# List of top-scoring protein chains for t2k-100-30-bys-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.soe.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 2arzA 247 1.76e-43 b.45.1.1 127225 1xhnA 184 9.65e-32 b.45.1.1 122007 1vl7A 157 3.21e-18 b.45.1.1 108732 1rfeA 162 3.21e-13 b.45.1.1 111796 2aq6A 147 1.69e-10 b.45.1.1 127156 1w9aA 147 1.86e-10 b.45.1.1 114408 2fhqA 141 2.03e-08 b.45.1.1 133497 2hq9A 149 5.77e-08 b.45.1.1 136659 1t9mA 214 7.34e-07 b.45.1.1 112364 1g79A 218 6.59e-06 1ci0A b.45.1.1 25752 2hhzA 150 7.56e-06 2ig6A 150 1.01e-05 1nrgA 261 1.07e-05 b.45.1.1 80694 1dnlA 199 1.34e-05 1ci0A b.45.1.1 25753 2htiA 185 1.88e-05 b.45.1.1 136744 1ty9A 222 2.49e-05 b.45.1.1 112827 2htdA 140 3.33e-05 2hq7A 146 4.26e-05 b.45.1.1 136657 2iabA 155 5.26e-05 2i02A 148 8.84e-05 b.45.1.1 136936 2a2jA 246 1.65e-04 b.45.1.1 126033 2asfA 137 2.55e-04 b.45.1.1 127253 2re7A 134 2.65e-04 1w3oA 216 5.83e-04 b.45.1.1 114142 2fg9A 178 2.01e-03 b.45.1.1 133426 3ba3A 145 4.87e-03 1ci0A 228 6.78e-03 1ci0A b.45.1.1 25750 2ou5A 175 7.16e-03 2furA 209 1.62e-02 b.45.1.1 134185 1nar 290 7.11e-02 1nar 1narA 290 7.11e-02 c.1.8.5 28988 2p19A 149 1.35e-01 1taq 832 1.93e-01 1taq 2i51A 195 3.09e-01 1jfuA 186 3.65e-01 c.47.1.10 62940 1ef1A 294 4.51e-01 1ef1A a.11.2.1,b.55.1.5,d.15.1.4 16368,27003,37611 2nrrA 159 4.83e-01 1wdeA 294 4.86e-01 c.90.1.1 114534 1xwtA 405 5.35e-01 a.102.1.2 122410 1b43A 340 5.94e-01 1a76 a.60.7.1,c.120.1.2 18092,33362 1j1nA 492 6.65e-01 c.94.1.1 83978 1gcvA 140 6.92e-01 1cg5B a.1.1.2 15410 1h12A 405 7.10e-01 a.102.1.2 83447 1xw2A 405 7.20e-01 a.102.1.2 122389 1hw5A 210 7.36e-01 2cgpA a.4.5.4,b.82.3.2 16098,28137 2id0A 644 7.57e-01 3cp3A 148 8.90e-01 1h4rA 314 1.07e+00 a.11.2.1,b.55.1.5,d.15.1.4 65616,65617,65618 2ix0A 663 1.09e+00 1ud9A 245 1.23e+00 d.131.1.2,d.131.1.2 107768,107769 2de3A 365 1.33e+00 1ffkI 194 1.54e+00 1ffkI d.12.1.2 37494 1vq0A 302 1.77e+00 d.193.1.1,g.81.1.1 114000,114001 1j5kA 89 1.79e+00 d.51.1.1 71565 1gvnB 287 1.83e+00 c.37.1.21 76354 1rwzA 245 1.83e+00 d.131.1.2,d.131.1.2 98005,98006 2hqyA 305 1.95e+00 2zatA 260 1.99e+00 1zzkA 82 2.03e+00 d.51.1.1 125909 2ej9A 237 2.08e+00 1ta3A 274 2.14e+00 c.1.8.5 106731 1mo7A 213 2.24e+00 d.220.1.1 85028 2ge7A 108 2.30e+00 d.254.1.2 135049 1uocA 289 2.43e+00 c.55.3.9 99686 2vnvA 129 2.49e+00 1rxzA 245 2.56e+00 d.131.1.2,d.131.1.2 98067,98068 3b9eA 584 3.17e+00 2vqeK 129 3.87e+00 1wmhA 89 4.02e+00 d.15.2.2 114744 