# 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 1s3iA 310 6.14e-01 b.46.1.1 -4111 c.65.1.1 -8042 1kxrA 339 7.38e-01 d.3.1.3 73175 1ndbA 596 8.02e-01 c.43.1.3 80411 c.43.1.3 80412 1emsA 440 1.07e+00 1emsA d.13.1.1 37520 d.160.1.1 42086 1xgsA 295 1.21e+00 1bn5 a.4.5.25 16216 d.127.1.1 41153 1kafA 108 1.41e+00 d.199.1.1 68372 1ukuA 102 1.68e+00 d.58.5.2 -9992 1kn0A 212 1.70e+00 d.50.1.3 77444 1ut7A 171 2.39e+00 unknown_sccs -4724 1nm8A 616 2.57e+00 c.43.1.3 85872 c.43.1.3 85873 1fa3A 96 3.04e+00 1molA d.17.1.1 37996 1m6kA 251 3.39e+00 e.3.1.1 78695 1r4pB 70 3.49e+00 b.40.2.1 -3887 1vjzA 341 3.76e+00 c.1.8.3 -5318 1mrj 247 4.33e+00 1mrj d.165.1.1 42177 1azqA 66 4.58e+00 1azpA b.34.13.1 37469 1azpA 66 4.78e+00 1azpA b.34.13.1 37467 1nbwA 607 5.38e+00 c.8.6.1 80393 c.55.1.6 80394 c.55.1.6 80395 1h4pA 408 5.39e+00 c.1.8.3 -5314 1ajsA 412 5.45e+00 1ajsA c.67.1.1 34276 1q1rA 431 5.46e+00 c.3.1.5 -6048 c.3.1.5 -6049 d.87.1.1 -10502 1rvkA 382 5.48e+00 c.1.11.2 -5568 d.54.1.1 -9826 1fdo 715 5.70e+00 2napA b.52.2.2 26917 c.81.1.1 35325 1btkB 169 5.71e+00 1btkA b.55.1.1 26960 1bqyA 234 5.92e+00 5ptp b.47.1.2 26332 1ex2A 189 6.43e+00 1ex2A c.51.4.2 33225 1m1hA 248 6.83e+00 b.114.1.1 78415 d.58.42.1 78416 1frvB 536 7.01e+00 1h2rL e.18.1.1 43296 1eno 312 7.25e+00 1enp c.2.1.2 29905 1lxtA 561 7.54e+00 3pmgA c.84.1.1 35432 c.84.1.1 35433 c.84.1.1 35434 d.129.2.1 41309 1ybvA 283 7.97e+00 1ybvA c.2.1.2 29948 1fdi 715 8.16e+00 2napA b.52.2.2 26918 c.81.1.1 35326 1o97D 320 8.16e+00 c.26.2.3 81233 c.31.1.2 81234 1g0oA 283 8.52e+00 1ybvA c.2.1.2 60181 1onqA 283 8.72e+00 b.1.1.2 -2640 d.19.1.1 -9390 1l7jA 347 8.76e+00 b.30.5.4 73660 1kczA 413 8.91e+00 c.1.11.2 68451 d.54.1.1 68452 1k38A 254 8.97e+00 e.3.1.1 84303 1js8A 394 9.01e+00 a.86.1.1 67219 b.112.1.1 67220 1fgp 70 9.49e+00 1g3p b.37.1.1 24795 1jssA 224 9.53e+00 d.129.3.2 71844 1efuB 282 1.05e+01 1efuB a.5.2.2 58975 d.43.1.1 58976 d.43.1.1 38677 1op0A 234 1.07e+01 1rxyA 253 1.09e+01 c.56.2.1 -7834 1ca4A 168 1.12e+01 1d0aB b.8.1.1 23238 h.1.2.1 45445 2bosA 68 1.13e+01 2bosA b.40.2.1 25025 1lx7A 253 1.15e+01 c.56.2.1 74329 1jsdB 176 1.17e+01 h.3.1.1 63259 1f35A 162 1.18e+01 1f35A b.94.1.1 59628 1czyC 168 1.19e+01 1d0aB b.8.1.1 23222 h.1.2.1 45429 1enp 312 1.19e+01 1enp c.2.1.2 29906 1mmuA 347 1.20e+01 b.30.5.4 79303 1aj6 219 1.21e+01 1aj6 d.122.1.2 41106 1r62A 160 1.24e+01 1l7jB 347 1.25e+01 b.30.5.4 73661 1czyA 168 1.25e+01 1d0aB b.8.1.1 23220 h.1.2.1 45427 1jx4A 352 1.28e+01 unknown_sccs -10188 unknown_sccs -11898 