# List of top-scoring protein chains for T0373.t06-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 2a61A 145 1.06e-15 2fbhA 146 3.12e-15 1s3jA 155 2.10e-14 a.4.5.28 98437 2fbkA 181 3.11e-14 1jgsA 138 4.46e-14 a.4.5.28 66683 2ethA 154 6.71e-14 2fbiA 142 8.95e-14 1lnwA 147 1.19e-13 a.4.5.28 78104 1z91A 147 1.23e-13 1lj9A 144 1.05e-12 a.4.5.28 78035 2fxaA 207 3.79e-10 1ku9A 152 1.23e-08 a.4.5.36 77544 2ev0A 142 2.10e-08 1on2A 142 2.39e-08 a.4.5.24,a.76.1.1 87103,87104 1fx7A 230 4.16e-08 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 60088,60089,60090 1b1bA 140 7.38e-08 1bi0 a.4.5.24,a.76.1.1 16215,18421 2tdx 226 1.58e-07 1bi0 a.4.5.24,a.76.1.1 16201,18407 2dtr 226 1.99e-07 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 16193,18399,24450 1c0wA 225 2.07e-07 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 16211,18417,24455 1g3yA 226 2.63e-07 a.4.5.24,a.76.1.1,b.34.1.2 65136,65137,65138 1fwzA 226 2.64e-07 a.4.5.24,a.76.1.1,b.34.1.2 60077,60078,60079 1g3tA 226 2.73e-07 a.4.5.24,a.76.1.1,b.34.1.2 65127,65128,65129 1xcvA 139 3.88e-07 1p92A 226 4.26e-07 a.4.5.24,a.76.1.1,b.34.1.2 104085,104086,104087 1hsjA 487 1.08e-06 4mbp a.4.5.28,c.94.1.1 61237,61238 1sfxA 109 1.16e-06 a.4.5.50 105505 1ulyA 192 1.24e-06 1ub9A 100 1.44e-06 a.4.5.28 99159 1ixcA 294 1.62e-06 a.4.5.37,c.94.1.1 83764,83765 1i1gA 141 1.67e-06 a.4.5.32,d.58.4.2 65982,65983 1mkmA 249 3.20e-06 a.4.5.33,d.110.2.2 79242,79243 1xnpA 202 3.32e-06 1r22A 122 3.43e-06 a.4.5.5 104777 1yyvA 131 3.56e-06 1r1tA 122 4.73e-06 a.4.5.5 104769 1p4xA 250 5.85e-06 a.4.5.28,a.4.5.28 87784,87785 1f5tA 121 1.02e-05 1bi0 a.4.5.24,a.76.1.1 16203,18409 1z7uA 112 1.37e-05 2fnpA 124 1.67e-05 2frhA 127 2.76e-05 1fzpB 123 2.86e-05 1fznD a.4.5.28 19008 2cfxA 144 3.33e-05 1xmaA 145 4.07e-05 1r1uA 106 4.56e-05 a.4.5.5 104771 2g7uA 257 6.16e-05 1okrA 123 1.26e-04 a.4.5.39 93269 2fswA 107 1.71e-04 1sd6A 123 1.76e-04 a.4.5.39 98803 1ri7A 171 1.94e-04 a.4.5.32,d.58.4.2 97504,97505 2eshA 118 2.18e-04 2dbbA 151 2.74e-04 2b0lA 102 3.30e-04 1b9mA 265 3.90e-04 1b9mA a.4.5.8,b.40.6.2,b.40.6.2 16118,58938,58939 1o7lA 262 4.11e-04 a.4.5.8,b.40.6.2,b.40.6.2 81147,81148,81149 2co5A 99 7.00e-04 1lea 84 1.02e-03 1lea a.4.5.2 16085 1jhfA 202 1.20e-03 a.4.5.2,b.87.1.1 63057,63058 1u2wA 122 1.21e-03 1jhhA 202 1.33e-03 a.4.5.2,b.87.1.1 63060,63061 1tbxA 99 1.42e-03 a.4.5.48 106748 1sd4A 