# List of top-scoring protein chains for t04-80-60-80-str2+near-backbone-11-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 2a84A 300 5.42e-02 1v8fA 276 7.29e-02 c.26.1.4 100503 1n2eA 300 1.13e-01 c.26.1.4 85268 2b20A 403 1.83e-01 1ebfA 358 1.91e-01 1ebuA c.2.1.3,d.81.1.2 30033,39948 1y7rA 133 4.31e-01 1jae 471 4.36e-01 1smd b.71.1.1,c.1.8.1 27773,28760 1ohpA 125 4.63e-01 1q33A 292 4.76e-01 d.113.1.1 95657 1wgkA 114 5.38e-01 1ocvA 125 6.16e-01 d.17.4.3 86810 1dmhA 311 8.61e-01 1dmhA b.3.6.1 22633 1dkgA 197 8.99e-01 1dkgA b.73.1.1,h.1.9.1 27812,45626 1e19A 314 1.06e+00 1b7bA c.73.1.1 34967 2a2lA 145 1.07e+00 1skoA 143 1.12e+00 d.110.7.1 105676 2b18A 164 1.14e+00 1qwtA 255 1.14e+00 b.26.1.3 96501 2as0A 396 1.23e+00 1vr3A 191 1.42e+00 1gcb 454 1.54e+00 3gcb d.3.1.1 37034 1veaA 148 1.60e+00 d.275.1.1 108529 1t5yA 190 1.64e+00 b.122.1.1,d.17.6.3 106495,106496 1v25A 541 1.67e+00 e.23.1.1 108275 1wfuA 120 1.80e+00 1tvjA 166 1.88e+00 1cl8A 276 1.91e+00 1ckqA c.52.1.1 33230 1smd 496 2.08e+00 1smd b.71.1.1,c.1.8.1 27768,28755 1i1iP 681 2.14e+00 1i1iP d.92.1.5 40297 1uwdA 103 2.15e+00 1sqwA 188 2.15e+00 2bmoB 194 2.16e+00 1vetA 124 2.27e+00 d.110.7.1 108553 1sc6A 404 2.29e+00 1iwmA 186 2.48e+00 b.125.1.2 83758 1tu1A 148 2.76e+00 d.107.1.3 107316 1twuA 139 3.10e+00 d.32.1.8 107413 1tiqA 180 3.12e+00 d.108.1.1 107010 1u04A 771 3.15e+00 b.34.14.1,c.55.3.10 107539,107540 1vm6A 228 3.23e+00 c.2.1.3,d.81.1.3 108876,108877 1qwzA 235 3.27e+00 b.100.1.1 96510 1wz9A 375 3.36e+00 1v3yA 192 3.61e+00 1wddS 128 3.72e+00 3gcb 470 3.79e+00 3gcb d.3.1.1 37032 1ecrA 309 3.81e+00 1ecrA e.2.1.1 42678 1ugjA 141 3.91e+00 b.41.1.3 107826 1pea 385 3.91e+00 1pea c.93.1.1 35662 1w44A 331 4.00e+00 1zpvA 91 4.35e+00 1vdeA 454 4.41e+00 1vdeA b.86.1.2,d.95.2.2,d.95.2.2 28378,40581,40582 1zbpA 273 4.53e+00 1qxrA 189 4.64e+00 b.82.1.7 96552 2f4iA 197 4.73e+00 1hx0A 496 4.95e+00 b.71.1.1,c.1.8.1 61346,61347 2a8jA 420 5.31e+00 1aqm 453 5.65e+00 1smd b.71.1.1,c.1.8.1 27717,28704 1rz2A 254 5.97e+00 b.100.1.1 105130 2a74A 643 6.30e+00 1e2wA 251 6.33e+00 1hcz b.2.6.1,b.84.2.2 22466,28252 3proC 166 6.34e+00 3proC d.52.1.1,d.52.1.1 38812,38813 1nqzA 194 6.54e+00 d.113.1.1 86077 1y12A 165 6.70e+00 2ff4A 388 6.84e+00 3pcgA 200 6.88e+00 3pchA b.3.6.1 22647 1dkiA 371 6.99e+00 1dkiA d.3.1.1 37090 2gj8A 172 7.43e+00 1q1oA 98 7.77e+00 d.15.2.2 95596 1miwA 404 7.79e+00 a.173.1.1,d.218.1.4 79162,79163 2exnA 136 7.84e+00 2basA 