# 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 2fe5A 94 6.40e-18 1tp5A 119 2.12e-17 1bfeA 119 3.77e-17 1pdr b.36.1.1 24775 1be9A 119 4.79e-17 1pdr b.36.1.1 24774 1pdr 99 5.82e-17 1pdr b.36.1.1 24771 1g9oA 91 6.34e-17 1pdr b.36.1.1 60400 1n7eA 97 6.67e-17 b.36.1.1 91691 1i92A 91 1.20e-16 1pdr b.36.1.1 61990 1n7fA 97 8.94e-16 b.36.1.1 91692 2fcfA 103 1.68e-15 1qavA 90 1.93e-15 1qauA b.36.1.1 24777 1mfgA 95 2.73e-15 b.36.1.1 79043 1q3oA 109 2.84e-15 b.36.1.1 95700 1ihjA 98 3.01e-15 1pdr b.36.1.1 62382 1l6oA 95 2.04e-14 b.36.1.1 84534 1i16 130 8.48e-14 1i16 b.36.1.2 24787 1kwaA 88 1.35e-13 1kwaA b.36.1.1 24772 1n99A 166 1.51e-13 b.36.1.1,b.36.1.1 85459,85460 1m5zA 91 2.11e-13 b.36.1.1 78676 2f0aA 98 3.05e-13 1kwaB 88 7.10e-13 1kwaA b.36.1.1 24773 1wf7A 103 8.02e-13 1nf3C 128 1.47e-12 b.36.1.1 85596 2f5yA 91 2.16e-12 1qavB 115 2.43e-12 1qauA b.36.1.1 24780 1qauA 112 2.74e-12 1qauA b.36.1.1 24779 1v5lA 103 6.81e-12 b.36.1.1 108378 1nteA 82 6.55e-11 b.36.1.1 86163 1b8qA 127 8.09e-11 1qauA b.36.1.1 24781 1r6jA 82 1.33e-10 b.36.1.1 97151 1fc6A 388 1.50e-08 1fc6A b.36.1.3,c.14.1.2 64738,64739 1lcyA 325 3.81e-07 b.36.1.4,b.47.1.1 73834,73835 1te0A 318 4.25e-07 1ky9B 448 1.84e-04 b.36.1.4,b.36.1.4,b.47.1.1 73200,73201,73202 1y8tA 324 2.13e-03 1ky9A 448 7.40e-03 b.36.1.4,b.47.1.1 73198,73199 1fxlA 167 1.07e-02 1b7fA d.58.7.1,d.58.7.1 39183,39184 1sotA 320 5.43e-02 b.36.1.4,b.47.1.1 105852,105853 1y9wA 140 5.14e-01 1cis 66 8.21e-01 2sniI k.1.1.1 46375 1vkcA 158 1.09e+00 1r13A 148 1.38e+00 d.169.1.1,h.1.1.1 96782,96783 2c5qA 240 1.46e+00 1b7fA 168 1.53e+00 1b7fA d.58.7.1,d.58.7.1 39169,39170 2fl4A 149 1.56e+00 1eujA 166 1.64e+00 1eujA b.40.4.4 25316 1fxrA 64 1.82e+00 1fxd d.58.1.4 38993 1db3A 372 1.85e+00 1db3A c.2.1.2 29813 1yjmA 110 1.93e+00 1fl0A 171 2.00e+00 1eujA b.40.4.4 25315 3sxlA 184 2.08e+00 1b7fA d.58.7.1,d.58.7.1 39173,39174 1eulA 994 2.18e+00 1eulA 1xebA 150 2.19e+00 2brfA 110 2.24e+00 1s3zA 165 2.49e+00 d.108.1.1 105250 1coaI 64 2.58e+00 2sniI d.40.1.1 38574 1f9zA 135 2.61e+00 1qipA d.32.1.1 38484 2sniI 83 2.79e+00 2sniI d.40.1.1 38573 1bo4B 168 2.80e+00 1bo4A d.108.1.1 40799 1kb5A 115 2.85e+00 1tvdA b.1.1.1 20611 1ggrA 168 3.04e+00 1gpr b.84.3.1 28279 1glaF 168 3.37e+00 1gpr b.84.3.1 28274 1fa8A 135 3.43e+00 1qipA d.32.1.1 38486 1mjc 69 3.85e+00 1mjc b.40.4.5 25319 1yagG 125 3.87e+00 1d0nA d.109.1.1 40846 1rl2A 137 3.96e+00 1rl2A b.34.5.3,b.40.4.5 24610,25342 