# List of top-scoring protein chains for t2k-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 2gvkA 317 9.96e-56 1jeoA 180 5.83e-03 c.80.1.3 66611 1qwrA 319 2.94e-01 b.82.1.3 96491 2bkyX 89 9.25e-01 2gnpA 266 1.00e+00 2bl9A 238 1.13e+00 2amlA 373 1.77e+00 1hcrA 52 1.99e+00 1hcrA a.4.1.2 16020 1l1sA 113 2.17e+00 c.114.1.1 73484 1lepA 99 2.33e+00 1lepA b.35.1.1 24649 1pch 88 2.46e+00 1ptf d.94.1.1 40564 1t0tV 248 2.62e+00 d.58.4.10 106229 1v4sA 455 2.72e+00 c.55.1.3,c.55.1.3 100309,100310 2blcA 238 2.88e+00 1m3sA 186 2.90e+00 c.80.1.3 78573 1gh6A 114 3.03e+00 a.2.3.1 65191 1moq 368 3.38e+00 1moq c.80.1.1 35302 1r8oB 71 3.65e+00 1vimA 200 3.99e+00 c.80.1.3 100758 2bgiA 272 4.34e+00 1fm0E 150 4.37e+00 1fmaE d.41.5.1 38629 1chmA 401 4.40e+00 1chmA c.55.2.1,d.127.1.1 33545,41142 2bklA 695 4.46e+00 1gtvA 214 4.48e+00 c.37.1.1 70537 1udvA 89 4.54e+00 d.68.6.1 99224 1nm1G 125 4.55e+00 d.109.1.1 80653 1zkcA 197 4.73e+00 1g3uA 214 4.91e+00 c.37.1.1 65132 1xnaA 183 5.06e+00 1xnaA b.18.1.8 23773 1omzA 293 5.14e+00 c.68.1.15 87093 1gt8C 1025 5.22e+00 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70428,70429,70430,70431,70432 1d4xG 126 5.63e+00 1d0nA d.109.1.1 59109 1z6kA 293 5.83e+00 1vggA 161 5.84e+00 1p4cA 380 6.03e+00 c.1.4.1 94100 1fmaE 150 6.13e+00 1fmaE d.41.5.1 38630 1xkrA 206 6.31e+00 1huvA 380 6.34e+00 c.1.4.1 61277 1nh9A 87 6.39e+00 d.68.6.1 91878 1jqeA 292 6.58e+00 c.66.1.19 71789 1r8gA 372 6.80e+00 d.128.1.3 104845 1a6jA 163 6.90e+00 1a6jA d.112.1.1 40915 2dlbA 80 6.98e+00 1d7yA 408 7.28e+00 1d7yA c.3.1.5,c.3.1.5,d.87.1.1 30565,30566,40204 1igs 248 7.36e+00 1a53 c.1.2.4 28565 1a53 247 7.46e+00 1a53 c.1.2.4 28564 1e1oA 504 7.70e+00 1lylA b.40.4.1,d.104.1.1 25258,40714 1l1qA 186 7.76e+00 c.61.1.1 77653 1yagG 125 7.92e+00 1d0nA d.109.1.1 40846 2b25A 336 8.14e+00 1juk 248 8.49e+00 1a53 c.1.2.4 28567 1dkrA 317 8.92e+00 1dkuA c.61.1.2,c.61.1.2 34114,34115 2aotA 292 8.96e+00 1wu4A 396 9.85e+00 1j7lA 264 1.00e+01 d.144.1.6 62697 1t6cA 315 1.01e+01 c.55.1.8,c.55.1.8 106558,106559 2hppP 79 1.01e+01 5hpgA g.14.1.1 44654 1jkoC 52 1.06e+01 a.4.1.2 66809 1v64A 108 1.12e+01 a.21.1.1 108392 1hkcA 917 1.12e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33475,33476,33477,33478 1wkaA 147 1.14e+01 1uf2A 1019 1.16e+01 e.28.1.2 99289 1j5uA 136 1.17e+01 