# 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 1dq3A 454 1.50e-02 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1d2eA 397 2.59e-02 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25701,25741,32136 1xngA 268 2.50e-01 1kk1A 410 3.04e-01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 2bwrA 401 5.51e-01 1hfuA 503 5.59e-01 b.6.1.3,b.6.1.3,b.6.1.3 65827,65828,65829 1zvnA 99 6.32e-01 1hoe 74 7.65e-01 1hoe b.5.1.1 22833 1f6fB 210 7.72e-01 1axiB b.1.2.1,b.1.2.1 22033,22034 1yhfA 115 8.27e-01 1ok0A 74 1.00e+00 b.5.1.1 93191 1a65A 504 1.04e+00 1a65A b.6.1.3,b.6.1.3,b.6.1.3 23148,23149,23150 1zxkA 98 1.10e+00 1theA 260 1.10e+00 1theB d.3.1.1 37056 1gmyA 261 1.47e+00 d.3.1.1 76236 1nciA 110 1.61e+00 1edhA b.1.6.1 22191 1z6bA 154 1.70e+00 1eylA 186 2.08e+00 1wba b.42.4.1 25593 1umhA 184 2.11e+00 b.18.1.21 99605 1j83A 180 2.22e+00 b.18.1.12 66430 1khoA 370 2.57e+00 a.124.1.1,b.12.1.3 72489,72490 1gg4A 452 2.58e+00 1gg4A c.59.1.1,c.98.1.1,c.72.2.1 33957,58985,58986 1rzfL 213 2.83e+00 b.1.1.1,b.1.1.2 98152,98153 1sz6B 263 2.98e+00 1ca1 370 3.16e+00 1ca1 a.124.1.1,b.12.1.3 19340,23648 1tul 108 3.22e+00 1tul b.85.5.1 28373 1qmeA 702 3.31e+00 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37487,37488,42560,42769 1h09A 338 3.37e+00 b.109.1.1,c.1.8.8 83420,83421 1pmzA 86 3.40e+00 a.39.1.10 104195 1el5A 389 3.49e+00 1b3mA c.3.1.2,d.16.1.3 30369,37937 1lkdA 297 3.51e+00 d.32.1.3,d.32.1.3 78059,78060 1han 297 3.73e+00 1han d.32.1.3,d.32.1.3 38506,38507 1qwrA 319 3.80e+00 b.82.1.3 96491 2gpzA 111 4.08e+00 1yhpA 212 4.36e+00 1s0uA 408 5.01e+00 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 1sznA 417 5.16e+00 b.71.1.1,c.1.8.1 106162,106163 1dg6A 191 5.23e+00 1d4vB b.22.1.1 23883 1gpmA 525 5.47e+00 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 2cokA 113 5.55e+00 1vr8A 142 5.60e+00 1jmcA 246 5.86e+00 1jmcA b.40.4.3,b.40.4.3 25300,25301 1wh0A 134 6.03e+00 1t9fA 187 6.17e+00 b.42.6.1 106710 1f5aA 513 6.97e+00 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39337,75835,75836 1ut1A 148 7.11e+00 b.2.3.6 108014 1hq3D 103 7.12e+00 1aoiB a.22.1.1 16464 1tzyD 103 7.12e+00 a.22.1.1 107533 1tlyA 278 7.29e+00 f.4.6.1 107143 1q79A 514 7.79e+00 a.160.1.1,d.218.1.3,d.58.16.1 104548,104549,104550 1kx5B 102 7.94e+00 a.22.1.1 77594 1io1A 398 8.61e+00 1io1A e.32.1.1 62611 2brcA 214 8.67e+00 1wckA 220 8.77e+00 2breA 219 8.97e+00 1f3lA 321 9.08e+00 1g6q2 c.66.1.6 59630 1j9bA 141 9.24e+00 c.47.1.12 66459 1s3cA 141 9.25e+00 1xe1A 116 9.48e+00 b.43.3.1 109571 1psuA 