# List of top-scoring protein chains for t2k-100-30-str 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 1lfpA 249 2.14e-49 1konA 249 2.95e-45 1b4aA 149 5.21e-03 1b4aA a.4.5.3 16088 d.74.2.1 39721 1pytA 94 1.02e-01 1pytA d.58.3.1 39064 1qaxA 428 1.21e-01 1qaxA d.58.20.1 39376 d.179.1.1 42597 1qc9A 276 2.01e-01 1ckqA c.52.1.1 33235 1hf2A 210 2.52e-01 1hf2A b.80.3.1 60992 c.102.1.1 60993 1kwmA 402 2.70e-01 1ckqA 276 2.85e-01 1ckqA c.52.1.1 33229 1afi 72 2.91e-01 1aw0 d.58.17.1 39339 1qm9A 198 3.25e-01 1qm9A d.58.7.1 39207 d.58.7.1 39208 1gmuA 143 3.62e-01 b.107.1.1 65335 d.58.38.1 65336 1cl8A 276 3.72e-01 1ckqA c.52.1.1 33230 1earA 147 4.07e-01 b.107.1.1 64875 d.58.38.1 64876 1eriA 276 4.84e-01 1ckqA c.52.1.1 33231 1eb0A 147 4.92e-01 b.107.1.1 64890 d.58.38.1 64891 1uae 419 5.36e-01 1uae d.68.2.2 39574 1qpsA 261 5.54e-01 1ckqA c.52.1.1 33234 1l9fA 389 6.54e-01 1el5A 389 6.63e-01 1b3mA c.3.1.2 30369 d.16.1.3 37937 2hqi 72 7.06e-01 1aw0 d.58.17.1 39340 1i9yA 347 7.21e-01 1i9yA d.151.1.2 62101 1i9zA 347 7.23e-01 1i9yA d.151.1.2 62102 1ejdA 419 7.99e-01 1uae d.68.2.2 39576 1xxaA 78 8.26e-01 1xxaA d.74.2.1 39700 1aw0 72 9.46e-01 1aw0 d.58.17.1 39342 1bmtA 246 9.51e-01 1bmtA a.46.1.1 17757 c.23.6.1 31235 1dqeA 137 9.71e-01 1dqeA a.39.2.1 17388 1lpuA 332 1.03e+00 1jdiA 231 1.07e+00 c.74.1.1 66551 1aye 401 1.13e+00 1aye c.56.5.1 33824 d.58.3.1 39065 1a58 177 1.17e+00 2cpl b.62.1.1 27495 1kmnD 424 1.32e+00 1adjA c.51.1.1 33185 d.104.1.1 40734 1csn 298 1.44e+00 1csn d.144.1.1 41664 1psdA 409 1.48e+00 1psdA c.2.1.4 30097 c.23.12.1 31357 d.58.18.1 39354 1i1dA 161 1.63e+00 1i21A d.108.1.1 61526 1jh6A 189 1.66e+00 d.61.1.1 66707 1ad3A 452 1.73e+00 1ad3A c.82.1.1 35335 1reqA 727 1.74e+00 1reqA c.1.19.1 29620 c.23.6.1 31247 1xxcA 78 1.76e+00 1xxaA d.74.2.1 39712 3uagA 437 1.79e+00 4uagA c.5.1.1 30652 c.59.1.1 33953 c.72.2.1 34956 1ckiA 317 1.84e+00 1csn d.144.1.1 41660 1bwzA 274 1.88e+00 1bwzA d.21.1.1 38337 d.21.1.1 38338 1d1rA 116 1.92e+00 1d1rA d.64.1.1 39548 1i12A 160 2.04e+00 1i21A d.108.1.1 61515 1fecA 490 2.14e+00 3grs c.3.1.5 30489 c.3.1.5 30490 d.87.1.1 40176 4uagA 437 2.19e+00 4uagA c.5.1.1 30651 c.59.1.1 33952 c.72.2.1 