# 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 5.01e-02 1ev7A 317 1.43e-01 1ev7B c.52.1.9 33315 1uliA 460 7.38e-01 b.33.1.2,d.129.3.3 107921,107922 1ev7B 317 8.62e-01 1ev7B c.52.1.9 33316 1gt91 357 8.94e-01 2a72A 146 9.01e-01 1t1gA 364 9.09e-01 c.41.1.2 106246 1autC 250 9.41e-01 5ptp b.47.1.2 26348 1wkrA 340 9.67e-01 b.50.1.2 109395 1mzyA 333 1.25e+00 b.6.1.3,b.6.1.3 103848,103849 2bwqA 129 1.27e+00 1mjc 69 1.54e+00 1mjc b.40.4.5 25319 1tdhA 364 1.69e+00 a.156.1.2,b.113.1.1,g.39.1.8 106772,106773,106774 1j9qA 341 1.74e+00 1nif b.6.1.3,b.6.1.3 62765,62766 1iawA 317 1.77e+00 c.52.1.9 62126 1nif 340 1.79e+00 1nif b.6.1.3,b.6.1.3 23048,23049 1aw7A 194 1.86e+00 1aw7A b.40.2.2,d.15.6.1 25164,37753 1snrA 341 1.92e+00 b.6.1.3,b.6.1.3 105823,105824 1as8A 343 1.99e+00 1nif b.6.1.3,b.6.1.3 23074,23075 1afsA 323 2.12e+00 1frb c.1.7.1 28694 2aheA 267 2.14e+00 1as6A 343 2.17e+00 1nif b.6.1.3,b.6.1.3 23090,23091 2f9nA 245 2.20e+00 1el6A 219 2.70e+00 1el6B d.182.1.1 42606 1jt8A 102 2.77e+00 b.40.4.5 63279 1gj7B 253 2.79e+00 1ga1A 372 2.82e+00 1ga1A c.41.1.2 32557 1kcbA 340 2.83e+00 b.6.1.3,b.6.1.3 90951,90952 1zvkA 358 2.97e+00 1c5yB 253 3.06e+00 5ptp 1et7A 341 3.57e+00 1nif b.6.1.3,b.6.1.3 23070,23071 1bcg 77 3.65e+00 1aho g.3.7.1 44130 1zkpA 268 3.90e+00 1lkxA 697 3.93e+00 c.37.1.9 73981 1el6B 219 4.24e+00 1el6B d.182.1.1 42607 1ga6A 372 4.31e+00 1ga1A c.41.1.2 32556 1ltoA 245 4.32e+00 b.47.1.2 84707 1juvA 193 4.43e+00 c.71.1.1 90912 1o6aA 96 4.90e+00 b.139.1.1 92562 1a5iA 265 5.18e+00 5ptp b.47.1.2 26331 1ic6A 279 5.27e+00 1gci c.41.1.1 62257 1rtfB 252 5.31e+00 5ptp 2bw4A 340 5.34e+00 1vq0A 302 5.75e+00 1tueA 212 5.96e+00 c.37.1.20 107323 1ve4A 206 6.00e+00 2cgaA 245 6.01e+00 5ptp b.47.1.2 26028 1k3sA 113 6.08e+00 d.198.1.1 68120 1yphE 97 6.26e+00 2anyA 241 6.42e+00 1a0lA 244 6.51e+00 5ptp b.47.1.2 26286 2anwA 241 6.55e+00 2fjbA 643 7.22e+00 1jnrA 643 7.26e+00 a.7.3.1,c.3.1.4,d.168.1.1 66966,66967,66968 1se8A 301 7.41e+00 b.40.4.3 105448 2fdiA 211 7.61e+00 1qnjA 240 7.90e+00 5ptp b.47.1.2 26238 1gvkB 240 7.99e+00 b.47.1.2 70610 1sf9A 128 8.41e+00 b.34.15.1 98831 1vhsA 175 8.61e+00 d.108.1.1 100698 1mb4A 370 8.72e+00 c.2.1.3,d.81.1.1 78908,78909 1afqC 96 8.87e+00 5ptp 1zy9A 564 9.02e+00 1ab9C 97 9.28e+00 5ptp 1d2tA 231 9.72e+00 1d2tA a.111.1.1 19052 1tjoA 182 1.00e+01 1mojA 182 1.01e+01 a.25.1.1 91367 1wrvA 308 1.01e+01 