# List of top-scoring protein chains for t04-100-40-40-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 1z9lA 128 3.32e-01 1qwtA 255 5.36e-01 b.26.1.3 96501 1udxA 416 7.05e-01 b.117.1.1,c.37.1.8,d.242.1.1 99228,99229,99230 1on0A 158 1.40e+00 d.108.1.1 87095 1ifqA 138 1.74e+00 1ifqA d.110.4.1 62350 1kaeA 434 1.92e+00 c.82.1.2 72247 1bymA 97 2.19e+00 1bi0 b.34.1.2 24458 1bywA 110 2.48e+00 1bywA d.110.3.6 40912 1rw2A 152 2.66e+00 a.118.19.1 97961 1xeeA 91 2.70e+00 1x47A 98 2.83e+00 1xaoA 121 3.22e+00 2a9mH 126 3.24e+00 1gg4A 452 3.39e+00 1gg4A c.59.1.1,c.98.1.1,c.72.2.1 33957,58985,58986 1onqA 283 4.22e+00 b.1.1.2,d.19.1.1 93365,93366 1k3yA 221 4.84e+00 a.45.1.1,c.47.1.5 77245,77246 1k4nA 192 5.47e+00 d.32.1.5 72059 3hhrB 203 5.70e+00 1axiB b.1.2.1,b.1.2.1 22005,22006 2aabH 243 5.74e+00 2adgB 222 5.81e+00 1rypB 250 6.03e+00 1rypB d.153.1.4 41933 1ze3D 125 6.19e+00 1vpkA 378 6.45e+00 1tjgH 237 6.56e+00 1yb3A 175 6.78e+00 2cxaA 256 7.15e+00 1vkcA 158 7.51e+00 1msk 331 7.53e+00 1msk d.173.1.1 42495 8fabB 224 7.65e+00 1igtB b.1.1.1,b.1.1.2 19773,20883 1f3aA 222 8.78e+00 1pgtA a.45.1.1,c.47.1.5 17701,32995 1nrgA 261 9.44e+00 b.45.1.1 80694 1x4rA 99 9.95e+00 2gaiA 633 1.01e+01 1hilB 220 1.02e+01 1igtB b.1.1.1,b.1.1.2 19787,20897 1x0oA 119 1.04e+01 1zcjA 463 1.05e+01 1ho8A 480 1.07e+01 1ho8A a.118.1.9 61107 1r77A 103 1.13e+01 3daaA 277 1.13e+01 1daaA e.17.1.1 43272 1yk3A 210 1.16e+01 1tiqA 180 1.17e+01 d.108.1.1 107010 1rlmA 271 1.18e+01 1dykA 394 1.19e+01 1dykA b.29.1.4,b.29.1.4 24223,24224 1go4E 100 1.21e+01 h.1.22.1 70296 1u20A 212 1.25e+01 1ujrA 110 1.25e+01 1lzlA 323 1.25e+01 c.69.1.2 78306 1ze3H 122 1.26e+01 1g79A 218 1.28e+01 1ci0A b.45.1.1 25752 1j1xH 114 1.28e+01 b.1.1.1 77063 1wcuA 153 1.31e+01 1xygD 359 1.37e+01 2a9nH 126 1.40e+01 1rybA 212 1.41e+01 c.56.3.1 98098 1lqtA 456 1.41e+01 c.3.1.1,c.4.1.1 74198,74199 2af6A 258 1.44e+01 1k3bA 119 1.47e+01 b.61.5.1 72016 1uacH 114 1.50e+01 b.1.1.1 99132 2bjfA 329 1.54e+01 1rylA 167 1.58e+01 d.276.1.1 105124 1x1mA 107 1.60e+01 1aquA 297 1.62e+01 1aquA c.37.1.5 31942 1x6oA 174 1.64e+01 b.34.5.2,b.40.4.5 109493,109494 1y75A 118 1.69e+01 2c4jA 218 1.75e+01 1suwA 249 1.76e+01 e.52.1.1 106027 1wguA 136 1.77e+01 1rgxA 114 1.77e+01 g.77.1.1 104932 2b8eA 273 1.77e+01 1zvhA 134 1.81e+01 1z0sA 278 1.87e+01 1nslA 184 1.88e+01 d.108.1.1 86137 1s3zA 165 1.95e+01 d.108.1.1 105250 1wgoA 123 1.95e+01 1nt2A 210 1.98e+01 