# List of top-scoring protein chains for t2k-100-30-str2-scores 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 1neiA 60 9.50e-02 d.253.1.1 91843 1guqA 348 1.70e-01 1guqA d.13.1.2,d.13.1.2 37522,37523 1gupA 348 1.74e-01 1guqA d.13.1.2,d.13.1.2 37534,37535 1hxpA 348 2.01e-01 1guqA d.13.1.2,d.13.1.2 37530,37531 1udh 244 2.51e-01 3eugA c.18.1.1 31015 1jtdB 273 3.47e-01 b.69.5.2 67265 1vbuA 328 3.56e-01 1g99A 408 3.75e-01 1g99A c.55.1.2,c.55.1.2 33457,33458 1x3mA 415 4.54e-01 1udg 244 5.29e-01 3eugA c.18.1.1 31016 1wyuB 474 1.10e+00 2aehA 369 2.07e+00 1vhxA 150 2.25e+00 c.55.3.8 100712 2avtA 378 2.81e+00 2awaA 390 2.87e+00 2bkyA 97 3.44e+00 1u2eA 289 3.61e+00 1pujA 282 3.94e+00 c.37.1.8 88294 1sspE 223 4.09e+00 3eugA c.18.1.1 31009 2al6A 375 4.16e+00 1akz 223 4.72e+00 3eugA c.18.1.1 31007 4eugA 229 4.72e+00 3eugA c.18.1.1 31019 3eugA 229 4.76e+00 3eugA c.18.1.1 31018 1eu1A 780 5.00e+00 1dmr b.52.2.2,c.81.1.1 26903,35311 1dnpA 471 5.00e+00 1qnf a.99.1.1,c.28.1.1 18775,31630 1yn8A 59 5.16e+00 1s7iA 124 5.17e+00 d.58.4.9 105353 1uteA 313 5.27e+00 1uteA d.159.1.1 42078 1dd3A 128 5.52e+00 1dd3C a.108.1.1,d.45.1.1 19031,38760 1ih7A 903 5.55e+00 1clqA c.55.3.5,e.8.1.1 62375,62376 1ituA 369 5.86e+00 c.1.9.7 71423 1yixA 265 6.03e+00 1clqA 903 6.06e+00 1clqA c.55.3.5,e.8.1.1 33717,43006 1a12A 413 6.22e+00 1a12A b.69.5.1 27663 1khqA 212 6.47e+00 d.3.1.1 90964 1flzA 228 6.51e+00 3eugA c.18.1.1 31027 1m5yA 408 6.57e+00 a.167.1.1,d.26.1.1,d.26.1.1 78664,78665,78666 1ppn 212 6.60e+00 1cs8A d.3.1.1 37004 2cioA 212 6.67e+00 1awcA 110 6.87e+00 1awcA a.4.5.21 16167 1eugA 229 6.96e+00 3eugA c.18.1.1 31021 9pap 212 6.98e+00 1cs8A d.3.1.1 37006 1u59A 287 7.40e+00 d.144.1.7 107681 1sazA 381 7.42e+00 1euiA 228 7.82e+00 3eugA c.18.1.1 31028 1dvh 79 7.82e+00 1c53 a.3.1.1 15802 3nodB 423 7.99e+00 1nseA d.174.1.1 42513 1r6dA 337 8.03e+00 c.2.1.2 97148 1h6kX 97 8.12e+00 d.58.7.1 60684 1xat 212 8.41e+00 2xat b.81.1.3 28059 2sniI 83 8.96e+00 2sniI d.40.1.1 38573 1n0qA 93 8.99e+00 k.37.1.1 79754 1i2tA 61 9.26e+00 1i2tA a.144.1.1 61582 1icwA 72 9.44e+00 1tvxA d.9.1.1 37357 1dd3C 32 9.44e+00 1dd3C a.108.1.1 19033 2bjdA 101 9.91e+00 2xat 212 9.98e+00 2xat b.81.1.3 28058 1h6kZ 98 1.01e+01 d.58.7.1 60686 1ko9A 345 1.02e+01 