# List of top-scoring protein chains for t04-100-30-alpha 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 2.83e-23 a.24.16.2 77142 1dk8A 147 1.40e-01 1agrE a.91.1.1 18548 1mb3A 124 2.27e-01 c.23.1.1 78907 1pa7A 130 4.67e-01 a.40.1.1 -896 1o3uA 135 5.76e-01 a.24.16.3 86615 2cxbA 124 6.75e-01 1ycc a.3.1.1 15891 1cxc 124 7.51e-01 1ycc a.3.1.1 15890 1ezfA 340 1.32e+00 1ezfA a.128.1.2 19440 1cxzB 86 1.37e+00 1cxzB a.2.6.1 15705 2tct 207 1.38e+00 2tct a.4.1.9 16063 a.121.1.1 19240 1s7zA 117 1.38e+00 unknown_sccs -344 1or7A 194 1.39e+00 a.4.13.2 87332 a.177.1.1 87333 1amf 233 1.51e+00 1wod c.94.1.1 35833 1wod 233 1.54e+00 1wod c.94.1.1 35832 1buoA 121 1.63e+00 1buoA d.42.1.1 38631 1e6yB 433 1.83e+00 1mroB a.89.1.1 18535 d.58.31.2 39453 1rxxA 421 1.84e+00 unknown_sccs -10982 1k6wA 426 2.16e+00 b.92.1.2 68236 c.1.9.5 68237 1p9bA 442 2.22e+00 c.37.1.10 -7115 1i58A 189 2.41e+00 1b3qA d.122.1.3 61773 1qzzA 374 2.47e+00 a.4.5.29 -277 c.66.1.12 -8045 1nnwA 252 2.62e+00 d.159.1.5 80674 1fjgD 209 2.76e+00 1c05A d.66.1.2 39553 1jvsA 400 2.77e+00 a.69.3.1 77187 c.2.1.3 77188 d.81.1.3 77189 1q0qA 406 2.82e+00 1dcs 311 2.83e+00 1dcs b.82.2.1 28124 1a0p 290 2.89e+00 1a0p a.60.9.1 18105 d.163.1.1 42165 1rx0A 393 3.09e+00 a.29.3.1 -742 e.6.1.1 -11858 1f74A 293 3.29e+00 1nal3 c.1.10.1 29079 7a3hA 303 3.54e+00 7a3hA c.1.8.3 28817 1nksA 194 3.82e+00 1nksA c.37.1.1 31886 1tmy 120 3.99e+00 1dbwA c.23.1.1 31083 1mvoA 136 4.08e+00 c.23.1.1 79513 1mp4A 292 4.22e+00 c.68.1.6 79376 1hf8A 289 4.31e+00 1hg5A unknown_sccs -399 unknown_sccs -1628 1nznA 126 4.41e+00 a.118.8.1 -1616 1i39A 225 4.56e+00 1ekeA c.55.3.1 61585 1i8jA 323 4.75e+00 1b4kA c.1.10.3 61968 1e4yA 214 4.75e+00 1zin c.37.1.1 31901 g.41.2.1 45181 1miwA 404 4.81e+00 a.173.1.1 79162 d.218.1.4 79163 1l6sA 323 4.96e+00 c.1.10.3 73627 1pq9A 253 5.37e+00 a.123.1.1 -1687 1qgoA 264 5.52e+00 1qgoA c.92.1.2 35596 1m1nA 491 5.62e+00 c.92.2.3 78417 1dat 174 5.94e+00 2fha a.25.1.1 16677 2igd 61 6.01e+00 2igd d.15.7.1 37821 1auiB 169 6.10e+00 1auiB a.39.1.5 17325 1q08A 99 6.39e+00 a.6.1.3 -381 1b8dA 164 6.40e+00 1cpcA a.1.1.3 15665 1aua 296 6.65e+00 1aua a.5.3.1 16290 c.13.1.1 30882 1icrA 217 6.71e+00 1vfrA d.90.1.1 62274 1q1aA 289 6.89e+00 c.31.1.5 -6781 1k4nA 192 7.14e+00 d.32.1.5 72059 1qwgA 251 7.25e+00 unknown_sccs -5678 1hlvA 131 7.41e+00 a.4.1.7 65854 a.4.1.7 65855 1izmA 