# List of top-scoring protein chains for t2k-100-30-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 2a61A 145 8.95e-14 2fbhA 146 5.75e-13 1z91A 147 8.30e-13 2fbiA 142 8.41e-13 1jgsA 138 1.17e-12 a.4.5.28 66683 1s3jA 155 4.17e-12 a.4.5.28 98437 1lnwA 147 4.94e-12 a.4.5.28 78104 2ethA 154 1.42e-11 1lj9A 144 5.20e-11 a.4.5.28 78035 1p4xA 250 1.88e-08 a.4.5.28,a.4.5.28 87784,87785 2fxaA 207 2.67e-08 1ub9A 100 5.15e-06 a.4.5.28 99159 1on2A 142 1.53e-05 a.4.5.24,a.76.1.1 87103,87104 1ddnA 226 2.48e-04 1bi0 a.4.5.24,a.76.1.1 16207,18413 1f5tA 121 2.96e-04 1bi0 a.4.5.24,a.76.1.1 16203,18409 1z7uA 112 4.09e-04 1fx7A 230 4.43e-04 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 60088,60089,60090 1b1bA 140 6.16e-04 1bi0 a.4.5.24,a.76.1.1 16215,18421 1bi0 226 6.28e-04 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 16202,18408,24453 1c0wA 225 7.10e-04 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 16211,18417,24455 2dtr 226 1.15e-03 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 16193,18399,24450 1yyvA 131 1.24e-03 1tbxA 99 2.09e-03 a.4.5.48 106748 1sfxA 109 2.28e-03 a.4.5.50 105505 1mkmA 249 2.64e-03 a.4.5.33,d.110.2.2 79242,79243 1okrA 123 4.03e-03 a.4.5.39 93269 1xmaA 145 4.18e-03 2co5A 99 4.74e-03 2fswA 107 5.94e-03 1ulyA 192 1.01e-02 2f2eA 146 1.28e-02 2cfxA 144 1.33e-02 1i1sA 96 1.34e-02 1bjaA a.4.5.9 16124 1bjaA 95 1.67e-02 1bjaA a.4.5.9 16122 1sd4A 126 1.81e-02 a.4.5.39 105428 2b0lA 102 2.94e-02 1smtB 122 3.25e-02 1smtA a.4.5.5 16110 1hw5A 210 3.31e-02 2cgpA a.4.5.4,b.82.3.2 16098,28137 1dpuA 99 3.54e-02 1dpuA a.4.5.16 16150 1r1tA 122 3.89e-02 a.4.5.5 104769 1xnpA 202 4.13e-02 1z1dA 103 4.72e-02 1smtA 122 4.75e-02 1smtA a.4.5.5 16109 1i6xA 209 5.24e-02 a.4.5.4,b.82.3.2 83673,83674 2g7uA 257 8.69e-02 1ft9A 222 9.68e-02 1ft9A a.4.5.4,b.82.3.1 16107,28131 1u2wA 122 1.07e-01 2cgpA 210 1.12e-01 2cgpA a.4.5.4,b.82.3.2 16102,28141 1ixcA 294 1.18e-01 a.4.5.37,c.94.1.1 83764,83765 1xn7A 78 1.21e-01 1g6nA 210 1.43e-01 2cgpA a.4.5.4,b.82.3.2 16100,28139 1iz1A 294 1.58e-01 a.4.5.37,c.94.1.1 83823,83824 1r1uA 106 1.83e-01 a.4.5.5 104771 1ge9A 184 1.89e-01 1dd5A d.67.3.1 60463 1i1gA 141 1.90e-01 a.4.5.32,d.58.4.2 65982,65983 1q1hA 110 2.00e-01 a.4.5.41 95580 2fu4A 83 2.06e-01 6paxA 133 2.19e-01 6paxA a.4.1.5,a.4.1.5 64758,64759 2dbbA 151 2.22e-01 2eshA 118 2.26e-01 1qgpA 77 3.60e-01 1qbjA a.4.5.19 16158 1r7jA 