140 9.85e+00 d.38.1.5 88285 1ax0 239 1.00e+01 1led b.29.1.1 24042 1o6sB 105 1.02e+01 b.1.6.1 81096 1pov1 302 1.03e+01 1pov1 2fs2A 151 1.04e+01 1iloA 77 1.09e+01 c.47.1.1 66205 2fimA 276 1.10e+01 1sh0A 510 1.10e+01 e.8.1.4 98876 1xnkA 196 1.13e+01 2b43A 526 1.14e+01 1widA 130 1.16e+01 1v04A 355 1.16e+01 b.68.6.2 100240 2eifA 136 1.17e+01 1bkb b.34.5.2,b.40.4.5 24607,25339 1q9jA 422 1.20e+01 c.43.1.2,c.43.1.2 104590,104591 1yruA 364 1.21e+01 1m6yA 301 1.23e+01 a.60.13.1,c.66.1.23 78716,78717 2fhxA 246 1.29e+01 1ylnA 252 1.30e+01 2aehA 369 1.34e+01 1hxs1 302 1.38e+01 1ih8A 271 1.42e+01 2nsyA c.26.2.1 62377 1ifrA 121 1.44e+01 b.1.16.1 71203 2fcbA 173 1.44e+01 2fcbA b.1.1.4,b.1.1.4 21781,21782 1suwA 249 1.45e+01 e.52.1.1 106027 2cw8A 537 1.47e+01 1zxfA 155 1.48e+01 1bb8 71 1.50e+01 2bb8 d.10.1.1 37478 1ofdA 1520 1.53e+01 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 1ha3A 405 1.54e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 1pu5A 164 1.57e+01 b.95.1.1 104310 1g13A 162 1.60e+01 1g13A b.95.1.1 60194 1ah6 220 1.61e+01 1yer d.122.1.1 41094 1obpA 159 1.69e+01 1obpA b.60.1.1 27092 1gt1A 159 1.70e+01 b.60.1.1 90515 1m2tB 263 1.70e+01 b.42.2.1,b.42.2.1 84762,84763 1hn2A 159 1.70e+01 b.60.1.1 65890 1h1aA 191 1.75e+01 b.29.1.11 83450 1bkb 136 1.82e+01 1bkb b.34.5.2,b.40.4.5 24609,25341 1vj2A 126 1.89e+01 b.82.1.10 100796 1kqpA 271 1.93e+01 c.26.2.1 72883 1zljA 78 1.94e+01 2a2pA 129 1.95e+01 1exrA 148 1.97e+01 1cll a.39.1.5 17299 1q7hA 153 1.99e+01 b.122.1.1,d.17.6.2 96042,96043 1z4xA 532 2.01e+01 1rl2A 137 2.01e+01 1rl2A b.34.5.3,b.40.4.5 24610,25342 1vqoE 178 2.01e+01 1x8hA 228 2.02e+01 1yruB 74 2.04e+01 1wdcC 156 2.07e+01 1wdcC a.39.1.5 17317 2av9A 147 2.10e+01 1g1kA 143 2.10e+01 1aohA b.2.2.2 22404 1nlqA 108 2.13e+01 b.121.3.1 85853 1vk3A 615 2.13e+01 d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 100846,100847,100848,100849 2d4qA 257 2.15e+01 1zkiA 133 2.18e+01 1gppA 237 2.18e+01 b.86.1.2 76262 1z4vA 532 2.18e+01 1tif 78 2.19e+01 1tif d.15.8.1 37836 1n4xH 120 2.19e+01 b.1.1.1 85324 1z0sA 278 2.19e+01 1jpyA 137 2.25e+01 g.17.1.6 67065 2c78A 405 2.32e+01 1uebA 184 2.34e+01 b.34.5.2,b.40.4.5,b.40.4.5 107782,107783,107784 1v6tA 255 2.34e+01 1jnyA 435 2.37e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1jenA 267 2.40e+01 1jenA 1m2xA 223 2.42e+01 d.157.1.1 84764 1yrtA 364 2.43e+01 2bl0C 142 2.43e+01 2ew2A 316 2.43e+01 2al6A 375 2.45e+01 2g1lA 104 2.49e+01 1jj2E 177 2.57e+01 1ffk1 d.141.1.1,d.141.1.1 63089,63090 1smlA 269 2.61e+01 1smlA d.157.1.1 