# List of top-scoring protein chains for T0323.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 1mpgA 282 2.51e-22 1mpgA a.96.1.3,d.129.1.2 18747,41296 1ornA 226 3.83e-22 a.96.1.1 87342 1p59A 226 3.85e-22 a.96.1.1 87794 2abk 211 2.57e-21 2abk a.96.1.1 18743 1ko9A 345 1.36e-17 a.96.1.3,d.129.1.2 68717,68718 1lwyA 324 1.61e-17 a.96.1.3,d.129.1.2 78285,78286 1fn7A 317 1.61e-17 1ebmA a.96.1.3,d.129.1.2 59892,59893 1ebmA 317 3.16e-17 1ebmA a.96.1.3,d.129.1.2 18751,41300 1yqkA 319 5.55e-17 1n3cA 317 5.87e-17 a.96.1.3,d.129.1.2 85293,85294 1m3qA 317 6.81e-17 a.96.1.3,d.129.1.2 91184,91185 1kg6A 225 7.20e-17 a.96.1.2 77382 1kg5A 225 8.15e-17 a.96.1.2 77381 1kg2A 225 9.04e-17 a.96.1.2 77378 1weiA 225 9.39e-17 a.96.1.2 109339 1rrsA 369 1.02e-16 a.96.1.2,d.113.1.3 97800,97801 1yqrA 319 1.10e-16 1kqjA 225 1.12e-16 a.96.1.2 72879 1kg7A 225 1.15e-16 a.96.1.2 77383 1n3aA 317 1.24e-16 a.96.1.3,d.129.1.2 85291,85292 1kg4A 225 1.33e-16 a.96.1.2 77380 1rrqA 369 1.34e-16 a.96.1.2,d.113.1.3 97798,97799 1mun 225 3.42e-16 1mun a.96.1.2 18744 1keaA 221 4.73e-15 a.96.1.2 68491 1pu6A 218 5.14e-13 a.96.1.5 95123 1ngnA 155 3.21e-06 a.96.1.2 85697 2csbA 519 2.71e-02 1vddA 228 7.58e-02 e.49.1.1 108519 1d8lA 149 2.11e-01 1hjp a.60.2.1,b.40.4.2 17948,25267 1hjp 203 2.20e-01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16274,17947,25266 1cuk 203 2.32e-01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16273,17946,25265 1ixrA 191 2.43e-01 a.60.2.1,b.40.4.2 76925,76926 2bhnA 214 8.02e-01 2bgwA 219 8.79e-01 1j8yF 297 1.23e+00 1ng1 a.24.13.1,c.37.1.10 62747,62748 1o9uA 350 1.56e+00 d.144.1.7 92691 1h8fB 350 1.66e+00 d.144.1.7 65734 1h8fA 352 1.67e+00 d.144.1.7 65733 1j8mF 297 1.69e+00 1ng1 a.24.13.1,c.37.1.10 62742,62743 1x2iA 75 1.81e+00 1uv5A 350 1.96e+00 d.144.1.7 100029 1cl3A 138 2.04e+00 2jhbA b.54.1.1 26949 1r0eA 391 2.06e+00 1q5kA 414 2.11e+00 d.144.1.7 104537 1io4D 141 2.12e+00 2jhbA b.54.1.1 62617 1j1bA 420 2.12e+00 d.144.1.7 90758 1pyxA 422 2.13e+00 d.144.1.7 95383 1q41A 424 2.13e+00 d.144.1.7 95774 1h9dB 134 2.14e+00 2jhbA b.54.1.1 60822 2jhbA 143 2.16e+00 2jhbA b.54.1.1 26950 1gngA 378 2.17e+00 d.144.1.7 76239 1iqpA 327 3.40e+00 