# List of top-scoring protein chains for t04-100-30-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 1grx 85 2.56e-03 1kte c.47.1.1 32766 1kte 105 8.04e-02 1kte c.47.1.1 32771 1s4nA 348 1.38e-01 unknown_sccs -8262 1k3yA 221 2.37e-01 a.45.1.1 77245 c.47.1.5 77246 1t1vA 93 3.90e-01 1f3aA 222 5.21e-01 1pgtA a.45.1.1 17701 c.47.1.5 32995 1j3vA 289 6.38e-01 a.100.1.1 -1303 c.2.1.6 -5947 1ksiA 642 7.28e-01 1ksiB b.30.2.1 24408 d.17.2.1 38043 d.17.2.1 38044 1j0fA 100 7.73e-01 unknown_sccs -7483 1eu8A 409 9.21e-01 1eu8A c.94.1.1 59502 1pbjA 125 9.96e-01 d.37.1.1 -9608 d.37.1.1 -9609 3daaA 277 1.09e+00 1daaA e.17.1.1 43272 1o0wA 252 1.19e+00 a.149.1.1 80751 d.50.1.1 80752 1h75A 81 1.21e+00 1h75A c.47.1.1 60716 1whsA 255 1.31e+00 1ivyA c.69.1.5 34649 1zfjA 491 1.40e+00 1ak5 c.1.5.1 28638 d.37.1.1 38540 d.37.1.1 38541 1eg5A 384 1.49e+00 1ecxA c.67.1.3 34429 1whtA 256 1.67e+00 1ivyA c.69.1.5 34646 1ig3A 263 1.74e+00 1ig3A b.82.6.1 62358 c.100.1.1 62359 1ayl 541 2.10e+00 1ayl c.91.1.1 64718 c.109.1.1 64719 1us8A 147 2.15e+00 c.37.1.12 -7194 1m2dA 110 2.24e+00 c.47.1.11 78476 1mvoA 136 2.36e+00 c.23.1.1 79513 1jx4A 352 2.40e+00 unknown_sccs -10188 unknown_sccs -11898 1iyeA 309 2.42e+00 e.17.1.1 83786 1iloA 77 2.45e+00 c.47.1.1 66205 1d3yA 301 2.50e+00 1d3yA e.12.1.1 43252 1r5pA 108 2.51e+00 unknown_sccs -7487 1a8y 367 2.61e+00 1a8y c.47.1.3 32781 c.47.1.3 32782 c.47.1.3 32783 1s48A 609 2.72e+00 e.8.1.4 -11955 1sra 151 2.74e+00 1sra a.39.1.3 17190 1dq3A 454 2.75e+00 1dq3A b.86.1.2 28380 d.50.3.1 38798 d.95.2.2 40585 d.95.2.2 40586 1i1kA 309 2.89e+00 1daaA e.17.1.1 61533 2hhmA 276 2.90e+00 1imbA e.7.1.1 42955 1fgyA 127 3.08e+00 1faoA b.55.1.1 26976 1xgsA 295 3.30e+00 1bn5 a.4.5.25 16216 d.127.1.1 41153 1a8i 842 3.37e+00 1a8i c.87.1.4 35490 1fsz 372 3.48e+00 1fsz c.32.1.1 31750 d.79.2.1 39802 1j79A 347 3.75e+00 1j79A c.1.9.4 62675 1jo0A 98 3.81e+00 d.68.4.1 77140 1cl8A 276 3.88e+00 1ckqA c.52.1.1 33230 1sb8A 352 4.00e+00 1fn9A 365 4.00e+00 1fn9A d.196.1.1 59894 1fsgA 233 4.16e+00 1qk3A c.61.1.1 34029 1qnaA 200 4.60e+00 1ytbA d.129.1.1 41226 d.129.1.1 41227 1io2A 213 4.93e+00 1ekeA c.55.3.1 62612 1co4A 42 5.10e+00 1co4A g.47.1.1 45347 1imbA 277 5.11e+00 1imbA e.7.1.1 42957 1ry9A 145 5.22e+00 d.198.1.1 -9020 1b1cA 181 5.84e+00 1amoA c.23.5.2 31212 1sr9A 644 5.88e+00 1g6hA 257 5.88e+00 1gajA c.37.1.12 60318 1pvmA 184 6.02e+00 d.37.1.1 -9612 d.37.1.1 -9613 unknown_sccs -12799 1mo0A 275 6.10e+00 c.1.1.1 79329 1f2tA 149 6.30e+00 1f2tA c.37.1.12 32373 1j08A 226 6.93e+00 c.47.1.2 83855 c.47.1.2 83856 1igwA 434 7.32e+00 c.1.12.7 62370 1f37A 110 7.79e+00 1f37A c.47.1.11 33088 1g5aA 628 8.47e+00 b.71.1.1 65152 c.1.8.1 65153 3vub 101 8.78e+00 3vub b.34.6.1 24613 1bu8A 452 9.03e+00 1gpl b.12.1.2 23647 c.69.1.19 34795 1vjpA 394 