# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7-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 1vjkA 98 2.50e-03 d.15.3.1 108631 2bb6A 414 2.49e-02 1xlqA 106 8.27e-02 1frrA 95 1.21e-01 1awd d.15.4.1 37674 1oqqA 106 1.32e-01 d.15.4.1 93422 1yqbA 100 1.78e-01 1fmaD 81 2.89e-01 1fmaD d.15.3.1 37643 1ryjA 70 2.95e-01 d.15.3.2 98104 1uwmA 106 3.08e-01 2rgf 97 3.37e-01 1lfdA d.15.1.5 37627 2bwfA 77 3.44e-01 1vc3B 97 3.94e-01 1e9mA 106 4.06e-01 1ayfA d.15.4.1 59397 1l7yA 94 4.17e-01 d.15.1.6 73676 1drw 273 4.79e-01 1drw c.2.1.3,d.81.1.3 30057,39972 1dih 273 6.32e-01 1drw c.2.1.3,d.81.1.3 30056,39971 1put 106 7.38e-01 1ayfA d.15.4.1 37680 1dmhA 311 8.66e-01 1dmhA b.3.6.1 22633 1zq7A 207 8.88e-01 1qorA 327 9.47e-01 1qorA b.35.1.2,c.2.1.1 24766,29782 2dafA 118 1.12e+00 1frd 98 1.14e+00 1awd d.15.4.1 37648 1fm0D 81 1.18e+00 1fmaD d.15.3.1 37642 1euvB 86 1.22e+00 1a5r d.15.1.1 37598 1zud2 66 1.31e+00 1nbfD 76 1.32e+00 d.15.1.1 80390 1awd 94 1.32e+00 1awd d.15.4.1 37673 1lfdA 87 1.61e+00 1lfdA d.15.1.5 37622 1wi0A 113 1.62e+00 2bpsA 81 1.62e+00 1yj1A 76 1.66e+00 1wgrA 100 1.68e+00 1offA 97 1.78e+00 d.15.4.1 86947 2cu3A 64 1.79e+00 1pt1A 143 1.82e+00 b.52.2.1 95084 1d4vB 163 1.95e+00 1d4vB b.22.1.1 23884 1c1yB 77 2.02e+00 1c1yB d.15.1.5 37618 1arzC 273 2.12e+00 1drw c.2.1.3,d.81.1.3 30061,39976 1uh6A 100 2.21e+00 d.15.1.1 99394 1aw8B 91 2.31e+00 1aw8B 1lxdA 100 2.33e+00 1lfdA d.15.1.5 37624 1dg6A 191 2.35e+00 1d4vB b.22.1.1 23883 1prxA 224 2.42e+00 1prxA c.47.1.10 33076 1rwsA 77 2.48e+00 d.15.3.2 97991 1ubi 76 2.67e+00 1ubi d.15.1.1 37584 1s0uA 408 2.90e+00 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 1qt9A 98 2.97e+00 1awd d.15.4.1 37647 1a70 97 3.16e+00 1awd d.15.4.1 37678 1guaB 81 3.17e+00 1c1yB d.15.1.5 37619 1d3zA 76 3.29e+00 1ubi d.15.1.1 37592 1ubq 76 3.35e+00 1ubi d.15.1.1 37585 1f0zA 66 3.49e+00 1f0zA d.15.3.2 37644 1czpA 98 3.50e+00 1awd d.15.4.1 37645 1wjnA 97 3.50e+00 1woqA 267 3.60e+00 c.55.1.10,c.55.1.10 109462,109463 1fxiA 96 3.61e+00 1awd d.15.4.1 37664 1v86A 95 3.69e+00 d.15.1.1 108421 1k07A 263 3.86e+00 d.157.1.1 77218 1kf6B 243 4.08e+00 a.1.2.1,d.15.4.2 72397,72398 1l5pA 93 4.21e+00 d.15.4.1 73598 1u94A 356 4.26e+00 c.37.1.11,d.48.1.1 107743,107744 1pl8A 356 4.35e+00 b.35.1.2,c.2.1.1 94878,94879 1raxA 115 4.38e+00 