# List of top-scoring protein chains for t2k-100-30-near-backbone-11 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 1dbuA 158 4.41e-20 1dbuA d.116.1.1 40930 1dbxA 158 4.50e-20 1dbuA d.116.1.1 40928 1vkiA 181 1.75e-13 1vjfA 180 8.06e-13 d.116.1.1 -10941 3grx 82 3.01e-02 1aba c.47.1.1 32769 1t1vA 93 6.33e-02 1o4vA 183 1.62e-01 c.23.8.1 86628 1rktA 205 1.66e-01 a.4.1.9 -210 a.121.1.1 -1663 1j0fA 100 1.93e-01 unknown_sccs -7483 2frvB 536 2.37e-01 1h2rL e.18.1.1 43291 1frvB 536 3.81e-01 1h2rL e.18.1.1 43296 1qgpA 77 4.50e-01 1qbjA a.4.5.19 16158 1qahA 136 5.68e-01 d.79.1.1 -10377 1qbjA 81 7.60e-01 1qbjA a.4.5.19 16155 1vgyA 393 7.74e-01 c.56.5.4 -7882 d.58.19.1 -10106 1l7mA 211 9.29e-01 c.108.1.4 73664 1oniA 137 1.18e+00 d.79.1.1 87144 1j97A 211 1.38e+00 1f5sA c.108.1.4 62753 1j0aA 325 1.49e+00 c.79.1.1 83871 1fpzA 212 1.51e+00 1fpzA c.45.1.1 59976 1pytA 94 1.60e+00 1pytA d.58.3.1 39064 2gbp 309 1.62e+00 1gca c.93.1.1 35657 1pamA 686 1.70e+00 1cxlA b.1.18.2 21846 b.3.1.1 22515 b.71.1.1 27753 c.1.8.1 28740 1vicA 262 1.84e+00 c.68.1.13 -8252 1mkmA 249 1.99e+00 a.4.5.33 79242 d.110.2.2 79243 1f5sA 211 2.05e+00 1f5sA c.108.1.4 59656 1nmeA 146 2.10e+00 c.17.1.1 85874 1evlA 401 2.13e+00 1qf6A c.51.1.1 33202 d.104.1.1 40751 1vjqA 79 2.17e+00 unknown_sccs -13478 1ng4A 390 2.53e+00 c.3.1.2 85666 d.16.1.3 85667 1lvaA 258 2.58e+00 a.4.5.35 74276 a.4.5.35 74277 a.4.5.35 74278 a.4.5.35 74279 1o6uA 403 2.58e+00 a.5.3.1 -366 unknown_sccs -3048 c.13.1.1 -6221 1ub0A 258 2.78e+00 c.72.1.2 88394 1f6bA 198 2.78e+00 c.37.1.8 64986 1tia 279 2.84e+00 3tgl c.69.1.17 34737 1pufB 73 2.85e+00 a.4.1.1 -192 1gca 309 3.05e+00 1gca c.93.1.1 35659 1qyaA 307 3.14e+00 1pauA 147 3.32e+00 1pauA c.17.1.1 30994 1b72B 87 3.61e+00 1akhA a.4.1.1 16001 1jqeA 292 3.66e+00 c.66.1.19 71789 1d4oA 184 3.70e+00 1d4oA c.31.1.4 31748 1cxlA 686 3.78e+00 1cxlA b.1.18.2 21829 b.3.1.1 22498 b.71.1.1 27736 c.1.8.1 28723 1d3cA 686 3.81e+00 1cxlA b.1.18.2 21827 b.3.1.1 22496 b.71.1.1 27734 c.1.8.1 28721 1qu9A 128 3.84e+00 1qu9A d.79.1.1 39755 1qu9C 128 3.84e+00 1qu9A d.79.1.1 39757 1nbwB 117 3.90e+00 c.51.3.2 80396 1eikA 