1vjlA 164 1.01e+01 d.257.1.1 100822 1qhsA 178 1.02e+01 1qhsA c.37.1.3 31938 2fp7A 54 1.03e+01 1iw8A 231 1.05e+01 a.111.1.1 76866 1ze3D 125 1.05e+01 1tygB 87 1.11e+01 d.15.3.2 107455 3hmgA 328 1.13e+01 1hgeA b.19.1.2 23825 1vbkA 307 1.16e+01 1pv5A 264 1.17e+01 d.251.1.1 95150 1gg6C 97 1.20e+01 5ptp 1vjvA 415 1.26e+01 d.3.1.9 108632 1hgeA 328 1.28e+01 1hgeA b.19.1.2 23816 1iv3A 152 1.29e+01 d.79.5.1 76828 1btu 240 1.30e+01 5ptp b.47.1.2 26241 2ff4A 388 1.33e+01 1x3lA 440 1.33e+01 1yjmA 110 1.38e+01 1esfA 233 1.50e+01 3seb b.40.2.2,d.15.6.1 25146,37735 1mtnC 97 1.51e+01 5ptp 1iyeA 309 1.52e+01 e.17.1.1 83786 1nykA 165 1.53e+01 b.33.1.1 86408 1y88A 199 1.54e+01 1k2i1 245 1.56e+01 1dyqA 234 1.60e+01 3seb b.40.2.2,d.15.6.1 59140,59141 1ubpA 101 1.60e+01 1ubpA d.8.1.1 37353 1z64A 26 1.61e+01 1yr1A 119 1.61e+01 4ubpA 101 1.61e+01 1ubpA d.8.1.1 37352 2bkyX 89 1.64e+01 1j96A 323 1.70e+01 c.1.7.1 71616 1a2vA 655 1.71e+01 1a2vA b.30.2.1,d.17.2.1,d.17.2.1 24416,38059,38060 3c2c 112 1.74e+01 1ycc a.3.1.1 15885 1m7vA 363 1.79e+01 d.174.1.1 78748 1txoA 237 1.80e+01 2fpeA 62 1.80e+01 1iqyA 638 1.81e+01 b.30.2.1,d.17.2.1,d.17.2.1 76763,76764,76765 1iqqA 200 1.81e+01 d.124.1.1 66274 1qhxA 178 1.83e+01 1qhsA c.37.1.3 31936 1vfqA 143 1.85e+01 1eu3A 210 1.90e+01 1an8 b.40.2.2,d.15.6.1 25206,37795 1udvA 89 1.98e+01 d.68.6.1 99224 2biiA 424 1.98e+01 3kvt 115 1.99e+01 1t1dA d.42.1.2 38642 1taxA 302 2.00e+01 1taxA 1wdtA 665 2.00e+01 1yozA 116 2.01e+01 1ecfA 504 2.04e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 1ts3A 194 2.12e+01 1aw7A b.40.2.2,d.15.6.1 25168,37757 1p1mA 406 2.12e+01 b.92.1.4,c.1.9.9 87696,87697 1t0aA 159 2.13e+01 1p4dA 330 2.16e+01 d.89.1.5 94101 1jsdA 319 2.18e+01 b.19.1.2 63258 2bh8A 101 2.18e+01 1u69A 163 2.21e+01 d.32.1.7 107699 2dg5B 190 2.23e+01 2bzvA 181 2.26e+01 1jtdB 273 2.27e+01 b.69.5.2 67265 1el3A 316 2.29e+01 1frb c.1.7.1 28672 1m4uL 139 2.29e+01 g.17.1.2 78626 2bzuA 181 2.30e+01 1yt3A 375 2.31e+01 1ecfB 504 2.33e+01 1ecfB c.61.1.1,d.153.1.1 34054,41821 1t0gA 109 2.34e+01 d.120.1.2 99063 2scuB 388 2.36e+01 2scuB c.23.4.1,d.142.1.4 31141,41562 1j03A 102 2.42e+01 d.120.1.2 90733 1gy7A 125 2.44e+01 d.17.4.2 70738 1us0A 316 2.44e+01 c.1.7.1 99850 1hnr 47 2.52e+01 1hnr a.155.1.1 17896 1tux 301 2.53e+01 1taxA c.1.8.3 28907 3ullA 132 2.53e+01 3ullA b.40.4.3 25282 1zsyA 357 2.54e+01 2agtA 319 2.56e+01 2acr 315 