# List of top-scoring protein chains for t04-100-30-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 1guqA 348 3.48e-60 1guqA d.13.1.2 37522 d.13.1.2 37523 1kpeA 126 2.59e-23 1kpf d.13.1.1 37508 1kpf 126 4.76e-23 1kpf d.13.1.1 37507 1fit 147 2.59e-21 1fit d.13.1.1 37499 2fhi 147 5.05e-21 1fit d.13.1.1 37505 1st0A 337 1.10e-06 1oihA 301 3.63e-02 1itvA 195 4.87e-02 b.66.1.1 76791 1iuqA 367 9.62e-02 1k30A 368 1.13e-01 c.112.1.1 68067 1a9xA 1058 1.56e-01 a.92.1.1 18550 c.24.1.1 31479 c.30.1.1 31657 c.30.1.1 31658 d.142.1.2 41502 d.142.1.2 41503 1f2tB 148 1.58e-01 1f2tB 1byfA 125 2.30e-01 1byfA d.169.1.1 42419 1azsA 220 2.47e-01 1azsA d.58.29.1 39416 1vhmA 195 2.75e-01 3csuA 310 3.39e-01 3csuA c.78.1.1 35094 c.78.1.1 35095 1k0eA 453 4.38e-01 d.161.1.1 67938 1dfeA 37 4.97e-01 1dfeA g.42.1.1 45318 1jyhA 157 5.32e-01 d.60.1.3 71956 1ukkA 142 7.55e-01 1gwmA 153 7.66e-01 b.18.1.19 83348 1duvG 333 7.75e-01 1othA c.78.1.1 35228 c.78.1.1 35229 1g0oA 283 9.67e-01 1ybvA c.2.1.2 60181 1ng4A 390 1.08e+00 c.3.1.2 85666 d.16.1.3 85667 1mbxC 106 1.19e+00 d.45.1.2 78929 1squA 155 1.26e+00 1f7lA 121 1.27e+00 1f7lA d.150.1.2 59666 1mmiA 366 1.47e+00 1ci3M 249 1.57e+00 1hcz b.2.6.1 22480 b.84.2.2 28266 1gheA 177 1.73e+00 d.108.1.1 76222 1iz0A 302 1.96e+00 b.35.1.2 83821 c.2.1.1 83822 2cmd 312 1.97e+00 2cmd c.2.1.5 30135 d.162.1.1 42102 1xel 338 1.99e+00 1xel c.2.1.2 29786 1ten 90 2.13e+00 1ten b.1.2.1 21990 1v33A 366 2.37e+00 1huuA 90 2.40e+00 1huuA a.55.1.1 17897 1g71A 347 2.41e+00 1g71A e.16.1.1 43268 1phk 298 2.42e+00 1cdkA d.144.1.7 41635 1azsB 212 2.49e+00 1azsA d.58.29.1 39423 1ptmA 329 2.54e+00 1h8mA 140 2.69e+00 1h8mA d.110.4.1 60782 1j9lA 247 2.72e+00 c.106.1.1 62762 1ji8A 111 2.82e+00 d.203.1.1 66733 1elqA 390 2.85e+00 1elqA c.67.1.3 34436 1ev0A 58 2.85e+00 1ev0A d.71.1.1 39594 1up8A 598 2.98e+00 1udc 338 3.18e+00 1xel c.2.1.2 29785 1j1uA 306 3.24e+00 c.26.1.1 83980 1qe3A 489 3.35e+00 2bce c.69.1.1 34630 1qpxA 218 3.39e+00 1qpxA b.1.11.1 22318 b.7.2.1 23200 1q67A 231 3.53e+00 1ml4A 308 3.58e+00 c.78.1.1 79255 c.78.1.1 79256 1lucA 355 3.82e+00 1lucA c.1.16.1 29547 1m55A 197 3.83e+00 d.89.1.3 74469 2prd 174 3.92e+00 2prd b.40.5.1 25435 1jvnA 555 3.93e+00 c.1.2.1 67355 c.23.16.1 67356 1gvnA 90 3.93e+00 a.8.2.1 76353 1pwxA 254 4.16e+00 1r94A 118 4.35e+00 1sdjA 310 4.37e+00 1ab8A 220 4.43e+00 