# List of top-scoring protein chains for t2k-80-60-80-str2+near-backbone-11-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 1g9oA 91 7.42e-13 1pdr b.36.1.1 60400 1i92A 91 2.20e-12 1pdr b.36.1.1 61990 2fe5A 94 2.60e-12 1bfeA 119 5.21e-12 1pdr b.36.1.1 24775 1tp5A 119 7.67e-12 1be9A 119 1.22e-11 1pdr b.36.1.1 24774 1mfgA 95 1.51e-11 b.36.1.1 79043 1q3oA 109 1.90e-11 b.36.1.1 95700 2fcfA 103 2.03e-11 1n7eA 97 2.23e-11 b.36.1.1 91691 1n7fA 97 2.34e-11 b.36.1.1 91692 1qavA 90 3.23e-11 1qauA b.36.1.1 24777 1ihjA 98 4.02e-11 1pdr b.36.1.1 62382 1pdr 99 5.30e-11 1pdr b.36.1.1 24771 2f5yA 91 3.12e-10 1n99A 166 3.41e-10 b.36.1.1,b.36.1.1 85459,85460 1kwaA 88 3.71e-10 1kwaA b.36.1.1 24772 1kwaB 88 6.03e-10 1kwaA b.36.1.1 24773 1l6oA 95 7.95e-10 b.36.1.1 84534 1m5zA 91 1.56e-09 b.36.1.1 78676 1nf3C 128 1.62e-09 b.36.1.1 85596 2f0aA 98 2.15e-09 1qavB 115 2.82e-09 1qauA b.36.1.1 24780 1nteA 82 3.29e-09 b.36.1.1 86163 1qauA 112 4.73e-09 1qauA b.36.1.1 24779 1wf7A 103 6.53e-09 1r6jA 82 6.88e-09 b.36.1.1 97151 1i16 130 8.26e-09 1i16 b.36.1.2 24787 1b8qA 127 3.59e-08 1qauA b.36.1.1 24781 1v5lA 103 9.70e-08 b.36.1.1 108378 1fc6A 388 1.75e-06 1fc6A b.36.1.3,c.14.1.2 64738,64739 1lcyA 325 3.93e-05 b.36.1.4,b.47.1.1 73834,73835 1te0A 318 2.14e-04 1y8tA 324 3.40e-03 1ky9B 448 9.14e-02 b.36.1.4,b.36.1.4,b.47.1.1 73200,73201,73202 1fxlA 167 2.56e-01 1b7fA d.58.7.1,d.58.7.1 39183,39184 1zh1A 163 3.46e-01 1svy 114 4.08e-01 1svy d.109.1.1 40831 1s3zA 165 4.92e-01 d.108.1.1 105250 1db3A 372 5.74e-01 1db3A c.2.1.2 29813 1y7rA 133 6.87e-01 1y9kA 157 9.07e-01 2c5qA 240 9.61e-01 1vkcA 158 1.19e+00 1cq3A 233 1.29e+00 1cq3A b.27.1.1 23923 1vkbA 161 1.82e+00 d.269.1.1 108643 1yvkA 163 1.89e+00 1lh0A 213 1.99e+00 c.61.1.1 73896 1stmA 157 2.24e+00 1stmA b.121.7.1 23281 2d4pA 141 2.32e+00 1tiqA 180 2.35e+00 d.108.1.1 107010 1nm1G 125 2.71e+00 d.109.1.1 80653 1xewX 182 2.89e+00 1kzlA 208 2.96e+00 b.43.4.3,b.43.4.3 77635,77636 1bo4B 168 2.97e+00 1bo4A d.108.1.1 40799 1f2tA 149 2.98e+00 1f2tA c.37.1.12 32373 1lw6I 64 3.21e+00 d.40.1.1 74294 1opr 213 3.44e+00 1opr c.61.1.1 34091 1wlgA 299 3.52e+00 1yagG 125 3.54e+00 1d0nA d.109.1.1 40846 2fvgA 340 3.67e+00 1o12A 376 3.93e+00 b.92.1.5,c.1.9.10 80758,80759 3sxlA 184 3.93e+00 1b7fA d.58.7.1,d.58.7.1 39173,39174 1xebA 150 4.20e+00 2fl4A 149 4.30e+00 1azsC 388 4.30e+00 1cipA a.66.1.1,c.37.1.8 18203,32086 1i4uA 181 4.32e+00 b.60.1.1 61732 1khiA 176 4.38e+00 b.34.5.2,b.40.4.5 