# List of top-scoring protein chains for T0311.t2k-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 8.28e-06 a.35.1.3 108034 2b5aA 77 8.84e-05 1lliA 92 4.77e-04 1lmb3 a.35.1.2 17025 1y7yA 74 1.38e-03 1bw6A 56 1.92e-03 1bw6A a.4.1.7 16052 2a6cA 83 2.27e-03 1lmb3 92 2.96e-03 1lmb3 1rioA 98 3.03e-03 a.35.1.2 97513 1sq8A 64 3.63e-03 a.35.1.2 105888 1hlvA 131 4.12e-03 a.4.1.7,a.4.1.7 65854,65855 2r63 63 1.26e-02 1r69 a.35.1.2 17036 1y9qA 192 1.36e-02 1r69 69 1.70e-02 1r69 a.35.1.2 17028 1r63 63 2.46e-02 1r69 a.35.1.2 17035 1lccA 51 2.47e-02 1pru a.35.1.5 17110 1lqc 56 2.64e-02 1pru a.35.1.5 17109 1cjgA 62 2.82e-02 1pru a.35.1.5 17112 1l1mA 62 2.84e-02 a.35.1.5 73474 1adr 76 3.96e-02 1r69 a.35.1.2 17042 2bjcA 62 6.74e-02 1x57A 91 1.18e-01 1xnpA 202 1.61e-01 1efaA 333 2.80e-01 1tlfA a.35.1.5,c.93.1.1 17106,35691 1b0nA 111 2.86e-01 1b0nA a.34.1.1,a.35.1.3 17001,17064 1jyfA 349 2.92e-01 c.93.1.1 67456 1jyeA 349 2.93e-01 c.93.1.1 67455 1lbiA 360 2.97e-01 1tlfA c.93.1.1 35694 1umqA 81 2.98e-01 a.4.1.12 99625 1r22A 122 4.77e-01 a.4.5.5 104777 1uxc 65 6.01e-01 1uxc a.35.1.5 17119 1zvvA 332 6.24e-01 1dwkA 156 6.25e-01 1dw9A a.35.1.4,d.72.1.1 17075,39606 1rzrA 332 6.26e-01 2bnmA 198 7.85e-01 2ftcG 145 1.00e+00 1d1mA 65 1.03e+00 1orc a.35.1.2 17056 2cu3A 64 1.16e+00 6croA 60 1.18e+00 1orc a.35.1.2 17047 1a6i 217 1.20e+00 2tct a.4.1.9,a.121.1.1 16066,19243 3orcA 65 1.23e+00 1orc a.35.1.2 17061 5croA 66 1.31e+00 1orc a.35.1.2 17044 1d1lA 61 1.34e+00 1orc a.35.1.2 17057 1orc 71 1.34e+00 1orc a.35.1.2 17054 1qpiA 203 2.02e+00 2tct a.4.1.9,a.121.1.1 16072,19249 2tct 207 2.04e+00 2tct a.4.1.9,a.121.1.1 16063,19240 1bjz 207 2.04e+00 2tct a.4.1.9,a.121.1.1 16065,19242 2trt 217 2.09e+00 2tct a.4.1.9,a.121.1.1 16064,19241 1cfr 285 2.37e+00 1cfr c.52.1.7 33312 1pru 56 3.17e+00 1pru a.35.1.5 17104 1r1tA 122 3.49e+00 a.4.5.5 104769 1hw1A 239 3.67e+00 1e2xA a.4.5.6,a.78.1.1 16111,18441 1e2xA 243 3.71e+00 1e2xA a.4.5.6,a.78.1.1 16113,18443 1wpkA 146 3.97e+00 2auwA 170 4.07e+00 1u8bA 133 4.22e+00 1zgwA 139 4.35e+00 1am4D 177 4.38e+00 1ctqA c.37.1.8 32068 1eesA 178 4.46e+00 1eesA c.37.1.8 32073 2aseA 178 4.47e+00 1gzsA 180 4.49e+00 c.37.1.8 76424 1ceeA 179 4.50e+00 1ctqA c.37.1.8 32072 1rvgA 305 4.54e+00 c.1.10.2 97920 1cf4A 184 4.71e+00 1eesA c.37.1.8 32075 1ki1A 188 4.74e+00 c.37.1.8 72496 1an0A 190 4.76e+00 1ctqA c.37.1.8 32066 2ngrA 191 4.78e+00 1ctqA c.37.1.8 32061 1doaA 191 4.78e+00 1ctqA c.37.1.8 32065 1a4rA 191 4.82e+00 1ctqA c.37.1.8 32063 2dfkB 194 4.83e+00 1aje 194 4.88e+00 1ctqA c.37.1.8 32071 1nf3A 195 4.90e+00 c.37.1.8 