# 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 1fezA 256 2.52e-01 1fezA c.108.1.3 43343 1rqlA 267 2.74e-01 c.108.1.3 97750 1swvA 267 3.07e-01 2ap1A 327 3.61e-01 1zd9A 188 8.38e-01 1zoyC 140 9.12e-01 1pysA 350 1.08e+00 1pysA d.104.1.1 40775 1z5bA 469 1.15e+00 1ofgA 381 1.16e+00 1ofgA c.2.1.3,d.81.1.5 30064,39979 1h6dA 433 1.29e+00 c.2.1.3,d.81.1.5 65656,65657 1r0pA 312 1.31e+00 d.144.1.7 96734 1f20A 435 1.36e+00 b.43.4.1,c.25.1.4 64932,64933 1h2kA 349 1.39e+00 b.82.2.6 76572 2h88C 140 1.67e+00 1nrjA 158 2.33e+00 d.110.4.4 86124 1yrvA 169 2.36e+00 1b7yA 350 2.52e+00 1pysA d.104.1.1 40776 1kvkA 395 2.62e+00 d.14.1.5,d.58.26.3 73060,73061 1tllA 688 2.84e+00 b.43.4.1,c.23.5.2,c.25.1.4 107128,107129,107130 1wg8A 285 2.91e+00 1fseA 74 2.93e+00 1fseA a.4.6.2 60000 2fbwC 141 2.94e+00 1b5pA 385 3.02e+00 c.67.1.1 90403 1s72M 194 3.12e+00 d.12.1.2 105332 1u9aA 160 3.52e+00 1u9aA d.20.1.1 38333 1vqoM 195 4.02e+00 1jj2L 194 4.02e+00 1ffkI d.12.1.2 63097 1z8uA 102 4.10e+00 1bjwA 382 4.12e+00 1bjwA c.67.1.1 34349 1s1qA 145 4.50e+00 d.20.1.2 98351 2bjkA 516 4.80e+00 1wxcB 134 4.93e+00 1uzbA 516 5.04e+00 c.82.1.1 100220 2a3qA 170 5.09e+00 1o04A 500 5.35e+00 c.82.1.1 86508 1jl5A 454 5.38e+00 c.10.2.6 66830 1wzvA 155 5.44e+00 1r8sA 164 5.66e+00 c.37.1.8 97247 1w0bA 102 5.71e+00 a.7.11.1 108985 1jsdA 319 5.79e+00 b.19.1.2 63258 1gg3A 279 5.88e+00 1ef1A a.11.2.1,b.55.1.5,d.15.1.4 16372,27007,37615 1u7kA 131 5.93e+00 2ddrA 306 6.04e+00 1sjiA 350 6.23e+00 1jy2O 56 6.36e+00 h.1.8.1 67441 1vmiA 355 6.38e+00 2bpsA 81 6.49e+00 2grrA 161 6.96e+00 1rypA 243 7.11e+00 1pmaA d.153.1.4 41932 1zfpE 98 7.16e+00 1griA d.93.1.1 40465 1wf9A 107 7.20e+00 1g0uG 252 7.24e+00 d.153.1.4 41952 1a8y 367 7.25e+00 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 1ufiA 64 7.43e+00 a.30.4.1 99336 1auiA 521 7.79e+00 1auiA d.159.1.3 42085 1fzqA 181 8.25e+00 1hurA c.37.1.8 32060 1innA 166 8.37e+00 1j98A d.185.1.2 62608 1yirA 408 8.48e+00 2fi9A 128 8.56e+00 1uj8A 77 8.67e+00 2aegA 268 9.14e+00 1u19A 349 9.24e+00 1lvfA 110 9.30e+00 a.47.2.1 74280 1exrA 148 9.37e+00 1cll a.39.1.5 17299 1lkkA 105 9.57e+00 1lckA d.93.1.1 40412 1yx1A 264 9.70e+00 1l9hA 349 9.78e+00 