# List of top-scoring protein chains for t04-100-30-bys-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 2d4pA 141 5.02e-01 1je0A 236 7.92e-01 c.56.2.1 66581 1vhmA 195 8.20e-01 d.110.2.1 100691 1z5nA 242 1.05e+00 1jysA 242 1.30e+00 c.56.2.1 77216 1vc1A 110 1.64e+00 c.13.2.1 108493 1z5oA 242 1.71e+00 1pjcA 361 2.02e+00 1sayA c.2.1.4,c.23.12.2 30101,31361 1zbfA 142 2.78e+00 1k9sA 237 2.95e+00 c.56.2.1 68359 2bh1X 96 3.02e+00 1lx7A 253 3.06e+00 c.56.2.1 74329 2cxcA 144 3.51e+00 1vk8A 106 3.71e+00 d.58.48.1 108636 1a8s 273 3.94e+00 1brt c.69.1.12 34710 2bl1A 172 4.17e+00 1rxyA 253 4.19e+00 c.56.2.1 98065 1v37A 177 4.58e+00 1ecpA 238 4.73e+00 1ecpA c.56.2.1 33775 1kyhA 276 4.81e+00 c.72.1.4 73222 2fg9A 178 4.88e+00 1ec7A 446 5.79e+00 1bqg c.1.11.2,d.54.1.1 29218,38862 1ryp2 233 5.97e+00 1ryp2 1pb1A 416 6.15e+00 c.77.1.1 88014 3nul 130 6.19e+00 3nul d.110.1.1 40891 1ygmA 118 6.78e+00 1yqtA 538 6.89e+00 1innA 166 7.19e+00 1j98A d.185.1.2 62608 1qlmA 316 7.40e+00 1qlmA d.147.1.1 41765 1j8mF 297 7.40e+00 1ng1 a.24.13.1,c.37.1.10 62742,62743 1y1nA 291 7.60e+00 1lucA 355 7.70e+00 1lucA c.1.16.1 29547 1yvoA 172 7.93e+00 1g3p 217 8.09e+00 1g3p b.37.1.1,b.37.1.1 24788,24789 1z4rA 168 8.12e+00 1vhsA 175 8.40e+00 d.108.1.1 100698 1okjA 251 8.50e+00 c.55.1.9,c.55.1.9 103998,103999 1ujmA 342 9.05e+00 1gw5S 142 9.67e+00 d.110.4.2 70633 1i1dA 161 1.05e+01 1i21A d.108.1.1 61526 1sc3B 88 1.12e+01 1hi9A 274 1.12e+01 1hi9A c.99.1.1 61063 1wu7A 434 1.14e+01 1j8yF 297 1.14e+01 1ng1 a.24.13.1,c.37.1.10 62747,62748 1a0p 290 1.17e+01 1a0p a.60.9.1,d.163.1.1 18105,42165 1zo0A 126 1.17e+01 1hqsA 423 1.18e+01 1iso c.77.1.1 61154 1u55A 188 1.21e+01 d.278.1.1 107677 1vlwA 217 1.21e+01 c.1.10.1 108868 1zejA 293 1.23e+01 1i12A 160 1.25e+01 1i21A d.108.1.1 61515 1iso 416 1.27e+01 1iso c.77.1.1 35065 1vhwA 253 1.27e+01 c.56.2.1 100706 1v6tA 255 1.29e+01 1vjeA 166 1.29e+01 d.185.1.2 100807 1w36C 1122 1.36e+01 2plc 274 1.38e+01 2plc c.1.18.2 29614 1h70A 255 1.51e+01 1h70A d.126.1.3 60711 1y1pA 342 1.52e+01 1h6zA 913 1.53e+01 c.1.12.2,c.8.1.1,d.142.1.5 70906,70907,70908 2a1iA 146 1.56e+01 