# 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 1t62A 166 7.37e-02 1khiA 176 1.17e-01 b.34.5.2 77408 b.40.4.5 77409 1devC 196 3.23e-01 1ygs b.26.1.1 23915 1hh2P 344 4.87e-01 b.40.4.5 65835 d.52.3.1 65836 d.52.3.1 65837 d.202.1.1 65838 1o9yA 84 6.23e-01 unknown_sccs -4105 1k0eA 453 6.89e-01 d.161.1.1 67938 1r6xA 395 7.55e-01 b.122.1.3 -5125 c.26.1.5 -6620 1vie 62 1.24e+00 1vie b.34.4.1 24592 2cpgA 45 1.25e+00 2cpgA unknown_sccs 17455 1nscA 390 1.44e+00 2qwc b.68.1.1 27591 1bif 469 1.47e+00 1bif c.37.1.7 31961 c.60.1.4 34003 3bifA 468 1.68e+00 1bif c.37.1.7 31962 c.60.1.4 34008 1uheA 97 1.71e+00 1ixlA 131 1.83e+00 d.38.1.5 -9705 1qzzA 374 1.83e+00 a.4.5.29 -277 c.66.1.12 -8045 1iyeA 309 1.96e+00 e.17.1.1 83786 1i1kA 309 1.97e+00 1daaA e.17.1.1 61533 1e8uA 454 2.02e+00 1e8tA b.68.1.1 59389 1g8fA 511 2.05e+00 1g8fA b.122.1.3 60348 c.26.1.5 60349 c.37.1.15 60350 1khxA 227 2.06e+00 b.26.1.1 68631 1a3gA 308 2.27e+00 1daaA e.17.1.1 43286 1lj2C 28 2.41e+00 1vif 62 2.47e+00 1vie b.34.4.1 24593 1b8qA 127 2.50e+00 1qauA b.36.1.1 24781 1ov3A 138 2.57e+00 b.34.2.1 87451 b.34.2.1 87452 1qd6C 240 2.59e+00 1qd5A 1o6aA 96 2.68e+00 unknown_sccs -4101 1xgsA 295 2.70e+00 1bn5 a.4.5.25 16216 d.127.1.1 41153 1bax 94 2.71e+00 1bax a.61.1.3 18133 1pedA 351 2.82e+00 1pedA b.35.1.2 24753 c.2.1.1 29769 2bifA 469 2.87e+00 1bif c.37.1.7 31963 c.60.1.4 34009 1fbtA 190 2.91e+00 1bif c.60.1.4 34004 1dmr 823 3.28e+00 1dmr b.52.2.2 26904 c.81.1.1 35312 1jokA 149 3.58e+00 1snc b.40.1.1 63214 1eu1A 780 3.58e+00 1dmr b.52.2.2 26903 c.81.1.1 35311 1e8tA 454 3.58e+00 1e8tA b.68.1.1 59387 1k0gA 453 3.66e+00 d.161.1.1 67940 2eifA 136 3.78e+00 1bkb b.34.5.2 24607 b.40.4.5 25339 1usrA 454 3.84e+00 b.68.1.1 -4569 1i7kA 179 3.87e+00 1u9aA d.20.1.1 61889 1iz6A 138 4.01e+00 b.34.5.2 76976 b.40.4.5 76977 1su4A 994 4.24e+00 b.82.7.1 -4927 c.108.1.7 -6854 d.220.1.1 -11668 f.33.1.1 -12333 1ng2A 193 4.40e+00 b.34.2.1 85660 b.34.2.1 85661 1ckaA 57 4.44e+00 1ckaA b.34.2.1 24459 1ksfX 758 4.45e+00 a.174.1.1 77522 c.37.1.20 77523 c.37.1.20 77524 1gmwA 143 4.98e+00 b.107.1.1 65347 d.58.38.1 65348 1qauA 112 5.13e+00 1qauA b.36.1.1 24779 1kevA 351 5.35e+00 1pedA b.35.1.2 24749 c.2.1.1 29765 1qd5A 275 5.48e+00 1qd5A f.4.2.1 43748 1gmuA 143 5.71e+00 b.107.1.1 65335 