# List of top-scoring protein chains for t2k-100-30-stride-ebghtl 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 1ck9A 104 5.19e-19 1ck9A d.79.3.1 39806 1jj2F 119 3.77e-18 1ffkE d.79.3.1 63091 1ffkE 119 1.06e-17 1ffkE d.79.3.1 39812 1dbuA 158 9.03e-03 1dbuA d.116.1.1 40930 1dt9A 437 1.66e-02 1dt9A c.55.4.2 33738 d.79.3.2 39815 d.91.1.1 40257 3uagA 437 3.27e-02 4uagA c.5.1.1 30652 c.59.1.1 33953 c.72.2.1 34956 1f5sA 211 4.55e-02 1f5sA c.108.1.4 59656 1j97A 211 4.55e-02 1f5sA c.108.1.4 62753 4uagA 437 4.64e-02 4uagA c.5.1.1 30651 c.59.1.1 33952 c.72.2.1 34955 1uag 437 4.70e-02 4uagA c.5.1.1 30653 c.59.1.1 33954 c.72.2.1 34957 1dbxA 158 5.17e-02 1dbuA d.116.1.1 40928 1l7mA 211 5.19e-02 1jqaA 370 1.06e-01 e.22.1.2 67085 1tif 78 1.45e-01 1tif d.15.8.1 37836 1jq5A 370 1.48e-01 e.22.1.2 67084 1f6yA 262 1.68e-01 1f6yA c.1.21.2 29673 1jpnA 296 1.97e-01 a.24.13.1 67039 c.37.1.10 67040 1bw0A 416 2.04e-01 1bw0A c.67.1.1 34385 1cs1A 386 2.44e-01 1ibjA c.67.1.3 34399 2hmiA 558 2.59e-01 1rthA c.55.3.1 33604 e.8.1.2 43106 1cs1C 386 2.64e-01 1ibjA c.67.1.3 34401 1gc5A 467 3.77e-01 1gc5A c.72.1.3 60429 1gv4A 528 3.91e-01 2liv 344 4.00e-01 2liv c.93.1.1 35708 1ng1 294 4.38e-01 1ng1 a.24.13.1 16961 c.37.1.10 32272 1pszA 303 4.44e-01 1toaA c.92.2.2 35600 2ng1 293 4.61e-01 1ng1 a.24.13.1 16962 c.37.1.10 32273 1fts 295 6.43e-01 1ng1 a.24.13.1 16968 c.37.1.10 32279 1bif 469 6.66e-01 1bif c.37.1.7 31961 c.60.1.4 34003 2lbp 346 7.05e-01 2liv c.93.1.1 35709 1yacA 208 7.58e-01 1yacA c.33.1.2 31757 1b93A 152 8.01e-01 1b93A c.24.1.2 31507 1ha3A 405 8.13e-01 1efcA b.43.3.1 60869 b.44.1.1 60870 c.37.1.8 60871 1igs 248 8.24e-01 1a53 c.1.2.4 28565 1j8mF 297 8.27e-01 1ng1 a.24.13.1 62742 c.37.1.10 62743 1rthA 560 8.68e-01 1rthA c.55.3.1 33576 e.8.1.2 43028 1a53 247 8.74e-01 1a53 c.1.2.4 28564 1juk 248 9.09e-01 1a53 c.1.2.4 28567 1qc5A 192 9.26e-01 1aoxA c.62.1.1 34147 1im5A 180 9.53e-01 c.33.1.2 66211 1b93B 152 9.84e-01 1b93A c.24.1.2 31508 1hrhA 136 1.02e+00 1rthA c.55.3.1 33577 1d3hA 367 1.03e+00 1d3gA c.1.4.1 28601 1jjfA 268 1.10e+00 c.69.1.2 66765 1d3gA 367 1.14e+00 1d3gA c.1.4.1 28600 1dttA 560 1.14e+00 1rthA c.55.3.1 33611 e.8.1.2 43088 1b7gO 340 1.15e+00 1b7gO c.2.1.3 29992 d.81.1.1 39907 1dkrA 317 1.16e+00 1dkuA c.61.1.2 34114 c.61.1.2 34115 1i7qB 193 1.23e+00 1qdlB c.23.16.1 61902 1dkuA 317 1.51e+00 1dkuA c.61.1.2 34118 c.61.1.2 34119 1in4A 334 1.57e+00 1hqcA a.4.5.11 62597 c.37.1.13 62598 1bjx 110 1.58e+00 1bjx c.47.1.2 