# List of top-scoring protein chains for t04-100-30-bys 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 1e19A 314 1.01e-03 1b7bA c.73.1.1 34967 1j97A 211 1.29e-02 1f5sA c.108.1.4 62753 1l7mA 211 1.36e-02 c.108.1.4 73664 2cro 71 7.60e-02 1r69 a.35.1.2 17038 1r7lA 110 1.45e-01 1onxA 390 1.47e-01 b.92.1.7 87176 c.1.9.13 87177 1lrzA 426 1.63e-01 a.2.7.4 78167 d.108.1.4 78168 d.108.1.4 78169 1d7yA 408 1.81e-01 1d7yA c.3.1.5 30565 c.3.1.5 30566 d.87.1.1 40204 1onwA 390 2.34e-01 b.92.1.7 87172 c.1.9.13 87173 1q7zA 566 3.14e-01 c.1.21.2 -5638 c.1.26.1 -5666 1nteA 82 3.37e-01 b.36.1.1 86163 1umgA 362 3.83e-01 1r6jA 82 3.84e-01 b.36.1.1 -3732 1qflA 389 4.24e-01 1afwA c.95.1.1 35908 c.95.1.1 35909 1dekA 241 4.31e-01 1dekA c.37.1.1 31842 1qmvA 197 4.75e-01 1qq2A c.47.1.10 33066 1pcfA 66 5.72e-01 1pcfA d.18.1.1 38142 1a05A 358 5.76e-01 1cnzA c.77.1.1 35059 1lktA 104 6.00e-01 1lktA b.90.1.1 28398 1deuA 277 6.87e-01 1theB d.3.1.1 37085 1m4tA 392 7.57e-01 c.95.1.1 78617 c.95.1.1 78618 1dd9A 338 7.93e-01 1dd9A e.13.1.1 43254 2cpl 165 8.69e-01 2cpl b.62.1.1 27420 1f53A 84 9.81e-01 1f53A b.11.1.4 23632 1j1nA 492 9.95e-01 c.94.1.1 83978 1sjwA 144 1.04e+00 unknown_sccs -9296 1awqA 164 1.06e+00 2cpl b.62.1.1 27461 4uagA 437 1.06e+00 4uagA c.5.1.1 30651 c.59.1.1 33952 c.72.2.1 34955 1ivg 388 1.19e+00 2qwc b.68.1.1 27578 1j6pA 418 1.23e+00 b.92.1.4 77089 c.1.9.9 77090 1p1mA 406 1.25e+00 b.92.1.4 87696 c.1.9.9 87697 1gadO 330 1.28e+00 1dssG c.2.1.3 29950 d.81.1.1 39865 1bag 425 1.29e+00 1bag b.71.1.1 27720 c.1.8.1 28707 1rhfA 182 1.30e+00 b.1.1.1 -2335 b.1.1.4 -2684 1euwA 152 1.49e+00 1dupA b.85.4.1 28349 1dypA 271 1.50e+00 1dypA b.29.1.2 24185 1hp1A 516 1.52e+00 d.114.1.1 70976 d.159.1.2 70977 1ush 550 1.57e+00 1ush d.114.1.1 40923 d.159.1.2 42079 1ogwA 76 1.65e+00 d.15.1.1 87001 1f60B 94 1.72e+00 1b64 d.58.12.1 39307 1mkaA 171 1.77e+00 1mkaA d.38.1.2 38543 1awsA 164 1.81e+00 2cpl b.62.1.1 27431 1qd6C 240 1.85e+00 1qd5A 1theA 260 1.87e+00 1theB d.3.1.1 37056 1g9oA 91 1.92e+00 1pdr b.36.1.1 60400 16pk 415 2.21e+00 16pk c.86.1.1 35454 1je0A 236 2.31e+00 c.56.2.1 66581 1e4fT 419 2.43e+00 1e4fT c.55.1.1 33453 