# 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 1efcA 393 2.54e-01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25680,25720,32113 1efuA 385 2.83e-01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25682,25722,32115 6gsvA 217 7.37e-01 1b8xA a.45.1.1,c.47.1.5 17633,32925 2furA 209 7.37e-01 1b4pA 217 7.66e-01 a.45.1.1,c.47.1.5 83158,83159 1ugpA 203 9.15e-01 d.149.1.1 107831 1ireA 204 1.01e+00 d.149.1.1 76769 1jpaA 312 1.18e+00 d.144.1.7 67011 1zd3A 555 1.42e+00 1etu 394 1.46e+00 1efcA c.37.1.8 64737 2wrpR 107 1.59e+00 1jhgA a.4.12.1 19010 1vj5A 555 1.67e+00 c.108.1.2,c.69.1.11 100799,100800 3crxA 343 1.78e+00 4crxA a.60.9.1,d.163.1.1 18101,42161 1ggzA 148 1.80e+00 a.39.1.5 70176 1trrA 107 1.92e+00 1jhgA a.4.12.1 19017 1e6iA 121 2.12e+00 1b91A a.29.2.1 16969 1cll 148 2.38e+00 1cll a.39.1.5 17263 1hx1B 114 2.46e+00 1hx1B a.7.7.1 61350 1kbuA 349 2.58e+00 a.60.9.1,d.163.1.1 72284,72285 1o9rA 162 2.65e+00 a.25.1.1 86706 2bl0C 142 2.73e+00 1eni 138 2.83e+00 2end a.18.1.1 16403 2a2fX 325 2.88e+00 1m48A 133 3.14e+00 a.26.1.2 74443 2c4jA 218 3.23e+00 2b1eA 564 3.24e+00 1n3gA 113 3.26e+00 d.204.1.1 79962 1cr6B 554 3.38e+00 1cr6B c.69.1.11,c.108.1.2 34688,43338 3cln 148 3.49e+00 1cll a.39.1.5 17286 2ccmA 191 3.49e+00 1xw5A 217 3.58e+00 1ahr 146 3.61e+00 1cll a.39.1.5 17287 1m6kA 251 4.59e+00 e.3.1.1 78695 1enj 138 4.70e+00 2end a.18.1.1 16401 1jhgA 101 5.31e+00 1jhgA a.4.12.1 19009 2esnA 310 5.33e+00 1vkmA 297 5.62e+00 c.138.1.1 108670 2occH 85 5.83e+00 2occH a.51.1.1 17796 1xo0A 324 5.91e+00 1x6vA 630 5.96e+00 1eemA 241 6.19e+00 1eemA a.45.1.1,c.47.1.5 17717,33011 1vasA 137 7.01e+00 2end a.18.1.1 16404 1b48A 221 7.04e+00 1pgtA a.45.1.1,c.47.1.5 17703,32997 1tbmA 326 7.10e+00 a.211.1.2 106744 1v54G 85 7.58e+00 f.23.2.1 100328 1osa 148 7.60e+00 1cll a.39.1.5 17300 1qo7A 394 7.62e+00 1qo7A c.69.1.11 34697 1hwxA 501 8.17e+00 1hwyA c.2.1.7,c.58.1.1 30250,33898 1enk 138 8.23e+00 2end a.18.1.1 16402 1tn4 159 8.43e+00 1ncx a.39.1.5 17248 2occG 84 8.63e+00 2occG f.23.2.1 43522 1crxA 322 8.65e+00 4crxA a.60.9.1,d.163.1.1 18097,42157 1hwyA 501 8.88e+00 1hwyA c.2.1.7,c.58.1.1 30262,33910 1ig6A 107 9.20e+00 1ig6A a.4.3.1 62364 1zs3A 182 9.58e+00 1gqeA 365 9.98e+00 e.38.1.1 70351 1a6q 382 1.02e+01 1a6q a.159.1.1,d.219.1.1 75801,75802 1v54H 85 1.08e+01 a.51.1.1 100329 1nk4A 580 1.08e+01 c.55.3.5,e.8.1.1 91923,91924 1gewA 356 1.09e+01 1gewA c.67.1.1 60470 2a1dD 