# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7-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 1jnyA 435 1.18e-23 b.43.3.1 66982 b.44.1.1 66983 c.37.1.8 66984 1aipE 405 1.39e-23 1efcA b.43.3.1 25699 b.44.1.1 25739 c.37.1.8 32134 1efcA 393 1.56e-23 1efcA b.43.3.1 25680 b.44.1.1 25720 c.37.1.8 32113 1exmA 405 5.18e-23 1efcA b.43.3.1 25696 b.44.1.1 25736 c.37.1.8 32131 1ha3A 405 1.43e-22 1efcA b.43.3.1 60869 b.44.1.1 60870 c.37.1.8 60871 1d2eA 397 8.51e-22 1efcA b.43.3.1 25701 b.44.1.1 25741 c.37.1.8 32136 1f60A 458 7.26e-21 1efcA b.43.3.1 25705 b.44.1.1 25745 c.37.1.8 32140 1kk1A 410 4.89e-10 b.43.3.1 72634 b.44.1.1 72635 c.37.1.8 72636 1s0uA 408 1.59e-09 1g7tA 594 1.24e-05 1g7rA b.43.3.1 25714 b.43.3.1 25715 c.20.1.1 31033 c.37.1.8 32148 1g7sA 594 1.50e-05 1g7rA b.43.3.1 25712 b.43.3.1 25713 c.20.1.1 31032 c.37.1.8 32147 1g7rA 594 1.76e-05 1g7rA b.43.3.1 25716 b.43.3.1 25717 c.20.1.1 31034 c.37.1.8 32149 1d1nA 99 4.70e-04 1d1nA b.43.3.1 25718 1n0uA 842 9.94e-03 b.43.3.1 79757 c.37.1.8 79758 d.14.1.1 79759 d.58.11.1 79760 d.58.11.1 79761 1mq7A 154 3.99e-02 b.85.4.1 79404 1sixA 174 6.68e-02 1dar 691 1.18e-01 1dar b.43.3.1 25707 c.37.1.8 32142 d.14.1.1 37547 d.58.11.1 39300 1wwcA 118 1.75e-01 1wwcA b.1.1.4 21778 1qfgA 725 4.17e-01 1by5A f.4.3.3 43803 1fnmA 691 4.44e-01 1dar b.43.3.1 25709 c.37.1.8 32144 d.14.1.1 37546 d.58.11.1 39302 d.58.11.1 39303 1n7eA 97 4.46e-01 1hh2P 344 4.56e-01 b.40.4.5 65835 d.52.3.1 65836 d.52.3.1 65837 d.202.1.1 65838 1fiwA 290 5.26e-01 5ptp 1q5hA 147 6.60e-01 1euwA 152 6.71e-01 1dupA b.85.4.1 28349 1dupA 152 7.20e-01 1dupA b.85.4.1 28351 1pmy 123 7.79e-01 1bqk b.6.1.1 22888 1by5A 714 8.00e-01 1by5A f.4.3.3 43800 1j5qA 437 8.82e-01 b.121.2.3 77084 b.121.2.3 77085 1pkoA 139 1.10e+00 b.1.1.1 88147 1eysH 259 1.18e+00 6prcH b.41.1.1 25484 f.23.10.1 43517 1rtfB 252 1.57e+00 5ptp 2eifA 136 1.67e+00 1bkb b.34.5.2 24607 b.40.4.5 25339 1e96B 203 1.67e+00 1e96B a.118.8.1 19211 1nglA 179 1.69e+00 1nglA b.60.1.1 27146 1d7qA 143 1.74e+00 1d7qA b.40.4.5 25331 1bb9 115 1.76e+00 1bb9 b.34.2.1 24554 1oi1A 221 1.94e+00 b.34.9.3 87037 b.34.9.3 87038 1n7fA 97 2.05e+00 2cgaA 245 