95 3.66e-01 a.4.5.49 104836 1zybA 232 4.06e-01 1yqyA 523 4.89e-01 2bgcA 238 5.43e-01 1k78A 149 5.46e-01 a.4.1.5,a.4.1.5 68255,68256 1mzbA 136 7.04e-01 a.4.5.42 91497 1yg2A 179 8.73e-01 1qzzA 374 8.79e-01 a.4.5.29,c.66.1.12 96719,96720 1j75A 67 9.16e-01 a.4.5.19 62673 1puoA 170 1.08e+00 a.101.1.1,a.101.1.1 95134,95135 1jhfA 202 1.11e+00 a.4.5.2,b.87.1.1 63057,63058 1qbjA 81 1.11e+00 1qbjA a.4.5.19 16155 1b9mA 265 1.15e+00 1b9mA a.4.5.8,b.40.6.2,b.40.6.2 16118,58938,58939 2cohA 202 1.21e+00 1lea 84 1.41e+00 1lea a.4.5.2 16085 1fzpB 123 1.55e+00 1fznD a.4.5.28 19008 2bgsA 344 1.55e+00 1zljA 78 1.57e+00 1bw6A 56 1.58e+00 1bw6A a.4.1.7 16052 1wi9A 72 1.78e+00 2bjcA 62 1.81e+00 1kn6A 90 1.82e+00 d.58.3.3 72770 1sfuA 75 1.87e+00 a.4.5.19 105503 1cjgA 62 1.88e+00 1pru a.35.1.5 17112 1lqc 56 1.94e+00 1pru a.35.1.5 17109 1iawA 317 2.05e+00 c.52.1.9 62126 1omiA 248 2.07e+00 b.82.3.3,a.4.5.4 87079,87080 1lcdA 51 2.21e+00 1pru a.35.1.5 17111 1lccA 51 2.24e+00 1pru a.35.1.5 17110 1j5yA 187 2.50e+00 a.4.5.1,d.94.2.1 71592,71593 1ev7B 317 2.63e+00 1ev7B c.52.1.9 33316 1j7nA 776 2.77e+00 d.92.1.14,d.92.1.14,d.166.1.1 66409,66410,66411 1lvaA 258 2.85e+00 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 1ev7A 317 3.11e+00 1ev7B c.52.1.9 33315 1y0uA 96 3.13e+00 1ri7A 171 3.16e+00 a.4.5.32,d.58.4.2 97504,97505 1hlvA 131 3.37e+00 a.4.1.7,a.4.1.7 65854,65855 2cu6A 103 3.43e+00 1j7nB 776 3.63e+00 d.92.1.14,d.92.1.14,d.166.1.1 66412,66413,66414 1in6A 334 3.95e+00 1hqcA a.4.5.11,c.37.1.20 62601,62602 2cg4A 152 4.10e+00 1c8bA 371 4.10e+00 1c8bA c.56.1.2 59082 1t98A 287 4.15e+00 1s7oA 113 4.32e+00 a.4.13.3 105354 1hw1A 239 4.34e+00 1e2xA a.4.5.6,a.78.1.1 16111,18441 2acjA 66 4.60e+00 1efaA 333 4.64e+00 1tlfA a.35.1.5,c.93.1.1 17106,35691 1je8A 82 4.80e+00 a.4.6.2 77108 1tuoA 464 5.05e+00 1e2xA 243 5.28e+00 1e2xA a.4.5.6,a.78.1.1 16113,18443 2bx9A 53 5.30e+00 1in4A 334 5.44e+00 1hqcA a.4.5.11,c.37.1.20 62597,62598 1odd 118 5.46e+00 1opc a.4.6.1 16232 1opc 110 5.75e+00 1opc a.4.6.1 16231 1ldjA 760 6.35e+00 a.4.5.34,a.118.17.1,e.40.1.1 73847,73848,73849 1b0nA 111 6.45e+00 1b0nA a.34.1.1,a.35.1.3 17001,17064 1puzA 82 6.65e+00 a.218.1.1 104320 1di6A 195 7.46e+00 1di6A c.57.1.1 33863 1zkrA 153 7.77e+00 1ys7A 233 7.80e+00 1xd7A 145 7.92e+00 a.4.5.55 109566 1t6sA 162 8.14e+00 2lfb 100 8.15e+00 1lfb a.4.1.1 15990 1utxA 66 8.59e+00 a.35.1.3 108034 