1chd 203 1.57e+01 1chd c.40.1.1 32478 1ezm 301 1.61e+01 1hyt d.92.1.2 58980 1k8kA 418 1.67e+01 c.55.1.1,c.55.1.1 68305,68306 1ct5A 256 1.73e+01 1ct5A c.1.6.2 28663 1cyw 205 1.75e+01 1cyx b.6.1.2 23024 1e79G 272 1.76e+01 1e79G c.49.2.1 33158 1z85A 234 1.77e+01 2ffcA 353 1.81e+01 1pkp 150 1.85e+01 1pkp d.14.1.1,d.50.1.2 37551,38787 2d2eA 250 1.86e+01 1iibA 106 1.87e+01 1iibA c.44.2.1 32648 1h7nA 342 1.90e+01 1b4kA c.1.10.3 60726 2ptd 298 1.94e+01 2plc c.1.18.2 29605 1tfuA 157 1.96e+01 c.26.1.3 106859 1o8uA 257 2.01e+01 c.14.1.3 81194 1zu1A 127 2.03e+01 1ohlA 342 2.04e+01 c.1.10.3 87035 1ujcA 161 2.05e+01 1h75A 81 2.05e+01 1h75A c.47.1.1 60716 1ej6D 418 2.06e+01 i.7.1.1 45970 1kssA 571 2.06e+01 a.138.1.3,c.3.1.4,d.168.1.1 72928,72929,72930 1q6cA 495 2.07e+01 c.1.8.1 95970 1cyx 205 2.09e+01 1cyx b.6.1.2 23023 2g0qA 173 2.11e+01 1e39A 571 2.14e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19694,30431,42314 1ypfA 336 2.14e+01 1go2A 304 2.15e+01 b.43.4.2,c.25.1.1 76243,76244 1wa3A 205 2.16e+01 1kdj 102 2.16e+01 1plc b.6.1.1 22864 2bhuA 602 2.20e+01 1xm7A 195 2.20e+01 1que 303 2.23e+01 1fnc b.43.4.2,c.25.1.1 25647,31537 1odkA 235 2.24e+01 c.56.2.1 86863 1oj4A 283 2.24e+01 d.14.1.5,d.58.26.5 93083,93084 1q1gA 276 2.26e+01 c.56.2.1 95574 1p2hA 571 2.27e+01 a.138.1.3,c.3.1.4,d.168.1.1 93930,93931,93932 2bkaA 242 2.28e+01 1w34A 304 2.29e+01 1szoA 257 2.30e+01 c.14.1.3 106164 1dj0A 264 2.32e+01 1dj0A d.265.1.1 90337 1ogiA 303 2.33e+01 b.43.4.2,c.25.1.1 92914,92915 1y0pA 571 2.37e+01 1wy7A 207 2.39e+01 1vj1A 363 2.40e+01 b.35.1.2,c.2.1.1 100794,100795 1zclA 180 2.43e+01 1zccA 248 2.43e+01 2bsaA 303 2.52e+01 1va4A 279 2.52e+01 c.69.1.12 108458 1wy1A 172 2.54e+01 1zesA 125 2.65e+01 2dbyA 368 2.66e+01 1ckmA 330 2.67e+01 1ckmA b.40.4.6,d.142.2.3 25358,41585 2bmwA 304 2.71e+01 1fftB 315 2.72e+01 1cyx b.6.1.2,f.17.2.1 23025,43628 1r5jA 337 2.74e+01 c.77.1.5 97097 1xt8A 292 2.75e+01 1igs 248 2.81e+01 1a53 c.1.2.4 28565 2a2nA 176 2.82e+01 1ylqA 96 2.86e+01 1ixcA 294 2.87e+01 a.4.5.37,c.94.1.1 83764,83765 1x24A 180 2.93e+01 1yw5A 177 2.95e+01 1t6aA 126 2.95e+01 d.129.8.1 