# List of top-scoring protein chains for t2k-100-30-near-backbone-11-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 1v7lA 163 7.55e-03 2gp4A 628 1.59e-01 3ullA 132 5.12e-01 3ullA b.40.4.3 25282 1q7hA 153 7.15e-01 b.122.1.1,d.17.6.2 96042,96043 1zvyA 136 8.99e-01 1kqfA 1015 9.63e-01 b.52.2.2,c.81.1.1 72871,72872 1pguA 615 1.23e+00 b.69.4.1,b.69.4.1 88069,88070 1dl5A 317 1.42e+00 1dl5A c.66.1.7,d.197.1.1 64720,64721 1t0hB 224 1.88e+00 c.37.1.1 106208 1ox3A 109 2.18e+00 h.1.17.1 93668 1eu3A 210 2.30e+00 1an8 b.40.2.2,d.15.6.1 25206,37795 1a5z 319 2.59e+00 1ceqA c.2.1.5,d.162.1.1 30181,42148 1ivyA 452 2.71e+00 1ivyA c.69.1.5 34654 1iz6A 138 2.72e+00 b.34.5.2,b.40.4.5 76976,76977 1aquA 297 3.00e+00 1aquA c.37.1.5 31942 1zeqX 84 3.04e+00 1t3lA 337 3.23e+00 b.34.2.1,c.37.1.1 106358,106359 1b8qA 127 3.37e+00 1qauA b.36.1.1 24781 1wmmA 145 3.55e+00 1ue1A 164 3.71e+00 b.40.4.3 99243 1x3eA 165 3.77e+00 1ng4A 390 4.10e+00 c.3.1.2,d.16.1.3 85666,85667 1ryiA 382 4.16e+00 1akp 114 4.90e+00 2mcm b.1.7.1 22212 1pch 88 4.93e+00 1ptf d.94.1.1 40564 2fxqA 264 5.03e+00 1k3sA 113 5.20e+00 d.198.1.1 68120 1qvcA 145 5.88e+00 3ullA b.40.4.3 25284 1i12A 160 7.12e+00 1i21A d.108.1.1 61515 1pydA 556 7.58e+00 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31735,31773,31774 1wocA 103 8.07e+00 1e0tA 470 8.12e+00 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 1yfqA 342 8.23e+00 1qauA 112 8.27e+00 1qauA b.36.1.1 24779 2gjgA 248 8.29e+00 1i1dA 161 8.44e+00 1i21A d.108.1.1 61526 1i21A 159 8.47e+00 1i21A d.108.1.1 61549 1zx8A 136 8.79e+00 1p42A 270 8.88e+00 d.14.1.7,d.14.1.7 87754,87755 1vpjA 192 8.89e+00 2go3A 267 8.90e+00 1xovA 326 9.02e+00 1ckv 141 9.21e+00 1ckv d.137.1.1 41452 1r3eA 309 9.64e+00 b.122.1.1,d.265.1.2 96907,96908 1v1qA 134 9.80e+00 1tvxA 75 9.97e+00 1tvxA d.9.1.1 37441 1tvxB 75 1.09e+01 1tvxA d.9.1.1 37442 1qavB 115 1.09e+01 1qauA b.36.1.1 24780 1uebA 184 1.10e+01 b.34.5.2,b.40.4.5,b.40.4.5 107782,107783,107784 2cyeA 133 1.16e+01 1mh1 186 1.16e+01 1eesA c.37.1.8 32002 1whzA 70 1.27e+01 2crvA 120 1.39e+01 1ireB 228 1.42e+01 b.34.4.4 76770 1pwt 61 1.43e+01 1tud b.34.2.1 24490 1g8fA 511 1.46e+01 1g8fA b.122.1.3,c.26.1.5,c.37.1.15 60348,60349,60350 1afp 51 1.48e+01 1afp g.26.1.1 44947 1shg 62 1.49e+01 1ckaA b.34.2.1 24493 1nkqA 259 1.54e+01 d.177.1.1 103862 1r6xA 395 1.56e+01 b.122.1.3,c.26.1.5 97167,97168 1b34B 118 1.59e+01 1b34B b.38.1.1 24797 1txyA 104 1.59e+01 1jsdA 