# 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 1tzbA 302 4.09e-07 1moq 368 9.97e-03 1moq c.80.1.1 35302 1b0zA 445 6.74e-01 2pgi c.80.1.2 35309 2pgi 445 6.74e-01 2pgi c.80.1.2 35308 1a6dA 545 7.44e-01 1a6dA a.129.1.2 19488 c.8.5.2 30819 d.56.1.2 38936 1c7qA 445 1.29e+00 2pgi c.80.1.2 35307 1g0hA 252 1.38e+00 1dk4A e.7.1.1 60171 1m3sA 186 1.65e+00 c.80.1.3 78573 1brwA 433 1.90e+00 1brwA a.46.2.1 17764 c.27.1.1 31628 d.41.3.1 38626 1t35A 191 1.93e+00 unknown_sccs -7285 1o57A 291 2.00e+00 unknown_sccs -249 c.61.1.1 -7960 1p41A 291 2.00e+00 1fezA 256 2.04e+00 1fezA c.108.1.3 43343 1ho8A 480 2.06e+00 1ho8A a.118.1.9 61107 1dk4A 252 2.22e+00 1dk4A e.7.1.1 42970 1f0kA 364 2.36e+00 1f0kA c.87.1.2 35465 1b3tA 147 2.36e+00 1b3tA d.58.8.1 39228 1kzyC 259 2.70e+00 c.15.1.4 73383 c.15.1.4 73384 1h2sA 225 2.71e+00 f.13.1.1 76578 1rqlA 267 2.80e+00 c.108.1.3 -6814 1efcA 393 2.87e+00 1efcA b.43.3.1 25680 b.44.1.1 25720 c.37.1.8 32113 1yer 228 2.91e+00 1yer d.122.1.1 41101 1uylA 236 3.10e+00 1vhiA 142 3.52e+00 1b3tA d.58.8.1 39230 1a1s 314 3.55e+00 1othA c.78.1.1 35258 c.78.1.1 35259 1ml4A 308 4.18e+00 c.78.1.1 79255 c.78.1.1 79256 1io7A 368 4.24e+00 1f4tA a.104.1.1 18971 1k4nA 192 4.29e+00 d.32.1.5 72059 1d3uB 201 4.48e+00 1aisB a.74.1.2 18386 a.74.1.2 18387 1tx4A 198 4.65e+00 1tx4A a.116.1.1 19098 1ckv 141 4.73e+00 1ckv d.137.1.1 41452 1l0lB 439 4.80e+00 d.185.1.1 84484 d.185.1.1 84485 1garA 212 5.05e+00 2gar c.65.1.1 34162 1m15A 357 5.13e+00 a.83.1.1 78368 d.128.1.2 78369 1qy5A 269 5.35e+00 d.122.1.1 -10958 1efdN 266 5.62e+00 1efdN c.92.2.1 35597 1byqA 228 5.86e+00 1yer d.122.1.1 41100 1ohuA 175 6.00e+00 f.1.4.1 -12058 1ezvB 352 6.05e+00 1ezvB d.185.1.1 59543 d.185.1.1 59544 1jw9B 249 6.12e+00 c.111.1.1 67377 1jgjA 217 6.14e+00 1c3wA f.13.1.1 62952 1h68A 239 6.60e+00 f.13.1.1 60664 1ihp 438 6.62e+00 1ihp c.60.1.2 33993 1j5xA 342 6.70e+00 c.80.1.1 71591 1jeoA 180 6.87e+00 c.80.1.3 66611 1pkp 150 6.87e+00 1pkp d.14.1.1 37551 d.50.1.2 38787 1bg0 356 7.01e+00 1qh4A a.83.1.1 18476 d.128.1.2 41211 2cblA 305 7.22e+00 2cblA a.39.1.7 17380 a.48.1.1 17774 d.93.1.1 40528 1pvvA 315 7.99e+00 c.78.1.1 -8495 c.78.1.1 -8496 1hr6A 475 8.06e+00 1hr6A d.185.1.1 61164 d.185.1.1 61165 1kid 203 8.25e+00 1derA c.8.5.1 30771 1jjfA 268 8.97e+00 c.69.1.2 66765 1keaA 221 9.20e+00 a.96.1.2 68491 1kkhA 317 9.35e+00 d.14.1.5 72645 d.58.26.3 72646 1p8xA 344 9.52e+00 d.109.1.1 -10813 d.109.1.1 -10814 d.109.1.1 -10815 1lucB 324 9.56e+00 1lucA c.1.16.1 29548 1nsyA 271 9.76e+00 2nsyA c.26.2.1 31614 1volA 204 9.78e+00 1tfb a.74.1.2 18370 a.74.1.2 18371 1fukA 165 1.03e+01 1fukA c.37.1.19 32409 1dar 691 1.03e+01 1dar b.43.3.1 25707 c.37.1.8 32142 d.14.1.1 37547 d.58.11.1 39300 1fxxA 482 1.05e+01 1fxxA c.55.3.5 33726 1v8gA 329 1.08e+01 a.46.2.1 -953 c.27.1.1 -6644 1ny6A 267 1.09e+01 c.37.1.20 -7221 1m22A 503 1.11e+01 c.117.1.1 78464 1jlnA 297 1.12e+01 1pty c.45.1.2 63172 1jayA 212 1.14e+01 c.2.1.6 66478 1vimA 200 1.18e+01 c.80.1.3 -8532 1qe3A 489 1.21e+01 2bce c.69.1.1 34630 1duvG 333 1.22e+01 1othA c.78.1.1 35228 c.78.1.1 35229 1b1cA 181 1.23e+01 1amoA c.23.5.2 31212 1b6rA 355 1.23e+01 1b6rA b.84.2.1 28241 c.30.1.1 31648 d.142.1.2 41493 1kb9B 352 1.25e+01 d.185.1.1 77313 d.185.1.1 77314 1r8sE 203 1.27e+01 a.118.3.1 -1579 1in0A 163 1.28e+01 d.58.49.1 83694 d.58.49.1 83695 1knvA 293 1.28e+01 c.52.1.7 68707 1ih8A 271 1.31e+01 2nsyA c.26.2.1 62377 1i8tA 367 1.37e+01 c.4.1.3 66094 d.16.1.7 66095 1b47A 304 1.39e+01 2cblA a.39.1.7 17381 a.48.1.1 17775 d.93.1.1 40529 1ah6 220 1.39e+01 1yer d.122.1.1 41094 1ja1A 622 1.43e+01 1amoA b.43.4.1 62803 c.23.5.2 62804 c.25.1.4 62805 1l6rA 227 1.45e+01 c.108.1.10 77768 1k66A 149 1.47e+01 c.23.1.1 -6406 2nsyA 271 1.48e+01 2nsyA c.26.2.1 31612 1jaxA 212 1.50e+01 c.2.1.6 66476 1j7nA 776 1.52e+01 d.92.1.14 66409 d.92.1.14 66410 d.166.1.1 66411 1o58A 303 1.56e+01 c.79.1.1 -8503 1j6nA 303 1.58e+01 1brlB 324 1.58e+01 1lucA c.1.16.1 29554 1aisB 200 1.61e+01 1aisB a.74.1.2 18384 a.74.1.2 18385 1hvd 319 1.67e+01 1avc a.65.1.1 18154 1b6sA 355 1.69e+01 1b6rA b.84.2.1 28242 c.30.1.1 31649 d.142.1.2 41494 1l9vA 317 1.70e+01 d.13.2.1 73760 d.216.1.1 73761 1kwkA 645 1.73e+01 b.71.1.1 77565 c.1.8.1 77566 c.23.16.5 77567 1iq4A 179 1.73e+01 1iq4A d.77.1.1 62641 1gp4A 356 1.76e+01 b.82.2.1 65439 1tc1A 220 1.77e+01 1tc1A c.61.1.1 34083 1e29A 135 1.78e+01 1e29A a.3.1.1 59161 1pmaP 211 1.78e+01 1pmaP d.153.1.4 41863 1ppjB 439 1.82e+01 1kqpA 271 1.82e+01 c.26.2.1 72883 4pfk 319 1.83e+01 3pfk c.89.1.1 35582 1j4wA 174 1.84e+01 d.51.1.1 71529 d.51.1.1 71530 1fnmA 691 1.84e+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 2ay1A 394 1.86e+01 1ajsA c.67.1.1 34357 1p1lA 102 1.87e+01 d.58.5.2 87695 1oroA 213 1.89e+01 1opr c.61.1.1 34093 1prxA 224 1.89e+01 1prxA c.47.1.10 33076 1nytA 271 1.90e+01 c.2.1.7 86417 c.58.1.5 86418 1gp6A 356 1.94e+01 b.82.2.1 