# 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 1je0A 236 6.77e-02 c.56.2.1 66581 1k3fA 253 3.23e-01 c.56.2.1 68105 1ex2A 189 4.19e-01 1ex2A c.51.4.2 33225 1lx7A 253 4.73e-01 1jmxA 494 5.53e-01 a.3.1.7 66901 a.3.1.7 66902 b.1.1.6 66903 b.1.1.6 66904 b.61.4.1 66905 1fjgI 128 7.88e-01 1fjfI d.14.1.1 37559 1ir6A 424 8.26e-01 1rgs 288 1.02e+00 1rgs b.82.3.2 28146 b.82.3.2 28147 1b63A 333 1.24e+00 1b63A d.14.1.3 37566 d.122.1.2 41107 1dr8B 344 1.31e+00 1cnzA c.77.1.1 35052 1idm 343 1.33e+00 1cnzA c.77.1.1 35035 1fcjA 322 1.58e+00 1oasA c.79.1.1 35289 1azwA 313 1.63e+00 1qtrA c.69.1.7 34658 1lxtA 561 1.64e+00 3pmgA c.84.1.1 35432 c.84.1.1 35433 c.84.1.1 35434 d.129.2.1 41309 1qd1A 325 1.71e+00 1qd1A d.58.34.1 39493 d.58.34.1 39494 3pmgA 561 1.83e+00 3pmgA c.84.1.1 35408 c.84.1.1 35409 c.84.1.1 35410 d.129.2.1 41301 1d5yA 292 1.83e+00 1d5yA a.4.1.8 16055 a.4.1.8 16056 d.60.1.2 39532 1ipd 345 2.34e+00 1cnzA c.77.1.1 35038 1qhtA 775 2.51e+00 1tgoA c.55.3.5 33722 e.8.1.1 43011 1jmkC 230 2.66e+00 1oasA 322 2.81e+00 1oasA c.79.1.1 35293 1prxA 224 2.87e+00 1prxA c.47.1.10 33076 2at2A 300 2.88e+00 3csuA c.78.1.1 35196 c.78.1.1 35197 1a8h 500 3.11e+00 1a8h a.27.1.1 16922 c.26.1.1 31589 1ex1A 605 3.29e+00 1ex1A c.1.8.7 29013 c.23.11.1 31347 1hw7A 255 3.42e+00 1i7fA d.193.1.1 61297 1dquA 538 3.79e+00 1dquA c.1.12.6 29314 1jj2E 177 3.92e+00 1ffk1 d.141.1.1 63089 d.141.1.1 63090 1uby 367 4.37e+00 1uby a.128.1.1 19435 1qmpA 130 4.55e+00 1dz3A c.23.1.1 31106 1hyeA 313 4.57e+00 2cmd c.2.1.5 61400 d.162.1.1 61401 1prxB 224 4.60e+00 1prxA c.47.1.10 33077 1ap8 213 4.67e+00 1ap8 d.86.1.1 40151 1i58A 189 5.32e+00 1b3qA d.122.1.3 61773 1dosA 358 5.33e+00 1dosA c.1.10.2 29175 1dz3A 130 5.41e+00 1dz3A c.23.1.1 31105 1l0oA 150 5.66e+00 1dg3A 592 5.80e+00 1dg3A a.114.1.1 19078 c.37.1.8 32153 1ast 200 5.96e+00 1iae d.92.1.8 40310 1iae 200 6.30e+00 1iae d.92.1.8 40311 1d3vA 323 6.36e+00 1d3vA c.42.1.1 32559 2pth 193 6.40e+00 2pth c.56.3.1 33793 1cm7A 363 6.47e+00 1cnzA c.77.1.1 35063 1lehA 364 6.50e+00 1bw9A c.2.1.7 30268 c.58.1.1 33916 1iab 200 6.68e+00 1iae d.92.1.8 40312 1sup 275 6.73e+00 1gci c.41.1.1 32510 1dcfA 136 6.88e+00 1dcfA c.23.1.2 31124 1rlaA 323 6.89e+00 1d3vA c.42.1.1 32561 1ihvA 52 7.04e+00 1ihvA b.34.7.1 24629 1ffk1 177 7.22e+00 1ffk1 1geqA 248 7.50e+00 2tysA c.1.2.4 28589 1jq3A 296 8.01e+00 c.66.1.17 67079 1dih 273 8.20e+00 1drw c.2.1.3 30056 d.81.1.3 39971 1srrA 124 