# List of top-scoring protein chains for t04-100-30-str2-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 4.90e-16 2fneA 117 1.01e-15 1tp5A 119 1.69e-15 1qavA 90 1.99e-15 1qauA b.36.1.1 24777 2fcfA 103 2.01e-15 1be9A 119 2.42e-15 1pdr b.36.1.1 24774 1g9oA 91 6.56e-15 1pdr b.36.1.1 60400 2h2bA 107 4.37e-14 1n7eA 97 4.55e-14 b.36.1.1 91691 1n7fA 97 1.12e-13 b.36.1.1 91692 1q3oA 109 1.14e-13 b.36.1.1 95700 1ihjA 98 1.69e-13 1pdr b.36.1.1 62382 1l6oA 95 2.20e-13 b.36.1.1 84534 1nf3C 128 5.38e-13 b.36.1.1 85596 2f0aA 98 7.93e-13 1mfgA 95 8.44e-13 b.36.1.1 79043 1kwaA 88 9.18e-13 1kwaA b.36.1.1 24772 2h3lA 103 9.50e-13 1qauA 112 2.57e-12 1qauA b.36.1.1 24779 1wf7A 103 5.87e-12 2f5yA 91 8.82e-12 1nteA 82 4.18e-11 b.36.1.1 86163 1v5lA 103 6.43e-11 b.36.1.1 108378 1r6jA 82 7.71e-11 b.36.1.1 97151 1fc6A 388 4.13e-07 1fc6A b.36.1.3,c.14.1.2 64738,64739 1lcyA 325 1.59e-06 b.36.1.4,b.47.1.1 73834,73835 1te0A 318 3.62e-06 1y8tA 324 1.39e-04 1sotA 320 9.88e-03 b.36.1.4,b.47.1.1 105852,105853 1zn8A 180 2.10e-01 1kk1A 410 6.58e-01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 2d4pA 141 6.63e-01 1xebA 150 1.12e+00 2bshA 125 1.18e+00 1fxlA 167 1.49e+00 1b7fA d.58.7.1,d.58.7.1 39183,39184 2bsjA 133 1.61e+00 1yezA 68 1.68e+00 2brfA 110 1.68e+00 2bhoA 130 1.76e+00 1se8A 301 2.06e+00 b.40.4.3 105448 1r13A 148 2.60e+00 d.169.1.1,h.1.1.1 96782,96783 1un8A 552 2.70e+00 c.119.1.2,a.208.1.1 103806,99661 1x3mA 415 2.82e+00 1yjmA 110 2.93e+00 2fe7A 166 3.12e+00 2bsyA 278 3.45e+00 2gwnA 452 3.74e+00 1h3gA 601 4.02e+00 b.1.18.2,b.71.1.1,c.1.8.1 90594,90595,90596 1o6dA 163 4.19e+00 c.116.1.3 92567 1y9wA 140 4.29e+00 1vj0A 380 4.48e+00 b.35.1.2,c.2.1.1 100786,100787 2f4wA 187 4.90e+00 2c5qA 240 4.98e+00 1ad3A 452 5.25e+00 1ad3A c.82.1.1 35335 1g57A 217 5.28e+00 1g57A d.115.1.2 60253 1htrB 329 5.31e+00 1smrA 2bh8A 101 5.51e+00 1yloA 348 5.85e+00 1t6t1 118 6.06e+00 1hh1A 143 6.20e+00 1gefA c.52.1.18 61036 1rutX 188 6.72e+00 1fr3A 67 7.07e+00 1fr3A b.40.6.1 25436 1y791 680 7.24e+00 1yg9A 330 8.01e+00 1cq3A 233 8.36e+00 1cq3A b.27.1.1 23923 2bs3A 656 8.90e+00 1a62 130 9.14e+00 1a62 a.140.3.1,b.40.4.5 64708,64709 1mkmA 249 9.17e+00 a.4.5.33,d.110.2.2 79242,79243 1yvcA 70 9.29e+00 1s0uA 408 9.43e+00 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 1qlaA 656 9.64e+00 1qlaA