34955 1uag 437 2.19e+00 4uagA c.5.1.1 30653 c.59.1.1 33954 c.72.2.1 34957 1efuB 282 2.30e+00 1efuB a.5.2.2 58975 d.43.1.1 58976 d.43.1.1 38677 1mla 309 2.35e+00 1mla c.19.1.1 31031 d.58.23.1 39383 1i1gA 141 2.38e+00 a.4.5.32 65982 d.58.37.1 65983 1l7mA 211 2.40e+00 1jg8A 347 2.44e+00 1jg8A c.67.1.1 62946 1j97A 211 2.51e+00 1f5sA c.108.1.4 62753 1f5sA 211 2.52e+00 1f5sA c.108.1.4 59656 1bh5A 183 2.64e+00 1qipA d.32.1.1 38476 1f1eA 154 2.71e+00 a.22.1.2 64927 2gbp 309 2.74e+00 1gca c.93.1.1 35657 1eqcA 394 2.79e+00 1cz1A c.1.8.3 28811 1hnnA 282 2.82e+00 c.66.1.15 65895 1b33N 67 2.83e+00 1b33N d.30.1.1 38459 1hh2P 344 2.89e+00 b.40.4.5 65835 d.52.3.1 65836 d.52.3.1 65837 d.202.1.1 65838 1eu8A 409 2.92e+00 1eu8A c.94.1.1 59502 1pil 112 2.98e+00 2pii d.58.5.1 39072 1dtyA 429 2.98e+00 1dtyA c.67.1.4 34495 1phnB 172 3.03e+00 1qgwC a.1.1.3 15642 1httA 423 3.03e+00 1adjA c.51.1.1 33178 d.104.1.1 40727 1ovaA 386 3.09e+00 1ovaA e.1.1.1 42619 1qj5A 429 3.15e+00 1dtyA c.67.1.4 34493 1qipA 183 3.19e+00 1qipA d.32.1.1 38470 1cz1A 394 3.23e+00 1cz1A c.1.8.3 28839 1kskA 234 3.57e+00 1aogA 485 3.66e+00 3grs c.3.1.5 30517 c.3.1.5 30518 d.87.1.1 40190 1g60A 260 3.72e+00 1gx1A 160 3.96e+00 1gca 309 3.99e+00 1gca c.93.1.1 35659 1jy8A 159 4.02e+00 d.79.5.1 67452 1awqA 164 4.23e+00 2cpl b.62.1.1 27461 1gtqA 140 4.25e+00 1b66A d.96.1.2 40661 1i21A 159 4.27e+00 1i21A d.108.1.1 61549 1b66A 140 4.31e+00 1b66A d.96.1.2 40657 1gnlA 544 4.41e+00 1fjgT 106 4.52e+00 1fjfT a.7.6.1 16338 1g7rA 594 4.58e+00 1g7rA b.43.3.1 25716 b.43.3.1 25717 c.20.1.1 31034 c.37.1.8 32149 1cwoA 165 4.73e+00 2cpl b.62.1.1 27445 1ifqA 138 4.77e+00 1ifqA d.110.4.1 62350 2pii 112 4.78e+00 2pii d.58.5.1 39071 2cpl 165 4.87e+00 2cpl b.62.1.1 27420 1qlmA 316 5.05e+00 1qlmA d.147.1.1 41765 1k4jA 230 5.37e+00 1awsA 164 5.47e+00 2cpl b.62.1.1 27431 1vokA 200 5.74e+00 1ytbA d.129.1.1 41242 d.129.1.1 41243 1mroC 247 5.97e+00 1mroC d.58.31.1 39437 2rmcA 182 6.16e+00 2cpl b.62.1.1 27491 1fe0A 68 6.21e+00 1cc8A d.58.17.1 39345 1kkhA 317 6.31e+00 1hbnC 248 6.33e+00 1mroC d.58.31.1 60902 1ktpB 172 6.34e+00 1qu9A 128 6.74e+00 1qu9A d.79.1.1 39755 1qu9C 128 6.74e+00 1qu9A d.79.1.1 39757 