# List of top-scoring protein chains for t2k-100-30-bys 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 1jogA 146 4.10e-26 a.24.16.2 77142 1cxzB 86 2.15e-01 1cxzB a.2.6.1 15705 1s7zA 117 2.79e-01 unknown_sccs -344 1dk8A 147 3.11e-01 1agrE a.91.1.1 18548 1mb3A 124 3.38e-01 c.23.1.1 78907 1m5tA 124 3.42e-01 c.23.1.1 78660 1dgmA 363 3.95e-01 1bx4A c.72.1.1 34936 1rktA 205 4.41e-01 a.4.1.9 -210 a.121.1.1 -1663 1pa7A 130 5.28e-01 a.40.1.1 -896 2cxbA 124 5.36e-01 1ycc a.3.1.1 15891 1rx0A 393 8.02e-01 a.29.3.1 -742 e.6.1.1 -11858 1cxc 124 8.03e-01 1ycc a.3.1.1 15890 1buoA 121 8.98e-01 1buoA d.42.1.1 38631 1r8iA 213 1.03e+00 unknown_sccs -411 1aua 296 1.22e+00 1aua a.5.3.1 16290 c.13.1.1 30882 1im4A 221 1.35e+00 unknown_sccs 62581 1h5vA 304 1.36e+00 c.1.8.3 70898 7a3hA 303 1.39e+00 7a3hA c.1.8.3 28817 1a3h 300 1.48e+00 7a3hA c.1.8.3 28819 1qspA 165 1.53e+00 1qspA a.24.10.2 16639 1pq9A 253 1.67e+00 a.123.1.1 -1687 1m5yA 408 1.75e+00 a.167.1.1 78664 d.26.1.1 78665 d.26.1.1 78666 2pflA 759 1.87e+00 1cm5A c.7.1.1 30675 3pflA 759 1.89e+00 1cm5A c.7.1.1 30673 1lis 136 1.92e+00 1lis a.19.1.1 16406 2lisA 136 1.92e+00 1lis a.19.1.1 16405 1a0p 290 1.95e+00 1a0p a.60.9.1 18105 d.163.1.1 42165 1m6kA 251 2.13e+00 e.3.1.1 78695 1cm5A 759 2.13e+00 1cm5A c.7.1.1 30671 1l3lA 234 2.17e+00 a.4.6.2 73541 d.110.5.1 73542 1l9hA 349 2.33e+00 f.13.1.2 73720 1qlaC 256 2.39e+00 1qlaC f.21.2.1 43722 1jvsA 400 2.42e+00 a.69.3.1 77187 c.2.1.3 77188 d.81.1.3 77189 1q0qA 406 2.70e+00 1b4eA 323 2.88e+00 1b4kA c.1.10.3 29186 1mvoA 136 2.91e+00 c.23.1.1 79513 1h16A 759 3.06e+00 c.7.1.1 76462 3lynA 136 3.10e+00 1lis a.19.1.1 16413 1ail 73 3.25e+00 1ail a.16.1.1 16381 1k8cA 322 3.27e+00 c.1.7.1 72172 1mi3A 322 3.30e+00 c.1.7.1 -5257 1ns1A 73 3.52e+00 1ail a.16.1.1 16382 2sas 185 3.64e+00 2sas a.39.1.5 17258 1k6wA 426 3.66e+00 b.92.1.2 68236 c.1.9.5 68237 1op1A 82 3.68e+00 a.13.1.1 -456 1fjgD 209 3.77e+00 1c05A d.66.1.2 39553 1i50B 1224 3.78e+00 e.29.1.1 61755 1l6sA 323 3.84e+00 c.1.10.3 73627 1i8jA 323 3.99e+00 1b4kA c.1.10.3 61968 1q08A 99 4.03e+00 a.6.1.3 -381 1lre 81 4.05e+00 1lre a.13.1.1 16376 3crxA 343 4.24e+00 4crxA a.60.9.1 18101 d.163.1.1 42161 1kbuA 349 4.25e+00 a.60.9.1 72284 d.163.1.1 72285 1js8A 394 4.36e+00 a.86.1.1 67219 b.112.1.1 67220 1fpoA 171 4.49e+00 1fpoA a.2.3.1 15693 a.23.1.1 16487 2igd 61 4.50e+00 2igd d.15.7.1 37821 1p9bA 442 4.51e+00 c.37.1.10 -7115 1igd 61 4.52e+00 2igd d.15.7.1 37822 1qwgA 