# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7 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 1s72T 120 2.35e-20 1jj2S 119 2.95e-20 1ffkQ b.34.5.1 63104 1ffkQ 119 6.73e-18 1ffkQ b.34.5.1 24605 1omiA 248 3.44e-02 a.4.5.4 87079 b.82.3.3 87080 1bbzE 58 1.02e-01 1bbzA b.34.2.1 24479 1bbzA 58 1.08e-01 1bbzA b.34.2.1 24477 1hjdA 101 1.88e-01 b.34.2.1 65846 1aboA 62 2.17e-01 1bbzA b.34.2.1 24474 1t6aA 126 2.52e-01 1s72Q 96 2.88e-01 1jj2P 95 4.15e-01 1ffkN b.34.5.1 63101 1i0cA 60 4.19e-01 1aojA b.34.2.1 61485 1jj2A 239 4.41e-01 1rl2A b.34.5.3 63084 b.40.4.5 63085 1bxvA 91 5.60e-01 1aac b.6.1.1 22875 1tuc 63 6.57e-01 1tuc b.34.2.1 24492 1ljoA 77 6.91e-01 b.38.1.1 73941 1ugpB 226 7.04e-01 2cuaA 135 7.40e-01 2cuaA b.6.1.2 23039 2phlA 397 7.88e-01 1dgwA b.82.1.2 28082 b.82.1.2 28083 1jegA 83 8.30e-01 b.34.2.1 66610 1uw6A 211 8.50e-01 1lplA 95 9.49e-01 b.34.10.1 74173 1d3bA 75 9.66e-01 1d3bA b.38.1.1 24798 1gmeA 151 9.98e-01 b.15.1.1 65305 1gcqA 61 1.02e+00 1ckaA b.34.2.1 60434 1eikA 77 1.04e+00 1eikA d.78.1.1 39751 1jotA 133 1.11e+00 1jotA 1i8fA 81 1.13e+00 1i8fA b.38.1.1 61959 1mtnC 97 1.13e+00 5ptp 1cskA 71 1.19e+00 1ckaA b.34.2.1 24513 1ab9C 97 1.20e+00 5ptp 1kvdB 77 1.28e+00 1kveB 1d2pA 373 1.29e+00 1d2oA b.3.5.1 22629 b.3.5.1 22630 b.3.5.1 22631 b.3.5.1 22632 1tovA 98 1.32e+00 1ireB 228 1.39e+00 b.34.4.4 76770 1luzA 88 1.42e+00 b.40.4.5 74271 1ckaA 57 1.51e+00 1ckaA b.34.2.1 24459 1jacA 133 1.52e+00 1jotA 1txlA 215 1.70e+00 1nhp 447 1.72e+00 1nhp c.3.1.5 30549 c.3.1.5 30550 d.87.1.1 40196 1qlyA 58 1.76e+00 1bbzA b.34.2.1 24530 1o97D 320 1.77e+00 c.26.2.3 81233 c.31.1.2 81234 1kveB 77 1.85e+00 1kveB 1sfdA 105 1.86e+00 1qniA 581 1.89e+00 1qniA b.6.1.4 23042 b.69.3.1 27642 1oejA 193 1.96e+00 1ou8A 111 1.97e+00 1lfo 128 2.07e+00 1hmt b.60.1.2 27223 1shfA 59 2.10e+00 1bbzA b.34.2.1 24462 1trb 320 2.18e+00 1trb c.3.1.5 30529 c.3.1.5 30530 1pwt 61 2.26e+00 1tud b.34.2.1 24490 1noa 113 2.31e+00 2mcm b.1.7.1 22208 1jpyB 137 2.32e+00 g.17.1.6 67066 1hdkA 141 2.41e+00 b.29.1.3 65807 1gg6C 97 2.42e+00 5ptp 1dwkA 156 