# 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 5.43e-20 2f6sA 201 1.63e-19 1d5rA 324 3.64e-02 1d5rA b.7.1.1,c.45.1.1 23181,32697 1e2aA 105 2.84e-01 1e2aA a.7.2.1 16322 2e2aA 105 3.38e-01 a.7.2.1 88499 1sxjE 354 4.20e-01 a.80.1.1,c.37.1.20 106089,106090 1bupA 386 7.76e-01 1ba1 c.55.1.1,c.55.1.1 33377,33378 1bn7A 294 9.16e-01 1bn6A c.69.1.8 34677 1qv1A 195 9.45e-01 a.39.1.5 96347 1bn6A 294 9.74e-01 1bn6A c.69.1.8 34678 1kay 381 1.00e+00 1ba1 c.55.1.1,c.55.1.1 33385,33386 1cqwA 295 1.02e+00 1b6g c.69.1.8 34679 1atr 386 1.09e+00 1ba1 c.55.1.1,c.55.1.1 33421,33422 1hpm 386 1.13e+00 1ba1 c.55.1.1,c.55.1.1 33381,33382 1f0jA 377 1.15e+00 1f0jA a.211.1.2 19346 1ba1 386 1.40e+00 1ba1 c.55.1.1,c.55.1.1 33387,33388 1ats 386 1.44e+00 1ba1 c.55.1.1,c.55.1.1 33423,33424 1aerA 205 1.78e+00 1aerA d.166.1.1 42249 1jf2A 195 2.04e+00 1ej3A a.39.1.5 62930 1ea2A 131 2.14e+00 d.17.4.3 64860 1d4fA 431 2.25e+00 1b3rA c.2.1.4,c.23.12.3 30110,31370 1vf1A 229 2.30e+00 1o1zA 234 2.82e+00 c.1.18.3 86555 2bh7A 261 3.00e+00 2d2mB 142 3.09e+00 1el4A 195 3.29e+00 1ej3A a.39.1.5 59453 1cv2A 296 3.29e+00 1bn6A c.69.1.8 34680 2bgxA 261 3.61e+00 1wddS 128 3.87e+00 1jf0A 195 3.90e+00 1ej3A a.39.1.5 62926 1aerB 195 4.04e+00 1aerA d.166.1.1 42250 2avpA 70 4.12e+00 1iz7A 295 4.31e+00 c.69.1.8 76982 2gupA 292 4.58e+00 2shpA 525 4.76e+00 2shpA c.45.1.2,d.93.1.1,d.93.1.1 32683,40533,40534 1nj4A 363 4.78e+00 b.105.1.1,e.3.1.1 80545,80546 1dmaA 214 4.91e+00 1aerA d.166.1.1 42251 1na3A 91 4.98e+00 k.38.1.1 85481 1hd8A 363 5.38e+00 b.105.1.1,e.3.1.1 65803,65804 1y1xA 191 5.43e+00 1wcrA 103 5.49e+00 1b3rA 431 5.55e+00 1b3rA c.2.1.4,c.23.12.3 30106,31366 1v5xA 203 5.78e+00 c.1.2.4 100377 2ffuA 501 5.94e+00 1ny1A 240 6.16e+00 c.6.2.3 86395 1mj5A 302 6.95e+00 c.69.1.8 91285 1y5eA 169 6.97e+00 1h7sA 365 7.01e+00 d.14.1.3,d.122.1.2 65705,65706 1ydhA 216 7.38e+00 1hkvA 453 7.42e+00 b.49.2.3,c.1.6.1 83559,83560 1opy 131 7.98e+00 1opy d.17.4.3 38113 2f22A 144 8.02e+00 1b48A 221 8.06e+00 1pgtA a.45.1.1,c.47.1.5 17703,32997 1rr7A 129 8.09e+00 a.4.1.14 105075 1neiA 60 8.32e+00 d.253.1.1 91843 1nzoA 363 8.33e+00 b.105.1.1,e.3.1.1 92383,92384 1z6fA 363 8.65e+00 1dmmA 131 8.71e+00 1opy d.17.4.3 38114 1xwfA 431 8.86e+00 1oh0A 131 8.87e+00 d.17.4.3 87004 1zk8A 183 9.94e+00 2b3oA 532 1.04e+01 1y2kA 349 1.06e+01 1aw1A 256 1.09e+01 1amk c.1.1.1 28515 1gadO 330 1.10e+01 1dssG c.2.1.3,d.81.1.1 29950,39865 1xxaA 78 1.16e+01 1xxaA d.74.2.1 39700 1ikpA 613 1.18e+01 b.29.1.7,d.166.1.1,f.1.5.1 66182,66183,66184 1tbbA 332 1.28e+01 a.211.1.2 106741 1z3eA 132 1.34e+01 1xxcA 78 1.37e+01 1xxaA d.74.2.1 39712 1xo0A 324 