# List of top-scoring protein chains for t04-100-30-alpha-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 2c1vA 338 2.27e-01 2ggcA 263 3.97e-01 1xnzA 264 5.08e-01 2b81A 323 5.38e-01 1c24A 263 5.93e-01 1c24A d.127.1.1 41148 2aucA 126 6.34e-01 1oa8A 133 8.79e-01 b.145.1.1 92698 1zip 217 1.04e+00 1zin c.37.1.1,g.41.2.1 31916,45179 1zin 217 1.12e+00 1zin c.37.1.1,g.41.2.1 31915,45178 1rec 201 1.29e+00 1rec a.39.1.5 17326 1xt8A 292 1.35e+00 1ax4A 467 1.52e+00 1ax4A c.67.1.2 34391 1omrA 201 1.65e+00 a.39.1.5 93349 2eu8A 216 1.73e+00 2fhpA 187 1.94e+00 2b0cA 206 2.05e+00 1ghpA 258 2.35e+00 1btl e.3.1.1 60520 1qycA 308 2.36e+00 c.2.1.2 96581 1w7jB 151 2.74e+00 1uufA 369 2.89e+00 b.35.1.2,c.2.1.1 100006,100007 16vpA 366 2.96e+00 16vpA d.180.1.1 42601 1p3jA 217 3.30e+00 c.37.1.1,g.41.2.1 94022,94023 1gu2A 124 3.50e+00 a.3.1.1 76348 2azeA 155 3.66e+00 1jbkA 195 4.05e+00 c.37.1.20 71631 2d2eA 250 4.08e+00 2bl0B 145 4.15e+00 2cvzA 289 4.29e+00 1vlrA 350 4.55e+00 d.13.1.3,d.246.1.1 108860,108861 1yruB 74 4.64e+00 2csbA 519 4.95e+00 1aky 221 5.04e+00 1zin c.37.1.1,g.41.2.1 31896,45197 9gafA 295 5.16e+00 1apyA d.153.1.5 42008 1iwhB 146 5.73e+00 a.1.1.2 76883 2a7oA 112 6.23e+00 1th8A 145 6.53e+00 d.122.1.3 106908 2gwhA 298 6.57e+00 1ng6A 148 6.94e+00 a.182.1.1 85670 1gcuA 295 6.97e+00 1gcuA c.2.1.3,d.81.1.4 30063,39978 2d5xB 146 7.14e+00 1j09A 468 7.14e+00 a.97.1.1,c.26.1.1 77025,77026 1bqbA 301 7.28e+00 1hyt d.92.1.2 58962 1njhA 119 7.28e+00 b.128.1.1 85787 1p4kA 295 7.41e+00 d.153.1.5 87772 1m45A 148 7.44e+00 a.39.1.5 78598 2ftxB 64 7.95e+00 1i39A 225 8.08e+00 1ekeA c.55.3.1 61585 1b04A 318 8.18e+00 1b04A d.142.2.2 41579 1lc0A 294 8.23e+00 c.2.1.3,d.81.1.4 73823,73824 1sq5A 308 8.63e+00 c.37.1.6 105882 1zcjA 463 8.74e+00 1egaA 301 8.86e+00 1egaA c.37.1.8,d.52.3.1 32150,38836 1t3qA 168 9.10e+00 a.56.1.1,d.15.4.2 106367,106368 1kk8B 139 9.38e+00 a.39.1.5 77430 1gln 468 9.45e+00 1gln a.97.1.1,c.26.1.1 18752,31588 1wjuA 100 9.53e+00 1qf5A 431 9.67e+00 1adeA c.37.1.10 32212 1vzyA 291 9.69e+00 1z5hA 780 1.00e+01 1fmjA 351 1.02e+01 c.37.1.5 59879 1auiB 169 1.03e+01 1auiB a.39.1.5 17325 1ug3A 339 1.04e+01 1e7lA 157 