# 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 1prxA 224 1.57e-03 1prxA c.47.1.10 33076 1prxB 224 1.62e-03 1prxA c.47.1.10 33077 1qmvA 197 2.03e-01 1qq2A c.47.1.10 33066 1g5pA 289 4.32e-01 1cp2A c.37.1.10 32253 1fp6A 289 4.58e-01 1cp2A c.37.1.10 32243 1nipA 289 7.51e-01 1cp2A c.37.1.10 32263 1gky 187 1.10e+00 1gky c.37.1.1 31839 1ex7A 186 1.18e+00 1gky c.37.1.1 59537 1o13A 136 1.72e+00 c.55.5.1 80762 1bob 320 1.72e+00 1bob d.108.1.1 40816 1itpA 77 1.87e+00 d.58.3.2 66371 1izmA 184 1.95e+00 unknown_sccs -1233 1qm9A 198 3.24e+00 1qm9A d.58.7.1 39207 d.58.7.1 39208 1okrA 123 3.28e+00 unknown_sccs -235 1ls6A 295 3.63e+00 c.37.1.5 -7026 1b5tA 275 4.02e+00 1b5tA c.1.23.1 29676 1aquA 297 4.41e+00 1aquA c.37.1.5 31942 1rh5B 74 4.50e+00 unknown_sccs -12198 1n81A 186 4.99e+00 a.185.1.1 85388 1lliA 92 5.40e+00 1lmb3 a.35.1.2 17025 1nv8A 284 6.30e+00 c.66.1.30 86224 1gpuA 680 6.58e+00 c.36.1.6 65455 c.36.1.10 65454 c.48.1.1 65456 1sbp 310 6.81e+00 1sbp c.94.1.1 35760 1b9oA 123 7.05e+00 3lzt d.2.1.2 36597 1gks 78 7.08e+00 1cc5 a.3.1.1 15909 1faoA 126 7.42e+00 1faoA b.55.1.1 26974 1htqA 477 7.43e+00 d.15.9.1 71035 d.128.1.1 71036 1hfx 123 7.49e+00 3lzt d.2.1.2 36600 1f60B 94 7.51e+00 1b64 d.58.12.1 39307 1n8jA 186 7.68e+00 c.47.1.10 85401 1csjA 531 8.26e+00 1quvA e.8.1.4 43120 1cor 82 8.39e+00 451c a.3.1.1 15903 1fjgM 126 9.23e+00 1fjfM a.156.1.1 16293 1hml 142 9.28e+00 3lzt d.2.1.2 36598 1quvA 578 9.47e+00 1quvA e.8.1.4 43119 1m6sA 347 9.78e+00 c.67.1.1 78701 1eqfA 280 9.82e+00 1eqfA a.29.2.1 16972 a.29.2.1 16973 1ne2A 200 9.87e+00 c.66.1.32 85586 1hy3A 294 9.89e+00 c.37.1.5 71090 1g3mA 294 1.00e+01 c.37.1.5 83268 1gzqA 300 1.05e+01 b.1.1.2 70818 d.19.1.1 70819 1jg8A 347 1.07e+01 1jg8A c.67.1.1 62946 1eiyB 785 1.09e+01 1pysB a.6.1.1 16305 a.6.1.1 16306 b.40.4.4 25314 d.58.13.1 39313 d.104.1.1 40782 d.138.1.1 41458 1g7cB 94 1.15e+01 1b64 d.58.12.1 39308 1gx5A 536 1.19e+01 e.8.1.4 70682 1htoA 477 1.22e+01 d.15.9.1 70987 d.128.1.1 70988 1ig5A 75 1.23e+01 4icb a.39.1.1 62363 1trkA 680 1.27e+01 1trkA c.36.1.6 31804 c.36.1.10 31803 c.48.1.1 33090 1cch 82 1.27e+01 451c a.3.1.1 15902 1e5uI 187 1.30e+01 1f00I b.1.14.1 22372 d.169.1.3 42441 1k8kA 418 1.31e+01 c.55.1.1 68305 c.55.1.1 68306 1tkaA 678 1.33e+01 1trkA c.36.1.6 31816 c.36.1.10 31815 c.48.1.1 33096 1h1nA 305 1.35e+01 c.1.8.3 70855 1irp 153 1.37e+01 