# 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 2cw8A 537 9.46e-02 1gt91 357 2.51e-01 1t1gA 364 2.62e-01 c.41.1.2 106246 1uliA 460 2.89e-01 b.33.1.2,d.129.3.3 107921,107922 1wkrA 340 5.87e-01 b.50.1.2 109395 1tdhA 364 6.25e-01 a.156.1.2,b.113.1.1,g.39.1.8 106772,106773,106774 1mzyA 333 8.26e-01 b.6.1.3,b.6.1.3 103848,103849 2a72A 146 1.08e+00 1nif 340 1.17e+00 1nif b.6.1.3,b.6.1.3 23048,23049 2aheA 267 1.32e+00 1el6A 219 1.43e+00 1el6B d.182.1.1 42606 2bwqA 129 1.51e+00 1snrA 341 1.53e+00 b.6.1.3,b.6.1.3 105823,105824 1j9qA 341 1.59e+00 1nif b.6.1.3,b.6.1.3 62765,62766 1ga6A 372 1.63e+00 1ga1A c.41.1.2 32556 1mjc 69 1.79e+00 1mjc b.40.4.5 25319 1kcbA 340 1.97e+00 b.6.1.3,b.6.1.3 90951,90952 2f9nA 245 1.97e+00 1o6aA 96 2.17e+00 b.139.1.1 92562 1k3sA 113 2.55e+00 d.198.1.1 68120 1ev7A 317 2.66e+00 1ev7B c.52.1.9 33315 1gj7B 253 2.88e+00 1zkpA 268 3.07e+00 1ltoA 245 3.10e+00 b.47.1.2 84707 1vjlA 164 3.14e+00 d.257.1.1 100822 1c5yB 253 3.26e+00 5ptp 1tueA 212 3.26e+00 c.37.1.20 107323 4ubpA 101 3.28e+00 1ubpA d.8.1.1 37352 2fdiA 211 3.56e+00 1ic6A 279 3.68e+00 1gci c.41.1.1 62257 1d2tA 231 4.15e+00 1d2tA a.111.1.1 19052 2bw4A 340 4.17e+00 1iw8A 231 4.26e+00 a.111.1.1 76866 1jnrA 643 4.33e+00 a.7.3.1,c.3.1.4,d.168.1.1 66966,66967,66968 2fjbA 643 4.34e+00 1rtfB 252 4.62e+00 5ptp 1tjoA 182 5.15e+00 1mojA 182 5.16e+00 a.25.1.1 91367 1vq0A 302 5.73e+00 1qnjA 240 6.15e+00 5ptp b.47.1.2 26238 1gvkB 240 6.18e+00 b.47.1.2 70610 1sf9A 128 6.47e+00 b.34.15.1 98831 2anwA 241 6.49e+00 2anyA 241 6.85e+00 2ff4A 388 7.03e+00 1juvA 193 7.25e+00 c.71.1.1 90912 1se8A 301 7.25e+00 b.40.4.3 105448 1yphE 97 7.47e+00 1mb4A 370 7.63e+00 c.2.1.3,d.81.1.1 78908,78909 1ve4A 206 7.94e+00 1wrvA 308 8.17e+00 1z64A 26 8.21e+00 1vhsA 175 8.31e+00 d.108.1.1 100698 1tygB 87 8.32e+00 d.15.3.2 107455 1iv3A 152 8.40e+00 d.79.5.1 76828 1p1mA 406 8.42e+00 b.92.1.4,c.1.9.9 87696,87697 1vbkA 307 8.43e+00 1t0aA 159 8.95e+00 1jsdA 319 9.17e+00 b.19.1.2 63258 1zy9A 564 9.25e+00 1yjmA 110 9.94e+00 1nykA 165 1.03e+01 b.33.1.1 86408 1qhxA 178 1.04e+01 1qhsA c.37.1.3 31936 1j6pA 418 1.06e+01 b.92.1.4,c.1.9.9 77089,77090 2fpeA 62 1.06e+01 1rqpA 299 1.12e+01 b.141.1.1,c.132.1.1 97754,97755 2biiA 424 1.13e+01 1tcvA 287 1.13e+01 2dg5B 190 1.21e+01 1hnr 47 1.23e+01 1hnr a.155.1.1 17896 2fp7A 54 1.23e+01 1iyeA 309 1.25e+01 e.17.1.1 83786 1eu3A 210 1.26e+01 1an8 b.40.2.2,d.15.6.1 25206,37795 1pv5A 264 1.30e+01 d.251.1.1 95150 1dyqA 