431 8.19e+00 2gkpA 167 8.31e+00 1g94A 448 8.41e+00 b.71.1.1,c.1.8.1 65169,65170 1kao 167 8.50e+00 1ctqA c.37.1.8 32014 2bzuA 181 8.52e+00 1fjrA 195 8.62e+00 1fjrA b.102.1.1 59855 2b06A 155 8.85e+00 1w2lA 99 8.86e+00 1luzA 88 8.87e+00 b.40.4.5 74271 1xt9A 212 9.02e+00 1ei6A 406 9.08e+00 c.76.1.4 90443 2cyeA 133 9.09e+00 1ti6B 274 9.10e+00 b.3.5.1,d.58.1.5 106976,106977 2nlrA 234 9.15e+00 2nlrA b.29.1.11 24344 1cojA 212 9.20e+00 1avmA a.2.11.1,d.44.1.1 15737,38734 1djrD 103 9.46e+00 3chbD b.40.2.1 24865 2a8mA 420 9.50e+00 1zkdA 387 9.53e+00 7taa 478 9.54e+00 7taa b.71.1.1,c.1.8.1 27778,28765 1t3lA 337 9.80e+00 b.34.2.1,c.37.1.1 106358,106359 1uw4A 91 9.95e+00 d.58.7.4 100071 2atvA 196 1.01e+01 1zq4A 693 1.01e+01 1mai 131 1.02e+01 1mai b.55.1.1 26951 1wtaA 275 1.04e+01 1bcpF 99 1.05e+01 1prtF b.40.2.1 25142 1ki0A 253 1.07e+01 g.14.1.1,g.14.1.1,g.14.1.1 72493,72494,72495 1cqxA 403 1.09e+01 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 2stv 195 1.09e+01 2stv b.121.7.1 23287 1j08A 226 1.11e+01 c.47.1.2,c.47.1.2 83855,83856 2bukA 196 1.12e+01 1b65A 375 1.12e+01 1b65A d.154.1.1 42020 1vqoH 171 1.13e+01 2c5lC 117 1.14e+01 1ogaE 252 1.15e+01 b.1.1.1,b.1.1.2 86992,86993 2biiA 424 1.15e+01 1a8l 226 1.15e+01 1a8l c.47.1.2,c.47.1.2 32777,32778 1uch 230 1.16e+01 1uch d.3.1.6 37129 2fvhA 120 1.17e+01 1lc5A 364 1.17e+01 c.67.1.1 73827 2kfnA 605 1.18e+01 1xwl c.55.3.5,e.8.1.1 33682,42975 2fug7 129 1.19e+01 4ubpA 101 1.21e+01 1ubpA d.8.1.1 37352 1y6hA 177 1.21e+01 1avmA 201 1.23e+01 1avmA a.2.11.1,d.44.1.1 15782,38745 1xs0A 136 1.27e+01 1qsoA 149 1.28e+01 1qsmA d.108.1.1 40812 1zynA 202 1.30e+01 3tdt 274 1.30e+01 3tdt b.81.1.2 28053 2axjA 242 1.32e+01 1p0zA 131 1.32e+01 d.110.6.1 93882 1quqB 121 1.33e+01 1quqB b.40.4.3 25305 1xo3A 101 1.34e+01 2faoA 309 1.34e+01 2fmlA 273 1.35e+01 1unnC 115 1.36e+01 d.240.1.1 99680 1zjcA 418 1.36e+01 1rk8A 165 1.37e+01 d.58.7.1 97603 2dbbA 151 1.39e+01 1fzqA 181 1.39e+01 1hurA c.37.1.8 32060 1x9pA 523 1.40e+01 1fjgD 209 1.41e+01 1c05A d.66.1.2 39553 1wnfA 328 1.41e+01 1pvl 301 1.43e+01 1pvl f.6.1.1 43819 1jkxA 212 1.44e+01 c.65.1.1 66813 1tmxA 293 1.45e+01 1x6oA 174 1.49e+01 b.34.5.2,b.40.4.5 109493,109494 1g9oA 91 1.52e+01 1pdr b.36.1.1 60400 1yghA 164 1.53e+01 1yghA d.108.1.1 40802 2carA 196 1.54e+01 1x82A 190 1.55e+01 1j9bA 141 1.55e+01 c.47.1.12 66459 1u58A 253 1.56e+01 1bcpD 110 1.56e+01 1bcpD b.40.2.1 25132 1lp9E 194 1.57e+01 b.1.1.1,b.1.1.2 