# List of top-scoring protein chains for T0311.t04-w0.5 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 1utxA 66 1.73e-04 a.35.1.3 108034 1lliA 92 2.25e-03 1lmb3 a.35.1.2 17025 2a6cA 83 2.62e-03 2b5aA 77 3.56e-03 1rioA 98 8.76e-03 a.35.1.2 97513 1lmb3 92 8.81e-03 1lmb3 1bw6A 56 1.77e-02 1bw6A a.4.1.7 16052 1lccA 51 3.85e-02 1pru a.35.1.5 17110 1lqc 56 4.12e-02 1pru a.35.1.5 17109 1sq8A 64 4.15e-02 a.35.1.2 105888 1cjgA 62 4.39e-02 1pru a.35.1.5 17112 1l1mA 62 4.41e-02 a.35.1.5 73474 1hlvA 131 4.61e-02 a.4.1.7,a.4.1.7 65854,65855 2r63 63 7.82e-02 1r69 a.35.1.2 17036 1y7yA 74 8.51e-02 2bjcA 62 9.23e-02 1r69 69 1.92e-01 1r69 a.35.1.2 17028 1r63 63 3.07e-01 1r69 a.35.1.2 17035 1efaA 333 3.90e-01 1tlfA a.35.1.5,c.93.1.1 17106,35691 1jyfA 349 4.18e-01 c.93.1.1 67456 1jyeA 349 4.19e-01 c.93.1.1 67455 1lbiA 360 4.26e-01 1tlfA c.93.1.1 35694 1rzrA 332 5.00e-01 1zvvA 332 5.05e-01 1dwkA 156 6.11e-01 1dw9A a.35.1.4,d.72.1.1 17075,39606 2cu3A 64 6.45e-01 1y9qA 192 7.04e-01 1xnpA 202 7.10e-01 1r22A 122 8.93e-01 a.4.5.5 104777 1umqA 81 1.07e+00 a.4.1.12 99625 1uxc 65 1.40e+00 1uxc a.35.1.5 17119 1cfr 285 1.42e+00 1cfr c.52.1.7 33312 1adr 76 1.48e+00 1r69 a.35.1.2 17042 1d1mA 65 2.17e+00 1orc a.35.1.2 17056 2ftcG 145 2.25e+00 6croA 60 2.64e+00 1orc a.35.1.2 17047 3orcA 65 2.71e+00 1orc a.35.1.2 17061 1pru 56 2.77e+00 1pru a.35.1.5 17104 5croA 66 2.80e+00 1orc a.35.1.2 17044 1orc 71 2.84e+00 1orc a.35.1.2 17054 1d1lA 61 2.90e+00 1orc a.35.1.2 17057 1b0nA 111 4.92e+00 1b0nA a.34.1.1,a.35.1.3 17001,17064 1a6i 217 5.14e+00 2tct a.4.1.9,a.121.1.1 16066,19243 1r1tA 122 5.49e+00 a.4.5.5 104769 2auwA 170 7.24e+00 1efm 393 8.63e+00 1efcA c.37.1.8 64732 1qpiA 203 9.41e+00 2tct a.4.1.9,a.121.1.1 16072,19249 2tct 207 9.55e+00 2tct a.4.1.9,a.121.1.1 16063,19240 1bjz 207 9.55e+00 2tct a.4.1.9,a.121.1.1 16065,19242 1hw1A 239 9.61e+00 1e2xA a.4.5.6,a.78.1.1 16111,18441 1e2xA 243 9.66e+00 1e2xA a.4.5.6,a.78.1.1 16113,18443 2trt 217 9.85e+00 2tct a.4.1.9,a.121.1.1 16064,19241 1khcA 147 1.00e+01 b.34.9.2 68608 1bc5A 269 1.03e+01 1af7 a.58.1.1,c.66.1.8 17929,34204 2cw1A 65 1.04e+01 1af7 274 1.04e+01 1af7 a.58.1.1,c.66.1.8 17928,34203 1am4D 177 1.08e+01 1ctqA c.37.1.8 32068 1eesA 178 1.08e+01 1eesA c.37.1.8 32073 2aseA 178 1.09e+01 1gzsA 180 1.09e+01 c.37.1.8 76424 1etu 394 1.09e+01 1efcA c.37.1.8 64737 1ceeA 179 1.09e+01 1ctqA c.37.1.8 32072 1cf4A 184 1.11e+01 