.23.13.1 70539 1rec 201 5.88e+00 1rec a.39.1.5 17326 2pcfB 250 6.04e+00 1hcz i.4.1.1 45911 2f6uA 234 6.75e+00 2fclA 169 7.54e+00 2ewrA 170 7.59e+00 1qg0A 308 8.25e+00 1fnc b.43.4.2,c.25.1.1 25639,31529 1wekA 217 8.72e+00 1fdd 106 8.96e+00 1a6l d.58.1.2 38960 2av9A 147 9.94e+00 1a5mC 566 1.03e+01 1ubpC b.92.1.1,c.1.9.2 28423,29045 4sli 679 1.05e+01 2sli b.29.1.9,b.68.1.1 24275,27612 2sli 679 1.05e+01 2sli b.29.1.9,b.68.1.1 24274,27611 1a5kC 566 1.06e+01 1ubpC b.92.1.1,c.1.9.2 28425,29047 1a5lC 566 1.06e+01 1ubpC b.92.1.1,c.1.9.2 28426,29048 1fd2 106 1.09e+01 1a6l d.58.1.2 38962 2fnaA 357 1.13e+01 3uagA 437 1.15e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30652,33953,34956 1lybB 241 1.16e+01 1smrA 1fwcC 567 1.16e+01 1ubpC b.92.1.1,c.1.9.2 28410,29032 1ejrC 567 1.17e+01 1ubpC b.92.1.1,c.1.9.2 28420,29042 1ejxC 567 1.18e+01 b.92.1.1,c.1.9.2 83184,83185 1y0gA 191 1.21e+01 1uag 437 1.21e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30653,33954,34957 1cqqA 180 1.23e+01 1cqqA b.47.1.4 26422 4uagA 437 1.24e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30651,33952,34955 1cur 155 1.28e+01 1rcy b.6.1.1 23021 1yg9A 330 1.31e+01 7fd1A 106 1.33e+01 1a6l d.58.1.2 38953 2essA 248 1.33e+01 1ycoA 279 1.39e+01 1v7wA 807 1.39e+01 a.102.1.4,b.30.5.3 108411,108412 1b0vA 106 1.47e+01 1a6l d.58.1.2 38982 1xfjA 261 1.55e+01 d.194.1.2 109585 1hka 158 1.63e+01 1hka d.58.30.1 39433 1mxmA 254 1.67e+01 b.38.1.3,d.58.43.1,f.34.1.1 79647,79648,79649 1shyB 551 1.99e+01 b.69.12.1,g.16.2.1 105565,105566 1h2rL 534 2.02e+01 1h2rL e.18.1.1 43298 1jihA 531 2.02e+01 d.240.1.1,e.8.1.7 90374,90375 1ubkL 534 2.05e+01 e.18.1.1 88422 1fl9A 161 2.07e+01 c.37.1.18 70137 1ofzA 312 2.08e+01 b.68.8.1 86978 1a8z 153 2.11e+01 1rcy b.6.1.1 23020 1g7sA 594 2.12e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 2hrvA 142 2.12e+01 2hrvA b.47.1.4 26429 1xtqA 177 2.19e+01 1mo9A 523 2.23e+01 c.3.1.5,c.3.1.5,d.87.1.1 79341,79342,79343 1z5hA 780 2.23e+01 1wuiL 534 2.24e+01 1q47A 495 2.24e+01 b.69.12.1 104532 2c78A 405 2.27e+01 2a40B 260 2.27e+01 1gzqA 300 2.34e+01 b.1.1.2,d.19.1.1 70818,70819 1w6sA 599 2.38e+01 1vkdA 338 2.40e+01 b.67.2.4 108644 1umzA 278 2.54e+01 b.29.1.2 99639 1xhkA 187 2.56e+01 2calA 154 2.58e+01 1mqvA 125 2.59e+01 a.24.3.2 79415 1exmA 405 2.65e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 1o97D 320 2.68e+01 c.26.2.3,c.31.1.2 81233,81234 1br9 194 2.69e+01 1br9 b.40.3.1 25235 