# 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 1ri7A 171 1.04e-21 a.4.5.32,d.58.4.2 97504,97505 1i1gA 141 1.20e-19 a.4.5.32,d.58.4.2 65982,65983 2cg4A 152 1.11e-18 2cfxA 144 9.83e-17 1sfxA 109 4.38e-05 a.4.5.50 105505 1s3jA 155 1.67e-04 a.4.5.28 98437 1ulyA 192 2.79e-04 2a61A 145 8.42e-04 1xnpA 202 1.62e-03 1lj9A 144 2.08e-03 a.4.5.28 78035 1ub9A 100 3.76e-03 a.4.5.28 99159 2fbiA 142 4.36e-03 2csbA 519 4.80e-03 2fbhA 146 5.56e-03 2b0lA 102 6.63e-03 1je8A 82 6.90e-03 a.4.6.2 77108 2g7uA 257 7.55e-03 1z91A 147 7.65e-03 1q1hA 110 1.90e-02 a.4.5.41 95580 1u2wA 122 1.99e-02 2cgpA 210 2.24e-02 2cgpA a.4.5.4,b.82.3.2 16102,28141 1lnwA 147 2.44e-02 a.4.5.28 78104 1smtB 122 2.75e-02 1smtA a.4.5.5 16110 1r1tA 122 3.21e-02 a.4.5.5 104769 1i6xA 209 3.25e-02 a.4.5.4,b.82.3.2 83673,83674 1zljA 78 3.39e-02 1g6nA 210 4.09e-02 2cgpA a.4.5.4,b.82.3.2 16100,28139 1xd7A 145 4.12e-02 a.4.5.55 109566 1bib 321 4.17e-02 1bia a.4.5.1,b.34.1.1,d.104.1.2 16084,24448,40788 1smtA 122 4.26e-02 1smtA a.4.5.5 16109 1hw5A 210 4.57e-02 2cgpA a.4.5.4,b.82.3.2 16098,28137 1lvaA 258 5.56e-02 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 1bia 321 5.80e-02 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1b1bA 140 6.27e-02 1bi0 a.4.5.24,a.76.1.1 16215,18421 1ft9A 222 9.95e-02 1ft9A a.4.5.4,b.82.3.1 16107,28131 1mkmA 249 1.16e-01 a.4.5.33,d.110.2.2 79242,79243 1a04A 215 1.67e-01 1a04A a.4.6.2,c.23.1.1 16234,31089 1jhfA 202 1.71e-01 a.4.5.2,b.87.1.1 63057,63058 1j5yA 187 1.96e-01 a.4.5.1,d.94.2.1 71592,71593 1fx7A 230 2.27e-01 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 60088,60089,60090 1lea 84 2.53e-01 1lea a.4.5.2 16085 1f5tA 121 2.88e-01 1bi0 a.4.5.24,a.76.1.1 16203,18409 1okrA 123 2.94e-01 a.4.5.39 93269 2fxaA 207 3.05e-01 1aisB 200 3.34e-01 1aisB a.74.1.2,a.74.1.2 18384,18385 3crd 100 3.83e-01 3crd a.77.1.3 18429 1fseA 74 3.85e-01 1fseA a.4.6.2 60000 1d3uB 201 4.09e-01 1aisB a.74.1.2,a.74.1.2 18386,18387 2ethA 154 4.10e-01 1e2xA 243 4.78e-01 1e2xA a.4.5.6,a.78.1.1 16113,18443 1hw1A 239 5.20e-01 1e2xA a.4.5.6,a.78.1.1 16111,18441 1g2hA 61 5.52e-01 1g2hA a.4.1.12 60224 1ddnA 226 6.28e-01 1bi0 a.4.5.24,a.76.1.1 16207,18413 1p4xA 250 6.42e-01 a.4.5.28,a.4.5.28 87784,87785 1sd4A 126 7.20e-01 a.4.5.39 105428 1xmaA 145 8.26e-01 1c0wA 225 8.56e-01 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 16211,18417,24455 1xmkA 79 8.98e-01 1jgsA 138 9.63e-01 a.4.5.28 66683 1on2A 142 1.10e+00 a.4.5.24,a.76.1.1 87103,87104 1xn7A 