# List of top-scoring protein chains for t2k-100-30-bys-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.soe.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 1jtgB 165 2.89e-07 d.98.1.1 67267 2g2uB 165 5.45e-07 d.98.1.1 134541 2h36X 112 5.00e-03 2nvmA 126 9.26e-01 d.326.1.1 138631 1cc1L 498 1.43e+00 1h2rL e.18.1.1 43301 1vz0A 230 1.57e+00 a.4.14.1,d.268.1.1 108929,108930 1soxA 466 1.65e+00 1soxA b.1.18.6,d.120.1.1,d.176.1.1 21947,41090,42563 2dkoA 146 1.86e+00 1a99A 344 2.08e+00 1pot c.94.1.1 35812 2c9wA 169 2.14e+00 1ogpA 393 2.28e+00 b.1.18.6,d.176.1.1 92927,92928 1ylxA 103 2.32e+00 d.82.5.1 123677 1cp3A 277 2.43e+00 1pauA c.17.1.1 30992 2afbA 351 2.53e+00 c.72.1.1 126674 1nmsA 249 2.68e+00 c.17.1.1 85879 2reiA 318 2.78e+00 2bjfA 329 2.87e+00 1ta8A 332 2.94e+00 d.142.2.2 112375 2fueA 262 2.95e+00 c.108.1.10 134119 2glcA 342 2.95e+00 1zckA 154 3.04e+00 1jofA 365 3.05e+00 b.69.10.1 71775 2amyA 246 3.10e+00 c.108.1.10 127026 2dekA 265 3.12e+00 c.90.1.1 131430 1ucrA 78 3.17e+00 a.4.5.45 99188 2a9dA 372 3.21e+00 b.1.18.6,d.176.1.1 126431,126432 2g6yA 217 3.29e+00 1gq6A 313 3.60e+00 c.42.1.1 70341 2o35A 105 3.61e+00 1ne6A 283 3.63e+00 b.82.3.2,b.82.3.2 91831,91832 3brbA 313 3.71e+00 2p36A 335 3.76e+00 2iskA 230 4.16e+00 2ivfA 976 4.42e+00 1rxdA 159 4.56e+00 c.45.1.1 111959 1shkA 173 4.61e+00 1shkA c.37.1.2 31932 1e6cA 173 5.09e+00 1shkA c.37.1.2 59296 1d7pM 159 5.28e+00 1cztA b.18.1.2 23718 1h6vA 499 5.84e+00 3grs c.3.1.5,c.3.1.5,d.87.1.1 60693,60694,60695 1y8cA 246 5.85e+00 c.66.1.43 116563 1rl3A 288 6.17e+00 b.82.3.2,b.82.3.2 104975,104976 1jhgA 101 6.48e+00 1jhgA a.4.12.1 19009 2iorA 235 6.49e+00 2pbiB 354 6.92e+00 2iwxA 214 7.09e+00 d.122.1.1 137758 1x24A 180 7.34e+00 2c2aA 258 7.57e+00 a.30.2.1,d.122.1.3 129662,129663 2rdyA 803 7.68e+00 1rgs 288 7.68e+00 1rgs 1b56A 135 7.89e+00 b.60.1.2 27183 1vzyA 291 7.92e+00 d.193.1.1,g.81.1.1 114042,114043 1r4aA 165 8.00e+00 c.37.1.8 96986 1jl0A 334 8.05e+00 1jenA d.156.1.1 63155 1zuhA 168 8.06e+00 3bxoA 239 8.09e+00 1js8A 394 8.11e+00 a.86.1.1,b.112.1.1 67219,67220 1wdvA 152 8.21e+00 d.116.1.1 114539 1whzA 70 8.61e+00 d.50.3.2 114656 1aoeA 192 9.02e+00 1aoeA c.71.1.1 34923 1tuaA 191 9.04e+00 d.51.1.1,d.51.1.1 107321,107322 2a1hA 365 9.56e+00 e.17.1.1 125997 2gmqA 118 9.61e+00 1zclA 180 1.02e+01 1a49A 530 1.02e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27026,29255,33109 2h27A 73 1.02e+01 a.4.13.2 135993 1g7nA 131 1.06e+01 b.60.1.2 83274 1b74A 254 1.06e+01 1b74A c.78.2.1,c.78.2.1 35264,35265 2ofyA 86 1.07e+01 1z82A 335 1.07e+01 1b1gA 75 1.09e+01 1psrA a.39.1.1 17151 2f94F 350 