1eesA c.37.1.8 32075 1an0A 190 1.12e+01 1ctqA c.37.1.8 32066 2ngrA 191 1.12e+01 1ctqA c.37.1.8 32061 1ki1A 188 1.12e+01 c.37.1.8 72496 1nf3A 195 1.13e+01 c.37.1.8 85594 2dfkB 194 1.13e+01 1a4rA 191 1.13e+01 1ctqA c.37.1.8 32063 1doaA 191 1.13e+01 1ctqA c.37.1.8 32065 1aje 194 1.15e+01 1ctqA c.37.1.8 32071 1x57A 91 1.23e+01 1drw 273 1.33e+01 1drw c.2.1.3,d.81.1.3 30057,39972 2cg4A 152 1.46e+01 2acjA 66 1.53e+01 1eztA 166 1.61e+01 1agrE a.91.1.1 18541 1dg1G 394 1.73e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25684,25724,32117 1ob2A 393 1.75e+01 b.43.3.1,b.44.1.1,c.37.1.8 103900,103901,103902 1efcA 393 1.75e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25680,25720,32113 1d8tA 393 1.75e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25686,25726,32119 1h4bA 84 1.82e+01 a.39.1.10 90608 1x1nA 524 1.86e+01 2b0tA 738 1.88e+01 1rzsA 61 1.92e+01 a.35.1.2 105139 1pnf 314 1.97e+01 1pgs b.121.1.1,b.121.1.1 23655,23656 1pgs 314 2.01e+01 1pgs b.121.1.1,b.121.1.1 23653,23654 2cro 71 2.03e+01 1r69 a.35.1.2 17038 1wpkA 146 2.04e+01 1agrE 205 2.10e+01 1agrE a.91.1.1 18538 1efuA 385 2.12e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25682,25722,32115 1sovA 328 2.12e+01 2deoA 230 2.15e+01 1j75A 67 2.18e+01 a.4.5.19 62673 1u8bA 133 2.19e+01 2fbhA 146 2.21e+01 1qbjA 81 2.23e+01 1qbjA a.4.5.19 16155 1zgwA 139 2.28e+01 1qgpA 77 2.29e+01 1qbjA a.4.5.19 16158 1ab4 493 2.29e+01 1ab4 e.11.1.1 43251 1nw1A 429 2.49e+01 d.144.1.8 86286 1wzoA 246 2.55e+01 1i6zA 135 2.75e+01 a.7.7.1 61861 1yq8A 191 2.88e+01 1ngr 85 2.92e+01 1ngr a.77.1.2 18422 2bs3B 239 2.92e+01 1rvgA 305 2.94e+01 c.1.10.2 97920 1ic8A 194 2.95e+01 a.4.1.1,a.35.1.1 76740,76741 1e3yA 104 2.97e+01 1fadA a.77.1.2 18426 1pmzA 86 3.03e+01 a.39.1.10 104195 2btvC 349 3.08e+01 1bvp1 a.115.1.1,b.19.1.1 19086,23782 1wd5A 208 3.09e+01 1jpaA 312 3.14e+01 d.144.1.7 67011 1x2iA 75 3.19e+01 1jh9A 340 3.26e+01 a.35.1.5,c.93.1.1 66710,66711 1vpwA 340 3.29e+01 1qpzA a.35.1.5,c.93.1.1 17087,35680 1jfsA 340 3.29e+01 a.35.1.5,c.93.1.1 66650,66651 2ge4A 177 3.31e+01 1g90A 176 3.31e+01 1bxwA f.4.1.1 60388 1bvp1 349 3.34e+01 1bvp1 1qqbA 340 3.35e+01 1qpzA a.35.1.5,c.93.1.1 17099,35674 1vz0A 230 3.36e+01 a.4.14.1,d.268.1.1 108929,108930 2cskA 146 3.37e+01 2pucA 340 3.37e+01 1qpzA a.35.1.5,c.93.1.1 17094,35684 1qpzA 340 3.37e+01 1qpzA a.35.1.5,c.93.1.1 17097,35673 2pugA 340 3.37e+01 1qpzA a.35.1.5,c.93.1.1 