# 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 1hn6A 110 3.41e-21 g.61.1.1 76721 1tocR 120 3.20e-02 1tocR g.8.1.2 44558 g.8.1.2 44559 1m6bA 621 1.28e-01 c.10.2.5 74521 c.10.2.5 74522 g.3.9.1 74523 g.3.9.1 74524 1j58A 385 2.81e-01 b.82.1.2 71531 1e32A 458 9.19e-01 1e32A b.52.2.3 59183 c.37.1.20 59184 d.31.1.1 59185 1ljrA 244 1.03e+00 1ljrA a.45.1.1 17707 c.47.1.5 33001 2eng 210 1.20e+00 2eng b.52.1.1 26895 1nstA 325 1.22e+00 1nstA c.37.1.5 31951 1a49A 530 1.36e+00 1a49A b.58.1.1 27026 c.1.12.1 29255 c.49.1.1 33109 1pkn 530 1.46e+00 1a49A b.58.1.1 27042 c.1.12.1 29271 c.49.1.1 33125 2knt 58 1.65e+00 1bpi g.8.1.1 44537 1hd5A 213 1.71e+00 2eng b.52.1.1 26896 1gadO 330 1.79e+00 1dssG c.2.1.3 29950 d.81.1.1 39865 2sil 381 1.84e+00 3sil b.68.1.1 27543 1kthA 58 1.92e+00 g.8.1.1 68863 1ecfB 504 1.96e+00 1ecfB c.61.1.1 34054 d.153.1.1 41821 1o0iA 138 1.99e+00 d.38.1.5 86532 1knt 58 2.02e+00 1bpi g.8.1.1 44538 1bj7 156 2.13e+00 1bj7 b.60.1.1 27113 1shp 55 2.23e+00 1bpi g.8.1.1 44553 1l8fA 207 2.40e+00 b.52.1.1 84537 2pspA 106 2.44e+00 2pspA g.16.1.1 44730 g.16.1.1 44731 1ka9H 200 2.51e+00 c.23.16.1 77308 1fkj 107 2.58e+00 1fkj d.26.1.1 38384 3sil 379 2.63e+00 3sil b.68.1.1 27542 1onwA 390 2.86e+00 b.92.1.7 87172 c.1.9.13 87173 1dim 381 2.93e+00 3sil b.68.1.1 27544 1onxA 390 3.04e+00 b.92.1.7 87176 c.1.9.13 87177 1ecfA 504 3.07e+00 1ecfB c.61.1.1 34053 d.153.1.1 41820 1jt7A 146 3.26e+00 b.42.1.1 67255 1tdtA 259 3.45e+00 3tdt b.81.1.2 28055 1pcp 106 3.48e+00 2pspA g.16.1.1 44742 g.16.1.1 44743 1i50B 1224 3.51e+00 e.29.1.1 61755 2tdt 274 3.55e+00 3tdt b.81.1.2 28054 1n1mA 728 3.61e+00 b.70.3.1 79815 c.69.1.24 79816 1kgqA 274 3.66e+00 b.81.1.2 72447 1lvk 762 3.68e+00 1lvk b.34.3.1 24576 c.37.1.9 32173 3tdt 274 3.74e+00 3tdt b.81.1.2 28053 1b2rA 304 3.78e+00 1fnc b.43.4.2 25648 c.25.1.1 31538 1fkd 107 3.87e+00 1fkj d.26.1.1 38383 1bkf 107 3.93e+00 1fkj d.26.1.1 38382 1p63A 144 4.23e+00 b.42.1.1 -4002 1i50A 1733 4.26e+00 e.29.1.2 61754 1ogiA 303 4.35e+00 b.43.4.2 -4042 c.25.1.1 -6587 1fkf 107 4.43e+00 1fkj d.26.1.1 38386 1delA 241 4.44e+00 1dekA c.37.1.1 31844 2reb 352 4.49e+00 2reb c.37.1.11 32282 d.48.1.1 38767 1dekA 241 4.52e+00 1dekA c.37.1.1 31842 1k8eA 345 4.63e+00 1o17A 345 4.63e+00 a.46.2.1 80765 c.27.1.1 80766 1go2A 304 4.65e+00 b.43.4.2 76243 c.25.1.1 76244 1ndh 272 4.85e+00 1ndh b.43.4.2 25662 c.25.1.1 31552 1irk 306 5.07e+00 1fmk d.144.1.7 41703 1wad 112 5.36e+00 3cyr