# 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 2d4pA 141 2.02e-01 1z5oA 242 5.19e-01 1rxyA 253 6.41e-01 c.56.2.1 98065 1jysA 242 7.35e-01 c.56.2.1 77216 1je0A 236 7.47e-01 c.56.2.1 66581 1z5nA 242 8.41e-01 1lx7A 253 9.09e-01 c.56.2.1 74329 1ecpA 238 1.05e+00 1ecpA c.56.2.1 33775 1zbfA 142 1.33e+00 1q1gA 276 1.41e+00 c.56.2.1 95574 1k9sA 237 1.78e+00 c.56.2.1 68359 2bsxA 253 2.81e+00 1pjcA 361 2.97e+00 1sayA c.2.1.4,c.23.12.2 30101,31361 1o0xA 262 3.13e+00 d.127.1.1 80755 1vc1A 110 3.34e+00 c.13.2.1 108493 1bfd 528 3.49e+00 1bfd c.31.1.3,c.36.1.5,c.36.1.9 31745,31801,31802 1q6zA 528 3.77e+00 1a8s 273 3.82e+00 1brt c.69.1.12 34710 2a2nA 176 4.23e+00 1z4rA 168 4.45e+00 1dj0A 264 4.51e+00 1dj0A d.265.1.1 90337 1hi9A 274 4.91e+00 1hi9A c.99.1.1 61063 1k8kB 394 4.93e+00 c.55.1.1 68307 1k8kA 418 5.47e+00 c.55.1.1,c.55.1.1 68305,68306 1vhmA 195 5.48e+00 d.110.2.1 100691 1gw5S 142 5.76e+00 d.110.4.2 70633 1vhsA 175 5.94e+00 d.108.1.1 100698 1oj4A 283 6.41e+00 d.14.1.5,d.58.26.5 93083,93084 1ylqA 96 6.46e+00 1zosA 230 6.88e+00 1s62A 106 7.27e+00 1g3p 217 7.29e+00 1g3p b.37.1.1,b.37.1.1 24788,24789 2bh1X 96 7.31e+00 2c3zA 222 7.33e+00 1vk8A 106 7.34e+00 d.58.48.1 108636 1szoA 257 7.37e+00 c.14.1.3 106164 1o8uA 257 7.37e+00 c.14.1.3 81194 2gx9A 129 7.52e+00 1xm7A 195 7.71e+00 1v37A 177 7.87e+00 1h6zA 913 8.06e+00 c.1.12.2,c.8.1.1,d.142.1.5 70906,70907,70908 1vjeA 166 8.53e+00 d.185.1.2 100807 1y1pA 342 8.55e+00 1igs 248 8.62e+00 1a53 c.1.2.4 28565 1xtoA 311 8.70e+00 1w78A 422 8.81e+00 1odkA 235 8.90e+00 c.56.2.1 86863 1a53 247 9.19e+00 1a53 c.1.2.4 28564 1ujmA 342 9.37e+00 1yt3A 375 9.51e+00 2gd9A 189 9.72e+00 1g2rA 100 9.81e+00 1g2rA d.192.1.1 60231 1ec7A 446 1.03e+01 1bqg c.1.11.2,d.54.1.1 29218,38862 1zzoA 136 1.06e+01 1xo7A 166 1.11e+01 1vhwA 253 1.12e+01 c.56.2.1 100706 1y1nA 291 1.12e+01 3nul 130 1.13e+01 3nul d.110.1.1 40891 1innA 166 1.20e+01 1j98A d.185.1.2 62608 1h7nA 342 1.21e+01 1b4kA c.1.10.3 60726 1ohlA 342 1.23e+01 c.1.10.3 87035 1t6aA 126 1.25e+01 d.129.8.1 106555 4pfk 319 1.34e+01 3pfk c.89.1.1 35582 1e0tA 470 1.40e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 2bswA 146 1.41e+01 1th0A 226 1.41e+01 d.3.1.7 106903 1vj1A 363 1.43e+01 b.35.1.2,c.2.1.1 100794,100795 1zo0A 126 1.46e+01 1lwdA 413 1.46e+01 c.77.1.1 78265 1khtA 192 1.48e+01 c.37.1.1 84401 1v6tA 255 1.49e+01 1s12A 94 1.60e+01 1mgpA 313 1.60e+01 c.119.1.1 79098 2bhuA 602 1.63e+01 1aa8A 347 1.66e+01 1an9A 2ptd 298 1.69e+01 2plc c.1.18.2 29605 1l2uA 245 1.73e+01 c.1.2.3 73516 