# List of top-scoring protein chains for t04-100-30-str2 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 1rvaA 244 2.63e-02 1rvaA c.52.1.2 33240 1eonA 245 2.66e-02 1rvaA c.52.1.2 33238 1sx5A 244 2.79e-02 c.52.1.2 -7551 1vh5A 148 8.85e-02 d.38.1.5 -9677 1e44B 96 1.03e-01 1e44B b.101.1.1 59220 1gefA 123 1.28e-01 1gefA c.52.1.18 60465 1han 297 1.68e-01 1han d.32.1.3 38506 d.32.1.3 38507 1hh1A 143 2.35e-01 1gefA c.52.1.18 61036 1cliA 345 2.43e-01 1cliA d.79.4.1 39816 d.139.1.1 41459 1lkdA 297 2.64e-01 d.32.1.3 78059 d.32.1.3 78060 1bif 469 2.87e-01 1bif c.37.1.7 31961 c.60.1.4 34003 1b77A 228 4.46e-01 1b77A d.131.1.2 41362 d.131.1.2 41363 2igd 61 6.05e-01 2igd d.15.7.1 37821 1nhp 447 9.37e-01 1nhp c.3.1.5 30549 c.3.1.5 30550 d.87.1.1 40196 1iyeA 309 9.85e-01 e.17.1.1 83786 1o8uA 257 1.00e+00 c.14.1.3 81194 1skoB 130 1.01e+00 1szoA 257 1.11e+00 1nhs 447 1.12e+00 1nhp c.3.1.5 30555 c.3.1.5 30556 d.87.1.1 40199 1skoA 143 1.14e+00 1k0eA 453 1.38e+00 d.161.1.1 67938 1pbuA 162 1.38e+00 d.58.46.1 88030 1f52A 468 1.39e+00 1lgr d.15.9.1 37839 d.128.1.1 41169 1udxA 416 1.45e+00 b.117.1.1 -3546 c.37.1.8 -7101 unknown_sccs -9009 1o0iA 138 1.50e+00 d.38.1.5 86532 1pvtA 238 1.53e+00 c.74.1.1 -8444 1i1kA 309 1.87e+00 1daaA e.17.1.1 61533 1lxjA 104 2.24e+00 d.58.48.1 84736 1r62A 160 2.46e+00 1uq5A 263 2.47e+00 d.165.1.1 -11555 1ift 263 2.76e+00 1mrj d.165.1.1 42211 1pymA 295 2.82e+00 1pymA c.1.12.7 29308 1m2tA 254 3.98e+00 d.165.1.1 84761 1b43A 340 4.14e+00 1a76 a.60.7.1 18092 c.120.1.2 33362 1s2wA 295 4.22e+00 c.1.12.7 -5577 1j31A 262 4.32e+00 d.160.1.2 -11473 1pwxA 254 4.81e+00 c.2.1.2 -5858 1ujxA 119 5.07e+00 b.26.1.2 -3325 1fp1D 372 5.11e+00 1fpqA a.4.5.29 59939 c.66.1.12 59940 1aisA 182 5.18e+00 1ytbA d.129.1.1 41288 d.129.1.1 41289 1oi7A 288 5.56e+00 c.2.1.8 87049 c.23.4.1 87050 1sqzA 121 5.69e+00 a.133.1.2 -1971 1tk4A 121 5.77e+00 1vk6A 269 5.86e+00 unknown_sccs -10923 unknown_sccs -10924 1nf3C 128 5.97e+00 b.36.1.1 85596 1kutA 230 6.07e+00 d.143.1.1 73017 1g8pA 350 6.21e+00 1g8pA c.37.1.20 60376 1hc7A 477 6.23e+00 1hc7A c.51.1.1 60938 d.68.5.1 60940 d.104.1.1 60939 1tj9A 121 6.26e+00 1h7mA 102 6.40e+00 d.79.3.1 83485 1gqeA 365 6.63e+00 e.38.1.1 70351 1pqzA 238 6.66e+00 1fe7A 121 6.66e+00 1poa 1k8wA 327 7.07e+00 b.122.1.1 83094 unknown_sccs -10143 1q7fA 286 7.73e+00 unknown_sccs -4599 1f86A 115 7.86e+00 1etb1 b.3.4.1 59689 1mvfD 82 7.91e+00 b.129.1.1 85143 1n0wA 243 8.25e+00 c.37.1.11 79772 1ofzA 312 8.33e+00 b.68.8.1 86978 1o50A 157 9.17e+00 d.37.1.1 -9604 d.37.1.1 -9605 1sdwA 314 9.23e+00 b.121.1.2 -3024 b.121.1.2 -3025 1a79A 171 9.46e+00 1a79A c.52.2.1 33340 d.75.1.1 39739 1ogsA 497 9.55e+00 b.71.1.2 86997 c.1.8.3 86998 1bpoA 494 9.61e+00 1bpoA a.118.1.4 19143 b.69.6.1 27670 1regX 122 9.69e+00 1regX d.58.27.1 39406 1o5hA 214 9.77e+00 unknown_sccs -1078 1f4lA 551 9.91e+00 1qqtA a.27.1.1 59648 c.26.1.1 59649 g.41.1.1 59650 1tzbA 302 9.92e+00 1pfvA 551 9.93e+00 a.27.1.1 -727 c.26.1.1 -6603 g.41.1.1 -12765 1jeoA 180 1.03e+01 c.80.1.3 66611 1bzyA 217 1.04e+01 1qk3A c.61.1.1 34071 1dhpA 292 1.05e+01 1dhpA c.1.10.1 29097 1f1xA 322 1.07e+01 d.32.1.3 83208 d.32.1.3 83209 1vk3A 615 1.08e+01 d.79.4.1 -10416 d.79.4.1 -10417 d.139.1.1 -11154 d.139.1.1 -11155 1psuA 140 1.11e+01 d.38.1.5 88285 1sesA 421 1.12e+01 1sesA a.2.7.1 15710 d.104.1.1 40710 1t35A 191 1.12e+01 unknown_sccs -7285 1kw3B 292 1.15e+01 d.32.1.3 77549 d.32.1.3 77550 1gxrA 337 1.16e+01 b.69.4.1 70722 1vimA 200 1.17e+01 c.80.1.3 -8532 1p32A 209 1.20e+01 1p32A d.25.1.1 38379 1kkoA 413 1.20e+01 c.1.11.2 68675 d.54.1.1 68676 1abrA 251 1.23e+01 1mrj d.165.1.1 42196 1ou8A 111 1.28e+01 unknown_sccs -3799 1uuhA 159 1.32e+01 d.169.1.4 -11651 1phm 310 1.37e+01 1phm b.121.1.2 59015 b.121.1.2 59016 3erk 364 1.40e+01 1hcl d.144.1.7 41654 2prd 174 1.41e+01 2prd b.40.5.1 25435 1j8uA 325 1.42e+01 d.178.1.1 71611 1ax0 239 1.48e+01 1led b.29.1.1 24042 1o5zA 442 1.51e+01 c.59.1.2 -7939 c.72.2.2 -8418 4pah 308 1.51e+01 4pah d.178.1.1 42576 1sk4A 163 1.57e+01 1m4vA 204 1.65e+01 b.40.2.2 74459 d.15.6.1 74460 1vdwA 254 1.68e+01 e.7.1.1 -11868 1r6xA 395 1.70e+01 b.122.1.3 -5125 c.26.1.5 -6620 1e19A 314 1.71e+01 1b7bA c.73.1.1 34967 1q42A 201 1.72e+01 d.17.4.2 -9292 1jj2C 246 1.73e+01 1ffkC c.22.1.1 63087 1dp0A 1023 1.77e+01 b.1.4.1 22073 b.1.4.1 22074 b.18.1.5 23722 b.30.5.1 24346 c.1.8.3 28845 1wab 232 1.79e+01 1wab c.23.10.3 31341 1r4kA 169 1.79e+01 unknown_sccs -3625 1mo9A 523 1.82e+01 c.3.1.5 79341 c.3.1.5 79342 d.87.1.1 79343 1m7yA 435 1.83e+01 c.67.1.4 78761 1ile 821 1.84e+01 1ile a.27.1.1 16924 b.51.1.1 26889 c.26.1.1 31591 1s72C 246 1.87e+01 1f1uA 323 1.88e+01 d.32.1.3 83200 d.32.1.3 83201 1es9A 232 2.00e+01 1wab c.23.10.3 31340 1g94A 448 2.01e+01 b.71.1.1 65169 c.1.8.1 65170 1iirA 415 2.01e+01 1iirA c.87.1.5 62453 1ujnA 348 2.05e+01 e.22.1.1 -11998 1ok7A 366 2.05e+01 1uyrA 737 2.05e+01 c.14.1.4 -6258 c.14.1.4 -6259 1rg9A 383 2.07e+01 d.130.1.1 -11057 d.130.1.1 -11058 d.130.1.1 -11059 1lqaA 346 2.08e+01 c.1.7.1 84674 1htqA 477 2.11e+01 d.15.9.1 71035 