# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7-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 1jogA 146 1.90e-13 a.24.16.2 77142 1o3uA 135 4.69e-02 a.24.16.3 86615 1s7zA 117 8.70e-02 unknown_sccs -344 1ufbA 127 3.70e-01 a.24.16.3 -635 1ewqA 765 5.51e-01 1ewqA a.113.1.1 19069 c.37.1.12 32383 c.55.6.1 33740 d.75.2.1 39743 2cxbA 124 6.01e-01 1ycc a.3.1.1 15891 1cxc 124 6.50e-01 1ycc a.3.1.1 15890 1nksA 194 8.98e-01 1nksA c.37.1.1 31886 1b89A 449 1.13e+00 1b89A a.118.1.3 19138 1uaaA 673 1.90e+00 1pjr c.37.1.19 32401 c.37.1.19 32402 1oj7A 408 1.92e+00 1jdpA 441 2.10e+00 c.93.1.1 62906 1fmjA 351 2.77e+00 c.37.1.5 59879 1khyA 148 3.31e+00 a.174.1.1 77410 1qq7A 253 3.51e+00 1qq5A c.108.1.1 43329 1rxqA 178 3.59e+00 1vhrA 184 3.81e+00 1vhrA c.45.1.1 32651 1qq5A 253 3.82e+00 1qq5A c.108.1.1 43327 1mb3A 124 3.93e+00 c.23.1.1 78907 1om0A 274 3.94e+00 c.1.8.5 87058 1sqsA 242 3.95e+00 unknown_sccs -6433 1aq6A 253 4.26e+00 1qq5A c.108.1.1 43331 1b7eA 420 4.26e+00 1b7eA c.55.3.4 33680 1mw5A 187 4.38e+00 unknown_sccs -11213 1gzsB 165 4.44e+00 a.168.1.1 76425 1ta3A 274 4.73e+00 1ngvA 534 4.95e+00 c.111.1.2 85698 1rmi 160 5.25e+00 1ifa a.26.1.3 16891 2lisA 136 5.40e+00 1lis a.19.1.1 16405 1lis 136 5.52e+00 1lis a.19.1.1 16406 1jbwA 428 5.53e+00 c.59.1.2 62860 c.72.2.2 62861 1v25A 541 5.60e+00 1m5tA 124 5.89e+00 c.23.1.1 78660 1knyA 253 5.94e+00 1knyA a.24.16.1 75896 d.218.1.1 75897 1ebuA 358 6.08e+00 1ebuA c.2.1.3 30035 d.81.1.2 39950 1r5lA 262 6.56e+00 a.5.3.1 -360 c.13.1.1 -6215 1chkA 238 6.58e+00 1chkA d.2.1.7 36999 1bcfA 158 6.90e+00 1bcfA a.25.1.1 16648 1iygA 133 6.97e+00 a.118.8.1 76947 1jraA 117 7.41e+00 a.24.15.1 67117 1e4fT 419 7.44e+00 1e4fT c.55.1.1 33453 c.55.1.1 33454 1ltm 320 7.95e+00 1ltm d.2.1.6 36992 1hqcA 324 8.09e+00 1hqcA a.4.5.11 16127 c.37.1.20 32424 1dp4A 435 8.31e+00 1dp4A c.93.1.1 35710 1q0gA 117 8.50e+00 1di1A 300 8.55e+00 1di1A a.128.1.4 19446 1l3pA 102 8.68e+00 a.24.17.1 84520 1ebfA 358 8.98e+00 1ebuA c.2.1.3 30033 d.81.1.2 39948 1bk5A 422 9.10e+00 1bk5A a.118.1.1 19130 1cnv 299 9.18e+00 1cnv c.1.8.5 28989 1o9gA 250 9.51e+00 c.66.1.29 86692 1ee4A 423 9.54e+00 1ee4A a.118.1.1 19128 3lynA 136 9.79e+00 1lis a.19.1.1 16413 2sas 185 1.02e+01 2sas a.39.1.5 17258 1qrjB 199 1.04e+01 1qrjB a.28.3.1 16952 1crxA 322 1.06e+01 4crxA a.60.9.1 18097 d.163.1.1 42157 1ezfA 340 1.07e+01 1ezfA a.128.1.2 19440 2nsyA 271 1.08e+01 2nsyA c.26.2.1 31612 1p32A 209 1.09e+01 1p32A d.25.1.1 38379 1kqpA 271 1.09e+01 c.26.2.1 72883 1o08A 221 1.10e+01 c.108.1.6 86525 1myf 153 1.11e+01 1a6m a.1.1.2 15147 1kkcA 