2bkfA 87 4.06e+00 d.15.2.2 128699 1r3dA 264 4.07e+00 c.69.1.35 111680 1jb0D 138 4.11e+00 1jb0D d.187.1.1 62823 1rpuA 172 4.12e+00 d.255.1.1 97716 2bmbA 545 4.31e+00 1um8A 376 4.37e+00 c.37.1.20 99580 2ojwA 384 4.76e+00 1yz7A 188 4.86e+00 2jbvA 546 5.02e+00 1g6nA 210 5.17e+00 2cgpA a.4.5.4,b.82.3.2 16100,28139 1ryp1 222 5.34e+00 1ryp1 2on5A 206 5.38e+00 2uubK 129 5.39e+00 c.55.4.1 139942 2cgpA 210 5.42e+00 2cgpA a.4.5.4,b.82.3.2 16102,28141 1k1xA 659 5.47e+00 a.8.3.2,b.30.5.8,c.6.2.2 84279,84280,84281 1n9lA 109 5.64e+00 d.110.3.6 85468 3b50A 310 5.68e+00 1nk4A 580 5.75e+00 c.55.3.5,e.8.1.1 91923,91924 1wmhB 86 5.75e+00 d.15.2.2 114745 1g0uL 241 5.77e+00 d.153.1.4 41894 2qziA 103 6.08e+00 2z1dA 372 6.09e+00 3bgyA 237 6.10e+00 2bdpA 580 6.42e+00 1xwl c.55.3.5,e.8.1.1 33709,43002 2b8tA 223 6.47e+00 c.37.1.24,g.39.1.14 128109,128110 2hhvA 580 6.51e+00 c.55.3.5,e.8.1.1 136514,136515 1u2eA 289 6.60e+00 2rghA 571 6.62e+00 1l3sA 580 6.66e+00 c.55.3.5,e.8.1.1 84521,84522 2ebuA 112 6.74e+00 1xwl 580 6.75e+00 1xwl 1xx6A 191 6.77e+00 c.37.1.24,g.39.1.14 116139,116140 1u4bA 580 6.83e+00 c.55.3.5,e.8.1.1 107664,107665 1u0mA 382 6.93e+00 c.95.1.2,c.95.1.2 107557,107558 1fjgK 129 7.02e+00 1fjfK c.55.4.1 33733 2ogwA 310 7.12e+00 1vz6A 393 7.19e+00 d.154.1.2 108949 1wn5A 130 7.26e+00 c.97.1.1 121082 1wj6A 101 7.43e+00 d.15.2.2 114693 2p5tB 253 7.54e+00 2ceyA 306 7.63e+00 1vimA 200 7.72e+00 c.80.1.3 100758 2h1nA 567 7.94e+00 2z3hA 130 8.06e+00 1e8cA 498 8.32e+00 c.98.1.1,c.59.1.1,c.72.2.1 59377,59378,59379 1aua 296 8.34e+00 1aua 1auaA 296 8.34e+00 a.5.3.1,c.13.1.1 16290,30882 1i6xA 209 8.59e+00 a.4.5.4,b.82.3.2 83673,83674 1qsgA 265 9.22e+00 1eny c.2.1.2 29935 1y89A 238 9.31e+00 2qntA 141 9.48e+00 1kamA 194 9.55e+00 c.26.1.3 72254 1hl9A 449 9.61e+00 b.71.1.3,c.1.8.11 90650,90651 1yycA 174 9.62e+00 1gnlA 544 9.67e+00 e.26.1.1 70287 1ps9A 671 9.72e+00 c.1.4.1,c.3.1.1,c.4.1.1 95076,95077,95078 1u7bA 261 9.79e+00 d.131.1.2,d.131.1.2 113083,113084 2acvA 463 9.98e+00 2eq6A 464 1.05e+01 1f76A 336 1.06e+01 c.1.4.1 76160 1np8A 159 1.08e+01 a.39.1.8 92022 1a6dB 543 1.09e+01 1a6dA a.129.1.2,c.8.5.2,d.56.1.2 19489,30820,38937 1s3iA 310 1.09e+01 b.46.1.1,c.65.1.1 98435,98436 1iurA 88 1.11e+01 a.2.3.1 90704 1gxrA 337 1.13e+01 b.69.4.1 70722 1y3nA 490 1.14e+01 c.94.1.1 122597 1axj 122 1.16e+01 1axj 3b7nA 320 1.19e+01 1jf3A 147 1.21e+01 a.1.1.2 71642 1skoA 143 1.21e+01 d.110.7.1 105676 2o8gI 225 1.26e+01 2pzzA 147 