78 1.12e+00 2f06A 144 1.13e+00 1j75A 67 1.14e+00 a.4.5.19 62673 1bw6A 56 1.35e+00 1bw6A a.4.1.7 16052 2cohA 202 1.38e+00 1r1uA 106 1.48e+00 a.4.5.5 104771 2fu4A 83 1.52e+00 1ufmA 84 1.57e+00 a.4.5.47 107816 1qgpA 77 1.57e+00 1qbjA a.4.5.19 16158 6paxA 133 1.70e+00 6paxA a.4.1.5,a.4.1.5 64758,64759 1pk5A 248 1.80e+00 a.123.1.1 88139 1wi9A 72 1.95e+00 1s7oA 113 2.03e+00 a.4.13.3 105354 1qbjA 81 2.13e+00 1qbjA a.4.5.19 16155 1qzzA 374 2.34e+00 a.4.5.29,c.66.1.12 96719,96720 1zybA 232 2.42e+00 1hqcA 324 2.55e+00 1hqcA a.4.5.11,c.37.1.20 16127,32424 1mgtA 174 2.62e+00 1mgtA a.4.2.1,c.55.7.1 16078,33753 1in6A 334 2.75e+00 1hqcA a.4.5.11,c.37.1.20 62601,62602 1b0nA 111 2.79e+00 1b0nA a.34.1.1,a.35.1.3 17001,17064 1f08A 148 2.85e+00 1f08A d.89.1.2 59564 1bbpA 173 2.86e+00 1bbpA b.60.1.1 27147 1k78A 149 3.12e+00 a.4.1.5,a.4.1.5 68255,68256 1pdnC 128 3.16e+00 6paxA a.4.1.5 16047 1yucA 255 3.54e+00 2bj7A 138 3.68e+00 1fxxA 482 3.75e+00 1fxxA c.55.3.5 33726 1y0uA 96 3.82e+00 2exrA 524 3.84e+00 1yyvA 131 4.01e+00 1ksyA 154 4.62e+00 d.89.1.2 72948 1jr7A 311 4.77e+00 b.82.2.3 63255 1han 297 5.25e+00 1han d.32.1.3,d.32.1.3 38506,38507 1v05A 96 5.90e+00 1xt8A 292 5.93e+00 1lgtA 297 5.96e+00 d.32.1.3,d.32.1.3 77956,77957 2a6cA 83 6.03e+00 1lkdA 297 6.08e+00 d.32.1.3,d.32.1.3 78059,78060 1u8bA 133 6.90e+00 1z7uA 112 7.21e+00 1wbpA 397 7.50e+00 1m32A 366 7.53e+00 c.67.1.3 78508 1louA 101 7.67e+00 1ris d.58.14.1 39323 2aq4A 434 7.85e+00 1zgwA 139 7.88e+00 1t6sA 162 8.19e+00 2bznA 351 8.38e+00 1c3jA 351 8.95e+00 1c3jA c.87.1.1 35459 1bi0 226 9.09e+00 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 16202,18408,24453 1utxA 66 9.13e+00 a.35.1.3 108034 1f4kA 122 9.52e+00 1bm9A a.4.5.7 59646 1dhy 292 9.60e+00 1han d.32.1.3,d.32.1.3 38504,38505 1uxd 65 9.65e+00 1uxc a.35.1.5 17118 1s6lA 212 1.01e+01 2c6qA 351 1.03e+01 1p4wA 99 1.08e+01 a.4.6.2 87783 1t56A 216 1.09e+01 a.4.1.9,a.121.1.1 106428,106429 1in4A 334 1.13e+01 1hqcA a.4.5.11,c.37.1.20 62597,62598 2bgu 351 1.14e+01 1c3jA c.87.1.1 35460 2a19B 284 1.15e+01 2a5hA 416 1.16e+01 2f2eA 146 1.19e+01 2bjcA 62 1.23e+01 1uxc 65 1.26e+01 1uxc a.35.1.5 17119 1kw3B 292 1.27e+01 d.32.1.3,d.32.1.3 77549,77550 2or1L 69 1.34e+01 1r69 a.35.1.2 17031 2b5aA 77 1.39e+01 2c9wA 169 1.40e+01 1h6zA 913 1.42e+01 c.1.12.2,c.8.1.1,d.142.1.5 70906,70907,70908 2f46A 156 1.43e+01 1sc6A 404 1.46e+01 1b8iB 63 1.50e+01 1akhA a.4.1.1 16011 1cqmA 101 1.50e+01 1ris d.58.14.1 39321 1lqc 56 1.52e+01 1pru a.35.1.5 