# 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 1o8uA 257 4.56e-02 c.14.1.3 81194 1szoA 257 4.82e-02 1ezwA 349 1.27e-01 1ezwA c.1.16.3 29558 1hx0A 496 2.67e-01 b.71.1.1 61346 c.1.8.1 61347 1az3A 244 4.17e-01 1rvaA c.52.1.2 33276 1jkmA 358 4.45e-01 1jkmA c.69.1.2 34633 1tk4A 121 4.95e-01 1ho1A 242 5.64e-01 1ho1A c.1.24.1 61097 2rveA 244 5.71e-01 1rvaA c.52.1.2 33283 1o5zA 442 5.76e-01 c.59.1.2 -7939 c.72.2.2 -8418 1hh1A 143 5.82e-01 1gefA c.52.1.18 61036 1tj9A 121 5.84e-01 1kpmA 121 6.13e-01 a.133.1.2 72844 1fv0A 121 6.14e-01 a.133.1.2 70147 1umgA 362 6.64e-01 1kczA 413 6.77e-01 c.1.11.2 68451 d.54.1.1 68452 1a3gA 308 7.19e-01 1daaA e.17.1.1 43286 1su4A 994 7.54e-01 b.82.7.1 -4927 c.108.1.7 -6854 d.220.1.1 -11668 f.33.1.1 -12333 1gefA 123 7.96e-01 1gefA c.52.1.18 60465 1smd 496 9.16e-01 1smd b.71.1.1 27768 c.1.8.1 28755 3bifA 468 9.71e-01 1bif c.37.1.7 31962 c.60.1.4 34008 1mumA 295 9.87e-01 c.1.12.7 85108 2bifA 469 1.00e+00 1bif c.37.1.7 31963 c.60.1.4 34009 1mvfD 82 1.04e+00 b.129.1.1 85143 1a79A 171 1.05e+00 1a79A c.52.2.1 33340 d.75.1.1 39739 1o50A 157 1.06e+00 d.37.1.1 -9604 d.37.1.1 -9605 1pgx 83 1.10e+00 2igd d.15.7.1 37823 1sqzA 121 1.16e+00 a.133.1.2 -1971 1jae 471 1.18e+00 1smd b.71.1.1 27773 c.1.8.1 28760 1bif 469 1.21e+00 1bif c.37.1.7 31961 c.60.1.4 34003 1eulA 994 1.31e+00 1eulA 1igd 61 1.36e+00 2igd d.15.7.1 37822 2igd 61 1.36e+00 2igd d.15.7.1 37821 1g94A 448 1.38e+00 b.71.1.1 65169 c.1.8.1 65170 1sx5A 244 1.43e+00 c.52.1.2 -7551 1p32C 209 1.56e+00 1p32A d.25.1.1 38381 1eonA 245 1.57e+00 1rvaA c.52.1.2 33238 1thm 279 1.58e+00 1gci c.41.1.1 32544 1ujxA 119 1.60e+00 b.26.1.2 -3325 1m5wA 243 1.61e+00 c.1.24.1 84836 1rvaA 244 1.66e+00 1rvaA c.52.1.2 33240 1b5tA 275 1.77e+00 1b5tA c.1.23.1 29676 1kkoA 413 1.98e+00 c.1.11.2 68675 d.54.1.1 68676 1qatB 622 2.10e+00 1djxB a.39.1.7 17355 b.7.1.1 23172 c.1.18.1 29600 1vdwA 254 2.24e+00 e.7.1.1 -11868 1f07A 321 2.37e+00 1ezwA c.1.16.3 59560 1p32A 209 2.52e+00 1p32A d.25.1.1 38379 1cxvA 164 2.60e+00 1ck7A d.92.1.11 40404 1un7A 400 2.67e+00 b.92.1.5 -5077 c.1.9.10 -5429 1pkoA 139 