1fnhA 271 4.08e+00 1fnhA b.1.2.1,b.1.2.1,b.1.2.1 21976,21977,21978 1zh1A 163 4.15e+00 1p7tA 731 4.43e+00 c.1.13.1 94319 1y7rA 133 4.49e+00 1jj2D 176 4.78e+00 1ffkD d.77.1.1 63088 1f3z 161 4.97e+00 1gpr b.84.3.1 28273 1cvjA 190 5.20e+00 1cvjB d.58.7.1,d.58.7.1 39191,39192 1a79A 171 5.33e+00 1a79A c.52.2.1,d.75.1.1 33340,39739 1mt6A 280 5.35e+00 b.76.2.1,b.85.7.1 79446,79447 1viuA 203 5.45e+00 d.113.1.1 100771 1vbwA 68 5.78e+00 1h9jA 145 5.92e+00 1h9jA b.40.6.2,b.40.6.2 60829,60830 1d4xG 126 5.95e+00 1d0nA d.109.1.1 59109 1bo4A 168 6.31e+00 1bo4A d.108.1.1 40798 1xe1A 116 6.35e+00 b.43.3.1 109571 1s1qA 145 6.40e+00 d.20.1.2 98351 1kw4A 89 6.72e+00 a.60.1.2 73077 1nm1G 125 7.02e+00 d.109.1.1 80653 2fvgA 340 7.06e+00 2aexA 346 7.23e+00 2bsjA 133 7.23e+00 1svy 114 7.37e+00 1svy d.109.1.1 40831 1lw6I 64 7.39e+00 d.40.1.1 74294 1z4eA 153 7.44e+00 1su4A 994 7.89e+00 b.82.7.1,c.108.1.7,d.220.1.1,f.33.1.1 98993,98994,98995,98996 1xewX 182 7.94e+00 1wi0A 113 8.00e+00 1cvjB 190 8.25e+00 1cvjB d.58.7.1,d.58.7.1 39193,39194 1to2I 64 8.25e+00 1skyB 502 8.62e+00 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18313,26478,32358 2f7fA 494 8.74e+00 1vc3B 97 8.76e+00 1h9mA 145 9.12e+00 1h9jA b.40.6.2,b.40.6.2 60833,60834 1vyfA 135 9.28e+00 b.60.1.2 108902 1t9fA 187 9.43e+00 b.42.6.1 106710 1x3mA 415 9.51e+00 1h3iA 293 9.62e+00 b.76.2.1,b.85.7.1 76635,76636 1dax 64 1.03e+01 1fxd d.58.1.4 38996 1koe 172 1.06e+01 1koe d.169.1.5 42448 1bd2D 204 1.07e+01 1tcrA b.1.1.1,b.1.1.2 20622,21557 1y9kA 157 1.08e+01 2ghpA 292 1.09e+01 1gpr 162 1.10e+01 1gpr b.84.3.1 28267 1qf6A 642 1.17e+01 1qf6A c.51.1.1,d.15.10.1,d.67.1.1,d.104.1.1 33210,39551,39562,40759 1d8cA 723 1.20e+01 1d8cA c.1.13.1 29325 1vpqA 273 1.22e+01 2bshA 125 1.26e+01 2fk9A 157 1.27e+01 1r0vA 305 1.29e+01 c.52.2.1,c.52.2.1,d.75.1.1 96742,96743,96744 1r62A 160 1.31e+01 d.122.1.3 104816 1g65K 211 1.33e+01 d.153.1.4 41907 1ifyA 49 1.33e+01 a.5.2.1 71207 2sxl 88 1.34e+01 1b7fA d.58.7.1 39179 1mek 120 1.36e+01 1erv c.47.1.2 32775 2a8mA 420 1.36e+01 1dfd 64 1.39e+01 1fxd d.58.1.4 38995 1js8A 394 1.42e+01 a.86.1.1,b.112.1.1 67219,67220 1qstA 160 1.42e+01 1yghA d.108.1.1 40804 3mefA 69 1.45e+01 1mjc b.40.4.5 25320 2fsp 124 1.45e+01 1dz3A c.23.1.1 31119 1l7bA 92 1.52e+01 c.15.1.2 91053 2bhoA 130 1.53e+01 1uw0A 117 1.55e+01 g.39.1.12 108063 2a8jA 420 1.57e+01 1tif 78 1.61e+01 1tif d.15.8.1 37836 1o50A 157 1.64e+01 d.37.1.1,d.37.1.1 