# List of top-scoring protein chains for t04-100-30-bys 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 1l0iA 78 1.33e-07 a.28.1.1 77643 1f80D 81 2.45e-05 1acp a.28.1.1 59686 1uc2A 481 2.10e-01 unknown_sccs -11725 1lm8B 118 2.59e-01 d.15.1.1 74033 1vcbA 118 4.05e-01 1vcbA d.15.1.1 37603 1j3mA 129 5.35e-01 1ytfB 53 5.35e-01 1ytfB a.32.1.1 16997 1o4vA 183 5.63e-01 c.23.8.1 86628 1nh2B 53 5.91e-01 a.32.1.1 -777 1eg5A 384 6.44e-01 1ecxA c.67.1.3 34429 1jj2W 91 6.84e-01 1ffkU d.29.1.1 63108 1s72X 92 7.10e-01 1cby 259 8.65e-01 1cby d.103.1.1 40705 1qczA 169 1.02e+00 1qczA c.23.8.1 31276 1ireA 204 1.06e+00 d.149.1.1 76769 1ugpA 203 1.11e+00 1jr2A 286 1.12e+00 c.113.1.1 67111 1otfA 62 1.12e+00 1otfA d.80.1.1 39820 1fm0D 81 1.12e+00 1fmaD d.15.3.1 37642 1clxA 347 1.29e+00 1taxA c.1.8.3 28899 1rqtA 37 1.37e+00 a.108.1.1 -1473 1gd0A 122 1.42e+00 1dptA d.80.1.3 39834 1jidA 128 1.51e+00 d.201.1.1 66735 1jqeA 292 1.57e+00 c.66.1.19 71789 1nvpB 57 1.60e+00 a.32.1.1 -779 1oj4A 283 1.66e+00 d.14.1.5 -9088 d.58.26.5 -10133 1j6oA 268 1.69e+00 c.1.9.12 77088 1p3wA 404 1.69e+00 c.67.1.3 87752 1fwkA 296 1.71e+00 1fwkA d.14.1.5 37576 d.58.26.1 39398 1h72C 296 1.75e+00 d.14.1.5 60712 d.58.26.1 60713 1v9dA 340 1.76e+00 unknown_sccs -1762 1eluA 390 2.00e+00 1elqA c.67.1.3 34434 1g8mA 593 2.00e+00 1g8mA c.24.1.3 60371 c.97.2.1 60372 1j0aA 325 2.01e+00 c.79.1.1 83871 1elqA 390 2.11e+00 1elqA c.67.1.3 34436 1b25A 619 2.13e+00 1b25A a.110.1.1 19044 d.152.1.1 41796 1g61A 228 2.19e+00 1g61A d.126.1.1 41126 1se9A 126 2.31e+00 d.15.1.1 -9145 1h5wA 309 2.36e+00 e.27.1.1 65635 1lngA 87 2.45e+00 d.201.1.1 74045 1rkqA 282 2.80e+00 c.108.1.10 -6847 1tc5A 194 2.88e+00 1bolA 222 3.18e+00 1bolA d.124.1.1 41120 1bu8A 452 3.30e+00 1gpl b.12.1.2 23647 c.69.1.19 34795 1ct5A 256 3.32e+00 1ct5A c.1.6.2 28663 1bi5A 389 3.42e+00 1bi5A c.95.1.2 35985 c.95.1.2 35986 1i88A 389 3.45e+00 c.95.1.2 66070 c.95.1.2 66071 1lc5A 364 3.54e+00 c.67.1.1 73827 1v7nV 163 3.86e+00 a.26.1.2 -715 1bg6 359 4.01e+00 1bg6 a.100.1.5 18810 c.2.1.6 30214 1k47A 337 4.02e+00 d.14.1.5 72040 d.58.26.4 72041 1mlwA 301 4.03e+00 d.178.1.1 79289 1mwwA 128 4.12e+00 unknown_sccs -10451 1e1hA 287 4.17e+00 d.92.1.7 83167 1qj2B 809 4.18e+00 1qj2B 1go3F 107 4.44e+00 a.60.8.2 65407 1gx1A 160 4.54e+00 d.79.5.1 70675 1nnhA 294 4.58e+00 d.104.1.1 -10772 1n62B 809 4.78e+00 d.41.1.1 80092 d.133.1.1 80093 1dptA 117 4.95e+00 1dptA d.80.1.3 39862 