# List of top-scoring protein chains for t2k-w0.5 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 1bx0A 314 1.31e-01 1fnc b.43.4.2 25630 c.25.1.1 31520 1frqA 314 1.31e-01 1fnc b.43.4.2 25632 c.25.1.1 31522 1fnc 314 1.31e-01 1fnc b.43.4.2 25627 c.25.1.1 31517 1fnd 314 1.31e-01 1fnc b.43.4.2 25626 c.25.1.1 31516 1bx1A 314 1.31e-01 1fnc b.43.4.2 25629 c.25.1.1 31519 1frn 314 1.40e-01 1fnc b.43.4.2 25631 c.25.1.1 31521 1qnrA 344 2.57e-01 1qnoA c.1.8.3 28834 1qnoA 344 2.57e-01 1qnoA c.1.8.3 28838 1ht3A 279 3.02e-01 1gci c.41.1.1 61243 1d2zA 108 4.85e-01 1d2zA a.77.1.1 18437 1qo7A 394 6.85e-01 1qo7A c.69.1.11 34697 2prk 279 8.17e-01 1gci c.41.1.1 32548 2tldE 220 9.04e-01 5ptp b.47.1.2 25881 1ic6A 279 9.21e-01 1gci c.41.1.1 62257 1srdA 154 1.18e+00 1mfmA b.1.8.1 22275 1l0yD 221 1.24e+00 1b1zA 219 1.30e+00 3seb b.40.2.2 25216 d.15.6.1 37805 1elvA 333 1.39e+00 5ptp b.47.1.2 59454 g.18.1.1 59455 1fnuA 221 1.40e+00 3seb b.40.2.2 25212 d.15.6.1 37801 1ha5A 218 1.45e+00 1fohA 664 1.49e+00 1fohA c.3.1.2 30381 c.47.1.10 33078 d.16.1.2 37900 1e63A 304 1.85e+00 1fnc b.43.4.2 59287 c.25.1.1 59288 1f6dA 376 1.85e+00 1f6dA c.87.1.3 35467 1hj9A 223 1.94e+00 b.47.1.2 65845 1c5dB 215 2.11e+00 1igtB b.1.1.1 20415 b.1.1.2 21387 1a3gA 308 2.21e+00 1daaA e.17.1.1 43286 1i1kA 309 2.21e+00 1daaA e.17.1.1 61533 1jglH 218 2.26e+00 b.1.1.1 66679 b.1.1.2 66680 1g3fA 117 2.30e+00 1g3fA g.52.1.1 45378 1g73C 121 2.31e+00 1g3fA g.52.1.1 45375 1f9xA 120 2.32e+00 1g3fA g.52.1.1 59748 1e64A 304 2.38e+00 1fnc b.43.4.2 59289 c.25.1.1 59290 1rap 108 2.54e+00 1ycc a.3.1.1 15858 1raq 108 2.59e+00 1ycc a.3.1.1 15844 1mvmA 587 2.68e+00 2cas b.10.1.4 23383 1kipB 116 2.83e+00 1gc1H b.1.1.1 19957 4dpvZ 584 2.86e+00 2cas b.10.1.4 23377 1qgc4 438 2.99e+00 1igtB 1quf 303 3.01e+00 1fnc b.43.4.2 25650 c.25.1.1 31540 1qg0A 308 3.17e+00 1fnc b.43.4.2 25639 c.25.1.1 31529 1qgaA 308 3.17e+00 1fnc b.43.4.2 25637 c.25.1.1 31527 1qfzA 308 3.17e+00 1fnc b.43.4.2 25633 c.25.1.1 31523 1b2rA 304 3.25e+00 1fnc b.43.4.2 25648 c.25.1.1 31538 1gjrA 304 3.25e+00 1que 303 3.26e+00 1fnc b.43.4.2 25647 c.25.1.1 31537 1bqk 124 3.27e+00 1bqk b.6.1.1 22889 1ewyA 303 3.30e+00 1fnc b.43.4.2 25651 c.25.1.1 31541 1m6pA 152 3.47e+00 1m6pA b.64.1.1 27519 1keoA 154 3.50e+00 b.64.1.1 68534 1bvkB 117 3.54e+00 1gc1H b.1.1.1 20279 1g5aA 628 3.60e+00 b.71.1.1 65152 c.1.8.1 65153 1mfbH 219 3.75e+00 