# List of top-scoring protein chains for t2k-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 2g03A 194 3.89e-18 2f6sA 201 2.58e-17 1d5rA 324 8.61e-02 1d5rA b.7.1.1,c.45.1.1 23181,32697 2d2mB 142 8.36e-01 1e2aA 105 1.22e+00 1e2aA a.7.2.1 16322 2e2aA 105 1.62e+00 a.7.2.1 88499 1sxjE 354 3.01e+00 a.80.1.1,c.37.1.20 106089,106090 1nh1A 330 3.07e+00 e.45.1.1 91871 2avpA 70 3.15e+00 1y1xA 191 3.17e+00 1na3A 91 3.33e+00 k.38.1.1 85481 1fvrA 327 3.74e+00 d.144.1.7 60047 1vf1A 229 4.69e+00 1xxqA 161 4.85e+00 1d4fA 431 5.44e+00 1b3rA c.2.1.4,c.23.12.3 30110,31370 1rypG 244 6.11e+00 d.153.1.4 41938 2d0sA 79 6.74e+00 1ie9A 259 6.75e+00 1db1A a.123.1.1 62318 1aerB 195 7.27e+00 1aerA d.166.1.1 42250 1fsgA 233 8.35e+00 1qk3A c.61.1.1 34029 2ew8A 249 8.51e+00 1mkp 144 8.56e+00 1vhrA c.45.1.1 32654 1aerA 205 8.89e+00 1aerA d.166.1.1 42249 1dmaA 214 9.01e+00 1aerA d.166.1.1 42251 1a0p 290 9.20e+00 1a0p a.60.9.1,d.163.1.1 18105,42165 1v5xA 203 9.29e+00 c.1.2.4 100377 1qk3A 233 9.44e+00 1qk3A c.61.1.1 34031 3pflA 759 9.99e+00 1cm5A c.7.1.1 30673 1m0uA 249 1.01e+01 a.45.1.1,c.47.1.5 78359,78360 1tuwA 109 1.02e+01 d.58.4.8 107346 1h16A 759 1.03e+01 c.7.1.1 76462 1vprA 374 1.05e+01 1gadO 330 1.08e+01 1dssG c.2.1.3,d.81.1.1 29950,39865 1v9sA 208 1.10e+01 2ffuA 501 1.10e+01 1s95A 333 1.11e+01 d.159.1.3 105375 1o1zA 234 1.14e+01 c.1.18.3 86555 1ayg 80 1.15e+01 451c a.3.1.1 15831 2phh 394 1.15e+01 1pbe c.3.1.2,d.16.1.2 30353,37884 1f52A 468 1.16e+01 1lgr d.15.9.1,d.128.1.1 37839,41169 1rkbA 173 1.24e+01 1xqiA 195 1.26e+01 2d27A 149 1.29e+01 1lgr 468 1.29e+01 1lgr d.15.9.1,d.128.1.1 37837,41167 1w6uA 302 1.30e+01 1fus 106 1.31e+01 9rnt d.1.1.4 36050 1dbrA 231 1.31e+01 1qk3A c.61.1.1 34041 1jotA 133 1.33e+01 1jotA 1b3rA 431 1.43e+01 1b3rA c.2.1.4,c.23.12.3 30106,31366 1cnv 299 1.45e+01 1cnv c.1.8.5 28989 1db1A 259 1.45e+01 1db1A a.123.1.1 19329 2lgsA 468 1.49e+01 1lgr d.15.9.1,d.128.1.1 37838,41168 1zx0A 236 1.50e+01 2awdA 323 1.54e+01 1qqeA 292 1.56e+01 1qqeA a.118.8.1 19210 1fcdA 401 1.56e+01 1fcdA c.3.1.5,c.3.1.5,d.87.1.1 30593,30594,40218 1pbe 394 1.56e+01 1pbe c.3.1.2,d.16.1.2 30338,37869 2g7jA 124 1.59e+01 2pflA 759 1.60e+01 1cm5A c.7.1.1 30675 1b48A 221 1.61e+01 1pgtA a.45.1.1,c.47.1.5 17703,32997 1j3bA 529 1.61e+01 c.91.1.1,c.109.1.1 77071,77072 2f02A 323 1.63e+01 2h6bA 250 1.70e+01 1r03A 182 1.76e+01 a.25.1.1 104675 1qk4A 233 1.77e+01 1qk3A c.61.1.1 34037 1bed 181 1.79e+01 1fvkA c.47.1.13 90330 1d3uA 181 1.80e+01 1ytbA d.129.1.1,d.129.1.1 41290,41291 1bkb 136 1.87e+01 1bkb b.34.5.2,b.40.4.5 24609,25341 