# 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 1je0A 236 4.77e-02 c.56.2.1 66581 1lx7A 253 5.04e-02 1jeqB 565 1.15e-01 1jeqB e.31.1.2 62922 1bouB 302 1.15e-01 1bouB c.56.6.1 33859 1k3fA 253 2.11e-01 c.56.2.1 68105 1b57A 358 2.15e-01 1dosA c.1.10.2 29177 1jeyB 565 2.28e-01 1jeqB e.31.1.2 62925 1dosA 358 2.56e-01 1dosA c.1.10.2 29175 1geqA 248 2.85e-01 2tysA c.1.2.4 28589 1a8h 500 3.50e-01 1a8h a.27.1.1 16922 c.26.1.1 31589 2cevA 299 4.21e-01 1d3vA c.42.1.1 32576 1ex2A 189 6.58e-01 1ex2A c.51.4.2 33225 1trb 320 6.93e-01 1trb c.3.1.5 30529 c.3.1.5 30530 1jmkC 230 8.02e-01 1e39A 571 9.79e-01 1qjdA a.138.1.3 19694 c.3.1.4 30431 d.168.1.1 42314 1qjdA 571 1.00e+00 1qjdA a.138.1.3 19695 c.3.1.4 30432 d.168.1.1 42315 1rlaA 323 1.06e+00 1d3vA c.42.1.1 32561 1hdhA 536 1.07e+00 c.76.1.2 65805 1d3vA 323 1.11e+00 1d3vA c.42.1.1 32559 1jmxA 494 1.19e+00 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 1ctn 540 1.32e+00 1ctn b.1.1.5 21876 c.1.8.5 29005 d.26.3.1 38439 3ladA 476 1.40e+00 1lvl c.3.1.5 30573 c.3.1.5 30574 d.87.1.1 40208 1k6wA 426 1.50e+00 b.92.1.2 68236 c.1.9.5 68237 1qopA 268 1.80e+00 2tysA c.1.2.4 28570 1ap8 213 1.80e+00 1ap8 d.86.1.1 40151 1ex1A 605 1.88e+00 1ex1A c.1.8.7 29013 c.23.11.1 31347 2pth 193 2.05e+00 2pth c.56.3.1 33793 1gs5A 258 2.14e+00 1edqA 540 2.34e+00 1ctn b.1.1.5 21873 c.1.8.5 29002 d.26.3.1 38436 1iexA 605 2.41e+00 c.1.8.7 66127 c.23.11.1 66128 1b87A 181 2.43e+00 1b87A d.108.1.1 40797 1jy1A 464 2.44e+00 d.136.1.3 67438 d.136.1.3 67439 1scuA 288 2.47e+00 2scuA c.2.1.8 30307 c.23.4.1 31135 1c3pA 375 2.50e+00 1c3pA c.42.1.2 32606 1erw 105 2.57e+00 1erv c.47.1.1 32745 5tmpA 213 2.59e+00 5tmpA c.37.1.1 31931 1sup 275 2.89e+00 1gci c.41.1.1 32510 1f5sA 211 3.04e+00 1f5sA c.108.1.4 59656 1j97A 211 3.16e+00 1f5sA c.108.1.4 62753 2act 220 3.26e+00 1cs8A d.3.1.1 37002 2tysA 268 3.52e+00 2tysA c.1.2.4 28572 1cozA 129 3.53e+00 1cozA c.26.1.2 31598 4kbpA 432 3.73e+00 4kbpA b.1.12.1 22345 d.159.1.1 42064 1jfvA 131 3.78e+00 c.44.1.1 66654 1h61A 364 4.15e+00 1oyc c.1.4.1 60657 1jk7A 323 4.47e+00 1auiA d.159.1.3 63144 1l7mA 211 4.54e+00 1jf8A 131 4.64e+00 c.44.1.1 66621 1korA 400 4.71e+00 