# List of top-scoring protein chains for t2k-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.soe.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 3l1bA 233 6.40e-01 3kezA 461 8.22e-01 3k9vA 482 1.29e+00 2ixnA 310 1.36e+00 a.268.1.1 137777 1h6gA 256 1.54e+00 1h6gA a.24.9.1,a.24.9.1 60669,60670 2r40D 266 2.20e+00 a.123.1.1 151572 2btvA 901 2.27e+00 2btvA e.28.1.1 43376 1w2wA 211 2.87e+00 c.124.1.5 109130 2hkvA 149 2.93e+00 a.213.1.2 147306 2cwlA 302 3.12e+00 a.25.1.3 130927 1nv8A 284 3.85e+00 c.66.1.30 86224 2dpmA 284 4.04e+00 2dpmA c.66.1.28 34246 3dkaA 155 4.04e+00 1oshA 232 4.45e+00 a.123.1.1 93496 2f8lA 344 4.68e+00 c.66.1.45 133132 2v8tA 302 4.72e+00 1ymtA 246 5.07e+00 2pvqA 201 5.54e+00 3c8tA 451 5.95e+00 1mqvA 125 6.50e+00 a.24.3.2 79415 2j9wA 102 6.53e+00 1huw 166 6.78e+00 1huw 1p2xA 159 6.91e+00 a.40.1.1 104062 1d0yA 761 7.59e+00 1lvk b.34.3.1,c.37.1.9 24581,32178 3fxvA 233 7.63e+00 1s2xA 206 7.77e+00 a.47.3.1 105229 3enbA 222 7.87e+00 c.55.3.14 158189 3ejnA 474 8.30e+00 a.118.8.6 158180 2ntoA 201 8.55e+00 3ipiA 295 8.72e+00 3i6aA 222 8.77e+00 2wa5A 245 8.80e+00 1izmA 184 8.83e+00 a.199.1.1 90725 1g8xA 1010 9.55e+00 1lvk k.1.1.1 46378 2vl7A 540 9.70e+00 2fwtA 125 9.87e+00 3kraB 274 1.03e+01 1gv3A 248 1.04e+01 a.2.11.1,d.44.1.1 70585,70586 3gahA 194 1.09e+01 1cqxA 403 1.13e+01 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 1lvk 762 1.14e+01 1lvk 2o18A 340 1.15e+01 2okuA 131 1.16e+01 a.48.5.1 148809 3eqxA 373 1.20e+01 3mykX 762 1.21e+01 1otvA 259 1.23e+01 a.132.1.4 93526 1gseA 221 1.23e+01 1pgtA a.45.1.1,c.47.1.5 17667,32961 3h7nA 729 1.25e+01 3msuA 427 1.29e+01 3f5cB 268 1.32e+01 2nt8A 223 1.32e+01 2akaA 776 1.34e+01 1k3yA 221 1.35e+01 a.45.1.1,c.47.1.5 77245,77246 2gm6A 208 1.38e+01 b.82.1.19 147130 2gscA 128 1.42e+01 a.29.16.1 147169 3gaiA 194 1.43e+01 2of3A 266 1.45e+01 1jfgA 374 1.46e+01 a.128.1.5 66636 2cb5A 453 1.48e+01 3gcb d.3.1.1 37035 1wy1A 172 1.51e+01 2lbd 267 1.52e+01 2lbd 2k2vA 126 1.52e+01 3ci3A 194 1.58e+01 1fkmA 396 1.59e+01 1fkmA a.69.2.1,a.69.2.1 18315,18316 2pvpA 367 1.60e+01 1a7vA 125 1.67e+01 1cpq a.24.3.2 16562 3l6xA 584 1.67e+01 1vrmA 325 1.68e+01 d.96.2.1 120472 3mzoA 216 1.69e+01 3f3fC 570 1.69e+01 1xuqA 212 1.70e+01 2ot3A 274 1.71e+01 a.222.1.1 139311 1p5sA 203 1.77e+01 a.40.1.1 