# List of top-scoring protein chains for t04-100-30-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 2fh7A 595 8.72e-71 1larA 575 8.88e-70 1larA c.45.1.2,c.45.1.2 32693,32694 1p15A 253 6.77e-64 c.45.1.2 93894 2shpA 525 4.21e-62 2shpA c.45.1.2,d.93.1.1,d.93.1.1 32683,40533,40534 1g7fA 298 1.54e-61 1pty c.45.1.2 60330 2b49A 287 1.76e-61 2f71A 298 2.25e-61 2b3oA 532 7.97e-61 1pa1A 310 8.22e-61 c.45.1.2 94404 1ptvA 321 2.19e-60 1pty c.45.1.2 32665 1jlnA 297 2.43e-59 1pty c.45.1.2 63172 1wchA 315 8.93e-59 2bzlA 325 1.37e-58 2bijA 305 2.75e-58 2bv5A 282 6.64e-58 1ytw 306 1.61e-26 1ytw c.45.1.2 32689 1lyvA 306 5.68e-26 c.45.1.2 74348 1g4wR 383 2.86e-20 1g4uS a.24.11.1,c.45.1.2 16644,32692 1oheA 348 1.72e-18 c.45.1.1,c.45.1.1 87013,87014 1x24A 180 3.24e-16 1zckA 154 3.43e-15 1rxdA 159 3.46e-15 1zclA 180 4.20e-15 1fpzA 212 1.56e-11 1fpzA c.45.1.1 59976 1vhrA 184 2.59e-09 1vhrA c.45.1.1 32651 1d5rA 324 4.78e-09 1d5rA b.7.1.1,c.45.1.1 23181,32697 1i9sA 210 6.19e-08 1i9sA c.45.1.1 62099 1yn9A 169 6.94e-08 2c46A 241 7.20e-08 1wrmA 165 1.47e-07 1xriA 151 1.46e-06 1yz4A 160 1.53e-06 1mkp 144 6.13e-06 1vhrA c.45.1.1 32654 1zsqA 528 5.27e-05 1ywfA 296 9.66e-05 1lw3A 657 1.24e-04 b.55.1.8,c.45.1.3 91152,91153 1u24A 337 4.11e-04 2cy0A 263 2.55e-02 1wxdA 263 2.95e-02 2d5cA 263 2.96e-02 1wr2A 238 5.52e-02 1ihuA 589 6.79e-02 c.37.1.10,c.37.1.10 62394,62395 1wj7A 104 7.81e-02 1gvhA 396 1.72e-01 a.1.1.2,b.43.4.2,c.25.1.5 70601,70602,70603 1p2fA 220 2.07e-01 a.4.6.1,c.23.1.1 87720,87721 1npyA 271 3.13e-01 c.2.1.7,c.58.1.5 85995,85996 1t9kA 347 6.62e-01 c.124.1.5 106721 1yt8A 539 8.91e-01 1h65A 270 1.01e+00 c.37.1.8 65640 2ak4D 211 1.44e+00 1vj1A 363 1.51e+00 b.35.1.2,c.2.1.1 100794,100795 1b74A 254 1.62e+00 1b74A c.78.2.1,c.78.2.1 35264,35265 1m1zA 513 1.64e+00 c.26.2.1,d.153.1.1 78457,78458 1f2tA 149 1.76e+00 1f2tA c.37.1.12 32373 1jkmB 361 1.88e+00 1jkmA c.69.1.2 34634 1i45A 248 2.00e+00 1amk c.1.1.1 61665 1v37A 177 2.17e+00 1g60A 260 2.60e+00 c.66.1.11 70151 1e0cA 271 2.68e+00 1e0cA c.46.1.2,c.46.1.2 32717,32718 1zoiA 276 2.85e+00 2f46A 156 3.10e+00 1f2dA 341 3.15e+00 1f2dA c.79.1.1 35298 1fadA 99 3.41e+00 1fadA a.77.1.2 18428 1rj9A 304 3.56e+00 a.24.13.1,c.37.1.10 97553,97554 1sffA 426 3.60e+00 c.67.1.4 105482 1wddS 128 3.63e+00 1tzjA 338 3.67e+00 1j0dA 341 4.02e+00 c.79.1.1 83902 1z5vA 