a.138.1.1 19658 1que 303 5.48e+00 1fnc b.43.4.2 25647 c.25.1.1 31537 1adz 71 5.75e+00 1bpi g.8.1.1 44542 1e0lA 37 5.92e+00 1e0lA b.72.1.1 27804 1iso 416 6.08e+00 1iso c.77.1.1 35065 1oz7A 131 6.13e+00 d.169.1.1 -11622 1aozA 552 6.19e+00 1aozA b.6.1.3 23124 b.6.1.3 23125 b.6.1.3 23126 1v2bA 177 6.23e+00 1vom 762 6.26e+00 1lvk b.34.3.1 24577 c.37.1.9 32174 1ogoX 574 6.31e+00 unknown_sccs -3237 unknown_sccs -4783 1uolA 219 6.33e+00 b.2.5.2 -2886 1ezvA 430 6.41e+00 1be3A d.185.1.1 59541 d.185.1.1 59542 1jb7B 260 6.46e+00 1otcB b.40.4.3 62839 1gsmA 210 6.74e+00 b.1.1.4 65535 b.1.1.4 65536 1jqzA 146 6.98e+00 b.42.1.1 67109 1kb9A 431 7.31e+00 d.185.1.1 77311 d.185.1.1 77312 1otcB 260 7.32e+00 1otcB b.40.4.3 25310 1cczA 171 7.43e+00 1cczA b.1.1.1 19758 b.1.1.3 21683 7icd 416 7.66e+00 1iso c.77.1.1 35072 1dtx 59 7.71e+00 1bpi g.8.1.1 44551 1eyqA 222 7.73e+00 1eypA d.36.1.1 38534 1iznA 286 7.88e+00 e.43.1.1 83847 1jepA 222 7.90e+00 d.36.1.1 66612 1b77A 228 8.04e+00 1b77A d.131.1.2 41362 d.131.1.2 41363 1gmnA 183 8.13e+00 g.10.1.1 65315 g.14.1.1 65316 1qh0A 295 8.25e+00 b.43.4.2 68891 c.25.1.1 68892 1eagA 342 8.48e+00 1eagA b.50.1.2 26826 1uocA 289 8.50e+00 unknown_sccs -7671 1d0yA 761 8.52e+00 1lvk b.34.3.1 24581 c.37.1.9 32178 1g25A 65 8.62e+00 1g25A g.44.1.1 45325 1dyr 206 8.65e+00 1aoeA c.71.1.1 34916 1bfi 112 8.67e+00 1qadA d.93.1.1 40499 1liuA 528 8.93e+00 b.58.1.1 77970 c.1.12.1 77971 c.49.1.1 77972 1eybA 471 9.13e+00 1ey2A b.82.1.4 28115 1miwA 404 9.52e+00 a.173.1.1 79162 d.218.1.4 79163 1ir3A 306 9.81e+00 1fmk d.144.1.7 41702 1bhtA 176 9.91e+00 1bhtA g.10.1.1 44603 g.14.1.1 44663 1n67A 359 1.02e+01 b.2.3.4 85354 b.2.3.4 85355 1b91A 118 1.02e+01 1b91A 1e79A 510 1.03e+01 1skyB a.69.1.1 18269 b.49.1.1 26434 c.37.1.11 32314 1hp4A 512 1.05e+01 1hp4A c.1.8.6 61111 d.92.2.1 61112 1cjwA 166 1.05e+01 1cjwA d.108.1.1 40818 1jm4B 118 1.06e+01 a.29.2.1 71746 1cx8A 639 1.08e+01 1cx8B a.48.2.1 17782 c.8.4.1 30763 c.56.5.5 33851 1pb1A 416 1.08e+01 c.77.1.1 88014 1cx8B 639 1.12e+01 1cx8B a.48.2.1 17783 c.8.4.1 30764 c.56.5.5 33852 1mnd 762 1.13e+01 1lvk b.34.3.1 24591 c.37.1.9 32188 1g5vA 88 1.24e+01 1g5vA b.34.9.1 60292 1h9oA 112 1.24e+01 1qadA d.93.1.1 60837 1de4C 640 1.26e+01 1cx8B a.48.2.1 17779 c.8.4.1 30760 c.56.5.5 33848 1kuxA 207 1.26e+01 d.108.1.1 73021 1jakA 512 1.27e+01 c.1.8.6 66472 d.92.2.1 66473 1d6aB 262 1.30e+01 1qi7A d.165.1.1 42198 1tupA 219 1.36e+01 1tupA b.2.5.2 22434 