77 3.95e+00 1eikA d.78.1.1 39751 1o2dA 371 4.00e+00 e.22.1.2 86591 1n5dA 288 4.16e+00 c.2.1.2 80030 1ot1A 686 4.20e+00 b.1.18.2 87392 b.3.1.1 87393 b.71.1.1 87394 c.1.8.1 87395 1gqoF 143 4.32e+00 c.23.13.1 76300 1or7A 194 4.32e+00 a.4.13.2 87332 a.177.1.1 87333 1rec 201 4.36e+00 1rec a.39.1.5 17326 1omrA 201 4.40e+00 a.39.1.5 -854 2sas 185 4.44e+00 2sas a.39.1.5 17258 1gqoM 143 4.47e+00 c.23.13.1 76307 1aba 87 4.66e+00 1aba c.47.1.1 32760 1mu5A 471 4.71e+00 a.156.1.3 79472 d.14.1.3 79473 d.122.1.2 79474 1vj1A 363 4.80e+00 b.35.1.2 -3728 c.2.1.1 -5752 1at1A 310 4.83e+00 3csuA c.78.1.1 35168 c.78.1.1 35169 1p9vA 310 5.03e+00 1sdjA 310 5.03e+00 d.21.1.2 -9420 d.21.1.2 -9421 1ekxA 311 5.19e+00 3csuA c.78.1.1 35088 c.78.1.1 35089 1hu4A 288 5.28e+00 1hu4A 1gqoC 143 5.32e+00 c.23.13.1 76297 1gqoS 143 5.33e+00 c.23.13.1 76313 1ngr 85 5.42e+00 1ngr a.77.1.2 18422 1ncx 162 5.52e+00 1ncx a.39.1.5 17222 1gqoL 143 5.55e+00 c.23.13.1 76306 1gqoK 143 5.61e+00 c.23.13.1 76305 1j5rA 371 5.73e+00 1st9A 143 5.78e+00 c.47.1.10 -7503 1o1zA 234 5.80e+00 c.1.18.3 86555 1gqoQ 143 5.82e+00 c.23.13.1 76311 1np6A 174 5.88e+00 c.37.1.10 85954 1gqoO 143 5.96e+00 c.23.13.1 76309 1akhA 61 6.04e+00 1akhA a.4.1.1 15980 1irxA 523 6.05e+00 a.97.1.2 71378 c.26.1.1 71379 1uetA 437 6.15e+00 unknown_sccs -1144 unknown_sccs -9798 unknown_sccs -10058 1gqoG 143 6.43e+00 c.23.13.1 76301 1gqoU 143 6.46e+00 c.23.13.1 76315 1kngA 156 6.63e+00 c.47.1.10 72777 2tct 207 6.68e+00 2tct a.4.1.9 16063 a.121.1.1 19240 1j9iA 68 6.74e+00 a.6.1.5 71619 1o7bT 98 6.77e+00 d.169.1.4 -11647 1gqoV 143 6.87e+00 c.23.13.1 76316 1top 162 6.98e+00 1ncx a.39.1.5 17223 1p9qC 256 7.47e+00 1gvfA 286 7.52e+00 c.1.10.2 70599 1fjlA 81 7.52e+00 2hddA a.4.1.1 16017 1gqoD 143 7.54e+00 c.23.13.1 76298 1bmfA 510 7.64e+00 1skyB a.69.1.1 18281 b.49.1.1 26446 c.37.1.11 32326 1cp3A 277 7.71e+00 1pauA c.17.1.1 30992 1whi 122 7.72e+00 1whi b.39.1.1 24810 5pal 109 7.73e+00 1a75A a.39.1.4 17215 1ddeA 338 7.82e+00 1dd9A e.13.1.1 43255 1t95A 240 7.97e+00 1in4A 334 7.99e+00 1hqcA a.4.5.11 62597 c.37.1.20 62598 1gqoT 143 8.06e+00 c.23.13.1 76314 1c4oA 