2.61e+01 1frb c.1.7.1 28674 2bnjA 303 2.65e+01 1rl6A 177 2.66e+01 1rl6A d.141.1.1,d.141.1.1 41473,41474 2b1xA 470 2.67e+01 2d1yA 256 2.70e+01 1j6pA 418 2.70e+01 b.92.1.4,c.1.9.9 77089,77090 1rqpA 299 2.75e+01 b.141.1.1,c.132.1.1 97754,97755 2brfA 110 2.75e+01 1zbxB 141 2.84e+01 1pmt 203 2.87e+01 1a0fA a.45.1.1,c.47.1.5 17740,33034 1me4A 215 2.88e+01 d.3.1.1 79023 2prk 279 2.88e+01 1gci c.41.1.1 32548 1zk7A 467 2.88e+01 1fnlA 175 2.88e+01 2fcbA b.1.1.4,b.1.1.4 21783,21784 1pzxA 289 2.95e+01 c.119.1.1 95484 1xn5A 146 2.95e+01 1jsmA 325 2.95e+01 b.19.1.2 63264 1elt 236 3.00e+01 5ptp b.47.1.2 26281 1dmaA 214 3.03e+01 1aerA d.166.1.1 42251 1ui8A 638 3.04e+01 b.30.2.1,d.17.2.1,d.17.2.1 99419,99420,99421 1ui7A 638 3.05e+01 b.30.2.1,d.17.2.1,d.17.2.1 99413,99414,99415 1tcvA 287 3.10e+01 1pfxC 235 3.13e+01 5ptp b.47.1.2 26353 1p42A 270 3.21e+01 d.14.1.7,d.14.1.7 87754,87755 3tss 194 3.22e+01 1aw7A b.40.2.2,d.15.6.1 25160,37749 1s3eA 520 3.29e+01 c.3.1.2,d.16.1.5 98426,98427 1jbuH 254 3.32e+01 5ptp b.47.1.2 62856 1ivwA 638 3.43e+01 b.30.2.1,d.17.2.1,d.17.2.1 71456,71457,71458 1ojaA 520 3.44e+01 c.3.1.2,d.16.1.5 93096,93097 1me3A 215 3.52e+01 d.3.1.1 79022 1hpi 71 3.56e+01 1ckuA g.35.1.1 44995 1fnoA 417 3.58e+01 d.58.19.1,c.56.5.4 70145,75841 1y4wA 518 3.64e+01 2ai4A 119 3.66e+01 1uisA 231 3.76e+01 d.22.1.1 99431 1bmp 139 3.77e+01 2tgi g.17.1.2 44785 2viuA 328 3.78e+01 1hgeA b.19.1.2 23797 1aim 215 3.80e+01 1cs8A d.3.1.1 37044 1frb 315 3.80e+01 1frb c.1.7.1 28665 1lshA 1056 3.91e+01 a.118.4.1,f.7.1.1,f.7.1.1 74242,74243,74244 3ssi 113 4.02e+01 3ssi d.84.1.1 40032 1nr4A 71 4.04e+01 d.9.1.1 92077 1dleA 298 4.04e+01 1dleA b.47.1.2 26312 1o54A 277 4.06e+01 c.66.1.13 92482 1mroC 247 4.07e+01 1mroC d.58.31.1 39437 1ugmA 125 4.07e+01 d.15.1.3 107827 2f5yA 91 4.08e+01 1w6gA 646 4.08e+01 1v5vA 401 4.10e+01 1ytbA 180 4.24e+01 1ytbA d.129.1.1,d.129.1.1 41276,41277 1senA 164 4.26e+01 c.47.1.1 105465 1ixkA 315 4.36e+01 c.66.1.38 90716 2a1kA 233 4.40e+01 1pmlA 86 4.42e+01 5hpgA g.14.1.1 44632 1ozjA 144 4.43e+01 d.164.1.1 93846 1qd9A 124 4.43e+01 1qu9A d.79.1.1 39758 1ytbB 180 4.44e+01 1ytbA d.129.1.1,d.129.1.1 41278,41279 2gi3A 476 4.46e+01 1yr2A 741 4.59e+01 1l0wA 580 4.62e+01 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 2ahrA 259 4.63e+01 1rjoA 646 4.64e+01 1gokA 303 4.66e+01 c.1.8.3 65420 2ao0A 324 4.67e+01 1q74A 303 4.75e+01 c.134.1.1 