1azsA d.58.29.1 39414 1dosA 358 4.54e+00 1dosA c.1.10.2 29175 1eluA 390 4.65e+00 1elqA c.67.1.3 34434 1hw5A 210 4.80e+00 2cgpA a.4.5.4 16098 b.82.3.2 28137 1hyhA 309 4.84e+00 1hyhA c.2.1.5 30150 d.162.1.1 42117 1rypH 205 4.91e+00 d.153.1.4 41876 1f42A 306 4.92e+00 1f42A b.1.1.4 59636 b.1.2.1 59637 b.1.2.1 59638 1s3jA 155 5.03e+00 1ovlA 271 5.04e+00 a.123.1.1 87455 1forL 210 5.13e+00 8fabA b.1.1.1 19988 b.1.1.2 21044 2polA 366 5.58e+00 2polA d.131.1.1 41356 d.131.1.1 41357 d.131.1.1 41358 1im8A 244 5.67e+00 c.66.1.14 66212 1lldA 319 5.70e+00 3ldh c.2.1.5 30177 d.162.1.1 42144 1ow1A 195 5.71e+00 1o6aA 96 5.72e+00 1v4vA 376 5.90e+00 1l8bA 190 6.24e+00 d.86.1.1 73683 1qmeA 702 6.25e+00 1pmd d.11.1.1 37487 d.11.1.1 37488 d.175.1.1 42560 e.3.1.1 42769 1jyoA 130 6.28e+00 d.198.1.1 67483 1nepA 130 6.35e+00 b.1.18.7 80440 1fxqA 267 6.60e+00 1d9eA c.1.10.4 60108 1o8bA 219 6.66e+00 c.35.1.2 81180 d.58.40.1 81181 1oi2A 366 6.79e+00 c.32.1.2 87039 d.79.2.2 87040 1auoA 218 6.79e+00 1auoA c.69.1.14 34716 1lfaA 187 6.80e+00 1ido c.62.1.1 34122 1opoA 348 6.86e+00 b.121.4.7 87240 1s4nA 348 6.92e+00 1gcoA 261 7.00e+00 1ybvA c.2.1.2 29884 1a3c 181 7.09e+00 1a3c c.61.1.1 34095 1fwsA 267 7.27e+00 1d9eA c.1.10.4 60063 1i7pA 274 7.44e+00 b.43.4.2 66048 c.25.1.1 66049 1aohA 147 7.45e+00 1aohA b.2.2.2 22401 1kcxA 518 7.69e+00 1b2pA 119 7.71e+00 1b2pA b.78.1.1 27998 1pe1A 267 7.83e+00 1fnnA 389 7.89e+00 1fnnA a.4.5.11 16129 c.37.1.20 32426 1je8A 82 8.00e+00 a.4.6.2 77108 1b8aA 438 8.08e+00 1b8aA b.40.4.1 25244 d.104.1.1 40765 1r7aA 504 8.37e+00 1qyaA 307 8.39e+00 1b0uA 262 8.53e+00 1b0uA c.37.1.12 32370 1hkyA 86 8.68e+00 g.10.1.3 76714 1n4kA 381 8.78e+00 a.118.1.11 79992 b.42.6.1 79993 1dykA 394 8.78e+00 1dykA b.29.1.4 24223 b.29.1.4 24224 1pj5A 830 8.85e+00 1n0lA 224 8.95e+00 b.1.11.1 79744 b.7.2.1 79745 1o50A 157 9.01e+00 1jcxA 267 9.11e+00 c.1.10.4 66510 1gz8A 299 9.23e+00 d.144.1.7 83405 1jopA 155 9.56e+00 b.82.2.7 84187 1sqhA 312 9.57e+00 1t2dA 322 9.91e+00 1m1zA 513 1.00e+01 c.26.2.1 78457 d.153.1.1 78458 1jnrB 150 1.00e+01 d.58.1.5 66969 1d4vA 117 1.01e+01 1d4vA g.24.1.1 44915 g.24.1.1 44916 g.24.1.1 44917 1gjjA 168 1.03e+01 a.140.1.1 83291 a.140.1.1 83292 1h3nA 878 1.07e+01 a.27.1.1 76641 b.51.1.1 76642 c.26.1.1 76643 1rewC 135 1.07e+01 1p5vA 235 1.11e+01 b.1.11.1 87812 b.7.2.1 87813 1ldg 316 1.12e+01 