# List of top-scoring protein chains for T0305.t06-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 7.06e-58 2c7sA 313 1.43e-56 1larA 575 2.52e-56 1larA c.45.1.2,c.45.1.2 32693,32694 1yfoA 302 6.73e-56 2shpA c.45.1.2 32681 1rpmA 278 6.02e-55 2shpA c.45.1.2 32679 2ahsA 295 2.13e-54 2cfvA 316 1.79e-53 2gjtA 295 1.54e-52 2g59A 297 1.61e-52 1p15A 253 1.67e-52 c.45.1.2 93894 1ygrA 610 1.79e-51 2shpA 525 3.11e-50 2shpA c.45.1.2,d.93.1.1,d.93.1.1 32683,40533,40534 2b3oA 532 1.24e-49 2fjmA 310 1.51e-49 1q6nA 310 2.00e-49 c.45.1.2 95984 1lqfA 295 2.04e-49 c.45.1.2 74187 1l8kA 314 2.34e-49 c.45.1.2 73691 2f6fA 302 2.49e-49 1gwz 299 3.07e-49 2shpA c.45.1.2 32685 1bzhA 298 3.63e-49 1pty c.45.1.2 32664 2f71A 298 3.74e-49 2azrA 299 3.76e-49 1bzcA 321 3.79e-49 1pty c.45.1.2 32670 1oemX 321 3.96e-49 c.45.1.2 86916 1bzjA 297 4.06e-49 1pty c.45.1.2 32667 1c83A 298 5.46e-49 1pty c.45.1.2 32660 1l8gA 321 5.79e-49 c.45.1.2 73689 1c86A 298 6.55e-49 1pty c.45.1.2 32668 1i57A 310 7.16e-49 1pty c.45.1.2 61772 1pa1A 310 8.87e-49 c.45.1.2 94404 1fprA 284 9.26e-49 2shpA c.45.1.2 59949 1a5y 330 1.08e-48 1pty c.45.1.2 32673 1gfyA 298 1.21e-48 1pty c.45.1.2 32666 1nwlA 298 1.38e-48 c.45.1.2 86300 1eeoA 321 1.41e-48 1pty c.45.1.2 32655 1aax 321 1.44e-48 1pty c.45.1.2 32657 1g1fA 298 1.84e-48 1pty c.45.1.2 32662 1ptuA 321 2.01e-48 1pty c.45.1.2 32675 1ptvA 321 2.07e-48 1pty c.45.1.2 32665 2b49A 287 6.08e-48 2a3kA 296 1.70e-47 1zc0A 309 1.84e-47 2gp0A 309 2.47e-47 1wchA 315 1.19e-46 2a8bA 283 3.81e-46 1jlnA 297 9.97e-46 1pty c.45.1.2 63172 2bijA 305 3.33e-45 2bzlA 325 4.90e-45 2bv5A 282 1.77e-44 1pa9A 284 7.14e-19 c.45.1.2 94411 1yptA 305 7.21e-19 1ytw c.45.1.2 32686 1xxvA 306 7.21e-19 1qz0A 306 7.21e-19 c.45.1.2 96607 1yts 278 3.57e-18 1ytw c.45.1.2 32690 1lyvA 306 3.62e-18 c.45.1.2 74348 1xxpA 306 3.62e-18 1ohcA 348 3.93e-16 c.45.1.1,c.45.1.1 87009,87010 1g4wR 383 9.11e-16 1g4uS a.24.11.1,c.45.1.2 16644,32692 1oheA 348 2.04e-15 c.45.1.1,c.45.1.1 87013,87014 1x24A 180 9.99e-11 1zckA 154 1.01e-10 1rxdA 159 1.04e-10 1zclA 180 6.67e-10 1xm2A 173 7.10e-10 1v3aA 173 3.77e-09 1r6hA 172 3.85e-09 c.45.1.1 97150 1fpzA 212 9.90e-09 1fpzA c.45.1.1 59976 1d5rA 324 8.25e-07 1d5rA b.7.1.1,c.45.1.1 23181,32697 1yn9A 169 4.14e-05 1m3gA 145 7.37e-05 c.45.1.1 84783 1vhrA 184 1.18e-04 1vhrA c.45.1.1 32651 2c46A 241 1.22e-04 1i9sA 210 1.71e-04 1i9sA c.45.1.1 62099 1wrmA 165 1.97e-04 1j4xA 184 9.04e-04 c.45.1.1 66392 1yz4A 160 1.29e-03 1xriA 151 2.52e-03 1ywfA 296 9.47e-03 1mkp 144 1.00e-02 1vhrA c.45.1.1 32654 1zsqA 528 1.66e-02 1lw3A 657 1.71e-02 b.55.1.8,c.45.1.3 91152,91153 1h4jA 599 1.37e-01 4aahA b.70.1.1 60590 1h4iA 599 1.37e-01 4aahA b.70.1.1 60586 1w6sA 599 1.61e-01 1z6tA 591 3.32e-01 1u24A 337 4.36e-01 2d5cA 263 5.10e-01 1gvhA 396 5.38e-01 a.1.1.2,b.43.4.2,c.25.1.5 70601,70602,70603 1lrwA 600 7.26e-01 b.70.1.1 91111 1erjA 393 1.47e+00 1erjA b.69.4.1 27660 1fu5A 111 3.34e+00 1qadA d.93.1.1 40505 1x4zA 