221 1.12e+01 a.2.11.1 68660 d.44.1.1 68661 1bk6A 422 1.13e+01 1bk5A a.118.1.1 19133 1dbqA 289 1.16e+01 1qpzA c.93.1.1 35666 1jdlA 121 1.19e+01 a.3.1.1 66557 1miwA 404 1.19e+01 a.173.1.1 79162 d.218.1.4 79163 1i50A 1733 1.20e+01 e.29.1.2 61754 1i50B 1224 1.20e+01 e.29.1.1 61755 1f44A 324 1.21e+01 a.60.9.1 64982 d.163.1.1 64983 1n3kA 130 1.21e+01 a.77.1.4 79965 1qgoA 264 1.23e+01 1qgoA c.92.1.2 35596 1m1nA 491 1.24e+01 c.92.2.3 78417 2occE 109 1.25e+01 2occE a.118.11.1 19224 1fp4A 492 1.29e+01 c.92.2.3 76187 1qckA 89 1.32e+01 1qckA a.60.5.1 17976 1qusA 322 1.34e+01 1ltm d.2.1.6 36991 1gln 468 1.34e+01 1gln a.97.1.1 18752 c.26.1.1 31588 1j99A 293 1.36e+01 c.37.1.5 71618 1gr8A 412 1.37e+01 1ockA 412 1.37e+01 c.117.1.1 86802 3minC 491 1.38e+01 1qguA c.92.2.3 35607 1mx3A 347 1.38e+01 c.2.1.4 79638 c.23.12.1 79639 1pvyA 227 1.39e+01 d.115.1.2 -10937 1mrzA 293 1.39e+01 b.43.5.1 -4048 c.26.1.3 -6616 1qz5A 375 1.40e+01 c.55.1.1 -7590 c.55.1.1 -7591 1clqA 903 1.41e+01 1clqA c.55.3.5 33717 e.8.1.1 43006 1nsyA 271 1.41e+01 2nsyA c.26.2.1 31614 1in6A 334 1.42e+01 1hqcA a.4.5.11 62601 c.37.1.20 62602 1apyA 162 1.42e+01 1apyA d.153.1.5 42004 1m22A 503 1.43e+01 c.117.1.1 78464 1hvd 319 1.44e+01 1avc a.65.1.1 18154 1ntyA 311 1.44e+01 1b43A 340 1.44e+01 1a76 a.60.7.1 18092 c.120.1.2 33362 1kbuA 349 1.44e+01 a.60.9.1 72284 d.163.1.1 72285 1m48A 133 1.47e+01 a.26.1.2 74443 1in4A 334 1.47e+01 1hqcA a.4.5.11 62597 c.37.1.20 62598 1ig3A 263 1.50e+01 1ig3A b.82.6.1 62358 c.100.1.1 62359 1aca 86 1.52e+01 1aca a.11.1.1 16367 1a16 440 1.53e+01 1az9 c.55.2.1 33548 d.127.1.1 41165 1jr8A 117 1.54e+01 a.24.15.1 67115 1nznA 126 1.54e+01 a.118.8.1 -1616 1ccwA 137 1.54e+01 1be1 c.23.6.1 31238 4crxA 322 1.57e+01 4crxA a.60.9.1 18095 d.163.1.1 42155 1b5tA 275 1.59e+01 1b5tA c.1.23.1 29676 1jqjC 343 1.59e+01 a.80.1.1 67097 c.37.1.20 67098 3crxA 343 1.61e+01 4crxA a.60.9.1 18101 d.163.1.1 42161 1paqA 189 1.62e+01 unknown_sccs -1557 1au7A 146 1.64e+01 1au7A a.4.1.1 15995 a.35.1.1 17021 1hh7A 114 1.64e+01 1ycc a.3.1.1 15896 1jmkC 230 1.65e+01 c.69.1.22 71747 1ubeA 349 1.67e+01 c.37.1.11 88412 d.48.1.1 88413 1lk9A 448 1.68e+01 c.67.1.1 78057 1vpwA 340 1.68e+01 1qpzA a.35.1.5 17087 c.93.1.1 35680 1kfuS 184 1.70e+01 a.39.1.8 68574 1p32C 209 1.70e+01 1p32A d.25.1.1 38381 1um8A 376 1.74e+01 c.37.1.20 -7251 1v54E 109 1.77e+01 a.118.11.1 -1652 1ej5A 107 1.77e+01 1ej5A a.68.1.1 18268 1ih8A 271 1.79e+01 2nsyA c.26.2.1 62377 1az9 457 1.80e+01 1az9 c.55.2.1 33547 d.127.1.1 41164 1op1A 82 1.81e+01 a.13.1.1 -456 1fgs 428 1.82e+01 1fgs c.59.1.2 33959 