1.41e+01 1hlrA 907 1.46e+01 1vlbA 907 1.46e+01 a.56.1.1,d.15.4.2,d.41.1.1,d.133.1.1 108739,108740,108741,108742 2iw2A 494 1.47e+01 1aw2A 256 1.48e+01 1amk c.1.1.1 28523 1dqrA 557 1.54e+01 1dqrA c.80.1.2 35305 1a7aA 432 1.54e+01 1b3rA c.2.1.4,c.23.12.3 30104,31364 3crxA 343 1.55e+01 4crxA a.60.9.1,d.163.1.1 18101,42161 1li4A 432 1.56e+01 c.2.1.4,c.23.12.3 84616,84617 1xorA 349 1.56e+01 1nepA 130 1.56e+01 b.1.18.7 80440 2d0sA 79 1.60e+01 2ah5A 210 1.63e+01 1f44A 324 1.64e+01 a.60.9.1,d.163.1.1 64982,64983 1yuwA 554 1.66e+01 1r03A 182 1.68e+01 a.25.1.1 104675 1f2tA 149 1.69e+01 1f2tA c.37.1.12 32373 1xe7A 203 1.70e+01 1brlA 355 1.70e+01 1lucA c.1.16.1 29553 1m2oB 190 1.74e+01 c.37.1.8 78485 1r7lA 110 1.78e+01 d.277.1.1 104837 1uhkA 191 1.88e+01 487dH 224 1.92e+01 1ad2 i.1.1.2 45835 1ad2 228 1.94e+01 1ad2 e.24.1.1 43353 1il6 185 2.02e+01 1alu a.26.1.1 16827 1ecl 597 2.03e+01 1ecl e.10.1.1 43238 1wbsA 360 2.04e+01 1v9vA 114 2.06e+01 1v7rA 186 2.07e+01 c.51.4.1 100482 1ptmA 329 2.08e+01 c.77.1.3 95104 1us8A 147 2.08e+01 c.37.1.12 99859 1gulA 222 2.10e+01 1pgtA a.45.1.1,c.47.1.5 17675,32969 1ixxB 123 2.13e+01 1ixxB d.169.1.1 42336 1hywA 68 2.17e+01 1hywA d.186.1.1 61425 1kt8A 365 2.17e+01 e.17.1.1 77531 1rm4A 337 2.25e+01 c.2.1.3,d.81.1.1 105000,105001 1xg1A 67 2.34e+01 1crxA 322 2.34e+01 4crxA a.60.9.1,d.163.1.1 18097,42157 1fvrA 327 2.37e+01 d.144.1.7 60047 1tpfA 250 2.38e+01 1amk c.1.1.1 28467 1h96A 182 2.39e+01 2fha a.25.1.1 60811 1ie9A 259 2.45e+01 1db1A a.123.1.1 62318 1iba 101 2.51e+01 1iba d.95.1.1 40567 1gumA 222 2.55e+01 1pgtA a.45.1.1,c.47.1.5 17683,32977 2cxnA 557 2.58e+01 1ej3A 191 2.61e+01 1ej3A a.39.1.5 17259 1j2zA 270 2.64e+01 b.81.1.1 90805 1akz 223 2.66e+01 3eugA c.18.1.1 31007 1gupA 348 2.66e+01 1guqA d.13.1.2,d.13.1.2 37534,37535 1lb3A 182 2.67e+01 a.25.1.1 77873 1w78A 422 2.69e+01 1khyA 148 2.72e+01 a.174.1.1 77410 1u0fA 564 2.91e+01 4crxA 322 2.91e+01 4crxA a.60.9.1,d.163.1.1 18095,42155 1hm5A 558 2.92e+01 c.80.1.2 76717 1zz2A 360 2.92e+01 1q7sA 117 2.94e+01 c.131.1.1 96055 1kllA 130 3.01e+01 d.32.1.2 72720 1n55A 251 3.02e+01 c.1.1.1 80007 1aew 174 3.05e+01 2fha a.25.1.1 16676 1guqA 348 3.07e+01 1guqA d.13.1.2,d.13.1.2 37522,37523 1kbuA 349 3.09e+01 a.60.9.1,d.163.1.1 72284,72285 2a4xA 138 3.11e+01 1w0uA 55 3.12e+01 1dat 174 3.20e+01 2fha a.25.1.1 16677 1j34B 123 3.20e+01 d.169.1.1 84049 1sspE 223 3.23e+01 3eugA c.18.1.1 31009 3eugA 229 3.24e+01 3eugA c.18.1.1 31018 1oktA 211 3.31e+01 a.45.1.1,c.47.1.5 93272,93273 1u9kA 114 3.33e+01 1z2lA 423 3.36e+01 1vchA 175 3.36e+01 2fha 183 3.38e+01 2fha a.25.1.1 16674 1yyaA 250 3.43e+01 1nozA 