1irp b.42.1.2 25559 1e08A 371 1.39e+01 i.4.1.1 45914 1pwmA 316 1.44e+01 c.1.7.1 -5232 1el3A 316 1.50e+01 1frb c.1.7.1 28672 1sspE 223 1.50e+01 3eugA c.18.1.1 31009 1bed 181 1.51e+01 1fvkA unknown_sccs -7444 3icb 75 1.52e+01 4icb a.39.1.1 17147 1b7yB 785 1.53e+01 1pysB a.6.1.1 16301 a.6.1.1 16302 b.40.4.4 25312 d.58.13.1 39311 d.104.1.1 40780 d.138.1.1 41456 1p27B 106 1.55e+01 d.58.7.1 -10020 1ads 315 1.59e+01 1frb c.1.7.1 28671 1p8cA 145 1.60e+01 unknown_sccs -1927 1eu8A 409 1.62e+01 1eu8A c.94.1.1 59502 1c2pA 576 1.62e+01 1quvA e.8.1.4 43117 1p5jA 372 1.62e+01 1qxoA 388 1.63e+01 unknown_sccs -11161 1qwdA 177 1.68e+01 b.60.1.1 -4455 1a3yA 149 1.69e+01 1obpA b.60.1.1 27110 1ov3A 138 1.72e+01 b.34.2.1 87451 b.34.2.1 87452 1cb0A 283 1.76e+01 1cb0A c.56.2.1 33790 1eljA 381 1.76e+01 4mbp c.94.1.1 35791 1gdvA 85 1.79e+01 1ctj a.3.1.1 60458 1ixh 321 1.79e+01 1ixh c.94.1.1 35761 2acr 315 1.80e+01 1frb c.1.7.1 28674 1us0A 316 1.80e+01 c.1.7.1 -5233 1vjoA 393 1.89e+01 c.67.1.3 -8173 1qhdA 398 1.90e+01 1qhdA a.115.1.2 63324 b.19.1.1 63325 1qhqA 140 1.91e+01 1qhqA b.6.1.1 63326 1gnuA 117 1.92e+01 d.15.1.3 65403 1josA 128 1.94e+01 d.52.7.1 84191 1tsg 98 1.98e+01 1tsg 1dzkA 157 2.02e+01 1obpA b.60.1.1 27096 1oi1A 221 2.02e+01 b.34.9.3 87037 b.34.9.3 87038 1gxrA 337 2.07e+01 b.69.4.1 70722 1zfjA 491 2.09e+01 1ak5 c.1.5.1 28638 d.37.1.1 38540 d.37.1.1 38541 1llp 343 2.11e+01 1arv a.93.1.1 18578 1hw6A 278 2.14e+01 1frb c.1.7.1 61296 1ksyA 154 2.21e+01 d.89.1.2 72948 1frb 315 2.25e+01 1frb c.1.7.1 28665 4icb 76 2.25e+01 4icb a.39.1.1 17145 1dd5A 185 2.27e+01 1dd5A d.67.3.1 39564 1oe9A 795 2.30e+01 b.34.3.1 -3581 c.37.1.9 -7103 1uw4A 91 2.31e+01 unknown_sccs -10038 1s4qA 228 2.31e+01 c.37.1.1 -6975 1p6xA 334 2.36e+01 c.37.1.1 -6983 1b8oA 284 2.41e+01 1b8oA c.56.2.1 33762 1a5j 110 2.42e+01 1a5j a.4.1.3 16043 a.4.1.3 16044 1bt0A 76 2.46e+01 1ubi d.15.1.1 37607 1umqA 81 2.46e+01 unknown_sccs -203 1jwgA 147 2.48e+01 a.118.9.2 71911 1dax 64 2.48e+01 1fxd d.58.1.4 38996 1pbjA 125 2.50e+01 d.37.1.1 -9608 d.37.1.1 -9609 1l6rA 227 2.59e+01 c.108.1.10 77768 1lmb3 92 2.62e+01 1lmb3 1jm4B 118 2.62e+01 a.29.2.1 71746 1qpcA 279 2.65e+01 1fgkA d.144.1.7 41685 1e58A 249 2.67e+01 1qhfA c.60.1.1 59262 1lk3A 160 2.68e+01 a.26.1.3 73950 1cjxA 357 2.68e+01 1cjxA d.32.1.3 38516 d.32.1.3 38517 1dfd 64 2.71e+01 1fxd d.58.1.4 38995 