c.72.2.2 34962 1i8oA 114 1.83e+01 1ycc a.3.1.1 61979 1hkcA 917 1.83e+01 1qhaA c.55.1.3 33475 c.55.1.3 33476 c.55.1.3 33477 c.55.1.3 33478 2minA 491 1.83e+01 1qguA c.92.2.3 35609 1mc3A 296 1.84e+01 c.68.1.6 78943 1dm5A 315 1.84e+01 1avc a.65.1.1 18186 1vicA 262 1.87e+01 c.68.1.13 -8252 1r4pA 297 1.88e+01 d.165.1.2 -11560 1v4aA 440 1.88e+01 1kshA 186 1.89e+01 c.37.1.8 72914 1oqcA 125 1.90e+01 a.24.15.1 87264 1icrA 217 1.90e+01 1vfrA d.90.1.1 62274 1iwhA 141 1.91e+01 a.1.1.2 76882 1ci4A 89 1.91e+01 1qckA a.60.5.1 17970 1f0yA 302 1.92e+01 2hdhA a.100.1.3 18793 c.2.1.6 30197 1p3jA 217 1.94e+01 c.37.1.1 -6996 g.41.2.1 -12769 1ih7A 903 1.96e+01 1clqA c.55.3.5 62375 e.8.1.1 62376 1j6zA 376 1.98e+01 1yagA c.55.1.1 62667 c.55.1.1 62668 1snnA 227 1.98e+01 1tmy 120 1.99e+01 1dbwA c.23.1.1 31083 2pgd 482 2.00e+01 2pgd a.100.1.1 18778 c.2.1.6 30190 1i2oA 316 2.01e+01 1onrA c.1.10.1 61574 2ezxA 89 2.02e+01 1qckA a.60.5.1 17978 1ssqA 267 2.06e+01 1uj6A 227 2.08e+01 1ift 263 2.10e+01 1mrj d.165.1.1 42211 1g19A 350 2.19e+01 2reb c.37.1.11 32284 d.48.1.1 38770 1a2zA 220 2.20e+01 1a2zA c.56.4.1 33794 2cmkA 227 2.23e+01 1ckeA c.37.1.1 31847 1ezwA 349 2.24e+01 1ezwA c.1.16.3 29558 1nuuA 252 2.28e+01 c.26.1.3 86209 1oxkB 134 2.35e+01 c.23.1.1 -6411 1g7sA 594 2.35e+01 1g7rA b.43.3.1 25712 b.43.3.1 25713 c.20.1.1 31032 c.37.1.8 32147 1ffkO 154 2.36e+01 1ffkO d.55.1.1 38899 1ov2A 99 2.36e+01 a.13.1.1 -457 1fhvA 323 2.39e+01 1fhuA c.1.11.2 29235 d.54.1.1 38879 1h96A 182 2.39e+01 2fha a.25.1.1 60811 1lk5A 229 2.40e+01 unknown_sccs 73960 d.58.40.1 73961 1mrg 263 2.41e+01 1mrj d.165.1.1 42183 1im8A 244 2.47e+01 c.66.1.14 66212 1oi7A 288 2.47e+01 c.2.1.8 87049 c.23.4.1 87050 1j09A 468 2.47e+01 a.97.1.1 77025 c.26.1.1 77026 1jnyA 435 2.49e+01 b.43.3.1 66982 b.44.1.1 66983 c.37.1.8 66984 1gxlA 213 2.51e+01 d.215.1.1 70713 1l3lA 234 2.52e+01 a.4.6.2 73541 d.110.5.1 73542 1vhnA 318 2.52e+01 c.1.4.1 -5209 1f07A 321 2.53e+01 1ezwA c.1.16.3 59560 1bqg 451 2.54e+01 1bqg c.1.11.2 29217 d.54.1.1 38861 1yagA 375 2.55e+01 1yagA c.55.1.1 33449 c.55.1.1 33450 1ja1A 622 2.55e+01 1amoA b.43.4.1 62803 c.23.5.2 62804 c.25.1.4 62805 1mbd 153 2.57e+01 1a6m a.1.1.2 15033 1xikA 375 2.62e+01 1xikA a.25.1.2 16784 1ewkA 490 2.63e+01 1ewkA c.93.1.1 35712 1ac5 483 2.67e+01 1ac5 c.69.1.5 34653 1gm7B 557 2.71e+01 1amoA 615 2.74e+01 1amoA b.43.4.1 25669 c.23.5.2 31210 c.25.1.4 31557 1chrA 370 2.78e+01 1mucA c.1.11.2 29252 d.54.1.1 38896 1bmtA 246 2.80e+01 1bmtA a.46.1.1 17757 c.23.6.1 31235 5fbpA 335 2.81e+01 1frpA e.7.1.1 42873 1pu6A 218 2.81e+01 unknown_sccs -1282 