# List of top-scoring protein chains for t04-100-30-str2-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 2b06A 155 4.36e-01 1m7vA 363 1.09e+00 d.174.1.1 78748 1o50A 157 1.68e+00 d.37.1.1,d.37.1.1 92478,92479 1yspA 181 2.29e+00 1xg5A 279 2.30e+00 2b0lA 102 2.36e+00 1ofdA 1520 2.40e+00 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 1mmvB 419 2.61e+00 d.174.1.1 91318 1om4A 422 2.70e+00 d.174.1.1 87067 1khtA 192 4.81e+00 c.37.1.1 84401 1lrzA 426 4.89e+00 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 1r13A 148 5.21e+00 d.169.1.1,h.1.1.1 96782,96783 1pbyB 337 5.49e+00 b.69.2.2 94422 1ykiA 217 6.15e+00 1icrA 217 6.21e+00 1vfrA d.90.1.1 62274 2bjvA 265 6.32e+00 1zzmA 259 7.52e+00 1np7A 489 7.63e+00 a.99.1.1,c.28.1.1 80677,80678 2afwA 329 8.27e+00 1jmxB 349 8.61e+00 b.69.2.2 66906 1ps9A 671 8.76e+00 c.1.4.1,c.3.1.1,c.4.1.1 95076,95077,95078 1g6aA 271 8.82e+00 1btl e.3.1.1 42704 1u9iA 519 8.96e+00 1dv1A 449 9.67e+00 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28234,31641,41486 1xr4A 509 9.98e+00 1xseA 295 1.05e+01 1x38A 602 1.08e+01 2g8lA 299 1.11e+01 1f6fB 210 1.19e+01 1axiB b.1.2.1,b.1.2.1 22033,22034 1z94A 147 1.27e+01 1ex1A 605 1.34e+01 1ex1A c.1.8.7,c.23.11.1 29013,31347 1nksA 194 1.36e+01 1nksA c.37.1.1 31886 1amuA 563 1.43e+01 1amuA e.23.1.1 43351 2fq3A 104 1.48e+01 1gdoA 240 1.55e+01 1gdoA 1xffA 240 1.57e+01 d.153.1.1 109580 2gsq 202 1.66e+01 1pd21 a.45.1.1,c.47.1.5 17715,33009 1hstA 90 1.78e+01 1hstA a.4.5.13 16140 1ae7 119 1.82e+01 1poa a.133.1.2 19553 1z90A 469 1.85e+01 1s72E 178 1.85e+01 d.141.1.1,d.141.1.1 105323,105324 1q7bA 244 1.87e+01 c.2.1.2 96026 1xn5A 146 1.91e+01 1dd9A 338 1.97e+01 1dd9A e.13.1.1 43254 1dpjA 329 2.02e+01 1smrA b.50.1.2 26828 1jtvA 327 2.08e+01 c.2.1.2 84230 1fds 327 2.10e+01 1fds c.2.1.2 29838 2cu3A 64 2.17e+01 4pfk 319 2.20e+01 3pfk c.89.1.1 35582 1kveB 77 2.22e+01 1kveB 1xu9A 286 2.26e+01 1xeeA 91 2.27e+01 1wluA 136 2.27e+01 1vm8A 534 2.36e+01 3cox 507 2.38e+01 1b8sA c.3.1.2,d.16.1.1 30332,37863 1zemA 262 2.44e+01 1fkmA 396 2.54e+01 1fkmA a.69.2.1,a.69.2.1 18315,18316 1furA 467 2.55e+01 1furA a.127.1.1 19403 1xneA 113 2.57e+01 1ydhA 216 2.59e+01 2f6rA 281 2.62e+01 1j6oA 268 2.65e+01 c.1.9.12 77088 1jv1A 505 2.71e+01 c.68.1.5 