# List of top-scoring protein chains for t2k-w0.5 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 1efm 393 4.74e-03 1efcA c.37.1.8 64732 1etu 394 4.74e-03 1efcA c.37.1.8 64737 1d8tA 393 4.76e-03 1efcA b.43.3.1 25686 b.44.1.1 25726 c.37.1.8 32119 1efcA 393 4.76e-03 1efcA b.43.3.1 25680 b.44.1.1 25720 c.37.1.8 32113 1efuA 385 4.76e-03 1efcA b.43.3.1 25682 b.44.1.1 25722 c.37.1.8 32115 1dg1G 394 4.76e-03 1efcA b.43.3.1 25684 b.44.1.1 25724 c.37.1.8 32117 1dlgA 419 2.33e-01 1uae d.68.2.2 39580 1nawA 419 2.43e-01 1uae d.68.2.2 39582 1ejdA 419 2.44e-01 1uae d.68.2.2 39576 3tmkA 216 6.03e-01 3tmkA c.37.1.1 31920 2tmkA 216 6.03e-01 3tmkA c.37.1.1 31928 1jh3A 107 7.22e-01 1b7bA 310 8.42e-01 1b7bA c.73.1.1 34963 1jj2N 115 9.67e-01 1ffkL c.12.1.1 63099 1ffkL 115 9.67e-01 1ffkL c.12.1.1 30881 1id0A 152 1.12e+00 d.122.1.3 66111 1k2yX 463 1.59e+00 c.84.1.1 68063 c.84.1.1 68064 c.84.1.1 68065 c.84.1.1 68066 1ff9A 450 2.05e+00 1ff9A c.2.1.3 30039 d.81.1.2 39954 1e2o 233 2.10e+00 1eaf c.43.1.1 32631 4aig 201 2.12e+00 1atlA d.92.1.9 40318 3aig 202 2.13e+00 1atlA d.92.1.9 40321 1qdbA 473 2.40e+00 1qdbA a.138.1.3 19688 3rpbA 140 2.66e+00 1rsy b.7.1.2 23199 1eh1A 185 2.90e+00 1dd5A d.67.3.1 39565 1bf2 750 2.95e+00 1bf2 b.1.1.5 21860 b.71.1.1 27787 c.1.8.1 28774 2ts1 419 2.96e+00 2ts1 c.26.1.1 31564 1ihjA 98 3.00e+00 1pdr b.36.1.1 62382 1jx4A 352 3.12e+00 e.8.1.5 67405 1kvoA 124 3.30e+00 1poa a.133.1.2 19564 1k35A 463 3.39e+00 c.84.1.1 68094 c.84.1.1 68095 c.84.1.1 68096 c.84.1.1 68097 1d2eA 397 3.75e+00 1efcA b.43.3.1 25701 b.44.1.1 25741 c.37.1.8 32136 1jpmA 366 3.84e+00 c.1.11.2 67031 d.54.1.1 67032 1iag 202 4.38e+00 1atlA d.92.1.9 40319 1ktjA 129 4.44e+00 1a9v 129 4.53e+00 1a9v b.1.1.5 21946 1cmkE 350 4.56e+00 1cdkA d.144.1.1 41623 1cdkA 350 4.56e+00 1cdkA d.144.1.1 41620 1kqqA 139 4.76e+00 1jbpE 350 4.85e+00 1cdkA d.144.1.1 62849 1mioB 458 5.33e+00 1qguB c.92.2.3 35602 1a2n 419 5.47e+00 1uae d.68.2.2 39575 1ctpE 350 5.66e+00 1cdkA d.144.1.1 41622 1uae 419 5.68e+00 1uae d.68.2.2 39574 1atpE 350 5.75e+00 1cdkA d.144.1.1 41629 1exmA 405 5.90e+00 1efcA b.43.3.1 25696 b.44.1.1 25736 c.37.1.8 32131 1ha3A 405 5.90e+00 1efcA b.43.3.1 60869 b.44.1.1 60870 