# List of top-scoring protein chains for t2k-100-30-str2 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 1hw1A 239 3.13e-01 1e2xA a.4.5.6 16111 a.78.1.1 18441 1o4sA 389 3.20e-01 c.67.1.1 86620 1qkkA 155 6.27e-01 1dbwA c.23.1.1 31104 1l5zA 155 6.35e-01 c.23.1.1 77722 1ko9A 345 9.88e-01 a.96.1.3 68717 d.129.1.2 68718 1omrA 201 1.05e+00 1eemA 241 1.12e+00 1eemA a.45.1.1 17717 c.47.1.5 33011 1fftC 204 1.13e+00 1fftC f.25.1.1 43629 1peqA 714 1.16e+00 1rtwA 220 1.39e+00 1e2xA 243 1.43e+00 1e2xA a.4.5.6 16113 a.78.1.1 18443 1lwyA 324 1.60e+00 a.96.1.3 78285 d.129.1.2 78286 1izcA 339 1.68e+00 c.1.12.5 83838 1v74B 87 1.75e+00 1fonA 240 1.75e+00 5ptp b.47.1.2 26231 1s9pA 227 1.86e+00 1paqA 189 1.87e+00 1ebmA 317 1.95e+00 1ebmA a.96.1.3 18751 d.129.1.2 41300 1g8iA 190 1.98e+00 1rec a.39.1.5 60363 1lwdA 413 2.03e+00 c.77.1.1 78265 1i37A 260 2.14e+00 1a28A a.123.1.1 61583 1hlvA 131 2.40e+00 a.4.1.7 65854 a.4.1.7 65855 1iow 306 2.67e+00 1iow c.30.1.2 31713 d.142.1.1 41481 1klt 226 2.70e+00 5ptp b.47.1.2 26300 1j30A 144 2.80e+00 1iq3A 110 2.90e+00 1iq3A a.39.1.6 62640 1k8eA 345 3.02e+00 1o17A 345 3.02e+00 a.46.2.1 80765 c.27.1.1 80766 1or7A 194 3.24e+00 a.4.13.2 87332 a.177.1.1 87333 1h3fA 432 3.34e+00 c.26.1.1 76631 d.66.1.4 76632 1kf6A 602 3.37e+00 a.7.3.1 72394 c.3.1.4 72395 d.168.1.1 72396 1w7bA 339 3.60e+00 1m3qA 317 3.72e+00 1w0hA 204 3.90e+00 1n83A 270 3.94e+00 a.123.1.1 80276 1ois 223 4.36e+00 1a36A e.15.1.1 43267 1x9mA 698 4.44e+00 1n45A 233 4.75e+00 a.132.1.1 79981 1rfzA 168 4.80e+00 1odoA 408 5.15e+00 1mhyG 169 5.25e+00 1mtyG a.23.3.1 16518 2dln 306 5.37e+00 1iow c.30.1.2 31715 d.142.1.1 41483 1ltm 320 5.45e+00 1ltm d.2.1.6 36992 1rec 201 5.60e+00 1rec a.39.1.5 17326 1qusA 322 6.05e+00 1ltm d.2.1.6 36991 1kfuS 184 6.14e+00 a.39.1.8 68574 1jdpA 441 6.21e+00 c.93.1.1 62906 1twfF 155 6.23e+00 1ka2A 499 6.26e+00 d.92.1.5 77305 1i50F 155 6.42e+00 d.78.1.2 61760 1v7wA 807 6.48e+00 1pbp 321 6.57e+00 1ixh c.94.1.1 35768 1pu6A 218 6.62e+00 1dp4A 435 7.31e+00 1dp4A c.93.1.1 35710 1oe8A 211 7.75e+00 a.45.1.1 86905 c.47.1.5 86906 1tu3F 79 7.75e+00 1lnrI 134 7.82e+00 1ew6A 137 7.92e+00 1ewaA a.1.1.2 15637 1ewaA 137 7.92e+00 1ewaA a.1.1.2 15639 1s2xA 206 8.28e+00 1oshA 232 8.64e+00 1h99A 224 8.93e+00 a.142.1.1 60814 a.142.1.1 60815 1eh2 