2.46e+00 1dw9A a.35.1.4 17075 d.72.1.1 39606 1dw9A 156 2.56e+00 1dw9A a.35.1.4 17065 d.72.1.1 39596 1aac 105 2.58e+00 1aac b.6.1.1 22838 1jyoA 130 2.64e+00 d.198.1.1 67483 1v76A 96 2.67e+00 1i9bA 217 3.00e+00 1i9bA b.96.1.1 62084 1nhs 447 3.09e+00 1nhp c.3.1.5 30555 c.3.1.5 30556 d.87.1.1 40199 1ebaA 215 3.10e+00 1eerB b.1.2.1 22015 b.1.2.1 22016 1lckA 175 3.21e+00 1lckA b.34.2.1 24552 d.93.1.1 40421 1ku8A 133 3.32e+00 1mgqA 83 3.37e+00 b.38.1.1 79099 1ycsB 239 3.42e+00 1ycsB b.34.2.1 24553 d.211.1.1 19155 1m5q1 130 3.47e+00 1smxA 96 3.50e+00 1uj0A 62 3.66e+00 1awo 62 3.72e+00 1bbzA b.34.2.1 24482 1shg 62 3.79e+00 1ckaA b.34.2.1 24493 1d7qA 143 3.81e+00 1d7qA b.40.4.5 25331 1ejfA 125 3.82e+00 1ejfA b.15.1.2 23683 1kkeA 210 3.96e+00 b.21.1.2 68669 b.83.1.2 68670 1oebA 62 3.97e+00 b.34.2.1 86909 1bxaA 105 3.98e+00 1aac b.6.1.1 22839 2mcm 112 4.02e+00 2mcm b.1.7.1 22207 1irp 153 4.05e+00 1irp b.42.1.2 25559 1hw5A 210 4.05e+00 2cgpA a.4.5.4 16098 b.82.3.2 28137 1gd7A 109 4.22e+00 b.40.4.4 60441 1aaj 105 4.30e+00 1aac b.6.1.1 22841 1jh2A 99 4.33e+00 1gcqC 70 4.42e+00 1gcpA b.34.2.1 60436 1cuk 203 4.48e+00 1hjp a.5.1.1 16273 a.60.2.1 17946 b.40.4.2 25265 1a62 130 4.56e+00 1a62 a.140.3.1 64708 b.40.4.5 64709 1nwwA 149 4.73e+00 d.17.4.8 86306 1a49A 530 4.80e+00 1a49A b.58.1.1 27026 c.1.12.1 29255 c.49.1.1 33109 1gjuA 637 4.82e+00 b.71.1.1 60580 c.1.8.1 60581 1wkt 88 4.95e+00 1wkt b.11.1.2 23630 1joa 447 5.05e+00 1nhp c.3.1.5 30563 c.3.1.5 30564 d.87.1.1 40203 1rqpA 299 5.08e+00 1j48A 110 5.21e+00 b.1.7.1 84112 1jpyA 137 5.32e+00 g.17.1.6 67065 1umuA 116 5.39e+00 1umuA b.87.1.1 28382 1jacC 133 5.46e+00 1jotA 1ox8A 107 5.48e+00 1aipE 405 5.48e+00 1efcA b.43.3.1 25699 b.44.1.1 25739 c.37.1.8 32134 1lcl 142 5.48e+00 1lcl b.29.1.3 24216 1oqkA 97 5.52e+00 1ehkB 168 5.63e+00 2cuaA b.6.1.2 23041 f.17.2.1 43625 1m26A 133 5.67e+00 1ootA 60 5.81e+00 1bmfA 510 5.97e+00 1skyB a.69.1.1 18281 b.49.1.1 26446 c.37.1.11 32326 1c3mA 147 6.04e+00 1jotA b.77.3.1 27983 1vif 62 6.13e+00 1vie b.34.4.1 24593 1g86A 142 6.21e+00 b.29.1.3 70161 1nycA 