# 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 1rlhA 173 1.24e+00 1mxb 383 1.37e+00 1mxb d.130.1.1 41329 d.130.1.1 41330 d.130.1.1 41331 1fuxA 166 1.67e+00 1fjjA b.17.1.2 60034 1rg9A 383 1.69e+00 1riqA 465 2.76e+00 1bw4 125 3.80e+00 1bw4 b.52.1.2 26900 1jj2B 337 3.80e+00 1ffkB b.43.3.2 63086 1ffkB 338 4.84e+00 1ffkB b.43.3.2 25719 1bw3 125 5.36e+00 1bw4 b.52.1.2 26899 1a6bB 40 5.65e+00 1a6bB g.40.1.1 45172 1klo 162 5.83e+00 1klo g.3.11.2 44326 g.3.11.2 44327 g.3.11.2 44328 1qvjA 292 6.53e+00 1m4iA 181 6.60e+00 d.108.1.1 74457 1l5cA 92 7.55e+00 b.9.1.1 73577 1mxa 383 8.37e+00 1mxb d.130.1.1 41326 d.130.1.1 41327 d.130.1.1 41328 1nlr 234 8.65e+00 2nlrA b.29.1.11 24345 1q33A 292 8.94e+00 1q16B 512 9.21e+00 1hp4A 512 9.23e+00 1hp4A c.1.8.6 61111 d.92.2.1 61112 1l7lA 121 9.64e+00 b.18.1.16 77790 1jakA 512 1.03e+01 c.1.8.6 66472 d.92.2.1 66473 1bvzA 585 1.25e+01 1bvzA b.1.18.2 21856 b.71.1.1 27783 c.1.8.1 28770 1ji2A 585 1.33e+01 b.1.18.2 71672 b.71.1.1 71673 c.1.8.1 71674 1hp5A 512 1.35e+01 1hp4A c.1.8.6 61113 d.92.2.1 61114 3pmgA 561 1.35e+01 3pmgA c.84.1.1 35408 c.84.1.1 35409 c.84.1.1 35410 d.129.2.1 41301 4dpvZ 584 1.35e+01 2cas b.121.5.2 23377 1lslA 113 1.40e+01 g.60.1.1 78178 g.60.1.1 78179 1oa4A 222 1.55e+01 b.29.1.11 86731 1mpzA 41 1.60e+01 g.20.1.1 79391 2nlrA 234 1.60e+01 2nlrA b.29.1.11 24344 2bn2A 95 1.61e+01 1npoA b.9.1.1 23266 1h7dA 49 1.66e+01 j.88.1.1 65701 1i6uA 130 1.67e+01 d.140.1.1 61850 1fd9A 213 1.69e+01 1fd9A d.26.1.1 59771 2rveA 244 1.74e+01 1rvaA c.52.1.2 33283 2f5bH 235 1.78e+01 b.1.1.1 88506 b.1.1.2 88507 1npoC 95 1.84e+01 1npoA b.9.1.1 23271 1pamA 686 1.88e+01 1cxlA b.1.18.2 21846 b.3.1.1 22515 b.71.1.1 27753 c.1.8.1 28740 1kmxA 55 1.95e+01 g.25.1.1 72758 1s5lB 510 1.95e+01 1npoA 95 2.00e+01 1npoA b.9.1.1 23270 1o04A 500 2.12e+01 c.82.1.1 86508 1cr1A 296 2.37e+01 1cr1A c.37.1.11 32286 1bbi 71 2.38e+01 1pi2 g.3.13.1 44345 2cbh 36 2.46e+01 2cbh g.3.8.1 44181 1jj7A 260 2.47e+01 c.37.1.12 63114 1ciy 590 2.47e+01 1ciy b.18.1.3 23720 b.77.2.1 27977 f.1.3.1 43392 1j48A 110 2.51e+01 b.1.7.1 84112 1cqeA 580 2.61e+01 1cqeA a.93.1.2 18703 g.3.11.1 44246 1su8A 636 2.65e+01 1j7rA 86 2.69e+01 1j7rA a.39.1.5 62701 1en2A 89 2.82e+01 1hev g.3.1.1 44048 g.3.1.1 44049 1jjyA 636 2.86e+01 1jjyA e.26.1.2 63141 1h8vA 218 2.95e+01 2nlrA b.29.1.11 60795 1cr0A 296 2.97e+01 1cr1A c.37.1.11 32287 1fqgA 263 2.99e+01 1btl e.3.1.1 42699 1c3kA 147 3.08e+01 1jotA b.77.3.1 27984 1jk4A 89 3.11e+01 b.9.1.1 77130 1ey2A 471 3.12e+01 1ey2A b.82.1.4 28116 1kt9A 138 3.15e+01 d.113.1.1 72959 1lxtA 561 3.24e+01 3pmgA c.84.1.1 35432 c.84.1.1 35433 c.84.1.1 35434 d.129.2.1 41309 1lxa 262 3.32e+01 1lxa b.81.1.1 28052 1ueoA 63 3.33e+01 1nscA 390 3.35e+01 2qwc b.68.1.1 27591 1vgh 55 3.38e+01 2vgh g.25.1.1 44945 1lqaA 346 3.44e+01 c.1.7.1 84674 1iqbB 89 3.46e+01 g.3.1.1 66264 g.3.1.1 66265 1lmiA 131 3.48e+01 b.1.19.1 78098 1p4cA 380 3.50e+01 1hlqA 75 3.52e+01 g.35.1.1 83613 1mknA 59 3.59e+01 1mknA g.5.1.1 44383 1m40A 263 3.80e+01 e.3.1.1 74437 1eybA 471 3.83e+01 1ey2A b.82.1.4 28115 1gu7A 364 3.88e+01 b.35.1.2 83321 c.2.1.1 83322 1btl 263 3.95e+01 1btl e.3.1.1 42691