# List of top-scoring protein chains for t2k-100-30-dssp-ehl2-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 1njkA 156 4.24e-17 d.38.1.1 85818 2cyeA 133 1.09e-16 1z54A 132 1.64e-16 1s5uA 138 1.92e-16 d.38.1.1 98573 2av9A 147 1.45e-13 2aliA 158 1.07e-12 2gf6A 135 7.94e-12 1lo7A 141 9.62e-10 d.38.1.1 74144 1bvqA 141 1.69e-09 1bvqA d.38.1.1 38542 2essA 248 1.41e-08 2h4uA 145 9.69e-08 1yliA 153 1.93e-06 1wluA 136 2.81e-06 1j1yA 136 3.39e-06 d.38.1.5 90776 2gvhA 288 4.33e-05 1vpmA 169 6.85e-05 2fs2A 151 7.81e-05 1psuA 140 8.63e-05 d.38.1.5 88285 1t82A 155 1.04e-04 d.38.1.5 106639 2b3nA 159 1.25e-04 1zkiA 133 1.54e-04 1q4uA 151 4.25e-04 d.38.1.5 95828 1ixlA 131 4.34e-04 d.38.1.5 90717 2b6eA 146 1.75e-03 1o0iA 138 3.46e-03 d.38.1.5 86532 2cwzA 141 6.80e-03 1u1zA 168 7.79e-03 d.38.1.6 107602 1vh5A 148 1.01e-02 d.38.1.5 100642 1c8uA 285 2.62e-02 1c8uA d.38.1.3,d.38.1.3 38547,38548 1iq6A 134 1.16e-01 d.38.1.4 76755 1yocA 147 1.85e-01 3fib 249 3.09e-01 3fib d.171.1.1 42455 2fibA 269 3.10e-01 3fib d.171.1.1 42457 1b8aA 438 3.16e-01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1fib 269 3.17e-01 3fib d.171.1.1 42456 1sh8A 154 4.57e-01 d.38.1.5 105549 1z6bA 154 5.18e-01 1pa1A 310 7.71e-01 c.45.1.2 94404 1a5y 330 8.52e-01 1pty c.45.1.2 32673 1aax 321 8.78e-01 1pty c.45.1.2 32657 2f71A 298 9.01e-01 1pty 321 9.27e-01 1pty c.45.1.2 32656 1ptvA 321 1.37e+00 1pty c.45.1.2 32665 1eeoA 321 1.38e+00 1pty c.45.1.2 32655 2hnp 321 1.41e+00 1pty c.45.1.2 32678 1g7fA 298 1.82e+00 1pty c.45.1.2 60330 1yq2A 1024 1.97e+00 1aohB 147 2.64e+00 1aohA b.2.2.2 22402 2f4lA 297 2.79e+00 1w9aA 147 3.64e+00 1jeoA 180 3.69e+00 c.80.1.3 66611 1xxoA 147 3.81e+00 2aq6A 147 4.03e+00 1t3tA 1303 4.32e+00 a.5.10.1,c.23.16.1,d.284.1.2,d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 106381,106382,106383,106384,106385,106386,106387 1aohA 147 4.46e+00 1aohA b.2.2.2 22401 1df3A 162 4.75e+00 1mup b.60.1.1 27134 2ae5B 528 4.79e+00 1nmtA 392 5.25e+00 1nmtA d.108.1.2,d.108.1.2 40823,40824 1klqA 197 5.46e+00 d.135.1.1 68689 2bdvA 231 5.90e+00 1fm2B 520 6.54e+00 1fm2B 1aqjA 421 6.78e+00 2admA c.66.1.27 34242 1rbp 182 6.95e+00 1aqb b.60.1.1 27085 1ylxA 103 6.96e+00 1tc5A 194 7.16e+00 c.110.1.1 106752 1g38A 393 7.45e+00 2admA c.66.1.27 60235 2admA 421 7.95e+00 2admA c.66.1.27 34238 1txqA 93 7.98e+00 1rcqA 357 8.31e+00 b.49.2.2,c.1.6.1 104882,104883 1vcaA 202 8.88e+00 1vcaA b.1.1.3,b.1.1.4 21649,21685 1w9hA 427 9.35e+00 1gk1B 522 1.00e+01 1mup 166 1.01e+01 1mup b.60.1.1 27133 1m3sA 186 1.06e+01 c.80.1.3 78573 1clqA 903 1.07e+01 1clqA c.55.3.5,e.8.1.1 33717,43006 1ih7A 903 1.08e+01 1clqA c.55.3.5,e.8.1.1 62375,62376 