106555 1q6zA 528 2.96e+01 1uyjA 296 2.99e+01 f.8.1.2 108143 1nv8A 284 2.99e+01 c.66.1.30 86224 1v8bA 479 3.05e+01 1tiqA 180 3.06e+01 d.108.1.1 107010 1yruA 364 3.08e+01 1byb 495 3.12e+01 1byb c.1.8.1 28790 1yrtA 364 3.15e+01 1v3hA 495 3.22e+01 c.1.8.1 108303 1zotA 358 3.23e+01 1u4gA 301 3.24e+01 d.92.1.2 107670 1mtyD 512 3.25e+01 1mhyD a.25.1.2 16742 1a41 234 3.26e+01 1a41 d.163.1.2 42174 1wdpA 495 3.27e+01 1y5eA 169 3.35e+01 1r6wA 322 3.41e+01 c.1.11.2,d.54.1.1 97165,97166 1id1A 153 3.41e+01 1id1A c.2.1.9 62286 1q9iA 571 3.43e+01 a.138.1.3,c.3.1.4,d.168.1.1 96273,96274,96275 1zvdA 380 3.43e+01 1rcuA 195 3.48e+01 c.129.1.1 97295 8tlnE 316 3.51e+01 1hyt d.92.1.2 59075 1vggA 161 3.53e+01 1a53 247 3.56e+01 1a53 c.1.2.4 28564 2ajrA 331 3.58e+01 1rxdA 159 3.66e+01 1m2xA 223 3.69e+01 d.157.1.1 84764 1bmqB 88 3.74e+01 1pauB 1yw3A 208 3.75e+01 1q7zA 566 3.77e+01 c.1.21.2,c.1.26.1 96090,96091 1ws6A 171 3.78e+01 2d1yA 256 3.84e+01 1s62A 106 3.84e+01 1bfd 528 3.91e+01 1bfd c.31.1.3,c.36.1.5,c.36.1.9 31745,31801,31802 1vr8A 142 3.93e+01 1lqtA 456 3.99e+01 c.3.1.1,c.4.1.1 74198,74199 1o20A 427 3.99e+01 c.82.1.1 86556 1lssA 140 4.01e+01 c.2.1.9 74246 1wyzA 242 4.06e+01 1sl4A 155 4.06e+01 d.169.1.1 105710 1vk1A 242 4.07e+01 d.268.1.2 108634 1xo7A 166 4.22e+01 1t6sA 162 4.22e+01 1xccA 220 4.23e+01 1vefA 395 4.24e+01 2f5xA 312 4.26e+01 1lxjA 104 4.26e+01 d.58.48.1 84736 1uuyA 167 4.28e+01 c.57.1.1 108059 1yqdA 366 4.29e+01 1s72E 178 4.32e+01 d.141.1.1,d.141.1.1 105323,105324 1jj2E 177 4.33e+01 1ffk1 d.141.1.1,d.141.1.1 63089,63090 2akaB 299 4.39e+01 1kblA 873 4.43e+01 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 1efvB 255 4.47e+01 1efvB c.26.2.3 31634 1idsA 207 4.55e+01 1avmA a.2.11.1,d.44.1.1 15722,38730 830cA 168 4.55e+01 1ck7A d.92.1.11 40400 1dq3A 454 4.55e+01 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1atiA 505 4.55e+01 1atiA c.51.1.1,d.104.1.1 33196,40745 1nf2A 268 4.57e+01 c.108.1.10 91849 1ew4A 106 4.58e+01 1ew4A d.82.2.1 40023 2c60A 111 4.59e+01 1sbp 310 4.59e+01 1sbp c.94.1.1 35760 1yt3A 375 4.62e+01 2bh4X 134 4.66e+01 1t0qA 498 4.66e+01 a.25.1.2 