a.7.3.1,c.3.1.4,d.168.1.1 16328,30427,42310 1wwzA 159 1.03e+01 2cu5A 129 1.04e+01 2affA 120 1.08e+01 1qb7A 236 1.11e+01 1qb7A c.61.1.1 34087 1rl2A 137 1.11e+01 1rl2A b.34.5.3,b.40.4.5 24610,25342 1xdnA 277 1.14e+01 1g2qA 187 1.14e+01 c.61.1.1 65117 1ti6A 875 1.18e+01 b.52.2.2,c.81.1.1 106974,106975 2fvgA 340 1.19e+01 1uc2A 481 1.25e+01 d.261.1.1 99161 2a19A 175 1.25e+01 2adcA 229 1.28e+01 1avaC 181 1.29e+01 1avaC b.42.4.1 25604 1lw6I 64 1.34e+01 d.40.1.1 74294 1vkmA 297 1.36e+01 c.138.1.1 108670 1vqqA 646 1.42e+01 1a8vA 121 1.42e+01 1a62 a.140.3.1,b.40.4.5 64712,64713 2bw3A 534 1.49e+01 1qsmA 152 1.58e+01 1qsmA d.108.1.1 40808 1c9oA 66 1.64e+01 1mjc b.40.4.5 25325 1cliA 345 1.67e+01 1cliA d.79.4.1,d.139.1.1 39816,41459 2cwaA 263 1.71e+01 1hvyA 288 1.78e+01 1bkpA d.117.1.1 41049 1to2I 64 1.79e+01 1tr7A 164 1.85e+01 1w94A 156 1.87e+01 1zn6A 227 1.91e+01 1klfB 279 1.94e+01 b.2.3.2,b.2.3.2 72684,72685 2fxqA 264 1.95e+01 1uwfA 158 1.95e+01 1db3A 372 1.96e+01 1db3A c.2.1.2 29813 1eyqA 222 1.96e+01 1eypA d.36.1.1 38534 1s4iA 175 2.03e+01 1p7tA 731 2.07e+01 c.1.13.1 94319 1xtmA 175 2.10e+01 1a79A 171 2.11e+01 1a79A c.52.2.1,d.75.1.1 33340,39739 2apr 325 2.11e+01 2er7E b.50.1.2 26819 1ypcI 64 2.15e+01 2sniI d.40.1.1 38570 1qunB 279 2.18e+01 b.2.3.2,b.2.3.2 22411,22412 1g7sA 594 2.22e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 1xtlA 175 2.24e+01 1gztA 115 2.34e+01 b.115.1.1 76428 3aprE 325 2.40e+01 2er7E b.50.1.2 26820 1jnyA 435 2.43e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 2iu4A 336 2.44e+01 1jmuB 666 2.45e+01 1oxcA 114 2.46e+01 b.115.1.1 93683 2bnjA 303 2.48e+01 1rypB 250 2.49e+01 1rypB d.153.1.4 41933 1koe 172 2.50e+01 1koe d.169.1.5 42448 1ugmA 125 2.50e+01 d.15.1.3 107827 1o6aA 96 2.50e+01 b.139.1.1 92562 1k0rA 366 2.51e+01 b.40.4.5,d.52.3.1,d.52.3.1,d.202.1.1 67961,67962,67963,67964 1ltlA 279 2.52e+01 b.40.4.11 84701 1ym5A 300 2.53e+01 1llnA 262 2.57e+01 d.165.1.1 84625 1npuA 117 2.58e+01 b.1.1.1 92038 1fjgQ 105 2.59e+01 1fjfQ b.40.4.5 25352 1aop 497 2.76e+01 2aop d.58.36.1,d.58.36.1,d.134.1.1,d.134.1.1 39501,39502,41425,41426 2avtA 378 2.78e+01 1bo4A 168 2.80e+01 1bo4A d.108.1.1 40798 2f9dA 125 2.80e+01 1bx4A 345 2.86e+01 1bx4A c.72.1.1 34935 1d8cA 723 2.88e+01 1d8cA c.1.13.1 29325 1vdmA 153 2.89e+01 4gcr 174 2.93e+01 1amm b.11.1.1,b.11.1.1 