# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7 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 1ncx 162 1.58e-02 1ncx a.39.1.5 17222 1k94A 165 1.72e-02 a.39.1.8 68333 1top 162 2.54e-02 1ncx a.39.1.5 17223 1gw5B 591 2.63e-02 a.118.1.10 70630 1f4qA 165 5.87e-02 1alvA a.39.1.8 17360 1lnh 857 2.21e-01 1yge a.119.1.1 19237 b.12.1.1 23637 1qs0A 407 2.51e-01 1qs0A c.36.1.11 31829 1alvA 173 2.96e-01 1alvA a.39.1.8 17370 1kfuS 184 3.29e-01 a.39.1.8 68574 1t1dA 100 4.83e-01 1t1dA d.42.1.2 38637 1zac 90 4.93e-01 1ncx a.39.1.5 17236 1lla 628 5.73e-01 1lla a.85.1.1 18485 a.86.1.1 18496 b.1.18.3 21861 1omrA 201 7.38e-01 1m46A 148 8.61e-01 a.39.1.5 78599 1a68 95 8.99e-01 1t1dA d.42.1.2 38639 1dsxA 87 9.26e-01 1t1dA d.42.1.2 38644 1ggwA 140 9.53e-01 1ggwA a.39.1.5 60490 1g8iA 190 1.04e+00 1rec a.39.1.5 60363 1knzA 164 1.27e+00 e.34.1.1 68709 1g3jA 532 1.33e+00 3bct a.118.1.1 19114 1aijL 281 1.49e+00 6prcL f.26.1.1 43461 1n93X 375 1.74e+00 1vrtA 560 1.82e+00 1rthA c.55.3.1 33574 e.8.1.2 43023 1dqeA 137 1.87e+00 1dqeA a.39.2.1 17388 2mysB 166 2.12e+00 1wdcB a.39.1.5 17308 1j7rA 86 2.18e+00 1j7rA a.39.1.5 62701 7catA 506 2.28e+00 1cf9A e.5.1.1 42781 1qbkB 890 2.32e+00 1qbkB a.118.1.1 19127 1avsA 90 2.48e+00 1cll a.39.1.5 17226 1ll1 590 2.48e+00 1lla a.85.1.1 18488 a.86.1.1 18499 b.1.18.3 21864 1qltA 560 2.58e+00 1qltA d.58.32.1 39457 d.145.1.1 41720 1e8gA 560 2.81e+00 1qltA d.58.32.1 39455 d.145.1.1 41718 1ggzA 148 3.12e+00 a.39.1.5 70176 1v54A 514 3.13e+00 1cll 148 3.31e+00 1cll a.39.1.5 17263 2btfA 375 3.49e+00 1yagA c.55.1.1 33429 c.55.1.1 33430 1m45A 148 3.60e+00 a.39.1.5 78598 1gm7A 209 3.67e+00 d.153.1.2 65302 1o1fC 147 3.71e+00 i.15.1.1 80997 1qu1A 155 3.79e+00 1qu1A h.3.1.1 45670 1qcrC 378 3.81e+00 1be3C f.32.1.1 75931 f.21.1.2 75932 1iicA 422 3.88e+00 1nmtA d.108.1.2 62422 d.108.1.2 62423 2lbd 267 3.94e+00 2lbd a.123.1.1 19287 1hqvA 191 3.99e+00 1hqvA a.39.1.8 61160 3cln 148 4.07e+00 1cll a.39.1.5 17286 1dttA 560 4.14e+00 1rthA c.55.3.1 33611 e.8.1.2 43088 1ddf 127 4.62e+00 1ddf a.77.1.2 18423 1gkmA 509 4.69e+00 a.127.1.2 70228 1gweA 503 4.75e+00 e.5.1.1 70667 1i7gA 287 4.89e+00 a.123.1.1 71121 1rxwA 336 4.91e+00 1hbzA 498 5.04e+00 1cf9A e.5.1.1 60937 4lbd 267 5.14e+00 2lbd a.123.1.1 19289 1kiyA 374 5.27e+00 a.128.1.5 72555 1d4xA 375 5.33e+00 1yagA c.55.1.1 59107 c.55.1.1 59108 1jfaA 374 5.38e+00 a.128.1.5 66622 1wdcC 156 5.62e+00 1wdcC a.39.1.5 17317 1jdhA 529 5.74e+00 a.118.1.1 66549 