2.70e+00 b.1.1.1 88147 1qqtA 551 2.72e+00 1qqtA a.27.1.1 16923 c.26.1.1 31590 g.41.1.1 45175 1gjuA 637 2.75e+00 b.71.1.1 60580 c.1.8.1 60581 1qwgA 251 2.80e+00 unknown_sccs -5678 1aqm 453 2.80e+00 1smd b.71.1.1 27717 c.1.8.1 28704 1s2wA 295 2.89e+00 c.1.12.7 -5577 1pfvA 551 2.98e+00 a.27.1.1 -727 c.26.1.1 -6603 g.41.1.1 -12765 1jkmB 361 3.07e+00 1jkmA c.69.1.2 34634 830cA 168 3.12e+00 1ck7A d.92.1.11 40400 1f4lA 551 3.16e+00 1qqtA a.27.1.1 59648 c.26.1.1 59649 g.41.1.1 59650 1iyeA 309 3.18e+00 e.17.1.1 83786 1i1kA 309 3.24e+00 1daaA e.17.1.1 61533 1pymA 295 3.31e+00 1pymA c.1.12.7 29308 1a78A 134 3.56e+00 1c1lA b.29.1.3 24212 1p9oA 313 3.82e+00 unknown_sccs -8423 1vk3A 615 3.92e+00 d.79.4.1 -10416 d.79.4.1 -10417 d.139.1.1 -11154 d.139.1.1 -11155 1ipiA 123 4.10e+00 c.52.1.18 66255 1h8uA 117 4.12e+00 1h8uA d.169.1.1 60793 1rj9A 304 4.22e+00 a.24.13.1 -631 c.37.1.10 -7129 1v93A 296 4.26e+00 c.1.23.1 -5654 1gjwA 637 4.38e+00 b.71.1.1 60582 c.1.8.1 60583 1f1xA 322 4.88e+00 d.32.1.3 83208 d.32.1.3 83209 1cnv 299 4.91e+00 1cnv c.1.8.5 28989 1pzxA 289 5.09e+00 c.119.1.1 -8623 1vhh 162 5.27e+00 1vhh d.65.1.2 39550 1cye 129 5.41e+00 3chy c.23.1.1 31077 1b25A 619 5.55e+00 1b25A a.110.1.1 19044 d.152.1.1 41796 1edt 271 5.57e+00 2ebn c.1.8.5 28993 1dp0A 1023 5.72e+00 b.1.4.1 22073 b.1.4.1 22074 b.18.1.5 23722 b.30.5.1 24346 c.1.8.3 28845 1nf3C 128 5.90e+00 b.36.1.1 85596 1np6A 174 5.97e+00 c.37.1.10 85954 1k0eA 453 6.02e+00 d.161.1.1 67938 1pvmA 184 6.24e+00 d.37.1.1 -9612 d.37.1.1 -9613 unknown_sccs -12799 1gvmA 136 6.25e+00 b.109.1.1 70612 1qrqA 325 6.34e+00 1qrqA c.1.7.1 28667 1lvwA 295 6.75e+00 c.68.1.6 84723 1ex7A 186 6.77e+00 1gky c.37.1.1 59537 1mk4A 157 6.78e+00 d.108.1.1 84979 1lshA 1056 6.80e+00 a.118.4.1 74242 f.7.1.1 74243 f.7.1.1 74244 1exbA 332 6.83e+00 1qrqA c.1.7.1 28666 1hnuA 280 6.93e+00 1hnoA c.14.1.3 61096 1bglA 1023 7.04e+00 1bglA b.1.4.1 22097 b.1.4.1 22098 b.18.1.5 23734 b.30.5.1 24358 c.1.8.3 28857 1k0gA 453 7.09e+00 d.161.1.1 67940 1p5dX 463 7.31e+00 c.84.1.1 -8554 c.84.1.1 -8555 c.84.1.1 -8556 d.129.2.1 -11029 1pbuA 162 7.53e+00 