c.66.1.3 86149 1l3lA 234 2.01e+01 a.4.6.2,d.110.5.1 73541,73542 1g3mA 294 2.02e+01 c.37.1.5 83268 1vd3A 217 2.04e+01 1t0yA 122 2.06e+01 d.15.1.1 99066 1xw5A 217 2.07e+01 1n0lA 224 2.15e+01 b.1.11.1,b.7.2.1 79744,79745 1zkcA 197 2.19e+01 1oktA 211 2.22e+01 a.45.1.1,c.47.1.5 93272,93273 1z5lA 285 2.24e+01 1uu1A 335 2.25e+01 c.67.1.1 99993 1otgA 125 2.28e+01 1otgA d.80.1.2 39831 1r4xA 275 2.28e+01 b.1.10.3,d.105.1.2 97054,97055 1vj1A 363 2.33e+01 b.35.1.2,c.2.1.1 100794,100795 1tf9A 284 2.34e+01 1mqkH 127 2.34e+01 b.1.1.1 85053 1z4rA 168 2.37e+01 1rtqA 299 2.37e+01 c.56.5.4 97819 1rypC 244 2.37e+01 1rypC d.153.1.4 41934 2bpsA 81 2.37e+01 1vf1A 229 2.42e+01 1jguH 217 2.46e+01 b.1.1.1,b.1.1.2 66688,66689 1s6bA 119 2.46e+01 a.133.1.2 98592 1rloA 271 2.52e+01 2hrvA 142 2.56e+01 2hrvA b.47.1.4 26429 1gpl 432 2.57e+01 1gpl b.12.1.2,c.69.1.19 23645,34793 1hyxH 224 2.58e+01 1igtB b.1.1.1,b.1.1.2 20167,21191 1tkjA 284 2.61e+01 1oejA 193 2.64e+01 b.60.1.4 92798 1aboA 62 2.65e+01 1bbzA b.34.2.1 24474 1v32A 101 2.66e+01 a.42.1.1 100277 1s72N 187 2.70e+01 c.55.4.1 105333 1wr2A 238 2.71e+01 1ctqA 166 2.78e+01 1ctqA c.37.1.8 31965 1e3dB 542 2.87e+01 1h2rL e.18.1.1 59189 1t0tV 248 2.88e+01 d.58.4.10 106229 2ajuH 219 2.91e+01 2bh1A 250 2.94e+01 1u0tA 307 2.98e+01 e.52.1.1 107567 1mkyA 439 2.98e+01 c.37.1.8,c.37.1.8,d.52.5.1 79250,79251,79252 1bbzA 58 2.99e+01 1bbzA b.34.2.1 24477 6gsvA 217 2.99e+01 1b8xA a.45.1.1,c.47.1.5 17633,32925 2a6tA 271 2.99e+01 1xmbA 418 3.00e+01 1fsgA 233 3.00e+01 1qk3A c.61.1.1 34029 1dazC 99 3.03e+01 1hvc b.50.1.1 26501 1rowA 109 3.03e+01 b.1.11.2 97676 1t9mA 214 3.04e+01 1a2yB 116 3.11e+01 1gc1H b.1.1.1 19927 2g39A 497 3.12e+01 1ugjA 141 3.13e+01 b.41.1.3 107826 1jmtA 104 3.15e+01 d.58.7.3 63180 1difA 99 3.15e+01 1fmb b.50.1.1 26503 2msbA 115 3.18e+01 1rtm1 d.169.1.1 42355 1lfpA 249 3.20e+01 e.39.1.1 73885 1l7aA 318 3.35e+01 c.69.1.25 77772 1lj2A 110 3.41e+01 h.1.13.2 73926 1wwbX 103 3.45e+01 1wwcA b.1.1.4 21777 1xsnA 335 3.51e+01 2akrA 285 3.54e+01 1squA 155 3.54e+01 d.252.1.1 98971 1ncwH 222 3.56e+01 b.1.1.1,b.1.1.2 85555,85556 2ge3A 170 3.60e+01 1x82A 190 3.62e+01 2fckA 181 3.63e+01 1gkmA 509 3.64e+01 a.127.1.2 70228 1yf5L 254 3.68e+01 1nh0A 99 3.69e+01 b.50.1.1 91869 1i8kB 124 3.69e+01 b.1.1.1 71131 1uvqA 197 3.72e+01 b.1.1.2,d.19.1.1 100062,100063 1u5kA 244 3.75e+01 1dnlA 199 3.89e+01 1ci0A b.45.1.1 25753 1jyaA 130 3.90e+01 d.198.1.1 