1rthA 560 5.87e+00 1rthA c.55.3.1 33576 e.8.1.2 43028 1jr8A 117 5.95e+00 a.24.15.1 67115 1jeqA 609 6.25e+00 1jeqA a.140.2.1 64748 e.31.1.1 64749 1vaoA 560 6.52e+00 1qltA d.58.32.1 39461 d.145.1.1 41724 1ho8A 480 6.75e+00 1ho8A a.118.1.9 61107 1fmjA 351 6.77e+00 c.37.1.5 59879 2occA 514 6.81e+00 2occA f.24.1.1 43518 1dgaA 375 6.90e+00 1yagA 1okrA 123 7.17e+00 1fps 348 7.29e+00 1uby a.128.1.1 19436 1m48A 133 7.31e+00 a.26.1.2 74443 1jfkA 134 7.36e+00 a.39.1.5 66639 1lufA 343 7.59e+00 d.144.1.7 78223 1kk1A 410 8.10e+00 b.43.3.1 72634 b.44.1.1 72635 c.37.1.8 72636 1dceB 331 8.18e+00 1dceB a.102.4.3 18872 1a36A 592 8.66e+00 1a36A a.2.8.1 15715 d.163.1.2 42173 e.15.1.1 43266 1fcyA 236 8.67e+00 2lbd a.123.1.1 19282 1qlnA 883 8.98e+00 1cezA e.8.1.3 43111 1ai7A 209 9.20e+00 1ajqA d.153.1.2 41845 1jraA 117 9.46e+00 a.24.15.1 67117 1ajqA 209 9.60e+00 1ajqA d.153.1.2 41840 1uby 367 9.75e+00 1uby a.128.1.1 19435 1vi0A 206 1.00e+01 1f1sA 814 1.00e+01 a.102.3.2 64928 b.1.18.2 64929 b.24.1.1 64930 b.30.5.2 64931 1jfgA 374 1.09e+01 a.128.1.5 66636 1bi0 226 1.12e+01 1bi0 a.4.5.24 16202 a.76.1.1 18408 b.34.1.2 24453 1ovlA 271 1.12e+01 a.123.1.1 87455 1ju3A 583 1.13e+01 b.18.1.13 67300 c.69.1.21 67301 1nrlA 316 1.13e+01 1wgtA 186 1.13e+01 9wgaA g.3.1.1 44008 g.3.1.1 44009 g.3.1.1 44010 g.3.1.1 44011 1br1B 150 1.14e+01 1wdcC a.39.1.5 17309 1uhnA 189 1.15e+01 6prcM 323 1.15e+01 6prcM f.26.1.1 43435 1hy3A 294 1.15e+01 c.37.1.5 71090 1mxrA 375 1.15e+01 a.25.1.2 85197 1eg7A 557 1.16e+01 1eg7A c.37.1.10 32241 1b8fA 509 1.16e+01 1b8fA a.127.1.2 19434 1n3kA 130 1.18e+01 a.77.1.4 79965 1exrA 148 1.18e+01 1cll a.39.1.5 17299 1e9lA 377 1.19e+01 1e9lA c.1.8.5 59395 d.26.3.1 59396 1ngvA 534 1.21e+01 c.111.1.2 85698 1g4yR 148 1.28e+01 1cll a.39.1.5 60252 1taq 832 1.31e+01 1taq a.60.7.1 18082 c.120.1.2 33352 c.55.3.5 33698 e.8.1.1 42991 1biqA 375 1.33e+01 1xikA a.25.1.2 16786 1l7mA 211 1.35e+01 c.108.1.4 73664 1sva1 361 1.36e+01 1vpsA 1f5sA 211 1.37e+01 1f5sA c.108.1.4 59656 9wgaA 171 1.43e+01 9wgaA g.3.1.1 44000 g.3.1.1 44001 g.3.1.1 44002 g.3.1.1 44003 1fjgM 126 1.44e+01 1fjfM a.156.1.1 16293 1j6zA 376 1.45e+01 1yagA c.55.1.1 62667 c.55.1.1 62668 2hmiA 558 1.46e+01 1rthA c.55.3.1 33604 e.8.1.2 43106 1gh6A 114 1.49e+01 a.2.3.1 65191 1dxrM 323 1.54e+01 6prcM f.26.1.1 43432 1j97A 211 1.54e+01 1f5sA c.108.1.4 62753 1lg2A 365 1.55e+01 c.1.8.5 77950 d.26.3.1 77951 1ebmA 317 1.62e+01 1ebmA a.96.1.3 18751 d.129.1.2 41300 1e7uA 961 