# List of top-scoring protein chains for t2k-100-30-bys 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 1gr3A 160 2.61e-17 b.22.1.1 65476 1c3hA 137 1.01e-16 b.22.1.1 -3255 1c28A 135 3.96e-16 1c28A b.22.1.1 23857 1o91A 178 1.63e-15 b.22.1.1 -3282 1pk6C 129 3.07e-13 b.22.1.1 -3293 1pk6A 133 1.38e-12 b.22.1.1 -3287 1pk6B 132 6.31e-12 b.22.1.1 -3290 1jh5A 144 4.24e-02 b.22.1.1 66697 1iqaA 160 5.66e-02 b.22.1.1 71274 1rj8A 164 6.00e-02 b.22.1.1 -3263 1kxgA 152 7.05e-02 b.22.1.1 73145 2tnfA 156 2.03e-01 2tnfA b.22.1.1 23880 1d2qA 173 2.13e-01 1d4vB b.22.1.1 23894 1dg6A 191 2.25e-01 1d4vB b.22.1.1 23883 1tnrA 144 2.60e-01 2tnfA b.22.1.1 23867 1j83A 180 2.82e-01 b.18.1.12 66430 1v7wA 807 3.81e-01 1o6uA 403 3.87e-01 a.5.3.1 -366 unknown_sccs -3048 c.13.1.1 -6221 1a8p 258 4.92e-01 1fdr b.43.4.2 25654 c.25.1.1 31544 1d4vB 163 5.31e-01 1d4vB b.22.1.1 23884 1aly 146 6.08e-01 1aly b.22.1.1 23856 1jv4A 162 6.42e-01 b.60.1.1 67343 1hv9A 456 6.55e-01 1fwyA b.81.1.4 28060 c.68.1.5 34518 1k5nB 100 6.69e-01 b.1.1.2 77268 1i05A 180 7.03e-01 1mup b.60.1.1 27130 1duzB 100 7.58e-01 1agdB b.1.1.2 20671 1pfo 500 8.10e-01 1pfo f.9.1.1 43826 1i06A 180 8.58e-01 1mup b.60.1.1 27131 1huuA 90 1.03e+00 1huuA a.55.1.1 17897 1i4fB 100 1.12e+00 1agdB b.1.1.2 61689 1m3jA 471 1.42e+00 f.9.1.1 -12372 1hdmB 193 1.44e+00 1hdmB b.1.1.2 21584 d.19.1.1 38158 1agdB 99 1.57e+00 1agdB b.1.1.2 20742 1nuyA 337 1.65e+00 e.7.1.1 86213 1m3iA 471 1.68e+00 f.9.1.1 -12374 4tsvA 150 1.90e+00 2tnfA b.22.1.1 23860 1hsbB 99 1.96e+00 1agdB b.1.1.2 20737 2cb5A 453 2.02e+00 3gcb d.3.1.1 37035 1g4uS 383 2.16e+00 1g4uS a.24.11.1 16643 c.45.1.2 32691 1hfuA 503 2.27e+00 b.6.1.3 65827 b.6.1.3 65828 b.6.1.3 65829 1d5mB 192 2.53e+00 1iakB b.1.1.2 21618 d.19.1.1 38192 1p9qC 256 2.64e+00 1edqA 540 2.93e+00 1ctn b.1.18.2 21873 c.1.8.5 29002 d.26.3.1 38436 1gcuA 295 2.94e+00 1gcuA c.2.1.3 30063 d.81.1.4 39978 1pmd 675 3.01e+00 1pmd d.11.1.1 37491 d.11.1.1 37492 d.175.1.1 42562 e.3.1.1 42771 1o20A 427 3.21e+00 c.82.1.1 86556 1qy1A 174 3.38e+00 b.60.1.1 -4445 1i18A 97 3.44e+00 b.43.4.3 61520 1xgsA 295 3.47e+00 1bn5 a.4.5.25 16216 d.127.1.1 41153 1k9tA 540 3.52e+00 b.1.18.2 77298 c.1.8.5 77299 d.26.3.1 77300 1m4jA 142 3.59e+00 d.109.1.2 78602 1t95A 240 3.81e+00 1qwoA 442 3.96e+00 1pch 88 3.98e+00 1ptf d.94.1.1 40564 1sdwA 314 3.99e+00 b.121.1.2 -3024 b.121.1.2 -3025 1kzlA 208 4.05e+00 b.43.4.3 77635 b.43.4.3 77636 1uxzA 131 4.25e+00 b.18.1.10 -3110 1obpA 159 4.66e+00 1obpA b.60.1.1 27092 1iakA 199 4.85e+00 1iakA b.1.1.2 21625 d.19.1.1 38199 1mup 166 5.03e+00 1mup b.60.1.1 