d.208.1.1 71584 1dgkN 917 1.20e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33487,33488,33489,33490 2bkkA 264 1.23e+01 1o12A 376 1.24e+01 b.92.1.5,c.1.9.10 80758,80759 1czaN 917 1.30e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33463,33464,33465,33466 1nriA 306 1.31e+01 c.80.1.3 86123 1yzyA 413 1.37e+01 2cg4A 152 1.38e+01 1tiqA 180 1.43e+01 d.108.1.1 107010 1dciA 275 1.45e+01 1dciA c.14.1.3 30918 1yz7A 188 1.48e+01 1ugiA 84 1.48e+01 1ugiA d.17.5.1 38125 1qhaA 917 1.50e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33467,33468,33469,33470 1obpA 159 1.53e+01 1obpA b.60.1.1 27092 1je5A 206 1.57e+01 1je5A b.40.4.7 62909 1v5vA 401 1.58e+01 1aoeA 192 1.60e+01 1aoeA c.71.1.1 34923 2cx5A 158 1.64e+01 1vl7A 157 1.65e+01 b.45.1.1 108732 1df7A 159 1.66e+01 3dfr c.71.1.1 34885 1jg1A 235 1.68e+01 c.66.1.7 66661 1wi1A 126 1.75e+01 1buhB 79 1.82e+01 1puc d.97.1.1 40686 1uufA 369 1.85e+01 b.35.1.2,c.2.1.1 100006,100007 1c4kA 730 1.87e+01 1ordA c.23.1.4,c.67.1.5,d.125.1.1 31273,34502,41123 1kmqA 184 1.89e+01 c.37.1.8 84412 1vg8A 207 1.89e+01 c.37.1.8 108606 1jc9A 269 1.92e+01 d.171.1.1 66490 1hskA 326 1.97e+01 2mbr d.145.1.2,d.146.1.1 61241,61242 1gnkA 112 2.01e+01 2pii d.58.5.1 39073 2d0tA 406 2.03e+01 1j7iA 264 2.06e+01 1j7iA d.144.1.6 62694 1a6dB 543 2.12e+01 1a6dA a.129.1.2,c.8.5.2,d.56.1.2 19489,30820,38937 1q2lA 939 2.19e+01 1rwzA 245 2.22e+01 d.131.1.2,d.131.1.2 98005,98006 1ughI 82 2.23e+01 1ugiA d.17.5.1 38133 1ipaA 274 2.23e+01 c.116.1.1,d.79.3.3 71254,71255 2c3zA 222 2.24e+01 2f5gA 133 2.28e+01 1hp4A 512 2.30e+01 1hp4A c.1.8.6,d.92.2.1 61111,61112 1w5fA 353 2.32e+01 1jakA 512 2.32e+01 c.1.8.6,d.92.2.1 66472,66473 1hcgA 241 2.32e+01 5ptp b.47.1.2 26341 1esc 306 2.34e+01 1esc c.23.10.1 31334 1z0jA 170 2.35e+01 1tx4B 178 2.39e+01 1ctqA c.37.1.8 32045 1l9gA 192 2.40e+01 c.18.1.2 84568 1ordA 730 2.42e+01 1ordA c.23.1.4,c.67.1.5,d.125.1.1 31274,34503,41124 1im4A 221 2.42e+01 e.8.1.7 62581 2bcgG 453 2.44e+01 1rv9A 259 2.48e+01 d.194.1.2 105105 1dqsA 393 2.48e+01 1dqsA e.22.1.1 43347 1ni9A 338 2.51e+01 e.7.1.2 85739 2bbeA 108 2.53e+01 1sg6A 393 2.54e+01 e.22.1.1 105522 2b20A 403 2.54e+01 2f1kA 279 2.56e+01 1wmuA 141 2.59e+01 a.1.1.2 109416 2f8mA 244 2.60e+01 1ou0A 207 2.61e+01 c.23.17.1 93536 1vi2A 300 2.62e+01 c.2.1.7,c.58.1.5 