# 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.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 1zkoA 136 1.03e-01 1a65A 504 1.51e-01 1a65A b.6.1.3,b.6.1.3,b.6.1.3 23148,23149,23150 1hfuA 503 1.57e-01 b.6.1.3,b.6.1.3,b.6.1.3 65827,65828,65829 1crzA 403 1.79e-01 1crzA b.68.4.1,c.51.2.1 27629,33211 2hqsA 415 2.10e-01 b.68.4.1,c.51.2.1 136662,136663 1hpcA 131 2.22e-01 1htp b.84.1.1 28221 1htp 131 2.26e-01 1htp 1m1hA 248 2.74e-01 b.114.1.1,d.58.42.1 78415,78416 1brwA 433 4.32e-01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1gycA 499 5.61e-01 b.6.1.3,b.6.1.3,b.6.1.3 70748,70749,70750 1vdzA 588 5.94e-01 1y8oB 128 6.37e-01 b.84.1.1 122759 2ej8A 160 6.61e-01 1wp5A 323 7.59e-01 b.68.10.1 114780 2elaA 175 1.11e+00 2evbA 74 1.17e+00 1bteA 97 1.22e+00 1bteA g.7.1.3 44463 1aozA 552 1.41e+00 1aozA b.6.1.3,b.6.1.3,b.6.1.3 23124,23125,23126 1fm4A 159 1.70e+00 1bv1 d.129.3.1 76186 2hrvA 142 2.25e+00 2hrvA b.47.1.4 26429 2qt6A 498 2.46e+00 1ghj 79 2.89e+00 1ghj 1seiA 130 3.19e+00 1seiA d.140.1.1 41463 1b6fA 159 3.25e+00 1bv1 d.129.3.1 41316 1gpr 162 3.29e+00 1gpr 1gprA 162 3.29e+00 b.84.3.1 28267 1at0 145 3.80e+00 1at0 1at0A 145 3.80e+00 b.86.1.1 28374 2be1A 339 3.83e+00 1kyaA 499 3.95e+00 b.6.1.3,b.6.1.3,b.6.1.3 73203,73204,73205 1qjoA 80 4.03e+00 1iyu b.84.1.1 28229 2hrgA 496 4.37e+00 1yhpA 212 4.39e+00 2q3uA 383 4.84e+00 d.126.1.6 139809 1gjxA 81 5.00e+00 b.84.1.1 65222 2ghsA 326 5.08e+00 b.68.6.1 135209 1x1oA 286 5.10e+00 2gcuA 245 5.14e+00 1vkpA 383 5.42e+00 d.126.1.6 108686 1yu0A 381 5.45e+00 b.163.1.1,d.169.1.8 124025,124026 1yu1A 381 5.46e+00 b.163.1.1,d.169.1.8 124027,124028 1yu2A 381 5.46e+00 b.163.1.1,d.169.1.8 124029,124030 1yu4A 381 5.76e+00 b.163.1.1,d.169.1.8 124033,124034 1yu3A 381 5.93e+00 b.163.1.1,d.169.1.8 124031,124032 1j1yA 136 5.94e+00 d.38.1.5 90776 1hh1A 143 6.22e+00 1gefA c.52.1.18 61036 2dt4A 143 6.29e+00 1k8mA 93 6.35e+00 b.84.1.1 68314 1nr0A 611 6.37e+00 b.69.4.1,b.69.4.1 86078,86079 2aq5A 402 6.53e+00 3b9fI 395 6.55e+00 1wluA 136 6.92e+00 d.38.1.5 121015 2cy5A 140 7.03e+00 b.55.1.2 131018 1efnA 59 7.21e+00 1bbzA b.34.2.1 24465 2h62A 114 7.39e+00 g.17.1.2 136177 1lxiA 139 7.43e+00 g.17.1.2 84735 2qnkA 286 7.55e+00 1ntvA 152 7.93e+00 b.55.1.2 86168 1ixlA 131 8.15e+00 d.38.1.5 90717 2q1fA 1022 8.59e+00 1y2qA 143 8.68e+00 1bv1 159 9.00e+00 1bv1 2ol2A 395 9.21e+00 1shfA 59 9.51e+00 1bbzA b.34.2.1 24462 2e63A 170 9.97e+00 