# List of top-scoring protein chains for t2k-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 1g79A 218 9.73e-34 1ci0A b.45.1.1 25752 1dnlA 199 1.41e-33 1ci0A b.45.1.1 25753 1nrgA 261 1.27e-28 b.45.1.1 80694 1t9mA 214 1.23e-25 1ty9A 222 3.13e-24 1ci0A 228 2.96e-23 1ci0A b.45.1.1 25750 1rfeA 162 1.05e-14 2fhqA 141 8.83e-14 1vl7A 157 7.21e-11 b.45.1.1 108732 2fg9A 178 5.70e-10 2asfA 137 1.25e-09 2aq6A 147 4.49e-09 1w9aA 147 1.84e-08 1xxoA 147 3.36e-08 2arzA 247 5.44e-07 2furA 209 9.35e-07 1xhnA 184 8.17e-06 1flmA 122 2.53e-05 1axj b.45.1.1 25747 1axj 122 3.59e-05 1axj b.45.1.1 25749 1w3oA 216 9.05e-05 1ejeA 192 5.07e-03 1ejeA b.45.1.2 25757 1a0rB 340 3.11e-01 1tbgA b.69.4.1 27658 1wj9A 211 3.79e-01 2bh8A 101 4.16e-01 1gotB 340 5.96e-01 1tbgA b.69.4.1 27648 2a6sA 84 8.01e-01 1b7yA 350 1.19e+00 1pysA d.104.1.1 40776 1tbgA 340 1.39e+00 1tbgA b.69.4.1 27649 2bcjB 340 1.53e+00 1pysA 350 1.60e+00 1pysA d.104.1.1 40775 1wlgA 299 1.63e+00 2bgzA 299 1.66e+00 1m1hA 248 2.04e+00 b.114.1.1,d.58.42.1 78415,78416 1ylnA 252 2.29e+00 2cn3A 737 2.36e+00 1v0wA 506 2.40e+00 d.136.1.2,d.136.1.2 108220,108221 1f0iA 504 2.40e+00 1f0iA d.136.1.2,d.136.1.2 59566,59567 1mjc 69 2.70e+00 1mjc b.40.4.5 25319 2al6A 375 2.72e+00 1d8hA 311 2.82e+00 1d8iA d.63.1.1 39544 1vkkA 154 2.96e+00 d.109.1.2 108669 1gm6A 175 3.08e+00 b.60.1.1 70272 1wvhA 134 3.12e+00 2bgiA 272 3.35e+00 1mxgA 435 3.36e+00 b.71.1.1,c.1.8.1 85193,85194 1widA 130 3.43e+00 1ibvB 229 3.45e+00 1txyA 104 3.93e+00 1zt3A 80 4.17e+00 1pyaB 228 4.34e+00 1pyaB 1wocA 103 4.44e+00 1nar 290 4.60e+00 1nar c.1.8.5 28988 1d8iA 311 4.88e+00 1d8iA d.63.1.1 39541 1qyaA 307 5.07e+00 d.21.1.2,d.21.1.2 104653,104654 1a1aA 107 5.28e+00 1fmk d.93.1.1 40449 1r1bA 59 5.41e+00 1r1bA a.16.1.3 16396 1obpA 159 5.50e+00 1obpA b.60.1.1 27092 1b8aA 438 5.80e+00 1b8aA b.40.4.1,d.104.1.1 25244,40765 1mkmA 249 6.06e+00 a.4.5.33,d.110.2.2 79242,79243 1am2 199 7.21e+00 1am2 b.86.1.2 28381 1qp2A 70 7.46e+00 1pse b.34.4.2 24596 1uf2C 421 7.68e+00 a.115.1.3,b.19.1.1 99291,99292 1o4rA 108 7.86e+00 d.93.1.1 92469 1bax 94 8.10e+00 1bax a.61.1.3 18133 1h7zA 194 8.23e+00 1qhvA b.21.1.1 60733 2fp8A 322 8.49e+00 1d2dA 59 8.53e+00 1r1bA a.16.1.3 16397 1ln1A 214 1.00e+01 d.129.3.2 74038 1ew3A 159 1.00e+01 1mup b.60.1.1 27114 1f2fA 104 