121 3.45e+00 1ciu 683 4.81e+00 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21852,22521,27759,28746 1di6A 195 4.87e+00 1di6A c.57.1.1 33863 2pna 104 5.34e+00 1qadA d.93.1.1 40501 1p2fA 220 5.97e+00 a.4.6.1,c.23.1.1 87720,87721 1zpdA 568 6.01e+00 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31741,31785,31786 1edg 380 7.76e+00 1edg c.1.8.3 28807 1ot1A 686 9.13e+00 b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 87392,87393,87394,87395 1ihuA 589 9.20e+00 c.37.1.10,c.37.1.10 62394,62395 1ot2A 686 9.51e+00 b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 87396,87397,87398,87399 1xapA 267 9.69e+00 1pezA 686 1.03e+01 b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 94600,94601,94602,94603 1i6vC 1118 1.13e+01 e.29.1.1 61856 1kclA 686 1.14e+01 b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 68445,68446,68447,68448 1wj7A 104 1.17e+01 1pamA 686 1.19e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21846,22515,27753,28740 1v3jA 686 1.19e+01 b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 108305,108306,108307,108308 1v3kA 686 1.19e+01 b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 108313,108314,108315,108316 1d7fA 686 1.19e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21848,22517,27755,28742 1uksA 686 1.19e+01 b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 99517,99518,99519,99520 1tcmA 686 1.22e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21833,22502,27740,28727 1pj9A 686 1.22e+01 b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 94754,94755,94756,94757 1ynjC 1119 1.22e+01 1l9uC 1118 1.22e+01 i.8.1.1 73750 1dtuA 686 1.27e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21840,22509,27747,28734 1hqmC 1119 1.28e+01 i.8.1.1 45974 1kckA 686 1.29e+01 b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 68441,68442,68443,68444 1cgx 686 1.29e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21832,22501,27739,28726 1cdg 686 1.29e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21816,22485,27723,28710 1cxlA 686 1.29e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21829,22498,27736,28723 1cgy 686 1.29e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21823,22492,27730,28717 1cgw 686 1.29e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21822,22491,27729,28716 1cgv 686 1.29e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21820,22489,27727,28714 1d3cA 686 1.30e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21827,22496,27734,28721 1eo5A 686 1.30e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21828,22497,27735,28722 1zbxB 141 1.33e+01 1ylaA 202 1.53e+01 1fv3A 472 1.59e+01 b.29.1.6,b.42.4.2 60038,60039 1tw3A 360 1.62e+01 a.4.5.29,c.66.1.12 107373,107374 1xdkB 303 1.75e+01 1dkfB 235 1.94e+01 2lbd a.123.1.1 19281 1e9zA 238 2.01e+01 b.85.3.1,d.8.1.1 64850,64851 1fd0A 235 2.09e+01 a.123.1.1 76164 1fcyA 236 2.09e+01 2lbd a.123.1.1 19282 1exaA 246 2.17e+01 2lbd a.123.1.1 