# 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 3.29e-01 1d4oA 184 4.85e-01 1d4oA c.31.1.4 31748 1ffyA 917 6.42e-01 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16926,26891,31593 1qu2A 917 6.42e-01 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16925,26890,31592 1ui0A 205 6.49e-01 c.18.1.2 99411 1omiA 248 9.50e-01 b.82.3.3,a.4.5.4 87079,87080 134l 130 1.19e+00 3lzt d.2.1.2 36505 1lktA 104 1.19e+00 1lktA b.90.1.1 28398 1bb3A 130 1.43e+00 3lzt d.2.1.2 36544 1yaxA 153 1.60e+00 1ebdA 455 1.62e+00 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30577,30578,40210 1tzaA 134 1.70e+00 b.1.23.1 107468 1yksA 440 1.72e+00 1b7mA 130 1.73e+00 3lzt d.2.1.2 36569 1b24A 188 1.80e+00 1b24A d.95.2.1,d.95.2.1 40573,40574 1b5vA 130 1.97e+00 3lzt d.2.1.2 36563 2fafA 608 2.03e+00 1b5zA 130 2.07e+00 3lzt d.2.1.2 36567 1lz1 130 2.14e+00 3lzt d.2.1.2 36415 1tp6A 128 2.20e+00 d.17.4.12 107184 1jogA 146 2.33e+00 a.24.16.2 77142 1b7qA 130 2.34e+00 3lzt d.2.1.2 36549 1jsf 130 2.36e+00 3lzt d.2.1.2 36410 1qqyA 130 2.46e+00 3lzt d.2.1.2 36586 133l 130 2.49e+00 3lzt d.2.1.2 36524 1b7oA 130 2.51e+00 3lzt d.2.1.2 36491 1b5xA 130 2.60e+00 3lzt d.2.1.2 36550 1b7nA 130 2.61e+00 3lzt d.2.1.2 36468 1b5yA 130 2.66e+00 3lzt d.2.1.2 36570 1b7lA 130 2.78e+00 3lzt d.2.1.2 36515 1b7rA 130 2.79e+00 3lzt d.2.1.2 36436 1b7pA 130 2.83e+00 3lzt d.2.1.2 36551 1b5wA 130 3.06e+00 3lzt d.2.1.2 36557 1b5uA 130 3.08e+00 3lzt d.2.1.2 36453 1l9gA 192 3.73e+00 c.18.1.2 84568 1h7mA 102 3.87e+00 d.79.3.1 83485 2c3vA 102 3.96e+00 1lmt 136 4.38e+00 3lzt d.2.1.2 36416 1b7s 130 4.53e+00 3lzt d.2.1.2 36571 1mxiA 160 4.57e+00 c.116.1.1 79646 1w41A 101 5.07e+00 1yx1A 264 5.45e+00 1i3dA 146 5.65e+00 a.1.1.2 61587 1m7xA 617 6.09e+00 b.1.18.2,b.71.1.1,c.1.8.1 78749,78750,78751 1pufB 73 6.38e+00 a.4.1.1 95132 1t5yA 190 6.92e+00 b.122.1.1,d.17.6.3 106495,106496 1yrlA 491 7.19e+00 1tyyA 339 7.46e+00 1vq2A 193 7.46e+00 1e25A 282 7.49e+00 1e25A e.3.1.1 42731 1cch 82 8.28e+00 451c a.3.1.1 15902 1b8iB 63 8.36e+00 1akhA a.4.1.1 16011 1ny1A 240 8.76e+00 c.6.2.3 86395 1g5aA 628 8.88e+00 b.71.1.1,c.1.8.1 65152,65153 1ne9A 335 8.98e+00 d.108.1.4,d.108.1.4 