1bgj 394 1.89e+01 1pbe c.3.1.2,d.16.1.2 30352,37883 1cm5A 759 1.89e+01 1cm5A c.7.1.1 30671 1gks 78 1.89e+01 1cc5 a.3.1.1 15909 1xwfA 431 1.91e+01 1q77A 138 1.95e+01 c.26.2.4 96023 1vmeA 410 2.01e+01 c.23.5.1,d.157.1.3 108893,108894 1ikpA 613 2.11e+01 b.29.1.7,d.166.1.1,f.1.5.1 66182,66183,66184 1k0iA 394 2.13e+01 c.3.1.2,d.16.1.2 67942,67943 1fgyA 127 2.15e+01 1faoA b.55.1.1 26976 1x6oA 174 2.16e+01 b.34.5.2,b.40.4.5 109493,109494 1s9rA 410 2.18e+01 d.126.1.4 98758 1y51A 88 2.20e+01 1ckiA 317 2.29e+01 1csn d.144.1.7 41660 1txjA 171 2.36e+01 b.88.1.2 107424 1fjcA 96 2.37e+01 1fjcA d.58.7.1 39212 1y5eA 169 2.37e+01 1ykjA 394 2.38e+01 3cla 213 2.52e+01 3cla c.43.1.1 32610 1aw1A 256 2.56e+01 1amk c.1.1.1 28515 1cj3A 392 2.62e+01 1pbe c.3.1.2,d.16.1.2 30347,37878 1iarB 207 2.62e+01 1iarB b.1.2.1,b.1.2.1 22037,22038 2aaoA 166 2.70e+01 1aw2A 256 2.74e+01 1amk c.1.1.1 28523 1zk8A 183 2.75e+01 1mwwA 128 2.81e+01 d.80.1.4 91483 1aisA 182 2.83e+01 1ytbA d.129.1.1,d.129.1.1 41288,41289 1hkvA 453 2.86e+01 b.49.2.3,c.1.6.1 83559,83560 1qv9A 283 2.88e+01 c.127.1.1 96356 1qhtA 775 2.89e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 2fswA 107 3.05e+01 1otfA 62 3.05e+01 1otfA d.80.1.1 39820 1yirA 408 3.08e+01 1a70 97 3.10e+01 1awd d.15.4.1 37678 1lxyA 409 3.13e+01 d.126.1.4 91154 1cr0A 296 3.18e+01 1cr1A c.37.1.11 32287 2ajrA 331 3.24e+01 1buqA 125 3.31e+01 1opy d.17.4.3 38111 2iw2A 494 3.31e+01 1bupA 386 3.31e+01 1ba1 c.55.1.1,c.55.1.1 33377,33378 1r2rA 248 3.33e+01 c.1.1.1 96875 2f06A 144 3.33e+01 1hpm 386 3.35e+01 1ba1 c.55.1.1,c.55.1.1 33381,33382 1y0nA 78 3.36e+01 1cr1A 296 3.49e+01 1cr1A c.37.1.11 32286 1bbhA 131 3.54e+01 1bbhA a.24.3.2 16546 1kay 381 3.57e+01 1ba1 c.55.1.1,c.55.1.1 33385,33386 1jacA 133 3.59e+01 1jotA 2fha 183 3.62e+01 2fha a.25.1.1 16674 1d9tA 289 3.67e+01 1deaA 1ba1 386 3.69e+01 1ba1 c.55.1.1,c.55.1.1 33387,33388 1xgwA 176 3.73e+01 1ats 386 3.74e+01 1ba1 c.55.1.1,c.55.1.1 33423,33424 1rom 403 3.75e+01 1rom a.104.1.1 18963 1tgoA 773 3.78e+01 1tgoA c.55.3.5,e.8.1.1 33721,43010 2dh4A 340 3.82e+01 1jwgA 147 3.85e+01 a.118.9.2 71911 1rm4A 337 3.85e+01 c.2.1.3,d.81.1.1 105000,105001 1ne7A 289 3.85e+01 c.124.1.1 91833 1gqyA 475 3.86e+01 c.5.1.1,c.59.1.1,c.72.2.1 83305,83306,83307 1m26A 133 3.86e+01 1ae1A 273 3.88e+01 1bdb c.2.1.2 29943 1nfvA 179 3.89e+01 a.25.1.1 85642 1jacC 133 3.93e+01 1jotA 1pczA 191 4.01e+01 1ytbA d.129.1.1,d.129.1.1 41292,41293 1tueA 212 4.01e+01 c.37.1.20 107323 1fm0E 150 4.02e+01 1fmaE d.41.5.1 38629 1vlbA 907 4.12e+01 a.56.1.1,d.15.4.2,d.41.1.1,d.133.1.1 