92478,92479 1csp 67 1.65e+01 1mjc b.40.4.5 25321 1wlgA 299 1.65e+01 1zhhB 242 1.70e+01 2a5dA 175 1.71e+01 1qsoA 149 1.73e+01 1qsmA d.108.1.1 40812 1tin 69 1.79e+01 2sniI d.40.1.1 38580 1rxdA 159 1.82e+01 1hw7A 255 1.82e+01 1i7fA d.193.1.1 61297 1l7yA 94 1.82e+01 d.15.1.6 73676 1b8aA 438 1.84e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1s9aA 257 1.85e+01 b.3.6.1 105379 1ksyA 154 1.89e+01 d.89.1.2 72948 1vqoD 177 1.89e+01 2a8lA 420 1.97e+01 2bgzA 299 1.99e+01 2f1rA 171 2.00e+01 1xk5A 204 2.02e+01 1t3qB 788 2.04e+01 d.41.1.1,d.133.1.1 106369,106370 1muhA 481 2.04e+01 c.55.3.4 79485 1ecl 597 2.07e+01 1ecl e.10.1.1 43238 2fe7A 166 2.09e+01 2affA 120 2.11e+01 1hcz 252 2.13e+01 1hcz b.2.6.1,b.84.2.2 22464,28250 2d4pA 141 2.17e+01 1clqA 903 2.17e+01 1clqA c.55.3.5,e.8.1.1 33717,43006 1ypcI 64 2.18e+01 2sniI d.40.1.1 38570 1pwaA 162 2.20e+01 b.42.1.1 95211 1zyeA 220 2.27e+01 1rm6A 769 2.27e+01 2bs3A 656 2.30e+01 2atrA 138 2.30e+01 1zejA 293 2.30e+01 1plr 258 2.38e+01 1plq d.131.1.2,d.131.1.2 41390,41391 1vl7A 157 2.38e+01 b.45.1.1 108732 2a10A 125 2.40e+01 1wpgA 994 2.40e+01 1qo0D 196 2.44e+01 1qo0D c.23.1.3 31125 1jobA 162 2.61e+01 1f35A b.94.1.1 63207 2bkkA 264 2.61e+01 1iyu 79 2.62e+01 1iyu b.84.1.1 28227 1rypL 212 2.67e+01 d.153.1.4 41880 1ex2A 189 2.69e+01 1ex2A c.51.4.2 33225 1pt1A 143 2.71e+01 b.52.2.1 95084 1mw9X 592 2.73e+01 e.10.1.1 91480 1smxA 96 2.74e+01 b.40.4.5 105772 1p27B 106 2.79e+01 d.58.7.1 93908 1o3yA 166 2.80e+01 c.37.1.8 86618 1t6t1 118 2.82e+01 1qmvA 197 2.88e+01 1qq2A c.47.1.10 33066 1tiqA 180 2.95e+01 d.108.1.1 107010 1d6mA 653 2.98e+01 1d6mA e.10.1.1 43248 1r8sA 164 3.01e+01 c.37.1.8 97247 2f4wA 187 3.08e+01 1a8y 367 3.09e+01 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 1rxwA 336 3.10e+01 a.60.7.1,c.120.1.2 98059,98060 1cq3A 233 3.15e+01 1cq3A b.27.1.1 23923 1l0wA 580 3.17e+01 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1amx 180 3.17e+01 1amx b.2.3.1 22410 2bkfA 87 3.19e+01 1cy9A 264 3.23e+01 1ecl e.10.1.1 43236 1nqjA 119 3.29e+01 b.23.2.1 86031 1mit 69 3.32e+01 1hymA d.40.1.1 38582 2f1lA 187 3.34e+01 1uc7A 125 3.41e+01 c.47.1.1 99163 1p4fA 293 3.44e+01 d.144.1.7 104063 1a62 130 3.45e+01 1a62 a.140.3.1,b.40.4.5 64708,64709 1m1sA 116 3.47e+01 b.1.11.2 84747 1fqtA 112 3.47e+01 1fqtA b.33.1.1 24441 1kppA 145 3.50e+01 d.20.1.2 72846 1svr 114 3.52e+01 1svy d.109.1.1 40833 1lci 550 3.52e+01 1lci e.23.1.1 43349 1th7A 81 3.62e+01 1tllA 