# List of top-scoring protein chains for t2k-w0.5 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 1byyA 53 3.67e-16 j.12.1.1 46147 1orqC 223 2.41e-14 f.14.1.1 87348 1qdvA 99 9.15e-10 1t1dA d.42.1.2 38652 1t1dA 100 1.29e-08 1t1dA d.42.1.2 38637 1eodA 100 2.40e-08 1t1dA d.42.1.2 38641 1eoeA 100 2.41e-08 1t1dA d.42.1.2 38638 1eofA 100 4.52e-08 1t1dA d.42.1.2 38640 1bl8A 97 5.05e-08 1bl8A f.14.1.1 43652 1a68 95 5.25e-08 1t1dA d.42.1.2 38639 1exbE 103 6.92e-08 1t1dA d.42.1.2 38643 1j95A 125 7.25e-08 1bl8A f.14.1.1 62749 1r3jC 124 7.28e-08 1jvmA 125 7.34e-08 f.14.1.1 67351 1f6gA 160 7.74e-08 1bl8A f.14.1.1 43656 1dsxA 87 3.57e-07 1t1dA d.42.1.2 38644 1qdwA 87 3.61e-07 1t1dA d.42.1.2 38656 1nn7A 105 1.96e-05 d.42.1.2 85894 1qg9A 21 3.07e-04 j.35.1.1 46275 1ho2A 20 3.42e-04 j.35.1.1 70967 1oojA 149 9.56e-04 a.39.1.5 87198 1mxeA 148 1.02e-03 a.39.1.5 79644 1deg 142 1.03e-03 1cll a.39.1.5 17280 3cln 148 1.68e-03 1cll a.39.1.5 17286 1prwA 149 1.98e-03 1iq5A 149 2.05e-03 a.39.1.5 62643 1g4yR 148 2.18e-03 1cll a.39.1.5 60252 1cdlA 147 2.26e-03 1cll a.39.1.5 17272 5tnc 162 2.36e-03 1ncx a.39.1.5 17246 3kvt 115 2.51e-03 1t1dA d.42.1.2 38642 1tcf 159 2.64e-03 1ncx a.39.1.5 17250 1ahr 146 2.84e-03 1cll a.39.1.5 17287 1a2xA 159 3.02e-03 1ncx a.39.1.5 17251 1ggzA 148 3.03e-03 a.39.1.5 70176 1qtxA 148 3.88e-03 k.21.1.1 88375 1top 162 4.12e-03 1ncx a.39.1.5 17223 1vrkA 148 4.40e-03 1cll k.21.1.1 46451 1tnw 162 4.57e-03 1ncx a.39.1.5 17235 4tnc 162 5.01e-03 1ncx a.39.1.5 17228 1cdmA 144 5.21e-03 1cll a.39.1.5 17270 1npqA 90 6.98e-03 a.39.1.5 85983 1qs7A 145 8.45e-03 k.21.1.1 88373 1lkjA 146 1.05e-02 a.39.1.5 84623 1exrA 148 1.05e-02 1cll a.39.1.5 17299 1clm 148 1.11e-02 1cll a.39.1.5 17301 1k93D 144 1.57e-02 a.39.1.5 68330 1avsA 90 1.89e-02 1cll a.39.1.5 17226 1f70A 76 2.22e-02 1cll a.39.1.5 17288 1ak8 76 2.39e-02 1cll a.39.1.5 17281 1smg 90 2.87e-02 1ncx a.39.1.5 17234 1f54A 77 3.43e-02 a.39.1.5 83244 1oe9B 151 9.60e-02 9wgaA 171 1.39e-01 9wgaA g.3.1.1 44000 g.3.1.1 44001 g.3.1.1 44002 g.3.1.1 44003 1j7qA 86 1.40e-01 1j7rA a.39.1.5 62700 1um3B 160 1.57e-01 1wgtA 186 1.67e-01 9wgaA