1ceqA c.2.1.5 30165 d.162.1.1 42132 1i76A 163 1.12e+01 1hfc d.92.1.11 61877 1oe4A 247 1.13e+01 c.18.1.3 86895 1sfsA 240 1.13e+01 1lghA 56 1.16e+01 1lghA f.3.1.1 43733 1t9fA 187 1.17e+01 1o6zA 303 1.17e+01 c.2.1.5 81107 d.162.1.1 81108 1ej1A 190 1.19e+01 1ejhA d.86.1.1 40144 1jmsA 381 1.19e+01 a.60.6.1 66889 a.60.12.1 75862 d.218.1.2 75863 2oatA 439 1.19e+01 2dkb c.67.1.4 34452 1du3A 130 1.19e+01 1d4vA g.24.1.1 44927 g.24.1.1 44928 g.24.1.1 44929 1jhgA 101 1.20e+01 1jhgA a.4.12.1 19009 1px5A 349 1.21e+01 1m0uA 249 1.24e+01 a.45.1.1 78359 c.47.1.5 78360 1gd0A 122 1.25e+01 1dptA d.80.1.3 39834 1vhoA 346 1.26e+01 1ee8A 266 1.27e+01 1ee8A a.156.1.2 75823 b.113.1.1 75824 g.39.1.8 75825 1g6uA 48 1.27e+01 1g6uA k.9.1.1 46425 1h9sA 140 1.28e+01 1b9mA b.40.6.2 60843 b.40.6.2 60844 1b4bA 71 1.29e+01 1b4aA d.74.2.1 39718 1i52A 236 1.30e+01 1i52A c.68.1.13 61767 1k3yA 221 1.31e+01 a.45.1.1 77245 c.47.1.5 77246 1gowA 489 1.32e+01 1qvbA c.1.8.4 28981 1v9fA 325 1.34e+01 1nlnA 204 1.35e+01 1jl0A 334 1.37e+01 1jenA d.156.1.1 63155 1obwA 175 1.37e+01 2prd b.40.5.1 25416 1bob 320 1.43e+01 1bob d.108.1.1 40816 1oa2A 218 1.43e+01 b.29.1.11 86721 1ukmB 128 1.43e+01 1eg7A 557 1.48e+01 1eg7A c.37.1.10 32241 1rreA 200 1.52e+01 1s98A 107 1.53e+01 3fruA 269 1.54e+01 1agdA b.1.1.2 20657 d.19.1.1 38150 1m07A 111 1.54e+01 d.5.1.1 78328 1i50F 155 1.54e+01 d.78.1.2 61760 1o7jA 327 1.55e+01 c.88.1.1 81140 1q0sA 259 1.56e+01 1a6jA 163 1.56e+01 1a6jA d.112.1.1 40915 1e58A 249 1.57e+01 1qhfA c.60.1.1 59262 1csn 298 1.58e+01 1csn d.144.1.7 41664 1q2yA 140 1.63e+01 1k3eA 156 1.64e+01 d.198.1.1 68103 1fsgA 233 1.64e+01 1qk3A c.61.1.1 34029 1geeA 261 1.65e+01 1hh1A 143 1.66e+01 1gefA c.52.1.18 61036 1lnwA 147 1.68e+01 a.4.5.28 78104 1gy8A 397 1.69e+01 c.2.1.2 83376 1g0sA 209 1.72e+01 1g0sA d.113.1.1 60187 1ef8A 261 1.73e+01 1ef8A c.14.1.3 30921 1yuiA 54 1.75e+01 1yuiA g.37.1.1 45073 2cbp 96 1.78e+01 2cbp b.6.1.1 22895 1qwlA 505 1.78e+01 1hdcA 253 1.80e+01 1e6wA c.2.1.2 29862 1l9xA 315 1.81e+01 c.23.16.1 73762 1vj2A 126 1.82e+01 1hyeA 313 1.82e+01 2cmd c.2.1.5 61400 d.162.1.1 61401 1h8vA 218 1.82e+01 2nlrA b.29.1.11 60795 1q8bA 105 1.87e+01 1pcxA 810 1.88e+01 1nzyA 269 1.89e+01 1nzyA c.14.1.3 30903 1mjnA 179 1.90e+01 c.62.1.1 79210 1cseI 71 1.95e+01 1egpA d.40.1.1 38559 1k2xA 177 1.96e+01 1a04A 215 1.96e+01 1a04A a.4.6.2 