77408,77409 1to2I 64 4.41e+00 2ganA 190 4.45e+00 1us8A 147 4.70e+00 c.37.1.12 99859 1eulA 994 4.73e+00 1eulA 1rxxA 421 4.73e+00 d.126.1.4 98061 1d4xG 126 4.75e+00 1d0nA d.109.1.1 59109 2bgzA 299 4.86e+00 1ufhA 180 4.88e+00 d.108.1.1 88485 1vr7A 142 5.14e+00 1yjmA 110 5.22e+00 2bkfA 87 5.42e+00 1vheA 373 5.70e+00 b.49.3.1,c.56.5.4 100669,100670 2aexA 346 5.80e+00 1o3yA 166 6.30e+00 c.37.1.8 86618 1y9wA 140 6.33e+00 1xm8A 254 6.35e+00 1on0A 158 6.45e+00 d.108.1.1 87095 1cjxA 357 6.57e+00 1cjxA d.32.1.3,d.32.1.3 38516,38517 1fnhA 271 6.62e+00 1fnhA b.1.2.1,b.1.2.1,b.1.2.1 21976,21977,21978 2cxaA 256 6.73e+00 2cy2A 174 6.97e+00 1zn8A 180 7.09e+00 1quqA 129 7.27e+00 1quqA b.40.4.3 25303 2ewcA 126 7.34e+00 1ypcI 64 7.42e+00 2sniI d.40.1.1 38570 2f7fA 494 7.51e+00 2sniI 83 7.67e+00 2sniI d.40.1.1 38573 1coaI 64 7.79e+00 2sniI d.40.1.1 38574 1f20A 435 7.94e+00 b.43.4.1,c.25.1.4 64932,64933 1qyaA 307 7.97e+00 d.21.1.2,d.21.1.2 104653,104654 1qg3A 195 8.12e+00 1qg3A b.1.2.1,b.1.2.1 21993,21994 1g2qA 187 8.52e+00 c.61.1.1 65117 1ze3H 122 8.61e+00 2a10A 125 8.70e+00 1y0bA 197 8.95e+00 1su4A 994 8.95e+00 b.82.7.1,c.108.1.7,d.220.1.1,f.33.1.1 98993,98994,98995,98996 2gf9A 189 9.03e+00 1tllA 688 9.04e+00 b.43.4.1,c.23.5.2,c.25.1.4 107128,107129,107130 1np6A 174 9.12e+00 c.37.1.10 85954 1x3mA 415 9.18e+00 1cis 66 9.22e+00 2sniI k.1.1.1 46375 1gpr 162 9.25e+00 1gpr b.84.3.1 28267 1ciqA 40 9.40e+00 2sniI d.40.1.1 38576 1x6oA 174 9.46e+00 b.34.5.2,b.40.4.5 109493,109494 1l0wA 580 9.49e+00 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1k8mA 93 9.64e+00 b.84.1.1 68314 5p21 166 9.75e+00 1ctqA c.37.1.8 31966 7reqB 637 9.76e+00 1reqB c.1.19.1,c.23.6.1 29617,31244 1qw2A 102 9.81e+00 d.249.1.1 96456 1kcbA 340 9.83e+00 b.6.1.3,b.6.1.3 90951,90952 1tluA 130 9.87e+00 d.156.1.2 107139 1skyB 502 9.92e+00 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18313,26478,32358 1sdjA 310 9.94e+00 d.21.1.2,d.21.1.2 98807,98808 2bz1A 196 1.00e+01 1h70A 255 1.01e+01 1h70A d.126.1.3 60711 1s1qA 145 1.02e+01 d.20.1.2 98351 1h91A 180 1.02e+01 b.60.1.1 60805 2f4wA 187 1.05e+01 1xvaA 292 1.06e+01 1xvaA c.66.1.5 34183 2bw4A 340 1.08e+01 1svr 114 1.10e+01 1svy d.109.1.1 40833 3rabA 169 1.11e+01 1ctqA c.37.1.8 32018 1qhlA 227 1.11e+01 1qhlA c.37.1.12 32382 1reqD 637 1.12e+01 1reqB c.1.19.1,c.23.6.1 29623,31250 1f76A 336 1.12e+01 c.1.4.1 76160 2f1rA 171 1.13e+01 1rypH 205 1.13e+01 d.153.1.4 41876 1eujA 166 1.14e+01 1eujA b.40.4.4 