# 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 1ihrA 76 4.18e-12 1ihrA d.212.1.2 62392 1lr0A 129 3.44e-06 d.212.1.1 74213 1fjgJ 105 1.50e-01 1fjfJ d.58.15.1 39330 1cm5A 759 2.88e-01 1cm5A c.7.1.1 30671 1h16A 759 3.25e-01 c.7.1.1 76462 1hn2A 159 3.56e-01 b.60.1.1 65890 1esiA 262 4.55e-01 1skf e.3.1.1 42682 1gt1A 159 4.57e-01 b.60.1.1 -4436 1f5mA 180 8.45e-01 1f5mB d.110.2.1 40895 1obpA 159 8.49e-01 1obpA b.60.1.1 27092 1f39A 101 8.71e-01 1umuA b.87.1.1 28386 1qmvA 197 9.16e-01 1qq2A c.47.1.10 33066 1n8jA 186 1.14e+00 c.47.1.10 85401 1q0rA 298 1.18e+00 unknown_sccs -8330 1ospO 257 1.21e+00 1ospO b.76.1.1 27971 5croA 66 1.70e+00 1orc a.35.1.2 17044 1avyA 74 1.84e+00 1avyB h.1.17.1 45656 1dkzA 219 2.17e+00 1dkzA unknown_sccs -445 unknown_sccs -3060 1iow 306 2.24e+00 1iow c.30.1.2 31713 d.142.1.1 41481 1ox3A 109 2.37e+00 h.1.17.1 -12938 1cc1L 498 2.38e+00 1h2rL e.18.1.1 43301 1btl 263 2.64e+00 1btl e.3.1.1 42691 1ermA 263 2.67e+00 1btl e.3.1.1 42690 1js3A 486 2.70e+00 c.67.1.6 67215 3cox 507 2.86e+00 1b8sA c.3.1.2 30332 d.16.1.1 37863 1sdjA 310 2.87e+00 d.21.1.2 -9420 d.21.1.2 -9421 1st9A 143 2.95e+00 c.47.1.10 -7503 1h2rL 534 3.18e+00 1h2rL e.18.1.1 43298 1r26A 125 3.38e+00 c.47.1.1 -7389 1qyaA 307 3.43e+00 1orc 71 3.48e+00 1orc a.35.1.2 17054 1qe3A 489 3.60e+00 2bce c.69.1.1 34630 1oyeA 1049 4.07e+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 1jj2L 194 4.57e+00 1ffkI d.12.1.2 63097 1kngA 156 4.68e+00 c.47.1.10 72777 3pyp 125 4.87e+00 3pyp d.110.3.1 40897 1nwzA 125 4.90e+00 d.110.3.1 86370 1a2vA 655 4.90e+00 1a2vA b.30.2.1 24416 d.17.2.1 38059 d.17.2.1 38060 1skoB 130 5.03e+00 1ubkL 534 5.09e+00 e.18.1.1 88422 1svpA 161 5.11e+00 1svpA b.47.1.3 26384 1i2kA 269 5.11e+00 e.17.1.1 -11995 1itg 166 5.18e+00 1b9dA c.55.3.2 33661 1iloA 77 5.41e+00 c.47.1.1 66205 1m98A 317 5.58e+00 a.175.1.1 78866 d.17.4.6 78867 1jcfA 344 5.76e+00 c.55.1.1 62878 c.55.1.1 62879 1ocvA 125 6.05e+00 d.17.4.3 86810 1pj5A 830 6.29e+00 unknown_sccs -4066 c.3.1.2 -6031 d.16.1.5 -9251 unknown_sccs -10171 1vetB 125 6.36e+00 1t82A 155 6.62e+00 1gqpA 221 6.94e+00 b.18.1.9 70372 1pz4A 116 7.14e+00 d.106.1.1 -10780 1urrA 102 7.20e+00 1m40A 263 7.79e+00 e.3.1.1 74437 1gp1A 198 8.54e+00 1gp1A c.47.1.10 33059 1oh0A 131 8.84e+00 d.17.4.3 87004 2trxA 108 9.12e+00 1thx c.47.1.1 32719 1v3eA 431 9.21e+00 b.68.1.1 -4584 1lm8V 160 9.46e+00 b.3.3.1 74035 1bl3A 160 9.69e+00 1b9dA c.55.3.2 33655 1b5pA 385 9.84e+00 c.67.1.1 -8133 1ei5A 520 9.89e+00 1ei5A b.61.3.1 27418 b.61.3.1 27419 e.3.1.1 42772 1iwlA 182 1.12e+01 b.125.1.1 83757 1qnaA 200 1.18e+01 1ytbA d.129.1.1 41226 d.129.1.1 41227 1i50B 1224 1.20e+01 e.29.1.1 61755 1bjwA 382 1.25e+01 1bjwA c.67.1.1 34349 1o1zA 234 1.34e+01 c.1.18.3 86555 1xgsA 295 1.34e+01 