# List of top-scoring protein chains for t2k-100-30-stride-ebghtl-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 1t6sA 162 2.06e-01 a.4.5.60,a.4.5.60 112271,112272 3proC 166 4.73e-01 3proC d.52.1.1,d.52.1.1 38812,38813 2cnqA 306 4.92e-01 d.143.1.1 130646 1obdA 306 5.55e-01 d.143.1.1 86767 1a48 306 7.41e-01 1a48 1c44A 123 1.41e+00 1qndA d.106.1.1 40795 1ylxA 103 1.50e+00 d.82.5.1 123677 1m41A 380 1.64e+00 c.1.16.4 78595 2a3qA 170 2.21e+00 a.204.1.2 126092 1ykdA 398 3.02e+00 1nqkA 381 3.16e+00 c.1.16.4 92050 1n91A 108 3.33e+00 d.206.1.1 80326 3proD 166 3.39e+00 3proC d.52.1.1,d.52.1.1 38814,38815 1ohtA 215 3.60e+00 d.118.1.1 87036 2a2lA 145 3.69e+00 d.110.9.1 126035 1cnuA 137 3.87e+00 1cof d.109.1.2 40862 1d4oA 184 4.02e+00 1d4oA c.31.1.4 31748 1qndA 123 4.09e+00 1qndA d.106.1.1 40794 1h5wA 309 4.24e+00 e.27.1.1 65635 1jrmA 104 4.26e+00 d.206.1.1 67136 2gu3A 136 4.37e+00 1phk 298 5.74e+00 1cdkA 1jagA 241 6.23e+00 1th5A 74 6.24e+00 d.52.8.1 119263 1bs0A 384 6.69e+00 1bs0A c.67.1.4 34490 1mngA 203 7.18e+00 1avmA a.2.11.1,d.44.1.1 15776,38701 2nr1 27 7.45e+00 1hwyA 501 7.84e+00 1hwyA c.2.1.7,c.58.1.1 30262,33910 1sviA 195 8.60e+00 c.37.1.8 106048 1v5xA 203 9.34e+00 c.1.2.4 100377 1kutA 230 9.50e+00 d.143.1.1 73017 1s5jA 847 9.62e+00 c.55.3.5,e.8.1.1 112040,112041 1ospO 257 9.75e+00 1ospO b.76.1.1 27971 1ijgA 309 9.75e+00 1fouA e.27.1.1 62493 1a3qA 285 1.07e+01 1a3qA b.1.18.1,b.2.5.3 21932,22447 1oivA 191 1.13e+01 c.37.1.8 93076 1j4wA 174 1.23e+01 d.51.1.1,d.51.1.1 71529,71530 1i1iP 681 1.23e+01 1i1iP d.92.1.5 40297 1bywA 110 1.27e+01 1bywA d.110.3.6 40912 2aat 396 1.27e+01 1ajsA 1b9mA 265 1.31e+01 1b9mA a.4.5.8,b.40.6.2,b.40.6.2 16118,58938,58939 1em2A 229 1.38e+01 1em2A d.129.3.2 41321 3aig 202 1.50e+01 1atlA 2fo3A 125 1.51e+01 d.20.1.1 133868 2c6cA 707 1.54e+01 a.48.2.1,c.8.4.1,c.56.5.5 129989,129990,129991 1mjhA 162 1.55e+01 1mjhA c.26.2.4 31639 1mjhB 162 1.56e+01 1mjhA c.26.2.4 31640 1muwA 386 1.58e+01 c.1.15.3 79495 1kwaB 88 1.66e+01 1kwaA b.36.1.1 24773 1pvgA 418 1.68e+01 d.14.1.3,d.122.1.2 95161,95162 2gqrA 237 1.70e+01 1aqcA 172 1.75e+01 1x11A b.55.1.2 26983 1zgmA 248 1.76e+01 1s6cA 183 1.76e+01 a.39.1.5 98594 1u96A 69 1.78e+01 a.17.1.2 113232 2fnoA 248 1.78e+01 a.45.1.1,c.47.1.5 133821,133822 2cunA 410 1.83e+01 1k2yX 463 1.84e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 1p5dX 463 1.84e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 5csmA 256 1.88e+01 5csmA a.130.1.2 19494 1jbaA 204 1.90e+01 1rec a.39.1.5 17330 2amyA 246 1.90e+01 c.108.1.10 127026 1hwxA 501 1.90e+01 1hwyA c.2.1.7,c.58.1.1 30250,33898 1u04A 771 2.00e+01 b.34.14.1,c.55.3.10 107539,107540 1ysc 421 2.05e+01 1ivyA 1tiqA 180 2.08e+01 d.108.1.1 107010 1jnyA 435 2.13e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1cpy 421 2.31e+01 1ivyA 2lfb 100 2.32e+01 1lfb 1lfb 99 2.34e+01 1lfb 1c8cA 64 