# List of top-scoring protein chains for T0305.t04-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 2fh7A 595 1.92e-55 2c7sA 313 1.81e-54 1larA 575 4.12e-54 1larA c.45.1.2,c.45.1.2 32693,32694 1yfoA 302 4.25e-54 2shpA c.45.1.2 32681 1rpmA 278 1.14e-52 2shpA c.45.1.2 32679 2ahsA 295 1.97e-52 2cfvA 316 3.00e-51 2gjtA 295 1.16e-50 2g59A 297 1.18e-50 1ygrA 610 3.09e-50 1p15A 253 5.83e-50 c.45.1.2 93894 2shpA 525 5.09e-49 2shpA c.45.1.2,d.93.1.1,d.93.1.1 32683,40533,40534 2b3oA 532 3.07e-48 1gwz 299 7.28e-48 2shpA c.45.1.2 32685 2fjmA 310 9.84e-48 1q6nA 310 1.19e-47 c.45.1.2 95984 1lqfA 295 1.22e-47 c.45.1.2 74187 2f6fA 302 1.44e-47 1bzhA 298 1.76e-47 1pty c.45.1.2 32664 2f71A 298 1.79e-47 2azrA 299 1.79e-47 1bzcA 321 1.81e-47 1pty c.45.1.2 32670 1oemX 321 1.85e-47 c.45.1.2 86916 1bzjA 297 1.85e-47 1pty c.45.1.2 32667 1fprA 284 2.31e-47 2shpA c.45.1.2 59949 1l8kA 314 2.40e-47 c.45.1.2 73691 1c83A 298 2.49e-47 1pty c.45.1.2 32660 1l8gA 321 2.56e-47 c.45.1.2 73689 1c86A 298 3.04e-47 1pty c.45.1.2 32668 1i57A 310 4.28e-47 1pty c.45.1.2 61772 2b49A 287 4.41e-47 1a5y 330 4.91e-47 1pty c.45.1.2 32673 1pa1A 310 5.08e-47 c.45.1.2 94404 1nwlA 298 6.01e-47 c.45.1.2 86300 1gfyA 298 6.37e-47 1pty c.45.1.2 32666 1eeoA 321 6.65e-47 1pty c.45.1.2 32655 1aax 321 6.71e-47 1pty c.45.1.2 32657 1ptuA 321 8.83e-47 1pty c.45.1.2 32675 1g1fA 298 8.96e-47 1pty c.45.1.2 32662 1ptvA 321 9.24e-47 1pty c.45.1.2 32665 2a3kA 296 3.45e-46 1zc0A 309 3.58e-46 2gp0A 309 3.91e-46 2a8bA 283 2.72e-45 1wchA 315 3.45e-45 1jlnA 297 5.33e-45 1pty c.45.1.2 63172 2bijA 305 2.96e-44 2bzlA 325 3.08e-44 2bv5A 282 1.55e-43 1pa9A 284 1.26e-17 c.45.1.2 94411 1yptA 305 1.26e-17 1ytw c.45.1.2 32686 1qz0A 306 1.26e-17 c.45.1.2 96607 1xxvA 306 1.26e-17 1lyvA 306 6.28e-17 c.45.1.2 74348 1xxpA 306 6.28e-17 1yts 278 6.32e-17 1ytw c.45.1.2 32690 1ohcA 348 1.01e-16 c.45.1.1,c.45.1.1 87009,87010 1oheA 348 5.04e-16 c.45.1.1,c.45.1.1 87013,87014 1g4wR 383 3.67e-12 1g4uS a.24.11.1,c.45.1.2 16644,32692 1x24A 180 3.20e-11 1rxdA 159 3.79e-11 1zckA 154 3.91e-11 1zclA 180 1.99e-10 1xm2A 173 2.36e-10 1v3aA 173 1.32e-09 1r6hA 172 1.35e-09 c.45.1.1 97150 1fpzA 212 1.06e-07 1fpzA c.45.1.1 59976 1d5rA 324 1.51e-05 1d5rA b.7.1.1,c.45.1.1 23181,32697 1yn9A 169 4.77e-05 1m3gA 145 2.25e-04 c.45.1.1 84783 1vhrA 184 3.00e-04 1vhrA c.45.1.1 32651 1wrmA 165 4.96e-04 2c46A 241 6.01e-04 1i9sA 210 8.69e-04 1i9sA c.45.1.1 62099 1j4xA 184 2.16e-03 c.45.1.1 66392 1yz4A 160 5.16e-03 1mkp 144 1.11e-02 1vhrA c.45.1.1 32654 1ywfA 296 1.55e-02 1zsqA 528 2.33e-02 1lw3A 657 2.38e-02 b.55.1.8,c.45.1.3 91152,91153 1xriA 151 5.43e-02 1gvhA 396 6.99e-02 a.1.1.2,b.43.4.2,c.25.1.5 70601,70602,70603 1u24A 