9.42e+00 c.2.1.3 -5897 d.81.1.3 -10480 1f8mA 429 9.62e+00 1dquA c.1.12.7 29315 1nycA 111 9.72e+00 unknown_sccs -4522 1pzxA 289 9.72e+00 c.119.1.1 -8623 1jtdB 273 9.97e+00 b.69.5.2 67265 1nrfA 262 1.04e+01 e.3.1.1 -11780 1eazA 125 1.05e+01 b.55.1.1 70113 1vioA 243 1.07e+01 unknown_sccs -10154 d.66.1.5 -10240 1qqgA 264 1.09e+01 1qqgA b.55.1.2 26987 b.55.1.2 26988 1o6aA 96 1.10e+01 unknown_sccs -4101 1mai 131 1.12e+01 1mai b.55.1.1 26951 1s1hM 132 1.13e+01 1f61A 429 1.16e+01 1dquA c.1.12.7 29319 1p4xA 250 1.18e+01 a.4.5.28 87784 a.4.5.28 87785 1gpl 432 1.23e+01 1gpl b.12.1.2 23645 c.69.1.19 34793 1qhfA 240 1.25e+01 1qhfA c.60.1.1 33960 1vhxA 150 1.27e+01 unknown_sccs -7663 1b04A 318 1.27e+01 1b04A d.142.2.2 41579 1a8l 226 1.27e+01 1a8l c.47.1.2 32777 c.47.1.2 32778 1vjgA 218 1.28e+01 unknown_sccs -6447 1wkqA 164 1.28e+01 1fzqA 181 1.30e+01 1hurA c.37.1.8 32060 1xbrA 184 1.30e+01 1xbrA b.2.5.4 22458 1xxaA 78 1.36e+01 1xxaA d.74.2.1 39700 1r26A 125 1.36e+01 c.47.1.1 -7389 1ne6A 283 1.36e+01 b.82.3.2 -4918 b.82.3.2 -4919 1m2oA 768 1.39e+01 a.71.2.1 78480 b.2.8.1 78481 c.62.1.2 78482 d.109.2.1 78483 g.41.10.1 78484 1adoA 363 1.39e+01 1fbaA c.1.10.1 29124 1m48A 133 1.44e+01 a.26.1.2 74443 1h5uA 842 1.44e+01 1a8i c.87.1.4 60655 1a4iA 301 1.44e+01 1a4iA c.2.1.7 30278 c.58.1.2 33926 3gcb 470 1.46e+01 3gcb d.3.1.1 37032 1j98A 157 1.46e+01 1j98A d.185.1.2 62755 1bw0A 416 1.47e+01 1bw0A c.67.1.1 34385 1gesA 450 1.54e+01 3grs c.3.1.5 30473 c.3.1.5 30474 d.87.1.1 40168 1o1yA 239 1.56e+01 c.23.16.1 86554 1ja1A 622 1.59e+01 1amoA b.43.4.1 62803 c.23.5.2 62804 c.25.1.4 62805 1d1gA 168 1.59e+01 1d1gA c.71.1.1 34889 1s6yA 450 1.70e+01 1n2zA 245 1.72e+01 c.92.2.2 79865 1mkyA 439 1.73e+01 c.37.1.8 79250 c.37.1.8 79251 d.52.5.1 79252 1oivA 191 1.79e+01 c.37.1.8 -7074 1e6bA 221 1.82e+01 1e6bA a.45.1.1 59294 c.47.1.5 59295 1kkoA 413 1.88e+01 c.1.11.2 68675 d.54.1.1 68676 1exbA 332 1.93e+01 1qrqA c.1.7.1 28666 1qv9A 283 1.97e+01 unknown_sccs -6888 1f21A 155 1.97e+01 2rn2 c.55.3.1 33550 1eudA 311 2.00e+01 2scuA c.2.1.8 30312 c.23.4.1 31140 1vjqA 79 2.01e+01 unknown_sccs -13478 1smvA 260 2.07e+01 1smvA b.121.4.7 23288 1nu0A 138 2.10e+01 unknown_sccs -7658 1iyxA 432 2.11e+01 c.1.11.1 83815 d.54.1.1 83816 1hyhA 309 2.11e+01 1hyhA c.2.1.5 30150 d.162.1.1 42117 1jmsA 381 2.14e+01 a.60.6.1 66889 a.60.12.1 75862 d.218.1.2 75863 1hufA 140 2.15e+01 1hufA d.195.1.1 61272 1uedA 406 2.16e+01 a.104.1.1 -1459 1di6A 195 2.23e+01 1di6A c.57.1.1 33863 1lwdA 413 2.28e+01 c.77.1.1 78265 1shuX 182 2.28e+01 c.62.1.1 -7982 1r8sA 164 2.29e+01 c.37.1.8 -7082 3thiA 371 2.30e+01 2thiA c.94.1.1 35792 1jfrA 262 2.44e+01 1jfrA c.69.1.16 34724 1n71A 180 2.45e+01 d.108.1.1 85370 1m3uA 264 2.50e+01 c.1.12.8 84784 1jksA 294 2.52e+01 d.144.1.7 71710 1vi2A 300 2.53e+01 