329 1.11e+01 1vyiA 112 1.16e+01 1exrA 148 1.16e+01 1cll a.39.1.5 17299 1eumA 165 1.16e+01 1eumA a.25.1.1 59507 2end 138 1.16e+01 2end a.18.1.1 16400 1xwl 580 1.19e+01 1xwl c.55.3.5,e.8.1.1 33708,43001 1ak8 76 1.21e+01 1cll a.39.1.5 17281 1u4bA 580 1.24e+01 c.55.3.5,e.8.1.1 107664,107665 2f3yA 148 1.24e+01 1b8aA 438 1.26e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 3bdpA 580 1.31e+01 1xwl c.55.3.5,e.8.1.1 33711,43004 1i5jA 79 1.31e+01 1i5jA j.39.1.1 61788 1jhdA 396 1.33e+01 b.122.1.3,c.26.1.5 66712,66713 1wdcC 156 1.35e+01 1wdcC a.39.1.5 17317 1f7uA 607 1.38e+01 1bs2A a.27.1.1,c.26.1.1,d.67.2.1 59673,59674,59675 1g4yR 148 1.40e+01 1cll a.39.1.5 60252 1m9xC 146 1.43e+01 a.73.1.1 84907 1a1w 91 1.43e+01 1a1z a.77.1.4 18425 2ajfA 597 1.44e+01 2bdpA 580 1.48e+01 1xwl c.55.3.5,e.8.1.1 33709,43002 1tns 76 1.49e+01 1qpmA a.6.1.7 16228 1b35A 260 1.52e+01 1b35A b.121.4.1 23333 4crxA 322 1.54e+01 4crxA a.60.9.1,d.163.1.1 18095,42155 1y82A 157 1.57e+01 1vjrA 271 1.58e+01 c.108.1.14 100832 1kdxA 81 1.59e+01 1kdxA a.12.1.1 16375 1ttzA 87 1.61e+01 c.47.1.1 107309 2af8 86 1.62e+01 2af8 a.28.1.1 16933 2a6cA 83 1.65e+01 1yviA 149 1.66e+01 1yqyA 523 1.66e+01 1ftt 68 1.67e+01 2hddA a.4.1.1 15997 1br1B 150 1.74e+01 1wdcC a.39.1.5 17309 1rxqA 178 1.74e+01 a.213.1.1 105118 1l3sA 580 1.76e+01 c.55.3.5,e.8.1.1 84521,84522 2c5rA 67 1.79e+01 1pp7U 131 1.89e+01 a.4.5.44 94973 1whrA 124 1.91e+01 1i0aA 466 1.91e+01 1auwA a.127.1.1 61479 1sedA 117 1.93e+01 a.219.1.1 105449 1jogA 146 1.98e+01 a.24.16.2 77142 1afvA 151 2.00e+01 1ak4C a.73.1.1 18324 1lfpA 249 2.09e+01 e.39.1.1 73885 1i6zA 135 2.10e+01 a.7.7.1 61861 1zboA 210 2.16e+01 1yw0A 276 2.16e+01 2aheA 267 2.16e+01 2ew2A 316 2.18e+01 1xfxO 149 2.19e+01 1occG 84 2.19e+01 2occG f.23.2.1 43562 1irl 133 2.19e+01 3inkC a.26.1.2 16883 1b4cA 92 2.20e+01 1b4cA a.39.1.2 17169 1a1z 91 2.26e+01 1a1z a.77.1.4 18427 1rcsA 105 2.26e+01 1jhgA a.4.12.1 19025 1q9uA 130 2.32e+01 d.129.7.1 96314 1opjA 293 2.33e+01 d.144.1.7 87230 2f1sA 186 2.35e+01 1c7nA 399 2.35e+01 1d2fA c.67.1.3 34413 1bku 33 2.36e+01 1bku j.6.1.1 46104 1n3kA 130 2.37e+01 a.77.1.4 79965 2f9dP 43 2.38e+01 1v9dA 340 2.41e+01 a.207.1.1 100535 1ds1A 324 2.52e+01 1drtA b.82.2.2 28127 1lwbA 122 2.53e+01 a.133.1.3 84728 7catA 506 2.57e+01 1cf9A e.5.1.1 42781 1fazA 122 2.60e+01 1fazA a.133.1.3 59757 1fgkA 310 2.65e+01 1fgkA d.144.1.7 41693 1eu8A 409 2.68e+01 1eu8A c.94.1.1 59502 