17109 1n2aA 201 1.52e+01 a.45.1.1,c.47.1.5 91553,91554 1cjgA 62 1.60e+01 1pru a.35.1.5 17112 1lccA 51 1.68e+01 1pru a.35.1.5 17110 1lcdA 51 1.69e+01 1pru a.35.1.5 17111 1du6A 64 1.70e+01 1akhA a.4.1.1 16002 2ad9A 119 1.70e+01 1r69 69 1.71e+01 1r69 a.35.1.2 17028 1xyzA 347 1.71e+01 1taxA c.1.8.3 28804 1imjA 210 1.75e+01 c.69.1.23 71246 1u5xA 140 1.76e+01 1pufB 73 1.76e+01 a.4.1.1 95132 1f0lA 535 1.77e+01 1ddt b.2.1.1,d.166.1.1,f.1.2.1 22377,42239,43382 1tbxA 99 1.78e+01 a.4.5.48 106748 1ixcA 294 1.79e+01 a.4.5.37,c.94.1.1 83764,83765 2acjA 66 1.81e+01 1xgsA 295 1.82e+01 1bn5 a.4.5.25,d.127.1.1 16216,41153 1js3A 486 1.85e+01 c.67.1.6 67215 1iz1A 294 1.87e+01 a.4.5.37,c.94.1.1 83823,83824 1tlk 154 1.87e+01 1tlk b.1.1.4 21707 2fswA 107 1.93e+01 1b72B 87 1.94e+01 1akhA a.4.1.1 16001 2dtr 226 1.99e+01 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 16193,18399,24450 1or7A 194 1.99e+01 a.4.13.2,a.177.1.1 87332,87333 1jixA 351 1.99e+01 1c3jA c.87.1.1 63081 2g7gA 213 2.03e+01 1a0fA 201 2.04e+01 1a0fA a.45.1.1,c.47.1.5 17737,33031 1v95A 130 2.07e+01 c.51.1.1 108435 1bm9A 122 2.07e+01 1bm9A a.4.5.7 16116 1zarA 282 2.08e+01 1r9wA 145 2.09e+01 d.89.1.2 97264 1r7jA 95 2.10e+01 a.4.5.49 104836 1kxoA 184 2.13e+01 b.60.1.1 84475 1yq7A 374 2.18e+01 2a33A 215 2.27e+01 1yv5A 374 2.33e+01 1tqmA 282 2.36e+01 a.4.5.56,d.144.1.9 107236,107237 1ddt 535 2.37e+01 1ddt b.2.1.1,d.166.1.1,f.1.2.1 22379,42241,43384 1hlvA 131 2.37e+01 a.4.1.7,a.4.1.7 65854,65855 1vmbA 140 2.38e+01 1azsC 388 2.39e+01 1cipA a.66.1.1,c.37.1.8 18203,32086 1xsvA 113 2.40e+01 1mli 96 2.51e+01 1mli d.58.4.1 39070 2f1fA 164 2.54e+01 2aj0A 71 2.62e+01 1ris 101 2.63e+01 1ris d.58.14.1 39314 1fhgA 154 2.67e+01 1tlk b.1.1.4 21706 1rr7A 129 2.67e+01 a.4.1.14 105075 1dik 874 2.68e+01 1dik c.1.12.2,c.8.1.1,d.142.1.5 29304,30702,41572 1t95A 240 2.75e+01 a.5.8.1,d.235.1.2,d.58.11.3 106705,106706,106707 1qd1A 325 2.85e+01 1qd1A d.58.34.1,d.58.34.1 39493,39494 1dw9A 156 2.90e+01 1dw9A a.35.1.4,d.72.1.1 17065,39596 1k8tA 510 2.98e+01 e.41.1.1 68316 2fsxA 148 3.01e+01 1bebA 162 3.01e+01 1bebA b.60.1.1 27115 1jg7A 351 3.05e+01 1c3jA c.87.1.1 62945 1abv 134 3.10e+01 1abv a.70.1.1 18317 2fvx 138 3.11e+01 5nul c.23.5.1 31200 1dwkA 156 3.13e+01 1dw9A a.35.1.4,d.72.1.1 17075,39606 1pgjA 478 3.14e+01 2pgd a.100.1.1,c.2.1.6 18783,30195 1jo0A 98 3.16e+01 d.68.4.1 77140 1stfI 98 3.17e+01 1stfI d.17.1.2 38006 1uwmA 106 3.19e+01 2bkaA 242 3.20e+01 1n3gA 113 3.20e+01 d.204.1.1 79962 