1rzuA 485 2.73e+01 c.87.1.8 105140 1foaA 348 2.74e+01 1foaA c.68.1.10 59929 1xoyA 161 2.79e+01 1zvtA 256 2.82e+01 1oivA 191 2.84e+01 c.37.1.8 93076 1vquA 374 2.85e+01 2fomB 185 2.90e+01 1budA 197 2.94e+01 1atlA d.92.1.9 40328 2ai4A 119 2.99e+01 1oa4A 222 3.11e+01 b.29.1.11 86731 1s7jA 262 3.14e+01 d.21.1.2 98647 1ynlH 219 3.16e+01 1js8A 394 3.17e+01 a.86.1.1,b.112.1.1 67219,67220 1ev7A 317 3.19e+01 1ev7B c.52.1.9 33315 1exnB 290 3.20e+01 1exnA a.60.7.1,c.120.1.2 18089,33359 1ut8A 291 3.23e+01 a.60.7.1,c.120.1.2 99908,99909 1wucA 250 3.23e+01 1exnA 290 3.23e+01 1exnA a.60.7.1,c.120.1.2 18088,33358 1xo1A 291 3.30e+01 1exnA a.60.7.1,c.120.1.2 18086,33356 2bgiA 272 3.30e+01 1ciy 590 3.37e+01 1ciy b.18.1.3,b.77.2.1,f.1.3.1 23720,27977,43392 1ut9A 609 3.42e+01 a.102.1.2,b.1.18.2 99912,99913 1zynA 202 3.42e+01 1e30A 155 3.43e+01 1rcy b.6.1.1 23016 1fa8A 135 3.49e+01 1qipA d.32.1.1 38486 1ryaA 160 3.50e+01 d.113.1.5 105122 1vrmA 325 3.51e+01 1ug1A 92 3.56e+01 b.34.2.1 99360 1ac5 483 3.58e+01 1ac5 c.69.1.5 34653 1iawA 317 3.58e+01 c.52.1.9 62126 1nscA 390 3.71e+01 2qwc b.68.1.1 27591 1rl2A 137 3.73e+01 1rl2A b.34.5.3,b.40.4.5 24610,25342 1abbA 828 3.73e+01 1a8i c.87.1.4 35536 1ats 386 3.75e+01 1ba1 c.55.1.1,c.55.1.1 33423,33424 1oixA 191 3.75e+01 1jzuA 157 3.79e+01 b.60.1.1 84271 1cjtA 217 3.80e+01 1azsA d.58.29.1 39419 1a3z 155 3.85e+01 1rcy b.6.1.1 23019 1suuA 312 3.87e+01 b.68.10.1 99006 1f9zA 135 3.89e+01 1qipA d.32.1.1 38484 1kbvA 327 3.91e+01 b.6.1.3,b.6.1.3 68395,68396 1h2aL 567 3.96e+01 1h2rL e.18.1.1 43299 1fo8A 343 4.00e+01 1foaA c.68.1.10 59927 1x6zA 123 4.01e+01 1ton 235 4.02e+01 5ptp b.47.1.2 26307 1rcy 151 4.04e+01 1rcy b.6.1.1 23018 1fnd 314 4.05e+01 1fnc b.43.4.2,c.25.1.1 25626,31516 1fnb 314 4.08e+01 1fnc b.43.4.2,c.25.1.1 25628,31518 1fm2B 520 4.13e+01 1fm2B 1u9yA 284 4.15e+01 1fo9A 348 4.17e+01 1foaA c.68.1.10 59928 1ba1 386 4.18e+01 1ba1 c.55.1.1,c.55.1.1 33387,33388 1kay 381 4.20e+01 1ba1 c.55.1.1,c.55.1.1 33385,33386 1hpm 386 4.20e+01 1ba1 c.55.1.1,c.55.1.1 33381,33382 1bupA 386 4.20e+01 1ba1 c.55.1.1,c.55.1.1 33377,33378 1ha3A 405 4.23e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 1fjgR 88 4.27e+01 1fjfR a.4.8.1 16252 1dmhA 311 4.32e+01 1dmhA b.3.6.1 22633 1fzkA 274 4.34e+01 1agdA b.1.1.2,d.19.1.1 60149,60150 1yqfA 203 4.37e+01 2b5wA 357 4.45e+01 1qupA 222 4.50e+01 1qupA b.1.8.1,d.58.17.1 22301,39352 1uurA 473 4.65e+01 a.47.1.1,b.2.5.5,d.93.1.1 