32774 2bjxA 110 1.58e+00 1bjx c.47.1.2 32776 1iqrA 420 1.58e+00 a.99.1.1 66275 c.28.1.1 66276 1uae 419 1.60e+00 1uae d.68.2.2 39574 1qfeA 252 1.65e+00 1qfeA c.1.10.1 29167 1ly1A 181 1.78e+00 1kid 203 1.86e+00 1derA c.8.5.1 30771 1f2dA 341 2.17e+00 1f2dA c.79.1.1 35298 1fzaB 328 2.23e+00 3fib d.171.1.1 42480 h.1.8.1 45621 1gk8A 475 2.29e+00 c.1.14.1 65234 d.58.9.1 65235 1g5pA 289 2.32e+00 1cp2A c.37.1.10 32253 1jpmA 366 2.42e+00 c.1.11.2 67031 d.54.1.1 67032 1hv8A 367 2.44e+00 1hv8A c.37.1.13 32405 c.37.1.13 32406 1fmtA 314 2.49e+00 1fmtA b.46.1.1 25758 c.65.1.1 34174 1g97A 459 2.50e+00 1fwyA b.81.1.4 60394 c.68.1.5 60395 1jj2X 240 2.54e+00 1ffkV c.9.2.1 63109 1dcjA 81 2.64e+00 1dcjA d.68.3.1 59115 1tbgA 340 2.85e+00 1tbgA b.69.4.1 27649 1gotB 340 2.93e+00 1tbgA b.69.4.1 27648 1egaA 301 2.99e+00 1egaA c.37.1.8 32150 d.52.3.1 38836 1edoA 244 3.01e+00 1ybvA c.2.1.2 29896 1kaeA 434 3.02e+00 1f2tB 148 3.07e+00 1f2tB 2nacA 393 3.08e+00 2nadA c.2.1.4 30088 c.23.12.1 31348 1hm9A 468 3.19e+00 b.81.1.4 65866 c.68.1.5 65867 1fmtB 314 3.21e+00 1fmtA b.46.1.1 25759 c.65.1.1 34175 1fwrA 213 3.21e+00 1fwrA c.1.10.1 29164 1k75A 434 3.25e+00 c.82.1.2 68253 1dar 691 3.30e+00 1dar b.43.3.1 25707 c.37.1.8 32142 d.14.1.1 37547 d.58.11.1 39300 1jg8A 347 3.39e+00 1jg8A c.67.1.1 62946 1kao 167 3.48e+00 1ctqA c.37.1.8 32014 1ko7A 314 3.63e+00 1iibA 106 3.69e+00 1iibA c.44.2.1 32648 1srvA 145 3.83e+00 1derA c.8.5.1 30817 1b1a 137 3.83e+00 1be1 c.23.6.1 31242 1thtA 305 3.86e+00 1thtA c.69.1.13 34711 1dbiA 280 4.14e+00 1gci c.41.1.1 32543 1aoxA 203 4.44e+00 1aoxA c.62.1.1 34151 1byrA 155 4.58e+00 1byrA d.136.1.1 41450 1ja9A 274 4.65e+00 c.2.1.2 62817 1gx1A 160 4.91e+00 1d2kA 392 5.17e+00 1d2kA c.1.8.5 29008 d.26.3.1 38442 1ecl 597 5.33e+00 1ecl e.10.1.1 43238 1exmA 405 5.36e+00 1efcA b.43.3.1 25696 b.44.1.1 25736 c.37.1.8 32131 2nadA 393 5.47e+00 2nadA c.2.1.4 30090 c.23.12.1 31350 1drw 273 5.74e+00 1drw c.2.1.3 30057 d.81.1.3 39972 1eny 268 5.85e+00 1eny c.2.1.2 29910 1jy8A 159 5.92e+00 d.79.5.1 67452 1i1kA 309 5.93e+00 1daaA e.17.1.1 61533 1fp6A 289 5.96e+00 1cp2A c.37.1.10 32243 1gca 309 5.99e+00 1gca c.93.1.1 35659 1dosA 358 6.02e+00 1dosA c.1.10.2 29175 1dliA 402 6.04e+00 1dliA a.100.1.4 18809 c.2.1.6 30213 c.26.3.1 31622 1b57A 358 6.08e+00 1dosA c.1.10.2 29177 2fokA 579 6.21e+00 2fokA a.4.5.12 16131 a.4.5.12 16132 a.4.5.12 16133 c.52.1.12 33323 7odcA 424 6.35e+00 7odcA b.49.2.1 26488 c.1.6.1 28650 4pfk 319 6.49e+00 3pfk c.89.1.1 