100726,100727 1ow1A 195 2.64e+01 b.131.1.3 93625 1hp5A 512 2.65e+01 1hp4A c.1.8.6,d.92.2.1 61113,61114 1ibsA 317 2.67e+01 c.61.1.2,c.61.1.2 66107,66108 1fp6A 289 2.68e+01 1cp2A c.37.1.10 32243 1ri7A 171 2.69e+01 a.4.5.32,d.58.4.2 97504,97505 1rr7A 129 2.69e+01 a.4.1.14 105075 2bcgY 206 2.76e+01 1udiI 83 2.79e+01 1ugiA d.17.5.1 38124 1a0hA 159 2.79e+01 1a0hA b.47.1.2,g.14.1.1 26229,44655 1wb4A 297 2.90e+01 1ys4A 354 2.93e+01 2givA 295 2.95e+01 7reqA 727 2.98e+01 1reqA c.1.19.1,c.23.6.1 29616,31243 2a3nA 355 3.00e+01 5reqA 727 3.01e+01 1reqA c.1.19.1,c.23.6.1 29632,31259 1wpoB 256 3.05e+01 1lay b.57.1.1 27013 1g0hA 252 3.08e+01 1dk4A e.7.1.1 60171 2calA 154 3.16e+01 1hyhA 309 3.19e+01 1hyhA c.2.1.5,d.162.1.1 30150,42117 1sheA 103 3.23e+01 d.274.1.1 105551 2nef 136 3.27e+01 1efnB d.102.1.1 40704 1nz0A 118 3.36e+01 d.14.1.2 86433 1nnhA 294 3.37e+01 d.104.1.1 92005 1g03A 134 3.41e+01 1qrjB a.73.1.1 60162 1hkbA 917 3.44e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33479,33480,33481,33482 1sotA 320 3.46e+01 b.36.1.4,b.47.1.1 105852,105853 2fqxA 318 3.46e+01 2b61A 377 3.47e+01 1ukvG 453 3.52e+01 c.3.1.3,c.3.1.3,d.16.1.6 107915,107916,107917 1gklA 297 3.64e+01 c.69.1.2 65250 1g8oA 310 3.71e+01 1g8oA c.68.1.9 60375 1h0xA 100 3.74e+01 d.68.6.1 76451 2kfnA 605 3.77e+01 1xwl c.55.3.5,e.8.1.1 33682,42975 1azo 232 3.77e+01 1azo c.52.1.14 33329 1np6A 174 3.78e+01 c.37.1.10 85954 2a6aA 218 3.81e+01 1aqcA 172 3.97e+01 1x11A b.55.1.2 26983 3rubS 123 3.98e+01 1rboC d.73.1.1 39616 1qaxA 428 3.99e+01 1qaxA d.58.20.1,d.179.1.1 39376,42597 1yemA 179 4.00e+01 1z08A 170 4.01e+01 1m0wA 491 4.07e+01 c.30.1.4,d.142.1.6 78363,78364 1it2A 146 4.08e+01 a.1.1.2 66365 1oe4A 247 4.12e+01 c.18.1.3 86895 2a1iA 146 4.16e+01 1gt1A 159 4.16e+01 b.60.1.1 90515 1x8dA 104 4.17e+01 1e30A 155 4.20e+01 1rcy b.6.1.1 23016 1jw3A 140 4.31e+01 d.208.1.1 67373 1vjqA 79 4.32e+01 k.43.1.1 100830 1l6wA 220 4.33e+01 c.1.10.1 73632 1reqA 727 4.33e+01 1reqA c.1.19.1,c.23.6.1 29620,31247 1tv9A 335 4.34e+01 1g5pA 289 4.37e+01 1cp2A c.37.1.10 32253 1zy4A 303 4.43e+01 1udxA 416 4.43e+01 b.117.1.1,c.37.1.8,d.242.1.1 99228,99229,99230 1xkpC 143 4.44e+01 1vpkA 378 4.44e+01 1hn2A 159 4.46e+01 b.60.1.1 65890 1rcwA 231 4.54e+01 a.132.1.4 97299 1rboC 123 4.58e+01 1rboC d.73.1.1 39634 1d6zA 727 4.76e+01 