126 2.74e-03 a.4.5.39 105428 2f2eA 146 3.26e-03 1uthB 315 3.93e-03 c.94.1.1 108033 1o5lA 213 4.76e-03 b.82.3.2 92506 1je8A 82 4.95e-03 a.4.6.2 77108 1z1dA 103 5.11e-03 1dpuA 99 5.13e-03 1dpuA a.4.5.16 16150 1utbB 315 5.29e-03 c.94.1.1 108031 1utbA 315 5.35e-03 c.94.1.1 108030 1uthA 315 6.10e-03 c.94.1.1 108032 2cg4A 152 6.49e-03 1ft9A 222 7.15e-03 1ft9A a.4.5.4,b.82.3.1 16107,28131 1e2xA 243 1.03e-02 1e2xA a.4.5.6,a.78.1.1 16113,18443 1hw1A 239 1.11e-02 1e2xA a.4.5.6,a.78.1.1 16111,18441 1q1hA 110 1.12e-02 a.4.5.41 95580 2fu4A 83 1.47e-02 1bw6A 56 1.55e-02 1bw6A a.4.1.7 16052 1yg2A 179 2.51e-02 1al3 324 2.53e-02 1al3 c.94.1.1 35835 1a04A 215 2.58e-02 1a04A a.4.6.2,c.23.1.1 16234,31089 1tw3A 360 2.60e-02 a.4.5.29,c.66.1.12 107373,107374 1hw5A 210 2.63e-02 2cgpA a.4.5.4,b.82.3.2 16098,28137 1mzbA 136 2.66e-02 a.4.5.42 91497 1hlvA 131 2.78e-02 a.4.1.7,a.4.1.7 65854,65855 1j75A 67 3.19e-02 a.4.5.19 62673 1zlkA 95 3.51e-02 1zljA 78 3.55e-02 1o3sA 200 3.89e-02 a.4.5.4,b.82.3.2 86609,86610 1i6xA 209 3.90e-02 a.4.5.4,b.82.3.2 83673,83674 1p6rA 82 4.06e-02 a.4.5.39 94187 1v4rA 102 4.11e-02 1o3tA 200 4.14e-02 a.4.5.4,b.82.3.2 86611,86612 1i5zA 209 4.23e-02 a.4.5.4,b.82.3.2 83669,83670 1g6nA 210 4.26e-02 2cgpA a.4.5.4,b.82.3.2 16100,28139 1cgpA 205 4.64e-02 a.4.5.4,b.82.3.2 16096,28135 1stzA 338 6.55e-02 a.4.5.51,d.110.2.3 106009,106010 1y0uA 96 9.42e-02 1r7jA 95 9.44e-02 a.4.5.49 104836 1bia 321 9.89e-02 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 2h6bA 250 1.08e-01 1qzzA 374 1.09e-01 a.4.5.29,c.66.1.12 96719,96720 1ruoA 209 1.44e-01 2cgpA a.4.5.4,b.82.3.2 16105,28144 1xsvA 113 1.53e-01 1z05A 429 1.76e-01 1s7oA 113 2.33e-01 a.4.13.3 105354 2esnA 310 2.34e-01 1xn7A 78 3.17e-01 1e19A 314 3.53e-01 1b7bA c.73.1.1 34967 1j5yA 187 4.23e-01 a.4.5.1,d.94.2.1 71592,71593 1i1sA 96 4.67e-01 1bjaA a.4.5.9 16124 1bjaA 95 5.04e-01 1bjaA a.4.5.9 16122 1qgpA 77 5.22e-01 1qbjA a.4.5.19 16158 1fseA 74 5.34e-01 1fseA a.4.6.2 60000 1z6rA 406 6.25e-01 1qbjA 81 6.39e-01 1qbjA a.4.5.19 16155 2acjA 66 7.00e-01 2bgcA 238 7.72e-01 2beoA 236 7.85e-01 1omiA 248 8.38e-01 b.82.3.3,a.4.5.4 87079,87080 1lccA 51 8.63e-01 1pru a.35.1.5 17110 1p5dX 463 8.81e-01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1lqc 56 9.71e-01 1pru a.35.1.5 17109 2fkfA 462 1.01e+00 1p4wA 99 1.03e+00 a.4.6.2 87783 1l1mA 62 1.06e+00 a.35.1.5 73474 1cjgA 62 