# List of top-scoring protein chains for t06-100-30-str2-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 1bf2 750 1.50e-01 1bf2 b.1.18.2,b.71.1.1,c.1.8.1 21860,27787,28774 1c8uA 285 2.11e-01 1c8uA d.38.1.3,d.38.1.3 38547,38548 1n7oA 721 2.13e-01 a.102.3.2,b.24.1.1,b.30.5.2 80259,80260,80261 1gj7B 253 3.93e-01 1gy7A 125 4.29e-01 d.17.4.2 70738 1vjvA 415 5.45e-01 d.3.1.9 108632 1el6A 219 5.68e-01 1el6B d.182.1.1 42606 1jsdA 319 8.54e-01 b.19.1.2 63258 1wwzA 159 1.24e+00 1avaC 181 1.33e+00 1avaC b.42.4.1 25604 1bia 321 1.34e+00 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1c9oA 66 1.58e+00 1mjc b.40.4.5 25325 1eu3A 210 1.87e+00 1an8 b.40.2.2,d.15.6.1 25206,37795 1fjrA 195 2.00e+00 1fjrA b.102.1.1 59855 1n62C 288 2.01e+00 d.87.2.1,d.145.1.3 80094,80095 1wkrA 340 2.01e+00 b.50.1.2 109395 1a8q 274 2.12e+00 1brt c.69.1.12 34702 1rcqA 357 2.24e+00 b.49.2.2,c.1.6.1 104882,104883 1a3aA 148 2.56e+00 1a3aA d.112.1.1 40917 1o54A 277 2.71e+00 c.66.1.13 92482 1x82A 190 2.95e+00 1jsmA 325 3.09e+00 b.19.1.2 63264 1hpi 71 3.12e+00 1ckuA g.35.1.1 44995 2evbA 74 3.36e+00 1is3A 135 3.59e+00 b.29.1.3 76773 1gpc 218 3.63e+00 1gpc b.40.4.7 25393 1x9iA 302 4.22e+00 1snrA 341 4.23e+00 b.6.1.3,b.6.1.3 105823,105824 1vr9A 213 4.34e+00 1sluA 142 4.69e+00 1sluA b.16.1.1 23685 1g7sA 594 4.92e+00 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 1ts9A 102 5.04e+00 2mcm 112 5.13e+00 2mcm b.1.7.1 22207 1vhsA 175 5.28e+00 d.108.1.1 100698 1jb7A 495 5.38e+00 1otcA b.40.4.3,b.40.4.3,b.40.4.3 62836,62837,62838 1gkpA 458 5.53e+00 b.92.1.3,c.1.9.6 70231,70232 1euwA 152 5.68e+00 1dupA b.85.4.1 28349 1eaiC 61 5.95e+00 1eaiC g.22.1.1 44894 1v6pA 62 6.00e+00 1rm6A 769 6.02e+00 1v5vA 401 6.21e+00 1ahsA 126 6.30e+00 1ahsA b.19.1.1 23794 1jovA 270 6.38e+00 b.30.5.7 84192 1gy6A 127 7.07e+00 d.17.4.2 70736 1ev7A 317 7.29e+00 1ev7B c.52.1.9 33315 1ddjA 247 7.34e+00 5ptp b.47.1.2 26362 1elt 236 7.39e+00 5ptp b.47.1.2 26281 1gtzA 156 7.60e+00 c.23.13.1 70539 1gcqC 70 7.60e+00 1gcpA b.34.2.1 60436 1kcqA 104 7.65e+00 d.109.1.1 68449 1t2wA 145 7.75e+00 b.100.1.1 106289 1se8A 301 7.78e+00 b.40.4.3 105448 1ijaA 148 7.87e+00 1ijaA b.100.1.1 62484 1f06A 320 8.46e+00 1dapA c.2.1.3,d.81.1.3 59556,59557 1brwA 433 8.53e+00 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1g31A 111 8.61e+00 1g31A b.35.1.1 24656 1j79A 347 8.63e+00 1j79A c.1.9.4 62675 1sz7A 200 8.81e+00 1mfgA 95 8.86e+00 b.36.1.1 79043 1udzA 182 8.96e+00 b.51.1.1 99239 1ad2 228 9.00e+00 1ad2 e.24.1.1 43353 1d0dA 60 