108739,108740,108741,108742 1hlrA 907 4.12e+01 1ea2A 131 4.17e+01 d.17.4.3 64860 2gb7A 305 4.20e+01 1ku8A 133 4.22e+01 1yyaA 250 4.24e+01 1ab6A 125 4.24e+01 3chy c.23.1.1 31054 1atr 386 4.28e+01 1ba1 c.55.1.1,c.55.1.1 33421,33422 1wfdA 93 4.30e+01 1senA 164 4.30e+01 c.47.1.1 105465 1rr7A 129 4.33e+01 a.4.1.14 105075 2citA 282 4.35e+01 1fha 183 4.50e+01 2fha a.25.1.1 16675 1i45A 248 4.51e+01 1amk c.1.1.1 61665 1bmbA 123 4.52e+01 1griA d.93.1.1 40466 1fmaE 150 4.59e+01 1fmaE d.41.5.1 38630 1n2zA 245 4.60e+01 c.92.2.2 79865 1f2tA 149 4.65e+01 1f2tA c.37.1.12 32373 1cmnA 402 4.71e+01 1rom a.104.1.1 18958 3chy 128 4.78e+01 3chy c.23.1.1 31038 1xe7A 203 4.80e+01 1ab5A 125 4.87e+01 3chy c.23.1.1 31056 1oktA 211 4.88e+01 a.45.1.1,c.47.1.5 93272,93273 1ovlA 271 4.88e+01 a.123.1.1 87455 1v37A 177 4.89e+01 1jbeA 128 4.94e+01 3chy c.23.1.1 62845 1j5yA 187 4.95e+01 a.4.5.1,d.94.2.1 71592,71593 1uwvA 433 4.96e+01 b.40.4.12,c.66.1.40 100128,100129 1h96A 182 4.98e+01 2fha a.25.1.1 60811 1ocvA 125 5.00e+01 d.17.4.3 86810 1uwsA 489 5.12e+01 c.1.8.4 108073 1lb3A 182 5.12e+01 a.25.1.1 77873 1tpfA 250 5.14e+01 1amk c.1.1.1 28467 2b3oA 532 5.15e+01 2glsA 470 5.23e+01 1lgr d.15.9.1,d.128.1.1 37851,41181 1f24A 402 5.27e+01 1rom a.104.1.1 18953 1nepA 130 5.29e+01 b.1.18.7 80440 1ghhA 81 5.32e+01 1ghhA d.57.1.1 38940 1vchA 175 5.33e+01 8cho 125 5.34e+01 1opy d.17.4.3 38108 1ohpA 125 5.37e+01 1gjxA 81 5.42e+01 b.84.1.1 65222 1dat 174 5.42e+01 2fha a.25.1.1 16677 1ukz 203 5.46e+01 1zin c.37.1.1 31840 1jfbA 404 5.46e+01 a.104.1.1 66624 1onrA 316 5.47e+01 1onrA c.1.10.1 29169 1g8iA 190 5.50e+01 1rec a.39.1.5 60363 1ugxA 133 5.50e+01 1o0pA 104 5.51e+01 d.58.7.1 86535 1qjgA 125 5.58e+01 1opy d.17.4.3 38102 1i8fA 81 5.61e+01 1i8fA b.38.1.1 61959 1tsm 316 5.62e+01 1bkpA d.117.1.1 41024 2dbbA 151 5.63e+01 1se9A 126 5.75e+01 d.15.1.1 98821 2bsjA 133 5.76e+01 2abwA 227 5.76e+01 1p9qC 256 5.79e+01 a.5.8.1,d.235.1.2,d.58.11.3 104093,104094,104095 2gp5A 349 5.86e+01 1i2oA 316 5.87e+01 1onrA c.1.10.1 61574 2cdqA 510 5.87e+01 2ah5A 210 5.88e+01 2bszA 278 5.89e+01 1ig0A 319 5.90e+01 1ig0A b.82.6.1,c.100.1.1 62354,62355 1g31A 111 5.91e+01 1g31A b.35.1.1 24656 1lufA 343 5.93e+01 d.144.1.7 78223 1r26A 125 5.95e+01 c.47.1.1 96847 1q6aA 107 5.96e+01 a.186.1.1 95966 2evrA 246 5.99e+01 2bv9A 290 6.00e+01 1gakA 141 6.01e+01 1gakA a.19.1.1 16415 1bkrA 109 6.02e+01 1bkrA a.40.1.1 17394 1r0dA 206 6.02e+01 a.216.1.1 104715 2f22A 144 6.03e+01 1wcrA 103 6.03e+01 1a7aA 432 6.04e+01 1b3rA c.2.1.4,c.23.12.3 30104,31364 1at0 145 6.06e+01 