337 2.63e-01 1z6tA 591 3.87e-01 2d5cA 263 7.79e-01 1h4jA 599 1.15e+00 4aahA b.70.1.1 60590 1h4iA 599 1.21e+00 4aahA b.70.1.1 60586 1w6sA 599 1.24e+00 1ciu 683 1.62e+00 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21852,22521,27759,28746 1erjA 393 1.97e+00 1erjA b.69.4.1 27660 1p2fA 220 2.14e+00 a.4.6.1,c.23.1.1 87720,87721 1zpdA 568 3.50e+00 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31741,31785,31786 1ux6A 350 3.71e+00 b.29.1.16,g.75.1.1 100145,100146 1lrwA 600 3.96e+00 b.70.1.1 91111 1zunA 325 5.10e+00 1d7fA 686 6.25e+00 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21848,22517,27755,28742 1pamA 686 6.37e+00 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21846,22515,27753,28740 1v3jA 686 6.38e+00 b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 108305,108306,108307,108308 1uksA 686 6.48e+00 b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 99517,99518,99519,99520 1v3kA 686 6.50e+00 b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 108313,108314,108315,108316 1di6A 195 7.25e+00 1di6A c.57.1.1 33863 1wj7A 104 8.54e+00 1dytA 133 9.99e+00 7rsa d.5.1.1 37288 1h1hA 134 1.00e+01 d.5.1.1 76468 1uktA 686 1.05e+01 b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 99525,99526,99527,99528 1zbxB 141 1.09e+01 1urhA 280 1.10e+01 c.46.1.2,c.46.1.2 99829,99830 1ot1A 686 1.17e+01 b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 87392,87393,87394,87395 1pezA 686 1.20e+01 b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 94600,94601,94602,94603 1ot2A 686 1.22e+01 b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 87396,87397,87398,87399 1kckA 686 1.35e+01 b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 68441,68442,68443,68444 1cgw 686 1.36e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21822,22491,27729,28716 1pj9A 686 1.39e+01 b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 94754,94755,94756,94757 1cgx 686 1.40e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21832,22501,27739,28726 1cgv 686 1.42e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21820,22489,27727,28714 1cgy 686 1.42e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21823,22492,27730,28717 1cdg 686 1.43e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21816,22485,27723,28710 1kclA 686 1.45e+01 b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 68445,68446,68447,68448 1ys7A 233 1.48e+01 1eo5A 686 1.48e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21828,22497,27735,28722 1cxlA 686 1.49e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21829,22498,27736,28723 1d3cA 686 1.52e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21827,22496,27734,28721 