35582 1dd6A 228 6.52e+00 1a7tA d.157.1.1 42054 1ekfA 365 6.63e+00 1ekfA e.17.1.1 59445 1k6dA 220 6.82e+00 1fokA 568 7.00e+00 2fokA a.4.5.12 16137 a.4.5.12 16138 a.4.5.12 16139 c.52.1.12 33325 1jsrA 327 7.10e+00 c.88.1.1 67237 2tpsA 227 7.25e+00 2tpsA c.1.3.1 28591 1dljA 402 7.82e+00 1dliA a.100.1.4 18808 c.2.1.6 30212 c.26.3.1 31621 1pii 452 7.92e+00 1pii c.1.2.4 28559 c.1.2.4 28563 8rucA 475 8.04e+00 1burA c.1.14.1 29339 d.58.9.1 39245 3pfk 319 8.23e+00 3pfk c.89.1.1 35581 1euaA 213 8.43e+00 1fwrA c.1.10.1 29155 6pfkA 319 8.49e+00 3pfk c.89.1.1 35583 2gbp 309 8.51e+00 1gca c.93.1.1 35657 1fq0A 213 8.56e+00 1fwrA c.1.10.1 29161 1qnf 484 8.65e+00 1qnf a.99.1.1 18777 c.28.1.1 31632 1cyx 205 8.83e+00 1cyx b.6.1.2 23023 1zid 268 8.83e+00 1eny c.2.1.2 29911 1k92A 455 8.91e+00 c.26.2.1 68325 d.210.1.1 68326 1jmvA 141 9.09e+00 c.29.1.2 66897 1jljA 189 9.40e+00 c.57.1.1 63169 1bvyF 191 9.40e+00 1bvyF c.23.5.1 31207 2cbf 234 9.46e+00 1cbf c.90.1.1 35588 1d7kA 421 9.81e+00 7odcA b.49.2.1 26486 c.1.6.1 28648 1qdlB 195 1.03e+01 1qdlB c.23.16.1 31437 1ihcA 188 1.03e+01 1di6A c.57.1.1 62379 1kl1A 419 1.05e+01 1arzC 273 1.06e+01 1drw c.2.1.3 30061 d.81.1.3 39976 1nipA 289 1.06e+01 1cp2A c.37.1.10 32263 1atzB 189 1.11e+01 1atzA c.62.1.1 34133 1eo1A 124 1.11e+01 1eo1A c.55.5.1 33739 1korA 400 1.12e+01 2tysA 268 1.12e+01 2tysA c.1.2.4 28572 1gmlA 178 1.13e+01 8abp 306 1.13e+01 8abp c.93.1.1 35647 1ek6A 348 1.14e+01 1xel c.2.1.2 29800 1toaA 313 1.17e+01 1toaA c.92.2.2 35598 1qtrA 317 1.22e+01 1qtrA c.69.1.7 34660 1agx 331 1.25e+01 4pgaA c.88.1.1 35564 1fjmA 330 1.26e+01 1auiA d.159.1.3 42082 1jk7A 323 1.28e+01 1auiA d.159.1.3 63144 1l3kA 196 1.30e+01 1ea7A 310 1.31e+01 1jzxK 205 1.32e+01 i.1.1.2 67885 1gm6A 175 1.32e+01 1cydA 244 1.33e+01 1cydA c.2.1.2 29825 1ejdA 419 1.34e+01 1uae d.68.2.2 39576 1mup 166 1.35e+01 1mup b.60.1.1 27133 2scuB 388 1.35e+01 2scuB c.23.4.1 31141 d.142.1.4 41562 1c9kA 180 1.37e+01 1c9kB c.37.1.11 32363 7timA 247 1.37e+01 1amk c.1.1.1 28457 1vrtA 560 1.38e+01 1rthA c.55.3.1 33574 e.8.1.2 43023 1i06A 180 1.39e+01 1mup b.60.1.1 27131 1cbuA 180 1.39e+01 1c9kB c.37.1.11 32360 1jv4A 162 1.40e+01 b.60.1.1 67343 1i05A 180 1.41e+01 1mup b.60.1.1 27130 1dih 273 1.41e+01 1drw c.2.1.3 30056 d.81.1.3 39971 1uteA 313 1.41e+01 1uteA d.159.1.1 42078 1khbA 625 1.44e+01 c.91.1.1 68606 c.109.1.1 68607 1qfcA 306 1.44e+01 1uteA d.159.1.1 42077 1i3kA 348 1.48e+01 1xel c.2.1.2 61595 1e5pA 151 1.50e+01 1bj7 b.60.1.1 