# List of top-scoring protein chains for t2k-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 1o86A 589 2.68e-03 d.92.1.5 81177 1oo0A 147 1.03e-01 d.232.1.1 87182 1sur 215 1.98e-01 1sur c.26.2.2 31620 1hiwA 133 2.17e-01 1hiwA a.61.1.1 18122 1mhyB 395 2.48e-01 1mtyB a.25.1.2 16781 1cqxA 403 2.56e-01 1cqxA a.1.1.2 15635 b.43.4.2 25667 c.25.1.5 31562 1ut0A 190 3.03e-01 1tam 132 3.20e-01 1hiwA a.61.1.1 18128 1qgrA 876 3.74e-01 1qgrA a.118.1.1 19119 1ku2A 241 3.80e-01 a.4.13.1 83096 a.177.1.1 83097 1k8tA 510 5.61e-01 e.41.1.1 68316 1l6nA 289 5.76e-01 a.61.1.1 73624 a.73.1.1 73625 2hmx 133 6.30e-01 1hiwA a.61.1.1 18129 1pauB 102 1.05e+00 1pauB 1bolA 222 1.07e+00 1bolA d.124.1.1 41120 1qr0A 228 1.16e+00 1qr0A d.150.1.1 59038 d.150.1.1 59039 1nmeB 92 1.21e+00 1p2fA 220 1.22e+00 a.4.6.1 87720 c.23.1.1 87721 1guxB 152 1.50e+00 1guxB a.74.1.3 18389 1top 162 1.52e+00 1ncx a.39.1.5 17223 1ncx 162 2.06e+00 1ncx a.39.1.5 17222 1ucrA 78 2.06e+00 unknown_sccs -308 1cp3A 277 2.26e+00 1pauA c.17.1.1 30992 1eqfA 280 2.30e+00 1eqfA a.29.2.1 16972 a.29.2.1 16973 1j8yF 297 2.46e+00 1ng1 a.24.13.1 62747 c.37.1.10 62748 1j8mF 297 2.49e+00 1ng1 a.24.13.1 62742 c.37.1.10 62743 1hme 77 2.53e+00 1cktA a.21.1.1 16418 1kqfC 217 2.65e+00 f.21.1.1 72874 1k66A 149 2.70e+00 c.23.1.1 -6406 1o5hA 214 2.86e+00 unknown_sccs -1078 1iv8A 720 2.88e+00 b.71.1.1 76842 c.1.8.1 76843 1f7lA 121 3.17e+00 1f7lA d.150.1.2 59666 1g8qA 90 3.18e+00 1g8qA a.135.1.1 19621 1j78A 458 3.37e+00 a.126.1.1 66397 a.126.1.1 66398 a.126.1.1 66399 1n46A 258 3.44e+00 a.123.1.1 85315 1h6pA 203 3.45e+00 a.146.1.1 60690 1sk7A 198 3.59e+00 1guxA 218 3.65e+00 1guxA a.74.1.3 18388 2btvA 901 3.80e+00 2btvA e.28.1.1 43376 1pi1A 185 3.85e+00 unknown_sccs -762 1h6oA 204 3.86e+00 a.146.1.1 60689 1nrjA 158 3.99e+00 d.110.4.4 86124 1kxpD 458 4.11e+00 a.126.1.1 73160 a.126.1.1 73161 a.126.1.1 73162 1f7tA 122 4.16e+00 1f7lA d.150.1.2 59667 1g0uI 205 4.22e+00 d.153.1.4 41891 1a32 88 4.64e+00 1a32 a.16.1.2 16384 1iuqA 367 4.67e+00 c.112.1.1 -8440 1nt2B 258 4.67e+00 a.183.1.1 86150 1adt 356 4.84e+00 1anv a.54.1.1 17887 g.51.1.1 45362 g.51.1.1 45368 1dbqA 289 4.94e+00 1qpzA c.93.1.1 35666 1iwhB 146 4.94e+00 a.1.1.2 76883 1kyoG 126 4.97e+00 f.27.1.1 73259 1jm6A 407 5.14e+00 a.29.5.1 66876 d.122.1.4 66877 1hsm 79 5.66e+00 1cktA a.21.1.1 16421 1ek8A 185 5.69e+00 1ek8A d.67.3.1 59444 1hzdA 272 5.73e+00 c.14.1.3 65969 1tbmA 326 5.82e+00 1irdB 146 5.83e+00 a.1.1.2 66287 1n8vA 