17088,35683 1jftA 340 3.43e+01 a.35.1.5,c.93.1.1 66652,66653 2c7yA 404 3.45e+01 1cnsA 243 3.49e+01 1cnsA d.2.1.1 36241 1z0xA 220 3.50e+01 2c3vA 102 3.64e+01 2gn4A 344 3.67e+01 1ojlA 304 3.72e+01 1dxjA 242 3.95e+01 1cnsA d.2.1.1 36244 1k9oI 378 3.98e+01 e.1.1.1 68356 2d42A 249 4.01e+01 2af0A 146 4.07e+01 1jbwA 428 4.07e+01 c.59.1.2,c.72.2.2 62860,62861 1nxhA 126 4.08e+01 a.200.1.1 92300 2bnmA 198 4.24e+01 1wvoA 79 4.27e+01 1rioH 73 4.27e+01 a.4.13.2 97515 2cqyA 108 4.29e+01 1nw8A 319 4.32e+01 c.66.1.11 86292 1lsg 144 4.46e+01 3lzt d.2.1.2 36379 1xsvA 113 4.47e+01 1zb7A 455 4.47e+01 1sz2A 332 4.51e+01 2bt2A 161 4.54e+01 1zu1A 127 4.59e+01 1eg2A 319 4.60e+01 1eg2A c.66.1.11 34249 1s7oA 113 4.63e+01 a.4.13.3 105354 1ku3A 73 4.66e+01 a.4.13.2 73000 2ahrA 259 4.68e+01 1a2yC 129 4.85e+01 3lzt d.2.1.2 36305 1uib 127 4.95e+01 3lzt d.2.1.2 36312 1qb2A 109 4.99e+01 1qb2A a.36.1.1 17125 1w2yA 229 5.03e+01 a.204.1.1 109140 1uid 129 5.05e+01 3lzt d.2.1.2 36348 1kxx 129 5.06e+01 3lzt d.2.1.2 36319 1uif 129 5.14e+01 3lzt d.2.1.2 36342 1ozhA 566 5.16e+01 c.31.1.3,c.36.1.5,c.36.1.9 93833,93834,93835 1kxy 129 5.19e+01 3lzt d.2.1.2 36324 1uic 129 5.22e+01 3lzt d.2.1.2 36356 1ir7A 129 5.23e+01 d.2.1.2 66283 1ir8A 129 5.35e+01 d.2.1.2 66284 1uie 129 5.38e+01 3lzt d.2.1.2 36349 1kxw 129 5.51e+01 3lzt d.2.1.2 36355 1l3wA 546 5.53e+01 b.1.6.1,b.1.6.1,b.1.6.1,b.1.6.1,b.1.6.1 73553,73554,73555,73556,73557 1y8aA 332 5.53e+01 1h6mA 129 5.67e+01 d.2.1.2 60688 1heo 129 5.68e+01 3lzt d.2.1.2 36320 1gh0B 172 5.73e+01 1qgwC a.1.1.3 60492 3lzt 129 5.73e+01 3lzt d.2.1.2 36245 1fn5A 129 5.73e+01 3lzt d.2.1.2 36325 1her 129 5.73e+01 3lzt d.2.1.2 36340 2iffY 129 5.75e+01 3lzt d.2.1.2 36383 1iosA 129 5.78e+01 3lzt d.2.1.2 62636 1ndgC 129 5.81e+01 d.2.1.2 85580 1lze 129 5.84e+01 3lzt d.2.1.2 36323 1u3eM 174 5.86e+01 d.4.1.3,d.285.1.1 107640,107641 1ioqA 129 5.91e+01 3lzt d.2.1.2 62634 1mfqC 129 5.91e+01 a.36.1.1 79046 1ha7B 172 5.92e+01 a.1.1.3 70936 1s6lA 212 5.94e+01 1lzg 129 5.94e+01 3lzt d.2.1.2 36318 1puzA 82 5.96e+01 a.218.1.1 104320 1vydA 116 5.98e+01 a.3.1.1 108900 1iotA 129 6.15e+01 3lzt d.2.1.2 62637 2a1fA 247 6.16e+01 1qw2A 102 6.17e+01 d.249.1.1 96456 1fluA 129 6.22e+01 3lzt d.2.1.2 36321 1flwA 129 6.22e+01 3lzt d.2.1.2 36322 1k24A 253 6.26e+01 f.4.4.2 72002 1iorA 129 6.27e+01 3lzt d.2.1.2 62635 1lsy 147 6.33e+01 3lzt d.2.1.2 36347 1ovyA 120 6.35e+01 c.55.4.1 