1cqxA 403 5.23e+00 1cqxA a.1.1.2 15635 b.43.4.2 25667 c.25.1.5 31562 1edg 380 5.34e+00 1edg c.1.8.3 28807 1jq3A 296 5.61e+00 c.66.1.17 67079 1inlA 296 5.67e+00 c.66.1.17 66220 1bksA 268 5.69e+00 2tysA c.1.2.4 28585 1huxA 270 6.04e+00 1huxA c.55.1.5 61278 1qumA 285 6.11e+00 1qumA c.1.15.1 29393 1b37B 472 6.21e+00 1b37B c.3.1.2 30390 d.16.1.5 37954 1erv 105 6.51e+00 1erv c.47.1.1 32743 1d5yA 292 6.62e+00 1d5yA a.4.1.8 16055 a.4.1.8 16056 d.60.1.2 39532 2scuA 288 6.66e+00 2scuA c.2.1.8 30303 c.23.4.1 31131 1qqtA 551 6.68e+00 1qqtA a.27.1.1 16923 c.26.1.1 31590 g.41.1.1 45175 1eqjA 511 6.70e+00 1ejjA c.105.1.1 59495 c.76.1.3 59496 1cp2A 269 6.81e+00 1cp2A c.37.1.10 32269 1prxB 224 6.98e+00 1prxA c.47.1.10 33077 1prxA 224 6.98e+00 1prxA c.47.1.10 33076 1whsB 153 7.23e+00 1whtB 1whtB 153 7.34e+00 1whtB 4tmkA 213 7.52e+00 5tmpA c.37.1.1 31930 1tahB 318 7.67e+00 1cvl c.69.1.18 34774 1ejjA 511 7.78e+00 1ejjA c.105.1.1 59422 c.76.1.3 59423 1tahA 318 7.79e+00 1cvl c.69.1.18 34775 1hi9A 274 7.95e+00 1hi9A c.99.1.1 61063 1wab 232 7.95e+00 1wab c.23.10.3 31341 1f4lA 551 8.06e+00 1qqtA a.27.1.1 59648 c.26.1.1 59649 g.41.1.1 59650 1i3kA 348 8.09e+00 1xel c.2.1.2 61595 1g66A 207 8.40e+00 1bs9 c.23.9.1 31329 1ek6A 348 8.40e+00 1xel c.2.1.2 29800 1es9A 232 8.50e+00 1wab c.23.10.3 31340 1chuA 540 8.61e+00 1chuA a.7.3.1 16325 c.3.1.4 30424 d.168.1.1 42307 1qtwA 285 8.64e+00 1qumA c.1.15.1 29392 1ir6A 424 8.66e+00 1drw 273 8.68e+00 1drw c.2.1.3 30057 d.81.1.3 39972 1bs9 207 8.83e+00 1bs9 c.23.9.1 31330 1fjmA 330 9.39e+00 1auiA d.159.1.3 42082 1gr2A 279 9.41e+00 1gr2A c.94.1.1 35825 1fnnA 389 9.69e+00 1fnnA a.4.5.11 16129 c.37.1.13 32426 1kbpA 432 9.72e+00 4kbpA b.1.12.1 22349 d.159.1.1 42068 1gh2A 107 9.87e+00 1erv c.47.1.1 60515 1ftkA 279 1.00e+01 1gr2A c.94.1.1 35819 1qfjA 232 1.04e+01 1qfjA b.43.4.2 25655 c.25.1.1 31545 1nhs 447 1.05e+01 1nhp c.3.1.5 30555 c.3.1.5 30556 d.87.1.1 40199 1jgtA 513 1.07e+01 c.26.2.1 66684 d.153.1.1 66685 1dhs 344 1.10e+01 1dhs c.31.1.1 31727 1h6uA 308 1.10e+01 b.1.1.6 65688 c.10.2.1 65689 1b25A 619 1.12e+01 1b25A a.110.1.1 19044 d.152.1.1 41796 1g5pA 289 1.12e+01 1cp2A c.37.1.10 32253 1aiu 105 