# List of top-scoring protein chains for t2k-100-30-alpha-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 2f22A 144 5.09e-11 1rxqA 178 1.20e-02 a.213.1.1 105118 1bouB 302 1.01e+00 1bouB c.56.6.1 33859 1b4uB 302 1.18e+00 1bouB c.56.6.1 33861 1l3pA 102 1.45e+00 a.24.17.1 84520 1nw3A 416 2.04e+00 c.66.1.31 86288 5eat 548 3.02e+00 5eat a.102.4.1,a.128.1.3 18853,19445 1oxa 403 3.07e+00 1f4tA a.104.1.1 18965 1bco 327 3.50e+00 1bco b.48.1.1,c.55.3.3 26431,33676 1r71A 178 3.74e+00 a.4.14.1 104823 2bzlA 325 3.77e+00 1z8oA 404 3.90e+00 5eau 548 3.94e+00 5eat a.102.4.1,a.128.1.3 18851,19443 1fp3A 402 4.06e+00 1fp3A a.102.1.3 18842 1gx3A 284 4.06e+00 d.3.1.5 70678 2gnxA 365 4.16e+00 1f60B 94 4.39e+00 1b64 d.58.12.1 39307 1pi1A 185 4.60e+00 a.29.7.1 94699 1exzA 141 4.73e+00 1exzA a.26.1.2 16877 1p1xA 260 5.09e+00 c.1.10.1 104060 1eupA 403 5.14e+00 1rom a.104.1.1 18967 1ayl 541 5.21e+00 1ayl c.91.1.1,c.109.1.1 64718,64719 1wkyA 464 5.41e+00 1y8oA 419 5.88e+00 1g7cB 94 6.56e+00 1b64 d.58.12.1 39308 1s4kA 120 6.75e+00 a.35.1.6 105254 1s5lE 84 7.03e+00 2fh5A 185 7.05e+00 1xmeA 568 7.52e+00 1adjA 421 7.80e+00 1adjA c.51.1.1,d.104.1.1 33188,40737 2a6hC 1119 7.81e+00 1w5rA 278 8.76e+00 1am4A 199 9.37e+00 1tx4A a.116.1.1 19100 1iw7C 1119 9.45e+00 e.29.1.1 71474 1ljrA 244 9.71e+00 1ljrA a.45.1.1,c.47.1.5 17707,33001 1jclA 260 9.76e+00 c.1.10.1 66501 1qqtA 551 1.10e+01 1qqtA a.27.1.1,c.26.1.1,g.41.1.1 16923,31590,45175 1f4tA 368 1.25e+01 1f4tA a.104.1.1 18973 1sa0E 143 1.26e+01 a.137.10.1 98777 1yarO 237 1.27e+01 1qgtA 149 1.29e+01 1qgtA a.62.1.1 18135 1gd8A 118 1.29e+01 d.188.1.1 60445 1ehkA 562 1.29e+01 1ehkA f.24.1.1 43624 1mtpA 323 1.33e+01 e.1.1.1 85107 1kptA 105 1.35e+01 1kptA d.70.1.1 39588 1jipA 403 1.40e+01 a.104.1.1 66748 1f4lA 551 1.42e+01 1qqtA a.27.1.1,c.26.1.1,g.41.1.1 59648,59649,59650 1te6A 439 1.51e+01 c.1.11.1,d.54.1.1 106797,106798 1aw2A 256 1.53e+01 1amk c.1.1.1 28523 1ylhA 560 1.53e+01 1o5hA 214 1.57e+01 a.191.1.1 92497 1xg1A 67 1.58e+01 1pfvA 551 1.59e+01 a.27.1.1,c.26.1.1,g.41.1.1 94660,94661,94662 1on2A 142 1.63e+01 a.4.5.24,a.76.1.1 87103,87104 