1.07e+01 1en7A a.140.4.1,d.4.1.5 64728,64729 1esmA 316 1.07e+01 1esmA c.37.1.6 31953 1b3uA 588 1.10e+01 1b3uA a.118.1.2 19135 2gasA 307 1.11e+01 1pp0A 199 1.12e+01 d.103.1.1 104211 1f0yA 302 1.13e+01 2hdhA a.100.1.3,c.2.1.6 18793,30197 2c3nA 247 1.14e+01 1eqfA 280 1.15e+01 1eqfA a.29.2.1,a.29.2.1 16972,16973 2a5lA 200 1.16e+01 1e1hB 174 1.17e+01 2aobA 99 1.18e+01 1jsxA 207 1.20e+01 c.66.1.20 71846 1r9lA 309 1.21e+01 c.94.1.1 97262 1rcuA 195 1.25e+01 c.129.1.1 97295 1wmuA 141 1.26e+01 a.1.1.2 109416 1p4cA 380 1.32e+01 c.1.4.1 94100 1r5iD 216 1.33e+01 a.202.1.1 97091 1avsA 90 1.33e+01 1cll a.39.1.5 17226 1wdpA 495 1.34e+01 2gzaA 361 1.36e+01 1m1cA 680 1.36e+01 e.42.1.1 78395 1jgsA 138 1.40e+01 a.4.5.28 66683 2esrA 177 1.41e+01 2aumA 317 1.43e+01 1sgwA 214 1.49e+01 c.37.1.12 105541 1zfpE 98 1.50e+01 1griA d.93.1.1 40465 1a8s 273 1.53e+01 1brt c.69.1.12 34710 1yemA 179 1.53e+01 1bjaA 95 1.55e+01 1bjaA a.4.5.9 16122 2b0jA 358 1.55e+01 1g5cA 170 1.56e+01 1g5cA c.53.2.1 60264 1gpl 432 1.57e+01 1gpl b.12.1.2,c.69.1.19 23645,34793 2occJ 59 1.58e+01 2occJ f.23.4.1 43524 2ca6A 386 1.58e+01 1wrjA 156 1.59e+01 1rqtA 37 1.60e+01 a.108.1.1 97771 1g4yR 148 1.60e+01 1cll a.39.1.5 60252 1ccwB 483 1.61e+01 1cb7B c.1.19.2 29646 1wdcB 156 1.66e+01 1wdcB a.39.1.5 17302 1e17A 150 1.70e+01 2hfh a.4.5.14 16143 1dpuA 99 1.72e+01 1dpuA a.4.5.16 16150 1byb 495 1.73e+01 1byb c.1.8.1 28790 1dv0A 47 1.73e+01 1dv0A a.5.2.1 16289 2ao0A 324 1.74e+01 4tmkA 213 1.76e+01 5tmpA c.37.1.1 31930 1ekeA 230 1.79e+01 1ekeA c.55.3.1 33572 1hw6A 278 1.79e+01 1frb c.1.7.1 61296 1w4vA 119 1.81e+01 1dw0A 112 1.84e+01 1dw0A a.3.1.1 15911 1pufB 73 1.86e+01 a.4.1.1 95132 1vydA 116 1.87e+01 a.3.1.1 108900 1t0qA 498 1.92e+01 a.25.1.2 106220 1uvzA 119 1.93e+01 1v0lA 313 1.98e+01 c.1.8.3 108207 1od8A 313 1.99e+01 c.1.8.3 86838 1jyrA 96 2.01e+01 d.93.1.1 71969 1e0wA 313 2.03e+01 1taxA c.1.8.3 59150 1dgnA 89 2.04e+01 1dgnA a.77.1.3 18436 1st0A 337 2.08e+01 d.13.1.3,d.246.1.1 98979,98980 1mwqA 101 2.09e+01 d.58.4.7 91481 1mtyB 384 2.13e+01 1mtyB a.25.1.2 16740 1b72B 87 2.15e+01 1akhA a.4.1.1 16001 2f3yA 148 2.17e+01 1n1jA 93 2.18e+01 a.22.1.3 79813 1v54J 59 