d.58.46.1 88030 1gq2A 555 7.58e+00 c.2.1.7 70308 c.58.1.3 70309 1f1uA 323 7.60e+00 d.32.1.3 83200 d.32.1.3 83201 1v7rA 186 7.85e+00 c.51.4.1 -7546 1qasA 622 7.97e+00 1djxB a.39.1.7 17340 b.7.1.1 23157 c.1.18.1 29585 1ktbA 405 8.15e+00 b.71.1.1 72960 c.1.8.1 72961 1ow4A 129 8.20e+00 a.39.2.1 -876 1obfO 335 8.20e+00 c.2.1.3 86768 d.81.1.1 86769 1djxA 624 8.95e+00 1djxB a.39.1.7 17342 b.7.1.1 23159 c.1.18.1 29587 1e3sA 261 9.06e+00 1e6wA c.2.1.2 59201 1s6bB 119 9.33e+00 a.133.1.2 -1954 1vkdA 338 9.53e+00 1mnmA 100 9.59e+00 1mnmA d.88.1.1 40232 1q74A 303 9.60e+00 unknown_sccs -8121 1b43A 340 9.81e+00 1a76 a.60.7.1 18092 c.120.1.2 33362 1no5A 114 1.05e+01 unknown_sccs -9785 1iwgA 1053 1.09e+01 d.58.44.1 76874 d.58.44.1 76875 d.58.44.1 76876 d.58.44.1 76877 d.225.1.1 76878 d.225.1.1 76879 f.35.1.1 76880 f.35.1.1 76881 1djxB 624 1.11e+01 1djxB a.39.1.7 17343 b.7.1.1 23160 c.1.18.1 29588 1j0hA 588 1.12e+01 b.1.18.2 77027 b.71.1.1 77028 c.1.8.1 77029 1bli 483 1.12e+01 1bli b.71.1.1 27715 c.1.8.1 28702 1jz8A 1023 1.12e+01 b.1.4.1 67830 b.1.4.1 67831 b.18.1.5 67832 b.30.5.1 67833 c.1.8.3 67834 1psuA 140 1.13e+01 d.38.1.5 88285 1erzA 303 1.14e+01 1erzA d.160.1.2 59498 1vh5A 148 1.14e+01 d.38.1.5 -9677 1abrA 251 1.14e+01 1mrj d.165.1.1 42196 1k2yX 463 1.14e+01 c.84.1.1 68063 c.84.1.1 68064 c.84.1.1 68065 d.129.2.1 68066 1mhxA 65 1.15e+01 d.15.7.1 79134 1jxpA 186 1.16e+01 1jxpA b.47.1.3 26402 3chy 128 1.20e+01 3chy c.23.1.1 31038 1gypA 358 1.20e+01 1dssG c.2.1.3 30004 d.81.1.1 39919 1j09A 468 1.21e+01 a.97.1.1 77025 c.26.1.1 77026 1ceo 343 1.21e+01 1ceo c.1.8.3 28808 1h3fA 432 1.22e+01 c.26.1.1 76631 d.66.1.4 76632 2reb 352 1.24e+01 2reb c.37.1.11 32282 d.48.1.1 38767 1g5vA 88 1.25e+01 1g5vA b.34.9.1 60292 1lwjA 441 1.25e+01 b.71.1.1 74303 c.1.8.1 74304 1g59A 468 1.25e+01 a.97.1.1 60257 c.26.1.1 60258 1dj8A 89 1.31e+01 1bg8A a.57.1.1 17919 1daaA 282 1.32e+01 1daaA e.17.1.1 43270 1jceA 344 1.35e+01 c.55.1.1 62876 c.55.1.1 62877 1uf5A 303 1.37e+01 1gln 468 1.38e+01 1gln a.97.1.1 18752 c.26.1.1 31588 1n2zA 245 1.40e+01 c.92.2.2 79865 1bh6A 274 1.41e+01 1gci