c.37.1.8 60871 1ydrE 350 5.98e+00 1cdkA d.144.1.1 41624 1g6sA 427 6.09e+00 1eps d.68.2.2 39584 1eps 427 6.12e+00 1eps d.68.2.2 39586 1apmE 350 6.19e+00 1cdkA d.144.1.1 41628 1h6vE 499 6.20e+00 c.3.1.5 60705 c.3.1.5 60706 d.87.1.1 60707 1g61A 228 6.22e+00 1g61A d.126.1.1 41126 1mugA 168 6.25e+00 1mugA c.18.1.2 31030 1g71A 347 6.99e+00 1g71A e.16.1.1 43268 1fmoE 350 7.21e+00 1cdkA d.144.1.1 41630 1bx6 350 7.23e+00 1cdkA d.144.1.1 41631 1dd3A 128 7.36e+00 1dd3C a.108.1.1 19031 d.45.1.1 38760 1stcE 350 7.37e+00 1cdkA d.144.1.1 41627 1jxlA 352 7.38e+00 e.8.1.5 67419 1l3rE 350 7.39e+00 1c20A 128 7.60e+00 1c20A a.4.3.1 16079 2plt 98 7.65e+00 1plc b.6.1.1 22862 1qm4A 396 7.69e+00 1mxb d.130.1.1 41350 d.130.1.1 41351 d.130.1.1 41352 1b23P 405 7.81e+00 1efcA b.43.3.1 25689 b.44.1.1 25729 c.37.1.8 32124 1eft 405 7.87e+00 1efcA b.43.3.1 25688 b.44.1.1 25728 c.37.1.8 32123 1dvoA 152 8.36e+00 1dvoA a.136.1.1 19623 1aipE 405 9.11e+00 1efcA b.43.3.1 25699 b.44.1.1 25739 c.37.1.8 32134 1ctf 74 1.11e+01 1ctf d.45.1.1 38759 2tprA 490 1.17e+01 3grs c.3.1.5 30505 c.3.1.5 30506 d.87.1.1 40184 1tytB 486 1.18e+01 3grs c.3.1.5 30515 c.3.1.5 30516 d.87.1.1 40189 1tytA 487 1.18e+01 3grs c.3.1.5 30513 c.3.1.5 30514 d.87.1.1 40188 1fecA 490 1.18e+01 3grs c.3.1.5 30489 c.3.1.5 30490 d.87.1.1 40176 1typA 487 1.19e+01 3grs c.3.1.5 30509 c.3.1.5 30510 d.87.1.1 40186 1jvr 137 1.35e+01 1jvr a.61.1.2 18132 1b8aA 438 1.41e+01 1b8aA b.40.4.1 25244 d.104.1.1 40765 1af3 196 1.44e+01 1maz f.1.4.1 43397 1mmoB 384 1.46e+01 1mtyB a.25.1.2 16768 1evhA 112 1.52e+01 1evhA b.55.1.4 26997 1i39A 225 1.59e+01 1ekeA c.55.3.1 61585 2nadA 393 1.64e+01 2nadA c.2.1.4 30090 c.23.12.1 31350 2nacA 393 1.64e+01 2nadA c.2.1.4 30088 c.23.12.1 31348 1a0jA 223 1.64e+01 5ptp b.47.1.2 26002 1qoyA 318 1.67e+01 1qoyA h.4.4.1 45788 1aku 147 1.67e+01 5nul c.23.5.1 31161 1maz 221 1.70e+01 1maz f.1.4.1 43393 1treA 255 1.83e+01 1amk c.1.1.1 28505 1mtyB 384 1.84e+01 1mtyB a.25.1.2 16740 1fz7C 389 1.85e+01 1mtyB a.25.1.2 16754 1ahm 129 1.85e+01 1a9v b.1.1.5 21944 1hqz1 141 1.86e+01 1dkxA 219 1.86e+01 1dkzA e.20.1.1 43315 1gwjA 377 1.94e+01 1hv8A 367 1.96e+01 1hv8A c.37.1.13 32405 c.37.1.13 32406 1c3pA 375 