# List of top-scoring protein chains for t04-100-40-40-str2+CB_burial_14_7-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 1na3A 91 9.97e-03 k.38.1.1 85481 2avpA 70 1.00e-02 1elwA 118 1.18e-02 1a17 a.118.8.1 19207 1hz4A 373 2.02e-02 a.118.8.2 65960 2fbnA 198 2.20e-02 2fxaA 207 3.99e-02 1ihgA 370 5.94e-02 2cpl a.118.8.1,b.62.1.1 62380,62381 2ff4A 388 1.50e-01 1elrA 131 2.14e-01 1a17 a.118.8.1 19209 1wfdA 93 2.94e-01 1a17 166 3.05e-01 1a17 a.118.8.1 19206 1hh8A 213 3.34e-01 1e96B a.118.8.1 61042 1i1iP 681 3.69e-01 1i1iP d.92.1.5 40297 1s3jA 155 4.57e-01 a.4.5.28 98437 1wm5A 208 5.13e-01 2ethA 154 8.49e-01 1ydiA 263 1.05e+00 1nktA 922 1.16e+00 a.162.1.1,a.172.1.1,c.37.1.19,c.37.1.19 85830,85831,85832,85833 1zejA 293 1.27e+00 1wy6A 172 1.32e+00 1nznA 126 1.47e+00 a.118.8.1 92382 1top 162 1.88e+00 1ncx a.39.1.5 17223 1oshA 232 2.01e+00 a.123.1.1 93496 2a61A 145 2.23e+00 1w36B 1180 2.53e+00 1aisB 200 2.53e+00 1aisB a.74.1.2,a.74.1.2 18384,18385 1lfpA 249 2.55e+00 e.39.1.1 73885 1xkpC 143 2.76e+00 1pme 380 2.86e+00 1hcl d.144.1.7 41653 1f7uA 607 3.26e+00 1bs2A a.27.1.1,c.26.1.1,d.67.2.1 59673,59674,59675 1zybA 232 3.27e+00 1rkeA 262 3.38e+00 a.24.9.1,a.24.9.1 97608,97609 2ex5A 207 3.41e+00 1xnfA 275 3.60e+00 1tujA 123 3.71e+00 1qqeA 292 4.01e+00 1qqeA a.118.8.1 19210 1hhsA 664 4.05e+00 1hi0P e.8.1.6 61045 1zvzA 279 4.13e+00 1bkdS 439 4.46e+00 1bkdS a.117.1.1 19111 2f3yA 148 4.67e+00 1dvoA 152 4.67e+00 1dvoA a.136.1.1 19623 1uvjA 664 4.89e+00 e.8.1.6 100045 1liiA 363 5.00e+00 c.72.1.1 73921 1hb6A 86 5.37e+00 a.11.1.1 70959 1t01A 255 5.58e+00 a.24.9.1,a.24.9.1 106188,106189 1wf3A 301 5.86e+00 1yt3A 375 6.24e+00 1dc1A 323 6.48e+00 1dc1A c.52.1.11 33321 2awiA 317 6.57e+00 1f6fA 199 7.08e+00 1f6fA a.26.1.1 16839 1tf5A 844 7.09e+00 a.162.1.1,a.172.1.1,c.37.1.19,c.37.1.19 106834,106835,106836,106837 1w79A 489 7.85e+00 1bif 469 7.92e+00 1bif c.37.1.7,c.60.1.4 31961,34003 1yzxA 226 8.08e+00 2absA 383 8.20e+00 1vdyA 140 8.59e+00 2fldA 165 9.24e+00 2fnaA 357 9.48e+00 3erk 364 9.97e+00 1hcl d.144.1.7 41654 1z91A 147 1.00e+01 1nzyA 269 1.00e+01 1nzyA c.14.1.3 30903 1sfxA 109 1.03e+01 a.4.5.50 105505 1o20A 427 1.07e+01 c.82.1.1 86556 1gpmA 525 1.07e+01 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 