184 7.57e+00 unknown_sccs -1233 2gdm 153 7.74e+00 2gdm a.1.1.2 15212 1q5zA 177 7.88e+00 unknown_sccs -1215 1ufaA 520 8.38e+00 unknown_sccs -421 unknown_sccs -6065 1oxkB 134 8.48e+00 c.23.1.1 -6411 1l3lA 234 8.49e+00 a.4.6.2 73541 d.110.5.1 73542 1ockA 412 8.76e+00 c.117.1.1 86802 3kvt 115 8.87e+00 1t1dA d.42.1.2 38642 1oj7A 408 9.08e+00 3lynA 136 9.24e+00 1lis a.19.1.1 16413 1qgrA 876 9.33e+00 1qgrA a.118.1.1 19119 1mjhA 162 9.62e+00 1mjhA c.26.2.4 31639 1r8iA 213 1.00e+01 unknown_sccs -411 1fpoA 171 1.01e+01 1fpoA a.2.3.1 15693 a.23.1.1 16487 1c0eA 157 1.03e+01 1dg9A c.44.1.1 32638 1iw7C 1119 1.03e+01 e.29.1.1 71474 2lisA 136 1.05e+01 1lis a.19.1.1 16405 1fmjA 351 1.05e+01 c.37.1.5 59879 1dg9A 157 1.06e+01 1dg9A c.44.1.1 32637 2gsq 202 1.13e+01 1pd21 a.45.1.1 17715 c.47.1.5 33009 1lis 136 1.13e+01 1lis a.19.1.1 16406 1fcjA 322 1.16e+01 1oasA c.79.1.1 35289 1v54E 109 1.17e+01 a.118.11.1 -1652 1wdcB 156 1.19e+01 1wdcB a.39.1.5 17302 1b0b 142 1.20e+01 2fal a.1.1.2 15010 1c02A 166 1.23e+01 1qspA a.24.10.2 16633 1m3kA 392 1.25e+01 c.95.1.1 78565 c.95.1.1 78566 1e8gA 560 1.26e+01 1qltA d.58.32.1 39455 d.145.1.1 41718 1m4tA 392 1.27e+01 c.95.1.1 78617 c.95.1.1 78618 1j09A 468 1.27e+01 a.97.1.1 77025 c.26.1.1 77026 1cm5A 759 1.28e+01 1cm5A c.7.1.1 30671 1d1qA 161 1.29e+01 1dg9A c.44.1.1 32642 1g60A 260 1.29e+01 c.66.1.11 70151 1js8A 394 1.30e+01 a.86.1.1 67219 b.112.1.1 67220 1qflA 389 1.30e+01 1afwA c.95.1.1 35908 c.95.1.1 35909 1qq7A 253 1.31e+01 1qq5A c.108.1.1 43329 1h16A 759 1.32e+01 c.7.1.1 76462 1n1bA 549 1.32e+01 a.102.4.1 79799 a.128.1.3 79800 1rktA 205 1.33e+01 a.4.1.9 -210 a.121.1.1 -1663 1d8dA 377 1.34e+01 1ft1A a.118.6.1 19185 2sas 185 1.36e+01 2sas a.39.1.5 17258 1jipA 403 1.39e+01 a.104.1.1 66748 1qq5A 253 1.40e+01 1qq5A c.108.1.1 43327 1hrkA 359 1.41e+01 1hrkA c.92.1.1 61228 1udxA 416 1.42e+01 b.117.1.1 -3546 c.37.1.8 -7101 unknown_sccs -9009 1hvvA 75 1.45e+01 1hvvA h.1.15.1 45639 1jnyA 435 1.48e+01 b.43.3.1 66982 b.44.1.1 66983 c.37.1.8 66984 1mojA 182 1.56e+01 a.25.1.1 -669 1cpt 412 1.57e+01 1cpt a.104.1.1 18968 1rtwA 220 1.59e+01 unknown_sccs -1904 1isiA 265 1.70e+01 e.4.1.1 71394 1qmyA 167 1.73e+01 1qmyA d.3.1.2 37094 1k1xA 659 1.73e+01 a.8.3.2 84279 b.30.5.8 84280 c.6.2.2 84281 1vhnA 318 1.73e+01 c.1.4.1 -5209 3gcb 470 1.76e+01 3gcb d.3.1.1 37032 2occE 109 1.77e+01 2occE a.118.11.1 19224 