# List of top-scoring protein chains for t2k-100-30-alpha 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 2minB 522 7.74e-01 1qguB c.92.2.3 35610 3minB 522 8.51e-01 1qguB c.92.2.3 35606 1necA 216 1.01e+00 1vfrA d.90.1.1 40249 1icrA 217 1.54e+00 1vfrA d.90.1.1 62274 1g4yR 148 1.60e+00 1cll a.39.1.5 60252 1go3F 107 1.60e+00 a.60.8.2 65407 1g8iA 190 1.72e+00 1rec a.39.1.5 60363 1elqA 390 1.80e+00 1elqA c.67.1.3 34436 1rec 201 1.82e+00 1rec a.39.1.5 17326 1brwA 433 1.85e+00 1brwA a.46.2.1 17764 c.27.1.1 31628 d.41.3.1 38626 1fd9A 213 1.89e+00 1fd9A d.26.1.1 59771 3cln 148 2.17e+00 1cll a.39.1.5 17286 1eluA 390 2.18e+00 1elqA c.67.1.3 34434 1eluB 390 2.26e+00 1elqA c.67.1.3 34435 1cll 148 2.48e+00 1cll a.39.1.5 17263 1qguB 519 2.49e+00 1qguB c.92.2.3 35626 1rcd 173 2.52e+00 2fha a.25.1.1 16687 1qh8B 519 3.00e+00 1qguB c.92.2.3 35634 9gafA 295 3.08e+00 1apyA d.153.1.5 42008 1jndA 420 3.57e+00 1ggqA 174 4.07e+00 1ggqA a.24.12.1 60486 1io7A 368 4.28e+00 1f4tA a.104.1.1 18971 1exrA 148 4.44e+00 1cll a.39.1.5 17299 1gntA 553 4.53e+00 1a8h 500 4.53e+00 1a8h a.27.1.1 16922 c.26.1.1 31589 1clxA 347 4.60e+00 1taxA c.1.8.3 28899 1osa 148 4.70e+00 1cll a.39.1.5 17300 1dp0A 1023 5.04e+00 b.1.4.1 22073 b.1.4.1 22074 b.18.1.5 23722 b.30.1.1 24346 c.1.8.3 28845 2ezh 75 5.09e+00 2ezh a.4.1.2 16029 3adk 195 5.48e+00 1zin c.37.1.1 31885 1eyzA 392 5.73e+00 1ez1A b.84.2.1 28246 c.30.1.1 31653 d.142.1.2 41498 1pda 315 5.90e+00 1pda c.94.1.1 35751 d.50.2.1 38794 1bvsB 203 6.05e+00 1hjp a.5.1.1 16281 a.60.2.1 17956 b.40.4.2 25275 1bglA 1023 6.18e+00 1bglA b.1.4.1 22097 b.1.4.1 22098 b.18.1.5 23734 b.30.1.1 24358 c.1.8.3 28857 1tpt 440 6.20e+00 1brwA a.46.2.1 17763 c.27.1.1 31627 d.41.3.1 38625 1ljrA 244 6.31e+00 1ljrA a.45.1.1 17707 c.47.1.5 33001 1e1dA 553 6.34e+00 1e1dA e.26.1.1 43363 1e2uA 553 6.40e+00 1e1dA e.26.1.1 43362 1ukz 203 6.79e+00 1zin c.37.1.1 31840 1b1cA 181 7.04e+00 1amoA c.23.5.2 31212 1i50K 120 7.12e+00 d.74.3.2 61765 1kjqA 391 7.16e+00 1liaA 164 7.25e+00 1cpcA a.1.1.3 15661 1jz8A 1023 7.29e+00 b.1.4.1 67830 b.1.4.1 67831 b.18.1.5 67832 b.30.1.1 67833 c.1.8.3 67834 2ezi 75 7.89e+00 2ezh a.4.1.2 16028 1ggzA 148 8.22e+00 1jtyA 194 