c.55.1.1 33454 1mgqA 83 2.45e+00 b.38.1.1 79099 1nd4A 264 2.52e+00 d.144.1.6 -11381 1j1yA 136 2.54e+00 d.38.1.5 -9671 1p1lA 102 2.68e+00 d.58.5.2 87695 1r9lA 309 3.10e+00 c.94.1.1 -8700 4dpvZ 584 3.21e+00 2cas b.121.5.2 23377 1ubi 76 3.25e+00 1ubi d.15.1.1 37584 1s72Q 96 3.25e+00 1g3qA 237 3.27e+00 1hyqA c.37.1.10 60237 1dxrH 258 3.36e+00 6prcH b.41.1.1 25456 f.23.10.1 43433 1h9oA 112 3.37e+00 1qadA d.93.1.1 60837 1m3kA 392 3.40e+00 c.95.1.1 78565 c.95.1.1 78566 1jj2P 95 3.50e+00 1ffkN b.34.5.1 63101 1sv6A 269 3.51e+00 1ii7A 333 3.58e+00 1ii7A d.159.1.4 62415 1f97A 212 3.58e+00 1f97A b.1.1.1 19763 b.1.1.4 21764 1cjbA 231 4.08e+00 1qk3A c.61.1.1 34079 1nnhA 294 4.08e+00 d.104.1.1 -10772 1k6wA 426 4.09e+00 b.92.1.2 68236 c.1.9.5 68237 1je5A 206 4.11e+00 1je5A b.40.4.7 62909 1gmyA 261 4.67e+00 d.3.1.1 76236 1bdo 80 4.83e+00 1bdo b.84.1.1 28214 1iyeA 309 5.27e+00 e.17.1.1 83786 1pxgA 382 5.40e+00 c.1.20.1 -5616 1uoyA 64 5.44e+00 unknown_sccs -12525 1bia 321 5.72e+00 1bia a.4.5.1 16083 b.34.1.1 24447 d.104.1.2 40787 1pdqA 72 5.84e+00 b.34.13.2 -3613 1rzhM 307 5.90e+00 f.26.1.1 -12227 1wkqA 164 5.93e+00 1uiuA 502 6.04e+00 c.94.1.1 -8674 1gk9B 557 6.05e+00 1ubkL 534 6.18e+00 e.18.1.1 88422 1eejA 216 6.38e+00 1eejA c.47.1.9 33057 d.17.3.1 38071 1uunA 184 6.41e+00 unknown_sccs -12370 1h2rL 534 6.42e+00 1h2rL e.18.1.1 43298 1uv7A 110 6.57e+00 unknown_sccs -10256 1pbjA 125 6.64e+00 d.37.1.1 -9608 d.37.1.1 -9609 1nddA 76 6.92e+00 1ubi d.15.1.1 37599 1f7zA 233 7.05e+00 5ptp b.47.1.2 59681 1e3aB 560 7.41e+00 1ajqB 1ton 235 7.97e+00 5ptp b.47.1.2 26307 1nwwA 149 7.98e+00 d.17.4.8 86306 1psdA 409 8.00e+00 1psdA c.2.1.4 30097 c.23.12.1 31357 d.58.18.1 39354 1e3dB 542 8.01e+00 1h2rL e.18.1.1 59189 1fehA 574 8.05e+00 1fehA c.96.1.1 36015 d.15.4.2 37690 d.58.1.5 38998 1gpr 162 8.14e+00 1gpr b.84.3.1 28267 1jtgB 165 8.18e+00 d.98.1.1 67267 4ubpC 570 8.31e+00 1ubpC b.92.1.1 28431 c.1.9.2 29053 1b0uA 262 8.59e+00 1b0uA c.37.1.12 32370 1ebfA 358 8.68e+00 1ebuA c.2.1.3 30033 d.81.1.2 39948 1kr4A 125 8.86e+00 d.58.5.2 72889 1mctA 223 9.00e+00 5ptp b.47.1.2 25961 1oxkB 134 9.02e+00 c.23.1.1 -6411 1tuhA 156 9.05e+00 1th8A 