1.08e+00 1pru a.35.1.5 17112 2fkmX 462 1.09e+00 1wdvA 152 1.11e+00 2cohA 202 1.22e+00 2bjcA 62 1.22e+00 2csbA 519 1.28e+00 1utxA 66 1.33e+00 a.35.1.3 108034 1poy1 323 1.35e+00 1pot 1mgtA 174 1.37e+00 1mgtA a.4.2.1,c.55.7.1 16078,33753 1pot 325 1.43e+00 1pot c.94.1.1 35807 1ge9A 184 1.47e+00 1dd5A d.67.3.1 60463 1k2yX 463 1.49e+00 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 1t6sA 162 1.49e+00 1jhgA 101 1.51e+00 1jhgA a.4.12.1 19009 1vgjA 184 1.77e+00 2h6cA 232 1.79e+00 1ylfA 149 2.10e+00 1rr7A 129 2.15e+00 a.4.1.14 105075 2bboA 291 2.17e+00 1bvuA 418 2.27e+00 1hwyA c.2.1.7,c.58.1.1 30226,33874 1zx4A 192 2.45e+00 1lvaA 258 2.47e+00 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 1k78A 149 2.54e+00 a.4.1.5,a.4.1.5 68255,68256 1puzA 82 2.56e+00 a.218.1.1 104320 1g2hA 61 2.95e+00 1g2hA a.4.1.12 60224 1j7kA 334 2.98e+00 1hqcA a.4.5.11,c.37.1.20 62695,62696 1rcsA 105 3.11e+00 1jhgA a.4.12.1 19025 1trrA 107 3.19e+00 1jhgA a.4.12.1 19017 2wrpR 107 3.20e+00 1jhgA a.4.12.1 19010 3wrp 108 3.25e+00 1jhgA a.4.12.1 19015 1troA 108 3.50e+00 1jhgA a.4.12.1 19011 1wsuA 124 3.54e+00 1in8A 334 3.83e+00 1hqcA a.4.5.11,c.37.1.20 62605,62606 1in4A 334 3.97e+00 1hqcA a.4.5.11,c.37.1.20 62597,62598 1in5A 334 4.16e+00 1hqcA a.4.5.11,c.37.1.20 62599,62600 6paxA 133 4.17e+00 6paxA a.4.1.5,a.4.1.5 64758,64759 1in7A 334 4.24e+00 1hqcA a.4.5.11,c.37.1.20 62603,62604 1pdnC 128 4.30e+00 6paxA a.4.1.5 16047 2a6cA 83 4.36e+00 1q2lA 939 4.39e+00 1bjz 207 4.44e+00 2tct a.4.1.9,a.121.1.1 16065,19242 2tct 207 4.46e+00 2tct a.4.1.9,a.121.1.1 16063,19240 1qpiA 203 4.51e+00 2tct a.4.1.9,a.121.1.1 16072,19249 2trt 217 4.59e+00 2tct a.4.1.9,a.121.1.1 16064,19241 1in6A 334 4.62e+00 1hqcA a.4.5.11,c.37.1.20 62601,62602 1res 43 4.80e+00 1ret a.4.1.2 16023 2ao9A 155 5.11e+00 2gaiA 633 5.38e+00 2amiA 96 5.41e+00 1a6i 217 5.61e+00 2tct a.4.1.9,a.121.1.1 16066,19243 1pru 56 5.64e+00 1pru a.35.1.5 17104 1squA 155 5.74e+00 d.252.1.1 98971 1xkoA 159 5.96e+00 1zybA 232 6.19e+00 1sgoA 139 7.17e+00 d.82.3.1 98857 1xd7A 145 7.23e+00 a.4.5.55 109566 1vz0A 230 7.50e+00 a.4.14.1,d.268.1.1 108929,108930 1efaA 333 7.88e+00 1tlfA a.35.1.5,c.93.1.1 17106,35691 1jyeA 349 8.00e+00 c.93.1.1 67455 1jyfA 349 8.03e+00 c.93.1.1 67456 1lbiA 360 8.66e+00 1tlfA c.93.1.1 35694 1r71A 178 8.70e+00 a.4.14.1 104823 1x3uA 79 8.77e+00 1hqcA 324 9.77e+00 1hqcA a.4.5.11,c.37.1.20 