# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7 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 1dg3A 592 1.29e-01 1dg3A a.114.1.1 19078 c.37.1.8 32153 1h2vC 771 1.90e-01 a.118.1.2 76592 a.118.1.2 76593 a.118.1.2 76594 1h6kA 757 2.68e-01 a.118.1.2 60675 a.118.1.2 60676 a.118.1.2 60677 1b8xA 280 3.54e-01 1b8xA a.45.1.1 17739 c.47.1.5 33033 1hqvA 191 5.96e-01 1hqvA a.39.1.8 61160 1f5nA 592 7.06e-01 1dg3A a.114.1.1 19077 c.37.1.8 32152 2matA 264 8.30e-01 1c24A d.127.1.1 41146 1c24A 263 1.08e+00 1c24A d.127.1.1 41148 1qmyA 167 1.23e+00 1qmyA d.3.1.2 37094 1jffA 451 1.33e+00 c.32.1.1 62932 d.79.2.1 62933 1qqqA 264 1.41e+00 1bkpA d.117.1.1 40931 1pujA 282 1.51e+00 1ndbA 596 1.82e+00 c.43.1.3 80411 c.43.1.3 80412 1evfA 264 1.87e+00 1bkpA d.117.1.1 40932 1ezvG 93 1.92e+00 1ezvG f.23.13.1 59551 1a0hA 159 1.99e+00 1a0hA b.47.1.2 26229 g.14.1.1 44655 1mat 264 2.11e+00 1c24A d.127.1.1 41152 1t7pA 698 2.33e+00 1t7pA c.55.3.5 33712 e.8.1.1 43005 1kb9H 93 2.51e+00 f.23.13.1 77323 4matA 278 2.59e+00 1c24A d.127.1.1 41150 1o0wA 252 2.94e+00 a.149.1.1 80751 d.50.1.1 80752 1qayA 428 3.07e+00 1qaxA d.58.20.1 39378 d.179.1.1 42599 1umwA 237 3.12e+00 1anv 356 3.17e+00 1anv a.54.1.1 17890 g.51.1.1 45365 g.51.1.1 45371 1adt 356 3.20e+00 1anv a.54.1.1 17887 g.51.1.1 45362 g.51.1.1 45368 1tys 265 3.25e+00 1bkpA d.117.1.1 40937 1m9nA 613 3.37e+00 c.24.1.3 78870 c.97.2.1 78871 1ig8A 486 3.76e+00 2yhx c.55.1.3 64746 c.55.1.3 64747 1yghA 164 3.92e+00 1yghA d.108.1.1 40802 2tscA 264 3.99e+00 1bkpA d.117.1.1 40952 1alvA 173 4.10e+00 1alvA a.39.1.8 17370 1iw7C 1119 4.27e+00 e.29.1.1 71474 1lfaA 187 4.41e+00 1ido c.62.1.1 34122 1o0xA 262 4.63e+00 d.127.1.1 80755 1mlvA 444 4.67e+00 a.166.1.1 79283 b.85.7.3 79284 1iqrA 420 4.76e+00 a.99.1.1 66275 c.28.1.1 66276 1eq2A 310 5.00e+00 1eq2A c.2.1.2 29814 1kfuS 184 5.02e+00 a.39.1.8 68574 1h2kA 349 5.05e+00 b.82.2.6 76572 1vaoA 560 5.11e+00 1qltA d.58.32.1 39461 d.145.1.1 41724 1nrjB 218 5.22e+00 1r31A 428 5.33e+00 1ah6 220 5.59e+00 1yer d.122.1.1 41094 1g8mA 593 5.71e+00 1g8mA c.24.1.3 60371 c.97.2.1 60372 1eu1A 780 5.73e+00 1dmr b.52.2.2 26903 c.81.1.1 35311 1gqeA 365 6.23e+00 e.38.1.1 70351 1miuA 738 6.23e+00 a.170.1.1 79153 a.171.1.1 79154 b.40.4.3 79155 b.40.4.3 79156 b.40.4.3 79157 1a2vA 655 6.35e+00 1a2vA b.30.2.1 24416 