# List of top-scoring protein chains for t2k-100-30-str 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 1h2vC 771 1.09e-01 1fkmA 396 1.20e-01 1fkmA a.69.2.1 18315 a.69.2.1 18316 1qbkB 890 1.54e-01 1qbkB a.118.1.1 19127 1cjaA 342 2.96e-01 1cjaA d.144.1.3 41708 1h6kA 757 3.66e-01 a.118.1.2 60675 a.118.1.2 60676 a.118.1.2 60677 1e8yA 966 1.33e+00 1e8xA a.118.1.6 19152 b.7.1.1 23187 d.15.1.5 37635 d.144.1.4 41715 1jcqA 382 1.39e+00 a.118.6.1 66504 1ld8A 382 1.52e+00 1e7uA 961 1.76e+00 1e8xA a.118.1.6 19147 b.7.1.1 23182 d.15.1.5 37630 d.144.1.4 41710 1iapA 211 1.93e+00 a.91.1.1 62119 1mhyB 395 2.11e+00 1mtyB a.25.1.2 16781 1jipA 403 2.18e+00 a.104.1.1 66748 1eupA 403 2.48e+00 1rom a.104.1.1 18967 1t7pA 698 2.62e+00 1t7pA c.55.3.5 33712 e.8.1.1 43005 1mhyG 169 3.07e+00 1mtyG a.23.3.1 16518 1gw9A 388 3.51e+00 1j4nA 271 3.52e+00 1keyA 235 3.63e+00 4xis 387 3.75e+00 4xis c.1.15.3 29421 1xis 387 3.79e+00 4xis c.1.15.3 29422 1rmi 160 3.80e+00 1ifa a.26.1.3 16891 1jk0B 345 4.01e+00 a.25.1.2 63143 1kqfC 217 4.03e+00 1ah7 245 4.34e+00 1ah7 a.124.1.1 19339 1d6mA 653 4.60e+00 1d6mA e.10.1.1 43248 1be3C 379 4.69e+00 1be3C f.2.1.8 43665 2xis 387 4.86e+00 4xis c.1.15.3 29427 1tubA 440 4.97e+00 1tubA c.32.1.1 31751 d.79.2.1 39803 6cts 433 5.09e+00 1csh a.103.1.1 18891 1iqrA 420 5.35e+00 a.99.1.1 66275 c.28.1.1 66276 1jb0A 755 6.21e+00 1jb0A f.2.1.12 62820 1b43A 340 6.25e+00 1a76 a.60.7.1 18092 c.53.1.2 33362 1gaxA 862 6.40e+00 1gaxA a.27.1.1 16928 b.51.1.1 26893 c.26.1.1 31595 3xis 387 6.51e+00 4xis c.1.15.3 29423 2bidA 197 6.69e+00 2bidA f.1.4.1 43398 1lnh 857 6.72e+00 1yge a.119.1.1 19237 b.12.1.1 23637 2pflA 759 7.51e+00 1cm5A c.7.1.1 30675 1ezfA 340 7.64e+00 1ezfA a.128.1.2 19440 1qjbA 245 8.29e+00 1qjaA a.118.7.1 19202 1a76 326 8.67e+00 1a76 a.60.7.1 18091 c.53.1.2 33361 1fjgD 209 8.69e+00 1c05A d.66.1.2 39553 1d8dA 377 8.81e+00 1ft1A a.118.6.1 19185 1ft1A 377 9.02e+00 1ft1A a.118.6.1 19186 1ca1 370 9.16e+00 1ca1 a.124.1.1 19340 b.12.1.3 23648 1eguA 731 9.38e+00 1eguA a.102.3.2 18850 b.24.1.1 23899 b.30.3.1 24423 1oxa 403 9.39e+00 1f4tA a.104.1.1 18965 1ir6A 424 9.51e+00 1amoA 615 9.64e+00 1amoA b.43.4.1 25669 