# List of top-scoring protein chains for t2k-100-30-alpha 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 1gupA 348 2.65e-59 1guqA d.13.1.2 37534 d.13.1.2 37535 1hxpA 348 2.67e-59 1guqA d.13.1.2 37530 d.13.1.2 37531 1guqA 348 3.00e-59 1guqA d.13.1.2 37522 d.13.1.2 37523 1emsA 440 2.50e-16 1emsA d.13.1.1 37520 d.160.1.1 42086 1kpeA 126 7.95e-16 1kpf d.13.1.1 37508 1kpf 126 1.46e-15 1kpf d.13.1.1 37507 1fit 147 1.66e-14 1fit d.13.1.1 37499 2fhi 147 2.09e-14 1fit d.13.1.1 37505 1st0A 337 3.65e-03 1oihA 301 1.08e-01 1dfeA 37 1.50e-01 1dfeA g.42.1.1 45318 2polA 366 1.85e-01 2polA d.131.1.1 41356 d.131.1.1 41357 d.131.1.1 41358 1i7oA 429 1.99e-01 1i7oA d.177.1.1 61893 d.177.1.1 61894 1dgzA 37 2.14e-01 1dfeA g.42.1.1 45319 1mmiA 366 2.29e-01 1gttA 429 2.82e-01 d.177.1.1 70529 d.177.1.1 70530 1ka1A 357 6.28e-01 e.7.1.1 68369 1k30A 368 6.47e-01 c.112.1.1 68067 1iuqA 367 7.04e-01 1bk0 331 7.76e-01 1bk0 b.82.2.1 28118 1odmA 331 8.39e-01 b.82.2.1 86875 1g0sA 209 8.50e-01 1g0sA d.113.1.1 60187 1qgxA 357 8.96e-01 1qgxA e.7.1.1 42973 1bpyA 335 1.03e+00 1bpyA a.60.6.1 17980 a.60.12.1 75819 d.218.1.2 75820 1c52 131 1.17e+00 1c52 a.3.1.1 15810 1dun 134 1.32e+00 1dun b.85.4.1 28371 1ml4A 308 1.41e+00 c.78.1.1 79255 c.78.1.1 79256 1duvG 333 1.48e+00 1othA c.78.1.1 35228 c.78.1.1 35229 1jqfA 334 1.64e+00 c.94.1.2 67086 1dtgA 334 1.76e+00 1nnt c.94.1.2 35896 1eikA 77 1.76e+00 1eikA d.78.1.1 39751 1a8e 329 1.84e+00 1cb6A c.94.1.2 35888 1b2pA 119 1.86e+00 1b2pA b.78.1.1 27998 2at2A 300 1.91e+00 3csuA c.78.1.1 35196 c.78.1.1 35197 1m41A 380 1.94e+00 c.1.16.4 78595 1mbxC 106 1.95e+00 d.45.1.2 78929 1bawA 105 2.01e+00 1plc b.6.1.1 22868 1gvp 87 2.06e+00 1gvp b.40.4.7 25369 1h4pA 408 2.19e+00 1ckmA 330 2.21e+00 1ckmA b.40.4.6 25358 d.142.2.3 41585 1ukkA 142 2.22e+00 1s4nA 348 2.33e+00 1byfA 125 2.35e+00 1byfA d.169.1.1 42419 1d3kA 329 2.35e+00 1nnt c.94.1.2 35889 1f2tB 148 2.54e+00 1f2tB 1rr9A 200 2.56e+00 1b3eA 330 2.58e+00 1nnt c.94.1.2 35897 1ji8A 111 2.66e+00 d.203.1.1 66733 1vqb 87 2.86e+00 1gvp b.40.4.7 25370 1qmeA 702 2.92e+00 1pmd d.11.1.1 37487 d.11.1.1 37488 d.175.1.1 42560 e.3.1.1 42769 1xgsA 295 2.94e+00 1bn5 a.4.5.25 16216 d.127.1.1 41153 1tlgA 125 2.96e+00 1byfA d.169.1.1 42421 1rpl 251 3.04e+00 1bpyA a.60.12.1 75933 d.218.1.2 75934 1cknA 330 3.06e+00 1ckmA b.40.4.6 25360 d.142.2.3 41587 1hueA 90 3.10e+00 1huuA a.55.1.1 17900 1huuA 90 3.39e+00 1huuA