d.17.2.1 38059 d.17.2.1 38060 1p0yA 444 6.46e+00 1jpnA 296 6.78e+00 a.24.13.1 67039 c.37.1.10 67040 1h99A 224 6.79e+00 a.142.1.1 60814 a.142.1.1 60815 1bia 321 6.80e+00 1bia a.4.5.1 16083 b.34.1.1 24447 d.104.1.2 40787 1ngvA 534 7.10e+00 1dmr 823 7.23e+00 1dmr b.52.2.2 26904 c.81.1.1 35312 1qaxA 428 7.97e+00 1qaxA d.58.20.1 39376 d.179.1.1 42597 1eluB 390 8.04e+00 1elqA c.67.1.3 34435 1qu9A 128 8.25e+00 1qu9A d.79.1.1 39755 1qu9C 128 8.25e+00 1qu9A d.79.1.1 39757 1p4dA 330 8.25e+00 1msc 129 8.58e+00 1msc d.85.1.1 40039 1i2sA 282 8.70e+00 e.3.1.1 71104 4blmA 265 8.72e+00 1btl e.3.1.1 42721 1oxjA 173 9.38e+00 1elqA 390 9.56e+00 1elqA c.67.1.3 34436 1gthD 1025 9.70e+00 a.1.2.2 70498 c.1.4.1 70499 c.3.1.1 70500 c.4.1.1 70501 d.58.1.5 70502 1fadA 99 1.01e+01 1fadA a.77.1.2 18428 1mjnA 179 1.05e+01 c.62.1.1 79210 1eluA 390 1.06e+01 1elqA c.67.1.3 34434 1gln 468 1.06e+01 1gln a.97.1.1 18752 c.26.1.1 31588 1jl0A 334 1.06e+01 1jenA d.156.1.1 63155 1qltA 560 1.12e+01 1qltA d.58.32.1 39457 d.145.1.1 41720 1gthA 1025 1.14e+01 a.1.2.2 70483 c.1.4.1 70484 c.3.1.1 70485 c.4.1.1 70486 d.58.1.5 70487 1ocyA 198 1.16e+01 1qtqA 553 1.17e+01 1gtrA b.53.1.2 26940 c.26.1.1 31579 1hr6B 443 1.17e+01 1be3A d.185.1.1 61166 d.185.1.1 61167 1e8gA 560 1.20e+01 1qltA d.58.32.1 39455 d.145.1.1 41718 1g59A 468 1.22e+01 a.97.1.1 60257 c.26.1.1 60258 1mhlA 108 1.23e+01 1d2vA a.93.1.2 18699 1mzeA 351 1.24e+01 b.82.2.6 79694 1ddf 127 1.25e+01 1ddf a.77.1.2 18423 1mypB 108 1.26e+01 1mypB a.93.1.2 18702 1gkxA 388 1.28e+01 a.29.5.1 65266 d.122.1.4 65267 1n4kA 381 1.31e+01 a.118.1.11 79992 b.42.6.1 79993 1nn6A 228 1.33e+01 3kinB 117 1.35e+01 3kinB 1h7xD 1025 1.36e+01 a.1.2.2 15690 c.1.4.1 28635 c.3.1.1 30331 c.4.1.1 30616 d.58.1.5 39014 1e3yA 104 1.44e+01 1fadA a.77.1.2 18426 1h7xA 1025 1.46e+01 1h7wA a.1.2.2 15687 c.1.4.1 28632 c.3.1.1 30328 c.4.1.1 30613 d.58.1.5 39011 1mi3A 322 1.47e+01 1n93X 375 1.51e+01 1jb0A 755 1.55e+01 1jb0A f.29.1.1 62820 1dofA 403 1.56e+01 1c3cA a.127.1.1 19429 1k8cA 322 1.57e+01 c.1.7.1 72172 1h7wD 1025 1.58e+01 a.1.2.2 15686 c.1.4.1 28631 c.3.1.1 30327 c.4.1.1 30612 d.58.1.5 39010 1tx4A 198 1.61e+01 1tx4A a.116.1.1 19098 1jqjC 343 1.63e+01 a.80.1.1 67097 c.37.1.20 67098 1cxpA 104 1.63e+01 1d2vA a.93.1.2 18695 1d2vA 104 1.63e+01 1d2vA a.93.1.2 18697 1fgjA 546 