19285 1zunA 325 2.20e+01 1yumA 242 2.27e+01 2lbd 267 2.32e+01 2lbd a.123.1.1 19287 1ys7A 233 2.65e+01 1t3gA 159 2.68e+01 1zhiB 138 2.72e+01 1z1aA 142 2.75e+01 1b5qA 472 2.77e+01 1b37B c.3.1.2,d.16.1.5 30404,37968 1a8d 452 2.79e+01 1a8d b.29.1.6,b.42.4.2 24262,25607 1m1nB 522 2.88e+01 c.92.2.3 78418 1g20B 523 2.89e+01 1qguB c.92.2.3 35614 1qg0A 308 3.13e+01 1fnc b.43.4.2,c.25.1.1 25639,31529 1qfzA 308 3.13e+01 1fnc b.43.4.2,c.25.1.1 25633,31523 1qgaA 308 3.13e+01 1fnc b.43.4.2,c.25.1.1 25637,31527 2g2bA 150 3.36e+01 1jhzA 289 3.65e+01 c.93.1.1 66731 1jfsA 340 3.67e+01 a.35.1.5,c.93.1.1 66650,66651 1j58A 385 3.72e+01 b.82.1.2 71531 1vmaA 306 3.86e+01 a.24.13.1,c.37.1.10 108887,108888 1bu6O 501 3.91e+01 1glcG c.55.1.4,c.55.1.4 33499,33500 1skz 119 4.12e+01 1skz g.3.15.1,g.3.15.1 44366,44367 1rj9A 304 4.18e+01 a.24.13.1,c.37.1.10 97553,97554 1eft 405 4.34e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25688,25728,32123 1uktA 686 4.38e+01 b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 99525,99526,99527,99528 1glaG 501 4.40e+01 1glcG c.55.1.4,c.55.1.4 33507,33508 1ux6A 350 4.43e+01 b.29.1.16,g.75.1.1 100145,100146 1okkD 303 4.46e+01 a.24.13.1,c.37.1.10 93261,93262 1dbqA 289 4.49e+01 1qpzA c.93.1.1 35666 1vpwA 340 4.50e+01 1qpzA a.35.1.5,c.93.1.1 17087,35680 1qpzA 340 4.50e+01 1qpzA a.35.1.5,c.93.1.1 17097,35673 1qqbA 340 4.54e+01 1qpzA a.35.1.5,c.93.1.1 17099,35674 1hdmA 201 4.55e+01 1iakA b.1.1.2,d.19.1.1 21583,38157 1yymG 313 4.60e+01 1oadA 388 4.69e+01 c.1.15.3 81253 2tsrA 307 4.72e+01 1bkpA d.117.1.1 41043 2pugA 340 4.74e+01 1qpzA a.35.1.5,c.93.1.1 17088,35683 1l0fA 358 4.74e+01 e.3.1.1 73398 1b23P 405 4.78e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25689,25729,32124 1kpgA 287 4.81e+01 c.66.1.18 68735 2cryA 122 4.84e+01 1mvwA 840 4.88e+01 i.15.1.1 79523 2mysA 843 4.89e+01 1lvk b.34.3.1,c.37.1.9 24557,32154 2pucA 340 4.95e+01 1qpzA a.35.1.5,c.93.1.1 17094,35684 1diwA 441 5.00e+01 1a8d b.29.1.6,b.42.4.2 24264,25609 1jftA 340 5.02e+01 a.35.1.5,c.93.1.1 66652,66653 1s6rA 359 5.04e+01 e.3.1.1 98604 1gljO 501 5.05e+01 1glcG c.55.1.4,c.55.1.4 33525,33526 1jh9A 340 5.06e+01 a.35.1.5,c.93.1.1 66710,66711 1y54A 361 5.10e+01 1xmdA 612 5.19e+01 1xmcA 612 5.19e+01 1xl7A 612 5.33e+01 1zp3A 304 5.40e+01 1b5tA 275 5.45e+01 1b5tA c.1.23.1 29676 1zp4A 304 5.46e+01 1cyg 680 5.47e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21843,22512,27750,28737 1exmA 405 5.51e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 1gw9A 388 5.62e+01 c.1.15.3 70658 145l 164 5.65e+01 1l92 d.2.1.3 36860 1aipA 405 5.81e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25697,25737,32132 2glkA 388 5.81e+01 1o89A 345 5.88e+01 b.35.1.2,c.2.1.1 92644,92645 2fmnA 304 5.89e+01 1jkmA 358 5.92e+01 1jkmA c.69.1.2 34633 2g6yA 217 5.93e+01 2c77A 405 5.94e+01 1jkmB 361 5.98e+01 1jkmA c.69.1.2 34634 1wr2A 238 5.99e+01 2c78A 405 6.02e+01 1dfqA 444 6.06e+01 1a8d b.29.1.6,b.42.4.2 