# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7-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 1prxA 224 5.27e-03 1prxA c.47.1.10 33076 1prxB 224 7.34e-03 1prxA c.47.1.10 33077 1sknP 92 2.64e-01 1sknP a.37.1.1 17127 1g5pA 289 2.79e-01 1cp2A c.37.1.10 32253 1fp6A 289 2.81e-01 1cp2A c.37.1.10 32243 1nipA 289 3.94e-01 1cp2A c.37.1.10 32263 1b72B 87 7.01e-01 1akhA a.4.1.1 16001 1jbgA 109 1.14e+00 a.6.1.3 66480 1itpA 77 1.36e+00 d.58.3.2 66371 1e08A 371 1.38e+00 i.4.1.1 45914 1akhB 83 1.49e+00 1akhB a.4.1.1 15985 1yrnB 83 2.22e+00 1akhB a.4.1.1 15986 1ex7A 186 2.33e+00 1gky c.37.1.1 59537 1ctf 74 2.49e+00 1ctf d.45.1.1 38759 1jqaA 370 2.65e+00 e.22.1.2 67085 1wetA 340 2.75e+00 1qpzA a.35.1.5 17093 c.93.1.1 35670 1hn0A 1021 2.77e+00 a.102.3.2 83616 b.18.1.17 83617 b.24.1.1 83618 b.30.5.2 83619 1gky 187 2.94e+00 1gky c.37.1.1 31839 1a5j 110 3.08e+00 1a5j a.4.1.3 16043 a.4.1.3 16044 1m5tA 124 3.24e+00 c.23.1.1 78660 1qmvA 197 3.48e+00 1qq2A c.47.1.10 33066 1aye 401 3.50e+00 1aye c.56.5.1 33824 d.58.3.1 39065 1jj2O 148 3.52e+00 1ffkM a.94.1.1 63100 1pufA 77 3.54e+00 a.4.1.1 -191 1fjkA 52 3.58e+00 1fjkA j.37.1.1 46288 1qpzA 340 3.63e+00 1qpzA a.35.1.5 17097 c.93.1.1 35673 1n7lA 53 3.71e+00 j.37.1.1 -13363 1s72P 149 3.77e+00 1gln 468 3.84e+00 1gln a.97.1.1 18752 c.26.1.1 31588 1on2A 142 3.89e+00 a.4.5.24 87103 a.76.1.1 87104 1cp2A 269 4.01e+00 1cp2A c.37.1.10 32269 1m45A 148 4.11e+00 a.39.1.5 78598 1vpwA 340 4.66e+00 1qpzA a.35.1.5 17087 c.93.1.1 35680 1ffkM 148 4.94e+00 1ffkM a.94.1.1 18740 1a3yA 149 5.45e+00 1obpA b.60.1.1 27110 1dzkA 157 6.09e+00 1obpA b.60.1.1 27096 1lliA 92 6.13e+00 1lmb3 a.35.1.2 17025 1o7bT 98 6.60e+00 d.169.1.4 -11647 1k9uA 78 6.82e+00 a.39.1.10 84348 2occJ 59 6.99e+00 2occJ f.23.4.1 43524 1faoA 126 7.11e+00 1faoA b.55.1.1 26974 1b7bA 310 7.19e+00 1b7bA c.73.1.1 34963 1v54J 59 7.35e+00 f.23.4.1 -12112 1b4aA 149 7.42e+00 1b4aA a.4.5.3 16088 d.74.2.1 39721 1jv1A 505 7.97e+00 c.68.1.5 71892 1k68A 140 8.02e+00 c.23.1.1 -6403 1pbjA 125 8.06e+00 d.37.1.1 -9608 d.37.1.1 -9609 1b72A 97 8.50e+00 2hddA a.4.1.1 16000 1yacA 208 8.69e+00 1yacA unknown_sccs 31757 1i60A 278 8.71e+00 c.1.15.4 71118 1s4qA 228 9.02e+00 c.37.1.1 -6975 1a8d 452 9.04e+00 1a8d b.29.1.6 24262 b.42.4.2 25607 1rsoB 56 9.11e+00 unknown_sccs -1188 1utg 70 1.13e+01 1utg a.101.1.1 18813 1v64A 108 1.13e+01 1msc 129 1.14e+01 1msc d.85.1.1 40039 2utgA 70 1.19e+01 1utg a.101.1.1 18814 1bt3A 345 1.20e+01 1bt3A a.86.1.2 18507 1zfjA 491 1.20e+01 1ak5 c.1.5.1 28638 d.37.1.1 38540 d.37.1.1 38541 1us7B 265 