# List of top-scoring protein chains for t2k-100-30-alpha 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 1rz1A 161 1.93e-27 b.45.1.2 -4088 1i0rA 169 4.52e-22 1i0rA b.45.1.2 61489 1i0sA 169 5.13e-22 1i0rA b.45.1.2 61491 1uscA 178 2.49e-21 b.45.1.2 -4074 1ejeA 192 1.61e-20 1ejeA b.45.1.2 25757 1d1gA 168 6.04e-03 1d1gA c.71.1.1 34889 1cz3A 168 1.63e-02 1d1gA c.71.1.1 34891 1ne2A 200 5.18e-02 c.66.1.32 85586 1mkyA 439 1.09e-01 c.37.1.8 79250 c.37.1.8 79251 d.52.5.1 79252 1axj 122 2.64e-01 1axj b.45.1.1 25749 1hywA 68 3.85e-01 1hywA d.186.1.1 61425 1tlk 154 4.16e-01 1tlk b.1.1.4 21707 1uaqA 158 4.33e-01 c.97.1.2 88386 1p6oA 161 4.56e-01 c.97.1.2 -8774 1kwmA 402 4.83e-01 c.56.5.1 73079 d.58.3.1 73080 1flmA 122 5.33e-01 1axj b.45.1.1 25747 1krhA 338 5.73e-01 b.43.4.2 72891 c.25.1.2 72892 d.15.4.2 72893 1fthA 122 5.78e-01 d.150.1.2 60028 1fhgA 154 5.80e-01 1tlk b.1.1.4 21706 1rxxA 421 9.29e-01 unknown_sccs -10982 1smvA 260 1.14e+00 1smvA b.121.4.7 23288 1nx8A 273 1.25e+00 b.82.2.8 86374 1eqjA 511 1.32e+00 1ejjA c.105.1.1 59495 c.76.1.3 59496 1knvA 293 1.41e+00 c.52.1.7 68707 1ejjA 511 1.47e+00 1ejjA c.105.1.1 59422 c.76.1.3 59423 1o98A 511 1.48e+00 c.105.1.1 86684 c.76.1.3 86685 1iuhA 198 1.64e+00 d.61.1.2 83711 1l1eA 287 2.01e+00 c.66.1.18 73454 1go3E 187 2.26e+00 b.40.4.5 83054 d.230.1.1 83055 1vcaA 202 2.47e+00 1vcaA b.1.1.3 21649 b.1.1.4 21685 1uylA 236 2.55e+00 1obpA 159 2.96e+00 1obpA b.60.1.1 27092 1a53 247 3.05e+00 1a53 c.1.2.4 28564 1byqA 228 3.16e+00 1yer d.122.1.1 41100 1ucaA 190 3.33e+00 d.124.1.1 88462 1bk7A 190 3.37e+00 1bk7A d.124.1.1 41121 1i3cA 149 3.65e+00 c.23.1.1 71112 1gt1A 159 3.68e+00 b.60.1.1 -4436 1juk 248 3.77e+00 1a53 c.1.2.4 28567 1pg6A 243 4.23e+00 unknown_sccs -4997 1jnyA 435 4.65e+00 b.43.3.1 66982 b.44.1.1 66983 c.37.1.8 66984 1iakA 199 4.75e+00 1iakA b.1.1.2 21625 d.19.1.1 38199 1yer 228 5.00e+00 1yer d.122.1.1 41101 1f06A 320 5.08e+00 1dapA c.2.1.3 59556 d.81.1.3 59557 1ixlA 131 5.13e+00 d.38.1.5 -9705 1bdo 80 5.26e+00 1bdo b.84.1.1 28214 1ucdA 190 5.32e+00 1tvfA 369 5.32e+00 1igs 248 5.52e+00 1a53 c.1.2.4 28565 3dapA 320 5.61e+00 1dapA c.2.1.3 30051 d.81.1.3 39966 1aohA 147 5.76e+00 1aohA b.2.2.2 22401 1i58A 189 5.98e+00 1b3qA d.122.1.3 61773 1hn2A 159 6.28e+00 b.60.1.1 65890 1kvdB 77 6.75e+00 1kveB 1devB 41 