# List of top-scoring protein chains for t2k-100-30-dssp-ehl2-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 2cnqA 306 5.70e-01 d.143.1.1 130646 1obdA 306 7.22e-01 d.143.1.1 86767 1t6sA 162 9.35e-01 a.4.5.60,a.4.5.60 112271,112272 1a48 306 1.14e+00 1a48 1v5xA 203 1.93e+00 c.1.2.4 100377 2cunA 410 1.93e+00 1muwA 386 2.91e+00 c.1.15.3 79495 1jrmA 104 3.08e+00 d.206.1.1 67136 1ylxA 103 3.28e+00 d.82.5.1 123677 1u96A 69 3.32e+00 a.17.1.2 113232 3proC 166 3.77e+00 3proC d.52.1.1,d.52.1.1 38812,38813 2gu3A 136 4.07e+00 1n91A 108 4.17e+00 d.206.1.1 80326 1h5wA 309 4.22e+00 e.27.1.1 65635 1jnyA 435 4.49e+00 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 3proD 166 4.94e+00 3proC d.52.1.1,d.52.1.1 38814,38815 1rypK 198 5.61e+00 d.153.1.4 41879 1iu8A 206 6.19e+00 c.56.4.1 71436 1m41A 380 6.58e+00 c.1.16.4 78595 1ud0A 113 7.42e+00 a.8.4.1 99198 1dujA 187 7.78e+00 1dujA d.135.1.1 41449 2fwuA 157 7.90e+00 b.1.27.1 134262 2c6cA 707 7.92e+00 a.48.2.1,c.8.4.1,c.56.5.5 129989,129990,129991 2nr1 27 8.50e+00 1vm6A 228 8.68e+00 d.81.1.3,c.2.1.3 108877,118631 1ohtA 215 8.83e+00 d.118.1.1 87036 2a3qA 170 9.01e+00 a.204.1.2 126092 1qndA 123 9.17e+00 1qndA d.106.1.1 40794 1c44A 123 9.24e+00 1qndA d.106.1.1 40795 1ykdA 398 1.00e+01 1gw9A 388 1.03e+01 c.1.15.3 70658 2xis 387 1.04e+01 4xis 1cpy 421 1.06e+01 1ivyA 1ysc 421 1.06e+01 1ivyA 3xis 387 1.11e+01 4xis 1mnzA 388 1.11e+01 c.1.15.3 79328 1xis 387 1.11e+01 4xis 4xis 387 1.11e+01 4xis 1tr0A 108 1.14e+01 d.58.4.4 107261 1aqcA 172 1.16e+01 1x11A b.55.1.2 26983 1nqkA 381 1.16e+01 c.1.16.4 92050 1ijgA 309 1.17e+01 1fouA e.27.1.1 62493 1s5jA 847 1.18e+01 c.55.3.5,e.8.1.1 112040,112041 1klqA 197 1.18e+01 d.135.1.1 68689 1p5dX 463 1.18e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1s6cA 183 1.18e+01 a.39.1.5 98594 830cA 168 1.33e+01 1ck7A d.92.1.11 40400 1jdw 423 1.37e+01 1jdw 2jdxA 385 1.40e+01 1jdw d.126.1.2 41139 1a3qA 285 1.42e+01 1a3qA b.1.18.1,b.2.5.3 21932,22447 1d4oA 184 1.44e+01 1d4oA c.31.1.4 31748 1i1iP 681 1.50e+01 1i1iP d.92.1.5 40297 1cnuA 137 1.56e+01 1cof d.109.1.2 40862 1ywqA 200 1.56e+01 d.90.1.1 124162 1k2yX 463 1.57e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 1g8yA 279 1.63e+01 1g8yA c.37.1.11 32302 1nlfA 279 1.64e+01 c.37.1.11 85850 1cec 343 1.65e+01 1ceo 2aeuA 374 1.73e+01 c.67.1.8 126646 3aig 202 1.74e+01 1atlA 1squA 155 1.76e+01 d.252.1.1 98971 1bs0A 384 1.78e+01 1bs0A c.67.1.4 34490 1ospO 257 1.80e+01 1ospO b.76.1.1 27971 2gqrA 237 1.85e+01 1p9qC 256 2.01e+01 a.5.8.1,d.235.1.2,d.58.11.3 104093,104094,104095 1c1lA 136 2.10e+01 1c1lA b.29.1.3 24219 1u04A 771 2.12e+01 b.34.14.1,c.55.3.10 107539,107540 1qcsA 211 2.28e+01 1qcsA b.52.2.3,d.31.1.1 26927,38461 1mjhA 162 2.41e+01 1mjhA c.26.2.4 31639 1j6qA 136 2.48e+01 