# List of top-scoring protein chains for t2k-100-30-alpha-scores 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 2fhqA 141 7.91e-16 1dnlA 199 7.31e-14 1ci0A b.45.1.1 25753 1g79A 218 9.29e-14 1ci0A b.45.1.1 25752 1nrgA 261 5.66e-10 b.45.1.1 80694 1rfeA 162 1.06e-09 2fg9A 178 1.84e-09 1t9mA 214 6.23e-09 1ty9A 222 6.67e-08 2asfA 137 8.19e-07 1ci0A 228 1.62e-06 1ci0A b.45.1.1 25750 1vl7A 157 8.13e-06 b.45.1.1 108732 2aq6A 147 1.14e-05 1w9aA 147 4.89e-05 1xxoA 147 6.96e-05 2furA 209 9.64e-05 1flmA 122 1.17e-04 1axj b.45.1.1 25747 1axj 122 1.51e-04 1axj b.45.1.1 25749 1w3oA 216 1.29e-03 1ejeA 192 2.68e-03 1ejeA b.45.1.2 25757 1xhnA 184 2.41e-02 2arzA 247 3.27e-02 2bgiA 272 7.78e-02 1j58A 385 2.73e-01 b.82.1.2 71531 1ujqA 305 1.47e+00 c.1.12.7 99463 1pvtA 238 2.57e+00 c.74.1.1 95189 1vc1A 110 3.03e+00 c.13.2.1 108493 1ww7A 160 3.18e+00 2exnA 136 3.51e+00 1tfaA 329 3.84e+00 1nnt c.94.1.2 35880 1ye8A 178 3.94e+00 2ag5A 246 4.44e+00 1tr8A 102 4.49e+00 1x88A 359 5.05e+00 1pse 69 5.07e+00 1pse b.34.4.2 24595 1nftA 329 5.12e+00 1nnt c.94.1.2 35881 1s2wA 295 5.14e+00 c.1.12.7 98407 2etvA 346 6.17e+00 1vrtA 560 6.31e+00 1rthA c.55.3.1,e.8.1.2 33574,43023 1d8yA 605 6.40e+00 1xwl c.55.3.5,e.8.1.1 33684,42977 1j5kA 89 6.57e+00 d.51.1.1 71565 1hrhA 136 6.64e+00 1rthA c.55.3.1 33577 1uirA 314 6.78e+00 c.66.1.17 99429 1y0yA 353 6.93e+00 1w66A 232 6.95e+00 1zzkA 82 7.31e+00 1mhnA 59 7.87e+00 b.34.9.1 84964 2f4iA 197 8.02e+00 1iejA 332 8.13e+00 1nnt c.94.1.2 62328 1ofuA 320 8.22e+00 c.32.1.1,d.79.2.1 86972,86973 1klnA 605 8.28e+00 1xwl c.55.3.5,e.8.1.1 33693,42986 1nnt 328 8.41e+00 1nnt c.94.1.2 35884 1ii6A 368 8.54e+00 1bg2 c.37.1.9 62413 2fcjA 119 8.57e+00 1g5vA 88 8.73e+00 1g5vA b.34.9.1 60292 1pfxL 146 8.79e+00 1cfi g.3.11.1,g.3.11.1,g.32.1.1 44207,44208,44973 1p3wA 404 9.06e+00 c.67.1.3 87752 1q0bA 367 9.72e+00 c.37.1.9 95502 1r17A 343 1.00e+01 b.2.3.4,b.2.3.4 96796,96797 1o98A 511 1.01e+01 c.105.1.1,c.76.1.3 86684,86685 2conA 79 1.01e+01 1zpwX 90 1.04e+01 1fua 215 1.06e+01 2fua c.74.1.1 34973 1qp2A 70 1.06e+01 1pse b.34.4.2 24596 2fua 215 1.08e+01 2fua c.74.1.1 34977 1r0vA 305 1.09e+01 c.52.2.1,c.52.2.1,d.75.1.1 96742,96743,96744 1dttA 560 1.10e+01 1rthA c.55.3.1,e.8.1.2 33611,43088 2azeA 155 1.11e+01 1eqjA 511 1.12e+01 1ejjA c.105.1.1,c.76.1.3 59495,59496 1auz 116 1.20e+01 1auz c.13.2.1 30883 1jeyA 609 1.20e+01 1jeqA b.131.1.1,c.62.1.3 90370,90371 1xfoA 357 1.21e+01 1oj4A 283 1.23e+01 d.14.1.5,d.58.26.5 93083,93084 