111 6.43e+00 1ef1A 294 6.48e+00 1ef1A a.11.2.1 16368 b.55.1.5 27003 d.15.1.4 37611 1pm4A 119 6.61e+00 1aizA 129 6.65e+00 1nwpA b.6.1.1 22903 1my7A 114 6.70e+00 b.1.18.1 79675 1ffkN 95 6.73e+00 1ffkN b.34.5.1 24606 1f3uB 171 6.78e+00 1f3uB b.65.1.1 27525 1jdqA 98 6.81e+00 d.68.3.3 66559 1b12A 248 6.81e+00 1b12A b.87.1.2 28388 1ihfA 99 7.09e+00 1huuA a.55.1.1 17893 1ospL 214 7.34e+00 32c2A b.1.1.1 20116 b.1.1.2 21146 1x6oA 174 7.51e+00 1id2A 106 7.54e+00 1aac b.6.1.1 62288 1ekrA 161 7.55e+00 1ekrA d.58.21.1 39380 1g291 372 7.58e+00 1g291 1d6mA 653 7.58e+00 1d6mA e.10.1.1 43248 1csp 67 7.78e+00 1mjc b.40.4.5 25321 1jztA 246 7.81e+00 c.104.1.1 63319 1i1jA 108 8.01e+00 1i1jA b.34.2.1 61531 1ul7A 102 8.03e+00 1mkeA 152 8.13e+00 b.55.1.4 79231 1utiA 58 8.15e+00 1mhnA 59 8.26e+00 b.34.9.1 84964 1stmA 157 8.35e+00 1stmA b.121.7.1 23281 1iz6A 138 8.45e+00 b.34.5.2 76976 b.40.4.5 76977 1nnxA 109 8.77e+00 1dnlA 199 8.82e+00 1ci0A b.45.1.1 25753 1e2wA 251 8.84e+00 1hcz b.2.6.1 22466 b.84.2.2 28252 1fneA 192 8.94e+00 1iakA b.1.1.2 59896 d.19.1.1 59897 1h9mA 145 9.02e+00 1h9jA b.40.6.2 60833 b.40.6.2 60834 1bdyA 123 9.02e+00 1bdyA b.7.1.1 23190 1qq1A 559 9.03e+00 1tyv b.80.1.6 28041 1dj7B 75 9.05e+00 1dj7B b.34.4.3 24598 1nxzA 246 9.10e+00 b.122.1.2 86391 c.116.1.5 86392 1c3kA 147 9.26e+00 1jotA b.77.3.1 27984 1m4zA 238 9.31e+00 b.34.12.1 78630 1ft9A 222 9.35e+00 1ft9A a.4.5.4 16107 b.82.3.1 28131 1hr0W 71 9.51e+00 1ah9 b.40.4.5 25329 2pcfB 250 9.51e+00 1hcz i.4.1.1 45911 1ipiA 123 9.55e+00 c.52.1.18 66255 1d2oA 187 9.62e+00 1d2oA b.3.5.1 22625 b.3.5.1 22626 1g79A 218 9.64e+00 1ci0A b.45.1.1 25752 1umuB 116 9.82e+00 1umuA b.87.1.1 28383 2dtr 226 9.92e+00 1bi0 a.4.5.24 16193 a.76.1.1 18399 b.34.1.2 24450 1ri9A 102 9.98e+00 1g2bA 62 1.00e+01 1tud b.34.2.1 24488 1hjp 203 1.02e+01 1hjp a.5.1.1 16274 a.60.2.1 17947 b.40.4.2 25266 1ugxA 133 1.04e+01 1a3qA 285 1.05e+01 1a3qA b.1.18.1 21932 b.2.5.3 22447 1fngA 192 1.09e+01 1iakA b.1.1.2 59904 d.19.1.1 59905 1vie 62 1.09e+01 1vie b.34.4.1 24592 1iq6A 134 1.10e+01 d.38.1.4 76755 1ktbA 