1lfdA d.15.1.5 37626 1i7hA 111 4.63e+00 d.15.4.1 71122 1ucyH 150 4.84e+00 1ucyH 1aw8E 91 5.22e+00 1aw8B 1doi 128 5.43e+00 1awd d.15.4.1 37676 1e3jA 352 5.50e+00 1e3jA b.35.1.2,c.2.1.1 24765,29781 1u2cA 246 5.67e+00 b.1.6.2,d.272.1.1 107610,107611 1wwtA 88 5.78e+00 2c5lC 117 6.09e+00 1rdr 461 6.29e+00 1rdr e.8.1.4 43116 1ogwA 76 6.52e+00 d.15.1.1 87001 1gtkA 313 6.71e+00 c.94.1.1,d.50.2.1 76346,76347 1se9A 126 6.87e+00 d.15.1.1 98821 1b9rA 105 7.25e+00 1ayfA d.15.4.1 37683 2f4pA 147 7.76e+00 1nddD 76 7.99e+00 1ubi d.15.1.1 37602 1uheA 97 8.08e+00 1pqhA 143 8.33e+00 b.52.2.1 95017 1xccA 220 8.34e+00 1a5r 103 8.57e+00 1a5r d.15.1.1 37597 2ap1A 327 9.01e+00 1xc3A 302 9.22e+00 1z2mA 155 9.73e+00 1prxB 224 1.04e+01 1prxA c.47.1.10 33077 1wm3A 72 1.09e+01 2bkrB 77 1.11e+01 1ukmB 128 1.14e+01 d.169.1.1 99500 1rfkA 98 1.15e+01 1sv6A 269 1.18e+01 d.177.1.1 106043 1ygs 234 1.18e+01 1ygs b.26.1.1 23907 2a9sA 171 1.20e+01 2g1lA 104 1.25e+01 2mjpA 193 1.27e+01 1b78A c.51.4.1 33223 2al3A 90 1.34e+01 1ew4A 106 1.36e+01 1ew4A d.82.2.1 40023 1adqA 206 1.40e+01 1igtB b.1.1.2,b.1.1.2 21518,21519 2reb 352 1.46e+01 2reb c.37.1.11,d.48.1.1 32282,38767 2azpA 318 1.46e+01 1wriA 93 1.48e+01 1atiA 505 1.48e+01 1atiA c.51.1.1,d.104.1.1 33196,40745 1g19A 350 1.49e+01 2reb c.37.1.11,d.48.1.1 32284,38770 1se4 239 1.56e+01 3seb b.40.2.2,d.15.6.1 25187,37776 1xzoA 174 1.60e+01 1v7pB 128 1.61e+01 d.169.1.1 108407 1tmxA 293 1.63e+01 1e0zA 128 1.67e+01 1awd d.15.4.1 59153 2gm3A 175 1.68e+01 1qmvA 197 1.72e+01 1qq2A c.47.1.10 33066 1xe1A 116 1.76e+01 b.43.3.1 109571 1b78A 193 1.77e+01 1b78A c.51.4.1 33221 1qlaB 239 1.80e+01 1qlaB a.1.2.1,d.15.4.2 15679,37707 1v2yA 105 1.85e+01 d.15.1.1 100275 1w24A 182 1.87e+01 1ra6A 461 1.88e+01 e.8.1.4 104879 2b0vA 153 1.88e+01 1wj9A 211 1.88e+01 1zavA 180 1.92e+01 1wzlA 585 1.94e+01 1bt0A 76 1.97e+01 1ubi d.15.1.1 37607 2aefA 234 2.01e+01 1atiB 505 2.02e+01 1atiA c.51.1.1,d.104.1.1 33197,40746 2bw0A 329 2.02e+01 2bt6A 108 2.07e+01 1t0qC 86 2.13e+01 d.15.12.1 106222 1mgpA 313 2.16e+01 c.119.1.1 79098 1z2wA 192 2.17e+01 1xd3A 230 2.17e+01 1yb5A 351 2.18e+01 1cvrA 435 2.20e+01 1cvrA b.1.18.12,c.17.1.2 21949,31006 1mugA 168 2.21e+01 1mugA c.18.1.2 31030 1ji2A 585 2.27e+01 b.1.18.2,b.71.1.1,c.1.8.1 71672,71673,71674 2awgA 118 2.28e+01 1pkp 150 2.31e+01 