1.10e+01 2p3eA 420 1.11e+01 1oaoA 674 1.13e+01 e.26.1.2 86744 2fziA 206 1.13e+01 c.71.1.1 134448 3sil 379 1.14e+01 3sil 3silA 379 1.14e+01 b.68.1.1 27542 2g17A 337 1.15e+01 c.2.1.3,d.81.1.1 134512,134513 1yemA 179 1.17e+01 d.63.1.2 116646 2cobA 70 1.19e+01 a.4.1.15 130673 1ef4A 55 1.19e+01 1ef4A a.4.11.1 16272 2g50A 530 1.23e+01 b.58.1.1,c.1.12.1,c.49.1.1 134618,134619,134620 1ut1A 148 1.24e+01 b.2.3.6 108014 2r6uA 148 1.24e+01 1noyA 388 1.28e+01 1clqA c.55.3.5 33713 2va8A 715 1.31e+01 1r69 69 1.32e+01 1r69 1r69A 69 1.32e+01 a.35.1.2 17028 2dplA 308 1.35e+01 1byqA 228 1.36e+01 1yer d.122.1.1 41100 1b8iB 63 1.37e+01 1akhA a.4.1.1 16011 2hl7A 84 1.39e+01 1rkqA 282 1.39e+01 c.108.1.10 97621 1yv5A 374 1.42e+01 2iv2X 715 1.42e+01 b.52.2.2,c.81.1.1 137714,137715 1sfeA 180 1.43e+01 a.4.2.1,c.55.7.1 16073,33748 1lliA 92 1.45e+01 1lmb3 a.35.1.2 17025 2oh5A 248 1.49e+01 1zvdA 380 1.54e+01 2hnxA 136 1.56e+01 b.60.1.2 136633 1du6A 64 1.56e+01 1akhA a.4.1.1 16002 2breA 219 1.61e+01 d.122.1.1 128994 2a4vA 159 1.61e+01 c.47.1.10 126163 2gu1A 361 1.64e+01 1jenA 267 1.64e+01 1jenA 2z10A 194 1.65e+01 2qv6A 268 1.70e+01 1ecfB 504 1.71e+01 1ecfB c.61.1.1,d.153.1.1 34054,41821 1clqA 903 1.72e+01 1clqA c.55.3.5,e.8.1.1 33717,43006 2rcyA 262 1.76e+01 1or7A 194 1.77e+01 a.4.13.2,a.177.1.1 87332,87333 1b72B 87 1.80e+01 1akhA a.4.1.1 16001 2dvyA 226 1.83e+01 1y89A 238 1.86e+01 2isbA 192 1.88e+01 c.8.9.1 137601 2joyA 96 1.88e+01 2qisA 374 1.89e+01 1lmb3 92 1.90e+01 1lmb3 1nox 205 1.91e+01 1nox 1noxA 205 1.91e+01 d.90.1.1 40242 1lyvA 306 1.94e+01 c.45.1.2 74348 1u7pA 164 1.95e+01 c.108.1.17 113095 1mjfA 281 1.96e+01 c.66.1.17 79198 1j7jA 178 1.99e+01 c.61.1.1 84131 3bw8A 217 2.12e+01 1pufB 73 2.14e+01 a.4.1.1 95132 1j3wA 163 2.14e+01 d.110.7.1 90833 1v1hA 103 2.15e+01 b.83.1.1,h.1.17.1 108243,108244 2trxA 108 2.16e+01 1thx c.47.1.1 32719 1wxiA 275 2.17e+01 c.26.2.1 121400 1ecfA 504 2.27e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 1vqsA 116 2.28e+01 d.58.4.13 114019 1konA 249 2.28e+01 e.39.1.1 72823 1g0oA 283 2.30e+01 1ybvA c.2.1.2 60181 2b5aA 77 2.31e+01 a.35.1.3 127882 2i0oA 304 2.35e+01 2r9zA 463 2.36e+01 1yptA 305 2.39e+01 1ytw c.45.1.2 32686 2j3mA 572 2.42e+01 1r6jA 82 2.45e+01 b.36.1.1 97151 1q7fA 286 2.45e+01 b.68.9.1 96036 2btfA 375 2.51e+01 1yagA c.55.1.1,c.55.1.1 33429,33430 1vkmA 297 2.56e+01 c.138.1.1 108670 2oj5A 165 2.58e+01 2qfjA 216 2.61e+01 2a1jA 63 2.65e+01 a.60.2.5 126000 2yv4A 105 2.66e+01 1qi9A 556 2.69e+01 1qhbA a.111.1.2 19053 2bf5A 98 2.70e+01 d.137.1.1 128405 1wh8A 111 2.72e+01 a.35.1.7 114636 1wrrA 301 2.73e+01 d.96.1.4,d.96.1.4 