a.55.1.1 17897 1ffyA 917 3.56e+00 1qu2A a.27.1.1 16926 b.51.1.1 26891 c.26.1.1 31593 1qu2A 917 3.56e+00 1qu2A a.27.1.1 16925 b.51.1.1 26890 c.26.1.1 31592 1ryoA 327 3.65e+00 1nqkA 381 3.80e+00 1gwmA 153 3.89e+00 b.18.1.19 83348 1j6wA 175 4.08e+00 1j98A d.185.1.2 62663 1h8mA 140 4.26e+00 1h8mA d.110.4.1 60782 1azsB 212 4.26e+00 1azsA d.58.29.1 39423 2cmd 312 4.34e+00 2cmd c.2.1.5 30135 d.162.1.1 42102 1gr8A 412 4.57e+00 1ockA 412 4.57e+00 c.117.1.1 86802 1culA 217 4.89e+00 1azsA d.58.29.1 39417 1a31A 538 5.10e+00 1a36A d.163.1.2 42170 e.15.1.1 43263 1k0tA 80 5.32e+00 d.58.1.4 71976 1o6zA 303 5.33e+00 c.2.1.5 81107 d.162.1.1 81108 1othA 321 5.33e+00 1othA c.78.1.1 35260 c.78.1.1 35261 3dni 260 5.50e+00 3dni d.151.1.1 41791 1jyhA 157 5.54e+00 d.60.1.3 71956 1m55A 197 5.61e+00 d.89.1.3 74469 1rreA 200 5.90e+00 1lf7A 182 6.12e+00 b.60.1.1 73878 1r3nA 462 6.24e+00 1eluB 390 6.42e+00 1elqA c.67.1.3 34435 1lj9A 144 6.59e+00 a.4.5.28 78035 1lfaA 187 6.67e+00 1ido c.62.1.1 34122 1oe4A 247 6.74e+00 c.18.1.3 86895 1elqA 390 6.76e+00 1elqA c.67.1.3 34436 1c96A 753 6.87e+00 1amj c.8.2.1 30727 c.83.1.1 35403 1squA 155 7.31e+00 1phk 298 7.66e+00 1cdkA d.144.1.7 41635 1gy9A 283 7.70e+00 b.82.2.5 70742 1fpzA 212 7.90e+00 1fpzA c.45.1.1 59976 1cjtA 217 7.98e+00 1azsA d.58.29.1 39419 1n13B 113 8.31e+00 1bo1A 416 8.38e+00 1bo1A d.143.1.2 41591 1bpb 248 8.43e+00 1bpyA a.60.12.1 75811 d.218.1.2 75812 1eluA 390 8.45e+00 1elqA c.67.1.3 34434 1nom 248 8.62e+00 1bpyA a.60.12.1 75929 d.218.1.2 75930 1f7lA 121 8.76e+00 1f7lA d.150.1.2 59666 1dosA 358 8.83e+00 1dosA c.1.10.2 29175 1mz4A 137 9.10e+00 1a36A 592 9.20e+00 1a36A a.2.8.1 15715 d.163.1.2 42173 e.15.1.1 43266 1bjt 793 9.66e+00 1bjt e.11.1.1 43249 3nn9 388 9.77e+00 2qwc b.68.1.1 27566 1g61A 228 9.77e+00 1g61A d.126.1.1 41126 1nstA 325 9.82e+00 1nstA c.37.1.5 31951 1uwsA 489 1.01e+01 1nlbL 220 1.01e+01 b.1.1.1 80623 b.1.1.2 80624 1itvA 195 1.01e+01 b.66.1.1 76791 1azsA 220 1.04e+01 1azsA d.58.29.1 39416 5nn9 388 1.04e+01 2qwc b.68.1.1 27563 1nz0A 118 1.05e+01 d.14.1.2 86433 1s3jA 155 1.06e+01 1b0jA 754 1.08e+01 1amj c.8.2.1 30719 c.83.1.1 35395 1g0oA 283 1.10e+01 1ybvA c.2.1.2 60181 1b57A 358 1.12e+01 1dosA c.1.10.2 29177 1mjnA 179 1.13e+01 c.62.1.1 79210 1kq4A 232 1.13e+01 d.207.1.1 68791 1f8eA 388 1.14e+01 2qwc b.68.1.1 59694 8acn 754 1.16e+01 1amj c.8.2.1 30724 c.83.1.1 35400 1jpyB 137 1.18e+01 g.17.1.6 67066 