# List of top-scoring protein chains for t2k-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 2.43e-19 1g9oA 91 3.34e-18 1pdr b.36.1.1 60400 1tp5A 119 4.36e-18 1i92A 91 4.95e-18 1pdr b.36.1.1 61990 1bfeA 119 8.97e-18 1pdr b.36.1.1 24775 1n7eA 97 1.12e-17 b.36.1.1 91691 2fcfA 103 1.13e-17 1be9A 119 1.46e-17 1pdr b.36.1.1 24774 1pdr 99 3.77e-17 1pdr b.36.1.1 24771 1qavA 90 4.53e-17 1qauA b.36.1.1 24777 1n7fA 97 6.87e-17 b.36.1.1 91692 1ihjA 98 1.23e-16 1pdr b.36.1.1 62382 1q3oA 109 3.22e-16 b.36.1.1 95700 1i16 130 2.48e-15 1i16 b.36.1.2 24787 1mfgA 95 2.80e-15 b.36.1.1 79043 1kwaA 88 3.58e-15 1kwaA b.36.1.1 24772 1kwaB 88 4.52e-15 1kwaA b.36.1.1 24773 1qavB 115 1.11e-14 1qauA b.36.1.1 24780 1l6oA 95 1.11e-14 b.36.1.1 84534 2f0aA 98 1.26e-14 1nf3C 128 2.61e-14 b.36.1.1 85596 1n99A 166 2.65e-14 b.36.1.1,b.36.1.1 85459,85460 1qauA 112 2.68e-14 1qauA b.36.1.1 24779 1b8qA 127 6.32e-14 1qauA b.36.1.1 24781 1wf7A 103 2.58e-13 1m5zA 91 2.98e-13 b.36.1.1 78676 2f5yA 91 3.18e-13 1v5lA 103 7.96e-13 b.36.1.1 108378 1nteA 82 2.87e-12 b.36.1.1 86163 1r6jA 82 6.94e-12 b.36.1.1 97151 1fc6A 388 1.16e-10 1fc6A b.36.1.3,c.14.1.2 64738,64739 1te0A 318 8.48e-08 1lcyA 325 3.66e-07 b.36.1.4,b.47.1.1 73834,73835 1ky9B 448 2.24e-05 b.36.1.4,b.36.1.4,b.47.1.1 73200,73201,73202 1y8tA 324 5.18e-05 1sotA 320 1.05e-03 b.36.1.4,b.47.1.1 105852,105853 1ky9A 448 2.43e-03 b.36.1.4,b.47.1.1 73198,73199 1zn8A 180 3.14e-02 1yg9A 330 1.82e-01 1gph1 465 2.83e-01 1ecfB 1ao0A 459 2.97e-01 1ecfB c.61.1.1,d.153.1.1 34049,41816 1db3A 372 3.67e-01 1db3A c.2.1.2 29813 1yjmA 110 6.39e-01 1r13A 148 9.73e-01 d.169.1.1,h.1.1.1 96782,96783 2bsyA 278 1.02e+00 1t6t1 118 1.21e+00 2bh8A 101 1.49e+00 2brfA 110 1.51e+00 1h3iA 293 1.69e+00 b.76.2.1,b.85.7.1 76635,76636 1ciqA 40 1.72e+00 2sniI d.40.1.1 38576 1mt6A 280 1.75e+00 b.76.2.1,b.85.7.1 79446,79447 1fxlA 167 1.83e+00 1b7fA d.58.7.1,d.58.7.1 39183,39184 2fvgA 340 1.96e+00 1vheA 373 1.98e+00 b.49.3.1,c.56.5.4 100669,100670 2d4pA 141 2.06e+00 1n6aA 259 2.15e+00 b.76.2.1,b.85.7.1 80121,80122 1opr 213 2.29e+00 1opr c.61.1.1 34091 1qb7A 236 2.73e+00 1qb7A c.61.1.1 34087 2f4wA 187 3.00e+00 1fxrA 64 3.02e+00 1fxd d.58.1.4 38993 1y0bA 197 3.22e+00 1g7rA 594 3.35e+00 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25716,25717,31034,32149 1g2qA 187 3.73e+00 c.61.1.1 65117 1coaI 64 3.84e+00 2sniI d.40.1.1 38574 1eujA 166 4.04e+00 1eujA b.40.4.4 25316 2a8jA 420 4.08e+00 1lh0A 213 4.15e+00 c.61.1.1 73896 