# 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 2.61e-02 1ev7A 317 1.60e-01 1ev7B c.52.1.9 33315 1gt91 357 3.00e-01 1t1gA 364 3.06e-01 c.41.1.2 106246 1uliA 460 3.45e-01 b.33.1.2,d.129.3.3 107921,107922 1tdhA 364 5.01e-01 a.156.1.2,b.113.1.1,g.39.1.8 106772,106773,106774 1wkrA 340 7.60e-01 b.50.1.2 109395 1mzyA 333 9.89e-01 b.6.1.3,b.6.1.3 103848,103849 1zvkA 358 1.03e+00 1j9qA 341 1.13e+00 1nif b.6.1.3,b.6.1.3 62765,62766 2bwqA 129 1.21e+00 1snrA 341 1.22e+00 b.6.1.3,b.6.1.3 105823,105824 1nif 340 1.30e+00 1nif b.6.1.3,b.6.1.3 23048,23049 2a72A 146 1.37e+00 1aw7A 194 1.44e+00 1aw7A b.40.2.2,d.15.6.1 25164,37753 2aheA 267 1.70e+00 1el6A 219 1.78e+00 1el6B d.182.1.1 42606 1mjc 69 1.80e+00 1mjc b.40.4.5 25319 1kcbA 340 1.89e+00 b.6.1.3,b.6.1.3 90951,90952 2f9nA 245 2.05e+00 1ga6A 372 2.25e+00 1ga1A c.41.1.2 32556 1zkpA 268 2.49e+00 1o6aA 96 2.70e+00 b.139.1.1 92562 1gj7B 253 2.91e+00 1k3sA 113 2.95e+00 d.198.1.1 68120 1c5yB 253 3.25e+00 5ptp 1ltoA 245 3.35e+00 b.47.1.2 84707 2fdiA 211 3.46e+00 1ic6A 279 3.77e+00 1gci c.41.1.1 62257 2fjbA 643 3.85e+00 1jnrA 643 3.86e+00 a.7.3.1,c.3.1.4,d.168.1.1 66966,66967,66968 4ubpA 101 3.95e+00 1ubpA d.8.1.1 37352 2bw4A 340 4.24e+00 1tueA 212 4.32e+00 c.37.1.20 107323 1vjlA 164 4.38e+00 d.257.1.1 100822 1juvA 193 4.45e+00 c.71.1.1 90912 1rtfB 252 4.51e+00 5ptp 1mojA 182 4.74e+00 a.25.1.1 91367 1tjoA 182 4.77e+00 1sf9A 128 5.39e+00 b.34.15.1 98831 1x3lA 440 5.66e+00 1d2tA 231 5.97e+00 1d2tA a.111.1.1 19052 1vq0A 302 6.16e+00 1qnjA 240 6.17e+00 5ptp b.47.1.2 26238 1gvkB 240 6.23e+00 b.47.1.2 70610 1yphE 97 6.37e+00 2ff4A 388 6.38e+00 1iw8A 231 6.39e+00 a.111.1.1 76866 1mb4A 370 7.03e+00 c.2.1.3,d.81.1.1 78908,78909 2anyA 241 7.05e+00 2anwA 241 7.15e+00 1se8A 301 7.81e+00 b.40.4.3 105448 1p1mA 406 7.86e+00 b.92.1.4,c.1.9.9 87696,87697 1ze3D 125 8.29e+00 1vhsA 175 8.35e+00 d.108.1.1 100698 2fp7A 54 8.45e+00 1zy9A 564 8.71e+00 1tygB 87 8.99e+00 d.15.3.2 107455 1yjmA 110 9.09e+00 1nykA 165 9.23e+00 b.33.1.1 86408 1j6pA 418 9.77e+00 b.92.1.4,c.1.9.9 77089,77090 1t0aA 159 1.01e+01 1z64A 26 1.04e+01 1iv3A 152 1.04e+01 d.79.5.1 76828 1a2vA 655 1.07e+01 1a2vA b.30.2.1,d.17.2.1,d.17.2.1 24416,38059,38060 1vbkA 307 1.09e+01 1wrvA 308 1.09e+01 1ve4A 206 1.12e+01 2fpeA 62 1.22e+01 1vjvA 415 1.26e+01 d.3.1.9 108632 1gg6C 97 1.30e+01 5ptp 1jtdB 273 1.32e+01 b.69.5.2 67265 1eu3A 210 1.35e+01 1an8 b.40.2.2,d.15.6.1 25206,37795 1iyeA 309 1.36e+01 e.17.1.1 83786 2biiA 424 1.40e+01 3kvt 115 