# List of top-scoring protein chains for t2k-w0.5 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 1rkd 309 9.01e-27 1rkd c.72.1.1 34928 1bx4A 345 6.48e-19 1bx4A c.72.1.1 34935 1lioA 363 1.42e-17 1dgmA 363 2.09e-17 1bx4A c.72.1.1 34936 1liiA 363 2.12e-17 1jxhA 288 3.40e-03 c.72.1.2 67415 1ekqA 272 1.42e-01 1c3qA c.72.1.2 34941 1gc5A 467 2.70e-01 1gc5A c.72.1.3 60429 2tbvA 387 3.67e-01 2tbvA b.10.1.2 23302 1vpe 398 4.51e-01 16pk c.86.1.1 35453 1esjA 284 5.15e-01 1c3qA c.72.1.2 34943 1c3qA 272 5.37e-01 1c3qA c.72.1.2 34948 2ay8A 394 6.07e-01 1ajsA c.67.1.1 34359 1php 394 1.31e+00 16pk c.86.1.1 35452 1axcE 261 2.44e+00 1plq d.131.1.2 41396 d.131.1.2 41397 1axcA 261 2.44e+00 1plq d.131.1.2 41392 d.131.1.2 41393 1jr1A 514 4.59e+00 c.1.5.1 63241 d.37.1.1 63242 d.37.1.1 63243 1ibjA 464 4.76e+00 1ibjA c.67.1.3 62162 1gky 187 5.92e+00 1gky c.37.1.1 31839 1ex7A 186 5.97e+00 1gky c.37.1.1 59537 1mgtA 174 6.64e+00 1mgtA a.4.2.1 16078 c.55.7.1 33753 16pk 415 6.73e+00 16pk c.86.1.1 35454 1qoqB 396 6.75e+00 2tysB c.79.1.1 35271 1qopB 396 6.91e+00 2tysB c.79.1.1 35270 1k7xB 396 6.92e+00 2wsyB 396 6.94e+00 2tysB c.79.1.1 35288 1fdjA 363 6.95e+00 1fbaA c.1.10.1 59772 1bksB 397 6.95e+00 2tysB c.79.1.1 35285 2tysB 397 6.96e+00 2tysB c.79.1.1 35272 1fuyB 396 7.09e+00 2tysB c.79.1.1 35279 1b3oB 514 7.22e+00 1ak5 c.1.5.1 28641 d.37.1.1 38538 d.37.1.1 38539 1ubsB 397 7.61e+00 2tysB c.79.1.1 35273 1beuB 397 7.61e+00 2tysB c.79.1.1 35274 1kgdA 180 7.73e+00 c.37.1.1 68582 1cr6B 554 7.81e+00 1cr6B c.108.1.2 43338 c.69.1.11 34688 1ek1A 554 7.81e+00 1cr6B c.108.1.2 43335 c.69.1.11 34685 1cqzA 554 7.81e+00 1cr6B c.108.1.2 43339 c.69.1.11 34689 1k74D 283 8.09e+00 a.123.1.1 68252 1i7iA 292 8.12e+00 3prgA 278 8.13e+00 2prgA a.123.1.1 19318 1prgA 270 8.16e+00 2prgA a.123.1.1 19314 1jbqE 435 8.17e+00 c.79.1.1 62854 1fm9D 272 8.17e+00 2prgA a.123.1.1 19313 2prgA 271 8.18e+00 2prgA a.123.1.1 19311 1qo5A 363 8.34e+00 1fbaA c.1.10.1 29102 1e69B 322 8.36e+00 1e69B c.37.1.12 32377 1fsz 372 9.27e+00 1fsz c.32.1.1 31750 d.79.2.1 39802 1zakA 222 9.38e+00 1zin c.37.1.1 31913 g.41.2.1 45202 1h5yA 253 9.87e+00 c.1.2.1 65638 1g7tA 594 1.15e+01 1g7rA b.43.3.1 25714 b.43.3.1 25715 c.20.1.1 31033 c.37.1.8 32148 1g7sA 594 1.15e+01 