# 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 1ru3A 732 6.09e-02 e.26.1.3 -12021 1mdoA 393 1.39e-01 c.67.1.4 79013 1oaoC 729 1.50e-01 e.26.1.3 86746 1a3k 137 2.33e-01 1a3k b.29.1.3 24218 1hdkA 141 2.48e-01 b.29.1.3 65807 1cdy 178 3.97e-01 1cdy b.1.1.1 19719 b.1.1.3 21658 1tif 78 4.04e-01 1tif d.15.8.1 37836 1m1cA 680 4.27e-01 e.42.1.1 78395 1ux6A 350 4.49e-01 unknown_sccs -3451 unknown_sccs -12886 1kcbA 340 4.61e-01 b.6.1.3 -2950 b.6.1.3 -2951 1nif 340 4.90e-01 1nif b.6.1.3 23048 b.6.1.3 23049 1jv2B 692 6.61e-01 b.1.15.1 67338 c.62.1.1 67339 d.200.1.1 67340 g.3.11.6 67341 g.3.11.6 67342 1kyfA 247 7.59e-01 b.1.10.1 73220 d.105.1.1 73221 1qtsA 247 7.93e-01 1qtsA b.1.10.1 22313 d.105.1.1 40789 1j9qA 341 8.93e-01 1nif b.6.1.3 62765 b.6.1.3 62766 1lcl 142 9.33e-01 1lcl b.29.1.3 24216 1cfb 205 1.13e+00 1cfb b.1.2.1 21991 b.1.2.1 21992 1hfuA 503 1.15e+00 b.6.1.3 65827 b.6.1.3 65828 b.6.1.3 65829 1p5vA 235 1.21e+00 b.1.11.1 87812 b.7.2.1 87813 1odkA 235 1.29e+00 c.56.2.1 86863 1a65A 504 1.35e+00 1a65A b.6.1.3 23148 b.6.1.3 23149 b.6.1.3 23150 1snrA 341 1.37e+00 1jeyA 609 1.54e+00 1jeqA unknown_sccs -4426 unknown_sccs -7990 1bquA 215 1.59e+00 1bquA b.1.2.1 22066 b.1.2.1 22067 1l4iA 206 1.60e+00 b.1.11.1 73564 b.7.2.1 73565 1g6oA 330 1.68e+00 1g6oA c.37.1.11 32430 1meoA 209 1.72e+00 c.65.1.1 79035 1fmtA 314 1.80e+00 1fmtA b.46.1.1 25758 c.65.1.1 34174 1sltA 134 1.92e+00 1c1lA b.29.1.3 24186 1htrB 329 1.96e+00 1smrA 1avaC 181 1.99e+00 1avaC b.42.4.1 25604 1obwA 175 2.51e+00 2prd b.40.5.1 25416 1ds1A 324 2.66e+00 1drtA b.82.2.2 28127 1xgsA 295 3.10e+00 1bn5 a.4.5.25 16216 d.127.1.1 41153 1dkzA 219 3.13e+00 1dkzA unknown_sccs -445 unknown_sccs -3060 1senA 164 3.46e+00 1vhoA 346 3.75e+00 unknown_sccs -4283 c.56.5.4 -7893 1c1lA 136 3.83e+00 1c1lA b.29.1.3 24219 1a0p 290 3.93e+00 1a0p a.60.9.1 18105 d.163.1.1 42165 1kmtA 141 4.04e+00 b.1.18.8 77442 3daaA 277 4.12e+00 1daaA e.17.1.1 43272 1ha3A 405 4.19e+00 1efcA b.43.3.1 60869 b.44.1.1 60870 c.37.1.8 60871 1tlk 154 4.26e+00 1tlk b.1.1.4 21707 1ukgA 252 4.43e+00 b.29.1.1 -3390 1gu7A 364 4.52e+00 b.35.1.2 83321 c.2.1.1 83322 1i8aA 189 4.61e+00 1i82A b.1.9.2 61951 1jx2B 315 4.64e+00 c.37.1.8 67404 1uvjA 664 4.70e+00 e.8.1.6 -11964 1k8wA 327 4.77e+00 b.122.1.1 83094 unknown_sccs -10143 1iw7C 1119 4.80e+00 e.29.1.1 71474 1fhgA 154 4.81e+00 1tlk b.1.1.4 21706 1v9yA 167 4.96e+00 1e7uA 961 5.12e+00 1e8xA a.118.1.6 19147 b.7.1.1 23182 d.15.1.5 37630 d.144.1.4 41710 1r0kA 388 5.25e+00 1exmA 405 5.60e+00 1efcA