25316 1bn7A 294 1.15e+01 1bn6A c.69.1.8 34677 2brfA 110 1.16e+01 1d2gA 292 1.16e+01 1xvaA c.66.1.5 34187 1b7fA 168 1.16e+01 1b7fA d.58.7.1,d.58.7.1 39169,39170 1bdfA 235 1.17e+01 1bdfA d.74.3.1,d.181.1.1 39727,42602 1oe1A 336 1.17e+01 b.6.1.3,b.6.1.3 86891,86892 1sotA 320 1.18e+01 b.36.1.4,b.47.1.1 105852,105853 1vekA 84 1.19e+01 1d5cA 162 1.19e+01 1ctqA c.37.1.8 32021 1g5tA 196 1.21e+01 1g5rA c.37.1.11 32366 2bijA 305 1.22e+01 2fe7A 166 1.22e+01 2g3aA 152 1.23e+01 1wwzA 159 1.23e+01 1qsmA 152 1.24e+01 1qsmA d.108.1.1 40808 1bo4A 168 1.25e+01 1bo4A d.108.1.1 40798 1j9qA 341 1.25e+01 1nif b.6.1.3,b.6.1.3 62765,62766 1qh3A 260 1.26e+01 1qh5A d.157.1.2 42059 1ih7A 903 1.27e+01 1clqA c.55.3.5,e.8.1.1 62375,62376 1l0bA 229 1.28e+01 c.15.1.3,c.15.1.3 73391,73392 1et7A 341 1.28e+01 1nif b.6.1.3,b.6.1.3 23070,23071 2breA 219 1.29e+01 1xfoA 357 1.29e+01 1u6rA 380 1.32e+01 1wpgA 994 1.32e+01 1cvjA 190 1.34e+01 1cvjB d.58.7.1,d.58.7.1 39191,39192 1xe1A 116 1.35e+01 b.43.3.1 109571 1r13A 148 1.39e+01 d.169.1.1,h.1.1.1 96782,96783 1wi0A 113 1.40e+01 1v8yA 170 1.40e+01 1bn6A 294 1.43e+01 1bn6A c.69.1.8 34678 1qstA 160 1.43e+01 1yghA d.108.1.1 40804 1oroA 213 1.45e+01 1opr c.61.1.1 34093 1svq 114 1.45e+01 1svy d.109.1.1 40832 1f00I 282 1.51e+01 1f00I b.1.14.1,b.1.14.1,d.169.1.3 22368,22369,42439 1oxsC 353 1.52e+01 b.40.6.3,c.37.1.12 87519,87520 1ikpA 613 1.52e+01 b.29.1.7,d.166.1.1,f.1.5.1 66182,66183,66184 1d0nA 729 1.54e+01 1d0nA d.109.1.1,d.109.1.1,d.109.1.1,d.109.1.1,d.109.1.1,d.109.1.1 40834,40835,40836,40837,40838,40839 1qh5A 260 1.54e+01 1qh5A d.157.1.2 42057 1q0rA 298 1.55e+01 c.69.1.28 95508 1reqB 637 1.56e+01 1reqB c.1.19.1,c.23.6.1 29621,31248 1a4rA 191 1.57e+01 1ctqA c.37.1.8 32063 1u4nA 310 1.58e+01 1si6X 282 1.58e+01 1brt 277 1.59e+01 1brt c.69.1.12 34699 1ag8A 499 1.60e+01 1bpwA c.82.1.1 35341 2b99A 156 1.61e+01 1ipiA 123 1.62e+01 c.52.1.18 66255 1grwA 126 1.62e+01 b.1.11.2 70391 1i1iP 681 1.63e+01 1i1iP d.92.1.5 40297 1fnmA 691 1.63e+01 1dar b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1,d.58.11.1 25709,32144,37546,39302,39303 1gheA 177 1.63e+01 d.108.1.1 76222 1mdbA 539 1.66e+01 e.23.1.1 79008 1xtqA 177 1.66e+01 1ky9A 448 1.66e+01 b.36.1.4,b.47.1.1 73198,73199 1s72L 165 1.67e+01 c.12.1.1 105331 1jj2K 164 1.68e+01 1ffkJ c.12.1.1 63096 1qb7A 236 1.70e+01 1qb7A c.61.1.1 34087 1broA 277 1.70e+01 1brt c.69.1.12 34700 1ggrA 168 1.72e+01 1gpr b.84.3.1 28279 1yd9A 193 1.73e+01 1f9zA 135 