# 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 3.28e-21 unknown_sccs -10786 1ttzA 87 1.02e+00 1hyeA 313 1.44e+00 2cmd c.2.1.5 61400 d.162.1.1 61401 1gt91 357 2.58e+00 1gp4A 356 2.80e+00 b.82.2.1 65439 1skyB 502 2.84e+00 1skyB a.69.1.1 18313 b.49.1.1 26478 c.37.1.11 32358 1j0aA 325 3.11e+00 c.79.1.1 83871 1l6wA 220 3.28e+00 c.1.10.1 73632 1vih 71 3.54e+00 1vih d.51.1.1 38807 1gp6A 356 3.82e+00 b.82.2.1 65441 1nf5B 286 4.57e+00 c.68.1.2 80454 1ej0A 180 4.82e+00 1ej0A c.66.1.2 34179 1vig 71 5.04e+00 1vih d.51.1.1 38806 1pztA 286 5.55e+00 c.68.1.2 -8213 1gjwA 637 5.95e+00 b.71.1.1 60582 c.1.8.1 60583 1gjuA 637 6.38e+00 b.71.1.1 60580 c.1.8.1 60581 1lnqA 336 6.61e+00 c.2.1.9 74049 f.14.1.1 74050 1us8A 147 7.00e+00 c.37.1.12 -7194 1ujnA 348 7.32e+00 e.22.1.1 -11998 1h6kZ 98 8.01e+00 d.58.7.1 60686 1nmmB 286 8.38e+00 c.68.1.2 80662 1pa2A 306 8.79e+00 1bgp a.93.1.1 18693 1e1dA 553 9.75e+00 1e1dA e.26.1.1 43363 1fc4A 401 9.76e+00 1bs0A c.67.1.4 59760 1skoA 143 1.04e+01 1a1d 146 1.08e+01 1a1d b.40.4.8 25394 1oz9A 150 1.10e+01 unknown_sccs -10588 1vhmA 195 1.11e+01 d.110.2.1 -10828 1jn8B 273 1.12e+01 1j8wB 273 1.22e+01 1e2uA 553 1.22e+01 1e1dA e.26.1.1 43362 1f2tA 149 1.27e+01 1f2tA c.37.1.12 32373 1gntA 553 1.28e+01 e.26.1.1 70290 1q1oA 98 1.28e+01 d.15.2.2 -9172 1j79A 347 1.29e+01 1j79A c.1.9.4 62675 1qdlA 422 1.31e+01 1qdlA d.161.1.1 42088 2cmd 312 1.34e+01 2cmd c.2.1.5 30135 d.162.1.1 42102 1egr 85 1.35e+01 1kte c.47.1.1 32765 1rpuA 172 1.35e+01 unknown_sccs -10738 1brlA 355 1.41e+01 1lucA c.1.16.1 29553 1p1xA 260 1.48e+01 1jcjA 260 1.48e+01 c.1.10.1 66499 1o88A 353 1.52e+01 b.80.1.1 81178 1og6A 298 1.53e+01 c.1.7.1 86984 1budA 197 1.53e+01 1atlA d.92.1.9 40328 1h0cA 392 1.54e+01 c.67.1.3 83424 1h7wA 1025 1.55e+01 1h7wA a.1.2.2 15683 c.1.4.1 28628 c.3.1.1 30324 c.4.1.1 30609 d.58.1.5 39007 1air 353 1.61e+01 1air b.80.1.1 28018 1fgxA 288 1.66e+01 1fgxA c.68.1.2 34508 1h6kX 97 1.72e+01 d.58.7.1 60684 2bc2A 227 1.73e+01 1a7tA d.157.1.1 42031 1ex2A 189 1.74e+01 1ex2A c.51.4.2 33225 1jclA 260 1.75e+01 c.1.10.1 66501 2pec 353 1.75e+01 1air b.80.1.1 28019 1m3uA 264 1.76e+01 c.1.12.8 84784 1g8fA 511 1.78e+01 1g8fA b.122.1.3 60348 c.26.1.5 60349 c.37.1.15 60350 