1mfa b.1.1.1 19891 b.1.1.2 20985 1bjk 295 3.81e+00 1fnc b.43.4.2 25649 c.25.1.1 31539 1bqeA 295 3.90e+00 b.43.4.2 64760 c.25.1.1 64761 1b47A 304 3.94e+00 2cblA a.39.1.7 17381 a.48.1.1 17775 d.93.1.1 40529 2cblA 305 3.95e+00 2cblA a.39.1.7 17380 a.48.1.1 17774 d.93.1.1 40528 1jgiA 628 4.31e+00 b.71.1.1 66676 c.1.8.1 66677 2rig 144 4.37e+00 1d9cA a.26.1.3 16921 5ptp 223 4.40e+00 5ptp b.47.1.2 25831 1b9nA 265 4.45e+00 1b9mA a.4.5.8 16120 b.40.6.2 58942 b.40.6.2 58943 1h85A 295 4.45e+00 b.43.4.2 65716 c.25.1.1 65717 1a7nH 116 4.47e+00 1gc1H b.1.1.1 19941 1a2yB 116 4.47e+00 1gc1H b.1.1.1 19927 1vfaB 116 4.47e+00 1gc1H b.1.1.1 19929 1g7jB 116 4.47e+00 1f3rB b.1.1.1 19933 1kiqB 116 4.48e+00 1gc1H b.1.1.1 19939 1fbvA 388 4.86e+00 2cblA a.39.1.7 17384 a.48.1.1 17778 d.93.1.1 40532 g.44.1.1 45321 1ntp 223 5.17e+00 5ptp b.47.1.2 25858 1c5sA 223 5.21e+00 5ptp b.47.1.2 25903 1j8aA 223 5.21e+00 b.47.1.2 62737 1g3cA 228 5.47e+00 5ptp b.47.1.2 25921 1tgsZ 229 5.61e+00 5ptp b.47.1.2 25850 1tgb 229 5.81e+00 5ptp b.47.1.2 25875 1byqA 228 5.84e+00 1yer d.122.1.1 41100 1yer 228 5.84e+00 1yer d.122.1.1 41101 1zzzA 237 6.26e+00 5ptp b.47.1.2 25892 1qmuA 380 6.44e+00 1qmuA b.3.2.1 22534 c.56.5.1 33827 1qttA 117 6.54e+00 1a1x b.63.1.1 27516 1f0tA 243 6.54e+00 5ptp b.47.1.2 25937 1jhgA 101 6.86e+00 1jhgA a.107.1.1 19009 1hplA 449 6.97e+00 1gpl b.12.1.2 23639 c.69.1.19 34787 1bal 51 7.02e+00 1bbl a.9.1.1 16357 1bbl 51 7.02e+00 1bbl a.9.1.1 16356 1j4wA 174 7.20e+00 1b28A 53 7.25e+00 1bazA a.43.1.1 17445 1fryA 29 8.10e+00 1rcsA 105 8.21e+00 1jhgA a.107.1.1 19025 1fdlH 218 8.27e+00 1igtB b.1.1.1 19961 b.1.1.2 21021 1aroP 883 8.34e+00 1cezA e.8.1.3 43112 1e62A 304 8.34e+00 1fnc b.43.4.2 59285 c.25.1.1 59286 1qlnA 883 8.36e+00 1cezA e.8.1.3 43111 1cezA 883 8.36e+00 1cezA e.8.1.3 43110 4rnpA 883 8.36e+00 1cezA e.8.1.3 43113 2wrpR 107 8.40e+00 1jhgA a.107.1.1 19010 1trrA 107 8.62e+00 1jhgA a.107.1.1 19017 1fpv 584 8.67e+00 2cas b.10.1.4 23579 3wrp 108 8.77e+00 1jhgA a.107.1.1 19015 1nsnH 210 8.80e+00 1igtB b.1.1.1 20071 b.1.1.2 21103 1tawA 223 8.87e+00 5ptp b.47.1.2 25860 1troA 108 9.24e+00 1jhgA a.107.1.1 19011 1pls 113 9.55e+00 1pls b.55.1.1 26965 1b9mA 265 9.70e+00 1b9mA a.4.5.8 16118 b.40.6.2 58938 b.40.6.2 58939 1d2mA 665 1.01e+01 1d2mA c.37.1.13 32417 c.37.1.13 32418 1c4oA 664 1.01e+01 1d2mA c.37.1.13 32415 c.37.1.13 32416 1gq8A 319 1.04e+01 1dl7H 