# 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 2cw8A 537 2.30e-01 1uliA 460 2.92e-01 b.33.1.2,d.129.3.3 107921,107922 1wkrA 340 5.83e-01 b.50.1.2 109395 2a72A 146 5.94e-01 1gt91 357 6.89e-01 1t1gA 364 7.40e-01 c.41.1.2 106246 1autC 250 8.88e-01 5ptp b.47.1.2 26348 1ev7A 317 1.15e+00 1ev7B c.52.1.9 33315 1mjc 69 1.24e+00 1mjc b.40.4.5 25319 2bwqA 129 1.27e+00 1iawA 317 1.36e+00 c.52.1.9 62126 1tdhA 364 1.69e+00 a.156.1.2,b.113.1.1,g.39.1.8 106772,106773,106774 1ga1A 372 1.76e+00 1ga1A c.41.1.2 32557 1jt8A 102 1.99e+00 b.40.4.5 63279 1afsA 323 2.07e+00 1frb c.1.7.1 28694 1mzyA 333 2.08e+00 b.6.1.3,b.6.1.3 103848,103849 1el6A 219 2.22e+00 1el6B d.182.1.1 42606 1bcg 77 2.32e+00 1aho g.3.7.1 44130 1ev7B 317 2.50e+00 1ev7B c.52.1.9 33316 1ga6A 372 2.70e+00 1ga1A c.41.1.2 32556 2f9nA 245 2.80e+00 1gj7B 253 2.97e+00 1k3sA 113 3.19e+00 d.198.1.1 68120 1lkxA 697 3.21e+00 c.37.1.9 73981 1c5yB 253 3.25e+00 5ptp 2aheA 267 3.26e+00 1o6aA 96 3.36e+00 b.139.1.1 92562 1el6B 219 3.43e+00 1el6B d.182.1.1 42607 1tueA 212 3.47e+00 c.37.1.20 107323 1as8A 343 3.49e+00 1nif b.6.1.3,b.6.1.3 23074,23075 1rtfB 252 3.56e+00 5ptp 1snrA 341 3.64e+00 b.6.1.3,b.6.1.3 105823,105824 1as6A 343 3.75e+00 1nif b.6.1.3,b.6.1.3 23090,23091 1nif 340 3.75e+00 1nif b.6.1.3,b.6.1.3 23048,23049 1j9qA 341 3.84e+00 1nif b.6.1.3,b.6.1.3 62765,62766 1ltoA 245 3.94e+00 b.47.1.2 84707 1vbkA 307 4.67e+00 2cgaA 245 4.73e+00 5ptp b.47.1.2 26028 1vq0A 302 4.94e+00 1mb4A 370 4.97e+00 c.2.1.3,d.81.1.1 78908,78909 1ve4A 206 5.14e+00 1ic6A 279 5.16e+00 1gci c.41.1.1 62257 1zkpA 268 5.76e+00 1se8A 301 5.78e+00 b.40.4.3 105448 1wrvA 308 5.83e+00 1d2tA 231 5.94e+00 1d2tA a.111.1.1 19052 1kcbA 340 6.11e+00 b.6.1.3,b.6.1.3 90951,90952 1vhsA 175 6.14e+00 d.108.1.1 100698 1iw8A 231 6.17e+00 a.111.1.1 76866 1et7A 341 6.25e+00 1nif b.6.1.3,b.6.1.3 23070,23071 1qnjA 240 6.63e+00 5ptp b.47.1.2 26238 1qhsA 178 6.63e+00 1qhsA c.37.1.3 31938 2fdiA 211 6.67e+00 1gvkB 240 6.69e+00 b.47.1.2 70610 1yphE 97 6.81e+00 2anyA 241 6.96e+00 1vjlA 164 7.11e+00 d.257.1.1 100822 2anwA 241 7.14e+00 3hmgA 328 7.50e+00 1hgeA b.19.1.2 23825 2fjbA 643 7.79e+00 1jnrA 643 7.88e+00 a.7.3.1,c.3.1.4,d.168.1.1 66966,66967,66968 1sf9A 128 8.06e+00 b.34.15.1 98831 1zy9A 564 8.60e+00 1juvA 193 8.82e+00 c.71.1.1 90912 1hgeA 328 8.88e+00 1hgeA b.19.1.2 23816 1esfA 233 8.98e+00 3seb b.40.2.2,d.15.6.1 25146,37735 