85594 2cro 71 5.69e+00 1r69 a.35.1.2 17038 2acjA 66 5.71e+00 2deoA 230 5.89e+00 1s7oA 113 6.11e+00 a.4.13.3 105354 1e3yA 104 6.23e+00 1fadA a.77.1.2 18426 2cqyA 108 6.38e+00 1z0xA 220 7.08e+00 1nw1A 429 7.62e+00 d.144.1.8 86286 2fbhA 146 7.87e+00 1qbjA 81 7.99e+00 1qbjA a.4.5.19 16155 1qgpA 77 8.09e+00 1qbjA a.4.5.19 16158 1r9wA 145 9.35e+00 d.89.1.2 97264 2cg4A 152 1.04e+01 1bc5A 269 1.07e+01 1af7 a.58.1.1,c.66.1.8 17929,34204 1af7 274 1.08e+01 1af7 a.58.1.1,c.66.1.8 17928,34203 1j75A 67 1.11e+01 a.4.5.19 62673 1xsvA 113 1.15e+01 1efm 393 1.18e+01 1efcA c.37.1.8 64732 2b0tA 738 1.24e+01 2cw1A 65 1.29e+01 1etu 394 1.35e+01 1efcA c.37.1.8 64737 1khcA 147 1.40e+01 b.34.9.2 68608 1i6zA 135 1.44e+01 a.7.7.1 61861 1l3wA 546 1.47e+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 2btvC 349 1.50e+01 1bvp1 a.115.1.1,b.19.1.1 19086,23782 1bvp1 349 1.52e+01 1bvp1 1i2kA 269 1.58e+01 e.17.1.1 90661 1ic8A 194 1.62e+01 a.4.1.1,a.35.1.1 76740,76741 1ojlA 304 1.64e+01 1puzA 82 1.68e+01 a.218.1.1 104320 1g90A 176 1.80e+01 1bxwA f.4.1.1 60388 2ge4A 177 1.81e+01 1wzoA 246 1.83e+01 1yq8A 191 1.97e+01 1ulyA 192 2.00e+01 1eztA 166 2.02e+01 1agrE a.91.1.1 18541 1jpaA 312 2.04e+01 d.144.1.7 67011 1rzsA 61 2.11e+01 a.35.1.2 105139 1fadA 99 2.27e+01 1fadA a.77.1.2 18428 1wqaA 455 2.32e+01 2a1fA 247 2.33e+01 2cfxA 144 2.39e+01 1ngr 85 2.41e+01 1ngr a.77.1.2 18422 1q55A 880 2.42e+01 i.20.1.1 95862 1t56A 216 2.43e+01 a.4.1.9,a.121.1.1 106428,106429 1x1nA 524 2.49e+01 1jbwA 428 2.50e+01 c.59.1.2,c.72.2.2 62860,62861 1u9nA 236 2.54e+01 2af0A 146 2.56e+01 1agrE 205 2.63e+01 1agrE a.91.1.1 18538 1vqvA 306 3.13e+01 1ab4 493 3.13e+01 1ab4 e.11.1.1 43251 1o6dA 163 3.16e+01 c.116.1.3 92567 1pmzA 86 3.19e+01 a.39.1.10 104195 1h4bA 84 3.19e+01 a.39.1.10 90608 2bs3B 239 3.22e+01 1rioH 73 3.41e+01 a.4.13.2 97515 2bfwA 200 3.49e+01 1g8aA 227 3.52e+01 c.66.1.3 90506 3cox 507 3.56e+01 1b8sA c.3.1.2,d.16.1.1 30332,37863 1ku3A 73 3.69e+01 a.4.13.2 73000 1hsm 79 3.72e+01 1cktA a.21.1.1 16421 1hme 77 3.76e+01 1cktA a.21.1.1 16418 1pryA 227 3.77e+01 c.66.1.3 95063 1nhm 81 3.79e+01 1cktA a.21.1.1 16422 1wriA 93 3.82e+01 1lv5A 580 3.93e+01 c.55.3.5,e.8.1.1 84719,84720 1nk4A 580 3.94e+01 c.55.3.5,e.8.1.1 91923,91924 2bdpA 580 3.94e+01 1xwl c.55.3.5,e.8.1.1 33709,43002 1u4bA 580 3.94e+01 c.55.3.5,e.8.1.1 107664,107665 1lsg 144 4.10e+01 3lzt d.2.1.2 36379 2b2cA 314 4.14e+01 1uib 127 4.14e+01 3lzt d.2.1.2 36312 2g8lA 299 4.16e+01 1xngA 268 4.16e+01 1vz0A 230 4.18e+01 a.4.14.1,d.268.1.1 108929,108930 1a2yC 129 4.19e+01 3lzt d.2.1.2 36305 1s6lA 212 4.28e+01 1s1mA 