# List of top-scoring protein chains for t2k-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 1h1iB 350 2.76e-03 b.82.1.5 76470 1h1iC 350 4.69e-03 b.82.1.5 76471 1h1iD 350 9.51e-03 b.82.1.5 76472 1juhA 350 1.07e-02 b.82.1.5 71884 1plzA 189 3.31e-02 b.82.1.7 88160 1qxrA 189 4.24e-02 1j58A 385 5.28e-02 b.82.1.2 71531 1cawB 184 6.86e-02 1caxB b.82.1.2 28113 1amj 754 1.41e-01 1amj c.8.2.1 30725 c.83.1.1 35401 8acn 754 1.42e-01 1amj c.8.2.1 30724 c.83.1.1 35400 6acn 754 1.48e-01 1amj c.8.2.1 30721 c.83.1.1 35397 1c96A 753 1.73e-01 1amj c.8.2.1 30727 c.83.1.1 35403 7acn 754 1.99e-01 1amj c.8.2.1 30717 c.83.1.1 35393 1b0jA 754 2.37e-01 1amj c.8.2.1 30719 c.83.1.1 35395 1fxzA 476 3.73e-01 b.82.1.2 65059 b.82.1.2 65060 2pia 321 3.80e-01 2pia b.43.4.2 25663 c.25.1.2 31553 d.15.4.2 37704 1nnjA 271 5.56e-01 a.156.1.2 80669 b.113.1.1 80670 g.39.1.8 80671 1pjjA 271 5.65e-01 1cauB 184 5.68e-01 1caxB b.82.1.2 28103 1miuA 738 6.00e-01 a.170.1.1 79153 a.171.1.1 79154 b.40.4.3 79155 b.40.4.3 79156 b.40.4.3 79157 1nxmA 197 7.02e-01 b.82.1.1 86385 1caxB 184 8.57e-01 1caxB b.82.1.2 28105 1oo2A 119 9.89e-01 1krhA 338 1.19e+00 b.43.4.2 72891 c.25.1.2 72892 d.15.4.2 72893 1iscA 192 1.45e+00 1avmA a.2.11.1 15733 d.44.1.1 38726 1j1tA 233 1.52e+00 1isaA 192 1.53e+00 1avmA a.2.11.1 15731 d.44.1.1 38724 1gvmA 136 1.58e+00 b.109.1.1 70612 1jlxA 304 1.58e+00 1jlyA b.42.3.1 25583 b.42.3.1 25584 2phlA 397 1.64e+00 1dgwA b.82.1.2 28082 b.82.1.2 28083 1fw9A 164 1.65e+00 1fw9A d.190.1.1 60059 1cur 155 1.67e+00 1rcy b.6.1.1 23021 1fpzA 212 1.71e+00 1fpzA c.45.1.1 59976 1e1aA 314 1.80e+00 1e1aA b.68.6.1 59155 1m8uA 173 1.85e+00 1pjxA 314 1.95e+00 1fzdA 201 2.21e+00 3fib d.171.1.1 42484 1b9mA 265 2.23e+00 1b9mA a.4.5.8 16118 b.40.6.2 58938 b.40.6.2 58939 1o59A 355 2.29e+00 1hcxA 127 2.37e+00 b.109.1.1 65800 1h10A 125 2.55e+00 b.55.1.1 83446 2cgpA 210 2.76e+00 2cgpA a.4.5.4 16102 b.82.3.2 28141 1qqp2 218 2.85e+00 1qqp2 1nkr 201 2.91e+00 1nkr b.1.1.4 21799 b.1.1.4 21800 1aboA 62 3.66e+00 1bbzA b.34.2.1 24474 1itg 166 3.66e+00 1b9dA c.55.3.2 33661 1apf 49 3.71e+00 1ahl g.9.1.1 44602 1lox 662 3.94e+00 1lox a.119.1.2 19238 b.12.1.1 23638 1od5A 492 4.02e+00 b.82.1.2 86832 b.82.1.2 86833 1h4rA 314 4.12e+00 a.11.2.1 65616 b.55.1.5 65617 d.15.1.4 65618 1rcy 151 4.13e+00 