# List of top-scoring protein chains for t04-100-30-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 1u69A 163 3.04e-01 d.32.1.7 107699 1rybA 212 3.98e-01 c.56.3.1 98098 2gaiA 633 6.01e-01 1k3yA 221 8.46e-01 a.45.1.1,c.47.1.5 77245,77246 1phk 298 1.76e+00 1cdkA d.144.1.7 41635 1vcdA 126 2.42e+00 1f3aA 222 2.91e+00 1pgtA a.45.1.1,c.47.1.5 17701,32995 1zemA 262 3.39e+00 1vhmA 195 3.49e+00 d.110.2.1 100691 1vf1A 229 3.84e+00 1lj2A 110 3.88e+00 h.1.13.2 73926 1t9mA 214 3.92e+00 1sdoA 203 4.94e+00 c.52.1.21 98809 1xrkA 124 6.06e+00 1bylA 125 7.54e+00 1bylA d.32.1.2 38495 1v7cA 351 8.42e+00 c.79.1.1 100446 1kay 381 8.47e+00 1ba1 c.55.1.1,c.55.1.1 33385,33386 1cojA 212 8.49e+00 1avmA a.2.11.1,d.44.1.1 15737,38734 1bupA 386 8.57e+00 1ba1 c.55.1.1,c.55.1.1 33377,33378 1xd7A 145 8.80e+00 a.4.5.55 109566 2msbA 115 9.18e+00 1rtm1 d.169.1.1 42355 2c0cA 362 9.72e+00 1yuwA 554 1.01e+01 1womA 271 1.01e+01 1wwpA 119 1.02e+01 1qxrA 189 1.03e+01 b.82.1.7 96552 1ylkA 172 1.04e+01 1l3lA 234 1.09e+01 a.4.6.2,d.110.5.1 73541,73542 1y74A 57 1.12e+01 1sesA 421 1.13e+01 1sesA a.2.7.1,d.104.1.1 15710,40710 2f9sA 151 1.19e+01 1st9A 143 1.20e+01 c.47.1.10 98987 1rktA 205 1.25e+01 a.4.1.9,a.121.1.1 97623,97624 1x82A 190 1.27e+01 1u20A 212 1.30e+01 1hnjA 317 1.34e+01 1hn9A c.95.1.2,c.95.1.2 35969,35970 1avoA 60 1.38e+01 1avoA a.24.8.1 16619 1z6oM 191 1.45e+01 1zowA 313 1.48e+01 2f9lA 199 1.50e+01 1f5qB 252 1.61e+01 1f5qB a.74.1.1,a.74.1.1 18362,18363 1zl8A 53 1.63e+01 1vrpA 381 1.65e+01 1eijA 80 1.83e+01 1eijA a.5.6.1 16298 1qh4A 380 1.86e+01 1qh4A a.83.1.1,d.128.1.2 18462,41197 1nwzA 125 1.87e+01 d.110.3.1 86370 1ysjA 404 1.88e+01 1dugA 234 1.90e+01 1b8xA a.45.1.1,c.47.1.5 17718,33012 1z9lA 128 1.90e+01 1wr2A 238 2.03e+01 1zi8A 236 2.04e+01 1eudB 396 2.14e+01 2scuB c.23.4.1,d.142.1.4 31150,41571 1vpkA 378 2.19e+01 1rgxA 114 2.22e+01 g.77.1.1 104932 1jvnA 555 2.23e+01 c.1.2.1,c.23.16.1 67355,67356 1i1qA 520 2.30e+01 1qdlA d.161.1.1 61543 1su8A 636 2.30e+01 e.26.1.2 98999 1wucA 250 2.38e+01 1rw2A 152 2.42e+01 a.118.19.1 97961 1bbzA 58 2.46e+01 1bbzA b.34.2.1 24477 1go4E 100 2.47e+01 h.1.22.1 70296 1ze3H 122 2.48e+01 1jjyA 636 2.54e+01 1jjyA 3pviA 157 2.59e+01 3pviA c.52.1.6 33300 1q02A 52 2.63e+01 a.5.2.1 95490 1o70A 324 2.64e+01 b.118.1.1,b.118.1.1 81115,81116 1tu7A 208 2.70e+01 1owfB 94 2.75e+01 a.55.1.1 87488 1rtm1 149 2.78e+01 1rtm1 1jksA 294 2.79e+01 d.144.1.7 71710 1df7A 159 2.85e+01 3dfr c.71.1.1 34885 1y9lA 115 2.87e+01 1wxxA 382 2.95e+01 1lrzA 426 3.06e+01 