a.80.1.1,c.37.1.20 62649,62650 1pznA 349 3.53e+00 a.60.4.1,c.37.1.11 95456,95457 1bvsA 203 3.61e+00 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16280,17955,25274 2a6cA 83 3.98e+00 1y88A 199 4.02e+00 2fmpA 335 4.03e+00 1z00A 89 4.80e+00 1vqoY 241 4.91e+00 2fpmA 322 5.22e+00 1q46A 175 5.31e+00 b.40.4.5 95782 2a19A 175 5.32e+00 1x6mA 196 5.47e+00 1doi 128 5.56e+00 1awd d.15.4.1 37676 2f1jA 322 5.57e+00 1jj2X 240 5.65e+00 1ffkV c.9.2.1 63109 1e0zA 128 5.67e+00 1awd d.15.4.1 59153 2a1jB 91 5.68e+00 1vh1A 256 7.77e+00 c.68.1.13 100632 2bj7A 138 8.26e+00 1bpe 335 8.59e+00 1bpyA a.60.6.1,a.60.12.1,d.218.1.2 18076,75815,75816 1huzA 335 9.20e+00 1bpyA a.60.6.1,a.60.12.1,d.218.1.2 61281,75850,75851 1vicA 262 9.40e+00 c.68.1.13 100756 1w5bA 364 1.04e+01 1fsz 372 1.05e+01 1fsz c.32.1.1,d.79.2.1 31750,39802 1zetA 388 1.06e+01 2alzA 390 1.06e+01 1w5eA 364 1.10e+01 2fvoA 333 1.15e+01 2a7vA 490 1.28e+01 2aplA 157 1.35e+01 1rq0A 342 1.44e+01 e.38.1.1 105044 1i89A 389 1.46e+01 c.95.1.2,c.95.1.2 66074,66075 1k5oA 86 1.49e+01 a.165.1.1 77269 1j2mA 99 1.52e+01 a.165.1.1 84018 1yr2A 741 1.52e+01 1j2nA 99 1.54e+01 a.165.1.1 84019 1nc5A 373 1.66e+01 a.102.1.6 85548 1ma3A 253 1.76e+01 c.31.1.5 78883 1ko7A 314 1.85e+01 c.98.2.1,c.91.1.2 72797,72798 1i88A 389 1.92e+01 c.95.1.2,c.95.1.2 66070,66071 1ttyA 87 1.95e+01 1qobA 98 2.12e+01 1awd d.15.4.1 37655 1bccB 422 2.23e+01 1be3B d.185.1.1,d.185.1.1 58948,58949 1z9bA 135 2.43e+01 1qr0A 228 2.54e+01 1qr0A d.150.1.1,d.150.1.1 59038,59039 1j7cA 98 2.54e+01 1awd d.15.4.1 62679 1lq9A 112 2.55e+01 d.58.4.3 78129 1j7bA 98 2.57e+01 1awd d.15.4.1 62678 1czpA 98 2.57e+01 1awd d.15.4.1 37645 1f51A 182 2.60e+01 1ixmA d.123.1.1 41116 1d8cA 723 2.61e+01 1d8cA c.1.13.1 29325 1p7tA 731 2.63e+01 c.1.13.1 94319 1wf6A 132 2.67e+01 1ixmA 192 2.67e+01 1ixmA d.123.1.1 41114 1bgxT 832 2.72e+01 1taq a.60.7.1,c.120.1.2,c.55.3.5,e.8.1.1 18083,33353,33699,42992 1taq 832 2.74e+01 1taq a.60.7.1,c.120.1.2,c.55.3.5,e.8.1.1 18082,33352,33698,42991 1jmsA 381 2.75e+01 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 1uocA 289 2.78e+01 c.55.3.9 99686 1a6zA 275 2.90e+01 1agdA b.1.1.2,d.19.1.1 20781,38280 1kdhA 363 2.92e+01 