2g7sA 194 1.08e+01 1n0nA 199 1.08e+01 a.2.11.1,d.44.1.1 79750,79751 1evsA 187 1.08e+01 1evsA a.26.1.1 16845 2fbhA 146 1.18e+01 2ac5A 316 1.24e+01 1l3pA 102 1.25e+01 a.24.17.1 84520 2g38B 198 1.34e+01 1r9kA 172 1.35e+01 a.168.1.1 104869 1bh9B 89 1.36e+01 1bh9B a.22.1.3 16485 2gtrA 261 1.38e+01 1bx4A 345 1.38e+01 1bx4A c.72.1.1 34935 1tn6A 382 1.41e+01 1qwvA 142 1.45e+01 a.39.2.1 96506 1u9cA 224 1.45e+01 1rzsA 61 1.45e+01 a.35.1.2 105139 1v54E 109 1.46e+01 a.118.11.1 100326 1pl4A 198 1.52e+01 a.2.11.1,d.44.1.1 94854,94855 2cohA 202 1.52e+01 1qc7A 101 1.53e+01 1qc7A a.118.14.1 18456 1ltlA 279 1.58e+01 b.40.4.11 84701 1n3kA 130 1.59e+01 a.77.1.4 79965 1vkeA 133 1.62e+01 a.152.1.2 108650 1ub0A 258 1.63e+01 c.72.1.2 88394 1ap6A 198 1.67e+01 1avmA a.2.11.1,d.44.1.1 15746,38705 2g5cA 281 1.69e+01 1ic8A 194 1.71e+01 a.4.1.1,a.35.1.1 76740,76741 1odoA 408 1.71e+01 a.104.1.1 92783 2dfkA 402 1.73e+01 1dqeA 137 1.74e+01 1dqeA a.39.2.1 17388 2g7uA 257 1.76e+01 1jogA 146 1.78e+01 a.24.16.2 77142 1lj9A 144 1.79e+01 a.4.5.28 78035 1xizA 159 1.80e+01 1paqA 189 1.82e+01 a.118.1.14 94413 1wdcC 156 1.87e+01 1wdcC a.39.1.5 17317 1nrfA 262 1.89e+01 e.3.1.1 92086 2fa8A 105 1.89e+01 1r62A 160 1.94e+01 d.122.1.3 104816 1pbv 195 1.98e+01 1pbv a.118.3.1 19179 1zx4A 192 2.02e+01 1m9xC 146 2.02e+01 a.73.1.1 84907 1gvhA 396 2.02e+01 a.1.1.2,b.43.4.2,c.25.1.5 70601,70602,70603 2axyA 73 2.07e+01 2auwA 170 2.09e+01 1lvaA 258 2.16e+01 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 1vj7A 393 2.17e+01 a.211.1.1,d.218.1.8 100801,100802 1i6pA 220 2.18e+01 1ddzA c.53.2.1 61848 1w53A 84 2.18e+01 a.186.1.2 109175 1qwgA 251 2.19e+01 c.1.27.1 96473 1nmeB 92 2.21e+01 2g3bA 208 2.25e+01 1w9rA 119 2.25e+01 1nt2A 210 2.25e+01 c.66.1.3 86149 1f4qA 165 2.26e+01 1alvA a.39.1.8 17360 1d8dA 377 2.31e+01 1ft1A a.118.6.1 19185 1ux5A 411 2.33e+01 a.207.1.1 100144 1vlgA 176 2.34e+01 a.25.1.1 108816 1c7nA 399 2.36e+01 1d2fA c.67.1.3 34413 2c2aA 258 2.38e+01 1knyA 253 2.46e+01 1knyA a.24.16.1,d.218.1.1 75896,75897 2co5A 99 2.56e+01 1g8eA 116 2.60e+01 1g8eA a.145.1.1 60346 1ggzA 148 2.70e+01 a.39.1.5 70176 1s4bP 674 2.74e+01 d.92.1.5 105252 2cruA 118 2.76e+01 1nvvS 481 2.76e+01 a.117.1.1 86279 2bl0C 142 