b.43.3.1 25696 b.44.1.1 25736 c.37.1.8 32131 1gr0A 367 5.74e+00 c.2.1.3 70379 d.81.1.3 70380 1hhsA 664 5.79e+00 1hi0P e.8.1.6 61045 1j1uA 306 5.87e+00 c.26.1.1 83980 1n3oA 252 5.98e+00 b.29.1.1 79967 1pmy 123 6.01e+00 1bqk b.6.1.1 22888 1nrzA 164 6.24e+00 c.38.1.1 86131 1fsoA 139 6.46e+00 1rhoA b.1.18.8 60007 1od5A 492 6.53e+00 b.82.1.2 86832 b.82.1.2 86833 1sjyA 159 6.62e+00 d.113.1.1 -10908 1e19A 314 6.91e+00 1b7bA c.73.1.1 34967 1i40A 175 7.22e+00 b.40.5.1 66024 1g1cA 99 7.24e+00 b.1.1.4 65078 2tgi 112 7.28e+00 2tgi g.17.1.2 44777 1gl4B 98 7.38e+00 b.1.1.4 65288 1k0iA 394 7.64e+00 c.3.1.2 67942 d.16.1.2 67943 1pbe 394 7.65e+00 1pbe c.3.1.2 30338 d.16.1.2 37869 1bpoA 494 7.88e+00 1bpoA a.118.1.4 19143 b.69.6.1 27670 1gt1A 159 8.05e+00 b.60.1.1 -4436 1euvB 86 8.14e+00 1a5r d.15.1.1 37598 1utcA 363 8.27e+00 a.118.1.4 -1568 b.69.6.1 -4612 1hn2A 159 8.34e+00 b.60.1.1 65890 1oh0A 131 8.51e+00 d.17.4.3 87004 1nkqA 259 8.56e+00 1rvkA 382 8.83e+00 c.1.11.2 -5568 d.54.1.1 -9826 1ejxC 567 8.83e+00 b.92.1.1 83184 c.1.9.2 83185 1e42A 258 8.85e+00 1e42A b.1.10.1 22316 d.105.1.1 40792 1th8A 145 8.95e+00 1htyA 1015 9.28e+00 a.8.3.1 83064 b.30.5.6 83065 c.6.2.1 83066 2hft 218 9.31e+00 1boy b.1.2.1 21951 b.1.2.1 21952 1szwA 379 9.35e+00 unknown_sccs -10164 1mbyA 88 9.52e+00 d.223.1.1 78931 1eonA 245 9.57e+00 1rvaA c.52.1.2 33238 1oh4A 179 9.61e+00 b.18.1.18 -3123 1kq6A 141 9.70e+00 d.189.1.1 -9926 1mhyD 521 9.73e+00 1mhyD a.25.1.2 16780 1epfA 191 9.83e+00 2ncm b.1.1.4 21694 b.1.1.4 21695 1bt0A 76 9.92e+00 1ubi d.15.1.1 37607 1f37A 110 9.97e+00 1f37A c.47.1.11 33088 1rvaA 244 1.01e+01 1rvaA c.52.1.2 33240 1vjqA 79 1.04e+01 unknown_sccs -13478 1obpA 159 1.05e+01 1obpA b.60.1.1 27092 1qy6A 274 1.06e+01 b.47.1.1 -4126 1v84A 253 1.07e+01 3tgl 269 1.07e+01 3tgl c.69.1.17 34733 1c7gA 456 1.09e+01 c.67.1.2 -8153 1nciA 110 1.11e+01 1edhA b.1.6.1 22191 1eyzA 392 1.14e+01 1ez1A b.84.2.1 28246 c.30.1.1 31653 d.142.1.2 41498 1p7hL 286 1.16e+01 b.1.18.1 -2700 b.2.5.3 -2894 1of4A 179 1.17e+01 b.18.1.18 86932 1sefA 274 1.18e+01 1m6iA 493 1.20e+01 c.3.1.5 74533 c.3.1.5 74534 d.87.1.1 74535 1euaA 213 1.20e+01 1fwrA c.1.10.1 29155 1ixmA 192 1.22e+01 1ixmA d.123.1.1 41114 1f15A 218 1.24e+01 1f15B b.121.4.5 23320 1k0wA 231 1.24e+01 c.74.1.1 77220 1o7kA 131 1.25e+01 d.189.1.1 81144 1i3jA 116 1.25e+01 1i3jA e.30.1.1 61594 1qcsA 211 1.27e+01 1qcsA b.52.2.3 26927 d.31.1.1 38461 1vavA 222 1.29e+01 1jmaA 290 1.34e+01 b.1.1.1 63177 1f6fB 210 1.35e+01 1axiB b.1.2.1 22033 b.1.2.1 22034 