1gh8A 89 3.21e+01 1gh8A d.58.12.1 39309 2cb2A 318 3.30e+01 2gcfA 73 3.36e+01 1ew3A 159 3.40e+01 1mup b.60.1.1 27114 1hh1A 143 3.49e+01 1gefA c.52.1.18 61036 2guhA 214 3.50e+01 1g8aA 227 3.51e+01 c.66.1.3 90506 1jg8A 347 3.53e+01 1jg8A c.67.1.1 62946 2feaA 236 3.56e+01 1gk1B 522 3.57e+01 1jggA 60 3.62e+01 2hddA a.4.1.1 62950 1uwwA 191 3.66e+01 b.18.1.23 108079 1adr 76 3.67e+01 1r69 a.35.1.2 17042 1hn0A 1021 3.68e+01 a.102.3.2,b.18.1.17,b.24.1.1,b.30.5.2 83616,83617,83618,83619 1s69A 124 3.70e+01 a.1.1.1 105305 2fox 138 3.74e+01 5nul c.23.5.1 31197 1azo 232 3.75e+01 1azo c.52.1.14 33329 1m6sA 347 3.76e+01 c.67.1.1 78701 2tct 207 3.85e+01 2tct a.4.1.9,a.121.1.1 16063,19240 5nul 138 3.88e+01 5nul c.23.5.1 31191 3nll 138 3.89e+01 5nul c.23.5.1 31206 1psdA 409 3.89e+01 1psdA c.2.1.4,c.23.12.1,d.58.18.1 30097,31357,39354 1vfgA 390 4.00e+01 a.173.1.1,d.218.1.4 108570,108571 1w23A 360 4.03e+01 1gqaA 130 4.05e+01 a.24.3.2 76275 1z1dA 103 4.15e+01 1wdyA 285 4.16e+01 1fgyA 127 4.18e+01 1faoA b.55.1.1 26976 1cy9A 264 4.19e+01 1ecl e.10.1.1 43236 1rk8A 165 4.23e+01 d.58.7.1 97603 1a5dA 173 4.25e+01 1amm b.11.1.1,b.11.1.1 23614,23615 2b4gA 317 4.35e+01 1b4bA 71 4.56e+01 1b4aA d.74.2.1 39718 1or0B 528 4.69e+01 1kblA 873 4.70e+01 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 1d02A 202 4.73e+01 1d02A c.52.1.8 33313 1wosA 364 4.77e+01 b.44.2.1,d.250.1.1 109468,109469 1zug 71 4.82e+01 1r69 a.35.1.2 17041 1dpuA 99 4.85e+01 1dpuA a.4.5.16 16150 1uj6A 227 4.86e+01 c.124.1.4,d.58.40.1 107898,107899 1h8aC 128 4.88e+01 a.4.1.3,a.4.1.3 65731,65732 1tdj 514 4.96e+01 1tdj c.79.1.1,d.58.18.2,d.58.18.2 35297,39356,39357 1zkoA 136 5.02e+01 1pru 56 5.03e+01 1pru a.35.1.5 17104 1bjz 207 5.08e+01 2tct a.4.1.9,a.121.1.1 16065,19242 1xfxA 777 5.14e+01 1jroA 462 5.14e+01 a.56.1.1,d.15.4.2,d.87.2.1,d.145.1.3 67137,67138,67139,67140 1ne2A 200 5.16e+01 c.66.1.32 85586 1jh6A 189 5.28e+01 d.61.1.1 66707 1uxtA 501 5.29e+01 c.82.1.1 108125 1e9mA 106 5.35e+01 1ayfA d.15.4.1 59397 2ae5B 528 5.38e+01 1j7gA 144 5.38e+01 c.110.1.1 84130 1wpkA 146 5.40e+01 1nb5I 98 5.40e+01 d.17.1.2 80381 1l0oC 243 5.45e+01 a.4.13.2 73405 1vqtA 213 5.45e+01 1vjoA 393 5.48e+01 c.67.1.3 100827 1v4xB 146 5.48e+01 a.1.1.2 108364 1s72N 187 5.48e+01 c.55.4.1 105333 1p0yA 444 5.52e+01 a.166.1.1,b.85.7.3 87654,87655 1ta0A 197 5.60e+01 c.108.1.16 106729 1p9qC 256 5.64e+01 a.5.8.1,d.235.1.2,d.58.11.3 104093,104094,104095 2bjdA 101 5.74e+01 1mwyA 73 5.80e+01 d.58.17.1 79616 