6.76e+00 1devB j.64.1.1 46354 1oaiA 59 6.96e+00 a.5.2.3 81255 1cjsA 219 7.01e+00 1cjsA e.24.1.1 43354 1o8uA 257 7.13e+00 c.14.1.3 81194 1kveB 77 7.19e+00 1kveB 1szoA 257 7.21e+00 1zpdA 568 7.39e+00 1zpdA c.31.1.3 31741 c.36.1.5 31785 c.36.1.9 31786 1b1cA 181 7.87e+00 1amoA c.23.5.2 31212 1ig8A 486 7.90e+00 2yhx c.55.1.3 64746 c.55.1.3 64747 1efcA 393 7.97e+00 1efcA b.43.3.1 25680 b.44.1.1 25720 c.37.1.8 32113 1k9sA 237 8.00e+00 c.56.2.1 68359 1fxlA 167 8.02e+00 1b7fA d.58.7.1 39183 d.58.7.1 39184 1bovA 69 8.13e+00 2bosA b.40.2.1 25070 1jksA 294 8.20e+00 d.144.1.7 71710 1dapA 320 8.32e+00 1dapA c.2.1.3 30053 d.81.1.3 39968 1nktA 922 8.74e+00 a.162.1.1 85830 a.172.1.1 85831 c.37.1.19 85832 c.37.1.19 85833 1i2aA 219 9.30e+00 e.24.1.1 -12012 1dwtA 153 9.32e+00 1a6m a.1.1.2 15190 1gjnA 153 9.39e+00 a.1.1.2 70191 1odkA 235 9.45e+00 c.56.2.1 86863 1ecpA 238 9.57e+00 1ecpA c.56.2.1 33775 1nngA 153 9.68e+00 d.38.1.1 -9636 1pxfA 111 9.81e+00 b.40.4.4 88341 1s9aA 257 9.84e+00 1ngzB 220 1.00e+01 b.1.1.1 80502 b.1.1.2 80503 1hruA 188 1.01e+01 1hruA d.115.1.1 40926 1sriA 121 1.04e+01 1swuA b.61.1.1 27276 1iq8A 582 1.05e+01 b.122.1.1 83074 c.1.20.1 71270 d.17.6.1 83075 1a3k 137 1.06e+01 1a3k b.29.1.3 24218 1j1yA 136 1.06e+01 d.38.1.5 -9671 1hxs1 302 1.07e+01 2ucz 165 1.09e+01 1u9aA d.20.1.1 38330 1itvA 195 1.12e+01 b.66.1.1 76791 1i8dA 213 1.12e+01 b.43.4.3 61953 b.43.4.3 61954 2e2c 156 1.18e+01 1u9aA d.20.1.1 38336 1q8iA 783 1.20e+01 c.55.3.5 -7635 e.8.1.1 -11885 1ipwA 175 1.24e+01 2prd b.40.5.1 25427 1vjqA 79 1.25e+01 unknown_sccs -13478 1iejA 332 1.26e+01 1nnt c.94.1.2 62328 1ekeA 230 1.29e+01 1ekeA c.55.3.1 33572 2izgB 123 1.30e+01 1swuA b.61.1.1 27236 1n1bA 549 1.32e+01 a.102.4.1 79799 a.128.1.3 79800 1hyuA 521 1.35e+01 1hyuA c.3.1.5 30547 c.3.1.5 30548 c.47.1.2 32779 c.47.1.2 32780 1iqsA 88 1.37e+01 d.214.1.1 71278 1cuk 203 1.41e+01 1hjp a.5.1.1 16273 a.60.2.1 17946 b.40.4.2 25265 1ny6A 267 1.43e+01 c.37.1.20 -7221 1h6hA 143 1.45e+01 d.189.1.1 65681 1ee6A 197 1.45e+01 1ee6A b.80.1.1 28024 2pii 112 1.50e+01 2pii d.58.5.1 39071 1ceeB 59 1.51e+01 1ceeB 1v92A 46 1.52e+01 a.5.2.3 -357 1aohB 147 1.53e+01 1aohA b.2.2.2 22402 2prd 174 1.55e+01 2prd b.40.5.1 25435 2pcdA 200 1.56e+01 3pchA b.3.6.1 22665 1r9hA 135 1.57e+01 d.26.1.1 -9482 1f1sA 814 1.60e+01 a.102.3.2 