16127,32424 1fp2A 352 9.86e+00 1fpxA a.4.5.29,c.66.1.12 59941,59942 1zk8A 183 9.90e+00 1xmjA 290 1.02e+01 1xmiA 291 1.09e+01 1ixrC 312 1.13e+01 a.4.5.11,c.37.1.20 76930,76931 1ixsB 318 1.20e+01 a.4.5.11,c.37.1.20 76933,76934 1wyzA 242 1.30e+01 1u9nA 236 1.43e+01 1t56A 216 1.43e+01 a.4.1.9,a.121.1.1 106428,106429 1uhnA 189 1.48e+01 a.39.1.5 99399 1q4rA 112 1.48e+01 d.58.4.4 95823 1b0nA 111 1.51e+01 1b0nA a.34.1.1,a.35.1.3 17001,17064 1ev7A 317 1.52e+01 1ev7B c.52.1.9 33315 2bbsA 290 1.63e+01 2bbtA 290 1.64e+01 1or7A 194 1.69e+01 a.4.13.2,a.177.1.1 87332,87333 1g652 196 1.77e+01 1zauA 328 1.78e+01 1rypH 205 1.83e+01 d.153.1.4 41876 1uxc 65 1.87e+01 1uxc a.35.1.5 17119 1sq8A 64 1.87e+01 a.35.1.2 105888 2gyqA 173 1.88e+01 2ftuA 118 1.89e+01 1pwhA 327 1.93e+01 c.79.1.1 95224 3cox 507 1.96e+01 1b8sA c.3.1.2,d.16.1.1 30332,37863 2fcwA 109 2.06e+01 1oltA 457 2.09e+01 c.1.28.2 93334 2cw8A 537 2.13e+01 2b5aA 77 2.18e+01 1zbdB 134 2.27e+01 1zbdB g.50.1.1 45359 1vyuA 351 2.30e+01 b.34.2.1,c.37.1.1 108914,108915 1mt6A 280 2.44e+01 b.76.2.1,b.85.7.1 79446,79447 1h3iA 293 2.50e+01 b.76.2.1,b.85.7.1 76635,76636 1gw3 46 2.50e+01 1gw4 j.39.1.1 46298 1n6cA 297 2.65e+01 b.76.2.1,b.85.7.1 80123,80124 2g7gA 213 2.67e+01 1i7dA 659 2.70e+01 1d6mA e.10.1.1 61886 1d6mA 653 2.71e+01 1d6mA e.10.1.1 43248 1x8lA 351 2.72e+01 1puoA 170 2.73e+01 a.101.1.1,a.101.1.1 95134,95135 1euzA 419 2.76e+01 1k89 c.2.1.7,c.58.1.1 59513,59514 1wj5A 120 2.76e+01 2givA 295 2.79e+01 1mufA 257 2.80e+01 b.76.2.1,b.85.7.1 79483,79484 2a2jA 246 2.82e+01 2f6qA 280 2.83e+01 1xt9A 212 2.86e+01 1whzA 70 3.05e+01 1yqyA 523 3.07e+01 1h3fA 432 3.17e+01 c.26.1.1,d.66.1.4 76631,76632 1lqtA 456 3.17e+01 c.3.1.1,c.4.1.1 74198,74199 1ic8A 194 3.21e+01 a.4.1.1,a.35.1.1 76740,76741 1xqhA 264 3.26e+01 1sknP 92 3.26e+01 1sknP a.37.1.1 17127 1tviA 172 3.33e+01 2gwgA 350 3.36e+01 1g6uA 48 3.37e+01 1g6uA k.9.1.1 46425 1xf8A 335 3.48e+01 1g4mA 393 3.54e+01 b.1.18.11,b.1.18.11 65143,65144 1eysH 259 3.58e+01 6prcH b.41.1.1,f.23.10.1 25484,43517 2fnaA 357 3.63e+01 1a8y 367 3.83e+01 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 1ne9A 335 3.85e+01 d.108.1.4,d.108.1.4 91839,91840 1jsyA 418 3.96e+01 b.1.18.11,b.1.18.11 71847,71848 1fmjA 351 3.96e+01 c.37.1.5 59879 1odd 118 3.99e+01 1opc a.4.6.1 16232 1opc 110 4.05e+01 1opc a.4.6.1 16231 1cx4A 305 4.16e+01 b.82.3.2,b.82.3.2 59099,59100 