1g7rA b.43.3.1 25712 b.43.3.1 25713 c.20.1.1 31032 c.37.1.8 32147 1ax4A 467 1.17e+01 1ax4A c.67.1.2 34391 1fyeA 229 1.19e+01 1fyeA c.23.16.4 31477 1giyD 178 1.20e+01 i.1.1.1 60551 4enl 436 1.21e+01 4enl c.1.11.1 29202 d.54.1.1 38846 1l8pA 436 1.21e+01 1oneA 436 1.22e+01 4enl c.1.11.1 29200 d.54.1.1 38844 2oneA 436 1.22e+01 4enl c.1.11.1 29203 d.54.1.1 38847 1c1lA 136 1.26e+01 1c1lA b.29.1.3 24219 1gtxA 472 1.31e+01 1gtxA c.67.1.4 34464 2pia 321 1.33e+01 2pia b.43.4.2 25663 c.25.1.2 31553 d.15.4.2 37704 1pklG 499 1.38e+01 1a49A b.58.1.1 27058 c.1.12.1 29286 c.49.1.1 33140 1dxlA 470 1.52e+01 1lvl c.3.1.5 30585 c.3.1.5 30586 d.87.1.1 40214 1jh9A 340 1.53e+01 a.35.1.5 66710 c.93.1.1 66711 1gc0A 398 1.54e+01 1qm9A 198 1.67e+01 1qm9A d.58.7.1 39207 d.58.7.1 39208 1f4qA 165 1.70e+01 1alvA a.39.1.7 17360 4ubpC 570 1.74e+01 1ubpC b.92.1.1 28431 c.1.9.2 29053 1ubpC 570 1.74e+01 1ubpC b.92.1.1 28432 c.1.9.2 29054 1i01E 244 1.83e+01 1ybvA c.2.1.2 29901 1jehB 478 2.00e+01 c.3.1.5 62915 c.3.1.5 62916 d.87.1.1 62917 7mdhB 375 2.01e+01 1bmdA c.2.1.5 30131 d.162.1.1 42098 1hf0A 159 2.03e+01 a.4.1.1 65820 a.35.1.1 65821 1ie7C 570 2.03e+01 1ubpC b.92.1.1 62315 c.1.9.2 62316 1c3oB 382 2.06e+01 1c3oB c.8.3.1 30744 c.23.16.1 31421 1who 96 2.15e+01 1who b.7.3.1 23215 1ordA 730 2.17e+01 1ordA c.23.7.1 31274 c.67.1.5 34503 d.125.1.1 41124 1e7pG 655 2.17e+01 1qlaA a.7.3.1 59359 c.3.1.4 59360 d.168.1.1 59361 1e7pA 656 2.17e+01 1qlaA a.7.3.1 59347 c.3.1.4 59348 d.168.1.1 59349 1c4kA 730 2.18e+01 1ordA c.23.7.1 31273 c.67.1.5 34502 d.125.1.1 41123 1cqtA 163 2.20e+01 1au7A a.4.1.1 15992 a.35.1.1 17018 1octC 156 2.21e+01 1au7A a.4.1.1 15991 a.35.1.1 17017 1k94A 165 2.24e+01 a.39.1.7 68333 1b5eA 246 2.28e+01 1b5eA d.117.1.1 41056 1kkqA 269 2.31e+01 a.123.1.1 68679 1k7lA 288 2.33e+01 a.123.1.1 68268 1cs0B 382 2.35e+01 1c3oB c.8.3.1 30740 c.23.16.1 31417 1i7gA 287 2.35e+01 1jg8A 347 2.40e+01 1jg8A c.67.1.1 62946 1azwA 313 2.41e+01 1qtrA c.69.1.7 34658 1cozA 129 2.47e+01 1cozA c.26.1.2 31598 1eo1A 124 2.50e+01 1eo1A c.55.5.1 33739 1gca 309 2.51e+01 1gca c.93.1.1 35659 2dldA 337 2.51e+01 1dxy c.2.1.4 30099 c.23.12.1 31359 1a39 402 2.53e+01 1celA b.29.1.10 24305 1orc 71 2.56e+01 1orc a.35.1.2 17054 1g19A 350 2.56e+01 