27133 1hueA 90 5.19e+00 1huuA a.55.1.1 17900 1tnfA 158 5.45e+00 2tnfA b.22.1.1 23871 1fwxA 595 5.49e+00 b.6.1.4 60069 b.69.3.1 60070 1qmeA 702 5.89e+00 1pmd d.11.1.1 37487 d.11.1.1 37488 d.175.1.1 42560 e.3.1.1 42769 1g6gA 127 5.95e+00 1g6gA b.26.1.2 23916 1ctn 540 6.28e+00 1ctn b.1.18.2 21876 c.1.8.5 29005 d.26.3.1 38439 1spuB 727 6.37e+00 1oacA b.30.2.1 24399 d.17.2.1 38025 d.17.2.1 38026 d.82.1.1 40012 1rfs 139 6.47e+00 1rfs b.33.1.1 24434 3seb 238 6.56e+00 3seb b.40.2.2 25184 d.15.6.1 37773 1g4wR 383 6.69e+00 1g4uS a.24.11.1 16644 c.45.1.2 32692 1vjlA 164 6.98e+00 unknown_sccs -11117 1kxrA 339 7.04e+00 d.3.1.3 73175 1df3A 162 7.04e+00 1mup b.60.1.1 27134 2nlrA 234 7.09e+00 2nlrA b.29.1.11 24344 19hcA 292 7.11e+00 19hcA a.138.1.1 19668 1rdzA 337 7.20e+00 1frpA e.7.1.1 42882 1gt1A 159 7.21e+00 b.60.1.1 -4436 1cklB 126 7.33e+00 1cklB g.18.1.1 44853 g.18.1.1 44854 1ofwA 296 7.65e+00 a.138.1.1 -2035 1regX 122 7.95e+00 1regX d.58.27.1 39406 2bosA 68 8.06e+00 2bosA b.40.2.1 25025 1o5yA 193 8.17e+00 1d6zA 727 8.47e+00 1oacA b.30.2.1 24394 d.17.2.1 38015 d.17.2.1 38016 d.82.1.1 40007 1smlA 269 8.55e+00 1smlA d.157.1.1 42053 1ujxA 119 8.56e+00 b.26.1.2 -3325 1d5mC 239 8.96e+00 3seb b.40.2.2 25185 d.15.6.1 37774 1qfxA 460 9.18e+00 1qfxA c.60.1.2 33994 1oacA 727 9.29e+00 1oacA b.30.2.1 24390 d.17.2.1 38007 d.17.2.1 38008 d.82.1.1 40003 1ui8A 638 9.83e+00 b.30.2.1 -3525 d.17.2.1 -9272 d.17.2.1 -9273 1ajqB 557 9.86e+00 1ajqB 1r4pB 70 9.88e+00 b.40.2.1 -3887 1llnA 262 1.01e+01 d.165.1.1 84625 1d7kA 421 1.02e+01 7odcA b.49.2.3 26486 c.1.6.1 28648 1ew3A 159 1.03e+01 1mup b.60.1.1 27114 1ub4C 85 1.03e+01 b.129.1.1 88401 1a65A 504 1.04e+01 1a65A b.6.1.3 23148 b.6.1.3 23149 b.6.1.3 23150 1iqyA 638 1.06e+01 b.30.2.1 76763 d.17.2.1 76764 d.17.2.1 76765 1avk 638 1.09e+01 1a2vA b.30.2.1 24410 d.17.2.1 38047 d.17.2.1 38048 2ifeA 100 1.12e+01 1tig d.68.1.1 39567 1o5kA 306 1.13e+01 c.1.10.1 -5482 1pft 50 1.15e+01 1pft g.41.3.1 45206 1qniA 581 1.17e+01 1qniA b.6.1.4 23042 b.69.3.1 27642 1uc7A 125 1.18e+01 c.47.1.1 -7414 1nlr 234 1.27e+01 2nlrA b.29.1.11 24345 1cklA 126 1.27e+01 1cklB g.18.1.1 44851 g.18.1.1 44852 1dfx 125 1.33e+01 1dfx b.1.13.1 22367 g.41.5.2 45255 1qfhA 212 1.35e+01 1qfhA b.1.18.10 21893 b.1.18.10 21894 1dtoA 221 1.35e+01 1dtoA b.91.1.1 28405 1o60A 292 1.40e+01 c.1.10.4 -5549 1nh9A 87 1.41e+01 d.68.6.1 -10287 1cwvA 492 1.54e+01 1cwvA b.1.14.1 22373 b.1.14.1 22374 b.1.14.1 22375 b.1.14.1 22376 d.169.1.3 42442 1hdmA 201 1.54e+01 1iakA b.1.1.2 21583 d.19.1.1 38157 1aozA 552 1.58e+01 1aozA b.6.1.3 23124 