42053 1l1jA 239 2.75e+01 b.47.1.1 84516 1sacA 204 2.76e+01 1sacA b.29.1.5 24237 1u1zA 168 2.79e+01 d.38.1.6 107602 2f3yA 148 2.79e+01 2aioA 269 2.85e+01 1wy5A 317 2.88e+01 1sy6A 204 2.89e+01 b.1.1.4,b.1.1.4 106111,106112 1gzwA 134 2.90e+01 b.29.1.3 90535 1gzcA 239 2.92e+01 b.29.1.1 70803 1u3oA 82 2.95e+01 1dyoA 160 2.96e+01 1dyoA b.18.1.7 23771 1q87A 221 2.97e+01 e.47.1.1 96192 1qo3C 137 3.01e+01 1qo3C d.169.1.1 42350 2f4lA 297 3.02e+01 1fvuB 125 3.05e+01 1ixxB d.169.1.1 42346 1iq6A 134 3.08e+01 d.38.1.4 76755 1mpp 361 3.12e+01 2rmpA b.50.1.2 26856 1uv6A 210 3.16e+01 b.96.1.1 100030 1mspA 126 3.20e+01 1mspA b.1.11.2 22333 1h9sA 140 3.28e+01 1b9mA b.40.6.2,b.40.6.2 60843,60844 2axwA 134 3.30e+01 1b8oA 284 3.31e+01 1b8oA c.56.2.1 33762 2crvA 120 3.33e+01 2cyeA 133 3.44e+01 1b8kA 119 3.45e+01 1bndA g.17.1.3 44795 1xfxO 149 3.47e+01 1uaiA 224 3.48e+01 b.29.1.18 107761 1z2nX 324 3.49e+01 1wpnA 188 3.51e+01 1opoA 348 3.51e+01 b.121.4.7 87240 1xer 103 3.54e+01 1xer d.58.1.3 38990 2b3nA 159 3.56e+01 1wbiA 129 3.56e+01 2bh8A 101 3.56e+01 1k2yX 463 3.57e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 1p5dX 463 3.59e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1g4yR 148 3.61e+01 1cll a.39.1.5 60252 1qh7A 207 3.65e+01 1axkA b.29.1.11 24317 1ux2A 212 3.73e+01 b.96.1.1 100132 1h4gA 207 3.77e+01 b.29.1.11 70863 1qlpA 394 3.78e+01 1ovaA e.1.1.1 42628 1cd9B 215 3.80e+01 1cto b.1.2.1,b.1.2.1 22041,22042 1oaqL 120 3.82e+01 b.1.1.1 92708 1yu0A 381 3.83e+01 2g76A 335 3.84e+01 2fytA 340 3.85e+01 1ojjA 402 3.89e+01 b.29.1.10 93130 1sltA 134 3.90e+01 1c1lA b.29.1.3 24186 1ygaA 342 3.90e+01 2bkdN 134 3.92e+01 1y9qA 192 3.96e+01 1o91A 178 3.97e+01 b.22.1.1 92656 1quqB 121 3.97e+01 1quqB b.40.4.3 25305 1wlnA 120 4.02e+01 1nn6A 228 4.06e+01 b.47.1.2 85893 1ryiA 382 4.06e+01 1avsA 90 4.08e+01 1cll a.39.1.5 17226 2ak5A 64 4.12e+01 1v8hA 107 4.12e+01 1vdeA 454 4.21e+01 1vdeA b.86.1.2,d.95.2.2,d.95.2.2 28378,40581,40582 1cqxA 403 4.21e+01 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 1zkpA 268 4.26e+01 1odkA 235 4.28e+01 c.56.2.1 86863 1lucB 324 4.28e+01 1lucA c.1.16.1 29548 1faoA 126 4.29e+01 1faoA b.55.1.1 26974 2gjgA 248 4.30e+01 1neu 124 4.37e+01 1neu b.1.1.1 19704 1p5hA 428 4.38e+01 c.123.1.1 87802 1jjeA 222 4.38e+01 1a7tA d.157.1.1 63117 1v5wA 343 4.38e+01 c.37.1.11 108387 1wruA 379 4.39e+01 1dazC 99 4.41e+01 1hvc b.50.1.1 26501 1z9lA 128 4.43e+01 1ecfA 504 4.45e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 1shwB 181 4.46e+01 b.18.1.4 105563 1nezG 128 4.46e+01 