# List of top-scoring protein chains for t2k-100-30-alpha-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 7.24e-02 d.253.1.1 91843 1guqA 348 2.08e-01 1guqA d.13.1.2,d.13.1.2 37522,37523 1gupA 348 2.24e-01 1guqA d.13.1.2,d.13.1.2 37534,37535 1hxpA 348 2.68e-01 1guqA d.13.1.2,d.13.1.2 37530,37531 1uch 230 1.25e+00 1uch d.3.1.6 37129 1eu1A 780 1.28e+00 1dmr b.52.2.2,c.81.1.1 26903,35311 1bxeA 113 1.36e+00 1bxeA d.55.1.1 38898 1zyeA 220 1.48e+00 1i4jA 110 2.17e+00 d.55.1.1 76734 1v30A 124 2.82e+00 1ehaA 558 2.86e+00 1ehaA b.1.18.2,b.71.1.1,c.1.8.1 21859,27786,28773 1i2tA 61 3.16e+00 1i2tA a.144.1.1 61582 1yn8A 59 3.55e+00 2aehA 369 4.01e+00 1s7iA 124 4.45e+00 d.58.4.9 105353 1eh9A 558 4.52e+00 1ehaA b.1.18.2,b.71.1.1,c.1.8.1 21858,27785,28772 1bfeA 119 4.65e+00 1pdr b.36.1.1 24775 1xpjA 126 4.98e+00 2fd4A 122 5.20e+00 2fnbA 95 5.48e+00 2fnbA b.1.2.1 21979 1fc6A 388 6.00e+00 1fc6A b.36.1.3,c.14.1.2 64738,64739 2au5A 139 6.44e+00 1dd3C 32 6.73e+00 1dd3C a.108.1.1 19033 1dvh 79 6.85e+00 1c53 a.3.1.1 15802 2al6A 375 7.01e+00 1pc3A 350 7.04e+00 c.94.1.1 104102 1jvpP 298 7.10e+00 d.144.1.7 67371 1xd3A 230 7.20e+00 1m1zA 513 7.42e+00 c.26.2.1,d.153.1.1 78457,78458 1g9lA 144 7.45e+00 1g9lA a.144.1.1 60399 1udg 244 7.50e+00 3eugA c.18.1.1 31016 1gz8A 299 8.16e+00 d.144.1.7 83405 1awcA 110 8.27e+00 1awcA a.4.5.21 16167 1jgtA 513 8.37e+00 c.26.2.1,d.153.1.1 66684,66685 1u2xA 474 8.49e+00 c.72.1.3 107622 1zavU 30 8.72e+00 1wgvA 124 9.23e+00 1udh 244 9.33e+00 3eugA c.18.1.1 31015 1pujA 282 9.36e+00 c.37.1.8 88294 1n7fA 97 9.37e+00 b.36.1.1 91692 1nh9A 87 9.41e+00 d.68.6.1 91878 1h6kZ 98 9.79e+00 d.58.7.1 60686 1s0pA 176 9.87e+00 a.192.1.1 98300 1axn 323 9.88e+00 1avc a.65.1.1 18149 2dvh 79 9.99e+00 1c53 a.3.1.1 15803 1eylA 186 1.03e+01 1wba b.42.4.1 25593 1hjxA 362 1.03e+01 c.1.8.5,d.26.3.1 83512,83513 1h6kX 97 1.07e+01 d.58.7.1 60684 1rwrA 301 1.08e+01 b.80.1.11 97990 1e1xA 299 1.09e+01 1hcl d.144.1.7 59157 1n7eA 97 1.11e+01 b.36.1.1 91691 1vbuA 328 1.12e+01 1hkvA 453 1.13e+01 b.49.2.3,c.1.6.1 83559,83560 2sniI 83 1.14e+01 2sniI d.40.1.1 38573 1hcl 298 1.15e+01 1hcl d.144.1.7 41593 2pgd 482 1.15e+01 2pgd a.100.1.1,c.2.1.6 18778,30190 2bhoA 130 1.17e+01 1ciqA 40 1.19e+01 2sniI