1rtxA 123 5.86e+01 a.1.1.1 97827 1di1A 300 5.91e+01 1di1A a.128.1.4 19446 1dgnA 89 5.94e+01 1dgnA a.77.1.3 18436 1zirA 173 5.97e+01 1xfuA 747 5.98e+01 1rlkA 117 6.02e+01 c.131.1.1 97651 1mlvA 444 6.04e+01 a.166.1.1,b.85.7.3 79283,79284 1whtA 256 6.10e+01 1ivyA c.69.1.5 34646 1q2lA 939 6.15e+01 2cro 71 6.16e+01 1r69 a.35.1.2 17038 1ohtA 215 6.21e+01 d.118.1.1 87036 1ng0A 253 6.22e+01 b.121.4.7 80475 2f94F 350 6.26e+01 1x71A 178 6.30e+01 1tuzA 118 6.30e+01 1b79A 119 6.31e+01 1b79A a.81.1.1 18451 1ln4A 104 6.40e+01 d.68.4.1 74043 2f8mA 244 6.76e+01 1vqoN 187 6.78e+01 1whsA 255 6.93e+01 1ivyA c.69.1.5 34649 1sjqA 105 6.93e+01 d.58.7.1 105660 1gvdA 52 6.96e+01 a.4.1.3 83338 2esnA 310 7.01e+01 2b06A 155 7.02e+01 1h1dA 221 7.09e+01 c.66.1.1 83452 1h2vC 771 7.13e+01 a.118.1.14,a.118.1.14,a.118.1.14 76592,76593,76594 1fexA 59 7.15e+01 a.4.1.3 59803 1ax8 146 7.22e+01 1ax8 a.26.1.1 16844 1gyvA 120 7.25e+01 b.1.10.2 70790 1qo0D 196 7.25e+01 1qo0D c.23.1.3 31125 1chuA 540 7.26e+01 1chuA a.7.3.1,c.3.1.4,d.168.1.1 16325,30424,42307 1ulrA 88 7.34e+01 2bnh 457 7.34e+01 1a4yA c.10.1.1 30850 1kqfB 294 7.35e+01 d.58.1.5,f.23.22.1 75900,75901 1jj2M 186 7.36e+01 1ffkK c.55.4.1 63098 1gywA 128 7.45e+01 b.1.10.2 70791 2h21A 440 7.46e+01 1p32A 209 7.50e+01 1p32A d.25.1.1 38379 1kjnA 157 7.72e+01 c.115.1.1 72614 1a6i 217 7.79e+01 2tct a.4.1.9,a.121.1.1 16066,19243 1y37A 304 7.85e+01 1n25A 368 7.88e+01 c.37.1.20 85264 1neeA 138 7.91e+01 d.241.1.1,g.59.1.1 91841,91842 1cf7B 95 7.91e+01 1cf7B a.4.5.17 16152 1wwzA 159 7.92e+01 2ex3B 264 7.95e+01 1uocA 289 7.97e+01 c.55.3.9 99686 1nal1 297 7.97e+01 1nal3 1b9mA 265 7.99e+01 1b9mA a.4.5.8,b.40.6.2,b.40.6.2 16118,58938,58939 1khbA 625 8.00e+01 c.91.1.1,c.109.1.1 68606,68607 1sw5A 275 8.01e+01 c.94.1.1 106069 1txoA 237 8.05e+01 1h5yA 253 8.05e+01 c.1.2.1 65638 1bcsA 263 8.08e+01 1ivyA c.69.1.5 34647 1b5eA 246 8.09e+01 1b5eA d.117.1.1 41056 1mzbA 136 8.20e+01 a.4.5.42 91497 1qlaB 239 8.38e+01 1qlaB a.1.2.1,d.15.4.2 15679,37707 1vggA 161 8.39e+01 1v2xA 194 8.46e+01 c.116.1.1 100274 1xebA 150 8.58e+01 1fjlA 81 8.62e+01 2hddA a.4.1.1 16017 1z9tA 255 8.66e+01 1dgsA 667 8.69e+01 1dgsA a.60.2.2,b.40.4.6,d.142.2.2 17963,25365,41581 1q0uA 219 8.73e+01 c.37.1.19 95512 1sw5B 275 8.73e+01 c.94.1.1 106070 1jwwA 80 8.88e+01 d.58.17.1 71919 1zx4A 192 8.90e+01 1who 96 8.91e+01 1who b.7.3.1 23215 1xviA 275 8.91e+01 1wyuA 438 8.91e+01 1fdyA 297 8.94e+01 1nal3 c.1.10.1 29071 1j6wA 175 8.95e+01 1j98A d.185.1.2 62663