# List of top-scoring protein chains for t04-100-30-str2 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 1ucsA 64 2.02e-07 b.85.1.1 88466 1hg7A 66 1.47e-06 1msi b.85.1.1 28280 1lfaA 187 5.41e-02 1ido c.62.1.1 34122 1mjnA 179 8.22e-02 c.62.1.1 79210 1jhgA 101 2.74e-01 1jhgA a.4.12.1 19009 1uurA 473 6.98e-01 a.47.1.1 -968 b.2.5.5 -2904 d.93.1.1 -10632 1ml9A 302 7.54e-01 b.85.7.1 79282 1jhfA 202 7.85e-01 a.4.5.2 63057 b.87.1.1 63058 1innA 166 8.03e-01 1j98A d.185.1.2 62608 1vjeA 166 8.21e-01 d.185.1.2 -10261 1kay 381 8.74e-01 1ba1 c.55.1.1 33385 c.55.1.1 33386 1pcfA 66 1.00e+00 1pcfA d.18.1.1 38142 1ex1A 605 1.08e+00 1ex1A c.1.8.7 29013 c.23.11.1 31347 1giqA 413 1.10e+00 d.166.1.1 76224 d.166.1.1 76225 1go4A 205 1.23e+00 d.135.1.1 70292 1o0xA 262 1.34e+00 d.127.1.1 80755 1f4lA 551 1.49e+00 1qqtA a.27.1.1 59648 c.26.1.1 59649 g.41.1.1 59650 1pfvA 551 1.50e+00 a.27.1.1 -727 c.26.1.1 -6603 g.41.1.1 -12765 1k94A 165 1.54e+00 a.39.1.8 68333 1ks9A 291 1.81e+00 a.100.1.7 68857 c.2.1.6 68858 1fc6A 388 1.83e+00 1fc6A b.36.1.3 64738 c.14.1.2 64739 1mf7A 194 1.85e+00 c.62.1.1 84937 1mgtA 174 1.94e+00 1mgtA a.4.2.1 16078 c.55.7.1 33753 1n9lA 109 1.95e+00 d.110.3.6 85468 1qz5A 375 1.96e+00 c.55.1.1 -7590 c.55.1.1 -7591 1bo4A 168 2.10e+00 1bo4A d.108.1.1 40798 2sas 185 2.45e+00 2sas a.39.1.5 17258 1emvB 134 2.71e+00 1bxiB d.4.1.1 37135 1dik 874 2.76e+00 1dik c.1.12.2 29304 c.8.1.1 30702 d.142.1.5 41572 1l6pA 125 2.79e+00 b.1.17.1 73626 1f46A 140 2.89e+00 1f46A d.129.4.1 59643 1bupA 386 3.06e+00 1ba1 c.55.1.1 33377 c.55.1.1 33378 1j6zA 376 3.11e+00 1yagA c.55.1.1 62667 c.55.1.1 62668 1fr2B 134 3.27e+00 d.4.1.1 83257 1rqlA 267 3.29e+00 c.108.1.3 -6814 1jqlB 140 3.32e+00 c.37.1.20 63234 1top 162 3.33e+00 1ncx a.39.1.5 17223 1ido 192 3.37e+00 1ido c.62.1.1 34139 1d4xA 375 3.42e+00 1yagA c.55.1.1 59107 c.55.1.1 59108 1i50F 155 3.42e+00 d.78.1.2 61760 1pne 140 3.73e+00 1pne d.110.1.1 40866 1js8A 394 3.87e+00 a.86.1.1 67219 b.112.1.1 67220 1jf8A 131 3.97e+00 c.44.1.1 66621 1l7dA 384 4.03e+00 c.2.1.4 77774 c.23.12.2 77775 1omrA 201 4.12e+00 a.39.1.5 -854 1o5oA 221 4.15e+00 c.61.1.1 -7954 