2beiA 170 4.18e+01 1jpc 109 4.27e+01 1b2pA b.78.1.1 27986 1gm9A 209 4.30e+01 d.153.1.2 65304 1gm7A 209 4.30e+01 d.153.1.2 65302 1kecA 209 4.31e+01 d.153.1.2 90957 1k7dA 209 4.32e+01 d.153.1.2 90946 1gk9A 260 4.37e+01 d.153.1.2 65246 1wi9A 72 4.42e+01 1e31A 142 4.42e+01 1f3hA g.52.1.1 45379 1xe4A 335 4.50e+01 1ky8A 501 4.54e+01 c.82.1.1 77628 1r0wA 286 4.55e+01 c.37.1.12 96754 1f3hA 142 4.70e+01 1f3hA g.52.1.1 45381 1uxtA 501 4.76e+01 c.82.1.1 108125 1uxvA 501 4.77e+01 c.82.1.1 108127 1zkrA 153 4.81e+01 1b48A 221 4.82e+01 1pgtA a.45.1.1,c.47.1.5 17703,32997 1gukA 222 4.84e+01 1pgtA a.45.1.1,c.47.1.5 17705,32999 2a33A 215 4.85e+01 2aj6A 159 4.90e+01 2bx9A 53 4.92e+01 1zyqA 698 4.94e+01 1ep1B 261 4.97e+01 1ep2B b.43.4.2,c.25.1.3 25665,31555 1wp0A 165 4.98e+01 1ep3B 262 4.99e+01 1ep2B b.43.4.2,c.25.1.3 25664,31554 1x9mA 698 4.99e+01 2gqkA 173 5.14e+01 1ufzA 83 5.20e+01 a.5.9.1 107821 1neq 74 5.42e+01 1neq a.35.1.2 17063 1umqA 81 5.49e+01 a.4.1.12 99625 1av1A 201 5.55e+01 1av1A h.5.1.1 45796 1moxA 501 5.68e+01 c.10.2.5,c.10.2.5,g.3.9.1,g.3.9.1 91372,91373,91374,91375 1jioA 403 5.79e+01 a.104.1.1 66747 1z8oA 404 5.81e+01 1mtoA 319 5.85e+01 c.89.1.1 79458 2ggtA 164 5.89e+01 1u5lA 108 5.90e+01 1jipA 403 5.99e+01 a.104.1.1 66748 1z8pA 404 6.00e+01 1oryA 130 6.07e+01 a.24.19.1 93466 1eupA 403 6.28e+01 1rom a.104.1.1 18967 1ku1A 230 6.29e+01 a.118.3.1 72996 1z8qA 404 6.31e+01 1orjA 130 6.35e+01 a.24.19.1 93456 1yd7A 395 6.38e+01 1n6aA 259 6.39e+01 b.76.2.1,b.85.7.1 80121,80122 2f69A 261 6.41e+01 1s1dA 331 6.45e+01 b.67.3.1 98344 2h2nA 339 6.49e+01 2r63 63 6.59e+01 1r69 a.35.1.2 17036 3gcb 470 6.70e+01 3gcb d.3.1.1 37032 1a6r 471 6.74e+01 3gcb d.3.1.1 37033 1r63 63 6.86e+01 1r69 a.35.1.2 17035 1gcb 454 6.87e+01 3gcb d.3.1.1 37034 2a4nA 182 7.04e+01 1oh1A 109 7.14e+01 b.61.2.2 92977 2cpzA 115 7.14e+01 1xi1A 575 7.18e+01 2a01A 243 7.21e+01 1xfcA 384 7.34e+01 1nlnA 204 7.35e+01 d.3.1.7 91962 1wh6A 101 7.37e+01 1llc 325 7.49e+01 1hyhA c.2.1.5,d.162.1.1 30176,42143 1b87A 181 7.73e+01 1b87A d.108.1.1 40797 2gc9A 179 8.11e+01 1cp9A 205 8.12e+01 1ajqA d.153.1.2 41849 1b6a 478 8.38e+01 1bn5 a.4.5.25,d.127.1.1 16223,41160 1khyA 148 8.57e+01 a.174.1.1 77410 1vr5A 547 8.58e+01 1qzyA 478 8.60e+01 a.4.5.25,d.127.1.1 96717,96718 1j7nA 776 8.63e+01 d.92.1.14,d.92.1.14,d.166.1.1 66409,66410,66411 1jeiA 53 8.80e+01 1jeiA a.140.1.1 62918