319 1.60e+01 b.19.1.2 63258 1tuc 63 1.60e+01 1tuc b.34.2.1 24492 1uv4A 293 1.63e+01 1il8A 72 1.64e+01 1tvxA d.9.1.1 37365 1rerA 391 1.66e+01 b.1.18.4,f.10.1.1 97327,97328 1umzA 278 1.70e+01 b.29.1.2 99639 1plfA 72 1.72e+01 1tvxA d.9.1.1 37373 3il8 72 1.79e+01 1tvxA d.9.1.1 37356 1pk6A 133 1.84e+01 b.22.1.1 94801 1napA 70 1.96e+01 1tvxA d.9.1.1 37445 1oruA 195 1.99e+01 b.58.1.2 93464 1z9fA 153 2.02e+01 1k8kB 394 2.04e+01 c.55.1.1 68307 1lplA 95 2.04e+01 b.34.10.1 74173 2cwaA 263 2.05e+01 1te7A 103 2.07e+01 1kawA 135 2.13e+01 3ullA b.40.4.3 25288 1pn2A 280 2.16e+01 d.38.1.4,d.38.1.4 94930,94931 2bvlA 543 2.17e+01 1hruA 188 2.24e+01 1hruA d.115.1.1 40926 1jscA 630 2.27e+01 c.31.1.3,c.36.1.5,c.36.1.9 67224,67225,67226 1iqzA 81 2.29e+01 d.58.1.4 66281 1kqfB 294 2.31e+01 d.58.1.5,f.23.22.1 75900,75901 1fvrA 327 2.31e+01 d.144.1.7 60047 1oyzA 280 2.34e+01 a.118.1.16 93775 1guaA 167 2.34e+01 1ctqA c.37.1.8 32013 1i18A 97 2.34e+01 b.43.4.3 61520 1viuA 203 2.42e+01 d.113.1.1 100771 1s28A 132 2.45e+01 d.198.1.1 105223 1tovA 98 2.45e+01 b.34.10.1 107179 1ugpB 226 2.51e+01 b.34.4.4 107832 3htsB 102 2.57e+01 2hts a.4.5.22 16175 2furA 209 2.67e+01 2c6yA 111 2.69e+01 1icwA 72 2.69e+01 1tvxA d.9.1.1 37357 2hts 88 2.72e+01 2hts a.4.5.22 16174 1tk9A 188 2.75e+01 c.80.1.3 107082 1jdqA 98 2.75e+01 d.68.3.3 66559 1iweA 457 2.76e+01 c.37.1.10 71486 2aebA 322 2.77e+01 1wloA 136 2.82e+01 1vchA 175 2.83e+01 1k0hA 117 2.85e+01 b.106.1.2 71975 1o54A 277 2.86e+01 c.66.1.13 92482 1qpbA 563 2.87e+01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31739,31781,31782 1lr0A 129 2.98e+01 d.212.1.1 74213 2as9A 210 3.07e+01 1dmr 823 3.14e+01 1dmr b.52.2.2,c.81.1.1 26904,35312 1h95A 79 3.15e+01 b.40.4.5 65742 1owfA 99 3.20e+01 a.55.1.1 87487 1ihfA 99 3.35e+01 1huuA a.55.1.1 17893 1kao 167 3.37e+01 1ctqA c.37.1.8 32014 1vqvA 306 3.38e+01 2mcm 112 3.39e+01 2mcm b.1.7.1 22207 1mp8A 281 3.45e+01 d.144.1.7 91384 2cfxA 144 3.46e+01 1sawA 225 3.47e+01 1ywnA 316 3.47e+01 2fg9A 178 3.52e+01 1fjgD 209 3.54e+01 1c05A d.66.1.2 39553 1dg6A 191 3.58e+01 1d4vB b.22.1.1 23883 1u4cA 349 3.60e+01 b.69.4.2 107666 1lldA 319 3.64e+01 3ldh c.2.1.5,d.162.1.1 30177,42144 1pfkA 320 3.65e+01 3pfk c.89.1.1 35575 1k8kG 151 3.69e+01 a.118.13.1 68313 1cm9A 74 3.73e+01 1b3aA d.9.1.1 37405 1hjdA 101 3.77e+01 b.34.2.1 65846 2myo 118 3.78e+01 2myo d.211.1.1 19175 1bkb 136 3.85e+01 1bkb b.34.5.2,b.40.4.5 24609,25341 1gy9A 283 3.87e+01 