# 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 1c1dA 355 5.90e-01 1bw9A c.2.1.7 30270 c.58.1.1 33918 1qkmA 255 5.98e-01 3erdA a.123.1.1 19309 1qgwC 177 6.83e-01 1qgwC a.1.1.3 15673 1aqb 183 8.41e-01 1aqb b.60.1.1 27084 1hbq 183 8.48e-01 1aqb b.60.1.1 27078 1hbp 183 8.85e-01 1aqb b.60.1.1 27079 1bw9A 356 9.42e-01 1bw9A c.2.1.7 30274 c.58.1.1 33922 1ezm 301 1.05e+00 1hyt d.92.1.2 58980 1qo0D 196 1.11e+00 1qo0D c.23.1.3 31125 1a8y 367 1.18e+00 1a8y c.47.1.3 32781 c.47.1.3 32782 c.47.1.3 32783 1d0qA 103 1.73e+00 1d0qA g.41.3.2 45208 1go4A 205 2.13e+00 1ihfA 99 2.49e+00 1huuA a.55.1.1 17893 1f2tB 148 2.90e+00 1f2tB 1hjp 203 3.25e+00 1hjp a.5.1.1 16274 a.60.2.1 17947 b.40.4.2 25266 1crxA 322 3.38e+00 4crxA a.60.9.1 18097 d.163.1.1 42157 1pyaB 228 3.38e+00 1pyaB 1cnt2 187 3.80e+00 1cnt3 2dri 271 4.00e+00 2dri c.93.1.1 35637 1g24A 211 4.47e+00 1g24A d.166.1.1 42270 1jf0A 195 4.73e+00 1ej3A a.39.1.5 62926 1cec 343 4.78e+00 1ceo c.1.8.3 28809 1yuiA 54 5.04e+00 1yuiA g.37.1.1 45073 1bouA 139 5.45e+00 1bouA a.88.1.1 18521 1f44A 324 5.72e+00 a.60.9.1 64982 d.163.1.1 64983 1b4uA 139 5.88e+00 1bouA a.88.1.1 18523 1rbp 182 6.04e+00 1aqb b.60.1.1 27085 1pydA 556 6.21e+00 1zpdA c.31.1.3 31735 c.36.1.1 31773 c.36.1.1 31774 1lox 662 6.24e+00 1lox a.119.1.2 19238 b.12.1.1 23638 4crxA 322 6.45e+00 4crxA a.60.9.1 18095 d.163.1.1 42155 1pvdA 537 6.47e+00 1zpdA c.31.1.3 31737 c.36.1.1 31777 c.36.1.1 31778 3ertA 261 6.48e+00 3erdA a.123.1.1 19292 1ceo 343 6.53e+00 1ceo c.1.8.3 28808 2kinA 238 6.78e+00 1bg2 c.37.1.9 32190 1ej3A 191 6.82e+00 1ej3A a.39.1.5 17259 1kbuA 349 6.82e+00 1l2iA 261 6.87e+00 1ps1A 337 7.00e+00 1ps1A a.128.1.4 19450 1qlaC 256 7.04e+00 1qlaC f.2.1.9 43722 1tfe 145 7.13e+00 1tfe d.43.1.1 38680 1hu4A 288 7.41e+00 1hu4A c.2.1.2 61268 1dt6A 473 7.70e+00 1dt6A a.104.1.1 18977 3aig 202 7.79e+00 1atlA d.92.1.9 40321 3crxA 343 7.91e+00 4crxA a.60.9.1 18101 d.163.1.1 42161 1avqA 228 7.95e+00 1avqA c.52.1.13 33326 1qlpA 394 8.11e+00 1ovaA e.1.1.1 42628 3erdA 261 8.38e+00 3erdA a.123.1.1 19293 1ip9A 85 8.39e+00 1ip9A d.15.2.2 62638 1aw5 326 8.47e+00 1b4kA c.1.10.3 29181 1qpbA 563 8.56e+00 1zpdA c.31.1.3 31739 c.36.1.1 31781 c.36.1.1 31782 1k2yX 463 8.58e+00 c.84.1.1 68063 c.84.1.1 68064 c.84.1.1 68065 c.84.1.1 68066 1qu6A 179 8.76e+00 1qu6A d.50.1.1 38784 d.50.1.1 38785 1ekeA 230 9.28e+00 1ekeA c.55.3.1 33572 1i3dA 146 9.36e+00 a.1.1.2 