121204,121205 1r4uA 301 2.75e+01 d.96.1.4,d.96.1.4 97047,97048 1kkeA 210 2.81e+01 b.83.1.2,b.21.1.2 68669,68670 1u7eB 154 2.81e+01 2p3hA 101 2.82e+01 2gx9A 129 2.82e+01 d.299.1.1 135828 1kebA 108 2.86e+01 c.47.1.1 77341 2q3pA 112 2.87e+01 d.58.4.4 139798 1dpeA 507 2.90e+01 c.94.1.1 35799 1tuhA 156 2.90e+01 d.17.4.11 107345 2b30A 301 2.91e+01 c.108.1.10 127759 1vpvA 300 2.91e+01 c.119.1.1 113975 1nr0A 611 2.91e+01 b.69.4.1,b.69.4.1 86078,86079 1ekfA 365 2.93e+01 1ekfA e.17.1.1 59445 2cw9A 194 2.94e+01 d.17.4.13 130920 1oaqL 120 2.97e+01 b.1.1.1 92708 2gwfA 157 3.00e+01 c.46.1.4 135802 2pk8A 103 3.04e+01 d.274.1.1 139707 2r78A 117 3.06e+01 1g99A 408 3.09e+01 1g99A c.55.1.2,c.55.1.2 33457,33458 2oo9A 46 3.14e+01 2gudA 122 3.17e+01 b.77.3.1 135732 2nqwA 93 3.28e+01 2fug7 129 3.29e+01 1t70A 255 3.32e+01 d.159.1.9 112275 1smlA 269 3.34e+01 1smlA d.157.1.1 42053 2d9rA 104 3.36e+01 b.129.2.1 131350 2pkhA 148 3.41e+01 1dppA 507 3.44e+01 1dpe c.94.1.1 35800 1s55A 156 3.46e+01 b.22.1.1 118865 2d1wA 638 3.48e+01 b.30.2.1,d.17.2.1,d.17.2.1 131145,131146,131147 1vm6A 228 3.48e+01 d.81.1.3,c.2.1.3 108877,118631 2i5gA 325 3.49e+01 2phnA 254 3.51e+01 d.340.1.1 139696 2f22A 144 3.53e+01 a.213.1.2 132795 2oseA 234 3.54e+01 1keyA 235 3.55e+01 a.118.16.1 72389 1ni5A 433 3.57e+01 b.153.1.2,d.229.1.1,c.26.2.5 111592,111593,80533 2hpwA 233 3.57e+01 2fu5C 183 3.57e+01 c.37.1.8 134104 1bncA 449 3.65e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28236,31643,41488 2p10A 286 3.66e+01 2aioA 269 3.67e+01 d.157.1.1 126829 2bcgY 206 3.70e+01 c.37.1.8 128285 1agiA 125 3.73e+01 d.5.1.1 37303 1g55A 343 3.74e+01 1g55A c.66.1.26 34247 1j1jA 240 3.76e+01 a.118.16.1 90762 1ui8A 638 3.77e+01 b.30.2.1,d.17.2.1,d.17.2.1 99419,99420,99421 1el6A 219 3.77e+01 1el6B d.182.1.1 42606 1gotB 340 3.86e+01 1tbgA b.69.4.1 27648 2ismA 352 3.91e+01 2p7oA 133 3.91e+01 1r5mA 425 3.93e+01 1suuA 312 3.93e+01 b.68.10.1 99006 2hekA 371 3.98e+01 a.211.1.1 136354 2gdqA 382 4.10e+01 c.1.11.2,d.54.1.1 135020,135021 2o8xA 70 4.11e+01 1j8yF 297 4.12e+01 1ng1 a.24.13.1,c.37.1.10 62747,62748 1ytw 306 4.16e+01 1ytw 1w6gA 646 4.19e+01 b.30.2.1,d.17.2.1,d.17.2.1 120660,120661,120662 1vhvA 268 4.20e+01 c.90.1.1 100704 2g3wA 182 4.20e+01 1mx4A 168 4.22e+01 d.211.1.1 79640 2pz0A 252 4.26e+01 1trrA 107 4.29e+01 1jhgA a.4.12.1 19017 2dd7A 216 4.32e+01 1bia 321 4.32e+01 1bia 1biaA 321 4.32e+01 a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1rvgA 305 4.33e+01 c.1.10.2 97920 2d9sA 53 4.35e+01 2bjrA 368 4.36e+01 b.169.1.1,b.169.1.1 128628,128629 2i3oA 516 4.38e+01 d.153.1.6 137027 2gz4A 207 4.43e+01 