1fpoA 171 2.73e+01 1fpoA a.2.3.1,a.23.1.1 15693,16487 2fu4A 83 2.75e+01 1umgA 362 2.83e+01 d.280.1.1 107956 1ak4C 145 2.84e+01 1ak4C a.73.1.1 18321 1b79A 119 2.85e+01 1b79A a.81.1.1 18451 1ylmA 144 2.86e+01 2ctoA 93 2.88e+01 1oktA 211 2.88e+01 a.45.1.1,c.47.1.5 93272,93273 1ej2A 181 2.90e+01 1f9aA c.26.1.3 59414 2b0jA 358 2.91e+01 1y88A 199 2.92e+01 2myo 118 2.93e+01 2myo d.211.1.1 19175 1l8dA 112 2.96e+01 h.4.12.1 73687 1iieA 75 2.97e+01 1iieA a.109.1.1 19039 1yurA 98 3.00e+01 1m8jA 181 3.01e+01 c.26.1.3 84875 1pa7A 130 3.03e+01 a.40.1.1 94410 1fhuA 320 3.05e+01 1fhuA c.1.11.2,d.54.1.1 29234,38878 1nu7D 282 3.06e+01 a.8.6.1,a.8.6.1 92191,92192 1d5wC 126 3.10e+01 1dbwA c.23.1.1 31101 1u7lA 392 3.17e+01 1rzhL 281 3.19e+01 f.26.1.1 98164 1cnpA 90 3.20e+01 4icb a.39.1.2 17161 2bnkA 67 3.21e+01 1top 162 3.25e+01 1ncx a.39.1.5 17223 1aihA 170 3.29e+01 1aihA d.163.1.1 42149 1mvwB 145 3.30e+01 i.15.1.1 79524 1hssA 124 3.33e+01 1bea a.52.1.2 17819 1gvnB 287 3.44e+01 c.37.1.21 76354 1kk8B 139 3.45e+01 a.39.1.5 77430 1b06A 210 3.48e+01 1avmA a.2.11.1,d.44.1.1 15740,38737 2avuE 192 3.53e+01 1yrnB 83 3.56e+01 1akhB a.4.1.1 15986 1taq 832 3.56e+01 1taq a.60.7.1,c.120.1.2,c.55.3.5,e.8.1.1 18082,33352,33698,42991 2bbrA 195 3.60e+01 1se7A 83 3.60e+01 1xqiA 195 3.68e+01 1m7sA 484 3.68e+01 e.5.1.1 74574 1qhhA 167 3.71e+01 1pjr c.37.1.19 32393 2aawA 222 3.79e+01 1p4xA 250 3.84e+01 a.4.5.28,a.4.5.28 87784,87785 1eia 207 3.84e+01 1eia a.28.3.1,a.73.1.1 16951,18331 1jj21 48 3.87e+01 1ffkY 1mw5A 187 3.89e+01 d.259.1.1 91477 2ethA 154 3.89e+01 1vqo2 50 3.91e+01 1dryA 324 3.93e+01 1drtA b.82.2.2 28128 1sheA 103 3.93e+01 d.274.1.1 105551 1zv1A 65 3.94e+01 1w0bA 102 3.96e+01 a.7.11.1 108985 1guxA 218 3.98e+01 1guxA a.74.1.3 18388 1h3fA 432 3.99e+01 c.26.1.1,d.66.1.4 76631,76632 1z8uA 102 4.03e+01 1y01A 102 4.03e+01 1akhB 83 4.05e+01 1akhB a.4.1.1 15985 1ggwA 140 4.05e+01 1ggwA a.39.1.5 60490 1dmhA 311 4.05e+01 1dmhA b.3.6.1 22633 1bd8 156 4.08e+01 1bd8 d.211.1.1 19157 1myo 118 4.15e+01 2myo d.211.1.1 19174 1jm4B 118 4.23e+01 a.29.2.1 71746 1n45A 233 4.26e+01 a.132.1.1 79981 2gdjA 264 4.28e+01 1nwmX 142 4.33e+01 a.7.8.1 86301 1sb0A 87 4.35e+01 a.12.1.1 98789 1zbfA 142 4.36e+01 1amuA 563 4.38e+01 1amuA e.23.1.1 43351 1axdA 209 4.52e+01 1gnwA a.45.1.1,c.47.1.5 17730,33024 1w9yA 319 4.57e+01 1n1cA 217 4.59e+01 a.184.1.1 85254 1rijA 25 4.61e+01 k.32.1.1 104951 1aijL 281 4.64e+01 6prcL