9.63e+00 1kigI g.8.1.2 44566 1mj5A 302 1.03e+01 c.69.1.8 91285 1t92A 116 1.05e+01 1go3E 187 1.07e+01 b.40.4.5,d.230.1.1 83054,83055 1g4wR 383 1.09e+01 1g4uS a.24.11.1,c.45.1.2 16644,32692 1f53A 84 1.10e+01 1f53A b.11.1.4 23632 1b0uA 262 1.12e+01 1b0uA c.37.1.12 32370 1a8s 273 1.14e+01 1brt c.69.1.12 34710 1dwkA 156 1.14e+01 1dw9A a.35.1.4,d.72.1.1 17075,39606 1gvkB 240 1.17e+01 b.47.1.2 70610 1u8vA 490 1.20e+01 1cv8 174 1.21e+01 1cv8 d.3.1.1 37089 1hx0A 496 1.25e+01 b.71.1.1,c.1.8.1 61346,61347 1mhnA 59 1.28e+01 b.34.9.1 84964 1iq6A 134 1.28e+01 d.38.1.4 76755 1f20A 435 1.29e+01 b.43.4.1,c.25.1.4 64932,64933 1ebfA 358 1.30e+01 1ebuA c.2.1.3,d.81.1.2 30033,39948 1umgA 362 1.37e+01 d.280.1.1 107956 1pv5A 264 1.37e+01 d.251.1.1 95150 1yb3A 175 1.38e+01 1rutX 188 1.40e+01 1inlA 296 1.42e+01 c.66.1.17 66220 1y4wA 518 1.44e+01 1dzkA 157 1.49e+01 1obpA b.60.1.1 27096 1cqxA 403 1.51e+01 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 1p1mA 406 1.51e+01 b.92.1.4,c.1.9.9 87696,87697 1epxA 370 1.51e+01 1fbaA c.1.10.1 29150 1g4mA 393 1.55e+01 b.1.18.11,b.1.18.11 65143,65144 1n08A 163 1.56e+01 b.43.5.1 79730 1s3eA 520 1.56e+01 c.3.1.2,d.16.1.5 98426,98427 1eaxA 241 1.59e+01 b.47.1.2 64889 1whzA 70 1.63e+01 1jb0D 138 1.64e+01 1jb0D d.187.1.1 62823 1v30A 124 1.65e+01 1o1yA 239 1.66e+01 c.23.16.1 86554 1i8kA 107 1.67e+01 b.1.1.1 71130 1dkuA 317 1.68e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 1ogoX 574 1.69e+01 b.133.1.1,b.80.1.10 92925,92926 1gk9B 557 1.70e+01 1vp6A 138 1.75e+01 1f3lA 321 1.87e+01 1g6q2 c.66.1.6 59630 1a78A 134 1.91e+01 1c1lA b.29.1.3 24212 1h8eH 146 1.96e+01 1e79H b.93.1.1 60757 1d7qA 143 1.97e+01 1d7qA b.40.4.5 25331 1jyhA 157 2.00e+01 d.60.1.3 71956 1iyeA 309 2.01e+01 e.17.1.1 83786 1ewkA 490 2.07e+01 1ewkA c.93.1.1 35712 1npk 154 2.10e+01 1npk d.58.6.1 39099 1dcoA 104 2.22e+01 1dcpA d.74.1.1 39680 1pkoA 139 2.26e+01 b.1.1.1 88147 1bqsA 209 2.28e+01 1bqsA b.1.1.4,b.1.1.4 21704,21705 1ne9A 335 2.29e+01 d.108.1.4,d.108.1.4 91839,91840 1j3mA 129 2.29e+01 d.129.7.1 103836 1d4xG 126 2.31e+01 1d0nA d.109.1.1 59109 1ja1A 622 2.35e+01 1amoA b.43.4.1,c.23.5.2,c.25.1.4 62803,62804,62805 1ruwA 69 2.39e+01 1qwrA 319 2.50e+01 b.82.1.3 96491 1i8aA 189 2.61e+01 1i82A b.1.9.2 61951 1j96A 323 2.63e+01 c.1.7.1 71616 1dypA 271 2.67e+01 1dypA b.29.1.2 24185 1my7A 114 2.67e+01 b.1.18.1 79675 1k2eA 156 2.68e+01 d.113.1.1 72010 1dg6A 191 2.68e+01 1d4vB b.22.1.1 23883 1jtdB 273 2.71e+01 b.69.5.2 67265 1g94A 448 2.72e+01 b.71.1.1,c.1.8.1 