2.06e+01 1c3pA c.42.1.2 32606 1c3rA 375 2.07e+01 1c3pA c.42.1.2 32607 1dctA 324 2.08e+01 6mhtA c.66.1.10 34244 1atlA 202 2.18e+01 1atlA d.92.1.9 40322 1dthA 203 2.20e+01 1atlA d.92.1.9 40324 1iuz 98 2.20e+01 1plc b.6.1.1 22861 1bpr 191 2.29e+01 1dkzA e.20.1.1 43319 1j9eA 147 2.30e+01 c.23.5.1 62756 1g5jA 175 2.30e+01 1maz f.1.4.1 43394 1lci 550 2.34e+01 1lci e.23.1.1 43349 1bxlA 181 2.38e+01 1maz f.1.4.1 43396 1i1oA 147 2.42e+01 5nul c.23.5.1 61542 1b4rA 80 2.45e+01 1b4rA b.1.3.1 22072 1dkzA 219 2.45e+01 1dkzA e.20.1.1 43314 2if1 126 2.46e+01 2if1 d.64.1.1 39547 1gl2B 65 2.54e+01 h.1.15.1 65279 1f9aA 168 2.57e+01 1f9aA c.26.1.3 31602 1jeyB 565 2.60e+01 1jeqB e.31.1.2 62925 1jeqB 565 2.60e+01 1jeqB e.31.1.2 62922 1c7fA 147 2.61e+01 5nul c.23.5.1 31163 1lvl 458 2.64e+01 1lvl c.3.1.5 30567 c.3.1.5 30568 d.87.1.1 40205 1bu5A 147 2.67e+01 5nul c.23.5.1 31155 2fx2 147 2.67e+01 1rcf c.23.5.1 31158 1a5p 124 2.76e+01 7rsa d.5.1.1 37201 1aat 411 2.76e+01 1ajsA c.67.1.1 34275 1f4pA 147 2.78e+01 5nul c.23.5.1 59651 1fx1 148 2.79e+01 1rcf c.23.5.1 31169 1akw 147 2.83e+01 5nul c.23.5.1 31153 1i50C 318 2.84e+01 d.74.3.1 61756 d.181.1.1 61757 1eejA 216 2.88e+01 1eejA c.47.1.9 33057 d.17.3.1 38071 1akr 147 2.91e+01 1rcf c.23.5.1 31152 2pfkC 302 2.92e+01 3pfk c.89.1.1 35579 2pfkD 305 3.00e+01 3pfk c.89.1.1 35580 1akt 147 3.00e+01 5nul c.23.5.1 31157 1dfmA 223 3.02e+01 1d2iA c.52.1.5 33295 1d2iA 223 3.02e+01 1d2iA c.52.1.5 33297 1j9gA 147 3.08e+01 c.23.5.1 62757 1ag8A 499 3.20e+01 1bpwA c.82.1.1 35341 1azl 147 3.23e+01 5nul c.23.5.1 31154 1arb 268 3.24e+01 1arb b.47.1.1 25766 1pfkA 320 3.27e+01 3pfk c.89.1.1 35575 2pfkA 320 3.27e+01 3pfk c.89.1.1 35577 1jeqA 609 3.36e+01 1jeqA a.140.2.1 64748 e.31.1.1 64749 1jeyA 609 3.36e+01 1jeqA e.31.1.1 62924 1dq3A 454 3.48e+01 1dq3A b.86.1.2 28380 d.50.3.1 38798 d.95.2.2 40585 d.95.2.2 40586 1k1eA 180 3.51e+01 c.108.1.5 67995 1e54A 332 3.60e+01 1e54A f.4.3.1 59258 1r092 262 3.72e+01 1aym2 1j5eJ 104 3.83e+01 1fjgJ 105 3.87e+01 1fjfJ d.58.15.1 39330 2fheA 216 3.89e+01 1b8xA a.45.1.1 17724 c.47.1.5 33018 1bxsA 501 3.90e+01 1bpwA c.82.1.1 35357 1tin 69 3.90e+01 2sniI d.40.1.1 38580 1mit 69 3.95e+01 1hymA d.40.1.1 38582