a.60.6.1,a.60.12.1,d.218.1.2 72349,75882,75883 1alc 123 2.99e+01 3lzt d.2.1.2 36596 1vrgA 527 2.99e+01 1yc5A 246 3.03e+01 1qogA 98 3.10e+01 1awd d.15.4.1 37657 1i8bA 389 3.11e+01 c.95.1.2,c.95.1.2 66078,66079 2g9dA 350 3.13e+01 1doqA 69 3.20e+01 1coo a.60.3.1 17968 1qofA 98 3.35e+01 1awd d.15.4.1 37653 1mxgA 435 3.42e+01 b.71.1.1,c.1.8.1 85193,85194 2cvhA 220 3.47e+01 1o6bA 169 3.50e+01 c.26.1.3 92564 1qlaA 656 3.55e+01 1qlaA a.7.3.1,c.3.1.4,d.168.1.1 16328,30427,42310 2an1A 292 3.58e+01 1xwiA 322 3.65e+01 1jwxA 389 3.70e+01 c.95.1.2,c.95.1.2 71920,71921 1rpl 251 3.71e+01 1bpyA a.60.12.1,d.218.1.2 75933,75934 1cmcA 104 3.73e+01 1cmbA a.43.1.5 17462 1jn3A 251 3.75e+01 1bpyA a.60.12.1,d.218.1.2 75864,75865 2ferA 411 3.78e+01 1t85A 414 3.79e+01 a.104.1.1 106650 1qmqA 414 3.80e+01 1phd a.104.1.1 18907 2a1mA 415 3.80e+01 1dz4A 414 3.81e+01 1phd a.104.1.1 18903 1yrcA 414 3.81e+01 2a1nA 415 3.81e+01 1gekA 415 3.81e+01 1phd a.104.1.1 18915 6cp4 414 3.81e+01 1phd a.104.1.1 18924 1lwlA 417 3.81e+01 a.104.1.1 78273 1p2yA 420 3.82e+01 a.104.1.1 93961 2fe6A 421 3.82e+01 1m1zA 513 3.83e+01 c.26.2.1,d.153.1.1 78457,78458 1gebA 415 3.88e+01 1phd a.104.1.1 18932 2a1oA 415 3.88e+01 2cp4 414 3.88e+01 1phd a.104.1.1 18933 1i86A 389 4.06e+01 c.95.1.2,c.95.1.2 66068,66069 1qzxA 440 4.06e+01 a.24.13.1,a.36.1.1,c.37.1.10 96711,96712,96713 1iwjA 415 4.26e+01 a.104.1.1 71489 1d6hA 387 4.27e+01 1bi5A c.95.1.2,c.95.1.2 36005,36006 1chwA 389 4.28e+01 1bi5A c.95.1.2,c.95.1.2 35997,35998 1cmlA 389 4.30e+01 1bi5A c.95.1.2,c.95.1.2 35989,35990 1bq6A 388 4.35e+01 1bi5A c.95.1.2,c.95.1.2 35987,35988 1bi5A 389 4.35e+01 1bi5A c.95.1.2,c.95.1.2 35985,35986 1v3vA 333 4.37e+01 b.35.1.2,c.2.1.1 108345,108346 1uh9A 325 4.39e+01 b.50.1.2 107844 2a6hA 315 4.44e+01 2spcA 107 4.45e+01 2spcA a.7.1.1 16311 1vr8A 142 4.48e+01 1z7aA 308 4.53e+01 1j71A 334 4.57e+01 1eagA b.50.1.2 62669 2cyjA 118 4.71e+01 1mjoA 104 4.72e+01 1cmbA a.43.1.5 17466 1f74A 293 4.96e+01 1nal3 c.1.10.1 29079 1huxA 270 5.06e+01 1huxA c.55.1.5 61278 1yroA 123 5.08e+01 1v8oA 158 5.11e+01 c.120.1.1 100511 1k1gA 131 5.17e+01 d.51.1.1 68015 1jsdB 176 5.27e+01 h.3.1.1 63259 1f6fA 199 5.27e+01 1f6fA a.26.1.1 16839 