65441 1louA 101 1.95e+01 1ris d.58.14.1 39323 1m1zA 513 1.97e+01 c.26.2.1 78457 d.153.1.1 78458 1spa 396 1.98e+01 1ajsA c.67.1.1 34291 1di1A 300 2.02e+01 1di1A a.128.1.4 19446 1mwqA 101 2.03e+01 unknown_sccs -9962 2sxl 88 2.05e+01 1b7fA d.58.7.1 39179 1n1bA 549 2.10e+01 a.102.4.1 79799 a.128.1.3 79800 3pfk 319 2.12e+01 3pfk c.89.1.1 35581 3csuA 310 2.13e+01 3csuA c.78.1.1 35094 c.78.1.1 35095 1lh0A 213 2.19e+01 c.61.1.1 73896 1i1gA 141 2.21e+01 a.4.5.32 65982 d.58.4.2 65983 1kgnA 329 2.21e+01 a.25.1.2 68584 1kf6A 602 2.22e+01 a.7.3.1 72394 c.3.1.4 72395 d.168.1.1 72396 1bbhA 131 2.35e+01 1bbhA a.24.3.2 16546 1uw4A 91 2.38e+01 unknown_sccs -10038 1jkxA 212 2.38e+01 c.65.1.1 66813 1hr6B 443 2.40e+01 1be3A d.185.1.1 61166 d.185.1.1 61167 1j7nB 776 2.45e+01 d.92.1.14 66412 d.92.1.14 66413 d.166.1.1 66414 1cqmA 101 2.48e+01 1ris d.58.14.1 39321 1qwoA 442 2.48e+01 1qmhA 347 2.56e+01 1qmhA c.47.2.1 33082 d.68.2.1 39568 1jfmA 174 2.62e+01 d.19.1.1 66640 1iicA 422 2.62e+01 1nmtA d.108.1.2 62422 d.108.1.2 62423 1jgtA 513 2.76e+01 c.26.2.1 66684 d.153.1.1 66685 1ppjA 446 2.78e+01 1d2eA 397 2.98e+01 1efcA b.43.3.1 25701 b.44.1.1 25741 c.37.1.8 32136 1rbp 182 3.00e+01 1aqb b.60.1.1 27085 1ris 101 3.04e+01 1ris d.58.14.1 39314 1sqsA 242 3.07e+01 unknown_sccs -6433 1dqyA 283 3.11e+01 1dqyA c.69.1.3 34640 1i0lA 221 3.11e+01 c.61.1.1 71096 6pfkA 319 3.14e+01 3pfk c.89.1.1 35583 1uxoA 192 3.15e+01 1vreA 147 3.15e+01 2hbg a.1.1.2 15017 1bq0 103 3.19e+01 1bqz a.2.3.1 15698 1cliA 345 3.24e+01 1cliA d.79.4.1 39816 d.139.1.1 41459 1jr1A 514 3.34e+01 c.1.5.1 63241 d.37.1.1 63242 d.37.1.1 63243 1qisA 396 3.36e+01 1ajsA c.67.1.1 34284 1othA 321 3.37e+01 1othA c.78.1.1 35260 c.78.1.1 35261 1kwgA 645 3.37e+01 b.71.1.1 77561 c.1.8.1 77562 c.23.16.5 77563 1nxzA 246 3.41e+01 b.122.1.2 86391 c.116.1.5 86392 1h6oA 204 3.42e+01 a.146.1.1 60689 1n2zA 245 3.48e+01 c.92.2.2 79865 1rypA 243 3.51e+01 1pmaA d.153.1.4 41932 1lrzA 426 3.53e+01 a.2.7.4 78167 d.108.1.4 78168 d.108.1.4 78169 1aa7A 158 3.56e+01 1aa7A a.95.1.1 18741 1kngA 156 3.59e+01 c.47.1.10 72777 1do0A 442 3.61e+01 1do0A c.37.1.20 32432 5pal 109 3.69e+01 1a75A a.39.1.4 17215 1l0lA 446 3.73e+01 d.185.1.1 84482 d.185.1.1 84483 1musA 477 3.86e+01 c.55.3.4 79494 1bqz 77 3.89e+01 1bqz a.2.3.1 15699 1g0uG 252 3.93e+01 d.153.1.4 41952 1jzuA 157 3.94e+01 b.60.1.1 84271 1no5A 114 3.94e+01 unknown_sccs -9785 1vjqA 79 3.97e+01 unknown_sccs -13478