688 3.63e+01 b.43.4.1,c.23.5.2,c.25.1.4 107128,107129,107130 1wd5A 208 3.64e+01 2ganA 190 3.64e+01 1sc6A 404 3.65e+01 1iz5A 249 3.69e+01 d.131.1.2,d.131.1.2 83834,83835 1q5qA 259 3.73e+01 d.153.1.4 95904 1hl6A 165 3.75e+01 d.58.7.1 83609 1a4rA 191 3.81e+01 1ctqA c.37.1.8 32063 1aba 87 3.83e+01 1aba c.47.1.1 32760 1io1A 398 3.84e+01 1io1A e.32.1.1 62611 1euwA 152 3.84e+01 1dupA b.85.4.1 28349 1lngA 87 3.89e+01 d.201.1.1 74045 1jj2L 194 3.89e+01 1ffkI d.12.1.2 63097 2fywA 267 3.92e+01 1nepA 130 3.97e+01 b.1.18.7 80440 1srrA 124 3.98e+01 1dz3A c.23.1.1 31110 1z96A 40 3.98e+01 1c9oA 66 3.98e+01 1mjc b.40.4.5 25325 7reqB 637 4.03e+01 1reqB c.1.19.1,c.23.6.1 29617,31244 1yvkA 163 4.04e+01 1uzcA 71 4.08e+01 a.159.2.1 100222 1aj6 219 4.11e+01 1aj6 d.122.1.2 41106 1jalA 363 4.11e+01 c.37.1.8,d.15.10.2 84138,84139 1pvmA 184 4.18e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1reqD 637 4.19e+01 1reqB c.1.19.1,c.23.6.1 29623,31250 1k4mA 213 4.19e+01 c.26.1.3 77258 1ionA 243 4.21e+01 c.37.1.10 62633 1dupA 152 4.22e+01 1dupA b.85.4.1 28351 1ipiA 123 4.22e+01 c.52.1.18 66255 1jjiA 311 4.22e+01 c.69.1.2 66766 1y96A 86 4.26e+01 1a6q 382 4.27e+01 1a6q a.159.1.1,d.219.1.1 75801,75802 1zo0A 126 4.29e+01 1bcsB 160 4.31e+01 1whtB 2cy2A 174 4.35e+01 1avaC 181 4.36e+01 1avaC b.42.4.1 25604 1s72M 194 4.36e+01 d.12.1.2 105332 1zhvA 134 4.37e+01 1ge8A 249 4.37e+01 1plq d.131.1.2,d.131.1.2 41398,41399 1um0A 365 4.44e+01 d.258.1.1 107942 1ufhA 180 4.45e+01 d.108.1.1 88485 1n0qA 93 4.47e+01 k.37.1.1 79754 1dwmA 70 4.47e+01 1hymA d.40.1.1 38583 1yaiA 151 4.53e+01 1yaiA b.1.8.1 22289 1az3A 244 4.54e+01 1rvaA c.52.1.2 33276 1xwwA 157 4.55e+01 1ugmA 125 4.61e+01 d.15.1.3 107827 1vqoM 195 4.65e+01 1pqhA 143 4.68e+01 b.52.2.1 95017 2pcfB 250 4.71e+01 1hcz i.4.1.1 45911 1vr9A 213 4.72e+01 2g3aA 152 4.73e+01 1jc4A 148 4.74e+01 1jc4A d.32.1.4 62863 2mev1 277 4.77e+01 2mev1 1eso 154 4.81e+01 1yaiA b.1.8.1 22293 1qsmA 152 4.81e+01 1qsmA d.108.1.1 40808 1udzA 182 4.85e+01 b.51.1.1 99239 1cruA 454 4.87e+01 1c9uA b.68.2.1 27617 1cjxA 357 4.88e+01 1cjxA d.32.1.3,d.32.1.3 38516,38517 1u07A 90 4.90e+01 1g5tA 196 4.90e+01 1g5rA c.37.1.11 32366 1zckA 154 4.92e+01 1mvoA 136 4.92e+01 c.23.1.1 79513 1zclA 180 4.93e+01 1j0fA 100 4.97e+01 c.47.1.14 90739 1xv2A 237 4.97e+01 2fe8A 315 5.04e+01 1i7fA 292 5.04e+01 1i7fA d.193.1.1 61888 1dg9A 157 5.04e+01 1dg9A c.44.1.1 32637 1l1dA 152 5.07e+01 b.88.1.3 73452 1avv 