3bjkA 153 1.01e+01 2hl0A 143 1.01e+01 1uy4A 145 1.03e+01 b.18.1.10 108131 2dsjA 423 1.06e+01 1v10A 521 1.07e+01 b.6.1.3,b.6.1.3,b.6.1.3 108224,108225,108226 1azgB 67 1.08e+01 1bbzA b.34.2.1 24471 2p18A 311 1.08e+01 2vesA 299 1.14e+01 2qwvA 208 1.17e+01 2fp8A 322 1.18e+01 1xedA 117 1.19e+01 b.1.1.1 115229 3bjsA 428 1.20e+01 1qpoA 284 1.21e+01 1qpoA c.1.17.1,d.41.2.1 29561,38597 1dciA 275 1.23e+01 1dciA c.14.1.3 30918 1oc0A 379 1.23e+01 e.1.1.1 86790 1qwyA 291 1.23e+01 b.84.3.2 96509 2gaiA 633 1.28e+01 2d5lA 706 1.30e+01 2ptfA 233 1.35e+01 1vrmA 325 1.37e+01 d.96.2.1 120472 1udxA 416 1.41e+01 b.117.1.1,c.37.1.8,d.242.1.1 99228,99229,99230 2a2nA 176 1.43e+01 b.62.1.1 126041 1ej6A 1289 1.44e+01 i.7.1.1 45967 1mejA 223 1.48e+01 c.65.1.1 79029 2ivwA 113 1.48e+01 1nkqA 259 1.49e+01 d.177.1.1 103862 1rl2A 137 1.51e+01 1rl2A b.34.5.3,b.40.4.5 24610,25342 2gc1A 188 1.55e+01 b.82.1.7 134928 1lj5A 379 1.58e+01 e.1.1.1 73928 1yliA 153 1.61e+01 d.38.1.1 123651 1bdo 80 1.61e+01 1bdo 1bdoA 80 1.61e+01 b.84.1.1 28214 2j73A 103 1.63e+01 1xrkA 124 1.64e+01 d.32.1.2 115881 3c6kA 381 1.68e+01 2ahdA 165 1.69e+01 d.159.1.7 126752 2h5uA 499 1.69e+01 1meoA 209 1.69e+01 c.65.1.1 79035 1cqqA 180 1.71e+01 1cqqA b.47.1.4 26422 1bylA 125 1.72e+01 1bylA d.32.1.2 38495 2j5iA 276 1.74e+01 1nb9A 147 1.76e+01 b.43.5.1 85515 1a7cA 379 1.77e+01 1sek e.1.1.1 42660 2dlbA 80 1.79e+01 1k82A 268 1.81e+01 a.156.1.2,b.113.1.1,g.39.1.8 75866,75867,75868 3cnwA 148 1.85e+01 1a0nB 69 1.87e+01 1bbzA b.34.2.1 24469 1y7rA 133 1.87e+01 d.108.1.1 122716 1qftA 175 1.87e+01 1qftA b.60.1.1 27151 2a22A 215 1.93e+01 d.159.1.7 126025 2hgsA 474 1.93e+01 2hgsA c.30.1.4,d.142.1.6 31722,75997 2in0A 139 1.95e+01 2qfmA 364 1.96e+01 1h8gA 95 2.06e+01 b.109.1.1 65735 1qxrA 189 2.09e+01 b.82.1.7 96552 1ef8A 261 2.09e+01 1ef8A c.14.1.3 30921 1hcxA 127 2.10e+01 b.109.1.1 65800 2h4uA 145 2.12e+01 d.38.1.5 136082 2hdaA 64 2.17e+01 1zi0A 307 2.22e+01 1pz7A 204 2.26e+01 b.29.1.4 95405 1upiA 225 2.26e+01 b.82.1.1 99757 1db2A 377 2.27e+01 1sek e.1.1.1 42672 2gllA 171 2.28e+01 1gvmA 136 2.30e+01 b.109.1.1 70612 1h70A 255 2.35e+01 1h70A d.126.1.3 60711 2cdpA 160 2.38e+01 2z3zA 706 2.40e+01 2gj3A 120 2.41e+01 1icmA 131 2.45e+01 b.60.1.2 27174 1ifc 132 2.46e+01 1ifcA 132 2.46e+01 b.60.1.2 27173 1v1pA 211 2.46e+01 b.40.2.2,d.15.6.1 108268,108269 1j5pA 253 2.48e+01 d.81.1.3,c.2.1.3 71577,83092 1v25A 541 2.49e+01 e.23.1.1 108275 