1ejjA 511 1.26e+01 1ejjA c.105.1.1,c.76.1.3 59422,59423 2bw3A 534 1.31e+01 1k0mA 241 1.35e+01 a.45.1.1,c.47.1.5 67949,67950 1aim 215 1.37e+01 1cs8A d.3.1.1 37044 2g1uA 155 1.44e+01 1v9yA 167 1.44e+01 d.110.3.2 108454 1zvkA 358 1.44e+01 2g09A 297 1.47e+01 1bbpA 173 1.50e+01 1bbpA b.60.1.1 27147 2bvfA 459 1.50e+01 1rthA 560 1.51e+01 1rthA c.55.3.1,e.8.1.2 33576,43028 1fnuA 221 1.55e+01 3seb b.40.2.2,d.15.6.1 25212,37801 1ksyA 154 1.56e+01 d.89.1.2 72948 2a5sA 284 1.57e+01 1me4A 215 1.58e+01 d.3.1.1 79023 1rq2A 382 1.64e+01 c.32.1.1,d.79.2.1 105048,105049 1jb0F 164 1.74e+01 1jb0F f.23.16.1 62825 2alzA 390 1.76e+01 1gt91 357 1.78e+01 1umkA 275 1.78e+01 1jeqA 609 1.81e+01 1jeqA a.140.2.1,b.131.1.1,c.62.1.3 64748,90366,90367 1f2aA 215 1.81e+01 1cs8A d.3.1.1 37040 1rz3A 201 1.82e+01 c.37.1.6 98132 1xe1A 116 1.82e+01 b.43.3.1 109571 1lqbC 162 1.82e+01 b.3.3.1 74186 1fkoA 543 1.89e+01 1rthA c.55.3.1,e.8.1.2 33612,43094 2c1gA 431 1.89e+01 1k0nA 241 1.89e+01 a.45.1.1,c.47.1.5 67953,67954 1xtmA 175 1.92e+01 1qg3A 195 1.92e+01 1qg3A b.1.2.1,b.1.2.1 21993,21994 1a8p 258 1.96e+01 1fdr b.43.4.2,c.25.1.1 25654,31544 1wj9A 211 2.05e+01 1fk9A 543 2.09e+01 1rthA c.55.3.1,e.8.1.2 33607,43080 1gal 583 2.10e+01 1gpeA c.3.1.2,d.16.1.1 30386,37950 2dpmA 284 2.11e+01 2dpmA c.66.1.28 34246 1y1pA 342 2.12e+01 1div 149 2.14e+01 1div d.99.1.1,d.100.1.1 40692,40693 1ne9A 335 2.14e+01 d.108.1.4,d.108.1.4 91839,91840 1cf3A 583 2.17e+01 1gpeA c.3.1.2,d.16.1.1 30385,37949 1me3A 215 2.19e+01 d.3.1.1 79022 1lm8V 160 2.20e+01 b.3.3.1 74035 2d0oA 610 2.22e+01 1i9zA 347 2.28e+01 1i9yA d.151.1.2 62102 1n9lA 109 2.31e+01 d.110.3.6 85468 2bznA 351 2.47e+01 1b1zA 219 2.48e+01 3seb b.40.2.2,d.15.6.1 25216,37805 2c6qA 351 2.51e+01 1a8y 367 2.52e+01 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 2hmiA 558 2.53e+01 1rthA c.55.3.1,e.8.1.2 33604,43106 1o89A 345 2.54e+01 b.35.1.2,c.2.1.1 92644,92645 1gdoB 240 2.58e+01 1gdoA 2gw8A 114 2.61e+01 1i9yA 347 2.73e+01 1i9yA d.151.1.2 62101 2b4yA 271 2.76e+01 1i7pA 274 2.76e+01 b.43.4.2,c.25.1.1 66048,66049 1g6aA 271 2.77e+01 1btl e.3.1.1 42704 1ujmA 342 2.81e+01 1q7fA 286 2.83e+01 b.68.9.1 96036 1ryp2 233 2.83e+01 1ryp2 2fauA 341 2.84e+01 1z7dA 433 2.86e+01 1t3nA 388 2.86e+01 d.240.1.1,e.8.1.7 106363,106364 1qx4A 274 2.88e+01 b.43.4.2,c.25.1.1 104624,104625 1b76A 442 2.88e+01 1atiA c.51.1.1,d.104.1.1 33198,40747 1kijA 390 2.92e+01 d.14.1.3,d.122.1.2 72514,72515 1qrrA 394 2.95e+01 1qrrA c.2.1.2 29824 1xn9A 101 