151 5.08e+01 1efnB d.102.1.1 40703 1evlA 401 5.09e+01 1qf6A c.51.1.1,d.104.1.1 33202,40751 1vekA 84 5.09e+01 1qlaB 239 5.15e+01 1qlaB a.1.2.1,d.15.4.2 15679,37707 1j24A 143 5.17e+01 c.52.1.20 84008 1qbiA 454 5.19e+01 1c9uA b.68.2.1 27619 1tlk 154 5.23e+01 1tlk b.1.1.4 21707 2dvh 79 5.25e+01 1c53 a.3.1.1 15803 1phr 157 5.28e+01 1dg9A c.44.1.1 32635 1f2tA 149 5.31e+01 1f2tA c.37.1.12 32373 1fo0A 116 5.34e+01 1tvdA b.1.1.1 20610 1vi4A 174 5.34e+01 c.8.7.1 100731 2ew8A 249 5.36e+01 1l0bA 229 5.37e+01 c.15.1.3,c.15.1.3 73391,73392 1musA 477 5.38e+01 c.55.3.4 79494 1b96A 244 5.38e+01 1rvaA c.52.1.2 33268 1ad3A 452 5.39e+01 1ad3A c.82.1.1 35335 1dvh 79 5.40e+01 1c53 a.3.1.1 15802 1v5tA 90 5.42e+01 d.15.1.1 108385 1yr2A 741 5.45e+01 1f35A 162 5.47e+01 1f35A b.94.1.1 59628 1ze3H 122 5.51e+01 2mysC 149 5.51e+01 1wdcC a.39.1.5 17323 1wwkA 307 5.53e+01 2gpr 154 5.54e+01 1gpr b.84.3.1 28269 1g2hA 61 5.56e+01 1g2hA a.4.1.12 60224 1jnyA 435 5.57e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 5p21 166 5.58e+01 1ctqA c.37.1.8 31966 1ccwB 483 5.64e+01 1cb7B c.1.19.2 29646 1ti6A 875 5.65e+01 b.52.2.2,c.81.1.1 106974,106975 2ex4A 241 5.70e+01 1gnuA 117 5.71e+01 d.15.1.3 65403 1c0eA 157 5.74e+01 1dg9A c.44.1.1 32638 2gcuA 245 5.80e+01 1oxsC 353 5.81e+01 b.40.6.3,c.37.1.12 87519,87520 1rwzA 245 5.82e+01 d.131.1.2,d.131.1.2 98005,98006 1hkfA 122 5.85e+01 b.1.1.1 83553 1f3iA 481 5.85e+01 1b7eA 1uqvA 85 5.86e+01 a.60.1.2 99798 1ha1 184 5.86e+01 1ha1 d.58.7.1,d.58.7.1 39147,39148 1eerB 227 5.88e+01 1eerB b.1.2.1,b.1.2.1 22011,22012 1yg9A 330 5.90e+01 1g8sA 230 5.96e+01 c.66.1.3 90507 1j7lA 264 5.99e+01 d.144.1.6 62697 1qlaA 656 6.00e+01 1qlaA a.7.3.1,c.3.1.4,d.168.1.1 16328,30427,42310 1whsB 153 6.03e+01 1whtB 1rhfA 182 6.07e+01 b.1.1.1,b.1.1.4 97469,97470 1np6A 174 6.07e+01 c.37.1.10 85954 1qcsA 211 6.10e+01 1qcsA b.52.2.3,d.31.1.1 26927,38461 2bngA 149 6.11e+01 1kshA 186 6.12e+01 c.37.1.8 72914 2apsA 162 6.13e+01 1yaiA b.1.8.1 22298 2coqA 108 6.18e+01 1wvqA 167 6.20e+01 1i81A 83 6.24e+01 1d3bB b.38.1.1 61930 1j7iA 264 6.26e+01 1j7iA d.144.1.6 62694 1wvhA 134 6.27e+01 2ak4D 211 6.31e+01 1gvp 87 6.31e+01 1gvp b.40.4.7 25369 1o7iA 119 6.41e+01 b.40.4.3 86642 1d1nA 99 6.42e+01 1d1nA b.43.3.1 25718 1swuA 127 6.44e+01 1swuA b.61.1.1 27230 1yghA 164 6.46e+01 1yghA d.108.1.1 40802 1qy5A 269 6.51e+01 d.122.1.1 96573 1rsy 152 6.51e+01 1rsy 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