2afgA 140 1.36e+01 1bfg b.42.1.1 25514 1meyC 87 1.38e+01 2gliA k.12.1.1 46430 1k8kA 418 1.42e+01 c.55.1.1 68305 c.55.1.1 68306 1ep3B 262 1.45e+01 1ep2B b.43.4.2 25664 c.25.1.3 31554 1mp9A 198 1.46e+01 a.74.1.2 -1127 a.74.1.2 -1128 1cxvA 164 1.52e+01 1ck7A d.92.1.11 40404 1tsrA 219 1.56e+01 1tupA b.2.5.2 22437 1i1iP 681 1.57e+01 1i1iP d.92.1.5 40297 1qciA 262 1.58e+01 1qi7A d.165.1.1 42201 1avpA 204 1.62e+01 1avpA d.3.1.7 37132 1jyoA 130 1.64e+01 d.198.1.1 67483 1se9A 126 1.65e+01 d.15.1.1 -9145 1h8eA 510 1.67e+01 1skyB a.69.1.1 60738 b.49.1.1 60739 c.37.1.11 60740 1eo9A 209 1.67e+01 3pchA b.3.6.1 22731 1iqqA 200 1.69e+01 d.124.1.1 66274 1eypA 222 1.71e+01 1eypA d.36.1.1 38536 1crwG 333 1.71e+01 1dssG c.2.1.3 30026 d.81.1.1 39941 1tie 172 1.72e+01 1wba b.42.4.1 25592 1l8dA 112 1.74e+01 h.4.12.1 73687 1exmA 405 1.76e+01 1efcA b.43.3.1 25696 b.44.1.1 25736 c.37.1.8 32131 1tlk 154 1.77e+01 1tlk b.1.1.4 21707 1oghA 204 1.80e+01 b.85.4.1 86994 1f39A 101 1.81e+01 1umuA b.87.1.1 28386 1ln1A 214 1.92e+01 d.129.3.2 74038 1dceA 567 1.94e+01 1dceA a.118.6.1 19191 b.7.4.1 23218 c.10.2.2 30867 2hgf 97 1.99e+01 1bhtA g.10.1.1 44607 1toaA 313 2.00e+01 1toaA c.92.2.2 35598 1jj2Y 73 2.00e+01 1ffkW g.41.8.1 63110 1bbpA 173 2.01e+01 1bbpA b.60.1.1 27147 1gk8I 140 2.06e+01 d.73.1.1 65242 1skyB 502 2.06e+01 1skyB a.69.1.1 18313 b.49.1.1 26478 c.37.1.11 32358 1kxoA 184 2.07e+01 b.60.1.1 84475 1oalA 151 2.10e+01 b.1.8.1 86739 1bmfA 510 2.17e+01 1skyB a.69.1.1 18281 b.49.1.1 26446 c.37.1.11 32326 1ep2B 261 2.24e+01 1ep2B b.43.4.2 25666 c.25.1.3 31556 1kyoA 430 2.30e+01 d.185.1.1 73249 d.185.1.1 73250 1nngA 153 2.31e+01 d.38.1.1 -9636 1bk7A 190 2.34e+01 1bk7A d.124.1.1 41121 1hp5A 512 2.34e+01 1hp4A c.1.8.6 61113 d.92.2.1 61114 1umhA 184 2.34e+01 unknown_sccs -3127 1b6a 478 2.40e+01 1bn5 a.4.5.25 16223 d.127.1.1 41160 1dssG 333 2.42e+01 1dssG c.2.1.3 30022 d.81.1.1 39937 1igrA 478 2.44e+01 1igrA c.10.2.5 30877 c.10.2.5 30878 g.3.9.1 44188 1nlnA 204 2.44e+01 d.3.1.7 -8897 1rg9A 383 2.45e+01 d.130.1.1 -11057 d.130.1.1 -11058 d.130.1.1 -11059 1ksqA 75 2.45e+01 g.23.1.1 -12689 1abmA 198 2.46e+01 1avmA 1ey2A 471 2.47e+01 1ey2A b.82.1.4 28116 1mhnA 59 2.47e+01 b.34.9.1 84964 1fgyA 127 2.49e+01 1faoA b.55.1.1 26976 1hg4A 279 2.49e+01 1lbd a.123.1.1 19333 1lf6A 684 2.53e+01 a.102.1.5 77918 b.30.5.5 77919 1ucdA 190 2.55e+01 1ucaA 190 2.55e+01 d.124.1.1 88462 2asi 360 2.56e+01 2rmpA b.50.1.2 26824 1pl4A 