93624 1f0xA 571 6.36e+01 1f0xA d.58.32.2,d.145.1.1 39483,41746 1s1mA 545 6.38e+01 c.23.16.1,c.37.1.10 105201,105202 2bfwA 200 6.41e+01 1vqvA 306 6.65e+01 1sfxA 109 6.75e+01 a.4.5.50 105505 1mizB 201 6.81e+01 a.11.2.1,b.55.1.5 79172,79173 1ohmA 44 6.84e+01 j.106.1.1 93025 1mixA 206 6.84e+01 a.11.2.1,b.55.1.5 79166,79167 1c2rA 116 6.93e+01 1ycc a.3.1.1 15887 1mk7B 192 6.93e+01 a.11.2.1,b.55.1.5 79219,79220 1cqdA 221 7.00e+01 1cs8A d.3.1.1 37027 1souA 194 7.00e+01 c.124.1.6 105858 1jhlA 129 7.30e+01 3lzt d.2.1.2 36403 1s1hC 192 7.32e+01 i.1.1.1 105156 2avaA 82 7.33e+01 1fxjA 331 7.35e+01 1fwyA b.81.1.4,c.68.1.5 28062,34520 1z67A 135 7.42e+01 1m4uA 206 7.47e+01 g.17.1.7 78625 1x8lA 351 7.48e+01 1l0yA 236 7.53e+01 b.1.1.1,b.1.1.2 73440,73441 1juqA 171 7.56e+01 a.118.9.2 67322 1bec 238 7.60e+01 1bec b.1.1.1,b.1.1.2 20627,21561 1o3sA 200 7.61e+01 a.4.5.4,b.82.3.2 86609,86610 1q7xA 108 7.62e+01 b.36.1.1 96059 1prlC 64 7.67e+01 1ckaA b.34.2.1 24524 1nloC 64 7.67e+01 1ckaA b.34.2.1 24519 1xx6A 191 7.73e+01 2csbA 519 7.79e+01 1ghlA 130 7.85e+01 3lzt d.2.1.2 36401 1c2n 137 8.06e+01 1ycc a.3.1.1 15889 1l6wA 220 8.08e+01 c.1.10.1 73632 1ulyA 192 8.08e+01 1fo8A 343 8.14e+01 1foaA c.68.1.10 59927 1gvnB 287 8.17e+01 c.37.1.21 76354 1lv5A 580 8.17e+01 c.55.3.5,e.8.1.1 84719,84720 1nk4A 580 8.17e+01 c.55.3.5,e.8.1.1 91923,91924 1i6xA 209 8.18e+01 a.4.5.4,b.82.3.2 83673,83674 1u4bA 580 8.18e+01 c.55.3.5,e.8.1.1 107664,107665 2bdpA 580 8.21e+01 1xwl c.55.3.5,e.8.1.1 33709,43002 1fo9A 348 8.22e+01 1foaA c.68.1.10 59928 1y19B 202 8.24e+01 1rwrA 301 8.40e+01 b.80.1.11 97990 1o6yA 299 8.42e+01 d.144.1.7 81106 2g8lA 299 8.43e+01 1f75A 249 8.44e+01 1f75A c.101.1.1 59662 1mruA 311 8.51e+01 d.144.1.7 79425 1ltm 320 8.53e+01 1ltm d.2.1.6 36992 1qusA 322 8.55e+01 1ltm d.2.1.6 36991 1mwaB 237 8.57e+01 b.1.1.1,b.1.1.2 79560,79561 1hme 77 8.63e+01 1cktA a.21.1.1 16418 1hsm 79 8.63e+01 1cktA a.21.1.1 16421 1g8aA 227 8.66e+01 c.66.1.3 90506 1yseA 141 8.67e+01 1o3tA 200 8.68e+01 a.4.5.4,b.82.3.2 86611,86612 1kn1A 160 8.70e+01 a.1.1.3 77455 1hw5A 210 8.76e+01 2cgpA a.4.5.4,b.82.3.2 16098,28137 1nhm 81 8.78e+01 1cktA a.21.1.1 16422 1zkdA 387 8.78e+01 1cgpA 205 8.81e+01 a.4.5.4,b.82.3.2 16096,28135 1i5zA 209 8.86e+01 a.4.5.4,b.82.3.2 83669,83670 1g6nA 210 8.87e+01 2cgpA a.4.5.4,b.82.3.2 16100,28139 1flyA 129 8.89e+01 3lzt d.2.1.2 36346 1nzjA 298 8.91e+01 c.26.1.1 92377