1tcmA 686 1.52e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21833,22502,27740,28727 1bu6O 501 1.56e+01 1glcG c.55.1.4,c.55.1.4 33499,33500 1dtuA 686 1.66e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21840,22509,27747,28734 1glaG 501 1.66e+01 1glcG c.55.1.4,c.55.1.4 33507,33508 1x4zA 121 1.71e+01 1gljO 501 1.81e+01 1glcG c.55.1.4,c.55.1.4 33525,33526 1s58A 554 1.86e+01 b.121.5.2 105262 1z1aA 142 1.96e+01 1zhiB 138 1.96e+01 1e69A 322 1.98e+01 1e69B c.37.1.12 32376 1eu8A 409 2.11e+01 1eu8A c.94.1.1 59502 2tsrA 307 2.59e+01 1bkpA d.117.1.1 41043 1fv3A 472 2.69e+01 b.29.1.6,b.42.4.2 60038,60039 1jhzA 289 2.80e+01 c.93.1.1 66731 1jfsA 340 2.81e+01 a.35.1.5,c.93.1.1 66650,66651 2cryA 122 2.95e+01 1j8mF 297 3.06e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 2c9kA 612 3.06e+01 1jh9A 340 3.21e+01 a.35.1.5,c.93.1.1 66710,66711 1yb5A 351 3.23e+01 1dleA 298 3.26e+01 1dleA b.47.1.2 26312 1yumA 242 3.27e+01 1dbqA 289 3.28e+01 1qpzA c.93.1.1 35666 1qpzA 340 3.29e+01 1qpzA a.35.1.5,c.93.1.1 17097,35673 1vpwA 340 3.31e+01 1qpzA a.35.1.5,c.93.1.1 17087,35680 2pugA 340 3.35e+01 1qpzA a.35.1.5,c.93.1.1 17088,35683 1m1nB 522 3.39e+01 c.92.2.3 78418 1g20B 523 3.39e+01 1qguB c.92.2.3 35614 1qqbA 340 3.41e+01 1qpzA a.35.1.5,c.93.1.1 17099,35674 1a8d 452 3.45e+01 1a8d b.29.1.6,b.42.4.2 24262,25607 1jftA 340 3.50e+01 a.35.1.5,c.93.1.1 66652,66653 1aroP 883 3.57e+01 1cezA e.8.1.3 43112 1j8yF 297 3.58e+01 1ng1 a.24.13.1,c.37.1.10 62747,62748 1fu5A 111 3.73e+01 1qadA d.93.1.1 40505 1d0hA 469 3.86e+01 1a8d b.29.1.6,b.42.4.2 24265,25610 2pucA 340 3.88e+01 1qpzA a.35.1.5,c.93.1.1 17094,35684 1ja1A 622 3.93e+01 1amoA b.43.4.1,c.23.5.2,c.25.1.4 62803,62804,62805 1ja0A 620 3.94e+01 1amoA b.43.4.1,c.23.5.2,c.25.1.4 62798,62799,62800 1j9zA 622 3.95e+01 1amoA b.43.4.1,c.23.5.2,c.25.1.4 62792,62793,62794 1cyg 680 3.96e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21843,22512,27750,28737 1t3gA 159 3.96e+01 1diwA 441 3.98e+01 1a8d b.29.1.6,b.42.4.2 24264,25609 1okkD 303 4.12e+01 a.24.13.1,c.37.1.10 93261,93262 1amoA 615 4.21e+01 1amoA b.43.4.1,c.23.5.2,c.25.1.4 25669,31210,31557 1teeA 393 4.25e+01 c.95.1.2 106811 1eft 405 4.25e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25688,25728,32123 1tedA 393 4.30e+01 c.95.1.2 106807 1rj9A 304 4.33e+01 a.24.13.1,c.37.1.10 97553,97554 1b23P 405 4.42e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25689,25729,32124 2g2bA 150 4.47e+01 2g7zA 282 4.54e+01 1us8A 147 4.55e+01 c.37.1.12 99859 1f2tA 149 4.57e+01 1f2tA c.37.1.12 32373 2bivA 243 4.63e+01 1b5qA 472 4.72e+01 1b37B c.3.1.2,d.16.1.5 30404,37968 1wxuA 93 4.80e+01 1ii8A 195 4.86e+01 1f2tA c.37.1.12 62417 