1wsrA 375 1.74e+01 1o20A 427 1.76e+01 c.82.1.1 86556 1i12A 160 1.76e+01 1i21A d.108.1.1 61515 3cla 213 1.77e+01 3cla c.43.1.1 32610 1id1A 153 1.78e+01 1id1A c.2.1.9 62286 1zyeA 220 1.78e+01 1wosA 364 1.80e+01 b.44.2.1,d.250.1.1 109468,109469 1zejA 293 1.81e+01 1tcvA 287 1.84e+01 2bzpA 226 1.90e+01 1q67A 231 1.91e+01 b.55.1.7 95960 1usyA 275 1.91e+01 1m2xA 223 1.96e+01 d.157.1.1 84764 2c0cA 362 1.97e+01 1tvnA 293 2.05e+01 1i1dA 161 2.07e+01 1i21A d.108.1.1 61526 1t4oA 117 2.07e+01 d.50.1.1 106425 1a88A 275 2.09e+01 1brt c.69.1.12 34707 1va4A 279 2.19e+01 c.69.1.12 108458 1yymG 313 2.23e+01 1q2yA 140 2.23e+01 d.108.1.1 95655 1hyvA 166 2.28e+01 1b9dA c.55.3.2 61424 1x8hA 228 2.30e+01 2plc 274 2.31e+01 2plc c.1.18.2 29614 1yqdA 366 2.32e+01 1x8gA 227 2.34e+01 2akaB 299 2.34e+01 1vefA 395 2.39e+01 1esiA 262 2.40e+01 1skf e.3.1.1 42682 1q8iA 783 2.41e+01 c.55.3.5,e.8.1.1 96208,96209 1poiB 260 2.44e+01 1poiB c.124.1.3 34155 1qlmA 316 2.45e+01 1qlmA d.147.1.1 41765 1zvdA 380 2.48e+01 1ve9A 347 2.49e+01 c.4.1.2,d.16.1.3 100571,100572 1xfjA 261 2.50e+01 d.194.1.2 109585 1tyyA 339 2.52e+01 2g3aA 152 2.55e+01 1up6A 416 2.56e+01 c.2.1.5,d.162.1.2 107976,107977 1xxoA 147 2.56e+01 1gg4A 452 2.58e+01 1gg4A c.59.1.1,c.98.1.1,c.72.2.1 33957,58985,58986 1u04A 771 2.60e+01 b.34.14.1,c.55.3.10 107539,107540 1mw7A 240 2.60e+01 e.39.1.1 79557 1xjeA 644 2.60e+01 2arzA 247 2.60e+01 1on0A 158 2.61e+01 d.108.1.1 87095 1v6fA 151 2.62e+01 d.109.1.2 108395 1up7A 417 2.68e+01 1i4wA 353 2.70e+01 c.66.1.24 66028 1knqA 175 2.72e+01 c.37.1.17 72786 1vybA 238 2.72e+01 d.151.1.1 108897 2a1iA 146 2.73e+01 1rf6A 427 2.73e+01 d.68.2.2 97366 7a3hA 303 2.75e+01 7a3hA c.1.8.3 28817 1wnaA 131 2.77e+01 1ml8A 134 2.82e+01 d.227.1.2 85013 1qmvA 197 2.82e+01 1qq2A c.47.1.10 33066 1xjjA 644 2.87e+01 2d28C 149 2.88e+01 1tltA 319 2.89e+01 c.2.1.3,d.81.1.5 107135,107136 1p3dA 475 2.91e+01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 2afcA 168 2.91e+01 1pv9A 348 2.96e+01 c.55.2.1,d.127.1.1 95157,95158 1k8kF 168 2.97e+01 d.198.2.1 68312 1dq3A 454 2.97e+01 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1mgtA 174 2.98e+01 1mgtA a.4.2.1,c.55.7.1 16078,33753 1prxA 224 2.99e+01 1prxA c.47.1.10 33076 1sjdA 368 3.01e+01 c.1.11.2,d.54.1.1 105632,105633 1cliA 345 3.05e+01 1cliA d.79.4.1,d.139.1.1 39816,41459 1mc0A 368 3.05e+01 d.110.2.1,d.110.2.1 78937,78938 1dvjA 246 3.10e+01 1dvjA c.1.2.3 28546 1pb7A 292 3.13e+01 c.94.1.1 88025 2g5cA 281 3.16e+01 1j8mF 297 3.18e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 