g.3.1.1 44008 g.3.1.1 44009 g.3.1.1 44010 g.3.1.1 44011 2cwgA 171 2.11e-01 9wgaA g.3.1.1 44024 g.3.1.1 44025 g.3.1.1 44026 g.3.1.1 44027 1trf 76 3.51e-01 1ncx a.39.1.5 17247 1q9bA 43 3.75e-01 1ulkA 126 4.11e-01 1prxA 224 6.23e-01 1prxA c.47.1.10 33076 1ggwA 140 7.62e-01 1ggwA a.39.1.5 60490 1lnqA 336 7.69e-01 c.2.1.9 74049 f.14.1.1 74050 1p0hA 318 7.91e-01 1cojA 212 1.10e+00 1avmA a.2.11.1 15737 d.44.1.1 38734 1scmC 149 1.12e+00 1wdcC a.39.1.5 17319 1dflX 152 1.13e+00 1wdcC a.39.1.5 17321 1ulmA 82 1.13e+00 1wdcC 156 1.20e+00 1wdcC a.39.1.5 17317 1kk8C 154 1.24e+00 a.39.1.5 77431 1oyeA 1049 1.33e+00 d.58.44.1 87587 d.58.44.1 87588 d.58.44.1 87589 d.58.44.1 87590 d.225.1.1 87591 d.225.1.1 87592 f.35.1.1 87593 f.35.1.1 87594 1iwgA 1053 1.33e+00 d.58.44.1 76874 d.58.44.1 76875 d.58.44.1 76876 d.58.44.1 76877 d.225.1.1 76878 d.225.1.1 76879 f.35.1.1 76880 f.35.1.1 76881 1jb0B 740 1.53e+00 1jb0A f.29.1.1 62821 1q90D 159 1.78e+00 1orsC 132 1.93e+00 f.14.1.1 87353 1cjtC 402 2.04e+00 1cipA a.66.1.1 18206 c.37.1.8 32089 1azsC 402 2.48e+00 1cipA a.66.1.1 18203 c.37.1.8 32086 1pduA 244 2.53e+00 a.123.1.1 88034 1jpaA 312 2.61e+00 d.144.1.7 67011 1mvwB 145 2.73e+00 i.15.1.1 79524 1cs4C 394 3.00e+00 1cipA a.66.1.1 18205 c.37.1.8 32088 2mysB 166 3.18e+00 1wdcB a.39.1.5 17308 1culC 380 3.23e+00 1cipA a.66.1.1 18204 c.37.1.8 32087 1k26A 156 3.34e+00 d.113.1.1 72003 1i7pA 274 3.36e+00 b.43.4.2 66048 c.25.1.1 66049 1mmc 30 3.67e+00 g.3.1.2 44061 1jbaA 204 3.85e+00 1rec a.39.1.5 17330 1rtu 113 4.48e+00 9rnt d.1.1.4 36139 1ekeA 230 5.29e+00 1ekeA c.55.3.1 33572 1ctaA 35 5.52e+00 1ctdA a.39.1.5 17232 1n3bA 216 5.78e+00 c.37.1.1 79959 1ge9A 184 5.94e+00 1dd5A d.67.3.1 60463 1vhtA 218 5.95e+00 1fqjA 325 6.02e+00 1cipA a.66.1.1 18215 c.37.1.8 32098 1j7nA 776 6.03e+00 d.92.1.14 66409 d.92.1.14 66410 d.166.1.1 66411 1n4qB 377 6.04e+00 1nm1A 375 6.18e+00 c.55.1.1 80651 c.55.1.1 80652 1l7pA 211 6.34e+00 c.108.1.4 73670 1hyp 80 6.56e+00 1hyp a.52.1.1 17806 1pwuA 776 6.80e+00 1cp9A 205 6.94e+00 1ajqA d.153.1.2 41849 1gotA 350 7.13e+00 1cipA a.66.1.1 18213 c.37.1.8 32096 1ndh 272 7.20e+00 1ndh b.43.4.2 