106 9.04e+00 1eh2 a.39.1.6 17339 1uddA 226 9.21e+00 1dw0A 112 9.31e+00 1dw0A a.3.1.1 15911 1mhyB 395 9.33e+00 1mtyB a.25.1.2 16781 1syyA 346 9.49e+00 1j8uA 325 9.65e+00 d.178.1.1 71611 1kgsA 225 9.72e+00 a.4.6.1 68596 c.23.1.1 68597 1myt 146 9.85e+00 1a6m a.1.1.2 15207 1t7rA 269 1.01e+01 1ljrA 244 1.01e+01 1ljrA a.45.1.1 17707 c.47.1.5 33001 1ihoA 283 1.02e+01 1ihoA c.26.1.4 62390 1ng1 294 1.03e+01 1ng1 a.24.13.1 16961 c.37.1.10 32272 1jpnA 296 1.04e+01 a.24.13.1 67039 c.37.1.10 67040 1exeA 99 1.04e+01 1huuA a.55.1.1 17906 1ls1A 295 1.04e+01 a.24.13.1 78170 c.37.1.10 78171 1pv6A 417 1.05e+01 1am7A 158 1.06e+01 1am7A d.2.1.4 36981 1e3aB 560 1.06e+01 1ajqB 1r5qA 102 1.08e+01 2tct 207 1.09e+01 2tct a.4.1.9 16063 a.121.1.1 19240 1tqgA 105 1.09e+01 1a05A 358 1.09e+01 1cnzA c.77.1.1 35059 1f4qA 165 1.10e+01 1alvA a.39.1.8 17360 1ew6B 137 1.11e+01 1ewaA a.1.1.2 15638 1dmwA 307 1.15e+01 4pah d.178.1.1 42580 1dseA 292 1.16e+01 1ryc a.93.1.1 59130 1wdgA 94 1.18e+01 1qltA 560 1.18e+01 1qltA d.58.32.1 39457 d.145.1.1 41720 1r85A 379 1.20e+01 1jk0A 419 1.23e+01 a.25.1.2 63142 1o0wA 252 1.24e+01 a.149.1.1 80751 d.50.1.1 80752 1rkuA 206 1.25e+01 1mlwA 301 1.27e+01 d.178.1.1 79289 1ouvA 273 1.29e+01 1gkfB 557 1.29e+01 1f5sA 211 1.31e+01 1f5sA c.108.1.4 59656 1j97A 211 1.31e+01 1f5sA c.108.1.4 62753 1ryc 294 1.31e+01 1ryc a.93.1.1 18601 1fqvD 149 1.32e+01 1fqvD a.157.1.1 19263 d.42.1.1 38667 1gk9B 557 1.34e+01 1iuqA 367 1.35e+01 1huw 166 1.35e+01 1huw a.26.1.1 16831 4pah 308 1.36e+01 4pah d.178.1.1 42576 2cyp 294 1.36e+01 1ryc a.93.1.1 18600 1bed 181 1.37e+01 1fvkA a.44.1.1 17514 c.47.1.4 32808 1jgsA 138 1.40e+01 a.4.5.28 66683 1w1kA 560 1.42e+01 1u2zA 433 1.43e+01 1ds4A 292 1.43e+01 1ryc a.93.1.1 59129 1l7mA 211 1.43e+01 c.108.1.4 73664 1hizA 379 1.44e+01 c.1.8.3 65841 1pah 308 1.44e+01 4pah d.178.1.1 42578 1gm9B 557 1.45e+01 1csn 298 1.45e+01 1csn d.144.1.7 41664 1qcrA 446 1.46e+01 1be3A d.185.1.1 59025 d.185.1.1 59026 1dgsA 667 1.46e+01 1dgsA a.60.2.2 17963 b.40.4.6 25365 d.142.2.2 41581 1k04A 162 1.46e+01 a.24.14.1 67904 1qu7A 227 1.48e+01 1qu7A h.4.5.1 45789 1e96B 203 1.49e+01 1e96B a.118.8.1 19211 1colA 204 1.50e+01 1a87 f.1.1.1 43378 1qgjA 300 1.52e+01 1bgp a.93.1.1 18691 1emvB 134 1.52e+01 1bxiB d.4.1.1 37135 1k30A 368 1.55e+01 c.112.1.1 