a.96.1.3,d.129.1.2 68717,68718 1gz8A 299 1.09e+01 d.144.1.7 83405 1xnpA 202 1.10e+01 1wp1A 474 1.11e+01 1hcl 298 1.12e+01 1hcl d.144.1.7 41593 1e1xA 299 1.12e+01 1hcl d.144.1.7 59157 1s5dA 240 1.12e+01 d.166.1.1 98541 1g26A 31 1.15e+01 1g26A g.3.16.1 44381 1mnmC 87 1.19e+01 1akhB a.4.1.1 15983 1nh9A 87 1.24e+01 d.68.6.1 91878 1v8gA 329 1.25e+01 a.46.2.1,c.27.1.1 100505,100506 1li5B 461 1.26e+01 a.27.1.1,c.26.1.1 73914,73915 1xxbA 78 1.29e+01 1xxaA d.74.2.1 39706 2azpA 318 1.31e+01 1i4jA 110 1.32e+01 d.55.1.1 76734 1hxiA 121 1.34e+01 1hxiA a.118.8.1 61366 2booA 247 1.35e+01 2fcr 173 1.40e+01 1rcf c.23.5.1 31151 1li5A 461 1.41e+01 a.27.1.1,c.26.1.1 73912,73913 1k1vA 41 1.44e+01 a.37.1.1 71999 1wdvA 152 1.45e+01 1z2uA 150 1.45e+01 1hl9A 449 1.46e+01 b.71.1.3,c.1.8.11 90650,90651 1ciqA 40 1.48e+01 2sniI d.40.1.1 38576 1tuc 63 1.49e+01 1tuc b.34.2.1 24492 2fr1A 486 1.53e+01 1wj7A 104 1.55e+01 1aty 79 1.57e+01 1aty j.35.1.1 46259 1h0xA 100 1.62e+01 d.68.6.1 76451 1xbbA 291 1.63e+01 3il8 72 1.63e+01 1tvxA d.9.1.1 37356 1q4mA 221 1.64e+01 a.132.1.3 95805 2f2gA 221 1.66e+01 1hjxA 362 1.68e+01 c.1.8.5,d.26.3.1 83512,83513 1bxeA 113 1.73e+01 1bxeA d.55.1.1 38898 1r6fA 310 1.74e+01 e.46.1.1 97149 1wxrA 1048 1.74e+01 1vquA 374 1.77e+01 1jvpP 298 1.78e+01 d.144.1.7 67371 2dvh 79 1.78e+01 1c53 a.3.1.1 15803 1ykuA 136 1.81e+01 1cnzA 363 1.82e+01 1cnzA c.77.1.1 35061 1yoaA 159 1.85e+01 1coaI 64 1.86e+01 2sniI d.40.1.1 38574 1ehiA 377 1.86e+01 1iow c.30.1.2,d.142.1.1 31716,41484 1shg 62 1.90e+01 1ckaA b.34.2.1 24493 1axn 323 1.92e+01 1avc a.65.1.1 18149 1tufA 434 1.99e+01 b.49.2.3,c.1.6.1 107335,107336 1ehaA 558 2.05e+01 1ehaA b.1.18.2,b.71.1.1,c.1.8.1 21859,27786,28773 1b0uA 262 2.06e+01 1b0uA c.37.1.12 32370 1agrE 205 2.09e+01 1agrE a.91.1.1 18538 1hl8A 449 2.13e+01 b.71.1.3,c.1.8.11 90646,90647 1aii 323 2.19e+01 1avc a.65.1.1 18150 1w2lA 99 2.33e+01 1hbzA 498 2.34e+01 1cf9A e.5.1.1 60937 1gweA 503 2.36e+01 e.5.1.1 70667 1zwyA 185 2.38e+01 1to2I 64 2.38e+01 1cyx 205 2.41e+01 1cyx b.6.1.2 23023 1pwt 61 2.46e+01 1tud b.34.2.1 24490 1uj0A 62 2.48e+01 b.34.2.1 99449 1r6wA 322 2.53e+01 c.1.11.2,d.54.1.1 97165,97166 1qfcA 306 2.53e+01 1uteA d.159.1.1 42077 2aa4A 289 2.57e+01 1w97L 246 2.59e+01 1xxaA 78 