d.40.1.1 38576 1k1vA 41 1.22e+01 a.37.1.1 71999 2axwA 134 1.23e+01 1t6cA 315 1.23e+01 c.55.1.8,c.55.1.8 106558,106559 1aty 79 1.26e+01 1aty j.35.1.1 46259 1a12A 413 1.26e+01 1a12A b.69.5.1 27663 1mugA 168 1.27e+01 1mugA c.18.1.2 31030 1u04A 771 1.28e+01 b.34.14.1,c.55.3.10 107539,107540 1p0hA 318 1.30e+01 d.108.1.1 93866 1ti6A 875 1.31e+01 b.52.2.2,c.81.1.1 106974,106975 1zwyA 185 1.36e+01 1y02A 120 1.38e+01 1ex2A 189 1.38e+01 1ex2A c.51.4.2 33225 2c27A 315 1.39e+01 1hl9A 449 1.42e+01 b.71.1.3,c.1.8.11 90650,90651 1ituA 369 1.42e+01 c.1.9.7 71423 1otvA 259 1.44e+01 a.132.1.4 93526 2bsjA 133 1.47e+01 2awaA 390 1.47e+01 2avtA 378 1.50e+01 1w97L 246 1.50e+01 2c9aA 259 1.51e+01 1tie 172 1.51e+01 1wba b.42.4.1 25592 1dd3A 128 1.55e+01 1dd3C a.108.1.1,d.45.1.1 19031,38760 1jtdB 273 1.58e+01 b.69.5.2 67265 1s12A 94 1.59e+01 1sspE 223 1.72e+01 3eugA c.18.1.1 31009 1dnpA 471 1.74e+01 1qnf a.99.1.1,c.28.1.1 18775,31630 1akz 223 1.76e+01 3eugA c.18.1.1 31007 2fe5A 94 1.77e+01 1cis 66 1.81e+01 2sniI k.1.1.1 46375 1xnpA 202 1.85e+01 1stzA 338 1.87e+01 a.4.5.51,d.110.2.3 106009,106010 1irk 306 1.87e+01 1fmk d.144.1.7 41703 1p2hA 571 1.89e+01 a.138.1.3,c.3.1.4,d.168.1.1 93930,93931,93932 1to2I 64 1.93e+01 1hd8A 363 1.93e+01 b.105.1.1,e.3.1.1 65803,65804 1nj4A 363 1.94e+01 b.105.1.1,e.3.1.1 80545,80546 1jfmA 174 1.94e+01 d.19.1.1 66640 9pap 212 1.94e+01 1cs8A d.3.1.1 37006 1q9iA 571 1.94e+01 a.138.1.3,c.3.1.4,d.168.1.1 96273,96274,96275 1ppn 212 1.99e+01 1cs8A d.3.1.1 37004 1g26A 31 2.01e+01 1g26A g.3.16.1 44381 1lw6I 64 2.05e+01 d.40.1.1 74294 2cyjA 118 2.06e+01 1aii 323 2.07e+01 1avc a.65.1.1 18150 1qjdA 571 2.08e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19695,30432,42315 1z96A 40 2.10e+01 1ir3A 306 2.10e+01 1fmk d.144.1.7 41702 1be9A 119 2.12e+01 1pdr b.36.1.1 24774 1tp5A 119 2.12e+01 1dulA 69 2.14e+01 1dulA a.36.1.1 17121 1wnaA 131 2.21e+01 1coaI 64 2.27e+01 2sniI d.40.1.1 38574 1dm5A 315 2.28e+01 1avc a.65.1.1 18186 1c7jA 489 2.31e+01 2bce c.69.1.1 34631 1opjA 293 2.35e+01 d.144.1.7 87230 1khqA 212 2.35e+01 d.3.1.1 90964 2fywA 267 2.35e+01 2sli 679 2.39e+01 2sli b.29.1.9,b.68.1.1 24274,27611 4sli 679 2.43e+01 2sli b.29.1.9,b.68.1.1 24275,27612 1twiA 434 2.49e+01 