65169,65170 1dgwA 178 2.78e+01 1dgwA b.82.1.2 28090 1o7nA 449 2.78e+01 b.33.1.2,d.129.3.3 81162,81163 1ks8A 433 2.79e+01 a.102.1.2 77519 1i88A 389 2.79e+01 c.95.1.2,c.95.1.2 66070,66071 1k2xB 143 2.80e+01 1oh4A 179 2.83e+01 b.18.1.18 92978 1oruA 195 2.83e+01 b.58.1.2 93464 1jihA 531 2.86e+01 d.240.1.1,e.8.1.7 90374,90375 1senA 164 2.96e+01 c.47.1.1 105465 1o7iA 119 3.03e+01 b.40.4.3 86642 1a8y 367 3.04e+01 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 1bcpD 110 3.12e+01 1bcpD b.40.2.1 25132 1tl9A 339 3.13e+01 1jofA 365 3.14e+01 b.69.10.1 71775 1bywA 110 3.16e+01 1bywA d.110.3.6 40912 1hh8A 213 3.19e+01 1e96B a.118.8.1 61042 1bdfA 235 3.28e+01 1bdfA d.74.3.1,d.181.1.1 39727,42602 1y8oB 128 3.30e+01 1d2sA 170 3.32e+01 1d2sA b.29.1.4 24221 1hkyA 86 3.38e+01 g.10.1.3 76714 1bdo 80 3.38e+01 1bdo b.84.1.1 28214 1ooyA 481 3.38e+01 c.124.1.3,c.124.1.2 93388,93389 1gpr 162 3.42e+01 1gpr b.84.3.1 28267 1gttA 429 3.43e+01 d.177.1.1,d.177.1.1 70529,70530 1iyhA 198 3.45e+01 a.45.1.1,c.47.1.5 83790,83791 2cfuA 658 3.46e+01 1eu8A 409 3.52e+01 1eu8A c.94.1.1 59502 1qh5A 260 3.53e+01 1qh5A d.157.1.2 42057 1im3D 95 3.58e+01 1im3D b.1.18.5 62568 1gmuA 143 3.60e+01 b.107.1.1,d.58.38.1 65335,65336 1bxvA 91 3.66e+01 1aac b.6.1.1 22875 1oxxK 353 3.68e+01 b.40.6.3,c.37.1.12 93715,93716 1ji6A 589 3.70e+01 b.18.1.3,b.77.2.1,f.1.3.1 63066,63067,63068 2gfaA 119 3.71e+01 1gpiA 431 3.73e+01 b.29.1.10 65450 1l8bA 190 3.74e+01 d.86.1.1 73683 1i8dA 213 3.74e+01 b.43.4.3,b.43.4.3 61953,61954 1fehA 574 3.77e+01 1fehA c.96.1.1,d.15.4.2,d.58.1.5 36015,37690,38998 1b65A 375 3.84e+01 1b65A d.154.1.1 42020 1wp5A 323 3.85e+01 1fyhB 229 3.87e+01 1jrhI b.1.2.1,b.1.2.1 22055,22056 1ayl 541 3.88e+01 1ayl c.91.1.1,c.109.1.1 64718,64719 1ifrA 121 3.89e+01 b.1.16.1 71203 1gp6A 356 3.89e+01 b.82.2.1 65441 1e9gA 286 3.90e+01 1wgjA b.40.5.1 59393 1tkeA 224 3.90e+01 1odmA 331 3.93e+01 b.82.2.1 86875 1vfyA 73 4.01e+01 1vfyA g.50.1.1 45357 1ihjA 98 4.02e+01 1pdr b.36.1.1 62382 4fiv 113 4.06e+01 1fmb b.50.1.1 26762 1fc4A 401 4.12e+01 1bs0A c.67.1.4 59760 1i60A 278 4.14e+01 c.1.15.4 71118 1ajj 37 4.14e+01 1ajj g.12.1.1 44609 1f39A 101 4.16e+01 1umuA b.87.1.1 28386 1jlzA 23 4.20e+01 g.3.7.2 66869 1frb 315 4.26e+01 1frb c.1.7.1 28665 1lvmA 229 4.29e+01 b.47.1.3 78243 1b6rA 355 4.33e+01 1b6rA b.84.2.1,c.30.1.1,d.142.1.2 28241,31648,41493 1c7sA 858 4.39e+01 1qba b.1.18.2,b.2.2.3,c.1.8.6,d.92.2.1 21812,22408,29011,40410 1d4tA 104 4.46e+01 1d4tA d.93.1.1 40537 1pmi 440 4.49e+01 1pmi b.82.1.3 28114 