251 4.53e+00 unknown_sccs -5678 1eq1A 166 4.92e+00 a.63.1.1 64910 2tct 207 4.94e+00 2tct a.4.1.9 16063 a.121.1.1 19240 1k5hA 398 5.02e+00 a.69.3.1 68192 c.2.1.3 68193 d.81.1.3 68194 1au7A 146 5.05e+00 1au7A a.4.1.1 15995 a.35.1.1 17021 1i39A 225 5.05e+00 1ekeA c.55.3.1 61585 1f88A 348 5.05e+00 1f88A f.13.1.2 43429 1hzxA 349 5.07e+00 1f88A f.13.1.2 61466 1rxxA 421 5.12e+00 unknown_sccs -10982 1ciy 590 5.22e+00 1ciy b.18.1.3 23720 b.77.2.1 27977 f.1.3.1 43392 1aew 174 5.38e+00 2fha a.25.1.1 16676 1i58A 189 5.88e+00 1b3qA d.122.1.3 61773 1djxB 624 5.93e+00 1djxB a.39.1.7 17343 b.7.1.1 23160 c.1.18.1 29588 1ui7A 638 6.00e+00 b.30.2.1 -3523 d.17.2.1 -9268 d.17.2.1 -9269 1de6A 426 6.02e+00 1de5A c.1.15.2 29398 1o3uA 135 6.05e+00 a.24.16.3 86615 1akeA 214 6.08e+00 1zin c.37.1.1 31905 g.41.2.1 45185 1c02A 166 6.08e+00 1qspA a.24.10.2 16633 1h5rA 293 6.10e+00 c.68.1.6 65623 1ockA 412 6.11e+00 c.117.1.1 86802 1b0b 142 6.12e+00 2fal a.1.1.2 15010 1gr8A 412 6.15e+00 1oxkB 134 6.31e+00 c.23.1.1 -6411 1t7pA 698 6.37e+00 1t7pA c.55.3.5 33712 e.8.1.1 43005 1jcrA 377 6.39e+00 a.118.6.1 66506 1d8wA 426 6.40e+00 1de5A c.1.15.2 29394 1iw7C 1119 6.42e+00 e.29.1.1 71474 1ivwA 638 6.56e+00 b.30.2.1 71456 d.17.2.1 71457 d.17.2.1 71458 1ui8A 638 6.59e+00 b.30.2.1 -3525 d.17.2.1 -9272 d.17.2.1 -9273 1d1qA 161 6.60e+00 1dg9A c.44.1.1 32642 1bk6A 422 6.66e+00 1bk5A a.118.1.1 19133 1iqyA 638 6.77e+00 b.30.2.1 76763 d.17.2.1 76764 d.17.2.1 76765 1f44A 324 6.90e+00 a.60.9.1 64982 d.163.1.1 64983 2a0b 125 7.09e+00 2a0b a.24.10.1 16630 1f6kA 293 7.31e+00 1nal3 c.1.10.1 29081 1s72B 338 7.38e+00 1uqvA 85 7.52e+00 a.60.1.2 -1010 1moh 142 7.53e+00 1flp a.1.1.2 15012 1avk 638 7.65e+00 1a2vA b.30.2.1 24410 d.17.2.1 38047 d.17.2.1 38048 1hvvA 75 7.76e+00 1hvvA h.1.15.1 45639 6gsvA 217 7.83e+00 1b8xA a.45.1.1 17633 c.47.1.5 32925 1jnyA 435 7.89e+00 b.43.3.1 66982 b.44.1.1 66983 c.37.1.8 66984 1jthB 77 7.92e+00 h.1.15.1 67271 1miwA 404 7.98e+00 a.173.1.1 79162 d.218.1.4 79163 1jj2B 337 8.00e+00 1ffkB b.43.3.2 63086 1f74A 293 8.04e+00 1nal3 c.1.10.1 29079 1pgx 83 8.17e+00 2igd d.15.7.1 37823 1dat 174 8.17e+00 2fha a.25.1.1 16677 1nznA 126 8.24e+00 a.118.8.1 -1616 1ov2A 99 8.27e+00 a.13.1.1 -457 1qlaA 656 8.36e+00 1qlaA a.7.3.1 16328 c.3.1.4 30427 d.168.1.1 42310 1bp3A 191 8.49e+00 1huw a.26.1.1 16838 1s9aA 257 8.76e+00 1e6yB 433 8.79e+00 1mroB a.89.1.1 18535 d.58.31.2 39453 1qgrA 876 8.89e+00 1qgrA a.118.1.1 19119 1sfcB 83 