1.65e+01 1fgjA a.138.1.3 19679 1nm8A 616 1.69e+01 1bpb 248 1.71e+01 1bpyA a.60.12.1 75811 d.218.1.2 75812 1i7kA 179 1.71e+01 1u9aA d.20.1.1 61889 1f8nA 839 1.80e+01 1yge a.119.1.1 59703 b.12.1.1 59704 1gkzA 388 1.82e+01 a.29.5.1 65268 d.122.1.4 65269 1a41 234 1.86e+01 1a41 d.163.1.2 42174 1i5rA 327 1.87e+01 1gthC 1025 1.91e+01 a.1.2.2 70493 c.1.4.1 70494 c.3.1.1 70495 c.4.1.1 70496 d.58.1.5 70497 1h7xC 1025 1.93e+01 a.1.2.2 15689 c.1.4.1 28634 c.3.1.1 30330 c.4.1.1 30615 d.58.1.5 39013 1au7A 146 1.94e+01 1au7A a.4.1.1 15995 a.35.1.1 17021 1ddzA 496 1.97e+01 1ddzA c.53.2.1 33372 c.53.2.1 33373 1gwuA 309 1.99e+01 1ualA 274 2.00e+01 1n3kA 130 2.00e+01 a.77.1.4 79965 1m56B 264 2.02e+01 b.6.1.2 74472 f.17.2.1 74473 1e3dB 542 2.02e+01 1h2rL e.18.1.1 59189 1c0aA 585 2.05e+01 1c0aA b.40.4.1 25246 d.74.4.1 39731 d.104.1.1 40767 2occD 147 2.05e+01 1ocrD f.23.1.1 43521 1h7xB 1025 2.05e+01 a.1.2.2 15688 c.1.4.1 28633 c.3.1.1 30329 c.4.1.1 30614 d.58.1.5 39012 1o6uA 403 2.06e+01 1fiwA 290 2.10e+01 5ptp 1h7wB 1025 2.11e+01 a.1.2.2 15684 c.1.4.1 28629 c.3.1.1 30325 c.4.1.1 30610 d.58.1.5 39008 1ef1C 90 2.12e+01 1ef1C a.137.5.1 19642 1yagA 375 2.15e+01 1yagA c.55.1.1 33449 c.55.1.1 33450 1gt8C 1025 2.19e+01 a.1.2.2 70428 c.1.4.1 70429 c.3.1.1 70430 c.4.1.1 70431 d.58.1.5 70432 1pjpA 226 2.20e+01 5ptp b.47.1.2 26301 1jsqA 582 2.23e+01 i.13.1.1 63270 1j09A 468 2.23e+01 a.97.1.1 77025 c.26.1.1 77026 1eudA 311 2.26e+01 2scuA c.2.1.8 30312 c.23.4.1 31140 1cmxA 236 2.35e+01 1uch d.3.1.6 37130 1jwhC 215 2.37e+01 g.41.4.1 71915 1ocrD 147 2.38e+01 1ocrD f.23.1.1 43541 1gtrA 553 2.41e+01 1gtrA b.53.1.2 26939 c.26.1.1 31578 1h7wA 1025 2.41e+01 1h7wA a.1.2.2 15683 c.1.4.1 28628 c.3.1.1 30324 c.4.1.1 30609 d.58.1.5 39007 1budA 197 2.44e+01 1atlA d.92.1.9 40328 1irxA 523 2.46e+01 a.97.1.2 71378 c.26.1.1 71379 1k2eA 156 2.49e+01 d.113.1.1 72010 1bib 321 2.50e+01 1bia a.4.5.1 16084 b.34.1.1 24448 d.104.1.2 40788 1m2oA 768 2.53e+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 1eza 259 2.56e+01 1zymA a.60.10.1 18113 c.8.1.2 30708 1eg2A 319 2.56e+01 1eg2A c.66.1.11 34249 1jnrB 150 2.67e+01 d.58.1.5 66969 1j99A 293 2.69e+01 c.37.1.5 71618 7atjA 308 2.71e+01 1bgp a.93.1.1 18673 1pmt 203 2.74e+01 1a0fA a.45.1.1 17740 c.47.1.5 33034 1ngmB 72 2.75e+01 1jb1A 205 2.75e+01 1jb1A