59272 1gtxA 472 1.56e+01 1gtxA c.67.1.4 34464 1bksA 268 1.60e+01 2tysA c.1.2.4 28585 1fjgK 129 1.68e+01 1fjfK c.55.4.1 33733 2udpA 338 1.68e+01 1xel c.2.1.2 29791 1qsgA 265 1.68e+01 1eny c.2.1.2 29935 2ae2A 260 1.69e+01 1bdb c.2.1.2 29945 1c9kB 180 1.70e+01 1c9kB c.37.1.11 32364 1rkd 309 1.75e+01 1rkd c.72.1.1 34928 1d3yA 301 1.76e+01 1d3yA e.12.1.1 43252 1gjwA 637 1.80e+01 b.71.1.1 60582 c.1.8.1 60583 1aipE 405 1.82e+01 1efcA b.43.3.1 25699 b.44.1.1 25739 c.37.1.8 32134 1cjcA 460 1.84e+01 1cjcA c.3.1.1 30319 c.4.1.1 30604 1i45A 248 1.85e+01 1amk c.1.1.1 61665 1ivyA 452 1.86e+01 1ivyA c.69.1.5 34654 1kvs 338 1.87e+01 1xel c.2.1.2 29799 1xel 338 1.87e+01 1xel c.2.1.2 29786 1udc 338 1.87e+01 1xel c.2.1.2 29785 1gjuA 637 1.90e+01 b.71.1.1 60580 c.1.8.1 60581 1mil 104 1.94e+01 1d4tA d.93.1.1 40496 1kq3A 376 1.94e+01 e.22.1.2 68790 1fsz 372 1.96e+01 1fsz c.32.1.1 31750 d.79.2.1 39802 1a1z 91 1.97e+01 1a1z a.77.1.1 18427 1ezwA 349 1.98e+01 1ezwA c.1.16.3 29558 1ccwA 137 2.00e+01 1be1 c.23.6.1 31238 1ka1A 357 2.00e+01 e.7.1.1 68369 1qgxA 357 2.00e+01 1qgxA e.7.1.1 42973 1qapA 296 2.04e+01 1qpoA c.1.17.1 29559 d.41.2.1 38595 1fd2 106 2.06e+01 1a6l d.58.1.2 38962 1a6l 106 2.09e+01 1a6l d.58.1.2 38966 1asx 159 2.09e+01 1a6dA c.8.5.2 30821 7fd1A 106 2.12e+01 1a6l d.58.1.2 38953 1b73A 254 2.13e+01 1b74A c.78.2.1 35266 c.78.2.1 35267 1jscA 630 2.14e+01 c.31.1.3 67224 c.36.1.1 67225 c.36.1.1 67226 8ohm 435 2.17e+01 1heiA c.37.1.14 32469 c.37.1.14 32470 1eq2A 310 2.18e+01 1eq2A c.2.1.2 29814 1fr7A 260 2.21e+01 2cba b.74.1.1 27828 1atzA 189 2.24e+01 1atzA c.62.1.1 34132 1eluB 390 2.25e+01 1elqA c.67.1.3 34435 1eulA 994 2.26e+01 1eulA f.2.1.10 43726 1je3A 97 2.27e+01 1dppA 507 2.27e+01 1dpe c.94.1.1 35800 1bmtA 246 2.27e+01 1bmtA a.46.1.1 17757 c.23.6.1 31235 1ii7A 333 2.28e+01 1ii7A d.159.1.4 62415 2mnr 357 2.33e+01 2mnr c.1.11.2 29245 d.54.1.1 38889 1qopA 268 2.33e+01 2tysA c.1.2.4 28570 1j5eK 129 2.34e+01 1ejrC 567 2.39e+01 1ubpC b.92.1.1 28420 c.1.9.2 29042 1fcbA 511 2.45e+01 1gox c.1.4.1 28620 d.120.1.1 41087 1a76 326 2.54e+01 1a76 a.60.7.1 18091 c.53.1.2 33361 1e8yA 966 2.55e+01 1e8xA a.118.1.6 19152 b.7.1.1 23187 d.15.1.5 37635 d.144.1.4 41715 1h2rS 267 2.61e+01 2frvA e.19.1.1 43310 1udb 338 2.62e+01 1xel c.2.1.2 29787 2gd1O 334 2.69e+01 1dssG c.2.1.3 29978 d.81.1.1 39893 1b16A 254 2.69e+01 1b16A c.2.1.2 29875 4pgaA 337 2.70e+01 4pgaA c.88.1.1 35565 1cozA 129 2.71e+01 1cozA c.26.1.2 31598 1pjr 724 2.72e+01 1pjr