23589,23590 1yqfA 203 2.94e+01 1kssA 571 3.05e+01 a.138.1.3,c.3.1.4,d.168.1.1 72928,72929,72930 1y07A 128 3.06e+01 1e39A 571 3.09e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19694,30431,42314 2aamA 309 3.14e+01 1zdnA 158 3.15e+01 1xnzA 264 3.22e+01 1g8aA 227 3.24e+01 c.66.1.3 90506 1whi 122 3.26e+01 1whi b.39.1.1 24810 1fxrA 64 3.27e+01 1fxd d.58.1.4 38993 1rxxA 421 3.29e+01 d.126.1.4 98061 2ggcA 263 3.30e+01 1ze3H 122 3.32e+01 1amm 174 3.34e+01 1amm b.11.1.1,b.11.1.1 23587,23588 1c24A 263 3.35e+01 1c24A d.127.1.1 41148 2asbA 251 3.36e+01 1fdr 248 3.37e+01 1fdr b.43.4.2,c.25.1.1 25653,31543 1o50A 157 3.39e+01 d.37.1.1,d.37.1.1 92478,92479 1y0bA 197 3.40e+01 1gutA 68 3.45e+01 b.40.6.1 65576 1nqjA 119 3.52e+01 b.23.2.1 86031 1u3oA 82 3.55e+01 2b3hA 329 3.58e+01 1o63A 219 3.63e+01 c.94.1.1 92540 1mvwB 145 3.64e+01 i.15.1.1 79524 2g8oA 264 3.66e+01 1uzvA 114 3.74e+01 1yy6A 155 3.79e+01 2g8mA 264 3.79e+01 1i1wA 303 3.82e+01 c.1.8.3 76732 1ypvA 313 3.83e+01 1uurA 473 3.84e+01 a.47.1.1,b.2.5.5,d.93.1.1 100016,100017,100018 1evfA 264 3.85e+01 1bkpA d.117.1.1 40932 2f1wA 158 3.94e+01 1qqqA 264 3.97e+01 1bkpA d.117.1.1 40931 1epwA 1290 3.98e+01 b.29.1.6,b.42.4.2,d.92.1.7,h.4.2.1 24269,25614,40305,45785 1vpqA 273 3.99e+01 1y9kA 157 4.09e+01 1vc3B 97 4.09e+01 1tul 108 4.10e+01 1tul b.85.5.1 28373 1gv3A 248 4.13e+01 a.2.11.1,d.44.1.1 70585,70586 1zsyA 357 4.14e+01 1k8mA 93 4.17e+01 b.84.1.1 68314 1j3kA 280 4.21e+01 c.71.1.1 84070 1y0gA 191 4.23e+01 1p2hA 571 4.23e+01 a.138.1.3,c.3.1.4,d.168.1.1 93930,93931,93932 1y0pA 571 4.23e+01 1pm4A 119 4.25e+01 b.135.1.1 94891 1q9iA 571 4.26e+01 a.138.1.3,c.3.1.4,d.168.1.1 96273,96274,96275 1q52A 314 4.27e+01 c.14.1.3 95846 1u09A 476 4.37e+01 e.8.1.4 107545 1d4oA 184 4.39e+01 1d4oA c.31.1.4 31748 1qsoA 149 4.43e+01 1qsmA d.108.1.1 40812 1s29A 92 4.45e+01 a.4.5.46 98373 2b18A 164 4.46e+01 2cf8H 257 4.46e+01 1bob 320 4.48e+01 1bob d.108.1.1 40816 1earA 147 4.50e+01 b.107.1.1,d.58.38.1 64875,64876 1obwA 175 4.51e+01 2prd b.40.5.1 25416 1a8p 258 4.52e+01 1fdr b.43.4.2,c.25.1.1 25654,31544 1v93A 296 4.61e+01 c.1.23.1 100532 1vraB 215 4.72e+01 1j5pA 253 4.74e+01 d.81.1.3,c.2.1.3 71577,83092 1ema 236 4.75e+01 1ema d.22.1.1 38339 1z4rA 168 4.75e+01 1vzqH 250 4.77e+01 1h8dH 260 4.82e+01 5ptp 1wvqA 167 4.84e+01 2fojA 155 