112 1.06e+01 1f3rB b.1.1.1 20499 1a1x 108 1.12e+01 1a1x b.63.1.1 27514 1h4wA 224 1.15e+01 b.47.1.2 65622 1gawB 314 1.15e+01 1fnc b.43.4.2 25644 c.25.1.1 31534 1hg4E 279 1.19e+01 1lbd a.123.1.1 19337 1ggwA 140 1.23e+01 1ggwA a.39.1.5 60490 1ql0A 241 1.29e+01 1qaeA d.4.1.2 37139 1kqfA 1015 1.33e+01 1g8tA 245 1.34e+01 1qaeA d.4.1.2 37137 1smnA 245 1.34e+01 1qaeA d.4.1.2 37143 1qaeA 245 1.34e+01 1qaeA d.4.1.2 37141 1g94A 448 1.35e+01 b.71.1.1 65169 c.1.8.1 65170 1kxhA 448 1.36e+01 1aqm 453 1.37e+01 1smd b.71.1.1 27717 c.1.8.1 28704 1fxyA 228 1.41e+01 5ptp b.47.1.2 26347 1cynA 178 1.43e+01 2cpl b.62.1.1 27489 1ccr 112 1.45e+01 1ycc a.3.1.1 15877 2cy3 118 1.47e+01 3cyr a.138.1.1 19649 1dliA 402 1.47e+01 1dliA a.100.1.4 18809 c.2.1.6 30213 c.26.3.1 31622 1c05A 159 1.48e+01 1c05A d.66.1.2 39559 1g2nA 264 1.51e+01 1lbd a.123.1.1 60227 1fb3A 296 1.51e+01 1fnc b.43.4.2 25641 c.25.1.1 31531 1fvcB 120 1.52e+01 1igtB b.1.1.1 19863 1dljA 402 1.55e+01 1dliA a.100.1.4 18808 c.2.1.6 30212 c.26.3.1 31621 1k3vA 579 1.56e+01 b.10.1.4 68122 1i7pA 274 1.57e+01 b.43.4.2 66048 c.25.1.1 66049 1qgzA 295 1.61e+01 b.43.4.2 68889 c.25.1.1 68890 1eptC 98 1.63e+01 5ptp 1prtC 196 1.80e+01 1bcpB b.40.2.1 25117 d.169.1.2 42426 1bcpC 199 1.83e+01 1bcpB b.40.2.1 25121 d.169.1.2 42430 1a3lH 218 1.83e+01 1mfa b.1.1.1 20241 b.1.1.2 21253 1cz8V 94 1.99e+01 1vpfA g.17.1.1 44765 1i86A 389 2.00e+01 c.95.1.2 66068 c.95.1.2 66069 1ja9A 274 2.00e+01 c.2.1.2 62817 1i88A 389 2.01e+01 c.95.1.2 66070 c.95.1.2 66071 1i8bA 389 2.01e+01 c.95.1.2 66078 c.95.1.2 66079 1i89A 389 2.02e+01 c.95.1.2 66074 c.95.1.2 66075 1d6iA 388 2.03e+01 1bi5A c.95.1.2 36001 c.95.1.2 36002 1d9xA 658 2.05e+01 1d2mA c.37.1.13 32419 c.37.1.13 32420 1adwA 123 2.05e+01 1bqk b.6.1.1 22893 1dqiA 124 2.05e+01 1do6A b.1.13.1 22357 1do6A 124 2.05e+01 1do6A b.1.13.1 22361 1trnA 224 2.07e+01 5ptp b.47.1.2 26000 1fltV 98 2.12e+01 1vpfA g.17.1.1 44751 1eavA 162 2.13e+01 c.57.1.1 64877 1bq6A 388 2.13e+01 1bi5A c.95.1.2 35987 c.95.1.2 35988 1bi5A 389 2.13e+01 1bi5A c.95.1.2 35985 c.95.1.2 35986 1d6hA 387 2.17e+01 1bi5A c.95.1.2 36005 c.95.1.2 36006 1mlcB 218 2.20e+01 1igtB b.1.1.1 20053 b.1.1.2 21095 1ndh 272 2.26e+01 1ndh b.43.4.2 25662 c.25.1.1 31552 1hskA 326 2.26e+01 2mbr d.145.1.2 61241 d.146.1.1 61242 1chwA 389 2.32e+01 1bi5A c.95.1.2 35997 c.95.1.2 35998 1vppV 102 2.32e+01 1vpfA g.17.1.1 44753 1vpfA 102 