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 1q2zA 120 3.16e+01 a.118.19.1 95656 1uu3A 310 3.16e+01 d.144.1.7 99999 1g1pA 33 3.19e+01 1g1pA g.3.6.1 44099 2pviA 157 3.23e+01 3pviA c.52.1.6 33302 1k1xA 659 3.28e+01 a.8.3.2,b.30.5.8,c.6.2.2 84279,84280,84281 2bmeA 186 3.28e+01 1din 236 3.29e+01 1din c.69.1.9 34682 1v7lA 163 3.36e+01 1nh2D 121 3.36e+01 a.32.1.1,b.56.1.1 91876,91877 1ryp2 233 3.36e+01 1ryp2 1e1hA 287 3.37e+01 d.92.1.7 83167 1lba 146 3.41e+01 1lba d.118.1.1 41062 1uunA 184 3.46e+01 f.6.1.2 100012 1z90A 469 3.55e+01 1qc7A 101 3.66e+01 1qc7A a.118.14.1 18456 3pyp 125 3.70e+01 3pyp d.110.3.1 40897 1dseA 292 3.80e+01 1ryc a.93.1.1 59130 1elqA 390 3.81e+01 1elqA c.67.1.3 34436 1onqA 283 3.81e+01 b.1.1.2,d.19.1.1 93365,93366 6gsvA 217 3.82e+01 1b8xA a.45.1.1,c.47.1.5 17633,32925 1h1wA 289 3.97e+01 d.144.1.7 83460 1lpbA 95 3.97e+01 1lpbA g.3.10.1,g.3.10.1 44189,44190 1eluA 390 4.00e+01 1elqA c.67.1.3 34434 1e3dB 542 4.05e+01 1h2rL e.18.1.1 59189 1rypC 244 4.06e+01 1rypC d.153.1.4 41934 2a8lA 420 4.11e+01 3xis 387 4.17e+01 4xis c.1.15.3 29423 1pb1A 416 4.25e+01 c.77.1.1 88014 2gf9A 189 4.25e+01 4xis 387 4.30e+01 4xis c.1.15.3 29421 1k2xA 177 4.30e+01 d.153.1.5 90929 1go3F 107 4.33e+01 a.60.8.2 65407 1v5dA 386 4.34e+01 2cblA 305 4.35e+01 2cblA a.39.1.7,a.48.1.1,d.93.1.1 17380,17774,40528 1ptvA 321 4.40e+01 1pty c.45.1.2 32665 2c4jA 218 4.45e+01 1afb1 154 4.55e+01 1rtm1 1oxjA 173 4.56e+01 a.60.1.2,a.118.1.13 87517,87518 2b33A 140 4.57e+01 1z6oA 212 4.61e+01 2f71A 298 4.64e+01 1zwxA 301 4.66e+01 1x3sA 195 4.67e+01 2ae6A 166 4.68e+01 1mkp 144 4.71e+01 1vhrA c.45.1.1 32654 1mhdA 132 4.75e+01 1mhdA d.164.1.1 42175 1yoaA 159 4.78e+01 1qr0A 228 4.79e+01 1qr0A d.150.1.1,d.150.1.1 59038,59039 1hz6A 72 4.81e+01 2ptl d.15.7.1 61429 1xw5A 217 4.83e+01 1h12A 405 4.86e+01 a.102.1.2 83447 1r77A 103 4.87e+01 1e58A 249 4.89e+01 1qhfA c.60.1.1 59262 1uzpA 162 4.91e+01 g.3.11.1,g.3.11.1,g.23.1.1 100232,100233,100234 2g9iA 249 5.02e+01 1k4nA 192 5.05e+01 d.32.1.5 72059 1jgsA 138 5.08e+01 a.4.5.28 66683 1ytfD 121 5.09e+01 1ytfD a.32.1.1,b.56.1.1 16998,27011 2gq1A 332 5.24e+01 256bA 106 5.42e+01 256bA a.24.3.1 16539 2blkA 122 5.45e+01 1vk3A 615 5.48e+01 d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 100846,100847,100848,100849 1zmbA 290 5.66e+01 1muwA 386 5.80e+01 c.1.15.3 79495 1g5aA 628 5.83e+01 b.71.1.1,c.1.8.1 65152,65153 1xygD 359 5.90e+01 1xw2A 405 6.07e+01 1i52A 236 6.08e+01 1i52A c.68.1.13 61767 1y8oA 419 6.10e+01 1t8sA 484 6.15e+01 c.56.2.1 106679 