# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7-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 1q9uA 130 1.92e-01 unknown_sccs -11025 1qf6A 642 3.28e-01 1qf6A c.51.1.1 33210 d.15.10.1 39551 d.67.1.1 39562 d.104.1.1 40759 1edzA 320 3.56e-01 1ee9A c.2.1.7 30287 c.58.1.2 33935 1ee9A 320 5.31e-01 1ee9A c.2.1.7 30288 c.58.1.2 33936 1j3mA 129 5.43e-01 1ovqA 138 7.77e-01 unknown_sccs -7660 1ss4A 153 1.17e+00 2bpa1 426 1.25e+00 2bpa1 1i4wA 353 1.30e+00 c.66.1.24 66028 1nxiA 132 1.53e+00 d.58.47.1 86381 1cr1A 296 1.54e+00 1cr1A c.37.1.11 32286 1qipA 183 1.81e+00 1qipA d.32.1.1 38470 1m6iA 493 2.04e+00 c.3.1.5 74533 c.3.1.5 74534 d.87.1.1 74535 1cr0A 296 2.12e+00 1cr1A c.37.1.11 32287 1an9A 340 2.21e+00 1an9A c.4.1.2 30617 d.16.1.3 37904 1udxA 416 2.50e+00 b.117.1.1 -3546 c.37.1.8 -7101 unknown_sccs -9009 1ris 101 2.66e+00 1ris d.58.14.1 39314 1uxoA 192 2.74e+00 1mli 96 2.80e+00 1mli d.58.4.1 39070 1mvlA 209 2.86e+00 c.34.1.1 85146 6prcH 258 2.87e+00 6prcH b.41.1.1 25457 f.23.10.1 43436 1evlA 401 2.89e+00 1qf6A c.51.1.1 33202 d.104.1.1 40751 1nzjA 298 2.94e+00 c.26.1.1 -6600 1ks2A 219 3.32e+00 unknown_sccs 72908 d.58.40.1 72909 1o8bA 219 3.39e+00 unknown_sccs 81180 d.58.40.1 81181 1gv4A 528 3.49e+00 c.3.1.5 70589 c.3.1.5 70590 d.87.1.1 70591 1bh5A 183 3.59e+00 1qipA d.32.1.1 38476 1dhy 292 4.42e+00 1han d.32.1.3 38504 d.32.1.3 38505 1e20A 209 4.51e+00 1e20A c.34.1.1 31759 1qqhA 144 4.58e+00 1dtoA b.91.1.1 28404 1lkzA 219 4.60e+00 unknown_sccs 73991 d.58.40.1 73992 1uv7A 110 4.75e+00 unknown_sccs -10256 1cqmA 101 4.91e+00 1ris d.58.14.1 39321 1j2mA 99 5.46e+00 a.165.1.1 84018 4gr1 478 5.58e+00 3grs c.3.1.5 30461 c.3.1.5 30462 d.87.1.1 40162 1fw9A 164 6.18e+00 1fw9A d.190.1.1 60059 1fzrA 138 6.19e+00 1fzrA c.52.1.17 33336 1k8wA 327 6.23e+00 b.122.1.1 83094 unknown_sccs -10143 1o20A 427 6.49e+00 c.82.1.1 86556 1irf 112 6.65e+00 2irfG a.4.5.23 16192 1gp1A 198 6.67e+00 1gp1A c.47.1.10 33059 3grs 478 6.76e+00 3grs c.3.1.5 30441 c.3.1.5 30442 d.87.1.1 40152 1ve9A 347 6.89e+00 c.4.1.2 -6056 d.16.1.3 -9214 1aa8A 347 6.94e+00 1an9A 1dxrH 258 7.17e+00 6prcH b.41.1.1 25456 f.23.10.1 43433 1r0pA 312 7.24e+00 d.144.1.7 -11377 1jbaA 204 