2.61e+01 1xxaA d.74.2.1 39700 1be9A 119 2.62e+01 1pdr b.36.1.1 24774 1cyw 205 2.63e+01 1cyx b.6.1.2 23024 1z96A 40 2.64e+01 1rlzA 369 2.67e+01 c.31.1.1 104989 1v4pA 157 2.72e+01 2fggA 101 2.75e+01 1twiA 434 2.76e+01 b.49.2.3,c.1.6.1 107399,107400 1il8A 72 2.77e+01 1tvxA d.9.1.1 37365 1qtwA 285 2.79e+01 1qumA c.1.15.1 29392 1vg5A 73 2.79e+01 1s12A 94 2.80e+01 1kx5B 102 2.82e+01 a.22.1.1 77594 1h2vZ 156 2.92e+01 d.58.7.1 76595 2a6aA 218 3.06e+01 1xd3A 230 3.09e+01 1zk8A 183 3.14e+01 1dhs 344 3.19e+01 1dhs c.31.1.1 31727 1ayg 80 3.20e+01 451c a.3.1.1 15831 1lw6I 64 3.34e+01 d.40.1.1 74294 1pgl2 370 3.34e+01 1bssA 244 3.35e+01 1rvaA c.52.1.2 33256 1ty9A 222 3.37e+01 1xyzA 347 3.39e+01 1taxA c.1.8.3 28804 1xmxA 385 3.43e+01 2evwX 166 3.44e+01 1wehA 171 3.44e+01 1u7lA 392 3.45e+01 2bv2A 83 3.55e+01 1j3wA 163 3.57e+01 d.110.7.1 90833 1dulA 69 3.57e+01 1dulA a.36.1.1 17121 1np7A 489 3.66e+01 a.99.1.1,c.28.1.1 80677,80678 1fhuA 320 3.75e+01 1fhuA c.1.11.2,d.54.1.1 29234,38878 1khoA 370 3.78e+01 a.124.1.1,b.12.1.3 72489,72490 1iq8A 582 3.79e+01 c.1.20.1,b.122.1.1,d.17.6.1 71270,83074,83075 1m3qA 317 3.92e+01 a.96.1.3,d.129.1.2 91184,91185 1qumA 285 3.94e+01 1qumA c.1.15.1 29393 1v9nA 360 3.95e+01 1jsxA 207 3.95e+01 c.66.1.20 71846 1griA 217 3.97e+01 1griA b.34.2.1,b.34.2.1,d.93.1.1 24531,24532,40473 1hkvA 453 3.98e+01 b.49.2.3,c.1.6.1 83559,83560 1az3A 244 3.99e+01 1rvaA c.52.1.2 33276 1cm7A 363 4.01e+01 1cnzA c.77.1.1 35063 1jqnA 883 4.01e+01 c.1.12.3 77159 1xjdA 345 4.06e+01 1ti6A 875 4.08e+01 b.52.2.2,c.81.1.1 106974,106975 1fvaA 217 4.20e+01 1fvaA d.58.28.1 39409 1n9bA 265 4.20e+01 e.3.1.1 85463 1oo4A 111 4.25e+01 d.93.1.1 87185 1v3vA 333 4.31e+01 b.35.1.2,c.2.1.1 108345,108346 1x65A 89 4.32e+01 1fvgA 199 4.33e+01 1fvaA d.58.28.1 39408 2itg 163 4.34e+01 1b9dA c.55.3.2 33669 1v7oA 165 4.34e+01 d.67.1.2 100480 1pa4A 116 4.37e+01 d.52.7.1 94409 2a19B 284 4.37e+01 2rveA 244 4.48e+01 1rvaA c.52.1.2 33283 1bmv2 374 4.55e+01 1bmv2 1v30A 124 4.55e+01 1gngX 39 4.56e+01 1hzdA 272 4.56e+01 c.14.1.3 65969 2fdbM 164 4.56e+01 1otvA 259 4.57e+01 a.132.1.4 93526 1bfeA 119 4.62e+01 1pdr b.36.1.1 24775 1m1zA 513 4.66e+01 c.26.2.1,d.153.1.1 78457,78458 1jgtA 513 4.72e+01 c.26.2.1,d.153.1.1 66684,66685 1xqoA 256 