b.1.1.1 85592 1cid 177 4.49e+01 1cid b.1.1.1,b.1.1.3 19740,21679 1n26A 325 4.51e+01 b.1.1.4,b.1.2.1,b.1.2.1 79850,79851,79852 1i9bA 217 4.54e+01 1i9bA b.96.1.1 62084 1tvxA 75 4.55e+01 1tvxA d.9.1.1 37441 1xnzA 264 4.58e+01 1avwB 171 4.58e+01 1wba b.42.4.1 25599 1yhtA 367 4.62e+01 2bbkH 355 4.64e+01 2bbkH b.69.2.1 27634 1uw6A 211 4.65e+01 b.96.1.1 100079 1pne 140 4.66e+01 1pne d.110.1.1 40866 1bjmA 216 4.69e+01 8fabA b.1.1.1,b.1.1.2 20524,21460 1ixlA 131 4.72e+01 d.38.1.5 90717 1ogsA 497 4.74e+01 b.71.1.2,c.1.8.3 86997,86998 2absA 383 4.80e+01 1x0tA 120 4.84e+01 1fr3A 67 4.88e+01 1fr3A b.40.6.1 25436 1yb3A 175 4.91e+01 1yu2A 381 4.91e+01 1xl3C 92 4.97e+01 1tjyA 316 4.98e+01 c.93.1.1 107062 1exmA 405 5.02e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 1dymA 402 5.03e+01 1celA b.29.1.10 24304 1tbuA 118 5.11e+01 1uylA 236 5.23e+01 d.122.1.1 108147 1yu1A 381 5.23e+01 1c24A 263 5.24e+01 1c24A d.127.1.1 41148 1zxq 192 5.25e+01 1zxq b.1.1.3,b.1.1.4 21657,21693 1zkkA 167 5.26e+01 8fabA 212 5.32e+01 8fabA b.1.1.1,b.1.1.2 19772,20882 2bc4A 211 5.34e+01 1nr0A 611 5.34e+01 b.69.4.1,b.69.4.1 86078,86079 1t7lA 766 5.39e+01 2blnA 305 5.40e+01 2g6fX 59 5.41e+01 1afb1 154 5.42e+01 1rtm1 2bynA 227 5.44e+01 1pvc1 301 5.46e+01 1pov1 1oivA 191 5.48e+01 c.37.1.8 93076 1t82A 155 5.52e+01 d.38.1.5 106639 1w6nA 134 5.58e+01 1ebdC 41 5.60e+01 1ebdC a.9.1.1 16355 1zczA 464 5.68e+01 1wdcB 156 5.69e+01 1wdcB a.39.1.5 17302 1yu4A 381 5.73e+01 2asuB 234 5.74e+01 1byqA 228 5.75e+01 1yer d.122.1.1 41100 2bypA 214 5.83e+01 1lbvA 252 5.85e+01 e.7.1.1 73813 1oalA 151 5.85e+01 b.1.8.1 86739 1nw3A 416 5.86e+01 c.66.1.31 86288 1s72E 178 5.86e+01 d.141.1.1,d.141.1.1 105323,105324 1mfa 247 5.88e+01 1mfa b.1.1.1,b.1.1.1 19888,19889 1w24A 182 5.89e+01 2bgoA 140 5.93e+01 1m07A 111 5.94e+01 d.5.1.1 78328 1ts9A 102 6.06e+01 1zotA 358 6.07e+01 1ng4A 390 6.11e+01 c.3.1.2,d.16.1.3 85666,85667 1qw1A 121 6.14e+01 2azqA 311 6.20e+01 1hq0A 295 6.20e+01 1hzgA d.194.1.1 61122 2d13A 227 6.20e+01 1yu3A 381 6.21e+01 1lktA 104 6.33e+01 1lktA b.90.1.1 28398 1rcwA 231 6.34e+01 a.132.1.4 97299 1tltA 319 6.38e+01 c.2.1.3,d.81.1.5 107135,107136 1ukgA 252 6.46e+01 b.29.1.1 99489 1viaA 175 6.47e+01 c.37.1.2 100754 1g8iA 190 6.49e+01 1rec a.39.1.5 60363 1epwA 1290 6.50e+01 b.29.1.6,b.42.4.2,d.92.1.7,h.4.2.1 24269,25614,40305,45785 1jalA 363 6.51e+01 c.37.1.8,d.15.10.2 84138,84139 2cvhA 220 6.52e+01 1fs0E 138 6.54e+01 1aqt a.2.10.1,b.93.1.1 59997,59998 1ru8A 232 6.59e+01 c.26.2.1 97849 2ag4A 164 6.61e+01 1ebfA 358 6.65e+01 