b.49.2.3,c.1.6.1 107399,107400 1icwA 72 2.56e+01 1tvxA d.9.1.1 37357 1s7zA 117 2.58e+01 a.159.3.1 98715 1tufA 434 2.59e+01 b.49.2.3,c.1.6.1 107335,107336 2bshA 125 2.60e+01 1hyeA 313 2.64e+01 2cmd c.2.1.5,d.162.1.1 61400,61401 1q0sA 259 2.70e+01 c.66.1.28 95509 1vg5A 73 2.76e+01 1e39A 571 2.78e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19694,30431,42314 2cioA 212 2.84e+01 1aeiA 315 2.85e+01 1avc a.65.1.1 18180 1mmiA 366 2.86e+01 d.131.1.1,d.131.1.1,d.131.1.1 91309,91310,91311 1y0pA 571 2.88e+01 1wehA 171 2.91e+01 1lj1A 571 2.93e+01 a.138.1.3,c.3.1.4,d.168.1.1 78023,78024,78025 2bzpA 226 2.94e+01 1kssA 571 2.95e+01 a.138.1.3,c.3.1.4,d.168.1.1 72928,72929,72930 1ykuA 136 2.96e+01 1wyuB 474 2.96e+01 1r30A 369 3.11e+01 c.1.28.1 96895 1dmr 823 3.11e+01 1dmr b.52.2.2,c.81.1.1 26904,35312 1auiA 521 3.14e+01 1auiA d.159.1.3 42085 1m64A 571 3.19e+01 a.138.1.3,c.3.1.4,d.168.1.1 78683,78684,78685 1n0qA 93 3.21e+01 k.37.1.1 79754 1vhxA 150 3.26e+01 c.55.3.8 100712 1pdr 99 3.27e+01 1pdr b.36.1.1 24771 1miwA 404 3.36e+01 a.173.1.1,d.218.1.4 79162,79163 1ak1 310 3.39e+01 1ak1 c.92.1.1 35594 1r0kA 388 3.57e+01 a.69.3.1,c.2.1.3,d.81.1.3 104723,104724,104725 1e19A 314 3.75e+01 1b7bA c.73.1.1 34967 1fmk 452 3.75e+01 1fmk b.34.2.1,d.93.1.1,d.144.1.7 24511,40436,41690 2bh1A 250 3.78e+01 1wqsA 173 3.85e+01 1jqnA 883 3.87e+01 c.1.12.3 77159 1txnA 328 3.87e+01 1dmmA 131 3.92e+01 1opy d.17.4.3 38114 1hl8A 449 3.94e+01 b.71.1.3,c.1.8.11 90646,90647 1on0A 158 3.96e+01 d.108.1.1 87095 1az5 99 4.07e+01 1hvc b.50.1.1 26747 1jsxA 207 4.07e+01 c.66.1.20 71846 1agrE 205 4.08e+01 1agrE a.91.1.1 18538 1gvnA 90 4.08e+01 a.8.2.1 76353 1vg0A 650 4.09e+01 c.3.1.3,d.16.1.6 108596,108597 1z6fA 363 4.13e+01 1ng2A 193 4.15e+01 b.34.2.1,b.34.2.1 85660,85661 1yixA 265 4.20e+01 1xxoA 147 4.21e+01 1w9aA 147 4.22e+01 1xbbA 291 4.32e+01 1m70A 190 4.40e+01 a.3.1.4,a.3.1.4 91200,91201 1hxiA 121 4.41e+01 1hxiA a.118.8.1 61366 2dln 306 4.45e+01 1iow c.30.1.2,d.142.1.1 31715,41483 1c7iA 489 4.49e+01 1thg c.69.1.1 34632 1wj7A 104 4.52e+01 1wp1A 474 4.64e+01 2ac4A 309 4.65e+01 2b4gA 317 4.74e+01 1xreA 217 4.76e+01 3il8 72 4.78e+01 1tvxA d.9.1.1 37356 1ayg 80 4.78e+01 451c a.3.1.1 15831 1q5qA 259 4.78e+01 d.153.1.4 