24267,25612 1vz2A 710 6.19e+01 b.69.7.1,c.69.1.4 108945,108946 2c7bA 311 6.19e+01 1e8nA 710 6.21e+01 1qfmA b.69.7.1,c.69.1.4 27675,34643 1uwbB 427 6.22e+01 1rthA e.8.1.2 43063 1h2xA 710 6.26e+01 b.69.7.1,c.69.1.4 76598,76599 1jpiA 388 6.26e+01 c.1.22.1 67023 1vz3A 710 6.27e+01 b.69.7.1,c.69.1.4 108947,108948 1cqsA 131 6.28e+01 d.17.4.3 83165 1e5tA 710 6.37e+01 1qfmA b.69.7.1,c.69.1.4 27676,34644 1eu8A 409 6.41e+01 1eu8A c.94.1.1 59502 1hfeL 421 6.44e+01 1fehA c.96.1.1,d.58.1.5 36018,39001 1hniB 427 6.49e+01 1rthA e.8.1.2 43045 1h2wA 710 6.49e+01 b.69.7.1,c.69.1.4 76596,76597 1qx1A 1045 6.50e+01 a.8.3.1,b.30.5.6,c.6.2.1 96512,96513,96514 1jphA 388 6.52e+01 c.1.22.1 67022 1htyA 1015 6.53e+01 a.8.3.1,b.30.5.6,c.6.2.1 83064,83065,83066 1nf3C 128 6.56e+01 b.36.1.1 85596 1dllA 441 6.61e+01 1a8d b.29.1.6,b.42.4.2 24263,25608 1ps3A 1045 6.65e+01 a.8.3.1,b.30.5.6,c.6.2.1 95065,95066,95067 1qwnA 1045 6.65e+01 a.8.3.1,b.30.5.6,c.6.2.1 96487,96488,96489 1e5mA 416 6.68e+01 1dd8A c.95.1.1,c.95.1.1 58973,58974 1yb5A 351 6.75e+01 1r3vA 367 6.97e+01 c.1.22.1 96965 1w6yA 131 6.98e+01 1o1hA 387 7.03e+01 c.1.15.3 81044 1urhA 280 7.04e+01 c.46.1.2,c.46.1.2 99829,99830 2fnqA 699 7.08e+01 2b4wA 315 7.10e+01 1jpkA 388 7.21e+01 c.1.22.1 67026 1e08A 371 7.21e+01 i.4.1.1 45914 2b32A 131 7.23e+01 1u1gA 256 7.24e+01 2awfA 172 7.27e+01 1aroP 883 7.28e+01 1cezA e.8.1.3 43112 1oo3A 111 7.35e+01 d.93.1.1 87184 1qhhA 167 7.39e+01 1pjr c.37.1.19 32393 1yt8A 539 7.40e+01 1r3wA 367 7.47e+01 c.1.22.1 96966 1rxyA 253 7.48e+01 c.56.2.1 98065 1oi1A 221 7.69e+01 b.34.9.3,b.34.9.3 87037,87038 2bivA 243 7.71e+01 1bqnB 430 7.71e+01 1rthA e.8.1.2 43065 1b6iA 164 7.74e+01 1l92 d.2.1.3 36945 2acvA 463 7.79e+01 1hysB 425 7.81e+01 1rthA e.8.1.2 61419 1r3rA 367 7.82e+01 c.1.22.1 96962 1ikxB 427 7.82e+01 e.8.1.2 62535 2acwA 465 7.84e+01 1nx8A 273 7.85e+01 b.82.2.8 86374 1qe1B 427 7.86e+01 1rthA e.8.1.2 43055 1eetB 427 7.91e+01 1rthA e.8.1.2 43079 1dloB 427 7.92e+01 1rthA e.8.1.2 43041 1t05B 437 7.94e+01 e.8.1.2 99062 1ohoA 131 7.94e+01 1r31A 428 7.94e+01 d.58.20.1,d.179.1.1 96897,96898 2booA 247 7.96e+01 1jlaB 440 8.13e+01 e.8.1.2 66835 1lwjA 441 8.18e+01 b.71.1.1,c.1.8.1 74303,74304 1r3qA 367 8.18e+01 c.1.22.1 96961 3hvtB 428 8.19e+01 1rthA e.8.1.2 43067 1tqjA 230 8.29e+01 c.1.2.2 107228 2bdqA 224 8.32e+01 1nmaN 388 8.37e+01 2qwc b.68.1.1 27590 4thiA 362 8.39e+01 2thiA c.94.1.1 35793 1hquB 430 8.45e+01 1rthA e.8.1.2 61159 1r0aB 429 8.46e+01 e.8.1.2 104678 1w00A 131 8.46e+01 1j5oB 430 8.52e+01 e.8.1.2 71570 1wxuA 93 8.52e+01 2mev1 277 8.55e+01 2mev1 2be2B 430 8.60e+01 3thiA 371 8.61e+01 2thiA c.94.1.1 35792 1r3sA 367 8.61e+01 c.1.22.1 96963 1v37A 177 8.61e+01 1zx8A 136 8.68e+01 1p0iA 529 8.77e+01 c.69.1.1 93867 2a6hC 1119 8.78e+01 144l 164 8.82e+01 1l92 d.2.1.3 36893 1c1bB 440 8.93e+01 1rthA e.8.1.2 43077 1dgnA 89 8.94e+01 1dgnA a.77.1.3 18436 1ex9A 285 8.95e+01 1cvl c.69.1.18 34785 1ncdN 389 8.99e+01 2qwc b.68.1.1 27589