# List of top-scoring protein chains for t2k-100-30-str 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 1ggzA 148 1.66e-03 3cln 148 1.73e-03 1cll a.39.1.5 17286 1top 162 2.25e-03 1ncx a.39.1.5 17223 1ncx 162 2.40e-03 1ncx a.39.1.5 17222 1g4yR 148 4.40e-03 1cll a.39.1.5 60252 1t1dA 100 6.66e-03 1t1dA d.42.1.2 38637 1cll 148 6.85e-03 1cll a.39.1.5 17263 1jvmA 125 8.90e-03 f.2.1.11 67351 1k4cC 124 9.13e-03 f.2.1.11 68130 1j95A 125 9.91e-03 1bl8A f.2.1.11 62749 2mysB 166 1.37e-02 1wdcB a.39.1.5 17308 1bl8A 97 1.42e-02 1bl8A f.2.1.11 43652 1avsA 90 1.58e-02 1cll a.39.1.5 17226 1zac 90 2.97e-02 1ncx a.39.1.5 17236 1a68 95 3.13e-02 1t1dA d.42.1.2 38639 1jb0A 755 3.37e-02 1jb0A f.2.1.12 62820 1exrA 148 4.65e-02 1cll a.39.1.5 17299 1osa 148 5.79e-02 1cll a.39.1.5 17300 1dsxA 87 7.24e-02 1t1dA d.42.1.2 38644 1byyA 53 7.55e-02 j.12.1.1 46147 1iwgA 1053 9.03e-02 1lnh 857 1.13e-01 1yge a.119.1.1 19237 b.12.1.1 23637 1j7rA 86 1.26e-01 1j7rA a.39.1.5 62701 1ezvC 385 2.03e-01 1be3C f.2.1.8 59545 1ehkA 562 2.39e-01 1ehkA f.2.1.3 43624 1wdcC 156 2.66e-01 1wdcC a.39.1.5 17317 1wdcB 156 3.02e-01 1wdcB a.39.1.5 17302 1kyoC 385 3.35e-01 1be3C 379 3.55e-01 1be3C f.2.1.8 43665 1ho2A 20 4.07e-01 1qg9A 21 7.81e-01 j.35.1.1 46275 1dhx 967 8.27e-01 1dhx b.13.2.2 58971 b.13.2.2 58972 1ggwA 140 9.01e-01 1ggwA a.39.1.5 60490 1wgtA 186 1.17e+00 9wgaA g.3.1.1 44008 g.3.1.1 44009 g.3.1.1 44010 g.3.1.1 44011 9wgaA 171 1.35e+00 9wgaA g.3.1.1 44000 g.3.1.1 44001 g.3.1.1 44002 g.3.1.1 44003 1bf2 750 1.60e+00 1bf2 b.1.1.5 21860 b.71.1.1 27787 c.1.8.1 28774 1i50A 1733 1.84e+00 e.29.1.1 61754 1dceA 567 2.09e+00 1dceA a.118.6.1 19191 b.7.4.1 23218 c.10.2.2 30867 1aijL 281 2.16e+00 6prcL f.2.1.2 43461 1jbaA 204 2.22e+00 1rec a.39.1.5 17330 1dqeA 137 2.37e+00 1dqeA a.39.2.1 17388 1ezfA 340 2.66e+00 1ezfA a.128.1.2 19440 1gntA 553 2.72e+00 1e2uA 553 2.75e+00 1e1dA e.26.1.1 43362 1mmoD 512 3.21e+00 1mhyD a.25.1.2 16770 2pvbA 107 3.37e+00 1a75A a.39.1.4 17205 1e1dA 553 3.42e+00 1e1dA e.26.1.1 43363 1gupA 348 3.91e+00 1guqA d.13.1.2 37534 d.13.1.2 37535 1dugA 234 4.07e+00 1b8xA