# List of top-scoring protein chains for t2k-100-30-bys-scores 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 1gulA 222 2.44e-02 1pgtA a.45.1.1,c.47.1.5 17675,32969 1gumA 222 4.30e-02 1pgtA a.45.1.1,c.47.1.5 17683,32977 1u69A 163 1.91e-01 d.32.1.7 107699 1rybA 212 2.80e-01 c.56.3.1 98098 1b5sA 242 7.78e-01 1eaf c.43.1.1 32626 1k3yA 221 1.02e+00 a.45.1.1,c.47.1.5 77245,77246 1phk 298 1.09e+00 1cdkA d.144.1.7 41635 2gaiA 633 1.15e+00 1k3lA 221 1.54e+00 a.45.1.1,c.47.1.5 77229,77230 1gseA 221 1.92e+00 1pgtA a.45.1.1,c.47.1.5 17667,32961 1vcdA 126 2.28e+00 1t9mA 214 3.70e+00 1f3aA 222 3.78e+00 1pgtA a.45.1.1,c.47.1.5 17701,32995 1gzqA 300 3.85e+00 b.1.1.2,d.19.1.1 70818,70819 1vf1A 229 4.30e+00 2c0cA 362 5.45e+00 1vhmA 195 5.62e+00 d.110.2.1 100691 1sdoA 203 5.90e+00 c.52.1.21 98809 1xrkA 124 6.00e+00 1v7cA 351 6.21e+00 c.79.1.1 100446 1zemA 262 6.35e+00 2nef 136 6.95e+00 1efnB d.102.1.1 40704 1qxrA 189 8.17e+00 b.82.1.7 96552 1bylA 125 8.26e+00 1bylA d.32.1.2 38495 1lj2A 110 8.69e+00 h.1.13.2 73926 1st9A 143 8.89e+00 c.47.1.10 98987 2f9sA 151 8.95e+00 1eblB 317 9.28e+00 1hn9A c.95.1.2,c.95.1.2 35975,35976 1eyuA 157 9.34e+00 3pviA c.52.1.6 33304 1wwpA 119 9.71e+00 1rktA 205 9.92e+00 a.4.1.9,a.121.1.1 97623,97624 1x82A 190 1.03e+01 1hnjA 317 1.08e+01 1hn9A c.95.1.2,c.95.1.2 35969,35970 1zowA 313 1.08e+01 1cojA 212 1.11e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1hn9A 317 1.18e+01 1hn9A c.95.1.2,c.95.1.2 35977,35978 1y74A 57 1.20e+01 1zl8A 53 1.21e+01 1eblA 317 1.35e+01 1hn9A c.95.1.2,c.95.1.2 35973,35974 1vpkA 378 1.37e+01 1womA 271 1.38e+01 1z6oM 191 1.43e+01 1ihfB 94 1.44e+01 1huuA a.55.1.1 17894 1uunA 184 1.46e+01 f.6.1.2 100012 1nwzA 125 1.48e+01 d.110.3.1 86370 2phy 125 1.54e+01 3pyp d.110.3.1 40901 1xd7A 145 1.62e+01 a.4.5.55 109566 3pviA 157 1.62e+01 3pviA c.52.1.6 33300 1bbzA 58 1.64e+01 1bbzA b.34.2.1 24477 1l3lA 234 1.66e+01 a.4.6.2,d.110.5.1 73541,73542 1ba1 386 1.67e+01 1ba1 c.55.1.1,c.55.1.1 33387,33388 7icd 416 1.70e+01 1iso c.77.1.1 35072 1kay 381 1.71e+01 1ba1 c.55.1.1,c.55.1.1 33385,33386 1bupA 386 1.72e+01 1ba1 c.55.1.1,c.55.1.1 33377,33378 1hpm 386 1.74e+01 1ba1 c.55.1.1,c.55.1.1 33381,33382 2f9lA 199 1.77e+01 1avoA 60 1.92e+01 1avoA a.24.8.1 16619 1owfB 94 1.95e+01 a.55.1.1 87488 2pviA 157 2.01e+01 3pviA c.52.1.6 33302 1dugA 234 2.02e+01 1b8xA a.45.1.1,c.47.1.5 