2.38e+01 1azpA b.34.13.1 59084 1b57A 358 2.49e+01 1dosA c.1.10.2 29177 1ro0A 216 2.58e+01 d.264.1.2 97664 1y96B 85 2.60e+01 1o8xA 146 2.60e+01 c.47.1.10 86681 3bifA 468 2.66e+01 1bif c.37.1.7,c.60.1.4 31962,34008 1jc9A 269 2.69e+01 d.171.1.1 66490 1k0hA 117 2.71e+01 b.106.1.2 71975 1yarH 217 2.74e+01 d.153.1.4 122844 1shp 55 2.84e+01 1bpi 1ewxA 146 2.84e+01 1ewxA c.47.1.10 33062 1es2A 262 2.85e+01 1skf e.3.1.1 42680 3pyp 125 2.86e+01 3pyp 2gi9A 56 2.87e+01 2c2aA 258 2.88e+01 a.30.2.1,d.122.1.3 129662,129663 1hbxA 92 2.88e+01 1mnmA d.88.1.1 60930 1txvA 452 2.89e+01 b.69.8.1 112783 2f9lA 199 2.91e+01 c.37.1.8 133166 1vpkA 378 2.93e+01 d.131.1.1,d.131.1.1,d.131.1.1 113963,113964,113965 1w53A 84 3.04e+01 a.186.1.2 109175 1nwzA 125 3.05e+01 d.110.3.1 86370 1pgx 83 3.07e+01 2igd 1fc6A 388 3.12e+01 1fc6A b.36.1.3,c.14.1.2 64738,64739 1lxkA 721 3.17e+01 a.102.3.2,b.24.1.1,b.30.5.2 74331,74332,74333 2bwqA 129 3.19e+01 b.7.1.2 129380 1qk8A 146 3.24e+01 1ewxA c.47.1.10 33061 1jdw 423 3.25e+01 1jdw 1kufA 203 3.26e+01 d.92.1.9 73007 1nlfA 279 3.29e+01 c.37.1.11 85850 1kugA 203 3.30e+01 d.92.1.9 73008 1tr0A 108 3.31e+01 d.58.4.4 107261 1ywqA 200 3.32e+01 d.90.1.1 124162 2fw2A 260 3.34e+01 c.14.1.3 134231 1g8yA 279 3.35e+01 1g8yA c.37.1.11 32302 2phy 125 3.36e+01 3pyp 1skf 262 3.42e+01 1skf 1es5A 262 3.47e+01 1skf e.3.1.1 42679 1u0jA 267 3.47e+01 c.37.1.20 107546 1i1gA 141 3.48e+01 a.4.5.32,d.58.4.2 65982,65983 2bosA 68 3.49e+01 2bosA b.40.2.1 25025 1b06A 210 3.58e+01 1avmA a.2.11.1,d.44.1.1 15740,38737 1klqA 197 3.68e+01 d.135.1.1 68689 1ztuA 341 3.69e+01 1mgpA 313 3.70e+01 c.119.1.1 79098 2fueA 262 3.71e+01 c.108.1.10 134119 1uanA 227 3.73e+01 c.134.1.1 99135 1esiA 262 3.75e+01 1skf e.3.1.1 42682 1azqA 66 3.75e+01 1azpA b.34.13.1 37469 1fxxA 482 3.78e+01 1fxxA c.55.3.5 33726 1ud0A 113 3.83e+01 a.8.4.1 99198 1pguA 615 3.91e+01 b.69.4.1,b.69.4.1 88069,88070 1kvdB 77 4.00e+01 1kveB 1zceA 155 4.01e+01 b.122.1.8 124907 1kveB 77 4.01e+01 1kveB 2fbmA 291 4.02e+01 c.14.1.3 133251 1ro2A 216 4.06e+01 d.264.1.2 97665 1es4A 262 4.12e+01 1skf e.3.1.1 42683 1dosA 358 4.14e+01 1dosA c.1.10.2 29175 1h38B 883 4.17e+01 e.8.1.3 76626 1bf4A 63 4.17e+01 1azpA b.34.13.1 37461 1igd 61 4.20e+01 2igd 2igd 61 4.20e+01 2igd 1go4A 205 4.25e+01 d.135.1.1 70292 2ng1 293 4.33e+01 1ng1 2g3aA 152 4.33e+01 d.108.1.1 134557 1yewA 382 4.35e+01 1yqtA 538 4.39e+01 1xh9A 350 4.40e+01 1a1x 108 4.40e+01 1a1x 1v74A 107 4.42e+01 d.243.1.1 100442 2fwuA 157 4.47e+01 b.1.27.1 134262 4xis 387 4.48e+01 4xis 1pmaP 211 4.55e+01 1pmaP d.153.1.4 41863 1r4pB 70 4.56e+01 b.40.2.1 97026 1zejA 293 4.61e+01 1kwaA 88 4.61e+01 1kwaA b.36.1.1 24772 1j1uA 306 4.71e+01 c.26.1.1 83980 1wuiL 534 4.72e+01 e.18.1.1 121289 1ubkL 534 4.73e+01 e.18.1.1 88422 1o22A 170 4.78e+01 d.238.1.1 86557 1vh5A 148 4.90e+01 d.38.1.5 100642 1dujA 187 5.08e+01 1dujA d.135.1.1 