96019 1gosA 520 4.76e+01 c.3.1.2,d.16.1.5 65425,65426 1f2aA 215 4.78e+01 1cs8A d.3.1.1 37040 1l9gA 192 4.84e+01 c.18.1.2 84568 1i1wA 303 4.88e+01 c.1.8.3 76732 1ahsA 126 4.91e+01 1ahsA b.19.1.1 23794 1pvmA 184 4.91e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1bh5A 183 4.93e+01 1qipA d.32.1.1 38476 1x82A 190 4.95e+01 1k6aA 303 4.98e+01 c.1.8.3 72081 1eg9A 449 5.04e+01 1ndoA b.33.1.2,d.129.3.3 24443,41322 1jb7B 260 5.05e+01 1otcB b.40.4.3 62839 1pwmA 316 5.06e+01 c.1.7.1 95231 1wruA 379 5.10e+01 1dtdB 61 5.16e+01 1dtvA g.30.1.1 44962 1prtD 110 5.20e+01 1bcpD b.40.2.1 25128 1mo1A 87 5.24e+01 d.94.1.1 91363 1a8q 274 5.34e+01 1brt c.69.1.12 34702 1qxrA 189 5.34e+01 b.82.1.7 96552 1hh8A 213 5.35e+01 1e96B a.118.8.1 61042 1tkeA 224 5.38e+01 1wzvA 155 5.57e+01 1ndoA 449 5.60e+01 1ndoA b.33.1.2,d.129.3.3 24444,41323 1i1kA 309 5.66e+01 1daaA e.17.1.1 61533 1y7xA 113 5.66e+01 1az1 315 5.69e+01 1frb c.1.7.1 28677 1wm5A 208 5.73e+01 2bngA 149 5.84e+01 1o7nA 449 5.96e+01 b.33.1.2,d.129.3.3 81162,81163 1v8bA 479 5.99e+01 1vgjA 184 6.00e+01 2bz6H 254 6.02e+01 1o0pA 104 6.04e+01 d.58.7.1 86535 1ezvE 185 6.06e+01 1rie b.33.1.1,f.23.12.1 59548,59549 1jyhA 157 6.09e+01 d.60.1.3 71956 1hzgA 295 6.11e+01 1hzgA d.194.1.1 61436 1aiw 62 6.20e+01 1aiw b.72.2.1 27808 2bhgA 209 6.26e+01 1e9gA 286 6.27e+01 1wgjA b.40.5.1 59393 1krhA 338 6.27e+01 b.43.4.2,c.25.1.2,d.15.4.2 72891,72892,72893 1big 37 6.28e+01 1sco g.3.7.2 44145 1mpp 361 6.30e+01 2rmpA b.50.1.2 26856 1e96B 203 6.32e+01 1e96B a.118.8.1 19211 1xyn 178 6.34e+01 1axkA b.29.1.11 24322 2ffmA 91 6.37e+01 1l5jA 865 6.40e+01 a.118.15.1,c.8.2.1,c.83.1.1 73592,73593,73594 1hbq 183 6.44e+01 1aqb b.60.1.1 27078 1hbnC 248 6.44e+01 1mroC d.58.31.1 60902 3sicI 107 6.48e+01 3ssi d.84.1.1 40028 2cxaA 256 6.55e+01 1wmmA 145 6.55e+01 1whzA 70 6.64e+01 1whi 122 6.65e+01 1whi b.39.1.1 24810 1r8oB 71 6.75e+01 1siiA 646 6.76e+01 b.30.2.1,d.17.2.1,d.17.2.1 105578,105579,105580 1dnlA 199 6.77e+01 1ci0A b.45.1.1 25753 2fneA 117 6.80e+01 1xf1A 926 6.81e+01 1tlyA 278 6.83e+01 f.4.6.1 107143 1kliH 254 6.89e+01 b.47.1.2 77435 1i5hW 50 6.93e+01 1i5hW b.72.1.1 61785 1i50H 146 6.97e+01 b.40.4.8 61761 1i1qA 520 6.97e+01 1qdlA d.161.1.1 61543 1mbyA 88 7.05e+01 d.223.1.1 78931 1vcaA 202 7.07e+01 1vcaA b.1.1.3,b.1.1.4 21649,21685 1kpmA 121 7.12e+01 a.133.1.2 72844 1df7A 159 7.18e+01 3dfr c.71.1.1 34885 1u2xA 