2.32e+01 1vpfA g.17.1.1 44767 1rp1 441 2.33e+01 1gpl b.12.1.2 23646 c.69.1.19 34794 1cmlA 389 2.36e+01 1bi5A c.95.1.2 35989 c.95.1.2 35990 1jwxA 389 2.42e+01 5cytR 104 2.45e+01 1ycc a.3.1.1 15878 1lfmA 103 2.50e+01 1cgzA 389 2.52e+01 1bi5A c.95.1.2 35993 c.95.1.2 35994 1irw 108 2.60e+01 1ycc a.3.1.1 15855 1fhb 108 2.63e+01 1ycc a.3.1.1 15862 1pmy 123 2.65e+01 1bqk b.6.1.1 22888 1b6a 478 2.67e+01 1bn5 a.4.5.25 16223 d.127.1.1 41160 1bn5 478 2.68e+01 1bn5 a.4.5.25 16224 d.127.1.1 41161 1gnhA 206 2.69e+01 1sacA b.29.1.5 24252 1cyc 103 2.74e+01 1ycc a.3.1.1 15881 1ey2A 471 2.77e+01 1ey2A b.82.1.4 28116 1eybA 471 2.77e+01 1ey2A b.82.1.4 28115 1gwcA 230 2.83e+01 1nddA 76 2.88e+01 1ubi d.15.1.1 37599 1nddD 76 2.88e+01 1ubi d.15.1.1 37602 1fnsH 225 2.94e+01 1igtB b.1.1.1 20289 b.1.1.2 21281 1oakH 223 2.96e+01 1igtB b.1.1.1 20291 b.1.1.2 21283 1irv 108 2.99e+01 1ycc a.3.1.1 15857 1fvdB 223 3.04e+01 1igtB b.1.1.1 19867 b.1.1.2 20963 1cqyA 99 3.04e+01 1b9zA b.3.1.1 22527 1csx 108 3.06e+01 1ycc a.3.1.1 15841 1fveB 223 3.08e+01 1igtB b.1.1.1 19871 b.1.1.2 20967 1yfc 108 3.08e+01 1ycc a.3.1.1 15864 1kyoW 108 3.09e+01 1mctA 223 3.09e+01 5ptp b.47.1.2 25961 3hflH 215 3.10e+01 1igtB b.1.1.1 19969 b.1.1.2 21027 1yic 108 3.10e+01 1ycc a.3.1.1 15863 1a79A 171 3.15e+01 1a79A c.52.2.1 33340 d.75.1.1 39739 1giw 104 3.18e+01 1ycc a.3.1.1 15874 1a58 177 3.21e+01 2cpl b.62.1.1 27495 1wejF 105 3.22e+01 1ycc a.3.1.1 15865 1ycc 108 3.22e+01 1ycc a.3.1.1 15834 2ycc 108 3.23e+01 1ycc a.3.1.1 15856 1crh 109 3.26e+01 1ycc a.3.1.1 15849 1crg 109 3.27e+01 1ycc a.3.1.1 15854 1m60A 104 3.28e+01 1csw 108 3.31e+01 1ycc a.3.1.1 15839 1chh 108 3.31e+01 1ycc a.3.1.1 15852 1csv 108 3.36e+01 1ycc a.3.1.1 15850 1emtH 213 3.44e+01 1igtB b.1.1.1 20483 b.1.1.2 21447 1eiwA 111 3.56e+01 1eiwA c.23.3.1 31130 1cie 108 3.57e+01 1ycc a.3.1.1 15838 1csu 108 3.60e+01 1ycc a.3.1.1 15837 1gotA 350 3.63e+01 1cipA a.66.1.1 18213 c.37.1.8 32096 1jx4A 352 3.65e+01 e.8.1.5 67405 1eoeA 100 3.73e+01 1t1dA d.42.1.2 38638 1qh0A 295 3.74e+01 b.43.4.2 68891 c.25.1.1 68892 1chj 108 3.76e+01 1ycc a.3.1.1 15851 1qqfA 277 3.77e+01 1c3d a.102.4.4 18875 1qsjA 277 3.77e+01 1c3d a.102.4.4 18876 1jljA 189 3.77e+01 c.57.1.1 63169 1hh1A 143 3.78e+01 1gefA c.52.1.18 61036 2gsq 202 3.80e+01 1pd21 a.45.1.1 17715 c.47.1.5 33009 1chi 108 3.86e+01 1ycc a.3.1.1 15848 1c3tA 76 3.88e+01 1ubi d.15.1.1 37594