1.04e+01 1fmk d.93.1.1 40455 1m40A 263 1.04e+01 e.3.1.1 74437 1rgzA 363 1.05e+01 e.3.1.1 97457 2bc4A 211 1.06e+01 1v6fA 151 1.06e+01 d.109.1.2 108395 1btl 263 1.07e+01 1btl e.3.1.1 42691 1j5yA 187 1.07e+01 a.4.5.1,d.94.2.1 71592,71593 1shaA 104 1.07e+01 1fmk d.93.1.1 40424 1fqgA 263 1.08e+01 1btl e.3.1.1 42699 1hyhA 309 1.10e+01 1hyhA c.2.1.5,d.162.1.1 30150,42117 3mefA 69 1.10e+01 1mjc b.40.4.5 25320 1ae3 86 1.10e+01 1gvp b.40.4.7 25381 1shbA 104 1.13e+01 1fmk d.93.1.1 40425 1ermA 263 1.13e+01 1btl e.3.1.1 42690 1ga0A 364 1.17e+01 1gceA e.3.1.1 60410 1v1qA 134 1.22e+01 1gvp 87 1.23e+01 1gvp b.40.4.7 25369 1vqb 87 1.26e+01 1gvp b.40.4.7 25370 1vlyA 338 1.27e+01 b.44.2.1,d.250.1.1 108871,108872 1onhA 364 1.29e+01 e.3.1.1 93357 1qrrA 394 1.31e+01 1qrrA c.2.1.2 29824 1i24A 404 1.33e+01 c.2.1.2 83663 1k4fA 248 1.35e+01 e.3.1.1 68138 1hdmA 201 1.36e+01 1iakA b.1.1.2,d.19.1.1 21583,38157 1sdjA 310 1.43e+01 d.21.1.2,d.21.1.2 98807,98808 1zarA 282 1.46e+01 1fofA 246 1.46e+01 1fofA e.3.1.1 42763 1tqmA 282 1.46e+01 a.4.5.56,d.144.1.9 107236,107237 1pse 69 1.57e+01 1pse b.34.4.2 24595 1fmk 452 1.60e+01 1fmk b.34.2.1,d.93.1.1,d.144.1.7 24511,40436,41690 1ygtA 111 1.64e+01 1e8nA 710 1.67e+01 1qfmA b.69.7.1,c.69.1.4 27675,34643 2ddrA 306 1.70e+01 1pcxA 810 1.72e+01 a.71.2.1,b.2.8.1,c.62.1.2,d.109.2.1,g.41.10.1 94497,94498,94499,94500,94501 2f15A 96 1.76e+01 2d37A 176 1.77e+01 1k55A 246 1.78e+01 e.3.1.1 68156 2atfA 200 1.78e+01 1ollA 188 1.81e+01 b.1.1.4,b.1.1.4 93313,93314 1e3uA 246 1.83e+01 1fofA e.3.1.1 42755 1gceA 364 1.94e+01 1gceA e.3.1.1 42738 1vhtA 218 1.94e+01 c.37.1.1 100700 1a7j 290 1.96e+01 1a7j c.37.1.6 31952 1rocA 155 1.99e+01 b.1.22.1 97673 1qbeA 132 2.04e+01 1qbeA d.85.1.1 40138 2b5hA 200 2.13e+01 1enxA 190 2.20e+01 1axkA b.29.1.11 24325 2pil 159 2.20e+01 2pil d.24.1.1 38376 1ay2 159 2.23e+01 2pil d.24.1.1 38377 1kqwA 134 2.28e+01 b.60.1.2 72887 1pvtA 238 2.30e+01 c.74.1.1 95189 1shdA 107 2.31e+01 1fmk d.93.1.1 40440 2aehA 369 2.31e+01 1qfmA 710 2.35e+01 1qfmA b.69.7.1,c.69.1.4 27673,34641 1h2xA 710 2.40e+01 b.69.7.1,c.69.1.4 76598,76599 1k68A 140 2.45e+01 c.23.1.1 90943 1byqA 228 2.49e+01 1yer d.122.1.1 41100 2azeA 155 2.49e+01 1mwsA 646 2.50e+01 d.17.4.5,d.175.1.1,e.3.1.1 79592,79593,79594 2g6fX 59 2.51e+01 1h2wA 710 2.55e+01 