1zndA 174 1.15e+01 1i05A 180 1.18e+01 1mup b.60.1.1 27130 1i06A 180 1.19e+01 1mup b.60.1.1 27131 2bi0A 337 1.21e+01 1n4xH 120 1.21e+01 b.1.1.1 85324 1jv4A 162 1.21e+01 b.60.1.1 67343 2bx2L 517 1.27e+01 1kt6A 183 1.33e+01 b.60.1.1 84466 1hbp 183 1.34e+01 1aqb b.60.1.1 27079 1qy1A 174 1.37e+01 b.60.1.1 96568 1ztuA 341 1.38e+01 1ga3A 113 1.42e+01 1ga3A a.26.1.2 60411 1a14L 104 1.44e+01 8fabA b.1.1.1 20060 2eifA 136 1.49e+01 1bkb b.34.5.2,b.40.4.5 24607,25339 1iicA 422 1.54e+01 1nmtA d.108.1.2,d.108.1.2 62422,62423 1hbq 183 1.57e+01 1aqb b.60.1.1 27078 3kar 346 1.57e+01 1bg2 c.37.1.9 32198 1wleA 501 1.82e+01 1oo0A 147 1.87e+01 d.232.1.1 87182 1bjwA 382 1.91e+01 1bjwA c.67.1.1 34349 1b5pA 385 1.93e+01 c.67.1.1 90403 1lfo 128 1.93e+01 1hmt b.60.1.2 27223 2cwaA 263 2.07e+01 1mnmC 87 2.07e+01 1akhB a.4.1.1 15983 1adqL 213 2.10e+01 8fabA b.1.1.1,b.1.1.2 20272,21272 1dujA 187 2.12e+01 1dujA d.135.1.1 41449 1zwyA 185 2.20e+01 1s5jA 847 2.23e+01 1ymmE 249 2.24e+01 1spiA 358 2.25e+01 1frpA e.7.1.1 42939 1h6fA 193 2.35e+01 b.2.5.4 70901 1ig8A 486 2.46e+01 2yhx c.55.1.3,c.55.1.3 64746,64747 1mqoA 227 2.53e+01 d.157.1.1 103846 1rl4A 188 2.60e+01 d.167.1.1 97636 1yqgA 263 2.61e+01 1or0B 528 2.65e+01 1b66A 140 2.65e+01 1b66A d.96.1.2 40657 2as0A 396 2.66e+01 2pcdM 238 2.67e+01 3pchM b.3.6.1 22760 1dzkA 157 2.67e+01 1obpA b.60.1.1 27096 1l0wA 580 2.69e+01 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1mkaA 171 2.75e+01 1mkaA d.38.1.2 38543 1tf4A 605 2.75e+01 1tf4A a.102.1.2,b.2.2.2 18827,22393 1go4A 205 2.81e+01 d.135.1.1 70292 1a3yA 149 2.95e+01 1obpA b.60.1.1 27110 1xc3A 302 2.97e+01 1eal 127 3.02e+01 1hmt b.60.1.2 27227 1zrn 232 3.05e+01 1qq5A c.108.1.1 43323 1gtqA 140 3.07e+01 1b66A d.96.1.2 40661 1jud 232 3.07e+01 1qq5A c.108.1.1 43325 1cwvA 492 3.16e+01 1cwvA b.1.14.1,b.1.14.1,b.1.14.1,b.1.14.1,d.169.1.3 22373,22374,22375,22376,42442 2fsjA 346 3.20e+01 1i1dA 161 3.21e+01 1i21A d.108.1.1 61526 1zowA 313 3.23e+01 1b7yA 350 3.30e+01 1pysA d.104.1.1 40776 2db9A 149 3.33e+01 1aqb 183 3.47e+01 1aqb b.60.1.1 27084 1gotB 340 3.48e+01 1tbgA b.69.4.1 27648 1ouoA 210 3.51e+01 d.4.1.6 93554 4cms 323 3.52e+01 1smrA b.50.1.2 26866 1lkkA 105 3.55e+01 1lckA d.93.1.1 40412 1f9vA 347 3.60e+01 1bg2 c.37.1.9 59745 3pcgM 238 3.60e+01 3pchM b.3.6.1 22742 3pchM 238 3.60e+01 3pchM b.3.6.1 22748 1f3mA 80 3.63e+01 1f3mA j.66.1.1 46358 1kv9A 668 3.68e+01 a.3.1.6,b.70.1.1 73056,73057 1tyjA 170 3.72e+01 1pn2A 280 3.74e+01 d.38.1.4,d.38.1.4 94930,94931 1widA 130 3.74e+01 1fqtA 112 3.75e+01 1fqtA b.33.1.1 24441 2f6eA 127 3.80e+01 4pep 326 3.83e+01 1smrA b.50.1.2 26843 1zxkA 98 3.85e+01 1q15A 503 3.88e+01 