474 7.19e+01 c.72.1.3 107622 1c3gA 170 7.24e+01 1c3gA b.4.1.1,b.4.1.1 22831,22832 1cr5A 189 7.26e+01 1cr5A b.52.2.3,d.31.1.1 26931,38465 1khoA 370 7.29e+01 a.124.1.1,b.12.1.3 72489,72490 1q4gA 553 7.33e+01 a.93.1.2,g.3.11.1 95789,95790 1ee6A 197 7.39e+01 1ee6A b.80.1.1 28024 1aerA 205 7.43e+01 1aerA d.166.1.1 42249 2cfuA 658 7.44e+01 1gm7B 557 7.48e+01 1ounA 127 7.49e+01 1ounA d.17.4.2 38090 1avk 638 7.49e+01 1a2vA b.30.2.1,d.17.2.1,d.17.2.1 24410,38047,38048 487dH 224 7.56e+01 1ad2 i.1.1.2 45835 1gkfB 557 7.59e+01 1vi4A 174 7.60e+01 c.8.7.1 100731 1tbaB 180 7.63e+01 1ytbA d.129.1.1,d.129.1.1 41286,41287 1yagG 125 7.64e+01 1d0nA d.109.1.1 40846 1ae1A 273 7.65e+01 1bdb c.2.1.2 29943 1aisA 182 7.65e+01 1ytbA d.129.1.1,d.129.1.1 41288,41289 1oe1A 336 7.67e+01 b.6.1.3,b.6.1.3 86891,86892 1vdxA 184 7.67e+01 1ad2 228 7.68e+01 1ad2 e.24.1.1 43353 1bucA 383 7.69e+01 3mdeA a.29.3.1,e.6.1.1 16590,42851 1rc6A 261 7.70e+01 b.82.1.11 97287 1a3gA 308 7.71e+01 1daaA e.17.1.1 43286 1kt6A 183 7.74e+01 b.60.1.1 84466 1danH 254 7.77e+01 5ptp b.47.1.2 26292 1tk4A 121 7.96e+01 a.133.1.2 107073 1eso 154 7.97e+01 1yaiA b.1.8.1 22293 1htrB 329 8.01e+01 1smrA 1tj9A 121 8.04e+01 a.133.1.2 107015 1snnA 227 8.05e+01 d.115.1.2 105821 1php 394 8.05e+01 16pk c.86.1.1 35452 1hcnA 92 8.06e+01 1hcnA g.17.1.4 44809 1zwpA 121 8.15e+01 1ejxA 100 8.15e+01 d.8.1.1 83182 1hiaI 48 8.20e+01 1bx7 g.3.15.1 44357 1xttA 216 8.28e+01 1g47A 77 8.28e+01 1g47A g.39.1.3,g.39.1.3 45147,45148 1f2tB 148 8.28e+01 1f2tB 2sicI 107 8.36e+01 3ssi d.84.1.1 40031 1geeA 261 8.42e+01 c.2.1.2 90509 1sqzA 121 8.44e+01 a.133.1.2 98975 1enwA 114 8.49e+01 1enwA a.5.4.1 16291 1yt5A 258 8.49e+01 1ijvA 36 8.54e+01 g.9.1.1 66169 1ylxA 103 8.57e+01 1qk4A 233 8.59e+01 1qk3A c.61.1.1 34037 2mcm 112 8.60e+01 2mcm b.1.7.1 22207 1eo9B 241 8.63e+01 3pchM b.3.6.1 22826 1gk9B 557 8.63e+01 1ikpA 613 8.65e+01 b.29.1.7,d.166.1.1,f.1.5.1 66182,66183,66184 1kczA 413 8.73e+01 c.1.11.2,d.54.1.1 68451,68452 2a6qA 86 8.73e+01 1cqeA 580 8.74e+01 1cqeA a.93.1.2,g.3.11.1 18703,44246 1hq0A 295 8.75e+01 1hzgA d.194.1.1 61122 1lxiA 139 8.76e+01 g.17.1.2 84735 1rm6A 769 8.76e+01 1sur 215 8.82e+01 1sur c.26.2.2 31620 1sjqA 105 8.83e+01 d.58.7.1 105660 2c5qA 240 8.86e+01 1bzyA 217 8.91e+01 1qk3A c.61.1.1 34071 1mmiA 366 8.93e+01 d.131.1.1,d.131.1.1,d.131.1.1 91309,91310,91311 1gcoA 261 8.93e+01 1ybvA c.2.1.2 29884