# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7-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 5.85e-22 1g79A 218 1.23e-16 1ci0A b.45.1.1 25752 1dnlA 199 5.81e-16 1ci0A b.45.1.1 25753 1rfeA 162 3.19e-13 2fg9A 178 1.64e-12 1nrgA 261 2.40e-12 b.45.1.1 80694 1t9mA 214 7.10e-12 2asfA 137 1.68e-11 1ty9A 222 1.09e-10 1vl7A 157 1.02e-09 b.45.1.1 108732 1ci0A 228 6.92e-09 1ci0A b.45.1.1 25750 2furA 209 8.55e-09 1axj 122 3.98e-08 1axj b.45.1.1 25749 2aq6A 147 5.47e-08 1xxoA 147 1.04e-07 1w9aA 147 1.85e-07 1flmA 122 2.83e-07 1axj b.45.1.1 25747 1xhnA 184 9.57e-07 1w3oA 216 1.23e-06 2arzA 247 4.86e-05 1ejeA 192 1.64e-03 1ejeA b.45.1.2 25757 1ww7A 160 3.91e-01 1rz1A 161 3.97e-01 b.45.1.2 98124 1qhuA 460 6.55e-01 1qhuA b.66.1.1,b.66.1.1 27530,27531 1wgbA 159 7.22e-01 1rocA 155 7.27e-01 b.1.22.1 97673 1i0rA 169 8.05e-01 1i0rA b.45.1.2 61489 1yoaA 159 8.93e-01 1i0sA 169 1.22e+00 1i0rA b.45.1.2 61491 1xfkA 336 1.55e+00 1wj9A 211 1.68e+00 2bgiA 272 1.77e+00 1w0dA 337 2.06e+00 1nnwA 252 2.27e+00 d.159.1.5 80674 1wjxA 122 2.87e+00 1c0aA 585 3.07e+00 1c0aA b.40.4.1,d.74.4.1,d.104.1.1 25246,39731,40767 2bjfA 329 3.30e+00 1b09A 206 3.55e+00 1sacA b.29.1.5 24247 2cwzA 141 3.98e+00 1rgyA 360 3.99e+00 e.3.1.1 97456 1klnA 605 4.21e+00 1xwl c.55.3.5,e.8.1.1 33693,42986 1ry9A 145 4.34e+00 d.198.1.1 98094 2db1A 118 4.52e+00 1rq2A 382 5.18e+00 c.32.1.1,d.79.2.1 105048,105049 1k0mA 241 5.43e+00 a.45.1.1,c.47.1.5 67949,67950 2ffyA 358 5.46e+00 1gnhA 206 5.62e+00 1sacA b.29.1.5 24252 1m2kA 249 5.98e+00 c.31.1.5 84754 1ipd 345 5.98e+00 1cnzA c.77.1.1 35038 1quqB 121 6.06e+00 1quqB b.40.4.3 25305 1obpA 159 6.36e+00 1obpA b.60.1.1 27092 1qa7A 217 6.43e+00 1havA b.47.1.4 26425 1ofuA 320 6.43e+00 c.32.1.1,d.79.2.1 86972,86973 1lq9A 112 6.57e+00 d.58.4.3 78129 1k0nA 241 6.64e+00 a.45.1.1,c.47.1.5 67953,67954 1d2eA 397 6.79e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25701,25741,32136 2b4yA 271 6.93e+00 1cm7A 363 7.03e+00 1cnzA c.77.1.1 35063 1iciA 256 7.12e+00 1iciA c.31.1.5 62266 1l0gA 358 7.57e+00 e.3.1.1 73400 2d37A 176 7.58e+00 1wluA 136 7.60e+00 2dcnA 311 7.77e+00 1j1yA 136 7.84e+00 d.38.1.5 90776 1uscA 178 7.89e+00 b.45.1.2 99860 1nnjA 271 8.03e+00 a.156.1.2,b.113.1.1,g.39.1.8 80669,80670,80671 1d8yA 605 8.10e+00 1xwl c.55.3.5,e.8.1.1 33684,42977 1idm 343 8.20e+00 1cnzA c.77.1.1 35035 1kvlA 358 8.21e+00 e.3.1.1 73062 1gy7A 125 8.47e+00 d.17.4.2 70738 1zzkA 82 8.63e+00 2cxcA 144 8.70e+00 