f.13.1.2 73720 1vjeA 166 1.02e+01 d.185.1.2 100807 1pzlA 237 1.07e+01 a.123.1.1 104393 1ajsA 412 1.12e+01 1ajsA c.67.1.1 34276 1z21A 112 1.13e+01 1cuk 203 1.17e+01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16273,17946,25265 1nepA 130 1.17e+01 b.1.18.7 80440 1xttA 216 1.18e+01 1rdfA 267 1.19e+01 c.108.1.3 104884 1ug0A 88 1.19e+01 a.217.1.1 107822 1w9yA 319 1.23e+01 1bbpA 173 1.29e+01 1bbpA b.60.1.1 27147 2b20A 403 1.30e+01 1l8bA 190 1.34e+01 d.86.1.1 73683 1kxoA 184 1.36e+01 b.60.1.1 84475 1q2hA 69 1.43e+01 a.34.4.1 104498 2fjlA 150 1.48e+01 2aobA 99 1.48e+01 1uujA 88 1.49e+01 a.221.1.1 108046 1jchA 551 1.49e+01 b.101.1.1,b.110.1.1,h.4.9.1 66491,66492,66493 1wgxA 73 1.52e+01 1ufzA 83 1.53e+01 a.5.9.1 107821 1ls6A 295 1.61e+01 c.37.1.5 91115 1lre 81 1.61e+01 1lre a.13.1.1 16376 1zwwA 256 1.68e+01 1ev0A 58 1.70e+01 1ev0A d.71.1.1 39594 1hzxA 349 1.71e+01 1f88A f.13.1.2 61466 1ymmA 191 1.71e+01 1jggA 60 1.72e+01 2hddA a.4.1.1 62950 1xkpB 124 1.72e+01 1w77A 228 1.76e+01 1o5kA 306 1.80e+01 c.1.10.1 92504 1go4A 205 1.84e+01 d.135.1.1 70292 1qgtA 149 1.84e+01 1qgtA a.62.1.1 18135 2ahqA 76 1.84e+01 1ov2A 99 1.85e+01 a.13.1.1 93580 1lox 662 1.92e+01 1lox a.119.1.2,b.12.1.1 19238,23638 1kr4A 125 1.93e+01 d.58.5.2 72889 1eu8A 409 1.96e+01 1eu8A c.94.1.1 59502 1ujwB 135 1.97e+01 h.4.9.1 99472 2d81A 318 2.02e+01 1woqA 267 2.04e+01 c.55.1.10,c.55.1.10 109462,109463 1zyeA 220 2.09e+01 1k1fA 72 2.12e+01 a.147.1.1 68007 1ayaA 101 2.19e+01 1qadA d.93.1.1 40460 1w15A 153 2.22e+01 b.7.1.2 109041 1ej1A 190 2.23e+01 1ejhA d.86.1.1 40144 1f3z 161 2.25e+01 1gpr b.84.3.1 28273 1yg2A 179 2.26e+01 1td6A 306 2.30e+01 1o3yA 166 2.32e+01 c.37.1.8 86618 1hleB 31 2.35e+01 1hleB 1ebmA 317 2.36e+01 1ebmA a.96.1.3,d.129.1.2 18751,41300 1b3uA 588 2.39e+01 1b3uA a.118.1.2 19135 1sxjE 354 2.41e+01 a.80.1.1,c.37.1.20 106089,106090 1ois 223 2.42e+01 1a36A e.15.1.1 43267 1m3qA 317 2.47e+01 a.96.1.3,d.129.1.2 91184,91185 2bwfA 77 2.51e+01 2bwvA 440 2.63e+01 1wl9A 440 2.63e+01 1qsdA 106 2.72e+01 1qsdA a.7.5.1 16335 1q1vA 70 2.73e+01 a.159.4.1 104479 2db9A 149 2.74e+01 1stzA 338 2.77e+01 a.4.5.51,d.110.2.3 106009,106010 1wmhA 89 2.80e+01 1mlwA 301 