c.23.5.2 31210 c.25.1.4 31557 1br2A 791 9.74e+00 1lvk b.34.3.1 24558 c.37.1.9 32155 1mmoG 162 9.75e+00 1mtyG a.23.3.1 16512 1pot 325 1.00e+01 1pot c.94.1.1 35807 1j8rA 196 1.02e+01 1j8rA b.2.3.3 62745 1io7A 368 1.02e+01 1f4tA a.104.1.1 18971 1ayx 492 1.06e+01 1ayx a.102.1.1 18825 1kmmA 424 1.08e+01 1adjA c.51.1.1 33174 d.104.1.1 40723 1mtyG 162 1.09e+01 1mtyG a.23.3.1 16498 1l9hA 349 1.09e+01 1i7dA 659 1.11e+01 1d6mA e.10.1.1 61886 1gw5B 591 1.11e+01 1dugA 234 1.19e+01 1b8xA a.45.1.1 17718 c.47.1.5 33012 1csc 433 1.27e+01 1csh a.103.1.1 18886 1ja1A 622 1.28e+01 1amoA b.43.4.1 62803 c.23.5.2 62804 c.25.1.4 62805 1jcrA 377 1.32e+01 a.118.6.1 66506 1rpa 342 1.33e+01 1cviA c.60.1.2 33983 1hmcB 148 1.34e+01 1hmcB a.26.1.2 16868 1csmA 256 1.35e+01 5csmA a.130.1.2 19495 1ihgA 370 1.37e+01 2cpl a.118.8.1 62380 b.62.1.1 62381 1ecrA 309 1.39e+01 1ecrA e.2.1.1 42678 1sftA 388 1.40e+01 1bd0A b.49.2.1 26482 c.1.6.1 28644 1e8xA 961 1.42e+01 1e8xA a.118.1.6 19148 b.7.1.1 23183 d.15.1.5 37631 d.144.1.4 41711 1bd0A 388 1.42e+01 1bd0A b.49.2.1 26480 c.1.6.1 28642 1qjaA 245 1.45e+01 1qjaA a.118.7.1 19204 1hzxA 349 1.47e+01 1f88A f.2.1.1 61466 1dofA 403 1.48e+01 1c3cA a.127.1.1 19429 1h7eA 245 1.53e+01 c.68.1.13 60717 1by2 119 1.53e+01 1by2 d.170.1.1 42452 1fvzA 271 1.56e+01 1fvzA d.129.3.4 60050 1lkxA 697 1.56e+01 5csmA 256 1.60e+01 5csmA a.130.1.2 19494 1j78A 458 1.61e+01 a.126.1.1 66397 a.126.1.1 66398 a.126.1.1 66399 1amz 435 1.63e+01 1csh a.103.1.1 18884 1j99A 293 1.64e+01 1b9zA 516 1.71e+01 1b9zA b.3.1.1 22528 c.1.8.2 28798 1ndk 155 1.76e+01 1npk d.58.6.1 39118 1hmcA 148 1.78e+01 1hmcB a.26.1.2 16867 1npk 154 1.79e+01 1npk d.58.6.1 39099 1lpuA 332 1.83e+01 1qhbA 596 1.86e+01 1qhbA a.111.1.2 19055 1aisB 200 1.89e+01 1aisB a.74.1.2 18384 a.74.1.2 18385 2hpaA 342 1.89e+01 1cviA c.60.1.2 33985 1ea3A 164 1.93e+01 1aa7A a.95.1.1 59398 1dvkA 173 1.96e+01 1dvkA a.72.1.1 18319 1ifa 158 2.02e+01 1ifa a.26.1.3 16892 4crxA 322 2.04e+01 4crxA a.60.9.1 18095 d.163.1.1 42155 1f3fA 155 2.04e+01 1npk d.58.6.1 39101 1i36A 264 2.07e+01 1envA 123 2.10e+01 1envA h.3.2.1 45726 3pflA 759 2.12e+01 1cm5A c.7.1.1 30673 3crxA 343 2.13e+01 4crxA