# List of top-scoring protein chains for T0309.t2k-w0.5 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 2bdtA 189 8.72e-03 2afcA 168 1.78e-02 2bdqA 224 1.93e-02 2gxfA 142 2.52e-02 1xklA 273 2.68e-02 1tf7A 525 1.82e-01 c.37.1.11,c.37.1.11 106838,106839 1kjvA 284 2.09e-01 b.1.1.2,d.19.1.1 77421,77422 1xqbA 247 2.63e-01 1zxoA 291 5.03e-01 2g7lA 243 1.07e+00 1pe0A 197 1.17e+00 c.23.16.2 88045 1pdvA 197 1.18e+00 c.23.16.2 88036 2asbA 251 1.47e+00 1souA 194 1.51e+00 c.124.1.6 105858 1pn5A 159 1.62e+00 a.77.1.5 94948 1e1hB 174 1.69e+00 1rf3A 200 1.77e+00 b.8.1.1,h.1.2.1 104915,104916 1ydoA 307 1.81e+00 1zynA 202 1.82e+00 1ys5A 164 1.92e+00 1fl0A 171 1.93e+00 1eujA b.40.4.4 25315 1e7zA 174 1.94e+00 1eujA b.40.4.4 25318 1qysA 106 2.02e+00 k.41.1.1 96603 1yr2A 741 2.03e+00 1tq5A 242 2.28e+00 2f60K 64 2.48e+00 1znpA 154 2.78e+00 1k92A 455 2.83e+00 c.26.2.1,d.210.1.1 68325,68326 2c71A 216 3.14e+00 1n7hA 381 3.30e+00 c.2.1.2 80250 2fvtA 135 3.32e+00 1hyuA 521 3.57e+00 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1uv7A 110 3.58e+00 d.67.4.1 100040 1yhdA 100 3.89e+00 2aj2A 208 3.92e+00 2gtcA 111 4.12e+00 2g3tA 179 4.39e+00 2gbsA 145 4.41e+00 1qx7D 85 4.46e+00 1kkdA 102 4.53e+00 f.15.1.1 68668 1zvwA 378 4.73e+00 1kjmA 285 5.17e+00 b.1.1.2,d.19.1.1 77416,77417 1mejA 223 5.28e+00 c.65.1.1 79029 1xtoA 311 5.39e+00 1rz4A 226 5.59e+00 a.4.5.53,a.118.1.18 105131,105132 1d2oA 187 5.61e+00 1d2oA b.3.5.1,b.3.5.1 22625,22626 1xhsA 121 5.66e+00 1xdyA 298 5.81e+00 1ezkA 153 6.01e+00 1ewxA c.47.1.10 33063 1okdA 154 6.02e+00 c.47.1.10 93249 1xwvA 129 6.02e+00 1ln4A 104 7.04e+00 d.68.4.1 74043 2ex0A 399 7.37e+00 2c4xA 260 7.47e+00 1d2pA 373 7.54e+00 1d2oA b.3.5.1,b.3.5.1,b.3.5.1,b.3.5.1 22629,22630,22631,22632 1thqA 170 7.69e+00 f.4.1.2 106920 1rqcA 185 7.69e+00 d.167.1.1 97732 1jymA 183 7.94e+00 d.167.1.1 71957 1v30A 124 8.12e+00 2ct9A 208 8.29e+00 1u4aA 87 8.75e+00 1vddA 228 8.87e+00 e.49.1.1 108519 1wspA 84 8.89e+00 1jhhA 202 9.21e+00 a.4.5.2,b.87.1.1 63060,63061 1q59A 172 9.23e+00 f.1.4.1 95881 1xt8A 292 9.48e+00 1ju3A 583 9.50e+00 b.18.1.13,c.69.1.21 67300,67301 1kxd 159 9.60e+00 1svpA b.47.1.3 26392 1d1rA 116 9.68e+00 