2.81e+01 d.178.1.1 79289 1jyrA 96 2.83e+01 d.93.1.1 71969 1iyjB 817 2.86e+01 a.170.1.1,a.171.1.1,b.40.4.3,b.40.4.3,b.40.4.3 76948,76949,76950,76951,76952 1dat 174 2.86e+01 2fha a.25.1.1 16677 1wijA 140 2.95e+01 2a5lA 200 3.00e+01 1yovA 537 3.03e+01 1az9 457 3.10e+01 1az9 c.55.2.1,d.127.1.1 33547,41164 1s62A 106 3.16e+01 1sg7A 96 3.18e+01 1yruB 74 3.26e+01 2ae0X 345 3.29e+01 1xqaA 113 3.31e+01 1w3uA 362 3.31e+01 2glzA 153 3.32e+01 2c0rA 362 3.32e+01 1kveB 77 3.36e+01 1kveB 1xdfA 157 3.40e+01 1ztpA 251 3.41e+01 1gqeA 365 3.41e+01 e.38.1.1 70351 1wx1A 335 3.45e+01 1ei7A 158 3.49e+01 1rmvA a.24.5.1 16584 1akz 223 3.50e+01 3eugA c.18.1.1 31007 1p5zB 263 3.50e+01 c.37.1.1 87815 2gkpA 167 3.55e+01 1vgmA 378 3.56e+01 1g4yR 148 3.56e+01 1cll a.39.1.5 60252 1re9A 414 3.56e+01 2viuA 328 3.62e+01 1hgeA b.19.1.2 23797 1blxA 326 3.65e+01 1hcl d.144.1.7 41596 1v54E 109 3.66e+01 a.118.11.1 100326 1jr7A 311 3.66e+01 b.82.2.3 63255 1r1qA 100 3.68e+01 d.93.1.1 104763 1q18A 332 3.71e+01 c.55.1.7,c.55.1.7 104470,104471 2eueA 279 3.76e+01 2fa8A 105 3.78e+01 1xawA 140 3.80e+01 1sziA 247 3.80e+01 a.24.23.1 106159 1nqzA 194 3.81e+01 d.113.1.1 86077 1gd8A 118 3.84e+01 d.188.1.1 60445 1qmqA 414 3.88e+01 1phd a.104.1.1 18907 1euhA 475 3.88e+01 1euhA c.82.1.1 35369 1n00A 321 3.89e+01 a.65.1.1 85241 2c0wA 50 3.89e+01 1m0wA 491 3.91e+01 c.30.1.4,d.142.1.6 78363,78364 1yoeA 322 3.91e+01 1wduA 245 3.93e+01 d.151.1.1 109286 1g03A 134 3.97e+01 1qrjB a.73.1.1 60162 2occE 109 4.04e+01 2occE a.118.11.1 19224 1xn9A 101 4.04e+01 1lci 550 4.08e+01 1lci e.23.1.1 43349 1ggzA 148 4.14e+01 a.39.1.5 70176 2fqpA 97 4.17e+01 1yvhA 329 4.25e+01 1uqvA 85 4.28e+01 a.60.1.2 99798 2b6hA 192 4.28e+01 1k3tA 359 4.30e+01 c.2.1.3,d.81.1.1 72022,72023 1mdbA 539 4.31e+01 e.23.1.1 79008 2gd5A 179 4.34e+01 1p0hA 318 4.37e+01 d.108.1.1 93866 2bjhA 260 4.39e+01 2bydA 323 4.40e+01 1fi2A 201 4.41e+01 1fi2A b.82.1.2 59845 1g8iA 190 4.42e+01 1rec a.39.1.5 60363 2ex5A 207 4.43e+01 2ajrA 331 4.45e+01 1tkeA 224 4.45e+01 1iapA 211 4.48e+01 a.91.1.1 62119 1wpaA 114 4.49e+01 1sz2A 332 4.50e+01 1aj8A 371 4.54e+01 1aj8A a.103.1.1 18900 1pa2A 306 4.57e+01 1bgp a.93.1.1 18693 1sesA 421 4.59e+01 