1vjeA 166 1.82e+01 d.185.1.2 -10261 1oeyJ 107 1.85e+01 d.15.2.2 -9168 1ng1 294 1.85e+01 1ng1 a.24.13.1 16961 c.37.1.10 32272 1innA 166 1.88e+01 1j98A d.185.1.2 62608 1kq6A 141 1.90e+01 d.189.1.1 -9926 1cnt3 187 1.91e+01 1cnt3 1v1rA 400 1.91e+01 1h7wD 1025 1.95e+01 a.1.2.2 15686 c.1.4.1 28631 c.3.1.1 30327 c.4.1.1 30612 d.58.1.5 39010 1rj9A 304 1.96e+01 a.24.13.1 -631 c.37.1.10 -7129 1tz9A 367 1.96e+01 1cec 343 1.96e+01 1ceo c.1.8.3 28809 1d1rA 116 1.99e+01 1d1rA d.64.1.1 39548 1dvkA 173 2.00e+01 1dvkA a.72.1.1 18319 2bc2B 227 2.03e+01 1a7tA d.157.1.1 42032 1q0pA 223 2.12e+01 c.62.1.1 -7979 1ur3M 319 2.13e+01 c.1.7.1 -5248 1ub3A 220 2.14e+01 c.1.10.1 88395 1gteA 1025 2.16e+01 a.1.2.2 70440 c.1.4.1 70441 c.3.1.1 70442 c.4.1.1 70443 d.58.1.5 70444 1gteD 1025 2.18e+01 a.1.2.2 70455 c.1.4.1 70456 c.3.1.1 70457 c.4.1.1 70458 d.58.1.5 70459 1pvdA 537 2.18e+01 1zpdA c.31.1.3 31737 c.36.1.5 31777 c.36.1.9 31778 1h7wB 1025 2.19e+01 a.1.2.2 15684 c.1.4.1 28629 c.3.1.1 30325 c.4.1.1 30610 d.58.1.5 39008 1un8A 552 2.19e+01 unknown_sccs -1942 c.32.1.2 -6792 d.79.2.2 -10401 1a4iB 301 2.23e+01 1a4iA c.2.1.7 30279 c.58.1.2 33927 1dbwA 126 2.26e+01 1dbwA c.23.1.1 31095 1qpbA 563 2.32e+01 1zpdA c.31.1.3 31739 c.36.1.5 31781 c.36.1.9 31782 1pydA 556 2.37e+01 1zpdA c.31.1.3 31735 c.36.1.5 31773 c.36.1.9 31774 1d7yA 408 2.37e+01 1d7yA c.3.1.5 30565 c.3.1.5 30566 d.87.1.1 40204 1mzhA 225 2.38e+01 c.1.10.1 79698 1in0A 163 2.41e+01 d.58.49.1 83694 d.58.49.1 83695 1uiqA 351 2.47e+01 1v7cA 351 2.47e+01 c.79.1.1 -8512 1ls1A 295 2.50e+01 a.24.13.1 78170 c.37.1.10 78171 1ky3A 182 2.50e+01 c.37.1.8 73193 1k92A 455 2.51e+01 c.26.2.1 68325 d.210.1.1 68326 1viuA 203 2.52e+01 d.113.1.1 -10889 1esiA 262 2.53e+01 1skf e.3.1.1 42682 1uz5A 402 2.56e+01 b.85.6.1 -5029 b.103.1.1 -5069 c.57.1.2 -7902 1puiA 210 2.60e+01 c.37.1.8 88292 1qsoA 149 2.61e+01 1qsmA d.108.1.1 40812 1efvA 315 2.62e+01 1efvA c.26.2.3 31633 c.31.1.2 31728 1qfnA 85 2.63e+01 1qfnA c.47.1.1 32768 1k8kB 394 2.64e+01 c.55.1.1 68307 1twdA 256 2.66e+01 2hhmA 276 2.70e+01 1imbA e.7.1.1 42955 1ej6A 1289 2.75e+01 i.7.1.1 45967 1hl9A 449 2.75e+01 unknown_sccs -4694 unknown_sccs -5365 1kwaA 88 2.79e+01 1kwaA b.36.1.1 24772 1imdA 277 