1.41e+01 1t1dA d.42.1.2 38642 1jsdA 319 1.43e+01 b.19.1.2 63258 1pv5A 264 1.49e+01 d.251.1.1 95150 1qhxA 178 1.50e+01 1qhsA c.37.1.3 31936 1yozA 116 1.52e+01 2dg5B 190 1.59e+01 1hpi 71 1.64e+01 1ckuA g.35.1.1 44995 1hnr 47 1.65e+01 1hnr a.155.1.1 17896 2brfA 110 1.68e+01 1iqyA 638 1.68e+01 b.30.2.1,d.17.2.1,d.17.2.1 76763,76764,76765 1j96A 323 1.70e+01 c.1.7.1 71616 1dyqA 234 1.72e+01 3seb b.40.2.2,d.15.6.1 59140,59141 2bh8A 101 1.74e+01 1rqpA 299 1.76e+01 b.141.1.1,c.132.1.1 97754,97755 2bzvA 181 1.76e+01 1fnoA 417 1.81e+01 d.58.19.1,c.56.5.4 70145,75841 2bzuA 181 1.81e+01 1s3eA 520 1.86e+01 c.3.1.2,d.16.1.5 98426,98427 1lshA 1056 1.89e+01 a.118.4.1,f.7.1.1,f.7.1.1 74242,74243,74244 1fnlA 175 1.92e+01 2fcbA b.1.1.4,b.1.1.4 21783,21784 1ojaA 520 1.92e+01 c.3.1.2,d.16.1.5 93096,93097 1tcvA 287 1.92e+01 1m7vA 363 1.93e+01 d.174.1.1 78748 1vfqA 143 2.00e+01 2bnjA 303 2.03e+01 1zsyA 357 2.05e+01 1zbxB 141 2.07e+01 3c2c 112 2.15e+01 1ycc a.3.1.1 15885 1gy7A 125 2.16e+01 d.17.4.2 70738 2ptd 298 2.17e+01 2plc c.1.18.2 29605 1t0gA 109 2.20e+01 d.120.1.2 99063 1p42A 270 2.21e+01 d.14.1.7,d.14.1.7 87754,87755 3ullA 132 2.23e+01 3ullA b.40.4.3 25282 2viuA 328 2.24e+01 1hgeA b.19.1.2 23797 1u69A 163 2.25e+01 d.32.1.7 107699 1txoA 237 2.26e+01 1y4wA 518 2.27e+01 1ecfA 504 2.29e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 1iqqA 200 2.29e+01 d.124.1.1 66274 1hh8A 213 2.30e+01 1e96B a.118.8.1 61042 1wdtA 665 2.31e+01 1zk7A 467 2.36e+01 1yr1A 119 2.45e+01 2gi3A 476 2.46e+01 1wm5A 208 2.49e+01 3tss 194 2.49e+01 1aw7A b.40.2.2,d.15.6.1 25160,37749 2b1xA 470 2.50e+01 1yt3A 375 2.52e+01 1ejxA 100 2.53e+01 d.8.1.1 83182 1ahsA 126 2.54e+01 1ahsA b.19.1.1 23794 2ai4A 119 2.64e+01 2f5yA 91 2.88e+01 1jsmA 325 2.90e+01 b.19.1.2 63264 1ui7A 638 2.93e+01 b.30.2.1,d.17.2.1,d.17.2.1 99413,99414,99415 1us0A 316 2.93e+01 c.1.7.1 99850 1pzxA 289 2.95e+01 c.119.1.1 95484 1ui8A 638 2.96e+01 b.30.2.1,d.17.2.1,d.17.2.1 99419,99420,99421 2agtA 319 3.10e+01 1vgjA 184 3.15e+01 1mroC 247 3.16e+01 1mroC d.58.31.1 39437 1me4A 215 3.17e+01 d.3.1.1 79023 2d1yA 256 3.19e+01 1e9gA 286 3.29e+01 1wgjA b.40.5.1 59393 1y7xA 113 3.31e+01 1aiw 62 3.35e+01 1aiw b.72.2.1 27808 1y88A 199 3.37e+01 1dtdB 61 3.38e+01 1dtvA g.30.1.1 44962 1senA 164 3.42e+01 c.47.1.1 105465 1o54A 277 3.43e+01 c.66.1.13 92482 1rl6A 177 3.44e+01 1rl6A d.141.1.1,d.141.1.1 41473,41474 1elt 236 3.47e+01 5ptp b.47.1.2 26281 1ej6B 1275 3.56e+01 i.7.1.1 45968 2bhgA 209 3.60e+01 1i1wA 303 3.65e+01 