1tygB 87 8.98e+00 d.15.3.2 107455 1a0lA 244 9.11e+00 5ptp b.47.1.2 26286 1mojA 182 9.36e+00 a.25.1.1 91367 1tjoA 182 9.37e+00 1pv5A 264 9.56e+00 d.251.1.1 95150 1afqC 96 9.73e+00 5ptp 1iyeA 309 9.76e+00 e.17.1.1 83786 1dyqA 234 9.76e+00 3seb b.40.2.2,d.15.6.1 59140,59141 1ubpA 101 1.00e+01 1ubpA d.8.1.1 37353 4ubpA 101 1.01e+01 1ubpA d.8.1.1 37352 2dg5B 190 1.03e+01 1ab9C 97 1.03e+01 5ptp 1y88A 199 1.07e+01 1btu 240 1.11e+01 5ptp b.47.1.2 26241 1z64A 26 1.15e+01 1yjmA 110 1.18e+01 1iqqA 200 1.19e+01 d.124.1.1 66274 1t0gA 109 1.21e+01 d.120.1.2 99063 2fp7A 54 1.22e+01 1txoA 237 1.22e+01 1qhxA 178 1.22e+01 1qhsA c.37.1.3 31936 2bw4A 340 1.24e+01 1a5iA 265 1.26e+01 5ptp b.47.1.2 26331 1nykA 165 1.29e+01 b.33.1.1 86408 1iv3A 152 1.32e+01 d.79.5.1 76828 1t0aA 159 1.35e+01 1gg6C 97 1.36e+01 5ptp 2ff4A 388 1.36e+01 1tcvA 287 1.38e+01 1zk7A 467 1.38e+01 1j96A 323 1.41e+01 c.1.7.1 71616 1eu3A 210 1.42e+01 1an8 b.40.2.2,d.15.6.1 25206,37795 3c2c 112 1.47e+01 1ycc a.3.1.1 15885 1yr1A 119 1.48e+01 1mtnC 97 1.49e+01 5ptp 1k2i1 245 1.50e+01 2bzvA 181 1.51e+01 2scuB 388 1.52e+01 2scuB c.23.4.1,d.142.1.4 31141,41562 1nr4A 71 1.58e+01 d.9.1.1 92077 2bzuA 181 1.59e+01 2fpeA 62 1.59e+01 1wzvA 155 1.68e+01 1hnr 47 1.70e+01 1hnr a.155.1.1 17896 3ullA 132 1.71e+01 3ullA b.40.4.3 25282 1vfqA 143 1.73e+01 1p42A 270 1.73e+01 d.14.1.7,d.14.1.7 87754,87755 1yozA 116 1.86e+01 2biiA 424 1.88e+01 1p4dA 330 1.91e+01 d.89.1.5 94101 1jsdA 319 1.93e+01 b.19.1.2 63258 1s3eA 520 1.98e+01 c.3.1.2,d.16.1.5 98426,98427 1ojaA 520 1.99e+01 c.3.1.2,d.16.1.5 93096,93097 1vjvA 415 1.99e+01 d.3.1.9 108632 1ecfA 504 1.99e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 1jtdB 273 2.00e+01 b.69.5.2 67265 1j03A 102 2.01e+01 d.120.1.2 90733 2bh8A 101 2.06e+01 1ecfB 504 2.08e+01 1ecfB c.61.1.1,d.153.1.1 34054,41821 1p1mA 406 2.11e+01 b.92.1.4,c.1.9.9 87696,87697 1dmaA 214 2.21e+01 1aerA d.166.1.1 42251 1zbxB 141 2.23e+01 1iqyA 638 2.27e+01 b.30.2.1,d.17.2.1,d.17.2.1 76763,76764,76765 1wdtA 665 2.29e+01 1ahsA 126 2.30e+01 1ahsA b.19.1.1 23794 1rqpA 299 2.43e+01 b.141.1.1,c.132.1.1 97754,97755 1jsmA 325 2.44e+01 b.19.1.2 63264 1jb7B 260 2.46e+01 1otcB b.40.4.3 62839 2brfA 110 2.54e+01 1el3A 316 2.60e+01 1frb c.1.7.1 28672 2f5yA 91 2.64e+01 2gi3A 476 2.66e+01 2viuA 328 2.66e+01 1hgeA b.19.1.2 23797 1aw7A 194 2.69e+01 1aw7A b.40.2.2,d.15.6.1 25164,37753 1us0A 