17718,33012 1yuwA 554 2.03e+01 1i8xA 30 2.05e+01 g.3.16.1 71132 1vrpA 381 2.06e+01 1wucA 250 2.08e+01 1qh4A 380 2.12e+01 1qh4A a.83.1.1,d.128.1.2 18462,41197 1g1pA 33 2.14e+01 1g1pA g.3.6.1 44099 1ysjA 404 2.19e+01 1q02A 52 2.21e+01 a.5.2.1 95490 1i1qA 520 2.23e+01 1qdlA d.161.1.1 61543 1wb4A 297 2.25e+01 1gkkA 297 2.27e+01 c.69.1.2 65248 1gklA 297 2.27e+01 c.69.1.2 65250 1go4E 100 2.29e+01 h.1.22.1 70296 1su8A 636 2.29e+01 e.26.1.2 98999 1ylkA 172 2.30e+01 2msbA 115 2.35e+01 1rtm1 d.169.1.1 42355 1k1xA 659 2.36e+01 a.8.3.2,b.30.5.8,c.6.2.2 84279,84280,84281 1z9lA 128 2.42e+01 1jjyA 636 2.50e+01 1jjyA 1jvnA 555 2.62e+01 c.1.2.1,c.23.16.1 67355,67356 1ats 386 2.63e+01 1ba1 c.55.1.1,c.55.1.1 33423,33424 2bmeA 186 2.64e+01 1bbzE 58 2.65e+01 1bbzA b.34.2.1 24479 1eijA 80 2.68e+01 1eijA a.5.6.1 16298 1u20A 212 2.80e+01 2a8lA 420 2.82e+01 1eucB 396 2.88e+01 2scuB c.23.4.1,d.142.1.4 31149,41570 1plfA 72 2.91e+01 1tvxA d.9.1.1 37373 2f71A 298 2.98e+01 1pvuA 154 2.99e+01 3pviA c.52.1.6 33306 1wr2A 238 3.03e+01 1qc7A 101 3.06e+01 1qc7A a.118.14.1 18456 6gsvA 217 3.08e+01 1b8xA a.45.1.1,c.47.1.5 17633,32925 1ptvA 321 3.09e+01 1pty c.45.1.2 32665 3pyp 125 3.11e+01 3pyp d.110.3.1 40897 2hnp 321 3.12e+01 1pty c.45.1.2 32678 1qr0A 228 3.15e+01 1qr0A d.150.1.1,d.150.1.1 59038,59039 1eudB 396 3.15e+01 2scuB c.23.4.1,d.142.1.4 31150,41571 1aroL 151 3.17e+01 1lba d.118.1.1 41063 1p6xA 334 3.26e+01 c.37.1.1 94195 1f5qB 252 3.32e+01 1f5qB a.74.1.1,a.74.1.1 18362,18363 1zmbA 290 3.46e+01 1oxjA 173 3.46e+01 a.60.1.2,a.118.1.13 87517,87518 2ae6A 166 3.48e+01 2msbB 115 3.54e+01 1rtm1 d.169.1.1 42356 1eeoA 321 3.57e+01 1pty c.45.1.2 32655 1v7lA 163 3.59e+01 1y8oA 419 3.61e+01 1uu3A 310 3.61e+01 d.144.1.7 99999 1h12A 405 3.63e+01 a.102.1.2 83447 1tu7A 208 3.69e+01 1tdj 514 3.70e+01 1tdj c.79.1.1,d.58.18.2,d.58.18.2 35297,39356,39357 2cblA 305 3.73e+01 2cblA a.39.1.7,a.48.1.1,d.93.1.1 17380,17774,40528 1lpbA 95 3.75e+01 1lpbA g.3.10.1,g.3.10.1 44189,44190 1y9lA 115 3.76e+01 1nh2D 121 3.83e+01 a.32.1.1,b.56.1.1 91876,91877 1eluB 390 3.84e+01 1elqA c.67.1.3 34435 1rw2A 152 3.86e+01 a.118.19.1 97961 1k2xA 177 3.89e+01 d.153.1.5 90929 1pb1A 416 3.90e+01 c.77.1.1 88014 1e58A 249 3.92e+01 1qhfA c.60.1.1 59262 1jksA 294 4.01e+01 d.144.1.7 71710 1b8xA 280 4.07e+01 1b8xA a.45.1.1,c.47.1.5 17739,33033 1yoaA 159 4.11e+01 1jgsA 