1oacA b.30.2.1,d.17.2.1,d.17.2.1,d.82.1.1 24394,38015,38016,40007 2cb2A 318 4.82e+01 1k1gA 131 4.83e+01 d.51.1.1 68015 1wdnA 226 4.91e+01 1lst c.94.1.1 35816 1nw1A 429 4.91e+01 d.144.1.8 86286 1deuA 277 4.92e+01 1theB d.3.1.1 37085 2fb0A 94 4.97e+01 1p4xA 250 4.97e+01 a.4.5.28,a.4.5.28 87784,87785 1a99A 344 4.99e+01 1pot c.94.1.1 35812 1b3rA 431 5.00e+01 1b3rA c.2.1.4,c.23.12.3 30106,31366 1ge9A 184 5.01e+01 1dd5A d.67.3.1 60463 1d8yA 605 5.10e+01 1xwl c.55.3.5,e.8.1.1 33684,42977 1wn5A 130 5.12e+01 1sc6A 404 5.16e+01 1uu1A 335 5.27e+01 c.67.1.1 99993 2gnxA 365 5.28e+01 1d0nA 729 5.28e+01 1d0nA d.109.1.1,d.109.1.1,d.109.1.1,d.109.1.1,d.109.1.1,d.109.1.1 40834,40835,40836,40837,40838,40839 1p1lA 102 5.30e+01 d.58.5.2 87695 1ukvY 206 5.30e+01 c.37.1.8 107918 1qm4A 396 5.30e+01 1mxb d.130.1.1,d.130.1.1,d.130.1.1 41350,41351,41352 1l9hA 349 5.37e+01 f.13.1.2 73720 1bbpA 173 5.40e+01 1bbpA b.60.1.1 27147 1j6rA 214 5.43e+01 d.173.1.2 71598 1a6r 471 5.46e+01 3gcb d.3.1.1 37033 1cs8A 316 5.48e+01 1cs8A d.3.1.1 37065 1a6dA 545 5.49e+01 1a6dA a.129.1.2,c.8.5.2,d.56.1.2 19488,30819,38936 1d0qA 103 5.53e+01 1d0qA g.41.3.2 45208 1atx 46 5.56e+01 1ahl g.9.1.1 44600 1xfjA 261 5.62e+01 d.194.1.2 109585 1gkkA 297 5.69e+01 c.69.1.2 65248 1fj2A 232 5.70e+01 1auoA c.69.1.14 34720 1gcb 454 5.72e+01 3gcb d.3.1.1 37034 1oacA 727 5.78e+01 1oacA b.30.2.1,d.17.2.1,d.17.2.1,d.82.1.1 24390,38007,38008,40003 1z7dA 433 5.79e+01 1vehA 92 5.92e+01 1opc 110 5.96e+01 1opc a.4.6.1 16231 1gggA 226 5.97e+01 1lst c.94.1.1 35817 1h8eG 272 5.97e+01 1e79G c.49.2.1 60756 1b3qA 379 5.97e+01 1b3qA a.30.2.1,b.40.7.1,d.122.1.3 16993,25454,41112 1thqA 170 6.04e+01 f.4.1.2 106920 1egdA 396 6.04e+01 3mdeA a.29.3.1,e.6.1.1 16596,42857 3gcb 470 6.06e+01 3gcb d.3.1.1 37032 1no5A 114 6.07e+01 d.218.1.5 92014 1griA 217 6.08e+01 1griA b.34.2.1,b.34.2.1,d.93.1.1 24531,24532,40473 1uzbA 516 6.10e+01 c.82.1.1 100220 1yqeA 282 6.10e+01 1zejA 293 6.10e+01 1u24A 337 6.12e+01 1lay 256 6.15e+01 1lay b.57.1.1 27014 1tf4A 605 6.16e+01 1tf4A a.102.1.2,b.2.2.2 18827,22393 1npoC 95 6.16e+01 1npoA b.9.1.1 23271 1mo1A 87 6.37e+01 d.94.1.1 91363 2aobA 99 6.39e+01 1t6nA 220 6.46e+01 c.37.1.19 106576 1npdA 288 6.50e+01 c.2.1.7,c.58.1.5 80681,80682 1ko6A 187 6.52e+01 b.119.1.1 77471 1kq3A 376 6.56e+01 e.22.1.2 68790 