1d1rA d.64.1.1 39548 1ghtA 105 9.85e+00 2rslA c.53.1.1 60526 1ma3A 253 1.03e+01 c.31.1.5 78883 1n0lA 224 1.03e+01 b.1.11.1,b.7.2.1 79744,79745 1kxrA 339 1.04e+01 d.3.1.3 73175 1tl9A 339 1.04e+01 2af6A 258 1.05e+01 1k6lM 314 1.09e+01 f.26.1.1 72087 1repC 251 1.11e+01 1repC a.4.5.10,a.4.5.10 16125,16126 2ex1A 399 1.12e+01 1jul 248 1.12e+01 1a53 c.1.2.4 28566 1zbxB 141 1.12e+01 1a53 247 1.13e+01 1a53 c.1.2.4 28564 1n1iA 105 1.13e+01 g.3.11.4,g.3.11.4 79805,79806 2rslA 140 1.14e+01 2rslA c.53.1.1 33345 2ffiA 288 1.14e+01 2afrA 231 1.16e+01 1sjnA 170 1.16e+01 b.85.4.1 98896 2f9cA 334 1.18e+01 2snv 151 1.22e+01 1svpA b.47.1.3 26394 1riiA 265 1.23e+01 1yvkA 163 1.24e+01 1wykA 153 1.24e+01 1svpA b.47.1.3 26386 1t5cA 349 1.24e+01 1kxc 159 1.24e+01 1svpA b.47.1.3 26391 2snwA 158 1.25e+01 1svpA b.47.1.3 26381 1kxa 159 1.25e+01 1svpA b.47.1.3 26383 1uxc 65 1.26e+01 1uxc a.35.1.5 17119 1zp4A 304 1.27e+01 1wcuA 153 1.27e+01 1zp3A 304 1.27e+01 1d1sA 373 1.27e+01 2ohxA b.35.1.2,c.2.1.1 24727,29743 1d1tA 373 1.27e+01 2ohxA b.35.1.2,c.2.1.1 24719,29735 1v1qA 134 1.29e+01 2fmnA 304 1.30e+01 1kxe 159 1.31e+01 1svpA b.47.1.3 26393 1jidA 128 1.32e+01 d.201.1.1 66735 1k3kA 158 1.32e+01 f.1.4.1 72017 2f1mA 277 1.34e+01 1xwnA 174 1.35e+01 1zr4A 183 1.36e+01 1gdtA 183 1.36e+01 2rslA a.4.1.2,c.53.1.1 16021,33348 1wljA 189 1.37e+01 1rkgA 292 1.45e+01 a.123.1.1 97611 1kxb 159 1.45e+01 1svpA b.47.1.3 26390 1rrb 107 1.45e+01 1c1yB d.15.1.5 37621 1svpA 161 1.45e+01 1svpA b.47.1.3 26384 1kxf 264 1.48e+01 1svpA b.47.1.3 26380 1ld4A 264 1.48e+01 i.6.1.1 77886 1xb2B 291 1.48e+01 1ywmA 200 1.51e+01 1r7rA 816 1.51e+01 b.52.2.3,c.37.1.20,c.37.1.20,d.31.1.1 97203,97204,97205,97206 1yx0A 159 1.53e+01 1rtwA 220 1.53e+01 a.132.1.3 97823 1zboA 210 1.56e+01 2gm2A 132 1.56e+01 2g0uA 92 1.65e+01 2gslA 137 1.67e+01 1j8cA 125 1.71e+01 d.15.1.1 71601 1vckA 115 1.74e+01 1g4yB 101 1.76e+01 1g4yB f.15.1.1 60251 1o4yA 288 1.78e+01 b.29.1.2 92473 1jrlA 190 1.81e+01 c.23.10.5 84205 1ivnA 190 1.81e+01 c.23.10.5 83719 1j00A 190 1.82e+01 c.23.10.5 83854 2ew0A 192 1.83e+01 1vajA 214 1.83e+01 1s1gA 124 1.89e+01 d.42.1.2 98346 1f0kA 364 1.90e+01 1f0kA c.87.1.2 