2reb c.37.1.11 32284 d.48.1.1 38770 1ykfA 352 2.56e+01 1pedA b.35.1.2 24757 c.2.1.1 29773 1qlaA 656 2.60e+01 1qlaA a.7.3.1 16328 c.3.1.4 30427 d.168.1.1 42310 1qg7A 67 2.63e+01 1a15A d.9.1.1 37449 1l9fA 389 2.65e+01 1el5A 389 2.65e+01 1b3mA c.3.1.2 30369 d.16.1.3 37937 3gbp 305 2.76e+01 1gca c.93.1.1 35661 1fc4A 401 2.79e+01 1bs0A c.67.1.4 59760 1g7rA 594 2.80e+01 1g7rA b.43.3.1 25716 b.43.3.1 25717 c.20.1.1 31034 c.37.1.8 32149 3ladA 476 2.86e+01 1lvl c.3.1.5 30573 c.3.1.5 30574 d.87.1.1 40208 1qirA 396 2.87e+01 1ajsA c.67.1.1 34290 1jdbF 382 2.93e+01 c.8.3.1 30757 c.23.16.1 31434 1eamA 307 3.02e+01 3mag c.66.1.9 34212 3mct 297 3.08e+01 3mag c.66.1.9 34215 1bky 307 3.08e+01 3mag c.66.1.9 34214 1a9xB 379 3.08e+01 1c3oB c.8.3.1 30732 c.23.16.1 31409 1eqa 297 3.12e+01 3mag c.66.1.9 34216 1eboA 131 3.15e+01 2eboA h.3.2.1 45757 3orcA 65 3.17e+01 1orc a.35.1.2 17061 1pdz 434 3.17e+01 4enl c.1.11.1 29215 d.54.1.1 38859 4dcg 307 3.27e+01 3mag c.66.1.9 34208 1qtrA 317 3.28e+01 1qtrA c.69.1.7 34660 1lea 84 3.29e+01 1lea a.4.5.2 16085 1yoo 396 3.36e+01 1ajsA c.67.1.1 34295 5eaaA 396 3.37e+01 1ajsA c.67.1.1 34328 2puaA 340 3.41e+01 1qpzA a.35.1.5 17098 c.93.1.1 35685 2gbp 309 3.44e+01 1gca c.93.1.1 35657 1f3oA 235 3.50e+01 1b0uA c.37.1.12 59631 1vpt 348 3.51e+01 3mag c.66.1.9 34207 1k4yA 534 3.53e+01 1cpy 421 3.55e+01 1ivyA c.69.1.5 34651 1e3oC 160 3.57e+01 1au7A a.4.1.1 59197 a.35.1.1 59198 1rgs 288 3.64e+01 1rgs b.82.3.2 28146 b.82.3.2 28147 1d1mA 65 3.80e+01 1orc a.35.1.2 17056 1l9vA 317 3.85e+01 1vp3 348 3.88e+01 3mag c.66.1.9 34209 1v39 322 3.88e+01 3mag c.66.1.9 34206 1vp9 322 3.88e+01 3mag c.66.1.9 34210 1vpwA 340 3.89e+01 1qpzA a.35.1.5 17087 c.93.1.1 35680 1aop 497 3.91e+01 2aop d.58.36.1 39501 d.58.36.1 39502 d.134.1.1 41425 d.134.1.1 41426 2aop 497 3.91e+01 2aop d.58.36.1 39503 d.58.36.1 39504 d.134.1.1 41427 d.134.1.1 41428 1qpzA 340 3.94e+01 1qpzA a.35.1.5 17097 c.93.1.1 35673 1wetA 340 3.94e+01 1qpzA a.35.1.5 17093 c.93.1.1 35670 1ktbA 405 3.94e+01 1bdhA 340 3.96e+01 1qpzA a.35.1.5 17089 c.93.1.1 35668 2pfkC 302 3.96e+01 3pfk c.89.1.1 35579 1fezA 256 3.98e+01 1fezA c.108.1.3 43343 1dbqA 289 3.99e+01 1qpzA c.93.1.1 35666 1g7oA 215 4.00e+01 1g7oA a.45.1.1 60332 c.47.1.5 60333