106220 2b5gA 171 4.67e+01 1ykdA 398 4.68e+01 1fpzA 212 4.68e+01 1fpzA c.45.1.1 59976 1xkpC 143 4.76e+01 1fm0D 81 4.78e+01 1fmaD d.15.3.1 37642 1uirA 314 4.78e+01 c.66.1.17 99429 1xjeA 644 4.78e+01 1zpvA 91 4.85e+01 1kqzA 273 4.93e+01 c.1.8.5 68844 2azwA 148 4.96e+01 2exrA 524 4.98e+01 1nfp 228 4.99e+01 1nfp c.1.16.2 29555 1vliA 385 4.99e+01 b.85.1.1,c.1.10.6 108830,108831 2c3zA 222 5.01e+01 2aefA 234 5.04e+01 2cxxA 190 5.12e+01 1uteA 313 5.13e+01 1uteA d.159.1.1 42078 1q2yA 140 5.14e+01 d.108.1.1 95655 1vr5A 547 5.15e+01 1t9hA 307 5.20e+01 1c4oA 664 5.23e+01 1d2mA c.37.1.19,c.37.1.19 32415,32416 1l2tA 235 5.29e+01 c.37.1.12 73514 1b7yB 785 5.35e+01 1pysB a.6.1.1,a.6.1.1,b.40.4.4,d.58.13.1,d.104.1.1,d.138.1.1 16301,16302,25312,39311,40780,41456 1jf8A 131 5.36e+01 c.44.1.1 66621 1v4pA 157 5.39e+01 1hnuA 280 5.53e+01 1hnoA c.14.1.3 61096 1fnc 314 5.54e+01 1fnc b.43.4.2,c.25.1.1 25627,31517 1jykA 254 5.58e+01 c.68.1.13 67458 1qtwA 285 5.60e+01 1qumA c.1.15.1 29392 1zzmA 259 5.68e+01 1zosA 230 5.74e+01 1wt4A 73 5.74e+01 1emvA 86 5.74e+01 1cei a.28.2.1 16944 2bfwA 200 5.75e+01 1vjnA 220 5.76e+01 d.157.1.4 100825 1vybA 238 5.82e+01 d.151.1.1 108897 1rf6A 427 5.82e+01 d.68.2.2 97366 1qg9A 21 5.83e+01 j.35.1.1 46275 1gp6A 356 5.89e+01 b.82.2.1 65441 1vbkA 307 5.89e+01 1dz3A 130 5.92e+01 1dz3A c.23.1.1 31105 1zyeA 220 5.96e+01 1nvvS 481 5.99e+01 a.117.1.1 86279 1vp2A 208 6.02e+01 1hurA 180 6.07e+01 1hurA c.37.1.8 32052 1yb2A 275 6.09e+01 1fnd 314 6.10e+01 1fnc b.43.4.2,c.25.1.1 25626,31516 1zlqA 502 6.17e+01 1v74B 87 6.17e+01 a.24.20.1 100443 1vgwA 231 6.19e+01 c.68.1.13 100612 2awpA 198 6.19e+01 2aqwA 332 6.21e+01 1v9sA 208 6.24e+01 1b00A 127 6.25e+01 3chy c.23.1.1 31122 1o0xA 262 6.28e+01 d.127.1.1 80755 1uiuA 502 6.29e+01 c.94.1.1 99434 2tmnE 316 6.33e+01 1hyt d.92.1.2 59055 1xjjA 644 6.34e+01 1mzwB 31 6.35e+01 2bodX 286 6.40e+01 1usgA 346 6.41e+01 c.93.1.1 99864 1kpgA 287 6.42e+01 c.66.1.18 68735 1mvoA 136 6.43e+01 c.23.1.1 79513 1bx1A 314 6.44e+01 1fnc b.43.4.2,c.25.1.1 25629,31519 2a9uA 144 6.49e+01 1rl6A 177 6.53e+01 1rl6A d.141.1.1,d.141.1.1 41473,41474 