138 4.12e+01 a.4.5.28 66683 1xwtA 405 4.18e+01 1rgxA 114 4.20e+01 g.77.1.1 104932 2ashA 381 4.23e+01 2b33A 140 4.34e+01 1g7fA 298 4.34e+01 1pty c.45.1.2 60330 1h1wA 289 4.34e+01 d.144.1.7 83460 1aax 321 4.38e+01 1pty c.45.1.2 32657 1sesA 421 4.39e+01 1sesA a.2.7.1,d.104.1.1 15710,40710 1dseA 292 4.41e+01 1ryc a.93.1.1 59130 1elqA 390 4.44e+01 1elqA c.67.1.3 34436 1xw2A 405 4.50e+01 1lba 146 4.54e+01 1lba d.118.1.1 41062 1e3dB 542 4.58e+01 1h2rL e.18.1.1 59189 1eluA 390 4.63e+01 1elqA c.67.1.3 34434 2hqi 72 4.64e+01 1aw0 d.58.17.1 39340 1go3F 107 4.66e+01 a.60.8.2 65407 2gf9A 189 4.69e+01 2blkA 122 4.70e+01 1z90A 469 4.71e+01 1lrzA 426 4.76e+01 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 1zi8A 236 4.77e+01 1z6oA 212 4.79e+01 1osdA 72 4.92e+01 d.58.17.1 104022 2c4jA 218 5.00e+01 1htyA 1015 5.03e+01 a.8.3.1,b.30.5.6,c.6.2.1 83064,83065,83066 1b47A 304 5.07e+01 2cblA a.39.1.7,a.48.1.1,d.93.1.1 17381,17775,40529 1hxkA 1015 5.08e+01 a.8.3.1,b.30.5.6,c.6.2.1 83070,83071,83072 1q2zA 120 5.10e+01 a.118.19.1 95656 1pcn 93 5.10e+01 1lpbA g.3.10.1,g.3.10.1 44199,44200 1mkp 144 5.16e+01 1vhrA c.45.1.1 32654 1hwwA 1015 5.16e+01 a.8.3.1,b.30.5.6,c.6.2.1 83067,83068,83069 1jykA 254 5.23e+01 c.68.1.13 67458 1kxlA 199 5.27e+01 b.40.4.3 73155 1vk3A 615 5.29e+01 d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 100846,100847,100848,100849 1jr2A 286 5.29e+01 c.113.1.1 67111 1usgA 346 5.31e+01 c.93.1.1 99864 1qwnA 1045 5.34e+01 a.8.3.1,b.30.5.6,c.6.2.1 96487,96488,96489 1c6vX 81 5.37e+01 1ihvA b.34.7.1 24641 1wxxA 382 5.37e+01 1xw5A 217 5.38e+01 1hz6A 72 5.38e+01 2ptl d.15.7.1 61429 2ddrA 306 5.41e+01 1pa1A 310 5.48e+01 c.45.1.2 94404 1df7A 159 5.50e+01 3dfr c.71.1.1 34885 1mejA 223 5.51e+01 c.65.1.1 79029 1onqA 283 5.54e+01 b.1.1.2,d.19.1.1 93365,93366 1qgmA 30 5.58e+01 g.3.16.1 44380 1pty 321 5.61e+01 1pty c.45.1.2 32656 2a0kA 161 5.67e+01 1i52A 236 5.73e+01 1i52A c.68.1.13 61767 1a2yB 116 5.83e+01 1gc1H b.1.1.1 19927 1nouA 507 5.83e+01 c.1.8.6,d.92.2.1 85932,85933 1v5dA 386 5.84e+01 2f62A 161 5.92e+01 1atr 386 5.94e+01 1ba1 c.55.1.1,c.55.1.1 33421,33422 1bed 181 6.00e+01 1fvkA c.47.1.13 90330 1wgbA 159 6.05e+01 2a5jA 191 6.11e+01 2g9iA 249 6.13e+01 1wgzA 510 6.13e+01 1nt2A 210 6.24e+01 c.66.1.3 86149 1rypC 244 6.24e+01 1rypC d.153.1.4 41934 1aboA 62 6.28e+01 1bbzA b.34.2.1 24474 1ppjJ 62 6.29e+01 