# List of top-scoring protein chains for t06-80-60-80-str2+near-backbone-11-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 1vjkA 98 4.11e-11 d.15.3.1 108631 2bb6A 414 3.57e-09 1zud2 66 1.69e-07 1yqbA 100 1.84e-07 2bwfA 77 3.19e-07 1yj1A 76 2.95e-06 1nddA 76 3.21e-06 1ubi d.15.1.1 37599 1ogwA 76 7.72e-06 d.15.1.1 87001 2bpsA 81 9.38e-06 1lfdA 87 1.37e-05 1lfdA d.15.1.5 37622 1euvB 86 1.58e-05 1a5r d.15.1.1 37598 1oqqA 106 2.08e-05 d.15.4.1 93422 1z2mA 155 2.24e-05 1xlqA 106 2.83e-05 1c1yB 77 3.25e-05 1c1yB d.15.1.5 37618 2fazA 78 4.77e-05 1wm3A 72 6.57e-05 2cu3A 64 8.11e-05 1wwtA 88 8.67e-05 1t0qC 86 1.04e-04 d.15.12.1 106222 1frrA 95 1.48e-04 1awd d.15.4.1 37674 2c5lC 117 1.51e-04 1uwmA 106 3.10e-04 1gttA 429 3.86e-04 d.177.1.1,d.177.1.1 70529,70530 2al3A 90 5.47e-04 2aefA 234 8.22e-04 2ggcA 263 9.26e-04 1vc3B 97 1.04e-03 1wzoA 246 1.04e-03 1sawA 225 1.07e-03 1fm0D 81 1.17e-03 1fmaD d.15.3.1 37642 2dafA 118 1.45e-03 1rfkA 98 1.50e-03 2sak 121 1.72e-03 2sak d.15.5.1 37711 1pqhA 143 2.07e-03 b.52.2.1 95017 1frd 98 2.24e-03 1awd d.15.4.1 37648 1t3qA 168 2.48e-03 a.56.1.1,d.15.4.2 106367,106368 1l5pA 93 2.74e-03 d.15.4.1 73598 2b3hA 329 2.96e-03 1czpA 98 3.13e-03 1awd d.15.4.1 37645 1offA 97 3.75e-03 d.15.4.1 86947 2bt6A 108 4.70e-03 2c1iA 431 4.93e-03 1t0yA 122 4.95e-03 d.15.1.1 99066 1rm6C 161 5.33e-03 1l7yA 94 5.80e-03 d.15.1.6 73676 1y1nA 291 5.84e-03 1wgrA 100 6.01e-03 1awd 94 6.10e-03 1awd d.15.4.1 37673 2c7hA 86 6.69e-03 2fnjB 118 6.73e-03 1oeyA 83 7.39e-03 d.15.2.2 92800 1a70 97 8.01e-03 1awd d.15.4.1 37678 2bh1A 250 8.47e-03 1lm8B 118 8.61e-03 d.15.1.1 74033 1xnzA 264 9.82e-03 1e7uA 961 1.02e-02 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 1xgsA 295 1.04e-02 1bn5 a.4.5.25,d.127.1.1 16216,41153 1i7hA 111 1.10e-02 d.15.4.1 71122 2iugA 120 1.18e-02 2pia 321 1.28e-02 2pia b.43.4.2,c.25.1.2,d.15.4.2 25663,31553,37704 1aisA 182 1.34e-02 1ytbA d.129.1.1,d.129.1.1 41288,41289 1xe1A 116 1.36e-02 b.43.3.1 109571 1meoA 209 1.75e-02 c.65.1.1 79035 1nkqA 259 1.76e-02 d.177.1.1 103862 1jalA 363 1.92e-02 c.37.1.8,d.15.10.2 84138,84139 1v8cA 168 2.30e-02 d.15.3.1,d.129.5.1 100495,100496 1dm9A 133 2.31e-02 1dm9A d.66.1.3 39560 1doi 128 2.36e-02 1awd d.15.4.1 37676 1vj0A 380 2.38e-02 b.35.1.2,c.2.1.1 100786,100787 1wjuA 100 2.60e-02 1wmhA 89 2.70e-02 1vkkA 154 2.72e-02 d.109.1.2 108669 1dg6A 191 2.76e-02 1d4vB b.22.1.1 23883 1wgkA 114 2.99e-02 1zghA 260 3.15e-02 1y8xB 