1lfb 99 4.19e+00 1lfb a.4.1.1 15989 1iw7C 1119 4.41e+00 e.29.1.1 71474 1k2yX 463 4.56e+00 c.84.1.1 68063 c.84.1.1 68064 c.84.1.1 68065 d.129.2.1 68066 1p0hA 318 4.94e+00 d.108.1.1 -10802 1up8A 598 5.07e+00 a.111.1.2 -1480 1f4qA 165 5.21e+00 1alvA a.39.1.8 17360 1aym3 238 5.27e+00 1aym3 1f8gA 384 5.28e+00 1sayA c.2.1.4 59695 c.23.12.2 59696 1qwiA 143 5.44e+00 d.227.1.1 -11183 2mcm 112 5.44e+00 2mcm b.1.7.1 22207 2pviA 157 5.58e+00 3pviA c.52.1.6 33302 1fjjA 159 5.92e+00 1fjjA b.17.1.2 59852 3pviA 157 6.37e+00 3pviA c.52.1.6 33300 1v1aA 309 6.42e+00 c.72.1.1 -8400 1tk1A 260 6.46e+00 1eg3A 261 6.68e+00 1eg3A a.39.1.7 17376 a.39.1.7 17377 b.72.1.1 27805 1plq 258 6.72e+00 1plq d.131.1.2 41388 d.131.1.2 41389 1go3F 107 7.72e+00 a.60.8.2 65407 2fhi 147 7.91e+00 1fit d.13.1.1 37505 1nq7A 244 8.01e+00 a.123.1.1 -1682 1n83A 270 8.05e+00 a.123.1.1 80276 1hkkA 364 8.08e+00 c.1.8.5 -5384 d.26.3.1 -9506 1q4rA 112 8.21e+00 d.58.4.4 -9943 1tvlA 454 8.23e+00 1fezA 256 8.23e+00 1fezA c.108.1.3 43343 1kyqA 274 8.25e+00 c.2.1.11 73281 e.37.1.1 73282 1vi2A 300 8.47e+00 c.2.1.7 -5960 c.58.1.5 -6366 1fthA 122 9.07e+00 d.150.1.2 60028 1jg1A 235 9.38e+00 c.66.1.7 66661 1avsA 90 9.41e+00 1cll a.39.1.5 17226 1umdA 367 9.78e+00 c.36.1.11 -6969 1tqyA 424 1.01e+01 1pc6A 146 1.05e+01 unknown_sccs -11739 1dpgA 485 1.06e+01 1dpgA c.2.1.3 30074 d.81.1.5 39989 1fit 147 1.07e+01 1fit d.13.1.1 37499 1kliL 69 1.07e+01 g.3.11.1 77436 1f9yA 158 1.07e+01 d.58.30.1 83249 2sak 121 1.09e+01 2sak d.15.5.1 37711 1ivnA 190 1.11e+01 c.23.10.5 83719 1rcqA 357 1.11e+01 1a7j 290 1.11e+01 1a7j c.37.1.6 31952 1exrA 148 1.13e+01 1cll a.39.1.5 17299 1fuxA 166 1.13e+01 1fjjA b.17.1.2 60034 1r13A 148 1.15e+01 d.169.1.1 -11646 h.1.1.1 -12895 1jnuA 104 1.18e+01 d.110.3.6 71762 1ujnA 348 1.20e+01 e.22.1.1 -11998 1rec 201 1.21e+01 1rec a.39.1.5 17326 1eu1A 780 1.25e+01 1dmr b.52.2.2 26903 c.81.1.1 35311 1kqfA 1015 1.27e+01 b.52.2.2 72871 c.81.1.1 72872 1ul7A 102 1.28e+01 unknown_sccs -11020 1m33A 258 1.28e+01 c.69.1.26 78514 1efvA 315 1.28e+01 1efvA c.26.2.3 31633 c.31.1.2 31728 1v6sA 390 1.29e+01 c.86.1.1 -8567 1ggzA 148 1.34e+01 