d.58.38.1 65336 1qavB 115 5.83e+00 1qauA b.36.1.1 24780 1f5mB 180 6.10e+00 1f5mB d.110.2.1 40896 1o54A 277 6.45e+00 c.66.1.13 -8095 1irqA 71 6.71e+00 unknown_sccs 66297 1na6A 404 6.75e+00 unknown_sccs -4715 unknown_sccs -7564 1f5mA 180 6.84e+00 1f5mB d.110.2.1 40895 1k3yA 221 6.93e+00 a.45.1.1 77245 c.47.1.5 77246 1sty 150 7.00e+00 1snc b.40.1.1 24812 1snc 149 7.38e+00 1snc b.40.1.1 24813 1d7kA 421 7.86e+00 7odcA b.49.2.3 26486 c.1.6.1 28648 1hw1A 239 8.10e+00 1e2xA a.4.5.6 16111 a.78.1.1 18441 1ht9A 76 8.61e+00 4icb a.39.1.1 61252 1gseA 221 8.88e+00 1pgtA a.45.1.1 17667 c.47.1.5 32961 1k3lA 221 9.12e+00 a.45.1.1 77229 c.47.1.5 77230 1e2xA 243 9.22e+00 1e2xA a.4.5.6 16113 a.78.1.1 18443 1dm9A 133 9.74e+00 1dm9A d.66.1.3 39560 1ey4A 149 9.94e+00 1snc b.40.1.1 24815 1fa4A 105 1.02e+01 1plc b.6.1.1 22867 1q1gA 276 1.04e+01 c.56.2.1 -7846 2sns 149 1.06e+01 1snc b.40.1.1 24860 1e0tA 470 1.06e+01 1a49A b.58.1.1 27064 c.1.12.1 29292 c.49.1.1 33146 2dpmA 284 1.07e+01 2dpmA c.66.1.28 34246 2a0b 125 1.07e+01 2a0b a.24.10.1 16630 1mdc 133 1.11e+01 1hmt b.60.1.2 27198 1omzA 293 1.13e+01 c.68.1.15 87093 1i50B 1224 1.16e+01 e.29.1.1 61755 1rlkA 117 1.17e+01 unknown_sccs -7526 1e79A 510 1.19e+01 1skyB a.69.1.1 18269 b.49.1.1 26434 c.37.1.11 32314 1ufkA 254 1.20e+01 unknown_sccs -8103 1axn 323 1.23e+01 1avc a.65.1.1 18149 1fo1A 271 1.24e+01 1fo1A c.10.2.3 30869 d.58.7.2 39213 1nycA 111 1.25e+01 unknown_sccs -4522 1unkA 87 1.27e+01 1cei a.28.2.1 16935 1o7iA 119 1.27e+01 b.40.4.3 86642 1cmcA 104 1.31e+01 1cmbA unknown_sccs 17462 1aqjA 421 1.35e+01 2admA c.66.1.27 34242 1v5lA 103 1.35e+01 1ayyA 151 1.36e+01 1apyA d.153.1.5 42016 1jqbA 351 1.36e+01 b.35.1.2 77151 c.2.1.1 77152 1qx2A 76 1.37e+01 1o58A 303 1.38e+01 c.79.1.1 -8503 3ullA 132 1.39e+01 3ullA b.40.4.3 25282 1d2eA 397 1.39e+01 1efcA b.43.3.1 25701 b.44.1.1 25741 c.37.1.8 32136 1knyA 253 1.40e+01 1knyA a.24.16.1 75896 d.218.1.1 75897 1j6nA 303 1.40e+01 1h8eA 510 1.40e+01 1skyB a.69.1.1 60738 b.49.1.1 60739 c.37.1.11 60740 1l6oA 95 1.50e+01 b.36.1.1 84534 2cbp 96 1.51e+01 2cbp b.6.1.1 22895 1rec 201 1.53e+01 1rec a.39.1.5 17326 1sb8A 352 1.56e+01 1tyu 543 1.59e+01 1tyv b.80.1.6 28037 1uxxX 133 1.60e+01 b.18.1.10 -3107 1hrkA 359 1.63e+01 1hrkA c.92.1.1 61228 1cei 94 1.63e+01 