41449 2aeuA 374 5.12e+01 c.67.1.8 126646 1f1xA 322 5.20e+01 d.32.1.3,d.32.1.3 83208,83209 1vkcA 158 5.24e+01 d.108.1.1 113663 1fuxA 166 5.27e+01 1fjjA b.17.1.2 60034 2ex3B 264 5.31e+01 a.263.1.1 132500 1yw3A 208 5.32e+01 2bf6A 449 5.35e+01 1iu8A 206 5.37e+01 c.56.4.1 71436 1n7oA 721 5.37e+01 a.102.3.2,b.24.1.1,b.30.5.2 80259,80260,80261 1gv3A 248 5.38e+01 a.2.11.1,d.44.1.1 70585,70586 1e0tA 470 5.47e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 1eguA 731 5.51e+01 1eguA a.102.3.2,b.24.1.1,b.30.5.2 18850,23899,24423 1v93A 296 5.52e+01 c.1.23.1 100532 830cA 168 5.52e+01 1ck7A d.92.1.11 40400 1lvhA 221 5.58e+01 c.108.1.6 74282 2jdxA 385 5.68e+01 1jdw d.126.1.2 41139 1in0A 163 5.70e+01 d.58.49.1,d.58.49.1 83694,83695 1oxxK 353 5.72e+01 b.40.6.3,c.37.1.12 93715,93716 1b63A 333 5.79e+01 1b63A d.14.1.3,d.122.1.2 37566,41107 1gw9A 388 5.80e+01 c.1.15.3 70658 1xr4A 509 5.80e+01 c.124.1.2,c.124.1.2 115860,115861 1xis 387 5.80e+01 4xis 2xis 387 5.80e+01 4xis 1mnzA 388 5.80e+01 c.1.15.3 79328 3xis 387 5.80e+01 4xis 3phy 125 5.81e+01 3pyp 1uxxX 133 5.85e+01 b.18.1.10 100169 1q53A 112 5.88e+01 d.58.4.4 95858 1cec 343 5.90e+01 1ceo 2fhi 147 6.00e+01 1fit 1cdcA 99 6.11e+01 1cdcA b.1.1.1 19746 1cdcB 99 6.11e+01 1cdcA b.1.1.1 19747 1s1eA 224 6.18e+01 a.39.1.5 112007 1qmgA 524 6.18e+01 1qmgA a.100.1.2,c.2.1.6 18785,30182 1atlA 202 6.19e+01 1atlA d.92.1.9 40322 1aam 396 6.20e+01 1ajsA 1pd21 199 6.25e+01 1pd21 1yveI 524 6.26e+01 1qmgA a.100.1.2,c.2.1.6 18789,30186 1mzuA 129 6.27e+01 d.110.3.1 79714 1yveJ 524 6.33e+01 1qmgA a.100.1.2,c.2.1.6 18790,30187 1e4eA 343 6.34e+01 1iow c.30.1.2,d.142.1.1 59221,59222 1f1uA 323 6.35e+01 d.32.1.3,d.32.1.3 83200,83201 1jidA 128 6.39e+01 d.201.1.1 66735 1oxsC 353 6.40e+01 b.40.6.3,c.37.1.12 87519,87520 1c3oE 1073 6.52e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18564,31493,31685,31686,41530,41531 1keeE 1073 6.58e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 68508,68509,68510,68511,68512,68513 2bfdA 400 6.72e+01 1914 232 6.75e+01 1914 1g6aA 271 6.87e+01 1btl e.3.1.1 42704 2afbA 351 6.98e+01 c.72.1.1 126674 1olsA 400 6.98e+01 c.36.1.11 93331 1m6iA 493 7.00e+01 c.3.1.5,c.3.1.5,d.87.1.1 74533,74534,74535 1cs0C 1073 7.00e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18559,31488,31675,31676,41520,41521 1jdbB 1073 7.02e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18574,31503,31705,31706,41550,41551 1z47A 355 7.02e+01 1ilyA 90 7.07e+01 c.55.4.1 71245 1ykuA 136 7.08e+01 1b62A 349 7.19e+01 1b63A d.14.1.3,d.122.1.2 37567,41108 1f7sA 139 7.23e+01 1cof d.109.1.2 40857 1c3oC 1073 7.24e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18563,31492,31683,31684,41528,41529 1x7yA 400 7.26e+01 c.36.1.11 114944 1weyA 104 7.27e+01 d.58.7.1 114569 1gqoY 143 7.28e+01 c.23.13.1 76318 1u84A 90 7.29e+01 a.230.1.1 113114 1dmwA 307 7.30e+01 4pah d.178.1.1 