b.6.1.3 23125 b.6.1.3 23126 5fbpA 335 1.60e+01 1frpA e.7.1.1 42873 1lxkA 721 1.61e+01 a.102.3.2 74331 b.24.1.1 74332 b.30.5.2 74333 1l7lA 121 1.62e+01 b.18.1.16 77790 1b4rA 80 1.62e+01 1b4rA b.1.3.1 22072 1ggrA 168 1.63e+01 1gpr b.84.3.1 28279 1ivwA 638 1.65e+01 b.30.2.1 71456 d.17.2.1 71457 d.17.2.1 71458 1dzkA 157 1.66e+01 1obpA b.60.1.1 27096 1qubA 319 1.66e+01 1qubA g.18.1.1 44863 g.18.1.1 44864 g.18.1.1 44865 g.18.1.1 44866 g.18.1.1 44867 1cr8A 42 1.67e+01 1ajj g.12.1.1 44613 1phm 310 1.67e+01 1phm b.121.1.2 59015 b.121.1.2 59016 1e58A 249 1.67e+01 1qhfA c.60.1.1 59262 1k3bA 119 1.69e+01 b.61.5.1 72016 1a6r 471 1.69e+01 3gcb d.3.1.1 37033 1g97A 459 1.74e+01 1fwyA b.81.1.4 60394 c.68.1.5 60395 1m6sA 347 1.75e+01 c.67.1.1 78701 1i8dA 213 1.76e+01 b.43.4.3 61953 b.43.4.3 61954 1jg8A 347 1.76e+01 1jg8A c.67.1.1 62946 1g3gA 164 1.77e+01 1g6gA b.26.1.2 23918 1ewkA 490 1.77e+01 1ewkA c.93.1.1 35712 1n7oA 721 1.82e+01 a.102.3.2 80259 b.24.1.1 80260 b.30.5.2 80261 1dfcA 493 1.83e+01 1dfcA b.42.5.1 25616 b.42.5.1 25617 b.42.5.1 25618 b.42.5.1 25619 2bbvC 363 1.84e+01 2bbvA b.121.4.4 23325 1iwdA 215 1.92e+01 d.3.1.1 83756 1gm7B 557 1.93e+01 1ppfE 218 1.94e+01 1a7s b.47.1.2 26234 1pnkB 557 1.95e+01 1ajqB 1dlhB 188 1.96e+01 1iakB b.1.1.2 21598 d.19.1.1 38172 1h9sA 140 2.00e+01 1b9mA b.40.6.2 60843 b.40.6.2 60844 3gcb 470 2.02e+01 3gcb d.3.1.1 37032 1dd6A 228 2.03e+01 1a7tA d.157.1.1 42054 1fvuB 125 2.04e+01 1ixxB d.169.1.1 42346 1eguA 731 2.09e+01 1eguA a.102.3.2 18850 b.24.1.1 23899 b.30.5.2 24423 1ui7A 638 2.10e+01 b.30.2.1 -3523 d.17.2.1 -9268 d.17.2.1 -9269 2ebn 289 2.12e+01 2ebn c.1.8.5 28990 1ihp 438 2.14e+01 1ihp c.60.1.2 33993 1gm9B 557 2.16e+01 1o04A 500 2.21e+01 c.82.1.1 86508 1cqkA 101 2.22e+01 1cqkA b.1.1.2 21547 1e3aB 560 2.23e+01 1ajqB 1f3z 161 2.28e+01 1gpr b.84.3.1 28273 1mdwA 328 2.29e+01 d.3.1.3 84934 1rc6A 261 2.32e+01 unknown_sccs -4868 1rwrA 301 2.34e+01 unknown_sccs -4787 1pjbA 361 2.37e+01 1sayA c.2.1.4 30103 c.23.12.2 31363 1bxsA 501 2.38e+01 1bpwA c.82.1.1 35357 1hn2A 159 2.38e+01 b.60.1.1 65890 1mj5A 302 2.40e+01 c.69.1.8 -8326 1sayA 361 2.40e+01 1sayA c.2.1.4 30102 c.23.12.2 31362 1uvqA 197 2.40e+01 b.1.1.2 -2649 d.19.1.1 -9336 1gcb 454 2.46e+01 3gcb d.3.1.1 37034 1hilB 220 2.47e+01 1igtB b.1.1.1 19787 b.1.1.2 20897 1b9mA 265 2.50e+01 1b9mA a.4.5.8 16118 b.40.6.2 58938 b.40.6.2 58939 1pz4A 116 2.52e+01 d.106.1.1 -10780 1pjcA 361 2.53e+01 1sayA c.2.1.4 30101 c.23.12.2 31361 1gk9B 557 2.58e+01 1i8fA 81 2.63e+01 1i8fA b.38.1.1 61959 1uctA 218 2.63e+01 b.1.1.4 88467 b.1.1.4 88468 1gkfB 557 