8.54e+00 1dz3A c.23.1.1 31110 1iexA 605 8.69e+00 c.1.8.7 66127 c.23.11.1 66128 1aa8A 347 9.40e+00 1an9A c.4.1.2 30619 d.16.1.3 37906 1broA 277 9.78e+00 1brt c.69.1.12 34700 1jeyB 565 9.95e+00 1jeqB e.31.1.2 62925 1arzC 273 9.98e+00 1drw c.2.1.3 30061 d.81.1.3 39976 1io2A 213 1.04e+01 1ekeA c.55.3.1 62612 1jeqB 565 1.11e+01 1jeqB e.31.1.2 62922 1cvl 319 1.14e+01 1cvl c.69.1.18 34786 1inlA 296 1.16e+01 c.66.1.17 66220 1brt 277 1.19e+01 1brt c.69.1.12 34699 1a8q 274 1.25e+01 1brt c.69.1.12 34702 1i7fA 292 1.26e+01 1i7fA d.193.1.1 61888 1lvl 458 1.28e+01 1lvl c.3.1.5 30567 c.3.1.5 30568 d.87.1.1 40205 1an9A 340 1.30e+01 1an9A c.4.1.2 30617 d.16.1.3 37904 1cnzA 363 1.34e+01 1cnzA c.77.1.1 35061 1b3qA 379 1.35e+01 1b3qA a.30.2.1 16993 b.40.7.1 25454 d.122.1.3 41112 1fp1D 372 1.37e+01 1fpqA a.4.5.29 59939 c.66.1.12 59940 2cevA 299 1.38e+01 1d3vA c.42.1.1 32576 1j5eK 129 1.40e+01 1qtrA 317 1.41e+01 1qtrA c.69.1.7 34660 1tgsI 56 1.42e+01 1tgsI g.15.1.1 44706 1ig3A 263 1.45e+01 1ig3A b.82.6.1 62358 c.100.1.1 62359 1fsz 372 1.46e+01 1fsz c.32.1.1 31750 d.79.2.1 39802 1h61A 364 1.54e+01 1oyc c.1.4.1 60657 1d0qA 103 1.55e+01 1d0qA g.41.3.2 45208 1ehiA 377 1.58e+01 1iow c.30.1.2 31716 d.142.1.1 41484 2fsp 124 1.59e+01 1dz3A c.23.1.1 31119 1jmsA 381 1.61e+01 a.60.6.1 66889 e.9.1.1 66890 1dcjA 81 1.62e+01 1dcjA d.68.3.1 59115 1bmv2 374 1.65e+01 1bmv2 1qg8A 255 1.76e+01 1qg8A c.68.1.1 34505 1fps 348 1.78e+01 1uby a.128.1.1 19436 1krhA 338 1.78e+01 1tgoA 773 1.89e+01 1tgoA c.55.3.5 33721 e.8.1.1 43010 1f2tB 148 1.93e+01 1f2tB 1dfuP 94 1.96e+01 1dfuP b.53.1.1 26936 2scuB 388 2.01e+01 2scuB c.23.4.1 31141 d.142.1.4 41562 1thfD 253 2.07e+01 1thfD c.1.2.1 28535 1aa2 108 2.08e+01 1bkrA a.40.1.1 17395 1tml 286 2.10e+01 1tml c.6.1.1 30656 1igwA 434 2.12e+01 c.1.12.6 62370 1bouB 302 2.15e+01 1bouB c.56.6.1 33859 1pytA 94 2.23e+01 1pytA d.58.3.1 39064 1npsA 88 2.26e+01 1prs b.11.1.1 23622 1fu1B 203 2.26e+01 1fu1B b.59.1.1 27077 h.1.11.1 45631 1efvA 315 2.26e+01 1efvA c.29.1.1 31633 c.31.1.2 31728 1hjp 203 2.28e+01 1hjp a.5.1.1 16274 a.60.2.1 17947 b.40.4.2 25266 1h65A 270 2.30e+01 c.37.1.8 65640 1ntr 124 2.33e+01 1dbwA c.23.1.1 31092 2gd1O 334 2.43e+01 1dssG c.2.1.3 29978 d.81.1.1 39893 2act 220 2.44e+01 1cs8A d.3.1.1 37002 1afi 72 2.44e+01 1aw0 d.58.17.1 39339 1e69B 322 2.50e+01 1e69B c.37.1.12 32377 3cox 507 2.54e+01 1b8sA c.3.1.2 30332 d.16.1.1 37863 1c3pA 375 2.54e+01 1c3pA c.42.1.2 32606 