61587 1fxjA 331 9.40e+00 1fwyA b.81.1.4 28062 c.68.1.5 34520 1cuk 203 1.00e+01 1hjp a.5.1.1 16273 a.60.2.1 17946 b.40.4.2 25265 1b77A 228 1.05e+01 1b77A d.131.1.2 41362 d.131.1.2 41363 1fwyA 331 1.13e+01 1fwyA b.81.1.4 28064 c.68.1.5 34522 1k8eA 345 1.18e+01 1a0p 290 1.20e+01 1a0p a.60.9.1 18105 d.163.1.1 42165 1auwA 468 1.23e+01 1auwA a.127.1.1 19416 1f61A 429 1.23e+01 1dquA c.1.12.6 29319 1ax0 239 1.23e+01 1led b.29.1.1 24042 1de4C 640 1.26e+01 1cx8B a.48.2.1 17779 c.8.4.1 30760 c.56.5.5 33848 2bdpA 580 1.33e+01 1xwl c.55.3.5 33709 e.8.1.1 43002 1g8kA 825 1.33e+01 1g8jA b.52.2.2 26920 c.81.1.1 35328 1bcsA 263 1.38e+01 1ivyA c.69.1.5 34647 1kskA 234 1.41e+01 1gzcA 239 1.42e+01 1hv9A 456 1.45e+01 1fwyA b.81.1.4 28060 c.68.1.5 34518 1pfkA 320 1.45e+01 3pfk c.89.1.1 35575 1hy0A 466 1.47e+01 1auwA a.127.1.1 61392 1k7wA 468 1.50e+01 1gzgA 337 1.51e+01 1hn2A 159 1.52e+01 b.60.1.1 65890 1gaxA 862 1.52e+01 1gaxA a.27.1.1 16928 b.51.1.1 26893 c.26.1.1 31595 1f8mA 429 1.54e+01 1dquA c.1.12.6 29315 1bg2 325 1.60e+01 1bg2 c.37.1.9 32189 1ltm 320 1.61e+01 1ltm d.2.1.6 36992 3bifA 468 1.65e+01 1bif c.37.1.7 31962 c.60.1.4 34008 1obpA 159 1.67e+01 1obpA b.60.1.1 27092 1qusA 322 1.67e+01 1ltm d.2.1.6 36991 1eljA 381 1.69e+01 4mbp c.94.1.1 35791 1bif 469 1.70e+01 1bif c.37.1.7 31961 c.60.1.4 34003 1hueA 90 1.70e+01 1huuA a.55.1.1 17900 1xwl 580 1.71e+01 1xwl c.55.3.5 33708 e.8.1.1 43001 1vid 221 1.71e+01 1vid c.66.1.1 34178 1g8jA 825 1.75e+01 1g8jA b.52.2.2 26924 c.81.1.1 35332 1b4kA 337 1.79e+01 1b4kA c.1.10.3 29184 1io2A 213 1.80e+01 1ekeA c.55.3.1 62612 1qfeA 252 1.80e+01 1qfeA c.1.10.1 29167 1hv8A 367 1.81e+01 1hv8A c.37.1.13 32405 c.37.1.13 32406 1imvA 398 1.82e+01 e.1.1.1 62591 1nom 248 1.84e+01 1bpyA e.9.1.1 43220 3bdpA 580 1.85e+01 1xwl c.55.3.5 33711 e.8.1.1 43004 1jp3A 253 1.90e+01 1f75A c.101.1.1 63221 1whtA 256 1.92e+01 1ivyA c.69.1.5 34646 2pfkA 320 1.94e+01 3pfk c.89.1.1 35577 1efuB 282 2.06e+01 1efuB a.5.2.2 58975 d.43.1.1 58976 d.43.1.1 38677 1aua 296 2.08e+01 1aua a.5.3.1 16290 c.13.1.1 30882 1k3fA 253 2.08e+01 c.56.2.1 68105 9apiA 347 2.09e+01 1ovaA e.1.1.1 42630 1floA 422 2.18e+01 1floA a.60.9.1 18106 d.163.1.1 42166 1qr6A 584 2.21e+01 1qr6A c.2.1.7 30293 c.58.1.3 33941 1nf1A 333 2.21e+01 1nf1A a.116.1.2 19110 1eucB 396 2.22e+01 2scuB c.23.4.1 31149 d.142.1.4 41570 1eudB 396 2.25e+01 2scuB c.23.4.1 31150 d.142.1.4 41571 1whsA 255 