2.19e+00 5ptp b.47.1.2 26028 1m3yA 413 2.37e+00 b.121.2.3 78579 b.121.2.3 78580 1nb5I 98 2.52e+00 d.17.1.2 80381 1pm4A 119 2.57e+00 1gg6B 131 2.81e+00 5ptp 1bkb 136 3.00e+00 1bkb b.34.5.2 24609 b.40.4.5 25341 1v74A 107 3.09e+00 1whi 122 3.22e+00 1whi b.39.1.1 24810 1eaxA 241 3.25e+00 b.47.1.2 64889 1by3A 714 3.53e+00 1by5A f.4.3.3 43801 1vjnA 220 3.55e+00 1e79A 510 3.73e+00 1skyB a.69.1.1 18269 b.49.1.1 26434 c.37.1.11 32314 1gctA 245 3.87e+00 5ptp b.47.1.2 26021 1h8eA 510 3.96e+00 1skyB a.69.1.1 60738 b.49.1.1 60739 c.37.1.11 60740 1uebA 184 3.99e+00 1rmi 160 4.07e+00 1ifa a.26.1.3 16891 2fcpA 723 4.16e+00 1by5A f.4.3.3 43802 1umwA 237 4.25e+00 1k2i1 245 4.38e+00 1vi4A 174 4.38e+00 1uz5A 402 4.61e+00 1b2pA 119 4.79e+00 1b2pA b.78.1.1 27998 1gvhA 396 4.80e+00 a.1.1.2 70601 b.43.4.2 70602 c.25.1.5 70603 1m4vA 204 4.85e+00 b.40.2.2 74459 d.15.6.1 74460 1ospH 218 4.95e+00 1igtB b.1.1.1 20117 b.1.1.2 21147 1qovH 260 4.95e+00 6prcH b.41.1.1 25464 f.23.10.1 43457 1bmfA 510 4.96e+00 1skyB a.69.1.1 18281 b.49.1.1 26446 c.37.1.11 32326 3pmgA 561 5.00e+00 3pmgA c.84.1.1 35408 c.84.1.1 35409 c.84.1.1 35410 d.129.2.1 41301 1fa4A 105 5.05e+00 1plc b.6.1.1 22867 1sro 76 5.22e+00 1sro b.40.4.5 25327 1dmmA 131 5.24e+00 1opy d.17.4.3 38114 3dni 260 5.41e+00 3dni d.151.1.1 41791 1rzhH 260 5.53e+00 1h0jA 60 5.70e+00 g.7.1.1 83432 1eiyB 785 5.96e+00 1pysB a.6.1.1 16305 a.6.1.1 16306 b.40.4.4 25314 d.58.13.1 39313 d.104.1.1 40782 d.138.1.1 41458 1opy 131 6.03e+00 1opy d.17.4.3 38113 1nwpA 128 6.05e+00 1nwpA b.6.1.1 23011 1bjt 793 6.17e+00 1bjt e.11.1.1 43249 1k5dB 201 6.19e+00 b.55.1.3 68169 6prcH 258 6.75e+00 6prcH b.41.1.1 25457 f.23.10.1 43436 1gc1H 229 6.84e+00 1gc1H b.1.1.1 20265 b.1.1.2 21265 1dxrH 258 6.85e+00 6prcH b.41.1.1 25456 f.23.10.1 43433 4fiv 113 6.86e+00 1fmb b.50.1.1 26762 1hh8A 213 7.02e+00 1e96B a.118.8.1 61042 1i3uA 127 7.04e+00 1gc1H b.1.1.1 61636 1c5yB 253 7.19e+00 5ptp 1ehkB 168 7.25e+00 2cuaA b.6.1.2 23041 f.17.2.1 43625 1n99A 166 7.56e+00 b.36.1.1 85459 b.36.1.1 85460 1kwaB 88 7.77e+00 1kwaA b.36.1.1 24773 1pqhA 143 7.82e+00 1eylA 186 7.83e+00 1wba b.42.4.1 25593 1fivA 113 7.91e+00 1fmb b.50.1.1 