664 8.43e+00 1d2mA c.37.1.19 32415 c.37.1.19 32416 1ul7A 102 8.43e+00 unknown_sccs -11020 1h75A 81 8.48e+00 1h75A c.47.1.1 60716 1e44A 85 8.67e+00 3eipA d.26.2.1 59219 1hnjA 317 8.85e+00 1hn9A c.95.1.1 35969 c.95.1.1 35970 1dgsA 667 8.86e+00 1dgsA a.60.2.2 17963 b.40.4.6 25365 d.142.2.2 41581 1gqoE 143 8.97e+00 c.23.13.1 76299 1s9uA 207 8.97e+00 1ckv 141 8.98e+00 1ckv d.137.1.1 41452 3csuA 310 9.04e+00 3csuA c.78.1.1 35094 c.78.1.1 35095 1auoA 218 9.19e+00 1auoA c.69.1.14 34716 1on2A 142 9.22e+00 a.4.5.24 87103 a.76.1.1 87104 1eblA 317 9.30e+00 1hn9A c.95.1.1 35973 c.95.1.1 35974 1du6A 64 9.60e+00 1akhA a.4.1.1 16002 3eipA 84 9.74e+00 3eipA d.26.2.1 38434 1h4vB 421 9.87e+00 1adjA c.51.1.1 60624 d.104.1.1 60625 1vhnA 318 9.88e+00 c.1.4.1 -5209 1adjA 421 9.96e+00 1adjA c.51.1.1 33188 d.104.1.1 40737 1d2mA 665 1.01e+01 1d2mA c.37.1.19 32417 c.37.1.19 32418 1hn9A 317 1.03e+01 1hn9A c.95.1.1 35977 c.95.1.1 35978 1m6nA 802 1.03e+01 a.162.1.1 78697 a.172.1.1 78698 c.37.1.19 78699 c.37.1.19 78700 1in6A 334 1.04e+01 1hqcA a.4.5.11 62601 c.37.1.20 62602 1iioA 84 1.06e+01 a.39.4.1 66150 3tgl 269 1.07e+01 3tgl c.69.1.17 34733 1nrjA 158 1.08e+01 d.110.4.4 86124 1k3fA 253 1.09e+01 c.56.2.1 68105 1fbtA 190 1.11e+01 1bif c.60.1.4 34004 1r89A 437 1.11e+01 unknown_sccs -1147 unknown_sccs -9801 unknown_sccs -10061 1gln 468 1.19e+01 1gln a.97.1.1 18752 c.26.1.1 31588 1rxyA 253 1.22e+01 c.56.2.1 -7834 1bjz 207 1.26e+01 2tct a.4.1.9 16065 a.121.1.1 19242 1yrnA 61 1.27e+01 1akhA a.4.1.1 15981 1s7oA 113 1.27e+01 1v32A 101 1.27e+01 a.42.1.1 -912 1gqoY 143 1.27e+01 c.23.13.1 76318 1jqaA 370 1.28e+01 e.22.1.2 67085 1ex2A 189 1.29e+01 1ex2A c.51.4.2 33225 1p99A 295 1.30e+01 c.94.1.1 -8697 1pii 452 1.31e+01 1pii c.1.2.4 28559 c.1.2.4 28563 1e32A 458 1.35e+01 1e32A b.52.2.3 59183 c.37.1.20 59184 d.31.1.1 59185 1gqoB 143 1.37e+01 c.23.13.1 76296 1rz3A 201 1.39e+01 c.37.1.6 -7048 1eqnA 321 1.39e+01 1dd9A e.13.1.1 43256 1ru8A 232 1.40e+01 c.26.2.1 -6635 1lngA 87 1.42e+01 d.201.1.1 74045 1h8eA 510 1.47e+01 1skyB a.69.1.1 60738 b.49.1.1 60739 c.37.1.11 60740 1mjoA 104 1.48e+01 1cmbA unknown_sccs 17466 