1cei a.28.2.1 16939 1aac 105 1.66e+01 1aac b.6.1.1 22838 1cmbA 104 1.67e+01 1cmbA unknown_sccs 17460 1tsp 559 1.67e+01 1tyv b.80.1.6 28044 1r48A 35 1.68e+01 unknown_sccs -13006 1dvoA 152 1.68e+01 1dvoA a.136.1.1 19623 1ur3M 319 1.68e+01 c.1.7.1 -5248 1quvA 578 1.71e+01 1quvA e.8.1.4 43119 1fr0A 125 1.77e+01 2a0b a.24.10.1 59996 1n5dA 288 1.77e+01 c.2.1.2 80030 1jj2R 84 1.78e+01 1ffkP d.12.1.1 63103 1s72S 85 1.80e+01 1o0xA 262 1.81e+01 d.127.1.1 80755 1gdeA 389 1.81e+01 c.67.1.1 60456 1hu4A 288 1.81e+01 1hu4A 1aonO 97 1.82e+01 b.35.1.1 24642 1t82A 155 1.85e+01 1pl8A 356 1.86e+01 b.35.1.2 -3716 c.2.1.1 -5740 1g8aA 227 1.86e+01 c.66.1.3 -8049 1eulA 994 1.87e+01 1eulA 1aaj 105 1.89e+01 1aac b.6.1.1 22841 1nvmA 345 1.90e+01 a.5.7.1 86249 c.1.10.5 86250 1a4mA 349 1.94e+01 1a4mA c.1.9.1 29014 1lr1A 61 1.97e+01 a.155.1.1 78154 5croA 66 1.98e+01 1orc a.35.1.2 17044 1f3aA 222 1.98e+01 1pgtA a.45.1.1 17701 c.47.1.5 32995 1gd9A 389 2.01e+01 c.67.1.1 60454 1gsmA 210 2.01e+01 b.1.1.4 65535 b.1.1.4 65536 1exeA 99 2.06e+01 1huuA a.55.1.1 17906 1cq3A 233 2.08e+01 1cq3A b.27.1.1 23923 1ubpB 122 2.08e+01 1ubpB b.85.3.1 28346 1v38A 78 2.09e+01 a.60.1.2 -1016 1az3A 244 2.13e+01 1rvaA c.52.1.2 33276 1vj0A 380 2.17e+01 b.35.1.2 -3697 c.2.1.1 -5721 1s6cA 183 2.20e+01 a.39.1.5 -858 1o1fC 147 2.22e+01 i.15.1.1 80997 1g3gA 164 2.23e+01 1g6gA b.26.1.2 23918 1lcyA 325 2.24e+01 b.36.1.4 73834 b.47.1.1 73835 1bxaA 105 2.26e+01 1aac b.6.1.1 22839 1mfgA 95 2.29e+01 b.36.1.1 79043 1b5eA 246 2.36e+01 1b5eA d.117.1.1 41056 1i58A 189 2.39e+01 1b3qA d.122.1.3 61773 1azsA 220 2.39e+01 1azsA d.58.29.1 39416 1v54D 147 2.43e+01 f.23.1.1 -12100 1g38A 393 2.44e+01 2admA c.66.1.27 60235 7reqA 727 2.46e+01 1reqA c.1.19.1 29616 c.23.6.1 31243 1bqsA 209 2.49e+01 1bqsA b.1.1.4 21704 b.1.1.4 21705 2occD 147 2.51e+01 1ocrD f.23.1.1 43521 1pa2A 306 2.51e+01 1bgp a.93.1.1 18693 1ocrD 147 2.51e+01 1ocrD f.23.1.1 43541 1krhA 338 2.53e+01 b.43.4.2 72891 c.25.1.2 72892 d.15.4.2 72893 1te5A 257 2.55e+01 1ujxA 119 2.55e+01 b.26.1.2 -3325 4icb 76 2.58e+01 4icb a.39.1.1 17145 1fx3B 169 2.60e+01 1fx3B d.33.1.1 38525 1tyv 542 2.67e+01 1tyv b.80.1.6 28038 1qq1A 559 2.68e+01 1tyv b.80.1.6 28041 1qa1A 554 2.68e+01 1tyv b.80.1.6 28047 1dg3A 592 2.69e+01 1dg3A a.114.1.1 19078 c.37.1.8 