1sx5A 244 1.35e+01 c.52.1.2 -7551 1aohA 147 1.36e+01 1aohA b.2.2.2 22401 1k0sA 151 1.41e+01 b.40.7.1 67969 1t2aA 375 1.41e+01 c.2.1.2 -5764 1fe7A 121 1.41e+01 1poa 1gpmA 525 1.45e+01 1gpmA c.23.16.1 31405 c.26.2.1 31608 d.52.2.1 38826 1ktaA 365 1.45e+01 e.17.1.1 77533 1pxvA 183 1.46e+01 d.3.1.1 -8881 1jsmA 325 1.47e+01 b.19.1.2 63264 2shpA 525 1.47e+01 2shpA c.45.1.2 32683 d.93.1.1 40533 d.93.1.1 40534 1dq3A 454 1.49e+01 1dq3A b.86.1.2 28380 d.50.3.1 38798 d.95.2.2 40585 d.95.2.2 40586 1e8yA 966 1.50e+01 1e8xA a.118.1.6 19152 b.7.1.1 23187 d.15.1.5 37635 d.144.1.4 41715 1nbfD 76 1.50e+01 d.15.1.1 80390 1j96A 323 1.53e+01 c.1.7.1 71616 1kdj 102 1.53e+01 1plc b.6.1.1 22864 1ct5A 256 1.56e+01 1ct5A c.1.6.2 28663 1hdr 244 1.57e+01 1dhr c.2.1.2 29837 1mnnA 340 1.58e+01 b.2.5.7 79324 1qwnA 1045 1.66e+01 a.8.3.1 -414 b.30.5.6 -3517 c.6.2.1 -6058 1dyoA 160 1.66e+01 1dyoA b.18.1.7 23771 1sqzA 121 1.68e+01 a.133.1.2 -1971 1ogwA 76 1.70e+01 d.15.1.1 87001 1qfmA 710 1.72e+01 1qfmA b.69.7.1 27673 c.69.1.4 34641 1ekfA 365 1.76e+01 1ekfA e.17.1.1 59445 1nykA 165 1.78e+01 b.33.1.1 86408 1fbnA 230 1.79e+01 1fbnA c.66.1.3 34181 1ojaA 520 1.82e+01 c.3.1.2 -6000 d.16.1.5 -9220 1k8kC 372 1.83e+01 b.69.4.1 68308 1m2dA 110 1.85e+01 c.47.1.11 78476 1mvfD 82 1.85e+01 b.129.1.1 85143 1g8sA 230 1.88e+01 c.66.1.3 -8047 1umdA 367 1.88e+01 c.36.1.11 -6969 1rie 129 1.89e+01 1rie b.33.1.1 24427 1a49A 530 1.89e+01 1a49A b.58.1.1 27026 c.1.12.1 29255 c.49.1.1 33109 1tk4A 121 1.91e+01 1kjqA 391 1.95e+01 b.84.2.1 72616 c.30.1.1 72617 d.142.1.2 72618 1lfo 128 1.98e+01 1hmt b.60.1.2 27223 1tj9A 121 1.99e+01 1nkiA 135 2.03e+01 d.32.1.2 -9544 1nrvA 105 2.03e+01 d.93.1.1 86126 1ubi 76 2.06e+01 1ubi d.15.1.1 37584 1vjlA 164 2.08e+01 unknown_sccs -11117 1n9eA 787 2.10e+01 b.30.2.1 -3529 d.17.2.1 -9278 d.17.2.1 -9279 1mjc 69 2.12e+01 1mjc b.40.4.5 25319 1vyrA 364 2.12e+01 1nddA 76 2.13e+01 1ubi d.15.1.1 37599 1hyhA 309 2.17e+01 1hyhA c.2.1.5 30150 d.162.1.1 42117 1nrwA 288 2.19e+01 c.108.1.10 86128 1pba 81 2.22e+01 1pytA d.58.3.1 39067 1j6rA 214 2.30e+01 d.173.1.2 71598 1jsdA 319 2.31e+01 b.19.1.2 63258 1mx3A 347 2.32e+01 c.2.1.4 79638 c.23.12.1 79639 1lvoA 302 2.34e+01 b.47.1.4 74284 2dtr 226 2.34e+01 1bi0 a.4.5.24 16193 a.76.1.1 18399 b.34.1.2 24450 1gvoA 364 2.38e+01 c.1.4.1 76357 1ci3M 249 2.44e+01 1hcz b.2.6.1 22480 b.84.2.2 28266 1hkfA 122 2.45e+01 b.1.1.1 83553 1g9mG 321 2.47e+01 1gc1G d.172.1.1 42492 1h61A 364 2.50e+01 1oyc c.1.4.1 60657 1i8kA 107 2.52e+01 b.1.1.1 71130 1qtoA 