35465 2ab0A 205 1.91e+01 2b43A 526 1.92e+01 2c3zA 222 1.93e+01 2gswA 182 1.94e+01 2fkiA 126 1.95e+01 1nxiA 132 1.97e+01 d.58.47.1 86381 2a2pA 129 2.00e+01 2ffgA 87 2.08e+01 1ujqA 305 2.11e+01 c.1.12.7 99463 1dyqA 234 2.13e+01 3seb b.40.2.2,d.15.6.1 59140,59141 1yfsA 465 2.23e+01 1yx5B 98 2.26e+01 1wxcA 281 2.27e+01 1ob1C 99 2.27e+01 g.3.11.4,g.3.11.4 86752,86753 1a1w 91 2.30e+01 1a1z a.77.1.4 18425 1a1z 91 2.30e+01 1a1z a.77.1.4 18427 1k99A 99 2.33e+01 a.21.1.1 68341 1zy8K 229 2.34e+01 1a9v 129 2.43e+01 1a9v b.1.18.7 21946 1ktjA 129 2.43e+01 b.1.18.7 72974 2b3wA 168 2.48e+01 4matA 278 2.49e+01 1c24A d.127.1.1 41150 1xtqA 177 2.51e+01 1q1yA 191 2.52e+01 d.167.1.1 104480 1zn6A 227 2.56e+01 1kevA 351 2.57e+01 1pedA b.35.1.2,c.2.1.1 24749,29765 2b2hA 399 2.57e+01 1kqpA 271 2.60e+01 c.26.2.1 72883 1u6tA 121 2.61e+01 2a10A 125 2.62e+01 1k28A 584 2.65e+01 b.40.8.1,b.108.1.2,d.2.1.3 68049,68050,68051 1wthA 584 2.65e+01 1l3gA 136 2.69e+01 d.34.1.1 77675 1twdA 256 2.73e+01 c.1.30.1 107397 1z8fA 228 2.73e+01 2d2zA 261 2.74e+01 1q8kA 308 2.78e+01 b.40.4.5,d.58.51.1 104556,104557 1s4qA 228 2.82e+01 c.37.1.1 98507 2exnA 136 2.86e+01 2gwgA 350 2.88e+01 1vj7A 393 2.92e+01 a.211.1.1,d.218.1.8 100801,100802 1l5zA 155 2.93e+01 c.23.1.1 77722 1qkkA 155 2.93e+01 1dbwA c.23.1.1 31104 1yvwA 115 2.93e+01 1xedA 117 2.94e+01 2bdvA 231 2.96e+01 2d1uA 104 3.00e+01 1uelA 95 3.01e+01 d.15.1.1 99265 1vhuA 211 3.02e+01 c.50.1.2 100703 1y8tA 324 3.03e+01 2axwA 134 3.04e+01 1ge8A 249 3.08e+01 1plq d.131.1.2,d.131.1.2 41398,41399 1visA 324 3.10e+01 d.14.1.5,d.58.26.3 100769,100770 1sqrA 95 3.11e+01 1lo5D 233 3.11e+01 b.40.2.2,d.15.6.1 78120,78121 1t8pA 267 3.11e+01 c.60.1.1 106667 1q1rA 431 3.12e+01 c.3.1.5,c.3.1.5,d.87.1.1 95600,95601,95602 1esfA 233 3.12e+01 3seb b.40.2.2,d.15.6.1 25146,37735 1iz5A 249 3.13e+01 d.131.1.2,d.131.1.2 83834,83835 1iz4A 249 3.18e+01 d.131.1.2,d.131.1.2 83832,83833 1pc2A 152 3.19e+01 a.118.8.1 94427 1i4gA 233 3.20e+01 3seb b.40.2.2,d.15.6.1 25148,37737 1ttzA 87 3.21e+01 c.47.1.1 107309 1y41A 180 3.21e+01 1pls 113 3.21e+01 1pls b.55.1.1 26965 1xtfA 427 3.23e+01 1jheA 135 3.24e+01 b.87.1.1 63055 1zp6A 191 3.31e+01 