# 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 1qvcA 145 2.28e-21 3ullA b.40.4.3 25284 1kawA 135 2.97e-17 3ullA b.40.4.3 25288 3ullA 132 9.06e-15 3ullA b.40.4.3 25282 1je5A 206 9.22e-03 1je5A b.40.4.7 62909 1a8p 258 4.14e-01 1fdr b.43.4.2 25654 c.25.1.1 31544 1l9mA 692 1.08e+00 1bfeA 119 1.27e+00 1pdr b.36.1.1 24775 1be9A 119 1.44e+00 1pdr b.36.1.1 24774 1pdr 99 1.51e+00 1pdr b.36.1.1 24771 2prd 174 1.94e+00 2prd b.40.5.1 25435 1d1nA 99 2.63e+00 1d1nA b.43.3.1 25718 1qg0A 308 2.86e+00 1fnc b.43.4.2 25639 c.25.1.1 31529 1btkB 169 3.11e+00 1btkA b.55.1.1 26960 1at0 145 3.60e+00 1at0 b.86.1.1 28374 2oneA 436 3.68e+00 4enl c.1.11.1 29203 d.54.1.1 38847 1btkA 169 4.04e+00 1btkA b.55.1.1 26959 4enl 436 4.36e+00 4enl c.1.11.1 29202 d.54.1.1 38846 1d5yA 292 4.37e+00 1d5yA a.4.1.8 16055 a.4.1.8 16056 d.60.1.2 39532 1ge8A 249 4.43e+00 1plq d.131.1.2 41398 d.131.1.2 41399 1oneA 436 4.60e+00 4enl c.1.11.1 29200 d.54.1.1 38844 1ewjA 126 4.65e+00 1ecsA d.32.1.2 59526 1ecsA 126 5.07e+00 1ecsA d.32.1.2 59407 1e79A 510 5.08e+00 1skyB a.69.1.1 18269 b.49.1.1 26434 c.37.1.11 32314 1lylA 504 5.84e+00 1lylA b.40.4.1 25261 d.104.1.1 40717 1bmfA 510 5.99e+00 1skyB a.69.1.1 18281 b.49.1.1 26446 c.37.1.11 32326 1ff9A 450 6.39e+00 1ff9A c.2.1.3 30039 d.81.1.2 39954 1ggxA 223 6.59e+00 1ggxA d.22.1.1 38367 1ndoB 194 6.93e+00 1ndoB d.17.4.4 38121 1fnc 314 6.94e+00 1fnc b.43.4.2 25627 c.25.1.1 31517 1rlw 126 6.99e+00 1rlw b.7.1.1 23177 1dynA 125 7.10e+00 1dynA b.55.1.1 26955 1e1oA 504 7.18e+00 1lylA b.40.4.1 25258 d.104.1.1 40714 2dynA 122 7.51e+00 1dynA b.55.1.1 26957 1shaA 104 7.78e+00 1fmk d.93.1.1 40424 1shbA 104 7.93e+00 1fmk d.93.1.1 40425 2tdt 274 8.16e+00 3tdt b.81.1.2 28054 3tdt 274 8.19e+00 3tdt b.81.1.2 28053 1shdA 107 8.26e+00 1fmk d.93.1.1 40440 1b8aA 438 8.48e+00 1b8aA b.40.4.1 25244 d.104.1.1 40765 1cqqA 180 8.65e+00 1cqqA b.47.1.4 26422 1b8zA 90 8.71e+00 1huuA a.55.1.1 17902 1lj5A 379 8.94e+00 1h8eA 510 9.27e+00 1skyB a.69.1.1 60738 b.49.1.1 60739 c.37.1.11 60740 1fhgA 154 9.49e+00 1tlk b.1.1.4 21706 1tlk 154 9.54e+00 1tlk b.1.1.4 21707 1fnd 314 1.02e+01 1fnc b.43.4.2 25626 c.25.1.1 31516 1noyA 388 1.10e+01 1clqA c.55.3.5 33713 1cbjA 151 1.16e+01 1mfmA b.1.8.1 22213 1smrA 335 1.17e+01 1smrA b.50.1.2 26878 1j7xA 302 1.17e+01 c.14.1.2 66425 1pfo 500 1.25e+01 1pfo f.9.1.1 43826 2sodB 152 1.28e+01 1mfmA b.1.8.1 22242 1huuA 90 1.30e+01 1huuA a.55.1.1 17897 1gpeA 587 1.33e+01 1gpeA c.3.1.2 30387 d.16.1.4 37951 1i18A 97 1.42e+01 b.43.4.3 61520 1ds6B 180 1.49e+01 1rhoA b.1.1.5 21898 1fmk 452 1.50e+01 1fmk b.34.2.1 24511 d.93.1.1 40436 d.144.1.2 41690 1hrnA 337 1.56e+01 1smrA b.50.1.2 26869 1phd 414 1.61e+01 1phd a.104.1.1 18913 1phg 414 1.61e+01 1phd a.104.1.1 18910 1fxlA 167 1.63e+01 1b7fA d.58.7.1 39183 d.58.7.1 39184 1nnt 328 1.63e+01 1nnt c.94.1.2 35884 1jb7A 495 1.72e+01 1otcA b.40.4.3 62836 b.40.4.3 62837 b.40.4.3 62838 1fjgQ 105 1.72e+01 1fjfQ b.40.4.5 25352 1otcA 495 1.73e+01 1otcA b.40.4.3 25307 b.40.4.3 25308 b.40.4.3 