122 2.52e+01 1bylA d.32.1.2 38494 1orrA 347 2.53e+01 c.2.1.2 -5776 1c8uA 285 2.53e+01 1c8uA d.38.1.3 38547 d.38.1.3 38548 1i50C 318 2.58e+01 d.74.3.1 61756 d.181.1.1 61757 1i7oA 429 2.59e+01 1i7oA d.177.1.1 61893 d.177.1.1 61894 1ox0A 430 2.60e+01 c.95.1.1 87495 c.95.1.1 87496 1o0xA 262 2.66e+01 d.127.1.1 80755 1je0A 236 2.69e+01 c.56.2.1 66581 1giqA 413 2.71e+01 d.166.1.1 76224 d.166.1.1 76225 1lj9A 144 2.71e+01 a.4.5.28 78035 8dfr 189 2.73e+01 1aoeA c.71.1.1 34895 1rhfA 182 2.73e+01 b.1.1.1 -2335 b.1.1.4 -2684 1lqpA 135 2.73e+01 d.32.1.2 78151 1ois 223 2.74e+01 1a36A e.15.1.1 43267 1a02N 301 2.74e+01 1a02N b.1.18.1 21923 b.2.5.3 22440 1wm1A 317 2.76e+01 1qwtA 255 2.79e+01 unknown_sccs -3329 1eylA 186 2.81e+01 1wba b.42.4.1 25593 1jmmA 377 2.82e+01 b.30.6.1 71749 1c9oA 66 2.89e+01 1mjc b.40.4.5 25325 1kk1A 410 2.90e+01 b.43.3.1 72634 b.44.1.1 72635 c.37.1.8 72636 1c7sA 858 2.93e+01 1qba b.1.18.2 21812 b.2.2.3 22408 c.1.8.6 29011 d.92.2.1 40410 1e3jA 352 2.95e+01 1e3jA b.35.1.2 24765 c.2.1.1 29781 1dbgA 506 3.04e+01 1dbgA b.80.1.4 28033 1dykA 394 3.06e+01 1dykA b.29.1.4 24223 b.29.1.4 24224 1fna 93 3.14e+01 1fnf b.1.2.1 21971 1pqzA 238 3.15e+01 1k8tA 510 3.17e+01 e.41.1.1 68316 1gttA 429 3.18e+01 d.177.1.1 70529 d.177.1.1 70530 3gcb 470 3.18e+01 3gcb d.3.1.1 37032 2cpgA 45 3.21e+01 2cpgA unknown_sccs 17455 1res 43 3.26e+01 1ret a.4.1.2 16023 1lehA 364 3.27e+01 1bw9A c.2.1.7 30268 c.58.1.1 33916 1e0tA 470 3.31e+01 1a49A b.58.1.1 27064 c.1.12.1 29292 c.49.1.1 33146 2fcbA 173 3.33e+01 2fcbA b.1.1.4 21781 b.1.1.4 21782 1uwwA 191 3.37e+01 1kwiA 101 3.37e+01 d.17.1.3 77564 1vypX 364 3.37e+01 1r94A 118 3.38e+01 b.124.1.1 -4402 1iarB 207 3.41e+01 1iarB b.1.2.1 22037 b.1.2.1 22038 1o54A 277 3.48e+01 c.66.1.13 -8095 1dboA 506 3.48e+01 1dbgA b.80.1.4 28034 1q0bA 367 3.55e+01 c.37.1.9 -7105 1fy7A 278 3.56e+01 1fy7A d.108.1.1 40817 1s0yA 76 3.58e+01 d.80.1.1 -10434 1pqhA 143 3.58e+01 b.52.2.1 -4318 1dg6A 191 3.67e+01 1d4vB b.22.1.1 23883 1eo6A 117 3.69e+01 1eo6A d.15.1.3 37609 1j0hA 588 3.72e+01 b.1.18.2 77027 b.71.1.1 77028 c.1.8.1 77029 1e30A 155 3.72e+01 1rcy b.6.1.1 23016 1ollA 188 3.78e+01 b.1.1.4 -2690 b.1.1.4 -2691 1s5lO 246 3.81e+01 1gnlA 544 3.81e+01 e.26.1.1 70287 1mkaA 171 3.83e+01 1mkaA d.38.1.2 38543 1wdaA 670 3.87e+01 1j7nA 776 3.87e+01 d.92.1.14 66409 d.92.1.14 66410 d.166.1.1 66411 1ul7A 102 3.90e+01 unknown_sccs -11020 1oniA 137 3.94e+01 d.79.1.1 87144 1k8kD 300 3.96e+01 d.198.2.1 68309 d.198.2.1 68310 1p35A 299 3.97e+01 1p35A b.28.1.1 23925