# List of top-scoring protein chains for t2k-100-30-str2-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 1yhfA 115 5.42e-01 1hoe 74 5.72e-01 1hoe b.5.1.1 22833 1uebA 184 6.43e-01 b.34.5.2,b.40.4.5,b.40.4.5 107782,107783,107784 1ok0A 74 8.28e-01 b.5.1.1 93191 2gpzA 111 9.30e-01 2fs2A 151 1.05e+00 3ait 74 1.14e+00 1hoe b.5.1.1 22835 1psuA 140 1.15e+00 d.38.1.5 88285 2ait 74 1.78e+00 1hoe b.5.1.1 22837 1ifrA 121 1.91e+00 b.1.16.1 71203 1d2eA 397 1.96e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25701,25741,32136 1z6bA 154 2.02e+00 1x8mA 288 2.02e+00 b.82.1.13 109516 1cd8 114 2.42e+00 1cd8 b.1.1.1 19714 2cw8A 537 3.08e+00 1yhpA 212 3.29e+00 1h6yA 170 3.35e+00 b.18.1.7 70904 1akjD 120 3.44e+00 1cd8 b.1.1.1 19712 1ao5A 237 3.94e+00 5ptp b.47.1.2 26334 1gnhA 206 4.21e+00 1sacA b.29.1.5 24252 1ofdA 1520 4.63e+00 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 1quqB 121 4.75e+00 1quqB b.40.4.3 25305 1qpxA 218 5.24e+00 1qpxA b.1.11.1,b.7.2.1 22318,23200 1neu 124 5.43e+00 1neu b.1.1.1 19704 1a6vL 110 5.91e+00 1mfa b.1.1.1 20256 1cqxA 403 6.66e+00 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 1z9lA 128 7.01e+00 2fhxA 246 7.27e+00 1m8aA 70 7.42e+00 d.9.1.1 74579 1dyoA 160 7.59e+00 1dyoA b.18.1.7 23771 1vzyA 291 7.81e+00 1efcA 393 8.15e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25680,25720,32113 1khbA 625 8.17e+00 c.91.1.1,c.109.1.1 68606,68607 1b09A 206 8.72e+00 1sacA b.29.1.5 24247 1llwA 1520 9.45e+00 b.80.4.1,c.1.4.1,d.153.1.1 74017,74018,74019 1vk3A 615 9.50e+00 d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 100846,100847,100848,100849 1iq6A 134 9.60e+00 d.38.1.4 76755 1efuA 385 1.01e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25682,25722,32115 1tvxB 75 1.05e+01 1tvxA d.9.1.1 37442 1icwA 72 1.08e+01 1tvxA d.9.1.1 37357 1v6fA 151 1.17e+01 d.109.1.2 108395 1oaqL 120 1.18e+01 b.1.1.1 92708 1dq3A 454 1.19e+01 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1xx0A 127 1.19e+01 1zkiA 133 1.21e+01 2g1lA 104 1.21e+01 1awiA 138 1.21e+01 1pne d.110.1.1 40871 1z2nX 324 1.22e+01 1oalA 151 1.29e+01 b.1.8.1 86739 1wh0A 134 1.31e+01 1pkoA 139 1.33e+01 b.1.1.1 88147 1nqeA 594 1.33e+01 f.4.3.3 86027 1c0aA 585 1.35e+01 1c0aA b.40.4.1,d.74.4.1,d.104.1.1 25246,39731,40767 1ji6A 589 1.42e+01 b.18.1.3,b.77.2.1,f.1.3.1 63066,63067,63068 1grwA 126 1.51e+01 b.1.11.2 70391 1napA 70 1.52e+01 1tvxA d.9.1.1 37445 2c78A 405 1.56e+01 1ha3A 405 1.56e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 1x0tA 120 1.57e+01 1yruA 364 1.61e+01 1z4xA 532 1.72e+01 1z4vA 532 1.72e+01 1q87A 221 1.74e+01 e.47.1.1 96192 