b.40.9.1 77091 2gu2A 312 2.49e+01 2bifA 469 2.58e+01 1bif c.37.1.7,c.60.1.4 31963,34009 1j4wA 174 2.63e+01 d.51.1.1,d.51.1.1 71529,71530 1phk 298 2.70e+01 1cdkA 1o8xA 146 2.73e+01 c.47.1.10 86681 5csmA 256 2.76e+01 5csmA a.130.1.2 19494 1kwaB 88 2.76e+01 1kwaA b.36.1.1 24773 1v7cA 351 2.78e+01 c.79.1.1 100446 1bywA 110 2.78e+01 1bywA d.110.3.6 40912 1b9mA 265 2.78e+01 1b9mA a.4.5.8,b.40.6.2,b.40.6.2 16118,58938,58939 1kutA 230 2.79e+01 d.143.1.1 73017 2fueA 262 2.88e+01 c.108.1.10 134119 1w53A 84 2.93e+01 a.186.1.2 109175 1avwB 171 2.95e+01 1wba b.42.4.1 25599 1c3oC 1073 2.97e+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 3bifA 468 2.98e+01 1bif c.37.1.7,c.60.1.4 31962,34008 1c3oE 1073 3.01e+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 3.01e+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 1qk8A 146 3.02e+01 1ewxA c.47.1.10 33061 1ewxA 146 3.02e+01 1ewxA c.47.1.10 33062 2amyA 246 3.08e+01 c.108.1.10 127026 1nrlA 316 3.12e+01 a.123.1.1 92091 2gk9A 426 3.14e+01 1c3oG 1073 3.18e+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 1z5bA 469 3.19e+01 a.156.1.3,d.14.1.3,d.122.1.2 124464,124465,124466 2ajrA 331 3.22e+01 c.72.1.1 126892 1sviA 195 3.23e+01 c.37.1.8 106048 1keeG 1073 3.28e+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 1go4A 205 3.55e+01 d.135.1.1 70292 1gqoB 143 3.64e+01 c.23.13.1 76296 1mjhB 162 3.65e+01 1mjhA c.26.2.4 31640 1kugA 203 3.69e+01 d.92.1.9 73008 1kufA 203 3.71e+01 d.92.1.9 73007 1f1sA 814 3.72e+01 a.102.3.2,b.1.18.2,b.24.1.1,b.30.5.2 64928,64929,64930,64931 1bxrA 1073 3.79e+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 18570,31499,31697,31698,41542,41543 1gqoM 143 3.82e+01 c.23.13.1 76307 1gqoE 143 3.83e+01 c.23.13.1 76299 1gqoG 143 3.83e+01 c.23.13.1 76301 1kwaA 88 3.85e+01 1kwaA b.36.1.1 24772 1zceA 155 3.87e+01 b.122.1.8 124907 1shp 55 3.91e+01 1bpi 2fw2A 260 3.95e+01 c.14.1.3 134231 1nwzA 125 4.02e+01 d.110.3.1 86370 3pyp 125 4.02e+01 3pyp 2phy 125 4.05e+01 3pyp 1gqoF 143 4.06e+01 c.23.13.1 76300 1gqoR 143 4.07e+01 c.23.13.1 76312 1lfb 99 4.15e+01 1lfb 1914 232 4.18e+01 1914 1ceo 343 4.20e+01 1ceo 2bwqA 129 4.21e+01 b.7.1.2 129380 1yewA 382 4.22e+01 2a2lA 145 4.26e+01 d.110.9.1 126035 1gqoL 143 4.26e+01 c.23.13.1 76306 2cyjA 118 4.28e+01 c.103.1.1 131026 1r8gA 372 4.28e+01 d.128.1.3 104845 1gqoS 143 4.28e+01 c.23.13.1 76313 1ebuA 358 4.32e+01 1ebuA c.2.1.3,d.81.1.2 30035,39950 1mngA 203 4.33e+01 1avmA a.2.11.1,d.44.1.1 15776,38701 1dosA 358 4.36e+01 1dosA c.1.10.2 29175 1b57A 358 4.39e+01 1dosA c.1.10.2 29177 1jagA 241 4.42e+01 1q53A 112 4.43e+01 d.58.4.4 95858 1qa9A 102 4.43e+01 1qa9A b.1.1.1 19742 1oxsC 353 4.55e+01 b.40.6.3,c.37.1.12 87519,87520 1fobA 334 4.59e+01 c.1.8.3 83255 1kx5A 135 4.60e+01 a.22.1.1 77593 