2.99e+01 1t1gA 364 3.02e+01 c.41.1.2 106246 1f6bA 198 3.04e+01 c.37.1.8 64986 1vcbC 160 3.04e+01 1vcbC b.3.3.1 22535 1mw9X 592 3.05e+01 e.10.1.1 91480 1sbyA 254 3.13e+01 1viaA 175 3.13e+01 c.37.1.2 100754 1gdoA 240 3.13e+01 1gdoA 1o4uA 285 3.14e+01 c.1.17.1,d.41.2.1 86624,86625 1n67A 359 3.16e+01 b.2.3.4,b.2.3.4 85354,85355 1e5xA 486 3.17e+01 c.79.1.1 59283 1vmaA 306 3.23e+01 a.24.13.1,c.37.1.10 108887,108888 1a4uA 254 3.25e+01 1b16A c.2.1.2 29878 1b16A 254 3.28e+01 1b16A c.2.1.2 29875 1vmeA 410 3.34e+01 c.23.5.1,d.157.1.3 108893,108894 2bgzA 299 3.34e+01 1wbiA 129 3.35e+01 1wlgA 299 3.36e+01 1xffA 240 3.38e+01 d.153.1.1 109580 1uarA 285 3.38e+01 c.46.1.2,c.46.1.2 107762,107763 1z08A 170 3.43e+01 1y0hA 105 3.43e+01 1eetA 557 3.44e+01 1rthA c.55.3.1,e.8.1.2 33608,43078 1fsz 372 3.44e+01 1fsz c.32.1.1,d.79.2.1 31750,39802 1ecfB 504 3.45e+01 1ecfB c.61.1.1,d.153.1.1 34054,41821 1tx4B 178 3.45e+01 1ctqA c.37.1.8 32045 1dbqA 289 3.49e+01 1qpzA c.93.1.1 35666 2av5A 120 3.50e+01 1hmvA 560 3.55e+01 1rthA c.55.3.1,e.8.1.2 33587,43046 1ejbA 168 3.58e+01 1rvv1 c.16.1.1 59417 1i24A 404 3.59e+01 c.2.1.2 83663 1t1jA 125 3.64e+01 c.137.1.1 106249 1oo0A 147 3.66e+01 d.232.1.1 87182 1jr1A 514 3.70e+01 c.1.5.1,d.37.1.1,d.37.1.1 63241,63242,63243 1zd7A 159 3.74e+01 1z41A 338 3.77e+01 1pex 207 3.80e+01 1gen b.66.1.1 27540 1atiA 505 3.81e+01 1atiA c.51.1.1,d.104.1.1 33196,40745 1eu3A 210 3.86e+01 1an8 b.40.2.2,d.15.6.1 25206,37795 1dloA 556 3.91e+01 1rthA c.55.3.1,e.8.1.2 33584,43040 1ecfA 504 3.91e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 1zetA 388 3.91e+01 1xtlA 175 3.97e+01 1fivA 113 3.98e+01 1fmb b.50.1.1 26764 1zt3A 80 4.02e+01 1f08A 148 4.05e+01 1f08A d.89.1.2 59564 1fts 295 4.08e+01 1ng1 a.24.13.1,c.37.1.10 16968,32279 2ai4A 119 4.10e+01 1m7bA 184 4.14e+01 c.37.1.8 74572 1puiA 210 4.15e+01 c.37.1.8 88292 1nv8A 284 4.15e+01 c.66.1.30 86224 1gca 309 4.21e+01 1gca c.93.1.1 35659 1atiB 505 4.30e+01 1atiA c.51.1.1,d.104.1.1 33197,40746 1a79A 171 4.33e+01 1a79A c.52.2.1,d.75.1.1 33340,39739 1j4wA 174 4.41e+01 d.51.1.1,d.51.1.1 71529,71530 2bvaA 292 4.43e+01 1es5A 262 4.43e+01 1skf e.3.1.1 42679 1gpeA 587 4.47e+01 1gpeA c.3.1.2,d.16.1.1 30387,37951 2cr9A 139 4.49e+01 1wd6A 123 4.50e+01 1sjiA 350 4.51e+01 1fm2B 520 4.52e+01 1fm2B 2fgtA 417 4.54e+01 2czvC 120 4.55e+01 1agqA 135 4.56e+01 1agqA g.17.1.2 44789 1wsrA 375 4.59e+01 1dzkA 157 4.60e+01 1obpA b.60.1.1 27096 2d93A 134 4.66e+01 1hqkA 154 4.72e+01 c.16.1.1 65902 