1gu7A 364 5.01e+00 b.35.1.2 83321 c.2.1.1 83322 1jbeA 128 5.17e+00 3chy c.23.1.1 62845 1azsA 220 5.70e+00 1azsA d.58.29.1 39416 1oeyA 83 5.71e+00 d.15.2.2 -9162 1ijgA 309 5.76e+00 1fouA e.27.1.1 62493 1gpl 432 5.89e+00 1gpl b.12.1.2 23645 c.69.1.19 34793 1l5wA 796 6.19e+00 c.87.1.4 73605 3pmgA 561 6.25e+00 3pmgA c.84.1.1 35408 c.84.1.1 35409 c.84.1.1 35410 d.129.2.1 41301 1nv8A 284 6.58e+00 c.66.1.30 86224 3chy 128 6.67e+00 3chy c.23.1.1 31038 1h05A 146 6.88e+00 c.23.13.1 76433 1i1iP 681 7.20e+00 1i1iP d.92.1.5 40297 1fecA 490 7.21e+00 3grs c.3.1.5 30489 c.3.1.5 30490 d.87.1.1 40176 1guzA 310 7.38e+00 c.2.1.5 65586 d.162.1.1 65587 1qgoA 264 7.40e+00 1qgoA c.92.1.2 35596 1hfoA 113 7.42e+00 d.80.1.3 61006 1hnjA 317 7.42e+00 1hn9A c.95.1.1 35969 c.95.1.1 35970 1ojaA 520 7.62e+00 c.3.1.2 -6000 d.16.1.5 -9220 1s3eA 520 7.63e+00 c.3.1.2 -6022 d.16.1.5 -9242 1k0dA 260 7.68e+00 a.45.1.1 67930 c.47.1.5 67931 1dbxA 158 7.69e+00 1dbuA d.116.1.1 40928 1sedA 117 8.03e+00 1atlA 202 8.41e+00 1atlA d.92.1.9 40322 1k8kA 418 8.43e+00 c.55.1.1 68305 c.55.1.1 68306 1c3cA 429 8.45e+00 1c3cA a.127.1.1 19425 1fiy 883 8.52e+00 1fiy c.1.12.3 29307 1ofgA 381 8.60e+00 1ofgA c.2.1.3 30064 d.81.1.5 39979 1pyaB 228 8.96e+00 1pyaB 1so2A 420 9.37e+00 a.125.1.1 -1735 1cyo 93 9.43e+00 1cyo d.120.1.1 41065 1qlmA 316 9.52e+00 1qlmA d.147.1.1 41765 1vicA 262 9.87e+00 c.68.1.13 -8252 1j54A 186 1.01e+01 c.55.3.5 77077 1xsm 390 1.02e+01 1xsm a.25.1.2 16804 1nbwA 607 1.02e+01 c.8.6.1 80393 c.55.1.6 80394 c.55.1.6 80395 1a6jA 163 1.02e+01 1a6jA d.112.1.1 40915 1lucA 355 1.02e+01 1lucA c.1.16.1 29547 1szqA 483 1.05e+01 unknown_sccs -11791 1lmb3 92 1.05e+01 1lmb3 1h5qA 265 1.05e+01 1cydA c.2.1.2 60643 1f83A 425 1.05e+01 1f82A d.92.1.7 40306 1o4sA 389 1.05e+01 c.67.1.1 86620 1b5tA 275 1.07e+01 1b5tA c.1.23.1 29676 1f08A 148 1.08e+01 1f08A d.89.1.2 59564 1gu2A 124 1.09e+01 a.3.1.1 76348 1mpgA 282 1.09e+01 1mpgA a.96.1.3 18747 d.129.1.2 41296 1afwA 393 1.16e+01 1afwA c.95.1.1 35900 c.95.1.1 35901 1lucB 324 1.19e+01 1lucA c.1.16.1 29548 1mldA 314 1.20e+01 2cmd c.2.1.5 30122 d.162.1.1 42089 1m3kA 392 1.22e+01 c.95.1.1 78565 c.95.1.1 78566 1m4tA 392 1.22e+01 c.95.1.1 78617 c.95.1.1 78618 1mdbA 539 1.24e+01 e.23.1.1 79008 1e2tA 284 1.24e+01 1e2tA d.3.1.5 37121 1a4iA 301 1.26e+01 1a4iA c.2.1.7 30278 c.58.1.2 33926 1pzgA 331 1.27e+01 c.2.1.5 -5931 d.162.1.1 -11498 1t8hA 277 1.30e+01 1bkrA 109 1.31e+01 