234 1.33e+01 3seb b.40.2.2,d.15.6.1 59140,59141 1jtdB 273 1.41e+01 b.69.5.2 67265 1t0gA 109 1.42e+01 d.120.1.2 99063 1yozA 116 1.48e+01 1hpi 71 1.49e+01 1ckuA g.35.1.1 44995 2bzvA 181 1.53e+01 1gg6C 97 1.56e+01 5ptp 2bzuA 181 1.58e+01 3ullA 132 1.60e+01 3ullA b.40.4.3 25282 2f5yA 91 1.62e+01 1p42A 270 1.64e+01 d.14.1.7,d.14.1.7 87754,87755 1s3eA 520 1.64e+01 c.3.1.2,d.16.1.5 98426,98427 1ojaA 520 1.65e+01 c.3.1.2,d.16.1.5 93096,93097 1sqzA 121 1.70e+01 a.133.1.2 98975 1vjvA 415 1.71e+01 d.3.1.9 108632 1j96A 323 1.72e+01 c.1.7.1 71616 1u69A 163 1.78e+01 d.32.1.7 107699 1fnoA 417 1.80e+01 d.58.19.1,c.56.5.4 70145,75841 1tj9A 121 1.85e+01 a.133.1.2 107015 1zwpA 121 1.88e+01 1zk7A 467 1.88e+01 1tk4A 121 1.89e+01 a.133.1.2 107073 1ejxA 100 1.95e+01 d.8.1.1 83182 1txoA 237 1.96e+01 2ptd 298 1.99e+01 2plc c.1.18.2 29605 1iqqA 200 2.01e+01 d.124.1.1 66274 1ahsA 126 2.03e+01 1ahsA b.19.1.1 23794 3c2c 112 2.05e+01 1ycc a.3.1.1 15885 2viuA 328 2.07e+01 1hgeA b.19.1.2 23797 1zbxB 141 2.08e+01 1y4lA 121 2.09e+01 2brfA 110 2.10e+01 1nr4A 71 2.11e+01 d.9.1.1 92077 1zsyA 357 2.11e+01 1y4wA 518 2.12e+01 2bh8A 101 2.15e+01 1yr1A 119 2.15e+01 2gi3A 476 2.23e+01 1ecfA 504 2.23e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 2bnjA 303 2.27e+01 1vfqA 143 2.27e+01 1y88A 199 2.38e+01 1iqyA 638 2.41e+01 b.30.2.1,d.17.2.1,d.17.2.1 76763,76764,76765 2ai4A 119 2.48e+01 1pguA 615 2.50e+01 b.69.4.1,b.69.4.1 88069,88070 1v8bA 479 2.56e+01 1jsmA 325 2.65e+01 b.19.1.2 63264 1wzvA 155 2.66e+01 1i50H 146 2.67e+01 b.40.4.8 61761 1wdtA 665 2.67e+01 2g58A 121 2.69e+01 1hh8A 213 2.69e+01 1e96B a.118.8.1 61042 1jb7B 260 2.82e+01 1otcB b.40.4.3 62839 1wm5A 208 2.90e+01 1yt3A 375 3.00e+01 1lshA 1056 3.06e+01 a.118.4.1,f.7.1.1,f.7.1.1 74242,74243,74244 1mroC 247 3.07e+01 1mroC d.58.31.1 39437 2b1xA 470 3.08e+01 1e9gA 286 3.08e+01 1wgjA b.40.5.1 59393 1ej6B 1275 3.12e+01 i.7.1.1 45968 1us0A 316 3.15e+01 c.1.7.1 99850 2agtA 319 3.24e+01 1xn5A 146 3.27e+01 2d1yA 256 3.29e+01 1aerA 205 3.32e+01 1aerA d.166.1.1 42249 1koqA 253 3.35e+01 2cba b.74.1.1 27964 1dleA 298 3.42e+01 1dleA b.47.1.2 26312 1o54A 277 3.45e+01 c.66.1.13 92482 1a2vA 655 3.49e+01 1a2vA b.30.2.1,d.17.2.1,d.17.2.1 24416,38059,38060 2ahrA 259 3.49e+01 1elt 236 3.50e+01 5ptp b.47.1.2 26281 2bhgA 209 3.51e+01 1ixkA 315 3.59e+01 c.66.1.38 90716 1qd9A 124 3.59e+01 1qu9A d.79.1.1 39758 1gy7A 125 3.63e+01 d.17.4.2 70738 1ugmA 125 3.63e+01 d.15.1.3 107827 1yr2A 741 