2sniI 83 4.24e+00 2sniI d.40.1.1 38573 1fl0A 171 4.45e+00 1eujA b.40.4.4 25315 1g7sA 594 5.03e+00 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 1iyu 79 5.11e+00 1iyu b.84.1.1 28227 1cis 66 5.39e+00 2sniI k.1.1.1 46375 1zsyA 357 5.52e+00 2a8lA 420 5.93e+00 2a8mA 420 6.11e+00 1to2I 64 6.41e+00 3mefA 69 6.47e+00 1mjc b.40.4.5 25320 1csp 67 6.58e+00 1mjc b.40.4.5 25321 1lw6I 64 6.58e+00 d.40.1.1 74294 1xdnA 277 6.59e+00 1fmaE 150 6.67e+00 1fmaE d.41.5.1 38630 1q1rA 431 6.76e+00 c.3.1.5,c.3.1.5,d.87.1.1 95600,95601,95602 1koe 172 7.07e+00 1koe d.169.1.5 42448 2bs3A 656 7.13e+00 1xe1A 116 7.26e+00 b.43.3.1 109571 1qlaA 656 7.55e+00 1qlaA a.7.3.1,c.3.1.4,d.168.1.1 16328,30427,42310 2c5qA 240 7.64e+00 1fm0E 150 7.69e+00 1fmaE d.41.5.1 38629 2f69A 261 7.76e+00 1h3gA 601 8.17e+00 b.1.18.2,b.71.1.1,c.1.8.1 90594,90595,90596 1y0yA 353 8.40e+00 1ad3A 452 8.73e+00 1ad3A c.82.1.1 35335 1vpqA 273 8.93e+00 1xfoA 357 9.07e+00 6prcH 258 9.09e+00 6prcH b.41.1.1,f.23.10.1 25457,43436 1dxrH 258 9.12e+00 6prcH b.41.1.1,f.23.10.1 25456,43433 1q52A 314 9.17e+00 c.14.1.3 95846 1g7tA 594 9.17e+00 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25714,25715,31033,32148 1dax 64 9.63e+00 1fxd d.58.1.4 38996 1kzlA 208 9.85e+00 b.43.4.3,b.43.4.3 77635,77636 1reqD 637 1.01e+01 1reqB c.1.19.1,c.23.6.1 29623,31250 7reqB 637 1.05e+01 1reqB c.1.19.1,c.23.6.1 29617,31244 1w30A 201 1.10e+01 1eulA 994 1.11e+01 1eulA 1vdmA 153 1.13e+01 1p7tA 731 1.20e+01 c.1.13.1 94319 1o12A 376 1.22e+01 b.92.1.5,c.1.9.10 80758,80759 1x3mA 415 1.32e+01 1oi7A 288 1.36e+01 c.2.1.8,c.23.4.1 87049,87050 1zh1A 163 1.38e+01 1poiA 317 1.42e+01 1poiA c.124.1.2 34153 1o50A 157 1.43e+01 d.37.1.1,d.37.1.1 92478,92479 1b7aA 186 1.45e+01 1a44 b.17.1.1 23705 1a44 185 1.47e+01 1a44 b.17.1.1 23704 1lnh 857 1.49e+01 1yge a.119.1.1,b.12.1.1 19237,23637 1reqB 637 1.49e+01 1reqB c.1.19.1,c.23.6.1 29621,31248 1uh5A 329 1.53e+01 c.2.1.2 107840 1wpgA 994 1.56e+01 1fa8A 135 1.58e+01 1qipA d.32.1.1 38486 1l0bA 229 1.58e+01 c.15.1.3,c.15.1.3 73391,73392 1cq3A 233 1.59e+01 1cq3A b.27.1.1 23923 1skyB 502 1.66e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18313,26478,32358 1js8A 394 1.78e+01 a.86.1.1,b.112.1.1 67219,67220 1fr3A 67 1.80e+01 1fr3A b.40.6.1 25436 1xebA 150 1.85e+01 1kw4A 89 1.90e+01 a.60.1.2 73077 1f9zA 135 1.90e+01 1qipA d.32.1.1 38484 1mjc 69 1.95e+01 1mjc b.40.4.5 25319 1et7A 341 1.95e+01 1nif b.6.1.3,b.6.1.3 23070,23071 2aamA 309 2.01e+01 2cw8A 