1gheA 177 1.19e+01 d.108.1.1 76222 1cz1A 394 1.19e+01 1cz1A c.1.8.3 28839 1jpyA 137 1.19e+01 g.17.1.6 67065 1p5vA 235 1.20e+01 b.1.11.1 87812 b.7.2.1 87813 1dekA 241 1.21e+01 1dekA c.37.1.1 31842 1eqcA 394 1.23e+01 1cz1A c.1.8.3 28811 1uunA 184 1.23e+01 1jnxX 214 1.25e+01 c.15.1.3 63201 c.15.1.3 63202 1ris 101 1.25e+01 1ris d.58.14.1 39314 1iz0A 302 1.25e+01 b.35.1.2 83821 c.2.1.1 83822 1cmiA 85 1.28e+01 1cmiA d.39.1.1 38551 2prd 174 1.32e+01 2prd b.40.5.1 25435 1ee8A 266 1.33e+01 1ee8A a.156.1.2 75823 b.113.1.1 75824 g.39.1.8 75825 1amj 754 1.37e+01 1amj c.8.2.1 30725 c.83.1.1 35401 1tlk 154 1.38e+01 1tlk b.1.1.4 21707 1sesA 421 1.41e+01 1sesA a.2.7.1 15710 d.104.1.1 40710 1qstA 160 1.42e+01 1yghA d.108.1.1 40804 1nnwA 252 1.42e+01 d.159.1.5 80674 1focA 132 1.43e+01 1c52 a.3.1.1 15812 2gn5 87 1.46e+01 1gvp b.40.4.7 25386 1yuiA 54 1.47e+01 1yuiA g.37.1.1 45073 6acn 754 1.47e+01 1amj c.8.2.1 30721 c.83.1.1 35397 1j3mA 129 1.47e+01 1ge9A 184 1.52e+01 1dd5A d.67.3.1 60463 1r7aA 504 1.54e+01 1gyxA 76 1.58e+01 d.80.1.1 76387 1lghB 45 1.60e+01 1lghB f.3.1.1 43734 1jsrA 327 1.61e+01 c.88.1.1 67237 1at1A 310 1.61e+01 3csuA c.78.1.1 35168 c.78.1.1 35169 1httA 423 1.62e+01 1adjA c.51.1.1 33178 d.104.1.1 40727 1cec 343 1.62e+01 1ceo c.1.8.3 28809 1vhmA 195 1.63e+01 1udb 338 1.69e+01 1xel c.2.1.2 29787 1ortA 335 1.69e+01 1othA c.78.1.1 35204 c.78.1.1 35205 6cpa 307 1.71e+01 1aye c.56.5.1 33816 1yme 309 1.73e+01 1aye c.56.5.1 33804 1e69B 322 1.74e+01 1e69B c.37.1.12 32377 1nzyA 269 1.78e+01 1nzyA c.14.1.3 30903 2cbp 96 1.79e+01 2cbp b.6.1.1 22895 1otjA 283 1.79e+01 7acn 754 1.79e+01 1amj c.8.2.1 30717 c.83.1.1 35393 1jyoA 130 1.80e+01 d.198.1.1 67483 1k3lA 221 1.81e+01 a.45.1.1 77229 c.47.1.5 77230 1jnyA 435 1.83e+01 b.43.3.1 66982 b.44.1.1 66983 c.37.1.8 66984 1fneA 192 1.83e+01 1iakA b.1.1.2 59896 d.19.1.1 59897 1k1vA 41 1.84e+01 a.37.1.1 71999 1fngA 192 1.86e+01 1iakA b.1.1.2 59904 d.19.1.1 59905 1kyqA 274 1.86e+01 c.2.1.11 73281 e.37.1.1 73282 1jmsA 381 1.88e+01 a.60.6.1 66889 a.60.12.1 75862 d.218.1.2 75863 1rypH 205 1.88e+01 d.153.1.4 41876 1nepA 130 1.89e+01 b.1.18.7 80440 1i52A 236 1.90e+01 1i52A c.68.1.13 61767 1h4xA 117 1.92e+01 1auz c.13.2.1 60626 1a6q 382 1.93e+01 1a6q a.159.1.1 75801 d.219.1.1 75802 1fhgA 154 1.93e+01 1tlk b.1.1.4 21706 1kutA 230 1.93e+01 d.143.1.1 73017 1ieaA 192 1.94e+01 1iakA b.1.1.2 21631 d.19.1.1 38205 1b8pA 329 