# List of top-scoring protein chains for t2k-100-30-alpha 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 1gqpA 221 2.80e-05 b.18.1.9 70372 1euu 605 1.17e-03 1eut b.1.18.2 21892 b.18.1.1 23713 b.68.1.1 27610 1eut 605 1.28e-03 1eut b.1.18.2 21891 b.18.1.1 23712 b.68.1.1 27609 1jhjA 171 3.87e-03 b.18.1.9 66714 1hg8A 349 6.53e-02 b.80.1.3 65830 1k3iA 656 1.43e-01 b.1.18.2 68113 b.18.1.1 68114 b.69.1.1 68115 1dr9A 201 1.87e-01 1dr9A b.1.1.1 19762 b.1.1.3 21684 1goh 639 2.38e-01 1gof b.1.18.2 21809 b.18.1.1 23711 b.69.1.1 27633 1gof 639 5.19e-01 1gof b.1.18.2 21807 b.18.1.1 23709 b.69.1.1 27631 1fx3A 169 1.14e+00 1fx3B d.33.1.1 38524 1qoiA 177 1.17e+00 2cpl b.62.1.1 27490 1fx3B 169 1.21e+00 1fx3B d.33.1.1 38525 1ewsA 32 1.72e+00 1ewsA g.9.1.1 59534 1et7A 341 2.03e+00 1nif b.6.1.3 23070 b.6.1.3 23071 1nhcA 336 2.07e+00 1r0pA 312 2.23e+00 1fiqC 763 2.24e+00 1fiqC d.41.1.1 38588 d.133.1.1 41418 1fo4A 1332 3.37e+00 a.56.1.1 17910 d.15.4.2 37695 d.41.1.1 38586 d.87.2.1 40227 d.133.1.1 41416 d.145.1.3 41758 1j9qA 341 3.56e+00 1nif b.6.1.3 62765 b.6.1.3 62766 1tvdA 116 3.90e+00 1tvdA b.1.1.1 20650 1as8A 343 3.93e+00 1nif b.6.1.3 23074 b.6.1.3 23075 1kgcE 242 4.03e+00 b.1.1.1 77386 b.1.1.2 77387 1gci 269 4.31e+00 1gci c.41.1.1 32503 1bvyF 191 4.61e+00 1bvyF c.23.5.1 31207 1uj0A 62 5.01e+00 1nif 340 5.27e+00 1nif b.6.1.3 23048 b.6.1.3 23049 1seiA 130 5.48e+00 1seiA d.140.1.1 41463 1oe1A 336 5.76e+00 b.6.1.3 86891 b.6.1.3 86892 1larA 575 6.30e+00 1larA c.45.1.2 32693 c.45.1.2 32694 6prcH 258 6.99e+00 6prcH b.41.1.1 25457 f.23.10.1 43436 1iznA 286 7.12e+00 e.43.1.1 83847 1kexA 155 7.13e+00 b.18.1.2 77350 1dxrH 258 7.27e+00 6prcH b.41.1.1 25456 f.23.10.1 43433 1kbvA 327 7.56e+00 b.6.1.3 68395 b.6.1.3 68396 1de3A 150 8.26e+00 1aqzA d.1.1.3 36240 1qh7A 207 9.29e+00 1axkA b.29.1.11 24317 1gmmA 133 9.77e+00 b.18.1.10 65314 1ah2 269 9.83e+00 1gci c.41.1.1 32542 1r4yA 136 9.83e+00 1ollA 188 1.01e+01 1gcqA 61 1.02e+01 1ckaA b.34.2.1 60434 1q8bA 105 1.07e+01 1d7pM 159 1.07e+01 1cztA b.18.1.2 23718 1rwzA 245 1.10e+01 1mgrA 99 1.12e+01 d.1.1.2 79106 1ha1 184 1.15e+01 1ha1 d.58.7.1 39147 d.58.7.1 39148 1gfc 59 1.15e+01 1griA b.34.2.1 24537 1mzgA 146 1.17e+01 d.224.1.1 79696 1ee6A 197 1.18e+01 1ee6A b.80.1.1 28024 1kit 757 1.19e+01 1kit b.29.1.8 24272 b.29.1.8 24273 b.68.1.1 27616 1cq3A 233 1.21e+01 1cq3A b.27.1.1 23923 1vjhA 122 1.24e+01 1gw0A 559 1.29e+01 b.6.1.3 70623 b.6.1.3 70624 b.6.1.3 70625 1f3aA 222 1.36e+01 1pgtA a.45.1.1 17701 c.47.1.5 32995 1k0sA 151 1.57e+01 b.40.7.1 67969 1h4gA 207 1.60e+01 b.29.1.11 70863 1h9jA 145 1.62e+01 1h9jA b.40.6.2 60829 b.40.6.2 60830 1dctA 324 1.73e+01 6mhtA c.66.1.26 34244 1d0yA 761 1.78e+01 1lvk b.34.3.1 24581 c.37.1.9 32178 1hlcA 129 1.85e+01 1c1lA b.29.1.3 24208 1rhfA 