1sl4A 155 3.21e+01 d.169.1.1 105710 2aq6A 147 3.25e+01 1wstA 417 3.25e+01 2bgkA 278 3.32e+01 1itg 166 3.32e+01 1b9dA c.55.3.2 33661 1uyjA 296 3.43e+01 f.8.1.2 108143 1w9aA 147 3.46e+01 1kblA 873 3.47e+01 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 1km4A 247 3.47e+01 c.1.2.3 72740 1rvaA 244 3.49e+01 1rvaA c.52.1.2 33240 1an9A 340 3.51e+01 1an9A c.4.1.2,d.16.1.3 30617,37904 1j8yF 297 3.56e+01 1ng1 a.24.13.1,c.37.1.10 62747,62748 1jbwA 428 3.60e+01 c.59.1.2,c.72.2.2 62860,62861 1ixcA 294 3.64e+01 a.4.5.37,c.94.1.1 83764,83765 2cqsA 842 3.64e+01 1c24A 263 3.64e+01 1c24A d.127.1.1 41148 1xnzA 264 3.68e+01 1lssA 140 3.72e+01 c.2.1.9 74246 1iibA 106 3.79e+01 1iibA c.44.2.1 32648 2aefA 234 3.79e+01 2cxaA 256 3.83e+01 1stzA 338 3.86e+01 a.4.5.51,d.110.2.3 106009,106010 1914 232 3.88e+01 1914 d.49.1.1,d.49.1.1 83028,83029 1x1zA 252 3.89e+01 1uuyA 167 3.93e+01 c.57.1.1 108059 1bl3A 160 3.94e+01 1b9dA c.55.3.2 33655 1ki9A 192 3.95e+01 c.37.1.1 84404 1lucA 355 3.95e+01 1lucA c.1.16.1 29547 1qx4A 274 3.97e+01 b.43.4.2,c.25.1.1 104624,104625 1cnv 299 3.97e+01 1cnv c.1.8.5 28989 1fu1A 203 3.98e+01 1fu1B b.59.1.1,h.1.11.1 27076,45630 1ryp2 233 3.99e+01 1ryp2 1g4wR 383 4.01e+01 1g4uS a.24.11.1,c.45.1.2 16644,32692 2fg1A 158 4.03e+01 1exqA 154 4.04e+01 1b9dA c.55.3.2 33646 1uh5A 329 4.10e+01 c.2.1.2 107840 1y5eA 169 4.11e+01 1chd 203 4.12e+01 1chd c.40.1.1 32478 1eonA 245 4.14e+01 1rvaA c.52.1.2 33238 1jykA 254 4.18e+01 c.68.1.13 67458 1atiA 505 4.18e+01 1atiA c.51.1.1,d.104.1.1 33196,40745 2cvlA 124 4.18e+01 1umkA 275 4.20e+01 2fz4A 237 4.26e+01 1ydyA 356 4.28e+01 1ik9A 213 4.31e+01 b.59.1.1,h.1.11.1 66176,66177 1e39A 571 4.32e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19694,30431,42314 1t8qA 336 4.34e+01 c.1.18.3 106669 2bwvA 440 4.39e+01 2c5qA 240 4.39e+01 1wl9A 440 4.39e+01 1nvvS 481 4.42e+01 a.117.1.1 86279 1y0pA 571 4.43e+01 1r5jA 337 4.47e+01 c.77.1.5 97097 1tp9A 162 4.48e+01 1rcuA 195 4.49e+01 c.129.1.1 97295 1nksA 194 4.49e+01 1nksA c.37.1.1 31886 1bif 469 4.53e+01 1bif c.37.1.7,c.60.1.4 31961,34003 2bl1A 172 4.54e+01 1ws6A 171 4.54e+01 1bn7A 294 4.55e+01 1bn6A c.69.1.8 34677 1p2hA 571 4.65e+01 a.138.1.3,c.3.1.4,d.168.1.1 93930,93931,93932 1yw5A 177 4.71e+01 1bbpA 173 4.76e+01 1bbpA b.60.1.1 27147 1mvoA 136 4.76e+01 c.23.1.1 79513 2gm3A 175 4.77e+01 1va6A 518 4.78e+01 1hw7A 255 4.82e+01 1i7fA d.193.1.1 61297 1wryA 121 4.84e+01 1vr8A 142 4.84e+01 1wu7A 434 4.85e+01 1sx5A 244 4.87e+01 c.52.1.2 99023 1hxhA 253 4.95e+01 c.2.1.2 76725 