1.95e+01 1bmdA c.2.1.5 30147 d.162.1.1 42114 1rkxA 357 1.96e+01 1jlxA 304 1.96e+01 1jlyA b.42.3.1 25583 b.42.3.1 25584 1b3qA 379 1.96e+01 1b3qA a.30.2.1 16993 b.40.7.1 25454 d.122.1.3 41112 1hg2A 289 1.97e+01 1hg5A a.118.10.1 61024 1ghhA 81 1.98e+01 1ghhA d.57.1.1 38940 1jj2P 95 2.00e+01 1ffkN b.34.5.1 63101 3csuA 310 2.00e+01 3csuA c.78.1.1 35094 c.78.1.1 35095 1akp 114 2.01e+01 2mcm b.1.7.1 22212 1hf8A 289 2.03e+01 1hg5A a.118.10.1 19219 1hzfA 367 2.04e+01 a.102.4.4 76731 1t15A 214 2.07e+01 2qwc 388 2.09e+01 2qwc b.68.1.1 27547 1m1zA 513 2.15e+01 c.26.2.1 78457 d.153.1.1 78458 1delA 241 2.17e+01 1dekA c.37.1.1 31844 1lqtA 456 2.19e+01 c.3.1.1 74198 c.4.1.1 74199 1seiA 130 2.20e+01 1seiA d.140.1.1 41463 1lucA 355 2.21e+01 1lucA c.1.16.1 29547 1f3cA 89 2.21e+01 1cmiA d.39.1.1 38557 1r2fA 319 2.22e+01 1r2fA a.25.1.2 16800 1ev0A 58 2.23e+01 1ev0A d.71.1.1 39594 1otfA 62 2.23e+01 1otfA d.80.1.1 39820 1ab8A 220 2.23e+01 1azsA d.58.29.1 39414 1m4lA 307 2.26e+01 c.56.5.1 78604 1vdkA 466 2.27e+01 1dykA 394 2.28e+01 1dykA b.29.1.4 24223 b.29.1.4 24224 1f7tA 122 2.32e+01 1f7lA d.150.1.2 59667 1jslA 327 2.33e+01 c.88.1.1 67233 1xel 338 2.34e+01 1xel c.2.1.2 29786 1e58A 249 2.35e+01 1qhfA c.60.1.1 59262 1iakA 199 2.35e+01 1iakA b.1.1.2 21625 d.19.1.1 38199 1t9fA 187 2.35e+01 1m6bA 621 2.35e+01 c.10.2.5 74521 c.10.2.5 74522 g.3.9.1 74523 g.3.9.1 74524 1fo3A 460 2.39e+01 1dl2A a.102.2.1 18845 1aua 296 2.43e+01 1aua a.5.3.1 16290 c.13.1.1 30882 1i7nA 309 2.46e+01 c.30.1.5 83681 d.142.1.3 83682 3fruA 269 2.46e+01 1agdA b.1.1.2 20657 d.19.1.1 38150 1k0eA 453 2.47e+01 d.161.1.1 67938 1louA 101 2.48e+01 1ris d.58.14.1 39323 1dgqA 188 2.50e+01 1ido c.62.1.1 34131 1o7jA 327 2.51e+01 c.88.1.1 81140 1k3yA 221 2.53e+01 a.45.1.1 77245 c.47.1.5 77246 1ngkA 128 2.54e+01 a.1.1.1 85673 1a8b 318 2.55e+01 1avc a.65.1.1 18171 1v5xA 203 2.56e+01 1jlyA 304 2.57e+01 1jlyA b.42.3.1 25587 b.42.3.1 25588 1o5zA 442 2.57e+01 2ran 316 2.58e+01 1avc a.65.1.1 18170 1pvvA 315 2.62e+01 1ffk1 177 2.65e+01 1ffk1 1nn6A 228 2.67e+01 b.47.1.2 85893 1ekxA 311 2.69e+01 3csuA c.78.1.1 35088 c.78.1.1 35089 1rypK 198 2.72e+01 d.153.1.4 41879 1ffkN 95 2.73e+01 1ffkN b.34.5.1 24606 1uvqA 197 2.74e+01 1jksA 294 2.75e+01 d.144.1.7 71710 2ctc 307 2.76e+01 1aye c.56.5.1 33802 1ef8A 261 2.76e+01 1ef8A c.14.1.3 30921 1gumA 222 2.77e+01 1pgtA a.45.1.1 17683 c.47.1.5 32977 1gseA 221 2.81e+01 1pgtA a.45.1.1 