8.29e+00 a.4.1.9 67292 a.121.1.1 67293 1qe3A 489 8.51e+00 2bce c.69.1.1 34630 1adeA 431 8.61e+00 1adeA c.37.1.10 32213 4xiaA 393 8.68e+00 4xis c.1.15.3 29439 1exnB 290 8.71e+00 1exnA a.60.7.1 18089 c.53.1.2 33359 1ez1A 392 8.74e+00 1ez1A b.84.2.1 28248 c.30.1.1 31655 d.142.1.2 41500 1ja1A 622 9.53e+00 1amoA b.43.4.1 62803 c.23.5.2 62804 c.25.1.4 62805 1fx8A 281 9.68e+00 f.2.1.5 43651 1eulA 994 9.83e+00 1eulA f.2.1.10 43726 1aipE 405 9.88e+00 1efcA b.43.3.1 25699 b.44.1.1 25739 c.37.1.8 32134 1r69 69 1.03e+01 1r69 a.35.1.2 17028 1i5pA 633 1.04e+01 1i5pA b.18.1.3 61817 b.77.2.1 61818 f.1.3.1 61819 2sas 185 1.05e+01 2sas a.39.1.5 17258 1ej3A 191 1.07e+01 1ej3A a.39.1.5 17259 2or1L 69 1.10e+01 1r69 a.35.1.2 17031 1dz4A 414 1.11e+01 1phd a.104.1.1 18903 1hy0A 466 1.14e+01 1auwA a.127.1.1 61392 1ibrB 462 1.15e+01 1qgrA a.118.1.1 19120 8adh 374 1.16e+01 2ohxA b.35.1.2 24690 c.2.1.1 29706 1auwA 468 1.16e+01 1auwA a.127.1.1 19416 1uby 367 1.18e+01 1uby a.128.1.1 19435 1a59 378 1.18e+01 1aj8A a.103.1.1 18902 1czpA 98 1.26e+01 1awd d.15.4.1 37645 1qt9A 98 1.26e+01 1awd d.15.4.1 37647 1phd 414 1.27e+01 1phd a.104.1.1 18913 1dq3A 454 1.30e+01 1dq3A b.86.1.2 28380 d.50.3.1 38798 d.95.2.2 40585 d.95.2.2 40586 1exnA 290 1.38e+01 1exnA a.60.7.1 18088 c.53.1.2 33358 1qmqA 414 1.39e+01 1phd a.104.1.1 18907 1b8dA 164 1.40e+01 1cpcA a.1.1.3 15665 2cb5A 453 1.41e+01 3gcb d.3.1.1 37035 1ab4 477 1.44e+01 1ab4 e.11.1.1 43251 1toh 343 1.48e+01 4pah d.178.1.1 42573 1ekbB 235 1.48e+01 5ptp b.47.1.2 26282 1eg5A 384 1.48e+01 1ecxA c.67.1.3 34429 1jt6A 188 1.51e+01 a.4.1.9 67247 a.121.1.1 67248 5pal 109 1.52e+01 1a75A a.39.1.4 17215 1dhs 344 1.55e+01 1dhs c.31.1.1 31727 1emvA 86 1.60e+01 1cei a.28.2.1 16944 1dzaA 129 1.61e+01 7rsa d.5.1.1 37275 1gm5A 780 1.61e+01 a.29.4.1 65298 b.40.4.9 65299 c.37.1.13 65300 c.37.1.13 65301 1qhlA 227 1.62e+01 1qhlA c.37.1.12 32382 1dcnD 436 1.73e+01 1auwA a.127.1.1 19423 1ecxA 384 1.74e+01 1ecxA c.67.1.3 34431 1d9cA 121 1.76e+01 1d9cA a.26.1.3 16901 1phg 414 1.77e+01 1phd a.104.1.1 18910 2gsq 202 1.81e+01 1pd21 a.45.1.1 17715 c.47.1.5 33009 1qf5A 431 1.82e+01 1adeA c.37.1.10 32212 1eguA 731 1.84e+01 1eguA a.102.3.2 18850 