# 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 1lba 146 4.23e-15 1lba d.118.1.1 41062 1i05A 180 2.35e-02 1mup b.60.1.1 27130 1i06A 180 2.65e-02 1mup b.60.1.1 27131 1jv4A 162 2.74e-02 b.60.1.1 67343 1ew3A 159 2.81e-02 1mup b.60.1.1 27114 1gm6A 175 4.99e-02 1mup 166 1.27e-01 1mup b.60.1.1 27133 1bj7 156 1.30e-01 1bj7 b.60.1.1 27113 1hfoA 113 2.22e-01 d.80.1.3 61006 2mcm 112 3.08e-01 2mcm b.1.7.1 22207 2chsA 127 7.43e-01 2chsA d.79.1.2 39764 1dbfA 127 8.44e-01 2chsA d.79.1.2 39761 1f2tA 149 1.04e+00 1f2tA c.37.1.12 32373 1mfiA 114 1.28e+00 1dptA d.80.1.3 39856 1gd0A 122 1.36e+00 1dptA d.80.1.3 39834 1hlgA 371 1.42e+00 1hlgA c.69.1.6 34656 1bdfA 235 2.14e+00 1bdfA d.74.3.1 39727 d.181.1.1 42602 1ekeA 230 2.21e+00 1ekeA c.55.3.1 33572 3pflA 759 2.67e+00 1cm5A c.7.1.1 30673 1qu9A 128 2.78e+00 1qu9A d.79.1.1 39755 1qu9C 128 2.78e+00 1qu9A d.79.1.1 39757 1jmuB 666 2.97e+00 3dni 260 3.10e+00 3dni d.151.1.1 41791 1dzkA 157 3.12e+00 1obpA b.60.1.1 27096 1a3yA 149 3.19e+00 1obpA b.60.1.1 27110 1cm5A 759 3.63e+00 1cm5A c.7.1.1 30671 1e85A 127 3.92e+00 1bbhA a.24.3.2 16549 1qj4A 257 3.95e+00 1qj4A c.69.1.20 34796 1dptA 117 4.09e+00 1dptA d.80.1.3 39862 1cgo 127 4.12e+00 1cpq a.24.3.2 16550 2pflA 759 4.59e+00 1cm5A c.7.1.1 30675 1fezA 256 4.63e+00 1fezA c.108.1.3 43343 1yasA 257 4.89e+00 1qj4A c.69.1.20 34801 1iicA 422 5.40e+00 1nmtA d.108.1.2 62422 d.108.1.2 62423 1h2aS 317 5.54e+00 2frvA e.19.1.1 43311 1toh 343 5.70e+00 4pah d.178.1.1 42573 1ijyA 130 5.92e+00 1ijxA a.141.1.1 62517 1fj2A 232 6.33e+00 1auoA c.69.1.14 34720 1noa 113 6.36e+00 2mcm b.1.7.1 22208 1fljA 260 6.50e+00 2cba b.74.1.1 27954 1fohA 664 6.54e+00 1fohA c.3.1.2 30381 c.47.1.10 33078 d.16.1.2 37900 1e3dB 542 6.72e+00 1h2rL e.18.1.1 59189 1eqcA 394 6.80e+00 1cz1A c.1.8.3 28811 3pmgA 561 6.84e+00 3pmgA c.84.1.1 35408 c.84.1.1 35409 c.84.1.1 35410 d.129.2.1 41301 1cz1A 394 6.88e+00 1cz1A c.1.8.3 28839 1brt 277 7.01e+00 1brt c.69.1.12 34699 1j5wA 298 7.07e+00 1ivg 388 7.14e+00 2qwc b.68.1.1 27578 1f8xA 157 7.44e+00 1f8xA c.23.14.1 31397 1byuA 216 7.49e+00 1byuA c.37.1.8 32032 1h2rL 534 7.53e+00 1h2rL e.18.1.1 43298 1jnyA 435 7.55e+00 b.43.3.1 66982 b.44.1.1 66983 c.37.1.8 66984 5pal 109 7.67e+00 1a75A a.39.1.4 17215 1h2aL 567 7.87e+00 1h2rL e.18.1.1 43299 1g6oA 330 9.04e+00 1g6oA c.37.1.13 32430 1c8bA 371 9.30e+00 1c8bA c.56.1.2 59082 1eq6A 189 9.31e+00 1eq6A d.107.1.1 40796 1g5cA 170 9.33e+00 1g5cA c.53.2.1 60264 1hp8 68 9.58e+00 1hp8 a.17.1.1 16399 1cc1L 498 1.04e+01 1h2rL e.18.1.1 43301 