b.82.2.5 70742 2bf5A 98 3.89e+01 1d4vB 163 3.91e+01 1d4vB b.22.1.1 23884 1myo 118 3.92e+01 2myo d.211.1.1 19174 1fltY 95 3.96e+01 1fltX b.1.1.4 21766 2napA 723 4.05e+01 2napA b.52.2.2,c.81.1.1 26926,35334 2gsfA 373 4.09e+01 1jajA 174 4.13e+01 d.218.1.2 66471 1qfjA 232 4.15e+01 1qfjA b.43.4.2,c.25.1.1 25655,31545 1d2qA 173 4.17e+01 1d4vB b.22.1.1 23894 1z4hA 66 4.19e+01 1j1yA 136 4.41e+01 d.38.1.5 90776 2hcuA 213 4.42e+01 1a8p 258 4.44e+01 1fdr b.43.4.2,c.25.1.1 25654,31544 1nffA 260 4.45e+01 c.2.1.2 80457 1vs0A 310 4.49e+01 1l3iA 192 4.55e+01 c.66.1.22 77676 1pedA 351 4.56e+01 1pedA b.35.1.2,c.2.1.1 24753,29769 1vkyA 347 4.64e+01 e.53.1.1 108696 1wluA 136 4.75e+01 1z08A 170 4.75e+01 1i1jA 108 4.77e+01 1i1jA b.34.2.1 61531 1gm0A 142 4.86e+01 a.39.2.1 65297 1e3jA 352 4.92e+01 1e3jA b.35.1.2,c.2.1.1 24765,29781 1s12A 94 5.00e+01 1qlaB 239 5.08e+01 1qlaB a.1.2.1,d.15.4.2 15679,37707 1rkqA 282 5.12e+01 c.108.1.10 97621 1f39A 101 5.13e+01 1umuA b.87.1.1 28386 3hsf 92 5.18e+01 2hts a.4.5.22 16182 2gu2A 312 5.22e+01 1kzlA 208 5.22e+01 b.43.4.3,b.43.4.3 77635,77636 1ri9A 102 5.30e+01 b.34.2.1 97506 2cvbA 188 5.32e+01 1g7tA 594 5.35e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25714,25715,31033,32148 1t9bA 677 5.39e+01 1jlyA 304 5.45e+01 1jlyA b.42.3.1,b.42.3.1 25587,25588 1bteA 97 5.46e+01 1bteA g.7.1.3 44463 1up6A 416 5.47e+01 c.2.1.5,d.162.1.2 107976,107977 1g10A 102 5.52e+01 1g10A d.137.1.1 60191 1gkkA 297 5.52e+01 c.69.1.2 65248 1sazA 381 5.53e+01 1kevA 351 5.54e+01 1pedA b.35.1.2,c.2.1.1 24749,29765 1kl7A 514 5.57e+01 c.79.1.1 72678 1qpcA 279 5.76e+01 1fgkA d.144.1.7 41685 1vziA 126 5.79e+01 b.1.13.1,g.41.5.2 108967,108968 1obfO 335 5.88e+01 c.2.1.3,d.81.1.1 86768,86769 1c30B 382 5.93e+01 c.8.3.1,c.23.16.1 30736,31413 1jlxA 304 5.99e+01 1jlyA b.42.3.1,b.42.3.1 25583,25584 1kblA 873 6.10e+01 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 1c05A 159 6.11e+01 1c05A d.66.1.2 39559 1a9xB 379 6.16e+01 1c3oB c.8.3.1,c.23.16.1 30732,31409 1eza 259 6.18e+01 1zymA a.60.10.1,c.8.1.2 18113,30708 1jqbA 351 6.22e+01 b.35.1.2,c.2.1.1 77151,77152 1bu1A 57 6.27e+01 1bbzA b.34.2.1 24499 1ymmB 198 6.31e+01 1gttA 429 6.32e+01 d.177.1.1,d.177.1.1 70529,70530 1fltX 95 6.40e+01 1fltX b.1.1.4 21765 1wozA 177 6.42e+01 1skyB 502 6.49e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18313,26478,32358 2c2hA 192 6.50e+01 1vdmA 153 6.71e+01 1h0hA 977 6.71e+01 b.52.2.2,c.81.1.1 76435,76436 