94147 1i45A 248 1.84e+01 1amk c.1.1.1 61665 3jq1A 481 1.85e+01 3hgtA 328 1.86e+01 3dzvA 273 1.86e+01 2yrnA 129 1.90e+01 3c7jA 237 1.94e+01 1i5pA 633 1.97e+01 1i5pA b.18.1.3,b.77.2.1,f.1.3.1 61817,61818,61819 1z47A 355 1.98e+01 1rp4A 389 1.99e+01 a.227.1.1 105027 2dkyA 91 2.06e+01 a.60.1.3 146539 2rekA 199 2.10e+01 2bkhA 814 2.15e+01 2jjnA 411 2.16e+01 3cbuA 214 2.16e+01 2okcA 445 2.18e+01 c.66.1.45 148801 1vplA 256 2.20e+01 c.37.1.12 113966 3hc5A 232 2.27e+01 2ce0A 105 2.29e+01 1ztsA 139 2.29e+01 3gytA 244 2.30e+01 3hy0A 441 2.31e+01 1u2zA 433 2.32e+01 c.66.1.31 107626 1dhpA 292 2.36e+01 1dhpA c.1.10.1 29097 2igsA 219 2.37e+01 d.2.1.11 147659 1txuA 273 2.38e+01 a.222.1.1 107439 3dlsA 335 2.39e+01 2atsA 292 2.39e+01 c.1.10.1 127306 2rauA 354 2.42e+01 3i4gA 528 2.49e+01 1ps1A 337 2.50e+01 1ps1A a.128.1.4 19450 2a6lA 292 2.54e+01 c.1.10.1 126285 2ojpA 292 2.55e+01 3abdA 227 2.61e+01 2ps5A 374 2.62e+01 1wymA 155 2.62e+01 1kiyA 374 2.63e+01 a.128.1.5 72555 2ez6A 221 2.69e+01 a.149.1.1,d.50.1.1 132616,132617 3eweB 564 2.72e+01 1d2eA 397 2.77e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25701,25741,32136 3gwjA 674 2.86e+01 1gxqA 106 2.93e+01 a.4.6.1 70721 3l55A 353 2.93e+01 1j8yF 297 2.97e+01 1ng1 a.24.13.1,c.37.1.10 62747,62748 2purA 292 3.00e+01 1sceA 112 3.04e+01 1puc d.97.1.1 40676 3abbA 408 3.05e+01 2v26A 784 3.05e+01 1rtwA 220 3.08e+01 a.132.1.3 97823 1o5xA 248 3.08e+01 c.1.1.1 92528 2qw5A 335 3.08e+01 1gvhA 396 3.12e+01 a.1.1.2,b.43.4.2,c.25.1.5 70601,70602,70603 2x1gF 971 3.13e+01 3iopA 312 3.17e+01 1ej6D 418 3.19e+01 i.7.1.1 45970 1vj7A 393 3.20e+01 a.211.1.1,d.218.1.8 100801,100802 2aelA 374 3.21e+01 1j8mF 297 3.24e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 2p3nA 256 3.28e+01 1wa5C 960 3.31e+01 a.118.1.1 114433 3gd2A 229 3.32e+01 1l2tA 235 3.32e+01 c.37.1.12 73514 2qk1A 249 3.38e+01 1jd1A 129 3.40e+01 1qu9A d.79.1.1 62890 1dlwA 116 3.48e+01 1dlyA a.1.1.1 14982 3kh1A 200 3.49e+01 1svcP 365 3.49e+01 1a3qA b.1.18.1,b.2.5.3 21924,22443 2qgsA 225 3.53e+01 a.211.1.1 150782 3bmxA 642 3.55e+01 3iv3A 332 3.57e+01 3ed3A 298 3.62e+01 1au1A 166 3.64e+01 1ifa a.26.1.3 16889 2p0pA 126 3.69e+01 3h9oA 311 3.70e+01 1fcyA 236 3.75e+01 2lbd a.123.1.1 19282 3fvqA 359 3.75e+01 2aqjA 538 3.80e+01 2db0A 253 3.85e+01 2jdiD 482 