c.26.2.1,d.153.1.1 95538,95539 1n6eA 1071 3.89e+01 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 80149,80150,80151,80152 1iseA 185 3.99e+01 d.67.3.1 90691 1ne8A 117 4.00e+01 b.34.6.2 80424 1i1b 153 4.01e+01 2i1b b.42.1.2 25537 1ax0 239 4.02e+01 1led b.29.1.1 24042 2i1b 153 4.05e+01 2i1b b.42.1.2 25538 3cms 323 4.20e+01 1smrA b.50.1.2 26865 1wxcB 134 4.30e+01 1vprA 374 4.39e+01 1ek8A 185 4.39e+01 1ek8A d.67.3.1 59444 1c0pA 363 4.45e+01 1an9A c.4.1.2,d.16.1.3 30647,37934 1aihA 170 4.46e+01 1aihA d.163.1.1 42149 1mzeA 351 4.57e+01 b.82.2.6 79694 1oglA 283 4.64e+01 a.204.1.1 92922 2d1eA 248 4.66e+01 1eqkA 102 4.81e+01 1eqkA d.17.1.2 37998 2fxqA 264 4.84e+01 1l7jA 347 4.88e+01 b.30.5.4 73660 1bihA 395 4.91e+01 1bihA b.1.1.4,b.1.1.4,b.1.1.4,b.1.1.4 21752,21753,21754,21755 1oaqH 121 4.91e+01 b.1.1.1 92707 1smxA 96 4.98e+01 b.40.4.5 105772 2bm3A 166 5.00e+01 1ab0 131 5.00e+01 1hmt b.60.1.2 27190 1tbgA 340 5.00e+01 1tbgA b.69.4.1 27649 1ncwH 222 5.06e+01 b.1.1.1,b.1.1.2 85555,85556 1pkp 150 5.12e+01 1pkp d.14.1.1,d.50.1.2 37551,38787 1lid 131 5.15e+01 1hmt b.60.1.2 27184 1c30B 382 5.20e+01 c.8.3.1,c.23.16.1 30736,31413 1ytw 306 5.24e+01 1ytw c.45.1.2 32689 1ytn 306 5.24e+01 1ytw c.45.1.2 32688 2fhfA 1083 5.26e+01 1yts 278 5.28e+01 1ytw c.45.1.2 32690 1adl 131 5.32e+01 1hmt b.60.1.2 27186 1i12A 160 5.33e+01 1i21A d.108.1.1 61515 1lcjA 109 5.34e+01 1qadA d.93.1.1 40414 1tbuA 118 5.34e+01 1vj0A 380 5.35e+01 b.35.1.2,c.2.1.1 100786,100787 1h2kA 349 5.37e+01 b.82.2.6 76572 2pil 159 5.44e+01 2pil d.24.1.1 38376 2bcjB 340 5.47e+01 1ijhA 504 5.47e+01 c.3.1.2,d.16.1.1 66161,66162 1i21A 159 5.48e+01 1i21A d.108.1.1 61549 1jl2A 156 5.49e+01 c.55.3.1 66822 1dd5A 185 5.54e+01 1dd5A d.67.3.1 39564 1bwyA 132 5.57e+01 1hmt b.60.1.2 27172 2f96A 224 5.57e+01 1iq3A 110 5.59e+01 1iq3A a.39.1.6 62640 1v7rA 186 5.59e+01 c.51.4.1 100482 1lyvA 306 5.72e+01 c.45.1.2 74348 1wguA 136 5.76e+01 1epwA 1290 5.80e+01 b.29.1.6,b.42.4.2,d.92.1.7,h.4.2.1 24269,25614,40305,45785 2cb4A 291 5.86e+01 1oe9A 795 5.88e+01 b.34.3.1,c.37.1.9 92792,92793 1abbA 828 5.90e+01 1a8i c.87.1.4 35536 2b69A 343 5.94e+01 1uylA 236 6.03e+01 d.122.1.1 108147 1xsm 390 6.10e+01 1xsm a.25.1.2 16804 1mmuA 347 6.18e+01 b.30.5.4 79303 1l7jB 347 6.19e+01 b.30.5.4 73661 1nszA 347 6.22e+01 b.30.5.4 80724 1xqaA 113 6.23e+01 1h0oA 390 6.33e+01 a.25.1.2 70845 1hms 132 6.34e+01 1hmt b.60.1.2 27168 1hmr 132 6.41e+01 1hmt b.60.1.2 27170 1gzcA 239 6.42e+01 b.29.1.1 70803 1pcfA 66 6.50e+01 1pcfA d.18.1.1 38142 1r2mA 71 6.50e+01 b.138.1.1 96871 2b97A 71 6.50e+01 1gpb 842 6.59e+01 1a8i c.87.1.4 35478 1c5cH 215 6.61e+01 1igtB b.1.1.1,b.1.1.2 20475,21439 