1gs9A 165 5.28e+01 a.24.1.1 83313 1rv0I 160 5.35e+01 h.3.1.1 97896 1bkzA 135 5.43e+01 1a3k b.29.1.3 24202 1nyaA 176 5.65e+01 a.39.1.5 92335 1ydhA 216 5.67e+01 1r8uA 50 5.70e+01 j.96.1.1 97249 1bdfA 235 5.74e+01 1bdfA d.74.3.1,d.181.1.1 39727,42602 1iq6A 134 5.86e+01 d.38.1.4 76755 1b68A 191 5.93e+01 1nfn a.24.1.1 59076 1zq1C 633 5.98e+01 1t6mA 299 5.99e+01 1x0mA 403 6.16e+01 1xccA 220 6.28e+01 1dt1A 129 6.29e+01 1c52 a.3.1.1 15811 1c52 131 6.31e+01 1c52 a.3.1.1 15810 1focA 132 6.31e+01 1c52 a.3.1.1 15812 2fwlA 133 6.31e+01 1d6iA 388 6.41e+01 1bi5A c.95.1.2,c.95.1.2 36001,36002 1lm5A 214 6.48e+01 d.211.2.1 74029 1objA 414 6.52e+01 c.117.1.1 92757 1le4 144 6.55e+01 1nfn a.24.1.1 16528 1e7pG 655 6.61e+01 1qlaA a.7.3.1,c.3.1.4,d.168.1.1 59359,59360,59361 2bs3A 656 6.61e+01 2avyI 129 6.61e+01 1pfsA 78 6.67e+01 1pfsA b.40.4.7 25391 2g7cA 255 6.69e+01 1ou5A 448 6.73e+01 a.173.1.1,d.218.1.4 87445,87446 1fxiA 96 6.78e+01 1awd d.15.4.1 37664 1qcrB 423 6.80e+01 1be3B d.185.1.1,d.185.1.1 59027,59028 1j7aA 98 6.80e+01 1awd d.15.4.1 62677 1ww8A 439 6.83e+01 1roe 97 7.01e+01 1awd d.15.4.1 37672 1ppjB 439 7.01e+01 d.185.1.1,d.185.1.1 104254,104255 2vhbA 146 7.08e+01 2vhbA a.1.1.2 15629 1sqbB 453 7.15e+01 d.185.1.1,d.185.1.1 105892,105893 1e9zB 569 7.19e+01 b.92.1.1,c.1.9.2 64852,64853 1j51A 414 7.22e+01 a.104.1.1 66393 2azeA 155 7.29e+01 1y6iA 233 7.34e+01 1ynjA 314 7.36e+01 1c8jA 414 7.38e+01 1phd a.104.1.1 59085 1i6vA 314 7.44e+01 d.74.3.1,d.181.1.1 61852,61853 1b0yA 85 7.44e+01 1ckuA g.35.1.1 44980 1hip 85 7.44e+01 g.35.1.1 44983 1gpc 218 7.50e+01 1gpc b.40.4.7 25393 1p3cA 215 7.64e+01 b.47.1.1 93996 1zorA 399 7.72e+01 1xsnA 335 7.79e+01 2bcqA 335 7.81e+01 1rztA 331 7.81e+01 a.60.6.1,a.60.12.1,d.218.1.2 98224,98225,98226 2avyM 117 7.91e+01 2ao9A 155 8.01e+01 1hqmA 313 8.01e+01 i.8.1.1 45972 1ztbA 401 8.02e+01 2d62A 375 8.18e+01 1gwiA 411 8.18e+01 a.104.1.1 76364 1w2vA 348 8.22e+01 1ckuA 85 8.27e+01 1ckuA g.35.1.1 44981 1tezA 474 8.28e+01 1jsmB 176 8.33e+01 h.3.1.1 63265 1uiyA 253 8.34e+01 c.14.1.3 99448 1owlA 484 8.41e+01 a.99.1.1,c.28.1.1 93647,93648 1p88A 216 8.48e+01 1vejA 74 8.58e+01 2g64A 140 8.98e+01 1o3uA 135 8.99e+01 a.24.16.3 86615