2.82e+01 1imbA e.7.1.1 42968 1i1qA 520 2.82e+01 1qdlA d.161.1.1 61543 1ego 85 2.82e+01 1kte c.47.1.1 32767 1cd1A 315 2.89e+01 1cd1A b.1.1.2 21579 d.19.1.1 38155 1qj4A 257 2.94e+01 1qj4A c.69.1.20 34796 1s5aA 150 2.96e+01 unknown_sccs -9300 1j4wA 174 2.97e+01 d.51.1.1 71529 d.51.1.1 71530 1dl5A 317 2.97e+01 1dl5A c.66.1.7 64720 d.197.1.1 64721 1m41A 380 3.03e+01 c.1.16.4 78595 1qfeA 252 3.12e+01 1qfeA c.1.10.1 29167 1vjfA 180 3.13e+01 d.116.1.1 -10941 1a4iA 301 3.17e+01 1a4iA c.2.1.7 30278 c.58.1.2 33926 1i50H 146 3.18e+01 b.40.4.8 61761 1gqnA 252 3.18e+01 c.1.10.1 -5494 1yasA 257 3.18e+01 1qj4A c.69.1.20 34801 1rxyA 253 3.25e+01 c.56.2.1 -7834 1qsmA 152 3.27e+01 1qsmA d.108.1.1 40808 1jpnA 296 3.27e+01 a.24.13.1 67039 c.37.1.10 67040 1diaA 306 3.32e+01 1a4iA c.2.1.7 30280 c.58.1.2 33928 1h7xB 1025 3.32e+01 a.1.2.2 15688 c.1.4.1 28633 c.3.1.1 30329 c.4.1.1 30614 d.58.1.5 39012 1k3fA 253 3.36e+01 c.56.2.1 68105 2ng1 293 3.38e+01 1ng1 a.24.13.1 16962 c.37.1.10 32273 1dckA 126 3.45e+01 1dbwA c.23.1.1 31097 1zid 268 3.45e+01 1eny c.2.1.2 29911 1nv8A 284 3.49e+01 c.66.1.30 86224 1fehA 574 3.49e+01 1fehA c.96.1.1 36015 d.15.4.2 37690 d.58.1.5 38998 1j3vA 289 3.50e+01 a.100.1.1 -1303 c.2.1.6 -5947 1ceo 343 3.52e+01 1ceo c.1.8.3 28808 1o4vA 183 3.52e+01 c.23.8.1 86628 1imbA 277 3.54e+01 1imbA e.7.1.1 42957 1r5jA 337 3.58e+01 unknown_sccs -8471 1q4rA 112 3.62e+01 d.58.4.4 -9943 1kbjA 412 3.62e+01 c.1.4.1 72280 1dg3A 592 3.63e+01 1dg3A a.114.1.1 19078 c.37.1.8 32153 1p3dA 475 3.64e+01 c.5.1.1 87728 c.59.1.1 87729 c.72.2.1 87730 4pfk 319 3.67e+01 3pfk c.89.1.1 35582 1r26A 125 3.70e+01 c.47.1.1 -7389 1hv8A 367 3.73e+01 1hv8A c.37.1.19 32405 c.37.1.19 32406 1rfmA 344 3.73e+01 c.122.1.1 -8032 1di0A 158 3.73e+01 1di0A c.16.1.1 30957 1bxsA 501 3.74e+01 1bpwA c.82.1.1 35357 1l9wA 252 3.74e+01 c.1.10.1 84570 1f5nA 592 3.80e+01 1dg3A a.114.1.1 19077 c.37.1.8 32152 1k7jA 206 3.81e+01 d.115.1.1 72103 1jf9A 408 3.84e+01 1c0nA c.67.1.3 62931 1r9fA 136 3.85e+01 unknown_sccs -10736 1kzfA 230 3.85e+01 d.108.1.3 73354 1bg2 325 3.89e+01 1bg2 c.37.1.9 32189 1fcbA 511 3.94e+01 1gox c.1.4.1 28620 d.120.1.1 41087 1lucA 355 3.96e+01 1lucA c.1.16.1 29547 1suh 146 3.99e+01 1edhA b.1.6.1 22206