# List of top-scoring protein chains for 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 1i21A 159 5.22e-14 1i21A d.108.1.1 61549 1i12A 160 5.88e-14 1i21A d.108.1.1 61515 1i1dA 161 5.88e-14 1i21A d.108.1.1 61526 1qsoA 149 4.39e-13 1qsmA d.108.1.1 40812 1qsmA 152 7.48e-13 1qsmA d.108.1.1 40808 1bo4A 168 1.26e-12 1bo4A d.108.1.1 40798 1bo4B 168 1.26e-12 1bo4A d.108.1.1 40799 1b6bA 174 1.11e-10 1cjwA d.108.1.1 40819 1cjwA 166 1.11e-10 1cjwA d.108.1.1 40818 1kuxA 207 1.43e-10 1ib1E 200 1.45e-10 1cjwA d.108.1.1 62137 1b87A 181 1.99e-10 1b87A d.108.1.1 40797 1l0cA 207 3.61e-10 1qstA 160 3.03e-09 1yghA d.108.1.1 40804 1qsrA 162 3.05e-09 1yghA d.108.1.1 40805 5gcnA 166 3.11e-09 1yghA d.108.1.1 40807 1cm0A 168 2.29e-08 1yghA d.108.1.1 40800 1yghA 164 1.24e-05 1yghA d.108.1.1 40802 1bob 320 8.05e-04 1bob d.108.1.1 40816 1nmtA 392 1.58e-03 1nmtA d.108.1.2 40823 d.108.1.2 40824 1fy7A 278 3.04e-03 1fy7A d.108.1.1 40817 1iicA 422 3.69e-01 1nmtA d.108.1.2 62422 d.108.1.2 62423 1poy2 323 1.29e+00 1pot 1pot 325 1.31e+00 1pot c.94.1.1 35807 1l8tA 263 1.75e+00 1j7lA 264 1.75e+00 d.144.1.6 62697 1j7iA 264 1.75e+00 1j7iA d.144.1.6 62694 1exqA 154 2.41e+00 1b9dA c.55.3.2 33646 1fyc 106 2.56e+00 1fyc b.84.1.1 28230 1h4yA 117 2.89e+00 1auz c.13.2.1 60628 1i8kA 107 4.06e+00 1dtzA 689 4.17e+00 1cb6A c.94.1.2 59134 c.94.1.2 59135 1qf8A 182 4.50e+00 1qf8A g.41.4.1 45212 1ex4A 239 4.72e+00 1b9dA b.34.7.1 24627 c.55.3.2 33670 1jwhD 215 5.93e+00 1hqsA 423 6.17e+00 1iso c.77.1.1 61154 1fuiA 591 7.26e+00 1fuiA b.43.2.1 25674 c.85.1.1 35444 1eysH 259 7.36e+00 6prcH b.41.1.1 25484 f.2.1.2 43517 1qs4B 154 7.40e+00 1b9dA c.55.3.2 33659 1biuA 166 7.79e+00 1b9dA c.55.3.2 33663 1bisB 166 7.80e+00 1b9dA c.55.3.2 33651 1iag 202 7.83e+00 1atlA d.92.1.9 40319 1qgnA 445 8.48e+00 1ibjA c.67.1.3 34403 4rnt 104 8.60e+00 9rnt d.1.1.1 36126 1hyvA 166 8.75e+00 1b9dA c.55.3.2 61424 1jflA 228 9.20e+00 1pta 318 9.72e+00 1pscA c.1.9.3 29064 1bl0A 129 1.01e+01 1d5yA a.4.1.8 16053 a.4.1.8 16054 1hzyA 332 1.01e+01 1pscA c.1.9.3 61468 1i0dA 332 1.01e+01 1pscA c.1.9.3 61487 1dpmA 329 1.02e+01 1pscA c.1.9.3 29062 1eywA 331 1.02e+01 1pscA c.1.9.3 29057 1jgmA 336 1.02e+01 1pscA c.1.9.3 62953 2dorA 311 1.03e+01 2dorA c.1.4.1 28593 1dorA 311 1.03e+01 2dorA c.1.4.1 28595 1pscA 365 1.04e+01 1pscA c.1.9.3 29058 1dioB 224 1.07e+01 1dioB c.51.3.1 33219 1eexB 224 1.07e+01 1dioB c.51.3.1 33213 1b9dA 163 