c.41.1.1 32487 1hnoA 280 1.41e+01 1hnoA c.14.1.3 61095 1cf9A 753 1.43e+01 1cf9A c.23.16.3 31441 e.5.1.1 42815 1pwxA 254 1.44e+01 c.2.1.2 -5858 1eejA 216 1.47e+01 1eejA c.47.1.9 33057 d.17.3.1 38071 1mxgA 435 1.50e+01 b.71.1.1 85193 c.1.8.1 85194 1gheA 177 1.51e+01 d.108.1.1 76222 1kolA 398 1.57e+01 b.35.1.2 77474 c.2.1.1 77475 1jcfA 344 1.63e+01 c.55.1.1 62878 c.55.1.1 62879 1byrA 155 1.63e+01 1byrA d.136.1.1 41450 1eokA 290 1.65e+01 1eokA c.1.8.5 28991 1jysA 242 1.65e+01 c.56.2.1 77216 1cec 343 1.66e+01 1ceo c.1.8.3 28809 1o20A 427 1.67e+01 c.82.1.1 86556 1vgwA 231 1.67e+01 c.68.1.13 -8237 1gky 187 1.68e+01 1gky c.37.1.1 31839 3tgl 269 1.71e+01 3tgl c.69.1.17 34733 1oa8A 133 1.78e+01 unknown_sccs -5142 1nm2A 317 1.81e+01 c.19.1.1 80654 d.58.23.1 80655 1gtxA 472 1.81e+01 1gtxA 3daaA 277 1.83e+01 1daaA e.17.1.1 43272 1a76 326 1.86e+01 1a76 a.60.7.1 18091 c.120.1.2 33361 1ax0 239 1.87e+01 1led b.29.1.1 24042 1t82A 155 1.87e+01 2mjpA 193 1.88e+01 1b78A c.51.4.1 33223 1jg1A 235 1.88e+01 c.66.1.7 66661 1g8aA 227 1.92e+01 c.66.1.3 -8049 1rxyA 253 1.92e+01 c.56.2.1 -7834 1e43A 483 1.93e+01 1bli b.71.1.1 59217 c.1.8.1 59218 1jmsA 381 1.93e+01 a.60.6.1 66889 a.60.12.1 75862 d.218.1.2 75863 1poa 118 1.94e+01 1poa a.133.1.2 19514 1np3A 338 1.96e+01 a.100.1.2 85946 c.2.1.6 85947 1uzbA 516 1.97e+01 c.82.1.1 -8552 1n3lA 372 1.99e+01 c.26.1.1 79966 1de4C 640 2.01e+01 1cx8B a.48.2.1 17779 c.8.4.1 30760 c.56.5.5 33848 1q52A 314 2.03e+01 c.14.1.3 -6246 1ud9A 245 2.07e+01 1jvnA 555 2.08e+01 c.1.2.1 67355 c.23.16.1 67356 1e6mA 128 2.12e+01 3chy c.23.1.1 31039 1dg3A 592 2.24e+01 1dg3A a.114.1.1 19078 c.37.1.8 32153 1l2tA 235 2.26e+01 c.37.1.12 73514 1p80A 753 2.28e+01 c.23.16.3 -6547 e.5.1.1 -11840 1nhp 447 2.29e+01 1nhp c.3.1.5 30549 c.3.1.5 30550 d.87.1.1 40196 1rm4A 337 2.29e+01 1bzyA 217 2.32e+01 1qk3A c.61.1.1 34071 1d2eA 397 2.33e+01 1efcA b.43.3.1 25701 b.44.1.1 25741 c.37.1.8 32136 1m4vA 204 2.33e+01 b.40.2.2 74459 d.15.6.1 74460 1dysA 348 2.35e+01 1bvwA c.6.1.1 30669 1f5nA 592 2.37e+01 1dg3A a.114.1.1 19077 c.37.1.8 32152 1u02A 239 2.40e+01 1bg8A 89 