4.85e+01 1tzfA 259 4.86e+01 c.68.1.13 107476 2polA 366 4.89e+01 2polA d.131.1.1,d.131.1.1,d.131.1.1 41356,41357,41358 1dkgA 197 4.90e+01 1dkgA b.73.1.1,h.1.9.1 27812,45626 1w99A 558 4.91e+01 1aozA 552 4.95e+01 1aozA b.6.1.3,b.6.1.3,b.6.1.3 23124,23125,23126 1sflA 238 4.96e+01 1fm0E 150 5.02e+01 1fmaE d.41.5.1 38629 1l7bA 92 5.04e+01 c.15.1.2 91053 1zh5A 195 5.14e+01 1vqvA 306 5.15e+01 2mspA 126 5.21e+01 1mspA b.1.11.2 22335 1ifyA 49 5.28e+01 a.5.2.1 71207 1w77A 228 5.31e+01 1o8bA 219 5.35e+01 c.124.1.4,d.58.40.1 81180,81181 1o7dE 126 5.35e+01 1uheA 97 5.45e+01 1ikpA 613 5.45e+01 b.29.1.7,d.166.1.1,f.1.5.1 66182,66183,66184 1kw4A 89 5.47e+01 a.60.1.2 73077 1bdfA 235 5.54e+01 1bdfA d.74.3.1,d.181.1.1 39727,42602 2atrA 138 5.56e+01 2f6uA 234 5.57e+01 1h9oA 112 5.58e+01 1qadA d.93.1.1 60837 1fzoB 99 5.61e+01 1agdB b.1.1.2 60157 1tif 78 5.63e+01 1tif d.15.8.1 37836 1ta3B 303 5.64e+01 c.1.8.3 106732 1p42A 270 5.70e+01 d.14.1.7,d.14.1.7 87754,87755 2d8aA 348 5.73e+01 1r62A 160 5.75e+01 d.122.1.3 104816 1tllA 688 5.76e+01 b.43.4.1,c.23.5.2,c.25.1.4 107128,107129,107130 1r31A 428 5.79e+01 d.58.20.1,d.179.1.1 96897,96898 1ucyH 150 5.83e+01 1ucyH 1q2yA 140 5.98e+01 d.108.1.1 95655 1wvhA 134 5.98e+01 1l0bA 229 6.01e+01 c.15.1.3,c.15.1.3 73391,73392 1uc7A 125 6.02e+01 c.47.1.1 99163 1uh5A 329 6.05e+01 c.2.1.2 107840 1n7oA 721 6.06e+01 a.102.3.2,b.24.1.1,b.30.5.2 80259,80260,80261 1qzzA 374 6.12e+01 a.4.5.29,c.66.1.12 96719,96720 1eo6A 117 6.16e+01 1eo6A d.15.1.3 37609 1vheA 373 6.17e+01 b.49.3.1,c.56.5.4 100669,100670 2fb5A 205 6.20e+01 1z6bA 154 6.22e+01 1kv7A 488 6.23e+01 b.6.1.3,b.6.1.3,b.6.1.3 68873,68874,68875 1uzcA 71 6.26e+01 a.159.2.1 100222 1bg4 302 6.26e+01 1taxA c.1.8.3 28806 2anuA 255 6.29e+01 1iz5A 249 6.36e+01 d.131.1.2,d.131.1.2 83834,83835 1zkkA 167 6.37e+01 1e5xA 486 6.40e+01 c.79.1.1 59283 1bkzA 135 6.47e+01 1a3k b.29.1.3 24202 1dxrH 258 6.49e+01 6prcH b.41.1.1,f.23.10.1 25456,43433 2fl4A 149 6.50e+01 2fa1A 160 6.51e+01 1vzoA 355 6.51e+01 d.144.1.7 108971 1jihA 531 6.63e+01 d.240.1.1,e.8.1.7 90374,90375 2fwhA 134 6.63e+01 1wxxA 382 6.77e+01 1ukcA 522 6.81e+01 c.69.1.17 107911 1fzkB 99 6.82e+01 1agdB b.1.1.2 60151 1lk2B 99 6.82e+01 b.1.1.2 91058 1ukvG 453 6.86e+01 c.3.1.3,c.3.1.3,d.16.1.6 107915,107916,107917 1f20A 435 6.89e+01 b.43.4.1,c.25.1.4 