1g99A 408 1.05e+01 1g99A c.55.1.2 33457 c.55.1.2 33458 1otfA 62 1.07e+01 1otfA d.80.1.1 39820 1f5mA 180 1.09e+01 1f5mB d.110.2.1 40895 1f5mB 180 1.10e+01 1f5mB d.110.2.1 40896 1euvA 221 1.14e+01 1euvA d.3.1.7 37133 1oakA 196 1.16e+01 1auq c.62.1.1 34138 1broA 277 1.18e+01 1brt c.69.1.12 34700 1ek0A 170 1.19e+01 1ctqA c.37.1.8 32076 1jtkA 136 1.23e+01 1qhdA 398 1.25e+01 1qhdA a.115.1.2 63324 b.19.1.1 63325 1kngA 156 1.27e+01 1h2rS 267 1.28e+01 2frvA e.19.1.1 43310 1h9oA 112 1.29e+01 1qadA d.93.1.1 60837 1svq 114 1.32e+01 1svy d.109.1.1 40832 1qtwA 285 1.32e+01 1qumA c.1.15.1 29392 1kijA 390 1.35e+01 2sli 679 1.41e+01 2sli b.29.1.9 24274 b.68.1.1 27611 4sli 679 1.41e+01 2sli b.29.1.9 24275 b.68.1.1 27612 1i69A 219 1.45e+01 c.94.1.1 61825 1efcA 393 1.49e+01 1efcA b.43.3.1 25680 b.44.1.1 25720 c.37.1.8 32113 1jeoA 180 1.49e+01 c.80.1.3 66611 1auq 208 1.49e+01 1auq c.62.1.1 34137 1eq9A 222 1.51e+01 5ptp b.47.1.2 26068 3pte 349 1.59e+01 3pte e.3.1.1 42687 1qumA 285 1.61e+01 1qumA c.1.15.1 29393 1hvbA 349 1.66e+01 3pte e.3.1.1 42686 1onrA 316 1.71e+01 1onrA c.1.10.1 29169 1duvG 333 1.75e+01 1othA c.78.1.1 35228 c.78.1.1 35229 1dwnA 127 1.81e+01 1dwnA d.85.1.1 40141 1qd9A 124 1.81e+01 1qu9A d.79.1.1 39758 1h7sA 365 1.85e+01 d.14.1.3 65705 d.122.1.2 65706 1h6dA 433 1.89e+01 c.2.1.3 65656 d.81.1.5 65657 1be9A 119 1.98e+01 1pdr b.36.1.1 24774 1ifqA 138 2.01e+01 1ifqA d.110.4.1 62350 1atzB 189 2.06e+01 1atzA c.62.1.1 34133 1bfi 112 2.07e+01 1qadA d.93.1.1 40499 1ofgA 381 2.08e+01 1ofgA c.2.1.3 30064 d.81.1.5 39979 1hskA 326 2.09e+01 2mbr d.145.1.2 61241 d.146.1.1 61242 1a5j 110 2.12e+01 1a5j a.4.1.3 16043 a.4.1.3 16044 1svy 114 2.17e+01 1svy d.109.1.1 40831 1b3jA 274 2.19e+01 1agdA b.1.1.2 20855 d.19.1.1 38319 1gd5A 130 2.21e+01 1gd5A d.189.1.1 60439 1qhhA 167 2.24e+01 1pjr c.37.1.13 32393 1lxtA 561 2.31e+01 3pmgA c.84.1.1 35432 c.84.1.1 35433 c.84.1.1 35434 d.129.2.1 41309 2dnjA 260 2.31e+01 3dni d.151.1.1 41790 1cjaA 342 2.31e+01 1cjaA d.144.1.3 41708 1dmhA 311 2.33e+01 1dmhA b.3.6.1 22633 1phk 298 2.41e+01 1cdkA d.144.1.1 41635 1jer 138 2.45e+01 2cbp b.6.1.1 23022 1i9gA 280 2.48e+01 c.66.1.13 62090 1atzA 189 2.54e+01 1atzA c.62.1.1 34132 1fnd 314 2.56e+01 1fnc b.43.4.2 25626 c.25.1.1 31516 1spgB 147 2.60e+01 1cg5B a.1.1.2 15588 1qqsA 174 2.61e+01 1nglA b.60.1.1 27143 1fnsA 196 2.61e+01 1auq c.62.1.1 34136 1ijbA 202 2.63e+01 1b47A 304 2.66e+01 2cblA a.39.1.7 17381 a.48.1.1 17775 d.93.1.1 40529 1f6yA 262 2.67e+01 1f6yA c.1.21.2 29673 1g9oA 91 2.71e+01 1pdr