91839,91840 2jdxA 385 9.12e+00 1jdw d.126.1.2 41139 1gyxA 76 9.14e+00 d.80.1.1 76387 1oyiA 82 9.43e+00 a.4.5.19 93729 1qx4A 274 1.00e+01 b.43.4.2,c.25.1.1 104624,104625 1kutA 230 1.09e+01 d.143.1.1 73017 1yioA 208 1.12e+01 2eshA 118 1.21e+01 1szoA 257 1.22e+01 c.14.1.3 106164 2gclA 261 1.24e+01 1ugjA 141 1.26e+01 b.41.1.3 107826 1dk8A 147 1.34e+01 1agrE a.91.1.1 18548 2bgcA 238 1.34e+01 1iiyA 101 1.35e+01 b.89.1.1 66152 1z67A 135 1.36e+01 1zbfA 142 1.42e+01 1i56A 130 1.42e+01 d.2.1.2 66033 1jdw 423 1.45e+01 1jdw d.126.1.2 41129 1dc7A 124 1.47e+01 1dbwA c.23.1.1 31093 1iscA 192 1.50e+01 1avmA a.2.11.1,d.44.1.1 15733,38726 1o8uA 257 1.55e+01 c.14.1.3 81194 1cor 82 1.56e+01 451c a.3.1.1 15903 1hbg 147 1.62e+01 2hbg a.1.1.2 15015 1isaA 192 1.63e+01 1avmA a.2.11.1,d.44.1.1 15731,38724 1izoA 417 1.63e+01 a.104.1.1 83851 2cfuA 658 1.63e+01 1gm6A 175 1.64e+01 b.60.1.1 70272 1i86A 389 1.67e+01 c.95.1.2,c.95.1.2 66068,66069 1b72B 87 1.68e+01 1akhA a.4.1.1 16001 2hbg 147 1.68e+01 2hbg a.1.1.2 15014 1i88A 389 1.71e+01 c.95.1.2,c.95.1.2 66070,66071 1vr8A 142 1.73e+01 1byrA 155 1.73e+01 1byrA d.136.1.1 41450 1bb4A 130 1.76e+01 3lzt d.2.1.2 36583 1bj8 109 1.77e+01 1bquA b.1.2.1 22070 1bvh 157 1.77e+01 1dg9A c.44.1.1 32640 1jf3A 147 1.79e+01 a.1.1.2 71642 1s3rA 535 1.80e+01 1vbvA 105 1.80e+01 1jf4A 147 1.80e+01 a.1.1.2 71643 2gi9A 56 1.82e+01 1rgeA 96 1.89e+01 1rgeA d.1.1.2 36028 1gmpA 96 1.93e+01 1rgeA d.1.1.2 36036 1i8vA 96 1.93e+01 d.1.1.2 61985 1aa2 108 1.95e+01 1bkrA a.40.1.1 17395 1bkrA 109 1.97e+01 1bkrA a.40.1.1 17394 1nxuA 333 1.98e+01 c.122.1.1 86389 1aca 86 1.98e+01 1aca a.11.1.1 16367 1xewY 172 1.98e+01 1ktbA 405 1.99e+01 b.71.1.1,c.1.8.1 72960,72961 1xhcA 367 2.07e+01 1vfrA 218 2.24e+01 1vfrA d.90.1.1 40247 1ntr 124 2.29e+01 1dbwA c.23.1.1 31092 1r4gA 53 2.30e+01 a.8.5.1 96996 1is1A 185 2.36e+01 d.67.3.1 83704 1vhnA 318 2.40e+01 c.1.4.1 100693 1sedA 117 2.40e+01 a.219.1.1 105449 1yqtA 538 2.46e+01 1khbA 625 2.54e+01 c.91.1.1,c.109.1.1 68606,68607 2b59B 172 2.56e+01 1zkdA 387 2.57e+01 1uvqA 197 2.57e+01 b.1.1.2,d.19.1.1 100062,100063 1b9wA 89 2.63e+01 1b9wA g.3.11.4,g.3.11.4 44334,44335 1sqwA 188 2.66e+01 1cqyA 