1.62e+01 1e8xA a.118.1.6 19147 b.7.1.1 23182 d.15.1.5 37630 d.144.1.4 41710 1ivhA 394 1.62e+01 3mdeA a.29.3.1 16608 e.6.1.1 42869 1h7nA 342 1.62e+01 1b4kA c.1.10.3 60726 1itwA 741 1.64e+01 c.77.1.2 76793 1p49A 562 1.66e+01 1jbaA 204 1.66e+01 1rec a.39.1.5 17330 1aoa 275 1.66e+01 1aoa a.40.1.1 17396 a.40.1.1 17397 1csmA 256 1.68e+01 5csmA a.130.1.2 19495 1pw4A 451 1.74e+01 1m1eB 81 1.74e+01 a.161.1.1 78400 1de6A 426 1.77e+01 1de5A c.1.15.2 29398 1be3C 379 1.83e+01 1be3C f.32.1.1 75805 f.21.1.2 75806 1s0uA 408 1.84e+01 1jb0A 755 1.86e+01 1jb0A f.29.1.1 62820 1jeyA 609 1.94e+01 1jeqA e.31.1.1 62924 1lkxA 697 1.98e+01 c.37.1.9 73981 1skyB 502 1.99e+01 1skyB a.69.1.1 18313 b.49.1.1 26478 c.37.1.11 32358 1kl1A 419 2.04e+01 c.67.1.4 72663 1i7wA 538 2.08e+01 3bct a.118.1.1 61909 1gw5A 621 2.09e+01 a.118.1.10 70629 1dghB 498 2.11e+01 1cf9A e.5.1.1 42791 2hdhA 293 2.17e+01 2hdhA a.100.1.3 18795 c.2.1.6 30199 1ribA 375 2.18e+01 1xikA a.25.1.2 16788 1alq 266 2.20e+01 1btl e.3.1.1 42707 1aroP 883 2.23e+01 1cezA e.8.1.3 43112 1lwyA 324 2.23e+01 a.96.1.3 78285 d.129.1.2 78286 1m13A 316 2.24e+01 a.123.1.1 84746 1de5A 426 2.24e+01 1de5A c.1.15.2 29402 1jqcA 375 2.26e+01 1xikA a.25.1.2 63229 1fmk 452 2.28e+01 1fmk b.34.2.1 24511 d.93.1.1 40436 d.144.1.7 41690 1e1dA 553 2.31e+01 1e1dA e.26.1.1 43363 1gntA 553 2.33e+01 e.26.1.1 70290 1n7zA 334 2.33e+01 b.127.1.1 85380 1f83A 425 2.36e+01 1f82A d.92.1.7 40306 1mo9A 523 2.38e+01 c.3.1.5 79341 c.3.1.5 79342 d.87.1.1 79343 1e2uA 553 2.39e+01 1e1dA e.26.1.1 43362 1ylvA 342 2.42e+01 1b4kA c.1.10.3 29180 1fs0G 230 2.44e+01 1fs0G c.49.2.1 59999 1miuA 738 2.45e+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 1nmtA 392 2.46e+01 1nmtA d.108.1.2 40823 d.108.1.2 40824 2shpA 525 2.50e+01 2shpA c.45.1.2 32683 d.93.1.1 40533 d.93.1.1 40534 1dceA 567 2.51e+01 1dceA a.118.6.1 19191 b.7.4.1 23218 c.10.2.2 30867 3erk 364 2.53e+01 1hcl d.144.1.7 41654 1g0oA 283 2.53e+01 1ybvA c.2.1.2 60181 1yagA 375 2.53e+01 1yagA c.55.1.1 33449 c.55.1.1 33450 1l2lA 457 2.55e+01 c.72.1.3 77656 1cezA 883 2.57e+01 1cezA e.8.1.3 43110 1uf2A 1019 2.57e+01 1nstA 325 2.60e+01 1nstA c.37.1.5 31951 1dgfA 497 2.61e+01 1cf9A e.5.1.1 42782 1kjwA 295 2.68e+01 b.34.2.1 68643 c.37.1.1 68644 1fxxA 482 2.69e+01 1fxxA c.55.3.5 33726 1kkjA 419 2.69e+01 c.67.1.4 72647 1jeyB 565 2.75e+01 1jeqB e.31.1.2 62925 1e1hB 174 2.76e+01 1h77A 605 2.81e+01 1ci8A 392 2.81e+01 e.3.1.1 64765 1phnB 172 2.82e+01 1qgwC a.1.1.3 15642 