1.26e+01 2zmfA 189 1.28e+01 2fcjA 119 1.29e+01 c.136.1.1 133269 1gt0D 80 1.29e+01 a.21.1.1 76337 1uf3A 228 1.30e+01 d.159.1.6 99317 1uj6A 227 1.31e+01 c.124.1.4,d.58.40.1 107898,107899 1alvA 173 1.32e+01 1alvA a.39.1.8 17370 2c21A 144 1.32e+01 d.32.1.1 129649 1ohvA 472 1.38e+01 c.67.1.4 93031 1tedA 393 1.41e+01 c.95.1.2 106807 1rypK 198 1.45e+01 d.153.1.4 41879 2e4sA 189 1.47e+01 2ct8A 497 1.49e+01 1xksA 450 1.51e+01 b.69.14.1 115422 3cjnA 162 1.55e+01 1nvtA 287 1.55e+01 c.2.1.7,c.58.1.5 86270,86271 1gkzA 388 1.55e+01 a.29.5.1,d.122.1.4 65268,65269 2jabA 136 1.56e+01 3bt5A 177 1.61e+01 1f9zA 135 1.63e+01 1qipA d.32.1.1 38484 2bbeA 108 1.64e+01 1fa8A 135 1.64e+01 1qipA d.32.1.1 38486 1q2lA 939 1.65e+01 d.185.1.1,d.185.1.1,d.185.1.1,d.185.1.1 118731,118732,118733,118734 1u0tA 307 1.66e+01 e.52.1.1 107567 3cptA 143 1.67e+01 1pczA 191 1.73e+01 1ytbA d.129.1.1,d.129.1.1 41292,41293 2rcfA 91 1.74e+01 1gal 583 1.76e+01 1gpeA 1g8aA 227 1.77e+01 c.66.1.3 90506 2jvgA 72 1.78e+01 2qzjA 136 1.79e+01 1m6nA 802 1.79e+01 a.162.1.1,a.172.1.1,c.37.1.19,c.37.1.19 78697,78698,78699,78700 1gtdA 85 1.80e+01 d.284.1.1 76344 3b7cA 122 1.84e+01 2qe6A 274 1.85e+01 1bf5A 545 1.87e+01 1bg1A a.47.1.1,b.2.5.5,d.93.1.1 17766,22460,40526 1xvwA 160 1.89e+01 c.47.1.10 122387 1aisA 182 1.90e+01 1ytbA d.129.1.1,d.129.1.1 41288,41289 1pzdA 322 1.90e+01 b.1.10.3,d.105.1.2 95413,95414 2ashA 381 1.98e+01 2ebbA 101 1.99e+01 1u9cA 224 1.99e+01 c.23.16.2 113234 2frvB 536 2.00e+01 1h2rL e.18.1.1 43291 2nptA 106 2.01e+01 d.15.2.2 138448 1rypI 222 2.05e+01 d.153.1.4 41877 1u69A 163 2.07e+01 d.32.1.7 107699 1r4xA 275 2.14e+01 b.1.10.3,d.105.1.2 97054,97055 2cdcA 366 2.16e+01 2ol5A 202 2.17e+01 1d3uA 181 2.24e+01 1ytbA d.129.1.1,d.129.1.1 41290,41291 1v4xA 144 2.30e+01 a.1.1.2 108363 1dixA 208 2.30e+01 1bk7A d.124.1.1 41122 2cqsA 842 2.33e+01 2gjlA 328 2.33e+01 1iruK 201 2.34e+01 d.153.1.4 71362 2nsqA 155 2.35e+01 2jynA 146 2.38e+01 1flmA 122 2.38e+01 1axj b.45.1.1 25747 1x6vA 630 2.41e+01 b.122.1.3,c.26.1.5,c.37.1.4 121755,121756,121757 3cqcA 270 2.44e+01 1y4tA 322 2.46e+01 c.94.1.1 116464 1m40A 263 2.48e+01 e.3.1.1 74437 1ji8A 111 2.50e+01 d.203.1.1 66733 1efcA 393 2.51e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25680,25720,32113 3cgvA 397 2.51e+01 1xeoA 168 2.51e+01 d.167.1.1 121913 2ogeA 399 2.55e+01 1squA 155 2.56e+01 d.252.1.1 98971 2sak 121 2.56e+01 2sak 2sakA 121 2.56e+01 d.15.5.1 37711 3cncA 220 2.57e+01 1wl7A 312 