1.73e+01 1qipA d.32.1.1 38484 1vkyA 347 1.74e+01 e.53.1.1 108696 1nif 340 1.74e+01 1nif b.6.1.3,b.6.1.3 23048,23049 1mgtA 174 1.75e+01 1mgtA a.4.2.1,c.55.7.1 16078,33753 1mk4A 157 1.75e+01 d.108.1.1 84979 1fohA 664 1.78e+01 1fohA c.3.1.2,c.47.1.10,d.16.1.2 30381,33078,37900 1jqeA 292 1.78e+01 c.66.1.19 71789 1jj2D 176 1.80e+01 1ffkD d.77.1.1 63088 1ntfA 282 1.81e+01 d.151.1.2 92104 1e79A 510 1.84e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18269,26434,32314 2bhoA 130 1.84e+01 1qm4A 396 1.86e+01 1mxb d.130.1.1,d.130.1.1,d.130.1.1 41350,41351,41352 1ei1A 391 1.86e+01 1aj6 d.14.1.3,d.122.1.2 37570,41104 1ad3A 452 1.87e+01 1ad3A c.82.1.1 35335 2fsrA 195 1.87e+01 1qi6A 475 1.90e+01 1euhA c.82.1.1 35373 1iyu 79 1.93e+01 1iyu b.84.1.1 28227 1ifyA 49 1.93e+01 a.5.2.1 71207 1oxxK 353 1.94e+01 b.40.6.3,c.37.1.12 93715,93716 1pg4A 652 1.94e+01 e.23.1.1 88067 1kijA 390 1.94e+01 d.14.1.3,d.122.1.2 72514,72515 1uc7A 125 2.00e+01 c.47.1.1 99163 1ujxA 119 2.02e+01 b.26.1.2 99473 1vqoL 165 2.02e+01 1pk6C 129 2.02e+01 b.22.1.1 94803 2a5dA 175 2.04e+01 1i2mA 216 2.08e+01 1byuA c.37.1.8 61568 1y21A 282 2.10e+01 1knb 196 2.10e+01 1qhvA b.21.1.1 23841 1ixcA 294 2.10e+01 a.4.5.37,c.94.1.1 83764,83765 1xs1A 193 2.12e+01 1yghA 164 2.12e+01 1yghA d.108.1.1 40802 1dupA 152 2.13e+01 1dupA b.85.4.1 28351 1qsoA 149 2.13e+01 1qsmA d.108.1.1 40812 1acf 125 2.15e+01 3nul d.110.1.1 40882 1z5oA 242 2.16e+01 1rypJ 204 2.20e+01 d.153.1.4 41878 1aba 87 2.21e+01 1aba c.47.1.1 32760 1vj0A 380 2.25e+01 b.35.1.2,c.2.1.1 100786,100787 1kmqA 184 2.26e+01 c.37.1.8 84412 173l 164 2.27e+01 1l92 d.2.1.3 36728 1azwA 313 2.29e+01 1qtrA c.69.1.7 34658 1fhvA 323 2.30e+01 1fhuA c.1.11.2,d.54.1.1 29235,38879 1g5rA 196 2.31e+01 1g5rA c.37.1.11 32367 1vdmA 153 2.31e+01 1udc 338 2.32e+01 1xel c.2.1.2 29785 2mspA 126 2.32e+01 1mspA b.1.11.2 22335 1cvjB 190 2.32e+01 1cvjB d.58.7.1,d.58.7.1 39193,39194 1yagA 375 2.32e+01 1yagA c.55.1.1,c.55.1.1 33449,33450 1euhA 475 2.33e+01 1euhA c.82.1.1 35369 1zeqX 84 2.34e+01 1tif 78 2.35e+01 1tif d.15.8.1 37836 1xn9A 101 2.43e+01 1mqeA 207 2.45e+01 d.113.1.1 91394 1z4eA 153 2.47e+01 2bv5A 282 2.49e+01 1hkhA 279 2.50e+01 c.69.1.12 90628 1iwmA 186 2.52e+01 b.125.1.2 83758 2atvA 196 2.53e+01 1kvs 338 2.53e+01 1xel c.2.1.2 29799 1vrpA 381 2.54e+01 1a88A 275 2.54e+01 1brt c.69.1.12 34707 1cqwA 295 2.55e+01 1b6g c.69.1.8 34679 1a79A 171 2.56e+01 1a79A c.52.2.1,d.75.1.1 33340,39739 2bkkA 264 2.57e+01 1ne9A 