1ov2A 99 1.77e+01 a.13.1.1 -457 1lehA 364 1.77e+01 1bw9A c.2.1.7 30268 c.58.1.1 33916 1a8y 367 1.79e+01 1a8y c.47.1.3 32781 c.47.1.3 32782 c.47.1.3 32783 1cjcA 460 1.79e+01 1cjcA c.3.1.1 30319 c.4.1.1 30604 1sqgA 429 1.81e+01 1jy2N 53 1.83e+01 h.1.8.1 67440 1mi3A 322 1.84e+01 c.1.7.1 -5257 1bykA 255 1.84e+01 1bykA c.93.1.1 35706 1ld8A 382 1.88e+01 a.118.6.1 73838 1jjyA 636 1.90e+01 1jjyA 4crxA 322 1.91e+01 4crxA a.60.9.1 18095 d.163.1.1 42155 1f44A 324 1.94e+01 a.60.9.1 64982 d.163.1.1 64983 1kk8B 139 1.94e+01 a.39.1.5 77430 1lmzA 187 1.95e+01 a.96.1.4 74037 1vh7A 265 2.02e+01 c.1.2.1 -5159 1w1kA 560 2.02e+01 1i36A 264 2.04e+01 a.100.1.8 71108 c.2.1.6 71109 1cg2A 393 2.06e+01 1cg2A c.56.5.4 33844 d.58.19.1 39360 1brwA 433 2.07e+01 1brwA a.46.2.1 17764 c.27.1.1 31628 d.41.3.1 38626 1zin 217 2.08e+01 1zin c.37.1.1 31915 g.41.2.1 45178 1au1A 166 2.11e+01 1ifa a.26.1.3 16889 1thfD 253 2.12e+01 1thfD c.1.2.1 28535 1iqyA 638 2.14e+01 b.30.2.1 76763 d.17.2.1 76764 d.17.2.1 76765 1ui7A 638 2.15e+01 b.30.2.1 -3523 d.17.2.1 -9268 d.17.2.1 -9269 1iybA 208 2.15e+01 d.124.1.1 -10977 1ccwA 137 2.20e+01 1be1 c.23.6.1 31238 1ak0 270 2.20e+01 1ak0 a.124.1.2 19345 1eb7A 323 2.21e+01 1eb7A a.3.1.5 59404 a.3.1.5 59405 1qntA 176 2.21e+01 1sfe a.4.2.1 16074 c.55.7.1 33749 1ui8A 638 2.22e+01 b.30.2.1 -3525 d.17.2.1 -9272 d.17.2.1 -9273 1ko3A 230 2.22e+01 d.157.1.1 -11454 1wdgA 94 2.23e+01 1ox3A 109 2.24e+01 h.1.17.1 -12938 1n7sB 68 2.24e+01 h.1.15.1 80272 1w2wA 211 2.25e+01 1ojrA 274 2.25e+01 c.74.1.1 -8441 1li5A 461 2.27e+01 a.27.1.1 73912 c.26.1.1 73913 1mhdA 132 2.28e+01 1mhdA d.164.1.1 42175 1mxgA 435 2.30e+01 b.71.1.1 85193 c.1.8.1 85194 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 1q9uA 130 2.31e+01 unknown_sccs -11025 1fxqA 267 2.31e+01 1d9eA c.1.10.4 60108 1j3wA 163 2.31e+01 unknown_sccs -10870 1afrA 345 2.34e+01 1afrA a.25.1.2 16805 1fwsA 267 2.34e+01 1d9eA c.1.10.4 60063 1pe1A 267 2.35e+01 c.1.10.4 -5553 1ib3A 349 2.36e+01 1ib2A 1su8A 636 2.38e+01 e.26.1.2 -12015 1d8wA 426 2.38e+01 1de5A c.1.15.2 29394 1o60A 292 2.41e+01 c.1.10.4 -5549 1jcxA 267 2.43e+01 c.1.10.4 66510 1ib2A 349 2.43e+01 1ib2A a.118.1.8 62141 1k3yA 221 2.43e+01 a.45.1.1 77245 c.47.1.5 77246 1a7tA 232 2.46e+01 1a7tA d.157.1.1 42041 1k47A 337 2.46e+01 d.14.1.5 72040 d.58.26.4 72041 1o98A 511 2.47e+01 c.105.1.1 86684 c.76.1.3 86685 1f61A 429 