b.24.1.1 23899 b.30.3.1 24423 1phnA 162 1.85e+01 1cpcA a.1.1.3 15641 1h6oA 204 1.89e+01 a.146.1.1 60689 1phb 414 1.95e+01 1phd a.104.1.1 18906 1j6zA 376 1.97e+01 1yagA c.55.1.1 62667 c.55.1.1 62668 1li5A 461 1.97e+01 1dt9A 437 1.98e+01 1dt9A c.55.4.2 33738 d.79.3.2 39815 d.91.1.1 40257 1ei7A 158 1.99e+01 1rmvA a.24.5.1 16584 1k7wA 468 1.99e+01 1d4xA 375 2.00e+01 1yagA c.55.1.1 59107 c.55.1.1 59108 1h99A 224 2.00e+01 a.142.1.1 60814 a.142.1.1 60815 5cpp 414 2.00e+01 1phd a.104.1.1 18935 1fiy 883 2.05e+01 1fiy c.1.12.3 29307 1ihfA 99 2.05e+01 1huuA a.55.1.1 17893 7ahlA 293 2.06e+01 7ahlA f.6.1.1 43812 1be3F 110 2.10e+01 1be3F f.2.1.8 43668 1ha3A 405 2.11e+01 1efcA b.43.3.1 60869 b.44.1.1 60870 c.37.1.8 60871 1mmoB 384 2.11e+01 1mtyB a.25.1.2 16768 1hstA 90 2.19e+01 1hstA a.4.5.13 16140 1pbv 195 2.23e+01 1pbv a.118.3.1 19179 1yveI 524 2.27e+01 1qmgA a.100.1.2 18789 c.2.1.6 30186 1frrA 95 2.32e+01 1awd d.15.4.1 37674 1eqnA 321 2.33e+01 1dd9A e.13.1.1 43256 1atiA 505 2.35e+01 1atiA c.51.1.1 33196 d.104.1.1 40745 1i0aA 466 2.36e+01 1auwA a.127.1.1 61479 1gkuB 1054 2.42e+01 c.37.1.16 65257 c.37.1.16 65258 e.10.1.1 65259 1atiB 505 2.42e+01 1atiA c.51.1.1 33197 d.104.1.1 40746 1qcrF 103 2.42e+01 1be3F f.2.1.8 43676 1qmgA 524 2.43e+01 1qmgA a.100.1.2 18785 c.2.1.6 30182 1b78A 193 2.45e+01 1b78A c.51.4.1 33221 1ddeA 338 2.46e+01 1dd9A e.13.1.1 43255 1qs2A 401 2.51e+01 1qs1A d.166.1.1 42268 d.166.1.1 42269 1f1mA 164 2.53e+01 1ggqA a.24.12.1 59598 1vsd 152 2.57e+01 1cxqA c.55.3.2 33625 2mjpA 193 2.58e+01 1b78A c.51.4.1 33223 1qs1A 462 2.67e+01 1qs1A d.166.1.1 42260 d.166.1.1 42261 1bg7 176 2.70e+01 2fha a.25.1.1 16686 1a28A 256 2.71e+01 1a28A a.123.1.1 19290 1b0b 142 2.75e+01 2fal a.1.1.2 15010 1hjp 203 2.76e+01 1hjp a.5.1.1 16274 a.60.2.1 17947 b.40.4.2 25266 1cfr 285 2.76e+01 1cfr c.52.1.7 33312 1ktpA 162 2.79e+01 1flp 142 2.80e+01 1flp a.1.1.2 15011 1l8rA 101 2.91e+01 1bd3A 243 2.92e+01 1bd3A c.61.1.1 34098 1f8yA 157 2.93e+01 1f8xA c.23.14.1 31395 1dqiA 124 2.95e+01 1do6A b.1.13.1 22357 1btu 240 2.97e+01 5ptp b.47.1.2 26241 1cpcA 162 2.98e+01 1cpcA a.1.1.3 15643 1dd9A 338 2.99e+01 1dd9A e.13.1.1 43254 1jkw 323 3.00e+01 1jkw a.74.1.1 18356 