1rcy b.6.1.1 23018 1qhdA 398 4.19e+00 1qhdA a.115.1.2 63324 b.19.1.1 63325 1bbzA 58 4.38e+00 1bbzA b.34.2.1 24477 1a3z 155 4.43e+00 1rcy b.6.1.1 23019 1bbzE 58 4.44e+00 1bbzA b.34.2.1 24479 1ep0A 185 4.49e+00 1dzrA b.82.1.1 28080 1mu5A 471 4.56e+00 a.156.1.3 79472 d.14.1.3 79473 d.122.1.2 79474 1exqA 154 4.78e+00 1b9dA c.55.3.2 33646 1hw5A 210 4.84e+00 2cgpA a.4.5.4 16098 b.82.3.2 28137 1f7dA 136 5.03e+00 1dun b.85.4.1 28353 1hyvA 166 5.23e+00 1b9dA c.55.3.2 61424 1jegA 83 5.29e+00 b.34.2.1 66610 1b9dA 163 5.30e+00 1b9dA c.55.3.2 33649 1e30A 155 5.47e+00 1rcy b.6.1.1 23016 1jlyA 304 5.74e+00 1jlyA b.42.3.1 25587 b.42.3.1 25588 1dlc 584 5.76e+00 1ciy b.18.1.3 23719 b.77.2.1 27976 f.1.3.1 43391 1gpr 162 5.80e+00 1gpr b.84.3.1 28267 2itg 163 6.11e+00 1b9dA c.55.3.2 33669 1bl3A 160 6.20e+00 1b9dA c.55.3.2 33655 1jofA 365 6.52e+00 b.69.10.1 71775 1bu8A 452 6.86e+00 1gpl b.12.1.2 23647 c.69.1.19 34795 1c8uA 285 6.97e+00 1c8uA d.38.1.3 38547 d.38.1.3 38548 1c8zA 265 7.08e+00 1c8zA d.23.1.1 38375 1bag 425 7.24e+00 1bag b.71.1.1 27720 c.1.8.1 28707 8prkA 287 7.38e+00 1wgjA b.40.5.1 25395 1ckmA 330 7.47e+00 1ckmA b.40.4.6 25358 d.142.2.3 41585 1b4rA 80 7.84e+00 1b4rA b.1.3.1 22072 1dmaA 214 8.37e+00 1aerA d.166.1.1 42251 1aerA 205 8.86e+00 1aerA d.166.1.1 42249 1jjuA 489 9.11e+00 a.3.1.7 66774 a.3.1.7 66775 b.1.18.14 66776 b.1.18.14 66777 b.61.4.1 66778 1g1sA 162 9.14e+00 d.169.1.1 65100 g.3.11.1 65101 1e79A 510 9.49e+00 1skyB a.69.1.1 18269 b.49.1.1 26434 c.37.1.11 32314 1fxkC 133 9.49e+00 1fxkC a.2.5.1 15702 1g38A 393 9.62e+00 2admA c.66.1.27 60235 1bkb 136 9.63e+00 1bkb b.34.5.2 24609 b.40.4.5 25341 1pguA 615 9.98e+00 b.69.4.1 88069 b.69.4.1 88070 1apo 42 1.05e+01 1edmB g.3.11.1 44240 1mngA 203 1.09e+01 1avmA a.2.11.1 15776 d.44.1.1 38701 1cskA 71 1.12e+01 1ckaA b.34.2.1 24513 1elpA 173 1.12e+01 1amm b.11.1.1 23596 b.11.1.1 23597 1mxgA 435 1.14e+01 b.71.1.1 85193 c.1.8.1 85194 1dgrM 93 1.16e+01 1caxB b.82.1.2 28101 1jdc 429 1.18e+01 1jdc b.71.1.1 27789 c.1.8.1 28776 1ogsA 497 1.18e+01 b.71.1.2 86997 c.1.8.3 86998 1uesA 191 1.22e+01 1h9jA 145 1.23e+01 1h9jA b.40.6.2 60829 b.40.6.2 60830 1kb0A 677 1.24e+01 a.3.1.6 68378 b.70.1.1 68379 1pz7A 204 1.26e+01 1e43A 483 1.26e+01 1bli b.71.1.1 59217 c.1.8.1 59218 1aqjA 421 1.27e+01 2admA