1mj5A 302 9.00e+00 c.69.1.8 91285 1q8fA 313 9.04e+00 c.70.1.1 96203 1aisB 200 9.35e+00 1aisB a.74.1.2,a.74.1.2 18384,18385 1tu9A 134 9.83e+00 a.1.1.2 107320 1xmkA 79 9.92e+00 1orjA 130 1.05e+01 a.24.19.1 93456 1a04A 215 1.13e+01 1a04A a.4.6.2,c.23.1.1 16234,31089 1iae 200 1.18e+01 1iae d.92.1.8 40311 1ast 200 1.20e+01 1iae d.92.1.8 40310 1iz7A 295 1.24e+01 c.69.1.8 76982 1cv2A 296 1.24e+01 1bn6A c.69.1.8 34680 1z67A 135 1.27e+01 1zs9A 261 1.29e+01 1pdnC 128 1.38e+01 6paxA a.4.1.5 16047 1i50F 155 1.39e+01 a.143.1.2 61760 1fp2A 352 1.40e+01 1fpxA a.4.5.29,c.66.1.12 59941,59942 1iab 200 1.42e+01 1iae d.92.1.8 40312 1htjF 210 1.44e+01 1htjF a.91.1.1 61254 1twfF 155 1.44e+01 1irxA 523 1.44e+01 a.97.1.2,c.26.1.1 71378,71379 1ka2A 499 1.45e+01 d.92.1.5 77305 1whzA 70 1.49e+01 1fpxA 352 1.49e+01 1fpxA a.4.5.29,c.66.1.12 59950,59951 1wmqA 147 1.51e+01 1d3uB 201 1.55e+01 1aisB a.74.1.2,a.74.1.2 18386,18387 1x6iA 91 1.55e+01 1rr7A 129 1.57e+01 a.4.1.14 105075 1i6uA 130 1.58e+01 d.140.1.1 61850 1ufaA 520 1.61e+01 a.8.3.3,c.6.2.4 99329,99330 1ufmA 84 1.68e+01 a.4.5.47 107816 2tct 207 1.74e+01 2tct a.4.1.9,a.121.1.1 16063,19240 1m7kA 99 1.82e+01 a.7.7.1 74573 1uyrA 737 1.85e+01 c.14.1.4,c.14.1.4 100188,100189 1pru 56 1.86e+01 1pru a.35.1.5 17104 1zxtA 76 1.89e+01 1oyiA 82 1.89e+01 a.4.5.19 93729 1t95A 240 1.96e+01 a.5.8.1,d.235.1.2,d.58.11.3 106705,106706,106707 1hqcA 324 2.00e+01 1hqcA a.4.5.11,c.37.1.20 16127,32424 1fokA 568 2.01e+01 2fokA a.4.5.12,a.4.5.12,a.4.5.12,c.52.1.12 16137,16138,16139,33325 1qxhA 167 2.03e+01 c.47.1.10 96528 1uxd 65 2.04e+01 1uxc a.35.1.5 17118 1rm6A 769 2.06e+01 1bjz 207 2.07e+01 2tct a.4.1.9,a.121.1.1 16065,19242 1a6i 217 2.07e+01 2tct a.4.1.9,a.121.1.1 16066,19243 1sgoA 139 2.08e+01 d.82.3.1 98857 1w9iA 770 2.18e+01 1zx4A 192 2.19e+01 1urvA 190 2.24e+01 1ut0A 190 2.24e+01 a.1.1.2 108012 1b24A 188 2.33e+01 1b24A d.95.2.1,d.95.2.1 40573,40574 1q06A 135 2.36e+01 a.6.1.3 95493 1zvnA 99 2.44e+01 3mspA 126 2.64e+01 1mspA b.1.11.2 22343 1p9qC 256 2.65e+01 a.5.8.1,d.235.1.2,d.58.11.3 104093,104094,104095 1mgtA 174 2.69e+01 1mgtA a.4.2.1,c.55.7.1 16078,33753 2blfB 81 2.70e+01 1od2A 805 2.72e+01 c.14.1.4,c.14.1.4 86821,86822 1hx1B 114 2.80e+01 1hx1B a.7.7.1 61350 1v38A 78 2.82e+01 a.60.1.2 100280 1vj2A 126 2.82e+01 b.82.1.10 100796 1r71A 178 2.86e+01 a.4.14.1 104823 1w2xA 758 2.92e+01 c.14.1.4,c.14.1.4 109134,109135 