1pmaA 233 2.82e+01 1pmaA d.153.1.4 41918 1e9gA 286 2.85e+01 1wgjA b.40.5.1 59393 1e4yA 214 2.89e+01 1zin c.37.1.1 31901 g.41.2.1 45181 1o98A 511 2.90e+01 c.105.1.1 86684 c.76.1.3 86685 1e0zA 128 2.90e+01 1awd d.15.4.1 59153 1dgmA 363 2.94e+01 1bx4A c.72.1.1 34936 2abd 86 2.95e+01 1aca a.11.1.1 16366 1wetA 340 2.96e+01 1qpzA a.35.1.5 17093 c.93.1.1 35670 1omwA 689 2.98e+01 a.91.1.1 87086 b.55.1.1 87087 d.144.1.7 87088 1d4xA 375 2.99e+01 1yagA c.55.1.1 59107 c.55.1.1 59108 1myt 146 3.02e+01 1a6m a.1.1.2 15207 1jb0L 154 3.03e+01 1jb0L f.31.1.1 62829 1lb3A 182 3.04e+01 a.25.1.1 77873 1bjz 207 3.06e+01 2tct a.4.1.9 16065 a.121.1.1 19242 8abp 306 3.07e+01 8abp c.93.1.1 35647 1bzpA 153 3.07e+01 1a6m a.1.1.2 15020 1qpzA 340 3.09e+01 1qpzA a.35.1.5 17097 c.93.1.1 35673 1a6m 151 3.11e+01 1a6m a.1.1.2 15018 1r6wA 322 3.11e+01 c.1.11.2 -5563 d.54.1.1 -9821 2spo 154 3.14e+01 1a6m a.1.1.2 15053 1mgn 154 3.16e+01 1a6m a.1.1.2 15097 1gk9B 557 3.16e+01 1gm9B 557 3.18e+01 1uxoA 192 3.19e+01 1mvoA 136 3.19e+01 c.23.1.1 79513 1abrA 251 3.22e+01 1mrj d.165.1.1 42196 1gs5A 258 3.24e+01 c.73.1.2 70395 1ofcX 304 3.25e+01 a.4.1.3 -195 unknown_sccs -199 unknown_sccs -978 1rcd 173 3.27e+01 2fha a.25.1.1 16687 1e19A 314 3.27e+01 1b7bA c.73.1.1 34967 1fyhA 258 3.32e+01 1d9cA a.26.1.3 16907 a.26.1.3 16908 1j6rA 214 3.34e+01 d.173.1.2 71598 1i1nA 226 3.37e+01 c.66.1.7 71102 1zin 217 3.46e+01 1zin c.37.1.1 31915 g.41.2.1 45178 1g7rA 594 3.47e+01 1g7rA b.43.3.1 25716 b.43.3.1 25717 c.20.1.1 31034 c.37.1.8 32149 1pjr 724 3.52e+01 1pjr c.37.1.19 32391 c.37.1.19 32392 1avc 673 3.54e+01 1avc a.65.1.1 18178 a.65.1.1 18179 1mi3A 322 3.55e+01 c.1.7.1 -5257 1i58A 189 3.58e+01 1b3qA d.122.1.3 61773 1du6A 64 3.59e+01 1akhA a.4.1.1 16002 1irk 306 3.64e+01 1fmk d.144.1.7 41703 1r8sE 203 3.64e+01 a.118.3.1 -1579 1bykA 255 3.65e+01 1bykA c.93.1.1 35706 1gkfB 557 3.66e+01 1c3pA 375 3.73e+01 1c3pA c.42.1.2 32606 1jqcA 375 3.75e+01 1xikA a.25.1.2 63229 1guxB 152 3.76e+01 1guxB a.74.1.3 18389 1dt9A 437 3.76e+01 1dt9A c.55.4.2 33738 d.79.3.2 39815 d.91.1.1 40257 1e3mA 800 3.76e+01 1ewqA a.113.1.1 19075 c.37.1.12 32389 c.55.6.1 33746 d.75.2.1 39747 1uqvA 85 3.79e+01 a.60.1.2 -1010 2lbp 346 3.81e+01 2liv c.93.1.1 35709 1riqA 465 3.82e+01 unknown_sccs -1295 d.104.1.1 -10769 1dpgA 485 3.85e+01 1dpgA c.2.1.3 30074 d.81.1.5 39989 1ekeA 230 3.86e+01 1ekeA c.55.3.1 33572 1h5rA 293 3.89e+01 c.68.1.6 65623 1at3A 247 3.96e+01 1at3A b.57.1.1 27021 1kfiA 572 3.98e+01 c.84.1.1 68555 c.84.1.1 68556 c.84.1.1 68557 d.129.2.1 68558 2pvbA 107 3.99e+01 1a75A a.39.1.4 17205