1wsrA 375 6.54e+01 2dg5A 366 6.63e+01 2b99A 156 6.64e+01 1knqA 175 6.64e+01 c.37.1.17 72786 1s12A 94 6.66e+01 1bkdS 439 6.73e+01 1bkdS a.117.1.1 19111 1yz4A 160 6.76e+01 1ub3A 220 6.85e+01 c.1.10.1 88395 1shuX 182 6.86e+01 c.62.1.1 98882 1li5A 461 6.87e+01 a.27.1.1,c.26.1.1 73912,73913 1yfsA 465 6.96e+01 1l2uA 245 6.97e+01 c.1.2.3 73516 1hw7A 255 7.02e+01 1i7fA d.193.1.1 61297 1n6zA 105 7.05e+01 d.263.1.1 85369 1qd9A 124 7.06e+01 1qu9A d.79.1.1 39758 1dbwA 126 7.10e+01 1dbwA c.23.1.1 31095 1riqA 465 7.17e+01 a.203.1.1,d.104.1.1 97516,97517 1nzeA 149 7.21e+01 a.24.18.1 92374 1h1dA 221 7.30e+01 c.66.1.1 83452 1zxxA 319 7.32e+01 1bupA 386 7.36e+01 1ba1 c.55.1.1,c.55.1.1 33377,33378 1uwvA 433 7.36e+01 b.40.4.12,c.66.1.40 100128,100129 1dik 874 7.40e+01 1dik c.1.12.2,c.8.1.1,d.142.1.5 29304,30702,41572 1h4xA 117 7.45e+01 1auz c.13.2.1 60626 1tqzA 133 7.47e+01 1uh5A 329 7.50e+01 c.2.1.2 107840 1xxoA 147 7.58e+01 1vid 221 7.58e+01 1vid c.66.1.1 34178 1ef8A 261 7.71e+01 1ef8A c.14.1.3 30921 1vhoA 346 7.73e+01 b.49.3.1,c.56.5.4 100694,100695 1i5gA 144 7.74e+01 1ewxA c.47.1.10 61784 2fuvA 549 7.78e+01 1apyB 141 7.87e+01 1apyB 1opbA 135 7.87e+01 1hmt b.60.1.2 27216 1nm2A 317 7.95e+01 c.19.1.1,d.58.23.1 80654,80655 1ve5A 311 8.08e+01 1ytfB 53 8.08e+01 1ytfB a.32.1.1 16997 1ns5A 155 8.20e+01 c.116.1.3 80705 1qstA 160 8.22e+01 1yghA d.108.1.1 40804 1ru8A 232 8.23e+01 c.26.2.1 97849 1x9zA 188 8.24e+01 1yqhA 109 8.24e+01 1zczA 464 8.26e+01 1xkqA 280 8.27e+01 1qs0B 338 8.29e+01 1qs0B c.36.1.7,c.48.1.2 31830,33103 2fcjA 119 8.30e+01 1k6wA 426 8.31e+01 b.92.1.2,c.1.9.5 68236,68237 1vqoE 178 8.33e+01 1ezwA 349 8.34e+01 1ezwA c.1.16.3 29558 2bsxA 253 8.34e+01 1qmpA 130 8.47e+01 1dz3A c.23.1.1 31106 1wapA 75 8.48e+01 1wapA b.82.5.1 28153 1xmxA 385 8.62e+01 1o08A 221 8.68e+01 c.108.1.6 86525 1on0A 158 8.74e+01 d.108.1.1 87095 1avk 638 8.76e+01 1a2vA b.30.2.1,d.17.2.1,d.17.2.1 24410,38047,38048 1zdzA 302 8.78e+01 1fxd 58 8.85e+01 1fxd d.58.1.4 38941 1xewX 182 8.85e+01 1kay 381 8.89e+01 1ba1 c.55.1.1,c.55.1.1 33385,33386 1w9aA 147 8.90e+01 1nstA 325 8.92e+01 1nstA c.37.1.5 31951