26764 1ea2A 131 8.18e+00 d.17.4.3 64860 1dqaC 467 8.30e+00 1dqaA d.58.20.1 39366 d.179.1.1 42587 1gj7B 253 8.50e+00 1p42A 270 8.53e+00 d.14.1.7 87754 d.14.1.7 87755 1bawA 105 8.69e+00 1plc b.6.1.1 22868 1ia9A 280 8.72e+00 1ia9A d.144.1.5 62113 3fivA 116 8.80e+00 1fmb b.50.1.1 26768 1q48A 134 9.08e+00 1g8lA 411 9.29e+00 1g8lA b.85.6.1 60365 b.103.1.1 60366 c.57.1.2 60367 1kobA 387 9.32e+00 1tkiA d.144.1.7 41640 2cdx 60 9.40e+00 1tgxA g.7.1.1 44436 1khiA 176 9.53e+00 b.34.5.2 77408 b.40.4.5 77409 1paz 123 9.55e+00 1bqk b.6.1.1 22878 1cjcA 460 9.56e+00 1cjcA c.3.1.1 30319 c.4.1.1 30604 1oxxK 353 9.90e+00 2cuaA 135 9.99e+00 2cuaA b.6.1.2 23039 1lnrI 134 1.01e+01 1a34A 159 1.01e+01 1a34A b.121.7.1 23286 1oxsC 353 1.01e+01 b.40.6.3 87519 c.37.1.12 87520 1ejeA 192 1.03e+01 1ejeA b.45.1.2 25757 1f7dA 136 1.04e+01 1dun b.85.4.1 28353 1rqpA 299 1.06e+01 1mgtA 174 1.06e+01 1mgtA a.4.2.1 16078 c.55.7.1 33753 1sgc 181 1.07e+01 1qq4A b.47.1.1 25810 1mvuB 121 1.11e+01 1oruA 195 1.11e+01 1fsiA 189 1.13e+01 1fsiA d.61.1.1 39536 1grwA 126 1.13e+01 b.1.11.2 70391 1ohfA 644 1.13e+01 1lo6A 223 1.14e+01 b.47.1.2 74143 1k1zA 78 1.16e+01 b.34.2.1 68026 3tss 194 1.18e+01 1aw7A b.40.2.2 25160 d.15.6.1 37749 2sga 181 1.19e+01 1qq4A b.47.1.1 25808 2dnjA 260 1.20e+01 3dni d.151.1.1 41790 1pt1A 143 1.21e+01 1jj2A 239 1.23e+01 1rl2A b.34.5.3 63084 b.40.4.5 63085 1cdtA 60 1.24e+01 1tgxA g.7.1.1 44415 1uw6A 211 1.24e+01 1rllA 692 1.24e+01 1gcqC 70 1.25e+01 1gcpA b.34.2.1 60436 1jdqA 98 1.31e+01 d.68.3.3 66559 1f15A 218 1.31e+01 1f15B b.121.4.5 23320 1jmcA 246 1.33e+01 1jmcA b.40.4.3 25300 b.40.4.3 25301 1btu 240 1.33e+01 5ptp b.47.1.2 26241 1ocvA 125 1.36e+01 d.17.4.3 86810 1pwt 61 1.37e+01 1tud b.34.2.1 24490 1po0A 751 1.42e+01 1kb9A 431 1.43e+01 d.185.1.1 77311 d.185.1.1 77312 1o9wA 177 1.45e+01 b.2.3.5 86713 1gvkB 240 1.49e+01 b.47.1.2 70610 2sfa 191 1.49e+01 1qq4A b.47.1.1 25815 1kyoA 430 1.49e+01 d.185.1.1 73249 d.185.1.1 73250 1shcA 195 1.50e+01 1shcA b.55.1.2 26992 1asyA 490 1.52e+01 1b8aA b.40.4.1 25242 d.104.1.1 40763 1aw8B 91 1.53e+01 1aw8B 1gpr 162 1.55e+01 1gpr b.84.3.1 28267 1udxA 416 1.55e+01 1q0xH 221 1.57e+01 1h6yA 