405 1.11e+01 b.71.1.1 72960 c.1.8.1 72961 2azaA 129 1.13e+01 1nwpA b.6.1.1 22901 1k3bA 119 1.14e+01 b.61.5.1 72016 1owfA 99 1.14e+01 a.55.1.1 87487 1qa1A 554 1.16e+01 1tyv b.80.1.6 28047 1azeA 56 1.17e+01 b.34.2.1 24536 1tud 62 1.17e+01 1tud b.34.2.1 24489 1rgxA 114 1.18e+01 1ieaA 192 1.20e+01 1iakA b.1.1.2 21631 d.19.1.1 38205 1tyv 542 1.22e+01 1tyv b.80.1.6 28038 1ov3A 138 1.23e+01 b.34.2.1 87451 b.34.2.1 87452 1kn9A 249 1.25e+01 b.87.1.2 68699 1my5A 114 1.28e+01 b.1.18.1 79673 1kbvA 327 1.28e+01 b.6.1.3 68395 b.6.1.3 68396 1c9oA 66 1.32e+01 1mjc b.40.4.5 25325 1qz8A 113 1.34e+01 1div 149 1.36e+01 1div d.99.1.1 40692 d.100.1.1 40693 1exmA 405 1.38e+01 1efcA b.43.3.1 25696 b.44.1.1 25736 c.37.1.8 32131 1nngA 153 1.38e+01 1vhyA 257 1.39e+01 1h4rA 314 1.43e+01 a.11.2.1 65616 b.55.1.5 65617 d.15.1.4 65618 1jmtA 104 1.45e+01 d.58.7.3 63180 1h9jA 145 1.47e+01 1h9jA b.40.6.2 60829 b.40.6.2 60830 1h9dA 134 1.49e+01 1cmoA b.2.5.6 60821 2eifA 136 1.51e+01 1bkb b.34.5.2 24607 b.40.4.5 25339 3stdA 165 1.52e+01 3stdA d.17.4.1 38073 1fwxA 595 1.53e+01 b.6.1.4 60069 b.69.3.1 60070 1qmyA 167 1.54e+01 1qmyA d.3.1.2 37094 1n6aA 259 1.55e+01 b.76.2.1 80121 b.85.7.1 80122 1b34B 118 1.55e+01 1b34B b.38.1.1 24797 1a63 130 1.56e+01 1a62 a.140.3.1 64710 b.40.4.5 64711 1bymA 97 1.62e+01 1bi0 b.34.1.2 24458 2std 172 1.66e+01 3stdA d.17.4.1 38085 1i81A 83 1.66e+01 1d3bB b.38.1.1 61930 1meyC 87 1.72e+01 2gliA k.12.1.1 46430 1tyu 543 1.72e+01 1tyv b.80.1.6 28037 1fhoA 119 1.73e+01 1fhoA b.55.1.1 26982 1bal 51 1.73e+01 1bbl a.9.1.1 16357 1lvl 458 1.73e+01 1lvl c.3.1.5 30567 c.3.1.5 30568 d.87.1.1 40205 1shwA 138 1.74e+01 1m4uA 206 1.76e+01 g.17.1.7 78625 1cvsC 225 1.76e+01 1cvsC b.1.1.4 21726 b.1.1.4 21727 1mxmA 254 1.77e+01 b.38.1.3 79647 d.58.43.1 79648 f.34.1.1 79649 1uvqA 197 1.77e+01 1ujrA 110 1.78e+01 1vkkA 154 1.79e+01 1g4mA 393 1.83e+01 b.1.18.11 65143 b.1.18.11 65144 1jjgA 102 1.88e+01 b.40.4.5 71696 1u96A 69 1.88e+01 1tlk 154 1.89e+01 1tlk b.1.1.4 21707 1hk9A 74 1.89e+01 b.38.1.2 83541 1b56 135 1.94e+01 1hmt b.60.1.2 27183 1semA 58 