d.128.1.1 71036 1gqiA 708 2.19e+01 c.1.8.10 76279 d.92.2.2 76280 1pm3A 78 2.24e+01 unknown_sccs -3973 1qmyA 167 2.26e+01 1qmyA d.3.1.2 37094 1qlmA 316 2.29e+01 1qlmA d.147.1.1 41765 1pkoA 139 2.36e+01 b.1.1.1 88147 1si2A 149 2.42e+01 1djxA 624 2.45e+01 1djxB a.39.1.7 17342 b.7.1.1 23159 c.1.18.1 29587 1led 243 2.50e+01 1led b.29.1.1 24039 1qhxA 178 2.50e+01 1qhsA c.37.1.3 31936 1qnrA 344 2.55e+01 1qnoA c.1.8.3 28834 1n3oA 252 2.58e+01 b.29.1.1 79967 1cr1A 296 2.59e+01 1cr1A c.37.1.11 32286 1ezwA 349 2.66e+01 1ezwA c.1.16.3 29558 1rypF 233 2.66e+01 1rypF d.153.1.4 41937 1n35A 1267 2.68e+01 e.8.1.4 79935 1b78A 193 2.74e+01 1b78A c.51.4.1 33221 1utcA 363 2.77e+01 a.118.1.4 -1568 b.69.6.1 -4612 1hnuA 280 2.82e+01 1hnoA c.14.1.3 61096 1hrnA 337 2.96e+01 1smrA b.50.1.2 26869 1ud9A 245 2.96e+01 1ivzA 132 2.96e+01 d.58.41.1 76863 1v8cA 168 2.99e+01 d.15.3.1 -9175 unknown_sccs -11012 2hhmA 276 3.01e+01 1imbA e.7.1.1 42955 1bob 320 3.02e+01 1bob d.108.1.1 40816 1uptA 171 3.02e+01 c.37.1.8 -7085 1dysA 348 3.02e+01 1bvwA c.6.1.1 30669 1qahA 136 3.04e+01 d.79.1.1 -10377 1aqm 453 3.05e+01 1smd b.71.1.1 27717 c.1.8.1 28704 1f6dA 376 3.08e+01 1f6dA c.87.1.3 35467 1s72E 178 3.08e+01 830cA 168 3.09e+01 1ck7A d.92.1.11 40400 1pjjA 271 3.10e+01 1hl9A 449 3.10e+01 unknown_sccs -4694 unknown_sccs -5365 1ukgA 252 3.19e+01 b.29.1.1 -3390 1nrlA 316 3.20e+01 a.123.1.1 -1668 1p9oA 313 3.21e+01 unknown_sccs -8423 3proC 166 3.24e+01 3proC d.52.1.1 38812 d.52.1.1 38813 1b6rA 355 3.25e+01 1b6rA b.84.2.1 28241 c.30.1.1 31648 d.142.1.2 41493 1nycA 111 3.26e+01 unknown_sccs -4522 1s9rA 410 3.34e+01 unknown_sccs -10989 1i2aA 219 3.39e+01 e.24.1.1 -12012 1j97A 211 3.43e+01 1f5sA c.108.1.4 62753 1n1tA 641 3.49e+01 b.29.1.15 79821 b.68.1.1 79822 1e6uA 321 3.55e+01 1bsvA c.2.1.2 29805 1nlnA 204 3.56e+01 d.3.1.7 -8897 1mmiA 366 3.57e+01 d.131.1.1 -11093 d.131.1.1 -11094 d.131.1.1 -11095 1jj2E 177 3.60e+01 1ffk1 d.141.1.1 63089 d.141.1.1 63090 1m3sA 186 3.65e+01 c.80.1.3 78573 1rss 151 3.68e+01 1rss a.75.1.1 18392 1kg0C 136 3.70e+01 d.169.1.1 72445 1nbaA 264 3.76e+01 1nbaA unknown_sccs 31753 2ebn 289 3.77e+01 2ebn c.1.8.5 28990 1a76 326 3.80e+01 1a76 a.60.7.1 18091 c.120.1.2 33361 1pi1A 185 3.82e+01 unknown_sccs -762 1rkqA 282 3.83e+01 c.108.1.10 -6847 1l7mA 211 3.83e+01 c.108.1.4 73664 1mu5A 471 3.85e+01 a.156.1.3 79472 d.14.1.3 79473 d.122.1.2 79474 1gpr 162 3.94e+01 1gpr b.84.3.1 28267 1q9uA 130 3.99e+01 unknown_sccs -11025 1nnjA 271 3.99e+01 a.156.1.2 80669 b.113.1.1 80670 g.39.1.8 80671