b.36.1.1 60400 1gesA 450 2.74e+01 3grs c.3.1.5 30473 c.3.1.5 30474 d.87.1.1 40168 2bce 581 2.75e+01 2bce c.69.1.1 34625 1d0nA 729 2.75e+01 1d0nA d.109.1.1 40834 d.109.1.1 40835 d.109.1.1 40836 d.109.1.1 40837 d.109.1.1 40838 d.109.1.1 40839 1gosA 520 2.83e+01 c.3.1.2 65425 d.16.1.5 65426 1lbeA 258 2.85e+01 1lbeA e.4.1.1 42773 1fnc 314 2.85e+01 1fnc b.43.4.2 25627 c.25.1.1 31517 2bvwA 362 2.87e+01 1bvwA c.6.1.1 30666 1qamA 244 2.94e+01 2ercA c.66.1.9 34220 1emsA 440 3.06e+01 1emsA d.13.1.1 37520 d.160.1.1 42086 1mh1 186 3.06e+01 1eesA c.37.1.8 32002 1fnoA 417 3.06e+01 1d2oA 187 3.07e+01 1d2oA b.3.5.1 22625 b.3.5.1 22626 1kao 167 3.09e+01 1ctqA c.37.1.8 32014 1e5dA 402 3.13e+01 1e5dA c.23.5.1 31208 d.157.1.3 42061 1nfkA 325 3.17e+01 1a3qA b.1.1.5 21929 b.2.5.1 22444 1dypA 271 3.20e+01 1dypA b.29.1.2 24185 1ig6A 107 3.21e+01 1ig6A a.4.3.2 62364 1pdz 434 3.22e+01 4enl c.1.11.1 29215 d.54.1.1 38859 1i6wA 181 3.23e+01 1i6wA c.69.1.18 61859 1epaA 164 3.25e+01 1epaA b.60.1.1 27128 1lr0A 129 3.25e+01 1jdfA 447 3.26e+01 c.1.11.2 62897 d.54.1.1 62898 1ctqA 166 3.27e+01 1ctqA c.37.1.8 31965 1bbhA 131 3.28e+01 1bbhA a.24.3.2 16546 1epbA 164 3.28e+01 1epaA b.60.1.1 27126 1kz7A 353 3.29e+01 1hq0A 295 3.29e+01 1hzgA d.194.1.1 61122 1f8yA 157 3.33e+01 1f8xA c.23.14.1 31395 1bvoA 175 3.36e+01 1a3qA b.2.5.1 22457 1c8oA 300 3.37e+01 1c8oA e.1.1.1 42677 1gx3A 284 3.39e+01 1rfs 139 3.42e+01 1rfs b.33.1.1 24434 1bf6A 291 3.43e+01 1pscA c.1.9.3 29065 1bvh 157 3.45e+01 1dg9A c.44.1.1 32640 1kyqA 274 3.49e+01 1jpaA 312 3.56e+01 d.144.1.2 67011 1ej2A 181 3.58e+01 1f9aA c.26.1.3 59414 1kt9A 138 3.59e+01 3nul 130 3.60e+01 3nul d.110.1.1 40891 1shcA 195 3.60e+01 1shcA b.55.1.2 26992 1jb0D 138 3.62e+01 1jb0D d.187.1.1 62823 1qvbA 481 3.66e+01 1qvbA c.1.8.4 28983 1svr 114 3.66e+01 1svy d.109.1.1 40833 1lehA 364 3.67e+01 1bw9A c.2.1.7 30268 c.58.1.1 33916 1hzgA 295 3.73e+01 1hzgA d.194.1.1 61436 1e5pA 151 3.73e+01 1bj7 b.60.1.1 59272 1ejhA 190 3.77e+01 1ejhA d.86.1.1 40147 1bhgA 613 3.77e+01 1bhgA b.1.4.1 22161 b.18.1.5 23766 c.1.8.3 28889 1es9A 232 3.78e+01 1wab c.23.10.3 31340 1dkgD 383 3.81e+01 1ba1 c.55.1.1 33427 c.55.1.1 33428 1bvwA 360 3.84e+01 1bvwA c.6.1.1 30668 1i9sA 210 3.84e+01 1i9sA c.45.1.1 62099 1ga0A 364 3.84e+01 1gceA e.3.1.1 60410 1ku2A 241 3.86e+01 1qadA 111 3.91e+01 1qadA d.93.1.1 40498 1k8tA 510 3.92e+01 e.9.1.4 68316 1ceqA 316 3.93e+01 1ceqA c.2.1.5 30163 d.162.1.1 42130 1lki 180 3.94e+01 1lki a.26.1.1 16829 1cknA 330 3.95e+01 1ckmA b.40.4.6 25360 d.142.2.3 41587