# List of top-scoring protein chains for t2k-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 1fo5A 85 6.49e-04 1fo5A c.47.1.1 59922 1hyuA 521 1.09e-03 1hyuA c.3.1.5 30547 c.3.1.5 30548 c.47.1.2 32779 c.47.1.2 32780 1ego 85 1.30e-03 1kte c.47.1.1 32767 1grx 85 1.57e-03 1kte c.47.1.1 32766 1qfnA 85 4.75e-03 1qfnA c.47.1.1 32768 1egr 85 4.95e-03 1kte c.47.1.1 32765 1k3yA 221 2.96e-02 a.45.1.1 77245 c.47.1.5 77246 1kte 105 3.27e-02 1kte c.47.1.1 32771 1k3lA 221 4.29e-02 a.45.1.1 77229 c.47.1.5 77230 1gseA 221 4.29e-02 1pgtA a.45.1.1 17667 c.47.1.5 32961 1f3aA 222 7.00e-02 1pgtA a.45.1.1 17701 c.47.1.5 32995 1t1vA 93 7.13e-02 1ytbB 180 1.60e-01 1ytbA d.129.1.1 41278 d.129.1.1 41279 1ytbA 180 1.92e-01 1ytbA d.129.1.1 41276 d.129.1.1 41277 1pbjA 125 2.10e-01 d.37.1.1 -9608 d.37.1.1 -9609 1s4nA 348 2.23e-01 unknown_sccs -8262 1jhb 106 2.44e-01 1kte c.47.1.1 32772 1j0fA 100 2.51e-01 unknown_sccs -7483 1h75A 81 3.52e-01 1h75A c.47.1.1 60716 1ksiB 642 3.97e-01 1ksiB b.30.2.1 24409 d.17.2.1 38045 d.17.2.1 38046 1ksiA 642 4.43e-01 1ksiB b.30.2.1 24408 d.17.2.1 38043 d.17.2.1 38044 1tbaB 180 5.27e-01 1ytbA d.129.1.1 41286 d.129.1.1 41287 1jx4A 352 6.34e-01 unknown_sccs -10188 unknown_sccs -11898 1whsA 255 9.87e-01 1ivyA c.69.1.5 34649 3daaA 277 1.07e+00 1daaA e.17.1.1 43272 1fn9A 365 1.17e+00 1fn9A d.196.1.1 59894 1im4A 221 1.25e+00 unknown_sccs 62581 1co4A 42 1.25e+00 1co4A g.47.1.1 45347 1j3vA 289 1.30e+00 a.100.1.1 -1303 c.2.1.6 -5947 1io2A 213 1.38e+00 1ekeA c.55.3.1 62612 1daaA 282 1.46e+00 1daaA e.17.1.1 43270 1pvmA 184 1.51e+00 d.37.1.1 -9612 d.37.1.1 -9613 unknown_sccs -12799 1o1yA 239 1.52e+00 c.23.16.1 86554 1hmcA 148 1.55e+00 1hmcB a.26.1.2 16867 1ig3A 263 1.70e+00 1ig3A b.82.6.1 62358 c.100.1.1 62359 1ayl 541 1.72e+00 1ayl c.91.1.1 64718 c.109.1.1 64719 1bw0A 416 1.75e+00 1bw0A c.67.1.1 34385 3grx 82 1.77e+00 1aba c.47.1.1 32769 1dq3A 454 1.93e+00 1dq3A b.86.1.2 28380 d.50.3.1 38798 d.95.2.2 40585 d.95.2.2 40586 2dabA 282 2.02e+00 1daaA e.17.1.1 43274 1cdwA 179 2.07e+00 1ytbA d.129.1.1 41212 d.129.1.1 41213 1gulA 222 2.11e+00 1pgtA a.45.1.1 17675 c.47.1.5 32969 1a3gA 308 2.17e+00 1daaA e.17.1.1 43286 1m2dA 110 2.17e+00 c.47.1.11 78476 1whtA 256 2.19e+00 1ivyA c.69.1.5 34646 1gpl 432 2.20e+00 1gpl b.12.1.2 23645 c.69.1.19 34793 1jvwA 167 2.20e+00 d.26.1.1 71907 1a8y 367 2.22e+00 1a8y c.47.1.3 32781 c.47.1.3 32782 c.47.1.3 32783 1bu8A 452 2.22e+00 1gpl b.12.1.2 23647 c.69.1.19 34795 