3.86e+01 a.69.1.1,b.49.1.1,c.37.1.11 138263,138264,138265 2a6nA 292 3.88e+01 c.1.10.1 126289 3lewA 495 3.89e+01 1kblA 873 3.89e+01 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 3gajA 187 3.93e+01 3cqvA 199 3.95e+01 1wy0A 342 3.98e+01 3dbyA 269 4.06e+01 a.29.13.1,a.29.13.1 157486,157487 1dik 874 4.13e+01 1dik 1xn8A 131 4.15e+01 a.229.1.1 115577 1ypfA 336 4.22e+01 3hmlA 258 4.24e+01 2rioA 434 4.24e+01 2fulA 178 4.25e+01 2qwoB 92 4.25e+01 1zzpA 130 4.30e+01 1pg4A 652 4.32e+01 e.23.1.1 88067 2b5dX 528 4.33e+01 a.8.3.3,c.6.2.4 127886,127887 2g3kA 94 4.34e+01 a.24.28.1 134562 3b55A 451 4.34e+01 c.150.1.3 154832 1p16A 395 4.37e+01 b.40.4.6,d.142.2.3 87661,87662 1xjuA 163 4.42e+01 d.2.1.3 115394 2oikA 154 4.43e+01 d.13.1.1 148780 2ja2A 498 4.45e+01 2rcvA 202 4.48e+01 1j33A 335 4.52e+01 c.39.1.1 77069 3d3mA 168 4.52e+01 3mlgA 189 4.56e+01 3mekA 429 4.58e+01 1ymgA 263 4.58e+01 f.19.1.1 145918 2hc5A 117 4.61e+01 d.352.1.1 147255 3i24A 149 4.63e+01 2r5tA 373 4.68e+01 2gb7A 305 4.71e+01 2wcrA 159 4.74e+01 1p5qA 336 4.79e+01 a.118.8.1,d.26.1.1 104068,104069 2nugA 221 4.85e+01 a.149.1.1,d.50.1.1 148452,148453 16vpA 366 4.88e+01 16vpA d.180.1.1 42601 3m1iC 1049 4.91e+01 3hbeX 204 4.95e+01 2ex3B 264 4.98e+01 a.263.1.1 132500 1efcA 393 5.00e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25680,25720,32113 1w77A 228 5.13e+01 c.68.1.13 120679 1uu3A 310 5.17e+01 d.144.1.7 99999 2hq1A 247 5.19e+01 1howA 373 5.20e+01 1hcl d.144.1.7 41679 2awpA 198 5.20e+01 2kuaA 170 5.24e+01 2j9uA 96 5.29e+01 a.24.28.1 138155 1gm5A 780 5.30e+01 a.24.21.1,b.40.4.9,c.37.1.19,c.37.1.19 65298,65299,65300,65301 1xm5A 155 5.31e+01 d.92.1.15 115467 3hnhA 258 5.32e+01 1xx7A 184 5.35e+01 a.211.1.1 116143 1bs4A 168 5.35e+01 1bs4A d.167.1.1 42287 3f7fA 729 5.37e+01 3m5fA 244 5.44e+01 2ntxA 365 5.48e+01 2d0eA 407 5.49e+01 1vqrA 297 5.62e+01 a.211.1.3 114015 2ogiA 196 5.63e+01 1i0hA 205 5.65e+01 1avmA a.2.11.1,d.44.1.1 15760,38685 2q3mA 326 5.66e+01 c.37.1.5 139795 2fkcA 247 5.67e+01 3gi8C 444 5.70e+01 1tf5A 844 5.82e+01 a.162.1.1,a.172.1.1,c.37.1.19,c.37.1.19 106834,106835,106836,106837 3ibvA 980 5.83e+01 1sxjC 340 5.87e+01 a.80.1.1,c.37.1.20 106085,106086 2j6aA 141 5.89e+01 2gojA 197 5.89e+01 2b7uA 257 5.89e+01 1ohcA 348 5.89e+01 c.45.1.1,c.45.1.1 87009,87010 1vpqA 273 