c.66.1.27 34242 1idaA 99 1.29e+01 1fmb b.50.1.1 26715 1cdi 179 1.30e+01 1cdy b.1.1.1 19727 b.1.1.3 21666 2gpr 154 1.31e+01 1gpr b.84.3.1 28269 1ofnA 205 1.31e+01 1ahl 49 1.33e+01 1ahl g.9.1.1 44601 3pvaA 335 1.36e+01 3pvaA d.153.1.3 41854 1is2A 661 1.36e+01 a.29.3.2 71382 a.29.3.2 71383 e.6.1.2 71384 1qk3A 233 1.37e+01 1qk3A c.61.1.1 34031 1j9qA 341 1.38e+01 1nif b.6.1.3 62765 b.6.1.3 62766 2eifA 136 1.38e+01 1bkb b.34.5.2 24607 b.40.4.5 25339 1f86A 115 1.40e+01 1etb1 b.3.4.1 59689 1erjA 393 1.40e+01 1erjA b.69.4.1 27660 1ibyA 112 1.41e+01 1ibzA b.6.1.4 62233 1ibzA 112 1.41e+01 1ibzA b.6.1.4 62237 1i4uA 181 1.42e+01 b.60.1.1 61732 1dgrW 93 1.42e+01 1caxB 1khiA 176 1.45e+01 b.34.5.2 77408 b.40.4.5 77409 1qbiA 454 1.47e+01 1c9uA b.68.2.1 27619 1fhoA 119 1.49e+01 1fhoA b.55.1.1 26982 1a3k 137 1.50e+01 1a3k b.29.1.3 24218 1e9gA 286 1.50e+01 1wgjA b.40.5.1 59393 1bmfA 510 1.54e+01 1skyB a.69.1.1 18281 b.49.1.1 26446 c.37.1.11 32326 1r4pA 297 1.55e+01 1nif 340 1.57e+01 1nif b.6.1.3 23048 b.6.1.3 23049 1bix 287 1.60e+01 1bix d.151.1.1 41781 1nrhX 472 1.62e+01 1ksiB 642 1.63e+01 1ksiB b.30.2.1 24409 d.17.2.1 38045 d.17.2.1 38046 1p32C 209 1.64e+01 1p32A d.25.1.1 38381 1eta1 127 1.67e+01 1etb1 1g4mA 393 1.71e+01 b.1.18.11 65143 b.1.18.11 65144 2cavA 445 1.74e+01 1dgwA b.82.1.2 28094 b.82.1.2 28095 1f41A 127 1.80e+01 1etb1 b.3.4.1 22539 1oi6A 205 1.80e+01 1hrnA 337 1.81e+01 1smrA b.50.1.2 26869 1k07A 263 1.81e+01 d.157.1.1 77218 1h91A 180 1.82e+01 b.60.1.1 60805 1itwA 741 1.83e+01 c.77.1.2 76793 1qnnA 191 1.84e+01 1avmA a.2.11.1 15792 d.44.1.1 38755 1hdhA 536 1.85e+01 c.76.1.2 65805 1hn0A 1021 1.85e+01 a.102.3.2 83616 b.18.1.17 83617 b.24.1.1 83618 b.30.5.2 83619 1as8A 343 1.86e+01 1nif b.6.1.3 23074 b.6.1.3 23075 1lr5A 163 1.88e+01 b.82.1.2 74215 2pabA 127 1.88e+01 1etb1 b.3.4.1 22597 1etb1 127 1.91e+01 1etb1 1mpyA 307 1.94e+01 1mpyA d.32.1.3 38508 d.32.1.3 38509 1wgjA 286 1.98e+01 1wgjA b.40.5.1 25397 1h9sA 140 1.99e+01 1b9mA b.40.6.2 60843 b.40.6.2 60844 1ca4A 168 2.01e+01 1d0aB b.8.1.1 23238 h.1.2.1 45445 1jmcA 246 2.01e+01 1jmcA b.40.4.3 25300 b.40.4.3 25301 1kzkA 99 2.03e+01 b.50.1.1 73371 1h8eA 510 2.04e+01 1skyB a.69.1.1 60738 b.49.1.1 60739 c.37.1.11 60740 1hd7A 318 2.04e+01 1bix d.151.1.1 41780 1c3oB 382 2.07e+01 1c3oB c.8.3.1 