1n6zA 105 4.99e+01 d.263.1.1 85369 1xc3A 302 5.01e+01 1itwA 741 5.01e+01 c.77.1.2 76793 1qorA 327 5.04e+01 1qorA b.35.1.2,c.2.1.1 24766,29782 1rlmA 271 5.08e+01 1z6kA 293 5.10e+01 1zynA 202 5.11e+01 1crb 134 5.12e+01 1hmt b.60.1.2 27220 1dgaA 375 5.15e+01 1yagA 2ggcA 263 5.23e+01 2fl4A 149 5.24e+01 2ewcA 126 5.25e+01 1acf 125 5.30e+01 3nul d.110.1.1 40882 1akz 223 5.44e+01 3eugA c.18.1.1 31007 1rkqA 282 5.44e+01 c.108.1.10 97621 1nv8A 284 5.45e+01 c.66.1.30 86224 1w36C 1122 5.46e+01 1xmxA 385 5.54e+01 1ur3M 319 5.62e+01 c.1.7.1 99806 1wduA 245 5.70e+01 d.151.1.1 109286 1q9iA 571 5.82e+01 a.138.1.3,c.3.1.4,d.168.1.1 96273,96274,96275 1tvxA 75 5.82e+01 1tvxA d.9.1.1 37441 1efvB 255 5.86e+01 1efvB c.26.2.3 31634 1fecA 490 5.88e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30489,30490,40176 1vjlA 164 5.88e+01 d.257.1.1 100822 1mk0A 97 5.98e+01 d.226.1.1 79216 1l8bA 190 6.01e+01 d.86.1.1 73683 1hskA 326 6.01e+01 2mbr d.145.1.2,d.146.1.1 61241,61242 1wyzA 242 6.04e+01 2ftxA 90 6.05e+01 1f8fA 371 6.08e+01 b.35.1.2,c.2.1.1 83246,83247 1que 303 6.08e+01 1fnc b.43.4.2,c.25.1.1 25647,31537 1e8cA 498 6.08e+01 c.98.1.1,c.59.1.1,c.72.2.1 59377,59378,59379 1d4xA 375 6.09e+01 1yagA c.55.1.1,c.55.1.1 59107,59108 1l0qA 391 6.10e+01 b.1.3.1,b.69.2.3 77644,77645 1om1A 332 6.11e+01 d.144.1.7 93347 1m2rA 327 6.12e+01 d.144.1.7 84760 1pzxA 289 6.14e+01 c.119.1.1 95484 1uq5A 263 6.15e+01 d.165.1.1 99778 1hrhA 136 6.21e+01 1rthA c.55.3.1 33577 1kssA 571 6.25e+01 a.138.1.3,c.3.1.4,d.168.1.1 72928,72929,72930 1ff9A 450 6.28e+01 1ff9A c.2.1.3,d.81.1.2 30039,39954 1pvgA 418 6.28e+01 d.14.1.3,d.122.1.2 95161,95162 2kfnA 605 6.37e+01 1xwl c.55.3.5,e.8.1.1 33682,42975 1nwbA 124 6.38e+01 b.124.1.1 86296 1qahA 136 6.40e+01 d.79.1.1 96338 1h75A 81 6.43e+01 1h75A c.47.1.1 60716 1kxoA 184 6.48e+01 b.60.1.1 84475 1rjdA 334 6.53e+01 c.66.1.37 97558 1ogiA 303 6.53e+01 b.43.4.2,c.25.1.1 92914,92915 1kyhA 276 6.56e+01 c.72.1.4 73222 1ne2A 200 6.58e+01 c.66.1.32 85586 1i7pA 274 6.60e+01 b.43.4.2,c.25.1.1 66048,66049 2d1yA 256 6.62e+01 2gptA 523 6.68e+01 2bsaA 303 6.72e+01 2c4wA 176 6.74e+01 1onrA 316 6.75e+01 1onrA c.1.10.1 29169 1ej6D 418 6.77e+01 i.7.1.1 45970 1przA 252 6.78e+01 d.265.1.3 95064 1v5vA 401 6.78e+01 1go2A 304 6.78e+01 b.43.4.2,c.25.1.1 76243,76244 1t95A 240 6.80e+01 a.5.8.1,d.235.1.2,d.58.11.3 106705,106706,106707 1w34A 304 6.80e+01 1dik 874 6.85e+01 1dik c.1.12.2,c.8.1.1,d.142.1.5 29304,30702,41572 1xkqA 280 6.98e+01 1lxjA 104 6.98e+01 d.58.48.1 84736 1sbp 310 7.00e+01 