3.65e+01 1php 394 3.66e+01 16pk c.86.1.1 35452 1eg9A 449 3.72e+01 1ndoA b.33.1.2,d.129.3.3 24443,41322 1pzxA 289 3.73e+01 c.119.1.1 95484 1wruA 379 3.74e+01 1aw7A 194 3.85e+01 1aw7A b.40.2.2,d.15.6.1 25164,37753 1ui8A 638 3.98e+01 b.30.2.1,d.17.2.1,d.17.2.1 99419,99420,99421 1i1wA 303 4.01e+01 c.1.8.3 76732 1geeA 261 4.03e+01 c.2.1.2 90509 1ckeA 227 4.04e+01 1ckeA c.37.1.1 31846 1ppa 121 4.05e+01 1poa a.133.1.2 19550 1qexA 288 4.11e+01 1qexA b.32.1.1 24425 1v5vA 401 4.13e+01 1o0pA 104 4.20e+01 d.58.7.1 86535 2gd9A 189 4.21e+01 1senA 164 4.23e+01 c.47.1.1 105465 1ozjA 144 4.24e+01 d.164.1.1 93846 1i1kA 309 4.25e+01 1daaA e.17.1.1 61533 2cxaA 256 4.28e+01 1krhA 338 4.31e+01 b.43.4.2,c.25.1.2,d.15.4.2 72891,72892,72893 1o7nA 449 4.33e+01 b.33.1.2,d.129.3.3 81162,81163 1xttA 216 4.34e+01 1aiw 62 4.38e+01 1aiw b.72.2.1 27808 1gcoA 261 4.41e+01 1ybvA c.2.1.2 29884 1mo1A 87 4.41e+01 d.94.1.1 91363 1im3D 95 4.49e+01 1im3D b.1.18.5 62568 1tlyA 278 4.50e+01 f.4.6.1 107143 2bngA 149 4.50e+01 2a1kA 233 4.51e+01 1r8oB 71 4.54e+01 1a8y 367 4.56e+01 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 1sh7A 284 4.57e+01 1ui7A 638 4.63e+01 b.30.2.1,d.17.2.1,d.17.2.1 99413,99414,99415 1ikpA 613 4.63e+01 b.29.1.7,d.166.1.1,f.1.5.1 66182,66183,66184 1twfH 146 4.63e+01 1a8q 274 4.66e+01 1brt c.69.1.12 34702 1jyhA 157 4.68e+01 d.60.1.3 71956 1y7xA 113 4.71e+01 1hq0A 295 4.73e+01 1hzgA d.194.1.1 61122 1hcnA 92 4.85e+01 1hcnA g.17.1.4 44809 1yb2A 275 4.87e+01 1mtyB 384 4.89e+01 1mtyB a.25.1.2 16740 1dtdB 61 4.94e+01 1dtvA g.30.1.1 44962 1jnuA 104 4.96e+01 d.110.3.6 71762 1hbnC 248 5.01e+01 1mroC d.58.31.1 60902 1fmhA 33 5.16e+01 1fmhB k.6.1.1 46409 1ts9A 102 5.18e+01 1aisA 182 5.20e+01 1ytbA d.129.1.1,d.129.1.1 41288,41289 1v33A 366 5.30e+01 d.264.1.1 100278 1df7A 159 5.31e+01 3dfr c.71.1.1 34885 2sicI 107 5.32e+01 3ssi d.84.1.1 40031 1u02A 239 5.39e+01 c.108.1.15 107538 1oruA 195 5.46e+01 b.58.1.2 93464 1pvmA 184 5.47e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1whi 122 5.47e+01 1whi b.39.1.1 24810 1u2xA 474 5.52e+01 c.72.1.3 107622 1to2E 281 5.55e+01 1ylxA 103 5.63e+01 3tss 194 5.69e+01 1aw7A b.40.2.2,d.15.6.1 25160,37749 1xxsA 122 5.69e+01 1sjqA 105 5.72e+01 d.58.7.1 105660 1mpp 361 5.87e+01 2rmpA b.50.1.2 26856 1oe1A 336 5.88e+01 b.6.1.3,b.6.1.3 86891,86892 1h54A 754 5.89e+01 a.102.1.4,b.30.5.3 60634,60635 2fsrA 195 5.95e+01 1wraA 308 6.00e+01 1frb 315 6.05e+01 1frb c.1.7.1 28665 1mbyA 88 6.11e+01 