2.77e+01 2gmyA 153 2.78e+01 1cxqA 162 2.84e+01 1cxqA c.55.3.2 33621 2gd5A 179 2.85e+01 1e3aA 260 2.87e+01 1ajqA d.153.1.2 41838 1bmtA 246 2.96e+01 1bmtA a.46.1.1,c.23.6.1 17757,31235 1a6m 151 3.00e+01 1a6m a.1.1.2 15018 1ng6A 148 3.03e+01 a.182.1.1 85670 1gk9A 260 3.04e+01 d.153.1.2 65246 2g6tA 306 3.05e+01 1t98A 287 3.10e+01 1wovA 250 3.10e+01 1sqgA 429 3.14e+01 a.79.1.3,c.66.1.38 105912,105913 1miwA 404 3.19e+01 a.173.1.1,d.218.1.4 79162,79163 1bxm 99 3.19e+01 1bxm a.134.1.1 19618 1lriA 98 3.34e+01 a.134.1.1 74223 2c5uA 375 3.34e+01 2ac3A 316 3.34e+01 2d3dA 88 3.34e+01 2c6yA 111 3.36e+01 2bylA 439 3.40e+01 1nc5A 373 3.42e+01 a.102.1.6 85548 1r8mE 203 3.43e+01 a.118.3.1 97242 1iso 416 3.46e+01 1iso c.77.1.1 35065 1o0pA 104 3.46e+01 d.58.7.1 86535 2occE 109 3.58e+01 2occE a.118.11.1 19224 2gyqA 175 3.62e+01 1f08A 148 3.63e+01 1f08A d.89.1.2 59564 1jxhA 288 3.66e+01 c.72.1.2 67415 1g5cA 170 3.69e+01 1g5cA c.53.2.1 60264 2es9A 115 3.76e+01 1gvnA 90 3.77e+01 a.8.2.1 76353 3sdhA 146 3.80e+01 3sdhA a.1.1.2 14984 1gtkA 313 3.83e+01 c.94.1.1,d.50.2.1 76346,76347 1khtA 192 3.84e+01 c.37.1.1 84401 1yarA 233 3.88e+01 1wy9A 147 3.89e+01 1re9A 414 3.90e+01 9gafA 295 3.94e+01 1apyA d.153.1.5 42008 1zroA 602 3.97e+01 1qb2A 109 3.97e+01 1qb2A a.36.1.1 17125 1z7lA 276 4.00e+01 1f44A 324 4.00e+01 a.60.9.1,d.163.1.1 64982,64983 2iu1A 208 4.06e+01 1ef1A 294 4.12e+01 1ef1A a.11.2.1,b.55.1.5,d.15.1.4 16368,27003,37611 1o17A 345 4.18e+01 a.46.2.1,c.27.1.1 80765,80766 1wlmA 151 4.19e+01 1vkfA 188 4.29e+01 c.1.29.1 108656 2fq4A 192 4.30e+01 1h6pA 203 4.31e+01 a.146.1.1 60690 1fxxA 482 4.33e+01 1fxxA c.55.3.5 33726 2blkA 122 4.37e+01 1knqA 175 4.41e+01 c.37.1.17 72786 1p4kA 295 4.42e+01 d.153.1.5 87772 2f8kA 88 4.44e+01 2d9iA 96 4.45e+01 1qmqA 414 4.49e+01 1phd a.104.1.1 18907 1t33A 224 4.50e+01 a.4.1.9,a.121.1.1 106295,106296 1zclA 180 4.57e+01 1ei7A 158 4.57e+01 1rmvA a.24.5.1 16584 1or7A 194 4.59e+01 a.4.13.2,a.177.1.1 87332,87333 1oohA 126 4.60e+01 a.39.2.1 93383 2aq9A 262 4.60e+01 1t95A 240 4.63e+01 a.5.8.1,d.235.1.2,d.58.11.3 106705,106706,106707 1whxA 111 4.69e+01 1ppjF 110 4.70e+01 f.27.1.1 104262 1oxjA 173 4.76e+01 a.60.1.2,a.118.1.13 87517,87518 1txgA 335 4.77e+01 2ex4A 241 4.79e+01 