1zp2A 235 3.32e+01 1rq8A 104 3.32e+01 d.68.4.1 105056 1zg2A 107 3.33e+01 1tiwA 602 3.35e+01 1zbpA 273 3.36e+01 1zbsA 291 3.37e+01 2gsvA 80 3.38e+01 1h6xA 170 3.45e+01 b.18.1.7 70903 1nwbA 124 3.47e+01 b.124.1.1 86296 1n3lA 372 3.50e+01 c.26.1.1 79966 1ogaD 215 3.57e+01 b.1.1.1,b.1.1.2 86990,86991 1q48A 134 3.59e+01 d.224.1.2 95783 1mk3A 178 3.65e+01 f.1.4.1 84978 1sgvA 316 3.67e+01 b.122.1.1,d.265.1.2 98858,98859 2ce7A 476 3.67e+01 1sr3A 136 3.68e+01 b.40.9.1 98976 1kezA 300 3.69e+01 c.69.1.22 68546 1cf7B 95 3.71e+01 1cf7B a.4.5.17 16152 1ysgA 181 3.73e+01 1o57A 291 3.75e+01 a.4.5.40,c.61.1.1 92483,92484 1h6yA 170 3.77e+01 b.18.1.7 70904 1xngA 268 3.79e+01 1w61A 414 3.79e+01 1rwiA 270 3.79e+01 b.68.9.1 97987 2cq9A 130 3.81e+01 2cwsA 237 3.84e+01 1maz 221 3.85e+01 1maz f.1.4.1 43393 1mzgA 146 3.86e+01 d.224.1.1 79696 1ywzA 175 3.88e+01 1z00A 89 3.89e+01 1rhjB 110 3.92e+01 2aegA 268 3.93e+01 2c24A 206 3.98e+01 1nkvA 256 3.98e+01 c.66.1.21 80577 1tm0A 350 3.99e+01 d.21.1.3 107147 1xw8A 252 3.99e+01 1m93A 55 4.02e+01 e.1.1.1 91235 1tiyA 164 4.07e+01 c.97.1.2 107012 1m9sA 605 4.09e+01 b.1.18.15,b.34.11.1,b.34.11.1,b.34.11.1,c.10.2.1 78874,78875,78876,78877,78878 1k8mA 93 4.12e+01 b.84.1.1 68314 2a1bA 116 4.13e+01 1v7oA 165 4.16e+01 d.67.1.2 100480 1ny4A 82 4.17e+01 b.40.4.5 92316 1c7gA 456 4.20e+01 c.67.1.2 90415 1qx3A 257 4.21e+01 c.17.1.1 96515 1tmwA 149 4.24e+01 1rzwA 123 4.28e+01 1n57A 291 4.31e+01 c.23.16.2 85328 1xm3A 264 4.36e+01 2an3A 289 4.38e+01 1vfsA 386 4.39e+01 b.49.2.2,c.1.6.1 108584,108585 2gujA 155 4.40e+01 1taeA 332 4.43e+01 2b6eA 146 4.45e+01 1zceA 155 4.51e+01 1uuzA 137 4.55e+01 d.233.1.1 100024 1n91A 108 4.56e+01 d.206.1.1 80326 2bbkL 125 4.57e+01 2bbkL g.21.1.1 44882 1v7bA 185 4.58e+01 1wvoA 79 4.62e+01 1y7iA 268 4.63e+01 1v0aA 178 4.65e+01 2gtaA 119 4.65e+01 2madL 124 4.65e+01 2bbkL g.21.1.1 44887 1ta0A 197 4.72e+01 c.108.1.16 106729 1mg2B 131 4.73e+01 g.21.1.1 79060 1tplA 456 4.74e+01 1ax4A c.67.1.2 34387 1t9zA 197 4.75e+01 c.108.1.16 106728 1v58A 241 4.77e+01 c.47.1.9,d.17.3.1 108371,108372 1orrA 347 4.80e+01 c.2.1.2 93460 1gqfA 265 4.84e+01 c.17.1.1 65470 1ddf 127 4.84e+01 1ddf