2.57e+01 b.67.2.1 120996 2iruA 303 2.57e+01 2i8lA 156 2.58e+01 2a4xA 138 2.58e+01 d.32.1.2 126166 1ho1A 242 2.59e+01 1ho1A c.1.24.1 61097 2igiA 180 2.61e+01 3cx5B 352 2.64e+01 2pq8A 278 2.65e+01 1za0A 275 2.66e+01 a.25.1.2 124774 1tf3A 92 2.66e+01 1aayA g.37.1.1,g.37.1.1,g.37.1.1 45057,45058,45059 2burB 241 2.69e+01 b.3.6.1 129228 1p3dA 475 2.70e+01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1z8oA 404 2.73e+01 a.104.1.1 124722 2hd3A 103 2.76e+01 1wmuA 141 2.79e+01 a.1.1.2 109416 1btl 263 2.80e+01 1btl 2fp8A 322 2.81e+01 2it9A 127 2.82e+01 d.18.1.3 137634 2eisA 133 2.82e+01 3b5mA 205 2.83e+01 2qeaA 160 2.83e+01 1tf6A 190 2.85e+01 1tf6A g.37.1.1,g.37.1.1,g.37.1.1,g.37.1.1,g.37.1.1,g.37.1.1 45060,45061,45062,45063,45064,45065 1tjlA 151 2.95e+01 a.2.14.1,g.39.1.13 107027,107028 2bkxA 242 2.96e+01 1wybA 392 2.97e+01 1wwpA 119 2.99e+01 1o22A 170 3.00e+01 d.238.1.1 86557 1wycA 392 3.01e+01 2d37A 176 3.01e+01 2z99A 219 3.04e+01 1r9fA 136 3.04e+01 d.255.1.1 97257 2gqcA 70 3.08e+01 2k29A 53 3.11e+01 2v3kA 258 3.16e+01 1pmaA 233 3.16e+01 1pmaA d.153.1.4 41918 2boqA 331 3.17e+01 1bs4A 168 3.18e+01 1bs4A d.167.1.1 42287 2outA 131 3.24e+01 1wc1A 226 3.25e+01 d.58.29.1 114492 3cdxA 354 3.26e+01 2dcfA 392 3.27e+01 2prsA 284 3.27e+01 1cg5A 141 3.28e+01 1abwA a.1.1.2 15406 1c14A 262 3.29e+01 1eny c.2.1.2 29927 1jmtA 104 3.32e+01 d.58.7.3 63180 3cbgA 232 3.35e+01 2z43A 324 3.40e+01 1knqA 175 3.41e+01 c.37.1.17 72786 1b85A 351 3.43e+01 1arv a.93.1.1 18581 2uxyA 341 3.44e+01 1yudA 170 3.45e+01 b.82.1.16 124046 2gm6A 208 3.46e+01 1e3dB 542 3.50e+01 1h2rL e.18.1.1 59189 1fqgA 263 3.51e+01 1btl e.3.1.1 42699 1qg6A 261 3.52e+01 1eny c.2.1.2 29919 1vffA 423 3.54e+01 c.1.8.4 120033 1kutA 230 3.54e+01 d.143.1.1 73017 1prxA 224 3.55e+01 1prxA c.47.1.10 33076 1ogiA 303 3.55e+01 b.43.4.2,c.25.1.1 92914,92915 1n6aA 259 3.58e+01 b.76.2.1,b.85.7.1 80121,80122 2zgwA 235 3.59e+01 1olmA 403 3.61e+01 a.5.3.1,b.132.1.1,c.13.1.1 104008,104009,104010 1xtmA 175 3.67e+01 3bf2A 152 3.70e+01 1vjuA 309 3.75e+01 d.248.1.1 100835 1s4iA 175 3.77e+01 1ew6A 137 3.81e+01 1ewaA a.1.1.2 15637 2vfrA 422 3.89e+01 3bomA 142 3.89e+01 2a0nA 265 3.91e+01 c.1.2.1 125961 1eupA 403 3.93e+01 1rom a.104.1.1 18967 2vc7A 314 3.97e+01 1xtlA 175 3.98e+01 3b82A 842 3.99e+01 1s4vA 229 4.00e+01 d.3.1.1 98511 2fp7A 54 4.00e+01 2hr0A 645 4.03e+01 1v3wA 173 4.05e+01 b.81.1.5 100291 1ytaA 180 4.07e+01 c.55.3.5 124002 1yexA 186 4.11e+01 c.47.1.10 