9.63e+00 1sfcB h.1.15.1 45644 1flp 142 9.68e+00 1flp a.1.1.2 15011 1mp4A 292 9.76e+00 c.68.1.6 79376 1oj7A 408 9.99e+00 1dcs 311 1.02e+01 1dcs b.82.2.1 28124 1j99A 293 1.04e+01 c.37.1.5 71618 1ft1A 377 1.04e+01 1ft1A a.118.6.1 19186 1jigA 146 1.04e+01 a.25.1.1 71685 1gkpA 458 1.05e+01 b.92.1.3 70231 c.1.9.6 70232 1izmA 184 1.08e+01 unknown_sccs -1233 1n6eA 1071 1.09e+01 b.36.1.3 80149 b.68.7.1 80150 b.69.9.1 80151 c.14.1.2 80152 1d8dA 377 1.10e+01 1ft1A a.118.6.1 19185 1crxA 322 1.14e+01 4crxA a.60.9.1 18097 d.163.1.1 42157 1amf 233 1.15e+01 1wod c.94.1.1 35833 1wod 233 1.16e+01 1wod c.94.1.1 35832 1bk5A 422 1.17e+01 1bk5A a.118.1.1 19130 1dg9A 157 1.22e+01 1dg9A c.44.1.1 32637 1ee4A 423 1.22e+01 1ee4A a.118.1.1 19128 1dghB 498 1.23e+01 1cf9A e.5.1.1 42791 1cpt 412 1.23e+01 1cpt a.104.1.1 18968 1chkA 238 1.26e+01 1chkA d.2.1.7 36999 2minA 491 1.27e+01 1qguA c.92.2.3 35609 1egdA 396 1.29e+01 3mdeA a.29.3.1 16596 e.6.1.1 42857 1brwA 433 1.29e+01 1brwA a.46.2.1 17764 c.27.1.1 31628 d.41.3.1 38626 1azwA 313 1.31e+01 1qtrA c.69.1.7 34658 1gln 468 1.33e+01 1gln a.97.1.1 18752 c.26.1.1 31588 1aq6A 253 1.34e+01 1qq5A c.108.1.1 43331 1k32A 1045 1.35e+01 b.36.1.3 68068 b.68.7.1 68069 b.69.9.1 68070 c.14.1.2 68071 1oahA 519 1.35e+01 a.138.1.3 86736 1g59A 468 1.35e+01 a.97.1.1 60257 c.26.1.1 60258 1ezfA 340 1.38e+01 1ezfA a.128.1.2 19440 1hf8A 289 1.42e+01 1hg5A unknown_sccs -399 unknown_sccs -1628 1dgfA 497 1.42e+01 1cf9A e.5.1.1 42782 1hg2A 289 1.42e+01 1hg5A unknown_sccs -401 unknown_sccs -1630 1qgoA 264 1.43e+01 1qgoA c.92.1.2 35596 2gdm 153 1.44e+01 2gdm a.1.1.2 15212 1ej5A 107 1.44e+01 1ej5A a.68.1.1 18268 1hg5A 289 1.45e+01 1hg5A unknown_sccs -400 unknown_sccs -1629 1dgsA 667 1.45e+01 1dgsA a.60.2.2 17963 b.40.4.6 25365 d.142.2.2 41581 1c0eA 157 1.46e+01 1dg9A c.44.1.1 32638 1m1nA 491 1.48e+01 c.92.2.3 78417 1hkvA 453 1.48e+01 b.49.2.3 83559 c.1.6.1 83560 1or7A 194 1.50e+01 a.4.13.2 87332 a.177.1.1 87333 1qzzA 374 1.51e+01 a.4.5.29 -277 c.66.1.12 -8045 1joyA 67 1.51e+01 1joyA a.30.2.1 16991 1bhdA 118 1.54e+01 1bkrA a.40.1.1 17398 1j09A 468 1.55e+01 a.97.1.1 77025 c.26.1.1 77026 1n7sB 68 1.55e+01 h.1.15.1 80272 2cevA 299 1.56e+01 1d3vA c.42.1.1 32576 1qq5A 253 1.58e+01 1qq5A c.108.1.1 43327 1de5A 426 1.59e+01 1de5A c.1.15.2 29402 1a32 88 1.59e+01 1a32 a.16.1.2 16384 1phr 157 1.60e+01 1dg9A c.44.1.1 32635 3minC 491 1.60e+01 1qguA c.92.2.3 35607 1qq7A 253 1.61e+01 1qq5A c.108.1.1 43329 1qckA 