# List of top-scoring protein chains for t2k-100-30-stride-ebghtl 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 1pa4A 116 6.13e-02 d.52.7.1 -9780 2hqi 72 5.95e-01 1aw0 d.58.17.1 39340 1h8mA 140 6.36e-01 1h8mA d.110.4.1 60782 1osdA 72 9.61e-01 1afi 72 1.45e+00 1aw0 d.58.17.1 39339 1iupA 282 1.53e+00 c.69.1.10 76815 1s9rA 410 1.65e+00 unknown_sccs -10989 1lxyA 409 1.65e+00 unknown_sccs -10987 1cnuA 137 1.71e+00 1cof d.109.1.2 40862 1ge9A 184 2.09e+00 1dd5A d.67.3.1 60463 1rro 108 2.75e+00 1a75A a.39.1.4 17195 1cfyA 143 2.91e+00 1cof d.109.1.2 40858 1cof 143 2.98e+00 1cof d.109.1.2 40860 1a7tA 232 3.14e+00 1a7tA d.157.1.1 42041 1yprA 125 3.86e+00 3nul d.110.1.1 40888 1howA 373 4.15e+00 1hcl d.144.1.7 41679 1r26A 125 4.28e+00 c.47.1.1 -7389 1kid 203 4.29e+00 1derA c.8.5.1 30771 1josA 128 4.51e+00 d.52.7.1 84191 1lu4A 136 5.00e+00 c.47.1.10 -7509 1v58A 241 5.03e+00 7timA 247 6.63e+00 1amk c.1.1.1 28457 1b31A 302 6.76e+00 1taxA c.1.8.3 28892 1bg4 302 6.79e+00 1taxA c.1.8.3 28806 1qc9A 276 7.06e+00 1ckqA c.52.1.1 33235 1o6jA 150 7.17e+00 c.47.1.10 81089 1i5gA 144 7.19e+00 1ewxA c.47.1.10 61784 1sxjE 354 7.41e+00 1i1qB 192 8.97e+00 1qdlB c.23.16.1 61544 1qlaB 239 9.22e+00 1qlaB a.1.2.1 15679 d.15.4.2 37707 1qj2B 809 9.32e+00 1qj2B 1lxiA 139 9.51e+00 g.17.1.2 84735 1m4uL 139 9.79e+00 g.17.1.2 78626 1oj4A 283 1.04e+01 d.14.1.5 -9088 d.58.26.5 -10133 1uc2A 481 1.04e+01 unknown_sccs -11725 1gr5A 547 1.06e+01 i.16.1.1 65478 1o0pA 104 1.09e+01 d.58.7.1 86535 1hd2A 161 1.16e+01 c.47.1.10 60962 1eriA 276 1.18e+01 1ckqA c.52.1.1 33231 1cpzA 68 1.22e+01 1aw0 d.58.17.1 39351 1cl8A 276 1.23e+01 1ckqA c.52.1.1 33230 1ckqA 276 1.23e+01 1ckqA c.52.1.1 33229 1egr 85 1.25e+01 1kte c.47.1.1 32765 1bed 181 1.25e+01 1fvkA unknown_sccs -7444 1v7oA 165 1.37e+01 unknown_sccs -10249 1f7sA 139 1.41e+01 1cof d.109.1.2 40857 1bob 320 1.49e+01 1bob d.108.1.1 40816 1k9tA 540 1.51e+01 b.1.18.2 77298 c.1.8.5 77299 d.26.3.1 77300 1edqA 540 1.52e+01 1ctn b.1.18.2 21873 c.1.8.5 29002 d.26.3.1 38436 1f46A 140 1.53e+01 1f46A d.129.4.1 59643 1p9qC 256 1.53e+01 1v0wA 506 1.57e+01 1ctn 540 1.60e+01 1ctn b.1.18.2 21876 c.1.8.5 29005 d.26.3.1 38439 1cec 343 1.60e+01 1ceo c.1.8.3 28809 1h2vZ 156 1.63e+01 d.58.7.1 76595 1ceo 343 1.63e+01 1ceo c.1.8.3 28808 1tib 269 1.66e+01 3tgl c.69.1.17 34738 1ek8A 185 1.69e+01 1ek8A d.67.3.1 59444 1qpsA 261 1.71e+01 1ckqA c.52.1.1 33234 1o8xA 146 1.75e+01 c.47.1.10 