4.73e+01 1owqA 361 4.85e+01 c.1.8.5,d.26.3.1 104041,104042 1bdg 451 4.86e+01 1qhaA c.55.1.3,c.55.1.3 33461,33462 1c4oA 664 4.87e+01 1d2mA c.37.1.19,c.37.1.19 32415,32416 1wyxA 69 5.00e+01 1r7jA 95 5.02e+01 a.4.5.49 104836 1zhvA 134 5.03e+01 2bcfA 276 5.05e+01 1cis 66 5.07e+01 2sniI k.1.1.1 46375 2pac 82 5.09e+01 451c a.3.1.1 15907 1jv1A 505 5.18e+01 c.68.1.5 71892 1wba 175 5.19e+01 1wba b.42.4.1 25591 2a2nA 176 5.26e+01 2ajgA 196 5.27e+01 1b96A 244 5.29e+01 1rvaA c.52.1.2 33268 1qadA 111 5.30e+01 1qadA d.93.1.1 40498 1hynP 379 5.31e+01 1hynP d.112.1.2 61408 1tp5A 119 5.31e+01 2ghjA 118 5.46e+01 1mjhB 162 5.46e+01 1mjhA c.26.2.4 31640 1qahA 136 5.48e+01 d.79.1.1 96338 1s14A 194 5.52e+01 d.122.1.2 98329 1w6sB 74 5.58e+01 1sx5A 244 5.65e+01 c.52.1.2 99023 1b94A 244 5.66e+01 1rvaA c.52.1.2 33250 2c9aA 259 5.66e+01 1xreA 217 5.67e+01 1zmmA 33 5.68e+01 1ok7A 366 5.80e+01 d.131.1.1,d.131.1.1,d.131.1.1 103992,103993,103994 1kssA 571 5.83e+01 a.138.1.3,c.3.1.4,d.168.1.1 72928,72929,72930 1d2mA 665 5.84e+01 1d2mA c.37.1.19,c.37.1.19 32417,32418 1pinA 163 5.86e+01 1pinA b.72.1.1,d.26.1.1 27802,38431 2ewcA 126 5.86e+01 1mmiA 366 5.92e+01 d.131.1.1,d.131.1.1,d.131.1.1 91309,91310,91311 1xo7A 166 5.94e+01 2axtE 84 6.11e+01 2g7sA 194 6.11e+01 1ta0A 197 6.14e+01 c.108.1.16 106729 1ir3A 306 6.15e+01 1fmk d.144.1.7 41702 1qjdA 571 6.19e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19695,30432,42315 1irk 306 6.20e+01 1fmk d.144.1.7 41703 1wnaA 131 6.21e+01 1b97A 244 6.23e+01 1rvaA c.52.1.2 33252 1ybxA 143 6.29e+01 1ebmA 317 6.35e+01 1ebmA a.96.1.3,d.129.1.2 18751,41300 2sli 679 6.39e+01 2sli b.29.1.9,b.68.1.1 24274,27611 1ac5 483 6.44e+01 1ac5 c.69.1.5 34653 4sli 679 6.44e+01 2sli b.29.1.9,b.68.1.1 24275,27612 1azsB 212 6.48e+01 1azsA d.58.29.1 39423 1nj4A 363 6.49e+01 b.105.1.1,e.3.1.1 80545,80546 1f9aA 168 6.50e+01 1f9aA c.26.1.3 31602 1woyA 500 6.58e+01 1fhvA 323 6.58e+01 1fhuA c.1.11.2,d.54.1.1 29235,38879 1ng4A 390 6.60e+01 c.3.1.2,d.16.1.3 85666,85667 1eztA 166 6.60e+01 1agrE a.91.1.1 18541 1hd8A 363 6.64e+01 b.105.1.1,e.3.1.1 65803,65804 1hf2A 210 6.69e+01 1hf2A b.80.3.1,c.102.1.1 60992,60993 1m70A 190 6.71e+01 a.3.1.4,a.3.1.4 91200,91201 1s0pA 176 6.77e+01 a.192.1.1 98300 1m6yA 301 6.81e+01 