a.45.1.1 17718 c.47.1.5 33012 1mtyD 512 4.09e+00 1mhyD a.25.1.2 16742 1k94A 165 4.12e+00 a.39.1.7 68333 3kvt 115 4.22e+00 1t1dA d.42.1.2 38642 1guqA 348 4.42e+00 1guqA d.13.1.2 37522 d.13.1.2 37523 1gx5A 536 4.69e+00 1jk0A 419 4.69e+00 a.25.1.2 63142 1ctaA 36 4.77e+00 1ctdA a.39.1.5 17232 1pvaA 110 5.04e+00 1a75A a.39.1.4 17207 1pal 108 5.06e+00 1a75A a.39.1.4 17209 1f5aA 513 5.17e+00 1fa0B d.58.16.1 39337 e.9.1.2 43231 1f4qA 165 7.27e+00 1alvA a.39.1.7 17360 1gweA 503 7.61e+00 1g8iA 190 7.77e+00 1rec a.39.1.5 60363 4cpv 109 7.98e+00 1a75A a.39.1.4 17198 1phnA 162 8.15e+00 1cpcA a.1.1.3 15641 1quvA 578 8.37e+00 1quvA e.8.1.4 43119 1hev 43 8.40e+00 1hev g.3.1.1 44060 1c2pA 576 8.45e+00 1quvA e.8.1.4 43117 2scpA 174 8.50e+00 2scpA a.39.1.5 17256 1rec 201 8.76e+00 1rec a.39.1.5 17326 1kfuS 184 9.24e+00 a.39.1.7 68574 1qazA 351 9.29e+00 1qazA a.102.3.1 18848 2lbp 346 9.59e+00 2liv c.93.1.1 35709 1alvA 173 1.03e+01 1alvA a.39.1.7 17370 1hxpA 348 1.05e+01 1guqA d.13.1.2 37530 d.13.1.2 37531 1cdp 109 1.06e+01 1a75A a.39.1.4 17197 1drs 59 1.12e+01 3ebx g.7.1.2 44457 1cb0A 283 1.12e+01 1cb0A c.56.2.1 33790 1kq4A 232 1.13e+01 d.207.1.1 68791 6gsvA 217 1.13e+01 1b8xA a.45.1.1 17633 c.47.1.5 32925 1ctdA 36 1.14e+01 1ctdA a.39.1.5 17230 3erk 364 1.14e+01 1hcl d.144.1.1 41654 1bi0 226 1.17e+01 1bi0 a.4.5.24 16202 a.76.1.1 18408 b.34.1.2 24453 5pal 109 1.21e+01 1a75A a.39.1.4 17215 1dt6A 473 1.25e+01 1dt6A a.104.1.1 18977 1hbzA 498 1.26e+01 1cf9A e.5.1.1 60937 2frvB 536 1.28e+01 1h2rL e.18.1.1 43291 1j7dA 145 1.29e+01 1jatB d.20.1.1 62680 1b6a 478 1.37e+01 1bn5 a.4.5.25 16223 d.127.1.1 41160 1m48A 133 1.45e+01 1auiB 169 1.48e+01 1auiB a.39.1.5 17325 1e6fA 143 1.49e+01 1e6fA b.64.1.1 59304 1phnB 172 1.49e+01 1qgwC a.1.1.3 15642 1dlc 584 1.50e+01 1ciy b.18.1.3 23719 b.77.2.1 27976 f.1.3.1 43391 1dxrM 323 1.51e+01 6prcM f.2.1.2 43432 1dcnD 436 1.52e+01 1auwA a.127.1.1 19423 6prcM 323 1.53e+01 6prcM f.2.1.2 43435 1mmc 30 1.57e+01 g.3.1.2 44061 2liv 344 1.60e+01 2liv c.93.1.1 35708 1dttA 560 1.63e+01 1rthA c.55.3.1 33611 e.8.1.2 43088 1irxA 523 1.65e+01 1k75A 434 