2.21e+01 f.23.4.1 100331 1eca 136 2.21e+01 1flp a.1.1.2 15209 1wdjA 187 2.27e+01 1dbqA 289 2.28e+01 1qpzA c.93.1.1 35666 1i3dA 146 2.29e+01 a.1.1.2 61587 1xfxO 149 2.29e+01 1ss4A 153 2.30e+01 d.32.1.6 105976 1q6cA 495 2.34e+01 c.1.8.1 95970 1irdB 146 2.34e+01 a.1.1.2 66287 2awiA 317 2.35e+01 2d2mD 145 2.36e+01 1p7tA 731 2.36e+01 c.1.13.1 94319 1jk3A 158 2.36e+01 d.92.1.11 66790 1uhnA 189 2.37e+01 a.39.1.5 99399 1xn9A 101 2.38e+01 1babB 146 2.39e+01 1abwA a.1.1.2 15414 1oz9A 150 2.42e+01 d.92.1.15 93808 2ak3A 226 2.43e+01 1zin c.37.1.1,g.41.2.1 31892,45193 1ohlA 342 2.44e+01 c.1.10.3 87035 2bx6A 350 2.44e+01 1mvwB 145 2.45e+01 i.15.1.1 79524 2aaoA 166 2.55e+01 1qyiA 384 2.59e+01 c.108.1.13 96595 1v3hA 495 2.61e+01 c.1.8.1 108303 1eq2A 310 2.63e+01 1eq2A c.2.1.2 29814 1lk2A 274 2.65e+01 b.1.1.2,d.19.1.1 91056,91057 1vprA 374 2.68e+01 1dekA 241 2.68e+01 1dekA c.37.1.1 31842 2ran 316 2.74e+01 1avc a.65.1.1 18170 1jftA 340 2.78e+01 a.35.1.5,c.93.1.1 66652,66653 1z00B 84 2.79e+01 1repC 251 2.80e+01 1repC a.4.5.10,a.4.5.10 16125,16126 1tn4 159 2.82e+01 1ncx a.39.1.5 17248 2shpA 525 2.86e+01 2shpA c.45.1.2,d.93.1.1,d.93.1.1 32683,40533,40534 1z3eB 73 2.87e+01 1fzoA 274 2.87e+01 1agdA b.1.1.2,d.19.1.1 60155,60156 2b7kA 200 2.90e+01 1uwkA 557 2.98e+01 e.51.1.1 108065 1v8dA 235 2.98e+01 c.140.1.1 108425 2co5A 99 3.04e+01 1pmi 440 3.05e+01 1pmi b.82.1.3 28114 2h7bA 105 3.08e+01 1v32A 101 3.08e+01 a.42.1.1 100277 1fxrA 64 3.08e+01 1fxd d.58.1.4 38993 2g3bA 208 3.10e+01 1rh5A 436 3.14e+01 f.41.1.1 97464 1a8b 318 3.15e+01 1avc a.65.1.1 18171 6paxA 133 3.19e+01 6paxA a.4.1.5,a.4.1.5 64758,64759 1n82A 331 3.22e+01 c.1.8.3 91703 1z1dA 103 3.24e+01 1ngkA 128 3.27e+01 a.1.1.1 85673 2gh1A 301 3.27e+01 1z2cB 383 3.28e+01 1v2zA 111 3.28e+01 a.186.1.1 108300 2b3oA 532 3.29e+01 1uouA 474 3.33e+01 a.46.2.1,c.27.1.1,d.41.3.1 99706,99707,99708 1top 162 3.36e+01 1ncx a.39.1.5 17223 2ev7A 64 3.36e+01 3lynA 136 3.37e+01 1lis a.19.1.1 16413 1wlmA 151 3.38e+01 2b30A 301 3.45e+01 1vhnA 318 3.47e+01 c.1.4.1 100693 2cwyA 94 3.48e+01 1exrA 148 3.52e+01 1cll a.39.1.5 17299 2fcr 173 3.52e+01 1rcf c.23.5.1 31151 1hy0A 466 3.53e+01 1auwA