123021 1fp3A 402 4.13e+01 1fp3A a.102.1.3 18842 2buwB 241 4.14e+01 1zwyA 185 4.16e+01 c.51.4.3 125753 1oc2A 348 4.20e+01 c.2.1.2 92765 2d4gA 171 4.20e+01 1cqxA 403 4.21e+01 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 2vptA 215 4.23e+01 1vp2A 208 4.28e+01 c.51.4.1 113933 1f60A 458 4.30e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 2e52A 300 4.30e+01 2pljA 419 4.31e+01 2rjoA 332 4.31e+01 1han 297 4.38e+01 1han 1a8y 367 4.40e+01 1a8y 1a8yA 367 4.40e+01 c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 2qr7A 342 4.41e+01 1ewaA 137 4.42e+01 1ewaA a.1.1.2 15639 2op6A 152 4.45e+01 1gd7A 109 4.49e+01 b.40.4.4 60441 1lkdA 297 4.49e+01 d.32.1.3,d.32.1.3 78059,78060 1ermA 263 4.52e+01 1btl e.3.1.1 42690 2qenA 350 4.54e+01 1awcB 153 4.59e+01 1bd8 d.211.1.1 19156 1q15A 503 4.62e+01 c.26.2.1,d.153.1.1 95538,95539 1vqoU 66 4.65e+01 g.39.1.6 120382 2amlA 373 4.65e+01 2r79A 283 4.66e+01 1prtF 98 4.66e+01 1prtF b.40.2.1 25140 1vm6A 228 4.67e+01 d.81.1.3,c.2.1.3 108877,118631 1urvA 190 4.68e+01 a.1.1.2 113414 2d6yA 202 4.71e+01 a.4.1.9,a.121.1.1 131313,131314 1dtdA 303 4.75e+01 1aye c.56.5.1 33823 1v4eA 299 4.75e+01 a.128.1.1 100296 1zxzA 197 4.81e+01 2ozbB 260 4.84e+01 1v25A 541 4.92e+01 e.23.1.1 108275 1uuhA 159 4.92e+01 d.169.1.4 100008 2obxA 157 4.92e+01 1vh7A 265 4.92e+01 c.1.2.1 100646 1n6zA 105 4.93e+01 d.263.1.1 85369 1mzyA 333 4.94e+01 b.6.1.3,b.6.1.3 103848,103849 1p1lA 102 5.00e+01 d.58.5.2 87695 1wc3A 219 5.02e+01 d.58.29.1 114495 2asuB 234 5.02e+01 1gnxA 479 5.04e+01 c.1.8.4 76241 1hfoA 113 5.04e+01 d.80.1.3 61006 1vb5A 276 5.05e+01 c.124.1.5 113604 2acmA 66 5.06e+01 2jbwA 386 5.10e+01 2jheA 190 5.11e+01 1vkbA 161 5.11e+01 d.269.1.1 108643 1znbA 232 5.12e+01 1a7tA d.157.1.1 42039 1thfD 253 5.14e+01 1thfD c.1.2.1 28535 3czqA 304 5.14e+01 1vpsA 289 5.16e+01 1vpsA b.121.6.1 23336 2g84A 197 5.18e+01 c.97.1.2 134766 2i2cA 272 5.21e+01 1jmxA 494 5.23e+01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 66901,66902,66903,66904,66905 2bgzA 299 5.24e+01 1qf9A 194 5.26e+01 1zin c.37.1.1 31848 2c1cA 312 5.27e+01 c.56.5.1 129630 1wolA 122 5.28e+01 1lqyA 184 5.31e+01 d.167.1.1 74212 1aj5A 173 5.33e+01 1alvA a.39.1.8 17367 1e96B 203 5.36e+01 1e96B a.118.8.1 19211 1n0qA 93 5.39e+01 k.37.1.1 79754 1fn9A 365 5.42e+01 1fn9A d.196.1.1 59894 2pkfA 334 5.46e+01 1dm1A 146 5.46e+01 2fal a.1.1.2 15153 1xtnA 120 5.49e+01 d.189.1.1 116028 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