2czsA 80 6.77e+01 1ykfA 352 6.79e+01 1pedA b.35.1.2,c.2.1.1 24757,29773 821p 166 6.80e+01 1ctqA c.37.1.8 31969 1jx7A 117 6.80e+01 c.114.1.1 77195 1ru3A 732 6.80e+01 e.26.1.3 97835 1huuA 90 6.82e+01 1huuA a.55.1.1 17897 1x9uA 116 6.83e+01 1szhA 161 6.87e+01 a.226.1.1 106157 2gm5A 139 7.04e+01 1o0sA 605 7.09e+01 c.2.1.7,c.58.1.3 86540,86541 1gklA 297 7.10e+01 c.69.1.2 65250 1d3vA 323 7.10e+01 1d3vA c.42.1.1 32559 1mjc 69 7.13e+01 1mjc b.40.4.5 25319 1ckqA 276 7.24e+01 1ckqA c.52.1.1 33229 2alaA 391 7.25e+01 2pfkA 320 7.36e+01 3pfk c.89.1.1 35577 1cne 270 7.38e+01 1ndh b.43.4.2,c.25.1.1 25661,31551 1que 303 7.53e+01 1fnc b.43.4.2,c.25.1.1 25647,31537 2bx2L 517 7.56e+01 1otjA 283 7.56e+01 b.82.2.5 93517 1wb4A 297 7.61e+01 1i7oA 429 7.61e+01 1i7oA d.177.1.1,d.177.1.1 61893,61894 1up7A 417 7.62e+01 1r4pB 70 7.67e+01 b.40.2.1 97026 1g40A 244 7.68e+01 1e5gA g.18.1.1,g.18.1.1,g.18.1.1,g.18.1.1 44823,44824,44825,44826 1npyA 271 7.73e+01 c.2.1.7,c.58.1.5 85995,85996 1uayA 242 7.80e+01 c.2.1.2 88390 1hqkA 154 7.81e+01 c.16.1.1 65902 2f57A 317 7.83e+01 1xneA 113 7.86e+01 1hueA 90 7.89e+01 1huuA a.55.1.1 17900 1fdr 248 7.91e+01 1fdr b.43.4.2,c.25.1.1 25653,31543 1w19A 160 7.93e+01 1agp 166 7.94e+01 1ctqA c.37.1.8 31985 1kl9A 182 7.94e+01 b.40.4.5 72681 1hbzA 498 7.96e+01 1cf9A e.5.1.1 60937 3lck 271 8.04e+01 1fmk d.144.1.7 41686 1l5jA 865 8.12e+01 a.118.15.1,c.8.2.1,c.83.1.1 73592,73593,73594 2dpmA 284 8.13e+01 2dpmA c.66.1.28 34246 1k78A 149 8.18e+01 a.4.1.5,a.4.1.5 68255,68256 1jpaA 312 8.19e+01 d.144.1.7 67011 2fbyA 205 8.23e+01 1lgpA 116 8.26e+01 b.26.1.2 73890 2fdsA 352 8.31e+01 1qsvA 101 8.37e+01 1fltX b.1.1.4 21771 1c3oB 382 8.39e+01 1c3oB c.8.3.1,c.23.16.1 30744,31421 1j58A 385 8.42e+01 b.82.1.2 71531 1xxoA 147 8.48e+01 1gweA 503 8.55e+01 e.5.1.1 70667 1rlaA 323 8.56e+01 1d3vA c.42.1.1 32561 1kopA 223 8.74e+01 2cba b.74.1.1 27966 1pdnC 128 8.77e+01 6paxA a.4.1.5 16047 2aq6A 147 8.77e+01 1g6gA 127 8.79e+01 1g6gA b.26.1.2 23916 1a14H 120 8.81e+01 1mfa b.1.1.1 20061 1e6cA 173 8.81e+01 1shkA c.37.1.2 59296 6paxA 133 8.82e+01 6paxA a.4.1.5,a.4.1.5 64758,64759 1qtyT 101 8.83e+01 1fltX b.1.1.4 21769 1s98A 107 8.83e+01 b.124.1.1 105377 1ik6A 369 8.86e+01 c.36.1.7,c.48.1.2 66174,66175 1kjnA 157 8.93e+01 c.115.1.1 72614 1t46A 313 8.95e+01 d.144.1.7 106397 1g7rA 594 8.97e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25716,25717,31034,32149 2ak5A 64 8.97e+01 1w9aA 147 8.98e+01