1wcrA 103 4.92e+01 1pb1A 416 4.94e+01 c.77.1.1 88014 1yemA 179 5.02e+01 1gzsB 165 5.03e+01 a.168.1.1 76425 2crbA 97 5.05e+01 1f9yA 158 5.05e+01 d.58.30.1 83249 1s0aA 429 5.13e+01 c.67.1.4 98263 1qgiA 259 5.17e+01 1qgiA d.2.1.7 37001 1v1aA 309 5.20e+01 c.72.1.1 100249 2d2yA 145 5.20e+01 1repC 251 5.23e+01 1repC a.4.5.10,a.4.5.10 16125,16126 1nz6A 101 5.24e+01 a.2.3.1 86441 1xfuA 747 5.24e+01 1mvfD 82 5.30e+01 b.129.1.1 85143 1u55A 188 5.34e+01 d.278.1.1 107677 1wxiA 275 5.35e+01 1z3iX 644 5.35e+01 1k78A 149 5.36e+01 a.4.1.5,a.4.1.5 68255,68256 1iw0A 215 5.42e+01 a.132.1.1 83720 1zip 217 5.46e+01 1zin c.37.1.1,g.41.2.1 31916,45179 1rec 201 5.58e+01 1rec a.39.1.5 17326 1eqoA 158 5.58e+01 1hka 1v38A 78 5.62e+01 a.60.1.2 100280 1w7jB 151 5.63e+01 1lw1A 177 5.64e+01 a.152.1.1 74290 1zin 217 5.65e+01 1zin c.37.1.1,g.41.2.1 31915,45178 2ge3A 170 5.66e+01 1c3cA 429 5.70e+01 1c3cA a.127.1.1 19425 1qj5A 429 5.79e+01 1dtyA c.67.1.4 34493 2c46A 241 5.80e+01 1epwA 1290 5.82e+01 b.29.1.6,b.42.4.2,d.92.1.7,h.4.2.1 24269,25614,40305,45785 1ekjA 221 5.83e+01 1ekjB c.53.2.1 33364 1p9qC 256 5.86e+01 a.5.8.1,d.235.1.2,d.58.11.3 104093,104094,104095 1auiB 169 5.89e+01 1auiB a.39.1.5 17325 2gviA 204 5.93e+01 1jgsA 138 5.97e+01 a.4.5.28 66683 1t07A 94 5.99e+01 d.279.1.1 106196 1b24A 188 6.00e+01 1b24A d.95.2.1,d.95.2.1 40573,40574 1uhkA 191 6.00e+01 2aibA 98 6.07e+01 1vsd 152 6.07e+01 1cxqA c.55.3.2 33625 1us7B 265 6.07e+01 a.205.1.1 99858 1bt3A 345 6.09e+01 1bt3A a.86.1.2 18507 1y97A 238 6.09e+01 1pxvA 183 6.12e+01 d.3.1.1 95301 1v4aA 440 6.12e+01 a.24.16.4,d.218.1.9 108350,108351 2a6hE 99 6.16e+01 2abk 211 6.17e+01 2abk a.96.1.1 18743 2aexA 346 6.22e+01 1umnA 165 6.33e+01 a.25.1.1 99607 1wiwA 290 6.34e+01 1yx4A 132 6.35e+01 1wtyA 119 6.38e+01 2cwcA 303 6.40e+01 1tvoA 368 6.42e+01 1i9sA 210 6.46e+01 1i9sA c.45.1.1 62099 1mla 309 6.50e+01 1mla c.19.1.1,d.58.23.1 31031,39383 1tn4 159 6.50e+01 1ncx a.39.1.5 17248 1rwyA 109 6.52e+01 a.39.1.4 98002 1v4xB 146 6.57e+01 a.1.1.2 108364 1lxa 262 6.59e+01 1lxa b.81.1.1 28052 1kkcA 221 6.59e+01 a.2.11.1,d.44.1.1 68660,68661 2ewcA 126 6.65e+01 1v4eA 299 6.68e+01 a.128.1.1 100296 1ockA 412 6.71e+01 c.117.1.1 86802 1ho8A 480 6.76e+01 1ho8A a.118.1.9 61107 