71892 1ugpB 226 2.71e+01 b.34.4.4 107832 1pfkA 320 2.76e+01 3pfk c.89.1.1 35575 1yixA 265 2.83e+01 1tjyA 316 2.87e+01 c.93.1.1 107062 1hdr 244 2.93e+01 1dhr c.2.1.2 29837 1msk 331 2.96e+01 1msk d.173.1.1 42495 1wmhB 86 2.96e+01 1a62 130 3.01e+01 1a62 a.140.3.1,b.40.4.5 64708,64709 1wguA 136 3.02e+01 1zxxA 319 3.02e+01 1b67A 68 3.06e+01 1a7w a.22.1.2 16474 1stzA 338 3.10e+01 a.4.5.51,d.110.2.3 106009,106010 1rkbA 173 3.10e+01 1n9lA 109 3.11e+01 d.110.3.6 85468 2pfkA 320 3.15e+01 3pfk c.89.1.1 35577 1ra6A 461 3.20e+01 e.8.1.4 104879 1ooeA 236 3.23e+01 c.2.1.2 87196 1guzA 310 3.25e+01 c.2.1.5,d.162.1.1 65586,65587 1y2qA 143 3.27e+01 1vqoE 178 3.31e+01 1qpcA 279 3.35e+01 1fgkA d.144.1.7 41685 1rypI 222 3.40e+01 d.153.1.4 41877 1go4A 205 3.41e+01 d.135.1.1 70292 1rypC 244 3.42e+01 1rypC d.153.1.4 41934 1ub3A 220 3.44e+01 c.1.10.1 88395 1j1yA 136 3.45e+01 d.38.1.5 90776 1k7jA 206 3.51e+01 d.115.1.1 72103 1l3kA 196 3.55e+01 d.58.7.1,d.58.7.1 73539,73540 2au3A 407 3.59e+01 1vig 71 3.61e+01 1vih d.51.1.1 38806 1ur5A 309 3.64e+01 c.2.1.5,d.162.1.1 99807,99808 1v4pA 157 3.65e+01 1luzA 88 3.69e+01 b.40.4.5 74271 1gpmA 525 3.69e+01 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 1eqcA 394 3.70e+01 1cz1A c.1.8.3 28811 1ireB 228 3.79e+01 b.34.4.4 76770 1g3qA 237 3.80e+01 1hyqA c.37.1.10 60237 1y5mA 276 3.83e+01 1ru8A 232 3.93e+01 c.26.2.1 97849 1gpc 218 4.00e+01 1gpc b.40.4.7 25393 2pspA 106 4.02e+01 2pspA g.16.1.1,g.16.1.1 44730,44731 1dmlB 36 4.04e+01 1dmlB 1rfeA 162 4.06e+01 1jj2E 177 4.09e+01 1ffk1 d.141.1.1,d.141.1.1 63089,63090 1tuc 63 4.13e+01 1tuc b.34.2.1 24492 1io2A 213 4.13e+01 1ekeA c.55.3.1 62612 2bvyA 475 4.15e+01 1qyaA 307 4.16e+01 d.21.1.2,d.21.1.2 104653,104654 1cnzA 363 4.17e+01 1cnzA c.77.1.1 35061 1mkyA 439 4.29e+01 c.37.1.8,c.37.1.8,d.52.5.1 79250,79251,79252 1a8vA 121 4.30e+01 1a62 a.140.3.1,b.40.4.5 64712,64713 2g03A 194 4.33e+01 1lucA 355 4.37e+01 1lucA c.1.16.1 29547 1molA 94 4.39e+01 1molA d.17.1.1 37988 2a33A 215 4.40e+01 1o94A 729 4.45e+01 c.1.4.1,c.3.1.1,c.4.1.1 81200,81201,81202 2dkaA 544 4.46e+01 1yarH 217 4.46e+01 1ws6A 171 4.62e+01 1xjo 284 4.67e+01 1xjo c.56.5.4 33843 1w2yA 229 4.68e+01 a.204.1.1 109140 1owfB 94 4.72e+01 a.55.1.1 87488 1djqA 729 