1mvoA 136 2.32e+00 c.23.1.1 79513 1j79A 347 2.37e+00 1j79A c.1.9.4 62675 1j08A 226 2.41e+00 c.47.1.2 83855 c.47.1.2 83856 1bcsA 263 2.42e+00 1ivyA c.69.1.5 34647 1xgsA 295 2.52e+00 1bn5 a.4.5.25 16216 d.127.1.1 41153 1d3yA 301 2.54e+00 1d3yA e.12.1.1 43252 1gumA 222 2.80e+00 1pgtA a.45.1.1 17683 c.47.1.5 32977 1s1hM 132 3.05e+00 1oen 540 3.10e+00 1ayl c.91.1.1 64750 c.109.1.1 64751 1o0wA 252 3.11e+00 a.149.1.1 80751 d.50.1.1 80752 1zfjA 491 3.23e+00 1ak5 c.1.5.1 28638 d.37.1.1 38540 d.37.1.1 38541 1iyeA 309 3.25e+00 e.17.1.1 83786 1i1kA 309 3.43e+00 1daaA e.17.1.1 61533 1eu8A 409 3.48e+00 1eu8A c.94.1.1 59502 1g6hA 257 3.69e+00 1gajA c.37.1.12 60318 1jo0A 98 3.76e+00 d.68.4.1 77140 1b1cA 181 3.81e+00 1amoA c.23.5.2 31212 1r5pA 108 3.86e+00 unknown_sccs -7487 1hv8A 367 3.99e+00 1hv8A c.37.1.19 32405 c.37.1.19 32406 1m2bA 110 3.99e+00 c.47.1.11 78474 1jtdB 273 3.99e+00 b.69.5.2 67265 1m2aA 110 4.10e+00 c.47.1.11 78472 1jfrA 262 4.20e+00 1jfrA c.69.1.16 34724 1f37A 110 4.41e+00 1f37A c.47.1.11 33088 1gajA 257 4.50e+00 1gajA c.37.1.12 60416 1sviA 195 4.60e+00 1fgyA 127 4.64e+00 1faoA b.55.1.1 26976 1qnaA 200 4.75e+00 1ytbA d.129.1.1 41226 d.129.1.1 41227 1b8tA 192 4.96e+00 1b8tA g.39.1.3 45135 g.39.1.3 45136 g.39.1.3 45137 g.39.1.3 45138 1s6yA 450 4.97e+00 2hhmA 276 5.01e+00 1imbA e.7.1.1 42955 1a4uA 254 5.06e+00 1b16A c.2.1.2 29878 1hizA 379 5.07e+00 c.1.8.3 65841 1imdA 277 5.14e+00 1imbA e.7.1.1 42968 1vhxA 150 5.22e+00 unknown_sccs -7663 1cnv 299 5.29e+00 1cnv c.1.8.5 28989 1p4xA 250 5.33e+00 a.4.5.28 87784 a.4.5.28 87785 1cl8A 276 5.51e+00 1ckqA c.52.1.1 33230 1ipd 345 5.56e+00 1cnzA c.77.1.1 35038 1a8l 226 5.70e+00 1a8l c.47.1.2 32777 c.47.1.2 32778 1b16A 254 5.73e+00 1b16A c.2.1.2 29875 1qk3A 233 5.78e+00 1qk3A c.61.1.1 34031 1wkqA 164 5.85e+00 1mo0A 275 5.89e+00 c.1.1.1 79329 1idm 343 6.02e+00 1cnzA c.77.1.1 35035 1oyjA 231 6.08e+00 a.45.1.1 87597 c.47.1.5 87598 1qhfA 240 6.18e+00 1qhfA c.60.1.1 33960 1hmcB 148 6.25e+00 1hmcB a.26.1.2 16868 1ut9A 609 6.46e+00 a.102.1.2 -1326 b.1.18.2 -2710 1kx9A 112 6.62e+00 unknown_sccs 77602 1fsgA 233 6.74e+00 1qk3A c.61.1.1 34029 1s48A 609 7.04e+00 e.8.1.4 -11955 1ghsA 306 7.46e+00 1aq0A c.1.8.3 28840 1imbA 277 7.49e+00 1imbA e.7.1.1 42957 1f21A 155 7.52e+00 2rn2 c.55.3.1 33550 1o6aA 96 7.52e+00 unknown_sccs -4101 1igwA 434 7.58e+00 c.1.12.7 62370 1bq3B 246 7.68e+00 1qhfA c.60.1.1 33979 1qc9A 276 7.84e+00 1ckqA c.52.1.1 33235 1dr8B 344 8.01e+00 