1kagA 173 4.73e+01 c.37.1.2 72249 1pda 315 4.77e+01 1pda c.94.1.1,d.50.2.1 35751,38794 2abqA 306 4.81e+01 2c1iA 431 4.82e+01 1ndh 272 4.84e+01 1ndh b.43.4.2,c.25.1.1 25662,31552 1xkiA 162 4.84e+01 1odkA 235 4.87e+01 c.56.2.1 86863 1qm4A 396 4.88e+01 1mxb d.130.1.1,d.130.1.1,d.130.1.1 41350,41351,41352 1kmqA 184 4.89e+01 c.37.1.8 84412 1kv9A 668 4.90e+01 a.3.1.6,b.70.1.1 73056,73057 1br9 194 4.94e+01 1br9 b.40.3.1 25235 1z5hA 780 4.95e+01 1vpjA 192 5.03e+01 1bqnA 558 5.10e+01 1rthA c.55.3.1,e.8.1.2 33599,43064 1y21A 282 5.11e+01 2a4vA 159 5.13e+01 2bduA 297 5.13e+01 1kuuA 202 5.14e+01 d.153.2.1 73019 1xfkA 336 5.18e+01 1ntfA 282 5.18e+01 d.151.1.2 92104 1gk1B 522 5.20e+01 1a3yA 149 5.26e+01 1obpA b.60.1.1 27110 1gdtA 183 5.27e+01 2rslA a.4.1.2,c.53.1.1 16021,33348 2ghsA 326 5.32e+01 1or0B 528 5.32e+01 1e4cP 215 5.33e+01 2fua c.74.1.1 34969 2bjfA 329 5.34e+01 1scjB 71 5.34e+01 1scjB d.58.3.2 39069 2df7A 458 5.36e+01 1mkeA 152 5.42e+01 b.55.1.4 79231 1esiA 262 5.46e+01 1skf e.3.1.1 42682 1xknA 355 5.48e+01 1pguA 615 5.50e+01 b.69.4.1,b.69.4.1 88069,88070 1zybA 232 5.53e+01 2rspA 124 5.55e+01 2rspB b.50.1.1 26771 1hniA 558 5.56e+01 1rthA c.55.3.1,e.8.1.2 33586,43044 1yn9A 169 5.57e+01 1vpmA 169 5.65e+01 2asi 360 5.66e+01 2rmpA b.50.1.2 26824 1ioaA 240 5.69e+01 1led b.29.1.1 24168 1pvmA 184 5.71e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1ew3A 159 5.73e+01 1mup b.60.1.1 27114 1p3dA 475 5.75e+01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1wd5A 208 5.75e+01 1rwrA 301 5.76e+01 b.80.1.11 97990 1bw6A 56 5.77e+01 1bw6A a.4.1.7 16052 1g8kB 133 5.86e+01 1g8jB b.33.1.1 24435 1z7aA 308 5.89e+01 1gd7A 109 5.96e+01 b.40.4.4 60441 1es2A 262 5.96e+01 1skf e.3.1.1 42680 1f9yA 158 5.98e+01 d.58.30.1 83249 1gp0A 143 6.01e+01 b.64.1.1 70300 1vphA 149 6.05e+01 1rp0A 284 6.05e+01 4fiv 113 6.09e+01 1fmb b.50.1.1 26762 1mvpA 124 6.11e+01 2rspB b.50.1.1 26775 2fdiA 211 6.16e+01 1aod 289 6.17e+01 2plc c.1.18.2 29615 1v0wA 506 6.17e+01 d.136.1.2,d.136.1.2 108220,108221 1tvjA 166 6.20e+01 2bk9A 153 6.20e+01 1j27A 102 6.27e+01 d.58.50.1 90778 1pjr 724 6.28e+01 1pjr c.37.1.19,c.37.1.19 32391,32392 1nfiA 301 6.37e+01 1a3qA b.1.18.1,b.2.5.3 21942,22455 1xv5A 401 6.38e+01 1y3nA 490 6.38e+01 1s4iA 175 6.39e+01 1xmrA 243 6.43e+01 1inlA 296 6.50e+01 c.66.1.17 66220 1g0u1 266 6.58e+01 1nfiC 301 6.62e+01 b.1.18.1,b.2.5.3 21943,22456 1bpv 112 6.65e+01 1bpv b.1.2.1 22071 1si6X 282 6.70e+01 1snzA 344 6.71e+01 b.30.5.4 98930 1wi9A 72 