f.23.14.1 104266 1mw7A 240 6.30e+01 e.39.1.1 79557 1ytfD 121 6.30e+01 1ytfD a.32.1.1,b.56.1.1 16998,27011 1k52A 72 6.33e+01 d.15.7.1 68148 1r77A 103 6.38e+01 2ex0A 399 6.39e+01 2f6mA 65 6.42e+01 1nseA 444 6.51e+01 1nseA d.174.1.1 42534 2f2tA 161 6.56e+01 1lkvX 232 6.56e+01 a.118.14.1 73980 1jruA 89 6.65e+01 1jruA d.15.1.2 63257 1etpA 190 6.65e+01 1etpA a.3.1.4,a.3.1.4 15962,15963 1yq5A 144 6.66e+01 1mhdA 132 6.71e+01 1mhdA d.164.1.1 42175 1x3sA 195 6.76e+01 1h8mA 140 6.77e+01 1h8mA d.110.4.1 60782 1omwA 689 6.82e+01 a.91.1.1,b.55.1.1,d.144.1.7 87086,87087,87088 1khdA 345 6.84e+01 a.46.2.1,c.27.1.1 77400,77401 1uehA 253 6.85e+01 c.101.1.1 99259 1atzB 189 6.93e+01 1atzA c.62.1.1 34133 1ze3H 122 6.95e+01 1t8sA 484 7.00e+01 c.56.2.1 106679 1din 236 7.02e+01 1din c.69.1.9 34682 2occA 514 7.05e+01 2occA f.24.1.1 43518 256bA 106 7.07e+01 256bA a.24.3.1 16539 1g0u1 266 7.07e+01 1xygD 359 7.09e+01 1buuA 168 7.10e+01 1rtm1 d.169.1.1,h.1.1.1 42366,45388 2gq1A 332 7.11e+01 1v3vA 333 7.15e+01 b.35.1.2,c.2.1.1 108345,108346 1nowA 507 7.16e+01 c.1.8.6,d.92.2.1 85936,85937 1rtm1 149 7.31e+01 1rtm1 1yw5A 177 7.36e+01 1htxA 32 7.36e+01 1qfdA g.3.2.1 61261 1b48A 221 7.52e+01 1pgtA a.45.1.1,c.47.1.5 17703,32997 1e1hA 287 7.52e+01 d.92.1.7 83167 1bunB 61 7.70e+01 1bpi g.8.1.1 44552 1a5y 330 7.72e+01 1pty c.45.1.2 32673 2ar9A 278 7.84e+01 1xis 387 7.86e+01 4xis c.1.15.3 29422 2fd5A 180 7.88e+01 1tzjA 338 7.92e+01 1fggA 261 7.95e+01 1fggA c.68.1.7 34576 1ryp2 233 8.07e+01 1ryp2 1iso 416 8.09e+01 1iso c.77.1.1 35065 1rypB 250 8.12e+01 1rypB d.153.1.4 41933 1mrj 247 8.19e+01 1mrj d.165.1.1 42177 1ggvA 232 8.19e+01 1din c.69.1.9 34683 2av9A 147 8.25e+01 1y3nA 490 8.32e+01 2cw9A 194 8.35e+01 1o70A 324 8.35e+01 b.118.1.1,b.118.1.1 81115,81116 1jogA 146 8.35e+01 a.24.16.2 77142 2cxxA 190 8.38e+01 1x4rA 99 8.41e+01 2pkaB 152 8.42e+01 5ptp 1j30A 144 8.44e+01 a.25.1.1 90806 5nseA 444 8.52e+01 d.174.1.1 74644 1i42A 89 8.55e+01 1jruA d.15.1.2 61651 1mx4A 168 8.61e+01 d.211.1.1 79640 3phy 125 8.61e+01 3pyp d.110.3.1 40904 1g5aA 628 8.62e+01 b.71.1.1,c.1.8.1 65152,65153 1ykwA 435 8.69e+01 1k4nA 192 8.70e+01 d.32.1.5 72059 1m70A 190 8.71e+01 a.3.1.4,a.3.1.4 91200,91201 2a6vA 226 8.73e+01 1tf1A 198 8.78e+01 d.110.2.2 106826 1kwsA 261 8.78e+01 c.68.1.7 73083 1v54A 514 8.83e+01 f.24.1.1 100321 3xis 387 8.89e+01 4xis c.1.15.3 29423