1.20e+01 unknown_sccs -1518 1ggwA 140 1.21e+01 1ggwA a.39.1.5 60490 1dd3A 128 1.22e+01 1dd3C a.108.1.1 19031 d.45.1.1 38760 1qpcA 279 1.22e+01 1fgkA d.144.1.7 41685 1g8eA 116 1.25e+01 1g8eA a.145.1.1 60346 1qcrH 60 1.26e+01 1qcrH f.28.1.1 43678 1cds 77 1.29e+01 1cds g.7.1.3 44461 1josA 128 1.34e+01 d.52.7.1 84191 1cjcA 460 1.34e+01 1cjcA c.3.1.1 30319 c.4.1.1 30604 1fjgM 126 1.34e+01 1fjfM a.156.1.1 16293 1ck9A 104 1.39e+01 1ck9A d.79.3.1 39806 1g59A 468 1.42e+01 a.97.1.1 60257 c.26.1.1 60258 1gk8I 140 1.42e+01 d.73.1.1 65242 2ms2A 129 1.44e+01 1msc d.85.1.1 40049 1k66A 149 1.49e+01 c.23.1.1 -6406 1ftt 68 1.52e+01 2hddA a.4.1.1 15997 1p5jA 372 1.53e+01 1qo7A 394 1.55e+01 1qo7A c.69.1.11 34697 1diwA 441 1.56e+01 1a8d b.29.1.6 24264 b.42.4.2 25609 1i3cA 149 1.61e+01 c.23.1.1 71112 1kskA 234 1.64e+01 unknown_sccs -10150 d.66.1.5 72920 1wdcC 156 1.65e+01 1wdcC a.39.1.5 17317 1m93A 55 1.67e+01 e.1.1.1 -11751 3lck 271 1.70e+01 1fmk d.144.1.7 41686 1o1fC 147 1.71e+01 i.15.1.1 80997 1rh5B 74 1.73e+01 unknown_sccs -12198 1qm1A 143 1.74e+01 1b10A d.6.1.1 37312 1uw4A 91 1.74e+01 unknown_sccs -10038 1nslA 184 1.78e+01 d.108.1.1 86137 1ohzB 60 1.82e+01 a.139.1.1 -147 1ngmB 72 1.84e+01 j.104.1.1 85687 1lm8V 160 1.85e+01 b.3.3.1 74035 1fe6A 52 1.95e+01 1fe6A h.1.19.1 45662 1uklC 61 1.99e+01 a.38.1.1 -807 2xat 212 2.01e+01 2xat b.81.1.3 28058 1lmb3 92 2.03e+01 1lmb3 1fukA 165 2.06e+01 1fukA c.37.1.19 32409 1fe6C 52 2.07e+01 1fe6C h.1.19.1 45664 1pufB 73 2.13e+01 a.4.1.1 -192 1p27B 106 2.13e+01 d.58.7.1 -10020 1qm9A 198 2.14e+01 1qm9A d.58.7.1 39207 d.58.7.1 39208 1d0hA 469 2.17e+01 1a8d b.29.1.6 24265 b.42.4.2 25610 1qpmA 69 2.22e+01 1qpmA a.6.1.7 16230 1tfe 145 2.23e+01 1tfe d.43.1.1 38680 1aoiF 87 2.23e+01 1aoiB a.22.1.1 16471 1tdhA 364 2.27e+01 1gw5B 591 2.28e+01 a.118.1.10 70630 1s4kA 120 2.35e+01 3icb 75 2.36e+01 4icb a.39.1.1 17147 1tplA 426 2.36e+01 1ax4A c.67.1.2 34387 1ry3A 64 2.38e+01 unknown_sccs -13301 1g6uA 48 2.43e+01 1g6uA k.9.1.1 46425 1necA 216 2.47e+01 1vfrA d.90.1.1 40249 1g2rA 100 2.48e+01 1g2rA d.192.1.1 60231 1v54M 46 2.48e+01 f.23.7.1 -12124 2occM 46 2.49e+01 2occM f.23.7.1 43527 1hq3D 103 2.54e+01 1aoiB a.22.1.1 16464 1vj1A 363 2.55e+01 b.35.1.2 -3728 c.2.1.1 -5752 1qm3A 112 2.56e+01 1b10A d.6.1.1 37313 1h8aC 128 2.57e+01 a.4.1.3 65731 a.4.1.3 65732 1neq 74 2.59e+01 1neq a.35.1.2 17063 1jr1A 514 2.63e+01 c.1.5.1 63241 d.37.1.1 63242 d.37.1.1 63243 1ekjB 221 2.64e+01 1ekjB c.53.2.1 33365 1r26A 125 2.64e+01 c.47.1.1 -7389 1aoy 78 2.65e+01 1aoy a.4.5.3 16087 1fafA 79 2.70e+01 1fafA