545 4.29e+01 c.23.16.1,c.37.1.10 105201,105202 1l6wA 220 4.33e+01 c.1.10.1 73632 1jh9A 340 4.41e+01 a.35.1.5,c.93.1.1 66710,66711 1lj9A 144 4.47e+01 a.4.5.28 78035 1x2iA 75 4.47e+01 1vpwA 340 4.47e+01 1qpzA a.35.1.5,c.93.1.1 17087,35680 1jfsA 340 4.50e+01 a.35.1.5,c.93.1.1 66650,66651 1kxx 129 4.50e+01 3lzt d.2.1.2 36319 1uid 129 4.55e+01 3lzt d.2.1.2 36348 1kxy 129 4.57e+01 3lzt d.2.1.2 36324 1paz 123 4.57e+01 1bqk b.6.1.1 22878 1qqbA 340 4.58e+01 1qpzA a.35.1.5,c.93.1.1 17099,35674 1uic 129 4.59e+01 3lzt d.2.1.2 36356 1uie 129 4.59e+01 3lzt d.2.1.2 36349 1py0A 125 4.62e+01 1ir7A 129 4.65e+01 d.2.1.2 66283 1qpzA 340 4.66e+01 1qpzA a.35.1.5,c.93.1.1 17097,35673 2pugA 340 4.68e+01 1qpzA a.35.1.5,c.93.1.1 17088,35683 1jg1A 235 4.70e+01 c.66.1.7 66661 2pucA 340 4.72e+01 1qpzA a.35.1.5,c.93.1.1 17094,35684 6paz 123 4.74e+01 1bqk b.6.1.1 22886 1uif 129 4.78e+01 3lzt d.2.1.2 36342 2cskA 146 4.78e+01 1kxw 129 4.81e+01 3lzt d.2.1.2 36355 1s3qA 173 4.81e+01 1nr3A 122 4.81e+01 d.236.1.1 86092 1jftA 340 4.90e+01 a.35.1.5,c.93.1.1 66652,66653 1heo 129 4.91e+01 3lzt d.2.1.2 36320 1h6mA 129 4.94e+01 d.2.1.2 60688 1ir8A 129 4.95e+01 d.2.1.2 66284 3lzt 129 4.95e+01 3lzt d.2.1.2 36245 1her 129 4.96e+01 3lzt d.2.1.2 36340 1fn5A 129 4.96e+01 3lzt d.2.1.2 36325 1ndgC 129 4.96e+01 d.2.1.2 85580 1tc3C 51 4.97e+01 1tc3C a.4.1.2 16025 1ltm 320 5.02e+01 1ltm d.2.1.6 36992 1lze 129 5.03e+01 3lzt d.2.1.2 36323 2iffY 129 5.03e+01 3lzt d.2.1.2 36383 1qusA 322 5.03e+01 1ltm d.2.1.6 36991 1lzg 129 5.10e+01 3lzt d.2.1.2 36318 1e0eA 55 5.13e+01 1wjcA a.4.10.1 59147 1iosA 129 5.15e+01 3lzt d.2.1.2 62636 1vaxA 287 5.16e+01 1dg1G 394 5.17e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25684,25724,32117 1m4uA 206 5.20e+01 g.17.1.7 78625 1x8lA 351 5.20e+01 1efcA 393 5.21e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25680,25720,32113 1ob2A 393 5.21e+01 b.43.3.1,b.44.1.1,c.37.1.8 103900,103901,103902 1d8tA 393 5.21e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25686,25726,32119 1ioqA 129 5.23e+01 3lzt d.2.1.2 62634 1fluA 129 5.23e+01 3lzt d.2.1.2 36321 1q7xA 108 5.32e+01 b.36.1.1 96059 1flwA 129 5.34e+01 3lzt d.2.1.2 36322 1nw8A 319 5.44e+01 c.66.1.11 86292 2c7yA 404 5.47e+01 1gh0B 172 5.52e+01 1qgwC a.1.1.3 60492 2bt2A 161 5.52e+01 1lsy 147 5.54e+01 3lzt d.2.1.2 36347 1juqA 171 5.63e+01 a.118.9.2 67322 1mc7A 95 5.64e+01 b.36.1.1 91241 1cqdA 221 5.66e+01 1cs8A d.3.1.1 37027 1tedA 393 5.68e+01 c.95.1.2 106807 1teeA 393 5.69e+01 c.95.1.2 106811 1ha7B 172 5.72e+01 a.1.1.3 70936 1drw 273 5.72e+01 1drw c.2.1.3,d.81.1.3 30057,39972 