1.14e+01 1erv c.47.1.1 32746 1fp6A 289 1.14e+01 1cp2A c.37.1.10 32243 1svy 114 1.15e+01 1svy d.109.1.1 40831 1i5gA 144 1.15e+01 1ewxA c.47.1.10 61784 1pymA 295 1.18e+01 1pymA c.1.12.4 29308 1b4kA 337 1.18e+01 1b4kA c.1.10.3 29184 1e0cA 271 1.19e+01 1e0cA c.46.1.2 32717 c.46.1.2 32718 1nhp 447 1.19e+01 1nhp c.3.1.5 30549 c.3.1.5 30550 d.87.1.1 40196 1chd 203 1.20e+01 1chd c.40.1.1 32478 1fh9A 312 1.22e+01 1taxA c.1.8.3 28913 1faaA 124 1.23e+01 1erv c.47.1.1 32738 1djnA 729 1.23e+01 2tmdA c.1.4.1 28612 c.3.1.1 30313 c.4.1.1 30598 3cbh 365 1.24e+01 1bvwA c.6.1.1 30665 1edsA 31 1.24e+01 1edsA j.35.1.1 46240 1fps 348 1.25e+01 1uby a.128.1.1 19436 1fjgI 128 1.25e+01 1fjfI d.14.1.1 37559 1fhdA 312 1.26e+01 1taxA c.1.8.3 28915 3tmkA 216 1.26e+01 3tmkA c.37.1.1 31920 1d8wA 426 1.27e+01 1de5A c.1.15.2 29394 1eudA 311 1.28e+01 2scuA c.2.1.8 30312 c.23.4.1 31140 1h65A 270 1.28e+01 c.37.1.8 65640 1jeoA 180 1.30e+01 c.80.1.3 66611 1f9aA 168 1.31e+01 1f9aA c.26.1.3 31602 1krhA 338 1.35e+01 1iab 200 1.36e+01 1iae d.92.1.8 40312 1iae 200 1.36e+01 1iae d.92.1.8 40311 1ast 200 1.36e+01 1iae d.92.1.8 40310 1dg9A 157 1.37e+01 1dg9A c.44.1.1 32637 1b5qA 472 1.38e+01 1b37B c.3.1.2 30404 d.16.1.5 37968 1e5eA 404 1.38e+01 1ibjA c.67.1.3 59265 1hp1A 516 1.39e+01 1cvl 319 1.41e+01 1cvl c.69.1.18 34786 1oaa 259 1.41e+01 1oaa c.2.1.2 29829 1f9mA 112 1.43e+01 1erv c.47.1.1 32736 1fqiA 147 1.44e+01 1agrE a.91.1.1 18542 1fbaA 361 1.44e+01 1fbaA c.1.10.1 29120 1phr 157 1.47e+01 1dg9A c.44.1.1 32635 1joa 447 1.49e+01 1nhp c.3.1.5 30563 c.3.1.5 30564 d.87.1.1 40203 1qo2A 241 1.52e+01 1qo2A c.1.2.1 28533 1g3qA 237 1.55e+01 1hyqA c.37.1.10 60237 1arzC 273 1.58e+01 1drw c.2.1.3 30061 d.81.1.3 39976 2wsyA 268 1.65e+01 2tysA c.1.2.4 28588 1s01 283 1.66e+01 1gci c.41.1.1 32511 1uby 367 1.67e+01 1uby a.128.1.1 19435 1c0pA 363 1.71e+01 1an9A c.4.1.2 30647 d.16.1.3 37934 1ccwA 137 1.73e+01 1be1 c.23.6.1 31238 2pia 321 1.76e+01 2pia b.43.4.2 25663 c.25.1.2 31553 d.15.4.2 37704 1jvnA 555 1.77e+01 c.1.2.1 67355 c.23.16.1 67356 1c1yB 77 1.78e+01 1c1yB d.15.1.5 37618 1k6dA 220 1.78e+01 1mjhA 162 1.79e+01 1mjhA c.29.1.2 31639 2tmdA 729 1.82e+01 2tmdA