25662 c.25.1.1 31552 2nlrA 234 7.39e+00 2nlrA b.29.1.11 24344 2znc 258 7.83e+00 2cba b.74.1.1 27957 1lufA 343 8.10e+00 d.144.1.7 78223 1r42A 615 8.16e+00 1fxwF 229 8.29e+00 c.23.10.3 65058 1q0sA 259 8.58e+00 1b55A 169 8.96e+00 1btkA b.55.1.1 26963 1bwnA 169 9.20e+00 1btkA b.55.1.1 26961 1mjoA 104 9.24e+00 1cmbA a.43.1.2 17466 1g0xA 197 9.67e+00 1nkr b.1.1.4 21805 b.1.1.4 21806 1k9uA 78 9.93e+00 a.39.1.10 84348 2mgj 154 1.04e+01 1a6m a.1.1.2 15119 1eq1A 166 1.07e+01 a.63.1.1 64910 1mnjA 153 1.08e+01 1a6m a.1.1.2 15179 1dejA 374 1.10e+01 1yagA c.55.1.1 33445 c.55.1.1 33446 1cmcA 104 1.15e+01 1cmbA a.43.1.2 17462 1bowA 159 1.17e+01 1bowA d.60.1.1 39528 1nyhA 166 1.19e+01 h.1.23.1 86403 2mge 154 1.20e+01 1a6m a.1.1.2 15056 1btkA 169 1.23e+01 1btkA b.55.1.1 26959 1duxC 94 1.26e+01 1awcA a.4.5.21 16170 1b6a 478 1.27e+01 1bn5 a.4.5.25 16223 d.127.1.1 41160 1qzyA 478 1.27e+01 1e27A 276 1.31e+01 1agdA b.1.1.2 20763 d.19.1.1 38271 1fcs 154 1.33e+01 1a6m a.1.1.2 15055 1qs2A 401 1.38e+01 1qs1A d.166.1.1 42268 d.166.1.1 42269 1egjL 215 1.42e+01 32c2A b.1.1.1 20500 b.1.1.2 21456 1fx8A 281 1.44e+01 f.19.1.1 43651 1mgn 154 1.45e+01 1a6m a.1.1.2 15097 1qnf 484 1.47e+01 1qnf a.99.1.1 18777 c.28.1.1 31632 1ih0A 71 1.48e+01 a.39.1.5 66140 1mg7A 417 1.48e+01 d.14.1.6 84954 d.58.26.6 84955 1lgwA 164 1.49e+01 d.2.1.3 73894 1nkwH 174 1.50e+01 i.1.1.2 80593 102m 154 1.52e+01 1a6m a.1.1.2 15073 1je6A 275 1.52e+01 b.1.1.2 71638 d.19.1.1 71639 1cikA 154 1.52e+01 1a6m a.1.1.2 15039 1fz1A 527 1.55e+01 1mhyD a.25.1.2 16744 1hu3A 260 1.55e+01 1hu3A a.118.1.2 19137 1gv3A 248 1.56e+01 a.2.11.1 70585 d.44.1.1 70586 1ldfA 281 1.57e+01 f.19.1.1 73845 1c0gA 374 1.58e+01 1yagA c.55.1.1 33443 c.55.1.1 33444 1i3kA 348 1.64e+01 1xel c.2.1.2 61595 1jd0A 263 1.64e+01 2cba b.74.1.1 62888 1e28A 276 1.66e+01 1agdA b.1.1.2 20765 d.19.1.1 38272 1ozsA 73 1.70e+01 1cp0A 154 1.73e+01 1a6m a.1.1.2 15109 1mlo 154 1.74e+01 1a6m a.1.1.2 15085 1bn7A 294 1.75e+01 1bn6A c.69.1.8 34677 1l7mA 211 1.79e+01 c.108.1.4 73664 1h54A 754 1.81e+01 a.102.1.4 60634 b.30.5.3 60635 1q2kA 31 1.83e+01 1ceo 343 1.86e+01 1ceo c.1.8.3 28808 1f20A 