1h4vB 421 4.45e+01 1adjA c.51.1.1,d.104.1.1 60624,60625 2ip2A 334 4.47e+01 2cmzA 423 4.50e+01 1bsgA 266 4.50e+01 e.3.1.1 42729 2ibaA 302 4.50e+01 d.96.1.4,d.96.1.4 137178,137179 1uwwA 191 4.52e+01 b.18.1.23 108079 1grx 85 4.58e+01 1kte 1hzoA 271 4.60e+01 e.3.1.1 71092 1oqcA 125 4.61e+01 a.24.15.1 87264 2ibnA 250 4.61e+01 a.211.1.4 137195 2ib5A 233 4.65e+01 2dkfA 431 4.65e+01 3co4A 312 4.65e+01 1wwbX 103 4.70e+01 1wwcA b.1.1.4 21777 1ughI 82 4.74e+01 1ugiA d.17.5.1 38133 1ae9A 179 4.74e+01 1ae9A d.163.1.1 42153 1i4jA 110 4.78e+01 d.55.1.1 76734 1iyoA 262 4.79e+01 e.3.1.1 76970 1z00B 84 4.80e+01 a.60.2.5 124295 1g2yA 32 4.81e+01 a.34.2.1 17003 2g7bA 137 4.83e+01 1whbA 157 4.84e+01 c.46.1.4 114639 3bojA 213 4.88e+01 3co5A 143 4.90e+01 2cr5A 109 4.91e+01 d.15.1.2 130733 1rjoA 646 4.93e+01 b.30.2.1,d.17.2.1,d.17.2.1 111832,111833,111834 1yueA 427 4.96e+01 2omf 340 4.98e+01 2omf 2e0qA 104 5.00e+01 1b04A 318 5.01e+01 1b04A d.142.2.2 41579 2if6A 186 5.02e+01 1bihA 395 5.06e+01 1bihA b.1.1.4,b.1.1.4,b.1.1.4,b.1.1.4 21752,21753,21754,21755 2g29A 417 5.06e+01 1jpdX 324 5.06e+01 c.1.11.2,d.54.1.1 67014,67015 3ck6A 252 5.09e+01 1g8aA 227 5.12e+01 c.66.1.3 90506 1std 172 5.15e+01 3stdA 1awqA 164 5.19e+01 2cpl b.62.1.1 27461 2a6qA 86 5.23e+01 d.306.1.1 126293 2ie7A 318 5.24e+01 a.65.1.1 137293 1vkiA 181 5.29e+01 d.116.1.1 108664 1v5rA 97 5.29e+01 d.82.4.1 119854 2gqpA 236 5.31e+01 d.122.1.1 135513 1ihbA 162 5.31e+01 1bd8 d.211.1.1 19161 2g9iA 249 5.35e+01 d.340.1.1 134806 1kcw 1046 5.40e+01 1kcw 1kcwA 1046 5.40e+01 b.6.1.3,b.6.1.3,b.6.1.3,b.6.1.3,b.6.1.3,b.6.1.3 23151,23152,23153,23154,23155,23156 2od5A 116 5.41e+01 2i7vA 459 5.45e+01 1x0pA 143 5.45e+01 d.58.10.2 121552 3by6A 126 5.46e+01 2z3hA 130 5.48e+01 2odiA 238 5.48e+01 1mgpA 313 5.50e+01 c.119.1.1 79098 1xmzA 241 5.52e+01 1bxeA 113 5.52e+01 1bxeA d.55.1.1 38898 1usgA 346 5.54e+01 c.93.1.1 99864 2cxvA 219 5.57e+01 b.47.1.4 131012 1rwsA 77 5.64e+01 d.15.3.2 97991 1xfdA 723 5.65e+01 b.70.3.1,c.69.1.24 115251,115252 2nx9A 464 5.65e+01 1vr6A 350 5.65e+01 c.1.10.4 120439 2ootA 709 5.68e+01 a.48.2.1,c.8.4.1,c.56.5.5 139176,139177,139178 1wotA 98 5.75e+01 d.218.1.5 109470 1ggxA 223 5.76e+01 1ggxA d.22.1.1 38367 2ftbA 125 5.77e+01 b.60.1.2 134057 2eu8A 216 5.78e+01 2bjqA 345 5.78e+01 b.169.1.1,b.169.1.1 128626,128627 1wn5A 130 5.79e+01 c.97.1.1 121082 1ybvA 283 5.79e+01 1ybvA c.2.1.2 29948 2okfA 140 5.82e+01 2dhqA 146 5.89e+01 2dhqA c.23.13.1 31382 2okgA 255 5.90e+01 2dy1A 665 5.92e+01 2v75A 104 5.92e+01 1dptA 117 5.93e+01 1dptA d.80.1.3 39862 2a50B 168 5.96e+01 1ih7A 903 5.97e+01 1clqA c.55.3.5,e.8.1.1 