f.26.1.1 43461 1ockA 412 4.72e+01 c.117.1.1 86802 1aipA 405 4.73e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25697,25737,32132 2b1xA 470 4.82e+01 1hdiA 413 4.86e+01 16pk c.86.1.1 60964 1v37A 177 4.89e+01 1drtA 324 4.93e+01 1drtA b.82.2.2 28130 1zq9A 285 4.98e+01 2iu5A 195 5.07e+01 1ncx 162 5.07e+01 1ncx a.39.1.5 17222 1nwaA 203 5.13e+01 d.58.28.1 86295 1jeqA 609 5.13e+01 1jeqA a.140.2.1,b.131.1.1,c.62.1.3 64748,90366,90367 1q18A 332 5.19e+01 c.55.1.7,c.55.1.7 104470,104471 2mev2 256 5.19e+01 1aym2 2aucA 126 5.21e+01 1s722 50 5.21e+01 1k6iA 352 5.21e+01 c.2.1.2 68223 1buyA 166 5.26e+01 1eerA a.26.1.2 16848 1o8rA 94 5.28e+01 d.234.1.1 86677 1kqqA 139 5.28e+01 a.4.3.1 72885 1dckA 126 5.29e+01 1dbwA c.23.1.1 31097 2gsq 202 5.29e+01 1pd21 a.45.1.1,c.47.1.5 17715,33009 1wa8A 99 5.35e+01 1rh9A 373 5.37e+01 1sz2A 332 5.42e+01 1im5A 180 5.43e+01 c.33.1.3 66211 1x3zA 335 5.49e+01 1k6kA 143 5.64e+01 a.174.1.1 77274 1mw7A 240 5.72e+01 e.39.1.1 79557 1tqnA 486 5.72e+01 a.104.1.1 107238 1acp 77 5.74e+01 1acp a.28.1.1 16931 1af8 86 5.77e+01 2af8 a.28.1.1 16932 1tkeA 224 5.94e+01 1t0cA 31 5.95e+01 1sq5A 308 5.99e+01 c.37.1.6 105882 1kbhB 59 6.00e+01 a.153.1.1 68383 1x74A 360 6.07e+01 1ufzA 83 6.09e+01 a.5.9.1 107821 1im8A 244 6.15e+01 c.66.1.14 66212 1dg3A 592 6.15e+01 1dg3A a.114.1.1,c.37.1.8 19078,32153 1lvaA 258 6.17e+01 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 1gcvB 136 6.22e+01 1cg5B a.1.1.2 15589 1qb2A 109 6.23e+01 1qb2A a.36.1.1 17125 1mzbA 136 6.26e+01 a.4.5.42 91497 1q7lB 88 6.27e+01 1pyiA 96 6.29e+01 1pyiA g.38.1.1,h.1.3.1 45079,45512 1aipE 405 6.34e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25699,25739,32134 1jr3E 334 6.36e+01 a.80.1.1,c.37.1.20 63253,63254 1l4sA 112 6.37e+01 d.204.1.1 77693 1w7jB 151 6.39e+01 1r6xA 395 6.40e+01 b.122.1.3,c.26.1.5 97167,97168 1y0vH 146 6.42e+01 2d2sA 235 6.44e+01 2a6hE 99 6.45e+01 1zjjA 263 6.55e+01 1p4dA 330 6.60e+01 d.89.1.5 94101 1oxjA 173 6.61e+01 a.60.1.2,a.118.1.13 87517,87518 1lddA 74 6.63e+01 a.4.5.34 73841 5csmA 256 6.64e+01 5csmA a.130.1.2 19494 1ni4A 365 6.66e+01 c.36.1.11 85728 2genA 197 6.71e+01 2ct9A 208 6.73e+01 1sxgA 280 6.76e+01 1ux5A 411 6.76e+01 a.207.1.1 100144 1dbwA 126 6.84e+01 1dbwA c.23.1.1 31095 1ylqA 96 6.84e+01 1u59A 287 6.88e+01 d.144.1.7 107681 1wwuA 99 6.89e+01 1zb1A 392 6.98e+01 1ycqA 107 6.99e+01 1ycqA a.42.1.1 17419 2gfhA 260 7.00e+01 1pgtA 210 7.02e+01 1pgtA