c.1.4.1 28616 c.3.1.1 30317 c.4.1.1 30602 1epxA 370 1.82e+01 1fbaA c.1.10.1 29150 1jcxA 267 1.83e+01 c.1.10.4 66510 1brwA 433 1.83e+01 1brwA a.46.2.1 17764 c.27.1.1 31628 d.41.3.1 38626 1fwsA 267 1.83e+01 1d9eA c.1.10.4 60063 1ush 550 1.85e+01 1ush d.114.1.1 40923 d.159.1.2 42079 1b0uA 262 1.88e+01 1b0uA c.37.1.12 32370 2dorA 311 1.89e+01 2dorA c.1.4.1 28593 1fc4A 401 1.89e+01 1bs0A c.67.1.4 59760 1gt91 357 1.89e+01 1de5A 426 1.91e+01 1de5A c.1.15.2 29402 4eugA 229 1.92e+01 3eugA c.18.1.1 31019 1thfD 253 1.95e+01 1thfD c.1.2.1 28535 1cf3A 583 1.95e+01 1gpeA c.3.1.2 30385 d.16.1.4 37949 1ejhA 190 1.96e+01 1ejhA d.86.1.1 40147 1igwA 434 1.96e+01 c.1.12.6 62370 1jilA 420 1.96e+01 c.26.1.1 66745 1k30A 368 1.98e+01 c.112.1.1 68067 3eugA 229 1.99e+01 3eugA c.18.1.1 31018 1d0bA 213 1.99e+01 1d0bA c.10.2.1 30866 1dxeA 256 2.01e+01 1dxeA c.1.12.5 29310 1d0qA 103 2.03e+01 1d0qA g.41.3.2 45208 1qjwA 365 2.03e+01 1bvwA c.6.1.1 30657 1ppo 216 2.06e+01 1cs8A d.3.1.1 37020 1nipA 289 2.07e+01 1cp2A c.37.1.10 32263 1fthA 122 2.09e+01 d.150.1.2 60028 1dbiA 280 2.10e+01 1gci c.41.1.1 32543 1jbwA 428 2.17e+01 c.59.1.2 62860 c.72.2.2 62861 1rhs 296 2.21e+01 1rhs c.46.1.2 32703 c.46.1.2 32704 1fxqA 267 2.21e+01 1d9eA c.1.10.4 60108 1e9lA 377 2.22e+01 1e9lA c.1.8.5 59395 d.26.3.1 59396 1gal 583 2.23e+01 1gpeA c.3.1.2 30386 d.16.1.4 37950 1lehA 364 2.23e+01 1bw9A c.2.1.7 30268 c.58.1.1 33916 1ehiA 377 2.24e+01 1iow c.30.1.2 31716 d.142.1.1 41484 1bf6A 291 2.25e+01 1pscA c.1.9.3 29065 1mkp 144 2.25e+01 1vhrA c.45.1.1 32654 1d7yA 408 2.29e+01 1d7yA c.3.1.5 30565 c.3.1.5 30566 d.87.1.1 40204 1dorA 311 2.31e+01 2dorA c.1.4.1 28595 1qk8A 146 2.31e+01 1ewxA c.47.1.10 33061 1l0oA 150 2.32e+01 1fu1A 203 2.43e+01 1fu1B b.59.1.1 27076 h.1.11.1 45630 2ptd 298 2.46e+01 2plc c.1.18.2 29605 1bd0A 388 2.47e+01 1bd0A b.49.2.1 26480 c.1.6.1 28642 1j9lA 247 2.47e+01 c.106.1.1 62762 1ej2A 181 2.49e+01 1f9aA c.26.1.3 59414 1dquA 538 2.50e+01 1dquA c.1.12.6 29314 1ds6B 180 2.50e+01 1rhoA b.1.1.5 21898 1fmcA 255 2.51e+01 1cydA c.2.1.2 29856 1dcfA 136 2.58e+01 1dcfA c.23.1.2 31124 1cqwA 295 2.59e+01 1b6g c.69.1.8 34679 1h4xA 117 2.59e+01 1auz c.13.2.1 