388 3.46e+01 1clqA c.55.3.5 33715 1ly7A 121 3.47e+01 d.82.2.1 74339 1wt9B 123 3.49e+01 1np7A 489 3.50e+01 a.99.1.1,c.28.1.1 80677,80678 1qqeA 292 3.56e+01 1qqeA a.118.8.1 19210 2bszA 278 3.59e+01 2d4rA 147 3.62e+01 1xxbA 78 3.63e+01 1xxaA d.74.2.1 39706 1rypG 244 3.66e+01 d.153.1.4 41938 1x7oA 287 3.70e+01 1avmA 201 3.88e+01 1avmA a.2.11.1,d.44.1.1 15782,38745 1rw6A 210 3.90e+01 a.47.4.1 105113 1bam 213 3.92e+01 1bam c.52.1.3 33285 1gqnA 252 3.95e+01 c.1.10.1 90514 1h5wA 309 3.98e+01 e.27.1.1 65635 1ha3A 405 4.08e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 2bhoA 130 4.13e+01 2a19A 175 4.17e+01 1ul7A 102 4.22e+01 d.129.6.1 99540 1smoA 119 4.22e+01 b.1.1.1 105764 1f5xA 208 4.22e+01 1f5xA a.87.1.1 18516 1k0iA 394 4.23e+01 c.3.1.2,d.16.1.2 67942,67943 1zboA 210 4.24e+01 1euiA 228 4.32e+01 3eugA c.18.1.1 31028 1j98A 157 4.36e+01 1j98A d.185.1.2 62755 2hbjA 410 4.37e+01 1amk 251 4.38e+01 1amk c.1.1.1 28503 1gkkA 297 4.41e+01 c.69.1.2 65248 1bgj 394 4.42e+01 1pbe c.3.1.2,d.16.1.2 30352,37883 1yo3A 102 4.42e+01 2phh 394 4.47e+01 1pbe c.3.1.2,d.16.1.2 30353,37884 1eg9A 449 4.48e+01 1ndoA b.33.1.2,d.129.3.3 24443,41322 1a8y 367 4.59e+01 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 1nwwA 149 4.65e+01 d.17.4.8 86306 1rtm1 149 4.67e+01 1rtm1 1b2vA 188 4.75e+01 1b2vA d.35.1.1 38532 1tq4A 413 4.81e+01 c.37.1.8 107201 1ekgA 127 4.88e+01 1dlxA d.82.2.1 40021 1pbe 394 4.89e+01 1pbe c.3.1.2,d.16.1.2 30338,37869 2bjcA 62 4.97e+01 1rboC 123 4.99e+01 1rboC d.73.1.1 39634 2c78A 405 5.01e+01 1obbA 480 5.01e+01 c.2.1.5,d.162.1.2 86760,86761 1eugA 229 5.09e+01 3eugA c.18.1.1 31021 1ykjA 394 5.12e+01 1yuzA 202 5.14e+01 1bsmA 201 5.17e+01 1avmA a.2.11.1,d.44.1.1 15780,38743 1i45A 248 5.19e+01 1amk c.1.1.1 61665 1fouA 309 5.22e+01 1fouA e.27.1.1 43364 1ub0A 258 5.22e+01 c.72.1.2 88394 1q87A 221 5.23e+01 e.47.1.1 96192 1kv5A 250 5.29e+01 c.1.1.1 73052 3timA 250 5.32e+01 1amk c.1.1.1 28483 1vp7A 100 5.34e+01 1iatA 557 5.39e+01 1dqrA c.80.1.2 62123 1uc8A 280 5.40e+01 c.30.1.6,d.142.1.7 99165,99166 1zzlA 351 5.41e+01 1rypA 243 5.42e+01 1pmaA d.153.1.4 41932 1y89A 238 5.46e+01 1th0A 226 5.51e+01 d.3.1.7 106903 1a4fA 141 5.54e+01 1abwA a.1.1.2 15394 1qqcA 773 5.57e+01 1tgoA c.55.3.5,e.8.1.1 33724,43013 1dk0A 188 5.57e+01 1b2vA d.35.1.1 38530 1fha 183 5.58e+01 2fha a.25.1.1 16675 1flzA 228 5.60e+01 3eugA c.18.1.1 31027 8rucI 123 5.63e+01 1rboC d.73.1.1 39629 1qfeA 252 5.66e+01 1qfeA c.1.10.1 29167 1afb1 154 5.76e+01 1rtm1 1exmA 405 5.81e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 1v63A 101 5.81e+01 a.21.1.1 108391 1l9wA 252 5.81e+01 c.1.10.1 84570 