c.2.1.7 -5960 c.58.1.5 -6366 1mp9A 198 2.56e+01 a.74.1.2 -1127 a.74.1.2 -1128 1jndA 420 2.56e+01 c.1.8.5 71757 d.26.3.1 71758 1oyjA 231 2.57e+01 a.45.1.1 87597 c.47.1.5 87598 1aq0A 306 2.58e+01 1aq0A c.1.8.3 28842 1byrA 155 2.60e+01 1byrA d.136.1.1 41450 1l5wA 796 2.60e+01 c.87.1.4 73605 1oihA 301 2.61e+01 b.82.2.5 -4899 1noyA 388 2.62e+01 1clqA c.55.3.5 33713 1n8vA 112 2.62e+01 unknown_sccs 85457 1ahsA 126 2.65e+01 1ahsA b.19.1.1 23794 1gcb 454 2.65e+01 3gcb d.3.1.1 37034 1ac5 483 2.66e+01 1ac5 c.69.1.5 34653 1puiA 210 2.71e+01 c.37.1.8 88292 1b16A 254 2.71e+01 1b16A c.2.1.2 29875 1uouA 474 2.74e+01 a.46.2.1 -951 c.27.1.1 -6642 d.41.3.1 -9715 1a2vA 655 2.92e+01 1a2vA b.30.2.1 24416 d.17.2.1 38059 d.17.2.1 38060 1m1qA 91 2.93e+01 a.138.1.3 74419 1ccwA 137 2.96e+01 1be1 c.23.6.1 31238 1uw4A 91 2.96e+01 unknown_sccs -10038 1b78A 193 2.99e+01 1b78A c.51.4.1 33221 1jvwA 167 3.06e+01 d.26.1.1 71907 1hurA 180 3.08e+01 1hurA c.37.1.8 32052 1tiyA 164 3.09e+01 1se8A 301 3.11e+01 1sviA 195 3.15e+01 3lynA 136 3.15e+01 1lis a.19.1.1 16413 1f2dA 341 3.16e+01 1f2dA c.79.1.1 35298 1o3yA 166 3.16e+01 c.37.1.8 86618 1wer 334 3.24e+01 1wer a.116.1.2 19108 1hdr 244 3.26e+01 1dhr c.2.1.2 29837 1o2dA 371 3.27e+01 e.22.1.2 86591 1o94A 729 3.28e+01 c.1.4.1 81200 c.3.1.1 81201 c.4.1.1 81202 1jz8A 1023 3.29e+01 b.1.4.1 67830 b.1.4.1 67831 b.18.1.5 67832 b.30.5.1 67833 c.1.8.3 67834 1esmA 316 3.30e+01 1esmA c.37.1.6 31953 1nmoA 247 3.31e+01 unknown_sccs -8746 1lvwA 295 3.33e+01 c.68.1.6 84723 1aszB 490 3.36e+01 1b8aA b.40.4.1 25241 d.104.1.1 40762 1nmeA 146 3.37e+01 c.17.1.1 85874 1id0A 152 3.40e+01 d.122.1.3 66111 1oaqL 120 3.41e+01 b.1.1.1 -2163 1jakA 512 3.42e+01 c.1.8.6 66472 d.92.2.1 66473 1jhnA 424 3.44e+01 b.29.1.12 70060 b.104.1.1 66722 1o0pA 104 3.45e+01 d.58.7.1 86535 1aisA 182 3.47e+01 1ytbA d.129.1.1 41288 d.129.1.1 41289 1pi1A 185 3.47e+01 unknown_sccs -762 1e19A 314 3.55e+01 1b7bA c.73.1.1 34967 1dp0A 1023 3.60e+01 b.1.4.1 22073 b.1.4.1 22074 b.18.1.5 23722 b.30.5.1 24346 c.1.8.3 28845 1jfuA 186 3.64e+01 c.47.1.10 62940 1k0dA 260 3.66e+01 a.45.1.1 67930 c.47.1.5 67931 1mh1 186 3.66e+01 1eesA c.37.1.8 32002 1oxsC 353 3.68e+01 b.40.6.3 87519 c.37.1.12 87520 1o50A 157 3.68e+01 d.37.1.1 -9604 d.37.1.1 -9605 1oaa 259 3.69e+01 1oaa c.2.1.2 29829 2tmdA 729 3.76e+01 2tmdA c.1.4.1 28616 c.3.1.1 30317 c.4.1.1 30602 1n57A 291 3.77e+01 c.23.16.2 85328 1e1oA 504 3.80e+01 1lylA b.40.4.1 25258 d.104.1.1 40714 1pa7A 130 3.80e+01 a.40.1.1 -896 1gnwA 211 3.88e+01 1gnwA a.45.1.1 17727 c.47.1.5 33021 2trcP 217 3.91e+01 1b9yC c.47.1.6 33051 1oxxK 353 3.92e+01 b.40.6.3 -3969 c.37.1.12 -7187 1nrvA 105 3.92e+01 d.93.1.1 86126 1qb7A 236 3.93e+01 1qb7A c.61.1.1 34087 1bkrA 109 3.95e+01 1bkrA a.40.1.1 17394 1us5A 314 3.95e+01 c.94.1.1 -8686