# List of top-scoring protein chains for t2k-100-30-str2 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 8.73e-02 d.92.1.5 81177 1nxcA 478 1.01e-01 a.102.2.1 -1333 1oo0A 147 2.03e-01 d.232.1.1 87182 1rypJ 204 2.79e-01 d.153.1.4 41878 1g0uI 205 2.90e-01 d.153.1.4 41891 1guxA 218 4.46e-01 1guxA a.74.1.3 18388 1gw5B 591 6.17e-01 a.118.1.10 70630 1hiwA 133 6.23e-01 1hiwA a.61.1.1 18122 1mhyB 395 6.29e-01 1mtyB a.25.1.2 16781 1l6nA 289 8.00e-01 a.61.1.1 73624 a.73.1.1 73625 1lw3A 657 9.63e-01 unknown_sccs -4378 unknown_sccs -7358 1ku2A 241 1.07e+00 a.4.13.1 83096 a.177.1.1 83097 1j54A 186 1.08e+00 c.55.3.5 77077 1paqA 189 1.08e+00 unknown_sccs -1557 1fo3A 460 1.18e+00 1dl2A a.102.2.1 18845 1sur 215 1.25e+00 1sur c.26.2.2 31620 1ut0A 190 1.28e+00 1ur5A 309 1.43e+00 c.2.1.5 -5910 d.162.1.1 -11477 1dvkA 173 1.43e+00 1dvkA a.72.1.1 18319 2hrvA 142 1.49e+00 2hrvA b.47.1.4 26429 1aisB 200 1.58e+00 1aisB a.74.1.2 18384 a.74.1.2 18385 1dvpA 220 1.80e+00 1dvpA a.118.9.2 19216 g.50.1.1 45358 1i37A 260 2.02e+00 1a28A a.123.1.1 61583 1qciA 262 2.23e+00 1qi7A d.165.1.1 42201 1qr0A 228 2.31e+00 1qr0A d.150.1.1 59038 d.150.1.1 59039 1jksA 294 2.36e+00 d.144.1.7 71710 1dceA 567 2.55e+00 1dceA a.118.6.1 19191 b.7.4.1 23218 c.10.2.2 30867 2hmx 133 2.84e+00 1hiwA a.61.1.1 18129 1a1z 91 3.01e+00 1a1z a.77.1.4 18427 1cwyA 500 3.45e+00 1cwyA c.1.8.1 28789 1eswA 500 3.48e+00 1cwyA c.1.8.1 59500 1q5qA 259 3.49e+00 d.153.1.4 -11433 1ohuA 175 3.53e+00 f.1.4.1 -12058 1hkvA 453 3.79e+00 b.49.2.3 83559 c.1.6.1 83560 1fztA 211 3.99e+00 1qhfA c.60.1.1 60158 1tlqA 189 4.25e+00 1eqfA 280 4.91e+00 1eqfA a.29.2.1 16972 a.29.2.1 16973 1p7gA 222 5.18e+00 a.2.11.1 -108 d.44.1.1 -9742 1fg7A 356 5.67e+00 1gewA c.67.1.1 59819 1kblA 873 5.77e+00 c.1.12.2 68384 c.8.1.1 68385 d.142.1.5 68386 1c4qA 69 5.87e+00 2bosA b.40.2.1 25010 1hn0A 1021 5.98e+00 a.102.3.2 83616 b.18.1.17 83617 b.24.1.1 83618 b.30.5.2 83619 1fioA 196 6.30e+00 1fioA a.47.2.1 17773 1r71A 178 6.36e+00 1d6aB 262 6.51e+00 1qi7A d.165.1.1 42198 1tam 132 6.74e+00 1hiwA a.61.1.1 18128 1a6q 382 6.83e+00 1a6q a.159.1.1 75801 d.219.1.1 75802 1sfe 180 6.93e+00 1sfe a.4.2.1 16073 c.55.7.1 33748 1br2A 791 