2f41A 121 2.51e+01 d.38.1.5 132904 2j3tC 145 2.62e+01 1sfp 114 2.63e+01 1sfp 1sfpA 114 2.63e+01 b.23.1.1 23895 1ob8A 135 2.64e+01 c.52.1.18 111627 2aujD 309 2.67e+01 1jjoC 261 2.67e+01 1vj2A 126 2.70e+01 b.82.1.10 100796 1gx3A 284 2.71e+01 d.3.1.5 70678 1wuuA 399 2.78e+01 d.14.1.5,d.58.26.7 114900,114901 2fvgA 340 2.92e+01 b.49.3.1,c.56.5.4 134201,134202 2cxxA 190 2.92e+01 c.37.1.8 131013 1bpoA 494 2.98e+01 1bpoA a.118.1.4,b.69.6.1 19143,27670 2arrA 382 3.00e+01 2qm1A 326 3.08e+01 1n26A 325 3.09e+01 b.1.1.4,b.1.2.1,b.1.2.1 79850,79851,79852 2hd5A 359 3.10e+01 1jyhA 157 3.11e+01 d.60.1.3 71956 2q9oA 559 3.16e+01 1j99A 293 3.20e+01 c.37.1.5 71618 1qi7A 253 3.23e+01 1qi7A d.165.1.1 42210 1rxxA 421 3.30e+01 d.126.1.4 98061 3cbwA 353 3.33e+01 1l3aA 228 3.38e+01 d.18.1.2 73531 1ohpA 125 3.40e+01 d.17.4.3 118702 3c5mA 396 3.41e+01 1avzC 57 3.42e+01 1bbzA b.34.2.1 24467 2bbvA 363 3.43e+01 2bbvA b.121.4.4 23323 2ih8A 559 3.45e+01 b.6.1.3,b.6.1.3,b.6.1.3 137407,137408,137409 1s7iA 124 3.47e+01 d.58.4.9 105353 2qwuA 211 3.48e+01 1kj1D 109 3.50e+01 b.78.1.1 68639 1tdtA 259 3.53e+01 3tdt b.81.1.2 28055 1hzdA 272 3.61e+01 c.14.1.3 65969 2jraA 67 3.64e+01 1aqkH 226 3.64e+01 1igtB b.1.1.1,b.1.1.2 20193,21209 1ds6B 180 3.66e+01 1rhoA b.1.18.8 21898 2il5A 171 3.70e+01 1fmtA 314 3.72e+01 1fmtA b.46.1.1,c.65.1.1 25758,34174 2eenA 183 3.76e+01 2a9mH 126 3.78e+01 1xfpA 142 3.79e+01 b.1.1.1 109587 1m5sA 297 3.80e+01 d.58.33.1,d.58.33.1 74511,74512 1od3A 168 3.82e+01 b.18.1.10 86825 1m6kA 251 3.84e+01 e.3.1.1 78695 1p0iA 529 3.85e+01 c.69.1.1 93867 2dfbA 190 3.86e+01 b.29.1.11 131470 3csvA 333 3.89e+01 1w5rA 278 3.89e+01 d.3.1.5 120643 1bkb 136 3.97e+01 1bkb 1bkbA 136 3.97e+01 b.34.5.2,b.40.4.5 24609,25341 2a9gA 418 3.98e+01 d.126.1.4 126435 2zdiC 151 4.03e+01 1szwA 379 4.03e+01 d.265.1.4 99047 2aabH 243 4.04e+01 b.1.1.2 126470 8fabB 224 4.06e+01 1igtB b.1.1.1,b.1.1.2 19773,20883 1o7dC 159 4.08e+01 b.30.5.6 86640 1mdbA 539 4.11e+01 e.23.1.1 79008 2v2fF 390 4.13e+01 2f0xA 148 4.19e+01 d.38.1.5 132673 1xuqA 212 4.20e+01 2b3jA 159 4.21e+01 c.97.1.2 127787 1cb8A 678 4.21e+01 1cb8A a.102.3.2,b.24.1.1,b.30.5.2 18849,23898,24422 2gxfA 142 4.24e+01 1ajaA 449 4.26e+01 1b8jA c.76.1.1 35010 2o18A 340 4.26e+01 1rznA 205 4.29e+01 c.52.1.28 111981 2g50A 530 4.32e+01 b.58.1.1,c.1.12.1,c.49.1.1 134618,134619,134620 2b6hA 192 4.34e+01 c.37.1.8 127994 1mxgA 435 4.38e+01 b.71.1.1,c.1.8.1 