# List of top-scoring protein chains for t2k-100-30-near-backbone-11-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 2f4qA 346 2.31e-01 1ffyA 917 5.34e-01 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16926,26891,31593 1qu2A 917 5.34e-01 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16925,26890,31592 1ui0A 205 5.80e-01 c.18.1.2 99411 1lktA 104 9.54e-01 1lktA b.90.1.1 28398 134l 130 1.29e+00 3lzt d.2.1.2 36505 1bb3A 130 1.53e+00 3lzt d.2.1.2 36544 1jogA 146 1.56e+00 a.24.16.2 77142 1b7mA 130 1.95e+00 3lzt d.2.1.2 36569 2c3vA 102 2.03e+00 1b5vA 130 2.08e+00 3lzt d.2.1.2 36563 1tp6A 128 2.09e+00 d.17.4.12 107184 1b5zA 130 2.17e+00 3lzt d.2.1.2 36567 1qqyA 130 2.38e+00 3lzt d.2.1.2 36586 1lz1 130 2.43e+00 3lzt d.2.1.2 36415 1ebdA 455 2.48e+00 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30577,30578,40210 1b7qA 130 2.51e+00 3lzt d.2.1.2 36549 1jsf 130 2.62e+00 3lzt d.2.1.2 36410 133l 130 2.68e+00 3lzt d.2.1.2 36524 1b7oA 130 2.87e+00 3lzt d.2.1.2 36491 1b5yA 130 2.89e+00 3lzt d.2.1.2 36570 1l9gA 192 2.95e+00 c.18.1.2 84568 1t5yA 190 3.02e+00 b.122.1.1,d.17.6.3 106495,106496 1i3dA 146 3.04e+00 a.1.1.2 61587 1b7nA 130 3.04e+00 3lzt d.2.1.2 36468 1b5xA 130 3.07e+00 3lzt d.2.1.2 36550 1yksA 440 3.14e+00 1omiA 248 3.17e+00 b.82.3.3,a.4.5.4 87079,87080 1b7lA 130 3.27e+00 3lzt d.2.1.2 36515 1b7rA 130 3.28e+00 3lzt d.2.1.2 36436 2fafA 608 3.28e+00 1b7pA 130 3.32e+00 3lzt d.2.1.2 36551 1b5wA 130 3.45e+00 3lzt d.2.1.2 36557 1b5uA 130 3.46e+00 3lzt d.2.1.2 36453 1d4oA 184 3.56e+00 1d4oA c.31.1.4 31748 1b24A 188 3.74e+00 1b24A d.95.2.1,d.95.2.1 40573,40574 1tyyA 339 3.86e+00 1yaxA 153 4.85e+00 1lmt 136 5.10e+00 3lzt d.2.1.2 36416 1b7s 130 5.32e+00 3lzt d.2.1.2 36571 1szoA 257 5.40e+00 c.14.1.3 106164 1h7mA 102 5.63e+00 d.79.3.1 83485 1yx1A 264 6.30e+00 1yrlA 491 6.59e+00 1m7xA 617 6.63e+00 b.1.18.2,b.71.1.1,c.1.8.1 78749,78750,78751 1o8uA 257 6.95e+00 c.14.1.3 81194 1iiyA 101 7.20e+00 b.89.1.1 66152 1vq2A 193 7.66e+00 2gclA 261 8.25e+00 1oyiA 82 8.67e+00 a.4.5.19 93729 1g5aA 628 8.94e+00 b.71.1.1,c.1.8.1 65152,65153 1gyxA 76 8.95e+00 d.80.1.1 76387 1w41A 101 9.08e+00 1cch 82 9.21e+00 451c a.3.1.1 15902 1pufB 73 9.25e+00 a.4.1.1 95132 1qx4A 274 9.56e+00 b.43.4.2,c.25.1.1 104624,104625 2gw6A 123 9.68e+00 2jdxA 385 1.00e+01 1jdw d.126.1.2 41139 1ny1A 240 1.07e+01 c.6.2.3 86395 1i8vA 96 1.19e+01 d.1.1.2 61985 1b8iB 63 1.24e+01 1akhA a.4.1.1 16011 1rgeA 96 1.25e+01 1rgeA d.1.1.2 36028 1vbvA 105 1.26e+01 1gmpA 96 1.27e+01 1rgeA d.1.1.2 36036 1iscA 192 1.28e+01 1avmA