30744 c.23.16.1 31421 1j0hA 588 2.08e+01 b.1.18.2 77027 b.71.1.1 77028 c.1.8.1 77029 1dfnA 30 2.11e+01 g.9.1.1 44570 1fi4A 416 2.11e+01 1fi4A d.14.1.5 59847 d.58.26.2 59848 2pvaA 345 2.14e+01 3pvaA d.153.1.3 41850 1uxzA 131 2.14e+01 1kk1A 410 2.14e+01 b.43.3.1 72634 b.44.1.1 72635 c.37.1.8 72636 2izgB 123 2.15e+01 1swuA b.61.1.1 27236 1d0aB 168 2.16e+01 1d0aB b.8.1.1 23224 h.1.2.1 45431 1cruA 454 2.18e+01 1c9uA b.68.2.1 27617 1o8uA 257 2.18e+01 c.14.1.3 81194 1difA 99 2.22e+01 1fmb b.50.1.1 26503 1czyA 168 2.23e+01 1d0aB b.8.1.1 23220 h.1.2.1 45427 1g9mC 185 2.26e+01 1cdy b.1.1.1 19721 b.1.1.3 21660 2admA 421 2.26e+01 2admA c.66.1.27 34238 1neu 124 2.26e+01 1neu b.1.1.1 19704 1q1fA 151 2.28e+01 1a78A 134 2.28e+01 1c1lA b.29.1.3 24212 1ollA 188 2.29e+01 1a6q 382 2.30e+01 1a6q a.159.1.1 75801 d.219.1.1 75802 1ttbA 127 2.31e+01 1etb1 b.3.4.1 22543 1gutA 68 2.32e+01 b.40.6.1 65576 1iazA 179 2.33e+01 1iazA b.97.1.1 62131 8prkB 287 2.36e+01 1wgjA b.40.5.1 25396 1e9gB 286 2.36e+01 1wgjA b.40.5.1 59394 1tfpA 130 2.40e+01 1etb1 b.3.4.1 22623 1hkvA 453 2.40e+01 b.49.2.3 83559 c.1.6.1 83560 1k9jA 139 2.40e+01 d.169.1.1 68353 1nt0A 286 2.44e+01 b.23.1.1 86143 b.23.1.1 86144 g.3.11.1 86145 1qksA 567 2.44e+01 1qksA a.3.1.2 15951 b.70.2.1 27710 1aoqA 567 2.46e+01 1qksA a.3.1.2 15934 b.70.2.1 27692 1czyC 168 2.46e+01 1d0aB b.8.1.1 23222 h.1.2.1 45429 1pm3A 78 2.50e+01 1ng4A 390 2.51e+01 c.3.1.2 85666 d.16.1.3 85667 1ca9A 192 2.55e+01 1d0aB b.8.1.1 23244 h.1.2.1 45451 1snc 149 2.58e+01 1snc b.40.1.1 24813 1kyaA 499 2.63e+01 b.6.1.3 73203 b.6.1.3 73204 b.6.1.3 73205 1ju3A 583 2.64e+01 b.18.1.13 67300 c.69.1.21 67301 1smd 496 2.65e+01 1smd b.71.1.1 27768 c.1.8.1 28755 1gv3A 248 2.67e+01 a.2.11.1 70585 d.44.1.1 70586 1ey4A 149 2.67e+01 1snc b.40.1.1 24815 1fna 93 2.67e+01 1fnf b.1.2.1 21971 1ld8B 437 2.69e+01 a.102.4.3 73839 1gjwA 637 2.69e+01 b.71.1.1 60582 c.1.8.1 60583 1uvqA 197 2.70e+01 1jb0D 138 2.73e+01 1jb0D d.187.1.1 62823 1azeA 56 2.76e+01 b.34.2.1 24536 1q02A 52 2.80e+01 2dnjA 260 2.82e+01 3dni d.151.1.1 41790 1et7A 341 2.83e+01 1nif b.6.1.3 23070 b.6.1.3 23071 1nh0A 99 2.85e+01 1umhA 184 2.86e+01 1asyA 490 2.87e+01 1b8aA b.40.4.1 25242 d.104.1.1 40763 1quqA 129 2.94e+01 1quqA b.40.4.3 25303 1kv9A 668 2.96e+01 a.3.1.6 73056 b.70.1.1 