170 1.59e+01 b.18.1.7 70904 1f56A 91 1.60e+01 2cbp b.6.1.1 22896 1qnjA 240 1.60e+01 5ptp b.47.1.2 26238 1jx6A 342 1.60e+01 c.93.1.1 67406 1etu 394 1.61e+01 1efcA c.37.1.8 64737 1foeA 377 1.63e+01 1foeA a.87.1.1 18517 b.55.1.1 26969 35c8H 217 1.63e+01 8fabA b.1.1.1 20297 b.1.1.2 21289 1cf1A 404 1.68e+01 1cf1A b.1.18.11 21907 b.1.18.11 21908 1vjjA 692 1.70e+01 1kmoA 774 1.72e+01 f.4.3.3 72753 1o54A 277 1.73e+01 1fr3A 67 1.76e+01 1fr3A b.40.6.1 25436 1q9rA 219 1.80e+01 1tgxA 60 1.80e+01 1tgxA g.7.1.1 44398 1cyu 98 1.82e+01 1stfI d.17.1.2 38004 1ounA 127 1.83e+01 1ounA d.17.4.2 38090 1vjuA 309 1.83e+01 1tlk 154 1.86e+01 1tlk b.1.1.4 21707 1oh0A 131 1.86e+01 d.17.4.3 87004 1mv3A 213 1.89e+01 1jsdA 319 1.92e+01 b.19.1.2 63258 1fonA 240 1.94e+01 5ptp b.47.1.2 26231 2pkaB 152 1.95e+01 5ptp 1mhnA 59 1.95e+01 b.34.9.1 84964 1k8kF 168 1.96e+01 d.198.2.1 68312 1g2bA 62 1.96e+01 1tud b.34.2.1 24488 1gztA 115 1.96e+01 b.115.1.1 76428 1jcv 153 1.96e+01 1mfmA b.1.8.1 22279 1f15B 218 1.97e+01 1f15B b.121.4.5 23321 1tetL 216 1.98e+01 32c2A b.1.1.1 19902 b.1.1.2 20996 1t5eA 360 1.98e+01 2rhe 114 1.98e+01 8fabA b.1.1.1 20523 1f1gA 154 1.99e+01 b.1.8.1 76153 1mjuL 219 1.99e+01 1e15A 499 2.00e+01 1e15A b.72.2.1 27810 c.1.8.5 29006 d.26.3.1 38440 1mzgA 146 2.02e+01 d.224.1.1 79696 1i9bA 217 2.02e+01 1i9bA b.96.1.1 62084 1b7yB 785 2.03e+01 1pysB a.6.1.1 16301 a.6.1.1 16302 b.40.4.4 25312 d.58.13.1 39311 d.104.1.1 40780 d.138.1.1 41456 1ff4A 65 2.08e+01 g.7.1.1 83251 1e6oL 212 2.08e+01 32c2A b.1.1.1 20494 b.1.1.2 21452 1i16 130 2.09e+01 1i16 b.36.1.2 24787 1hpwA 129 2.09e+01 1hpwA d.24.1.1 61118 32c2A 217 2.12e+01 32c2A b.1.1.1 20438 b.1.1.2 21404 1mq8A 291 2.13e+01 b.1.1.3 79405 b.1.1.4 79406 1blr 137 2.13e+01 1hmt b.60.1.2 27208 1jpyB 137 2.14e+01 g.17.1.6 67066 1jvwA 167 2.18e+01 d.26.1.1 71907 1gnhA 206 2.18e+01 1sacA b.29.1.5 24252 1aw8E 91 2.24e+01 1aw8B 2fivA 116 2.24e+01 1fmb b.50.1.1 26766 1e0tA 470 2.25e+01 1a49A b.58.1.1 27064 c.1.12.1 29292 c.49.1.1 33146 1qjgA 125 2.28e+01 1opy d.17.4.3 38102 1k5wA 152 2.32e+01 b.7.1.2 68212 1jq3A 296 2.33e+01 c.66.1.17 67079 1pysB 785 2.34e+01 1pysB a.6.1.1 16299 a.6.1.1 16300 