c.1.8.3 76732 1xn5A 146 3.83e+01 1jb7B 260 3.83e+01 1otcB b.40.4.3 62839 1ixkA 315 3.85e+01 c.66.1.38 90716 1pguA 615 3.92e+01 b.69.4.1,b.69.4.1 88069,88070 1geeA 261 3.93e+01 c.2.1.2 90509 1ugmA 125 3.93e+01 d.15.1.3 107827 1vdxA 184 3.95e+01 1ozjA 144 4.05e+01 d.164.1.1 93846 1v8bA 479 4.05e+01 1dleA 298 4.09e+01 1dleA b.47.1.2 26312 1fmhA 33 4.11e+01 1fmhB k.6.1.1 46409 1o0pA 104 4.12e+01 d.58.7.1 86535 1i1kA 309 4.16e+01 1daaA e.17.1.1 61533 1whi 122 4.16e+01 1whi b.39.1.1 24810 2cxaA 256 4.24e+01 1gcoA 261 4.26e+01 1ybvA c.2.1.2 29884 1yr2A 741 4.27e+01 1w6gA 646 4.28e+01 1wmmA 145 4.30e+01 1aerA 205 4.32e+01 1aerA d.166.1.1 42249 1wzvA 155 4.34e+01 1i50H 146 4.40e+01 b.40.4.8 61761 1to2E 281 4.43e+01 1ckeA 227 4.51e+01 1ckeA c.37.1.1 31846 1eg9A 449 4.54e+01 1ndoA b.33.1.2,d.129.3.3 24443,41322 2bkyX 89 4.56e+01 1rjoA 646 4.58e+01 1uisA 231 4.62e+01 d.22.1.1 99431 1mbyA 88 4.66e+01 d.223.1.1 78931 1xttA 216 4.66e+01 2a1kA 233 4.67e+01 2ahrA 259 4.70e+01 1mo1A 87 4.71e+01 d.94.1.1 91363 1a8q 274 4.73e+01 1brt c.69.1.12 34702 2sicI 107 4.74e+01 3ssi d.84.1.1 40031 2gd9A 189 4.75e+01 1a8y 367 4.76e+01 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 1krhA 338 4.81e+01 b.43.4.2,c.25.1.2,d.15.4.2 72891,72892,72893 2bngA 149 4.91e+01 1ikpA 613 4.91e+01 b.29.1.7,d.166.1.1,f.1.5.1 66182,66183,66184 1hbnC 248 4.93e+01 1mroC d.58.31.1 60902 1x82A 190 4.97e+01 1tj9A 121 5.04e+01 a.133.1.2 107015 1zwpA 121 5.06e+01 1tk4A 121 5.09e+01 a.133.1.2 107073 1im3D 95 5.12e+01 1im3D b.1.18.5 62568 1pvmA 184 5.21e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1wruA 379 5.28e+01 1o7nA 449 5.32e+01 b.33.1.2,d.129.3.3 81162,81163 1f2aA 215 5.34e+01 1cs8A d.3.1.1 37040 1hcnA 92 5.35e+01 1hcnA g.17.1.4 44809 1yt5A 258 5.35e+01 2fneA 117 5.38e+01 1qxrA 189 5.41e+01 b.82.1.7 96552 1udvA 89 5.43e+01 d.68.6.1 99224 1y4lA 121 5.48e+01 1mpp 361 5.49e+01 2rmpA b.50.1.2 26856 1v5vA 401 5.49e+01 1jyhA 157 5.50e+01 d.60.1.3 71956 1u2xA 474 5.51e+01 c.72.1.3 107622 1sqzA 121 5.58e+01 a.133.1.2 98975 1i1qA 520 5.64e+01 1qdlA d.161.1.1 61543 1jnuA 104 5.69e+01 d.110.3.6 71762 1qd9A 124 5.73e+01 1qu9A d.79.1.1 39758 1frb 315 5.76e+01 1frb c.1.7.1 28665 1kqrA 179 5.82e+01 b.29.1.14 72886 1ounA 127 5.87e+01 1ounA d.17.4.2 38090 1yb2A 275 5.88e+01 1df7A 159 5.90e+01 3dfr c.71.1.1 34885 2fsrA 195 5.99e+01 1nr4A 71 6.03e+01 d.9.1.1 92077 1kd8A 36 6.13e+01 h.1.3.1 68460 1sh7A 284 6.13e+01 1pwmA 316 6.25e+01 c.1.7.1 95231 1tlyA 278 6.26e+01 