73057 1ri6A 343 2.98e+01 1jyoA 130 3.00e+01 d.198.1.1 67483 1n6eA 1071 3.02e+01 b.36.1.3 80149 b.68.7.1 80150 b.69.9.1 80151 c.14.1.2 80152 1hxs2 272 3.04e+01 1bli 483 3.04e+01 1bli b.71.1.1 27715 c.1.8.1 28702 1dm0A 287 3.06e+01 1dm0A d.165.1.2 42227 1yge 839 3.09e+01 1yge a.119.1.1 19234 b.12.1.1 23634 1i2hA 168 3.13e+01 b.55.1.4 71103 1gjuA 637 3.15e+01 b.71.1.1 60580 c.1.8.1 60581 2bb2 181 3.16e+01 2bb2 b.11.1.1 23604 b.11.1.1 23605 1oygA 447 3.19e+01 1fsb 40 3.21e+01 1fsb g.3.11.1 44283 1rdo1 113 3.23e+01 1rtm1 1tvdA 116 3.24e+01 1tvdA b.1.1.1 20650 1jjuB 337 3.24e+01 b.69.2.2 66779 1ef1A 294 3.27e+01 1ef1A a.11.2.1 16368 b.55.1.5 27003 d.15.1.4 37611 1pbyB 337 3.28e+01 1jgtA 513 3.30e+01 c.26.2.1 66684 d.153.1.1 66685 1jdlA 121 3.30e+01 a.3.1.1 66557 1c9uA 454 3.32e+01 1c9uA b.68.2.1 27623 1vjs 483 3.32e+01 1bli b.71.1.1 27714 c.1.8.1 28701 1cs0B 382 3.34e+01 1c3oB c.8.3.1 30740 c.23.16.1 31417 1aomA 567 3.36e+01 1qksA b.70.2.1 27694 1tgoA 773 3.37e+01 1tgoA c.55.3.5 33721 e.8.1.1 43010 1gppA 237 3.37e+01 b.86.1.2 76262 1ojqA 212 3.38e+01 1fgqA 839 3.38e+01 1yge a.119.1.1 59826 b.12.1.1 59827 1ngzB 220 3.43e+01 b.1.1.1 80502 b.1.1.2 80503 1hx0A 496 3.44e+01 b.71.1.1 61346 c.1.8.1 61347 1rdj1 113 3.44e+01 1rtm1 1h9mA 145 3.48e+01 1h9jA b.40.6.2 60833 b.40.6.2 60834 1awo 62 3.50e+01 1bbzA b.34.2.1 24482 1sty 150 3.54e+01 1snc b.40.1.1 24812 1afb1 154 3.56e+01 1rtm1 1oxsC 353 3.57e+01 b.40.6.3 87519 c.37.1.12 87520 3dni 260 3.57e+01 3dni d.151.1.1 41791 1vavA 222 3.59e+01 1dqsA 393 3.60e+01 1dqsA e.22.1.1 43347 1e42A 258 3.60e+01 1e42A b.1.10.1 22316 d.105.1.1 40792 1oxxK 353 3.61e+01 1ayfB 105 3.61e+01 1ayfA d.15.4.1 37685 1l3yA 41 3.63e+01 g.3.11.6 73558 1crzA 403 3.67e+01 1crzA b.68.4.1 27629 c.51.2.1 33211 1g8tA 245 3.71e+01 1qaeA d.4.1.2 37137 1k1tA 99 3.74e+01 b.50.1.1 71995 1ql0A 241 3.74e+01 1qaeA d.4.1.2 37139 1qaeA 245 3.75e+01 1qaeA d.4.1.2 37141 1smnA 245 3.77e+01 1qaeA d.4.1.2 37143 1cknA 330 3.78e+01 1ckmA b.40.4.6 25360 d.142.2.3 41587 1dazC 99 3.79e+01 1hvc b.50.1.1 26501 1aw8B 91 3.80e+01 1aw8B 1nc7A 138 3.83e+01 b.123.1.1 85549 1m6kA 251 3.85e+01 e.3.1.1 78695 1ei5A 520 3.91e+01 1ei5A b.61.3.1 27418 b.61.3.1 27419 e.3.1.1 42772 1oj6A 151 3.96e+01 1wdcC 156 3.97e+01 1wdcC a.39.1.5 17317 1nnxA 109 3.99e+01