a.39.1.5 70176 1phk 298 1.34e+01 1cdkA d.144.1.7 41635 1rwyA 109 1.34e+01 a.39.1.4 -825 1b4pA 217 1.37e+01 a.45.1.1 83158 c.47.1.5 83159 1oaoA 674 1.39e+01 e.26.1.2 86744 1qgeE 97 1.41e+01 1cvl 1mwvA 714 1.43e+01 a.93.1.3 85161 a.93.1.3 85162 2btfA 375 1.44e+01 1yagA c.55.1.1 33429 c.55.1.1 33430 1r0wA 286 1.44e+01 c.37.1.12 -7158 1j9bA 141 1.44e+01 c.47.1.12 66459 1amx 180 1.44e+01 1amx b.2.3.1 22410 1p5dX 463 1.45e+01 c.84.1.1 -8554 c.84.1.1 -8555 c.84.1.1 -8556 d.129.2.1 -11029 1jltA 122 1.46e+01 a.133.1.2 66867 1j08A 226 1.47e+01 c.47.1.2 83855 c.47.1.2 83856 1aqb 183 1.50e+01 1aqb b.60.1.1 27084 1wdcB 156 1.51e+01 1wdcB a.39.1.5 17302 1mu5A 471 1.54e+01 a.156.1.3 79472 d.14.1.3 79473 d.122.1.2 79474 1p65A 73 1.56e+01 unknown_sccs -10331 1s4nA 348 1.59e+01 unknown_sccs -8262 1lj5A 379 1.59e+01 e.1.1.1 73928 1a7cA 379 1.59e+01 1sek e.1.1.1 42660 1eqoA 158 1.62e+01 1hka 1mai 131 1.66e+01 1mai b.55.1.1 26951 1ew6A 137 1.69e+01 1ewaA a.1.1.2 15637 1ee8A 266 1.70e+01 1ee8A a.156.1.2 75823 b.113.1.1 75824 g.39.1.8 75825 1hdhA 536 1.72e+01 c.76.1.2 65805 1nzyA 269 1.73e+01 1nzyA c.14.1.3 30903 1n2fA 142 1.74e+01 d.227.1.1 79853 1q40B 219 1.78e+01 d.17.4.2 -9287 1h7eA 245 1.83e+01 c.68.1.13 60717 1yrgA 385 1.83e+01 1yrgA c.10.1.2 30854 1dzfA 215 1.83e+01 1dzfA c.52.3.1 33344 d.78.1.1 39753 1o22A 170 1.85e+01 d.238.1.1 86557 1vns 609 1.86e+01 1vns a.111.1.3 19061 1ajsA 412 1.86e+01 1ajsA c.67.1.1 34276 1r62A 160 1.86e+01 6gsvA 217 1.92e+01 1b8xA a.45.1.1 17633 c.47.1.5 32925 1l3aA 228 1.92e+01 d.18.1.2 73531 1ni4A 365 1.94e+01 c.36.1.7 85728 1eb7A 323 1.96e+01 1eb7A a.3.1.5 59404 a.3.1.5 59405 1uouA 474 1.96e+01 a.46.2.1 -951 c.27.1.1 -6642 d.41.3.1 -9715 1udzA 182 1.97e+01 b.51.1.1 -4307 1oahA 519 1.97e+01 a.138.1.3 86736 1vpi 122 1.97e+01 1poa a.133.1.2 19559 1gvoA 364 1.98e+01 c.1.4.1 76357 1vyrA 364 1.98e+01 1rl2A 137 1.98e+01 1rl2A b.34.5.3 24610 b.40.4.5 25342 1g4yR 148 1.99e+01 1cll a.39.1.5 60252 1h61A 364 2.00e+01 1oyc c.1.4.1 60657 1bd0A 388 2.00e+01 1bd0A b.49.2.2 26480 c.1.6.1 28642 1s8iA 121 2.02e+01 a.133.1.2 -1968 1v4xB 146 2.04e+01 1ow4A 129 2.06e+01 a.39.2.1 -876 1cjwA 166 2.08e+01 1cjwA d.108.1.1 40818 1ugpB 226 2.09e+01 1ogwA 76 2.09e+01 d.15.1.1 87001 1ubi 76 2.10e+01 1ubi d.15.1.1 37584 1l1oC 181 2.14e+01 b.40.4.3 73480 2cmd 312 2.14e+01 2cmd c.2.1.5 30135 d.162.1.1 42102 1ab4 477 2.14e+01 1ab4 e.11.1.1 43251 1vypX 364 2.17e+01 1cl8A 276 2.19e+01 1ckqA c.52.1.1 33230 1nbfD 76 2.20e+01 d.15.1.1 80390 1o08A 221 2.22e+01 c.108.1.6 86525 1a76 326 2.25e+01 1a76 a.60.7.1 18091 c.120.1.2 33361 1t0bA 252 2.26e+01 1ni9A 338 2.29e+01 e.7.1.2 85739 1k8tA 510 2.30e+01 e.41.1.1 68316 1nzoA 363 2.32e+01 b.105.1.1 -2933 e.3.1.1 -11784 1kblA 873 2.38e+01 c.1.12.2 68384 c.8.1.1 68385 d.142.1.5 68386 1lvaA 258 2.38e+01 a.4.5.35 74276 a.4.5.35 74277 a.4.5.35 74278 a.4.5.35 74279 1f1xA 322 2.39e+01 d.32.1.3 83208 d.32.1.3 83209 1c1dA 355 2.39e+01 1bw9A c.2.1.7 30270 c.58.1.1 33918 1s9rA 410 2.40e+01 unknown_sccs -10989 1vybA 238 2.41e+01 1f1uA 323 2.41e+01 d.32.1.3 83200 d.32.1.3 83201 1o91A 178 2.42e+01 b.22.1.1 -3282 1rwtA 232 2.43e+01 unknown_sccs -12345 1es5A 262 2.43e+01 1skf e.3.1.1 42679 1h5bA 113 2.50e+01 1tvdA b.1.1.1 60638 1ppa 121 2.51e+01 1poa a.133.1.2 19550 1twdA 256 2.57e+01 1fznD 123 2.59e+01 1fznD 1ed1A 135 2.59e+01 1hiwA a.61.1.1 18130 1rro 108 2.60e+01 1a75A a.39.1.4 17195 1jzuA 157 2.61e+01 b.60.1.1 84271 1e6yA 569 2.62e+01 1mroA a.89.1.1 18529 d.58.31.2 39447 1n3jA 119 2.68e+01 b.85.7.2 79963 1n3yA 198 2.73e+01 c.62.1.1 79976 1mqvA 125 2.78e+01 a.24.3.2 79415 1gkmA 509 2.78e+01 a.127.1.2 70228 1csn 298 2.80e+01 1csn d.144.1.7 41664 1ireB 228 2.80e+01 b.34.4.4 76770 1ax4A 467 2.81e+01 1ax4A c.67.1.2 34391 1nrzA 164 2.82e+01 c.38.1.1 86131 1v8qA 85 2.83e+01 1g6hA 257 2.84e+01 1gajA c.37.1.12 60318 1jhjA 171 2.86e+01 b.18.1.9 66714 4cpv 109 2.86e+01 1a75A a.39.1.4 17198 1ekjA 221 2.87e+01 1ekjB c.53.2.1 33364 1m40A 263 2.88e+01 e.3.1.1 74437 1dgaA 375 2.89e+01 1yagA 1hl9A 449 2.92e+01 unknown_sccs -4694 unknown_sccs -5365 1ile 821 2.96e+01 1ile a.27.1.1 16924 b.51.1.1 26889 c.26.1.1 31591 1h1nA 305 2.98e+01 c.1.8.3 70855 1r1uA 106 3.02e+01 1l1zA 274 3.02e+01 a.156.1.2 75911 b.113.1.1 75912 g.39.1.8 75913 1ermA 263 