1irsA 112 2.70e+01 1qqgA b.55.1.2 26991 1f5nA 592 2.74e+01 1dg3A a.114.1.1 19077 c.37.1.8 32152 1bksA 268 2.77e+01 2tysA c.1.2.4 28585 1ik9A 213 2.81e+01 b.59.1.1 66176 h.1.11.1 66177 1gt91 357 2.83e+01 1bia 321 2.85e+01 1bia a.4.5.1 16083 b.34.1.1 24447 d.104.1.2 40787 1jj7A 260 2.85e+01 c.37.1.12 63114 1aw0 72 2.87e+01 1aw0 d.58.17.1 39342 1chd 203 2.87e+01 1chd c.40.1.1 32478 1hz6A 72 2.89e+01 2ptl d.15.7.1 61429 1fu1A 203 2.90e+01 1fu1B b.59.1.1 27076 h.1.11.1 45630 1jf8A 131 2.92e+01 c.44.1.1 66621 1hwxA 501 2.92e+01 1hwyA c.2.1.7 30250 c.58.1.1 33898 1div 149 2.92e+01 1div d.99.1.1 40692 d.100.1.1 40693 1bbl 51 2.96e+01 1bbl a.9.1.1 16356 1bkrA 109 2.98e+01 1bkrA a.40.1.1 17394 1yrgB 385 2.99e+01 1yrgA c.10.1.2 30855 1yrgA 385 3.00e+01 1yrgA c.10.1.2 30854 1hdhA 536 3.01e+01 c.76.1.2 65805 1fjgD 209 3.02e+01 1c05A d.66.1.2 39553 1ad3A 452 3.02e+01 1ad3A c.82.1.1 35335 1korA 400 3.05e+01 2dri 271 3.12e+01 2dri c.93.1.1 35637 1g6hA 257 3.15e+01 1gajA c.37.1.12 60318 1f61A 429 3.23e+01 1dquA c.1.12.6 29319 1jztA 246 3.25e+01 c.104.1.1 63319 1drw 273 3.28e+01 1drw c.2.1.3 30057 d.81.1.3 39972 1fjgK 129 3.29e+01 1fjfK c.55.4.1 33733 3ladA 476 3.29e+01 1lvl c.3.1.5 30573 c.3.1.5 30574 d.87.1.1 40208 1hnuA 280 3.34e+01 1hnoA c.14.1.3 61096 1jjuA 489 3.40e+01 a.3.1.7 66774 a.3.1.7 66775 b.1.1.6 66776 b.1.1.6 66777 b.61.4.1 66778 1edsA 31 3.41e+01 1edsA j.35.1.1 46240 1fpqA 372 3.43e+01 1fpqA a.4.5.29 59947 c.66.1.12 59948 1qh4A 380 3.44e+01 1qh4A a.83.1.1 18462 d.128.1.2 41197 1cfr 285 3.47e+01 1cfr c.52.1.7 33312 1bal 51 3.48e+01 1bbl a.9.1.1 16357 1jpdX 324 3.51e+01 c.1.11.2 67014 d.54.1.1 67015 1fmk 452 3.54e+01 1fmk b.34.2.1 24511 d.93.1.1 40436 d.144.1.2 41690 1whsB 153 3.54e+01 1whtB 3csuA 310 3.55e+01 3csuA c.78.1.1 35094 c.78.1.1 35095 1ldg 316 3.57e+01 1ceqA c.2.1.5 30165 d.162.1.1 42132 1whtB 153 3.64e+01 1whtB 1add 349 3.65e+01 1a4mA c.1.9.1 29020 1ig0A 319 3.66e+01 1ig0A b.82.6.1 62354 c.100.1.1 62355 1eb6A 177 3.68e+01 d.92.1.12 64895 1tahA 318 3.68e+01 1cvl c.69.1.18 34775 1tahB 318 3.69e+01 1cvl c.69.1.18 34774 1lj2C 28 3.73e+01 1j5eC 239 3.75e+01 1gesA 450 3.76e+01 3grs c.3.1.5 30473 c.3.1.5 30474 d.87.1.1 40168 1csjA 531 3.77e+01 1quvA e.8.1.4 43120 1hwyA 501 3.84e+01 1hwyA c.2.1.7 30262 c.58.1.1 33910 1g66A 207 3.86e+01 1bs9 c.23.9.1 31329 1chmA 401 3.87e+01 1chmA c.55.2.1 33545 d.127.1.1 41142 1iatA 557 3.88e+01 1dqrA c.80.1.2 62123 1l7mA 211 3.90e+01