1dkuA 317 1.49e+01 1dkuA c.61.1.2 34118 c.61.1.2 34119 1rwyA 109 1.51e+01 a.39.1.4 -825 1orvA 728 1.52e+01 b.70.3.1 87354 c.69.1.24 87355 1dd9A 338 1.53e+01 1dd9A e.13.1.1 43254 1ibsA 317 1.57e+01 c.61.1.2 66107 c.61.1.2 66108 1gqoI 143 1.60e+01 c.23.13.1 76303 1gefA 123 1.60e+01 1gefA c.52.1.18 60465 1ihjA 98 1.61e+01 1pdr b.36.1.1 62382 1tplA 426 1.64e+01 1ax4A c.67.1.2 34387 1xjo 284 1.65e+01 1xjo c.56.5.4 33843 1q1hA 110 1.66e+01 unknown_sccs -262 1kafA 108 1.67e+01 d.199.1.1 68372 1dlyA 164 1.69e+01 1dlyA a.1.1.1 14983 1lliA 92 1.69e+01 1lmb3 a.35.1.2 17025 1eblB 317 1.71e+01 1hn9A c.95.1.1 35975 c.95.1.1 35976 1h70A 255 1.76e+01 1h70A d.126.1.3 60711 1cpzA 68 1.78e+01 1aw0 d.58.17.1 39351 1b24A 188 1.78e+01 1b24A d.95.2.1 40573 d.95.2.1 40574 1v5sA 126 1.78e+01 1v7rA 186 1.80e+01 c.51.4.1 -7546 1mgtA 174 1.82e+01 1mgtA a.4.2.1 16078 c.55.7.1 33753 1apmE 350 1.83e+01 1cdkA d.144.1.7 41628 1brwA 433 1.85e+01 1brwA a.46.2.1 17764 c.27.1.1 31628 d.41.3.1 38626 1rhcA 330 1.85e+01 c.1.16.3 -5606 1dkrA 317 1.85e+01 1dkuA c.61.1.2 34114 c.61.1.2 34115 1vsd 152 1.85e+01 1cxqA c.55.3.2 33625 1nv8A 284 1.88e+01 c.66.1.30 86224 1ugiA 84 1.89e+01 1ugiA d.17.5.1 38125 1mr3F 181 1.90e+01 c.37.1.8 79422 1ku3A 73 1.94e+01 a.4.13.2 73000 1kyqA 274 1.94e+01 c.2.1.11 73281 e.37.1.1 73282 1j5eK 129 1.95e+01 c.55.4.1 71554 1l3iA 192 1.96e+01 c.66.1.22 77676 1e79A 510 1.97e+01 1skyB a.69.1.1 18269 b.49.1.1 26434 c.37.1.11 32314 1ni9A 338 1.99e+01 e.7.1.2 85739 1fjgK 129 1.99e+01 1fjfK c.55.4.1 33733 1ogdA 131 2.01e+01 unknown_sccs -8007 1jr3A 373 2.03e+01 a.80.1.1 63245 c.37.1.20 63246 1m5tA 124 2.06e+01 c.23.1.1 78660 1gqoN 143 2.06e+01 c.23.13.1 76308 1cmbA 104 2.06e+01 1cmbA unknown_sccs 17460 1cmcA 104 2.06e+01 1cmbA unknown_sccs 17462 1vk8A 106 2.08e+01 1nnwA 252 2.15e+01 d.159.1.5 80674 1l1qA 186 2.16e+01 c.61.1.1 77653 1le6A 123 2.17e+01 a.133.1.2 73862 1a98A 152 2.17e+01 1nulA c.61.1.1 34021 1asu 162 2.18e+01 1cxqA c.55.3.2 33626 2napA 723 2.19e+01 2napA b.52.2.2 26926 c.81.1.1 35334 1r6fA 310 2.21e+01 unknown_sccs -11804 1cgt 684 2.21e+01 1cxlA b.1.18.2 21815 b.3.1.1 22484 