85193,85194 1vc1A 110 4.38e+01 c.13.2.1 108493 2c0zA 216 4.40e+01 b.82.1.1 129615 2b4uA 335 4.46e+01 1i52A 236 4.46e+01 1i52A c.68.1.13 61767 2pjhB 193 4.58e+01 2gpcA 194 4.59e+01 1i8kB 124 4.59e+01 b.1.1.1 71131 1fgyA 127 4.64e+01 1faoA b.55.1.1 26976 2hh8A 149 4.65e+01 1ciqA 40 4.67e+01 2sniI d.40.1.1 38576 1ed8A 449 4.69e+01 1b8jA c.76.1.1 34988 2audA 257 4.73e+01 2durA 253 4.74e+01 2qzvA 873 4.77e+01 1gwmA 153 4.79e+01 b.18.1.19 83348 1kv9A 668 4.79e+01 a.3.1.6,b.70.1.1 73056,73057 1alkA 449 4.79e+01 1b8jA c.76.1.1 34994 1z47A 355 4.80e+01 1y6vA 449 4.80e+01 c.76.1.1 122674 1gttA 429 4.86e+01 d.177.1.1,d.177.1.1 70529,70530 2r15A 212 4.94e+01 2yv7A 260 4.95e+01 1atnD 260 5.03e+01 3dni d.151.1.1 41793 2b2nA 344 5.04e+01 c.37.1.19 127710 1te5A 257 5.04e+01 d.153.1.1 106795 1zp7A 206 5.06e+01 1ff4A 65 5.06e+01 g.7.1.1 83251 1wk8A 194 5.09e+01 1zvtA 256 5.10e+01 1yavA 159 5.11e+01 d.37.1.1,d.37.1.1 116595,116596 1wduA 245 5.12e+01 d.151.1.1 109286 2d4zA 250 5.13e+01 d.37.1.1,d.37.1.1 131260,131261 1xx0A 127 5.13e+01 b.55.1.1 122412 2cw2A 226 5.13e+01 1vf8A 377 5.14e+01 c.1.8.5,d.26.3.1 120029,120030 1pg4A 652 5.21e+01 e.23.1.1 88067 1b8jA 449 5.22e+01 1b8jA c.76.1.1 34992 1p9bA 442 5.22e+01 c.37.1.10 94385 1k1xA 659 5.24e+01 a.8.3.2,b.30.5.8,c.6.2.2 84279,84280,84281 1aniA 446 5.33e+01 1b8jA c.76.1.1 35018 1z6bA 154 5.36e+01 d.38.1.6 124510 1suuA 312 5.37e+01 b.68.10.1 99006 1f8vA 355 5.39e+01 2bbvA b.121.4.4 23329 2oxgB 124 5.43e+01 2q35A 243 5.45e+01 1kh5A 449 5.49e+01 c.76.1.1 72475 1elyA 449 5.53e+01 1b8jA c.76.1.1 35028 1zelA 298 5.56e+01 2qddA 378 5.56e+01 2a6hC 1119 5.56e+01 e.29.1.1 126264 1jvwA 167 5.57e+01 d.26.1.1 71907 2anhA 446 5.58e+01 1b8jA c.76.1.1 35004 3cjxA 165 5.67e+01 1y9lA 115 5.79e+01 1aliA 449 5.83e+01 1b8jA c.76.1.1 34996 1j8yF 297 5.88e+01 1ng1 a.24.13.1,c.37.1.10 62747,62748 1wnyA 186 5.91e+01 1e9lA 377 5.95e+01 1e9lA c.1.8.5,d.26.3.1 59395,59396 1gcpA 70 6.03e+01 1gcpA b.34.2.1 60430 1b6a 478 6.07e+01 1bn5 1b6aA 478 6.07e+01 a.4.5.25,d.127.1.1 16223,41160 2jhpA 644 6.07e+01 1op3H 225 6.09e+01 b.1.1.1,b.1.1.2 87208,87209 2bnqD 203 6.10e+01 1v0aA 178 6.11e+01 b.18.1.30 119815 1klo 162 6.14e+01 1klo 1kloA 162 6.14e+01 g.3.11.2,g.3.11.2,g.3.11.2 44326,44327,44328 2phlA 397 6.17e+01 1dgwA b.82.1.2,b.82.1.2 28082,28083 2q0oA 236 6.19e+01 1si7A 369 6.21e+01 d.265.1.4 98883 1anjA 446 6.21e+01 1b8jA c.76.1.1 35008 2qmqA 286 6.26e+01 2h14A 