1bkrA a.40.1.1 17394 1pujA 282 1.32e+01 c.37.1.8 88294 1jjyA 636 1.32e+01 1jjyA 1jqnA 883 1.33e+01 c.1.12.3 77159 1jeoA 180 1.35e+01 c.80.1.3 66611 1p5sA 203 1.36e+01 a.40.1.1 -900 1fnnA 389 1.36e+01 1fnnA a.4.5.11 16129 c.37.1.20 32426 1mqiA 263 1.37e+01 c.94.1.1 -8681 1oz9A 150 1.37e+01 unknown_sccs -10588 1f2rI 100 1.38e+01 1c9fA d.15.2.1 37641 1h6dA 433 1.45e+01 c.2.1.3 65656 d.81.1.5 65657 1vjrA 271 1.46e+01 unknown_sccs -6853 1stfI 98 1.50e+01 1stfI d.17.1.2 38006 1p4wA 99 1.51e+01 a.4.6.2 87783 1hu4A 288 1.51e+01 1hu4A 1n5dA 288 1.52e+01 c.2.1.2 80030 1o60A 292 1.54e+01 c.1.10.4 -5549 1lzlA 323 1.54e+01 c.69.1.2 78306 1d1gA 168 1.56e+01 1d1gA c.71.1.1 34889 1e5xA 486 1.58e+01 c.79.1.1 59283 1jyoA 130 1.64e+01 d.198.1.1 67483 1pv6A 417 1.67e+01 unknown_sccs -12263 1l0wA 580 1.67e+01 b.40.4.1 73426 d.74.4.1 73427 d.104.1.1 73428 1ssqA 267 1.69e+01 1hlrA 907 1.69e+01 a.56.1.1 65850 d.15.4.2 65851 d.41.1.1 65852 d.133.1.1 65853 1l2tA 235 1.70e+01 c.37.1.12 73514 1szwA 379 1.70e+01 unknown_sccs -10164 1mucA 373 1.72e+01 1mucA c.1.11.2 29236 d.54.1.1 38880 1div 149 1.73e+01 1div d.99.1.1 40692 d.100.1.1 40693 1r9lA 309 1.73e+01 c.94.1.1 -8700 1ka2A 499 1.73e+01 d.92.1.5 77305 1odfA 290 1.74e+01 c.37.1.6 -7045 1ff9A 450 1.75e+01 1ff9A c.2.1.3 30039 d.81.1.2 39954 1o5uA 101 1.75e+01 b.82.1.8 -4845 1sur 215 1.76e+01 1sur c.26.2.2 31620 1c1dA 355 1.76e+01 1bw9A c.2.1.7 30270 c.58.1.1 33918 1sra 151 1.79e+01 1sra a.39.1.3 17190 1owfA 99 1.80e+01 a.55.1.1 87487 1gntA 553 1.83e+01 e.26.1.1 70290 1e2uA 553 1.84e+01 1e1dA e.26.1.1 43362 1qq5A 253 1.85e+01 1qq5A c.108.1.1 43327 1iv3A 152 1.85e+01 d.79.5.1 76828 1o22A 170 1.85e+01 d.238.1.1 86557 2dhqA 146 1.86e+01 2dhqA c.23.13.1 31382 1hyhA 309 1.90e+01 1hyhA c.2.1.5 30150 d.162.1.1 42117 1uv7A 110 1.90e+01 unknown_sccs -10256 1qq7A 253 1.91e+01 1qq5A c.108.1.1 43329 1vid 221 1.91e+01 1vid c.66.1.1 34178 1b4fA 82 1.93e+01 1b4fA a.60.1.2 17934 1a8e 329 1.97e+01 1cb6A c.94.1.2 35888 1i0dA 332 2.01e+01 1pscA c.1.9.3 61487 1hzyA 332 2.02e+01 1pscA c.1.9.3 61468 1s6yA 450 2.02e+01 1s0yA 76 2.04e+01 d.80.1.1 -10434 1j5vA 351 2.04e+01 c.72.1.1 71585 1p2xA 159 2.05e+01 1n97A 389 2.06e+01 a.104.1.1 80335 1gnlA 544 2.07e+01 e.26.1.1 70287 1ks9A 291 2.09e+01 a.100.1.7 68857 c.2.1.6 68858 2ng1 293 2.12e+01 1ng1 a.24.13.1 16962 c.37.1.10 32273 1qi9A 556 2.14e+01 1qhbA a.111.1.2 19053 1lssA 140 2.15e+01 c.2.1.9 74246 1sacA 204 