a.127.1.1 61392 1e6yA 569 3.54e+01 1mroA a.89.1.1,d.58.31.2 18529,39447 1qv1A 195 3.55e+01 a.39.1.5 96347 1y0vH 146 3.55e+01 1pbe 394 3.59e+01 1pbe c.3.1.2,d.16.1.2 30338,37869 1wi6A 88 3.65e+01 1h7nA 342 3.69e+01 1b4kA c.1.10.3 60726 1m98A 317 3.72e+01 a.175.1.1,d.17.4.6 78866,78867 2fueA 262 3.72e+01 1yg2A 179 3.75e+01 2a5kA 307 3.81e+01 1g8iA 190 3.84e+01 1rec a.39.1.5 60363 2arsA 262 3.86e+01 1jf2A 195 3.86e+01 1ej3A a.39.1.5 62930 1wyuA 438 3.86e+01 1zb1A 392 3.92e+01 1dszB 85 3.99e+01 2nllB g.39.1.2 45108 1r6uA 437 4.03e+01 c.26.1.1 97163 1y6vA 449 4.06e+01 1epxA 370 4.08e+01 1fbaA c.1.10.1 29150 2dc4A 165 4.10e+01 1bg6 359 4.11e+01 1bg6 a.100.1.5,c.2.1.6 18810,30214 1pvmA 184 4.11e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1zx4A 192 4.16e+01 1rss 151 4.26e+01 1rss a.75.1.1 18392 1r69 69 4.27e+01 1r69 a.35.1.2 17028 1mvwC 147 4.32e+01 i.15.1.1 79525 1swyA 164 4.37e+01 1sczA 233 4.40e+01 c.43.1.1 98802 1i74A 309 4.41e+01 1i74A c.107.1.1 61867 1ijqA 316 4.42e+01 1ijqA b.68.5.1,g.3.11.1 62506,62507 1kjvA 284 4.42e+01 b.1.1.2,d.19.1.1 77421,77422 1odoA 408 4.44e+01 a.104.1.1 92783 1i7dA 659 4.50e+01 1d6mA e.10.1.1 61886 1ah7 245 4.52e+01 1ah7 a.124.1.1 19339 1sx7A 164 4.54e+01 2cyeA 133 4.54e+01 1sfe 180 4.55e+01 1sfe a.4.2.1,c.55.7.1 16073,33748 1v5iB 76 4.55e+01 1a0rP 245 4.60e+01 1b9yC c.47.1.6 33054 1uocA 289 4.61e+01 c.55.3.9 99686 1xwoA 465 4.62e+01 1viaA 175 4.65e+01 c.37.1.2 100754 1p9eA 331 4.66e+01 d.157.1.5 104088 1iooA 196 4.68e+01 d.124.1.1 71250 2fokA 579 4.69e+01 2fokA a.4.5.12,a.4.5.12,a.4.5.12,c.52.1.12 16131,16132,16133,33323 2fcjA 119 4.71e+01 2f2gA 221 4.76e+01 1el4A 195 4.76e+01 1ej3A a.39.1.5 59453 2btdA 210 4.77e+01 1vkpA 383 4.80e+01 d.126.1.6 108686 1pvaA 110 4.82e+01 1a75A a.39.1.4 17207 1m40A 263 4.86e+01 e.3.1.1 74437 2aunA 317 4.87e+01 2b2aA 199 4.87e+01 1zrsA 317 4.88e+01 1lb2B 84 4.88e+01 a.60.3.1 77871 1fl2A 310 4.93e+01 1hyuA c.3.1.5,c.3.1.5 59869,59870 1fpzA 212 4.94e+01 1fpzA c.45.1.1 59976 1xdzA 240 4.95e+01 1yrgA 385 4.95e+01 1yrgA c.10.1.2 30854 1knzA 164 4.97e+01 e.34.1.1 68709 1u3eM 174 5.00e+01 d.4.1.3,d.285.1.1 107640,107641 1orjA 130 5.05e+01 a.24.19.1 