1mxtA 504 6.69e+01 c.3.1.2,d.16.1.1 79671,79672 1n1pA 504 6.69e+01 c.3.1.2,d.16.1.1 91546,91547 1n4wA 504 6.69e+01 c.3.1.2,d.16.1.1 91676,91677 1yp1A 202 6.73e+01 2aw2A 120 6.74e+01 1v2dA 381 6.75e+01 c.67.1.1 108281 1b4vA 504 6.77e+01 1b8sA c.3.1.2,d.16.1.1 30334,37865 1b8sA 504 6.80e+01 1b8sA c.3.1.2,d.16.1.1 30335,37866 1lf7A 182 6.86e+01 b.60.1.1 73878 1iw2A 182 6.88e+01 b.60.1.1 71468 1nstA 325 6.96e+01 1nstA c.37.1.5 31951 1hn0A 1021 7.05e+01 a.102.3.2,b.18.1.17,b.24.1.1,b.30.5.2 83616,83617,83618,83619 1g7sA 594 7.09e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 1pysA 350 7.13e+01 1pysA d.104.1.1 40775 1vzyA 291 7.14e+01 1wchA 315 7.18e+01 2gujA 155 7.20e+01 2g1lA 104 7.25e+01 1u2hA 99 7.27e+01 1jt8A 102 7.27e+01 b.40.4.5 63279 1uisA 231 7.28e+01 d.22.1.1 99431 1w68A 390 7.28e+01 a.25.1.2 109216 1t5rA 284 7.33e+01 f.6.1.1 106465 1zy9A 564 7.38e+01 1okjA 251 7.41e+01 c.55.1.9,c.55.1.9 103998,103999 1a0p 290 7.42e+01 1a0p a.60.9.1,d.163.1.1 18105,42165 2booA 247 7.48e+01 1anjA 446 7.50e+01 1b8jA c.76.1.1 35008 1qftA 175 7.57e+01 1qftA b.60.1.1 27151 1a6wH 120 7.59e+01 1mfa b.1.1.1 20253 1quqA 129 7.60e+01 1quqA b.40.4.3 25303 2b59A 187 7.62e+01 1ltm 320 7.65e+01 1ltm d.2.1.6 36992 31bi 153 7.66e+01 2i1b b.42.1.2 25541 1o9yA 84 7.66e+01 b.139.1.1 92692 1qusA 322 7.66e+01 1ltm d.2.1.6 36991 1forL 210 7.66e+01 8fabA b.1.1.1,b.1.1.2 19988,21044 1zn6A 227 7.68e+01 1f5mA 180 7.74e+01 1f5mB d.110.2.1 40895 1f5mB 180 7.74e+01 1f5mB d.110.2.1 40896 1wubA 178 7.75e+01 1yptA 305 7.76e+01 1ytw c.45.1.2 32686 487dH 224 7.82e+01 1ad2 i.1.1.2 45835 2b49A 287 7.86e+01 1ad2 228 7.87e+01 1ad2 e.24.1.1 43353 1s1dA 331 7.89e+01 b.67.3.1 98344 2bklA 695 7.98e+01 1fx3B 169 8.07e+01 1fx3B d.33.1.1 38525 1g7nA 131 8.09e+01 b.60.1.2 83274 1dzrA 183 8.13e+01 1dzrA b.82.1.1 28076 1dszA 86 8.13e+01 2nllB g.39.1.2 45129 1hmt 132 8.15e+01 1hmt b.60.1.2 27169 1ay2 159 8.17e+01 2pil d.24.1.1 38377 2auhB 59 8.18e+01 1dthA 203 8.24e+01 1atlA d.92.1.9 40324 1yer 228 8.24e+01 1yer d.122.1.1 41101 1m93C 41 8.27e+01 1aniA 446 8.37e+01 1b8jA c.76.1.1 35018 1u04A 771 8.38e+01 b.34.14.1,c.55.3.10 107539,107540 1em9A 154 8.42e+01 1d1dA a.73.1.1 18333 2bbkH 355 8.43e+01 2bbkH b.69.2.1 27634 1b5sA 242 8.44e+01 1eaf c.43.1.1 32626 1t23A 93 8.51e+01 1b0wA 108 8.65e+01 8fabA b.1.1.1 20532 1z5bA 469 8.66e+01 1c0aA 585 8.67e+01 1c0aA b.40.4.1,d.74.4.1,d.104.1.1 25246,39731,40767 1ljoA 77 8.77e+01 b.38.1.1 73941 1p6pA 125 8.78e+01 b.60.1.2 87839 1wxxA 382 8.80e+01 1qjoA 80 8.90e+01 1iyu b.84.1.1 28229 1ksiB 642 8.91e+01 1ksiB b.30.2.1,d.17.2.1,d.17.2.1 24409,38045,38046 1owfB 94 8.93e+01 a.55.1.1 87488