7.85e+00 1rec a.39.1.5 17330 1lvoA 302 7.93e+00 b.47.1.4 74284 1b73A 254 8.10e+00 1b74A c.78.2.1 35266 c.78.2.1 35267 1louA 101 8.16e+00 1ris d.58.14.1 39323 1mo9A 523 8.37e+00 c.3.1.5 79341 c.3.1.5 79342 d.87.1.1 79343 8ohm 435 8.92e+00 1heiA c.37.1.14 32469 c.37.1.14 32470 1ntvA 152 9.40e+00 b.55.1.2 86168 1uc8A 280 9.80e+00 unknown_sccs -6718 unknown_sccs -11230 1afb1 154 1.01e+01 1rtm1 1q4mA 221 1.01e+01 unknown_sccs -1910 1tdj 514 1.01e+01 1tdj c.79.1.1 35297 d.58.18.2 39356 d.58.18.2 39357 1aogA 485 1.01e+01 3grs c.3.1.5 30517 c.3.1.5 30518 d.87.1.1 40190 1pvvA 315 1.03e+01 c.78.1.1 -8495 c.78.1.1 -8496 1vsrA 136 1.05e+01 1vsrA c.52.1.15 33332 1nqzA 194 1.05e+01 d.113.1.1 86077 1a8y 367 1.07e+01 1a8y c.47.1.3 32781 c.47.1.3 32782 c.47.1.3 32783 1jjgA 102 1.07e+01 b.40.4.5 71696 1sur 215 1.08e+01 1sur c.26.2.2 31620 1p3wA 404 1.11e+01 c.67.1.3 87752 1p9uA 302 1.11e+01 b.47.1.4 88001 1gw5S 142 1.16e+01 d.110.4.2 70633 1m0dA 138 1.18e+01 c.52.1.17 74354 1erw 105 1.20e+01 1erv c.47.1.1 32745 1d7yA 408 1.21e+01 1d7yA c.3.1.5 30565 c.3.1.5 30566 d.87.1.1 40204 1ivnA 190 1.22e+01 c.23.10.5 83719 1iuz 98 1.22e+01 1plc b.6.1.1 22861 1rtm1 149 1.22e+01 1rtm1 1mm4A 170 1.22e+01 f.4.1.2 79294 1fukA 165 1.27e+01 1fukA c.37.1.19 32409 1rqlA 267 1.30e+01 c.108.1.3 -6814 1rec 201 1.30e+01 1rec a.39.1.5 17326 1jrmA 104 1.31e+01 d.206.1.1 67136 1mvoA 136 1.37e+01 c.23.1.1 79513 1a8rA 221 1.38e+01 1a8rA d.96.1.1 40587 1e3mA 800 1.39e+01 1ewqA a.113.1.1 19075 c.37.1.12 32389 c.55.6.1 33746 d.75.2.1 39747 1od6A 160 1.39e+01 c.26.1.3 86836 1g10A 102 1.40e+01 1g10A d.137.1.1 60191 1r94A 118 1.41e+01 b.124.1.1 -4402 1mb3A 124 1.42e+01 c.23.1.1 78907 1aiu 105 1.43e+01 1erv c.47.1.1 32746 1aim 215 1.43e+01 1cs8A d.3.1.1 37044 1al0F 426 1.44e+01 2bpa1 b.121.5.1 23274 1bowA 159 1.44e+01 1bowA d.60.1.1 39528 1oiaA 95 1.44e+01 d.58.7.1 87051 1jc4A 148 1.47e+01 1jc4A d.32.1.4 62863 1nu4A 97 1.48e+01 d.58.7.1 80731 1ptmA 329 1.51e+01 unknown_sccs -8456 1luzA 88 1.51e+01 b.40.4.5 74271 1mszA 86 1.56e+01 d.68.7.1 79428 1p5hA 428 1.57e+01 c.123.1.1 87802 1faaA 124 1.61e+01 1erv c.47.1.1 32738 1httA 423 1.63e+01 1adjA c.51.1.1 33178 d.104.1.1 40727 1a6q 382 