1pkp d.14.1.1,d.50.1.2 37551,38787 1fc1A 224 2.39e+01 1igtB b.1.1.2,b.1.1.2 21520,21521 1t3qA 168 2.39e+01 a.56.1.1,d.15.4.2 106367,106368 1gehA 444 2.40e+01 c.1.14.1,d.58.9.1 65181,65182 1owfB 94 2.43e+01 a.55.1.1 87488 1mhxA 65 2.49e+01 d.15.7.1 79134 1ihfB 94 2.49e+01 1huuA a.55.1.1 17894 1q8rA 120 2.51e+01 d.79.6.1 96225 1xg9A 260 2.52e+01 1zghA 260 2.52e+01 1vj1A 363 2.55e+01 b.35.1.2,c.2.1.1 100794,100795 1ayfA 105 2.56e+01 1ayfA d.15.4.1 37684 1ksiA 642 2.57e+01 1ksiB b.30.2.1,d.17.2.1,d.17.2.1 24408,38043,38044 1s3iA 310 2.57e+01 b.46.1.1,c.65.1.1 98435,98436 1x0rA 249 2.61e+01 1gsmA 210 2.68e+01 b.1.1.4,b.1.1.4 65535,65536 1a81A 254 2.69e+01 1a81A d.93.1.1,d.93.1.1 40507,40508 1zyeA 220 2.79e+01 1f53A 84 2.82e+01 1f53A b.11.1.4 23632 1g5hA 454 2.83e+01 1g5hA c.51.1.1,d.104.1.1 60270,60271 1umuB 116 2.83e+01 1umuA b.87.1.1 28383 1iueA 98 2.87e+01 d.15.4.1 90697 1xa0A 328 2.87e+01 2gpr 154 2.88e+01 1gpr b.84.3.1 28269 1bxnA 485 2.95e+01 1burA c.1.14.1,d.58.9.1 29376,39282 1lm8B 118 2.95e+01 d.15.1.1 74033 1e6eB 128 2.99e+01 1ayfA d.15.4.1 59300 1igtD 444 3.00e+01 1igtB b.1.1.1,b.1.1.2,b.1.1.2,b.1.1.2 19767,20871,20872,20873 1ihoA 283 3.05e+01 1ihoA c.26.1.4 62390 1wjuA 100 3.06e+01 1l6xA 207 3.07e+01 b.1.1.2,b.1.1.2 73642,73643 1fc2D 224 3.07e+01 1igtB b.1.1.2,b.1.1.2 21516,21517 1ayfB 105 3.14e+01 1ayfA d.15.4.1 37685 1z3qA 200 3.23e+01 1umuA 116 3.26e+01 1umuA b.87.1.1 28382 1qq2A 199 3.27e+01 1qq2A c.47.1.10 33064 1n2eA 300 3.27e+01 c.26.1.4 85268 2fcr 173 3.31e+01 1rcf c.23.5.1 31151 2ci9A 102 3.33e+01 1v8cA 168 3.34e+01 d.15.3.1,d.129.5.1 100495,100496 1igtB 444 3.37e+01 1igtB b.1.1.1,b.1.1.2,b.1.1.2,b.1.1.2 19765,20867,20868,20869 1mhcB 99 3.38e+01 1agdB b.1.1.2 20832 1dljA 402 3.49e+01 1dliA a.100.1.4,c.2.1.6,c.26.3.1 18808,30212,31621 1gvp 87 3.50e+01 1gvp b.40.4.7 25369 1vcbA 118 3.55e+01 1vcbA d.15.1.1 37603 2cwaA 263 3.59e+01 1vqb 87 3.61e+01 1gvp b.40.4.7 25370 2ciaA 102 3.67e+01 1rfa 79 3.67e+01 1c1yB d.15.1.5 37620 1ae3 86 3.68e+01 1gvp b.40.4.7 25381 1pz7A 204 3.73e+01 b.29.1.4 95405 1pzxA 289 3.74e+01 c.119.1.1 95484 1uufA 369 3.80e+01 b.35.1.2,c.2.1.1 100006,100007 1td2A 287 3.82e+01 c.72.1.5 106765 1ksiB 642 3.85e+01 1ksiB b.30.2.1,d.17.2.1,d.17.2.1 24409,38045,38046 1g0uL 241 3.85e+01 d.153.1.4 41894 1oeyA 83 3.90e+01 