c.37.1.13 32391 c.37.1.13 32392 1hg3A 225 2.75e+01 1hg3A c.1.1.1 61025 1hskA 326 2.75e+01 2mbr d.145.1.2 61241 d.146.1.1 61242 1ass 159 2.76e+01 1a6dA c.8.5.2 30818 1di0A 158 2.76e+01 1di0A c.16.1.1 30957 1b74A 254 2.79e+01 1b74A c.78.2.1 35264 c.78.2.1 35265 1e6mA 128 2.80e+01 3chy c.23.1.1 31039 2hvm 273 2.81e+01 1cnv c.1.8.5 28985 1qcwA 410 2.81e+01 1gox c.1.4.1 28622 1dpe 507 2.86e+01 1dpe c.94.1.1 35799 1cqzA 554 2.89e+01 1cr6B c.108.1.2 43339 c.69.1.11 34689 1add 349 2.91e+01 1a4mA c.1.9.1 29020 1ble 163 2.91e+01 1ble c.38.1.1 32475 1zrn 232 2.91e+01 1qq5A c.108.1.1 43323 1nal3 297 2.98e+01 1nal3 1dts 221 2.99e+01 1byi c.37.1.10 32200 3mddA 385 3.03e+01 3mdeA a.29.3.1 16592 e.6.1.1 42853 3mdeA 385 3.04e+01 3mdeA a.29.3.1 16594 e.6.1.1 42855 1mdl 359 3.05e+01 2mnr c.1.11.2 29247 d.54.1.1 38891 1hyuA 521 3.05e+01 1hyuA c.3.1.5 30547 c.3.1.5 30548 c.47.1.2 32779 c.47.1.2 32780 1huvA 380 3.06e+01 c.1.4.1 61277 1ecfB 504 3.09e+01 1ecfB c.61.1.1 34054 d.153.1.1 41821 1d2fA 390 3.10e+01 1d2fA c.67.1.3 34411 1qguB 519 3.14e+01 1qguB c.92.2.3 35626 1e8xA 961 3.18e+01 1e8xA a.118.1.6 19148 b.7.1.1 23183 d.15.1.5 37631 d.144.1.4 41711 1ecfA 504 3.19e+01 1ecfB c.61.1.1 34053 d.153.1.1 41820 1exbA 332 3.20e+01 1qrqA c.1.7.1 28666 1dhs 344 3.25e+01 1dhs c.31.1.1 31727 1a8y 367 3.26e+01 1a8y c.47.1.3 32781 c.47.1.3 32782 c.47.1.3 32783 2dhqA 146 3.33e+01 2dhqA c.23.13.1 31382 1bykA 255 3.44e+01 1bykA c.93.1.1 35706 1jeoA 180 3.45e+01 c.80.1.3 66611 1qfjA 232 3.46e+01 1qfjA b.43.4.2 25655 c.25.1.1 31545 1gcoA 261 3.49e+01 1ybvA c.2.1.2 29884 1qq5A 253 3.52e+01 1qq5A c.108.1.1 43327 1ghr 306 3.55e+01 1aq0A c.1.8.3 28844 1fnnA 389 3.60e+01 1fnnA a.4.5.11 16129 c.37.1.13 32426 1qq7A 253 3.61e+01 1qq5A c.108.1.1 43329 1thm 279 3.61e+01 1gci c.41.1.1 32544 1jj2M 186 3.61e+01 1ffkK c.55.4.1 63098 1d8wA 426 3.62e+01 1de5A c.1.15.2 29394 1fwcC 567 3.66e+01 1ubpC b.92.1.1 28410 c.1.9.2 29032 1b43A 340 3.66e+01 1a76 a.60.7.1 18092 c.53.1.2 33362 1aq6A 253 3.66e+01 1qq5A c.108.1.1 43331 1jnxX 214 3.74e+01 c.15.1.3 63201 c.15.1.3 63202 1eluA 390 3.75e+01 1elqA c.67.1.3 34434 1heiA 451 3.76e+01 1heiA c.37.1.14 32463 c.37.1.14 32464 1jf9A 408 3.78e+01 1c0nA c.67.1.3 62931 1ysc 421 3.79e+01 1ivyA c.69.1.5 34652 1c3oB 382 3.79e+01 1c3oB c.8.3.1 30744 c.23.16.1 31421 1jj2K 164 3.85e+01 1ffkJ c.12.1.1 63096 1hozA 339 3.86e+01 c.70.1.1 65898 1duvG 333 3.88e+01 1othA c.78.1.1 35228 c.78.1.1 35229 1cbf 285 3.89e+01 1cbf c.90.1.1 35587