316 2.72e+01 c.1.7.1 99850 1gy7A 125 2.74e+01 d.17.4.2 70738 1sqzA 121 2.76e+01 a.133.1.2 98975 1j6pA 418 2.78e+01 b.92.1.4,c.1.9.9 77089,77090 1pfxC 235 2.78e+01 5ptp b.47.1.2 26353 2d1yA 256 2.78e+01 2b1xA 470 2.79e+01 2agtA 319 2.79e+01 1ugmA 125 2.80e+01 d.15.1.3 107827 1pzxA 289 2.86e+01 c.119.1.1 95484 2ai4A 119 2.87e+01 2acr 315 2.88e+01 1frb c.1.7.1 28674 2prk 279 2.88e+01 1gci c.41.1.1 32548 1qd9A 124 2.89e+01 1qu9A d.79.1.1 39758 1ytbA 180 2.92e+01 1ytbA d.129.1.1,d.129.1.1 41276,41277 1u69A 163 2.92e+01 d.32.1.7 107699 1zsyA 357 2.93e+01 1tux 301 3.00e+01 1taxA c.1.8.3 28907 1ytbB 180 3.10e+01 1ytbA d.129.1.1,d.129.1.1 41278,41279 1elt 236 3.10e+01 5ptp b.47.1.2 26281 1gosA 520 3.11e+01 c.3.1.2,d.16.1.5 65425,65426 1rc6A 261 3.12e+01 b.82.1.11 97287 1yt3A 375 3.15e+01 1tk4A 121 3.15e+01 a.133.1.2 107073 1ixkA 315 3.16e+01 c.66.1.38 90716 1tj9A 121 3.18e+01 a.133.1.2 107015 1frb 315 3.19e+01 1frb c.1.7.1 28665 2ahrA 259 3.20e+01 1xn5A 146 3.23e+01 1zwpA 121 3.28e+01 1yr2A 741 3.31e+01 1ozjA 144 3.32e+01 d.164.1.1 93846 1i50H 146 3.33e+01 b.40.4.8 61761 2ao0A 324 3.35e+01 1ui8A 638 3.58e+01 b.30.2.1,d.17.2.1,d.17.2.1 99419,99420,99421 3ssi 113 3.66e+01 3ssi d.84.1.1 40032 2bngA 149 3.70e+01 1o54A 277 3.73e+01 c.66.1.13 92482 1taxA 302 3.80e+01 1taxA 1jbuH 254 3.82e+01 5ptp b.47.1.2 62856 1ounA 127 3.91e+01 1ounA d.17.4.2 38090 1ezvE 185 3.93e+01 1rie b.33.1.1,f.23.12.1 59548,59549 1uisA 231 4.01e+01 d.22.1.1 99431 1koqA 253 4.02e+01 2cba b.74.1.1 27964 1l9gA 192 4.02e+01 c.18.1.2 84568 1mo1A 87 4.04e+01 d.94.1.1 91363 1eg9A 449 4.15e+01 1ndoA b.33.1.2,d.129.3.3 24443,41322 3tss 194 4.21e+01 1aw7A b.40.2.2,d.15.6.1 25160,37749 1pmt 203 4.25e+01 1a0fA a.45.1.1,c.47.1.5 17740,33034 1dleA 298 4.27e+01 1dleA b.47.1.2 26312 1v8bA 479 4.34e+01 1a8q 274 4.34e+01 1brt c.69.1.12 34702 1ui7A 638 4.39e+01 b.30.2.1,d.17.2.1,d.17.2.1 99413,99414,99415 1prtD 110 4.39e+01 1bcpD b.40.2.1 25128 1earA 147 4.43e+01 b.107.1.1,d.58.38.1 64875,64876 1senA 164 4.45e+01 c.47.1.1 105465 1pguA 615 4.47e+01 b.69.4.1,b.69.4.1 88069,88070 2g58A 121 4.53e+01 1eso 154 4.53e+01 1yaiA b.1.8.1 22293 1ndoA 449 4.54e+01 1ndoA b.33.1.2,d.129.3.3 24444,41323 1ivwA 638 4.57e+01 b.30.2.1,d.17.2.1,d.17.2.1 71456,71457,71458 1o7nA 449 4.60e+01 b.33.1.2,d.129.3.3 81162,81163 1g47A 77 4.64e+01 1g47A g.39.1.3,g.39.1.3 45147,45148 2a1kA 233 4.65e+01 