16234 c.23.1.1 31089 1uvqB 198 1.97e+01 1gg4A 452 1.99e+01 1gg4A c.98.1.1 58985 c.59.1.1 33957 c.72.2.1 58986 1f9vA 347 1.99e+01 1bg2 c.37.1.9 59745 1nd4A 264 1.99e+01 1eu1A 780 2.00e+01 1dmr b.52.2.2 26903 c.81.1.1 35311 1ockA 412 2.05e+01 c.117.1.1 86802 1l4dB 122 2.06e+01 d.15.5.1 77684 1nnwA 252 2.07e+01 d.159.1.5 80674 1hfoA 113 2.07e+01 d.80.1.3 61006 1bwzA 274 2.08e+01 1bwzA d.21.1.1 38337 d.21.1.1 38338 1smd 496 2.16e+01 1smd b.71.1.1 27768 c.1.8.1 28755 1korA 400 2.16e+01 c.26.2.1 72824 d.210.1.1 72825 1nukA 183 2.17e+01 1nukA b.18.1.4 23721 1eexA 554 2.17e+01 1dioA c.1.19.3 29650 1lqtA 456 2.18e+01 c.3.1.1 74198 c.4.1.1 74199 1nezG 128 2.19e+01 b.1.1.1 85592 1gnxA 479 2.19e+01 c.1.8.4 76241 2ahjA 206 2.22e+01 2ahjA d.149.1.1 41772 1eg9A 449 2.24e+01 1ndoA b.33.1.2 24443 d.129.3.3 41322 1o7nA 449 2.24e+01 b.33.1.2 81162 d.129.3.3 81163 1m4lA 307 2.27e+01 c.56.5.1 78604 1jksA 294 2.27e+01 d.144.1.7 71710 1ckmA 330 2.27e+01 1ckmA b.40.4.6 25358 d.142.2.3 41585 1ithA 141 2.30e+01 1ithA a.1.1.2 15623 1kv9A 668 2.33e+01 a.3.1.6 73056 b.70.1.1 73057 1e3mA 800 2.33e+01 1ewqA a.113.1.1 19075 c.37.1.12 32389 c.55.6.1 33746 d.75.2.1 39747 1qksA 567 2.36e+01 1qksA a.3.1.2 15951 b.70.2.1 27710 1lxnA 99 2.39e+01 d.58.48.1 84737 1pinA 163 2.41e+01 1pinA b.72.1.1 27802 d.26.1.1 38431 1ndh 272 2.42e+01 1ndh b.43.4.2 25662 c.25.1.1 31552 1bmv1 198 2.43e+01 1bmv1 1prxA 224 2.46e+01 1prxA c.47.1.10 33076 1ka1A 357 2.48e+01 e.7.1.1 68369 1nstA 325 2.50e+01 1nstA c.37.1.5 31951 1uzpA 162 2.52e+01 1lghB 45 2.52e+01 1lghB f.3.1.1 43734 1rztA 331 2.53e+01 1jndA 420 2.55e+01 c.1.8.5 71757 d.26.3.1 71758 2plc 274 2.57e+01 2plc c.1.18.2 29614 2ctc 307 2.62e+01 1aye c.56.5.1 33802 1oatA 439 2.63e+01 2dkb c.67.1.4 34461 1othA 321 2.63e+01 1othA c.78.1.1 35260 c.78.1.1 35261 1f0iA 504 2.64e+01 1f0iA d.136.1.2 59566 d.136.1.2 59567 1h4pA 408 2.65e+01 1b8zA 90 2.67e+01 1huuA a.55.1.1 17902 1vhwA 253 2.70e+01 1uc7A 125 2.71e+01 2trcP 217 2.76e+01 1b9yC c.47.1.6 33051 1iqrA 420 2.78e+01 a.99.1.1 66275 c.28.1.1 66276 1pvvA 315 2.79e+01 1cmiA 85 2.80e+01 1cmiA d.39.1.1 38551 1kv7A 488 2.81e+01 b.6.1.3 68873 b.6.1.3 68874 b.6.1.3 68875 1svb 395 2.82e+01 1svb b.1.18.4 21814 f.10.1.1 43827 1j6wA 175 2.83e+01 1j98A d.185.1.2 62663 1t15A 214 2.84e+01 1r3sA 367 2.86e+01 1dpe 507 2.87e+01 1dpe c.94.1.1 35799 1fuiA 