1.07e+01 1b9dA c.55.3.2 33649 1itg 166 1.09e+01 1b9dA c.55.3.2 33661 1bizA 166 1.13e+01 1b9dA c.55.3.2 33652 1bhl 151 1.17e+01 1b9dA c.55.3.2 33662 1mat 264 1.20e+01 1c24A d.127.1.1 41152 1k6yB 288 1.22e+01 a.4.10.1 68241 c.55.3.2 68242 1hslA 238 1.23e+01 1lst c.94.1.1 35804 1dcjA 81 1.26e+01 1dcjA d.68.3.1 59115 1bi4B 160 1.28e+01 1b9dA c.55.3.2 33667 1b92A 163 1.29e+01 1b9dA c.55.3.2 33654 4aig 201 1.29e+01 1atlA d.92.1.9 40318 1adz 71 1.29e+01 1bpi g.8.1.1 44542 3aig 202 1.30e+01 1atlA d.92.1.9 40321 2pth 193 1.35e+01 2pth c.56.3.1 33793 1di1A 300 1.39e+01 1di1A a.128.1.4 19446 1b9fA 163 1.43e+01 1b9dA c.55.3.2 33648 1b00A 127 1.49e+01 3chy c.23.1.1 31122 1dbp 271 1.50e+01 2dri c.93.1.1 35639 1bl3A 160 1.52e+01 1b9dA c.55.3.2 33655 2itg 163 1.55e+01 1b9dA c.55.3.2 33669 2dri 271 1.57e+01 2dri c.93.1.1 35637 1hrkA 359 1.62e+01 1hrkA c.92.1.1 61228 1i94H 138 1.80e+01 1seiA d.140.1.1 61999 1e9zB 569 1.84e+01 b.92.1.1 64852 c.1.9.2 64853 1yua 122 1.84e+01 1yua g.41.3.3 45210 g.41.3.3 45211 1e9yB 569 1.86e+01 b.92.1.1 64848 c.1.9.2 64849 1qs0B 338 1.87e+01 1qs0B c.36.1.3 31830 c.48.1.2 33103 1drk 271 1.89e+01 2dri c.93.1.1 35638 1ymv 129 2.02e+01 3chy c.23.1.1 31045 1rhlA 104 2.05e+01 9rnt d.1.1.1 36082 2aadA 104 2.09e+01 9rnt d.1.1.1 36110 1h4xA 117 2.10e+01 1auz c.13.2.1 60626 1h4zA 117 2.13e+01 1auz c.13.2.1 60630 1det 104 2.14e+01 9rnt d.1.1.1 36101 1birA 104 2.14e+01 9rnt d.1.1.1 36083 1hyfA 104 2.18e+01 9rnt d.1.1.1 36065 2hohA 104 2.22e+01 9rnt d.1.1.1 36077 1fysA 104 2.22e+01 9rnt d.1.1.1 36104 3rnt 104 2.24e+01 9rnt d.1.1.1 36069 9rnt 104 2.24e+01 9rnt d.1.1.1 36055 1i0vA 104 2.24e+01 9rnt d.1.1.1 36054 1ygw 104 2.24e+01 9rnt d.1.1.1 36137 1g02A 104 2.25e+01 9rnt d.1.1.1 36076 1i2gA 104 2.25e+01 9rnt d.1.1.1 61567 1b37B 472 2.27e+01 1b37B c.3.1.2 30390 d.16.1.5 37954 1b5qA 472 2.27e+01 1b37B c.3.1.2 30404 d.16.1.5 37968 1rgl 104 2.36e+01 9rnt d.1.1.1 36094 7rnt 104 2.37e+01 9rnt d.1.1.1 36105 1tml 286 2.40e+01 1tml c.6.1.1 30656 1trqA 104 2.53e+01 9rnt d.1.1.1 36127 1trpB 104 2.56e+01 9rnt d.1.1.1 36135 1bf5A 545 2.57e+01 1bg1A a.47.1.1 17766 b.2.5.1 22460 d.93.1.1 40526 2otcA 333 2.68e+01 1othA c.78.1.1 35234 c.78.1.1 35235 1lh0A 213 2.69e+01 1opr 213 2.69e+01 1opr c.61.1.1 34091 1seiA 130 2.69e+01 1seiA d.140.1.1 41463 1hx8B 299 2.69e+01 1hg5A a.118.10.1 19223 1j77A 209 2.74e+01 1j77A a.132.1.2 62674 1sto 213 2.75e+01 1opr c.61.1.1 34092 