7.10e+00 1lvk b.34.3.1 24558 c.37.1.9 32155 1guxB 152 7.21e+00 1guxB a.74.1.3 18389 1k87A 669 7.41e+00 a.176.1.1 77286 c.1.23.2 77287 1av1A 201 7.59e+00 1av1A h.5.1.1 45796 1k8kA 418 7.62e+00 c.55.1.1 68305 c.55.1.1 68306 1kb9C 385 7.66e+00 f.32.1.1 77315 f.21.1.2 77316 1ezvC 385 7.69e+00 1be3C f.32.1.1 75833 f.21.1.2 75834 1om2A 95 7.72e+00 1om2A a.23.4.1 16520 1gewA 356 7.73e+00 1gewA c.67.1.1 60470 1dj8A 89 7.83e+00 1bg8A a.57.1.1 17919 1dxtB 147 7.91e+00 1abwA a.1.1.2 15450 1babB 146 7.92e+00 1abwA a.1.1.2 15414 1p4oA 322 8.10e+00 d.144.1.7 87775 1a1w 91 8.13e+00 1a1z a.77.1.4 18425 1n8vA 112 8.30e+00 unknown_sccs 85457 1f7tA 122 8.31e+00 1f7lA d.150.1.2 59667 1jqhA 308 8.54e+00 d.144.1.7 71793 1oeyJ 107 8.57e+00 d.15.2.2 -9168 1ki1B 352 8.57e+00 a.87.1.1 72497 b.55.1.1 72498 1sig 339 8.71e+00 1sig a.177.1.1 19068 1s6tA 285 8.92e+00 c.37.1.5 -7040 1vkjA 285 8.92e+00 1qoyA 318 9.07e+00 1qoyA h.4.4.1 45788 1j8iA 93 9.19e+00 d.9.1.1 66438 1v61A 132 9.40e+00 1nw1A 429 9.43e+00 d.144.1.8 86286 1gpmA 525 9.66e+00 1gpmA c.23.16.1 31405 c.26.2.1 31608 d.52.2.1 38826 1n46A 258 9.73e+00 a.123.1.1 85315 1k66A 149 9.90e+00 c.23.1.1 -6406 1oqvA 192 9.94e+00 d.24.1.2 87320 1jpnA 296 1.05e+01 a.24.13.1 67039 c.37.1.10 67040 1ls1A 295 1.06e+01 a.24.13.1 78170 c.37.1.10 78171 1d1dA 262 1.13e+01 1d1dA a.28.3.1 16958 a.73.1.1 18335 1uirA 314 1.15e+01 c.66.1.17 -8114 1r9dA 787 1.20e+01 1hbkA 94 1.22e+01 1aca a.11.1.1 60887 1n83A 270 1.28e+01 a.123.1.1 80276 1tbmA 326 1.31e+01 1pi1A 185 1.31e+01 unknown_sccs -762 1tuc 63 1.33e+01 1tuc b.34.2.1 24492 1nrjA 158 1.35e+01 d.110.4.4 86124 1k4wA 252 1.41e+01 a.123.1.1 72068 1irdB 146 1.42e+01 a.1.1.2 66287 1em2A 229 1.47e+01 1em2A d.129.3.2 41321 1yfm 488 1.48e+01 1furA a.127.1.1 19413 1r4pB 70 1.49e+01 b.40.2.1 -3887 1mv8A 436 1.52e+01 a.100.1.4 85128 c.2.1.6 85129 c.26.3.1 85130 1iv8A 720 1.55e+01 b.71.1.1 76842 c.1.8.1 76843 1vk3A 615 1.56e+01 d.79.4.1 -10416 d.79.4.1 -10417 d.139.1.1 -11154 d.139.1.1 -11155 1vnc 609 1.60e+01 1vns a.111.1.3 19065 1kx9A 112 1.61e+01 unknown_sccs 77602 1n6bA 473 1.61e+01 a.104.1.1 85359 1qsaA 618 1.62e+01 1qsaA a.118.5.1 19182 d.2.1.6 36988 1m2tA 254 1.64e+01 