b.71.1.1 27722 c.1.8.1 28709 1b56 135 2.22e+01 1hmt b.60.1.2 27183 1cmaA 104 2.22e+01 1cmbA unknown_sccs 17486 1f21A 155 2.22e+01 2rn2 c.55.3.1 33550 1cmkE 350 2.24e+01 1cdkA d.144.1.7 41623 1g33A 73 2.25e+01 a.39.1.4 65121 1aye 401 2.26e+01 1aye c.56.5.1 33824 d.58.3.1 39065 1aurA 218 2.26e+01 1auoA c.69.1.14 34718 1h5yA 253 2.26e+01 c.1.2.1 65638 1k1eA 180 2.30e+01 c.108.1.5 67995 2scuA 288 2.31e+01 2scuA c.2.1.8 30303 c.23.4.1 31131 1dzkA 157 2.34e+01 1obpA b.60.1.1 27096 1mqoA 227 2.34e+01 1eg5A 384 2.36e+01 1ecxA c.67.1.3 34429 1ecxA 384 2.36e+01 1ecxA c.67.1.3 34431 1o9lA 481 2.38e+01 unknown_sccs 81242 unknown_sccs 81241 1e0eA 55 2.39e+01 1wjcA a.4.10.1 59147 1lx7A 253 2.45e+01 c.56.2.1 74329 1lxnA 99 2.47e+01 d.58.48.1 84737 1nktA 922 2.47e+01 a.162.1.1 85830 a.172.1.1 85831 c.37.1.19 85832 c.37.1.19 85833 1nu0A 138 2.48e+01 unknown_sccs -7658 1ipiA 123 2.50e+01 c.52.1.18 66255 1mwyA 73 2.50e+01 d.58.17.1 79616 1h2rL 534 2.53e+01 1h2rL e.18.1.1 43298 4uagA 437 2.53e+01 4uagA c.5.1.1 30651 c.59.1.1 33952 c.72.2.1 34955 1ooyA 481 2.54e+01 unknown_sccs -6867 unknown_sccs -6873 1qq9A 284 2.54e+01 1xjo c.56.5.4 33841 1cxqA 162 2.60e+01 1cxqA c.55.3.2 33621 1nksA 194 2.61e+01 1nksA c.37.1.1 31886 1o0uA 429 2.61e+01 c.118.1.1 80743 1jepA 222 2.62e+01 d.36.1.1 66612 1qqjA 419 2.63e+01 1qcnA b.34.8.1 59034 d.177.1.1 59035 1qq2A 199 2.63e+01 1qq2A c.47.1.10 33064 1kmmA 424 2.65e+01 1adjA c.51.1.1 33174 d.104.1.1 40723 2prd 174 2.66e+01 2prd b.40.5.1 25435 1eu8A 409 2.78e+01 1eu8A c.94.1.1 59502 1ubkL 534 2.79e+01 e.18.1.1 88422 1v84A 253 2.81e+01 1hyoA 421 2.83e+01 1qcnA b.34.8.1 59001 d.177.1.1 59002 1e3tA 203 2.85e+01 1d4oA c.31.1.4 31749 2rn2 155 2.87e+01 2rn2 c.55.3.1 33551 1eypA 222 2.88e+01 1eypA d.36.1.1 38536 1g61A 228 2.94e+01 1g61A d.126.1.1 41126 1dc1A 323 2.94e+01 1dc1A c.52.1.11 33321 1sfe 180 2.95e+01 1sfe a.4.2.1 16073 c.55.7.1 33748 1uag 437 2.97e+01 4uagA c.5.1.1 30653 c.59.1.1 33954 c.72.2.1 34957 1mjhB 162 3.00e+01 1mjhA c.26.2.4 31640 1pq4A 291 3.01e+01 c.92.2.2 -8633 1b0nA 111 3.02e+01 1b0nA a.34.1.1 17001 a.35.1.3 17064 1p3jA 217 3.04e+01 c.37.1.1 -6996 g.41.2.1 -12769 1cg7A 93 3.04e+01 1cktA a.21.1.1 16428 1hvd 319 3.06e+01 1avc a.65.1.1 18154 1qlmA 316 3.08e+01 1qlmA d.147.1.1 41765 1vkmA 297 3.11e+01 1uj6A 227 3.19e+01 1qcnA 421 3.20e+01 1qcnA b.34.8.1 59017 d.177.1.1 59018 1hmt 132 3.21e+01 1hmt b.60.1.2 27169 1fjgM 126 3.22e+01 1fjfM a.156.1.1 16293 1jq5A 370 3.22e+01 e.22.1.2 67084 1b4aA 149 3.23e+01 1b4aA a.4.5.3 16088 d.74.2.1 39721 1npdA 288 3.23e+01 c.2.1.7 80681 c.58.1.5 80682 1ujsA 88 3.25e+01 a.14.1.1 -463 1fw9A 164 3.30e+01 1fw9A d.190.1.1 60059 1fxrA 64 3.32e+01 1fxd d.58.1.4 38993 1j5yA 187 3.32e+01 a.4.5.1 71592 d.94.2.1 71593 1kt9A 138 3.33e+01 d.113.1.1 72959 1l0oC 243 3.33e+01 a.4.13.2 73405 1s3jA 155 3.34e+01 a.4.5.28 -227 1isiA 265 3.36e+01 e.4.1.1 71394 1ionA 243 3.36e+01 c.37.1.10 62633 1i1gA 141 3.37e+01 a.4.5.32 65982 d.58.4.2 65983 1vkhA 273 3.40e+01 1eyqA 222 3.41e+01 1eypA d.36.1.1 38534 1ryjA 70 3.43e+01 d.15.3.2 -9179 1fmjA 351 3.45e+01 c.37.1.5 59879 1mx3A 347 3.46e+01 c.2.1.4 79638 c.23.12.1 79639 1ass 159 3.47e+01 1a6dA c.8.5.2 30818 1gqoX 143 3.50e+01 c.23.13.1 76317 1gqoJ 143 3.52e+01 c.23.13.1 76304 1lmb3 92 3.53e+01 1lmb3 1jvpP 298 3.57e+01 d.144.1.7 67371 1vh7A 265 3.63e+01 c.1.2.1 -5159 1kkhA 317 3.66e+01 d.14.1.5 72645 d.58.26.3 72646 1tyfA 193 3.66e+01 1tyfA c.14.1.1 30885 1e0gA 48 3.72e+01 1e01A d.7.1.1 37325 1qcoA 423 3.72e+01 1qcnA b.34.8.1 59021 d.177.1.1 59022 1gcqC 70 3.72e+01 1gcpA b.34.2.1 60436 1dpgA 485 3.74e+01 1dpgA c.2.1.3 30074 d.81.1.5 39989 1dq3A 454 3.74e+01 1dq3A b.86.1.2 28380 d.50.3.1 38798 d.95.2.2 40585 d.95.2.2 40586 1bebA 162 3.75e+01 1bebA b.60.1.1 27115 1gqoP 143 3.75e+01 c.23.13.1 76310 1pb6A 212 3.77e+01 a.4.1.9 88017 a.121.1.1 88018 1gvjA 146 3.79e+01 a.4.5.21 -293 1gqoH 143 3.83e+01 c.23.13.1 76302 1no5A 114 3.83e+01 unknown_sccs -9785 1jj2O 148 3.90e+01 1ffkM a.94.1.1 63100 1mzjA 339 3.90e+01 c.95.1.1 79700 c.95.1.1 79701 1s72P 149 3.91e+01 1v5xA 203 3.95e+01 c.1.2.4 -5169 1gtmA 419 3.97e+01 1hwyA c.2.1.7 30223 c.58.1.1 33871 1pszA 303 3.97e+01 1toaA c.92.2.2 35600 1dax 64 3.99e+01 1fxd d.58.1.4 38996 1d8jA 81 4.00e+01 1d8jA a.4.5.18 16153