68067 2ptd 298 1.55e+01 2plc c.1.18.2 29605 1bxiB 134 1.56e+01 1bxiB d.4.1.1 37136 1e8gA 560 1.57e+01 1qltA d.58.32.1 39455 d.145.1.1 41718 1pjpA 226 1.57e+01 5ptp b.47.1.2 26301 1fqvJ 149 1.58e+01 1fqvD a.157.1.1 19266 d.42.1.1 38670 1xsm 390 1.63e+01 1xsm a.25.1.2 16804 1fd9A 213 1.63e+01 1fd9A d.26.1.1 59771 1hh8A 213 1.67e+01 1e96B a.118.8.1 61042 1ajqB 557 1.69e+01 1ajqB 1guxB 152 1.70e+01 1guxB a.74.1.3 18389 1om2A 95 1.71e+01 1om2A a.23.4.1 16520 5pal 109 1.76e+01 1a75A a.39.1.4 17215 1mkrA 294 1.77e+01 a.93.1.1 84997 1fr2B 134 1.78e+01 d.4.1.1 83257 2ng1 293 1.80e+01 1ng1 a.24.13.1 16962 c.37.1.10 32273 1cm7A 363 1.81e+01 1cnzA c.77.1.1 35063 1ccg 291 1.83e+01 1ryc a.93.1.1 18627 1j4nA 271 1.83e+01 f.19.1.1 71510 1ixh 321 1.83e+01 1ixh c.94.1.1 35761 1seiA 130 1.85e+01 1seiA d.140.1.1 41463 1iyjB 817 1.86e+01 a.170.1.1 76948 a.171.1.1 76949 b.40.4.3 76950 b.40.4.3 76951 b.40.4.3 76952 1v10A 521 1.86e+01 1qqfA 277 1.87e+01 1c3d a.102.4.4 18875 3icb 75 1.87e+01 4icb a.39.1.1 17147 2btvA 901 1.92e+01 2btvA e.28.1.1 43376 1sr7A 259 1.92e+01 1iq0A 592 1.92e+01 a.27.1.1 66257 c.26.1.1 66258 d.67.2.1 66259 1vaoA 560 2.03e+01 1qltA d.58.32.1 39461 d.145.1.1 41724 1ntvA 152 2.05e+01 b.55.1.2 86168 1itkA 731 2.07e+01 a.93.1.3 71417 a.93.1.3 71418 1nn6A 228 2.13e+01 b.47.1.2 85893 1pc6A 146 2.16e+01 1a28A 256 2.19e+01 1a28A a.123.1.1 19290 1ig5A 75 2.20e+01 4icb a.39.1.1 62363 1sqnA 261 2.21e+01 1i5nA 146 2.21e+01 1i5nA a.24.10.3 61805 1p57B 255 2.22e+01 1enfA 212 2.22e+01 3seb b.40.2.2 25198 d.15.6.1 37787 1wmuA 141 2.23e+01 1skz 119 2.24e+01 1skz g.3.15.1 44366 g.3.15.1 44367 1jdrA 294 2.27e+01 1ryc a.93.1.1 62908 1mijA 152 2.27e+01 a.4.1.1 79150 1f7cA 231 2.30e+01 1f7cA a.116.1.1 19107 1hx1B 114 2.31e+01 1hx1B a.7.7.1 61350 1a4pA 96 2.33e+01 1b4cA a.39.1.2 17176 1fs1B 141 2.34e+01 1vcbB a.157.1.1 19252 d.42.1.1 38664 1go3F 107 2.38e+01 a.60.8.2 65407 1tlqA 189 2.38e+01 1lshA 1056 2.39e+01 a.118.4.1 74242 f.7.1.1 74243 f.7.1.1 74244 1ht9A 76 2.41e+01 4icb a.39.1.1 61252 1b4aA 149 2.41e+01 1b4aA a.4.5.3 16088 d.74.2.1 39721 1wkqA 164 2.46e+01 1go4E 100 2.49e+01 h.1.22.1 70296 1hmcB 148 2.51e+01 1hmcB a.26.1.2 16868 1cipA 353 2.58e+01 1cipA a.66.1.1 18210 c.37.1.8 32093 1b31A 302 2.61e+01 1taxA c.1.8.3 28892 1bg4 302 2.61e+01 