91086,91087 1vl4A 447 1.58e+01 d.283.1.1 108718 1h12A 405 1.59e+01 a.102.1.2 83447 1y0zA 330 1.60e+01 1tueA 212 1.61e+01 c.37.1.20 107323 1vjfA 180 1.61e+01 d.116.1.1 100809 3rubS 123 1.62e+01 1rboC d.73.1.1 39616 1xiwA 105 1.65e+01 1voqa 90 1.65e+01 2d27A 149 1.65e+01 1dk0A 188 1.65e+01 1b2vA d.35.1.1 38530 2fr5A 146 1.66e+01 1zldA 120 1.70e+01 1r8gA 372 1.71e+01 d.128.1.3 104845 1mml 265 1.75e+01 1mml e.8.1.2 43015 1qm4A 396 1.77e+01 1mxb d.130.1.1,d.130.1.1,d.130.1.1 41350,41351,41352 1lkfA 299 1.78e+01 1pvl f.6.1.1 43821 1uyrA 737 1.79e+01 c.14.1.4,c.14.1.4 100188,100189 1vioA 243 1.81e+01 d.265.1.3,d.66.1.5 100762,100763 1tdtA 259 1.82e+01 3tdt b.81.1.2 28055 1n71A 180 1.84e+01 d.108.1.1 85370 1hnf 182 1.85e+01 1qa9A b.1.1.1,b.1.1.3 19741,21680 1yhfA 115 1.86e+01 1wpkA 146 1.87e+01 1qstA 160 1.88e+01 1yghA d.108.1.1 40804 3chbD 104 1.90e+01 3chbD b.40.2.1 24970 1zhsA 113 1.90e+01 1jkmB 361 1.90e+01 1jkmA c.69.1.2 34634 1eazA 125 1.92e+01 b.55.1.1 70113 1dt9A 437 1.92e+01 1dt9A c.55.4.2,d.79.3.2,d.91.1.1 33738,39815,40257 1xizA 159 1.93e+01 1ckmA 330 1.94e+01 1ckmA b.40.4.6,d.142.2.3 25358,41585 1lj5A 379 1.95e+01 e.1.1.1 73928 1xw2A 405 1.95e+01 2bzvA 181 1.96e+01 2a4nA 182 1.97e+01 1oa4A 222 1.99e+01 b.29.1.11 86731 2acfA 182 2.00e+01 1ir21 140 2.00e+01 1z6nA 167 2.02e+01 1z2mA 155 2.03e+01 2a90A 240 2.10e+01 1x9gA 200 2.10e+01 c.33.1.3 109527 1gk8I 140 2.11e+01 d.73.1.1 65242 1y791 680 2.12e+01 1qb5D 99 2.13e+01 b.40.2.1 88357 1s4bP 674 2.14e+01 d.92.1.5 105252 2cy2A 174 2.14e+01 2aukA 190 2.16e+01 1bcpB 199 2.16e+01 1bcpB b.40.2.1,d.169.1.2 25120,42429 2erxA 172 2.17e+01 1xpiA 231 2.18e+01 2evwX 166 2.19e+01 1ogdA 131 2.19e+01 c.133.1.1 92893 1zsqA 528 2.19e+01 1pzxA 289 2.20e+01 c.119.1.1 95484 2a9sA 171 2.23e+01 1t7pA 698 2.23e+01 1t7pA c.55.3.5,e.8.1.1 33712,43005 1twyA 290 2.23e+01 2gaeA 346 2.24e+01 1s9aA 257 2.24e+01 b.3.6.1 105379 2d1sA 548 2.27e+01 1prtF 98 2.28e+01 1prtF b.40.2.1 25140 1ex2A 189 2.29e+01 1ex2A c.51.4.2 33225 1rgxA 114 2.32e+01 g.77.1.1 104932 1qhtA 775 2.33e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1oa8A 133 2.39e+01 b.145.1.1 92698 1svdM 110 2.40e+01 1q40B 219 2.41e+01 d.17.4.2 95771 2a8lA 420 2.43e+01 1es6A 296 2.44e+01 1es6A b.31.1.1,b.31.1.1 83048,83049 2blnA 305 2.44e+01 1idsA 207 2.44e+01 1avmA a.2.11.1,d.44.1.1 15722,38730 1l5xA 280 2.45e+01 c.106.1.1 77718 1wc3A 219 2.46e+01 1g8aA 227 2.47e+01 c.66.1.3 90506 1ejxA 100 