1ebuA c.2.1.3,d.81.1.2 30033,39948 1w85I 49 6.66e+01 1rkqA 282 6.69e+01 c.108.1.10 97621 1xzoA 174 6.76e+01 1p9bA 442 6.78e+01 c.37.1.10 94385 1fftB 315 6.80e+01 1cyx b.6.1.2,f.17.2.1 23025,43628 1g3kA 174 6.81e+01 1nedA d.153.1.4 41989 1w2tA 432 6.88e+01 1sb2A 133 6.90e+01 1r6vA 671 6.91e+01 2pil 159 6.92e+01 2pil d.24.1.1 38376 1kskA 234 6.93e+01 d.66.1.5,d.265.1.3 72920,90389 1oxsC 353 7.06e+01 b.40.6.3,c.37.1.12 87519,87520 1bqhG 129 7.06e+01 1cd8 b.1.1.1 19715 1nxmA 197 7.11e+01 b.82.1.1 86385 1vrmA 325 7.18e+01 2bz8A 58 7.21e+01 1i9gA 280 7.22e+01 c.66.1.13 62090 1tp5A 119 7.23e+01 1l1eA 287 7.26e+01 c.66.1.18 73454 1lfo 128 7.31e+01 1hmt b.60.1.2 27223 1jg1A 235 7.33e+01 c.66.1.7 66661 1f60A 458 7.35e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 1pguA 615 7.41e+01 b.69.4.1,b.69.4.1 88069,88070 2f9lA 199 7.44e+01 1k9uA 78 7.47e+01 a.39.1.10 84348 1vsrA 136 7.50e+01 1vsrA c.52.1.15 33332 1vzyA 291 7.51e+01 1n7eA 97 7.55e+01 b.36.1.1 91691 1lvmA 229 7.55e+01 b.47.1.3 78243 2ck3D 482 7.55e+01 1s55A 156 7.56e+01 1qpxA 218 7.58e+01 1qpxA b.1.11.1,b.7.2.1 22318,23200 2mev1 277 7.60e+01 2mev1 1njkA 156 7.70e+01 d.38.1.1 85818 1i8aA 189 7.71e+01 1i82A b.1.9.2 61951 2a7mA 250 7.74e+01 1mkaA 171 7.77e+01 1mkaA d.38.1.2 38543 1ayoA 130 7.81e+01 1ayoA b.2.4.1 22431 2c5qA 240 7.81e+01 1bymA 97 7.85e+01 1bi0 b.34.1.2 24458 2d1eA 248 7.96e+01 1oxxK 353 7.99e+01 b.40.6.3,c.37.1.12 93715,93716 1o4tA 133 8.01e+01 b.82.1.9 86622 1pk6B 132 8.04e+01 b.22.1.1 94802 1jjtA 228 8.05e+01 1a7tA d.157.1.1 63139 1a12A 413 8.06e+01 1a12A b.69.5.1 27663 1z54A 132 8.09e+01 1jl0A 334 8.13e+01 1jenA d.156.1.1 63155 1mdaH 368 8.16e+01 2bbkH b.69.2.1 27637 1iqaA 160 8.24e+01 b.22.1.1 71274 1z47A 355 8.25e+01 2mspA 126 8.25e+01 1mspA b.1.11.2 22335 1h05A 146 8.26e+01 c.23.13.1 76433 1wluA 136 8.28e+01 1kb0A 677 8.29e+01 a.3.1.6,b.70.1.1 68378,68379 1jmtA 104 8.35e+01 d.58.7.3 63180 1m4lA 307 8.39e+01 c.56.5.1 78604 1l0wA 580 8.42e+01 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1cv8 174 8.47e+01 1cv8 d.3.1.1 37089 1xrsA 516 8.50e+01 1e8cA 498 8.53e+01 c.98.1.1,c.59.1.1,c.72.2.1 59377,59378,59379 1q8iA 783 8.54e+01 c.55.3.5,e.8.1.1 96208,96209 2abwA 227 8.57e+01 1e79D 482 8.64e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 18272,26437,32317 1e8pA 46 8.67e+01 g.55.1.1 59385 1wdtA 665 8.68e+01 1lvwA 295 8.69e+01 c.68.1.6 84723 1t5jA 313 8.79e+01 a.209.1.1 99125 1jhfA 202 8.80e+01 a.4.5.2,b.87.1.1 63057,63058 1khbA 625 8.85e+01 c.91.1.1,c.109.1.1 68606,68607 1t77A 414 8.97e+01