474 4.04e+00 1us8A 147 4.30e+00 c.37.1.12 99859 2bm8A 236 4.34e+00 1k66A 149 4.75e+00 c.23.1.1 90941 1t3gA 159 5.23e+00 2ex4A 241 5.35e+00 1igwA 434 5.50e+00 c.1.12.7 62370 1jftA 340 5.80e+00 a.35.1.5,c.93.1.1 66652,66653 1zbqA 327 5.82e+00 1nnsA 326 5.91e+00 c.88.1.1 85910 1xodA 118 6.49e+00 1dbqA 289 6.55e+00 1qpzA c.93.1.1 35666 1zh2A 121 6.68e+00 1xzwA 426 7.98e+00 1ux6A 350 8.04e+00 b.29.1.16,g.75.1.1 100145,100146 1i1qB 192 8.23e+00 1qdlB c.23.16.1 61544 1ox0A 430 8.36e+00 c.95.1.1,c.95.1.1 87495,87496 1gmxA 108 8.64e+00 c.46.1.3 65355 1gskA 513 8.66e+00 b.6.1.3,b.6.1.3,b.6.1.3 83314,83315,83316 1z7dA 433 8.96e+00 2aamA 309 9.29e+00 1w6sA 599 9.55e+00 1xhlA 297 9.75e+00 c.2.1.2 109591 1i6wA 181 9.89e+00 1i6wA c.69.1.18 61859 1qj5A 429 9.92e+00 1dtyA c.67.1.4 34493 1a88A 275 1.07e+01 1brt c.69.1.12 34707 1ispA 181 1.13e+01 c.69.1.18 76778 1s0aA 429 1.14e+01 c.67.1.4 98263 2c78A 405 1.19e+01 2awfA 172 1.28e+01 1har 216 1.29e+01 1rthA e.8.1.2 43025 1wlzA 105 1.33e+01 2f8lA 344 1.37e+01 1e5mA 416 1.38e+01 1dd8A c.95.1.1,c.95.1.1 58973,58974 1cojA 212 1.38e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1auiB 169 1.40e+01 1auiB a.39.1.5 17325 1evyA 366 1.40e+01 1evyA a.100.1.6,c.2.1.6 18811,30215 2btoA 473 1.42e+01 1vmaA 306 1.42e+01 a.24.13.1,c.37.1.10 108887,108888 1ha3A 405 1.45e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 1mvoA 136 1.46e+01 c.23.1.1 79513 1nx8A 273 1.48e+01 b.82.2.8 86374 1x6oA 174 1.49e+01 b.34.5.2,b.40.4.5 109493,109494 1td2A 287 1.49e+01 c.72.1.5 106765 1vkrA 125 1.51e+01 c.44.2.1 108689 1ix9A 205 1.55e+01 a.2.11.1,d.44.1.1 76899,76900 1iscA 192 1.55e+01 1avmA a.2.11.1,d.44.1.1 15733,38726 1i0hA 205 1.56e+01 1avmA a.2.11.1,d.44.1.1 15760,38685 1xkqA 280 1.58e+01 1n2eA 300 1.65e+01 c.26.1.4 85268 1pujA 282 1.65e+01 c.37.1.8 88294 1zp4A 304 1.67e+01 1geqA 248 1.72e+01 2tysA c.1.2.4 28589 1vloA 381 1.74e+01 b.44.2.1,d.250.1.1 108838,108839 1zpdA 568 1.76e+01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31741,31785,31786 1isuA 62 1.84e+01 1isuA g.35.1.1 44978 1kqpA 271 1.84e+01 c.26.2.1 72883 1t6nA 220 1.86e+01 c.37.1.19 106576 1exmA 405 1.91e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 1pjr 724 1.94e+01 1pjr c.37.1.19,c.37.1.19 32391,32392 1vljA 407 1.95e+01 e.22.1.2 108832 1zq1A 438 1.98e+01 1ih8A 271 2.00e+01 2nsyA