1taxA c.1.8.3 28806 1klo 162 2.61e+01 1klo g.3.11.2 44326 g.3.11.2 44327 g.3.11.2 44328 1f82A 424 2.67e+01 1f82A d.92.1.7 40307 1p2xA 159 2.70e+01 1uxtA 501 2.72e+01 1spgA 144 2.72e+01 1abwA a.1.1.2 15409 1wer 334 2.74e+01 1wer a.116.1.2 19108 1itwA 741 2.78e+01 c.77.1.2 76793 4ubpA 101 2.81e+01 1ubpA d.8.1.1 37352 1g5gB 481 2.84e+01 f.12.1.1 65157 h.3.2.1 65158 1htjF 210 2.92e+01 1htjF a.91.1.1 61254 1v3wA 173 2.94e+01 1tfe 145 2.94e+01 1tfe d.43.1.1 38680 1alq 266 2.96e+01 1btl e.3.1.1 42707 1rp3B 88 2.98e+01 2occE 109 2.98e+01 2occE a.118.11.1 19224 1ckiA 317 2.99e+01 1csn d.144.1.7 41660 1pvaA 110 2.99e+01 1a75A a.39.1.4 17207 1aisA 182 2.99e+01 1ytbA d.129.1.1 41288 d.129.1.1 41289 1g5yA 238 3.06e+01 1lbd a.123.1.1 60294 2abk 211 3.07e+01 2abk a.96.1.1 18743 1je8A 82 3.10e+01 a.4.6.2 77108 1gm7B 557 3.11e+01 1qq8A 214 3.11e+01 1qq8A 1be3A 446 3.11e+01 1be3A d.185.1.1 58950 d.185.1.1 58951 1ash 150 3.14e+01 1ash a.1.1.2 15622 1pioA 257 3.14e+01 1btl e.3.1.1 42719 1j0mA 752 3.14e+01 a.102.3.2 83910 b.24.1.1 83911 b.30.5.2 83912 1pnkB 557 3.15e+01 1ajqB 1lea 84 3.17e+01 1lea a.4.5.2 16085 1fuxA 166 3.17e+01 1fjjA b.17.1.2 60034 1p5sA 203 3.18e+01 1ebuA 358 3.18e+01 1ebuA c.2.1.3 30035 d.81.1.2 39950 1njrA 284 3.19e+01 1e79D 482 3.19e+01 1skyE a.69.1.1 18272 b.49.1.1 26437 c.37.1.11 32317 1yrnB 83 3.26e+01 1akhB a.4.1.1 15986 1t07A 94 3.30e+01 1vp4A 425 3.33e+01 1ax4A 467 3.35e+01 1ax4A c.67.1.2 34391 1s3jA 155 3.36e+01 1n2aA 201 3.37e+01 1mgtA 174 3.38e+01 1mgtA a.4.2.1 16078 c.55.7.1 33753 1h6pA 203 3.44e+01 a.146.1.1 60690 1ddf 127 3.45e+01 1ddf a.77.1.2 18423 1kxpD 458 3.49e+01 a.126.1.1 73160 a.126.1.1 73161 a.126.1.1 73162 3vtk 343 3.52e+01 1qhiA c.37.1.1 31884 3blm 257 3.53e+01 1btl e.3.1.1 42709 1v2yA 105 3.56e+01 1xszA 356 3.59e+01 1vg0A 650 3.59e+01 2mysB 166 3.60e+01 1wdcB a.39.1.5 17308 1ghpA 258 3.64e+01 1btl e.3.1.1 60520 1pieA 419 3.65e+01 1iznA 286 3.67e+01 e.43.1.1 83847 1w53A 84 3.70e+01 1bjz 207 3.76e+01 2tct a.4.1.9 16065 a.121.1.1 19242 1hmcA 148 3.80e+01 1hmcB a.26.1.2 16867 1t46A 313 3.82e+01 1ppjA 446 3.83e+01 2lhb 149 3.84e+01 2fal a.1.1.2 15597 1k7hA 476 3.86e+01 c.76.1.1 72101 1ubpA 101 3.86e+01 1ubpA d.8.1.1 37353 1izlC 473 3.88e+01 i.5.1.1 76996 1octC 156 3.92e+01 1au7A a.4.1.1 15991 a.35.1.1 17017