5.91e+01 c.1.32.1 113974 1ciy 590 5.92e+01 1ciy 1ciyA 590 5.92e+01 b.18.1.3,b.77.2.1,f.1.3.1 23720,27977,43392 2gsqA 202 5.96e+01 a.45.1.1,c.47.1.5 17715,33009 1d5nA 205 6.01e+01 1avmA a.2.11.1,d.44.1.1 15762,38687 2o8pA 227 6.02e+01 a.118.7.1 148679 3hhgA 306 6.05e+01 3ferA 262 6.07e+01 1neyA 247 6.09e+01 c.1.1.1 80449 2e8gA 241 6.12e+01 2btzA 394 6.16e+01 2wzkA 391 6.17e+01 1h1wA 289 6.19e+01 d.144.1.7 83460 3a6pA 1204 6.21e+01 1vyiA 112 6.21e+01 d.293.1.1 114032 3hdxA 478 6.22e+01 3dx5A 286 6.26e+01 3cucA 291 6.28e+01 1vjvA 415 6.28e+01 d.3.1.9 108632 2is6A 680 6.33e+01 2hwvA 121 6.34e+01 1n4kA 381 6.42e+01 a.118.22.1,b.42.6.1 79992,79993 1iomA 377 6.45e+01 a.103.1.1 83698 1oheA 348 6.51e+01 c.45.1.1,c.45.1.1 87013,87014 2jkcA 538 6.54e+01 3gzuA 800 6.57e+01 3d3zA 247 6.59e+01 3hxrA 761 6.60e+01 1xeoA 168 6.64e+01 d.167.1.1 121913 1jmuB 666 6.66e+01 1qqiA 104 6.70e+01 1opc a.4.6.1 16233 1p4xA 250 6.75e+01 a.4.5.28,a.4.5.28 87784,87785 3kwsA 287 6.77e+01 3ih8A 456 6.77e+01 3ls8A 614 6.92e+01 3draB 390 6.92e+01 1pqzA 238 6.94e+01 b.1.1.2,d.19.1.1 104297,104298 3dwbA 670 6.95e+01 3cq0A 339 6.97e+01 1eceA 358 6.98e+01 1eceA c.1.8.3 28813 3l8nA 202 6.99e+01 2el9A 431 7.06e+01 c.51.1.1,d.104.1.1 146887,146888 1khvA 516 7.10e+01 e.8.1.4 68627 1u2xA 474 7.17e+01 c.72.1.3 107622 2hfkA 319 7.18e+01 1efuA 385 7.18e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25682,25722,32115 2bt2A 161 7.19e+01 1uzeA 589 7.20e+01 d.92.1.5 108174 2gk9A 426 7.22e+01 3ccgA 190 7.23e+01 2qhbA 86 7.34e+01 a.4.1.3 150786 1ix9A 205 7.37e+01 a.2.11.1,d.44.1.1 76899,76900 1mhlC 466 7.37e+01 1mhlC 3lr2A 137 7.41e+01 3c1jA 424 7.45e+01 2di3A 239 7.51e+01 1fnmA 691 7.52e+01 1dar b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1,d.58.11.1 25709,32144,37546,39302,39303 2gwgA 350 7.52e+01 c.1.9.15 135805 3c4bA 265 7.53e+01 3c7lA 137 7.57e+01 1a87 321 7.58e+01 1a87 2cjlA 204 7.58e+01 2ganA 190 7.58e+01 d.108.1.1 134889 3ebbA 304 7.64e+01 1puc 105 7.78e+01 1puc 1pucA 105 7.78e+01 d.97.1.1 40675 2gpcA 194 7.81e+01 3lr6A 137 7.81e+01 1hr6B 443 7.85e+01 1be3A d.185.1.1,d.185.1.1 61166,61167 1f44A 324 7.88e+01 a.60.9.1,d.163.1.1 64982,64983 2zfyA 234 7.89e+01 1ej6B 1275 7.90e+01 i.7.1.1 45968 1ls1A 295 7.93e+01 a.24.13.1,c.37.1.10 78170,78171 3lr4A 126 7.98e+01