60626 1cseE 274 2.59e+01 1gci c.41.1.1 32481 1sftA 388 2.59e+01 1bd0A b.49.2.1 26482 c.1.6.1 28644 1bn7A 294 2.59e+01 1bn6A c.69.1.8 34677 1g0cA 364 2.59e+01 7a3hA c.1.8.3 60165 1c7nA 399 2.63e+01 1d2fA c.67.1.3 34413 1uteA 313 2.64e+01 1uteA d.159.1.1 42078 1tph1 247 2.65e+01 1amk 1agrE 205 2.66e+01 1agrE a.91.1.1 18538 1de6A 426 2.66e+01 1de5A c.1.15.2 29398 1fcjA 322 2.67e+01 1oasA c.79.1.1 35289 1qmpA 130 2.70e+01 1dz3A c.23.1.1 31106 1d7oA 297 2.72e+01 1enp c.2.1.2 29907 1qr6A 584 2.73e+01 1qr6A c.2.1.7 30293 c.58.1.3 33941 1at1A 310 2.75e+01 3csuA c.78.1.1 35168 c.78.1.1 35169 1taq 832 2.80e+01 1taq a.60.7.1 18082 c.53.1.2 33352 c.55.3.5 33698 e.8.1.1 42991 1azwA 313 2.81e+01 1qtrA c.69.1.7 34658 1qh3A 260 2.81e+01 1qh5A d.157.1.2 42059 1itxA 419 2.83e+01 7odcA 424 2.89e+01 7odcA b.49.2.1 26488 c.1.6.1 28650 1h6tA 291 2.90e+01 b.1.1.6 65686 c.10.2.1 65687 2scuB 388 2.91e+01 2scuB c.23.4.1 31141 d.142.1.4 41562 1bn6A 294 2.91e+01 1bn6A c.69.1.8 34678 1eno 312 2.93e+01 1enp c.2.1.2 29905 1keeG 1073 2.96e+01 a.92.1.1 68516 c.24.1.1 68517 c.30.1.1 68518 c.30.1.1 68519 d.142.1.2 68520 d.142.1.2 68521 1c3oC 1073 2.96e+01 a.92.1.1 18563 c.24.1.1 31492 c.30.1.1 31683 c.30.1.1 31684 d.142.1.2 41528 d.142.1.2 41529 1ei9A 279 2.99e+01 1ei9A c.69.1.13 34713 1cb2A 365 2.99e+01 1bvwA c.6.1.1 30661 1dmgA 225 3.00e+01 1dmgA c.22.1.1 31036 1j9jA 247 3.03e+01 c.106.1.1 62758 1fu1B 203 3.05e+01 1fu1B b.59.1.1 27077 h.1.11.1 45631 1reqA 727 3.05e+01 1reqA c.1.19.1 29620 c.23.6.1 31247 1dih 273 3.11e+01 1drw c.2.1.3 30056 d.81.1.3 39971 1g7tA 594 3.14e+01 1g7rA b.43.3.1 25714 b.43.3.1 25715 c.20.1.1 31033 c.37.1.8 32148 1ep3A 311 3.15e+01 2dorA c.1.4.1 28597 1a88A 275 3.17e+01 1brt c.69.1.12 34707 1gosA 520 3.18e+01 c.3.1.2 65425 d.16.1.5 65426 1eqcA 394 3.19e+01 1cz1A c.1.8.3 28811 3lck 271 3.21e+01 1fmk d.144.1.2 41686 1fgs 428 3.23e+01 1fgs c.59.1.2 33959 c.72.2.2 34962 1e3dA 266 3.24e+01 2frvA e.19.1.1 59188 1ihnA 113 3.25e+01 1ihnA c.103.1.1 62388 1enp 312 3.26e+01 1enp c.2.1.2 29906 3csuA 310 3.27e+01 3csuA c.78.1.1 35094 c.78.1.1 35095 1f0nA 285 3.29e+01 1dqyA c.69.1.3 34636 1dciA 275 3.32e+01 1dciA c.14.1.3 30918 