1w78A 422 1.63e+01 1mioA 534 1.64e+01 1qguA c.92.2.3 35601 1tx4A 198 1.65e+01 1tx4A a.116.1.1 19098 1z0xA 220 1.66e+01 1h4vB 421 1.66e+01 1adjA c.51.1.1,d.104.1.1 60624,60625 1qi7A 253 1.66e+01 1qi7A d.165.1.1 42210 1k8kA 418 1.70e+01 c.55.1.1,c.55.1.1 68305,68306 1zx4A 192 1.78e+01 1aw1A 256 1.78e+01 1amk c.1.1.1 28515 2g7sA 194 1.84e+01 1io7A 368 1.89e+01 1f4tA a.104.1.1 18971 1tph1 247 1.93e+01 1amk 1r2rA 248 1.93e+01 c.1.1.1 96875 1ithA 141 1.95e+01 1ithA a.1.1.2 15623 1w0uA 55 2.00e+01 2akzA 439 2.13e+01 1sl8A 191 2.17e+01 1o5zA 442 2.19e+01 c.59.1.2,c.72.2.2 92530,92531 1wv2A 265 2.21e+01 1jweA 114 2.26e+01 1b79A a.81.1.1 18455 1q7sA 117 2.27e+01 c.131.1.1 96055 2gz4A 207 2.33e+01 1oq9A 363 2.48e+01 a.25.1.2 87257 1e3aA 260 2.49e+01 1ajqA d.153.1.2 41838 2bd0A 244 2.51e+01 1f7lA 121 2.51e+01 1f7lA d.150.1.2 59666 1b79A 119 2.52e+01 1b79A a.81.1.1 18451 2fjbA 643 2.53e+01 1zk7A 467 2.58e+01 1uhkA 191 2.61e+01 1a7m 180 2.64e+01 1lki a.26.1.1 16830 1jnrA 643 2.65e+01 a.7.3.1,c.3.1.4,d.168.1.1 66966,66967,66968 1f7tA 122 2.74e+01 1f7lA d.150.1.2 59667 1afrA 345 2.75e+01 1afrA a.25.1.2 16805 3ertA 261 2.78e+01 3erdA a.123.1.1 19292 1esxA 96 2.80e+01 1esxA j.11.1.1 59501 1v7bA 185 2.81e+01 1ajqA 209 2.95e+01 1ajqA d.153.1.2 41840 1jb1A 205 3.00e+01 1jb1A c.91.1.2 62832 1rz3A 201 3.02e+01 c.37.1.6 98132 2ex3B 264 3.04e+01 1gk9A 260 3.05e+01 d.153.1.2 65246 1ydgA 211 3.05e+01 1pnkA 209 3.09e+01 1ajqA d.153.1.2 41839 1ykjA 394 3.12e+01 1h12A 405 3.15e+01 a.102.1.2 83447 1xw2A 405 3.16e+01 1lki 180 3.18e+01 1lki a.26.1.1 16829 1l8cA 95 3.23e+01 g.53.1.1 73685 2axtE 84 3.29e+01 1xwtA 405 3.34e+01 1ecxA 384 3.35e+01 1ecxA c.67.1.3 34431 1k0iA 394 3.38e+01 c.3.1.2,d.16.1.2 67942,67943 1gm7A 209 3.43e+01 d.153.1.2 65302 1qgrA 876 3.43e+01 1qgrA a.118.1.1 19119 1ej3A 191 3.46e+01 1ej3A a.39.1.5 17259 1oen 540 3.52e+01 1ayl c.91.1.1,c.109.1.1 64750,64751 1dgjA 907 3.53e+01 1alo a.56.1.1,d.15.4.2,d.41.1.1,d.133.1.1 17909,37694,38585,41415 1ai7A 209 3.54e+01 1ajqA d.153.1.2 41845 1w5cE 84 3.62e+01 1nkpB 83 3.72e+01 a.38.1.1 80574 1nlwB 76 3.74e+01 a.38.1.1 80634 