1ekfA 365 5.83e+01 1ekfA e.17.1.1 59445 1ht6A 405 5.83e+01 b.71.1.1,c.1.8.1 83629,83630 1byfA 125 5.83e+01 1byfA d.169.1.1 42419 1db1A 259 5.90e+01 1db1A a.123.1.1 19329 2gfsA 372 5.94e+01 1xdzA 240 6.03e+01 1dgnA 89 6.10e+01 1dgnA a.77.1.3 18436 1g8iA 190 6.10e+01 1rec a.39.1.5 60363 2a26A 50 6.10e+01 1h03P 125 6.19e+01 g.18.1.1,g.18.1.1 83411,83412 1a4eA 488 6.30e+01 1cf9A e.5.1.1 42806 1h05A 146 6.41e+01 c.23.13.1 76433 1o7nA 449 6.44e+01 b.33.1.2,d.129.3.3 81162,81163 1ys4A 354 6.51e+01 5nseA 444 6.55e+01 d.174.1.1 74644 1e7uA 961 6.60e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 1g0uG 252 6.61e+01 d.153.1.4 41952 2cq8A 110 6.72e+01 1lkkA 105 6.74e+01 1lckA d.93.1.1 40412 2bwvA 440 6.76e+01 2aawA 222 6.82e+01 1y9lA 115 6.90e+01 1jdhA 529 6.96e+01 a.118.1.1 66549 1wl9A 440 7.10e+01 1jvbA 347 7.10e+01 b.35.1.2,c.2.1.1 77181,77182 1wn2A 121 7.10e+01 1toh 343 7.11e+01 4pah d.178.1.1 42573 1s9rA 410 7.17e+01 d.126.1.4 98758 1i1gA 141 7.20e+01 a.4.5.32,d.58.4.2 65982,65983 1g0uE 234 7.26e+01 d.153.1.4 41950 1ka6A 128 7.26e+01 d.93.1.1 68370 1w2wA 211 7.27e+01 c.124.1.5 109130 1tlgA 125 7.33e+01 1byfA d.169.1.1 42421 1cj3A 392 7.34e+01 1pbe c.3.1.2,d.16.1.2 30347,37878 1buuA 168 7.42e+01 1rtm1 d.169.1.1,h.1.1.1 42366,45388 2bsjA 133 7.49e+01 1mioB 458 7.51e+01 1qguB c.92.2.3 35602 1ndoA 449 7.51e+01 1ndoA b.33.1.2,d.129.3.3 24444,41323 1ytw 306 7.57e+01 1ytw c.45.1.2 32689 1rkiA 102 7.62e+01 2gaxA 135 7.64e+01 1qghA 156 7.66e+01 1qghA a.25.1.1 16728 1g0uL 241 7.66e+01 d.153.1.4 41894 1eft 405 7.68e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25688,25728,32123 2gw2A 198 7.68e+01 1k8uA 90 7.74e+01 a.39.1.2 72181 2cmwA 310 7.78e+01 2aneA 125 7.87e+01 1wb4A 297 7.89e+01 1yt8A 539 7.93e+01 2g8lA 299 7.94e+01 1cs0B 382 7.94e+01 1c3oB c.8.3.1,c.23.16.1 30740,31417 3bamA 213 7.96e+01 1bam c.52.1.3 33288 1sl8A 191 8.05e+01 1ntvA 152 8.13e+01 b.55.1.2 86168 2aclB 244 8.16e+01 1s3cA 141 8.17e+01 1ytn 306 8.18e+01 1ytw c.45.1.2 32688 1p27B 106 8.20e+01 d.58.7.1 93908 7timA 247 8.23e+01 1amk c.1.1.1 28457 1b7dA 61 8.24e+01 1aho g.3.7.1 44139 3pflA 759 8.35e+01 1cm5A c.7.1.1 30673 2b4rO 345 8.39e+01 2gshA 414 8.46e+01 2fq3A 104 8.49e+01 1bmfA 510 8.51e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18281,26446,32326 1pt7A 437 8.71e+01 c.123.1.1 95093 2booA 247 8.73e+01 1v2zA 111 8.78e+01 a.186.1.1 108300 2bshA 125 8.81e+01 1r3cA 366 8.81e+01 d.144.1.7 96906 1u59A 287 8.83e+01 d.144.1.7 107681 1qhtA 775 8.85e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1t98A 287 8.95e+01 1gklA 297 8.96e+01 c.69.1.2 65250 1ukfA 188 8.99e+01 d.3.1.10 99488