435 1.90e+01 b.43.4.1 64932 c.25.1.4 64933 1mod 154 1.92e+01 1a6m a.1.1.2 15107 1mtyD 512 1.94e+01 1mhyD a.25.1.2 16742 1bif 469 1.94e+01 1bif c.37.1.7 31961 c.60.1.4 34003 2bifA 469 1.94e+01 1bif c.37.1.7 31963 c.60.1.4 34009 1cec 343 1.97e+01 1ceo c.1.8.3 28809 3bifA 468 1.97e+01 1bif c.37.1.7 31962 c.60.1.4 34008 1cqwA 295 1.98e+01 1b6g c.69.1.8 34679 1a1oA 276 1.99e+01 1agdA b.1.1.2 20751 d.19.1.1 38265 1ch7A 154 1.99e+01 1a6m a.1.1.2 15083 1mti 154 2.02e+01 1a6m a.1.1.2 15114 1p49A 561 2.03e+01 1kvp 497 2.05e+01 2bpa1 b.121.5.1 23278 1a1mA 278 2.13e+01 1agdA b.1.1.2 20753 d.19.1.1 38266 1i9sA 210 2.14e+01 1i9sA c.45.1.1 62099 1ml5c 228 2.17e+01 1co8A 154 2.18e+01 1a6m a.1.1.2 15079 1ofk 154 2.19e+01 1a6m a.1.1.2 15061 1mnh 153 2.24e+01 1a6m a.1.1.2 15187 1eg0N 229 2.26e+01 1ad2 i.1.1.1 45820 1aec 218 2.35e+01 1cs8A d.3.1.1 37003 1ch2A 154 2.38e+01 1a6m a.1.1.2 15064 1cklA 126 2.46e+01 1cklB g.18.1.1 44851 g.18.1.1 44852 1hzjA 348 2.49e+01 1xel c.2.1.2 61450 1ek6A 348 2.50e+01 1xel c.2.1.2 29800 1m05A 277 2.52e+01 1agdA 276 2.53e+01 1agdA b.1.1.2 20741 d.19.1.1 38260 1eztA 166 2.54e+01 1agrE a.91.1.1 18541 1n7uA 554 2.55e+01 b.126.1.1 85376 1bjfA 193 2.55e+01 1rec a.39.1.5 17331 1n7vA 555 2.56e+01 b.126.1.1 85377 1mym 154 2.56e+01 1a6m a.1.1.2 15054 1ib2A 349 2.57e+01 1ib2A a.118.1.8 62141 1ai1L 215 2.58e+01 8fabA b.1.1.1 19882 b.1.1.2 20978 1gntA 553 2.60e+01 e.26.1.1 70290 1e1dA 553 2.60e+01 1e1dA e.26.1.1 43363 1l25 164 2.64e+01 1l92 d.2.1.3 36761 1ch3A 154 2.65e+01 1a6m a.1.1.2 15111 1hmkA 124 2.68e+01 3lzt d.2.1.2 36603 1jm6A 407 2.70e+01 a.29.5.1 66876 d.122.1.4 66877 1hfyA 123 2.71e+01 3lzt d.2.1.2 36604 1jw8A 154 2.72e+01 a.1.1.2 67376 1e3cP 489 2.73e+01 1auk c.76.1.2 59187 1ch5A 154 2.74e+01 1a6m a.1.1.2 15127 1m45A 148 2.77e+01 a.39.1.5 78598 1mls 154 2.80e+01 1a6m a.1.1.2 15058 1e1zP 489 2.81e+01 1auk c.76.1.2 59158 1dceA 567 2.81e+01 1dceA a.118.6.1 19191 b.7.4.1 23218 c.10.2.2 30867 1co9A 154 2.84e+01 1a6m a.1.1.2 15028 1i50I 122 2.85e+01 g.41.3.1 61762 g.41.3.1 61763 1jc2A 76 2.88e+01 a.39.1.5 62862 1gvnB 287 2.91e+01 c.37.1.21 76354 487dH 224 