1h70A 255 6.89e+00 1h70A d.126.1.3 60711 1dv1A 449 7.04e+00 1bncA b.84.2.1 28234 c.30.1.1 31641 d.142.1.2 41486 1jcjA 260 7.09e+00 c.1.10.1 66499 2ng1 293 7.74e+00 1ng1 a.24.13.1 16962 c.37.1.10 32273 1bvoA 175 7.77e+00 1a3qA b.2.5.1 22457 1e0tA 470 8.06e+00 1a49A b.58.1.1 27064 c.1.12.1 29292 c.49.1.1 33146 1eur 365 8.21e+00 1eut b.68.1.1 27607 1g7sA 594 8.26e+00 1g7rA b.43.3.1 25712 b.43.3.1 25713 c.20.1.1 31032 c.37.1.8 32147 1orc 71 8.38e+00 1orc a.35.1.2 17054 1kmmA 424 8.63e+00 1adjA c.51.1.1 33174 d.104.1.1 40723 4pfk 319 8.69e+00 3pfk c.89.1.1 35582 1jdpA 441 9.04e+00 c.93.1.1 62906 1b4bA 71 9.08e+00 1b4aA d.74.2.1 39718 1hh1A 143 9.22e+00 1gefA c.52.1.18 61036 1pea 385 9.24e+00 1pea c.93.1.1 35662 1bncB 449 9.35e+00 1bncA b.84.2.1 28237 c.30.1.1 31644 d.142.1.2 41489 1irxA 523 9.37e+00 1g9zA 152 9.65e+00 1bp7A d.95.2.1 60408 1bjt 793 9.90e+00 1bjt e.11.1.1 43249 1t7pA 698 9.94e+00 1t7pA c.55.3.5 33712 e.8.1.1 43005 1bp7A 152 1.00e+01 1bp7A d.95.2.1 40568 1bncA 449 1.02e+01 1bncA b.84.2.1 28236 c.30.1.1 31643 d.142.1.2 41488 1ej1A 190 1.03e+01 1ejhA d.86.1.1 40144 1ygs 234 1.04e+01 1ygs b.26.1.1 23907 1ppa 121 1.05e+01 1poa a.133.1.2 19550 1h8vA 218 1.05e+01 2nlrA b.29.1.11 60795 1fgkA 310 1.05e+01 1fgkA d.144.1.2 41693 1thm 279 1.06e+01 1gci c.41.1.1 32544 1im8A 244 1.07e+01 c.66.1.14 66212 1qd9A 124 1.07e+01 1qu9A d.79.1.1 39758 1m0dA 138 1.10e+01 1l9xA 315 1.13e+01 1fzrA 138 1.13e+01 1fzrA c.52.1.17 33336 6pfkA 319 1.16e+01 3pfk c.89.1.1 35583 1ihgA 370 1.17e+01 2cpl a.118.8.1 62380 b.62.1.1 62381 1jclA 260 1.18e+01 c.1.10.1 66501 1fsz 372 1.18e+01 1fsz c.32.1.1 31750 d.79.2.1 39802 1evlA 401 1.19e+01 1qf6A c.51.1.1 33202 d.104.1.1 40751 1g7tA 594 1.19e+01 1g7rA b.43.3.1 25714 b.43.3.1 25715 c.20.1.1 31033 c.37.1.8 32148 1jg5A 83 1.22e+01 d.205.1.1 66666 1k94A 165 1.23e+01 a.39.1.7 68333 1ffkS 70 1.25e+01 1ffkS a.2.2.1 15692 1ytbB 180 1.26e+01 1ytbA d.129.1.1 41278 d.129.1.1 41279 1xxbA 78 1.30e+01 1xxaA d.74.2.1 39706 1j8mF 297 1.31e+01 1ng1 a.24.13.1 62742 c.37.1.10 62743 1a8p 258 1.34e+01 1fdr b.43.4.2 25654 c.25.1.1 31544 3pfk 319 1.34e+01 3pfk c.89.1.1 35581 1ib8A 164 1.37e+01 1bg6 359 1.37e+01 1bg6 