98 3.29e-02 1ji6A 589 3.30e-02 b.18.1.3,b.77.2.1,f.1.3.1 63066,63067,63068 1qxyA 252 3.31e-02 d.127.1.1 96565 1zc6A 305 3.46e-02 1vajA 214 3.53e-02 1ty0A 211 3.82e-02 b.40.2.2,d.15.6.1 107440,107441 1fehA 574 3.86e-02 1fehA c.96.1.1,d.15.4.2,d.58.1.5 36015,37690,38998 1woqA 267 4.70e-02 c.55.1.10,c.55.1.10 109462,109463 1sv6A 269 4.95e-02 d.177.1.1 106043 2calA 154 5.13e-02 1w99A 558 5.38e-02 1jkxA 212 5.71e-02 c.65.1.1 66813 1chmA 401 5.89e-02 1chmA c.55.2.1,d.127.1.1 33545,41142 1n62A 166 7.16e-02 a.56.1.1,d.15.4.2 80090,80091 1wy2A 351 7.32e-02 2bwvA 440 9.40e-02 1rypB 250 9.66e-02 1rypB d.153.1.4 41933 2g1lA 104 1.06e-01 2a9dA 372 1.08e-01 1ni9A 338 1.14e-01 e.7.1.2 85739 1gr3A 160 1.14e-01 b.22.1.1 65476 1pk6B 132 1.15e-01 b.22.1.1 94802 2blnA 305 1.15e-01 2fbwB 252 1.19e-01 1brwA 433 1.22e-01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 2fm8A 135 1.31e-01 1bkb 136 1.33e-01 1bkb b.34.5.2,b.40.4.5 24609,25341 2dbyA 368 1.43e-01 1mugA 168 1.49e-01 1mugA c.18.1.2 31030 1b6a 478 1.50e-01 1bn5 a.4.5.25,d.127.1.1 16223,41160 1rypC 244 1.55e-01 1rypC d.153.1.4 41934 1vlbA 907 1.61e-01 a.56.1.1,d.15.4.2,d.41.1.1,d.133.1.1 108739,108740,108741,108742 1oeyJ 107 1.74e-01 d.15.2.2 92804 1q8rA 120 1.74e-01 d.79.6.1 96225 2a8jA 420 1.75e-01 1q1oA 98 1.77e-01 d.15.2.2 95596 1o91A 178 1.81e-01 b.22.1.1 92656 1b6rA 355 1.82e-01 1b6rA b.84.2.1,c.30.1.1,d.142.1.2 28241,31648,41493 1xteA 154 2.00e-01 1z3qA 200 2.13e-01 1vctA 205 2.19e-01 2h88B 252 2.24e-01 1o0xA 262 2.24e-01 d.127.1.1 80755 1nofA 383 2.47e-01 b.71.1.2,c.1.8.3 92020,92021 2b5wA 357 2.53e-01 2d0oA 610 2.53e-01 1q7hA 153 2.57e-01 b.122.1.1,d.17.6.2 96042,96043 1wriA 93 2.72e-01 1am2 199 2.76e-01 1am2 b.86.1.2 28381 2ci9A 102 2.88e-01 1tygB 87 2.91e-01 d.15.3.2 107455 1ip9A 85 2.95e-01 1ip9A d.15.2.2 62638 2f69A 261 2.96e-01 1h9oA 112 3.07e-01 1qadA d.93.1.1 60837 1vfsA 386 3.11e-01 b.49.2.2,c.1.6.1 108584,108585 1iueA 98 3.13e-01 d.15.4.1 90697 1ufyA 122 3.40e-01 d.79.1.2 88489 2bkfA 87 3.47e-01 1kk1A 410 3.48e-01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1srqA 341 3.49e-01 e.55.1.1 105967 1gsmA 210 3.55e-01 b.1.1.4,b.1.1.4 65535,65536 1yarH 217 3.55e-01 1pl8A 356 3.56e-01 b.35.1.2,c.2.1.1 94878,94879 1mi8A 158 3.67e-01 b.86.1.2 91279 2hbtA 247 3.67e-01 1h4rA 314 3.93e-01 a.11.2.1,b.55.1.5,d.15.1.4 65616,65617,65618 4tsvA 150 4.00e-01 2tnfA b.22.1.1 23860 1zx8A 136 4.06e-01 1uheA 97 4.07e-01 1kzlA 208 