c.26.2.1 62377 1i7qB 193 2.01e+01 1qdlB c.23.16.1 61902 1d2eA 397 2.04e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25701,25741,32136 1s6cA 183 2.06e+01 a.39.1.5 98594 1eu8A 409 2.06e+01 1eu8A c.94.1.1 59502 4pgaA 337 2.06e+01 4pgaA c.88.1.1 35565 1mn8A 100 2.10e+01 a.61.1.6 79318 1vi9A 299 2.12e+01 c.72.1.5 100750 1b5qA 472 2.20e+01 1b37B c.3.1.2,d.16.1.5 30404,37968 1pvyA 227 2.23e+01 d.115.1.2 95195 1gxyA 226 2.24e+01 d.166.1.3 76380 1foeA 377 2.28e+01 1foeA a.87.1.1,b.55.1.1 18517,26969 1rc9A 221 2.39e+01 2fe7A 166 2.45e+01 1mb3A 124 2.47e+01 c.23.1.1 78907 1t7sA 137 2.48e+01 a.7.7.1 106636 1hdmA 201 2.49e+01 1iakA b.1.1.2,d.19.1.1 21583,38157 1xm7A 195 2.49e+01 1b5tA 275 2.58e+01 1b5tA c.1.23.1 29676 1yb5A 351 2.63e+01 1xfcA 384 2.64e+01 1ujqA 305 2.66e+01 c.1.12.7 99463 1li5A 461 2.67e+01 a.27.1.1,c.26.1.1 73912,73913 1nf3C 128 2.70e+01 b.36.1.1 85596 1ako 268 2.73e+01 1ako d.151.1.1 41779 1n2zA 245 2.73e+01 c.92.2.2 79865 1cp2A 269 2.78e+01 1cp2A c.37.1.10 32269 2gzqA 200 2.81e+01 1rxyA 253 2.81e+01 c.56.2.1 98065 1y10A 407 2.87e+01 1snnA 227 2.88e+01 d.115.1.2 105821 1s58A 554 2.93e+01 b.121.5.2 105262 1rhs 296 2.93e+01 1rhs c.46.1.2,c.46.1.2 32703,32704 1x7dA 350 2.93e+01 1up8A 598 2.94e+01 a.111.1.2 99710 1uf3A 228 2.96e+01 d.159.1.6 99317 1d7uA 433 3.00e+01 2dkb c.67.1.4 34439 1ps1A 337 3.03e+01 1ps1A a.128.1.4 19450 1o7jA 327 3.11e+01 c.88.1.1 81140 1ys7A 233 3.12e+01 1zbxB 141 3.13e+01 1erjA 393 3.15e+01 1erjA b.69.4.1 27660 1oqcA 125 3.17e+01 a.24.15.1 87264 1hp5A 512 3.19e+01 1hp4A c.1.8.6,d.92.2.1 61113,61114 1yxyA 234 3.23e+01 1z41A 338 3.24e+01 1li5B 461 3.26e+01 a.27.1.1,c.26.1.1 73914,73915 1gp6A 356 3.27e+01 b.82.2.1 65441 1wpaA 114 3.32e+01 1oi7A 288 3.32e+01 c.2.1.8,c.23.4.1 87049,87050 1j8yF 297 3.34e+01 1ng1 a.24.13.1,c.37.1.10 62747,62748 2dkb 433 3.38e+01 2dkb c.67.1.4 34438 2awpA 198 3.48e+01 2cb2A 318 3.48e+01 1hyvA 166 3.48e+01 1b9dA c.55.3.2 61424 1pdo 135 3.61e+01 1pdo c.54.1.1 33376 1tiqA 180 3.61e+01 d.108.1.1 107010 1gewA 356 3.62e+01 1gewA c.67.1.1 60470 1neyA 247 3.67e+01 c.1.1.1 80449 1nvmA 345 3.69e+01 a.5.7.1,c.1.10.5 86249,86250 2bjvA 265 3.69e+01 1jakA 512 3.70e+01 c.1.8.6,d.92.2.1 66472,66473 1itg 166 3.73e+01 1b9dA c.55.3.2 33661 1h7cA 108 3.77e+01 a.7.5.1 70914 1ad2 228 3.77e+01 1ad2 e.24.1.1 43353 1zq4A 693 3.78e+01 