1bn5 a.4.5.25 16216 d.127.1.1 41153 1e3dB 542 1.51e+01 1h2rL e.18.1.1 59189 1ezvD 245 1.52e+01 1be3D a.3.1.3 59546 f.23.11.1 59547 1b6rA 355 1.53e+01 1b6rA b.84.2.1 28241 c.30.1.1 31648 d.142.1.2 41493 1kb9D 246 1.55e+01 a.3.1.3 77317 f.23.11.1 77318 1snzA 344 1.55e+01 b.30.5.4 -3496 1oo0A 147 1.63e+01 d.232.1.1 87182 1tuhA 156 1.69e+01 1f3uA 118 1.69e+01 1f3uA b.65.1.1 27521 1rh6A 55 1.69e+01 1opy 131 1.70e+01 1opy d.17.4.3 38113 1q48A 134 1.74e+01 unknown_sccs -9776 1vc4A 254 1.79e+01 c.1.2.4 -5172 1vcbC 160 1.79e+01 1vcbC b.3.3.1 22535 1dymA 402 1.80e+01 1celA b.29.1.10 24304 1s14A 194 1.80e+01 d.122.1.2 -10973 1ne9A 335 1.94e+01 d.108.1.4 -10805 d.108.1.4 -10806 1gqiA 708 1.96e+01 c.1.8.10 76279 d.92.2.2 76280 1r75A 141 2.03e+01 unknown_sccs -3243 1fecA 490 2.05e+01 3grs c.3.1.5 30489 c.3.1.5 30490 d.87.1.1 40176 1ehiA 377 2.06e+01 1iow c.30.1.2 31716 d.142.1.1 41484 1bh9B 89 2.07e+01 1bh9B a.22.1.3 16485 1nulA 152 2.09e+01 1nulA c.61.1.1 34011 1q98A 165 2.11e+01 c.47.1.10 -7499 1vlbA 907 2.14e+01 1hlrA 907 2.14e+01 a.56.1.1 65850 d.15.4.2 65851 d.41.1.1 65852 d.133.1.1 65853 1i9gA 280 2.15e+01 c.66.1.13 62090 1j8bA 112 2.18e+01 d.222.1.1 77101 1hyvA 166 2.23e+01 1b9dA c.55.3.2 61424 1gakA 141 2.27e+01 1gakA a.19.1.1 16415 1b25A 619 2.29e+01 1b25A a.110.1.1 19044 d.152.1.1 41796 1dmmA 131 2.32e+01 1opy d.17.4.3 38114 1ojjA 402 2.32e+01 b.29.1.10 -3473 1mrg 263 2.38e+01 1mrj d.165.1.1 42183 1uf5A 303 2.41e+01 1gen 218 2.43e+01 1gen b.66.1.1 27536 1aisA 182 2.43e+01 1ytbA d.129.1.1 41288 d.129.1.1 41289 1ovnA 248 2.47e+01 a.71.1.1 -1096 c.47.1.7 -7477 1erzA 303 2.47e+01 1erzA d.160.1.2 59498 1f89A 291 2.57e+01 d.160.1.1 64988 1tqyB 415 2.58e+01 1a79A 171 2.58e+01 1a79A c.52.2.1 33340 d.75.1.1 39739 1mp9A 198 2.65e+01 a.74.1.2 -1127 a.74.1.2 -1128 1qb5D 99 2.65e+01 b.40.2.1 88357 1pcfA 66 2.67e+01 1pcfA d.18.1.1 38142 1tiiD 99 2.77e+01 1tiiD b.40.2.1 24965 1o88A 353 2.79e+01 b.80.1.1 81178 1uufA 369 2.88e+01 b.35.1.2 -3706 c.2.1.1 -5730 1exqA 154 2.90e+01 1b9dA c.55.3.2 33646 1txlA 215 2.92e+01 1o22A 170 2.99e+01 d.238.1.1 86557 1pbjA 125 3.02e+01 d.37.1.1 -9608 d.37.1.1 -9609 1alo 907 3.10e+01 1alo 1air 353 3.16e+01 1air b.80.1.1 28018 2act 220 3.19e+01 1cs8A d.3.1.1 37002 1q47A 495 3.23e+01 1sgvA 316 3.25e+01 b.122.1.1 -5120 unknown_sccs -10148 1mo9A 523 3.28e+01 c.3.1.5 79341 c.3.1.5 79342 d.87.1.1 79343 1h7sA 365 3.31e+01 d.14.1.3 65705 d.122.1.2 65706 1oglA 283 3.32e+01 unknown_sccs -1512 1bykA 255 3.59e+01 1bykA c.93.1.1 35706 1ufmA 84 3.71e+01 1udxA 416 3.76e+01 b.117.1.1 -3546 c.37.1.8 -7101 unknown_sccs -9009 1i31A 314 3.83e+01 1bw8A b.2.7.1 22481 1nzyA 269 3.88e+01 1nzyA c.14.1.3 30903 1nxiA 132 3.95e+01 d.58.47.1 86381 1seiA 130 3.98e+01 1seiA d.140.1.1 41463