4.33e-01 b.43.4.3,b.43.4.3 77635,77636 1wywA 230 4.39e-01 1prxA 224 4.40e-01 1prxA c.47.1.10 33076 1nbwA 607 4.46e-01 c.8.6.1,c.55.1.6,c.55.1.6 80393,80394,80395 1pdo 135 4.66e-01 1pdo c.54.1.1 33376 1p4kA 295 4.72e-01 d.153.1.5 87772 1xc3A 302 4.75e-01 1oruA 195 4.81e-01 b.58.1.2 93464 2c2qA 199 4.82e-01 1vhoA 346 4.95e-01 b.49.3.1,c.56.5.4 100694,100695 1pq7A 224 4.99e-01 b.47.1.2 95002 1whvA 100 5.12e-01 1y8aA 332 5.12e-01 1aly 146 5.16e-01 1aly b.22.1.1 23856 2b7nA 273 5.23e-01 1uptA 171 5.23e-01 c.37.1.8 99767 1e30A 155 5.43e-01 1rcy b.6.1.1 23016 2h17A 181 5.43e-01 1fonA 240 5.64e-01 5ptp b.47.1.2 26231 1ksiA 642 5.87e-01 1ksiB b.30.2.1,d.17.2.1,d.17.2.1 24408,38043,38044 1rcqA 357 5.89e-01 b.49.2.2,c.1.6.1 104882,104883 1el6A 219 5.93e-01 1el6B d.182.1.1 42606 1wj9A 211 5.94e-01 1rj8A 164 6.18e-01 b.22.1.1 97547 2g5cA 281 6.51e-01 1o8xA 146 6.54e-01 c.47.1.10 86681 2fk9A 157 6.81e-01 1iz6A 138 6.95e-01 b.34.5.2,b.40.4.5 76976,76977 1jzgA 128 7.06e-01 b.6.1.1 67855 1t9fA 187 7.11e-01 b.42.6.1 106710 1wfyA 104 7.11e-01 1jztA 246 7.14e-01 c.104.1.1 63319 1i8dA 213 7.20e-01 b.43.4.3,b.43.4.3 61953,61954 1fwxA 595 7.40e-01 b.6.1.4,b.69.3.1 60069,60070 1mp9A 198 7.45e-01 d.129.1.1,d.129.1.1 91385,91386 1n6aA 259 7.52e-01 b.76.2.1,b.85.7.1 80121,80122 1o4tA 133 7.80e-01 b.82.1.9 86622 1ra6A 461 7.89e-01 e.8.1.4 104879 1yn3A 98 7.95e-01 1t1gA 364 8.00e-01 c.41.1.2 106246 1sgwA 214 8.62e-01 c.37.1.12 105541 2cdpA 160 8.82e-01 1drw 273 9.21e-01 1drw c.2.1.3,d.81.1.3 30057,39972 1g6gA 127 9.27e-01 1g6gA b.26.1.2 23916 2ft6A 124 9.43e-01 1zmaA 118 9.48e-01 1vplA 256 9.55e-01 1efdN 266 9.55e-01 1efdN c.92.2.1 35597 1yp2A 451 9.75e-01 2g19A 244 9.95e-01 1s3sG 127 1.00e+00 d.15.1.2 98457 1ri6A 343 1.02e+00 b.69.11.1 97503 1xk7A 408 1.02e+00 1o54A 277 1.05e+00 c.66.1.13 92482 1y2tA 142 1.07e+00 2fomB 185 1.09e+00 1uufA 369 1.11e+00 b.35.1.2,c.2.1.1 100006,100007 2ah5A 210 1.12e+00 1vqvA 306 1.14e+00 1ze3D 125 1.14e+00 2cdcA 366 1.15e+00 1npsA 88 1.20e+00 1prs b.11.1.1 23622 1k07A 263 1.20e+00 d.157.1.1 77218 1jl0A 334 1.21e+00 1jenA d.156.1.1 63155 3gcb 470 1.25e+00 3gcb d.3.1.1 37032 1pk6A 133 1.26e+00 b.22.1.1 94801 1q5hA 147 1.30e+00 b.85.4.1 95893 1wojA 214 1.32e+00 1zvkA 358 1.33e+00 1kxgA 152 1.35e+00 b.22.1.1 73145 1gveA 327 1.37e+00 c.1.7.1 70597 1a4iA 301 1.37e+00 1a4iA c.2.1.7,c.58.1.2 30278,33926 1p0yA 444 1.39e+00 a.166.1.1,b.85.7.3 87654,87655 2bw0A 329 1.43e+00 1p0fA 373 