1d0dA 60 2.73e+01 1kigI g.8.1.2 44566 1mo0A 275 2.75e+01 c.1.1.1 79329 1iuqA 367 2.75e+01 c.112.1.1 -8440 1mdwA 328 2.76e+01 d.3.1.3 84934 1ocrC 261 2.77e+01 1ocrC f.25.1.1 43540 1ls9A 91 2.77e+01 a.3.1.1 78177 1onqA 283 2.84e+01 b.1.1.2 -2640 d.19.1.1 -9390 1jbgA 109 2.85e+01 a.6.1.3 66480 1e6yC 247 2.94e+01 1mroC d.58.31.1 39441 1akz 223 2.94e+01 3eugA c.18.1.1 31007 1v54F 98 2.94e+01 g.41.5.3 -12788 1mypB 108 2.96e+01 1mypB a.93.1.2 18702 1m4rA 151 2.99e+01 a.26.1.3 84799 1d6gA 47 3.00e+01 1d6gA g.33.1.1 44976 1ek8A 185 3.01e+01 1ek8A d.67.3.1 59444 1dqcA 74 3.04e+01 1dqcA g.31.1.1 44964 1cp2A 269 3.05e+01 1cp2A c.37.1.10 32269 1hymB 24 3.07e+01 1ugmA 125 3.09e+01 1hekA 131 3.09e+01 a.61.1.5 65818 1dqpA 230 3.10e+01 1dqnA c.61.1.1 34069 1oa4A 222 3.10e+01 b.29.1.11 86731 2drpA 66 3.11e+01 2drpA g.37.1.1 45026 g.37.1.1 45027 1n2zA 245 3.15e+01 c.92.2.2 79865 3lck 271 3.16e+01 1fmk d.144.1.7 41686 5bcaA 516 3.17e+01 1b9zA b.3.1.1 22529 c.1.8.1 28799 1a8d 452 3.19e+01 1a8d b.29.1.6 24262 b.42.4.2 25607 1h2bA 359 3.22e+01 b.35.1.2 -3679 c.2.1.1 -5703 1m2dA 110 3.23e+01 c.47.1.11 78476 1vns 609 3.28e+01 1vns a.111.1.3 19061 1vnc 609 3.29e+01 1vns a.111.1.3 19065 1jqaA 370 3.31e+01 e.22.1.2 67085 1kigI 60 3.33e+01 1kigI g.8.1.2 44567 3thiA 371 3.38e+01 2thiA c.94.1.1 35792 1cm7A 363 3.40e+01 1cnzA c.77.1.1 35063 1b9zA 516 3.43e+01 1b9zA b.3.1.1 22528 c.1.8.1 28798 1pyfA 312 3.43e+01 c.1.7.1 -5251 1iraX 152 3.44e+01 1irp b.42.1.2 25556 1itcA 516 3.45e+01 b.3.1.1 83705 c.1.8.1 83706 1dqnA 230 3.46e+01 1dqnA c.61.1.1 34067 1uanA 227 3.46e+01 unknown_sccs -8129 1f00I 282 3.47e+01 1f00I b.1.14.1 22368 b.1.14.1 22369 d.169.1.3 42439 1mypA 108 3.51e+01 1d2vA a.93.1.2 18701 2afpA 129 3.51e+01 2afpA d.169.1.1 42349 2occF 98 3.53e+01 2occF g.41.5.3 45256 1pgvA 197 3.59e+01 c.10.1.1 88073 1p5fA 189 3.61e+01 c.23.16.2 -6508 1sqhA 312 3.63e+01 unknown_sccs -10812 1w0bA 102 3.66e+01 1ogaD 215 3.72e+01 b.1.1.1 86990 b.1.1.2 86991 1v8gA 329 3.73e+01 a.46.2.1 -953 c.27.1.1 -6644 2thiA 379 3.79e+01 2thiA c.94.1.1 35794 1b91A 118 3.82e+01 1b91A 1h5oA 42 3.86e+01 g.9.1.2 83484 1v54C 261 3.86e+01 f.25.1.1 -12239 1ois 223 3.88e+01 1a36A e.15.1.1 43267 1umgA 362 3.91e+01 1fjgI 128 3.93e+01 1fjfI d.14.1.1 37559 1hruA 188 3.99e+01 1hruA d.115.1.1 40926 2occC 261 3.99e+01 1ocrC f.25.1.1 43520 1k5rA 41 3.99e+01 b.72.1.1 68206