b.69.7.1,c.69.1.4 76596,76597 1ujmA 342 2.56e+01 1ryp2 233 2.58e+01 1ryp2 1j58A 385 2.63e+01 b.82.1.2 71531 2bltA 361 2.66e+01 1gceA e.3.1.1 42739 1y1pA 342 2.66e+01 1cbs 137 2.74e+01 1hmt b.60.1.2 27201 1pguA 615 2.76e+01 b.69.4.1,b.69.4.1 88069,88070 1eqnA 321 2.80e+01 1dd9A e.13.1.1 43256 1ywxA 102 2.82e+01 1xypA 190 2.83e+01 1axkA b.29.1.11 24327 1gtfA 74 2.85e+01 b.82.5.1 70460 1mhnA 59 2.85e+01 b.34.9.1 84964 1h4rA 314 2.86e+01 a.11.2.1,b.55.1.5,d.15.1.4 65616,65617,65618 2av1A 275 2.95e+01 1wi1A 126 2.98e+01 1tplA 426 3.05e+01 1ax4A c.67.1.2 34387 1yer 228 3.07e+01 1yer d.122.1.1 41101 2fo3A 125 3.09e+01 1uzxA 169 3.16e+01 d.20.1.2 100238 1ha1 184 3.28e+01 1ha1 d.58.7.1,d.58.7.1 39147,39148 1t77A 414 3.31e+01 2cr9A 139 3.32e+01 2coqA 108 3.35e+01 1xxlA 239 3.41e+01 1ofdA 1520 3.49e+01 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 1twfK 120 3.54e+01 1duzA 275 3.58e+01 1agdA b.1.1.2,d.19.1.1 20670,38224 2av7A 275 3.59e+01 1o7dE 126 3.59e+01 1vheA 373 3.61e+01 b.49.3.1,c.56.5.4 100669,100670 1quqB 121 3.64e+01 1quqB b.40.4.3 25305 1tvjA 166 3.65e+01 1m2vB 926 3.65e+01 a.71.2.1,b.2.8.1,c.62.1.2,d.109.2.1,g.41.10.1 78497,78498,78499,78500,78501 1ugiA 84 3.65e+01 1ugiA d.17.5.1 38125 1b04A 318 3.66e+01 1b04A d.142.2.2 41579 1msaA 109 3.67e+01 1b2pA b.78.1.1 27987 1bc8C 93 3.70e+01 1awcA a.4.5.21 16168 1tuhA 156 3.70e+01 d.17.4.11 107345 1dixA 208 3.71e+01 1bk7A d.124.1.1 41122 1i4fA 275 3.74e+01 1agdA b.1.1.2,d.19.1.1 61687,61688 1ta8A 332 3.75e+01 2bwrA 401 3.77e+01 1jssA 224 3.77e+01 d.129.3.2 71844 1n87A 56 3.78e+01 g.44.1.2 85390 1udiI 83 3.82e+01 1ugiA d.17.5.1 38124 1di2A 69 3.88e+01 1di2A d.50.1.1 38780 1aazA 87 3.89e+01 1aba c.47.1.1 32761 1aba 87 3.95e+01 1aba c.47.1.1 32760 1ae2 87 3.99e+01 1gvp b.40.4.7 25382 1n9lA 109 4.05e+01 d.110.3.6 85468 1wcdJ 441 4.11e+01 1eu3A 210 4.12e+01 1an8 b.40.2.2,d.15.6.1 25206,37795 1td5A 202 4.15e+01 d.110.2.2 106767 1icxA 155 4.23e+01 d.129.3.1 71191 1qawF 74 4.25e+01 1wapA b.82.5.1 28202 1lrv 244 4.26e+01 1lrv a.118.1.5 19146 1bbpA 173 4.30e+01 1bbpA b.60.1.1 27147 2a1vA 144 4.31e+01 1c0aA 585 4.36e+01 1c0aA b.40.4.1,d.74.4.1,d.104.1.1 25246,39731,40767 1ygs 234 4.43e+01 1ygs b.26.1.1 23907 1oz9A 150 4.44e+01 d.92.1.15 93808 1hmvB 440 4.50e+01 1rthA e.8.1.2 43047 1lepA 99 4.56e+01 