2mjpA 193 1.28e+01 1b78A c.51.4.1 33223 1molA 94 1.29e+01 1molA d.17.1.1 37988 1g6hA 257 1.29e+01 1gajA c.37.1.12 60318 1vjqA 79 1.31e+01 unknown_sccs -13478 1ub0A 258 1.31e+01 c.72.1.2 88394 1nszA 347 1.32e+01 b.30.5.4 80724 1d0aB 168 1.32e+01 1d0aB b.8.1.1 23224 h.1.2.1 45431 1bo1A 416 1.34e+01 1bo1A d.143.1.2 41591 1b78A 193 1.37e+01 1b78A c.51.4.1 33221 1jobA 162 1.39e+01 1f35A b.94.1.1 63207 1kmnD 424 1.41e+01 1adjA c.51.1.1 33185 d.104.1.1 40734 1q8iA 783 1.44e+01 c.55.3.5 -7635 e.8.1.1 -11885 1l4iA 206 1.53e+01 b.1.11.1 73564 b.7.2.1 73565 1gajA 257 1.54e+01 1gajA c.37.1.12 60416 1l2lA 457 1.57e+01 c.72.1.3 77656 1btkA 169 1.62e+01 1btkA b.55.1.1 26959 1ca9A 192 1.64e+01 1d0aB b.8.1.1 23244 h.1.2.1 45451 1evlA 401 1.64e+01 1qf6A c.51.1.1 33202 d.104.1.1 40751 1p9rA 418 1.66e+01 c.37.1.11 -7142 1kkoA 413 1.66e+01 c.1.11.2 68675 d.54.1.1 68676 1dtyA 429 1.67e+01 1dtyA c.67.1.4 34495 1d7oA 297 1.69e+01 1enp c.2.1.2 29907 1aisA 182 1.71e+01 1ytbA d.129.1.1 41288 d.129.1.1 41289 1914 232 1.74e+01 1914 d.49.1.1 83028 d.49.1.1 83029 1k3fA 253 1.76e+01 c.56.2.1 68105 1j2gA 319 1.79e+01 1ehkB 168 1.82e+01 2cuaA b.6.1.2 23041 f.17.2.1 43625 1pysA 350 1.83e+01 1pysA d.104.1.1 40775 1fgkA 310 1.86e+01 1fgkA d.144.1.7 41693 1lo7A 141 1.86e+01 d.38.1.1 74144 1mo9A 523 1.86e+01 c.3.1.5 79341 c.3.1.5 79342 d.87.1.1 79343 1rypH 205 1.87e+01 d.153.1.4 41876 1fnmA 691 1.89e+01 1dar b.43.3.1 25709 c.37.1.8 32144 d.14.1.1 37546 d.58.11.1 39302 d.58.11.1 39303 1uxzA 131 1.89e+01 b.18.1.10 -3110 1jq3A 296 1.91e+01 c.66.1.17 67079 1inlA 296 1.91e+01 c.66.1.17 66220 1fsz 372 1.97e+01 1fsz c.32.1.1 31750 d.79.2.1 39802 1b7yA 350 2.04e+01 1pysA d.104.1.1 40776 1eqcA 394 2.08e+01 1cz1A c.1.8.3 28811 1cz1A 394 2.08e+01 1cz1A c.1.8.3 28839 2frvB 536 2.08e+01 1h2rL e.18.1.1 43291 1b63A 333 2.09e+01 1b63A d.14.1.3 37566 d.122.1.2 41107 1q7zA 566 2.13e+01 c.1.21.2 -5638 c.1.26.1 -5666 1aa6 715 2.17e+01 2napA b.52.2.2 26916 c.81.1.1 35324 1b7eA 420 2.19e+01 1b7eA c.55.3.4 33680 1e3dB 542 2.22e+01 1h2rL e.18.1.1 59189 1bovA 69 2.22e+01 2bosA b.40.2.1 25070 1deuA 277 2.24e+01 1theB d.3.1.1 37085 1fd9A 213 2.27e+01 1fd9A d.26.1.1 59771 1e8cA 498 2.27e+01 c.98.1.1 59377 c.59.1.1 59378 c.72.2.1 59379 1o12A 376 2.32e+01 b.92.1.5 80758 c.1.9.10 80759 1usuA 260 2.33e+01 unknown_sccs -9045 1q5qA 259 2.41e+01 d.153.1.4 -11433 1gxuA 91 2.46e+01 d.58.10.1 76378 1nmeA 146 2.49e+01 c.17.1.1 85874 1bvqA 141 2.49e+01 1bvqA d.38.1.1 38542 2cuaA 135 2.51e+01 2cuaA b.6.1.2 23039 1khdA 345 