2.43e+01 1bg8A a.57.1.1 17925 1qrrA 394 2.43e+01 1qrrA c.2.1.2 29824 1q9uA 130 2.44e+01 unknown_sccs -11025 1dbiA 280 2.46e+01 1gci c.41.1.1 32543 1uyrA 737 2.47e+01 c.14.1.4 -6258 c.14.1.4 -6259 1pgs 314 2.50e+01 1pgs b.121.1.1 23653 b.121.1.1 23654 1ck7A 631 2.50e+01 1ck7A a.20.1.2 58969 b.66.1.1 27538 d.92.1.11 58970 g.14.1.2 44674 g.14.1.2 44675 g.14.1.2 44676 1vgvA 384 2.51e+01 c.87.1.3 -8575 1i24A 404 2.52e+01 c.2.1.2 83663 1n6aA 259 2.53e+01 b.76.2.1 80121 b.85.7.1 80122 1gd1O 334 2.58e+01 1dssG c.2.1.3 29962 d.81.1.1 39877 1cseE 274 2.58e+01 1gci c.41.1.1 32481 1h1nA 305 2.59e+01 c.1.8.3 70855 1qgwA 76 2.61e+01 1qgwA d.184.1.1 42616 1j8mF 297 2.61e+01 1ng1 a.24.13.1 62742 c.37.1.10 62743 1h3iA 293 2.63e+01 b.76.2.1 76635 b.85.7.1 76636 1iq6A 134 2.63e+01 d.38.1.4 76755 1josA 128 2.64e+01 d.52.7.1 84191 1udvA 89 2.65e+01 d.68.6.1 -10280 1euhA 475 2.67e+01 1euhA c.82.1.1 35369 1rss 151 2.68e+01 1rss a.75.1.1 18392 1pjhA 280 2.69e+01 c.14.1.3 -6229 1jpmA 366 2.69e+01 c.1.11.2 67031 d.54.1.1 67032 2dabA 282 2.69e+01 1daaA e.17.1.1 43274 1vizA 240 2.73e+01 c.1.4.1 -5212 1mw7A 240 2.75e+01 e.39.1.1 79557 1scs 237 2.77e+01 1nls b.29.1.1 23930 1egzA 291 2.77e+01 7a3hA c.1.8.3 28828 1fjgK 129 2.80e+01 1fjfK c.55.4.1 33733 1hfc 169 2.81e+01 1hfc d.92.1.11 40335 2aaa 484 2.82e+01 7taa b.71.1.1 27777 c.1.8.1 28764 1mhnA 59 2.84e+01 b.34.9.1 84964 1nouA 507 2.84e+01 c.1.8.6 85932 d.92.2.1 85933 1f6dA 376 2.85e+01 1f6dA c.87.1.3 35467 1b78A 193 2.86e+01 1b78A c.51.4.1 33221 1rlhA 173 2.91e+01 unknown_sccs -10786 1itwA 741 2.94e+01 c.77.1.2 76793 2trcP 217 2.96e+01 1b9yC c.47.1.6 33051 2fcr 173 2.99e+01 1rcf c.23.5.1 31151 1jxhA 288 3.03e+01 c.72.1.2 67415 1nls 237 3.07e+01 1nls b.29.1.1 23928 1nq6A 302 3.08e+01 c.1.8.3 -5332 1nhs 447 3.10e+01 1nhp c.3.1.5 30555 c.3.1.5 30556 d.87.1.1 40199 1okgA 373 3.11e+01 c.46.1.2 -7367 c.46.1.2 -7368 unknown_sccs -9494 1cliA 345 3.12e+01 1cliA d.79.4.1 39816 d.139.1.1 41459 1e44B 96 3.13e+01 1e44B b.101.1.1 59220 1g7sA 594 3.16e+01 1g7rA b.43.3.1 25712 b.43.3.1 25713 c.20.1.1 31032 c.37.1.8 32147 1js3A 486 