# 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.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 1wc1A 226 5.48e-02 d.58.29.1 114492 2fyxA 143 6.16e-02 d.58.57.1 134411 1wc3A 219 9.72e-02 d.58.29.1 114495 1d2mA 665 3.92e-01 1d2mA c.37.1.19 32417 c.37.1.19 32418 1k3xA 262 6.67e-01 a.156.1.2 77242 b.113.1.1 77243 g.39.1.8 77244 1s4kA 120 7.34e-01 a.35.1.6 105254 1c4oA 664 7.74e-01 1d2mA c.37.1.19 32415 c.37.1.19 32416 1x1fA 149 1.13e+00 b.55.1.1 121579 2cwpA 112 1.58e+00 2daqA 110 2.53e+00 b.34.9.2 131354 1j3mA 129 2.71e+00 d.129.7.1 103836 2hhiA 204 3.00e+00 2o35A 105 3.16e+00 1ag4 103 3.65e+00 1ag4 1qydA 313 3.85e+00 c.2.1.2 96583 1ztsA 139 4.95e+00 1m3kA 392 5.03e+00 c.95.1.1 78565 c.95.1.1 78566 5cytR 104 5.19e+00 1ycc a.3.1.1 15878 1u53A 196 5.47e+00 1l2iA 261 5.64e+00 a.123.1.1 73503 3erdA 261 6.12e+00 3erdA a.123.1.1 19293 1va6A 518 6.51e+00 d.128.1.4 113598 1m4tA 392 6.52e+00 c.95.1.1 78617 c.95.1.1 78618 1xo0A 324 6.64e+00 a.60.9.1 115674 d.163.1.1 115675 4crxA 322 6.79e+00 4crxA a.60.9.1 18095 d.163.1.1 42155 1v2xA 194 7.07e+00 c.116.1.1 100274 1bgpA 309 7.12e+00 a.93.1.1 18690 1qflA 389 7.49e+00 1afwA c.95.1.1 35908 c.95.1.1 35909 1ndbA 596 7.83e+00 c.43.1.3 80411 c.43.1.3 80412 2aiuA 105 9.11e+00 2qptA 550 9.35e+00 1vjyA 303 9.64e+00 d.144.1.7 108633 3cc1A 433 9.66e+00 1kbuA 349 9.99e+00 a.60.9.1 72284 d.163.1.1 72285 1crxA 322 1.02e+01 4crxA a.60.9.1 18097 d.163.1.1 42157 1py5A 326 1.06e+01 d.144.1.7 104389 1ic8A 194 1.07e+01 a.4.1.1 76740 a.35.1.1 76741 1b6cB 342 1.11e+01 1b6cB d.144.1.7 41673 1odmA 331 1.13e+01 b.82.2.1 86875 1rkqA 282 1.21e+01 c.108.1.10 97621 1f44A 324 1.21e+01 a.60.9.1 64982 d.163.1.1 64983 1xqwA 293 1.22e+01 1yqzA 438 1.23e+01 2ciuA 127 1.24e+01 1mtzA 293 1.25e+01 c.69.1.7 79467 1xxpA 306 1.29e+01 c.45.1.2 122423 2c0dA 221 1.30e+01 1ozhA 566 1.32e+01 c.31.1.3 93833 c.36.1.5 93834 c.36.1.9 93835 1khtA 192 1.36e+01 c.37.1.1 84401 2pfzA 301 1.37e+01 2i5nC 336 1.39e+01 a.138.1.2 137063 1dxrC 336 1.39e+01 6prcC a.138.1.2 19670 1sxjC 340 1.43e+01 a.80.1.1 106085 c.37.1.20 106086 2hm7A 310 1.43e+01 2i5hA 205 1.44e+01 1akhA 61 1.46e+01 1akhA a.4.1.1 15980 3cjeA 167 1.48e+01 1clqA 903 1.49e+01 1clqA c.55.3.5 33717 e.8.1.1 43006 1xn8A 131 1.53e+01 a.229.1.1 115577 1vajA 214 1.56e+01 d.309.1.1 119907 2gasA 307 1.65e+01 2gdtA 116 1.73e+01 3crxA 343 1.74e+01 4crxA a.60.9.1 18101 d.163.1.1 42161 1a52A 258 1.74e+01 3erdA a.123.1.1 19296 1u4nA 310 1.78e+01 c.69.1.2 113021 1lyvA 306 1.80e+01 c.45.1.2 74348 2pgzA 230 1.82e+01 2yxlA 450 1.86e+01 2e74G 37 1.86e+01 f.23.26.1 132052 2nudC 35 1.86e+01 1ytw 306 1.99e+01 1ytw 1kjsA 74 2.05e+01 a.50.1.1 17792 1bqg 451 2.23e+01 1bqg 1tlqA 189 2.29e+01 a.195.1.1 107134 1yqfA 203 2.32e+01 d.25.1.1 123880 2rdyA 803 2.40e+01 3cjhB 64 2.42e+01 2oikA 154 2.46e+01 1yptA 305 2.57e+01 1ytw c.45.1.2 32686 1zjrA 211 2.70e+01 2dznB 82 2.71e+01 2fltA 149 2.78e+01 1apxA 249 2.78e+01 1ryc a.93.1.1 18669 1ih7A 903 2.83e+01 1clqA c.55.3.5 62375 e.8.1.1 62376 2z98A 200 2.85e+01 1bqnA 558 2.87e+01 1rthA c.55.3.1 33599 e.8.1.2 43064 2pqqA 149 2.89e+01 1squA 155 2.93e+01 d.252.1.1 98971 3b7kA 333 2.96e+01 2b4zA 104 2.98e+01 1vp7A 100 3.11e+01 a.7.13.1 113941 2czlA 272 3.12e+01 c.94.1.1 131055 1ghhA 81 3.13e+01 1ghhA d.57.1.1 38940 2nsfA 261 3.13e+01 1t5bA 201 3.24e+01 c.23.5.3 106433 3c2cA 112 3.24e+01 a.3.1.1 15885 1duvG 333 3.24e+01 1othA c.78.1.1 35228 c.78.1.1 35229 1lriA 98 3.25e+01 a.134.1.1 74223 1waaA 93 3.26e+01 1bxm 99 3.26e+01 1bxm 1nnvA 110 3.29e+01 d.17.7.1 92012 1qnxA 209 3.32e+01 1qnxA d.111.1.1 40914 1tikA 213 3.43e+01 c.23.5.3 107003 1ghpA 258 3.45e+01 1btl e.3.1.1 60520 2odaA 196 3.46e+01 2a6sA 84 3.49e+01 d.298.1.1 126305 2bypA 214 3.59e+01 1zu0A 529 3.65e+01 1v54C 261 3.66e+01 f.25.1.1 100324 1ea0A 1479 3.68e+01 b.80.4.1 64854 c.1.4.1 64855 d.153.1.1 64856 1f75A 249 3.71e+01 1f75A c.101.1.1 59662 1ys1X 320 3.77e+01 1fit 147 3.82e+01 1fit 1fitA 147 3.82e+01 d.13.1.1 37499 2hfnA 153 3.82e+01 2dt9A 167 3.88e+01 2afwA 329 3.91e+01 c.56.5.8 126707 1ocrC 261 3.96e+01 1ocrC f.25.1.1 43540