1.96e+01 1ckaA b.34.2.1 24544 1vrtA 560 1.96e+01 1rthA c.55.3.1 33574 e.8.1.2 43023 1qexA 288 1.96e+01 1qexA b.32.1.1 24425 1fdr 248 1.97e+01 1fdr b.43.4.2 25653 c.25.1.1 31543 1ektA 53 1.98e+01 1ektA d.46.1.1 38764 1bwwA 109 1.99e+01 8fabA b.1.1.1 20518 1ds6B 180 2.00e+01 1rhoA b.1.18.8 21898 1dynA 125 2.00e+01 1dynA b.55.1.1 26955 1i7dA 659 2.06e+01 1d6mA e.10.1.1 61886 1tsp 559 2.09e+01 1tyv b.80.1.6 28044 1pcs 98 2.09e+01 1plc b.6.1.1 22871 1preB 470 2.14e+01 1preA d.169.1.2 42438 f.8.1.1 43825 1fl2A 310 2.17e+01 1hyuA c.3.1.5 59869 c.3.1.5 59870 1pwaA 162 2.18e+01 1usmA 80 2.20e+01 1r0pA 312 2.20e+01 1eerB 227 2.27e+01 1eerB b.1.2.1 22011 b.1.2.1 22012 1i7nA 309 2.27e+01 c.30.1.5 83681 d.142.1.3 83682 1lcyA 325 2.30e+01 b.36.1.4 73834 b.47.1.1 73835 1guiA 155 2.31e+01 b.18.1.14 76351 1gcpA 70 2.31e+01 1gcpA b.34.2.1 60430 1vhqA 232 2.34e+01 1ecrA 309 2.34e+01 1ecrA e.2.1.1 42678 1fa4A 105 2.36e+01 1plc b.6.1.1 22867 1jxmA 301 2.36e+01 b.34.2.1 67420 c.37.1.1 67421 1ibzA 112 2.37e+01 1ibzA b.6.1.4 62237 1v5mA 136 2.38e+01 1ha3A 405 2.41e+01 1efcA b.43.3.1 60869 b.44.1.1 60870 c.37.1.8 60871 1o5zA 442 2.43e+01 1uliB 187 2.43e+01 2dynA 122 2.44e+01 1dynA b.55.1.1 26957 2bpa1 426 2.47e+01 2bpa1 1xfsA 178 2.49e+01 1q0sA 259 2.49e+01 1b9mA 265 2.51e+01 1b9mA a.4.5.8 16118 b.40.6.2 58938 b.40.6.2 58939 1si2A 149 2.52e+01 1ogiA 303 2.53e+01 1dyzA 129 2.54e+01 1nwpA b.6.1.1 22917 1wdaA 670 2.56e+01 1pkn 530 2.57e+01 1a49A b.58.1.1 27042 c.1.12.1 29271 c.49.1.1 33125 1mt6A 280 2.60e+01 b.76.2.1 79446 b.85.7.1 79447 1cx4A 305 2.63e+01 b.82.3.2 59099 b.82.3.2 59100 7pcy 98 2.64e+01 1plc b.6.1.1 22863 1i12A 160 2.70e+01 1i21A d.108.1.1 61515 1hcz 252 2.70e+01 1hcz b.2.6.1 22464 b.84.2.2 28250 1hl6A 165 2.75e+01 d.58.7.1 83609 1jy3P 48 2.76e+01 h.1.8.1 67448 1ge8A 249 2.76e+01 1plq d.131.1.2 41398 d.131.1.2 41399 1g87A 614 2.77e+01 a.102.1.2 83275 b.2.2.2 83276 1uurA 473 2.82e+01 1i3uA 127 2.92e+01 1gc1H b.1.1.1 61636 1fr3A 67 2.93e+01 1fr3A b.40.6.1 25436 2hntE 81 2.94e+01 1ucyH 1i1dA 161 2.97e+01 1i21A d.108.1.1 61526 