2.15e+01 1sacA b.29.1.5 24237 1nrzA 164 2.16e+01 c.38.1.1 86131 1su8A 636 2.19e+01 e.26.1.2 -12015 1mp1A 111 2.22e+01 unknown_sccs -996 1lddA 74 2.25e+01 a.4.5.34 73841 1idrA 136 2.27e+01 1dlyA a.1.1.1 62301 1b0nA 111 2.30e+01 1b0nA a.34.1.1 17001 a.35.1.3 17064 1n3kA 130 2.30e+01 a.77.1.4 79965 1ryoA 327 2.32e+01 c.94.1.2 -8708 1k4nA 192 2.33e+01 d.32.1.5 72059 1ek6A 348 2.33e+01 1xel c.2.1.2 29800 1mqoA 227 2.35e+01 1fmjA 351 2.35e+01 c.37.1.5 59879 1a8i 842 2.35e+01 1a8i c.87.1.4 35490 1omhA 293 2.38e+01 unknown_sccs -10527 2kfnA 605 2.42e+01 1xwl c.55.3.5 33682 e.8.1.1 42975 1jhfA 202 2.44e+01 a.4.5.2 63057 b.87.1.1 63058 1dd3C 32 2.44e+01 1dd3C a.108.1.1 19033 1dbwA 126 2.46e+01 1dbwA c.23.1.1 31095 1uekA 275 2.50e+01 d.14.1.5 88483 d.58.26.5 88484 1cc1S 283 2.51e+01 2frvA e.19.1.1 43313 1v54E 109 2.53e+01 a.118.11.1 -1652 1iwmA 186 2.53e+01 b.125.1.2 83758 1n2zA 245 2.53e+01 c.92.2.2 79865 1s0yB 71 2.54e+01 d.80.1.1 -10442 1on2A 142 2.56e+01 a.4.5.24 87103 a.76.1.1 87104 1ro2A 216 2.56e+01 unknown_sccs -11391 1jpmA 366 2.57e+01 c.1.11.2 67031 d.54.1.1 67032 1ut7A 171 2.59e+01 unknown_sccs -4724 1nstA 325 2.60e+01 1nstA c.37.1.5 31951 1ci4A 89 2.62e+01 1qckA a.60.5.1 17970 1ughI 82 2.64e+01 1ugiA d.17.5.1 38133 2occE 109 2.65e+01 2occE a.118.11.1 19224 1i50J 70 2.65e+01 a.4.11.1 61764 1dqeA 137 2.66e+01 1dqeA a.39.2.1 17388 1j8yF 297 2.66e+01 1ng1 a.24.13.1 62747 c.37.1.10 62748 1ga6A 372 2.67e+01 1ga1A c.41.1.2 32556 1d2zB 153 2.69e+01 1d2zB a.77.1.2 18439 1ugiA 84 2.70e+01 1ugiA d.17.5.1 38125 1j9iA 68 2.71e+01 a.6.1.5 71619 1te5A 257 2.71e+01 1km4A 247 2.71e+01 c.1.2.3 72740 3kvt 115 2.72e+01 1t1dA d.42.1.2 38642 1fiqB 350 2.74e+01 1fiqB d.87.2.1 40229 d.145.1.3 41760 1vjtA 483 2.76e+01 c.2.1.5 -5941 d.162.1.2 -11508 1npyA 271 2.76e+01 c.2.1.7 85995 c.58.1.5 85996 1jihA 531 2.77e+01 unknown_sccs -10212 unknown_sccs -11922 1gx3A 284 2.78e+01 d.3.1.5 70678 1e5pA 151 2.79e+01 1bj7 b.60.1.1 59272 1ub9A 100 2.79e+01 a.4.5.28 -231 1eueA 86 2.79e+01 1cyo d.120.1.1 59504 1kcfA 258 2.83e+01 a.140.2.1 68434 c.55.3.7 68435 1huxA 270 2.85e+01 1huxA c.55.1.5 61278 1pieA 419 2.87e+01 d.14.1.5 -9075 unknown_sccs -10120 1g87A 614 2.89e+01 a.102.1.2 83275 b.2.2.2 83276 1jr8A 117 2.89e+01 a.24.15.1 67115 1ep3B 262 2.90e+01 1ep2B b.43.4.2 25664 c.25.1.3 31554 1b8aA 438 2.91e+01 1b8aA b.40.4.1 25244 d.104.1.1 40765 1g8eA 116 2.91e+01 1g8eA a.145.1.1 60346 1qf5A 431 