2.64e+01 1jotA 133 2.69e+01 1jotA 1owfA 99 2.70e+01 a.55.1.1 87487 1lk2B 99 2.72e+01 b.1.1.2 -2576 1o54A 277 2.81e+01 c.66.1.13 -8095 1a3yA 149 2.83e+01 1obpA b.60.1.1 27110 1kz8A 337 2.84e+01 e.7.1.1 77633 1ea2A 131 2.89e+01 d.17.4.3 64860 1ihfA 99 2.90e+01 1huuA a.55.1.1 17893 1efuB 282 2.94e+01 1efuB a.5.2.2 58975 d.43.1.1 58976 d.43.1.1 38677 1svpA 161 2.94e+01 1svpA b.47.1.3 26384 1n8nA 212 2.96e+01 unknown_sccs -6830 1vkdA 338 2.97e+01 1as8A 343 2.98e+01 1nif b.6.1.3 23074 b.6.1.3 23075 1b8aA 438 3.00e+01 1b8aA b.40.4.1 25244 d.104.1.1 40765 1mvfD 82 3.01e+01 b.129.1.1 85143 1owfB 94 3.01e+01 a.55.1.1 87488 1qvjA 292 3.05e+01 d.113.1.1 -10902 1ihfB 94 3.06e+01 1huuA a.55.1.1 17894 1knwA 425 3.12e+01 b.49.2.3 -4274 c.1.6.1 -5229 1a88A 275 3.14e+01 1brt c.69.1.12 34707 1mdbA 539 3.18e+01 e.23.1.1 79008 1kkhA 317 3.21e+01 d.14.1.5 72645 d.58.26.3 72646 1wwaX 109 3.22e+01 1wwcA b.1.1.4 21775 1umhA 184 3.23e+01 unknown_sccs -3127 1hm9A 468 3.23e+01 b.81.1.4 65866 c.68.1.5 65867 1ksr 100 3.24e+01 1qfhA b.1.18.10 21897 1snrA 341 3.26e+01 1nezG 128 3.27e+01 b.1.1.1 85592 2fcbA 173 3.27e+01 2fcbA b.1.1.4 21781 b.1.1.4 21782 1jjyA 636 3.29e+01 1jjyA 1oh0A 131 3.30e+01 d.17.4.3 87004 1q33A 292 3.32e+01 d.113.1.1 -10901 1iakB 185 3.34e+01 1iakB b.1.1.2 21626 d.19.1.1 38200 2snv 151 3.36e+01 1svpA b.47.1.3 26394 1su8A 636 3.37e+01 e.26.1.2 -12015 1g0sA 209 3.39e+01 1g0sA d.113.1.1 60187 1o4sA 389 3.43e+01 c.67.1.1 86620 1j9qA 341 3.43e+01 1nif b.6.1.3 62765 b.6.1.3 62766 1of5B 184 3.48e+01 d.17.4.2 86934 1fzoB 99 3.54e+01 1agdB b.1.1.2 60157 1b12A 248 3.54e+01 1b12A b.87.1.2 28388 1nct 106 3.57e+01 1wit b.1.1.4 21708 1n99A 166 3.58e+01 b.36.1.1 85459 b.36.1.1 85460 1jj2B 337 3.58e+01 1ffkB b.43.3.2 63086 1mjuH 227 3.62e+01 b.1.1.1 -2245 b.1.1.2 -2495 1im3D 95 3.64e+01 1im3D b.1.18.5 62568 1lam 484 3.64e+01 1lam c.56.5.3 33829 c.50.1.1 33166 1kjvB 100 3.66e+01 b.1.1.2 77423 1fg7A 356 3.68e+01 1gewA c.67.1.1 59819 5nn9 388 3.68e+01 2qwc b.68.1.1 27563 1k12A 158 3.71e+01 b.18.1.15 71978 1kgcE 242 3.74e+01 b.1.1.1 77386 b.1.1.2 77387 1hh1A 143 3.75e+01 1gefA c.52.1.18 61036 1cjcA 460 3.76e+01 1cjcA c.3.1.1 30319 c.4.1.1 30604 2bbvA 363 3.78e+01 2bbvA b.121.4.4 23323 1lap 488 3.79e+01 1lam c.56.5.3 33834 c.50.1.1 33171 1fzkB 99 3.79e+01 1agdB b.1.1.2 60151 1fuxA 166 3.79e+01 1fjjA b.17.1.2 60034 2rmcA 182 3.81e+01 2cpl b.62.1.1 27491 1cd8 114 3.83e+01 1cd8 b.1.1.1 19714 1kpuB 99 3.87e+01 b.1.1.2 84458 1et7A 341 3.87e+01 1nif b.6.1.3 23070 b.6.1.3 23071 1nkqA 259 3.90e+01 1el6B 219 3.94e+01 1el6B d.182.1.1 42607