2.26e+01 1ivyA c.69.1.5 34649 1kq4A 232 2.30e+01 d.207.1.1 68791 1b71A 191 2.40e+01 1ryt a.25.1.1 16647 g.41.5.1 45246 9gafA 295 2.42e+01 1apyA d.153.1.5 42008 1dzfA 215 2.42e+01 1dzfA c.52.3.1 33344 d.78.1.1 39753 1ncs 47 2.44e+01 1ncs g.37.1.1 45040 1hm6A 346 2.49e+01 1avc a.65.1.1 18147 1rpl 251 2.50e+01 1bpyA e.9.1.1 43212 1bed 181 2.51e+01 1fvkA a.44.1.1 17514 c.47.1.4 32808 1bcfA 158 2.61e+01 1bcfA a.25.1.1 16648 1dvbA 191 2.68e+01 1ryt a.25.1.1 16645 g.41.5.1 45244 1exnB 290 2.72e+01 1exnA a.60.7.1 18089 c.53.1.2 33359 1ryt 190 2.75e+01 1ryt a.25.1.1 16646 g.41.5.1 45245 1jygA 69 2.76e+01 a.60.11.1 67457 1pch 88 2.76e+01 1ptf d.94.1.1 40564 1nmtA 392 2.89e+01 1nmtA d.108.1.2 40823 d.108.1.2 40824 1hg5A 289 2.95e+01 1hg5A a.118.10.1 19221 1lrzA 426 2.97e+01 1eu8A 409 3.13e+01 1eu8A c.94.1.1 59502 1dnlA 199 3.15e+01 1ci0A b.45.1.1 25753 1d8dA 377 3.15e+01 1ft1A a.118.6.1 19185 1hg2A 289 3.18e+01 1hg5A a.118.10.1 61024 1jcrA 377 3.22e+01 a.118.6.1 66506 1jsbA 73 3.23e+01 d.15.3.2 67223 1dofA 403 3.27e+01 1c3cA a.127.1.1 19429 1huuA 90 3.27e+01 1huuA a.55.1.1 17897 1ylvA 342 3.29e+01 1b4kA c.1.10.3 29180 1gkuB 1054 3.31e+01 c.37.1.16 65257 c.37.1.16 65258 e.10.1.1 65259 1g0uE 234 3.33e+01 d.153.1.4 41950 1qbqA 333 3.35e+01 1ft1A a.118.6.1 19187 1trkA 680 3.44e+01 1trkA c.36.1.2 31803 c.36.1.2 31804 c.48.1.1 33090 1dcnD 436 3.45e+01 1auwA a.127.1.1 19423 1b3jA 274 3.45e+01 1agdA b.1.1.2 20855 d.19.1.1 38319 1hf8A 289 3.48e+01 1hg5A a.118.10.1 19219 1e0eA 55 3.48e+01 1wjcA a.4.10.1 59147 1p35A 299 3.51e+01 1p35A b.28.1.1 23925 1kn6A 90 3.53e+01 1a48 306 3.58e+01 1a48 d.143.1.1 41590 1qbjA 81 3.61e+01 1qbjA a.4.5.19 16155 1d6jA 211 3.64e+01 1d6jA c.37.1.4 31940 1gky 187 3.67e+01 1gky c.37.1.1 31839 1f7wA 144 3.71e+01 1f46A d.129.4.1 59679 1qgpA 77 3.72e+01 1qbjA a.4.5.19 16158 1lucB 324 3.73e+01 1lucA c.1.16.1 29548 1ji0A 240 3.73e+01 1bpb 248 3.81e+01 1bpyA e.9.1.1 43215 1bvsB 203 3.85e+01 1hjp a.5.1.1 16281 a.60.2.1 17956 b.40.4.2 25275 2abk 211 3.86e+01 2abk a.96.1.1 18743 1ebfA 358 3.90e+01 1ebuA c.2.1.3 30033 d.81.1.2 39948 1kqqA 139 3.90e+01 1dl5A 317 3.92e+01 1dl5A c.66.1.7 64720 d.197.1.1 64721 3proC 166 3.93e+01 3proC d.52.1.1 38812 d.52.1.1 38813 1h7nA 342 3.96e+01 1b4kA c.1.10.3 60726 1anv 356 3.97e+01 1anv a.54.1.1 17890 g.51.1.1 45365 g.51.1.1 45371 3proD 166 3.98e+01 3proC d.52.1.1 38814 d.52.1.1 38815 1m4zA 238 3.98e+01