a.60.9.1 18101 d.163.1.1 42161 1fz1C 389 2.15e+01 1mtyB a.25.1.2 16746 1byb 495 2.18e+01 1byb c.1.8.2 28790 1i5nA 146 2.32e+01 1i5nA a.24.10.3 61805 1crxA 322 2.32e+01 4crxA a.60.9.1 18097 d.163.1.1 42157 1csh 435 2.35e+01 1csh a.103.1.1 18880 1gcvA 140 2.42e+01 1cg5B a.1.1.2 15410 1cnsA 243 2.48e+01 1cnsA d.2.1.1 36241 1xsm 390 2.52e+01 1xsm a.25.1.2 16804 1cm5A 759 2.52e+01 1cm5A c.7.1.1 30671 2pgd 482 2.53e+01 2pgd a.100.1.1 18778 c.2.1.6 30190 1d3uB 201 2.56e+01 1aisB a.74.1.2 18386 a.74.1.2 18387 1h3qA 140 2.56e+01 1i37A 260 2.60e+01 1a28A a.123.1.1 61583 1c0aA 585 2.62e+01 1c0aA b.40.4.1 25246 d.74.4.1 39731 d.104.1.1 40767 1taq 832 2.71e+01 1taq a.60.7.1 18082 c.53.1.2 33352 c.55.3.5 33698 e.8.1.1 42991 1avc 673 2.75e+01 1avc a.65.1.1 18178 a.65.1.1 18179 1g71A 347 2.80e+01 1g71A e.16.1.1 43268 1fm9D 272 2.83e+01 2prgA a.123.1.1 19313 1qusA 322 2.87e+01 1ltm d.2.1.6 36991 1ltm 320 2.87e+01 1ltm d.2.1.6 36992 1f2fA 104 2.88e+01 1fmk d.93.1.1 40455 1mdaH 368 2.91e+01 2bbkH b.69.2.1 27637 1b77A 228 2.96e+01 1b77A d.131.1.2 41362 d.131.1.2 41363 1de6A 426 2.99e+01 1de5A c.1.15.2 29398 1dkiA 371 3.06e+01 1dkiA d.3.1.1 37090 1f8mA 429 3.07e+01 1dquA c.1.12.6 29315 1f61A 429 3.13e+01 1dquA c.1.12.6 29319 1ahpA 797 3.14e+01 1a8i c.87.1.4 35544 1ddbA 195 3.19e+01 1ddbA f.1.4.1 43399 1lxkA 721 3.19e+01 1prgA 270 3.23e+01 2prgA a.123.1.1 19314 1dxjA 242 3.27e+01 1cnsA d.2.1.1 36244 1kiyA 374 3.29e+01 1deoA 233 3.30e+01 1deoA c.23.10.4 31345 1f4tA 368 3.31e+01 1f4tA a.104.1.1 18973 1aw9 216 3.31e+01 1gnwA a.45.1.1 17736 c.47.1.5 33030 1b79A 119 3.31e+01 1b79A a.81.1.1 18451 1kbuA 349 3.35e+01 1h3nA 878 3.40e+01 1l7vA 326 3.40e+01 1jfgA 374 3.43e+01 a.128.1.5 66636 1lrv 244 3.46e+01 1lrv a.118.1.5 19146 1shdA 107 3.46e+01 1fmk d.93.1.1 40440 1ytfC 79 3.47e+01 1ytfC b.56.1.1 27010 1k7cA 233 3.67e+01 c.23.10.4 68267 1kz7A 353 3.79e+01 1e3oC 160 3.81e+01 1au7A a.4.1.1 59197 a.35.1.1 59198 2baa 243 3.89e+01 1cnsA d.2.1.1 36243 1dkqA 410 3.89e+01 1dklA c.60.1.3 33998 1a36A 592 3.91e+01 1a36A a.2.8.1 15715 d.163.1.2 42173 e.15.1.1 43266 1qbqA 333 3.92e+01 1ft1A a.118.6.1 19187 1aa7A 158 3.94e+01 1aa7A a.95.1.1 18741