1.64e+01 1a6q a.159.1.1 75801 d.219.1.1 75802 2wrpR 107 1.66e+01 1jhgA a.4.12.1 19010 1ezoA 370 1.69e+01 4mbp c.94.1.1 59539 1kafA 108 1.69e+01 d.199.1.1 68372 1b74A 254 1.70e+01 1b74A c.78.2.1 35264 c.78.2.1 35265 1m4uA 206 1.71e+01 g.17.1.7 78625 1nfp 228 1.71e+01 1nfp c.1.16.2 29555 1isiA 265 1.74e+01 e.4.1.1 71394 1heiA 451 1.75e+01 1heiA c.37.1.14 32463 c.37.1.14 32464 1g24A 211 1.78e+01 1g24A d.166.1.1 42270 1i1gA 141 1.80e+01 a.4.5.32 65982 d.58.4.2 65983 2ae2A 260 1.86e+01 1bdb c.2.1.2 29945 1mjhA 162 1.88e+01 1mjhA c.26.2.4 31639 8abp 306 1.89e+01 8abp c.93.1.1 35647 1em2A 229 1.96e+01 1em2A d.129.3.2 41321 1php 394 1.97e+01 16pk c.86.1.1 35452 1urnA 97 1.97e+01 1urnA d.58.7.1 39153 1gdgA 293 1.97e+01 1kw3B 292 2.00e+01 d.32.1.3 77549 d.32.1.3 77550 1g2iA 166 2.04e+01 1g2iA c.23.16.2 31438 1uzxA 169 2.05e+01 d.20.1.2 -9409 1ecxA 384 2.05e+01 1ecxA c.67.1.3 34431 1f9mA 112 2.09e+01 1erv c.47.1.1 32736 1jj21 48 2.13e+01 1ffkY 2shpA 525 2.24e+01 2shpA c.45.1.2 32683 d.93.1.1 40533 d.93.1.1 40534 1aye 401 2.30e+01 1aye c.56.5.1 33824 d.58.3.1 39065 1m5tA 124 2.30e+01 c.23.1.1 78660 1gseA 221 2.34e+01 1pgtA a.45.1.1 17667 c.47.1.5 32961 1bg2 325 2.36e+01 1bg2 c.37.1.9 32189 1h5qA 265 2.43e+01 1cydA c.2.1.2 60643 1pta 318 2.46e+01 1pscA c.1.9.3 29064 1kmnD 424 2.48e+01 1adjA c.51.1.1 33185 d.104.1.1 40734 1izcA 339 2.51e+01 c.1.12.5 83838 1a1s 314 2.53e+01 1othA c.78.1.1 35258 c.78.1.1 35259 1rifA 282 2.55e+01 unknown_sccs -7265 1ejxB 101 2.56e+01 b.85.3.1 83183 1apmE 350 2.58e+01 1cdkA d.144.1.7 41628 1fa8A 135 2.60e+01 1qipA d.32.1.1 38486 1buuA 168 2.63e+01 1rtm1 d.169.1.1 42366 h.1.1.1 45388 4fiv 113 2.70e+01 1fmb b.50.1.1 26762 1m5oC 100 2.73e+01 d.58.7.1 78654 1e1hB 174 2.74e+01 1o6jA 150 2.75e+01 c.47.1.10 81089 1cx0A 95 2.75e+01 1urnA d.58.7.1 39158 1nhs 447 2.76e+01 1nhp c.3.1.5 30555 c.3.1.5 30556 d.87.1.1 40199 1s72X 92 2.78e+01 1ag6 99 2.78e+01 1plc b.6.1.1 22857 1oywA 523 2.80e+01 unknown_sccs -270 c.37.1.19 -7209 c.37.1.19 -7210 1eg5A 384 2.83e+01 1ecxA c.67.1.3 34429 1q8uA 350 2.83e+01 d.144.1.7 -11331 2fivA 116 2.86e+01 1fmb b.50.1.1 26766 1cxqA 162 2.88e+01 1cxqA c.55.3.2 33621 1whtB 153 2.88e+01 1whtB 1b93B 152 