182 1.94e+01 1kjqA 391 1.95e+01 b.84.2.1 72616 c.30.1.1 72617 d.142.1.2 72618 1uxxX 133 1.99e+01 1l3kA 196 2.06e+01 d.58.7.1 73539 d.58.7.1 73540 1j3bA 529 2.11e+01 c.91.1.1 77071 c.109.1.1 77072 1kcbA 340 2.13e+01 1bxtA 234 2.13e+01 3seb b.40.2.2 25210 d.15.6.1 37799 1ojxA 263 2.15e+01 1pdkB 157 2.15e+01 1pdkB b.2.3.2 22427 1v3eA 431 2.16e+01 1hv2A 99 2.23e+01 d.42.1.1 61287 1np4A 184 2.25e+01 1np1A b.60.1.1 27166 1eagA 342 2.32e+01 1eagA b.50.1.2 26826 1a0i 348 2.39e+01 1a0i b.40.4.6 25363 d.142.2.1 41577 1srqA 341 2.41e+01 1vom 762 2.43e+01 1lvk b.34.3.1 24577 c.37.1.9 32174 1dq3A 454 2.44e+01 1dq3A b.86.1.2 28380 d.50.3.1 38798 d.95.2.2 40585 d.95.2.2 40586 1erxA 184 2.44e+01 1np1A b.60.1.1 27164 1kawA 135 2.47e+01 3ullA b.40.4.3 25288 1c8zA 265 2.48e+01 1c8zA d.23.1.1 38375 1omiA 248 2.50e+01 a.4.5.4 87079 b.82.3.3 87080 1gskA 513 2.52e+01 b.6.1.3 83314 b.6.1.3 83315 b.6.1.3 83316 1sy3A 184 2.53e+01 1lvk 762 2.54e+01 1lvk b.34.3.1 24576 c.37.1.9 32173 1cb0A 283 2.67e+01 1cb0A c.56.2.1 33790 1p9oA 313 2.68e+01 1hnf 182 2.70e+01 1qa9A b.1.1.1 19741 b.1.1.3 21680 1l2lA 457 2.71e+01 c.72.1.3 77656 1ez1A 392 2.74e+01 1ez1A b.84.2.1 28248 c.30.1.1 31655 d.142.1.2 41500 1b5fA 239 2.76e+01 1smrA b.50.1.2 26836 1eeoA 321 2.77e+01 1pty c.45.1.2 32655 1eyzA 392 2.77e+01 1ez1A b.84.2.1 28246 c.30.1.1 31653 d.142.1.2 41498 1np1A 184 2.79e+01 1np1A b.60.1.1 27155 1r1dA 247 2.83e+01 1sq9A 397 2.87e+01 1skoA 143 2.89e+01 1xnaA 183 2.91e+01 1xnaA b.18.1.8 23773 1kkeA 210 3.04e+01 b.21.1.2 68669 b.83.1.2 68670 2pleA 105 3.05e+01 1qadA d.93.1.1 40522 3daaA 277 3.12e+01 1daaA e.17.1.1 43272 1bhgA 613 3.16e+01 1bhgA b.1.4.1 22161 b.18.1.5 23766 c.1.8.3 28889 1eal 127 3.18e+01 1hmt b.60.1.2 27227 3psg 370 3.26e+01 1smrA b.50.1.2 26841 1jroB 777 3.27e+01 d.41.1.1 67141 d.133.1.1 67142 1koiA 184 3.38e+01 b.60.1.1 68725 1khiA 176 3.41e+01 b.34.5.2 77408 b.40.4.5 77409 1dnlA 199 3.46e+01 1ci0A b.45.1.1 25753 2dynA 122 3.46e+01 1dynA b.55.1.1 26957 1fs0E 138 3.49e+01 1aqt a.2.10.1 59997 b.93.1.1 59998 1qa9A 102 3.49e+01 1qa9A b.1.1.1 19742 1pty 321 3.50e+01 1pty c.45.1.2 32656 2dabA 282 3.51e+01 1daaA e.17.1.1 43274 1mwrA 646 3.55e+01 d.17.4.5 79586 d.175.1.1 79587 e.3.1.1 79588 1hfuA 503 3.56e+01 b.6.1.3 65827 b.6.1.3 65828 b.6.1.3 65829 1g7fA 298 3.59e+01 1pty c.45.1.2 60330 1rpmA 278 3.64e+01 2shpA c.45.1.2 32679 1od3A 168 3.65e+01 b.18.1.10 86825 3mhtA 327 3.66e+01 6mhtA c.66.1.26 34234 1egdA 396 3.70e+01 3mdeA a.29.3.1 16596 e.6.1.1 42857 1gkuB 1054 3.72e+01 c.37.1.16 65257 c.37.1.16 65258 e.10.1.1 65259 1v7oA 165 3.74e+01 1ii2A 524 3.79e+01 c.91.1.1 66146 c.109.1.1 66147 1kb5B 117 3.82e+01 1kb5B b.1.1.1 20632 1rhoC 145 3.86e+01 1rhoA b.1.18.8 21901 1q4uA 151 3.87e+01 2pldA 105 3.93e+01 1qadA d.93.1.1 40521