1.44e+00 b.35.1.2,c.2.1.1 87642,87643 1y8oB 128 1.45e+00 1ryp1 222 1.47e+00 1ryp1 1oo0A 147 1.48e+00 d.232.1.1 87182 1eluA 390 1.50e+00 1elqA c.67.1.3 34434 1fviA 297 1.51e+00 1fviA b.40.4.6,d.142.2.1 25364,41578 2fk8A 318 1.52e+00 1xzoA 174 1.54e+00 1csn 298 1.54e+00 1csn d.144.1.7 41664 1i2mA 216 1.55e+00 1byuA c.37.1.8 61568 2h21A 440 1.57e+00 1stmA 157 1.57e+00 1stmA b.121.7.1 23281 1bd0A 388 1.57e+00 1bd0A b.49.2.2,c.1.6.1 26480,28642 1z1zA 131 1.68e+00 1wdiA 345 1.68e+00 1fr3A 67 1.69e+00 1fr3A b.40.6.1 25436 1u09A 476 1.71e+00 e.8.1.4 107545 2cy5A 140 1.78e+00 1h8eA 510 1.81e+00 1skyB a.69.1.1,b.49.1.1,c.37.1.11 60738,60739,60740 1kxoA 184 1.82e+00 b.60.1.1 84475 1gtkA 313 1.87e+00 c.94.1.1,d.50.2.1 76346,76347 1wdtA 665 1.90e+00 1s28A 132 1.95e+00 d.198.1.1 105223 2ciaA 102 1.95e+00 2an3A 289 1.96e+00 1kzyC 259 1.96e+00 c.15.1.4,c.15.1.4 73383,73384 1r6vA 671 1.98e+00 1ywxA 102 2.00e+00 1oi2A 366 2.01e+00 c.119.1.2 103802 1k94A 165 2.01e+00 a.39.1.8 68333 1dp4A 435 2.03e+00 1dp4A c.93.1.1 35710 1tqyA 424 2.04e+00 c.95.1.1,c.95.1.1 107245,107246 1wi0A 113 2.05e+00 1zavA 180 2.05e+00 1iq4A 179 2.08e+00 1iq4A d.77.1.1 62641 1whi 122 2.12e+00 1whi b.39.1.1 24810 1ijbA 202 2.12e+00 c.62.1.1 71229 1bvoA 175 2.15e+00 1a3qA b.2.5.3 22457 1yarA 233 2.15e+00 1h2bA 359 2.15e+00 b.35.1.2,c.2.1.1 90543,90544 1ten 90 2.22e+00 1ten b.1.2.1 21990 1sjyA 159 2.23e+00 d.113.1.1 98900 1z6bA 154 2.24e+00 1cbf 285 2.26e+00 1cbf c.90.1.1 35587 1s9jA 341 2.28e+00 2fxqA 264 2.29e+00 1pt6A 213 2.33e+00 c.62.1.1 95091 1q4rA 112 2.33e+00 d.58.4.4 95823 2eryA 172 2.34e+00 1rgyA 360 2.34e+00 e.3.1.1 97456 1x67A 146 2.35e+00 1fxlA 167 2.38e+00 1b7fA d.58.7.1,d.58.7.1 39183,39184 2a2nA 176 2.41e+00 1nlnA 204 2.42e+00 d.3.1.7 91962 1at0 145 2.42e+00 1at0 b.86.1.1 28374 1pzxA 289 2.42e+00 c.119.1.1 95484 1v30A 124 2.42e+00 1zejA 293 2.43e+00 1p4oA 322 2.46e+00 d.144.1.7 87775 1p9kA 79 2.47e+00 d.66.1.6 94392 1v73A 342 2.48e+00 2h1tA 188 2.50e+00 1epfA 191 2.52e+00 2ncm b.1.1.4,b.1.1.4 21694,21695 1b9mA 265 2.52e+00 1b9mA a.4.5.8,b.40.6.2,b.40.6.2 16118,58938,58939 1zj6A 187 2.54e+00 1k8rB 110 2.56e+00 d.15.1.5 72180 1xx6A 191 2.59e+00 1vzyA 291 2.69e+00 1vqoY 241 2.70e+00 1g7sA 594 2.72e+00 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 1oxwA 373 2.77e+00 c.19.1.3 87539 2c2nA 339 2.77e+00 2al6A 375 2.79e+00 1q79A 514 2.81e+00 a.160.1.1,d.218.1.3,d.58.16.1 104548,104549,104550 1twiA 434 