335 2.58e+01 d.108.1.4,d.108.1.4 91839,91840 1qy5A 269 2.59e+01 d.122.1.1 96573 2b4aA 138 2.59e+01 1z4rA 168 2.59e+01 2d1eA 248 2.60e+01 1u07A 90 2.61e+01 1qp8A 303 2.61e+01 1qp8A c.2.1.4,c.23.12.1 30092,31352 1ppjB 439 2.62e+01 d.185.1.1,d.185.1.1 104254,104255 2b0vA 153 2.65e+01 1xmpA 170 2.66e+01 1xzzA 246 2.67e+01 1kw3B 292 2.68e+01 d.32.1.3,d.32.1.3 77549,77550 1fl0A 171 2.68e+01 1eujA b.40.4.4 25315 1l0lB 439 2.68e+01 d.185.1.1,d.185.1.1 84484,84485 1muhA 481 2.70e+01 c.55.3.4 79485 1k4mA 213 2.70e+01 c.26.1.3 77258 1n6eA 1071 2.70e+01 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 80149,80150,80151,80152 1xv5A 401 2.72e+01 1as8A 343 2.73e+01 1nif b.6.1.3,b.6.1.3 23074,23075 1j7iA 264 2.73e+01 1j7iA d.144.1.6 62694 1a9y 338 2.73e+01 1xel c.2.1.2 29789 1ao0A 459 2.73e+01 1ecfB c.61.1.1,d.153.1.1 34049,41816 1k7kA 221 2.77e+01 c.51.4.1 72104 1qh4A 380 2.77e+01 1qh4A a.83.1.1,d.128.1.2 18462,41197 1ecl 597 2.78e+01 1ecl e.10.1.1 43238 1zejA 293 2.78e+01 1huqA 164 2.79e+01 1byuA c.37.1.8 32020 1vpqA 273 2.80e+01 1g0uI 205 2.80e+01 d.153.1.4 41891 1h8eA 510 2.81e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 60738,60739,60740 2bsyA 278 2.81e+01 1crkA 380 2.82e+01 1qh4A a.83.1.1,d.128.1.2 18458,41193 2cokA 113 2.84e+01 1yprA 125 2.86e+01 3nul d.110.1.1 40888 2cw8A 537 2.88e+01 1euwA 152 2.89e+01 1dupA b.85.4.1 28349 1cliA 345 2.90e+01 1cliA d.79.4.1,d.139.1.1 39816,41459 1k3fA 253 2.94e+01 c.56.2.1 68105 1y0yA 353 2.94e+01 1bhjA 292 2.95e+01 1xvaA c.66.1.5 34189 1a62 130 2.97e+01 1a62 a.140.3.1,b.40.4.5 64708,64709 1iv0A 98 2.98e+01 c.55.3.8 90706 1aazA 87 2.99e+01 1aba c.47.1.1 32761 1gph1 465 2.99e+01 1ecfB 1lngA 87 3.01e+01 d.201.1.1 74045 1mw9X 592 3.01e+01 e.10.1.1 91480 1a63 130 3.02e+01 1a62 a.140.3.1,b.40.4.5 64710,64711 1r4aA 165 3.03e+01 c.37.1.8 96986 1vicA 262 3.04e+01 c.68.1.13 100756 1a8uA 277 3.05e+01 1brt c.69.1.12 34703 1q5qA 259 3.06e+01 d.153.1.4 95904 1p3dA 475 3.06e+01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 2a2pA 129 3.09e+01 1x84A 189 3.09e+01 2bshA 125 3.10e+01 1z2aA 168 3.12e+01 1na6A 404 3.14e+01 b.142.1.1,c.52.1.22 91748,91749 1prq 125 3.16e+01 3nul d.110.1.1 40883 1zkpA 268 3.17e+01 2gpr 154 3.22e+01 1gpr b.84.3.1 28269 1yoxA 250 3.22e+01 1vfaB 116 3.23e+01 1gc1H b.1.1.1 19929 1snrA 341 3.24e+01 b.6.1.3,b.6.1.3 105823,105824 1lci 550 3.24e+01 1lci e.23.1.1 43349 2atrA 138 3.25e+01 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