a.2.3.1 15700 1rboC 123 2.71e+01 1rboC d.73.1.1 39634 1b9kA 238 2.72e+01 1qtsA b.1.10.1 22315 d.105.1.1 40791 1gseA 221 2.78e+01 1pgtA a.45.1.1 17667 c.47.1.5 32961 1mb3A 124 2.80e+01 c.23.1.1 78907 1snzA 344 2.81e+01 b.30.5.4 -3496 1mbe 53 2.85e+01 1mbe a.4.1.3 16038 1r6rA 100 2.95e+01 unknown_sccs -1071 1h70A 255 2.99e+01 1h70A d.126.1.3 60711 1fgkA 310 3.00e+01 1fgkA d.144.1.7 41693 1aoiB 87 3.03e+01 1aoiB a.22.1.1 16470 1pbe 394 3.04e+01 1pbe c.3.1.2 30338 d.16.1.2 37869 1xat 212 3.08e+01 2xat b.81.1.3 28059 1j09A 468 3.09e+01 a.97.1.1 77025 c.26.1.1 77026 1n9lA 109 3.09e+01 d.110.3.6 85468 1jyoE 105 3.11e+01 d.184.1.2 67487 1vcbC 160 3.12e+01 1vcbC b.3.3.1 22535 1p4dA 330 3.13e+01 unknown_sccs -10522 1hsm 79 3.14e+01 1cktA a.21.1.1 16421 1s96A 219 3.19e+01 c.37.1.1 -6972 1qhqA 140 3.20e+01 1qhqA b.6.1.1 63326 1kq4A 232 3.21e+01 d.207.1.1 68791 1o13A 136 3.22e+01 c.55.5.1 80762 1qtsA 247 3.26e+01 1qtsA b.1.10.1 22313 d.105.1.1 40789 1g61A 228 3.28e+01 1g61A d.126.1.1 41126 1gxrA 337 3.29e+01 b.69.4.1 70722 1aab 83 3.31e+01 1cktA a.21.1.1 16420 1ppjJ 62 3.32e+01 1dfd 64 3.37e+01 1fxd d.58.1.4 38995 1nd7A 374 3.38e+01 d.148.1.1 -11394 1g7sA 594 3.39e+01 1g7rA b.43.3.1 25712 b.43.3.1 25713 c.20.1.1 31032 c.37.1.8 32147 1pvaA 110 3.41e+01 1a75A a.39.1.4 17207 4icb 76 3.42e+01 4icb a.39.1.1 17145 8rucI 123 3.44e+01 1rboC d.73.1.1 39629 1bm9A 122 3.45e+01 1bm9A a.4.5.7 16116 1dx0A 219 3.46e+01 1b10A d.6.1.1 37324 1fioA 196 3.47e+01 1fioA a.47.2.1 17773 1cch 82 3.50e+01 451c a.3.1.1 15902 1kx5B 102 3.50e+01 a.22.1.1 77594 1ao6A 585 3.50e+01 1bj5 a.126.1.1 19354 a.126.1.1 19355 a.126.1.1 19356 1dv0A 47 3.53e+01 1dv0A a.5.2.1 16289 1k8kG 151 3.57e+01 a.118.13.1 68313 1xgsA 295 3.58e+01 1bn5 a.4.5.25 16216 d.127.1.1 41153 1r0kA 388 3.59e+01 1kbuA 349 3.61e+01 a.60.9.1 72284 d.163.1.1 72285 1hw7A 255 3.62e+01 1i7fA d.193.1.1 61297 1bgj 394 3.63e+01 1pbe c.3.1.2 30352 d.16.1.2 37883 1guuA 52 3.64e+01 a.4.1.3 83332 1iieA 75 3.65e+01 1iieA a.109.1.1 19039 1jw2A 72 3.68e+01 a.23.5.1 67372 1n8jA 186 3.72e+01 c.47.1.10 85401 1uyrA 737 3.76e+01 c.14.1.4 -6258 c.14.1.4 -6259 1g4yB 101 3.79e+01 1g4yB f.15.1.1 60251 1mwwA 128 3.80e+01 unknown_sccs -10451 1gt1A 159 3.84e+01 b.60.1.1 -4436 1hn2A 159 3.84e+01 b.60.1.1 65890 1o4sA 389 3.84e+01 c.67.1.1 86620 1gp8A 40 3.87e+01 2gp8A j.58.1.1 46342 1ekjA 221 3.89e+01 1ekjB c.53.2.1 33364 1oyiA 82 3.90e+01 a.4.5.19 -292 1m5yA 408 3.90e+01 a.167.1.1 78664 d.26.1.1 78665 d.26.1.1 78666 1lvhA 221 3.94e+01 c.108.1.6 74282 1fxrA 64 3.96e+01 1fxd d.58.1.4 38993