b.40.4.4 25311 d.58.13.1 39310 d.104.1.1 40779 d.138.1.1 41455 1itpA 77 2.35e+01 d.58.3.2 66371 1ezvA 430 2.35e+01 1be3A d.185.1.1 59541 d.185.1.1 59542 1efyA 350 2.36e+01 1a26 a.41.1.1 17413 d.166.1.2 42275 1ic1A 190 2.37e+01 1zxq b.1.1.3 21654 b.1.1.4 21690 1jpyA 137 2.38e+01 g.17.1.6 67065 1bv4A 118 2.40e+01 1rtm1 d.169.1.1 42380 1vf7A 369 2.42e+01 1i18A 97 2.43e+01 b.43.4.3 61520 1hyxL 216 2.43e+01 8fabA b.1.1.1 20166 b.1.1.2 21190 1shfA 59 2.44e+01 1bbzA b.34.2.1 24462 1ly7A 121 2.51e+01 d.82.2.1 74339 1d2pA 373 2.54e+01 1d2oA b.3.5.1 22629 b.3.5.1 22630 b.3.5.1 22631 b.3.5.1 22632 3pyp 125 2.56e+01 3pyp d.110.3.1 40897 1inlA 296 2.56e+01 c.66.1.17 66220 1lp4A 332 2.57e+01 d.144.1.7 74170 1aohA 147 2.59e+01 1aohA b.2.2.2 22401 1pjpA 226 2.59e+01 5ptp b.47.1.2 26301 1pj5A 830 2.60e+01 1qqsA 174 2.63e+01 1nglA b.60.1.1 27143 5ptp 223 2.63e+01 5ptp b.47.1.2 25831 2gpr 154 2.64e+01 1gpr b.84.3.1 28269 1earA 147 2.64e+01 b.107.1.1 64875 d.58.38.1 64876 1jhfA 202 2.65e+01 a.4.5.2 63057 b.87.1.1 63058 1iyu 79 2.65e+01 1iyu b.84.1.1 28227 1im3D 95 2.66e+01 1im3D b.1.18.5 62568 1dmr 823 2.70e+01 1dmr b.52.2.2 26904 c.81.1.1 35312 1nwzA 125 2.71e+01 d.110.3.1 86370 1fhgA 154 2.72e+01 1tlk b.1.1.4 21706 1dun 134 2.72e+01 1dun b.85.4.1 28371 1qpcA 279 2.74e+01 1fgkA d.144.1.7 41685 1tud 62 2.76e+01 1tud b.34.2.1 24489 1jysA 242 2.78e+01 c.56.2.1 77216 1h9jA 145 2.81e+01 1h9jA b.40.6.2 60829 b.40.6.2 60830 2phy 125 2.84e+01 3pyp d.110.3.1 40901 1fm0D 81 2.85e+01 1fmaD d.15.3.1 37642 1nls 237 2.86e+01 1nls b.29.1.1 23928 1wba 175 2.88e+01 1wba b.42.4.1 25591 1esgA 213 2.88e+01 1bam c.52.1.3 33286 1q7hA 153 2.89e+01 1fwxA 595 2.93e+01 b.6.1.4 60069 b.69.3.1 60070 1nlbL 220 2.93e+01 b.1.1.1 80623 b.1.1.2 80624 1cghA 224 2.96e+01 1a7s b.47.1.2 26290 1h0hA 977 2.97e+01 b.52.2.2 76435 c.81.1.1 76436 1mexL 213 2.98e+01 12e8L 214 2.99e+01 8fabA b.1.1.1 20268 b.1.1.2 21268 1hl9A 449 2.99e+01 8cho 125 3.02e+01 1opy d.17.4.3 38108 1h5bA 113 3.03e+01 1tvdA b.1.1.1 60638 1qcsA 211 3.09e+01 1qcsA b.52.2.3 26927 d.31.1.1 38461 1aohB 147 3.11e+01 1aohA b.2.2.2 22402 1diwA 441 3.11e+01 1a8d b.29.1.6 24264 b.42.4.2 25609 