62375,62376 2ivsA 314 6.07e+01 1jv4A 162 6.10e+01 b.60.1.1 67343 1h2kA 349 6.15e+01 b.82.2.6 76572 2e1vA 454 6.18e+01 1hmt 132 6.21e+01 1hmt 1hmtA 132 6.21e+01 b.60.1.2 27169 1fx7A 230 6.22e+01 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 60088,60089,60090 1ge8A 249 6.23e+01 1plq d.131.1.2,d.131.1.2 41398,41399 2c60A 111 6.27e+01 d.15.2.2 129966 1bkjA 240 6.28e+01 1bkjA d.90.1.1 40243 1qntA 176 6.30e+01 1sfe a.4.2.1,c.55.7.1 16074,33749 1caxB 184 6.31e+01 1caxB b.82.1.2 28105 2p84A 145 6.32e+01 1j8mF 297 6.35e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 2cx5A 158 6.36e+01 1hdmB 193 6.37e+01 1hdmB b.1.1.2,d.19.1.1 21584,38158 1oy3D 282 6.39e+01 d.211.1.1 87554 1ti6A 875 6.45e+01 b.52.2.2,c.81.1.1 106974,106975 1hxxA 340 6.46e+01 2omf f.4.3.1 61385 1cwvA 492 6.58e+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 1ywuA 149 6.66e+01 b.45.2.1 124164 1yljA 263 6.69e+01 1w7jB 151 6.74e+01 a.39.1.5 120690 1squA 155 6.74e+01 d.252.1.1 98971 1e0bA 68 6.85e+01 1e0bA b.34.13.2 37476 1yzxA 226 6.89e+01 1i7kA 179 6.91e+01 1u9aA d.20.1.1 61889 1p3jA 217 6.92e+01 c.37.1.1,g.41.2.1 94022,94023 1h65A 270 6.93e+01 c.37.1.8 65640 1ulyA 192 6.95e+01 a.4.5.58 113297 2dxqA 150 6.96e+01 1s14A 194 6.98e+01 d.122.1.2 98329 1vjnA 220 6.98e+01 d.157.1.4 100825 2otmA 154 6.99e+01 1nogA 177 7.00e+01 a.25.2.2 85923 1swvA 267 7.00e+01 c.108.1.3 112134 1anxA 319 7.00e+01 1avc a.65.1.1 18161 2hkjA 469 7.04e+01 a.156.1.3,d.14.1.3,d.122.1.2 136553,136554,136555 2o2kA 355 7.04e+01 2eqaA 352 7.06e+01 2ia1A 178 7.07e+01 1r1a1 287 7.07e+01 1aym1 2z0xA 158 7.07e+01 1udiI 83 7.12e+01 1ugiA d.17.5.1 38124 1zkeA 83 7.13e+01 a.30.6.1 125186 1idpA 172 7.15e+01 d.17.4.1 83685 2gdnA 267 7.15e+01 2bk8A 97 7.20e+01 1mzeA 351 7.26e+01 b.82.2.6 79694 2ntkA 222 7.32e+01 d.153.2.1 138583 1ass 159 7.32e+01 1a6dA 1assA 159 7.32e+01 c.8.5.2 30818 1dv1A 449 7.38e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28234,31641,41486 1ukvY 206 7.42e+01 c.37.1.8 107918 3cswA 285 7.42e+01 1yukA 103 7.46e+01 2hzmA 212 7.53e+01 1aerA 205 7.54e+01 1aerA d.166.1.1 42249 1a76 326 7.58e+01 1a76 1a76A 326 7.58e+01 a.60.7.1,c.120.1.2 18091,33361 1ud9A 245 7.60e+01 d.131.1.2,d.131.1.2 107768,107769 1k3zD 282 7.60e+01 d.211.1.1 77251 1awsA 164 7.62e+01 2cpl b.62.1.1 27431 1dd3A 128 7.70e+01 1dd3C a.108.1.1,d.45.1.1 19031,38760 2iakA 224 7.71e+01 3bhxA 709 7.76e+01 3bi1A 709 7.77e+01 1iznB 277 7.79e+01 e.43.1.2 83848 1cvrA 435 7.81e+01 1cvrA b.1.18.12,c.17.1.2 21949,31006 2i0xA 85 7.81e+01 1g6aA 271 7.89e+01 1btl e.3.1.1 42704 1gqvA 135 7.97e+01 d.5.1.1 70376 2yvyA 278 7.97e+01