145 9.38e+00 1j7lA 264 9.48e+00 d.144.1.6 62697 1srvA 145 9.53e+00 1derA c.8.5.1 30817 1nykA 165 9.65e+00 b.33.1.1 86408 1q3eA 207 9.86e+00 b.82.3.2 -4922 1oo2A 119 1.04e+01 b.3.4.1 -2925 1skoA 143 1.05e+01 1erjA 393 1.08e+01 1erjA b.69.4.1 27660 1nscA 390 1.08e+01 2qwc b.68.1.1 27591 1sefA 274 1.10e+01 1ngmB 72 1.12e+01 j.104.1.1 85687 1adt 356 1.12e+01 1anv a.54.1.1 17887 g.51.1.1 45362 g.51.1.1 45368 1l6oA 95 1.13e+01 b.36.1.1 84534 1nrzA 164 1.13e+01 c.38.1.1 86131 1ehiA 377 1.13e+01 1iow c.30.1.2 31716 d.142.1.1 41484 1pgl2 370 1.15e+01 1bcpB 199 1.17e+01 1bcpB b.40.2.1 25120 d.169.1.2 42429 1bqyA 234 1.18e+01 5ptp b.47.1.2 26332 1bkpA 278 1.18e+01 1bkpA d.117.1.1 41029 1jx2B 315 1.19e+01 c.37.1.8 67404 1rypJ 204 1.20e+01 d.153.1.4 41878 1fvgA 199 1.20e+01 1fvaA d.58.28.1 39408 1sdwA 314 1.20e+01 b.121.1.2 -3024 b.121.1.2 -3025 1t82A 155 1.21e+01 1pfbA 55 1.22e+01 b.34.13.2 -3614 1uqxA 113 1.27e+01 b.115.1.1 -3230 1s6tA 285 1.27e+01 c.37.1.5 -7040 1vkjA 285 1.27e+01 1v58A 241 1.31e+01 1n8jA 186 1.31e+01 c.47.1.10 85401 1ieaA 192 1.33e+01 1iakA b.1.1.2 21631 d.19.1.1 38205 1ktaA 365 1.37e+01 e.17.1.1 77533 1hgxA 183 1.38e+01 1tc1A c.61.1.1 34027 1vi4A 174 1.41e+01 c.8.7.1 -6073 1thfD 253 1.41e+01 1thfD c.1.2.1 28535 1sj1A 66 1.43e+01 1eu1A 780 1.45e+01 1dmr b.52.2.2 26903 c.81.1.1 35311 1cs6A 382 1.46e+01 1cs6A b.1.1.4 21760 b.1.1.4 21761 b.1.1.4 21762 b.1.1.4 21763 1pzwA 80 1.48e+01 unknown_sccs -12740 1sy6A 204 1.49e+01 1ecsA 126 1.52e+01 1ecsA d.32.1.2 59407 1gqzA 274 1.52e+01 d.21.1.1 83311 d.21.1.1 83312 1a0jA 223 1.53e+01 5ptp b.47.1.2 26002 1am2 199 1.57e+01 1am2 b.86.1.2 28381 1a65A 504 1.61e+01 1a65A b.6.1.3 23148 b.6.1.3 23149 b.6.1.3 23150 1kdgA 546 1.61e+01 c.3.1.2 77337 d.16.1.1 77338 1phm 310 1.63e+01 1phm b.121.1.2 59015 b.121.1.2 59016 1bmv2 374 1.63e+01 1bmv2 1gcuA 295 1.64e+01 1gcuA c.2.1.3 30063 d.81.1.4 39978 3daaA 277 1.69e+01 1daaA e.17.1.1 43272 1lk2B 99 1.74e+01 b.1.1.2 -2576 2trxA 108 1.77e+01 1thx c.47.1.1 32719 2pgd 482 1.77e+01 2pgd a.100.1.1 18778 c.2.1.6 30190 1op0A 234 1.77e+01 1pzxA 289 1.79e+01 c.119.1.1 -8623 1i7qA 519 1.79e+01 1qdlA d.161.1.1 61901 