1vp9 322 8.91e+00 3mag c.66.1.25 34210 2cxvA 219 9.56e+00 2dkaA 544 9.70e+00 2f62A 161 1.01e+01 1k8kD 300 1.02e+01 d.198.2.1,d.198.2.1 68309,68310 1pi4A 358 1.05e+01 e.3.1.1 94700 1fsz 372 1.05e+01 1fsz c.32.1.1,d.79.2.1 31750,39802 1tuhA 156 1.06e+01 d.17.4.11 107345 1crzA 403 1.06e+01 1crzA b.68.4.1,c.51.2.1 27629,33211 1i3zA 103 1.11e+01 d.93.1.1 83667 1z94A 147 1.11e+01 2blsA 358 1.14e+01 1gceA e.3.1.1 42747 2f2tA 161 1.14e+01 1v39 322 1.15e+01 3mag c.66.1.25 34206 2a0kA 161 1.18e+01 2ga9A 297 1.19e+01 2d0iA 333 1.19e+01 1fsyA 358 1.20e+01 1gceA e.3.1.1 60016 1mqeA 207 1.21e+01 d.113.1.1 91394 1qf6A 642 1.22e+01 1qf6A c.51.1.1,d.15.10.1,d.67.1.1,d.104.1.1 33210,39551,39562,40759 1frvA 264 1.31e+01 2frvA e.19.1.1 43308 1at0 145 1.31e+01 1at0 b.86.1.1 28374 1smpI 101 1.31e+01 1smpI b.61.2.1 27417 1jsmA 325 1.32e+01 b.19.1.2 63264 1vpt 348 1.32e+01 3mag c.66.1.25 34207 1tdzA 272 1.36e+01 a.156.1.2,b.113.1.1,g.39.1.8 106787,106788,106789 1asyA 490 1.38e+01 1b8aA b.40.4.1,d.104.1.1 25242,40763 1zzoA 136 1.42e+01 2cwsA 237 1.42e+01 2awdA 323 1.44e+01 3mag 307 1.45e+01 3mag c.66.1.25 34205 1rttA 193 1.47e+01 c.23.5.4 105098 1wbpA 397 1.47e+01 1fr1A 361 1.49e+01 1gceA e.3.1.1 42734 1fxlA 167 1.49e+01 1b7fA d.58.7.1,d.58.7.1 39183,39184 1ylnA 252 1.49e+01 2pviA 157 1.49e+01 3pviA c.52.1.6 33302 2gnqA 336 1.50e+01 1konA 249 1.50e+01 e.39.1.1 72823 1xqbA 247 1.52e+01 1pvuA 154 1.53e+01 3pviA c.52.1.6 33306 2f02A 323 1.58e+01 1bywA 110 1.62e+01 1bywA d.110.3.6 40912 1p97A 114 1.63e+01 d.110.3.7 94382 1pjjA 271 1.63e+01 a.156.1.2,b.113.1.1,g.39.1.8 104164,104165,104166 1vh5A 148 1.64e+01 d.38.1.5 100642 1nb9A 147 1.67e+01 b.43.5.1 85515 3pviA 157 1.76e+01 3pviA c.52.1.6 33300 1xaa 345 1.77e+01 1cnzA c.77.1.1 35033 1av6A 289 1.78e+01 3mag c.66.1.25 34218 1rowA 109 1.78e+01 b.1.11.2 97676 1j5kA 89 1.79e+01 d.51.1.1 71565 2bgcA 238 1.87e+01 2c6qA 351 1.97e+01 1u04A 771 1.99e+01 b.34.14.1,c.55.3.10 107539,107540 1wbiA 129 2.00e+01 2bznA 351 2.01e+01 1i7fA 292 2.05e+01 1i7fA d.193.1.1 61888 2bypA 214 2.07e+01 1mkyA 439 2.07e+01 c.37.1.8,c.37.1.8,d.52.5.1 79250,79251,79252 1uisA 231 2.08e+01 d.22.1.1 99431 1eyuA 157 2.09e+01 3pviA c.52.1.6 33304 1xv5A 401 2.11e+01 1mw9X 592 2.13e+01 e.10.1.1 91480 1y55X 126 2.13e+01 1pvtA 238 2.16e+01 c.74.1.1 95189 1wdtA 665 2.16e+01 1tfe 145 2.19e+01 1tfe d.43.1.1 38680 1qz8A 113 2.19e+01 b.140.1.1 96619 1dr8B 344 2.22e+01 1cnzA c.77.1.1 35052 1e8oB 106 