2.48e+01 d.8.1.1 83182 1njhA 119 2.48e+01 b.128.1.1 85787 1kskA 234 2.48e+01 d.66.1.5,d.265.1.3 72920,90389 2b4yA 271 2.48e+01 1psdA 409 2.52e+01 1psdA c.2.1.4,c.23.12.1,d.58.18.1 30097,31357,39354 1ifrA 121 2.53e+01 b.1.16.1 71203 1u3eM 174 2.54e+01 d.4.1.3,d.285.1.1 107640,107641 1s3cA 141 2.55e+01 1k4tA 592 2.57e+01 a.2.8.1,d.163.1.2,e.15.1.1 77263,77264,77265 1xwtA 405 2.59e+01 1n0nA 199 2.61e+01 a.2.11.1,d.44.1.1 79750,79751 1aiu 105 2.63e+01 1erv c.47.1.1 32746 1nxiA 132 2.64e+01 d.58.47.1 86381 1s72E 178 2.65e+01 d.141.1.1,d.141.1.1 105323,105324 1sxjE 354 2.67e+01 a.80.1.1,c.37.1.20 106089,106090 2a5jA 191 2.69e+01 1wlsA 328 2.69e+01 1qipA 183 2.69e+01 1qipA d.32.1.1 38470 1jv4A 162 2.70e+01 b.60.1.1 67343 1eluA 390 2.70e+01 1elqA c.67.1.3 34434 1ycoA 279 2.71e+01 1w79A 489 2.71e+01 1lcyA 325 2.72e+01 b.36.1.4,b.47.1.1 73834,73835 1z4rA 168 2.72e+01 1hyuA 521 2.72e+01 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 2cttA 104 2.75e+01 1jyhA 157 2.78e+01 d.60.1.3 71956 1x4rA 99 2.78e+01 1aqcA 172 2.78e+01 1x11A b.55.1.2 26983 2cg4A 152 2.83e+01 2atrA 138 2.84e+01 2db9A 149 2.93e+01 1t0qC 86 2.95e+01 d.15.12.1 106222 2iwrA 178 2.95e+01 1tl0D 103 2.96e+01 1iuhA 198 2.99e+01 d.61.1.2 83711 2glfA 450 3.00e+01 2b67A 204 3.01e+01 1k7kA 221 3.01e+01 c.51.4.1 72104 1ako 268 3.07e+01 1ako d.151.1.1 41779 1bsmA 201 3.07e+01 1avmA a.2.11.1,d.44.1.1 15780,38743 1u07A 90 3.08e+01 1f35A 162 3.10e+01 1f35A b.94.1.1 59628 1y3jA 77 3.11e+01 1sqhA 312 3.12e+01 d.108.1.5 98966 1rg9A 383 3.13e+01 d.130.1.1,d.130.1.1,d.130.1.1 97427,97428,97429 1pl4A 198 3.13e+01 a.2.11.1,d.44.1.1 94854,94855 1mw9X 592 3.15e+01 e.10.1.1 91480 1vc3B 97 3.16e+01 1wkaA 147 3.17e+01 1lt5D 103 3.17e+01 3chbD b.40.2.1 24875 1v60A 123 3.17e+01 1c44A 123 3.23e+01 1qndA d.106.1.1 40795 2fsqA 243 3.24e+01 2essA 248 3.24e+01 1n8yC 608 3.27e+01 c.10.2.5,c.10.2.5,g.3.9.1,g.3.9.1 80314,80315,80316,80317 1f5mA 180 3.28e+01 1f5mB d.110.2.1 40895 1qy1A 174 3.29e+01 b.60.1.1 96568 2f1nA 262 3.30e+01 2gk4A 232 3.32e+01 1cjwA 166 3.32e+01 1cjwA d.108.1.1 40818 1oatA 439 3.32e+01 2dkb c.67.1.4 34461 1f15A 218 3.35e+01 1f15B b.121.4.5 23320 1jj2P 95 3.35e+01 1ffkN b.34.5.1 63101 1mkmA 249 3.36e+01 a.4.5.33,d.110.2.2 79242,79243 1jqeA 292 3.36e+01 c.66.1.19 71789 1y9qA 192 3.39e+01 1olrA 224 3.40e+01 b.29.1.11 93330 2bjuA 453 3.40e+01 2bidA 197 3.41e+01 2bidA f.1.4.1 43398 1mtpA 323 3.42e+01 e.1.1.1 85107 1chd 203 3.45e+01 