1eg5A 384 3.74e+01 1ecxA c.67.1.3 34429 1l3eB 101 3.74e+01 g.53.1.1 73536 1o17A 345 3.77e+01 a.46.2.1,c.27.1.1 80765,80766 1mdwA 328 3.84e+01 d.3.1.3 84934 1pioA 257 3.90e+01 1btl e.3.1.1 42719 1swvA 267 3.93e+01 1nb5I 98 3.99e+01 d.17.1.2 80381 1tazA 365 4.11e+01 a.211.1.2 106734 1mxrA 375 4.15e+01 a.25.1.2 85197 2exrA 524 4.18e+01 1scfA 273 4.25e+01 1exzA a.26.1.2 16873 1cj3A 392 4.27e+01 1pbe c.3.1.2,d.16.1.2 30347,37878 1wq3A 322 4.27e+01 1kw4A 89 4.27e+01 a.60.1.2 73077 1pea 385 4.27e+01 1pea c.93.1.1 35662 1xpcA 248 4.30e+01 2b0tA 738 4.43e+01 2a5yA 204 4.43e+01 2hmx 133 4.44e+01 1hiwA a.61.1.1 18129 2phh 394 4.44e+01 1pbe c.3.1.2,d.16.1.2 30353,37884 1lyxA 248 4.47e+01 c.1.1.1 78304 2czlA 272 4.53e+01 1a52A 258 4.54e+01 3erdA a.123.1.1 19296 1fc3A 120 4.63e+01 1fc3A a.4.6.3 16237 1pbe 394 4.65e+01 1pbe c.3.1.2,d.16.1.2 30338,37869 1wf3A 301 4.71e+01 1bgj 394 4.74e+01 1pbe c.3.1.2,d.16.1.2 30352,37883 1idpA 172 4.74e+01 d.17.4.1 83685 1jqcA 375 4.79e+01 1xikA a.25.1.2 63229 1ezfA 340 4.79e+01 1ezfA a.128.1.2 19440 1hizA 379 4.82e+01 c.1.8.3 65841 1xm3A 264 4.82e+01 1rqlA 267 4.83e+01 c.108.1.3 97750 1go4A 205 4.87e+01 d.135.1.1 70292 1ahr 146 4.88e+01 1cll a.39.1.5 17287 3blm 257 4.90e+01 1btl e.3.1.1 42709 1biqA 375 4.95e+01 1xikA a.25.1.2 16786 1syyA 346 5.01e+01 a.25.1.2 106126 1ghpA 258 5.07e+01 1btl e.3.1.1 60520 1fezA 256 5.07e+01 1fezA c.108.1.3 43343 1y01A 102 5.08e+01 1r3dA 264 5.09e+01 1quuA 250 5.12e+01 1quuA a.7.1.1,a.7.1.1 16320,16321 1yge 839 5.16e+01 1yge a.119.1.1,b.12.1.1 19234,23634 2f6kA 307 5.16e+01 1o66A 275 5.18e+01 c.1.12.8 92547 1av8A 340 5.26e+01 1xikA a.25.1.2 16796 1o5xA 248 5.43e+01 c.1.1.1 92528 1nhyA 219 5.44e+01 a.45.1.1,c.47.1.5 80520,80521 3inkC 133 5.45e+01 3inkC a.26.1.2 16881 1wwpA 119 5.47e+01 2g19A 244 5.48e+01 1std 172 5.52e+01 3stdA d.17.4.1 38089 1lrrA 131 5.52e+01 d.228.1.1 78165 1lldA 319 5.67e+01 3ldh c.2.1.5,d.162.1.1 30177,42144 1t7lA 766 5.72e+01 2cx9A 387 5.79e+01 1ad3A 452 5.82e+01 1ad3A c.82.1.1 35335 1ws9A 387 5.86e+01 1a4iA 301 5.88e+01 1a4iA c.2.1.7,c.58.1.2 30278,33926 1bolA 222 5.91e+01 1bolA