2.89e+01 1b93A c.24.1.2 31508 1ia9A 280 2.89e+01 1ia9A d.144.1.5 62113 1iufA 144 2.91e+01 a.4.1.7 71439 a.4.1.7 71440 1mdyA 68 3.00e+01 1mdyA a.38.1.1 17132 1nhp 447 3.05e+01 1nhp c.3.1.5 30549 c.3.1.5 30550 d.87.1.1 40196 1nzhA 282 3.05e+01 d.151.1.2 -11398 2plt 98 3.09e+01 1plc b.6.1.1 22862 1d06A 130 3.09e+01 1drmA d.110.3.2 40906 1lkyA 77 3.10e+01 a.60.1.1 73985 1mn3A 54 3.10e+01 a.5.2.4 85024 1qovH 260 3.13e+01 6prcH b.41.1.1 25464 f.23.10.1 43457 1qamA 244 3.14e+01 2ercA c.66.1.24 34220 1j0wA 103 3.15e+01 b.55.1.2 -4364 1obwA 175 3.17e+01 2prd b.40.5.1 25416 1s722 50 3.31e+01 1hqsA 423 3.32e+01 1iso c.77.1.1 61154 1i0dA 332 3.36e+01 1pscA c.1.9.3 61487 1g8sA 230 3.37e+01 c.66.1.3 -8047 1cjsA 219 3.38e+01 1cjsA e.24.1.1 43354 1f9zA 135 3.39e+01 1qipA d.32.1.1 38484 1qc9A 276 3.40e+01 1ckqA c.52.1.1 33235 1uwvA 433 3.42e+01 unknown_sccs -3950 unknown_sccs -8107 1dckA 126 3.45e+01 1dbwA c.23.1.1 31097 1top 162 3.49e+01 1ncx a.39.1.5 17223 1imvA 398 3.49e+01 e.1.1.1 62591 1dpe 507 3.51e+01 1dpe c.94.1.1 35799 1i40A 175 3.54e+01 b.40.5.1 66024 1garA 212 3.58e+01 2gar c.65.1.1 34162 1jj2W 91 3.58e+01 1ffkU d.29.1.1 63108 16pk 415 3.60e+01 16pk c.86.1.1 35454 1lfpA 249 3.61e+01 e.39.1.1 73885 1eywA 331 3.62e+01 1pscA c.1.9.3 29057 1i1qB 192 3.70e+01 1qdlB c.23.16.1 61544 2ts1 419 3.71e+01 2ts1 c.26.1.1 31564 1jkxA 212 3.72e+01 c.65.1.1 66813 1s29A 92 3.74e+01 unknown_sccs -315 1pwxA 254 3.75e+01 c.2.1.2 -5858 1fezA 256 3.78e+01 1fezA c.108.1.3 43343 1eo1A 124 3.78e+01 1eo1A c.55.5.1 33739 1upaA 573 3.80e+01 c.31.1.3 -6745 c.36.1.5 -6903 c.36.1.9 -6943 1g5qA 181 3.81e+01 1g5qA c.34.1.1 60288 1gox 370 3.82e+01 1gox c.1.4.1 28607 1cw0A 155 3.82e+01 1vsrA c.52.1.15 33333 1whsB 153 3.84e+01 1whtB 1mjhB 162 3.86e+01 1mjhA c.26.2.4 31640 1kbqA 273 3.87e+01 c.23.5.3 68391 1dtyA 429 3.89e+01 1dtyA c.67.1.4 34495 1k5oA 86 3.89e+01 a.165.1.1 77269 2irfG 113 3.90e+01 2irfG a.4.5.23 16185 1is8K 84 3.91e+01 d.205.1.1 66331 1s0aA 429 3.92e+01 c.67.1.4 -8201 1jyeA 349 3.94e+01 c.93.1.1 67455 1a5r 103 3.95e+01 1a5r d.15.1.1 37597 1icrA 217 3.96e+01 1vfrA d.90.1.1 62274 1fbnA 230 3.97e+01 1fbnA c.66.1.3 34181 2prd 174 3.98e+01 2prd b.40.5.1 25435