1chd c.40.1.1 32478 1ne9A 335 3.45e+01 d.108.1.4,d.108.1.4 91839,91840 1y07A 128 3.51e+01 1jj2E 177 3.53e+01 1ffk1 d.141.1.1,d.141.1.1 63089,63090 1tedA 393 3.53e+01 c.95.1.2 106807 1tvxA 75 3.54e+01 1tvxA d.9.1.1 37441 2bjfA 329 3.54e+01 1qqrA 138 3.55e+01 1bmlC d.15.5.1 37721 1vggA 161 3.56e+01 1xk7A 408 3.59e+01 1q38A 89 3.68e+01 b.1.2.1 95663 1sh8A 154 3.78e+01 d.38.1.5 105549 1ujrA 110 3.84e+01 1vl2A 421 3.85e+01 c.26.2.1,d.210.1.1 108708,108709 1wduA 245 3.89e+01 d.151.1.1 109286 1s5jA 847 3.92e+01 1y51A 88 3.92e+01 1nu0A 138 3.92e+01 c.55.3.8 92165 1amuA 563 3.94e+01 1amuA e.23.1.1 43351 1omwA 689 3.95e+01 a.91.1.1,b.55.1.1,d.144.1.7 87086,87087,87088 1chuA 540 3.98e+01 1chuA a.7.3.1,c.3.1.4,d.168.1.1 16325,30424,42307 1bsg 266 3.99e+01 1btl e.3.1.1 42729 1xzzA 246 4.03e+01 1vj0A 380 4.05e+01 b.35.1.2,c.2.1.1 100786,100787 2ak4E 245 4.07e+01 1ois 223 4.08e+01 1a36A e.15.1.1 43267 1hpi 71 4.11e+01 1ckuA g.35.1.1 44995 1vhxA 150 4.12e+01 c.55.3.8 100712 1gcqC 70 4.13e+01 1gcpA b.34.2.1 60436 1vdc 333 4.14e+01 1trb c.3.1.5,c.3.1.5 30545,30546 1m4iA 181 4.18e+01 d.108.1.1 74457 1i06A 180 4.18e+01 1mup b.60.1.1 27131 2aq4A 434 4.23e+01 1xg8A 111 4.25e+01 1bpyA 335 4.29e+01 1bpyA a.60.6.1,a.60.12.1,d.218.1.2 17980,75819,75820 1fjjA 159 4.29e+01 1fjjA b.17.1.2 59852 1xakA 83 4.30e+01 1q2yA 140 4.31e+01 d.108.1.1 95655 1wteA 272 4.35e+01 1ryaA 160 4.36e+01 d.113.1.5 105122 8rucI 123 4.38e+01 1rboC d.73.1.1 39629 1g4wR 383 4.45e+01 1g4uS a.24.11.1,c.45.1.2 16644,32692 1je5A 206 4.54e+01 1je5A b.40.4.7 62909 1zndA 174 4.55e+01 2aotA 292 4.55e+01 1xodA 118 4.57e+01 1fl2A 310 4.60e+01 1hyuA c.3.1.5,c.3.1.5 59869,59870 1g6oA 330 4.60e+01 1g6oA c.37.1.11 32430 1mgpA 313 4.61e+01 c.119.1.1 79098 1h6lA 353 4.64e+01 b.68.3.1 60687 1qtqA 553 4.66e+01 1gtrA b.53.1.2,c.26.1.1 26940,31579 1ndh 272 4.67e+01 1ndh b.43.4.2,c.25.1.1 25662,31552 1x1rA 178 4.70e+01 1o7iA 119 4.77e+01 b.40.4.3 86642 1u7eB 154 4.80e+01 1erw 105 4.80e+01 1erv c.47.1.1 32745 1bg2 325 4.80e+01 1bg2 c.37.1.9 32189 1aly 146 4.81e+01 1aly b.22.1.1 23856 1vkiA 181 4.83e+01 d.116.1.1 108664 1d3bB 91 4.84e+01 1d3bB b.38.1.1 24804 2bw8A 227 4.87e+01 1h2rL 534 4.89e+01 1h2rL e.18.1.1 43298 2oatA 439 4.89e+01 2dkb c.67.1.4 34452 1jj2F 119 4.89e+01 1ffkE d.79.3.1 63091 1dbxA 158 4.94e+01 1dbuA d.116.1.1 40928 1lw3A 657 4.96e+01 b.55.1.8,c.45.1.3 91152,91153 2bkrA 212 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