1lkxA 697 3.32e+01 1cz1A 394 3.32e+01 1cz1A c.1.8.3 28839 1g8jA 825 3.33e+01 1g8jA b.52.2.2 26924 c.81.1.1 35332 1jjuA 489 3.35e+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 1svr 114 3.38e+01 1svy d.109.1.1 40833 1dp0A 1023 3.41e+01 b.1.4.1 22073 b.1.4.1 22074 b.18.1.5 23722 b.30.1.1 24346 c.1.8.3 28845 1li5A 461 3.42e+01 1jz8A 1023 3.42e+01 b.1.4.1 67830 b.1.4.1 67831 b.18.1.5 67832 b.30.1.1 67833 c.1.8.3 67834 3uagA 437 3.42e+01 4uagA c.5.1.1 30652 c.59.1.1 33953 c.72.2.1 34956 1mdiA 105 3.42e+01 1erv c.47.1.1 32755 1kvs 338 3.43e+01 1xel c.2.1.2 29799 1thtA 305 3.44e+01 1thtA c.69.1.13 34711 1jndA 420 3.48e+01 1e9gB 286 3.49e+01 1wgjA b.40.5.1 59394 1jl1A 155 3.50e+01 c.55.3.1 66821 1thm 279 3.51e+01 1gci c.41.1.1 32544 1dz3A 130 3.51e+01 1dz3A c.23.1.1 31105 1tpt 440 3.53e+01 1brwA a.46.2.1 17763 c.27.1.1 31627 d.41.3.1 38625 1tkaA 678 3.53e+01 1trkA c.36.1.2 31815 c.36.1.2 31816 c.48.1.1 33096 1mjhB 162 3.53e+01 1mjhA c.29.1.2 31640 1qh5A 260 3.54e+01 1qh5A d.157.1.2 42057 1gpeA 587 3.56e+01 1gpeA c.3.1.2 30387 d.16.1.4 37951 1ewxA 146 3.56e+01 1ewxA c.47.1.10 33062 1tr1A 447 3.57e+01 1e70M c.1.8.4 28957 2rn2 155 3.59e+01 2rn2 c.55.3.1 33551 1fmk 452 3.64e+01 1fmk b.34.2.1 24511 d.93.1.1 40436 d.144.1.2 41690 1bglA 1023 3.65e+01 1bglA b.1.4.1 22097 b.1.4.1 22098 b.18.1.5 23734 b.30.1.1 24358 c.1.8.3 28857 1oasA 322 3.70e+01 1oasA c.79.1.1 35293 1g8kA 825 3.70e+01 1g8jA b.52.2.2 26920 c.81.1.1 35328 1fpzA 212 3.70e+01 1fpzA c.45.1.1 59976 2tpsA 227 3.74e+01 2tpsA c.1.3.1 28591 1d0sA 356 3.77e+01 1d0vA c.39.1.1 32477 1hzmA 154 3.80e+01 c.46.1.1 65975 1f21A 155 3.82e+01 2rn2 c.55.3.1 33550 4uagA 437 3.82e+01 4uagA c.5.1.1 30651 c.59.1.1 33952 c.72.2.1 34955 1b3tA 147 3.90e+01 1b3tA d.58.8.1 39228 1hdj 77 3.91e+01 1bqz a.2.3.1 15696 2tysB 397 3.93e+01 2tysB c.79.1.1 35272 1fuiA 591 3.93e+01 1fuiA b.43.2.1 25674 c.85.1.1 35444 1udb 338 3.93e+01 1xel c.2.1.2 29787 8prkB 287 3.94e+01 1wgjA b.40.5.1 25396 1akz 223 3.94e+01 3eugA c.18.1.1 31007 1l9fA 389 3.94e+01 1i58A 189 3.96e+01 1b3qA d.122.1.3 61773 1qd1A 325 3.98e+01 1qd1A d.58.34.1 39493 d.58.34.1 39494 1bqcA 302 3.99e+01 1bqcA c.1.8.3 28831