99 2.71e+01 1b9zA b.3.1.1 22527 1hb6A 86 2.73e+01 a.11.1.1 70959 2d2mD 145 2.81e+01 1phr 157 2.86e+01 1dg9A c.44.1.1 32635 1gmwA 143 2.88e+01 b.107.1.1,d.58.38.1 65347,65348 1vjfA 180 2.90e+01 d.116.1.1 100809 1ttzA 87 2.95e+01 c.47.1.1 107309 3ezmA 101 3.02e+01 3ezmA b.89.1.1 28395 1lwdA 413 3.03e+01 c.77.1.1 78265 1lniA 96 3.04e+01 d.1.1.2 74046 1ew3A 159 3.11e+01 1mup b.60.1.1 27114 1ri9A 102 3.13e+01 b.34.2.1 97506 1txkA 498 3.13e+01 b.1.18.2,b.30.5.9 107425,107426 1rpyA 114 3.14e+01 d.93.1.1 97718 1omrA 201 3.25e+01 a.39.1.5 93349 1bi5A 389 3.29e+01 1bi5A c.95.1.2,c.95.1.2 35985,35986 1zin 217 3.33e+01 1zin c.37.1.1,g.41.2.1 31915,45178 1pulA 125 3.34e+01 1v0jA 399 3.38e+01 1cds 77 3.44e+01 1cds g.7.1.3 44461 2gw6A 123 3.47e+01 1nuuA 252 3.47e+01 c.26.1.3 86209 1xwwA 157 3.48e+01 1vreA 147 3.51e+01 2hbg a.1.1.2 15017 1dxtB 147 3.56e+01 1abwA a.1.1.2 15450 1s4nA 348 3.69e+01 c.68.1.16 98501 1qgtA 149 3.75e+01 1qgtA a.62.1.1 18135 2a25A 193 3.89e+01 1bquA 215 3.96e+01 1bquA b.1.2.1,b.1.2.1 22066,22067 1fecA 490 4.02e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30489,30490,40176 1vjlA 164 4.05e+01 d.257.1.1 100822 1gmuA 143 4.09e+01 b.107.1.1,d.58.38.1 65335,65336 1c75A 71 4.12e+01 451c a.3.1.1 15796 1d1rA 116 4.13e+01 1d1rA d.64.1.1 39548 1xb2B 291 4.15e+01 1hbyA 123 4.17e+01 7rsa d.5.1.1 60936 1b1jA 123 4.18e+01 7rsa d.5.1.1 37298 1tr0A 108 4.19e+01 d.58.4.4 107261 1z1lA 345 4.19e+01 1irdB 146 4.21e+01 a.1.1.2 66287 1ci4A 89 4.30e+01 1qckA a.60.5.1 17970 1iseA 185 4.41e+01 d.67.3.1 90691 2h00A 254 4.42e+01 1ztcA 221 4.44e+01 1c0dA 358 4.46e+01 1eceA c.1.8.3 28815 2abd 86 4.48e+01 1aca a.11.1.1 16366 2gk3A 256 4.53e+01 1idm 343 4.57e+01 1cnzA c.77.1.1 35035 1o7fA 469 4.65e+01 a.4.5.31,b.82.3.2,b.82.3.2 81131,81132,81133 1o7xD 377 4.71e+01 a.103.1.1 81174 2abwA 227 4.72e+01 1j3bA 529 4.74e+01 c.91.1.1,c.109.1.1 77071,77072 1v32A 101 4.74e+01 a.42.1.1 100277 1a8h 500 4.75e+01 1a8h a.27.1.1,c.26.1.1 16922,31589 1babB 146 4.79e+01 1abwA a.1.1.2 15414 1vnc 609 4.79e+01 1vns a.111.1.3 19065 2fa8A 105 4.79e+01 1o7xC 377 4.83e+01 a.103.1.1 81173 1u07A 90 4.84e+01 1eceA 358 4.89e+01 1eceA c.1.8.3 