1dfqA 444 4.87e+01 1a8d b.29.1.6,b.42.4.2 24267,25612 1exmA 405 4.90e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 1npyA 271 4.92e+01 c.2.1.7,c.58.1.5 85995,85996 1aipA 405 5.00e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25697,25737,32132 1qgzA 295 5.07e+01 b.43.4.2,c.25.1.1 68889,68890 1ihuA 589 5.14e+01 c.37.1.10,c.37.1.10 62394,62395 1vmaA 306 5.18e+01 a.24.13.1,c.37.1.10 108887,108888 1i6vC 1118 5.18e+01 e.29.1.1 61856 2c77A 405 5.20e+01 2fl7A 232 5.22e+01 1o89A 345 5.24e+01 b.35.1.2,c.2.1.1 92644,92645 1sz6A 249 5.28e+01 2c78A 405 5.29e+01 1hdmA 201 5.30e+01 1iakA b.1.1.2,d.19.1.1 21583,38157 1dllA 441 5.31e+01 1a8d b.29.1.6,b.42.4.2 24263,25608 2pna 104 5.35e+01 1qadA d.93.1.1 40501 1qhhA 167 5.46e+01 1pjr c.37.1.19 32393 1oi1A 221 5.64e+01 b.34.9.3,b.34.9.3 87037,87038 1tqjA 230 5.66e+01 c.1.2.2 107228 2b06A 155 5.67e+01 1qg0A 308 5.69e+01 1fnc b.43.4.2,c.25.1.1 25639,31529 1qgaA 308 5.70e+01 1fnc b.43.4.2,c.25.1.1 25637,31527 1qfzA 308 5.70e+01 1fnc b.43.4.2,c.25.1.1 25633,31523 1n0xH 230 5.83e+01 b.1.1.1,b.1.1.2 91528,91529 1l0fA 358 6.05e+01 e.3.1.1 73398 1cqsA 131 6.05e+01 d.17.4.3 83165 1nyrA 645 6.06e+01 c.51.1.1,d.15.10.1,d.67.1.1,d.104.1.1 92354,92355,92356,92357 2mev1 277 6.07e+01 2mev1 1w6yA 131 6.10e+01 1qh0A 295 6.11e+01 b.43.4.2,c.25.1.1 68891,68892 1dkfB 235 6.14e+01 2lbd a.123.1.1 19281 1j58A 385 6.28e+01 b.82.1.2 71531 1oqsB 122 6.28e+01 a.133.1.2 93428 1ynjC 1119 6.29e+01 1l9uC 1118 6.32e+01 i.8.1.1 73750 1hqmC 1119 6.37e+01 i.8.1.1 45974 1j1nA 492 6.40e+01 c.94.1.1 83978 2c7bA 311 6.63e+01 1oqcA 125 6.64e+01 a.24.15.1 87264 1hzwA 290 6.78e+01 1bkpA d.117.1.1 61464 1edg 380 6.79e+01 1edg c.1.8.3 28807 1hvyA 288 6.81e+01 1bkpA d.117.1.1 41049 1tw3A 360 6.89e+01 a.4.5.29,c.66.1.12 107373,107374 1ypvA 313 7.22e+01 1ju6A 313 7.43e+01 d.117.1.1 63289 1jkmB 361 7.48e+01 1jkmA c.69.1.2 34634 1wr2A 238 7.52e+01 1jkmA 358 7.54e+01 1jkmA c.69.1.2 34633 2aa4A 289 7.72e+01 2b32A 131 7.73e+01 1uwbB 427 7.74e+01 1rthA e.8.1.2 43063 1mec1 274 7.74e+01 2mev1 1w00A 131 7.78e+01 1ylaA 202 7.86e+01 1w72A 274 7.87e+01 1rrkA 497 7.90e+01 1xapA 267 8.05e+01 1rl9A 357 8.08e+01 a.83.1.1,d.128.1.2 104979,104980 1hniB 427 8.20e+01 1rthA e.8.1.2 43045 1w01A 131 8.24e+01 d.17.4.3 108979 1xmcA 612 8.24e+01 1hw4A 355 8.25e+01 1bkpA d.117.1.1 41054 1p52A 357 8.33e+01 a.83.1.1,d.128.1.2 87792,87793 1xmdA 612 8.39e+01 1igoA 205 8.40e+01 b.29.1.11 71209 1r31A 428 8.43e+01 d.58.20.1,d.179.1.1 96897,96898 1mswD 883 8.57e+01 e.8.1.3 79427 1bqnB 430 8.60e+01 1rthA e.8.1.2 43065 1xl7A 612 8.63e+01 1vrbA 342 8.68e+01 1pda 313 8.69e+01 1pda c.94.1.1,d.50.2.1 35751,38794 1suh 146 8.69e+01 1edhA b.1.6.1 22206