3mspA 126 1.78e+01 1mspA b.1.11.2 22343 2brcA 214 1.80e+01 1amw 214 1.83e+01 1yer d.122.1.1 41093 2mspA 126 1.89e+01 1mspA b.1.11.2 22335 1pz4A 116 1.90e+01 d.106.1.1 95400 1lu4A 136 1.91e+01 c.47.1.10 91124 1qppA 218 1.96e+01 1qpxA b.1.11.1,b.7.2.1 22320,23202 1ugjA 141 1.97e+01 b.41.1.3 107826 1kl9A 182 1.97e+01 b.40.4.5 72681 1aipE 405 1.98e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25699,25739,32134 1uaiA 224 2.00e+01 b.29.1.18 107761 1u1zA 168 2.05e+01 d.38.1.6 107602 1aqt 138 2.06e+01 1aqt a.2.10.1,b.93.1.1 15718,28435 1tvxA 75 2.07e+01 1tvxA d.9.1.1 37441 1fil 139 2.10e+01 1pne d.110.1.1 40869 1tu7A 208 2.10e+01 1mspA 126 2.18e+01 1mspA b.1.11.2 22333 2aw2A 120 2.20e+01 1v70A 105 2.21e+01 1zn8A 180 2.22e+01 1x8hA 228 2.23e+01 1xruA 282 2.24e+01 1jeyA 609 2.31e+01 1jeqA b.131.1.1,c.62.1.3 90370,90371 2d4qA 257 2.35e+01 1yrtA 364 2.36e+01 1tbuA 118 2.36e+01 2breA 219 2.37e+01 1n99A 166 2.39e+01 b.36.1.1,b.36.1.1 85459,85460 1jeqA 609 2.46e+01 1jeqA a.140.2.1,b.131.1.1,c.62.1.3 64748,90366,90367 1hxs1 302 2.48e+01 1mfa 247 2.49e+01 1mfa b.1.1.1,b.1.1.1 19888,19889 1m2xA 223 2.50e+01 d.157.1.1 84764 1suwA 249 2.52e+01 e.52.1.1 106027 1ah6 220 2.52e+01 1yer d.122.1.1 41094 1z54A 132 2.57e+01 2bgoA 140 2.62e+01 1a6uL 108 2.62e+01 1mfa b.1.1.1 20254 1ltoA 245 2.66e+01 b.47.1.2 84707 1e69B 322 2.69e+01 1e69B c.37.1.12 32377 1zhxA 438 2.77e+01 1zm0A 114 2.78e+01 2gvaA 87 2.79e+01 1gvp b.40.4.7 25389 1o4yA 288 2.85e+01 b.29.1.2 92473 2aynA 404 2.85e+01 1yukB 120 2.93e+01 1cid 177 2.97e+01 1cid b.1.1.1,b.1.1.3 19740,21679 1xauA 122 2.97e+01 1v88A 130 3.05e+01 b.55.1.1 108423 2bwrA 401 3.07e+01 1zotA 358 3.10e+01 1j05B 121 3.11e+01 b.1.1.1 90736 1ar61 302 3.17e+01 1pov1 1al21 302 3.18e+01 1pov1 1e8pA 46 3.18e+01 g.55.1.1 59385 1pov1 302 3.19e+01 1pov1 1csp 67 3.25e+01 1mjc b.40.4.5 25321 1a4h 230 3.28e+01 1yer d.122.1.1 41099 1am1 213 3.29e+01 1yer d.122.1.1 41095 1aipA 405 3.29e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25697,25737,32132 1njkA 156 3.31e+01 d.38.1.1 85818 1k9vF 201 3.32e+01 c.23.16.1 68365 2fimA 276 3.33e+01 1z0sA 278 3.37e+01 1fs0E 138 3.42e+01 1aqt a.2.10.1,b.93.1.1 59997,59998 1cv8 174 3.45e+01 1cv8 d.3.1.1 37089 1ar71 302 3.48e+01 1pov1 1mgsA 73 3.49e+01 1tvxA d.9.1.1 37389 1dcuA 357 3.50e+01 1frpA e.7.1.1 42943 1jjeA 222 3.50e+01 1a7tA d.157.1.1 63117 1eft 405 3.51e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25688,25728,32123 1ixlA 131 3.52e+01 d.38.1.5 90717 1s5jA 847 3.60e+01 1mjc 69 3.63e+01 1mjc b.40.4.5 25319 2alaA 391 3.65e+01 1qwrA 319 3.70e+01 b.82.1.3 96491 1yaiA 151 