f.4.6.1 107143 1qhoA 686 6.32e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21844,22513,27751,28738 1siiA 646 6.36e+01 b.30.2.1,d.17.2.1,d.17.2.1 105578,105579,105580 1r8oB 71 6.41e+01 1vcbC 160 6.42e+01 1vcbC b.3.3.1 22535 1mtyB 384 6.42e+01 1mtyB a.25.1.2 16740 1wraA 308 6.45e+01 1koqA 253 6.52e+01 2cba b.74.1.1 27964 2fp7B 172 6.63e+01 2ao0A 324 6.66e+01 2mcm 112 6.68e+01 2mcm b.1.7.1 22207 1sjqA 105 6.74e+01 d.58.7.1 105660 1hdlA 55 6.77e+01 g.68.1.2 65808 1ylxA 103 6.81e+01 1eso 154 6.85e+01 1yaiA b.1.8.1 22293 1ts9A 102 6.94e+01 1wlmA 151 6.97e+01 1xf1A 926 6.97e+01 1c3gA 170 6.99e+01 1c3gA b.4.1.1,b.4.1.1 22831,22832 1tkeA 224 7.02e+01 1ppa 121 7.04e+01 1poa a.133.1.2 19550 1ijvA 36 7.12e+01 g.9.1.1 66169 1avk 638 7.20e+01 1a2vA b.30.2.1,d.17.2.1,d.17.2.1 24410,38047,38048 1li1A 229 7.22e+01 d.169.1.6,d.169.1.6 73898,73899 1hq0A 295 7.23e+01 1hzgA d.194.1.1 61122 1oe1A 336 7.24e+01 b.6.1.3,b.6.1.3 86891,86892 2g58A 121 7.29e+01 1ad2 228 7.33e+01 1ad2 e.24.1.1 43353 1twfH 146 7.36e+01 1aisA 182 7.38e+01 1ytbA d.129.1.1,d.129.1.1 41288,41289 1xd5A 112 7.42e+01 1ee6A 197 7.47e+01 1ee6A b.80.1.1 28024 1nbaA 264 7.47e+01 1nbaA c.33.1.3 31753 1v37A 177 7.49e+01 1php 394 7.57e+01 16pk c.86.1.1 35452 2c43A 323 7.61e+01 1tl2A 236 7.75e+01 1tl2A b.67.1.1 27541 1ms9A 648 7.76e+01 b.29.1.15,b.68.1.1 85088,85089 1m1zA 513 7.84e+01 c.26.2.1,d.153.1.1 78457,78458 1q74A 303 7.86e+01 c.134.1.1 96019 1vcaA 202 7.90e+01 1vcaA b.1.1.3,b.1.1.4 21649,21685 2ffmA 91 7.93e+01 2btzA 394 7.96e+01 16pk 415 7.96e+01 16pk c.86.1.1 35454 1h54A 754 8.04e+01 a.102.1.4,b.30.5.3 60634,60635 1e6eB 128 8.09e+01 1ayfA d.15.4.1 59300 1jfuA 186 8.17e+01 c.47.1.10 62940 1t5oA 351 8.21e+01 c.124.1.5 106459 1sdjA 310 8.22e+01 d.21.1.2,d.21.1.2 98807,98808 1mmiA 366 8.26e+01 d.131.1.1,d.131.1.1,d.131.1.1 91309,91310,91311 2b4wA 315 8.27e+01 1rm6A 769 8.37e+01 1snnA 227 8.41e+01 d.115.1.2 105821 1q4gA 553 8.43e+01 a.93.1.2,g.3.11.1 95789,95790 1sur 215 8.44e+01 1sur c.26.2.2 31620 2a4vA 159 8.49e+01 1nh8A 304 8.50e+01 c.94.1.1,d.58.5.3 80507,80508 1gk9B 557 8.54e+01 1a4sA 503 8.59e+01 1bpwA c.82.1.1 35361 1hbq 183 8.67e+01 1aqb b.60.1.1 27078 1htrB 329 8.73e+01 1smrA 1eo9B 241 8.73e+01 3pchM b.3.6.1 22826 1jigA 146 8.74e+01 a.25.1.1 71685 1q98A 165 8.84e+01 c.47.1.10 96253 1w96A 554 8.84e+01 1yfsA 465 8.89e+01 1mfgA 95 8.93e+01 b.36.1.1 79043 1l0wA 580 8.97e+01 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1p0zA 131 8.98e+01 d.110.6.1 93882