112 6.10e+00 unknown_sccs 85457 1c24A 263 6.12e+00 1c24A d.127.1.1 41148 1q0gA 117 6.22e+00 1ngmB 72 6.45e+00 j.104.1.1 85687 1rdr 461 6.48e+00 1rdr e.8.1.4 43116 1rxxA 421 6.66e+00 unknown_sccs -10982 1mv8A 436 6.69e+00 a.100.1.4 85128 c.2.1.6 85129 c.26.3.1 85130 1hbkA 94 6.77e+00 1aca a.11.1.1 60887 1p7gA 222 6.88e+00 a.2.11.1 -108 d.44.1.1 -9742 1nw1A 429 7.16e+00 d.144.1.8 86286 1babB 146 7.33e+00 1abwA a.1.1.2 15414 1anv 356 7.36e+00 1anv a.54.1.1 17890 g.51.1.1 45365 g.51.1.1 45371 1k30A 368 7.51e+00 c.112.1.1 68067 1dxtB 147 7.59e+00 1abwA a.1.1.2 15450 2matA 264 7.66e+00 1c24A d.127.1.1 41146 1ls1A 295 7.78e+00 a.24.13.1 78170 c.37.1.10 78171 1wetA 340 7.81e+00 1qpzA a.35.1.5 17093 c.93.1.1 35670 1q9jA 422 7.86e+00 1j7yB 146 7.93e+00 a.1.1.2 66427 1mgn 154 7.96e+00 1a6m a.1.1.2 15097 1vkiA 181 7.98e+00 1vpwA 340 8.10e+00 1qpzA a.35.1.5 17087 c.93.1.1 35680 1i37A 260 8.41e+00 1a28A a.123.1.1 61583 1orsC 132 8.58e+00 f.14.1.1 87353 1or4A 178 8.70e+00 a.1.1.2 -91 1q5qA 259 8.70e+00 d.153.1.4 -11433 2hddA 61 8.83e+00 2hddA a.4.1.1 15971 1jalA 363 9.01e+00 c.37.1.8 84138 d.15.10.2 84139 1jpnA 296 9.33e+00 a.24.13.1 67039 c.37.1.10 67040 1i3dA 146 9.39e+00 a.1.1.2 61587 1rypJ 204 9.42e+00 d.153.1.4 41878 1kfiA 572 9.51e+00 c.84.1.1 68555 c.84.1.1 68556 c.84.1.1 68557 d.129.2.1 68558 1rj1A 151 9.68e+00 unknown_sccs -753 1ezvF 125 9.87e+00 1be3F f.27.1.1 59550 1kb9G 125 9.87e+00 f.27.1.1 77322 1ha2A 585 1.01e+01 1bj5 a.126.1.1 60866 a.126.1.1 60867 a.126.1.1 60868 1kgnA 329 1.03e+01 a.25.1.2 68584 1dchA 104 1.03e+01 1dcpA d.74.1.1 39692 1zymA 258 1.05e+01 1zymA a.60.10.1 18110 c.8.1.2 30705 1gw5B 591 1.06e+01 a.118.1.10 70630 1dhn 121 1.08e+01 1dhn d.96.1.3 40663 1dkxA 219 1.09e+01 1dkzA unknown_sccs -446 unknown_sccs -3061 4matA 278 1.09e+01 1c24A d.127.1.1 41150 1lvfA 110 1.10e+01 a.47.2.1 74280 1avoB 140 1.11e+01 1avoB 1fz1C 389 1.15e+01 1mtyB a.25.1.2 16746 1vnc 609 1.16e+01 1vns a.111.1.3 19065 1ng1 294 1.17e+01 1ng1 a.24.13.1 16961 c.37.1.10 32272 1n97A 389 1.19e+01 a.104.1.1 80335 1qpzA 340 1.19e+01 1qpzA a.35.1.5 17097 c.93.1.1 35673 1hkvA 453 1.19e+01 b.49.2.3 83559 c.1.6.1 83560 2hrvA 142 1.20e+01 2hrvA b.47.1.4 26429 1eza 259 1.20e+01 1zymA a.60.10.1 18113 c.8.1.2 30708 1fioA 196 1.23e+01 1fioA a.47.2.1 17773 2cblA 305 1.27e+01 2cblA a.39.1.7 17380 a.48.1.1 17774 d.93.1.1 40528 1gk9A 260 1.27e+01 d.153.1.2 65246 1bj5 585 1.31e+01 1bj5 a.126.1.1 19369 a.126.1.1 19370 a.126.1.1 19371 