1apmE 350 6.76e+01 1cdkA d.144.1.7 41628 1mw7A 240 6.80e+01 e.39.1.1 79557 1yfsA 465 6.82e+01 1v8fA 276 6.84e+01 c.26.1.4 100503 1kzfA 230 6.84e+01 d.108.1.3 73354 2ge7A 108 6.85e+01 1z6oM 191 6.85e+01 1y4hA 188 6.88e+01 1k7wA 468 6.89e+01 a.127.1.1 72130 1t1dA 100 6.93e+01 1t1dA d.42.1.2 38637 1f0jA 377 6.94e+01 1f0jA a.211.1.2 19346 1puzA 82 6.98e+01 a.218.1.1 104320 1t7lA 766 6.99e+01 1he1A 135 7.01e+01 1he1A a.24.11.1 16641 1i6xA 209 7.07e+01 a.4.5.4,b.82.3.2 83673,83674 2a0iA 330 7.12e+01 1np3A 338 7.19e+01 a.100.1.2,c.2.1.6 85946,85947 1xtpA 254 7.31e+01 1wmuB 146 7.38e+01 a.1.1.2 109417 1wbsA 360 7.39e+01 2g0dA 409 7.39e+01 2sas 185 7.41e+01 2sas a.39.1.5 17258 2anxA 146 7.41e+01 1x91A 153 7.42e+01 2gnoA 305 7.44e+01 1qm9A 198 7.44e+01 1qm9A d.58.7.1,d.58.7.1 39207,39208 1i3jA 116 7.46e+01 1i3jA d.285.1.1 61594 1ash 150 7.48e+01 1ash a.1.1.2 15622 1ppjH 78 7.51e+01 f.28.1.1 104264 2br9A 234 7.54e+01 1u3aA 189 7.56e+01 1muwA 386 7.61e+01 c.1.15.3 79495 2a6qA 86 7.64e+01 1bhdA 118 7.77e+01 1bkrA a.40.1.1 17398 1n81A 186 7.78e+01 a.185.1.1 85388 2f1sA 186 7.87e+01 1f8mA 429 7.88e+01 1dquA c.1.12.7 29315 1wp1A 474 7.95e+01 1ia6A 441 7.98e+01 a.102.1.2 76738 1f61A 429 8.00e+01 1dquA c.1.12.7 29319 1g4yR 148 8.08e+01 1cll a.39.1.5 60252 2b3nA 159 8.10e+01 1aky 221 8.13e+01 1zin c.37.1.1,g.41.2.1 31896,45197 1ug7A 128 8.14e+01 a.24.24.1 107824 2arhA 203 8.15e+01 1r5iD 216 8.19e+01 a.202.1.1 97091 2cdcA 366 8.19e+01 1xfxO 149 8.22e+01 1ow4A 129 8.23e+01 a.39.2.1 93628 1q77A 138 8.28e+01 c.26.2.4 96023 1vefA 395 8.29e+01 1fp2A 352 8.34e+01 1fpxA a.4.5.29,c.66.1.12 59941,59942 1l0iA 78 8.34e+01 a.28.1.1 77643 1d2dA 59 8.38e+01 1r1bA a.16.1.3 16397 1rkpA 326 8.43e+01 a.211.1.2 97620 1yarO 237 8.49e+01 2f2eA 146 8.51e+01 2c4bA 143 8.52e+01 1zt2B 212 8.54e+01 1uw0A 117 8.56e+01 g.39.1.12 108063 1a41 234 8.58e+01 1a41 d.163.1.2 42174 2d0eA 407 8.61e+01 1vejA 74 8.61e+01 1r3cA 366 8.62e+01 d.144.1.7 96906 1gsoA 431 8.65e+01 1gsoA b.84.2.1,c.30.1.1,d.142.1.2 28240,31647,41492 2b6cA 220 8.73e+01 1i0aA 466 8.77e+01 1auwA a.127.1.1 61479 1wzdA 215 8.79e+01 2h1rA 299 8.83e+01 1uehA 253 8.87e+01 c.101.1.1 99259 1anf 370 8.97e+01 4mbp c.94.1.1 35776 1qqfA 277 8.97e+01 1c3d a.102.4.4 18875