28813 1v4eA 299 4.90e+01 a.128.1.1 100296 1j7gA 144 4.94e+01 c.110.1.1 84130 1c0eA 157 4.96e+01 1dg9A c.44.1.1 32638 1vjqA 79 4.99e+01 k.43.1.1 100830 1nzjA 298 5.03e+01 c.26.1.1 92377 1dghB 498 5.19e+01 1cf9A e.5.1.1 42791 1xaa 345 5.20e+01 1cnzA c.77.1.1 35033 1y8qB 640 5.21e+01 2esnA 310 5.23e+01 2dbnA 461 5.27e+01 1b1iA 123 5.28e+01 7rsa d.5.1.1 37295 1ek8A 185 5.32e+01 1ek8A d.67.3.1 59444 1zcxA 178 5.34e+01 1iakA 199 5.44e+01 1iakA b.1.1.2,d.19.1.1 21625,38199 1vjvA 415 5.44e+01 d.3.1.9 108632 1tlfA 301 5.47e+01 1tlfA c.93.1.1 35687 1a4yB 123 5.57e+01 7rsa d.5.1.1 37296 1k2fA 190 5.61e+01 b.8.1.2 68054 1u5kA 244 5.68e+01 1un3A 123 5.69e+01 d.5.1.1 99646 1dr8B 344 5.77e+01 1cnzA c.77.1.1 35052 1k59A 123 5.79e+01 d.5.1.1 72073 1vmjA 151 5.80e+01 1cdq 77 5.83e+01 1cds g.7.1.3 44459 1hh7A 114 5.84e+01 1ycc a.3.1.1 15896 1woyA 500 5.92e+01 2ghjA 118 5.92e+01 1azsA 220 5.99e+01 1azsA d.58.29.1 39416 1ris 101 6.02e+01 1ris d.58.14.1 39314 2ct5A 73 6.03e+01 1tqzA 133 6.03e+01 1cmyB 146 6.03e+01 1abwA a.1.1.2 15544 1tie 172 6.04e+01 1wba b.42.4.1 25592 1j7yB 146 6.04e+01 a.1.1.2 66427 1culA 217 6.05e+01 1azsA d.58.29.1 39417 1izmA 184 6.12e+01 a.199.1.1 90725 1i0cA 60 6.12e+01 1aojA b.34.2.1 61485 1y9wA 140 6.15e+01 1cjtA 217 6.16e+01 1azsA d.58.29.1 39419 2ezxA 89 6.28e+01 1qckA a.60.5.1 17978 1cwyA 500 6.34e+01 1cwyA c.1.8.1 28789 1fjgK 129 6.36e+01 1fjfK c.55.4.1 33733 1b2vA 188 6.36e+01 1b2vA d.35.1.1 38532 1mpyA 307 6.38e+01 1mpyA d.32.1.3,d.32.1.3 38508,38509 2bj0A 203 6.43e+01 2igd 61 6.46e+01 2igd d.15.7.1 37821 1fjgP 88 6.52e+01 1emwA d.27.1.1 38444 2fbmA 291 6.52e+01 1lrwA 600 6.54e+01 b.70.1.1 91111 1igd 61 6.55e+01 2igd d.15.7.1 37822 1gyzA 60 6.57e+01 a.144.2.1 70793 1zip 217 6.63e+01 1zin c.37.1.1,g.41.2.1 31916,45179 1i8oA 114 6.63e+01 1ycc a.3.1.1 61979 1fx7A 230 6.67e+01 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 60088,60089,60090 1qhoA 686 6.70e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21844,22513,27751,28738 1zy9A 564 6.72e+01 1o7xB 377 6.77e+01 a.103.1.1 81172 1qauA 112 6.81e+01 1qauA b.36.1.1 24779 1qmvA 197 6.88e+01 1qq2A c.47.1.10 33066 1q4rA 112 6.94e+01 d.58.4.4 