1iotA 129 5.73e+01 3lzt d.2.1.2 62637 1wvoA 79 5.74e+01 1iorA 129 5.79e+01 3lzt d.2.1.2 62635 1sfxA 109 5.81e+01 a.4.5.50 105505 1bxwA 172 5.81e+01 1bxwA f.4.1.1 43743 1qjpA 171 5.81e+01 1bxwA f.4.1.1 43742 1tpc1 247 5.85e+01 1amk 1eg2A 319 5.89e+01 1eg2A c.66.1.11 34249 1tpb1 247 5.92e+01 1amk 2c3vA 102 5.98e+01 1ohmA 44 6.04e+01 j.106.1.1 93025 1kn1A 160 6.25e+01 a.1.1.3 77455 1efuA 385 6.31e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25682,25722,32115 1nxhA 126 6.42e+01 a.200.1.1 92300 1qb2A 109 6.47e+01 1qb2A a.36.1.1 17125 1pk6C 129 6.48e+01 b.22.1.1 94803 1flyA 129 6.50e+01 3lzt d.2.1.2 36346 1hu3A 260 6.66e+01 1hu3A a.118.1.14 19137 1pnf 314 6.72e+01 1pgs b.121.1.1,b.121.1.1 23655,23656 1bl0A 129 6.73e+01 1d5yA a.4.1.8,a.4.1.8 16053,16054 2cwnA 332 6.74e+01 1ea6A 364 6.75e+01 d.14.1.3,d.122.1.2 64871,64872 2gn4A 344 6.76e+01 1pgs 314 6.77e+01 1pgs b.121.1.1,b.121.1.1 23653,23654 1h7sA 365 6.78e+01 d.14.1.3,d.122.1.2 65705,65706 1wxpA 110 6.80e+01 1u3eM 174 6.81e+01 d.4.1.3,d.285.1.1 107640,107641 1l0yA 236 6.90e+01 b.1.1.1,b.1.1.2 73440,73441 1xs9A 132 6.91e+01 1bec 238 6.98e+01 1bec b.1.1.1,b.1.1.2 20627,21561 1bdyA 123 6.99e+01 1bdyA b.7.1.1 23190 1eswA 500 7.00e+01 1cwyA c.1.8.1 59500 1fp8A 500 7.02e+01 c.1.8.1 90498 1o6yA 299 7.04e+01 d.144.1.7 81106 1cnsA 243 7.07e+01 1cnsA d.2.1.1 36241 1mruA 311 7.18e+01 d.144.1.7 79425 3hdhA 302 7.25e+01 2hdhA a.100.1.3,c.2.1.6 18805,30209 1mwaB 237 7.31e+01 b.1.1.1,b.1.1.2 79560,79561 1mfqC 129 7.36e+01 a.36.1.1 79046 1k9oI 378 7.49e+01 e.1.1.1 68356 1j6pA 418 7.56e+01 b.92.1.4,c.1.9.9 77089,77090 1g2hA 61 7.57e+01 1g2hA a.4.1.12 60224 1qw2A 102 7.69e+01 d.249.1.1 96456 1rmtA 212 7.71e+01 1hen 129 7.87e+01 3lzt d.2.1.2 36326 1hem 129 7.90e+01 3lzt d.2.1.2 36317 1hep 129 7.90e+01 3lzt d.2.1.2 36327 1heq 129 7.93e+01 3lzt d.2.1.2 36316 1dkkA 129 7.97e+01 3lzt d.2.1.2 36404 1zu1A 127 8.00e+01 2b82A 211 8.02e+01 1ovyA 120 8.06e+01 c.55.4.1 93624 1bwzA 274 8.07e+01 1bwzA d.21.1.1,d.21.1.1 38337,38338 4paz 123 8.09e+01 1bqk b.6.1.1 22881 1nbyC 129 8.14e+01 d.2.1.2 85540 1eaxA 241 8.20e+01 b.47.1.2 64889 2gkeA 274 8.21e+01 1ozhA 566 8.22e+01 c.31.1.3,c.36.1.5,c.36.1.9 93833,93834,93835 1sz2A 332 8.24e+01 1jhlA 129 8.33e+01 3lzt d.2.1.2 36403 1o3sA 200 8.41e+01 a.4.5.4,b.82.3.2 86609,86610 1yseA 141 8.45e+01 1i6xA 209 8.58e+01 a.4.5.4,b.82.3.2 83673,83674 1xvuA 408 8.62e+01 1xk7A 408 8.67e+01 1xa3A 437 8.75e+01 1vydA 116 8.75e+01 a.3.1.1 108900 1t57A 206 8.91e+01 c.49.1.2 106430 2azoA 232 8.94e+01 1azo c.52.1.14 33330 1azo 232 9.00e+01 1azo c.52.1.14 33329