d.165.1.1 84761 1mldA 314 1.64e+01 2cmd c.2.1.5 30122 d.162.1.1 42089 1pnkA 209 1.67e+01 1ajqA d.153.1.2 41839 1lvaA 258 1.67e+01 a.4.5.35 74276 a.4.5.35 74277 a.4.5.35 74278 a.4.5.35 74279 1bovA 69 1.69e+01 2bosA b.40.2.1 25070 1kyoC 385 1.73e+01 f.32.1.1 75904 f.21.1.2 75905 1f5qB 252 1.75e+01 1f5qB a.74.1.1 18362 a.74.1.1 18363 1q0gA 117 1.76e+01 1ub9A 100 1.77e+01 a.4.5.28 -231 1mrg 263 1.77e+01 1mrj d.165.1.1 42183 1ad6 185 1.79e+01 1guxA a.74.1.3 18390 1kpkA 473 1.81e+01 f.20.1.1 68776 1vns 609 1.81e+01 1vns a.111.1.3 19061 1f7lA 121 1.83e+01 1f7lA d.150.1.2 59666 1j1qA 261 1.85e+01 d.165.1.1 -11546 1jztA 246 1.87e+01 c.104.1.1 63319 1ng1 294 1.87e+01 1ng1 a.24.13.1 16961 c.37.1.10 32272 1hzdA 272 1.91e+01 c.14.1.3 65969 1hkfA 122 1.95e+01 b.1.1.1 83553 1nq7A 244 1.95e+01 a.123.1.1 -1682 1pwt 61 1.95e+01 1tud b.34.2.1 24490 1shg 62 1.97e+01 1ckaA b.34.2.1 24493 2cmd 312 1.97e+01 2cmd c.2.1.5 30135 d.162.1.1 42102 1dik 874 2.00e+01 1dik c.1.12.2 29304 c.8.1.1 30702 d.142.1.5 41572 1oxjA 173 2.00e+01 a.60.1.2 87517 a.118.1.13 87518 1nt2B 258 2.03e+01 a.183.1.1 86150 1guzA 310 2.03e+01 c.2.1.5 65586 d.162.1.1 65587 1wer 334 2.05e+01 1wer a.116.1.2 19108 1n3lA 372 2.07e+01 c.26.1.1 79966 1nmeB 92 2.09e+01 1n97A 389 2.13e+01 a.104.1.1 80335 1d8vA 263 2.16e+01 1mrj d.165.1.1 42193 1idrA 136 2.19e+01 1dlyA a.1.1.1 62301 1dkxA 219 2.21e+01 1dkzA unknown_sccs -446 unknown_sccs -3061 1em9A 154 2.24e+01 1d1dA a.73.1.1 18333 1lnwA 147 2.29e+01 a.4.5.28 78104 1pbwA 216 2.31e+01 1pbwA a.116.1.1 19103 1j7yB 146 2.32e+01 a.1.1.2 66427 1hm6A 346 2.35e+01 1avc a.65.1.1 18147 1qz8A 113 2.39e+01 unknown_sccs -4264 1d3uB 201 2.46e+01 1aisB a.74.1.2 18386 a.74.1.2 18387 1j6rA 214 2.48e+01 d.173.1.2 71598 1pauB 102 2.49e+01 1pauB 1lvk 762 2.51e+01 1lvk b.34.3.1 24576 c.37.1.9 32173 2bosA 68 2.52e+01 2bosA b.40.2.1 25025 1lfkA 398 2.54e+01 a.104.1.1 77926 1dxrL 273 2.59e+01 6prcL f.26.1.1 43431 1j8mF 297 2.62e+01 1ng1 a.24.13.1 62742 c.37.1.10 62743 1k30A 368 2.63e+01 c.112.1.1 68067 1j8yF 297 2.63e+01 1ng1 a.24.13.1 62747 c.37.1.10 62748 1l4sA 112 2.65e+01 d.204.1.1 77693 1gnwA 211 2.65e+01 1gnwA a.45.1.1 17727 c.47.1.5 33021 1rj1A 151 2.67e+01 