a.2.11.1,d.44.1.1 15733,38726 1isaA 192 1.28e+01 1avmA a.2.11.1,d.44.1.1 15731,38724 1sqwA 188 1.29e+01 1ne9A 335 1.30e+01 d.108.1.4,d.108.1.4 91839,91840 1vhnA 318 1.30e+01 c.1.4.1 100693 1sedA 117 1.40e+01 a.219.1.1 105449 1bj8 109 1.41e+01 1bquA b.1.2.1 22070 1e25A 282 1.42e+01 1e25A e.3.1.1 42731 1vfrA 218 1.46e+01 1vfrA d.90.1.1 40247 1izoA 417 1.55e+01 a.104.1.1 83851 1bvh 157 1.58e+01 1dg9A c.44.1.1 32640 1i56A 130 1.58e+01 d.2.1.2 66033 1vr8A 142 1.59e+01 3ezmA 101 1.61e+01 3ezmA b.89.1.1 28395 1xhcA 367 1.63e+01 1b9wA 89 1.67e+01 1b9wA g.3.11.4,g.3.11.4 44334,44335 1jdw 423 1.67e+01 1jdw d.126.1.2 41129 1cor 82 1.75e+01 451c a.3.1.1 15903 1zbfA 142 1.80e+01 1aca 86 1.80e+01 1aca a.11.1.1 16367 1cqyA 99 1.84e+01 1b9zA b.3.1.1 22527 1xewY 172 1.85e+01 2eshA 118 1.90e+01 1ugjA 141 1.91e+01 b.41.1.3 107826 1bb4A 130 1.93e+01 3lzt d.2.1.2 36583 2cfuA 658 1.96e+01 1aa2 108 1.97e+01 1bkrA a.40.1.1 17395 1lniA 96 1.99e+01 d.1.1.2 74046 1bkrA 109 2.03e+01 1bkrA a.40.1.1 17394 1hbg 147 2.09e+01 2hbg a.1.1.2 15015 1txkA 498 2.12e+01 b.1.18.2,b.30.5.9 107425,107426 2hbg 147 2.21e+01 2hbg a.1.1.2 15014 1r4gA 53 2.25e+01 a.8.5.1 96996 1khbA 625 2.25e+01 c.91.1.1,c.109.1.1 68606,68607 1omrA 201 2.31e+01 a.39.1.5 93349 1zkdA 387 2.34e+01 1jf3A 147 2.37e+01 a.1.1.2 71642 1dxtB 147 2.37e+01 1abwA a.1.1.2 15450 1dk8A 147 2.38e+01 1agrE a.91.1.1 18548 1j7gA 144 2.45e+01 c.110.1.1 84130 2b59B 172 2.48e+01 1s4nA 348 2.51e+01 c.68.1.16 98501 1z67A 135 2.51e+01 1hb6A 86 2.52e+01 a.11.1.1 70959 1jf4A 147 2.59e+01 a.1.1.2 71643 1z1lA 345 2.63e+01 1phr 157 2.66e+01 1dg9A c.44.1.1 32635 1gmwA 143 2.66e+01 b.107.1.1,d.58.38.1 65347,65348 1ri9A 102 2.77e+01 b.34.2.1 97506 2gi9A 56 2.78e+01 1irdB 146 2.81e+01 a.1.1.2 66287 1b72B 87 2.83e+01 1akhA a.4.1.1 16001 2d2mD 145 2.88e+01 1c75A 71 2.95e+01 451c a.3.1.1 15796 2abwA 227 2.96e+01 1cds 77 2.96e+01 1cds g.7.1.3 44461 1dc7A 124 2.97e+01 1dbwA c.23.1.1 31093 1tqzA 133 2.98e+01 1yioA 208 3.06e+01 1tr0A 108 3.15e+01 d.58.4.4 107261 1hbyA 123 3.24e+01 7rsa d.5.1.1 60936 1is1A 185 3.26e+01 d.67.3.1 83704 1babB 146 3.26e+01 1abwA a.1.1.2 15414 2a25A 193 3.38e+01 1xwwA 157 3.38e+01 1mpyA 307 3.45e+01 1mpyA d.32.1.3,d.32.1.3 38508,38509 1bquA 215 3.47e+01 1bquA b.1.2.1,b.1.2.1 22066,22067 1ttzA 87 3.49e+01 c.47.1.1 107309 1b1jA 123 3.52e+01 7rsa d.5.1.1 37298 1u0tA 307 3.55e+01 e.52.1.1 107567 1i0cA 60 3.57e+01 1aojA b.34.2.1 61485 1uvqA 197 3.59e+01 b.1.1.2,d.19.1.1 100062,100063 1zin 217 3.60e+01 1zin c.37.1.1,g.41.2.1 31915,45178 1vjlA 164 3.71e+01 d.257.1.1 