2.49e+01 1dquA c.1.12.7 29319 1djxB 624 2.55e+01 1djxB a.39.1.7 17343 b.7.1.1 23160 c.1.18.1 29588 1eqjA 511 2.59e+01 1ejjA c.105.1.1 59495 c.76.1.3 59496 1jdw 423 2.64e+01 1jdw d.126.1.2 41129 1f8mA 429 2.65e+01 1dquA c.1.12.7 29315 5ukdA 194 2.67e+01 1zin c.37.1.1 31851 1avk 638 2.70e+01 1a2vA b.30.2.1 24410 d.17.2.1 38047 d.17.2.1 38048 1eswA 500 2.71e+01 1cwyA c.1.8.1 59500 1qf9A 194 2.73e+01 1zin c.37.1.1 31848 1v9mA 323 2.76e+01 unknown_sccs -12292 1jae 471 2.77e+01 1smd b.71.1.1 27773 c.1.8.1 28760 1kz1A 159 2.79e+01 c.16.1.1 73318 1gln 468 2.81e+01 1gln a.97.1.1 18752 c.26.1.1 31588 1ax4A 467 2.93e+01 1ax4A c.67.1.2 34391 1riqA 465 2.94e+01 unknown_sccs -1295 d.104.1.1 -10769 1knqA 175 2.96e+01 c.37.1.17 72786 1db3A 372 2.97e+01 1db3A c.2.1.2 29813 1ek0A 170 3.04e+01 1ctqA c.37.1.8 32076 1jigA 146 3.07e+01 a.25.1.1 71685 1gxqA 106 3.12e+01 a.4.6.1 70721 1snnA 227 3.12e+01 1ee4A 423 3.13e+01 1ee4A a.118.1.1 19128 1h6zA 913 3.13e+01 c.1.12.2 70906 c.8.1.1 70907 d.142.1.5 70908 1vhzA 198 3.14e+01 d.113.1.1 -10897 1ozjA 144 3.14e+01 d.164.1.1 -11537 1tqnA 486 3.22e+01 1oq9A 363 3.25e+01 a.25.1.2 87257 1bif 469 3.26e+01 1bif c.37.1.7 31961 c.60.1.4 34003 1im8A 244 3.29e+01 c.66.1.14 66212 1e7uA 961 3.31e+01 1e8xA a.118.1.6 19147 b.7.1.1 23182 d.15.1.5 37630 d.144.1.4 41710 1r5zA 323 3.33e+01 unknown_sccs -12289 1n8mA 38 3.34e+01 g.3.7.2 -12455 2cblA 305 3.36e+01 2cblA a.39.1.7 17380 a.48.1.1 17774 d.93.1.1 40528 1hw1A 239 3.44e+01 1e2xA a.4.5.6 16111 a.78.1.1 18441 1b43A 340 3.48e+01 1a76 a.60.7.1 18092 c.120.1.2 33362 1q6hA 224 3.54e+01 d.26.1.1 -9487 1a76 326 3.61e+01 1a76 a.60.7.1 18091 c.120.1.2 33361 1pvyA 227 3.65e+01 d.115.1.2 -10937 1cs1A 386 3.68e+01 1ibjA c.67.1.3 34399 1oniA 137 3.68e+01 d.79.1.1 87144 1ka2A 499 3.69e+01 d.92.1.5 77305 1n3kA 130 3.70e+01 a.77.1.4 79965 1qh8A 478 3.76e+01 1qguA c.92.2.3 35633 1m6kA 251 3.76e+01 e.3.1.1 78695 1ou0A 207 3.78e+01 c.23.17.1 -6498 1q06A 135 3.80e+01 a.6.1.3 -375 1e19A 314 3.86e+01 1b7bA c.73.1.1 34967 1gxyA 226 3.86e+01 d.166.1.3 76380 1r5pA 108 3.88e+01 unknown_sccs -7487 1uxoA 192 3.90e+01 1kl7A 514 3.91e+01 c.79.1.1 72678 1mbxC 106 3.92e+01 d.45.1.2 78929 1ls6A 295 3.92e+01 c.37.1.5 -7026 1jj2B 337 3.95e+01 1ffkB b.43.3.2 63086 1s72B 338 3.95e+01 1v8gA 329 3.96e+01 a.46.2.1 -953 c.27.1.1 -6644 1jhfA 202 3.99e+01 a.4.5.2 63057 b.87.1.1 63058