591 2.89e+01 1fuiA b.43.2.1 25674 c.85.1.1 35444 1jj2E 177 2.89e+01 1ffk1 d.141.1.1 63089 d.141.1.1 63090 1d4aA 273 2.89e+01 1d4aA c.23.5.3 31219 1dekA 241 2.89e+01 1dekA c.37.1.1 31842 1apyB 141 2.90e+01 1apyB 1ujnA 348 2.91e+01 1a6o 332 2.91e+01 1a6o 1kwaA 88 2.93e+01 1kwaA b.36.1.1 24772 2napA 723 2.93e+01 2napA b.52.2.2 26926 c.81.1.1 35334 1js8A 394 2.94e+01 a.86.1.1 67219 b.112.1.1 67220 1jenA 267 2.94e+01 1jenA 1hcl 298 2.99e+01 1hcl d.144.1.7 41593 1g9oA 91 2.99e+01 1pdr b.36.1.1 60400 1bpoA 494 2.99e+01 1bpoA a.118.1.4 19143 b.69.6.1 27670 1uroA 367 3.01e+01 1uroA c.1.22.1 29675 1odmA 331 3.03e+01 b.82.2.1 86875 1lvmA 229 3.05e+01 b.47.1.3 78243 1hc7A 477 3.06e+01 1hc7A c.51.1.1 60938 d.68.5.1 60940 d.104.1.1 60939 1bqhG 129 3.08e+01 1cd8 b.1.1.1 19715 1mu5A 471 3.12e+01 a.156.1.3 79472 d.14.1.3 79473 d.122.1.2 79474 1i40A 175 3.13e+01 b.40.5.1 66024 1q7zA 566 3.14e+01 1hl9A 449 3.14e+01 1uebA 184 3.20e+01 1ieaA 192 3.21e+01 1iakA b.1.1.2 21631 d.19.1.1 38205 1lrzA 426 3.22e+01 a.2.7.4 78167 d.108.1.4 78168 d.108.1.4 78169 1gzwA 134 3.22e+01 1jpyA 137 3.29e+01 g.17.1.6 67065 1a62 130 3.30e+01 1a62 a.140.3.1 64708 b.40.4.5 64709 1om1A 332 3.37e+01 1tetL 216 3.38e+01 32c2A b.1.1.1 19902 b.1.1.2 20996 1f7dA 136 3.38e+01 1dun b.85.4.1 28353 1jtaA 361 3.46e+01 b.80.1.1 71859 1f8eA 388 3.46e+01 2qwc b.68.1.1 59694 1ur5A 309 3.48e+01 1gp6A 356 3.49e+01 b.82.2.1 65441 1rcqA 357 3.50e+01 1msk 331 3.54e+01 1msk d.173.1.1 42495 1nijA 318 3.56e+01 c.37.1.10 85741 d.237.1.1 85742 1ckiA 317 3.56e+01 1csn d.144.1.7 41660 1g61A 228 3.62e+01 1g61A d.126.1.1 41126 1jj2P 95 3.64e+01 1ffkN b.34.5.1 63101 1e29A 135 3.64e+01 1e29A a.3.1.1 59161 1a8vA 121 3.68e+01 1a62 a.140.3.1 64712 b.40.4.5 64713 1gal 583 3.71e+01 1gpeA c.3.1.2 30386 d.16.1.1 37950 1b00A 127 3.73e+01 3chy c.23.1.1 31122 1m2rA 327 3.74e+01 d.144.1.7 84760 1pg5A 299 3.77e+01 2hrvA 142 3.77e+01 2hrvA b.47.1.4 26429 1mjuL 219 3.78e+01 1r4vA 171 3.79e+01 1g8iA 190 3.79e+01 1rec a.39.1.5 60363 1l3lA 234 3.85e+01 a.4.6.2 73541 d.110.5.1 73542 1esc 306 3.88e+01 1esc c.23.10.1 31334 1qm4A 396 3.89e+01 1mxb d.130.1.1 41350 d.130.1.1 41351 d.130.1.1 41352 1sixA 174 3.90e+01 1ew4A 106 3.93e+01 1ew4A d.82.2.1 40023 1mldA 314 3.94e+01 2cmd c.2.1.5 30122 d.162.1.1 42089 1qtnA 164 3.94e+01 1pauA c.17.1.1 30999 1nf9A 207 3.96e+01 c.33.1.2 85631