1oivA 191 4.63e+01 c.37.1.8 93076 1cs0C 1073 4.65e+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 1ykuA 136 4.65e+01 1oxxK 353 4.65e+01 b.40.6.3,c.37.1.12 93715,93716 1jbaA 204 4.66e+01 1rec a.39.1.5 17330 1o0pA 104 4.66e+01 d.58.7.1 86535 1xr4A 509 4.67e+01 c.124.1.2,c.124.1.2 115860,115861 1exnB 290 4.68e+01 1exnA a.60.7.1,c.120.1.2 18089,33359 1fit 147 4.69e+01 1fit 1cs0A 1073 4.69e+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 1enp 312 4.77e+01 1enp 1tiqA 180 4.84e+01 d.108.1.1 107010 2lfb 100 4.84e+01 1lfb 1uasA 362 4.85e+01 b.71.1.1,c.1.8.1 88388,88389 1rzmA 338 4.89e+01 c.1.10.4 105137 1c3oA 1073 4.90e+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 1ztuA 341 4.92e+01 1pd21 199 4.93e+01 1pd21 1jdbB 1073 4.93e+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 1bif 469 4.97e+01 1bif 1zbfA 142 5.01e+01 c.55.3.1 124850 1mu5A 471 5.15e+01 a.156.1.3,d.14.1.3,d.122.1.2 79472,79473,79474 1fcdA 401 5.17e+01 1fcdA c.3.1.5,c.3.1.5,d.87.1.1 30593,30594,40218 3phy 125 5.18e+01 3pyp 1gqoH 143 5.24e+01 c.23.13.1 76302 1rxwA 336 5.24e+01 a.60.7.1,c.120.1.2 98059,98060 1keeC 1073 5.24e+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 68500,68501,68502,68503,68504,68505 2bosA 68 5.26e+01 2bosA b.40.2.1 25025 1zgmA 248 5.28e+01 2fnoA 248 5.28e+01 a.45.1.1,c.47.1.5 133821,133822 1aoiA 116 5.37e+01 1aoiA a.22.1.1 16462 1pguA 615 5.39e+01 b.69.4.1,b.69.4.1 88069,88070 1es2A 262 5.41e+01 1skf e.3.1.1 42680 2abqA 306 5.44e+01 c.72.1.1 126528 1hwyA 501 5.55e+01 1hwyA c.2.1.7,c.58.1.1 30262,33910 2fo3A 125 5.57e+01 d.20.1.1 133868 1gqoI 143 5.57e+01 c.23.13.1 76303 1gqoO 143 5.57e+01 c.23.13.1 76309 1gqoP 143 5.57e+01 c.23.13.1 76310 1t95A 240 5.62e+01 a.5.8.1,d.235.1.2,d.58.11.3 106705,106706,106707 1flp 142 5.65e+01 1flp 1moh 142 5.65e+01 1flp 1s1eA 224 5.65e+01 a.39.1.5 112007 1vggA 161 5.68e+01 d.256.1.1 113647 1uy4A 145 5.70e+01 b.18.1.10 108131 1i1gA 141 5.74e+01 a.4.5.32,d.58.4.2 65982,65983 1gqoQ 143 5.77e+01 c.23.13.1 76311 1r4pB 70 5.77e+01 b.40.2.1 97026 1gqoC 143 5.86e+01 c.23.13.1 76297 1weyA 104 5.87e+01 d.58.7.1 114569 1gqoJ 143 5.88e+01 c.23.13.1 76304 1tn6B 437 5.90e+01 a.102.4.3 112528 1uanA 227 5.99e+01 c.134.1.1 99135 1mixA 206 6.02e+01 a.11.2.1,b.55.1.5 79166,79167 1a9xA 1058 6.19e+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 1em2A 229 6.24e+01 1em2A d.129.3.2 41321 1gqoY 143 6.24e+01 c.23.13.1 76318 1gqoK 143 6.32e+01 c.23.13.1 76305 2cvdA 198 6.35e+01 a.45.1.1,c.47.1.5 130861,130862 1u0jA 267 6.38e+01 c.37.1.20 107546 1cezA 883 6.42e+01 1cezA e.8.1.3 43110 1es5A 262 6.48e+01 1skf e.3.1.1 42679 1skf 262 6.49e+01 1skf 1fc6A 388 6.51e+01 1fc6A b.36.1.3,c.14.1.2 64738,64739 1hwxA 501 6.55e+01 1hwyA c.2.1.7,c.58.1.1 30250,33898 1bg2 325 