1w36B 1180 3.97e+01 1mk4A 157 4.00e+01 d.108.1.1 84979 1nh1A 330 4.05e+01 e.45.1.1 91871 1fgs 428 4.11e+01 1fgs c.59.1.2,c.72.2.2 33959,34962 1e8gA 560 4.20e+01 1qltA d.58.32.1,d.145.1.1 39455,41718 1vgwA 231 4.22e+01 c.68.1.13 100612 1q4mA 221 4.22e+01 a.132.1.3 95805 1mumA 295 4.33e+01 c.1.12.7 85108 1bu6O 501 4.35e+01 1glcG c.55.1.4,c.55.1.4 33499,33500 1j33A 335 4.36e+01 c.39.1.1 77069 1mnaA 298 4.38e+01 c.69.1.22 79322 1yixA 265 4.39e+01 1whbA 157 4.42e+01 1uufA 369 4.44e+01 b.35.1.2,c.2.1.1 100006,100007 1gox 370 4.51e+01 1gox c.1.4.1 28607 1w8sA 263 4.55e+01 2g8mA 264 4.59e+01 1rxxA 421 4.60e+01 d.126.1.4 98061 4ubpB 126 4.61e+01 1ubpB b.85.3.1 28345 1gveA 327 4.62e+01 c.1.7.1 70597 1t2bA 397 4.63e+01 1ujpA 271 4.63e+01 c.1.2.4 99462 1yy5B 513 4.71e+01 1fqiA 147 4.77e+01 1agrE a.91.1.1 18542 1xtpA 254 4.80e+01 1wx1A 335 4.88e+01 2atpB 115 4.89e+01 1ca1 370 4.90e+01 1ca1 a.124.1.1,b.12.1.3 19340,23648 1whuA 104 4.90e+01 1tedA 393 4.96e+01 c.95.1.2 106807 2g8oA 264 5.00e+01 2aa4A 289 5.00e+01 2a6hA 315 5.03e+01 1h7sA 365 5.12e+01 d.14.1.3,d.122.1.2 65705,65706 1rw2A 152 5.19e+01 a.118.19.1 97961 2a4aA 281 5.22e+01 1vr5A 547 5.25e+01 2bepA 159 5.29e+01 1l0gA 358 5.31e+01 e.3.1.1 73400 1d0vA 356 5.33e+01 1d0vA c.39.1.1 32476 1hdoA 206 5.33e+01 1he2A c.2.1.2 60965 1fmjA 351 5.37e+01 c.37.1.5 59879 1fo0A 116 5.39e+01 1tvdA b.1.1.1 20610 1qqqA 264 5.39e+01 1bkpA d.117.1.1 40931 1kllA 130 5.46e+01 d.32.1.2 72720 2a9gA 418 5.47e+01 1lx7A 253 5.54e+01 c.56.2.1 74329 1pytA 94 5.58e+01 1pytA d.58.3.1 39064 1ojxA 263 5.61e+01 c.1.10.1 93164 1omiA 248 5.63e+01 b.82.3.3,a.4.5.4 87079,87080 1ujnA 348 5.65e+01 e.22.1.1 99460 2fsxA 148 5.73e+01 1rqbA 539 5.74e+01 a.5.7.2,c.1.10.5 105057,105058 1sjwA 144 5.83e+01 d.17.4.9 98899 1vefA 395 5.87e+01 1ac5 483 5.88e+01 1ac5 c.69.1.5 34653 1a8s 273 5.91e+01 1brt c.69.1.12 34710 1gqnA 252 5.91e+01 c.1.10.1 90514 1sotA 320 5.96e+01 b.36.1.4,b.47.1.1 105852,105853 1lbeA 258 5.96e+01 1lbeA e.4.1.1 42773 1vrbA 342 5.98e+01 1y44A 320 5.99e+01 1yo8A 634 6.13e+01 1mswD 883 6.14e+01 e.8.1.3 79427 1xg4A 295 6.16e+01 1fp2A 352 6.22e+01 1fpxA a.4.5.29,c.66.1.12 59941,59942 1koqA 253 6.25e+01 2cba b.74.1.1 27964 2bgcA 238 6.33e+01 1evfA 264 6.35e+01 1bkpA d.117.1.1 40932 1d2mA 665 6.37e+01 1d2mA c.37.1.19,c.37.1.19 32417,32418 1vzoA 355 6.39e+01 d.144.1.7 