537 2.02e+01 1gr2A 279 2.03e+01 1gr2A c.94.1.1 35825 1ftkA 279 2.03e+01 1gr2A c.94.1.1 35819 1llnA 262 2.04e+01 d.165.1.1 84625 1o91A 178 2.09e+01 b.22.1.1 92656 1d8cA 723 2.10e+01 1d8cA c.1.13.1 29325 1vkmA 297 2.16e+01 c.138.1.1 108670 1dfd 64 2.21e+01 1fxd d.58.1.4 38995 1s3zA 165 2.24e+01 d.108.1.1 105250 1ecfA 504 2.30e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 3ezmA 101 2.33e+01 3ezmA b.89.1.1 28395 1jnyA 435 2.37e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1ah1 129 2.37e+01 1ah1 b.1.1.1 20652 1ujxA 119 2.38e+01 b.26.1.2 99473 1vc3B 97 2.51e+01 1vqqA 646 2.54e+01 1rurH 218 2.64e+01 b.1.1.1,b.1.1.2 97879,97880 1mqiA 263 2.67e+01 c.94.1.1 91398 1su4A 994 2.69e+01 b.82.7.1,c.108.1.7,d.220.1.1,f.33.1.1 98993,98994,98995,98996 1s5lO 246 2.71e+01 1c9oA 66 2.73e+01 1mjc b.40.4.5 25325 2bgzA 299 2.75e+01 1y7rA 133 2.82e+01 1ypcI 64 2.84e+01 2sniI d.40.1.1 38570 1f3uB 171 2.85e+01 1f3uB b.65.1.1 27525 1vraB 215 2.87e+01 1d4vB 163 2.89e+01 1d4vB b.22.1.1 23884 1behA 187 2.92e+01 1a44 b.17.1.1 23700 1fl2A 310 2.93e+01 1hyuA c.3.1.5,c.3.1.5 59869,59870 1nglA 179 3.00e+01 1nglA b.60.1.1 27146 1i52A 236 3.15e+01 1i52A c.68.1.13 61767 1ifyA 49 3.17e+01 a.5.2.1 71207 1ecfB 504 3.18e+01 1ecfB c.61.1.1,d.153.1.1 34054,41821 1m5eA 263 3.19e+01 c.94.1.1 78642 1a3lH 218 3.19e+01 1mfa b.1.1.1,b.1.1.2 20241,21253 2gvaA 87 3.23e+01 1gvp b.40.4.7 25389 1l7bA 92 3.30e+01 c.15.1.2 91053 2cc0A 195 3.33e+01 2adcA 229 3.33e+01 1hkfA 122 3.34e+01 b.1.1.1 83553 1mqdA 261 3.36e+01 c.94.1.1 85049 1m5dA 263 3.36e+01 c.94.1.1 78641 1wlgA 299 3.38e+01 1t3qB 788 3.39e+01 d.41.1.1,d.133.1.1 106369,106370 1jalA 363 3.42e+01 c.37.1.8,d.15.10.2 84138,84139 2bsjA 133 3.43e+01 1vqwA 457 3.44e+01 1npuA 117 3.48e+01 b.1.1.1 92038 1xx6A 191 3.51e+01 1c44A 123 3.54e+01 1qndA d.106.1.1 40795 1u9yA 284 3.58e+01 1iiyA 101 3.63e+01 b.89.1.1 66152 1uc7A 125 3.70e+01 c.47.1.1 99163 2az4A 429 3.72e+01 1vqb 87 3.72e+01 1gvp b.40.4.7 25370 1vf7A 369 3.72e+01 f.46.1.1 108557 1gvp 87 3.72e+01 1gvp b.40.4.7 25369 1p99A 295 3.74e+01 c.94.1.1 94384 1vyfA 135 3.76e+01 b.60.1.2 108902 1rutX 188 3.81e+01 1o9yA 84 3.96e+01 b.139.1.1 92692 3sxlA 184 3.97e+01 1b7fA d.58.7.1,d.58.7.1 39173,39174 1c9uA 454 3.98e+01 1c9uA b.68.2.1 27623 1zm8A 259 4.00e+01 1oroA 213 4.02e+01 1opr c.61.1.1 34093 1m1hA 248 4.03e+01 b.114.1.1,d.58.42.1 78415,78416 1rovA 857 4.05e+01 a.119.1.1,b.12.1.1 97674,97675 1x47A 98 4.10e+01 1vchA 175 4.10e+01 1rl2A 137 