1sbp c.94.1.1 35760 1wxdA 263 7.04e+01 2cy0A 263 7.11e+01 2d5cA 263 7.12e+01 1riqA 465 7.15e+01 a.203.1.1,d.104.1.1 97516,97517 2fymA 431 7.18e+01 1n1xA 124 7.21e+01 d.5.1.1 91548 1t9bA 677 7.25e+01 1zjjA 263 7.25e+01 1a0p 290 7.32e+01 1a0p a.60.9.1,d.163.1.1 18105,42165 1az9 457 7.33e+01 1az9 c.55.2.1,d.127.1.1 33547,41164 1qkkA 155 7.38e+01 1dbwA c.23.1.1 31104 1rloA 271 7.39e+01 1wdnA 226 7.41e+01 1lst c.94.1.1 35816 1vp2A 208 7.41e+01 2booA 247 7.45e+01 1v4pA 157 7.45e+01 1u55A 188 7.46e+01 d.278.1.1 107677 1yhvA 297 7.46e+01 1srqA 341 7.49e+01 e.55.1.1 105967 1wy2A 351 7.50e+01 1d4xG 126 7.54e+01 1d0nA d.109.1.1 59109 1kamA 194 7.55e+01 c.26.1.3 72254 1gnkA 112 7.59e+01 2pii d.58.5.1 39073 1e79G 272 7.64e+01 1e79G c.49.2.1 33158 1vd6A 224 7.65e+01 2cxcA 144 7.69e+01 1qd9A 124 7.73e+01 1qu9A d.79.1.1 39758 1hyuA 521 7.80e+01 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1rl6A 177 7.82e+01 1rl6A d.141.1.1,d.141.1.1 41473,41474 1opbA 135 7.88e+01 1hmt b.60.1.2 27216 1vk1A 242 7.89e+01 d.268.1.2 108634 2a5sA 284 7.95e+01 1vpqA 273 7.96e+01 1fx2A 235 7.96e+01 1fx2A d.58.29.1 39430 1fgs 428 7.98e+01 1fgs c.59.1.2,c.72.2.2 33959,34962 1i2oA 316 7.99e+01 1onrA c.1.10.1 61574 1t9hA 307 8.00e+01 1yq5A 144 8.02e+01 1wjxA 122 8.02e+01 2bmwA 304 8.03e+01 2bh7A 261 8.05e+01 2aeuA 374 8.06e+01 1v8eA 224 8.07e+01 1yvoA 172 8.07e+01 1jetA 517 8.20e+01 1jevA c.94.1.1 35718 2ae2A 260 8.20e+01 1bdb c.2.1.2 29945 1rz3A 201 8.25e+01 c.37.1.6 98132 1txdA 385 8.28e+01 a.87.1.1,b.55.1.1 107422,107423 1ns5A 155 8.28e+01 c.116.1.3 80705 1v3vA 333 8.33e+01 b.35.1.2,c.2.1.1 108345,108346 1mrp 309 8.35e+01 1mrp c.94.1.1 35796 1ygmA 118 8.36e+01 1ybdA 239 8.38e+01 2a4aA 281 8.40e+01 1t44G 147 8.44e+01 d.109.1.1 106395 1wy7A 207 8.45e+01 1tfuA 157 8.45e+01 c.26.1.3 106859 1u60A 310 8.45e+01 e.3.1.2 107692 1wzuA 300 8.47e+01 1l6rA 227 8.50e+01 c.108.1.10 77768 1p1cA 199 8.50e+01 c.66.1.16 87669 1gx5A 536 8.50e+01 e.8.1.4 70682 1ztcA 221 8.53e+01 2fu0A 160 8.54e+01 1tidB 119 8.55e+01 c.13.2.1 107000 1vkkA 154 8.56e+01 d.109.1.2 108669 1fpzA 212 8.57e+01 1fpzA c.45.1.1 59976 1vkhA 273 8.60e+01 c.69.1.32 108662 1khiA 176 8.62e+01 b.34.5.2,b.40.4.5 77408,77409 2azpA 318 8.64e+01 1nm1G 125 8.65e+01 d.109.1.1 80653 4ubpC 570 8.67e+01 1ubpC b.92.1.1,c.1.9.2 28431,29053 1wz7A 111 8.83e+01 1pkp 150 8.87e+01 1pkp d.14.1.1,d.50.1.2 37551,38787 1rxdA 159 8.87e+01 1h1dA 221 8.93e+01 c.66.1.1 83452 1zu4A 320 8.94e+01 1vjoA 393 8.95e+01 c.67.1.3 100827 2olbA 517 8.97e+01 1jevA c.94.1.1 35721