1om2A 95 1.33e+01 1om2A a.23.4.1 16520 1f4lA 551 1.34e+01 1qqtA a.27.1.1 59648 c.26.1.1 59649 g.41.1.1 59650 1guzA 310 1.34e+01 c.2.1.5 65586 d.162.1.1 65587 1a6q 382 1.35e+01 1a6q a.159.1.1 75801 d.219.1.1 75802 1gvnA 90 1.35e+01 a.8.2.1 76353 1pjhA 280 1.40e+01 c.14.1.3 -6229 1dt6A 473 1.41e+01 1dt6A a.104.1.1 18977 1n3lA 372 1.43e+01 c.26.1.1 79966 1v8cA 168 1.45e+01 d.15.3.1 -9175 unknown_sccs -11012 1m2oA 768 1.47e+01 a.71.2.1 78480 b.2.8.1 78481 c.62.1.2 78482 d.109.2.1 78483 g.41.10.1 78484 1pbwA 216 1.47e+01 1pbwA a.116.1.1 19103 1gewA 356 1.48e+01 1gewA c.67.1.1 60470 1jw2A 72 1.49e+01 a.23.5.1 67372 1my6A 199 1.50e+01 a.2.11.1 85232 d.44.1.1 85233 1kx9A 112 1.53e+01 unknown_sccs 77602 1f16A 192 1.54e+01 1f16A f.1.4.1 43400 1lk5A 229 1.54e+01 unknown_sccs 73960 d.58.40.1 73961 1hrdA 449 1.56e+01 1k89 c.2.1.7 30219 c.58.1.1 33867 1fslA 143 1.58e+01 2gdm a.1.1.2 15229 1hnoA 280 1.60e+01 1hnoA c.14.1.3 61095 1pfvA 551 1.61e+01 a.27.1.1 -727 c.26.1.1 -6603 g.41.1.1 -12765 1ub9A 100 1.62e+01 a.4.5.28 -231 1kpsB 171 1.62e+01 a.118.12.1 68787 1b47A 304 1.64e+01 2cblA a.39.1.7 17381 a.48.1.1 17775 d.93.1.1 40529 1ad3A 452 1.65e+01 1ad3A c.82.1.1 35335 1mat 264 1.70e+01 1c24A d.127.1.1 41152 1hx6A 394 1.72e+01 1cjdA b.121.2.1 58995 b.121.2.1 58996 1rypD 241 1.72e+01 1rypD d.153.1.4 41935 1hs6A 611 1.74e+01 1hs6A a.118.1.7 61233 b.98.1.1 61234 d.92.1.13 61235 1fg7A 356 1.76e+01 1gewA c.67.1.1 59819 1em9A 154 1.76e+01 1d1dA a.73.1.1 18333 1vns 609 1.81e+01 1vns a.111.1.3 19061 1na3A 91 1.81e+01 k.38.1.1 85481 1hb5A 394 1.82e+01 i.6.1.1 65752 1qkfA 92 1.84e+01 1qkfA d.28.1.1 38456 1m6nA 802 1.85e+01 a.162.1.1 78697 a.172.1.1 78698 c.37.1.19 78699 c.37.1.19 78700 1mtyB 384 1.91e+01 1mtyB a.25.1.2 16740 1j4wA 174 2.00e+01 d.51.1.1 71529 d.51.1.1 71530 1pnkA 209 2.03e+01 1ajqA d.153.1.2 41839 1brwA 433 2.11e+01 1brwA a.46.2.1 17764 c.27.1.1 31628 d.41.3.1 38626 1dkzA 219 2.14e+01 1dkzA unknown_sccs -445 unknown_sccs -3060 1mjgM 729 2.15e+01 e.26.1.3 79204 1be3C 379 2.17e+01 1be3C f.32.1.1 75805 f.21.1.2 75806 1oaoC 729 2.18e+01 e.26.1.3 86746 1paqA 189 2.18e+01 unknown_sccs -1557 1gnwA 211 2.19e+01 1gnwA a.45.1.1 17727 c.47.1.5 33021 1uhnA 189 2.29e+01 a.39.1.5 -853 1fsgA 233 2.30e+01 1qk3A c.61.1.1 34029 1n5uA 585 2.34e+01 a.126.1.1 85339 a.126.1.1 85340 a.126.1.1 85341 1bqk 124 2.36e+01 1bqk b.6.1.1 22889 1bgvA 449 2.37e+01 1k89 c.2.1.7 30217 c.58.1.1 33865 1cjbA 231 2.37e+01 1qk3A c.61.1.1 