67453 1p57B 255 4.00e+01 b.47.1.2 94126 2fbyA 205 4.01e+01 1z8gA 372 4.02e+01 1w36C 1122 4.02e+01 1tu7A 208 4.05e+01 1txlA 215 4.10e+01 b.60.1.4 107429 1s0uA 408 4.10e+01 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 1io7A 368 4.12e+01 1f4tA a.104.1.1 18971 1lam 484 4.13e+01 1lam c.50.1.1,c.56.5.3 33166,33829 1b5eA 246 4.21e+01 1b5eA d.117.1.1 41056 1oaqH 121 4.21e+01 b.1.1.1 92707 1qhqA 140 4.21e+01 1qhqA b.6.1.1 63326 1kzkA 99 4.22e+01 b.50.1.1 73371 1g7jB 116 4.22e+01 1f3rB b.1.1.1 19933 1qq9A 284 4.26e+01 1xjo c.56.5.4 33841 1a5t 334 4.30e+01 1a5t a.80.1.1,c.37.1.20 18450,32423 1wgrA 100 4.32e+01 1wurA 220 4.35e+01 1mvuB 121 4.36e+01 b.1.1.1 91475 2g3aA 152 4.40e+01 2aawA 222 4.40e+01 1y75B 118 4.42e+01 1qxrA 189 4.49e+01 b.82.1.7 96552 1q0xH 221 4.51e+01 b.1.1.1,b.1.1.2 95517,95518 1rzfH 235 4.51e+01 b.1.1.1,b.1.1.2 98150,98151 1iruK 201 4.56e+01 d.153.1.4 71362 1u69A 163 4.63e+01 d.32.1.7 107699 1rdr 461 4.67e+01 1rdr e.8.1.4 43116 2bmeA 186 4.74e+01 1h5bA 113 4.84e+01 1tvdA b.1.1.1 60638 1dlfH 124 4.95e+01 1igtB b.1.1.1 20383 1t3uA 104 4.96e+01 d.244.1.1 99120 1alu 186 5.04e+01 1alu a.26.1.1 16826 1zx5A 300 5.07e+01 1zanH 224 5.07e+01 1y4oA 104 5.09e+01 1qpoA 284 5.11e+01 1qpoA c.1.17.1,d.41.2.1 29561,38597 1m70A 190 5.15e+01 a.3.1.4,a.3.1.4 91200,91201 1bylA 125 5.20e+01 1bylA d.32.1.2 38495 2asfA 137 5.29e+01 1p2fA 220 5.34e+01 a.4.6.1,c.23.1.1 87720,87721 1pz4A 116 5.35e+01 d.106.1.1 95400 1b8fA 509 5.38e+01 1b8fA a.127.1.2 19434 1t2jA 116 5.44e+01 1fc6A 388 5.44e+01 1fc6A b.36.1.3,c.14.1.2 64738,64739 1vqoZ 83 5.50e+01 1pd21 199 5.52e+01 1pd21 1b4pA 217 5.55e+01 a.45.1.1,c.47.1.5 83158,83159 1qi7A 253 5.55e+01 1qi7A d.165.1.1 42210 1f08A 148 5.59e+01 1f08A d.89.1.2 59564 1v54B 227 5.63e+01 b.6.1.2,f.17.2.1 100322,100323 1cbs 137 5.67e+01 1hmt b.60.1.2 27201 1iyeA 309 5.68e+01 e.17.1.1 83786 1q7lA 198 5.70e+01 c.56.5.4 96044 1uspA 139 5.71e+01 d.227.1.1 99879 1tyjA 170 5.77e+01 1he7A 126 5.78e+01 1wwcA b.1.1.4 60970 1tw7A 99 5.78e+01 1m0uA 249 5.81e+01 a.45.1.1,c.47.1.5 78359,78360 1qo7A 394 5.87e+01 1qo7A c.69.1.11 34697 1a6wH 120 5.90e+01 1mfa b.1.1.1 20253 1wwpA 119 5.93e+01 1mg4A 113 5.93e+01 d.15.11.1 84953 1j05B 121 5.93e+01 b.1.1.1 90736 1dqqB 210 5.95e+01 1igtB b.1.1.1,b.1.1.2 20421,21391 1j6rA 214 5.99e+01 d.173.1.2 71598 1gowA 489 6.03e+01 1qvbA c.1.8.4 28981 1mkfA 382 6.09e+01 b.116.1.1 79232 2c0cA 362 6.11e+01 1gz2A 142 