64928 b.1.18.2 64929 b.24.1.1 64930 b.30.5.2 64931 1ocxA 182 1.60e+01 b.81.1.3 86814 1pov1 302 1.62e+01 1pov1 1ri5A 298 1.64e+01 unknown_sccs -8063 1j8hD 212 1.73e+01 b.1.1.1 71606 b.1.1.2 71607 2izhB 123 1.74e+01 1swuA b.61.1.1 27234 1t0hB 224 1.80e+01 1jqgA 433 1.81e+01 c.56.5.1 71791 d.58.3.1 71792 1q40B 219 1.84e+01 d.17.4.2 -9287 1pkoA 139 1.84e+01 b.1.1.1 88147 1fzkB 99 1.86e+01 1agdB b.1.1.2 60151 1rgs 288 1.87e+01 1rgs b.82.3.2 28146 b.82.3.2 28147 1pxvA 183 1.88e+01 d.3.1.1 -8881 1is2A 661 1.88e+01 a.29.3.2 71382 a.29.3.2 71383 e.6.1.2 71384 1ne6A 283 1.90e+01 b.82.3.2 -4918 b.82.3.2 -4919 1gx3A 284 1.91e+01 d.3.1.5 70678 1qynA 153 1.94e+01 d.33.1.1 -9585 1b7gO 340 1.95e+01 1b7gO c.2.1.3 29992 d.81.1.1 39907 1hjp 203 1.97e+01 1hjp a.5.1.1 16274 a.60.2.1 17947 b.40.4.2 25266 1h2vZ 156 2.00e+01 d.58.7.1 76595 1iqpA 327 2.00e+01 a.80.1.1 62649 c.37.1.20 62650 1dcfA 136 2.00e+01 1dcfA c.23.1.2 31124 1v8cA 168 2.02e+01 d.15.3.1 -9175 unknown_sccs -11012 1swuA 127 2.02e+01 1swuA b.61.1.1 27230 1bvp1 349 2.02e+01 1bvp1 1ytn 306 2.05e+01 1ytw c.45.1.2 32688 1n1tA 641 2.13e+01 b.29.1.15 79821 b.68.1.1 79822 1e19A 314 2.15e+01 1b7bA c.73.1.1 34967 1cf1A 404 2.16e+01 1cf1A b.1.18.11 21907 b.1.18.11 21908 1cwvA 492 2.23e+01 1cwvA b.1.14.1 22373 b.1.14.1 22374 b.1.14.1 22375 b.1.14.1 22376 d.169.1.3 42442 1ax4A 467 2.25e+01 1ax4A c.67.1.2 34391 1j1xL 107 2.25e+01 b.1.1.1 77064 1shyB 551 2.31e+01 1iqoA 88 2.32e+01 d.214.1.1 71277 1rypH 205 2.36e+01 d.153.1.4 41876 1kb5A 115 2.36e+01 1tvdA b.1.1.1 20611 1nd4A 264 2.46e+01 d.144.1.6 -11381 2bbkH 355 2.48e+01 2bbkH b.69.2.1 27634 1ewfA 456 2.48e+01 1bp1 d.83.1.1 40024 d.83.1.1 40025 1focA 132 2.51e+01 1c52 a.3.1.1 15812 1jyhA 157 2.52e+01 d.60.1.3 71956 1fg7A 356 2.55e+01 1gewA c.67.1.1 59819 1nsj 205 2.56e+01 1nsj c.1.2.4 28560 1rw7A 243 2.58e+01 c.23.16.2 -6530 1gewA 356 2.60e+01 1gewA c.67.1.1 60470 1mgn 154 2.61e+01 1a6m a.1.1.2 15097 1vk9A 151 2.62e+01 1c52 131 2.63e+01 1c52 a.3.1.1 15810 1bx2B 191 2.63e+01 1iakB b.1.1.2 21610 d.19.1.1 38184 1ooeA 236 2.68e+01 c.2.1.2 87196 1qpxA 218 2.69e+01 1qpxA b.1.11.1 22318 b.7.2.1 23200 1l6oA 95 2.70e+01 b.36.1.1 84534 1stfI 98 2.72e+01 1stfI d.17.1.2 38006 1gkuB 1054 2.73e+01 c.37.1.16 65257 c.37.1.16 65258 e.10.1.1 65259 1gmxA 108 2.78e+01 c.46.1.3 65355 