a.74.1.1 18357 1amoA 615 3.02e+01 1amoA b.43.4.1 25669 c.23.5.2 31210 c.25.1.4 31557 1cipA 353 3.03e+01 1cipA a.66.1.1 18210 c.37.1.8 32093 1gaxA 862 3.04e+01 1gaxA a.27.1.1 16928 b.51.1.1 26893 c.26.1.1 31595 1csn 298 3.08e+01 1csn d.144.1.1 41664 1qnjA 240 3.09e+01 5ptp b.47.1.2 26238 1e79A 510 3.10e+01 1skyB a.69.1.1 18269 b.49.1.1 26434 c.37.1.11 32314 1iapA 211 3.10e+01 a.91.1.1 62119 1qlaA 656 3.13e+01 1qlaA a.7.3.1 16328 c.3.1.4 30427 d.168.1.1 42310 1h8eA 510 3.18e+01 1skyB a.69.1.1 60738 b.49.1.1 60739 c.37.1.11 60740 1vsgA 364 3.18e+01 1vsgA h.4.1.1 45782 1f8xA 157 3.24e+01 1f8xA c.23.14.1 31397 1e5dA 402 3.24e+01 1e5dA c.23.5.1 31208 d.157.1.3 42061 1mtnC 97 3.25e+01 5ptp 1af7 274 3.28e+01 1af7 a.58.1.1 17928 c.66.1.8 34203 1e6iA 121 3.28e+01 1b91A a.29.2.1 16969 1g7dA 106 3.35e+01 1g7dA a.71.1.1 18318 1fyhA 258 3.37e+01 1d9cA a.26.1.3 16907 a.26.1.3 16908 1jihA 531 3.37e+01 e.8.1.5 66740 1aisB 200 3.37e+01 1aisB a.74.1.2 18384 a.74.1.2 18385 1ee2A 373 3.40e+01 2ohxA b.35.1.2 24663 c.2.1.1 29679 3ertA 261 3.42e+01 3erdA a.123.1.1 19292 1fcjA 322 3.45e+01 1oasA c.79.1.1 35289 1h8eD 482 3.46e+01 1skyE a.69.1.1 60747 b.49.1.1 60748 c.37.1.11 60749 1qj2A 166 3.46e+01 1qj2A a.56.1.1 17913 d.15.4.2 37698 1dgsA 667 3.50e+01 1dgsA a.60.2.2 17963 b.40.4.6 25365 d.142.2.2 41581 1qqtA 551 3.54e+01 1qqtA a.27.1.1 16923 c.26.1.1 31590 g.41.1.1 45175 1kxu 333 3.56e+01 1jkw a.74.1.1 18358 a.74.1.1 18359 1yveJ 524 3.59e+01 1qmgA a.100.1.2 18790 c.2.1.6 30187 1f7zA 233 3.61e+01 5ptp b.47.1.2 59681 12asA 330 3.62e+01 12asA d.104.1.1 40783 1id0A 152 3.66e+01 d.122.1.3 66111 1oasA 322 3.69e+01 1oasA c.79.1.1 35293 1f24A 402 3.69e+01 1rom a.104.1.1 18953 1mtyB 384 3.70e+01 1mtyB a.25.1.2 16740 1cl1A 395 3.71e+01 1cl2A c.67.1.3 34395 1hw7A 255 3.73e+01 1i7fA d.193.1.1 61297 1aogA 485 3.76e+01 3grs c.3.1.5 30517 c.3.1.5 30518 d.87.1.1 40190 1bc5A 269 3.80e+01 1af7 a.58.1.1 17929 c.66.1.8 34204 1g6hA 257 3.81e+01 1gajA c.37.1.12 60318 1ea5A 537 3.84e+01 2bce c.69.1.1 34592 1cseI 71 3.92e+01 1egpA d.40.1.1 38559 1l2iA 261 3.92e+01 1tml 286 3.92e+01 1tml c.6.1.1 30656 1a7s 221 3.96e+01 1a7s b.47.1.2 26284 1xyzA 347 3.98e+01 1taxA c.1.8.3 28804