93456 1fxoA 293 5.12e+01 1g0rA c.68.1.6 34524 1bkjA 240 5.12e+01 1bkjA d.90.1.1 40243 1ykjA 394 5.13e+01 2c4nA 250 5.17e+01 1w36D 608 5.18e+01 1tf5A 844 5.18e+01 a.162.1.1,a.172.1.1,c.37.1.19,c.37.1.19 106834,106835,106836,106837 1ed8A 449 5.19e+01 1b8jA c.76.1.1 34988 1khdA 345 5.20e+01 a.46.2.1,c.27.1.1 77400,77401 1sjdA 368 5.21e+01 c.1.11.2,d.54.1.1 105632,105633 1o69A 394 5.26e+01 c.67.1.4 92560 1wfdA 93 5.33e+01 1xhfA 123 5.34e+01 2g2kA 170 5.40e+01 1q4mA 221 5.42e+01 a.132.1.3 95805 1v6zA 228 5.44e+01 2cblA 305 5.50e+01 2cblA a.39.1.7,a.48.1.1,d.93.1.1 17380,17774,40528 1gk7A 39 5.57e+01 h.1.20.1 70212 1zthA 258 5.69e+01 1k68A 140 5.70e+01 c.23.1.1 90943 1jb0M 31 5.70e+01 1jb0M f.23.19.1 62830 1byi 224 5.72e+01 1byi c.37.1.10 32199 1yoeA 322 5.72e+01 5pal 109 5.75e+01 1a75A a.39.1.4 17215 1wi0A 113 5.75e+01 1hcuA 503 5.77e+01 a.102.2.1 65796 1ov9A 50 5.79e+01 a.155.1.1 93591 2ex0A 399 5.80e+01 1ash 150 5.80e+01 1ash a.1.1.2 15622 1k7kA 221 5.85e+01 c.51.4.1 72104 1d8cA 723 5.89e+01 1d8cA c.1.13.1 29325 1uarA 285 5.90e+01 c.46.1.2,c.46.1.2 107762,107763 1f7uA 607 5.91e+01 1bs2A a.27.1.1,c.26.1.1,d.67.2.1 59673,59674,59675 2a6aA 218 5.98e+01 1q1fA 151 6.02e+01 a.1.1.2 104476 1c52 131 6.04e+01 1c52 a.3.1.1 15810 1e2uA 553 6.09e+01 1e1dA e.26.1.1 43362 1wq3A 322 6.13e+01 1ii7A 333 6.14e+01 1ii7A d.159.1.4 62415 2fu4A 83 6.18e+01 1gx1A 160 6.18e+01 d.79.5.1 70675 1kk1A 410 6.27e+01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 2d0eA 407 6.30e+01 2fh7A 595 6.30e+01 3thiA 371 6.31e+01 2thiA c.94.1.1 35792 1yhtA 367 6.32e+01 1s1fA 406 6.33e+01 1gntA 553 6.39e+01 e.26.1.1 70290 1bm9A 122 6.44e+01 1bm9A a.4.5.7 16116 1nq6A 302 6.45e+01 c.1.8.3 92046 1xl7A 612 6.47e+01 2f9dA 125 6.53e+01 1pprM 312 6.60e+01 1pprM a.131.1.1,a.131.1.1 19502,19503 1uj6A 227 6.65e+01 c.124.1.4,d.58.40.1 107898,107899 1o3yA 166 6.71e+01 c.37.1.8 86618 1zl0A 311 6.79e+01 1h4pA 408 6.83e+01 c.1.8.3 90617 1wlsA 328 6.83e+01 1yhuB 144 6.87e+01 1iqcA 308 6.89e+01 a.3.1.5,a.3.1.5 66266,66267 1xwwA 157 6.89e+01 1xknA 355 6.92e+01 1pzlA 237 6.93e+01 a.123.1.1 104393 1v8eA 224 7.04e+01 3c2c 112 7.04e+01 1ycc a.3.1.1 15885 