1fd3A 41 4.53e+01 1fd3A g.9.1.1 44572 1j8rA 196 4.54e+01 1j8rA b.2.3.3 62745 1earA 147 4.55e+01 b.107.1.1,d.58.38.1 64875,64876 1p0zA 131 4.56e+01 d.110.6.1 93882 1oi6A 205 4.58e+01 b.82.1.1 103940 1j1tA 233 4.61e+01 b.29.1.18 90771 1yg9A 330 4.61e+01 1aiw 62 4.62e+01 1aiw b.72.2.1 27808 1h54A 754 4.62e+01 a.102.1.4,b.30.5.3 60634,60635 1rkqA 282 4.64e+01 c.108.1.10 97621 1et9A 204 4.73e+01 1an8 b.40.2.2,d.15.6.1 25204,37793 1iro 54 4.79e+01 1rb9 g.41.5.1 45223 1jo8A 58 4.80e+01 b.34.2.1 71774 1qddA 144 4.92e+01 1qddA d.169.1.1 42324 1f60A 458 4.95e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 1eluA 390 5.04e+01 1elqA c.67.1.3 34434 1ojrA 274 5.06e+01 c.74.1.1 93147 1rqpA 299 5.06e+01 b.141.1.1,c.132.1.1 97754,97755 1whi 122 5.14e+01 1whi b.39.1.1 24810 1kolA 398 5.14e+01 b.35.1.2,c.2.1.1 77474,77475 1h2wA 710 5.15e+01 b.69.7.1,c.69.1.4 76596,76597 1l7lA 121 5.21e+01 b.18.1.16 77790 1fnlA 175 5.29e+01 2fcbA b.1.1.4,b.1.1.4 21783,21784 1e0nA 27 5.36e+01 b.72.1.1 27807 1gnuA 117 5.36e+01 d.15.1.3 65403 1fcdA 401 5.40e+01 1fcdA c.3.1.5,c.3.1.5,d.87.1.1 30593,30594,40218 1n9eA 787 5.40e+01 b.30.2.1,d.17.2.1,d.17.2.1 91708,91709,91710 1fjgP 88 5.43e+01 1emwA d.27.1.1 38444 1br9 194 5.49e+01 1br9 b.40.3.1 25235 1us0A 316 5.54e+01 c.1.7.1 99850 1jfuA 186 5.56e+01 c.47.1.10 62940 1fhgA 154 5.60e+01 1tlk b.1.1.4 21706 1gycA 499 5.61e+01 b.6.1.3,b.6.1.3,b.6.1.3 70748,70749,70750 1gtkA 313 5.65e+01 c.94.1.1,d.50.2.1 76346,76347 1qxyA 252 5.66e+01 d.127.1.1 96565 1wdvA 152 5.71e+01 1gvhA 396 5.73e+01 a.1.1.2,b.43.4.2,c.25.1.5 70601,70602,70603 1gsmA 210 5.82e+01 b.1.1.4,b.1.1.4 65535,65536 1i2aA 219 5.83e+01 e.24.1.1 90660 1q74A 303 5.83e+01 c.134.1.1 96019 1ckaA 57 5.83e+01 1ckaA b.34.2.1 24459 1hzoA 271 5.83e+01 e.3.1.1 71092 1dmhA 311 5.84e+01 1dmhA b.3.6.1 22633 1d1gA 168 5.86e+01 1d1gA c.71.1.1 34889 2blnA 305 5.97e+01 1bdmA 327 5.97e+01 1bmdA c.2.1.5,d.162.1.1 30137,42104 1jb7B 260 5.98e+01 1otcB b.40.4.3 62839 1iz6A 138 6.01e+01 b.34.5.2,b.40.4.5 76976,76977 1w99A 558 6.04e+01 1fiqB 350 6.12e+01 1fiqB d.87.2.1,d.145.1.3 40229,41760 1onwA 390 6.14e+01 b.92.1.7,c.1.9.13 87172,87173 1l6xA 207 6.19e+01 b.1.1.2,b.1.1.2 73642,73643 1eu1A 780 6.25e+01 1dmr b.52.2.2,c.81.1.1 26903,35311 1oi2A 366 6.28e+01 c.119.1.2 103802 1chkA 238 6.29e+01 1chkA d.2.1.7 36999 1xdzA 240 6.46e+01 1agqA 135 6.51e+01 1agqA g.17.1.2 44789 1juvA 193 6.54e+01 c.71.1.1 90912 1cr5A 189 6.54e+01 1cr5A b.52.2.3,d.31.1.1 26931,38465 1g1cA 99 6.58e+01 b.1.1.4 65078 1gz2A 