95904 1xat 212 4.79e+01 2xat b.81.1.3 28059 1k1gA 131 4.79e+01 d.51.1.1 68015 2d4pA 141 4.80e+01 2ajrA 331 4.81e+01 1bbzE 58 4.85e+01 1bbzA b.34.2.1 24479 1gngX 39 4.86e+01 1il8A 72 4.88e+01 1tvxA d.9.1.1 37365 1a8vA 121 4.88e+01 1a62 a.140.3.1,b.40.4.5 64712,64713 1aboA 62 5.00e+01 1bbzA b.34.2.1 24474 1v9nA 360 5.01e+01 2xat 212 5.03e+01 2xat b.81.1.3 28058 1xhkA 187 5.07e+01 1zwwA 256 5.11e+01 1np7A 489 5.17e+01 a.99.1.1,c.28.1.1 80677,80678 1v3vA 333 5.27e+01 b.35.1.2,c.2.1.1 108345,108346 1yoaA 159 5.28e+01 1pu6A 218 5.29e+01 a.96.1.5 95123 1zk8A 183 5.39e+01 1lybB 241 5.43e+01 1smrA 1ew0A 130 5.49e+01 1drmA d.110.3.2 40905 1bbzA 58 5.50e+01 1bbzA b.34.2.1 24477 2polA 366 5.50e+01 2polA d.131.1.1,d.131.1.1,d.131.1.1 41356,41357,41358 1tx2A 297 5.56e+01 c.1.21.1 107420 1vajA 214 5.56e+01 1ih7A 903 5.56e+01 1clqA c.55.3.5,e.8.1.1 62375,62376 1ebmA 317 5.59e+01 1ebmA a.96.1.3,d.129.1.2 18751,41300 1fiy 883 5.60e+01 1fiy c.1.12.3 29307 2fqmA 75 5.61e+01 1ea2A 131 5.63e+01 d.17.4.3 64860 4bcl 366 5.63e+01 4bcl b.75.1.1 27968 1d06A 130 5.64e+01 1drmA d.110.3.2 40906 2fneA 117 5.65e+01 1wg8A 285 5.67e+01 1vggA 161 5.74e+01 1qb4A 883 5.78e+01 c.1.12.3 74640 1khoA 370 5.78e+01 a.124.1.1,b.12.1.3 72489,72490 1etpA 190 5.82e+01 1etpA a.3.1.4,a.3.1.4 15962,15963 1uuhA 159 5.85e+01 d.169.1.4 100008 1gweA 503 5.87e+01 e.5.1.1 70667 2cobA 70 5.93e+01 1bdg 451 5.97e+01 1qhaA c.55.1.3,c.55.1.3 33461,33462 2bjdA 101 5.97e+01 1m3qA 317 5.98e+01 a.96.1.3,d.129.1.2 91184,91185 1ok7A 366 6.02e+01 d.131.1.1,d.131.1.1,d.131.1.1 103992,103993,103994 1hbzA 498 6.05e+01 1cf9A e.5.1.1 60937 2au3A 407 6.07e+01 1qb2A 109 6.13e+01 1qb2A a.36.1.1 17125 1imvA 398 6.17e+01 e.1.1.1 62591 1iieA 75 6.18e+01 1iieA a.109.1.1 19039 2c4xA 260 6.21e+01 2g7sA 194 6.30e+01 1lwyA 324 6.31e+01 a.96.1.3,d.129.1.2 78285,78286 1oaiA 59 6.37e+01 a.5.2.3 81255 1cyj 90 6.39e+01 1ctj a.3.1.1 15805 1kllA 130 6.40e+01 d.32.1.2 72720 1sknP 92 6.54e+01 1sknP a.37.1.1 17127 1wyxA 69 6.54e+01 2astA 159 6.55e+01 1ym5A 300 6.56e+01 1wgbA 159 6.67e+01 1euiA 228 6.68e+01 3eugA c.18.1.1 31028 1eugA 229 6.71e+01 3eugA c.18.1.1 31021 1xmxA 385 6.71e+01 1pk1B 89 6.83e+01 1hh1A 143 6.90e+01 1gefA c.52.1.18 61036 1q2yA 140 