4.73e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28614,30315,30600 1vjpA 394 4.76e+01 c.2.1.3,d.81.1.3 100828,100829 1mxgA 435 4.77e+01 b.71.1.1,c.1.8.1 85193,85194 1nar 290 4.79e+01 1nar c.1.8.5 28988 1l6rA 227 4.79e+01 c.108.1.10 77768 1p6oA 161 4.83e+01 c.97.1.2 94185 1djnA 729 4.84e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28612,30313,30598 1qq9A 284 4.88e+01 1xjo c.56.5.4 33841 1aboA 62 4.88e+01 1bbzA b.34.2.1 24474 1amf 233 4.96e+01 1wod c.94.1.1 35833 1awd 94 4.97e+01 1awd d.15.4.1 37673 2b18A 164 4.98e+01 1g0oA 283 5.00e+01 1ybvA c.2.1.2 60181 1gln 468 5.01e+01 1gln a.97.1.1,c.26.1.1 18752,31588 1geeA 261 5.04e+01 c.2.1.2 90509 1gcoA 261 5.05e+01 1ybvA c.2.1.2 29884 1bbzA 58 5.10e+01 1bbzA b.34.2.1 24477 1ev7A 317 5.12e+01 1ev7B c.52.1.9 33315 1wod 233 5.16e+01 1wod c.94.1.1 35832 1olmA 403 5.23e+01 a.5.3.1,b.132.1.1,c.13.1.1 104008,104009,104010 1oshA 232 5.23e+01 a.123.1.1 93496 1j09A 468 5.24e+01 a.97.1.1,c.26.1.1 77025,77026 1fxlA 167 5.24e+01 1b7fA d.58.7.1,d.58.7.1 39183,39184 1r6lA 239 5.25e+01 d.14.1.4,d.101.1.1 97153,97154 1vjzA 341 5.27e+01 c.1.8.3 100838 1d0cA 444 5.30e+01 d.174.1.1 64769 1pj5A 830 5.31e+01 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 2tmdA 729 5.34e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28616,30317,30602 1s2oA 244 5.35e+01 1okrA 123 5.35e+01 a.4.5.39 93269 1lm4A 194 5.38e+01 d.167.1.1 84626 1qwgA 251 5.39e+01 c.1.27.1 96473 1iqrA 420 5.45e+01 a.99.1.1,c.28.1.1 66275,66276 1im5A 180 5.47e+01 c.33.1.3 66211 1i1nA 226 5.50e+01 c.66.1.7 71102 2a6hD 1524 5.56e+01 2d00A 109 5.64e+01 1rypK 198 5.66e+01 d.153.1.4 41879 1s0uA 408 5.67e+01 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 2ffjA 300 5.73e+01 1sfxA 109 5.74e+01 a.4.5.50 105505 1af7 274 5.76e+01 1af7 a.58.1.1,c.66.1.8 17928,34203 2azwA 148 5.84e+01 1zhxA 438 5.87e+01 1vquA 374 5.90e+01 1g8kA 825 6.02e+01 1g8jA b.52.2.2,c.81.1.1 26920,35328 1ed5A 444 6.10e+01 1nseA d.174.1.1 42530 1v8hA 107 6.19e+01 2aucA 126 6.19e+01 2bryA 497 6.19e+01 1jnuA 104 6.20e+01 d.110.3.6 71762 1bcpA 235 6.23e+01 1bcpA d.166.1.1 42255 1wzvA 155 6.24e+01 1u69A 163 6.26e+01 d.32.1.7 107699 2ge3A 170 6.28e+01 2fo3A 125 6.32e+01 1qwrA 319 6.36e+01 b.82.1.3 96491 1j5sA 463 6.47e+01 c.1.9.8 71580 