1sesA a.2.7.1,d.104.1.1 15710,40710 1kllA 130 4.60e+01 d.32.1.2 72720 1mu5A 471 4.63e+01 a.156.1.3,d.14.1.3,d.122.1.2 79472,79473,79474 1dz4A 414 4.66e+01 1phd a.104.1.1 18903 1wovA 250 4.66e+01 1uyrA 737 4.69e+01 c.14.1.4,c.14.1.4 100188,100189 1gk8I 140 4.70e+01 d.73.1.1 65242 7aatA 401 4.74e+01 1ajsA c.67.1.1 34250 2ck3A 510 4.75e+01 1yleA 342 4.80e+01 1qj4A 257 4.80e+01 1qj4A c.69.1.20 34796 2f3yA 148 4.81e+01 1yz4A 160 4.85e+01 1w7bA 339 4.90e+01 1rrmA 386 4.98e+01 e.22.1.2 105081 1r4aA 165 4.98e+01 c.37.1.8 96986 1xqoA 256 5.03e+01 1yasA 257 5.04e+01 1qj4A c.69.1.20 34801 1ywxA 102 5.08e+01 2gaeA 346 5.15e+01 2fupA 168 5.17e+01 2a0iA 330 5.17e+01 1bs0A 384 5.22e+01 1bs0A c.67.1.4 34490 1sfcD 87 5.23e+01 1sfcD h.1.15.1 45646 1k28A 584 5.23e+01 b.40.8.1,b.108.1.2,d.2.1.3 68049,68050,68051 2dfkA 402 5.39e+01 1go4E 100 5.39e+01 h.1.22.1 70296 1uwcA 261 5.40e+01 c.69.1.17 100101 2cglA 489 5.43e+01 1qlnA 883 5.43e+01 1cezA e.8.1.3 43111 1jsmA 325 5.46e+01 b.19.1.2 63264 1tn4 159 5.46e+01 1ncx a.39.1.5 17248 1eqfA 280 5.50e+01 1eqfA a.29.2.1,a.29.2.1 16972,16973 1j33A 335 5.52e+01 c.39.1.1 77069 2b0tA 738 5.53e+01 1btkA 169 5.53e+01 1btkA b.55.1.1 26959 1zg2A 107 5.58e+01 1a17 166 5.59e+01 1a17 a.118.8.1 19206 1qqgA 264 5.61e+01 1qqgA b.55.1.2,b.55.1.2 26987,26988 1d9cA 121 5.67e+01 1d9cA a.26.1.3 16901 2et1A 201 5.67e+01 1gvfA 286 5.68e+01 c.1.10.2 70599 1uliA 460 5.70e+01 b.33.1.2,d.129.3.3 107921,107922 1tvfA 369 5.81e+01 b.105.1.2,e.3.1.1 107358,107359 2ffsA 157 5.84e+01 1uptC 170 5.88e+01 c.37.1.8 99769 1szoA 257 5.89e+01 c.14.1.3 106164 1jyoE 105 5.91e+01 d.184.1.2 67487 1tjxA 159 5.95e+01 2fh1A 344 5.96e+01 2a5dA 175 5.96e+01 2g0uA 92 6.01e+01 1p8xA 344 6.02e+01 d.109.1.1,d.109.1.1,d.109.1.1 94365,94366,94367 1q02A 52 6.02e+01 a.5.2.1 95490 1ckmA 330 6.06e+01 1ckmA b.40.4.6,d.142.2.3 25358,41585 1uzcA 71 6.11e+01 a.159.2.1 100222 1opjA 293 6.17e+01 d.144.1.7 87230 2c5rA 67 6.21e+01 1brwA 433 6.30e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 2covD 104 6.30e+01 1p4oA 322 6.32e+01 d.144.1.7 87775 1xtnA 120 6.32e+01 1uptA 171 6.34e+01 c.37.1.8 99767 2cxcA 144 6.37e+01 1ukxA 137 6.46e+01 d.20.1.3 107919 