3.72e+01 1yaiA b.1.8.1 22289 2asi 360 3.77e+01 2rmpA b.50.1.2 26824 2cvhA 220 3.82e+01 1h54A 754 3.83e+01 a.102.1.4,b.30.5.3 60634,60635 1exmA 405 3.85e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 1g7sA 594 3.88e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 1gpwB 201 3.88e+01 c.23.16.1 65461 1cf9A 753 3.94e+01 1cf9A c.23.16.3,e.5.1.1 31441,42815 1e79D 482 3.96e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 18272,26437,32317 2ck3D 482 3.98e+01 2f9nA 245 4.03e+01 1g65K 211 4.15e+01 d.153.1.4 41907 1a6wL 109 4.16e+01 1mfa b.1.1.1 20252 1rypL 212 4.27e+01 d.153.1.4 41880 1c01A 76 4.30e+01 1c01A b.11.1.5 23633 1w0pA 781 4.31e+01 b.29.1.8,b.29.1.8,b.68.1.1 109038,109039,109040 1yz1A 174 4.32e+01 1m5sA 297 4.33e+01 d.58.33.1,d.58.33.1 74511,74512 1g7rA 594 4.47e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25716,25717,31034,32149 1fr3A 67 4.53e+01 1fr3A b.40.6.1 25436 1plfA 72 4.54e+01 1tvxA d.9.1.1 37373 1h6qA 168 4.54e+01 1h6qA b.88.1.2 60692 1uvqA 197 4.59e+01 b.1.1.2,d.19.1.1 100062,100063 1ao0A 459 4.64e+01 1ecfB c.61.1.1,d.153.1.1 34049,41816 1fvuB 125 4.76e+01 1ixxB d.169.1.1 42346 1zkkA 167 4.80e+01 1p80A 753 4.95e+01 c.23.16.3,e.5.1.1 94337,94338 1pvc1 301 5.00e+01 1pov1 1vkkA 154 5.07e+01 d.109.1.2 108669 2a6aA 218 5.11e+01 1h9sA 140 5.14e+01 1b9mA b.40.6.2,b.40.6.2 60843,60844 1faoA 126 5.15e+01 1faoA b.55.1.1 26974 1z47A 355 5.22e+01 1g7tA 594 5.22e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25714,25715,31033,32148 1h8eD 482 5.24e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 60747,60748,60749 1914 232 5.39e+01 1914 d.49.1.1,d.49.1.1 83028,83029 1e8oA 85 5.40e+01 1914 d.49.1.1 38773 2av9A 147 5.47e+01 1skyB 502 5.48e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18313,26478,32358 1umhA 184 5.50e+01 b.18.1.21 99605 1c0pA 363 5.55e+01 1an9A c.4.1.2,d.16.1.3 30647,37934 1jmtA 104 5.68e+01 d.58.7.3 63180 1mvuB 121 5.68e+01 b.1.1.1 91475 1zkpA 268 5.70e+01 1qqhA 144 5.75e+01 1dtoA b.91.1.1 28404 1pne 140 5.78e+01 1pne d.110.1.1 40866 1q8iA 783 5.78e+01 c.55.3.5,e.8.1.1 96208,96209 1gvhA 396 5.81e+01 a.1.1.2,b.43.4.2,c.25.1.5 70601,70602,70603 1ap2B 123 5.83e+01 1mfa b.1.1.1 20183 3mefA 69 5.91e+01 1mjc b.40.4.5 25320 1jgtA 513 5.96e+01 c.26.2.1,d.153.1.1 66684,66685 1gv9A 260 6.07e+01 b.29.1.13 70596 1bvqA 141 6.10e+01 1bvqA d.38.1.1 38542 1t77A 414 6.11e+01 1ylnA 252 6.16e+01 1e8cA 498 6.22e+01 c.98.1.1,c.59.1.1,c.72.2.1 59377,59378,59379 1mla 309 6.24e+01 1mla c.19.1.1,d.58.23.1 31031,39383 1w9hA 427 6.37e+01 1m1zA 513 6.37e+01 c.26.2.1,d.153.1.1 78457,78458 2b5hA 200 6.41e+01 