d.223.1.1 78931 1rjoA 646 6.11e+01 1kd8A 36 6.20e+01 h.1.3.1 68460 1w6gA 646 6.26e+01 2erfA 209 6.27e+01 1nbaA 264 6.29e+01 1nbaA c.33.1.3 31753 2mcm 112 6.47e+01 2mcm b.1.7.1 22207 1fnlA 175 6.52e+01 2fcbA b.1.1.4,b.1.1.4 21783,21784 1hn4A 131 6.54e+01 a.133.1.2 65893 1pwmA 316 6.61e+01 c.1.7.1 95231 2azpA 318 6.63e+01 2a4vA 159 6.71e+01 1sdjA 310 6.86e+01 d.21.1.2,d.21.1.2 98807,98808 1mfgA 95 6.88e+01 b.36.1.1 79043 1jigA 146 6.88e+01 a.25.1.1 71685 1mmiA 366 6.94e+01 d.131.1.1,d.131.1.1,d.131.1.1 91309,91310,91311 1rl6A 177 6.99e+01 1rl6A d.141.1.1,d.141.1.1 41473,41474 1tkeA 224 7.14e+01 1xnzA 264 7.19e+01 1ee6A 197 7.25e+01 1ee6A b.80.1.1 28024 1rifA 282 7.26e+01 c.37.1.23 97507 1tl2A 236 7.27e+01 1tl2A b.67.1.1 27541 2ao0A 324 7.29e+01 1gtdA 85 7.33e+01 d.284.1.1 76344 1e6eB 128 7.38e+01 1ayfA d.15.4.1 59300 1m1zA 513 7.40e+01 c.26.2.1,d.153.1.1 78457,78458 1ounA 127 7.46e+01 1ounA d.17.4.2 38090 1kqrA 179 7.49e+01 b.29.1.14 72886 1earA 147 7.49e+01 b.107.1.1,d.58.38.1 64875,64876 1q4gA 553 7.53e+01 a.93.1.2,g.3.11.1 95789,95790 1mvfD 82 7.62e+01 b.129.1.1 85143 1ijvA 36 7.69e+01 g.9.1.1 66169 1nh8A 304 7.71e+01 c.94.1.1,d.58.5.3 80507,80508 2c43A 323 7.71e+01 1ms9A 648 7.73e+01 b.29.1.15,b.68.1.1 85088,85089 1uynX 308 7.74e+01 f.4.5.1 100174 1c3gA 170 7.76e+01 1c3gA b.4.1.1,b.4.1.1 22831,22832 1snnA 227 7.77e+01 d.115.1.2 105821 1eso 154 7.78e+01 1yaiA b.1.8.1 22293 1s8iA 121 7.80e+01 a.133.1.2 98735 1zkoA 136 7.81e+01 1kzlA 208 7.82e+01 b.43.4.3,b.43.4.3 77635,77636 1q98A 165 7.88e+01 c.47.1.10 96253 1hdlA 55 7.90e+01 g.68.1.2 65808 1sv6A 269 7.94e+01 d.177.1.1 106043 1uisA 231 7.99e+01 d.22.1.1 99431 1ezvF 125 8.00e+01 1be3F f.27.1.1 59550 2bz6H 254 8.00e+01 1c24A 263 8.07e+01 1c24A d.127.1.1 41148 2c5qA 240 8.15e+01 2ffmA 91 8.18e+01 1kb9G 125 8.24e+01 f.27.1.1 77322 1t5oA 351 8.28e+01 c.124.1.5 106459 1g4iA 123 8.29e+01 1poa a.133.1.2 60241 1p0zA 131 8.30e+01 d.110.6.1 93882 1gk9B 557 8.37e+01 1i1qA 520 8.39e+01 1qdlA d.161.1.1 61543 1rie 129 8.39e+01 1rie b.33.1.1 24427 1cleA 534 8.41e+01 1thg c.69.1.17 34771 1yoyA 175 8.41e+01 1lm8V 160 8.48e+01 b.3.3.1 74035 2btiA 63 8.49e+01 1dgwA 178 8.49e+01 1dgwA b.82.1.2 28090 1vquA 374 8.56e+01 1pvyA 227 8.60e+01 d.115.1.2 95195 2fm8A 135 8.61e+01 1enwA 114 8.67e+01 1enwA a.5.4.1 16291 1siiA 646 8.85e+01 b.30.2.1,d.17.2.1,d.17.2.1 105578,105579,105580 1xd5A 112 8.88e+01 1w96A 554 8.92e+01 1sur 215 8.96e+01 1sur c.26.2.2 31620