100016,100017,100018 1ywmA 200 4.67e+01 1f9yA 158 4.71e+01 d.58.30.1 83249 1eqoA 158 4.72e+01 1hka 1kshB 152 4.73e+01 b.1.18.8 72915 1h65A 270 4.76e+01 c.37.1.8 65640 1k24A 253 4.77e+01 f.4.4.2 72002 1iq6A 134 4.85e+01 d.38.1.4 76755 1c8kA 842 4.93e+01 1a8i c.87.1.4 35491 2gjgA 248 4.95e+01 1wp5A 323 4.95e+01 2cy2A 174 4.99e+01 1dhkB 223 5.01e+01 1led b.29.1.1 24157 2dddA 225 5.04e+01 1i1iP 681 5.05e+01 1i1iP d.92.1.5 40297 1fnc 314 5.05e+01 1fnc b.43.4.2,c.25.1.1 25627,31517 1mkeA 152 5.09e+01 b.55.1.4 79231 1hbnC 248 5.16e+01 1mroC d.58.31.1 60902 1atr 386 5.21e+01 1ba1 c.55.1.1,c.55.1.1 33421,33422 1qpxA 218 5.22e+01 1qpxA b.1.11.1,b.7.2.1 22318,23200 1bx1A 314 5.23e+01 1fnc b.43.4.2,c.25.1.1 25629,31519 1uisA 231 5.26e+01 d.22.1.1 99431 1oe4A 247 5.29e+01 c.18.1.3 86895 1lm8V 160 5.40e+01 b.3.3.1 74035 1sr8A 298 5.41e+01 e.54.1.1 105959 2govA 195 5.42e+01 1xssA 225 5.43e+01 1lj5A 379 5.45e+01 e.1.1.1 73928 1ospO 257 5.51e+01 1ospO b.76.1.1 27971 1smd 496 5.51e+01 1smd b.71.1.1,c.1.8.1 27768,28755 1a8i 842 5.56e+01 1a8i c.87.1.4 35490 1atnD 260 5.58e+01 3dni d.151.1.1 41793 2gc9A 179 5.62e+01 1onqA 283 5.65e+01 b.1.1.2,d.19.1.1 93365,93366 1rz3A 201 5.68e+01 c.37.1.6 98132 1gthD 1025 5.71e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70498,70499,70500,70501,70502 1v10A 521 5.76e+01 b.6.1.3,b.6.1.3,b.6.1.3 108224,108225,108226 1hcz 252 5.79e+01 1hcz b.2.6.1,b.84.2.2 22464,28250 1gutA 68 5.87e+01 b.40.6.1 65576 1tmxA 293 5.92e+01 2aaa 484 5.93e+01 7taa b.71.1.1,c.1.8.1 27777,28764 1vcbC 160 5.94e+01 1vcbC b.3.3.1 22535 1mroC 247 5.97e+01 1mroC d.58.31.1 39437 1mqoA 227 5.99e+01 d.157.1.1 103846 3dni 260 6.01e+01 3dni d.151.1.1 41791 1pyoA 167 6.06e+01 c.17.1.1 95370 2d4qA 257 6.09e+01 1aipE 405 6.11e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25699,25739,32134 1l5jA 865 6.11e+01 a.118.15.1,c.8.2.1,c.83.1.1 73592,73593,73594 1lk2A 274 6.11e+01 b.1.1.2,d.19.1.1 91056,91057 1tafB 70 6.16e+01 1tafB a.22.1.3 16482 1h7xA 1025 6.20e+01 1h7wA a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15687,28632,30328,30613,39011 2fvhA 120 6.20e+01 1hcnB 145 6.42e+01 1hcnB g.17.1.4 44810 1bkb 136 6.44e+01 1bkb b.34.5.2,b.40.4.5 24609,25341 1n7vA 555 6.46e+01 b.126.1.1 85377 1gthB 1025 6.64e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70488,70489,70490,70491,70492 2ae5B 528 6.64e+01 1h5uA 842 6.71e+01 1a8i c.87.1.4 60655 2af4C 333 6.75e+01 2bx2L 517 