3.06e+01 1btl e.3.1.1 42690 1ithA 141 3.12e+01 1ithA a.1.1.2 15623 1spgA 144 3.14e+01 1abwA a.1.1.2 15409 1hn0A 1021 3.15e+01 a.102.3.2 83616 b.18.1.17 83617 b.24.1.1 83618 b.30.5.2 83619 1psrA 100 3.18e+01 1psrA a.39.1.2 17180 1a7w 69 3.19e+01 1a7w a.22.1.2 16477 1nj4A 363 3.19e+01 b.105.1.1 80545 e.3.1.1 80546 1btl 263 3.20e+01 1btl e.3.1.1 42691 19hcA 292 3.21e+01 19hcA a.138.1.1 19668 1g24A 211 3.23e+01 1g24A d.166.1.1 42270 1ur5A 309 3.31e+01 c.2.1.5 -5910 d.162.1.1 -11477 1i8nA 126 3.31e+01 1i8nA g.10.1.2 61976 1dkzA 219 3.31e+01 1dkzA unknown_sccs -445 unknown_sccs -3060 1xxaA 78 3.32e+01 1xxaA d.74.2.1 39700 1mkeA 152 3.36e+01 b.55.1.4 79231 1c52 131 3.37e+01 1c52 a.3.1.1 15810 1s3iA 310 3.37e+01 b.46.1.1 -4111 c.65.1.1 -8042 1s72V 71 3.40e+01 1jj2U 70 3.40e+01 1ffkS a.2.2.1 63106 1b8fA 509 3.40e+01 1b8fA a.127.1.2 19434 1io2A 213 3.41e+01 1ekeA c.55.3.1 62612 1p4wA 99 3.42e+01 a.4.6.2 87783 1rl6A 177 3.44e+01 1rl6A d.141.1.1 41473 d.141.1.1 41474 1kk8B 139 3.46e+01 a.39.1.5 77430 1hp5A 512 3.52e+01 1hp4A c.1.8.6 61113 d.92.2.1 61114 1o0pA 104 3.55e+01 d.58.7.1 86535 1isiA 265 3.56e+01 e.4.1.1 71394 1jakA 512 3.56e+01 c.1.8.6 66472 d.92.2.1 66473 1o6vA 466 3.57e+01 b.1.18.15 81099 c.10.2.1 81100 1rfmA 344 3.58e+01 c.122.1.1 -8032 1jx4A 352 3.59e+01 unknown_sccs -10188 unknown_sccs -11898 7odcA 424 3.63e+01 7odcA b.49.2.3 26488 c.1.6.1 28650 1wdcC 156 3.63e+01 1wdcC a.39.1.5 17317 1cvl 319 3.69e+01 1cvl c.69.1.18 34786 1d8hA 311 3.74e+01 1d8iA d.63.1.1 39544 1g291 372 3.75e+01 1g291 1kfwA 435 3.78e+01 c.1.8.5 77376 d.26.3.1 77377 1v4xA 144 3.79e+01 1seiA 130 3.79e+01 1seiA d.140.1.1 41463 1v5xA 203 3.83e+01 c.1.2.4 -5169 1me4A 215 3.83e+01 d.3.1.1 79023 1h2wA 710 3.85e+01 b.69.7.1 76596 c.69.1.4 76597 1qfmA 710 3.85e+01 1qfmA b.69.7.1 27673 c.69.1.4 34641 1oeyJ 107 3.86e+01 d.15.2.2 -9168 1f2aA 215 3.86e+01 1cs8A d.3.1.1 37040 1ayl 541 3.88e+01 1ayl c.91.1.1 64718 c.109.1.1 64719 1otjA 283 3.89e+01 b.82.2.5 -4893 1jdpA 441 3.93e+01 c.93.1.1 62906 1jsxA 207 3.94e+01 c.66.1.20 71846 1ox0A 430 3.95e+01 c.95.1.1 87495 c.95.1.1 87496 5pal 109 3.97e+01 1a75A a.39.1.4 17215