2fulA 178 6.50e+01 1a02F 56 6.54e+01 1a02F h.1.3.1 45534 1obr 326 6.57e+01 1aye c.56.5.2 33828 1ul7A 102 6.62e+01 d.129.6.1 99540 2d7vA 162 6.71e+01 1w4tA 299 6.73e+01 2feaA 236 6.74e+01 1wk2A 121 6.75e+01 1adn 92 6.78e+01 1adn g.48.1.1 45348 1z08A 170 6.81e+01 1uowA 159 6.87e+01 b.7.1.2 107975 1up8A 598 6.92e+01 a.111.1.2 99710 1xkzA 255 6.96e+01 1p5fA 189 7.09e+01 c.23.16.2 94142 1a8d 452 7.10e+01 1a8d b.29.1.6,b.42.4.2 24262,25607 2a19A 175 7.10e+01 1i37A 260 7.12e+01 1a28A a.123.1.1 61583 1zdyA 307 7.13e+01 1xiuA 230 7.13e+01 1uovA 159 7.15e+01 b.7.1.2 107974 1f89A 291 7.17e+01 d.160.1.1 64988 1jy1A 464 7.19e+01 d.136.1.3,d.136.1.3 67438,67439 1rec 201 7.19e+01 1rec a.39.1.5 17326 1zotA 358 7.22e+01 1pmmA 466 7.25e+01 c.67.1.6 94901 1c4xA 285 7.29e+01 1c4xA c.69.1.10 34684 1yrcA 414 7.34e+01 2dgkA 452 7.36e+01 1yruA 364 7.42e+01 1zgdA 312 7.44e+01 2afdA 88 7.44e+01 1xsjA 778 7.49e+01 1guxA 218 7.56e+01 1guxA a.74.1.3 18388 1mml 265 7.57e+01 1mml e.8.1.2 43015 1e79A 510 7.64e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18269,26434,32314 2ga9D 469 7.64e+01 1gkzA 388 7.73e+01 a.29.5.1,d.122.1.4 65268,65269 1gypA 358 7.77e+01 1dssG c.2.1.3,d.81.1.1 30004,39919 1nlqA 108 7.80e+01 b.121.3.1 85853 1qx2A 76 7.91e+01 a.39.1.1 104622 1sk4A 163 8.04e+01 d.118.1.1 105664 1fjlA 81 8.07e+01 2hddA a.4.1.1 16017 1cpcA 162 8.08e+01 1cpcA a.1.1.3 15643 2fs3A 282 8.20e+01 1u2eA 289 8.23e+01 2f2hA 773 8.25e+01 1sur 215 8.29e+01 1sur c.26.2.2 31620 1rvgA 305 8.38e+01 c.1.10.2 97920 1gpuA 680 8.38e+01 c.36.1.10,c.36.1.6,c.48.1.1 65454,65455,65456 1wad 112 8.38e+01 3cyr a.138.1.1 19658 1vd2A 89 8.39e+01 d.15.2.2 108517 2d2sA 235 8.39e+01 2h1nA 567 8.40e+01 2a2pA 129 8.43e+01 1zwxA 301 8.47e+01 1s9kD 53 8.49e+01 1aohA 147 8.50e+01 1aohA b.2.2.2 22401 2c43A 323 8.50e+01 1v2zA 111 8.50e+01 a.186.1.1 108300 1otsA 465 8.54e+01 f.20.1.1 87415 1iq4A 179 8.57e+01 1iq4A d.77.1.1 62641 1rm4A 337 8.57e+01 c.2.1.3,d.81.1.1 105000,105001 1j54A 186 8.71e+01 c.55.3.5 77077 1zhcA 76 8.72e+01 1vhnA 318 8.76e+01 c.1.4.1 100693 1xkrA 206 8.84e+01 1w6sB 74 8.89e+01 1r5zA 323 8.90e+01 f.40.1.1 97135 1gs9A 165 8.91e+01 a.24.1.1 83313 1xn5A 146 8.92e+01