1sflA 238 6.48e+01 1a32 88 6.50e+01 1a32 a.16.1.2 16384 1t9xA 1049 6.54e+01 2fckA 181 6.56e+01 1tf9A 284 6.59e+01 1qqfA 277 6.60e+01 1c3d a.102.4.4 18875 1ylnA 252 6.61e+01 1tr7A 164 6.77e+01 2b0rA 202 6.80e+01 1xvsA 126 6.82e+01 1pkoA 139 6.83e+01 b.1.1.1 88147 1ykdA 398 6.94e+01 1bn7A 294 7.05e+01 1bn6A c.69.1.8 34677 1fm0D 81 7.08e+01 1fmaD d.15.3.1 37642 1r0vA 305 7.11e+01 c.52.2.1,c.52.2.1,d.75.1.1 96742,96743,96744 2adgA 214 7.12e+01 1tyyA 339 7.16e+01 1s8nA 205 7.22e+01 c.23.1.1 105374 1n3kA 130 7.27e+01 a.77.1.4 79965 1a79A 171 7.28e+01 1a79A c.52.2.1,d.75.1.1 33340,39739 1v1aA 309 7.29e+01 c.72.1.1 100249 2cxcA 144 7.31e+01 1o6uA 403 7.33e+01 a.5.3.1,b.132.1.1,c.13.1.1 92589,92590,92591 1pzgA 331 7.35e+01 c.2.1.5,d.162.1.1 95425,95426 2gaiA 633 7.35e+01 1zo2A 129 7.37e+01 1nslA 184 7.38e+01 d.108.1.1 86137 1ufkA 254 7.42e+01 c.66.1.39 99340 2fhzA 109 7.49e+01 2fu4A 83 7.52e+01 1d1vA 444 7.59e+01 1nseA d.174.1.1 59101 1ehyA 294 7.62e+01 1ehyA c.69.1.11 34693 2a1kA 233 7.63e+01 1sfjA 238 7.67e+01 1dhr 241 7.68e+01 1dhr c.2.1.2 29832 1ctj 89 7.71e+01 1ctj a.3.1.1 15798 1tfjA 219 7.72e+01 2g7uA 257 7.75e+01 2aelA 374 7.75e+01 1vrmA 325 7.76e+01 2c1dA 264 7.76e+01 1vib 55 7.79e+01 1vib g.2.2.1 43999 1z8sA 146 7.85e+01 1s0yA 76 7.88e+01 d.80.1.1 98314 1sdjA 310 7.92e+01 d.21.1.2,d.21.1.2 98807,98808 1swxA 209 7.93e+01 a.224.1.1 106075 1y6lA 149 7.97e+01 1ls9A 91 8.05e+01 a.3.1.1 78177 1uu1A 335 8.10e+01 c.67.1.1 99993 1l8aA 886 8.17e+01 c.36.1.10,c.36.1.6,c.48.1.1 73677,73678,73679 1z83A 196 8.18e+01 1fsz 372 8.25e+01 1fsz c.32.1.1,d.79.2.1 31750,39802 2a6hC 1119 8.28e+01 1n4wA 504 8.28e+01 c.3.1.2,d.16.1.1 91676,91677 1ayl 541 8.33e+01 1ayl c.91.1.1,c.109.1.1 64718,64719 1mxtA 504 8.33e+01 c.3.1.2,d.16.1.1 79671,79672 1xc3A 302 8.41e+01 1h0hA 977 8.42e+01 b.52.2.2,c.81.1.1 76435,76436 1a34A 159 8.43e+01 1a34A b.121.7.1 23286 1i8kA 107 8.45e+01 b.1.1.1 71130 1b4vA 504 8.45e+01 1b8sA c.3.1.2,d.16.1.1 30334,37865 1i0dA 332 8.48e+01 1pscA c.1.9.3 61487 1hzyA 332 8.65e+01 1pscA c.1.9.3 61468 1sedA 117 8.78e+01 a.219.1.1 105449 1tkjA 284 8.85e+01 1t6sA 162 8.92e+01 1p32A 209 8.92e+01 1p32A d.25.1.1 38379 1r5jA 337 8.99e+01 c.77.1.5 97097 1uxjA 309 9.00e+01 c.2.1.5,d.162.1.1 108112,108113