1cnzA c.77.1.1 35052 1gnwA 211 8.29e+00 1gnwA a.45.1.1 17727 c.47.1.5 33021 3vub 101 8.60e+00 3vub b.34.6.1 24613 1ecxA 384 8.66e+00 1ecxA c.67.1.3 34431 1iloA 77 8.70e+00 c.47.1.1 66205 1vokA 200 8.84e+00 1ytbA d.129.1.1 41242 d.129.1.1 41243 1qpsA 261 9.19e+00 1ckqA c.52.1.1 33234 1gpb 842 9.47e+00 1a8i c.87.1.4 35478 1di6A 195 9.59e+00 1di6A c.57.1.1 33863 1eg5A 384 9.65e+00 1ecxA c.67.1.3 34429 1eriA 276 9.87e+00 1ckqA c.52.1.1 33231 1pzxA 289 1.03e+01 c.119.1.1 -8623 1vioA 243 1.07e+01 unknown_sccs -10154 d.66.1.5 -10240 1qk4A 233 1.12e+01 1qk3A c.61.1.1 34037 1cne 270 1.13e+01 1ndh b.43.4.2 25661 c.25.1.1 31551 1sra 151 1.13e+01 1sra a.39.1.3 17190 1fsz 372 1.16e+01 1fsz c.32.1.1 31750 d.79.2.1 39802 1ckqA 276 1.17e+01 1ckqA c.52.1.1 33229 1ja1A 622 1.19e+01 1amoA b.43.4.1 62803 c.23.5.2 62804 c.25.1.4 62805 1r26A 125 1.19e+01 c.47.1.1 -7389 1m2oA 768 1.20e+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 1eazA 125 1.25e+01 b.55.1.1 70113 1f89A 291 1.25e+01 d.160.1.1 64988 1nrfA 262 1.26e+01 e.3.1.1 -11780 1gwcA 230 1.28e+01 a.45.1.1 70660 c.47.1.5 70661 2rn2 155 1.29e+01 2rn2 c.55.3.1 33551 1tiyA 164 1.29e+01 1mai 131 1.30e+01 1mai b.55.1.1 26951 1kk9A 221 1.32e+01 d.115.1.1 77432 1awe 130 1.32e+01 1awe b.55.1.1 26968 1o0pA 104 1.33e+01 d.58.7.1 86535 1sr9A 644 1.34e+01 1gp4A 356 1.35e+01 b.82.2.1 65439 1jhnA 424 1.37e+01 b.29.1.12 70060 b.104.1.1 66722 1eucB 396 1.37e+01 2scuB c.23.4.1 31149 d.142.1.4 41570 1xbrA 184 1.39e+01 1xbrA b.2.5.4 22458 1dp4A 435 1.40e+01 1dp4A c.93.1.1 35710 1rg9A 383 1.43e+01 d.130.1.1 -11057 d.130.1.1 -11058 d.130.1.1 -11059 1fw1A 216 1.46e+01 a.45.1.1 60051 c.47.1.5 60052 1kmqA 184 1.47e+01 c.37.1.8 84412 1on3A 523 1.47e+01 c.14.1.4 87107 c.14.1.4 87108 1pms 136 1.48e+01 1awe b.55.1.1 26966 1vjgA 218 1.50e+01 unknown_sccs -6447 1esmA 316 1.50e+01 1esmA c.37.1.6 31953 1tx4B 178 1.55e+01 1ctqA c.37.1.8 32045 1orrA 347 1.55e+01 c.2.1.2 -5776 1a8i 842 1.58e+01 1a8i c.87.1.4 35490 1j6oA 268 1.59e+01 c.1.9.12 77088 1oktA 211 1.62e+01 a.45.1.1 -942 c.47.1.5 -7467 1ne6A 283 1.66e+01 b.82.3.2 -4918 b.82.3.2 -4919 1n57A 291 1.67e+01 c.23.16.2 85328 1n8vA 112 1.67e+01 unknown_sccs 85457 1iy8A 267 1.69e+01 c.2.1.2 83774 1qqgA 264 1.73e+01 1qqgA b.55.1.2 26987 b.55.1.2 26988 1nmoA 247 1.73e+01 unknown_sccs -8746 1bkrA 109 1.73e+01 1bkrA a.40.1.1 17394 1vjqA 79 1.77e+01 unknown_sccs -13478 1oxsC 353 1.77e+01 b.40.6.3 87519 c.37.1.12 87520 1pauA 147 1.77e+01 