1keyA 235 2.83e+01 a.118.16.1 72389 1vhvA 268 2.84e+01 5csmA 256 2.89e+01 5csmA a.130.1.2 19494 1fgkA 310 2.90e+01 1fgkA d.144.1.7 41693 1nvvS 481 2.90e+01 a.117.1.1 86279 1ltdA 506 2.91e+01 1gox c.1.4.1 28618 d.120.1.1 41086 1htmB 138 2.95e+01 1htmB h.3.1.1 45677 1ybvA 283 2.97e+01 1ybvA c.2.1.2 29948 1m1jA 491 2.99e+01 h.1.8.1 74369 1ohlA 342 3.01e+01 c.1.10.3 87035 1aoiG 116 3.02e+01 1aoiC a.22.1.1 16441 5ldh 334 3.07e+01 3ldh c.2.1.5 30158 d.162.1.1 42125 1lshA 1056 3.10e+01 a.118.4.1 74242 f.7.1.1 74243 f.7.1.1 74244 1hz4A 373 3.12e+01 a.118.8.2 65960 1rec 201 3.12e+01 1rec a.39.1.5 17326 1pal 108 3.12e+01 1a75A a.39.1.4 17209 1gk9A 260 3.12e+01 d.153.1.2 65246 1pnkA 209 3.14e+01 1ajqA d.153.1.2 41839 1upkA 341 3.14e+01 1dnpA 471 3.25e+01 1qnf a.99.1.1 18775 c.28.1.1 31630 1aipE 405 3.25e+01 1efcA b.43.3.1 25699 b.44.1.1 25739 c.37.1.8 32134 1fgqA 839 3.27e+01 1yge a.119.1.1 59826 b.12.1.1 59827 1efdN 266 3.27e+01 1efdN c.92.2.1 35597 1m2oA 768 3.28e+01 a.71.2.1 78480 b.2.8.1 78481 c.62.1.2 78482 d.109.2.1 78483 g.41.10.1 78484 1f2dA 341 3.28e+01 1f2dA c.79.1.1 35298 1k0rA 366 3.28e+01 b.40.4.5 67961 d.52.3.1 67962 d.52.3.1 67963 d.202.1.1 67964 2dtr 226 3.29e+01 1bi0 a.4.5.24 16193 a.76.1.1 18399 b.34.1.2 24450 1yge 839 3.32e+01 1yge a.119.1.1 19234 b.12.1.1 23634 1bla 155 3.36e+01 1bfg b.42.1.1 25502 1cdp 109 3.38e+01 1a75A a.39.1.4 17197 1ko9A 345 3.42e+01 a.96.1.3 68717 d.129.1.2 68718 1ci9A 392 3.43e+01 e.3.1.1 64767 1uetA 437 3.45e+01 1f8nA 839 3.46e+01 1yge a.119.1.1 59703 b.12.1.1 59704 3lynA 136 3.47e+01 1lis a.19.1.1 16413 1qhtA 775 3.47e+01 1tgoA c.55.3.5 33722 e.8.1.1 43011 3bct 457 3.51e+01 3bct a.118.1.1 19112 1ahpA 797 3.52e+01 1a8i c.87.1.4 35544 1kzhA 555 3.53e+01 c.89.1.1 73361 2dpg 485 3.58e+01 1dpgA c.2.1.3 30076 d.81.1.5 39991 2pvbA 107 3.58e+01 1a75A a.39.1.4 17205 1gseA 221 3.59e+01 1pgtA a.45.1.1 17667 c.47.1.5 32961 1n81A 186 3.60e+01 a.185.1.1 85388 1bn7A 294 3.61e+01 1bn6A c.69.1.8 34677 1bn6A 294 3.68e+01 1bn6A c.69.1.8 34678 1d8wA 426 3.69e+01 1de5A c.1.15.2 29394 1j7nB 776 3.72e+01 d.92.1.14 66412 d.92.1.14 66413 d.166.1.1 66414 1j5eB 256 3.73e+01 c.23.15.1 71543 1osa 148 3.81e+01 1cll a.39.1.5 17300 1qapA 296 3.81e+01 1qpoA c.1.17.1 29559 d.41.2.1 38595 1qz5A 375 3.81e+01 1rpa 342 3.86e+01 1cviA c.60.1.2 33983 1sek 378 3.91e+01 1sek e.1.1.1 42675 1gpb 842 3.95e+01 1a8i c.87.1.4 35478 2scpA 174 3.98e+01 2scpA a.39.1.5 17256 5pal 109 3.99e+01 1a75A a.39.1.4 17215