1v6tA 255 2.95e+01 1fehA 574 2.99e+01 1fehA c.96.1.1,d.15.4.2,d.58.1.5 36015,37690,38998 1stzA 338 3.03e+01 a.4.5.51,d.110.2.3 106009,106010 1wj5A 120 3.18e+01 1g3uA 214 3.28e+01 c.37.1.1 65132 1mkp 144 3.29e+01 1vhrA c.45.1.1 32654 1ecrA 309 3.29e+01 1ecrA e.2.1.1 42678 1qtrA 317 3.50e+01 1qtrA c.69.1.7 34660 2a6cA 83 3.59e+01 1uxc 65 3.63e+01 1uxc a.35.1.5 17119 1zxkA 98 3.66e+01 1eudA 311 3.87e+01 2scuA c.2.1.8,c.23.4.1 30312,31140 1khyA 148 3.87e+01 a.174.1.1 77410 2b5aA 77 3.91e+01 1e3aA 260 3.93e+01 1ajqA d.153.1.2 41838 2g7gA 213 4.14e+01 1bdg 451 4.14e+01 1qhaA c.55.1.3,c.55.1.3 33461,33462 1a2xA 159 4.18e+01 1ncx a.39.1.5 17251 1d2fA 390 4.26e+01 1d2fA c.67.1.3 34411 1jweA 114 4.27e+01 1b79A a.81.1.1 18455 1b4aA 149 4.29e+01 1b4aA a.4.5.3,d.74.2.1 16088,39721 1v88A 130 4.30e+01 b.55.1.1 108423 1mspA 126 4.30e+01 1mspA b.1.11.2 22333 2mspA 126 4.31e+01 1mspA b.1.11.2 22335 1foeA 377 4.32e+01 1foeA a.87.1.1,b.55.1.1 18517,26969 1vqoY 241 4.43e+01 1h10A 125 4.43e+01 b.55.1.1 83446 2culA 232 4.46e+01 2bnmA 198 4.48e+01 1wdvA 152 4.50e+01 1fy7A 278 4.57e+01 1fy7A d.108.1.1 40817 1i60A 278 4.63e+01 c.1.15.4 71118 1s72Y 241 4.72e+01 c.9.2.1 105344 2cw8A 537 4.72e+01 1y9uA 323 4.74e+01 1myt 146 4.76e+01 1a6m a.1.1.2 15207 1g5tA 196 4.77e+01 1g5rA c.37.1.11 32366 1qs2A 401 4.79e+01 1qs1A d.166.1.1,d.166.1.1 42268,42269 4dfrA 159 4.80e+01 1vdrA c.71.1.1 34822 1ajqA 209 4.84e+01 1ajqA d.153.1.2 41840 1jj2X 240 4.87e+01 1ffkV c.9.2.1 63109 1pnkA 209 4.87e+01 1ajqA d.153.1.2 41839 1ai7A 209 4.99e+01 1ajqA d.153.1.2 41845 1gtvA 214 4.99e+01 c.37.1.1 70537 1lmhA 184 5.01e+01 d.167.1.1 74036 1gm7A 209 5.03e+01 d.153.1.2 65302 1ddgA 374 5.05e+01 1amoA b.43.4.1,c.25.1.4 25671,31559 1lqwA 183 5.10e+01 d.167.1.1 74210 1eblB 317 5.13e+01 1hn9A c.95.1.2,c.95.1.2 35975,35976 1m2oB 190 5.14e+01 c.37.1.8 78485 1eucA 311 5.19e+01 2scuA c.2.1.8,c.23.4.1 30311,31139 1moh 142 5.37e+01 1flp a.1.1.2 15012 2dc3A 193 5.43e+01 1xdzA 240 5.49e+01 1unqA 125 5.53e+01 b.55.1.1 107968 1c9fA 90 5.63e+01 1c9fA d.15.2.1 37639 1mc0A 368 5.69e+01 d.110.2.1,d.110.2.1 78937,78938 1trrA 107 5.70e+01 1jhgA a.4.12.1 19017 1a58 177 5.73e+01 2cpl b.62.1.1 27495 1gk9A 260 5.75e+01 d.153.1.2 65246 1jftA 340 5.84e+01 a.35.1.5,c.93.1.1 66652,66653 1r69 69 5.91e+01 1r69 a.35.1.2 17028 1ci3M 249 5.95e+01 1hcz b.2.6.1,b.84.2.2 22480,28266 2or1L 69 5.98e+01 1r69 a.35.1.2 