1hufA 140 7.13e+01 1hufA d.195.1.1 61272 1yvhA 329 7.15e+01 1zd8A 227 7.20e+01 2a0jA 149 7.21e+01 1w53A 84 7.28e+01 a.186.1.2 109175 1n62A 166 7.32e+01 a.56.1.1,d.15.4.2 80090,80091 1p36A 164 7.40e+01 d.2.1.3 93978 2gakA 391 7.48e+01 1u3aA 189 7.51e+01 1r1dA 247 7.54e+01 c.69.1.29 96813 1lw9A 164 7.60e+01 d.2.1.3 84727 1svdA 473 7.63e+01 1c0eA 157 7.65e+01 1dg9A c.44.1.1 32638 2aaxA 275 7.70e+01 1i0aA 466 7.72e+01 1auwA a.127.1.1 61479 1iv3A 152 7.79e+01 d.79.5.1 76828 1ng7A 60 7.86e+01 a.178.1.1 85671 1t6cA 315 7.87e+01 c.55.1.8,c.55.1.8 106558,106559 1y60A 169 7.90e+01 1rwxA 178 7.91e+01 2lisA 136 7.95e+01 1lis a.19.1.1 16405 1qorA 327 8.00e+01 1qorA b.35.1.2,c.2.1.1 24766,29782 2trcP 217 8.02e+01 1b9yC c.47.1.6 33051 2bi7A 384 8.04e+01 119l 164 8.05e+01 1l92 d.2.1.3 36622 1deoA 233 8.08e+01 1deoA c.23.10.4 31345 1914 232 8.09e+01 1914 d.49.1.1,d.49.1.1 83028,83029 1k0iA 394 8.10e+01 c.3.1.2,d.16.1.2 67942,67943 1y93A 159 8.12e+01 1dcfA 136 8.12e+01 1dcfA c.23.1.2 31124 1sc3A 178 8.15e+01 c.17.1.1 105416 1w7bA 339 8.19e+01 1nynA 131 8.20e+01 d.235.1.1 86410 1z02A 446 8.22e+01 1q1hA 110 8.23e+01 a.4.5.41 95580 1ib8A 164 8.26e+01 b.38.2.1,d.52.4.1 71168,71169 2jdxA 385 8.30e+01 1jdw d.126.1.2 41139 2bwbA 46 8.33e+01 1iqqA 200 8.33e+01 d.124.1.1 66274 1vd6A 224 8.35e+01 1k7cA 233 8.36e+01 c.23.10.4 68267 1z6uA 150 8.36e+01 2ae8A 221 8.38e+01 1lis 136 8.39e+01 1lis a.19.1.1 16406 1k6xA 352 8.40e+01 c.2.1.2 68238 1miuA 738 8.41e+01 a.170.1.1,a.171.1.1,b.40.4.3,b.40.4.3,b.40.4.3 79153,79154,79155,79156,79157 1m12A 84 8.43e+01 a.64.1.1 84745 1dg9A 157 8.44e+01 1dg9A c.44.1.1 32637 2bzlA 325 8.45e+01 1f8fA 371 8.45e+01 b.35.1.2,c.2.1.1 83246,83247 1adoA 363 8.48e+01 1fbaA c.1.10.1 29124 1l1dA 152 8.49e+01 b.88.1.3 73452 1oj6A 151 8.54e+01 a.1.1.2 93088 2fmlA 273 8.56e+01 2amdA 311 8.61e+01 1zaiA 363 8.67e+01 1w5rA 278 8.69e+01 2dfbA 190 8.72e+01 1dzfA 215 8.77e+01 1dzfA c.52.3.1,d.78.1.1 33344,39753 1r3eA 309 8.82e+01 b.122.1.1,d.265.1.2 96907,96908 1u9yA 284 8.87e+01 1vaxA 287 8.87e+01 1mp9A 198 8.93e+01 d.129.1.1,d.129.1.1 91385,91386 1q2wA 308 8.94e+01 b.47.1.4 88355 2fh1A 344 8.96e+01 1u2eA 289 8.97e+01