34079 1ixmA 192 2.41e+01 1ixmA d.123.1.1 41114 1hnuA 280 2.42e+01 1hnoA c.14.1.3 61096 1ihuA 589 2.50e+01 c.37.1.10 62394 c.37.1.10 62395 1k1vA 41 2.51e+01 a.37.1.1 71999 1gm7A 209 2.53e+01 d.153.1.2 65302 1k9uA 78 2.56e+01 a.39.1.10 84348 1g5bA 221 2.57e+01 1g5bA d.159.1.3 60261 1k6iA 352 2.62e+01 c.2.1.2 68223 1qqiA 104 2.63e+01 1opc a.4.6.1 16233 1mmoB 384 2.66e+01 1mtyB a.25.1.2 16768 1dvkA 173 2.69e+01 1dvkA a.72.1.1 18319 1binA 143 2.70e+01 2gdm a.1.1.2 15231 1oxjA 173 2.70e+01 a.60.1.2 87517 a.118.1.13 87518 1xgsA 295 2.74e+01 1bn5 a.4.5.25 16216 d.127.1.1 41153 1cjdA 394 2.75e+01 1cjdA b.121.2.1 58963 b.121.2.1 58964 1kr7A 110 2.76e+01 a.1.1.4 72890 1eriA 276 2.77e+01 1ckqA c.52.1.1 33231 1vf6C 72 2.80e+01 unknown_sccs -1180 1fjgS 93 2.80e+01 1qkfA d.28.1.1 38451 1o0wA 252 2.85e+01 a.149.1.1 80751 d.50.1.1 80752 1k89 449 2.88e+01 1k89 c.2.1.7 30218 c.58.1.1 33866 1qc7A 101 2.88e+01 1qc7A a.118.14.1 18456 1gxqA 106 2.89e+01 a.4.6.1 70721 1cl8A 276 2.89e+01 1ckqA c.52.1.1 33230 1ciy 590 2.95e+01 1ciy b.18.1.3 23720 b.77.2.1 27977 f.1.3.1 43392 1wer 334 2.97e+01 1wer a.116.1.2 19108 1ajqA 209 2.99e+01 1ajqA d.153.1.2 41840 1ash 150 3.04e+01 1ash a.1.1.2 15622 1ho8A 480 3.05e+01 1ho8A a.118.1.9 61107 1k87A 669 3.08e+01 a.176.1.1 77286 c.1.23.2 77287 1tfe 145 3.10e+01 1tfe d.43.1.1 38680 1rcf 169 3.11e+01 1rcf c.23.5.1 31170 1bzpA 153 3.37e+01 1a6m a.1.1.2 15020 1ao6A 585 3.41e+01 1bj5 a.126.1.1 19354 a.126.1.1 19355 a.126.1.1 19356 1dcoA 104 3.43e+01 1dcpA d.74.1.1 39680 1e3aA 260 3.46e+01 1ajqA d.153.1.2 41838 1zac 90 3.46e+01 1ncx a.39.1.5 17236 1vjqA 79 3.47e+01 unknown_sccs -13478 1m2tA 254 3.55e+01 d.165.1.1 84761 1kplA 473 3.56e+01 f.20.1.1 68782 1it2A 146 3.58e+01 a.1.1.2 66365 1v54A 514 3.62e+01 f.24.1.1 -12235 1ngvA 534 3.66e+01 c.111.1.2 85698 1wdgA 94 3.67e+01 1qoyA 318 3.68e+01 1qoyA h.4.4.1 45788 1oboA 169 3.69e+01 c.23.5.1 86776 1lvaA 258 3.71e+01 a.4.5.35 74276 a.4.5.35 74277 a.4.5.35 74278 a.4.5.35 74279 1f93A 104 3.72e+01 1dcpA d.74.1.1 39688 1j54A 186 3.75e+01 c.55.3.5 77077 1gvhA 396 3.78e+01 a.1.1.2 70601 b.43.4.2 70602 c.25.1.5 70603 1rvkA 382 3.82e+01 c.1.11.2 -5568 d.54.1.1 -9826 1k6xA 352 3.82e+01 c.2.1.2 68238 1dmuA 299 3.84e+01 1dmuA c.52.1.4 33294 1pd3A 58 3.85e+01 unknown_sccs -767 1lnwA 147 3.91e+01 a.4.5.28 78104 1tn3 137 3.95e+01 1htn d.169.1.1 42423 1e7aA 585 3.98e+01 1bj5 a.126.1.1 19360 a.126.1.1 19361 a.126.1.1 19362 1ckqA 276 3.99e+01 1ckqA c.52.1.1 33229