17031 1r3dA 264 6.01e+01 1a52A 258 6.02e+01 3erdA a.123.1.1 19296 2b1xA 470 6.07e+01 1wpbA 172 6.08e+01 1du6A 64 6.11e+01 1akhA a.4.1.1 16002 1z5bA 469 6.16e+01 1b79A 119 6.22e+01 1b79A a.81.1.1 18451 1w9cA 321 6.28e+01 1cqa 133 6.33e+01 3nul d.110.1.1 40890 1mai 131 6.44e+01 1mai b.55.1.1 26951 1q4rA 112 6.45e+01 d.58.4.4 95823 1wm1A 317 6.53e+01 c.69.1.7 109405 1b9aA 108 6.55e+01 1a75A a.39.1.4 17204 1flp 142 6.56e+01 1flp a.1.1.2 15011 1ylvA 342 6.58e+01 1b4kA c.1.10.3 29180 1iyeA 309 6.59e+01 e.17.1.1 83786 1g5rA 196 6.59e+01 1g5rA c.37.1.11 32367 1eswA 500 6.63e+01 1cwyA c.1.8.1 59500 1qpzA 340 6.69e+01 1qpzA a.35.1.5,c.93.1.1 17097,35673 1ls9A 91 6.70e+01 a.3.1.1 78177 1u7eB 154 6.73e+01 1y7yA 74 6.83e+01 1ku1A 230 6.86e+01 a.118.3.1 72996 1f3lA 321 6.87e+01 1g6q2 c.66.1.6 59630 1vpwA 340 6.92e+01 1qpzA a.35.1.5,c.93.1.1 17087,35680 1bib 321 6.93e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16084,24448,40788 1zug 71 7.02e+01 1r69 a.35.1.2 17041 1wzdA 215 7.08e+01 1cwyA 500 7.18e+01 1cwyA c.1.8.1 28789 3erdA 261 7.24e+01 3erdA a.123.1.1 19293 1nhkL 144 7.43e+01 1npk d.58.6.1 39142 1c9bA 207 7.44e+01 1tfb a.74.1.2,a.74.1.2 18372,18373 1cdq 77 7.48e+01 1cds g.7.1.3 44459 1yhfA 115 7.53e+01 1lnzA 342 7.56e+01 b.117.1.1,c.37.1.8 78112,78113 1d9nA 75 7.56e+01 1d9nA d.10.1.3 37486 1zj6A 187 7.65e+01 1nekA 588 7.67e+01 a.7.3.1,c.3.1.4,d.168.1.1 80426,80427,80428 1sctB 151 7.72e+01 3sdhA a.1.1.2 15003 1xmbA 418 7.74e+01 1iujA 106 7.86e+01 d.58.4.5 90701 1qusA 322 7.94e+01 1ltm d.2.1.6 36991 5ldh 334 8.00e+01 3ldh c.2.1.5,d.162.1.1 30158,42125 2cro 71 8.03e+01 1r69 a.35.1.2 17038 1eo1A 124 8.03e+01 1eo1A c.55.5.1 33739 1ohlA 342 8.07e+01 c.1.10.3 87035 2wrpR 107 8.15e+01 1jhgA a.4.12.1 19010 1mg2B 131 8.16e+01 g.21.1.1 79060 1dwtA 153 8.21e+01 1a6m a.1.1.2 15190 1wfxA 186 8.22e+01 2cujA 108 8.22e+01 1wetA 340 8.25e+01 1qpzA a.35.1.5,c.93.1.1 17093,35670 1qawF 74 8.33e+01 1wapA b.82.5.1 28202 1cm9A 74 8.35e+01 1b3aA d.9.1.1 37405 1b0b 142 8.40e+01 2fal a.1.1.2 15010 1x0vA 354 8.46e+01 1vjoA 393 8.56e+01 c.67.1.3 100827 1u5tC 202 8.61e+01 a.4.5.54,a.4.5.54 107688,107689 1whrA 124 8.63e+01 1q2lA 939 8.70e+01 1c1bB 440 8.75e+01 1rthA e.8.1.2 43077 2c1xA 456 8.81e+01 1jhgA 101 8.82e+01 1jhgA a.4.12.1 19009 1z02A 446 8.89e+01 2agaA 190 8.89e+01 1ra9 159 8.92e+01 1vdrA c.71.1.1 34820 1zzcA 198 8.93e+01 1wi5A 119 9.00e+01