6.91e+01 d.108.1.1 95655 1yf3A 259 6.92e+01 1jqhA 308 6.97e+01 d.144.1.7 71793 1kyhA 276 6.97e+01 c.72.1.4 73222 2bhvA 246 7.01e+01 1zq7A 207 7.03e+01 1u59A 287 7.05e+01 d.144.1.7 107681 1l0qA 391 7.10e+01 b.1.3.1,b.69.2.3 77644,77645 1uteA 313 7.12e+01 1uteA d.159.1.1 42078 1q15A 503 7.12e+01 c.26.2.1,d.153.1.1 95538,95539 1u5pA 216 7.14e+01 1gbs 185 7.17e+01 153l d.2.1.5 36986 1u8vA 490 7.17e+01 1tuc 63 7.32e+01 1tuc b.34.2.1 24492 1y37A 304 7.50e+01 1z3eA 132 7.51e+01 2d4rA 147 7.61e+01 1c4kA 730 7.64e+01 1ordA c.23.1.4,c.67.1.5,d.125.1.1 31273,34502,41123 2gaiA 633 7.74e+01 1uwdA 103 7.76e+01 3eugA 229 7.82e+01 3eugA c.18.1.1 31018 2c26A 260 7.82e+01 1qavB 115 7.86e+01 1qauA b.36.1.1 24780 153l 185 7.87e+01 153l d.2.1.5 36984 1nzoA 363 7.89e+01 b.105.1.1,e.3.1.1 92383,92384 1buuA 168 7.93e+01 1rtm1 d.169.1.1,h.1.1.1 42366,45388 1opy 131 7.99e+01 1opy d.17.4.3 38113 2booA 247 8.04e+01 2f2lX 167 8.07e+01 1o9gA 250 8.09e+01 c.66.1.29 86692 1qauA 112 8.14e+01 1qauA b.36.1.1 24779 1fr3A 67 8.19e+01 1fr3A b.40.6.1 25436 1fqvD 149 8.20e+01 1fqvD a.157.1.1,d.42.1.1 19263,38667 1ktbA 405 8.20e+01 b.71.1.1,c.1.8.1 72960,72961 1o7nA 449 8.22e+01 b.33.1.2,d.129.3.3 81162,81163 1occG 84 8.24e+01 2occG f.23.2.1 43562 1ovqA 138 8.24e+01 c.55.3.8 93607 1zkiA 133 8.35e+01 1ordA 730 8.39e+01 1ordA c.23.1.4,c.67.1.5,d.125.1.1 31274,34503,41124 2occG 84 8.46e+01 2occG f.23.2.1 43522 1ufhA 180 8.51e+01 d.108.1.1 88485 2abqA 306 8.52e+01 1vf5F 35 8.53e+01 f.23.25.1 100586 2aucA 126 8.56e+01 1a2xA 159 8.57e+01 1ncx a.39.1.5 17251 1a62 130 8.63e+01 1a62 a.140.3.1,b.40.4.5 64708,64709 1wqjB 80 8.65e+01 1r7jA 95 8.66e+01 a.4.5.49 104836 1ix9A 205 8.68e+01 a.2.11.1,d.44.1.1 76899,76900 1zzmA 259 8.68e+01 1flzA 228 8.78e+01 3eugA c.18.1.1 31027 1allA 160 8.79e+01 1qgwC a.1.1.3 15647 1shyB 551 8.81e+01 b.69.12.1,g.16.2.1 105565,105566 1cyi 90 8.81e+01 1ctj a.3.1.1 15804 1r7mA 235 8.82e+01 1cch 82 8.84e+01 451c a.3.1.1 15902 4eugA 229 8.85e+01 3eugA c.18.1.1 31019 1ln1A 214 8.90e+01 d.129.3.2 74038 1r9kA 172 8.95e+01 a.168.1.1 104869 1t0qB 330 8.97e+01 a.25.1.2 106221 1to6A 371 8.97e+01 c.141.1.1 107170 1i6kA 328 8.98e+01 c.26.1.1 66040 2fggA 101 8.98e+01 1i12A 160 8.99e+01 1i21A d.108.1.1 61515