317 6.26e+01 1l1nA 183 6.29e+01 b.47.1.4 73476 1j8mF 297 6.31e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 2p3pA 207 6.31e+01 1azo 232 6.33e+01 1azo 1azoA 232 6.33e+01 c.52.1.14 33329 1wriA 93 6.37e+01 d.15.4.1 114838 1v6iA 232 6.39e+01 b.29.1.1 100383 1ocvA 125 6.41e+01 d.17.4.3 86810 2p8gA 162 6.41e+01 1erjA 393 6.42e+01 1erjA b.69.4.1 27660 1yc7A 124 6.43e+01 1qapA 296 6.43e+01 1qpoA c.1.17.1,d.41.2.1 29559,38595 1itcA 516 6.43e+01 b.3.1.1,c.1.8.1 83705,83706 1pszA 303 6.47e+01 1toaA c.92.2.2 35600 1mdc 133 6.49e+01 1hmt 1k1zA 78 6.49e+01 b.34.2.1 68026 1whi 122 6.51e+01 1whi 1whiA 122 6.51e+01 b.39.1.1 24810 2aorA 223 6.52e+01 1mpxA 615 6.54e+01 b.18.1.13,c.69.1.21 85041,85042 2cl2A 298 6.55e+01 2rcvA 202 6.56e+01 2askA 113 6.57e+01 1ri6A 343 6.57e+01 b.69.11.1 97503 3b98A 475 6.69e+01 1yezA 68 6.70e+01 b.40.4.12 123026 1j5yA 187 6.71e+01 a.4.5.1,d.94.2.1 71592,71593 2eigA 234 6.74e+01 2dfuA 264 6.74e+01 1udzA 182 6.75e+01 b.51.1.1 99239 2b4pA 334 6.77e+01 2drwA 363 6.79e+01 e.3.1.1 131674 2iagA 482 6.80e+01 1nzaA 103 6.87e+01 d.58.5.2 86444 1us8A 147 6.89e+01 c.37.1.12 99859 1wdjA 187 6.95e+01 c.52.1.27 114536 1qhqA 140 6.95e+01 1qhqA b.6.1.1 63326 2biwA 490 7.01e+01 1alhA 446 7.04e+01 1b8jA c.76.1.1 35016 1ad0B 220 7.07e+01 1igtB b.1.1.1,b.1.1.2 20125,21155 2hmhA 152 7.07e+01 1dcuA 357 7.08e+01 1frpA e.7.1.1 42943 2fmyA 220 7.08e+01 2bnuA 203 7.10e+01 2bm0A 691 7.10e+01 b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1,d.58.11.1 128748,128749,128750,128751,128752 1mdcA 131 7.24e+01 b.60.1.2 27198 3c9hA 355 7.25e+01 3b6hA 498 7.32e+01 1qh5A 260 7.33e+01 1qh5A d.157.1.2 42057 1e32A 458 7.34e+01 1e32A b.52.2.3,c.37.1.20,d.31.1.1 59183,59184,59185 1utcA 363 7.37e+01 a.118.1.4,b.69.6.1 99914,99915 2a6hD 1524 7.38e+01 e.29.1.2 126265 1lnzA 342 7.39e+01 b.117.1.1,c.37.1.8 78112,78113 1x82A 190 7.41e+01 b.82.1.7 114955 2j01Z 206 7.49e+01 1vhmA 195 7.51e+01 d.110.2.1 100691 2ftbA 125 7.52e+01 b.60.1.2 134057 1ruwA 69 7.52e+01 1lktA 104 7.56e+01 1lktA b.90.1.1 28398 1u24A 337 7.64e+01 c.45.1.4 112968 1g6nA 210 7.66e+01 2cgpA a.4.5.4,b.82.3.2 16100,28139 2a5hA 416 7.70e+01 1o0iA 138 7.83e+01 d.38.1.5 86532 2qybA 181 7.88e+01 1yqyA 523 7.88e+01 d.92.1.14,d.166.1.1 123903,123904 1lfkA 398 7.89e+01 a.104.1.1 77926 1tvkA 440 7.94e+01 c.32.1.1,d.79.2.1 107362,107363 2dkb 433 7.96e+01 2dkb 2cmwA 310 7.99e+01 1td5A 202 7.99e+01 d.110.2.2 106767