100822 1vjfA 180 3.73e+01 d.116.1.1 100809 1fjgP 88 3.75e+01 1emwA d.27.1.1 38444 2gk3A 256 3.75e+01 1ci4A 89 3.79e+01 1qckA a.60.5.1 17970 1gm6A 175 3.91e+01 b.60.1.1 70272 1idm 343 3.93e+01 1cnzA c.77.1.1 35035 1rpyA 114 3.94e+01 d.93.1.1 97718 1emwA 88 4.09e+01 1emwA d.27.1.1 38448 1o7xD 377 4.14e+01 a.103.1.1 81174 1o7xC 377 4.15e+01 a.103.1.1 81173 2ct5A 73 4.15e+01 1j7yB 146 4.18e+01 a.1.1.2 66427 2fa8A 105 4.19e+01 1q4rA 112 4.22e+01 d.58.4.4 95823 1uzcA 71 4.28e+01 a.159.2.1 100222 1v4eA 299 4.28e+01 a.128.1.1 100296 1xaa 345 4.29e+01 1cnzA c.77.1.1 35033 1v0jA 399 4.29e+01 1y8qB 640 4.34e+01 1gmuA 143 4.35e+01 b.107.1.1,d.58.38.1 65335,65336 2dg5B 190 4.37e+01 1vreA 147 4.43e+01 2hbg a.1.1.2 15017 1ktbA 405 4.44e+01 b.71.1.1,c.1.8.1 72960,72961 1t2lA 141 4.45e+01 1nxuA 333 4.47e+01 c.122.1.1 86389 2bgcA 238 4.58e+01 1cdq 77 4.59e+01 1cds g.7.1.3 44459 1cmyB 146 4.60e+01 1abwA a.1.1.2 15544 2abd 86 4.60e+01 1aca a.11.1.1 16366 1dr8B 344 4.67e+01 1cnzA c.77.1.1 35052 1b1iA 123 4.71e+01 7rsa d.5.1.1 37295 2dchX 216 4.84e+01 1k2fA 190 4.87e+01 b.8.1.2 68054 1vjvA 415 4.87e+01 d.3.1.9 108632 1a4yB 123 4.91e+01 7rsa d.5.1.1 37296 1y9wA 140 4.93e+01 1qhoA 686 4.95e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21844,22513,27751,28738 1f5vA 240 4.98e+01 1bkjA d.90.1.1 40255 1un3A 123 5.09e+01 d.5.1.1 99646 1lwdA 413 5.11e+01 c.77.1.1 78265 1k59A 123 5.19e+01 d.5.1.1 72073 1c0eA 157 5.23e+01 1dg9A c.44.1.1 32638 1yqtA 538 5.27e+01 2ezxA 89 5.33e+01 1qckA a.60.5.1 17978 1pulA 125 5.34e+01 1mxiA 160 5.40e+01 c.116.1.1 79646 1ntr 124 5.44e+01 1dbwA c.23.1.1 31092 1ijqA 316 5.46e+01 1ijqA b.68.5.1,g.3.11.1 62506,62507 1u5kA 244 5.47e+01 1dvoA 152 5.60e+01 1dvoA a.136.1.1 19623 1oksA 56 5.62e+01 a.8.5.1 93271 1a01B 146 5.65e+01 1abwA a.1.1.2 15448 1gv3A 248 5.70e+01 a.2.11.1,d.44.1.1 70585,70586 1tlfA 301 5.74e+01 1tlfA c.93.1.1 35687 1izmA 184 5.78e+01 a.199.1.1 90725 1qgtA 149 5.78e+01 1qgtA a.62.1.1 18135 1e19A 314 5.78e+01 1b7bA c.73.1.1 34967 1o5oA 221 5.84e+01 c.61.1.1 92509 1ur1A 378 5.85e+01 c.1.8.3 99804 1ddmA 135 5.89e+01 2nmbA b.55.1.2 26993 1b54 257 5.90e+01 1ct5A c.1.6.2 28664 1tie 172 5.91e+01 1wba b.42.4.1 25592 1b2vA 188 5.91e+01 1b2vA d.35.1.1 38532 1kutA 230 5.95e+01 d.143.1.1 73017 1hn2A 159 5.96e+01 b.60.1.1 65890 1qmvA 197 5.97e+01 1qq2A c.47.1.10 33066 1gt1A 159 5.98e+01 b.60.1.1 90515 1obpA 159 6.09e+01 1obpA b.60.1.1 27092 1j79A 347 6.13e+01 1j79A c.1.9.4 62675 1lgpA 116 6.17e+01 b.26.1.2 73890 1o7xB 377 6.39e+01 a.103.1.1 81172 1ztcA 221 6.46e+01 1xxoA 