89 1.63e+01 1qckA a.60.5.1 17976 1r5lA 262 1.65e+01 a.5.3.1 -360 c.13.1.1 -6215 1fp4A 492 1.65e+01 c.92.2.3 76187 1d1gA 168 1.67e+01 1d1gA c.71.1.1 34889 1fc3A 120 1.68e+01 1fc3A a.4.6.3 16237 1ffk1 177 1.70e+01 1ffk1 1qmyA 167 1.71e+01 1qmyA d.3.1.2 37094 1gxqA 106 1.71e+01 a.4.6.1 70721 1auiB 169 1.72e+01 1auiB a.39.1.5 17325 1cbg 490 1.72e+01 1e70M c.1.8.4 28933 1bykA 255 1.75e+01 1bykA c.93.1.1 35706 1fcjA 322 1.76e+01 1oasA c.79.1.1 35289 2ezxA 89 1.76e+01 1qckA a.60.5.1 17978 1k4nA 192 1.79e+01 d.32.1.5 72059 1tmy 120 1.82e+01 1dbwA c.23.1.1 31083 4crxA 322 1.83e+01 4crxA a.60.9.1 18095 d.163.1.1 42155 1pvyA 227 1.83e+01 d.115.1.2 -10937 1au1A 166 1.84e+01 1ifa a.26.1.3 16889 2gsq 202 1.88e+01 1pd21 a.45.1.1 17715 c.47.1.5 33009 1umdA 367 1.88e+01 c.36.1.11 -6969 1cjcA 460 1.90e+01 1cjcA c.3.1.1 30319 c.4.1.1 30604 1ujnA 348 1.90e+01 e.22.1.1 -11998 1e4yA 214 1.91e+01 1zin c.37.1.1 31901 g.41.2.1 45181 1oasA 322 1.95e+01 1oasA c.79.1.1 35293 1qbqA 333 1.98e+01 1ft1A a.118.6.1 19187 1fr0A 125 2.00e+01 2a0b a.24.10.1 59996 1mc3A 296 2.02e+01 c.68.1.6 78943 1oshA 232 2.04e+01 a.123.1.1 -1697 1h40A 71 2.05e+01 1d3uB 201 2.05e+01 1aisB a.74.1.2 18386 a.74.1.2 18387 1b43A 340 2.09e+01 1a76 a.60.7.1 18092 c.120.1.2 33362 1a76 326 2.09e+01 1a76 a.60.7.1 18091 c.120.1.2 33361 1liaA 164 2.14e+01 1cpcA a.1.1.3 15661 2cblA 305 2.15e+01 2cblA a.39.1.7 17380 a.48.1.1 17774 d.93.1.1 40528 1uzcA 71 2.17e+01 a.159.2.1 -339 1agrH 205 2.17e+01 1agrE a.91.1.1 18539 1fmjA 351 2.19e+01 c.37.1.5 59879 1vkeA 133 2.24e+01 1ofnA 205 2.25e+01 b.82.1.1 -4830 2fokA 579 2.30e+01 2fokA a.4.5.12 16131 a.4.5.12 16132 a.4.5.12 16133 c.52.1.12 33323 1mjhA 162 2.31e+01 1mjhA c.26.2.4 31639 1brlA 355 2.32e+01 1lucA c.1.16.1 29553 1ig6A 107 2.32e+01 1ig6A a.4.3.1 62364 1gdj 153 2.36e+01 2gdm a.1.1.2 15213 1v54E 109 2.38e+01 a.118.11.1 -1652 1snnA 227 2.44e+01 1cz3A 168 2.44e+01 1d1gA c.71.1.1 34891 1rlzA 369 2.48e+01 1qflA 389 2.51e+01 1afwA c.95.1.1 35908 c.95.1.1 35909 1o5hA 214 2.52e+01 unknown_sccs -1078 1q1aA 289 2.52e+01 c.31.1.5 -6781 1n3kA 130 2.55e+01 a.77.1.4 79965 1il6 185 2.56e+01 1alu a.26.1.1 16827 1k1xA 659 2.59e+01 a.8.3.2 84279 b.30.5.8 84280 c.6.2.2 84281 1yrnA 61 2.60e+01 1akhA a.4.1.1 15981 1m3kA 392 2.66e+01 c.95.1.1 78565 c.95.1.1 78566 1m4tA 392 2.68e+01 c.95.1.1 78617 c.95.1.1 78618 1uzbA 516 2.68e+01 c.82.1.1 -8552 1qhlA 227 2.69e+01 1qhlA c.37.1.12 32382 1gkxA 388 2.73e+01 a.29.5.1 65266 