1mo2A 294 6.63e+01 c.69.1.22 79331 8rucI 123 6.66e+01 1rboC d.73.1.1 39629 1bk0 331 6.66e+01 1bk0 b.82.2.1 28118 1k75A 434 6.67e+01 c.82.1.2 68253 1kfd 605 6.71e+01 1xwl c.55.3.5,e.8.1.1 33694,42987 1vkjA 285 6.78e+01 c.37.1.5 108666 1jljA 189 6.86e+01 c.57.1.1 63169 1b8yA 167 6.92e+01 1hfc d.92.1.11 40377 1qsmA 152 6.92e+01 1qsmA d.108.1.1 40808 1senA 164 7.01e+01 c.47.1.1 105465 1ni4B 341 7.01e+01 c.36.1.7,c.48.1.2 85729,85730 1ibcB 88 7.05e+01 1pauB 1sgvA 316 7.05e+01 b.122.1.1,d.265.1.2 98858,98859 1fjgJ 105 7.06e+01 1fjfJ d.58.15.1 39330 1wpoA 256 7.07e+01 1lay b.57.1.1 27012 1o0xA 262 7.08e+01 d.127.1.1 80755 1sfe 180 7.12e+01 1sfe a.4.2.1,c.55.7.1 16073,33748 1cjl 312 7.26e+01 1cs8A d.3.1.1 37066 1sxrA 183 7.28e+01 d.118.1.1 106101 2ct5A 73 7.29e+01 2bkyA 97 7.38e+01 2avnA 260 7.39e+01 2fp7A 54 7.41e+01 1kb9B 352 7.45e+01 d.185.1.1,d.185.1.1 77313,77314 1o54A 277 7.45e+01 c.66.1.13 92482 1q4rA 112 7.54e+01 d.58.4.4 95823 1m7bA 184 7.58e+01 c.37.1.8 74572 2faoA 309 7.64e+01 1r1mA 164 7.66e+01 d.79.7.1 96820 1a7aA 432 7.66e+01 1b3rA c.2.1.4,c.23.12.3 30104,31364 1riqA 465 7.74e+01 a.203.1.1,d.104.1.1 97516,97517 1g2qA 187 7.75e+01 c.61.1.1 65117 4ts1A 319 7.75e+01 2ts1 c.26.1.1 31565 1r8sA 164 7.77e+01 c.37.1.8 97247 1kxrA 339 7.80e+01 d.3.1.3 73175 1sc3B 88 7.86e+01 1fjsA 234 7.90e+01 1ucyE b.47.1.2 26336 1hy7A 173 8.04e+01 d.92.1.11 65957 1fkmA 396 8.09e+01 1fkmA a.69.2.1,a.69.2.1 18315,18316 1z54A 132 8.16e+01 1xjuA 163 8.16e+01 1u19A 349 8.23e+01 1kmvA 186 8.31e+01 c.71.1.1 72757 1dkuA 317 8.35e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 2ga9D 469 8.36e+01 1tl9A 339 8.38e+01 1klnA 605 8.38e+01 1xwl c.55.3.5,e.8.1.1 33693,42986 1wruA 379 8.40e+01 2g8lA 299 8.44e+01 1b4kA 337 8.44e+01 1b4kA c.1.10.3 29184 1gzgA 337 8.45e+01 c.1.10.3 70805 1nd4A 264 8.48e+01 d.144.1.6 91815 1dk4A 252 8.52e+01 1dk4A e.7.1.1 42970 1li4A 432 8.55e+01 c.2.1.4,c.23.12.3 84616,84617 1wddS 128 8.56e+01 1yfsA 465 8.56e+01 1u0tA 307 8.58e+01 e.52.1.1 107567 1ftrA 296 8.61e+01 1ftrA d.58.33.1,d.58.33.1 39485,39486 1pq9A 253 8.62e+01 a.123.1.1 95004 1rhs 296 8.65e+01 1rhs c.46.1.2,c.46.1.2 32703,32704 1odmA 331 8.66e+01 b.82.2.1 86875 2ae6A 166 8.76e+01 1f88A 348 8.82e+01 1f88A f.13.1.2 43429 1etu 394 8.85e+01 1efcA c.37.1.8 64737 1bmqB 88 8.86e+01 1pauB