a.100.1.5 18810 c.2.1.6 30214 1fhdA 312 1.37e+01 1taxA c.1.8.3 28915 1j7iA 264 1.37e+01 1j7iA d.144.1.6 62694 1bs0A 384 1.39e+01 1bs0A c.67.1.4 34490 1qnaA 200 1.39e+01 1ytbA d.129.1.1 41226 d.129.1.1 41227 1a6q 382 1.40e+01 1a6q d.158.1.1 42063 1eumA 165 1.40e+01 1eumA a.25.1.1 59507 1g3qA 237 1.42e+01 1hyqA c.37.1.10 60237 1dywA 173 1.43e+01 2cpl b.62.1.1 27505 1c3yA 108 1.43e+01 1c3yA a.39.2.1 17387 1edoA 244 1.44e+01 1ybvA c.2.1.2 29896 1cgo 127 1.44e+01 1cpq a.24.3.2 16550 2oneA 436 1.45e+01 4enl c.1.11.1 29203 d.54.1.1 38847 1eal 127 1.45e+01 1hmt b.60.1.2 27227 1ko7A 314 1.47e+01 1ytbA 180 1.48e+01 1ytbA d.129.1.1 41276 d.129.1.1 41277 1abrA 251 1.49e+01 1mrj d.165.1.1 42196 1gntA 553 1.51e+01 1jsmB 176 1.51e+01 h.3.1.1 63265 1pa2A 306 1.53e+01 1bgp a.93.1.1 18693 1idrA 136 1.53e+01 1dlyA a.1.1.1 62301 1t1dA 100 1.55e+01 1t1dA d.42.1.2 38637 4enl 436 1.57e+01 4enl c.1.11.1 29202 d.54.1.1 38846 1nfkA 325 1.58e+01 1a3qA b.1.1.5 21929 b.2.5.1 22444 1io1A 398 1.59e+01 1io1A e.32.1.1 62611 1qmhA 347 1.61e+01 1qmhA c.47.2.1 33082 d.68.2.1 39568 1eut 605 1.61e+01 1eut b.1.1.5 21891 b.18.1.1 23712 b.68.1.1 27609 1b7yA 350 1.63e+01 1pysA d.104.1.1 40776 1aisA 182 1.63e+01 1ytbA d.129.1.1 41288 d.129.1.1 41289 1e3oC 160 1.64e+01 1au7A a.4.1.1 59197 a.35.1.1 59198 1e85A 127 1.65e+01 1bbhA a.24.3.2 16549 1adjA 421 1.66e+01 1adjA c.51.1.1 33188 d.104.1.1 40737 3sxlA 184 1.67e+01 1b7fA d.58.7.1 39173 d.58.7.1 39174 1imuA 107 1.68e+01 d.204.1.1 66218 1l1eA 287 1.70e+01 1g10A 102 1.76e+01 1g10A d.137.1.1 60191 2occF 98 1.78e+01 2occF g.41.5.3 45256 1ecsA 126 1.78e+01 1ecsA d.32.1.2 59407 1e1dA 553 1.80e+01 1e1dA e.26.1.1 43363 1clqA 903 1.81e+01 1clqA c.55.3.5 33717 e.8.1.1 43006 1rthA 560 1.82e+01 1rthA c.55.3.1 33576 e.8.1.2 43028 1e2uA 553 1.86e+01 1e1dA e.26.1.1 43362 1fh9A 312 1.86e+01 1taxA c.1.8.3 28913 1ggxA 223 1.87e+01 1ggxA d.22.1.1 38367 1pba 81 1.87e+01 1pytA d.58.3.1 39067 1a8vA 121 1.89e+01 1a62 a.140.3.1 64712 b.40.4.5 64713 1c0nA 406 1.90e+01 1c0nA c.67.1.3 34433 1ash 150 1.91e+01 1ash a.1.1.2 15622 1euu 605 1.92e+01 1eut b.1.1.5 21892 b.18.1.1 23713 b.68.1.1 27610 1jceA 344 1.94e+01 c.55.1.1 62876 c.55.1.1 