1danH 254 3.11e+01 5ptp b.47.1.2 26292 1h9mA 145 3.11e+01 1h9jA b.40.6.2 60833 b.40.6.2 60834 1i8fA 81 3.12e+01 1i8fA b.38.1.1 61959 1f7zA 233 3.15e+01 5ptp b.47.1.2 59681 2hts 88 3.16e+01 2hts a.4.5.22 16174 1p4uA 153 3.16e+01 b.1.10.2 87780 1fmaD 81 3.19e+01 1fmaD d.15.3.1 37643 1bbzA 58 3.19e+01 1bbzA b.34.2.1 24477 1hxmA 229 3.20e+01 1hxmA b.1.1.1 61367 b.1.1.2 61368 1jv2A 957 3.22e+01 b.1.15.1 67334 b.1.15.1 67335 b.1.15.1 67336 b.69.8.1 67337 1jb2A 127 3.24e+01 d.17.4.2 71624 1nn6A 228 3.25e+01 b.47.1.2 85893 2hmx 133 3.25e+01 1hiwA a.61.1.1 18129 1ncwH 222 3.25e+01 b.1.1.1 85555 b.1.1.2 85556 1mlvA 444 3.28e+01 a.166.1.1 79283 b.85.7.3 79284 1bbzE 58 3.29e+01 1bbzA b.34.2.1 24479 1qcrA 446 3.29e+01 1be3A d.185.1.1 59025 d.185.1.1 59026 1mdc 133 3.30e+01 1hmt b.60.1.2 27198 1d0nA 729 3.30e+01 1d0nA d.109.1.1 40834 d.109.1.1 40835 d.109.1.1 40836 d.109.1.1 40837 d.109.1.1 40838 d.109.1.1 40839 1gcpA 70 3.34e+01 1gcpA b.34.2.1 60430 1dm9A 133 3.38e+01 1dm9A d.66.1.3 39560 1hj9A 226 3.42e+01 b.47.1.2 65845 1dqaA 467 3.43e+01 1dqaA d.58.20.1 39364 d.179.1.1 42585 1ten 90 3.48e+01 1ten b.1.2.1 21990 1bqk 124 3.48e+01 1bqk b.6.1.1 22889 1op3H 225 3.48e+01 b.1.1.1 87208 b.1.1.2 87209 1qcxA 359 3.49e+01 1qcxA b.80.1.2 28028 1mai 131 3.53e+01 1mai b.55.1.1 26951 1ja1A 622 3.54e+01 1amoA b.43.4.1 62803 c.23.5.2 62804 c.25.1.4 62805 2plt 98 3.55e+01 1plc b.6.1.1 22862 1os8A 223 3.57e+01 1eq9A 222 3.62e+01 5ptp b.47.1.2 26068 1fvuB 125 3.63e+01 1ixxB d.169.1.1 42346 1hr6B 443 3.63e+01 1be3A d.185.1.1 61166 d.185.1.1 61167 1qq4A 198 3.65e+01 1qq4A b.47.1.1 25768 1aac 105 3.74e+01 1aac b.6.1.1 22838 1l9mA 692 3.78e+01 b.1.18.9 73732 b.1.5.1 73733 b.1.5.1 73734 d.3.1.4 73735 1ar0A 127 3.79e+01 1ounA d.17.4.2 38092 1mtnC 97 3.79e+01 5ptp 1g2lA 235 3.80e+01 b.47.1.2 65112 2hft 218 3.82e+01 1boy b.1.2.1 21951 b.1.2.1 21952 1oz2A 331 3.85e+01 1ssxA 198 3.87e+01 1bxaA 105 3.90e+01 1aac b.6.1.1 22839 1vppV 102 3.90e+01 1vpfA g.17.1.1 44753 1aw7A 194 3.90e+01 1aw7A b.40.2.2 25164 d.15.6.1 37753 1iz6A 138 3.91e+01 b.34.5.2 76976 b.40.4.5 76977 1lr0A 129 3.96e+01 d.212.1.1 74213 1aboA 62 3.97e+01 1bbzA b.34.2.1 24474