95823 1dg9A 157 6.96e+01 1dg9A c.44.1.1 32637 1xfsA 178 7.00e+01 d.129.3.5 109589 2ciaA 102 7.13e+01 1oksA 56 7.16e+01 a.8.5.1 93271 1dvoA 152 7.26e+01 1dvoA a.136.1.1 19623 1eiyB 785 7.27e+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 16305,16306,25314,39313,40782,41458 1vr9A 213 7.36e+01 1ycqA 107 7.37e+01 1ycqA a.42.1.1 17419 2ewcA 126 7.40e+01 1zgzA 122 7.41e+01 1zvpA 133 7.48e+01 1hv2A 99 7.50e+01 d.42.1.1 61287 1ijqA 316 7.59e+01 1ijqA b.68.5.1,g.3.11.1 62506,62507 2cu3A 64 7.61e+01 1a01B 146 7.62e+01 1abwA a.1.1.2 15448 1b1eA 123 7.67e+01 7rsa d.5.1.1 37300 1b54 257 7.67e+01 1ct5A c.1.6.2 28664 1uasA 362 7.74e+01 b.71.1.1,c.1.8.1 88388,88389 1u0tA 307 7.77e+01 e.52.1.1 107567 1pgx 83 7.85e+01 2igd d.15.7.1 37823 2dg5B 190 7.86e+01 1s9uA 207 7.87e+01 a.184.1.1 105390 1npsA 88 7.95e+01 1prs b.11.1.1 23622 1obpA 159 7.95e+01 1obpA b.60.1.1 27092 1rhd 293 7.95e+01 1rhs c.46.1.2,c.46.1.2 32715,32716 1gv3A 248 8.00e+01 a.2.11.1,d.44.1.1 70585,70586 2cevA 299 8.04e+01 1d3vA c.42.1.1 32576 1korA 400 8.07e+01 c.26.2.1,d.210.1.1 72824,72825 1aoiC 116 8.07e+01 1aoiC a.22.1.1 16440 2fhxA 246 8.12e+01 1i6wA 181 8.14e+01 1i6wA c.69.1.18 61859 1emwA 88 8.14e+01 1emwA d.27.1.1 38448 1cqmA 101 8.17e+01 1ris d.58.14.1 39321 1qavB 115 8.20e+01 1qauA b.36.1.1 24780 1mi0A 65 8.21e+01 d.15.7.1 79135 2go8A 122 8.23e+01 1uzcA 71 8.25e+01 a.159.2.1 100222 1sur 215 8.28e+01 1sur c.26.2.2 31620 1vns 609 8.32e+01 1vns a.111.1.3 19061 1du6A 64 8.35e+01 1akhA a.4.1.1 16002 1hn2A 159 8.40e+01 b.60.1.1 65890 1dgfA 497 8.41e+01 1cf9A e.5.1.1 42782 1sphA 88 8.48e+01 1ptf d.94.1.1 40544 1jb7B 260 8.48e+01 1otcB b.40.4.3 62839 1aoiG 116 8.51e+01 1aoiC a.22.1.1 16441 1lqaA 346 8.54e+01 c.1.7.1 84674 1vkrA 125 8.57e+01 c.44.2.1 108689 1xoyA 161 8.60e+01 1gt1A 159 8.61e+01 b.60.1.1 90515 1j79A 347 8.65e+01 1j79A c.1.9.4 62675 1efaA 333 8.72e+01 1tlfA a.35.1.5,c.93.1.1 17106,35691 1s3cA 141 8.72e+01 7catA 506 8.85e+01 1cf9A e.5.1.1 42781 1htjF 210 8.86e+01 1htjF a.91.1.1 61254 1g5vA 88 8.87e+01 1g5vA b.34.9.1 60292 1f5vA 240 8.89e+01 1bkjA d.90.1.1 40255 1b7bA 310 8.92e+01 1b7bA c.73.1.1 34963 1jofA 365 8.97e+01 b.69.10.1 71775