2.95e+01 1adeA c.37.1.10 32212 1uvjA 664 2.98e+01 e.8.1.6 -11964 1qgdA 662 2.99e+01 c.36.1.6 88367 c.36.1.10 88368 c.48.1.1 88369 2rslA 140 3.00e+01 2rslA c.53.1.1 33345 1pzxA 289 3.03e+01 c.119.1.1 -8623 1kugA 203 3.04e+01 d.92.1.9 73008 1ftkA 279 3.04e+01 1gr2A c.94.1.1 35819 1qz9A 416 3.04e+01 c.67.1.3 -8180 1si2A 149 3.05e+01 1uxy 340 3.08e+01 2mbr d.145.1.2 41748 d.146.1.1 41761 1n0wA 243 3.10e+01 c.37.1.11 79772 1xvaA 292 3.12e+01 1xvaA c.66.1.5 34183 1n2eA 300 3.16e+01 c.26.1.4 85268 1o50A 157 3.20e+01 d.37.1.1 -9604 d.37.1.1 -9605 1alo 907 3.20e+01 1alo 1guqA 348 3.22e+01 1guqA d.13.1.2 37522 d.13.1.2 37523 1jy2P 48 3.24e+01 h.1.8.1 67442 1ngr 85 3.24e+01 1ngr a.77.1.2 18422 1ubi 76 3.25e+01 1ubi d.15.1.1 37584 1io7A 368 3.25e+01 1f4tA a.104.1.1 18971 1r31A 428 3.25e+01 d.58.20.1 -10108 d.179.1.1 -11716 1nu0A 138 3.26e+01 unknown_sccs -7658 2bc2A 227 3.26e+01 1a7tA d.157.1.1 42031 1j0lA 98 3.31e+01 unknown_sccs -9789 1sr7A 259 3.34e+01 1jg8A 347 3.35e+01 1jg8A c.67.1.1 62946 1riqA 465 3.36e+01 unknown_sccs -1295 d.104.1.1 -10769 1udvA 89 3.37e+01 d.68.6.1 -10280 1lh0A 213 3.37e+01 c.61.1.1 73896 1qmyA 167 3.38e+01 1qmyA d.3.1.2 37094 1h99A 224 3.39e+01 a.142.1.1 60814 a.142.1.1 60815 1hhsA 664 3.42e+01 1hi0P e.8.1.6 61045 4uagA 437 3.42e+01 4uagA c.5.1.1 30651 c.59.1.1 33952 c.72.2.1 34955 1qflA 389 3.42e+01 1afwA c.95.1.1 35908 c.95.1.1 35909 1ufoA 238 3.42e+01 unknown_sccs -8303 1orrA 347 3.45e+01 c.2.1.2 -5776 1mp4A 292 3.46e+01 c.68.1.6 79376 1m6sA 347 3.46e+01 c.67.1.1 78701 1js3A 486 3.49e+01 c.67.1.6 67215 1i60A 278 3.55e+01 c.1.15.4 71118 1a99A 344 3.57e+01 1pot c.94.1.1 35812 1mszA 86 3.58e+01 d.68.7.1 79428 1h0oA 390 3.58e+01 a.25.1.2 70845 1np6A 174 3.59e+01 c.37.1.10 85954 1pa7A 130 3.59e+01 a.40.1.1 -896 1gjsA 65 3.59e+01 1gab a.8.1.2 60578 1r6uA 437 3.59e+01 c.26.1.1 -6594 1gqpA 221 3.60e+01 b.18.1.9 70372 1i3dA 146 3.61e+01 a.1.1.2 61587 1i74A 309 3.61e+01 1i74A c.107.1.1 61867 4pah 308 3.62e+01 4pah d.178.1.1 42576 1ogwA 76 3.63e+01 d.15.1.1 87001 1jetA 517 3.63e+01 1jevA c.94.1.1 35718 1r4kA 169 3.65e+01 unknown_sccs -3625 1iomA 377 3.65e+01 a.103.1.1 83698 6paxA 133 3.66e+01 6paxA a.4.1.5 64758 a.4.1.5 64759 1v5sA 126 3.66e+01 1vpt 348 3.70e+01 3mag c.66.1.25 34207 1gouA 116 3.75e+01 d.1.1.2 65429 1jnyA 435 3.75e+01 b.43.3.1 66982 b.44.1.1 66983 c.37.1.8 66984 1gp6A 356 3.80e+01 b.82.2.1 65441 1ugmA 125 3.91e+01 1v97A 1332 3.96e+01