142 6.64e+01 d.169.1.1 83392 1ez0A 510 6.64e+01 1eyyA c.82.1.1 35385 1fvuA 133 6.65e+01 1ixxB d.169.1.1 42345 1ecfA 504 6.67e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 1ogwA 76 6.74e+01 d.15.1.1 87001 1fjgK 129 6.80e+01 1fjfK c.55.4.1 33733 1kt6A 183 6.85e+01 b.60.1.1 84466 1s3cA 141 6.85e+01 1hfuA 503 6.92e+01 b.6.1.3,b.6.1.3,b.6.1.3 65827,65828,65829 1bio 228 6.96e+01 5ptp b.47.1.2 26314 1i1qA 520 6.98e+01 1qdlA d.161.1.1 61543 1g6gA 127 6.98e+01 1g6gA b.26.1.2 23916 2arcA 164 7.01e+01 2arcA b.82.4.1 28148 1xmtA 103 7.12e+01 1ejfA 125 7.12e+01 1ejfA b.15.1.2 23683 1h2bA 359 7.13e+01 b.35.1.2,c.2.1.1 90543,90544 1pvmA 184 7.14e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1h9hE 223 7.20e+01 b.47.1.2 103810 1bhtA 176 7.22e+01 1bhtA g.10.1.1,g.14.1.1 44603,44663 1f2tB 148 7.24e+01 1f2tB 1g6hA 257 7.28e+01 1gajA c.37.1.12 60318 1df7A 159 7.39e+01 3dfr c.71.1.1 34885 1iseA 185 7.40e+01 d.67.3.1 90691 1a2yA 107 7.40e+01 8fabA b.1.1.1 19926 1ffyA 917 7.49e+01 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16926,26891,31593 1anf 370 7.52e+01 4mbp c.94.1.1 35776 1i7hA 111 7.55e+01 d.15.4.1 71122 2trxA 108 7.59e+01 1thx c.47.1.1 32719 1t61A 229 7.62e+01 d.169.1.6,d.169.1.6 106529,106530 1b12A 248 7.63e+01 1b12A b.87.1.2 28388 1gqeA 365 7.69e+01 e.38.1.1 70351 1ytvA 366 7.70e+01 1f7dA 136 7.73e+01 1dun b.85.4.1 28353 1cnt1 187 7.75e+01 1cnt3 1m9xC 146 7.75e+01 a.73.1.1 84907 1eyqA 222 7.87e+01 1eypA d.36.1.1 38534 1jltA 122 7.87e+01 a.133.1.2 66867 1pmhX 185 7.97e+01 b.18.1.18 104193 1jnrA 643 8.04e+01 a.7.3.1,c.3.1.4,d.168.1.1 66966,66967,66968 1xg0A 76 8.04e+01 1lycA 343 8.04e+01 a.93.1.1 74344 1gd8A 118 8.17e+01 d.188.1.1 60445 1brfA 53 8.29e+01 1rb9 g.41.5.1 45236 1bx7 55 8.30e+01 1bx7 g.3.15.1 44355 1khcA 147 8.33e+01 b.34.9.2 68608 1ro7A 259 8.35e+01 c.130.1.1 97667 1ahl 49 8.36e+01 1ahl g.9.1.1 44601 1extA 162 8.37e+01 1extA g.24.1.1,g.24.1.1,g.24.1.1 44900,44901,44902 1mk4A 157 8.42e+01 d.108.1.1 84979 1hlqA 75 8.45e+01 g.35.1.1 83613 1dcs 311 8.46e+01 1dcs b.82.2.1 28124 1tvxA 75 8.59e+01 1tvxA d.9.1.1 37441 1bsg 266 8.67e+01 1btl e.3.1.1 42729 1fmhA 33 8.68e+01 1fmhB k.6.1.1 46409 1gkmA 509 8.69e+01 a.127.1.2 70228 1bd0A 388 8.72e+01 1bd0A b.49.2.2,c.1.6.1 26480,28642 1kllA 130 8.74e+01 d.32.1.2 72720 1enwA 114 8.77e+01 1enwA a.5.4.1 16291 1eejA 216 8.79e+01 1eejA c.47.1.9,d.17.3.1 33057,38071 1s99A 200 8.81e+01 1k5nB 100 8.81e+01 b.1.1.2 77268 1lniA 96 8.90e+01 d.1.1.2 74046 1i7dA 659 8.98e+01 1d6mA e.10.1.1 61886