2viuA 328 1.82e+01 1hgeA b.19.1.2 23797 1fh0A 221 1.83e+01 1cs8A d.3.1.1 59832 1uf5A 303 1.84e+01 1q33A 292 1.85e+01 d.113.1.1 -10901 1ifqA 138 1.86e+01 1ifqA d.110.4.1 62350 1s4nA 348 1.87e+01 unknown_sccs -8262 1a9xB 379 1.88e+01 1c3oB c.8.3.1 30732 c.23.16.1 31409 1iu8A 206 1.90e+01 c.56.4.1 71436 1erzA 303 1.92e+01 1erzA d.160.1.2 59498 1o4tA 133 1.93e+01 b.82.1.9 86622 1kptA 105 1.95e+01 1kptA d.70.1.1 39588 1pz4A 116 1.95e+01 d.106.1.1 -10780 1fzkB 99 1.96e+01 1agdB b.1.1.2 60151 1viaA 175 1.96e+01 c.37.1.2 -7021 1lc0A 294 1.97e+01 c.2.1.3 73823 d.81.1.4 73824 1hkxA 147 1.98e+01 d.17.4.7 83567 1g1cA 99 1.99e+01 b.1.1.4 65078 1p5fA 189 2.00e+01 c.23.16.2 -6508 1fzoB 99 2.00e+01 1agdB b.1.1.2 60157 1orc 71 2.02e+01 1orc a.35.1.2 17054 1g13A 162 2.07e+01 1g13A b.95.1.1 60194 1khqA 212 2.07e+01 d.3.1.1 -8868 1ekfA 365 2.09e+01 1ekfA e.17.1.1 59445 1o6dA 163 2.09e+01 c.116.1.3 -6689 1kzfA 230 2.10e+01 d.108.1.3 73354 1pu5A 164 2.14e+01 1hj8A 222 2.16e+01 b.47.1.2 65844 1pv5A 264 2.22e+01 unknown_sccs -10182 1kwsA 261 2.27e+01 c.68.1.7 73083 1k8wA 327 2.28e+01 b.122.1.1 83094 unknown_sccs -10143 1bupA 386 2.28e+01 1ba1 c.55.1.1 33377 c.55.1.1 33378 2tbs 222 2.30e+01 5ptp b.47.1.2 26009 1dvoA 152 2.30e+01 1dvoA a.136.1.1 19623 1pwmA 316 2.34e+01 c.1.7.1 -5232 1s5aA 150 2.34e+01 unknown_sccs -9300 1ignA 246 2.35e+01 1ignA a.4.1.6 16048 a.4.1.6 16049 1cyj 90 2.38e+01 1ctj a.3.1.1 15805 3seb 238 2.39e+01 3seb b.40.2.2 25184 d.15.6.1 37773 1us0A 316 2.39e+01 c.1.7.1 -5233 1e5xA 486 2.40e+01 c.79.1.1 59283 1aop 497 2.43e+01 2aop d.58.36.1 39501 d.58.36.1 39502 d.134.1.1 41425 d.134.1.1 41426 1o5uA 101 2.44e+01 b.82.1.8 -4845 1obfO 335 2.44e+01 c.2.1.3 86768 d.81.1.1 86769 1gxqA 106 2.46e+01 a.4.6.1 70721 1huxA 270 2.47e+01 1huxA c.55.1.5 61278 1e8pA 46 2.50e+01 g.55.1.1 59385 1h9mA 145 2.51e+01 1h9jA b.40.6.2 60833 b.40.6.2 60834 1iomA 377 2.53e+01 a.103.1.1 83698 1qkkA 155 2.53e+01 1dbwA c.23.1.1 31104 1v04A 355 2.54e+01 unknown_sccs -4592 1m0wA 491 2.61e+01 c.30.1.4 78363 d.142.1.6 78364 1kay 381 2.61e+01 1ba1 c.55.1.1 33385 c.55.1.1 33386 1k2eA 156 2.67e+01 d.113.1.1 72010 1eswA 500 2.67e+01 1cwyA