1zbfA 142 6.42e+01 1vj2A 126 6.46e+01 b.82.1.10 100796 1uteA 313 6.47e+01 1uteA d.159.1.1 42078 1q7sA 117 6.51e+01 c.131.1.1 96055 1ixmA 192 6.55e+01 1ixmA d.123.1.1 41114 1n12A 138 6.81e+01 b.2.3.2 79779 2a7mA 250 6.88e+01 1c9oA 66 6.89e+01 1mjc b.40.4.5 25325 2fcbA 173 6.93e+01 2fcbA b.1.1.4,b.1.1.4 21781,21782 1aw7A 194 6.94e+01 1aw7A b.40.2.2,d.15.6.1 25164,37753 1bmc 221 6.95e+01 1a7tA d.157.1.1 42038 1eaqA 140 6.97e+01 b.2.5.6 76144 1txvB 440 6.99e+01 1forH 219 7.01e+01 1igtB b.1.1.1,b.1.1.2 19989,21045 1jjtA 228 7.15e+01 1a7tA d.157.1.1 63139 1bk0 331 7.36e+01 1bk0 b.82.2.1 28118 1mjuH 227 7.37e+01 b.1.1.1,b.1.1.2 91302,91303 1r9fA 136 7.39e+01 d.255.1.1 97257 1ixmB 192 7.44e+01 1ixmA d.123.1.1 41115 1q9jA 422 7.45e+01 c.43.1.2,c.43.1.2 104590,104591 1oxxK 353 7.48e+01 b.40.6.3,c.37.1.12 93715,93716 2crvA 120 7.50e+01 1oxsC 353 7.53e+01 b.40.6.3,c.37.1.12 87519,87520 1lnsA 763 7.58e+01 a.40.2.1,b.18.1.13,c.69.1.21 78101,78102,78103 1bshA 138 7.60e+01 1aqt a.2.10.1,b.93.1.1 15720,28437 2a8jA 420 7.60e+01 1khoA 370 7.62e+01 a.124.1.1,b.12.1.3 72489,72490 1gph1 465 7.64e+01 1ecfB 1vfvA 366 7.66e+01 c.37.1.9 108592 1hzgA 295 7.66e+01 1hzgA d.194.1.1 61436 1hfuA 503 7.67e+01 b.6.1.3,b.6.1.3,b.6.1.3 65827,65828,65829 1hq0A 295 7.70e+01 1hzgA d.194.1.1 61122 1e1hA 287 7.78e+01 d.92.1.7 83167 2bz6H 254 7.81e+01 2a8lA 420 7.84e+01 2bw2A 140 7.89e+01 1odmA 331 7.91e+01 b.82.2.1 86875 1dkuA 317 8.02e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 1c8pA 102 8.07e+01 1c8pA b.1.2.1 22040 2atfA 200 8.09e+01 1o9wA 177 8.12e+01 b.2.3.5 86713 1a65A 504 8.15e+01 1a65A b.6.1.3,b.6.1.3,b.6.1.3 23148,23149,23150 1snzA 344 8.20e+01 b.30.5.4 98930 1vcbC 160 8.22e+01 1vcbC b.3.3.1 22535 2g8yA 385 8.25e+01 1yvhA 329 8.35e+01 1n7fA 97 8.36e+01 b.36.1.1 91692 1azzA 226 8.38e+01 5ptp b.47.1.2 26072 1nekA 588 8.40e+01 a.7.3.1,c.3.1.4,d.168.1.1 80426,80427,80428 1h54B 754 8.45e+01 a.102.1.4,b.30.5.3 60636,60637 1pc0A 61 8.52e+01 b.137.1.1 94426 1eb0A 147 8.55e+01 b.107.1.1,d.58.38.1 64890,64891 1dkrA 317 8.56e+01 1dkuA c.61.1.2,c.61.1.2 34114,34115 1lqbC 162 8.58e+01 b.3.3.1 74186 2bc2B 227 8.58e+01 1a7tA d.157.1.1 42032 1c05A 159 8.60e+01 1c05A d.66.1.2 39559 1gsmA 210 8.64e+01 b.1.1.4,b.1.1.4 65535,65536 1ogsA 497 8.66e+01 b.71.1.2,c.1.8.3 86997,86998 1qfgA 725 8.77e+01 1by5A f.4.3.3 43803 2a8mA 420 8.81e+01 1y1oA 203 8.84e+01 1o4tA 133 8.90e+01 b.82.1.9 86622 2cblA 305 8.91e+01 2cblA a.39.1.7,a.48.1.1,d.93.1.1 17380,17774,40528 2a74A 643 8.93e+01 2fcpA 723 8.94e+01 1by5A f.4.3.3 43802 1lo6A 223 8.96e+01 b.47.1.2 74143 1w2tA 432 8.99e+01