4.12e+01 1rl2A b.34.5.3,b.40.4.5 24610,25342 1hjdA 101 4.13e+01 b.34.2.1 65846 1x6vA 630 4.14e+01 1scuA 288 4.15e+01 2scuA c.2.1.8,c.23.4.1 30307,31135 1bx4A 345 4.16e+01 1bx4A c.72.1.1 34935 1ojhA 65 4.18e+01 a.214.1.1 103976 1viuA 203 4.23e+01 d.113.1.1 100771 2bshA 125 4.31e+01 1iieA 75 4.32e+01 1iieA a.109.1.1 19039 1rz3A 201 4.34e+01 c.37.1.6 98132 1kkcA 221 4.35e+01 a.2.11.1,d.44.1.1 68660,68661 1ae3 86 4.35e+01 1gvp b.40.4.7 25381 1wlsA 328 4.37e+01 1xv5A 401 4.41e+01 1uheA 97 4.41e+01 1ugmA 125 4.50e+01 d.15.1.3 107827 1l1dA 152 4.52e+01 b.88.1.3 73452 1e6oH 219 4.52e+01 1igtB b.1.1.1,b.1.1.2 20495,21453 2sxl 88 4.55e+01 1b7fA d.58.7.1 39179 1tfzA 424 4.55e+01 d.32.1.3,d.32.1.3 106886,106887 2bb3A 221 4.55e+01 1wb4A 297 4.57e+01 1qbiA 454 4.63e+01 1c9uA b.68.2.1 27619 2scuA 288 4.66e+01 2scuA c.2.1.8,c.23.4.1 30303,31131 2fpmA 322 4.71e+01 1jzxK 205 4.77e+01 i.1.1.2 67885 1l5aA 436 4.77e+01 c.43.1.2,c.43.1.2 75923,75924 1bqhG 129 4.93e+01 1cd8 b.1.1.1 19715 1iezA 217 4.95e+01 d.115.1.2 66129 1jjiA 311 4.95e+01 c.69.1.2 66766 1aw8B 91 4.99e+01 1aw8B 1bxaA 105 4.99e+01 1aac b.6.1.1 22839 1zkpA 268 5.07e+01 1t5hX 504 5.08e+01 e.23.1.1 106449 1g8sA 230 5.09e+01 c.66.1.3 90507 1wnfA 328 5.11e+01 1fjrA 195 5.22e+01 1fjrA b.102.1.1 59855 2apsA 162 5.22e+01 1yaiA b.1.8.1 22298 1g57A 217 5.23e+01 1g57A d.115.1.2 60253 2ahqA 76 5.24e+01 1bd2D 204 5.28e+01 1tcrA b.1.1.1,b.1.1.2 20622,21557 1mdbA 539 5.39e+01 e.23.1.1 79008 2ampA 304 5.40e+01 1gkkA 297 5.47e+01 c.69.1.2 65248 2cyjA 118 5.50e+01 1fbnA 230 5.50e+01 1fbnA c.66.1.3 34181 1wwkA 307 5.60e+01 1pt1A 143 5.66e+01 b.52.2.1 95084 1cruA 454 5.67e+01 1c9uA b.68.2.1 27617 1t5eA 360 5.68e+01 f.46.1.1 106436 1egpA 45 5.81e+01 1egpA d.40.1.1 38561 1gklA 297 5.85e+01 c.69.1.2 65250 1sw5A 275 5.89e+01 c.94.1.1 106069 1y07A 128 5.90e+01 2f6uA 234 5.95e+01 1l7yA 94 5.98e+01 d.15.1.6 73676 1th7A 81 6.10e+01 1mwsA 646 6.25e+01 d.17.4.5,d.175.1.1,e.3.1.1 79592,79593,79594 2bhoA 130 6.26e+01 1mak 113 6.28e+01 8fabA b.1.1.1 19825 2fokA 579 6.30e+01 2fokA a.4.5.12,a.4.5.12,a.4.5.12,c.52.1.12 16131,16132,16133,33323 1hyuA 521 6.31e+01 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1qk4A 233 6.39e+01 1qk3A c.61.1.1 34037 1umzA 278 6.42e+01 b.29.1.2 99639 1dg6A 191 6.47e+01 1d4vB b.22.1.1 23883 2atrA 138 6.48e+01 1gpr 162 6.50e+01 1gpr b.84.3.1 28267 1oqvA 192 6.52e+01 d.24.1.2 87320 1o63A 219 6.60e+01 c.94.1.1 92540 1uzcA 71 6.71e+01 a.159.2.1 100222 1nm1G 