c.1.8.1 59500 1kjqA 391 2.74e+01 b.84.2.1 72616 c.30.1.1 72617 d.142.1.2 72618 1mp9A 198 2.82e+01 a.74.1.2 -1127 a.74.1.2 -1128 1hdmB 193 2.82e+01 1hdmB b.1.1.2 21584 d.19.1.1 38158 1nxjA 183 2.85e+01 c.8.7.1 86382 1gdhA 320 2.85e+01 1gdhA c.2.1.4 30095 c.23.12.1 31355 1k5nB 100 2.86e+01 b.1.1.2 77268 1vk6A 269 2.87e+01 unknown_sccs -10923 unknown_sccs -10924 1ytfB 53 2.89e+01 1ytfB a.32.1.1 16997 1bwzA 274 2.89e+01 1bwzA d.21.1.1 38337 d.21.1.1 38338 1i1qA 520 2.90e+01 1qdlA d.161.1.1 61543 1vh7A 265 2.92e+01 c.1.2.1 -5159 1bmv1 198 2.93e+01 1bmv1 1ppn 212 2.94e+01 1cs8A d.3.1.1 37004 1dnlA 199 2.99e+01 1ci0A b.45.1.1 25753 1fmb 104 3.01e+01 1fmb b.50.1.1 26777 1pgl1 185 3.02e+01 1memA 215 3.05e+01 1cs8A d.3.1.1 37069 1uypA 432 3.08e+01 unknown_sccs -3480 unknown_sccs -4554 1thjA 214 3.08e+01 1qreA b.81.1.5 28072 1nh2B 53 3.08e+01 a.32.1.1 -777 1s14A 194 3.15e+01 d.122.1.2 -10973 1v5sA 126 3.16e+01 1gvzA 237 3.17e+01 b.47.1.2 76360 1hd2A 161 3.17e+01 c.47.1.10 60962 1h09A 338 3.20e+01 b.109.1.1 83420 c.1.8.8 83421 1h4wA 224 3.21e+01 b.47.1.2 65622 1lx7A 253 3.27e+01 c.56.2.1 74329 1g5cA 170 3.27e+01 1g5cA c.53.2.1 60264 1jtdB 273 3.28e+01 b.69.5.2 67265 1qmeA 702 3.31e+01 1pmd d.11.1.1 37487 d.11.1.1 37488 d.175.1.1 42560 e.3.1.1 42769 1k92A 455 3.32e+01 c.26.2.1 68325 d.210.1.1 68326 1k7jA 206 3.33e+01 d.115.1.1 72103 1lbvA 252 3.37e+01 e.7.1.1 73813 1tiyA 164 3.40e+01 1sbxA 106 3.41e+01 1qreA 247 3.42e+01 1qreA b.81.1.5 28066 1p4oA 322 3.45e+01 d.144.1.7 87775 1nh2D 121 3.45e+01 a.32.1.1 -780 b.56.1.1 -4384 1pxwA 128 3.45e+01 d.79.3.1 -10406 1qx2A 76 3.50e+01 1ospO 257 3.52e+01 1ospO b.76.1.1 27971 1a7tA 232 3.56e+01 1a7tA d.157.1.1 42041 1anv 356 3.59e+01 1anv a.54.1.1 17890 g.51.1.1 45365 g.51.1.1 45371 1aiu 105 3.64e+01 1erv c.47.1.1 32746 1fx2A 235 3.67e+01 1fx2A d.58.29.1 39430 1j1bA 420 3.75e+01 d.144.1.7 -11312 1he7A 126 3.83e+01 1wwcA b.1.1.4 60970 1nw2A 105 3.84e+01 c.47.1.1 -7380 1jli 112 3.87e+01 1jli a.26.1.2 16884 1cvrA 435 3.88e+01 1cvrA b.1.18.12 21949 c.17.1.2 31006 1jmxB 349 3.92e+01 b.69.2.2 66906 1oboA 169 3.92e+01 c.23.5.1 86776 1fb6A 105 4.00e+01 1thx c.47.1.1 32739