6.78e+01 2a74A 643 6.83e+01 1smxA 96 6.97e+01 b.40.4.5 105772 2bsaA 303 6.98e+01 1w34A 304 6.99e+01 2g84A 197 7.02e+01 2fsjA 346 7.05e+01 1gt8B 1025 7.14e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70423,70424,70425,70426,70427 1u55A 188 7.25e+01 d.278.1.1 107677 2a8yA 270 7.26e+01 1i50B 1224 7.27e+01 e.29.1.1 61755 1go2A 304 7.28e+01 b.43.4.2,c.25.1.1 76243,76244 1gt8D 1025 7.29e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70433,70434,70435,70436,70437 5gcnA 166 7.37e+01 1yghA d.108.1.1 40807 1hyuA 521 7.41e+01 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1d2gA 292 7.43e+01 1xvaA c.66.1.5 34187 1orrA 347 7.45e+01 c.2.1.2 93460 2aieP 203 7.45e+01 1shwB 181 7.50e+01 b.18.1.4 105563 1aipA 405 7.51e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25697,25737,32132 2aaiB 262 7.57e+01 1abrB b.42.2.1,b.42.2.1 25561,25562 1b2rA 304 7.72e+01 1fnc b.43.4.2,c.25.1.1 25648,31538 1ogiA 303 7.72e+01 b.43.4.2,c.25.1.1 92914,92915 1gthA 1025 7.74e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70483,70484,70485,70486,70487 1gthC 1025 7.76e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70493,70494,70495,70496,70497 1fi4A 416 7.79e+01 1fi4A d.14.1.5,d.58.26.2 59847,59848 1jofA 365 7.80e+01 b.69.10.1 71775 1ixlA 131 7.97e+01 d.38.1.5 90717 1ema 236 8.00e+01 1ema d.22.1.1 38339 1lm4A 194 8.15e+01 d.167.1.1 84626 1am2 199 8.15e+01 1am2 b.86.1.2 28381 1kr7A 110 8.16e+01 a.1.1.4 72890 1g8iA 190 8.16e+01 1rec a.39.1.5 60363 1jz8A 1023 8.19e+01 b.1.4.1,b.1.4.1,b.18.1.5,b.30.5.1,c.1.8.3 67830,67831,67832,67833,67834 1qwyA 291 8.20e+01 b.84.3.2 96509 1dp0A 1023 8.29e+01 b.1.4.1,b.1.4.1,b.18.1.5,b.30.5.1,c.1.8.3 22073,22074,23722,24346,28845 1bglA 1023 8.31e+01 1bglA b.1.4.1,b.1.4.1,b.18.1.5,b.30.5.1,c.1.8.3 22097,22098,23734,24358,28857 1g7pA 274 8.36e+01 b.1.1.2,d.19.1.1 70153,70154 1ov3A 138 8.39e+01 b.34.2.1,b.34.2.1 87451,87452 1a8l 226 8.54e+01 1a8l c.47.1.2,c.47.1.2 32777,32778 2a6hC 1119 8.56e+01 1v61A 132 8.60e+01 b.55.1.1 108389 1lf6A 684 8.68e+01 a.102.1.5,b.30.5.5 77918,77919 1xttA 216 8.72e+01 1dp4A 435 8.75e+01 1dp4A c.93.1.1 35710 1lqbC 162 8.77e+01 b.3.3.1 74186 1iw7C 1119 8.77e+01 e.29.1.1 71474 1g7rA 594 8.78e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25716,25717,31034,32149 1c8zA 265 8.82e+01 1c8zA d.23.1.1 38375 1yqzA 438 8.84e+01 2cr4A 126 8.84e+01 1zn6A 227 8.95e+01 2g6tA 306 8.98e+01 1dzoA 123 8.99e+01 1dzoA d.24.1.1 38378