198 2.57e+01 a.2.11.1 -132 d.44.1.1 -9733 1m9sA 605 2.59e+01 b.1.18.15 78874 b.34.11.1 78875 b.34.11.1 78876 b.34.11.1 78877 c.10.2.1 78878 1mfgA 95 2.69e+01 b.36.1.1 79043 1lv3A 68 2.70e+01 g.39.1.9 78231 1v7oA 165 2.70e+01 unknown_sccs -10249 1bn5 478 2.71e+01 1bn5 a.4.5.25 16224 d.127.1.1 41161 1gtxA 472 2.71e+01 1gtxA 1g8jB 133 2.71e+01 1g8jB b.33.1.1 24439 1n0nA 199 2.74e+01 a.2.11.1 79750 d.44.1.1 79751 1hh1A 143 2.76e+01 1gefA c.52.1.18 61036 1ycsA 199 2.78e+01 1tupA b.2.5.2 22433 1a3z 155 2.79e+01 1rcy b.6.1.1 23019 1oruA 195 2.85e+01 unknown_sccs -4390 2rel 57 2.85e+01 1fleI g.3.14.1 44353 2xat 212 2.88e+01 2xat b.81.1.3 28058 1pkhA 204 2.90e+01 b.85.4.1 -5053 1ap6A 198 2.94e+01 1avmA a.2.11.1 15746 d.44.1.1 38705 1cnzA 363 2.96e+01 1cnzA c.77.1.1 35061 5pti 58 3.04e+01 1bpi g.8.1.1 44467 1bqsA 209 3.06e+01 1bqsA b.1.1.4 21704 b.1.1.4 21705 1efvA 315 3.07e+01 1efvA c.26.2.3 31633 c.31.1.2 31728 1a26 361 3.13e+01 1a26 a.41.1.1 17412 d.166.1.2 42274 1svpA 161 3.16e+01 1svpA b.47.1.3 26384 1bpi 58 3.16e+01 1bpi g.8.1.1 44468 1qhvA 195 3.17e+01 1qhvA b.21.1.1 23842 2snv 151 3.18e+01 1svpA b.47.1.3 26394 16pk 415 3.21e+01 16pk c.86.1.1 35454 1ofwA 296 3.25e+01 a.138.1.1 -2035 1q2wA 308 3.25e+01 b.47.1.4 88355 1qrrA 394 3.27e+01 1qrrA c.2.1.2 29824 3nodB 423 3.29e+01 1nseA d.174.1.1 42513 1g8kB 133 3.30e+01 1g8jB b.33.1.1 24435 1vj0A 380 3.37e+01 b.35.1.2 -3697 c.2.1.1 -5721 1go3F 107 3.42e+01 a.60.8.2 65407 1p3wA 404 3.45e+01 c.67.1.3 87752 1htwA 158 3.46e+01 c.37.1.18 71083 1nmtA 392 3.50e+01 1nmtA d.108.1.2 40823 d.108.1.2 40824 1efyA 350 3.53e+01 1a26 a.41.1.1 17413 d.166.1.2 42275 1pil 112 3.54e+01 2pii d.58.5.1 39072 1dec 39 3.59e+01 1dec g.3.15.2 44376 1dupA 152 3.59e+01 1dupA b.85.4.1 28351 1q16A 1247 3.61e+01 b.52.2.2 -4337 c.81.1.1 -8547 1apa 266 3.62e+01 1qi7A d.165.1.1 42205 1iw7C 1119 3.64e+01 e.29.1.1 71474 1p8kZ 254 3.70e+01 d.95.2.1 -10648 d.95.2.1 -10649 2hvm 273 3.79e+01 1cnv c.1.8.5 28985 1ixlA 131 3.83e+01 d.38.1.5 -9705 1lrwA 600 3.84e+01 b.70.1.1 -4629 1p65A 73 3.84e+01 unknown_sccs -10331 1fleI 57 3.85e+01 1fleI g.3.14.1 44352 1dxrL 273 3.86e+01 6prcL f.26.1.1 43431 1fecA 490 3.86e+01 3grs c.3.1.5 30489 c.3.1.5 30490 d.87.1.1 40176 2tgpI 58 3.87e+01 1bpi g.8.1.1 44494 1q8iA 783 3.88e+01 c.55.3.5 -7635 e.8.1.1 -11885 1uypA 432 3.89e+01 unknown_sccs -3480 unknown_sccs -4554 1c55A 40 3.93e+01 1sco g.3.7.2 44158 1vjnA 220 3.97e+01 unknown_sccs -11458