1u1zA 168 2.99e+01 1iraX 152 3.01e+01 1irp b.42.1.2 25556 1dzfA 215 3.02e+01 1dzfA c.52.3.1 33344 d.78.1.1 39753 1j1tA 233 3.03e+01 1be9A 119 3.05e+01 1pdr b.36.1.1 24774 1ci3M 249 3.07e+01 1hcz b.2.6.1 22480 b.84.2.2 28266 1bawA 105 3.08e+01 1plc b.6.1.1 22868 1nnvA 110 3.11e+01 1k2fA 190 3.11e+01 b.8.1.2 68054 1ibyA 112 3.12e+01 1ibzA b.6.1.4 62233 2pcdM 238 3.19e+01 3pchM b.3.6.1 22760 1jxcA 68 3.21e+01 g.3.7.5 77201 1bgyE 196 3.29e+01 1bgyE f.23.12.1 43683 1hyxL 216 3.32e+01 8fabA b.1.1.1 20166 b.1.1.2 21190 1gjwA 637 3.32e+01 b.71.1.1 60582 c.1.8.1 60583 1e79A 510 3.33e+01 1skyB a.69.1.1 18269 b.49.1.1 26434 c.37.1.11 32314 1r13A 148 3.34e+01 1skyE 473 3.38e+01 1skyE a.69.1.1 18314 b.49.1.1 26479 c.37.1.11 32359 1lvk 762 3.39e+01 1lvk b.34.3.1 24576 c.37.1.9 32173 1fzkA 274 3.41e+01 1agdA b.1.1.2 60149 d.19.1.1 60150 1p32A 209 3.43e+01 1p32A d.25.1.1 38379 1gfc 59 3.45e+01 1griA b.34.2.1 24537 1p32C 209 3.45e+01 1p32A d.25.1.1 38381 1ff4A 65 3.47e+01 g.7.1.1 83251 1dqqA 214 3.52e+01 8fabA b.1.1.1 20420 b.1.1.2 21390 1aqb 183 3.52e+01 1aqb b.60.1.1 27084 1e1oA 504 3.60e+01 1lylA b.40.4.1 25258 d.104.1.1 40714 1ebpA 211 3.60e+01 1eerB b.1.2.1 22023 b.1.2.1 22024 1mwsA 646 3.62e+01 d.17.4.5 79592 d.175.1.1 79593 e.3.1.1 79594 1sy7A 715 3.67e+01 12e8L 214 3.71e+01 8fabA b.1.1.1 20268 b.1.1.2 21268 1n67A 359 3.71e+01 b.2.3.4 85354 b.2.3.4 85355 1nepA 130 3.72e+01 b.1.18.7 80440 1l7iL 214 3.72e+01 b.1.1.1 73658 b.1.1.2 73659 1d0yA 761 3.73e+01 1lvk b.34.3.1 24581 c.37.1.9 32178 1sro 76 3.74e+01 1sro b.40.4.5 25327 1i21A 159 3.76e+01 1i21A d.108.1.1 61549 1nrgA 261 3.79e+01 b.45.1.1 80694 1s5lO 246 3.80e+01 1iuz 98 3.82e+01 1plc b.6.1.1 22861 1evhA 112 3.83e+01 1evhA b.55.1.4 26997 1jkgA 140 3.84e+01 d.17.4.2 66795 1eg9B 194 3.84e+01 1ndoB d.17.4.4 38120 1ntyA 311 3.85e+01 1k8bA 52 3.86e+01 g.59.1.1 72171 1gefA 123 3.91e+01 1gefA c.52.1.18 60465 1ollA 188 3.92e+01 1cb8A 678 3.93e+01 1cb8A a.102.3.2 18849 b.24.1.1 23898 b.30.5.2 24422 1b2rA 304 3.99e+01 1fnc b.43.4.2 25648 c.25.1.1 31538 1k1zA 78 3.99e+01 b.34.2.1 68026