1ts3A 194 4.67e+01 1aw7A b.40.2.2,d.15.6.1 25168,37757 1hzgA 295 4.69e+01 1hzgA d.194.1.1 61436 1kpmA 121 4.69e+01 a.133.1.2 72844 1a2vA 655 4.70e+01 1a2vA b.30.2.1,d.17.2.1,d.17.2.1 24416,38059,38060 1e9gA 286 4.71e+01 1wgjA b.40.5.1 59393 1w6gA 646 4.71e+01 1rjoA 646 4.72e+01 1ejxA 100 4.77e+01 d.8.1.1 83182 1wruA 379 4.78e+01 1m4uL 139 4.80e+01 g.17.1.2 78626 3sicI 107 4.83e+01 3ssi d.84.1.1 40028 2bgu 351 4.85e+01 1c3jA c.87.1.1 35460 1tkeA 224 4.89e+01 1fnoA 417 4.89e+01 d.58.19.1,c.56.5.4 70145,75841 1tbaB 180 4.91e+01 1ytbA d.129.1.1,d.129.1.1 41286,41287 1i1kA 309 4.93e+01 1daaA e.17.1.1 61533 1big 37 5.04e+01 1sco g.3.7.2 44145 1krhA 338 5.09e+01 b.43.4.2,c.25.1.2,d.15.4.2 72891,72892,72893 1tlyA 278 5.25e+01 f.4.6.1 107143 1cr5A 189 5.42e+01 1cr5A b.52.2.3,d.31.1.1 26931,38465 1mpp 361 5.43e+01 2rmpA b.50.1.2 26856 1r8oB 71 5.45e+01 1y4wA 518 5.47e+01 1aisA 182 5.62e+01 1ytbA d.129.1.1,d.129.1.1 41288,41289 1az1 315 5.63e+01 1frb c.1.7.1 28677 1v5vA 401 5.64e+01 1u2xA 474 5.65e+01 c.72.1.3 107622 1o0pA 104 5.68e+01 d.58.7.1 86535 1pwmA 316 5.75e+01 c.1.7.1 95231 1aerA 205 5.76e+01 1aerA d.166.1.1 42249 1hcnA 92 5.78e+01 1hcnA g.17.1.4 44809 1hh8A 213 5.80e+01 1e96B a.118.8.1 61042 1gy6A 127 5.93e+01 d.17.4.2 70736 1whi 122 5.93e+01 1whi b.39.1.1 24810 2bnjA 303 5.97e+01 2fm8A 135 6.06e+01 1l5jA 865 6.10e+01 a.118.15.1,c.8.2.1,c.83.1.1 73592,73593,73594 1twfH 146 6.12e+01 1bmp 139 6.13e+01 2tgi g.17.1.2 44785 1eqtA 68 6.17e+01 1b3aA d.9.1.1 37412 1y7xA 113 6.19e+01 1hq0A 295 6.21e+01 1hzgA d.194.1.1 61122 2bz6H 254 6.29e+01 1ej6B 1275 6.30e+01 i.7.1.1 45968 1q4gA 553 6.34e+01 a.93.1.2,g.3.11.1 95789,95790 1wm5A 208 6.36e+01 1e96B 203 6.37e+01 1e96B a.118.8.1 19211 1snnA 227 6.41e+01 d.115.1.2 105821 1xyn 178 6.43e+01 1axkA b.29.1.11 24322 2kauA 100 6.44e+01 1ubpA d.8.1.1 37335 1hbq 183 6.44e+01 1aqb b.60.1.1 27078 1i1qA 520 6.47e+01 1qdlA d.161.1.1 61543 1vi4A 174 6.49e+01 c.8.7.1 100731 1hpi 71 6.49e+01 1ckuA g.35.1.1 44995 1mvfD 82 6.50e+01 b.129.1.1 85143 2ffmA 91 6.51e+01 1jyhA 157 6.52e+01 d.60.1.3 71956 1ar0A 127 6.53e+01 1ounA d.17.4.2 38092 1lshA 1056 6.55e+01 a.118.4.1,f.7.1.1,f.7.1.1 74242,74243,74244 1ae1A 273 6.55e+01 1bdb c.2.1.2 29943 2sicI 107 6.58e+01 3ssi d.84.1.1 40031 1f2tB 148 6.59e+01 1f2tB 1a3gA 308 6.60e+01 1daaA e.17.1.1 43286 1sjqA 105 6.62e+01 d.58.7.1 105660 1whzA 70 6.68e+01 1ijvA 