1.69e+01 c.82.1.2 68253 1gp0A 143 1.74e+01 1jwhA 337 1.82e+01 1dceB 331 1.83e+01 1dceB a.102.4.3 18872 1bn5 478 1.83e+01 1bn5 a.4.5.25 16224 d.127.1.1 41161 1jpaA 312 1.85e+01 d.144.1.2 67011 1kaeA 434 1.87e+01 1fa0B 537 1.93e+01 1fa0B d.58.16.1 39336 e.9.1.2 43230 1e19A 314 1.96e+01 1b7bA c.73.1.1 34967 1hcuA 503 2.07e+01 a.102.2.1 65796 2lbd 267 2.11e+01 2lbd a.123.1.1 19287 1f6fA 199 2.15e+01 1f6fA a.26.1.1 16839 1mh1 186 2.18e+01 1eesA c.37.1.8 32002 1csjA 531 2.18e+01 1quvA e.8.1.4 43120 1g33A 73 2.19e+01 a.39.1.4 65121 1h2rL 534 2.28e+01 1h2rL e.18.1.1 43298 2dtr 226 2.32e+01 1bi0 a.4.5.24 16193 a.76.1.1 18399 b.34.1.2 24450 1qlaA 656 2.32e+01 1qlaA a.7.3.1 16328 c.3.1.4 30427 d.168.1.1 42310 4lbd 267 2.33e+01 2lbd a.123.1.1 19289 1allA 160 2.45e+01 1qgwC a.1.1.3 15647 1dmuA 299 2.50e+01 1dmuA c.52.1.4 33294 1c3cA 429 2.53e+01 1c3cA a.127.1.1 19425 1ponA 36 2.62e+01 1ponA a.39.1.5 17239 1f5sA 211 2.65e+01 1f5sA c.108.1.4 59656 1j97A 211 2.66e+01 1f5sA c.108.1.4 62753 1egdA 396 2.72e+01 3mdeA a.29.3.1 16596 e.6.1.1 42857 1fa0A 537 2.74e+01 1fa0B d.58.16.1 39335 e.9.1.2 43229 1pme 380 2.77e+01 1hcl d.144.1.1 41653 1fqyA 269 2.88e+01 1fqyA f.2.1.5 43649 1txb 73 2.91e+01 1txb g.7.1.1 44455 1l7mA 211 2.94e+01 1ezvE 185 3.08e+01 1rie b.33.1.1 59548 f.2.1.8 59549 1a4iA 301 3.20e+01 1a4iA c.2.1.7 30278 c.58.1.2 33926 1dx5I 118 3.30e+01 1dx5I g.3.11.1 44302 g.3.11.1 44303 g.3.11.1 44304 2btvA 901 3.33e+01 2btvA e.28.1.1 43376 1diaA 306 3.34e+01 1a4iA c.2.1.7 30280 c.58.1.2 33928 1c3wA 222 3.45e+01 1c3wA f.2.1.1 43405 1h2aL 567 3.48e+01 1h2rL e.18.1.1 43299 1iqbB 89 3.55e+01 g.3.1.1 66264 g.3.1.1 66265 1g5hA 454 3.55e+01 1g5hA c.51.1.1 60270 d.104.1.1 60271 1htxA 32 3.58e+01 1qfdA g.3.2.1 61261 1en2A 89 3.63e+01 1hev g.3.1.1 44048 g.3.1.1 44049 6prcL 273 3.70e+01 6prcL f.2.1.2 43434 1apxA 249 3.75e+01 1ryc a.93.1.1 18669 1jf0A 195 3.82e+01 1ej3A a.39.1.5 62926 1fokA 568 3.83e+01 2fokA a.4.5.12 16137 a.4.5.12 16138 a.4.5.12 16139 c.52.1.12 33325 1g6q2 328 3.85e+01 1g6q2 1btkB 169 3.89e+01 1btkA b.55.1.1 26960 1csh 435 3.92e+01 1csh a.103.1.1 18880