1lepA b.35.1.1 24649 1f3uA 118 4.66e+01 1f3uA b.65.1.1 27521 1ysjA 404 4.66e+01 1v2bA 177 4.67e+01 d.107.1.2 108279 1g0uE 234 4.68e+01 d.153.1.4 41950 1vmfA 145 4.70e+01 1fzkA 274 4.70e+01 1agdA b.1.1.2,d.19.1.1 60149,60150 1pbyA 489 4.71e+01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 94417,94418,94419,94420,94421 2fggA 101 4.73e+01 1ughI 82 4.77e+01 1ugiA d.17.5.1 38133 1lk2A 274 4.84e+01 b.1.1.2,d.19.1.1 91056,91057 1kpuA 274 4.87e+01 b.1.1.2,d.19.1.1 84456,84457 1feuA 206 4.87e+01 1feuA b.53.1.1 59801 1sjyA 159 4.87e+01 d.113.1.1 98900 1g7pA 274 4.87e+01 b.1.1.2,d.19.1.1 70153,70154 1uylA 236 4.88e+01 d.122.1.1 108147 1wvnA 82 4.88e+01 1asyA 490 4.92e+01 1b8aA b.40.4.1,d.104.1.1 25242,40763 1qwdA 177 4.93e+01 b.60.1.1 96471 1aszB 490 4.98e+01 1b8aA b.40.4.1,d.104.1.1 25241,40762 2c60A 111 5.01e+01 2eifA 136 5.02e+01 1bkb b.34.5.2,b.40.4.5 24607,25339 1lc5A 364 5.04e+01 c.67.1.1 73827 2fvgA 340 5.09e+01 2fxqA 264 5.18e+01 1j5kA 89 5.20e+01 d.51.1.1 71565 1wi6A 88 5.39e+01 2bayA 61 5.43e+01 1rowA 109 5.46e+01 b.1.11.2 97676 1a8p 258 5.62e+01 1fdr b.43.4.2,c.25.1.1 25654,31544 1y0hA 105 5.62e+01 1kit 757 5.62e+01 1kit b.29.1.8,b.29.1.8,b.68.1.1 24272,24273,27616 1dd9A 338 5.64e+01 1dd9A e.13.1.1 43254 1ddeA 338 5.73e+01 1dd9A e.13.1.1 43255 2bgcA 238 5.74e+01 1z0pA 84 5.81e+01 1sacA 204 5.88e+01 1sacA b.29.1.5 24237 1xa1A 255 5.89e+01 e.3.1.1 109529 1d8yA 605 5.91e+01 1xwl c.55.3.5,e.8.1.1 33684,42977 1r0vA 305 5.92e+01 c.52.2.1,c.52.2.1,d.75.1.1 96742,96743,96744 1at0 145 5.94e+01 1at0 b.86.1.1 28374 1ntfA 282 5.96e+01 d.151.1.2 92104 1wlpB 138 5.97e+01 1si6X 282 5.97e+01 1aquA 297 6.03e+01 1aquA c.37.1.5 31942 1q79A 514 6.03e+01 a.160.1.1,d.218.1.3,d.58.16.1 104548,104549,104550 1mjfA 281 6.06e+01 c.66.1.17 79198 1xkiA 162 6.07e+01 1y21A 282 6.08e+01 1n71A 180 6.15e+01 d.108.1.1 85370 2bitX 165 6.16e+01 1usyA 275 6.18e+01 1ox8A 107 6.18e+01 b.136.1.1 93671 2a14A 263 6.25e+01 1q3iA 214 6.26e+01 d.220.1.1 104524 1e88A 160 6.27e+01 g.14.1.2,g.14.1.2,g.27.1.1 44669,44670,44950 1r2zA 274 6.33e+01 a.156.1.2,b.113.1.1,g.39.1.8 96892,96893,96894 1i50K 120 6.40e+01 d.74.3.2 61765 1z4xA 532 6.40e+01 2fe7A 166 6.44e+01 1l1zA 274 6.51e+01 a.156.1.2,b.113.1.1,g.39.1.8 75911,75912,75913 1dioB 224 6.60e+01 1dioB c.51.3.1 33219 1rz3A 