86681 1l3iA 192 1.76e+01 c.66.1.22 77676 1um0A 365 1.83e+01 1gt6A 269 1.86e+01 c.69.1.17 76342 1k38A 254 1.87e+01 e.3.1.1 84303 1n62B 809 1.90e+01 d.41.1.1 80092 d.133.1.1 80093 1v6fA 151 1.90e+01 1fiqC 763 1.91e+01 1fiqC d.41.1.1 38588 d.133.1.1 41418 1lyxA 248 1.97e+01 c.1.1.1 78304 1r3eA 309 2.02e+01 b.122.1.1 -5118 unknown_sccs -10146 1t95A 240 2.13e+01 1f47B 144 2.16e+01 1f46A d.129.4.1 59645 1o5xA 248 2.18e+01 c.1.1.1 -5157 1derA 547 2.24e+01 1derA 1i45A 248 2.38e+01 1amk c.1.1.1 61665 1q8yA 373 2.42e+01 d.144.1.7 -11319 1is1A 185 2.48e+01 d.67.3.1 83704 1qk8A 146 2.48e+01 1ewxA c.47.1.10 33061 1ifqA 138 2.54e+01 1ifqA d.110.4.1 62350 1ewxA 146 2.58e+01 1ewxA c.47.1.10 33062 1ef8A 261 2.62e+01 1ef8A c.14.1.3 30921 1eejA 216 2.68e+01 1eejA c.47.1.9 33057 d.17.3.1 38071 1b9lA 120 2.71e+01 1b9lA d.96.1.3 40665 1qfnA 85 2.72e+01 1qfnA c.47.1.1 32768 1sr9A 644 2.73e+01 1j3kA 280 2.75e+01 c.71.1.1 84070 1b8aA 438 2.75e+01 1b8aA b.40.4.1 25244 d.104.1.1 40765 1rpuA 172 2.83e+01 unknown_sccs -10738 1a3aC 148 2.87e+01 1a3aA d.112.1.1 40919 1gokA 303 2.91e+01 c.1.8.3 65420 1fxmA 302 2.91e+01 1taxA 1k6aA 303 2.92e+01 c.1.8.3 72081 1mo9A 523 2.95e+01 c.3.1.5 79341 c.3.1.5 79342 d.87.1.1 79343 1qupA 222 2.99e+01 1qupA b.1.8.1 22301 d.58.17.1 39352 1b7yA 350 3.01e+01 1pysA d.104.1.1 40776 1qysA 106 3.01e+01 unknown_sccs -13432 1cawB 184 3.02e+01 1caxB b.82.1.2 28113 1fp3A 402 3.09e+01 1fp3A a.102.1.3 18842 1lw6E 281 3.10e+01 c.41.1.1 74293 1sup 275 3.10e+01 1gci c.41.1.1 32510 2scuB 388 3.11e+01 2scuB c.23.4.1 31141 d.142.1.4 41562 1sdoA 203 3.21e+01 unknown_sccs -7558 1hw8A 467 3.32e+01 1dqaA d.58.20.1 61298 d.179.1.1 61299 1thx 115 3.33e+01 1thx c.47.1.1 32732 1k3sA 113 3.37e+01 d.198.1.1 68120 1fjgQ 105 3.37e+01 1fjfQ b.40.4.5 25352 1dqaA 467 3.37e+01 1dqaA d.58.20.1 39364 d.179.1.1 42585 1f7wA 144 3.44e+01 1f46A d.129.4.1 59679 1dqaC 467 3.50e+01 1dqaA d.58.20.1 39366 d.179.1.1 42587 1n62C 288 3.51e+01 d.87.2.1 80094 d.145.1.3 80095 1fvgA 199 3.51e+01 1fvaA d.58.28.1 39408 1nrzA 164 3.52e+01 c.38.1.1 86131 3rubS 123 3.57e+01 1rboC d.73.1.1 39616 1qjcA 158 3.73e+01 1b6tA c.26.1.3 63328 1ek9A 428 3.73e+01 1ek9A f.5.1.1 43809 1dozA 309 3.82e+01 1ak1 c.92.1.1 35592 1i1wA 303 3.85e+01 c.1.8.3 76732 1b6tA 159 3.86e+01 1b6tA c.26.1.3 31600 1fvaA 217 3.89e+01 1fvaA d.58.28.1 39409 1fo5A 85 3.89e+01 1fo5A c.47.1.1 59922 1mg7A 417 3.94e+01 d.14.1.6 84954 d.58.26.6 84955