2.23e+01 1914 d.49.1.1 38775 2fs2A 151 2.24e+01 1rliA 184 2.24e+01 c.23.5.6 97647 1e4fT 419 2.31e+01 1e4fT c.55.1.1,c.55.1.1 33453,33454 1qqsA 174 2.32e+01 1nglA b.60.1.1 27143 1ddlA 188 2.35e+01 1auyA b.121.4.6 23317 1zkkA 167 2.37e+01 2gjgA 248 2.39e+01 1rgzA 363 2.40e+01 e.3.1.1 97457 1ltlA 279 2.41e+01 b.40.4.11 84701 2a50B 168 2.41e+01 1gt1A 159 2.42e+01 b.60.1.1 90515 1ym5A 300 2.43e+01 1gdoA 240 2.46e+01 1gdoA 2gar 212 2.46e+01 2gar c.65.1.1 34161 1havA 217 2.51e+01 1havA b.47.1.4 26423 1hn2A 159 2.52e+01 b.60.1.1 65890 1pda 315 2.54e+01 1pda c.94.1.1,d.50.2.1 35751,38794 1r2zA 274 2.56e+01 a.156.1.2,b.113.1.1,g.39.1.8 96892,96893,96894 1kfd 605 2.57e+01 1xwl c.55.3.5,e.8.1.1 33694,42987 2eueA 279 2.59e+01 1b2pA 119 2.60e+01 1b2pA b.78.1.1 27998 2bltA 361 2.62e+01 1gceA e.3.1.1 42739 1m4uL 139 2.62e+01 g.17.1.2 78626 1vr4A 103 2.63e+01 1xwyA 264 2.64e+01 1t94A 459 2.65e+01 d.240.1.1,e.8.1.7 106701,106702 1ga0A 364 2.66e+01 1gceA e.3.1.1 60410 2atxA 194 2.67e+01 2a1vA 144 2.68e+01 1xd5A 112 2.69e+01 1k1gA 131 2.70e+01 d.51.1.1 68015 1orvA 728 2.71e+01 b.70.3.1,c.69.1.24 87354,87355 2ax3A 502 2.72e+01 1a7cA 379 2.72e+01 1sek e.1.1.1 42660 1uocA 289 2.74e+01 c.55.3.9 99686 2bfxA 284 2.75e+01 1dv8A 128 2.77e+01 1ixxB d.169.1.1 42352 2g8lA 299 2.80e+01 1yphC 131 2.80e+01 2arhA 203 2.83e+01 1vkbA 161 2.87e+01 d.269.1.1 108643 1z4xA 532 2.88e+01 1ze3C 205 2.88e+01 1psuA 140 2.95e+01 d.38.1.5 88285 2bl5A 140 2.95e+01 1mw7A 240 2.98e+01 e.39.1.1 79557 1tq4A 413 3.04e+01 c.37.1.8 107201 1e2tA 284 3.06e+01 1e2tA d.3.1.5 37121 1preB 470 3.10e+01 1preA d.169.1.2,f.8.1.1 42438,43825 1w5fA 353 3.10e+01 1pydA 556 3.11e+01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31735,31773,31774 1cnzA 363 3.12e+01 1cnzA c.77.1.1 35061 1ok8A 394 3.12e+01 b.1.18.4,f.10.1.1 93236,93237 1a4rA 191 3.15e+01 1ctqA c.37.1.8 32063 1y08A 323 3.16e+01 1v3rA 116 3.19e+01 1pvdA 537 3.22e+01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31737,31777,31778 1qa7B 217 3.22e+01 1havA b.47.1.4 26426 2auaA 224 3.26e+01 1c5kA 439 3.28e+01 1crzA b.68.4.1,c.51.2.1 27630,33212 1zavA 180 3.34e+01 1kpeA 126 3.36e+01 1kpf d.13.1.1 37508 1e0tA 470 3.38e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 1lj5A 379 3.39e+01 e.1.1.1 73928 2frvA 264 3.39e+01 2frvA e.19.1.1 43303 2fmr 65 3.40e+01 2fmr d.51.1.1 38808 1i35A 95 3.43e+01 d.15.1.5 66017 1h9dB 134 3.44e+01 2jhbA b.54.1.1 60822 1jalA 363 3.46e+01 c.37.1.8,d.15.10.2 