62877 1oneA 436 1.94e+01 4enl c.1.11.1 29200 d.54.1.1 38844 1g5pA 289 1.95e+01 1cp2A c.37.1.10 32253 1jltB 122 1.99e+01 a.133.1.2 66868 1eljA 381 2.02e+01 4mbp c.94.1.1 35791 1jc4A 148 2.04e+01 1jc4A d.32.1.4 62863 1fp6A 289 2.04e+01 1cp2A c.37.1.10 32243 1ewjA 126 2.04e+01 1ecsA d.32.1.2 59526 1tfb 208 2.05e+01 1tfb a.74.1.2 18382 a.74.1.2 18383 1mpyA 307 2.06e+01 1mpyA d.32.1.3 38508 d.32.1.3 38509 1e6yC 247 2.08e+01 1mroC d.58.31.1 39441 1eu1A 780 2.09e+01 1dmr b.52.2.2 26903 c.81.1.1 35311 1k20A 310 2.15e+01 c.107.1.1 68027 1jcfA 344 2.17e+01 c.55.1.1 62878 c.55.1.1 62879 1hlvA 131 2.19e+01 a.4.1.7 65854 a.4.1.7 65855 1l1lA 739 2.20e+01 1hruA 188 2.21e+01 1hruA d.115.1.1 40926 1pamA 686 2.23e+01 1cxlA b.1.1.5 21846 b.3.1.1 22515 b.71.1.1 27753 c.1.8.1 28740 1lfo 128 2.24e+01 1hmt b.60.1.2 27223 1ab4 477 2.26e+01 1ab4 e.11.1.1 43251 1ca1 370 2.28e+01 1ca1 a.124.1.1 19340 b.12.1.3 23648 1ofgA 381 2.29e+01 1ofgA c.2.1.3 30064 d.81.1.5 39979 1eylA 186 2.29e+01 1wba b.42.4.1 25593 1iciA 256 2.30e+01 1iciA c.31.1.5 62266 1ka8A 100 2.32e+01 1jfzA 154 2.33e+01 a.149.1.1 66655 1h4vB 421 2.34e+01 1adjA c.51.1.1 60624 d.104.1.1 60625 1h6dA 433 2.34e+01 c.2.1.3 65656 d.81.1.5 65657 1iq0A 592 2.38e+01 a.27.1.1 66257 c.26.1.1 66258 d.67.2.1 66259 2mysB 166 2.39e+01 1wdcB a.39.1.5 17308 1tdj 514 2.39e+01 1tdj c.79.1.1 35297 d.58.18.2 39356 d.58.18.2 39357 1ejhA 190 2.42e+01 1ejhA d.86.1.1 40147 1ezvB 352 2.43e+01 1ezvB d.185.1.1 59543 d.185.1.1 59544 1ipcA 217 2.44e+01 1a8q 274 2.46e+01 1brt c.69.1.12 34702 1jf9A 408 2.46e+01 1c0nA c.67.1.3 62931 1b7fA 168 2.47e+01 1b7fA d.58.7.1 39169 d.58.7.1 39170 1f0xA 571 2.48e+01 1f0xA d.58.32.2 39483 d.145.1.1 41746 1pcfA 66 2.49e+01 1pcfA d.18.1.1 38142 1fa8A 135 2.49e+01 1qipA d.32.1.1 38486 1copD 66 2.52e+01 1orc a.35.1.2 17058 1j75A 67 2.55e+01 a.4.5.19 62673 1pysB 785 2.61e+01 1pysB a.6.1.1 16299 a.6.1.1 16300 b.40.4.4 25311 d.58.13.1 39310 d.104.1.1 40779 d.138.1.1 41455 1dq3A 454 2.63e+01 1dq3A b.86.1.2 28380 d.50.3.1 38798 d.95.2.2 40585 d.95.2.2 40586 1f3vA 179 2.64e+01 1f3vA d.58.22.1 39382 1sup 275 2.70e+01 1gci c.41.1.1 32510 1cdwA 179 2.70e+01 1ytbA d.129.1.1 41212 d.129.1.1 