1miuA 738 2.80e+01 a.170.1.1 79153 a.171.1.1 79154 b.40.4.3 79155 b.40.4.3 79156 b.40.4.3 79157 1zxq 192 2.80e+01 1zxq b.1.1.3 21657 b.1.1.4 21693 2spo 154 2.80e+01 1a6m a.1.1.2 15053 1p0kA 349 2.81e+01 c.1.4.1 87648 1bzpA 153 2.83e+01 1a6m a.1.1.2 15020 1mbd 153 2.84e+01 1a6m a.1.1.2 15033 1mz5A 638 2.88e+01 b.29.1.15 79679 b.68.1.1 79680 1u02A 239 2.90e+01 1o8vA 134 2.91e+01 b.60.1.2 86680 1poiA 317 2.97e+01 1poiA unknown_sccs 34153 1a6m 151 3.00e+01 1a6m a.1.1.2 15018 1utwA 432 3.01e+01 3pcnA 200 3.02e+01 3pchA b.3.6.1 22725 1pvtA 238 3.04e+01 c.74.1.1 -8444 1vhyA 257 3.07e+01 b.122.1.2 -5129 c.116.1.5 -6705 1lk2B 99 3.08e+01 b.1.1.2 -2576 1uypA 432 3.08e+01 unknown_sccs -3480 unknown_sccs -4554 1sl4A 155 3.13e+01 1cseE 274 3.13e+01 1gci c.41.1.1 32481 1ukcA 522 3.15e+01 1h9mA 145 3.17e+01 1h9jA b.40.6.2 60833 b.40.6.2 60834 1iq6A 134 3.17e+01 d.38.1.4 76755 1uzxA 169 3.18e+01 d.20.1.2 -9409 1e69B 322 3.18e+01 1e69B c.37.1.12 32377 1lyvA 306 3.21e+01 c.45.1.2 74348 1epfA 191 3.21e+01 2ncm b.1.1.4 21694 b.1.1.4 21695 1npuA 117 3.23e+01 b.1.1.1 -2339 1pvc1 301 3.24e+01 1pov1 1ok8A 394 3.25e+01 b.1.18.4 -2737 f.10.1.1 -12384 1kzlA 208 3.28e+01 b.43.4.3 77635 b.43.4.3 77636 1j0sA 157 3.28e+01 b.42.1.2 -4016 1bmdA 327 3.30e+01 1bmdA c.2.1.5 30139 d.162.1.1 42106 1nwbA 124 3.30e+01 b.124.1.1 86296 1gmlA 178 3.30e+01 c.8.5.2 70273 1pba 81 3.37e+01 1pytA d.58.3.1 39067 3pchA 200 3.42e+01 3pchA b.3.6.1 22653 3pcgA 200 3.42e+01 3pchA b.3.6.1 22647 2tgi 112 3.47e+01 2tgi g.17.1.2 44777 1nftA 329 3.48e+01 1nnt c.94.1.2 35881 1u9aA 160 3.49e+01 1u9aA d.20.1.1 38333 1ub9A 100 3.49e+01 a.4.5.28 -231 1v2bA 177 3.50e+01 1louA 101 3.50e+01 1ris d.58.14.1 39323 1h7mA 102 3.56e+01 d.79.3.1 83485 1pk9A 237 3.56e+01 c.56.2.1 -7734 1bg2 325 3.59e+01 1bg2 c.37.1.9 32189 1b3qA 379 3.63e+01 1b3qA a.30.2.1 16993 b.40.7.1 25454 d.122.1.3 41112 1uag 437 3.77e+01 4uagA c.5.1.1 30653 c.59.1.1 33954 c.72.2.1 34957 1p0iA 529 3.77e+01 c.69.1.1 -8291 1c4qA 69 3.79e+01 2bosA b.40.2.1 25010 3sxlA 184 3.80e+01 1b7fA d.58.7.1 39173 d.58.7.1 39174 1yts 278 3.84e+01 1ytw c.45.1.2 32690 1r0rE 274 3.85e+01 c.41.1.1 -7293 1mk0A 97 3.87e+01 d.226.1.1 79216 1nnt 328 3.90e+01 1nnt c.94.1.2 35884 1f7tA 122 3.90e+01 1f7lA d.150.1.2 59667 1jj2A 239 3.98e+01 1rl2A b.34.5.3 63084 b.40.4.5 63085