108971 1x6iA 91 6.41e+01 1j79A 347 6.42e+01 1j79A c.1.9.4 62675 2fl7A 232 6.44e+01 1xawA 140 6.47e+01 1go3F 107 6.48e+01 a.60.8.2 65407 1wc3A 219 6.49e+01 1zkpA 268 6.50e+01 1p7gA 222 6.54e+01 a.2.11.1,d.44.1.1 94223,94224 1kb9D 246 6.62e+01 a.3.1.3,f.23.11.1 77317,77318 1q7zA 566 6.65e+01 c.1.21.2,c.1.26.1 96090,96091 1fg7A 356 6.66e+01 1gewA c.67.1.1 59819 1f61A 429 6.69e+01 1dquA c.1.12.7 29319 1o12A 376 6.73e+01 b.92.1.5,c.1.9.10 80758,80759 2cw6A 298 6.78e+01 1je5A 206 6.79e+01 1je5A b.40.4.7 62909 2bjnA 160 6.84e+01 1l5oA 356 6.85e+01 c.39.1.1 77711 1j8mF 297 6.90e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 1t0iA 191 6.92e+01 c.23.5.4 106209 1vrtA 560 6.93e+01 1rthA c.55.3.1,e.8.1.2 33574,43023 1wwbX 103 6.98e+01 1wwcA b.1.1.4 21777 1f8mA 429 6.99e+01 1dquA c.1.12.7 29315 1qfeA 252 7.03e+01 1qfeA c.1.10.1 29167 1pi4A 358 7.06e+01 e.3.1.1 94700 1dqiA 124 7.15e+01 1do6A b.1.13.1 22357 1c02A 166 7.21e+01 1qspA a.24.10.2 16633 1g6oA 330 7.22e+01 1g6oA c.37.1.11 32430 3rubS 123 7.23e+01 1rboC d.73.1.1 39616 1sz6A 249 7.31e+01 1g4yR 148 7.33e+01 1cll a.39.1.5 60252 1w34A 304 7.36e+01 1p4oA 322 7.36e+01 d.144.1.7 87775 1xuqA 212 7.40e+01 1k24A 253 7.40e+01 f.4.4.2 72002 1ii2A 524 7.42e+01 c.91.1.1,c.109.1.1 66146,66147 1rsgA 516 7.44e+01 1l9xA 315 7.44e+01 c.23.16.1 73762 1f5nA 592 7.45e+01 1dg3A a.114.1.1,c.37.1.8 19077,32152 2f2gA 221 7.45e+01 1xmiA 291 7.48e+01 1q1fA 151 7.54e+01 a.1.1.2 104476 1ezvD 245 7.60e+01 1be3D a.3.1.3,f.23.11.1 59546,59547 1rthA 560 7.69e+01 1rthA c.55.3.1,e.8.1.2 33576,43028 1puiA 210 7.72e+01 c.37.1.8 88292 1uddA 226 7.77e+01 a.132.1.3 107776 1rgyA 360 7.77e+01 e.3.1.1 97456 1s57A 153 7.86e+01 1kpgA 287 7.97e+01 c.66.1.18 68735 1vp7A 100 8.05e+01 2ajtA 500 8.08e+01 1qf5A 431 8.16e+01 1adeA c.37.1.10 32212 2fhqA 141 8.19e+01 1kyfA 247 8.34e+01 b.1.10.1,d.105.1.1 73220,73221 1jj2F 119 8.36e+01 1ffkE d.79.3.1 63091 2cxxA 190 8.41e+01 1qtsA 247 8.54e+01 1qtsA b.1.10.1,d.105.1.1 22313,40789 1ei6A 406 8.58e+01 c.76.1.4 90443 1xvqA 175 8.67e+01 2calA 154 8.71e+01 1qo7A 394 8.72e+01 1qo7A c.69.1.11 34697 1iw0A 215 8.74e+01 a.132.1.1 83720 2ffyA 358 8.74e+01 1tvkA 440 8.76e+01 c.32.1.1,d.79.2.1 107362,107363 2ae0X 345 8.78e+01 1lrwA 600 8.78e+01 b.70.1.1 91111 2g8lA 299 8.82e+01 1yqyA 523 8.83e+01 1fsyA 358 8.97e+01 1gceA e.3.1.1 60016