d.122.1.4 65267 1lucA 355 2.75e+01 1lucA c.1.16.1 29547 1oa4A 222 2.76e+01 b.29.1.11 86731 2lh2 153 2.77e+01 2gdm a.1.1.2 15220 1f07A 321 2.77e+01 1ezwA c.1.16.3 59560 1dkgB 197 2.77e+01 1dkgA b.73.1.1 27813 h.1.9.1 45627 1q0sA 259 2.79e+01 c.66.1.28 -8110 1ot5A 477 2.85e+01 b.18.1.20 87409 c.41.1.1 87410 1ipd 345 2.91e+01 1cnzA c.77.1.1 35038 1zin 217 2.93e+01 1zin c.37.1.1 31915 g.41.2.1 45178 1h6gA 256 2.93e+01 1h6gA a.24.9.1 60669 a.24.9.1 60670 1huw 166 2.95e+01 1huw a.26.1.1 16831 1dy5A 124 2.95e+01 7rsa d.5.1.1 37163 1ci4A 89 3.00e+01 1qckA a.60.5.1 17970 1idm 343 3.02e+01 1cnzA c.77.1.1 35035 1dzaA 129 3.02e+01 7rsa d.5.1.1 37275 1qrjB 199 3.03e+01 1qrjB a.28.3.1 16952 1nwmX 142 3.10e+01 a.7.8.1 86301 1jcqA 382 3.11e+01 a.118.6.1 66504 1ihbA 162 3.17e+01 1bd8 d.211.1.1 19161 1ibrB 462 3.18e+01 1qgrA a.118.1.1 19120 1pyiA 96 3.20e+01 1pyiA g.38.1.1 45079 h.1.3.1 45512 1j3mA 129 3.22e+01 1oaiA 59 3.25e+01 a.5.2.3 81255 1lb3A 182 3.26e+01 a.25.1.1 77873 1pot 325 3.27e+01 1pot c.94.1.1 35807 1jj2L 194 3.28e+01 1ffkI d.12.1.2 63097 1iybA 208 3.29e+01 d.124.1.1 -10977 1q6hA 224 3.31e+01 d.26.1.1 -9487 1sqc 631 3.31e+01 2sqcA a.102.4.2 18858 a.102.4.2 18859 1wdcB 156 3.31e+01 1wdcB a.39.1.5 17302 1jipA 403 3.32e+01 a.104.1.1 66748 1ccwA 137 3.33e+01 1be1 c.23.6.1 31238 1h96A 182 3.34e+01 2fha a.25.1.1 60811 1tk9A 188 3.36e+01 1jthD 77 3.37e+01 h.1.15.1 67273 1dhs 344 3.42e+01 1dhs c.31.1.1 31727 1ld8A 382 3.44e+01 a.118.6.1 73838 1q9uA 130 3.52e+01 unknown_sccs -11025 1hrkA 359 3.52e+01 1hrkA c.92.1.1 61228 1dr8B 344 3.57e+01 1cnzA c.77.1.1 35052 1na3A 91 3.58e+01 k.38.1.1 85481 16vpA 366 3.58e+01 16vpA d.180.1.1 42601 1mx3A 347 3.58e+01 c.2.1.4 79638 c.23.12.1 79639 1hyqA 263 3.61e+01 1hyqA c.37.1.10 61412 1b8dA 164 3.65e+01 1cpcA a.1.1.3 15665 1qhhA 167 3.66e+01 1pjr c.37.1.19 32393 2lbp 346 3.67e+01 2liv c.93.1.1 35709 1p32C 209 3.68e+01 1p32A d.25.1.1 38381 1ufaA 520 3.69e+01 unknown_sccs -421 unknown_sccs -6065 1cs1A 386 3.70e+01 1ibjA c.67.1.3 34399 1fts 295 3.74e+01 1ng1 a.24.13.1 16968 c.37.1.10 32279 1qqiA 104 3.77e+01 1opc a.4.6.1 16233 1b22A 114 3.78e+01 1b22A a.60.4.1 17969 1ffkB 338 3.83e+01 1ffkB b.43.3.2 25719 1k8tA 510 3.85e+01 e.41.1.1 68316 1viuA 203 3.86e+01 d.113.1.1 -10889 1mhdA 132 3.87e+01 1mhdA d.164.1.1 42175 1ak0 270 3.88e+01 1ak0 a.124.1.2 19345 1nksA 194 3.94e+01 1nksA c.37.1.1 31886 1gt7A 274 3.99e+01 c.74.1.1 70398 1r5pA 108 4.00e+01 unknown_sccs -7487