a.60.13.1,c.66.1.23 78716,78717 1axdA 209 6.85e+01 1gnwA a.45.1.1,c.47.1.5 17730,33024 1nzoA 363 6.86e+01 b.105.1.1,e.3.1.1 92383,92384 1q9iA 571 6.88e+01 a.138.1.3,c.3.1.4,d.168.1.1 96273,96274,96275 1xpjA 126 6.89e+01 1ryiA 382 6.93e+01 1h9oA 112 6.95e+01 1qadA d.93.1.1 60837 1el6A 219 6.96e+01 1el6B d.182.1.1 42606 1y0pA 571 6.99e+01 1y02A 120 7.05e+01 1y43A 39 7.06e+01 1a91 79 7.11e+01 1a91 f.17.1.1 43635 1yzfA 195 7.17e+01 1cr6B 554 7.22e+01 1cr6B c.69.1.11,c.108.1.2 34688,43338 1cch 82 7.26e+01 451c a.3.1.1 15902 1a8vA 121 7.26e+01 1a62 a.140.3.1,b.40.4.5 64712,64713 2etxA 209 7.30e+01 1ysc 421 7.33e+01 1ivyA c.69.1.5 34652 1r6vA 671 7.33e+01 4blmA 265 7.38e+01 1btl e.3.1.1 42721 1ulrA 88 7.39e+01 1wgbA 159 7.40e+01 1cqzA 554 7.41e+01 1cr6B c.69.1.11,c.108.1.2 34689,43339 1vf5F 35 7.41e+01 f.23.25.1 100586 821p 166 7.43e+01 1ctqA c.37.1.8 31969 1dm5A 315 7.47e+01 1avc a.65.1.1 18186 1hyeA 313 7.50e+01 2cmd c.2.1.5,d.162.1.1 61400,61401 1dtyA 429 7.56e+01 1dtyA c.67.1.4 34495 2aqwA 332 7.57e+01 1qb4A 883 7.61e+01 c.1.12.3 74640 1m6pA 152 7.67e+01 1m6pA b.64.1.1 27519 1te5A 257 7.68e+01 d.153.1.1 106795 1z6fA 363 7.69e+01 1bs9 207 7.84e+01 1bs9 c.69.1.30 31330 1pzlA 237 7.84e+01 a.123.1.1 104393 1g66A 207 7.90e+01 1bs9 c.69.1.30 31329 1aeiA 315 7.90e+01 1avc a.65.1.1 18180 2faoA 309 7.91e+01 2fd4A 122 7.94e+01 1y9aA 360 7.95e+01 1rwrA 301 7.96e+01 b.80.1.11 97990 1fiy 883 7.99e+01 1fiy c.1.12.3 29307 1s0aA 429 8.03e+01 c.67.1.4 98263 1lwyA 324 8.08e+01 a.96.1.3,d.129.1.2 78285,78286 1qj5A 429 8.16e+01 1dtyA c.67.1.4 34493 2bhvA 246 8.21e+01 1bvzA 585 8.30e+01 1bvzA b.1.18.2,b.71.1.1,c.1.8.1 21856,27783,28770 1vm8A 534 8.30e+01 2bh4X 134 8.38e+01 1aoeA 192 8.40e+01 1aoeA c.71.1.1 34923 1e39A 571 8.51e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19694,30431,42314 1xfsA 178 8.51e+01 d.129.3.5 109589 1pzqA 60 8.53e+01 a.34.3.1 95466 1el6B 219 8.54e+01 1el6B d.182.1.1 42607 1rvaA 244 8.66e+01 1rvaA c.52.1.2 33240 1pdr 99 8.75e+01 1pdr b.36.1.1 24771 1sfkA 76 8.80e+01 a.190.1.1 105488 1tie 172 8.82e+01 1wba b.42.4.1 25592 1i2sA 282 8.83e+01 e.3.1.1 71104 1fsu 492 8.83e+01 1auk c.76.1.2 35032 1bw0A 416 8.90e+01 1bw0A c.67.1.1 34385 1ml8A 134 8.93e+01 d.227.1.2 85013 2fuvA 549 8.95e+01