1x4rA 99 6.27e+01 1h8mA 140 6.27e+01 1h8mA d.110.4.1 60782 1ty9A 222 6.27e+01 1jykA 254 6.32e+01 c.68.1.13 67458 1kwsA 261 6.40e+01 c.68.1.7 73083 1c6vX 81 6.44e+01 1ihvA b.34.7.1 24641 1atzA 189 6.48e+01 1atzA c.62.1.1 34132 1htyA 1015 6.52e+01 a.8.3.1,b.30.5.6,c.6.2.1 83064,83065,83066 1wb4A 297 6.52e+01 1g7fA 298 6.57e+01 1pty c.45.1.2 60330 1gklA 297 6.57e+01 c.69.1.2 65250 1llmC 88 6.59e+01 g.37.1.1,g.37.1.1 91059,91060 1avqA 228 6.60e+01 1avqA c.52.1.13 33326 1xwtA 405 6.69e+01 1wgbA 159 6.84e+01 1qwnA 1045 6.88e+01 a.8.3.1,b.30.5.6,c.6.2.1 96487,96488,96489 1yw5A 177 6.91e+01 1jr2A 286 6.93e+01 c.113.1.1 67111 1a2yB 116 6.99e+01 1gc1H b.1.1.1 19927 2eutA 294 6.99e+01 1z53A 294 7.01e+01 1ufaA 520 7.03e+01 a.8.3.3,c.6.2.4 99329,99330 1zbyA 294 7.06e+01 2occA 514 7.10e+01 2occA f.24.1.1 43518 2fp4B 395 7.11e+01 1ykwA 435 7.12e+01 2ethA 154 7.24e+01 1jogA 146 7.25e+01 a.24.16.2 77142 1uh4A 637 7.32e+01 b.1.18.2,b.71.1.1,c.1.8.1 99391,99392,99393 1bed 181 7.38e+01 1fvkA c.47.1.13 90330 1uehA 253 7.43e+01 c.101.1.1 99259 1jdrA 294 7.43e+01 1ryc a.93.1.1 62908 2f6mA 65 7.47e+01 1wloA 136 7.48e+01 2eryA 172 7.50e+01 1ox6A 555 7.55e+01 c.1.2.1,c.23.16.1 87505,87506 1ji1A 637 7.58e+01 b.1.18.2,b.71.1.1,c.1.8.1 71666,71667,71668 1i6xA 209 7.59e+01 a.4.5.4,b.82.3.2 83673,83674 1mw7A 240 7.60e+01 e.39.1.1 79557 1usgA 346 7.82e+01 c.93.1.1 99864 2ex0A 399 8.02e+01 1j30A 144 8.06e+01 a.25.1.1 90806 1v1hA 103 8.16e+01 b.83.1.1,h.1.17.1 108243,108244 1v3vA 333 8.21e+01 b.35.1.2,c.2.1.1 108345,108346 2fd5A 180 8.28e+01 1wgzA 510 8.31e+01 1mkrA 294 8.32e+01 a.93.1.1 84997 1nowA 507 8.34e+01 c.1.8.6,d.92.2.1 85936,85937 1opd 85 8.34e+01 1ptf d.94.1.1 40560 1omwA 689 8.34e+01 a.91.1.1,b.55.1.1,d.144.1.7 87086,87087,87088 1khdA 345 8.34e+01 a.46.2.1,c.27.1.1 77400,77401 1ppjJ 62 8.37e+01 f.23.14.1 104266 1pa1A 310 8.39e+01 c.45.1.2 94404 1h5qA 265 8.40e+01 1cydA c.2.1.2 60643 1i7wB 151 8.41e+01 1i7wB j.71.1.1 61910 1mrj 247 8.43e+01 1mrj d.165.1.1 42177 1hw7A 255 8.43e+01 1i7fA d.193.1.1 61297 1vp2A 208 8.58e+01 1g3mA 294 8.59e+01 c.37.1.5 83268 1y3nA 490 8.60e+01 2f60K 64 8.61e+01 1k3bA 119 8.62e+01 b.61.5.1 72016 1odfA 290 8.66e+01 c.37.1.6 92782 1fjlA 81 8.70e+01 2hddA a.4.1.1 16017 1i19A 561 8.72e+01 1i19A d.58.32.3,d.145.1.1 61522,61523 1d1vA 444 8.77e+01 1nseA d.174.1.1 59101 2ddrA 306 8.79e+01 1v54A 514 8.82e+01 f.24.1.1 100321 1rypI 222 8.83e+01 d.153.1.4 41877 12asA 330 8.93e+01 12asA d.104.1.1 40783 2fuqA 747 8.96e+01 1iso 416 8.98e+01 1iso c.77.1.1 35065