17667 c.47.1.5 32961 1iqzA 81 2.82e+01 d.58.1.4 66281 1cqmA 101 2.83e+01 1ris d.58.14.1 39321 1f76A 336 2.84e+01 c.1.4.1 76160 1ybvA 283 2.85e+01 1ybvA c.2.1.2 29948 1hizA 379 2.85e+01 c.1.8.3 65841 1a8a 318 2.86e+01 1avc a.65.1.1 18169 1ae1A 273 2.94e+01 1bdb c.2.1.2 29943 1gmpA 96 2.94e+01 1rgeA d.1.1.2 36036 1ku1A 230 2.99e+01 a.118.3.1 72996 1kaeA 434 3.00e+01 c.82.1.2 72247 1ovlA 271 3.00e+01 a.123.1.1 87455 1q53A 112 3.01e+01 1gvnA 90 3.05e+01 a.8.2.1 76353 1ckiA 317 3.09e+01 1csn d.144.1.7 41660 1kk1A 410 3.09e+01 b.43.3.1 72634 b.44.1.1 72635 c.37.1.8 72636 1a1s 314 3.11e+01 1othA c.78.1.1 35258 c.78.1.1 35259 1o6aA 96 3.14e+01 1s0yB 71 3.16e+01 1fc2C 58 3.18e+01 1fc2C a.8.1.1 16345 1f3mA 80 3.21e+01 1f3mA j.66.1.1 46358 1ten 90 3.23e+01 1ten b.1.2.1 21990 1gulA 222 3.24e+01 1pgtA a.45.1.1 17675 c.47.1.5 32969 1qrdA 273 3.24e+01 1d4aA c.23.5.3 31217 1orjA 130 3.26e+01 1k75A 434 3.29e+01 c.82.1.2 68253 1pft 50 3.29e+01 1pft g.41.3.1 45206 1f2eA 201 3.32e+01 1a0fA a.45.1.1 17745 c.47.1.5 33039 2dvh 79 3.33e+01 1c53 a.3.1.1 15803 1ceqA 316 3.33e+01 1ceqA c.2.1.5 30163 d.162.1.1 42130 1im8A 244 3.36e+01 c.66.1.14 66212 1cne 270 3.36e+01 1ndh b.43.4.2 25661 c.25.1.1 31551 1kb9F 74 3.36e+01 f.28.1.1 77321 1o0xA 262 3.38e+01 d.127.1.1 80755 1uspA 139 3.39e+01 1f56A 91 3.41e+01 2cbp b.6.1.1 22896 1ceo 343 3.43e+01 1ceo c.1.8.3 28808 1vhwA 253 3.49e+01 1q4rA 112 3.49e+01 1gqwA 283 3.51e+01 b.82.2.5 70377 1b0zA 445 3.51e+01 2pgi c.80.1.2 35309 2pgi 445 3.51e+01 2pgi c.80.1.2 35308 1hg5A 289 3.52e+01 1hg5A a.118.10.1 19221 1pv9A 348 3.55e+01 1repC 251 3.56e+01 1repC a.4.5.10 16125 a.4.5.10 16126 1udc 338 3.64e+01 1xel c.2.1.2 29785 1jb0C 80 3.66e+01 1jb0C d.58.1.4 62822 1r94A 118 3.66e+01 1kwaA 88 3.67e+01 1kwaA b.36.1.1 24772 1qhuA 460 3.68e+01 1qhuA b.66.1.1 27530 b.66.1.1 27531 1kbqA 273 3.69e+01 c.23.5.3 68391 1d4aA 273 3.70e+01 1d4aA c.23.5.3 31219 1uzpA 162 3.70e+01 1ptmA 329 3.71e+01 1ovnA 248 3.74e+01 1n93X 375 3.74e+01 1ipwA 175 3.76e+01 2prd b.40.5.1 25427 1jgtA 513 3.77e+01 c.26.2.1 66684 d.153.1.1 66685 1pgl1 185 3.78e+01 1v1aA 309 3.81e+01 1kvs 338 3.82e+01 1xel c.2.1.2 29799 1iw2A 182 3.83e+01 b.60.1.1 71468 1pgvA 197 3.84e+01 c.10.1.1 88073 1pc6A 146 3.94e+01 1a4mA 349 3.95e+01 1a4mA c.1.9.1 29014 1v1rA 400 3.95e+01 1cmaA 104 3.97e+01 1cmbA a.43.1.2 17486 1ez3A 127 3.98e+01 1dn1B a.47.2.1 17768 1opoA 348 3.99e+01 b.121.4.7 87240