64932,64933 1txvB 440 6.91e+01 1fjrA 195 6.93e+01 1fjrA b.102.1.1 59855 2gm5A 139 6.98e+01 1n3jA 119 7.04e+01 b.85.7.2 79963 1sfjA 238 7.07e+01 1w30A 201 7.08e+01 1j71A 334 7.14e+01 1eagA b.50.1.2 62669 1vhxA 150 7.19e+01 c.55.3.8 100712 1smrA 335 7.23e+01 1smrA b.50.1.2 26878 1vie 62 7.27e+01 1vie b.34.4.1 24592 1ojhA 65 7.31e+01 a.214.1.1 103976 1nm1G 125 7.49e+01 d.109.1.1 80653 1wbiA 129 7.51e+01 1xo3A 101 7.54e+01 1oalA 151 7.54e+01 b.1.8.1 86739 1eso 154 7.56e+01 1yaiA b.1.8.1 22293 1od5A 492 7.59e+01 b.82.1.2,b.82.1.2 86832,86833 1eexA 554 7.60e+01 1dioA c.1.19.3 29650 1h72C 296 7.61e+01 d.14.1.5,d.58.26.1 60712,60713 1csh 435 7.67e+01 1csh a.103.1.1 18880 2beiA 170 7.68e+01 1zhhB 242 7.72e+01 1on0A 158 7.76e+01 d.108.1.1 87095 1vkcA 158 7.76e+01 1tc5A 194 7.78e+01 c.110.1.1 106752 1dq3A 454 7.82e+01 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1pzxA 289 7.86e+01 c.119.1.1 95484 1t44G 147 7.90e+01 d.109.1.1 106395 1fl2A 310 7.95e+01 1hyuA c.3.1.5,c.3.1.5 59869,59870 1q3iA 214 7.95e+01 d.220.1.1 104524 2awaA 390 7.99e+01 1e3jA 352 8.00e+01 1e3jA b.35.1.2,c.2.1.1 24765,29781 1ogdA 131 8.05e+01 c.133.1.1 92893 1i52A 236 8.08e+01 1i52A c.68.1.13 61767 1pz7A 204 8.14e+01 b.29.1.4 95405 2ghpA 292 8.22e+01 1n8kA 374 8.25e+01 b.35.1.2,c.2.1.1 80298,80299 1stzA 338 8.25e+01 a.4.5.51,d.110.2.3 106009,106010 1iieA 75 8.25e+01 1iieA a.109.1.1 19039 1l1dA 152 8.26e+01 b.88.1.3 73452 1hetA 374 8.33e+01 2ohxA b.35.1.2,c.2.1.1 60975,60976 2gu2A 312 8.34e+01 1wyzA 242 8.35e+01 2d1eA 248 8.37e+01 2cvdA 198 8.40e+01 1sv6A 269 8.41e+01 d.177.1.1 106043 1u8vA 490 8.41e+01 1f8fA 371 8.46e+01 b.35.1.2,c.2.1.1 83246,83247 1o59A 355 8.48e+01 b.18.1.22,b.18.1.22 92495,92496 1y43B 173 8.48e+01 1fwkA 296 8.56e+01 1fwkA d.14.1.5,d.58.26.1 37576,39398 1ok7A 366 8.58e+01 d.131.1.1,d.131.1.1,d.131.1.1 103992,103993,103994 1d4xG 126 8.62e+01 1d0nA d.109.1.1 59109 1z96A 40 8.62e+01 1lf2A 331 8.65e+01 b.50.1.2 77914 1td5A 202 8.68e+01 d.110.2.2 106767 1vf7A 369 8.71e+01 f.46.1.1 108557 1t5eA 360 8.78e+01 f.46.1.1 106436 1gg6B 131 8.85e+01 5ptp 1e0tA 470 8.87e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 1rypI 222 8.89e+01 d.153.1.4 41877 1gvhA 396 8.91e+01 a.1.1.2,b.43.4.2,c.25.1.5 70601,70602,70603 1qorA 327 8.97e+01 1qorA b.35.1.2,c.2.1.1 24766,29782 2cyjA 118 8.99e+01