1aop 497 2.78e+01 2aop d.58.36.1 39501 d.58.36.1 39502 d.134.1.1 41425 d.134.1.1 41426 2aop 497 2.78e+01 2aop d.58.36.1 39503 d.58.36.1 39504 d.134.1.1 41427 d.134.1.1 41428 1i6uA 130 2.78e+01 d.140.1.1 61850 2birA 104 2.80e+01 9rnt d.1.1.1 36133 9gacA 295 2.81e+01 1apyA d.153.1.5 42010 1fxjA 331 2.84e+01 1fwyA b.81.1.4 28062 c.68.1.5 34520 1fwyA 331 2.84e+01 1fwyA b.81.1.4 28064 c.68.1.5 34522 1ch0A 104 2.93e+01 9rnt d.1.1.1 36129 1vie 62 2.94e+01 1vie b.34.4.1 24592 1vif 62 2.94e+01 1vie b.34.4.1 24593 1lra 104 2.94e+01 9rnt d.1.1.1 36112 5birB 104 2.94e+01 9rnt d.1.1.1 36107 3bir 104 2.99e+01 9rnt d.1.1.1 36132 1an7A 136 3.02e+01 1seiA d.140.1.1 41465 1eg0E 138 3.03e+01 1seiA i.1.1.1 45811 1qo8A 566 3.03e+01 1qjdA a.138.1.3 19696 c.3.1.4 30433 d.168.1.1 42316 1hi8A 664 3.04e+01 1hi0P e.8.1.6 61061 1l1nA 183 3.08e+01 1drj 271 3.09e+01 2dri c.93.1.1 35642 1a0qL 212 3.11e+01 8fabA b.1.1.1 20286 b.1.1.2 21278 2matA 264 3.18e+01 1c24A d.127.1.1 41146 3matA 265 3.19e+01 1c24A d.127.1.1 41149 1d3yA 301 3.22e+01 1d3yA e.12.1.1 43252 1frfS 264 3.23e+01 2frvA e.19.1.1 43312 4matA 278 3.25e+01 1c24A d.127.1.1 41150 1ggjA 753 3.26e+01 1cf9A c.23.16.3 31457 e.5.1.1 42831 1c24A 263 3.27e+01 1c24A d.127.1.1 41148 1ggkA 753 3.28e+01 1cf9A c.23.16.3 31453 e.5.1.1 42827 1cf9A 753 3.31e+01 1cf9A c.23.16.3 31441 e.5.1.1 42815 1ggeA 753 3.31e+01 1cf9A c.23.16.3 31449 e.5.1.1 42823 1kbzA 299 3.31e+01 1gghA 753 3.31e+01 1cf9A c.23.16.3 31465 e.5.1.1 42839 1gg9A 753 3.32e+01 1cf9A c.23.16.3 31445 e.5.1.1 42819 1gdhA 320 3.32e+01 1gdhA c.2.1.4 30095 c.23.12.1 31355 1hv9A 456 3.36e+01 1fwyA b.81.1.4 28060 c.68.1.5 34518 1jew3 238 3.39e+01 1qf7A 753 3.40e+01 1cf9A c.23.16.3 31461 e.5.1.1 42835 1qtfA 246 3.48e+01 1agjA b.47.1.1 25830 1eapA 213 3.48e+01 8fabA b.1.1.1 20014 b.1.1.2 21068 1dliA 402 3.51e+01 1dliA a.100.1.4 18809 c.2.1.6 30213 c.26.3.1 31622 1dljA 402 3.55e+01 1dliA a.100.1.4 18808 c.2.1.6 30212 c.26.3.1 31621 1ak7 174 3.57e+01 1cof d.109.1.2 40864 4thiA 362 3.58e+01 2thiA c.94.1.1 35793 1i3fA 104 3.63e+01 9rnt d.1.1.1 61591 1e19A 314 3.64e+01 1b7bA c.73.1.1 34967 1hvc 203 3.66e+01 1hvc b.50.1.1 26614 3thiA 371 3.67e+01 2thiA c.94.1.1 35792 2thiA 379 3.70e+01 2thiA c.94.1.1 35794 3hohA 104 3.77e+01 9rnt d.1.1.1 36085 1l0oA 150 3.88e+01 1i0sA 169 3.93e+01 1i0rA b.45.1.2 61491 1i0rA 169 3.93e+01 1i0rA b.45.1.2 61489 1g652 196 3.94e+01 1i51B 105 3.97e+01