41213 1nmtA 392 2.73e+01 1nmtA d.108.1.2 40823 d.108.1.2 40824 1l8bA 190 2.75e+01 1dttA 560 2.77e+01 1rthA c.55.3.1 33611 e.8.1.2 43088 1jj2U 70 2.79e+01 1ffkS a.2.2.1 63106 1fcdA 401 2.79e+01 1fcdA c.3.1.5 30593 c.3.1.5 30594 d.87.1.1 40218 1vhh 162 2.80e+01 1vhh d.65.1.2 39550 1cc8A 73 2.80e+01 1cc8A d.58.17.1 39343 1ecmA 109 2.84e+01 1ecmA a.130.1.1 19492 1ihrA 76 2.87e+01 1ihrA d.191.1.1 62392 1gx3A 284 2.89e+01 1fpxA 352 2.92e+01 1fpxA a.4.5.29 59950 c.66.1.12 59951 1vrtA 560 2.94e+01 1rthA c.55.3.1 33574 e.8.1.2 43023 1c9oA 66 2.96e+01 1mjc b.40.4.5 25325 1dar 691 2.97e+01 1dar b.43.3.1 25707 c.37.1.8 32142 d.14.1.1 37547 d.58.11.1 39300 1lqc 56 2.97e+01 1pru a.35.1.5 17109 1a6jA 163 2.97e+01 1a6jA d.112.1.1 40915 1tr1A 447 3.01e+01 1e70M c.1.8.4 28957 1hy3A 294 3.04e+01 1gv9A 260 3.05e+01 1bg7 176 3.06e+01 2fha a.25.1.1 16686 1b0nB 57 3.11e+01 1b0nB a.34.1.1 17002 1b8aA 438 3.21e+01 1b8aA b.40.4.1 25244 d.104.1.1 40765 2hmiA 558 3.22e+01 1rthA c.55.3.1 33604 e.8.1.2 43106 1lg7A 182 3.24e+01 1jpnA 296 3.26e+01 a.24.13.1 67039 c.37.1.10 67040 1kxlA 199 3.31e+01 1cjxA 357 3.33e+01 1cjxA d.32.1.3 38516 d.32.1.3 38517 1ho1A 242 3.36e+01 1ho1A c.1.24.1 61097 1f3hA 142 3.36e+01 1f3hA g.52.1.1 45381 1grj 158 3.43e+01 1grj a.2.1.1 15691 d.26.1.2 38433 1hjp 203 3.46e+01 1hjp a.5.1.1 16274 a.60.2.1 17947 b.40.4.2 25266 1l3lA 234 3.48e+01 1qsaA 618 3.51e+01 1qsaA a.118.5.1 19182 d.2.1.6 36988 1pysA 350 3.56e+01 1pysA d.104.1.1 40775 1i5nA 146 3.56e+01 1i5nA a.24.10.3 61805 1ir6A 424 3.56e+01 1fg7A 356 3.57e+01 1gewA c.67.1.1 59819 1cpq 129 3.61e+01 1cpq a.24.3.2 16556 1k47A 337 3.63e+01 1f44A 324 3.66e+01 a.60.9.1 64982 d.163.1.1 64983 1a8y 367 3.68e+01 1a8y c.47.1.3 32781 c.47.1.3 32782 c.47.1.3 32783 1c4kA 730 3.69e+01 1ordA c.23.7.1 31273 c.67.1.5 34502 d.125.1.1 41123 1dbqA 289 3.70e+01 1qpzA c.93.1.1 35666 1p35A 299 3.74e+01 1p35A b.28.1.1 23925 1euvB 86 3.75e+01 1a5r d.15.1.1 37598 1gewA 356 3.85e+01 1gewA c.67.1.1 60470 2fcr 173 3.91e+01 1rcf c.23.5.1 31151 1ihvA 52 3.91e+01 1ihvA b.34.7.1 24629 1ktbA 405 3.94e+01 2pabA 127 3.96e+01 1etb1 b.3.4.1 22597 1jwhA 337 3.96e+01 1b89A 449 3.98e+01 1b89A a.118.1.3 19138