6.72e+01 2arpA 116 6.75e+01 1vbvA 105 6.79e+01 2fjrA 189 6.86e+01 1rttA 193 6.87e+01 c.23.5.4 105098 1tidB 119 6.90e+01 c.13.2.1 107000 2tmp 127 6.98e+01 1br9 b.40.3.1 25236 2fivA 116 6.99e+01 1fmb b.50.1.1 26766 1ecl 597 7.00e+01 1ecl e.10.1.1 43238 1w9hA 427 7.01e+01 2ae5B 528 7.01e+01 2bwqA 129 7.04e+01 2eifA 136 7.05e+01 1bkb b.34.5.2,b.40.4.5 24607,25339 2bwrA 401 7.06e+01 1spbP 78 7.14e+01 1scjB d.58.3.2 39068 1ehaA 558 7.16e+01 1ehaA b.1.18.2,b.71.1.1,c.1.8.1 21859,27786,28773 3fivA 116 7.19e+01 1fmb b.50.1.1 26768 2d0iA 333 7.21e+01 1vqoE 178 7.24e+01 1mqeA 207 7.28e+01 d.113.1.1 91394 1hqi 90 7.28e+01 1hqi d.137.1.1 41454 1d5wC 126 7.31e+01 1dbwA c.23.1.1 31101 1o5oA 221 7.31e+01 c.61.1.1 92509 1cydA 244 7.35e+01 1cydA c.2.1.2 29825 1y44A 320 7.37e+01 1sy6A 204 7.46e+01 b.1.1.4,b.1.1.4 106111,106112 1nu7D 282 7.48e+01 a.8.6.1,a.8.6.1 92191,92192 1v9sA 208 7.53e+01 1xj4A 119 7.56e+01 2c1lA 358 7.57e+01 1w5fA 353 7.59e+01 1zd3A 555 7.62e+01 2f62A 161 7.63e+01 1ew0A 130 7.67e+01 1drmA d.110.3.2 40905 1f3lA 321 7.74e+01 1g6q2 c.66.1.6 59630 1f0iA 504 7.76e+01 1f0iA d.136.1.2,d.136.1.2 59566,59567 1skoA 143 7.82e+01 d.110.7.1 105676 2b0jA 358 7.82e+01 1jx2B 315 7.83e+01 c.37.1.8 67404 1mbmA 198 7.89e+01 b.47.1.3 78916 1gqyA 475 7.91e+01 c.5.1.1,c.59.1.1,c.72.2.1 83305,83306,83307 1f76A 336 7.91e+01 c.1.4.1 76160 1es4A 262 7.93e+01 1skf e.3.1.1 42683 2bmfA 451 7.97e+01 1x3lA 440 7.98e+01 1l6oA 95 8.02e+01 b.36.1.1 84534 1pieA 419 8.06e+01 d.14.1.5,d.58.26.7 94706,94707 1k0gA 453 8.14e+01 d.161.1.1 67940 1ag6 99 8.14e+01 1plc b.6.1.1 22857 2plc 274 8.20e+01 2plc c.1.18.2 29614 1bywA 110 8.26e+01 1bywA d.110.3.6 40912 1nxuA 333 8.28e+01 c.122.1.1 86389 1n71A 180 8.38e+01 d.108.1.1 85370 2rslA 140 8.38e+01 2rslA c.53.1.1 33345 1lxnA 99 8.45e+01 d.58.48.1 84737 1e5dA 402 8.47e+01 1e5dA c.23.5.1,d.157.1.3 31208,42061 2rmpA 361 8.53e+01 2rmpA b.50.1.2 26825 1w6sA 599 8.56e+01 1h4rA 314 8.64e+01 a.11.2.1,b.55.1.5,d.15.1.4 65616,65617,65618 1vkiA 181 8.65e+01 d.116.1.1 108664 1wetA 340 8.65e+01 1qpzA a.35.1.5,c.93.1.1 17093,35670 1hka 158 8.72e+01 1hka d.58.30.1 39433 1khoA 370 8.79e+01 a.124.1.1,b.12.1.3 72489,72490 1rfs 139 8.82e+01 1rfs b.33.1.1 24434 1mmsA 140 8.82e+01 1mmsA a.4.7.1,d.47.1.1 16247,38766 1uf2C 421 8.87e+01 a.115.1.3,b.19.1.1 99291,99292 1h3iA 293 8.89e+01 b.76.2.1,b.85.7.1 76635,76636 1skf 262 8.92e+01 1skf e.3.1.1 42684 1eur 365 8.98e+01 1eut b.68.1.1 27607 1yj7A 171 8.99e+01 1zxtA 76 8.99e+01