d.15.2.2 92800 1v6fA 151 3.90e+01 d.109.1.2 108395 1kk1A 410 3.91e+01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1dceA 567 3.92e+01 1dceA a.118.6.1,b.7.4.1,c.10.2.2 19191,23218,30867 1aqzB 149 3.93e+01 1aqzA d.1.1.3 36239 1meoA 209 3.95e+01 c.65.1.1 79035 1wywA 230 3.96e+01 1h0hA 977 4.10e+01 b.52.2.2,c.81.1.1 76435,76436 2gptA 523 4.10e+01 2cbf 234 4.13e+01 1cbf c.90.1.1 35588 1r6vA 671 4.21e+01 1cqkA 101 4.27e+01 1cqkA b.1.1.2 21547 3sicI 107 4.32e+01 3ssi d.84.1.1 40028 1nddA 76 4.43e+01 1ubi d.15.1.1 37599 1qw9A 502 4.55e+01 b.71.1.2,c.1.8.3 96466,96467 2cwpA 112 4.56e+01 1ryp1 222 4.56e+01 1ryp1 2b5wA 357 4.67e+01 3seb 238 4.71e+01 3seb b.40.2.2,d.15.6.1 25184,37773 1uxxX 133 4.71e+01 b.18.1.10 100169 1mopA 300 4.75e+01 c.26.1.4 85035 1cbf 285 4.75e+01 1cbf c.90.1.1 35587 1eo6A 117 4.85e+01 1eo6A d.15.1.3 37609 1iyu 79 4.92e+01 1iyu b.84.1.1 28227 2matA 264 4.96e+01 1c24A d.127.1.1 41146 1knmA 130 4.97e+01 b.42.2.1 72781 2fazA 78 4.97e+01 1dmzA 158 4.99e+01 1qu5A b.26.1.2 23921 2b4wA 315 5.04e+01 2sak 121 5.09e+01 2sak d.15.5.1 37711 2iadB 205 5.12e+01 1iakB b.1.1.2,d.19.1.1 21640,38214 1wloA 136 5.19e+01 1d5mC 239 5.26e+01 3seb b.40.2.2,d.15.6.1 25185,37774 1rq2A 382 5.27e+01 c.32.1.1,d.79.2.1 105048,105049 1aqzA 149 5.27e+01 1aqzA d.1.1.3 36238 1agnA 373 5.46e+01 2ohxA b.35.1.2,c.2.1.1 24737,29753 1ubeA 349 5.50e+01 c.37.1.11,d.48.1.1 88412,88413 1fiqC 763 5.64e+01 1fiqC d.41.1.1,d.133.1.1 38588,41418 1dywA 173 5.69e+01 2cpl b.62.1.1 27505 1uhgA 385 5.72e+01 e.1.1.1 88491 1bvzA 585 5.72e+01 1bvzA b.1.18.2,b.71.1.1,c.1.8.1 21856,27783,28770 1f47B 144 5.85e+01 1f46A d.129.4.1 59645 1atr 386 5.89e+01 1ba1 c.55.1.1,c.55.1.1 33421,33422 1gmmA 133 5.93e+01 b.18.1.10 65314 1pda 315 5.95e+01 1pda c.94.1.1,d.50.2.1 35751,38794 2ggcA 263 6.07e+01 1llwA 1520 6.10e+01 b.80.4.1,c.1.4.1,d.153.1.1 74017,74018,74019 2fomB 185 6.12e+01 1n8jA 186 6.19e+01 c.47.1.10 85401 2agyA 361 6.20e+01 1cd1A 315 6.23e+01 1cd1A b.1.1.2,d.19.1.1 21579,38155 1jjuB 337 6.27e+01 b.69.2.2 66779 1vi9A 299 6.28e+01 c.72.1.5 100750 1ba1 386 6.36e+01 1ba1 c.55.1.1,c.55.1.1 33387,33388 2sicI 107 6.37e+01 3ssi d.84.1.1 40031 1grwA 126 6.47e+01 b.1.11.2 70391 2cu1A 103 6.50e+01 1c24A 263 6.51e+01 1c24A d.127.1.1 41148 1h9oA 112 6.55e+01 1qadA d.93.1.1 60837 1z0wA 207 