3.16e+01 c.67.1.6 67215 1uaqA 158 3.20e+01 c.97.1.2 88386 1vi9A 299 3.20e+01 c.72.1.5 -8393 2bbkH 355 3.22e+01 2bbkH b.69.2.1 27634 1p6oA 161 3.24e+01 c.97.1.2 -8774 1gpmA 525 3.24e+01 1gpmA c.23.16.1 31405 c.26.2.1 31608 d.52.2.1 38826 1ub3A 220 3.24e+01 c.1.10.1 88395 1vc4A 254 3.32e+01 c.1.2.4 -5172 1o0iA 138 3.36e+01 d.38.1.5 86532 1f8xA 157 3.37e+01 1f8xA c.23.14.1 31397 1bag 425 3.37e+01 1bag b.71.1.1 27720 c.1.8.1 28707 1kq1A 77 3.39e+01 b.38.1.2 72848 1ohvA 472 3.43e+01 c.67.1.4 -8181 1bzsA 165 3.44e+01 1hfc d.92.1.11 40348 1bhgA 613 3.44e+01 1bhgA b.1.4.1 22161 b.18.1.5 23766 c.1.8.3 28889 1thfD 253 3.46e+01 1thfD c.1.2.1 28535 1kijA 390 3.46e+01 d.14.1.3 72514 d.122.1.2 72515 1qmyA 167 3.52e+01 1qmyA d.3.1.2 37094 1i76A 163 3.53e+01 1hfc d.92.1.11 61877 1gci 269 3.53e+01 1gci c.41.1.1 32503 1a88A 275 3.54e+01 1brt c.69.1.12 34707 1han 297 3.57e+01 1han d.32.1.3 38506 d.32.1.3 38507 1dfd 64 3.60e+01 1fxd d.58.1.4 38995 1lrzA 426 3.61e+01 a.2.7.4 78167 d.108.1.4 78168 d.108.1.4 78169 1a05A 358 3.61e+01 1cnzA c.77.1.1 35059 1iktA 120 3.61e+01 d.106.1.1 66188 1g0rA 293 3.61e+01 1g0rA c.68.1.6 34532 1egiA 147 3.61e+01 1eggA d.169.1.1 42331 3ezmA 101 3.65e+01 3ezmA b.89.1.1 28395 1nqkA 381 3.67e+01 c.1.16.4 -5607 1s6cA 183 3.70e+01 a.39.1.5 -858 1lx7A 253 3.70e+01 c.56.2.1 74329 1mt6A 280 3.72e+01 b.76.2.1 79446 b.85.7.1 79447 1ipaA 274 3.74e+01 c.116.1.1 71254 d.79.3.3 71255 1j31A 262 3.74e+01 d.160.1.2 -11473 1od2A 805 3.76e+01 c.14.1.4 86821 c.14.1.4 86822 1nfp 228 3.79e+01 1nfp c.1.16.2 29555 1vjzA 341 3.83e+01 c.1.8.3 -5318 1dtyA 429 3.88e+01 1dtyA c.67.1.4 34495 1dekA 241 3.89e+01 1dekA c.37.1.1 31842 1r3nA 462 3.89e+01 c.56.5.4 -7872 d.58.19.1 -10096 1fneA 192 3.92e+01 1iakA b.1.1.2 59896 d.19.1.1 59897 1fngA 192 3.92e+01 1iakA b.1.1.2 59904 d.19.1.1 59905 1rhcA 330 3.92e+01 c.1.16.3 -5606 1rw7A 243 3.92e+01 c.23.16.2 -6530 1qvzA 237 3.94e+01 c.23.16.2 -6537 1rpxA 230 3.96e+01 1rpxA c.1.2.2 28536 1joa 447 3.97e+01 1nhp c.3.1.5 30563 c.3.1.5 30564 d.87.1.1 40203 1ktzB 122 3.98e+01 g.7.1.3 68868 2rslA 140 3.98e+01 2rslA c.53.1.1 33345