a.45.1.1,c.47.1.5 17515,32809 1n2fA 142 7.04e+01 d.227.1.1 79853 2ar0A 541 7.06e+01 1ycsB 239 7.06e+01 1ycsB d.211.1.1,b.34.2.1 19155,24553 2bidA 197 7.08e+01 2bidA f.1.4.1 43398 1i9gA 280 7.08e+01 c.66.1.13 62090 1dipA 78 7.10e+01 1dipA h.1.12.1 45632 1csmA 256 7.11e+01 5csmA a.130.1.2 19495 1uk5A 111 7.15e+01 a.7.7.1 99487 2beiA 170 7.20e+01 1ax8 146 7.20e+01 1ax8 a.26.1.1 16844 1ulyA 192 7.21e+01 1wv9A 94 7.31e+01 1cmcA 104 7.31e+01 1cmbA a.43.1.5 17462 1v2xA 194 7.34e+01 c.116.1.1 100274 1z3eB 73 7.38e+01 1w9iA 770 7.39e+01 1yewA 382 7.43e+01 1xgkA 352 7.44e+01 1y3nA 490 7.44e+01 2fg9A 178 7.45e+01 1gumA 222 7.47e+01 1pgtA a.45.1.1,c.47.1.5 17683,32977 1umnA 165 7.50e+01 a.25.1.1 99607 1wpbA 172 7.50e+01 1u6rA 380 7.51e+01 1p2hA 571 7.52e+01 a.138.1.3,c.3.1.4,d.168.1.1 93930,93931,93932 1tu7A 208 7.59e+01 1d6gA 47 7.72e+01 1d6gA g.33.1.1 44976 1whtB 153 7.75e+01 1whtB 1o65A 246 7.78e+01 b.58.1.2 92544 1w2fA 276 7.81e+01 d.143.1.3 109125 1jggA 60 7.84e+01 2hddA a.4.1.1 62950 1ltsC 41 7.92e+01 1ltsC 1o5hA 214 7.92e+01 a.191.1.1 92497 1wpkA 146 7.93e+01 1ow4A 129 7.96e+01 a.39.2.1 93628 1vqoI 162 7.97e+01 2occF 98 8.00e+01 2occF g.41.5.3 45256 1xkzA 255 8.01e+01 1eh2 106 8.07e+01 1eh2 a.39.1.6 17339 2gpjA 252 8.10e+01 1jnrB 150 8.17e+01 d.58.1.5 66969 1fg7A 356 8.22e+01 1gewA c.67.1.1 59819 1m8oB 47 8.22e+01 j.60.1.1 78776 1p5dX 463 8.24e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1aua 296 8.24e+01 1aua a.5.3.1,c.13.1.1 16290,30882 1uehA 253 8.27e+01 c.101.1.1 99259 1q5nA 454 8.28e+01 a.127.1.1 95901 1kkuA 279 8.29e+01 c.26.1.3 72661 1gdeA 389 8.32e+01 c.67.1.1 60456 1jokA 149 8.32e+01 1snc b.40.1.1 63214 1w9rA 119 8.37e+01 1zybA 232 8.38e+01 1oqcA 125 8.40e+01 a.24.15.1 87264 1erd 40 8.43e+01 1erd a.10.1.1 16362 3lck 271 8.44e+01 1fmk d.144.1.7 41686 1q8cA 151 8.50e+01 a.79.1.2 96202 2ahjA 206 8.53e+01 2ahjA d.149.1.1 41772 1p9bA 442 8.54e+01 c.37.1.10 94385 2occE 109 8.59e+01 2occE a.118.11.1 19224 1kv4A 42 8.61e+01 j.4.1.3 73051 2ahjC 206 8.70e+01 2ahjA d.149.1.1 41773 1imuA 107 8.72e+01 d.204.1.1 66218 1ltaC 49 8.73e+01 1ltaC 1n1bA 549 8.78e+01 a.102.4.1,a.128.1.3 79799,79800 1a41 234 8.81e+01 1a41 d.163.1.2 42174 1nlwB 76 8.84e+01 a.38.1.1 80634 1zxoA 291 8.87e+01 1glqA 209 8.92e+01 1pgtA a.45.1.1,c.47.1.5 17588,32882 2fqmA 75 8.92e+01 1qovH 260 8.93e+01 6prcH b.41.1.1,f.23.10.1 25464,43457 1rzhH 260 8.98e+01 b.41.1.1,f.23.10.1 98162,98163