2.82e+00 b.49.2.3,c.1.6.1 107399,107400 1gwmA 153 2.85e+00 b.18.1.19 83348 1ng2A 193 2.88e+00 b.34.2.1,b.34.2.1 85660,85661 2a9sA 171 2.95e+00 1yzfA 195 2.95e+00 1lb6A 160 2.97e+00 b.8.1.1 73798 2nlrA 234 3.00e+00 2nlrA b.29.1.11 24344 1mg4A 113 3.00e+00 d.15.11.1 84953 2tnfA 156 3.00e+00 2tnfA b.22.1.1 23880 2eulA 156 3.01e+00 1ql0A 241 3.03e+00 1qaeA d.4.1.2 37139 1u20A 212 3.04e+00 1vjpA 394 3.04e+00 c.2.1.3,d.81.1.3 100828,100829 2a5dA 175 3.05e+00 1ztdA 133 3.07e+00 1xccA 220 3.07e+00 1ik9A 213 3.10e+00 b.59.1.1,h.1.11.1 66176,66177 1e43A 483 3.12e+00 1bli b.71.1.1,c.1.8.1 59217,59218 1ckmA 330 3.14e+00 1ckmA b.40.4.6,d.142.2.3 25358,41585 2a8nA 144 3.16e+00 1xl7A 612 3.23e+00 1eo6A 117 3.27e+00 1eo6A d.15.1.3 37609 1go3E 187 3.28e+00 b.40.4.5,d.230.1.1 83054,83055 1y0bA 197 3.28e+00 1vl1A 232 3.31e+00 c.124.1.1 108707 1whbA 157 3.31e+00 1u8zA 168 3.33e+00 1zaiA 363 3.34e+00 1t8hA 277 3.36e+00 d.194.1.2 106664 1twfK 120 3.39e+00 1wmhB 86 3.42e+00 1qysA 106 3.43e+00 k.41.1.1 96603 1zsyA 357 3.44e+00 1mxgA 435 3.48e+00 b.71.1.1,c.1.8.1 85193,85194 1f46A 140 3.52e+00 1f46A d.129.4.1 59643 1ddjA 247 3.53e+00 5ptp b.47.1.2 26362 1fmtA 314 3.56e+00 1fmtA b.46.1.1,c.65.1.1 25758,34174 1x9pA 523 3.58e+00 1mtpA 323 3.63e+00 e.1.1.1 85107 2a6zA 222 3.65e+00 1ysjA 404 3.66e+00 1wvhA 134 3.68e+00 1ikoP 178 3.69e+00 b.6.1.5 71243 1x8qA 184 3.76e+00 1rqwA 207 3.83e+00 b.25.1.1 97781 1jykA 254 3.88e+00 c.68.1.13 67458 2bt9A 90 3.94e+00 1gvp 87 3.95e+00 1gvp b.40.4.7 25369 1z2lA 423 3.97e+00 1rgzA 363 4.01e+00 e.3.1.1 97457 1f9vA 347 4.05e+00 1bg2 c.37.1.9 59745 1rg9A 383 4.06e+00 d.130.1.1,d.130.1.1,d.130.1.1 97427,97428,97429 1gnuA 117 4.11e+00 d.15.1.3 65403 1dceA 567 4.12e+00 1dceA a.118.6.1,b.7.4.1,c.10.2.2 19191,23218,30867 1x1rA 178 4.18e+00 1ofdA 1520 4.18e+00 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 1y51A 88 4.24e+00 1nd6A 354 4.25e+00 c.60.1.2 80407 1u6eA 335 4.26e+00 1fjgQ 105 4.29e+00 1fjfQ b.40.4.5 25352 1d9uA 154 4.30e+00 1am7A d.2.1.4 59111 1vl4A 447 4.38e+00 d.283.1.1 108718 1v8fA 276 4.38e+00 c.26.1.4 100503 1v7pB 128 4.40e+00 d.169.1.1 108407 2f9hA 129 4.40e+00 1wkqA 164 4.41e+00 c.97.1.2 109393 1hdhA 536 4.42e+00 c.76.1.2 65805 1hbnC 248 4.42e+00 1mroC d.58.31.1 60902 1f7sA 139 4.42e+00 1cof d.109.1.2 40857 1u2cA 246 4.45e+00 b.1.6.2,d.272.1.1 107610,107611 1krhA 338 4.48e+00 b.43.4.2,c.25.1.2,d.15.4.2 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