6.12e+01 d.169.1.1 83392 1mslA 109 6.15e+01 1mslA f.16.1.1 43660 1orvA 728 6.17e+01 b.70.3.1,c.69.1.24 87354,87355 2aheA 267 6.17e+01 1y6hA 177 6.21e+01 1mkp 144 6.26e+01 1vhrA c.45.1.1 32654 1jj2M 186 6.32e+01 1ffkK c.55.4.1 63098 2gqrA 237 6.37e+01 1p5vA 235 6.41e+01 b.1.11.1,b.7.2.1 87812,87813 1fzoA 274 6.42e+01 1agdA b.1.1.2,d.19.1.1 60155,60156 1yarA 233 6.45e+01 1y74A 57 6.53e+01 1ol0A 121 6.53e+01 b.1.1.1 93296 1p9eA 331 6.55e+01 d.157.1.5 104088 1x31D 99 6.57e+01 1gjwA 637 6.57e+01 b.71.1.1,c.1.8.1 60582,60583 2bl9A 238 6.61e+01 1vqoN 187 6.61e+01 1iyhA 198 6.65e+01 a.45.1.1,c.47.1.5 83790,83791 1g55A 343 6.65e+01 1g55A c.66.1.26 34247 2gmyA 153 6.66e+01 1oe8A 211 6.71e+01 a.45.1.1,c.47.1.5 86905,86906 1zr5A 214 6.75e+01 2b4vA 468 6.79e+01 1ejxB 101 6.82e+01 b.85.3.1 83183 1g5tA 196 6.93e+01 1g5rA c.37.1.11 32366 2fji1 399 7.02e+01 1spvA 184 7.02e+01 c.50.1.2 98957 1r5iD 216 7.03e+01 a.202.1.1 97091 1r8sA 164 7.06e+01 c.37.1.8 97247 1wucA 250 7.07e+01 1xzpB 150 7.07e+01 1xrkA 124 7.07e+01 1qh3A 260 7.09e+01 1qh5A d.157.1.2 42059 1s72Z 73 7.13e+01 g.41.8.1 105345 1trb 320 7.20e+01 1trb c.3.1.5,c.3.1.5 30529,30530 1mfa 247 7.20e+01 1mfa b.1.1.1,b.1.1.1 19888,19889 1gheA 177 7.26e+01 d.108.1.1 76222 1qh5A 260 7.29e+01 1qh5A d.157.1.2 42057 1k2xA 177 7.33e+01 d.153.1.5 90929 1dyoA 160 7.42e+01 1dyoA b.18.1.7 23771 1go4A 205 7.62e+01 d.135.1.1 70292 1y08A 323 7.66e+01 1vmfA 145 7.67e+01 1axiB 236 7.76e+01 1axiB b.1.2.1,b.1.2.1 21997,21998 1kutA 230 7.77e+01 d.143.1.1 73017 1qqhA 144 7.81e+01 1dtoA b.91.1.1 28404 1xjo 284 7.81e+01 1xjo c.56.5.4 33843 1rw1A 114 7.87e+01 1jhjA 171 7.89e+01 b.18.1.9 66714 1yn4A 99 7.89e+01 2cvdA 198 7.90e+01 1pvl 301 8.02e+01 1pvl f.6.1.1 43819 2mspA 126 8.03e+01 1mspA b.1.11.2 22335 1rklA 36 8.10e+01 f.23.30.1 97615 1t5eA 360 8.14e+01 f.46.1.1 106436 1d3vA 323 8.16e+01 1d3vA c.42.1.1 32559 2pviA 157 8.18e+01 3pviA c.52.1.6 33302 1xwtA 405 8.24e+01 2fikA 287 8.28e+01 1amy 403 8.34e+01 1jdc b.71.1.1,c.1.8.1 27799,28786 1g5aA 628 8.42e+01 b.71.1.1,c.1.8.1 65152,65153 2ex0A 399 8.48e+01 1sffA 426 8.68e+01 c.67.1.4 105482 1t8sA 484 8.68e+01 c.56.2.1 106679 1bmtA 246 8.69e+01 1bmtA a.46.1.1,c.23.6.1 17757,31235 1mnaA 298 8.74e+01 c.69.1.22 79322 1xw2A 405 8.78e+01 2bhgA 209 8.79e+01 1nfkA 325 8.80e+01 1a3qA b.1.18.1,b.2.5.3 21929,22444 2aebA 322 8.81e+01 1stfI 98 8.95e+01 1stfI d.17.1.2 38006 1xfpA 142 8.97e+01 b.1.1.1 109587