6.58e+01 1rcqA 357 6.58e+01 b.49.2.2,c.1.6.1 104882,104883 1ovaA 386 6.59e+01 1ovaA e.1.1.1 42619 1o89A 345 6.61e+01 b.35.1.2,c.2.1.1 92644,92645 1kshB 152 6.75e+01 b.1.18.8 72915 1hpm 386 6.76e+01 1ba1 c.55.1.1,c.55.1.1 33381,33382 2h88B 252 6.76e+01 2fp7B 172 6.78e+01 1mq7A 154 6.86e+01 b.85.4.1 79404 1knlA 130 6.90e+01 b.42.2.1 72780 1dfaA 454 6.95e+01 1vdeA b.86.1.2,d.95.2.2,d.95.2.2 28375,40575,40576 2ag4A 164 6.97e+01 1ay9A 108 7.03e+01 1umuA b.87.1.1 28384 1uzkA 162 7.05e+01 2fnjB 118 7.09e+01 1ao0A 459 7.13e+01 1ecfB c.61.1.1,d.153.1.1 34049,41816 1wxaA 116 7.13e+01 1vf7A 369 7.18e+01 f.46.1.1 108557 2fbwB 252 7.19e+01 1bmg 98 7.27e+01 1agdB b.1.1.2 20667 1mejA 223 7.30e+01 c.65.1.1 79029 4matA 278 7.30e+01 1c24A d.127.1.1 41150 1m9zA 111 7.32e+01 g.7.1.3 78881 1j5eE 161 7.32e+01 d.14.1.1,d.50.1.2 71547,71548 1gzqA 300 7.35e+01 b.1.1.2,d.19.1.1 70818,70819 2db2A 119 7.36e+01 1dlc 584 7.42e+01 1ciy b.18.1.3,b.77.2.1,f.1.3.1 23719,27976,43391 2h0bA 184 7.45e+01 1gttA 429 7.59e+01 d.177.1.1,d.177.1.1 70529,70530 1xnzA 264 7.67e+01 2fkbA 180 7.70e+01 1wf9A 107 7.72e+01 1efdN 266 7.73e+01 1efdN c.92.2.1 35597 1bupA 386 7.73e+01 1ba1 c.55.1.1,c.55.1.1 33377,33378 1hrhA 136 7.75e+01 1rthA c.55.3.1 33577 1t5eA 360 7.79e+01 f.46.1.1 106436 1y07A 128 7.80e+01 1azdA 237 7.80e+01 1nls b.29.1.1 24020 1ae2 87 7.86e+01 1gvp b.40.4.7 25382 2f9zC 159 7.87e+01 1b4rA 80 7.93e+01 1b4rA b.1.3.1 22072 1fmtB 314 7.95e+01 1fmtA b.46.1.1,c.65.1.1 25759,34175 2fggA 101 8.00e+01 2ah5A 210 8.07e+01 1kjvB 100 8.09e+01 b.1.1.2 77423 1f42A 306 8.16e+01 1f42A b.1.1.4,b.1.2.1,b.1.2.1 59636,59637,59638 2gupA 292 8.21e+01 1v97A 1332 8.32e+01 a.56.1.1,d.15.4.2,d.41.1.1,d.87.2.1,d.133.1.1,d.145.1.3 108436,108437,108438,108439,108440,108441 1f7wA 144 8.33e+01 1f46A d.129.4.1 59679 1g5cA 170 8.36e+01 1g5cA c.53.2.1 60264 1b76A 442 8.60e+01 1atiA c.51.1.1,d.104.1.1 33198,40747 2aj2A 208 8.63e+01 1onqA 283 8.63e+01 b.1.1.2,d.19.1.1 93365,93366 1vdeA 454 8.63e+01 1vdeA b.86.1.2,d.95.2.2,d.95.2.2 28378,40581,40582 1xteA 154 8.66e+01 1p99A 295 8.67e+01 c.94.1.1 94384 1befA 181 8.70e+01 1befA b.47.1.3 26419 1wgoA 123 8.73e+01 1dliA 402 8.74e+01 1dliA a.100.1.4,c.2.1.6,c.26.3.1 18809,30213,31622 3ait 74 8.77e+01 1hoe b.5.1.1 22835 1ats 386 8.80e+01 1ba1 c.55.1.1,c.55.1.1 33423,33424