unknown_sccs -753 1ezvF 125 2.70e+01 1be3F f.27.1.1 59550 1kb9G 125 2.74e+01 f.27.1.1 77322 1ciy 590 2.81e+01 1ciy b.18.1.3 23720 b.77.2.1 27977 f.1.3.1 43392 1jiwP 470 2.82e+01 1sat unknown_sccs 63079 d.92.1.6 63080 1sva1 361 2.82e+01 1vpsA 1gu9A 177 2.83e+01 a.152.1.1 65540 1a32 88 2.84e+01 1a32 a.16.1.2 16384 1m2oA 768 2.93e+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 2ng1 293 2.95e+01 1ng1 a.24.13.1 16962 c.37.1.10 32273 1kncA 177 2.97e+01 a.152.1.1 68703 1k1vA 41 2.99e+01 a.37.1.1 71999 1fjgS 93 3.01e+01 1qkfA d.28.1.1 38451 1dkzA 219 3.01e+01 1dkzA unknown_sccs -445 unknown_sccs -3060 1v4eA 299 3.02e+01 a.128.1.1 -1781 1colA 204 3.04e+01 1a87 f.1.1.1 43378 4ull 69 3.05e+01 2bosA b.40.2.1 25100 1knvA 293 3.07e+01 c.52.1.7 68707 1n3gA 113 3.09e+01 d.204.1.1 79962 2hddA 61 3.10e+01 2hddA a.4.1.1 15971 1i3dA 146 3.11e+01 a.1.1.2 61587 1uwsA 489 3.13e+01 1d2mA 665 3.15e+01 1d2mA c.37.1.19 32417 c.37.1.19 32418 1cnzA 363 3.15e+01 1cnzA c.77.1.1 35061 1e2xA 243 3.16e+01 1e2xA a.4.5.6 16113 a.78.1.1 18443 1vkeA 133 3.16e+01 1o5hA 214 3.16e+01 unknown_sccs -1078 1oedC 260 3.21e+01 f.36.1.1 86913 1vf6C 72 3.24e+01 unknown_sccs -1180 1rdr 461 3.26e+01 1rdr e.8.1.4 43116 1g8qA 90 3.34e+01 1g8qA a.135.1.1 19621 1f93A 104 3.36e+01 1dcpA d.74.1.1 39688 1ls6A 295 3.37e+01 c.37.1.5 -7026 1mjgM 729 3.40e+01 e.26.1.3 79204 1na3A 91 3.42e+01 k.38.1.1 85481 2matA 264 3.43e+01 1c24A d.127.1.1 41146 1vkiA 181 3.44e+01 1hlvA 131 3.46e+01 a.4.1.7 65854 a.4.1.7 65855 1omwA 689 3.46e+01 a.91.1.1 87086 b.55.1.1 87087 d.144.1.7 87088 1gikA 261 3.49e+01 d.165.1.1 -11545 1iuqA 367 3.54e+01 c.112.1.1 -8440 1cby 259 3.54e+01 1cby d.103.1.1 40705 1k28A 584 3.56e+01 b.40.8.1 68049 b.108.1.2 68050 d.2.1.3 68051 1qkfA 92 3.57e+01 1qkfA d.28.1.1 38456 1cp3A 277 3.58e+01 1pauA c.17.1.1 30992 1ssqA 267 3.59e+01 1a87 321 3.60e+01 1a87 f.1.1.1 43380 1t0iA 191 3.60e+01 1gd8A 118 3.67e+01 d.188.1.1 60445 1in4A 334 3.77e+01 1hqcA a.4.5.11 62597 c.37.1.20 62598 1snzA 344 3.78e+01 b.30.5.4 -3496 1fhjB 146 3.81e+01 1abwA a.1.1.2 59838 1urrA 102 3.82e+01 1nwbA 124 3.86e+01 b.124.1.1 86296 1otsA 465 3.90e+01 f.20.1.1 87415 1eazA 125 3.93e+01 b.55.1.1 70113