32153 2admA 421 2.69e+01 2admA c.66.1.27 34238 4ubpB 126 2.70e+01 1ubpB b.85.3.1 28345 1exzA 141 2.70e+01 1exzA a.26.1.2 16877 1l4iA 206 2.71e+01 b.1.11.1 73564 b.7.2.1 73565 1mtyB 384 2.74e+01 1mtyB a.25.1.2 16740 1jsmA 325 2.74e+01 b.19.1.2 63264 1fz1C 389 2.75e+01 1mtyB a.25.1.2 16746 1akr 147 2.84e+01 1rcf c.23.5.1 31152 7odcA 424 2.84e+01 7odcA b.49.2.3 26488 c.1.6.1 28650 1tmy 120 2.90e+01 1dbwA c.23.1.1 31083 1qcsA 211 2.90e+01 1qcsA b.52.2.3 26927 d.31.1.1 38461 1fkx 349 2.93e+01 1a4mA c.1.9.1 29018 1ndh 272 2.97e+01 1ndh b.43.4.2 25662 c.25.1.1 31552 1og6A 298 2.97e+01 c.1.7.1 86984 1add 349 2.99e+01 1a4mA c.1.9.1 29020 1mmoB 384 3.02e+01 1mtyB a.25.1.2 16768 1q1lA 401 3.05e+01 unknown_sccs -11166 1fjgD 209 3.05e+01 1c05A d.66.1.2 39553 1bmfA 510 3.06e+01 1skyB a.69.1.1 18281 b.49.1.1 26446 c.37.1.11 32326 1oafA 261 3.08e+01 a.93.1.1 86734 1ugxA 133 3.09e+01 1e2o 233 3.10e+01 1eaf c.43.1.1 32631 1c2pA 576 3.10e+01 1quvA e.8.1.4 43117 1bu5A 147 3.11e+01 5nul c.23.5.1 31155 1ig5A 75 3.14e+01 4icb a.39.1.1 62363 1ky3A 182 3.15e+01 c.37.1.8 73193 1bxvA 91 3.18e+01 1aac b.6.1.1 22875 1hrzA 76 3.20e+01 1hryA a.21.1.1 16430 1jltA 122 3.28e+01 a.133.1.2 66867 1v74A 107 3.29e+01 unknown_sccs -9319 1cof 143 3.29e+01 1cof d.109.1.2 40860 1omrA 201 3.30e+01 a.39.1.5 -854 1hq3B 126 3.33e+01 1aoiD a.22.1.1 16444 2lgsA 468 3.42e+01 1lgr d.15.9.1 37838 d.128.1.1 41168 1vcaA 202 3.47e+01 1vcaA b.1.1.3 21649 b.1.1.4 21685 1rcb 129 3.50e+01 1rcb a.26.1.2 16854 1mmoD 512 3.51e+01 1mhyD a.25.1.2 16770 1fjgQ 105 3.56e+01 1fjfQ b.40.4.5 25352 1gx5A 536 3.59e+01 e.8.1.4 70682 1sx5A 244 3.63e+01 c.52.1.2 -7551 1uebA 184 3.63e+01 1gttA 429 3.66e+01 d.177.1.1 70529 d.177.1.1 70530 1ed7A 45 3.68e+01 1ed7A b.72.2.1 27809 2polA 366 3.72e+01 2polA d.131.1.1 41356 d.131.1.1 41357 d.131.1.1 41358 1f20A 435 3.73e+01 b.43.4.1 64932 c.25.1.4 64933 1hryA 76 3.74e+01 1hryA a.21.1.1 16429 1lgr 468 3.75e+01 1lgr d.15.9.1 37837 d.128.1.1 41167 1nykA 165 3.80e+01 b.33.1.1 86408 1iqqA 200 3.80e+01 d.124.1.1 66274 1mwvA 714 3.81e+01 a.93.1.3 85161 a.93.1.3 85162 1g60A 260 3.81e+01 c.66.1.11 70151 1gh8A 89 3.95e+01 1gh8A d.58.12.1 39309 1chmA 401 3.96e+01 1chmA c.55.2.1 33545 d.127.1.1 41142 5reqA 727 4.00e+01 1reqA c.1.19.1 29632 c.23.6.1 31259