c.91.1.2 62832 1jatA 155 2.76e+01 1u9aA d.20.1.1 62818 3rp2A 224 2.82e+01 1a7s b.47.1.2 26298 1nw8A 319 2.95e+01 1do0A 442 2.96e+01 1do0A c.37.1.20 32432 1k8tA 510 2.96e+01 e.41.1.1 68316 1fds 327 2.97e+01 1fds c.2.1.2 29838 1gr8A 412 2.97e+01 c.117.1.1 70385 1ockA 412 2.97e+01 1fbtA 190 2.99e+01 1bif c.60.1.4 34004 1m4lA 307 2.99e+01 c.56.5.1 78604 1l8qA 324 3.04e+01 a.4.12.2 77809 c.37.1.20 77810 2atjA 308 3.04e+01 1bgp a.93.1.1 18675 1bxkA 355 3.06e+01 1bxkA c.2.1.2 29803 2ctb 307 3.10e+01 1aye c.56.5.1 33803 1qy5A 269 3.11e+01 1k26A 156 3.20e+01 d.113.1.1 72003 3csuA 310 3.21e+01 3csuA c.78.1.1 35094 c.78.1.1 35095 1qcrG 70 3.23e+01 1be3G f.23.13.1 43677 1qpsA 261 3.27e+01 1ckqA c.52.1.1 33234 1n9bA 265 3.30e+01 1i4mA 108 3.31e+01 d.6.1.1 66025 1byqA 228 3.33e+01 1yer d.122.1.1 41100 1fr1A 361 3.35e+01 1gceA e.3.1.1 42734 1hkbA 917 3.36e+01 1qhaA c.55.1.3 33479 c.55.1.3 33480 c.55.1.3 33481 c.55.1.3 33482 1ihgA 370 3.39e+01 2cpl a.118.8.1 62380 b.62.1.1 62381 1pme 380 3.40e+01 1hcl d.144.1.1 41653 1u9aA 160 3.43e+01 1u9aA d.20.1.1 38333 1chmA 401 3.45e+01 1chmA c.55.2.1 33545 d.127.1.1 41142 1gt8B 1025 3.48e+01 a.1.2.2 70423 c.1.4.1 70424 c.3.1.1 70425 c.4.1.1 70426 d.58.1.5 70427 1pytA 94 3.49e+01 1pytA d.58.3.1 39064 1mypA 108 3.50e+01 1d2vA a.93.1.2 18701 1tubA 440 3.55e+01 1tubA c.32.1.1 31751 d.79.2.1 39803 1im2A 444 3.58e+01 1do0A c.37.1.20 62564 1trkA 680 3.61e+01 1trkA c.36.1.2 31803 c.36.1.2 31804 c.48.1.1 33090 2ucz 165 3.65e+01 1u9aA d.20.1.1 38330 1ckmA 330 3.66e+01 1ckmA b.40.4.6 25358 d.142.2.3 41585 1h38D 883 3.68e+01 e.8.1.3 76628 1ls1A 295 3.74e+01 a.24.13.1 78170 c.37.1.10 78171 1fs0E 138 3.76e+01 1aqt a.2.10.1 59997 b.93.1.1 59998 1ng1 294 3.83e+01 1ng1 a.24.13.1 16961 c.37.1.10 32272 1gt8D 1025 3.86e+01 a.1.2.2 70433 c.1.4.1 70434 c.3.1.1 70435 c.4.1.1 70436 d.58.1.5 70437 1tkaA 678 3.87e+01 1trkA c.36.1.2 31815 c.36.1.2 31816 c.48.1.1 33096 1hvyA 288 3.87e+01 1bkpA d.117.1.1 41049 1g6wA 261 3.90e+01 1hqoA a.45.1.1 17751 c.47.1.5 33045 1dvpA 220 3.92e+01 1dvpA a.118.9.2 19216 g.50.1.1 45358 1ucyH 150 3.96e+01 1ucyH 1kjnA 157 3.97e+01 c.115.1.1 72614 1gt8A 1025 3.99e+01 a.1.2.2 70418 c.1.4.1 70419 c.3.1.1 70420 c.4.1.1 70421 d.58.1.5 70422 1gthB 1025 3.99e+01 a.1.2.2 70488 c.1.4.1 70489 c.3.1.1 70490 c.4.1.1 70491 d.58.1.5 70492