6.61e+01 1bg2 1keeA 1073 6.62e+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 1crzA 403 6.65e+01 1crzA b.68.4.1,c.51.2.1 27629,33211 1tf5A 844 6.74e+01 a.162.1.1,a.172.1.1,c.37.1.19,c.37.1.19 106834,106835,106836,106837 1gqoD 143 6.81e+01 c.23.13.1 76298 1gqoU 143 6.81e+01 c.23.13.1 76315 1qlnA 883 6.84e+01 1cezA e.8.1.3 43111 1vcbB 112 6.85e+01 1vcbB d.42.1.1 38633 1b06A 210 6.86e+01 1avmA a.2.11.1,d.44.1.1 15740,38737 1esiA 262 6.87e+01 1skf e.3.1.1 42682 1v02A 565 6.91e+01 c.1.8.4 108194 1f66A 136 6.92e+01 1aoiA a.22.1.1 16460 1is1A 185 6.95e+01 d.67.3.1 83704 1ld8B 437 6.96e+01 a.102.4.3 73839 1cdzA 96 6.98e+01 1cdzA c.15.1.1 30925 1yarH 217 7.01e+01 d.153.1.4 122844 1joyA 67 7.02e+01 1joyA a.30.2.1 16991 1jc9A 269 7.06e+01 d.171.1.1 66490 1ilyA 90 7.06e+01 c.55.4.1 71245 1b63A 333 7.18e+01 1b63A d.14.1.3,d.122.1.2 37566,41107 1b43A 340 7.23e+01 1a76 a.60.7.1,c.120.1.2 18092,33362 1c5kA 439 7.24e+01 1crzA b.68.4.1,c.51.2.1 27630,33212 2f9lA 199 7.26e+01 c.37.1.8 133166 1wr2A 238 7.33e+01 1mgpA 313 7.34e+01 c.119.1.1 79098 1hjsA 332 7.45e+01 c.1.8.3 83492 2essA 248 7.50e+01 d.38.1.8,d.38.1.8 132346,132347 1qttA 117 7.61e+01 1a1x b.63.1.1 27516 2aq4A 434 7.75e+01 1jovA 270 7.78e+01 b.30.5.7 84192 1a6pA 94 7.78e+01 1cdcA b.1.1.1 19748 1jidA 128 7.82e+01 d.201.1.1 66735 1a64A 97 7.96e+01 1cdcA b.1.1.1 19750 1l0qA 391 8.02e+01 b.1.3.1,b.69.2.3 77644,77645 1q4rA 112 8.06e+01 d.58.4.4 95823 1o58A 303 8.07e+01 c.79.1.1 92491 1zxzA 197 8.14e+01 1dqtA 117 8.19e+01 1ah1 b.1.1.1 20653 1hnf 182 8.20e+01 1qa9A 1u0sA 86 8.20e+01 d.58.24.1 107565 2c2aA 258 8.24e+01 a.30.2.1,d.122.1.3 129662,129663 1ebfA 358 8.26e+01 1ebuA c.2.1.3,d.81.1.2 30033,39948 1eguA 731 8.27e+01 1eguA a.102.3.2,b.24.1.1,b.30.5.2 18850,23899,24423 1d2eA 397 8.29e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25701,25741,32136 2bfdA 400 8.32e+01 1x7yA 400 8.32e+01 c.36.1.11 114944 1ut8A 291 8.33e+01 a.60.7.1,c.120.1.2 99908,99909 1tqzA 133 8.39e+01 b.55.1.11 119327 2c7hA 86 8.41e+01 1pmaP 211 8.41e+01 1pmaP d.153.1.4 41863 1vpkA 378 8.42e+01 d.131.1.1,d.131.1.1,d.131.1.1 113963,113964,113965 1es4A 262 8.44e+01 1skf e.3.1.1 42683 1i27A 73 8.51e+01 1i27A a.4.5.30 61555 1gqoT 143 8.55e+01 c.23.13.1 76314 1gqoX 143 8.58e+01 c.23.13.1 76317 1xn5A 146 8.59e+01 d.129.3.5 115574 1r2jA 366 8.60e+01 a.29.3.1,e.6.1.1 96869,96870 1obr 326 8.65e+01 1aye 1jic 62 8.72e+01 1azpA 1xovA 326 8.75e+01 b.34.11.4,c.56.5.6 122206,122207 1y2mA 716 8.78e+01 1ogaD 215 8.80e+01 b.1.1.1,b.1.1.2 86990,86991 1fi4A 416 8.86e+01 1fi4A d.14.1.5,d.58.26.2 59847,59848 1ex1A 605 8.87e+01 1ex1A c.1.8.7,c.23.11.1 29013,31347 1wt6A 81 8.94e+01 1mszA 86 8.94e+01 d.68.7.1 79428 1xh9A 350 8.95e+01 1fwkA 296 8.96e+01 1fwkA d.14.1.5,d.58.26.1 37576,39398