1at0 b.86.1.1 28374 1yuzA 202 6.15e+01 2bptA 861 6.21e+01 1gulA 222 6.28e+01 1pgtA a.45.1.1,c.47.1.5 17675,32969 1jkeA 145 6.30e+01 c.110.1.1 66791 1xw4X 110 6.42e+01 1rkxA 357 6.43e+01 c.2.1.2 97631 1top 162 6.47e+01 1ncx a.39.1.5 17223 1ryp2 233 6.48e+01 1ryp2 1li4A 432 6.54e+01 c.2.1.4,c.23.12.3 84616,84617 1aew 174 6.56e+01 2fha a.25.1.1 16676 1mzgA 146 6.59e+01 d.224.1.1 79696 1z3eA 132 6.59e+01 1zd0A 150 6.62e+01 2a7kA 250 6.63e+01 1gowA 489 6.67e+01 1qvbA c.1.8.4 28981 1jbwA 428 6.79e+01 c.59.1.2,c.72.2.2 62860,62861 1mhqA 148 6.81e+01 a.118.9.2 84973 1ul7A 102 6.83e+01 d.129.6.1 99540 1w0hA 204 6.85e+01 1v7bA 185 6.90e+01 1i1sA 96 6.91e+01 1bjaA a.4.5.9 16124 1kyqA 274 7.03e+01 c.2.1.11,e.37.1.1 73281,73282 1t0qB 330 7.04e+01 a.25.1.2 106221 1ncx 162 7.04e+01 1ncx a.39.1.5 17222 1hz4A 373 7.11e+01 a.118.8.2 65960 1auoA 218 7.15e+01 1auoA c.69.1.14 34716 1u2xA 474 7.20e+01 c.72.1.3 107622 1pxgA 382 7.21e+01 c.1.20.1 95287 1bc9 200 7.25e+01 1pbv a.118.3.1 19180 2aawA 222 7.28e+01 1dgfA 497 7.29e+01 1cf9A e.5.1.1 42782 2ar0A 541 7.40e+01 1pu6A 218 7.46e+01 a.96.1.5 95123 1j1uA 306 7.48e+01 c.26.1.1 83980 1u46A 291 7.55e+01 d.144.1.7 107656 8rucI 123 7.59e+01 1rboC d.73.1.1 39629 1n55A 251 7.62e+01 c.1.1.1 80007 1t6sA 162 7.63e+01 1g0u1 266 7.63e+01 1us8A 147 7.68e+01 c.37.1.12 99859 1ji6A 589 7.69e+01 b.18.1.3,b.77.2.1,f.1.3.1 63066,63067,63068 1i4yA 114 7.74e+01 2mhr a.24.4.1 61738 1y9uA 323 7.76e+01 1usmA 80 7.81e+01 d.74.1.1 99876 2fwkA 121 7.84e+01 1v2zA 111 7.89e+01 a.186.1.1 108300 1whrA 124 8.02e+01 1n2aA 201 8.15e+01 a.45.1.1,c.47.1.5 91553,91554 2g3kA 94 8.19e+01 1kshA 186 8.21e+01 c.37.1.8 72914 1q7sA 117 8.25e+01 c.131.1.1 96055 1kepA 348 8.31e+01 c.2.1.2 68536 2b7kA 200 8.32e+01 7timA 247 8.33e+01 1amk c.1.1.1 28457 3timA 250 8.34e+01 1amk c.1.1.1 28483 2gshA 414 8.35e+01 1kq8A 100 8.46e+01 a.4.5.14 68797 1i7xB 151 8.46e+01 1i7xB j.71.1.1 61914 1g8oA 310 8.47e+01 1g8oA c.68.1.9 60375 1rboC 123 8.48e+01 1rboC d.73.1.1 39634 1a4uA 254 8.53e+01 1b16A c.2.1.2 29878 3sgbI 56 8.57e+01 2ovo g.68.1.1 44679 1gd9A 389 8.59e+01 c.67.1.1 60454 1pud 386 8.59e+01 1pud c.1.20.1 29658 1t95A 240 8.60e+01 a.5.8.1,d.235.1.2,d.58.11.3 106705,106706,106707 1dulA 69 8.65e+01 1dulA a.36.1.1 17121 2c7xA 436 8.69e+01 1odoA 408 8.73e+01 a.104.1.1 92783 1pveA 72 8.76e+01 a.189.1.1 104322 1no1A 126 8.77e+01 a.179.1.1 85913 1u00A 227 8.81e+01 1xw3A 110 8.82e+01 1neyA 247 8.82e+01 c.1.1.1 80449 1o0yA 260 8.84e+01 c.1.10.1 80756 1j2zA 270 8.95e+01 b.81.1.1 90805 1eyhA 144 8.96e+01 1eduA a.118.9.1 19214