2.94e+01 1ad2 i.1.1.2 45835 1fmd2 218 2.97e+01 1qqp2 1nr3A 122 2.97e+01 d.236.1.1 86092 2mgb 154 2.99e+01 1a6m a.1.1.2 15102 1jr3D 343 3.00e+01 a.80.1.1 63251 c.37.1.20 63252 1c0fA 367 3.01e+01 1yagA c.55.1.1 33447 c.55.1.1 33448 1mll 154 3.02e+01 1a6m a.1.1.2 15057 1p85H 142 3.05e+01 i.1.1.1 87877 3ctn 76 3.05e+01 1ncx a.39.1.5 17241 1kjyA 325 3.07e+01 a.66.1.1 72624 c.37.1.8 72625 1j97A 210 3.12e+01 1f5sA c.108.1.4 62753 189l 164 3.13e+01 1l92 d.2.1.3 36960 1qqp2 218 3.13e+01 1qqp2 1l76 164 3.21e+01 1l92 d.2.1.3 36822 1bihA 395 3.22e+01 1bihA b.1.1.4 21752 b.1.1.4 21753 b.1.1.4 21754 b.1.1.4 21755 1oa4A 222 3.27e+01 b.29.1.11 86731 1cioA 154 3.30e+01 1a6m a.1.1.2 15029 1kkcA 221 3.30e+01 a.2.11.1 68660 d.44.1.1 68661 1onoA 398 3.32e+01 a.69.3.1 87159 c.2.1.3 87160 d.81.1.3 87161 1qnnA 191 3.33e+01 1avmA a.2.11.1 15792 d.44.1.1 38755 1bh2 315 3.33e+01 1cipA a.66.1.1 18214 c.37.1.8 32097 1jvsA 400 3.39e+01 a.69.3.1 77187 c.2.1.3 77188 d.81.1.3 77189 1ad2 228 3.43e+01 1ad2 e.24.1.1 43353 2mgg 154 3.46e+01 1a6m a.1.1.2 15069 1ch9A 154 3.49e+01 1a6m a.1.1.2 15062 1efxA 278 3.56e+01 1agdA b.1.1.2 20767 d.19.1.1 38273 1nijA 318 3.56e+01 c.37.1.10 85741 d.237.1.1 85742 1br1B 150 3.57e+01 1wdcC a.39.1.5 17309 1irc 154 3.58e+01 1a6m a.1.1.2 15141 1fjrA 195 3.64e+01 1fjrA b.102.1.1 59855 1n8zC 607 3.66e+01 c.10.2.5 80322 c.10.2.5 80323 g.3.9.1 80324 g.3.9.1 80325 1a6m 151 3.67e+01 1a6m a.1.1.2 15018 1eybA 471 3.67e+01 1ey2A b.82.1.4 28115 1mniA 153 3.70e+01 1a6m a.1.1.2 15173 1fx5A 242 3.77e+01 1led b.29.1.1 24135 1cp5A 154 3.78e+01 1a6m a.1.1.2 15123 1g26A 31 3.78e+01 1g26A g.3.16.1 44381 1bzpA 153 3.81e+01 1a6m a.1.1.2 15020 1alvA 173 3.84e+01 1alvA a.39.1.8 17370 1e2sP 489 3.84e+01 1auk c.76.1.2 35031 1fkvA 124 3.85e+01 3lzt d.2.1.2 36602 1iu8A 206 3.91e+01 c.56.4.1 71436 1lam 484 3.92e+01 1lam c.56.5.3 33829 c.50.1.1 33166 1drs 59 3.95e+01 3ebx g.7.1.2 44457 1l37 164 3.95e+01 1l92 d.2.1.3 36721 1jpfA 281 3.96e+01 b.1.1.2 67016 d.19.1.1 67017 1i7fA 292 3.96e+01 1i7fA d.193.1.1 61888 1n3nA 280 3.98e+01 b.1.1.2 85303 d.19.1.1 85304 1p7bA 333 3.99e+01 b.1.18.16 87844 f.14.1.1 87845