201 6.67e+01 c.37.1.6 98132 2bt9A 90 6.67e+01 1eziA 228 6.73e+01 1eyrA c.68.1.13 34512 1qy6A 274 6.76e+01 b.47.1.1 96574 2a4nA 182 6.76e+01 1mkfA 382 6.77e+01 b.116.1.1 79232 1qveA 126 6.82e+01 d.24.1.1 104594 1klnA 605 6.93e+01 1xwl c.55.3.5,e.8.1.1 33693,42986 1xdfA 157 6.97e+01 2bt6A 108 6.97e+01 1vqoB 338 6.98e+01 1eexB 224 7.01e+01 1dioB c.51.3.1 33213 2ak5A 64 7.03e+01 2fauA 341 7.12e+01 1l3kA 196 7.25e+01 d.58.7.1,d.58.7.1 73539,73540 2fnjA 226 7.28e+01 1kb0A 677 7.31e+01 a.3.1.6,b.70.1.1 68378,68379 1gvjA 146 7.32e+01 a.4.5.21 90525 1z4vA 532 7.32e+01 1mvpA 124 7.35e+01 2rspB b.50.1.1 26775 2kfnA 605 7.38e+01 1xwl c.55.3.5,e.8.1.1 33682,42975 2rspB 124 7.40e+01 2rspB b.50.1.1 26772 1pczA 191 7.40e+01 1ytbA d.129.1.1,d.129.1.1 41292,41293 2cwaA 263 7.43e+01 1fzoA 274 7.47e+01 1agdA b.1.1.2,d.19.1.1 60155,60156 1kfd 605 7.47e+01 1xwl c.55.3.5,e.8.1.1 33694,42987 1txvA 452 7.48e+01 1oz2A 331 7.54e+01 b.34.9.3,b.34.9.3,b.34.9.3 93781,93782,93783 1jl2A 156 7.56e+01 c.55.3.1 66822 1l0gA 358 7.59e+01 e.3.1.1 73400 1ukgA 252 7.61e+01 b.29.1.1 99489 1zxfA 155 7.66e+01 1xkzA 255 7.68e+01 2cwsA 237 7.74e+01 1n3oA 252 7.75e+01 b.29.1.1 79967 1ko3A 230 7.76e+01 d.157.1.1 90974 2a74A 643 7.80e+01 1lurA 339 7.83e+01 b.30.5.4 84717 1wxcA 281 7.90e+01 2cr5A 109 7.95e+01 2bvbA 137 7.95e+01 2cfxA 144 8.01e+01 1jfmA 174 8.01e+01 d.19.1.1 66640 1llnA 262 8.04e+01 d.165.1.1 84625 2a9sA 171 8.04e+01 1r8nA 185 8.07e+01 b.42.4.1 104851 1yfnA 118 8.12e+01 2ffyA 358 8.16e+01 1b87A 181 8.18e+01 1b87A d.108.1.1 40797 1wexA 104 8.19e+01 1nrkA 328 8.21e+01 b.44.2.1,d.250.1.1 92089,92090 1aotF 106 8.22e+01 1lckA d.93.1.1 40458 1gt1A 159 8.26e+01 b.60.1.1 90515 1hn2A 159 8.26e+01 b.60.1.1 65890 2gcfA 73 8.26e+01 1ywsA 82 8.27e+01 2c3nA 247 8.27e+01 1ye8A 178 8.30e+01 1yqdA 366 8.31e+01 2ffeA 311 8.32e+01 1skyB 502 8.43e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18313,26478,32358 1qgwA 76 8.53e+01 1qgwA d.184.1.1 42616 1xg0A 76 8.53e+01 2carA 196 8.67e+01 1b37A 472 8.79e+01 1b37B c.3.1.2,d.16.1.5 30389,37953 1h30A 422 8.81e+01 b.29.1.4,b.29.1.4 76604,76605 1b5qA 472 8.87e+01 1b37B c.3.1.2,d.16.1.5 30404,37968 1mwrA 646 8.95e+01 d.17.4.5,d.175.1.1,e.3.1.1 79586,79587,79588 2occG 84 8.98e+01 2occG f.23.2.1 43522 1xsoA 150 8.99e+01 1mfmA b.1.8.1 22273