25309 1qunB 279 1.73e+01 b.2.3.2 22411 b.2.3.2 22412 1qoiA 177 1.76e+01 2cpl b.62.1.1 27490 1dtoA 221 1.77e+01 1dtoA b.91.1.1 28405 1iakA 199 1.77e+01 1iakA b.1.1.2 21625 d.19.1.1 38199 3rp2A 224 1.78e+01 1a7s b.47.1.2 26298 1fdr 248 1.87e+01 1fdr b.43.4.2 25653 c.25.1.1 31543 1xsoA 150 1.88e+01 1mfmA b.1.8.1 22273 1i40A 175 1.91e+01 b.40.5.1 66024 1g13A 162 1.92e+01 1g13A b.95.1.1 60194 1nozA 388 2.01e+01 1clqA c.55.3.5 33715 1qfhA 212 2.02e+01 1qfhA b.1.1.5 21893 b.1.1.5 21894 1h8eG 272 2.03e+01 1e79G c.49.2.1 60756 1qdbA 473 2.06e+01 1qdbA a.138.1.3 19688 1kxrA 339 2.12e+01 1eut 605 2.13e+01 1eut b.1.1.5 21891 b.18.1.1 23712 b.68.1.1 27609 1lkkA 105 2.15e+01 1lckA d.93.1.1 40412 1e54A 332 2.17e+01 1e54A f.4.3.1 59258 1tdtA 259 2.18e+01 3tdt b.81.1.2 28055 1c0aA 585 2.18e+01 1c0aA b.40.4.1 25246 d.74.4.1 39731 d.104.1.1 40767 1f9zA 135 2.20e+01 1qipA d.32.1.1 38484 1yaiA 151 2.23e+01 1yaiA b.1.8.1 22289 1pkn 530 2.24e+01 1a49A b.58.1.1 27042 c.1.12.1 29271 c.49.1.1 33125 1behA 187 2.26e+01 1a44 b.17.1.1 23700 1eg9B 194 2.26e+01 1ndoB d.17.4.4 38120 5cpp 414 2.27e+01 1phd a.104.1.1 18935 1yghA 164 2.29e+01 1yghA d.108.1.1 40802 3cox 507 2.32e+01 1b8sA c.3.1.2 30332 d.16.1.1 37863 1wit 93 2.34e+01 1wit b.1.1.4 21714 1b33N 67 2.39e+01 1b33N d.30.1.1 38459 1ciy 590 2.45e+01 1ciy b.18.1.3 23720 b.77.2.1 27977 f.1.3.1 43392 1fs7A 485 2.46e+01 1qdbA a.138.1.3 19691 1i6iA 366 2.53e+01 1bg2 c.37.1.9 61844 1hh1A 143 2.56e+01 1gefA c.52.1.18 61036 1hqkA 154 2.63e+01 c.16.1.1 65902 1phb 414 2.67e+01 1phd a.104.1.1 18906 1amuA 563 2.77e+01 1amuA e.23.1.1 43351 1a8vA 121 2.81e+01 1a62 a.140.3.1 64712 b.40.4.5 64713 1jbuH 254 2.83e+01 5ptp b.47.1.2 62856 1gm5A 780 2.86e+01 a.29.4.1 65298 b.40.4.9 65299 c.37.1.13 65300 c.37.1.13 65301 1fa8A 135 2.86e+01 1qipA d.32.1.1 38486 1br9 194 2.87e+01 1br9 b.40.3.1 25235 1d5rA 324 2.90e+01 1d5rA b.7.1.1 23181 c.45.1.1 32697 1gqvA 135 2.93e+01 1iejA 332 2.96e+01 1nnt c.94.1.2 62328 1ijaA 148 2.99e+01 1ijaA b.100.1.1 62484 1obwA 175 3.12e+01 2prd b.40.5.1 25416 1f15B 218 3.14e+01 1f15B b.10.1.2 23321 1emwA 88 3.37e+01 1emwA d.27.1.1 38448 1jb3A 131 3.38e+01 1jc7A b.40.3.2 62833 1amx 180 3.39e+01 1amx b.2.3.1 22410 1f46A 140 3.46e+01 1f46A d.129.4.1 59643 1gmuA 143 3.50e+01 b.107.1.1 65335 d.58.38.1 65336 1al3 324 3.52e+01 1al3 c.94.1.1 35835 1cliA 345 3.52e+01 1cliA d.79.4.1 39816 d.139.1.1 41459 1a62 130 3.54e+01 1a62 a.140.3.1 64708 b.40.4.5 64709 1iioA 84 3.55e+01 a.39.4.1 66150 1que 303 3.58e+01 1fnc b.43.4.2 25647 c.25.1.1 31537 2aviA 128 3.60e+01 1swuA b.61.1.1 27411 2cpl 165 3.62e+01 2cpl b.62.1.1 27420 1euu 605 3.62e+01 1eut b.1.1.5 21892 b.18.1.1 23713 b.68.1.1 27610 1bovA 69 3.64e+01 2bosA b.40.2.1 25070 1jc7A 131 3.70e+01 1jc7A b.40.3.2 62873 1cwoA 165 3.75e+01 2cpl b.62.1.1 27445 1a7cA 379 3.76e+01 1sek e.1.1.1 42660 1k89 449 3.82e+01 1k89 c.2.1.7 30218 c.58.1.1 33866 1bgvA 449 3.93e+01 1k89 c.2.1.7 30217 c.58.1.1 33865 1hrdA 449 3.93e+01 1k89 c.2.1.7 30219 c.58.1.1 33867