84138,84139 1i9yA 347 3.48e+01 1i9yA d.151.1.2 62101 2bu3A 254 3.48e+01 1q79A 514 3.48e+01 a.160.1.1,d.218.1.3,d.58.16.1 104548,104549,104550 1cruA 454 3.50e+01 1c9uA b.68.2.1 27617 1l1zA 274 3.50e+01 a.156.1.2,b.113.1.1,g.39.1.8 75911,75912,75913 1b7fA 168 3.51e+01 1b7fA d.58.7.1,d.58.7.1 39169,39170 1ylqA 96 3.52e+01 1aohB 147 3.54e+01 1aohA b.2.2.2 22402 1zxfA 155 3.54e+01 1ecl 597 3.55e+01 1ecl e.10.1.1 43238 1gceA 364 3.55e+01 1gceA e.3.1.1 42738 1xgkA 352 3.55e+01 1lxiA 139 3.56e+01 g.17.1.2 84735 2kfnA 605 3.60e+01 1xwl c.55.3.5,e.8.1.1 33682,42975 1vphA 149 3.62e+01 2dnjA 260 3.63e+01 3dni d.151.1.1 41790 2fiuA 99 3.66e+01 1dih 273 3.66e+01 1drw c.2.1.3,d.81.1.3 30056,39971 2fauA 341 3.68e+01 1aohA 147 3.68e+01 1aohA b.2.2.2 22401 2aheA 267 3.70e+01 2f1fA 164 3.72e+01 1drw 273 3.81e+01 1drw c.2.1.3,d.81.1.3 30057,39972 1y4hA 188 3.82e+01 1gdhA 320 3.86e+01 1gdhA c.2.1.4,c.23.12.1 30095,31355 1kshB 152 3.90e+01 b.1.18.8 72915 1wocA 103 3.91e+01 1memA 215 3.93e+01 1cs8A d.3.1.1 37069 2ffeA 311 3.93e+01 1ybdA 239 3.94e+01 1xfoA 357 3.94e+01 2fdiA 211 3.95e+01 1onhA 364 3.98e+01 e.3.1.1 93357 1sflA 238 3.98e+01 1x0lA 333 4.02e+01 1qvcA 145 4.02e+01 3ullA b.40.4.3 25284 1gs5A 258 4.07e+01 c.73.1.2 70395 2bb3A 221 4.08e+01 1pfxL 146 4.13e+01 1cfi g.3.11.1,g.3.11.1,g.32.1.1 44207,44208,44973 1i9zA 347 4.13e+01 1i9yA d.151.1.2 62102 1dkiA 371 4.18e+01 1dkiA d.3.1.1 37090 1t3gA 159 4.23e+01 1xn9A 101 4.23e+01 1x54A 434 4.27e+01 1v1qA 134 4.28e+01 1nni1 174 4.30e+01 1rl6A 177 4.31e+01 1rl6A d.141.1.1,d.141.1.1 41473,41474 1tu6A 215 4.32e+01 d.3.1.1 107318 1ib8A 164 4.33e+01 b.38.2.1,d.52.4.1 71168,71169 1dar 691 4.33e+01 1dar b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1 25707,32142,37547,39300 1wwkA 307 4.34e+01 1b8aA 438 4.39e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1wmmA 145 4.41e+01 1jkxA 212 4.44e+01 c.65.1.1 66813 1nlnA 204 4.45e+01 d.3.1.7 91962 1l4iA 206 4.46e+01 b.1.11.1,b.7.2.1 73564,73565 1gdoB 240 4.51e+01 1gdoA 1arzC 273 4.55e+01 1drw c.2.1.3,d.81.1.3 30061,39976 1e87A 118 4.55e+01 1b6e d.169.1.1 42327 2d0oA 610 4.57e+01 1zbtA 371 4.60e+01 2bwqA 129 4.61e+01 1l7dA 384 4.62e+01 c.2.1.4,c.23.12.2 77774,77775 1vggA 161 4.69e+01 1l2lA 457 4.73e+01 c.72.1.3 77656 1gnkA 112 4.74e+01 2pii d.58.5.1 39073 1xe7A 203 4.78e+01 1k6iA 352 4.79e+01 c.2.1.2 68223 1t5bA 201 4.85e+01 c.23.5.3 106433 1tkeA 224 4.87e+01 1jsrA 327 4.90e+01 c.88.1.1 67237 1i50K 