42580 1dthA 203 7.32e+01 1atlA d.92.1.9 40324 1art 396 7.35e+01 1ajsA 1bxrA 1073 7.36e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18570,31499,31697,31698,41542,41543 1dqtA 117 7.38e+01 1ah1 b.1.1.1 20653 1crzA 403 7.39e+01 1crzA b.68.4.1,c.51.2.1 27629,33211 1sr9A 644 7.41e+01 a.5.7.1,c.1.10.5,d.270.1.1 105960,105961,105962 1jovA 270 7.47e+01 b.30.5.7 84192 1j8uA 325 7.51e+01 d.178.1.1 71611 1gqoC 143 7.54e+01 c.23.13.1 76297 1cof 143 7.54e+01 1cof 1qttA 117 7.55e+01 1a1x b.63.1.1 27516 1keeA 1073 7.61e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 68492,68493,68494,68495,68496,68497 1v1rA 400 7.66e+01 c.36.1.11 108272 1cfyA 143 7.68e+01 1cof d.109.1.2 40858 1gqoQ 143 7.76e+01 c.23.13.1 76311 1c3oG 1073 7.76e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18565,31494,31687,31688,41532,41533 1cs0A 1073 7.76e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18558,31487,31673,31674,41518,41519 1xccA 220 7.78e+01 c.47.1.10 115113 1csmA 256 7.79e+01 5csmA a.130.1.2 19495 1a9xA 1058 7.79e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18550,31479,31657,31658,41502,41503 1keeG 1073 7.80e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 68516,68517,68518,68519,68520,68521 1ceo 343 7.81e+01 1ceo 1cojA 212 7.86e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1c5kA 439 7.90e+01 1crzA b.68.4.1,c.51.2.1 27630,33212 1spa 396 7.91e+01 1ajsA 1wt6A 81 7.96e+01 2cyjA 118 7.98e+01 c.103.1.1 131026 1pprM 312 7.99e+01 1pprM a.131.1.1,a.131.1.1 19502,19503 1viwB 198 8.03e+01 1led b.29.1.1 24170 1fxzA 476 8.05e+01 b.82.1.2,b.82.1.2 65059,65060 1h2rL 534 8.11e+01 1h2rL e.18.1.1 43298 1ars 396 8.16e+01 1ajsA 2bwfA 77 8.20e+01 d.15.1.1 129363 2cqsA 842 8.22e+01 1joyA 67 8.24e+01 1joyA a.30.2.1 16991 1apmE 350 8.25e+01 1cdkA d.144.1.7 41628 1qisA 396 8.28e+01 1ajsA c.67.1.1 34284 1jpmA 366 8.33e+01 c.1.11.2,d.54.1.1 67031,67032 1q8uA 350 8.33e+01 d.144.1.7 96230 1ng1 294 8.34e+01 1ng1 1c3oA 1073 8.38e+01 1c3oA a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18562,31491,31681,31682,41526,41527 1wr2A 238 8.38e+01 1pah 308 8.47e+01 4pah 1flrL 219 8.50e+01 8fabA b.1.1.1,b.1.1.2 19904,20998 1jm1A 204 8.52e+01 b.33.1.1 71745 1keeC 1073 8.56e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 68500,68501,68502,68503,68504,68505 2av5A 120 8.56e+01 1aiaA 396 8.57e+01 1ajsA c.67.1.1 34306 2gk9A 426 8.62e+01 1e8oA 85 8.66e+01 1914 d.49.1.1 38773 1nekA 588 8.66e+01 a.7.3.1,c.3.1.4,d.168.1.1 80426,80427,80428 1ariA 396 8.67e+01 1ajsA c.67.1.1 34331 1at0 145 8.74e+01 1at0 2bifA 469 8.74e+01 1bif c.37.1.7,c.60.1.4 31963,34009 1qq2A 199 8.80e+01 1qq2A c.47.1.10 33064 1ogaD 215 8.80e+01 b.1.1.1,b.1.1.2 86990,86991 1iuhA 198 8.80e+01 d.61.1.2 83711 4pah 308 8.82e+01 4pah 1asg 396 8.85e+01 1ajsA 1jlvA 209 8.92e+01 a.45.1.1,c.47.1.5 71729,71730 1gqoP 143 8.92e+01 c.23.13.1 76310