1pauA c.17.1.1 30994 1npdA 288 1.80e+01 c.2.1.7 80681 c.58.1.5 80682 1g5aA 628 1.80e+01 b.71.1.1 65152 c.1.8.1 65153 1dcfA 136 1.80e+01 1dcfA c.23.1.2 31124 1toh 343 1.81e+01 4pah d.178.1.1 42573 1ghr 306 1.82e+01 1aq0A c.1.8.3 28844 1oxxK 353 1.83e+01 b.40.6.3 -3969 c.37.1.12 -7187 1ry9A 145 1.89e+01 d.198.1.1 -9020 1f8mA 429 1.90e+01 1dquA c.1.12.7 29315 1nycA 111 1.90e+01 unknown_sccs -4522 1thx 115 1.91e+01 1thx c.47.1.1 32732 1vsd 152 1.93e+01 1cxqA c.55.3.2 33625 1uw4A 91 1.94e+01 unknown_sccs -10038 1pmt 203 1.97e+01 1a0fA a.45.1.1 17740 c.47.1.5 33034 1rch 155 1.97e+01 2rn2 c.55.3.1 33570 1e6bA 221 2.01e+01 1e6bA a.45.1.1 59294 c.47.1.5 59295 1aq0A 306 2.03e+01 1aq0A c.1.8.3 28842 1sep 261 2.04e+01 1oaa c.2.1.2 29830 1jl1A 155 2.05e+01 c.55.3.1 66821 1hmpA 217 2.06e+01 1qk3A c.61.1.1 34075 1knvA 293 2.08e+01 c.52.1.7 68707 1pi1A 185 2.11e+01 unknown_sccs -762 1smvA 260 2.11e+01 1smvA b.121.4.7 23288 1aba 87 2.15e+01 1aba c.47.1.1 32760 1dd9A 338 2.16e+01 1dd9A e.13.1.1 43254 1aa2 108 2.19e+01 1bkrA a.40.1.1 17395 1oaa 259 2.20e+01 1oaa c.2.1.2 29829 1o50A 157 2.24e+01 d.37.1.1 -9604 d.37.1.1 -9605 1lwdA 413 2.24e+01 c.77.1.1 78265 2scuB 388 2.24e+01 2scuB c.23.4.1 31141 d.142.1.4 41562 1b04A 318 2.29e+01 1b04A d.142.2.2 41579 1bykA 255 2.33e+01 1bykA c.93.1.1 35706 1nu0A 138 2.33e+01 unknown_sccs -7658 1qq7A 253 2.34e+01 1qq5A c.108.1.1 43329 1aq6A 253 2.40e+01 1qq5A c.108.1.1 43331 1qq5A 253 2.42e+01 1qq5A c.108.1.1 43327 1ovqA 138 2.42e+01 unknown_sccs -7660 1f61A 429 2.44e+01 1dquA c.1.12.7 29319 1dxeA 256 2.45e+01 1dxeA c.1.12.5 29310 1hufA 140 2.49e+01 1hufA d.195.1.1 61272 1e6qM 501 2.52e+01 1e70M c.1.8.4 28920 1ak5 503 2.53e+01 1ak5 c.1.5.1 28639 1mh1 186 2.54e+01 1eesA c.37.1.8 32002 1e4mM 501 2.55e+01 1e70M c.1.8.4 59226 1cz3A 168 2.56e+01 1d1gA c.71.1.1 34891 1l5wA 796 2.57e+01 c.87.1.4 73605 1f4qA 165 2.57e+01 1alvA a.39.1.8 17360 1r7lA 110 2.59e+01 1hfbA 370 2.62e+01 c.1.10.4 76706 1ahpA 797 2.67e+01 1a8i c.87.1.4 35544 1nozA 388 2.67e+01 1clqA c.55.3.5 33715 1se8A 301 2.68e+01 3lynA 136 2.68e+01 1lis a.19.1.1 16413 1f2tA 149 2.70e+01 1f2tA c.37.1.12 32373 1g7eA 122 2.71e+01 1g7eA c.47.1.7 33055 1iyxA 432 2.74e+01 c.1.11.1 83815 d.54.1.1 83816 1b0uA 262 2.76e+01 1b0uA c.37.1.12 32370 1ukuA 102 2.76e+01 d.58.5.2 -9992 1d1gA 168 2.76e+01 1d1gA c.71.1.1 34889 1kebA 108 2.76e+01 c.47.1.1 77341 1us8A 147 2.80e+01 c.37.1.12 -7194 1ahsA 126 2.83e+01 1ahsA b.19.1.1 23794 