120 4.91e+01 d.74.3.2 61765 1ha1 184 4.93e+01 1ha1 d.58.7.1,d.58.7.1 39147,39148 1jz8A 1023 4.97e+01 b.1.4.1,b.1.4.1,b.18.1.5,b.30.5.1,c.1.8.3 67830,67831,67832,67833,67834 1jslA 327 4.98e+01 c.88.1.1 67233 1nbcA 155 5.01e+01 1nbcA b.2.2.2 22390 1dmhA 311 5.02e+01 1dmhA b.3.6.1 22633 2ag5A 246 5.03e+01 1g8yA 279 5.04e+01 1g8yA c.37.1.11 32302 1i6aA 219 5.06e+01 c.94.1.1 61827 2d28C 149 5.06e+01 2axoA 270 5.11e+01 1lm8V 160 5.13e+01 b.3.3.1 74035 2dbqA 334 5.14e+01 1di2A 69 5.15e+01 1di2A d.50.1.1 38780 1ma3A 253 5.16e+01 c.31.1.5 78883 1fm5A 199 5.17e+01 1fm5A d.169.1.1 42330 1vheA 373 5.30e+01 b.49.3.1,c.56.5.4 100669,100670 1wvqA 167 5.30e+01 1z4vA 532 5.34e+01 2cfxA 144 5.38e+01 1ufhA 180 5.43e+01 d.108.1.1 88485 1j9eA 147 5.44e+01 c.23.5.1 62756 1mgpA 313 5.48e+01 c.119.1.1 79098 1x89A 178 5.48e+01 1x71A 178 5.50e+01 1sfjA 238 5.51e+01 1iu8A 206 5.55e+01 c.56.4.1 71436 1l3kA 196 5.57e+01 d.58.7.1,d.58.7.1 73539,73540 1vmfA 145 5.65e+01 1w1hA 151 5.68e+01 2bjqA 345 5.74e+01 1vyoA 128 5.76e+01 1f5aA 513 5.76e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39337,75835,75836 2pvaA 345 5.78e+01 3pvaA d.153.1.3 41850 1vdnA 162 5.78e+01 1xffA 240 5.78e+01 d.153.1.1 109580 2bk9A 153 5.80e+01 1raxA 115 5.83e+01 1lfdA d.15.1.5 37626 1fbnA 230 5.83e+01 1fbnA c.66.1.3 34181 1autC 250 5.88e+01 5ptp b.47.1.2 26348 1s57A 153 5.88e+01 1dp0A 1023 5.95e+01 b.1.4.1,b.1.4.1,b.18.1.5,b.30.5.1,c.1.8.3 22073,22074,23722,24346,28845 1qhlA 227 6.09e+01 1qhlA c.37.1.12 32382 1j6oA 268 6.16e+01 c.1.9.12 77088 2bynA 227 6.16e+01 1txgA 335 6.16e+01 1kkcA 221 6.16e+01 a.2.11.1,d.44.1.1 68660,68661 1sotA 320 6.17e+01 b.36.1.4,b.47.1.1 105852,105853 1g6aA 271 6.18e+01 1btl e.3.1.1 42704 2gviA 204 6.19e+01 1hdj 77 6.19e+01 1bqz a.2.3.1 15696 1z52A 470 6.21e+01 1awiA 138 6.26e+01 1pne d.110.1.1 40871 2a5lA 200 6.27e+01 1pil 112 6.29e+01 2pii d.58.5.1 39072 1r5tA 142 6.33e+01 c.97.1.1 104812 1olmA 403 6.34e+01 a.5.3.1,b.132.1.1,c.13.1.1 104008,104009,104010 1mhnA 59 6.36e+01 b.34.9.1 84964 2a9sA 171 6.36e+01 1e50B 134 6.38e+01 2jhbA b.54.1.1 59245 1ioaA 240 6.38e+01 1led b.29.1.1 24168 1hl9A 449 6.44e+01 b.71.1.3,c.1.8.11 90650,90651 2bkqA 212 6.45e+01 1c9uA 454 6.46e+01 1c9uA b.68.2.1 27623 1cv8 174 6.47e+01 1cv8 d.3.1.1 37089 1xygD 359 6.47e+01 1g8sA 230 6.55e+01 c.66.1.3 90507 1twdA 256 6.55e+01 c.1.30.1 107397 1u32A 293 6.60e+01 d.159.1.3 107631 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