125 6.78e+01 d.109.1.1 80653 2b18A 164 6.81e+01 1yagG 125 6.82e+01 1d0nA d.109.1.1 40846 1x05A 129 6.92e+01 2cokA 113 6.99e+01 1h70A 255 7.02e+01 1h70A d.126.1.3 60711 1axiA 191 7.05e+01 1huw a.26.1.1 16832 1rhd 293 7.06e+01 1rhs c.46.1.2,c.46.1.2 32715,32716 1o3yA 166 7.16e+01 c.37.1.8 86618 1n0qA 93 7.17e+01 k.37.1.1 79754 1d7oA 297 7.19e+01 1enp c.2.1.2 29907 1g7jB 116 7.23e+01 1f3rB b.1.1.1 19933 1hcz 252 7.26e+01 1hcz b.2.6.1,b.84.2.2 22464,28250 1d4oA 184 7.42e+01 1d4oA c.31.1.4 31748 1bxvA 91 7.43e+01 1aac b.6.1.1 22875 1b7fA 168 7.44e+01 1b7fA d.58.7.1,d.58.7.1 39169,39170 1fdr 248 7.45e+01 1fdr b.43.4.2,c.25.1.1 25653,31543 1ueoA 63 7.51e+01 j.107.1.1 99269 1u09A 476 7.52e+01 e.8.1.4 107545 1tc5A 194 7.58e+01 c.110.1.1 106752 1g2hA 61 7.58e+01 1g2hA a.4.1.12 60224 1qk3A 233 7.62e+01 1qk3A c.61.1.1 34031 1lnzA 342 7.64e+01 b.117.1.1,c.37.1.8 78112,78113 1sflA 238 7.69e+01 1enp 312 7.71e+01 1enp c.2.1.2 29906 2fsxA 148 7.74e+01 1shsA 147 7.75e+01 1shsA b.15.1.1 23675 1tr7A 164 7.82e+01 1uwfA 158 7.85e+01 2bw4A 340 7.86e+01 1jj2D 176 7.91e+01 1ffkD d.77.1.1 63088 1d4xG 126 7.94e+01 1d0nA d.109.1.1 59109 1ggrA 168 7.98e+01 1gpr b.84.3.1 28279 2f1lA 187 8.00e+01 1cjxA 357 8.03e+01 1cjxA d.32.1.3,d.32.1.3 38516,38517 1aaj 105 8.06e+01 1aac b.6.1.1 22841 1eno 312 8.06e+01 1enp c.2.1.2 29905 1q5qA 259 8.06e+01 d.153.1.4 95904 2f6rA 281 8.06e+01 1fdlH 218 8.07e+01 1igtB b.1.1.1,b.1.1.2 19961,21021 1kf6A 602 8.11e+01 a.7.3.1,c.3.1.4,d.168.1.1 72394,72395,72396 1whi 122 8.12e+01 1whi b.39.1.1 24810 1e5xA 486 8.16e+01 c.79.1.1 59283 1zkkA 167 8.17e+01 2gpr 154 8.23e+01 1gpr b.84.3.1 28269 1g6sA 427 8.25e+01 1eps d.68.2.2 39584 1fsgA 233 8.29e+01 1qk3A c.61.1.1 34029 1s72H 171 8.30e+01 d.41.4.1 105327 2b8tA 223 8.34e+01 1nwaA 203 8.35e+01 d.58.28.1 86295 1yloA 348 8.38e+01 1s9aA 257 8.39e+01 b.3.6.1 105379 1lghB 45 8.43e+01 1lghB f.3.1.1 43734 1at0 145 8.44e+01 1at0 b.86.1.1 28374 1cliA 345 8.50e+01 1cliA d.79.4.1,d.139.1.1 39816,41459 1aac 105 8.59e+01 1aac b.6.1.1 22838 1sfdA 105 8.60e+01 b.6.1.1 105480 2rmpA 361 8.67e+01 2rmpA b.50.1.2 26825 1mwrA 646 8.70e+01 d.17.4.5,d.175.1.1,e.3.1.1 79586,79587,79588 1rxdA 159 8.72e+01 2affA 120 8.79e+01 2pcfB 250 8.81e+01 1hcz i.4.1.1 45911 1tluA 130 8.84e+01 d.156.1.2 107139 1f3z 161 8.90e+01 1gpr b.84.3.1 28273 2b8wA 328 8.93e+01 1ako 268 8.94e+01 1ako d.151.1.1 41779 1qy5A 269 8.97e+01 d.122.1.1 96573 1bu6O 501 8.99e+01 1glcG c.55.1.4,c.55.1.4 33499,33500