1c55A 40 2.84e+01 1sco g.3.7.2 44158 2mjpA 193 2.86e+01 1b78A c.51.4.1 33223 1b78A 193 2.87e+01 1b78A c.51.4.1 33221 1hph 37 2.87e+01 1hph j.15.1.1 46159 1h5yA 253 2.92e+01 c.1.2.1 65638 2ay1A 394 2.93e+01 1ajsA c.67.1.1 34357 1ru8A 232 3.01e+01 c.26.2.1 -6635 1iyhA 198 3.04e+01 a.45.1.1 83790 c.47.1.5 83791 1pd21 199 3.09e+01 1pd21 1lp3A 519 3.12e+01 b.121.5.2 74169 1oivA 191 3.12e+01 c.37.1.8 -7074 1usmA 80 3.14e+01 d.74.1.1 -10334 1jqeA 292 3.15e+01 c.66.1.19 71789 1ccwA 137 3.15e+01 1be1 c.23.6.1 31238 1aisA 182 3.16e+01 1ytbA d.129.1.1 41288 d.129.1.1 41289 1nnwA 252 3.19e+01 d.159.1.5 80674 1gp6A 356 3.25e+01 b.82.2.1 65441 2trxA 108 3.26e+01 1thx c.47.1.1 32719 1jakA 512 3.27e+01 c.1.8.6 66472 d.92.2.1 66473 1ilr1 152 3.29e+01 1irp 1h70A 255 3.35e+01 1h70A d.126.1.3 60711 1e19A 314 3.35e+01 1b7bA c.73.1.1 34967 1ekeA 230 3.36e+01 1ekeA c.55.3.1 33572 1f2dA 341 3.36e+01 1f2dA c.79.1.1 35298 1fzqA 181 3.39e+01 1hurA c.37.1.8 32060 1qipA 183 3.40e+01 1qipA d.32.1.1 38470 2tmdA 729 3.40e+01 2tmdA c.1.4.1 28616 c.3.1.1 30317 c.4.1.1 30602 1sb8A 352 3.40e+01 1vi2A 300 3.42e+01 c.2.1.7 -5960 c.58.1.5 -6366 1j98A 157 3.43e+01 1j98A d.185.1.2 62755 1eesA 178 3.50e+01 1eesA c.37.1.8 32073 1exbA 332 3.58e+01 1qrqA c.1.7.1 28666 1k32A 1045 3.59e+01 b.36.1.3 68068 b.68.7.1 68069 b.69.9.1 68070 c.14.1.2 68071 1kf6A 602 3.60e+01 a.7.3.1 72394 c.3.1.4 72395 d.168.1.1 72396 1o94A 729 3.62e+01 c.1.4.1 81200 c.3.1.1 81201 c.4.1.1 81202 1asu 162 3.62e+01 1cxqA c.55.3.2 33626 1bglA 1023 3.65e+01 1bglA b.1.4.1 22097 b.1.4.1 22098 b.18.1.5 23734 b.30.5.1 24358 c.1.8.3 28857 1gqoI 143 3.67e+01 c.23.13.1 76303 1n2zA 245 3.69e+01 c.92.2.2 79865 2ovo 56 3.73e+01 2ovo unknown_sccs 44701 1b87A 181 3.73e+01 1b87A d.108.1.1 40797 1t35A 191 3.75e+01 unknown_sccs -7285 1c8kA 842 3.80e+01 1a8i c.87.1.4 35491 1k0dA 260 3.82e+01 a.45.1.1 67930 c.47.1.5 67931 1lvwA 295 3.84e+01 c.68.1.6 84723 1bo4A 168 3.86e+01 1bo4A d.108.1.1 40798 1aszB 490 3.86e+01 1b8aA b.40.4.1 25241 d.104.1.1 40762 1n6eA 1071 3.86e+01 b.36.1.3 80149 b.68.7.1 80150 b.69.9.1 80151 c.14.1.2 80152 1efvB 255 3.86e+01 1efvB c.26.2.3 31634 1puiA 210 3.88e+01 c.37.1.8 88292 1g5yA 238 3.89e+01 1lbd a.123.1.1 60294 1mfiA 114 3.90e+01 1dptA d.80.1.3 39856 1mp9A 198 3.91e+01 a.74.1.2 -1127 a.74.1.2 -1128 8abp 306 3.92e+01 8abp c.93.1.1 35647 1dypA 271 3.95e+01 1dypA b.29.1.2 24185 1or0A 160 3.95e+01 d.153.1.2 -11415 1cxqA 162 3.99e+01 1cxqA c.55.3.2 33621