a.77.1.2 18423 1u4cA 349 4.91e+01 b.69.4.2 107666 2fm2A 200 4.92e+01 2gf4A 100 4.93e+01 2g01A 370 4.94e+01 1zhvA 134 4.96e+01 1zwvA 58 4.97e+01 1l8yA 91 4.98e+01 a.21.1.1 73708 1xjuA 163 4.98e+01 1rtlA 200 4.98e+01 1t2mA 101 4.99e+01 1d2dA 59 5.03e+01 1r1bA a.16.1.3 16397 1wv3A 238 5.05e+01 2dlbA 80 5.08e+01 2ajaA 376 5.09e+01 2d3jA 157 5.09e+01 1lw3A 657 5.11e+01 b.55.1.8,c.45.1.3 91152,91153 1t6kA 278 5.16e+01 2g2xA 157 5.18e+01 1sq1A 370 5.19e+01 d.258.1.1 98961 2b7eA 59 5.19e+01 1snlA 103 5.21e+01 a.39.1.7 105820 1ny8A 97 5.23e+01 d.52.6.1 103876 2eucA 130 5.24e+01 1y8mA 144 5.26e+01 2ap6A 112 5.33e+01 2fj6A 82 5.35e+01 1bc9 200 5.36e+01 1pbv a.118.3.1 19180 1xhjA 88 5.36e+01 2ffmA 91 5.38e+01 2acaA 189 5.39e+01 1zb7A 455 5.39e+01 1wg0A 243 5.39e+01 2deoA 230 5.43e+01 1o4zA 346 5.43e+01 b.29.1.2 92474 2bv9A 290 5.49e+01 1ztsA 139 5.51e+01 1vhmA 195 5.56e+01 d.110.2.1 100691 1yw6A 335 5.61e+01 2f4mA 295 5.63e+01 1sj6A 101 5.65e+01 1zy2A 150 5.66e+01 1i1cA 239 5.66e+01 1igtB b.1.1.2,b.1.1.2 21536,21537 1u5jA 539 5.72e+01 a.5.7.2,c.1.10.5 107682,107683 1rqbA 539 5.72e+01 a.5.7.2,c.1.10.5 105057,105058 1s3hA 539 5.72e+01 a.5.7.2,c.1.10.5 105235,105236 2f9sA 151 5.80e+01 1xsqA 168 5.84e+01 2bdrA 175 5.84e+01 2covD 104 5.86e+01 1pvdA 555 5.88e+01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31737,31777,31778 2fk6A 320 5.92e+01 1pydA 556 5.92e+01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31735,31773,31774 1qyiA 384 5.93e+01 c.108.1.13 96595 1k2eA 156 5.94e+01 d.113.1.1 72010 1xhfA 123 5.95e+01 1yxbA 98 5.98e+01 1efhA 292 5.99e+01 1aquA c.37.1.5 31948 1rrvA 416 6.01e+01 c.87.1.5 105083 2go8A 122 6.04e+01 1y44A 320 6.05e+01 1rl4A 188 6.05e+01 d.167.1.1 97636 1ni7A 155 6.10e+01 d.224.1.1 85738 1xfsA 178 6.12e+01 d.129.3.5 109589 1qpbA 563 6.12e+01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31739,31781,31782 1y67A 229 6.22e+01 1xjtA 191 6.23e+01 1yfkA 262 6.26e+01 1ybhA 590 6.28e+01 2eveA 157 6.32e+01 2ganA 190 6.33e+01 1wxcB 134 6.35e+01 1jhcA 137 6.35e+01 b.87.1.1 63054 1r55A 214 6.39e+01 2br9A 234 6.44e+01 1zq7A 207 6.44e+01 1jh3A 107 6.47e+01 d.66.1.4 71661 1yw4A 341 6.48e+01 1gd0A 