d.124.1.1 41120 2cqnA 77 5.91e+01 1lw7A 365 5.96e+01 c.26.1.3,c.37.1.1 74295,74296 1ac5 483 6.02e+01 1ac5 c.69.1.5 34653 2amlA 373 6.09e+01 1fwkA 296 6.19e+01 1fwkA d.14.1.5,d.58.26.1 37576,39398 1vf1A 229 6.19e+01 1b08A 158 6.21e+01 1rtm1 d.169.1.1,h.1.1.1 42416,45423 1sazA 381 6.31e+01 2axtF 45 6.34e+01 1uj2A 252 6.36e+01 c.37.1.6 99452 1qoxN 449 6.40e+01 1qoxN c.1.8.4 28978 1nz0A 118 6.46e+01 d.14.1.2 86433 2std 172 6.47e+01 3stdA d.17.4.1 38085 2hbtA 247 6.50e+01 1d2fA 390 6.51e+01 1d2fA c.67.1.3 34411 1w6uA 302 6.58e+01 2oneA 436 6.61e+01 4enl c.1.11.1,d.54.1.1 29203,38847 1h72C 296 6.67e+01 d.14.1.5,d.58.26.1 60712,60713 1f2eA 201 6.78e+01 1a0fA a.45.1.1,c.47.1.5 17745,33039 1aj0 282 6.80e+01 1aj2 c.1.21.1 29667 1m12A 84 6.81e+01 a.64.1.1 84745 1h6qA 168 6.83e+01 1h6qA b.88.1.2 60692 1sw6A 327 6.99e+01 1sw6A d.211.1.1 19176 1ib8A 164 7.03e+01 b.38.2.1,d.52.4.1 71168,71169 1h4pA 408 7.06e+01 c.1.8.3 90617 1hiwA 133 7.06e+01 1hiwA a.61.1.1 18122 1gypA 358 7.14e+01 1dssG c.2.1.3,d.81.1.1 30004,39919 1ohuA 175 7.25e+01 f.1.4.1 93029 1xikA 375 7.25e+01 1xikA a.25.1.2 16784 1yhtA 367 7.26e+01 2d29A 387 7.31e+01 1jj7A 260 7.35e+01 c.37.1.12 63114 1ywzA 175 7.39e+01 1fpxA 352 7.40e+01 1fpxA a.4.5.29,c.66.1.12 59950,59951 1l3iA 192 7.55e+01 c.66.1.22 77676 1of8A 370 7.66e+01 c.1.10.4 92819 1y1nA 291 7.70e+01 2f7fA 494 7.75e+01 2genA 197 7.77e+01 1aj2 282 7.79e+01 1aj2 c.1.21.1 29665 1sumB 235 7.79e+01 a.7.12.1 106025 3stdA 165 7.88e+01 3stdA d.17.4.1 38073 1fp2A 352 7.89e+01 1fpxA a.4.5.29,c.66.1.12 59941,59942 1tn4 159 7.91e+01 1ncx a.39.1.5 17248 1jcjA 260 7.91e+01 c.1.10.1 66499 2g2dA 193 7.92e+01 1ribA 375 7.94e+01 1xikA a.25.1.2 16788 1l8bA 190 8.03e+01 d.86.1.1 73683 1fmcA 255 8.04e+01 1cydA c.2.1.2 29856 1t2bA 397 8.10e+01 1xrsA 516 8.17e+01 153l 185 8.40e+01 153l d.2.1.5 36984 1w0hA 204 8.40e+01 1ef8A 261 8.46e+01 1ef8A c.14.1.3 30921 2bptA 861 8.53e+01 1exqA 154 8.65e+01 1b9dA c.55.3.2 33646 1ycoA 279 8.74e+01 1diaA 306 8.75e+01 1a4iA c.2.1.7,c.58.1.2 30280,33928 1is1A 185 8.81e+01 d.67.3.1 83704 1mwmA 320 8.92e+01 c.55.1.1,c.55.1.1 79580,79581