36 6.71e+01 g.9.1.1 66169 1xttA 216 6.77e+01 1fv0A 121 6.77e+01 a.133.1.2 70147 1mroC 247 6.79e+01 1mroC d.58.31.1 39437 1fnlA 175 6.79e+01 2fcbA b.1.1.4,b.1.1.4 21783,21784 1mmoB 384 6.81e+01 1mtyB a.25.1.2 16768 1geeA 261 6.81e+01 c.2.1.2 90509 1jnuA 104 6.82e+01 d.110.3.6 71762 2mcm 112 6.84e+01 2mcm b.1.7.1 22207 1h54B 754 6.91e+01 a.102.1.4,b.30.5.3 60636,60637 1nh8A 304 7.11e+01 c.94.1.1,d.58.5.3 80507,80508 1y4lA 121 7.12e+01 1aiw 62 7.16e+01 1aiw b.72.2.1 27808 1mtyB 384 7.16e+01 1mtyB a.25.1.2 16740 1yagG 125 7.18e+01 1d0nA d.109.1.1 40846 1pvyA 227 7.19e+01 d.115.1.2 95195 1gcoA 261 7.22e+01 1ybvA c.2.1.2 29884 1fz1C 389 7.25e+01 1mtyB a.25.1.2 16746 1d0iA 156 7.34e+01 2dhqA c.23.13.1 31383 1enwA 114 7.35e+01 1enwA a.5.4.1 16291 1cqeA 580 7.35e+01 1cqeA a.93.1.2,g.3.11.1 18703,44246 1yb2A 275 7.36e+01 1qcsA 211 7.41e+01 1qcsA b.52.2.3,d.31.1.1 26927,38461 2cxaA 256 7.44e+01 1df7A 159 7.45e+01 3dfr c.71.1.1 34885 2c5qA 240 7.48e+01 1tl2A 236 7.51e+01 1tl2A b.67.1.1 27541 1p5dX 463 7.53e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1wxcA 281 7.53e+01 2apsA 162 7.55e+01 1yaiA b.1.8.1 22298 2azpA 318 7.60e+01 1p0zA 131 7.67e+01 d.110.6.1 93882 1h54A 754 7.75e+01 a.102.1.4,b.30.5.3 60634,60635 1gkfB 557 7.81e+01 1sur 215 7.82e+01 1sur c.26.2.2 31620 1yb3A 175 7.84e+01 1tvxA 75 7.86e+01 1tvxA d.9.1.1 37441 1kddA 36 7.89e+01 h.1.3.1 68472 1kliH 254 7.90e+01 b.47.1.2 77435 1fwcA 100 7.94e+01 1ubpA d.8.1.1 37331 1gm7B 557 7.95e+01 2bhgA 209 7.97e+01 1mbyA 88 7.99e+01 d.223.1.1 78931 1c3gA 170 8.02e+01 1c3gA b.4.1.1,b.4.1.1 22831,22832 1siiA 646 8.03e+01 b.30.2.1,d.17.2.1,d.17.2.1 105578,105579,105580 1jfuA 186 8.05e+01 c.47.1.10 62940 1pvmA 184 8.10e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1kd9A 36 8.11e+01 h.1.3.1 68466 1t3yA 141 8.20e+01 1ogoX 574 8.33e+01 b.133.1.1,b.80.1.10 92925,92926 2arpF 152 8.36e+01 1danH 254 8.37e+01 5ptp b.47.1.2 26292 8prkA 287 8.41e+01 1wgjA b.40.5.1 25395 1p9uA 302 8.52e+01 b.47.1.4 88001 2fsrA 195 8.58e+01 1rl6A 177 8.62e+01 1rl6A d.141.1.1,d.141.1.1 41473,41474 487dH 224 8.76e+01 1ad2 i.1.1.2 45835 1rie 129 8.82e+01 1rie b.33.1.1 24427 2erfA 209 8.86e+01 1mmiA 366 8.87e+01 d.131.1.1,d.131.1.1,d.131.1.1 91309,91310,91311 1aogA 485 8.89e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30517,30518,40190 1gk9B 557 8.90e+01 1ad2 228 8.90e+01 1ad2 e.24.1.1 43353