2.56e+01 a.46.2.1 77400 c.27.1.1 77401 1nrlA 316 2.64e+01 a.123.1.1 -1668 1ap8 213 2.66e+01 1ap8 d.86.1.1 40151 1ubpB 122 2.67e+01 1ubpB b.85.3.1 28346 1e0bA 68 2.71e+01 1e0bA b.34.13.2 37476 1b6a 478 2.75e+01 1bn5 a.4.5.25 16223 d.127.1.1 41160 1bn5 478 2.76e+01 1bn5 a.4.5.25 16224 d.127.1.1 41161 1qj5A 429 2.79e+01 1dtyA c.67.1.4 34493 1hd2A 161 2.81e+01 c.47.1.10 60962 1f3iA 481 2.82e+01 1b7eA 1h65A 270 2.84e+01 c.37.1.8 65640 1oyeA 1049 2.88e+01 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 1ubkL 534 2.91e+01 e.18.1.1 88422 1h2rL 534 2.91e+01 1h2rL e.18.1.1 43298 1txlA 215 3.00e+01 1by2 119 3.01e+01 1by2 d.170.1.1 42452 1aqb 183 3.03e+01 1aqb b.60.1.1 27084 7taa 478 3.05e+01 7taa b.71.1.1 27778 c.1.8.1 28765 1i8fA 81 3.07e+01 1i8fA b.38.1.1 61959 1s0aA 429 3.08e+01 c.67.1.4 -8201 1ryp1 222 3.08e+01 1ryp1 1a62 130 3.11e+01 1a62 a.140.3.1 64708 b.40.4.5 64709 1tfe 145 3.14e+01 1tfe d.43.1.1 38680 1hbq 183 3.16e+01 1aqb b.60.1.1 27078 1g0uL 241 3.17e+01 d.153.1.4 41894 1umnA 165 3.25e+01 a.25.1.1 -656 1qj2B 809 3.26e+01 1qj2B 1nbaA 264 3.28e+01 1nbaA unknown_sccs 31753 1e4fT 419 3.30e+01 1e4fT c.55.1.1 33453 c.55.1.1 33454 1eexB 224 3.33e+01 1dioB c.51.3.1 33213 1a8vA 121 3.34e+01 1a62 a.140.3.1 64712 b.40.4.5 64713 1s14A 194 3.34e+01 d.122.1.2 -10973 1dioB 224 3.35e+01 1dioB c.51.3.1 33219 1pauA 147 3.45e+01 1pauA c.17.1.1 30994 1ua4A 455 3.49e+01 c.72.1.3 -8416 2mbr 340 3.51e+01 2mbr d.145.1.2 41749 d.146.1.1 41762 1h2aL 567 3.55e+01 1h2rL e.18.1.1 43299 1mugA 168 3.56e+01 1mugA c.18.1.2 31030 1knvA 293 3.56e+01 c.52.1.7 68707 1g61A 228 3.57e+01 1g61A d.126.1.1 41126 1pieA 419 3.60e+01 d.14.1.5 -9075 unknown_sccs -10120 1h9sA 140 3.61e+01 1b9mA b.40.6.2 60843 b.40.6.2 60844 1mdwA 328 3.61e+01 d.3.1.3 84934 4ubpB 126 3.63e+01 1ubpB b.85.3.1 28345 1irl 133 3.64e+01 3inkC a.26.1.2 16883 1pkp 150 3.67e+01 1pkp d.14.1.1 37551 d.50.1.2 38787 1rgxA 114 3.71e+01 1qhlA 227 3.73e+01 1qhlA c.37.1.12 32382 1nm1G 125 3.74e+01 d.109.1.1 80653 1yagG 125 3.75e+01 1d0nA d.109.1.1 40846 1mgtA 174 3.77e+01 1mgtA a.4.2.1 16078 c.55.7.1 33753 1fj7A 101 3.81e+01 1fj7A d.58.7.1 39209 1p5jA 372 3.82e+01 1dtx 59 3.82e+01 1bpi g.8.1.1 44551 1n62B 809 3.82e+01 d.41.1.1 80092 d.133.1.1 80093 1qf6A 642 3.85e+01 1qf6A c.51.1.1 33210 d.15.10.1 39551 d.67.1.1 39562 d.104.1.1 40759 1nu5A 370 3.92e+01 c.1.11.2 -5565 d.54.1.1 -9823 1c0dA 358 3.93e+01 1eceA c.1.8.3 28815 1knmA 130 3.97e+01 b.42.2.1 72781 1pwt 61 3.99e+01 1tud b.34.2.1 24490 1agx 331 3.99e+01 4pgaA c.88.1.1 35564