147 6.51e+01 1nuuA 252 6.55e+01 c.26.1.3 86209 1vr9A 213 6.60e+01 1iseA 185 6.62e+01 d.67.3.1 90691 2fbmA 291 6.67e+01 2a2pA 129 6.67e+01 1bxwA 172 6.72e+01 1bxwA f.4.1.1 43743 1vfqA 143 6.73e+01 1sphA 88 6.74e+01 1ptf d.94.1.1 40544 1asx 159 6.78e+01 1a6dA c.8.5.2 30821 1zip 217 6.78e+01 1zin c.37.1.1,g.41.2.1 31916,45179 1i88A 389 6.78e+01 c.95.1.2,c.95.1.2 66070,66071 1lqaA 346 6.81e+01 c.1.7.1 84674 1w4xA 542 6.89e+01 c.3.1.5,c.3.1.5 109171,109172 1zy9A 564 6.90e+01 1h8eG 272 6.90e+01 1e79G c.49.2.1 60756 1vrvA 101 6.94e+01 1b1eA 123 6.98e+01 7rsa d.5.1.1 37300 1dghB 498 7.00e+01 1cf9A e.5.1.1 42791 1ek8A 185 7.00e+01 1ek8A d.67.3.1 59444 1aw0 72 7.01e+01 1aw0 d.58.17.1 39342 1qauA 112 7.03e+01 1qauA b.36.1.1 24779 1zgzA 122 7.04e+01 1wchA 315 7.09e+01 1zcxA 178 7.12e+01 1i86A 389 7.17e+01 c.95.1.2,c.95.1.2 66068,66069 2fhxA 246 7.22e+01 1u07A 90 7.26e+01 2ciaA 102 7.28e+01 1lrwA 600 7.31e+01 b.70.1.1 91111 1nvpB 57 7.36e+01 a.32.1.1 92211 1t3yA 141 7.36e+01 1pczA 191 7.50e+01 1ytbA d.129.1.1,d.129.1.1 41292,41293 1dg9A 157 7.51e+01 1dg9A c.44.1.1 32637 1rec 201 7.52e+01 1rec a.39.1.5 17326 2cw8A 537 7.53e+01 1o5xA 248 7.58e+01 c.1.1.1 92528 1jotA 133 7.63e+01 1jotA 1vmjA 151 7.65e+01 1ew3A 159 7.67e+01 1mup b.60.1.1 27114 1jb7B 260 7.70e+01 1otcB b.40.4.3 62839 1h91A 180 7.72e+01 b.60.1.1 60805 1v32A 101 7.75e+01 a.42.1.1 100277 1aoiG 116 7.81e+01 1aoiC a.22.1.1 16441 1b07A 59 7.85e+01 1ckaA b.34.2.1 24461 1jyoE 105 7.86e+01 d.184.1.2 67487 1aoiC 116 7.90e+01 1aoiC a.22.1.1 16440 1o7fA 469 7.92e+01 a.4.5.31,b.82.3.2,b.82.3.2 81131,81132,81133 1rf6A 427 7.92e+01 d.68.2.2 97366 2f9zC 159 7.92e+01 1vkrA 125 7.97e+01 c.44.2.1 108689 5eau 548 8.03e+01 5eat a.102.4.1,a.128.1.3 18851,19443 1efaA 333 8.10e+01 1tlfA a.35.1.5,c.93.1.1 17106,35691 1i4uA 181 8.20e+01 b.60.1.1 61732 1ipd 345 8.26e+01 1cnzA c.77.1.1 35038 1hjp 203 8.27e+01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16274,17947,25266 1cv8 174 8.27e+01 1cv8 d.3.1.1 37089 1a00B 146 8.28e+01 1abwA a.1.1.2 15469 2dbnA 461 8.30e+01 1b7bA 310 8.32e+01 1b7bA c.73.1.1 34963 1qq2A 199 8.34e+01 1qq2A c.47.1.10 33064 1vnc 609 8.45e+01 1vns a.111.1.3 19065 1fecA 490 8.47e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30489,30490,40176 1j3bA 529 8.48e+01 c.91.1.1,c.109.1.1 77071,77072 1xg1A 67 8.63e+01 1s72L 165 8.69e+01 c.12.1.1 105331 1mbg 53 8.70e+01 a.4.1.3 16033 1iakA 199 8.79e+01 1iakA b.1.1.2,d.19.1.1 21625,38199 1jj2K 164 8.83e+01 1ffkJ c.12.1.1 63096 1ckaA 57 8.85e+01 1ckaA b.34.2.1 24459 1w9aA 147 8.88e+01