122 6.50e+01 1dptA d.80.1.3 39834 1t2eA 322 6.53e+01 c.2.1.5,d.162.1.1 99086,99087 2bcmA 165 6.54e+01 2fo1E 373 6.57e+01 2gh1A 301 6.57e+01 2bwbA 46 6.59e+01 1sqhA 312 6.65e+01 d.108.1.5 98966 1xsrA 168 6.66e+01 1hrkA 359 6.70e+01 1hrkA c.92.1.1 61228 2gefA 217 6.76e+01 2a7wA 116 6.80e+01 2b86A 67 6.81e+01 1yw3A 208 6.83e+01 2ffeA 311 6.85e+01 1s20A 340 6.86e+01 c.122.1.1 98356 2czsA 80 6.86e+01 2a55A 133 6.86e+01 1z0hA 438 6.89e+01 1qxfA 66 6.89e+01 g.41.8.4 96527 2bweA 50 6.90e+01 2apsA 162 6.93e+01 1yaiA b.1.8.1 22298 2a3vA 320 6.96e+01 1zc6A 305 7.06e+01 1xbfA 140 7.18e+01 d.273.1.1 109538 1s1pA 331 7.19e+01 c.1.7.1 98350 1zmbA 290 7.19e+01 2axpA 173 7.22e+01 1o9qA 414 7.24e+01 c.117.1.1 92683 1tzaA 134 7.29e+01 b.1.23.1 107468 2g7jA 124 7.39e+01 2bh1A 250 7.42e+01 1yf5L 254 7.45e+01 1sqsA 242 7.46e+01 c.23.5.5 98968 1oy1A 228 7.47e+01 c.23.16.2 87548 2f0aA 98 7.52e+01 1ykeB 151 7.57e+01 1ockA 412 7.63e+01 c.117.1.1 86802 1sbkA 144 7.63e+01 d.38.1.5 98791 1o9nA 414 7.64e+01 c.117.1.1 92677 2a8eA 220 7.65e+01 1uuqA 440 7.66e+01 c.1.8.3 100015 1objA 414 7.66e+01 c.117.1.1 92757 1obkA 414 7.69e+01 c.117.1.1 92759 1urxA 282 7.69e+01 b.29.1.2 99837 1fnoA 417 7.72e+01 d.58.19.1,c.56.5.4 70145,75841 1oblA 414 7.74e+01 c.117.1.1 92761 1wyzA 242 7.77e+01 1obiA 414 7.80e+01 c.117.1.1 92755 1o9pA 414 7.80e+01 c.117.1.1 92681 1pms 136 7.86e+01 1awe b.55.1.1 26966 5gcnA 166 7.89e+01 1yghA d.108.1.1 40807 1c5kA 439 7.92e+01 1crzA b.68.4.1,c.51.2.1 27630,33212 2bcoA 350 7.92e+01 1l5xA 280 7.98e+01 c.106.1.1 77718 1r6uA 437 8.12e+01 c.26.1.1 97163 1do0A 442 8.22e+01 1do0A c.37.1.20 32432 1vicA 262 8.23e+01 c.68.1.13 100756 1g4aE 443 8.24e+01 1do0A c.37.1.20 32444 1nssA 347 8.29e+01 b.30.5.4 80716 1ns8A 347 8.31e+01 b.30.5.4 80709 1mmuA 347 8.32e+01 b.30.5.4 79303 1wu6A 396 8.39e+01 1vqoI 162 8.40e+01 1nszA 347 8.42e+01 b.30.5.4 80724 1nsuA 347 8.46e+01 b.30.5.4 80718 1jmaA 290 8.53e+01 b.1.1.1 63177 1ns4A 347 8.56e+01 b.30.5.4 80703 1p5tA 127 8.61e+01 b.55.1.2 94148 2ewoA 377 8.64e+01 1r1mA 164 8.74e+01 d.79.7.1 96820 2gwrA 238 8.75e+01 1ns7A 347 8.89e+01 b.30.5.4 80707 1jhfA 202 8.93e+01 a.4.5.2,b.87.1.1 63057,63058