# 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 2fe7A 166 3.83e-18 1yr0A 175 4.05e-17 1yvoA 172 1.07e-16 2bl1A 172 1.18e-16 2ge3A 170 3.17e-16 2beiA 170 5.45e-16 2cy2A 174 5.25e-15 1vhsA 175 1.12e-14 d.108.1.1 100698 1tiqA 180 1.34e-14 d.108.1.1 107010 1z4eA 153 1.49e-14 2b5gA 171 3.43e-14 1u6mA 199 3.44e-14 1s3zA 165 6.08e-14 d.108.1.1 105250 1qsoA 149 1.25e-13 1qsmA d.108.1.1 40812 2ae6A 166 1.32e-13 1qsmA 152 1.65e-13 1qsmA d.108.1.1 40808 1wwzA 159 1.83e-13 1y9kA 157 1.03e-12 1gheA 177 1.55e-12 d.108.1.1 76222 1on0A 158 8.69e-12 d.108.1.1 87095 1ufhA 180 1.03e-11 d.108.1.1 88485 1mk4A 157 1.27e-11 d.108.1.1 84979 2fl4A 149 1.29e-11 1yx0A 159 1.60e-11 1vkcA 158 2.18e-11 2c27A 315 2.87e-11 1p0hA 318 4.58e-11 d.108.1.1 93866 1i12A 160 5.17e-11 1i21A d.108.1.1 61515 1cjwA 166 6.95e-11 1cjwA d.108.1.1 40818 1i1dA 161 7.40e-11 1i21A d.108.1.1 61526 1i21A 159 1.01e-10 1i21A d.108.1.1 61549 1nslA 184 1.16e-10 d.108.1.1 86137 1yreA 197 1.52e-10 2bswA 146 1.71e-10 1q2yA 140 1.90e-10 d.108.1.1 95655 1kuxA 207 2.77e-10 d.108.1.1 73021 1y9wA 140 4.15e-10 2g3aA 152 4.49e-10 1yvkA 163 4.71e-10 2ganA 190 1.44e-09 1b87A 181 1.75e-09 1b87A d.108.1.1 40797 2a4nA 182 2.08e-09 2atrA 138 2.14e-09 1b6bA 174 2.16e-09 1cjwA d.108.1.1 40819 1s7kA 182 2.24e-09 1n71A 180 2.33e-09 d.108.1.1 85370 1xebA 150 3.51e-09 2fckA 181 4.49e-09 1qstA 160 5.08e-09 1yghA d.108.1.1 40804 1z4rA 168 1.15e-08 1bo4A 168 1.96e-08 1bo4A d.108.1.1 40798 5gcnA 166 2.60e-08 1yghA d.108.1.1 40807 1bo4B 168 3.44e-08 1bo4A d.108.1.1 40799 2aj6A 159 8.92e-08 1y7rA 133 1.21e-07 1sqhA 312 1.48e-07 d.108.1.5 98966 1m4iA 181 1.90e-07 d.108.1.1 74457 1yghA 164 3.21e-07 1yghA d.108.1.1 40802 2fsrA 195 3.88e-06 1nmtA 392 5.91e-05 1nmtA d.108.1.2,d.108.1.2 40823,40824 1yk3A 210 7.62e-05 1fy7A 278 7.91e-04 1fy7A d.108.1.1 40817 2d4pA 141 1.20e-03 1bob 320 2.28e-03 1bob d.108.1.1 40816 1yleA 342 4.62e-03 2givA 295 8.68e-03 1xmtA 103 9.45e-03 1iicA 422 1.09e-02 1nmtA d.108.1.2,d.108.1.2 62422,62423 1ne9A 335 4.90e-02 d.108.1.4,d.108.1.4 91839,91840 1kzfA 230 5.68e-02 d.108.1.3 73354 1k4jA 230 7.69e-02 d.108.1.3 72057 1ro5A 201 2.15e-01 d.108.1.3 105023 1shdA 107 1.00e+00 1fmk d.93.1.1 40440 2bhmA 164 1.03e+00 1svjA 156 1.41e+00 d.220.1.1 106049 1pxtB 390 2.09e+00 1afwA c.95.1.1,c.95.1.1 35906,35907 1vicA 262 2.32e+00 c.68.1.13 100756 1qflA 389 2.57e+00 1afwA c.95.1.1,c.95.1.1 35908,35909 1afwA 393 2.61e+00 1afwA c.95.1.1,c.95.1.1 35900,35901 1m3kA 392 2.72e+00 c.95.1.1,c.95.1.1 78565,78566 1m4tA 392 2.76e+00 c.95.1.1,c.95.1.1 78617,78618 1eysH 259 3.15e+00 6prcH b.41.1.1,f.23.10.1 25484,43517 1d5tA 433 3.36e+00 1gnd c.3.1.3,d.16.1.6 30422,37986 1xtlA 175 4.00e+00 1v2xA 194 4.04e+00 c.116.1.1 100274 1s4iA 175 4.17e+00 1xtmA 175 4.26e+00 1o50A 157 4.46e+00 d.37.1.1,d.37.1.1 92478,92479 1diiC 80 4.84e+00 1diiC a.3.1.1 15925 1tuoA 464 5.10e+00 1rfmA 344 5.43e+00 c.122.1.1 97385 1y1uA 585 6.23e+00 3minC 491 6.40e+00 1qguA c.92.2.3 35607 1ndk 155 6.94e+00 1npk d.58.6.1 39118 1aup 449 6.98e+00 1k89 c.2.1.7,c.58.1.1 30222,33870 1qysA 106 7.13e+00 k.41.1.1 96603 1qhqA 140 7.75e+00 1qhqA b.6.1.1 63326 1k89 449 7.77e+00 1k89 c.2.1.7,c.58.1.1 30218,33866 1iznB 277 8.35e+00 e.43.1.2 83848 1ox6A 555 8.67e+00 c.1.2.1,c.23.16.1 87505,87506 1vdnA 162 9.24e+00 1s57A 153 9.28e+00 1pu1A 94 9.33e+00 d.266.1.1 104307 1y0bA 197 9.73e+00 1ayzA 169 1.00e+01 1u9aA d.20.1.1 38326 1rvgA 305 1.01e+01 c.1.10.2 97920 2cpl 165 1.09e+01 2cpl b.62.1.1 27420 1kolA 398 1.20e+01 b.35.1.2,c.2.1.1 77474,77475 1agjA 242 1.20e+01 1agjA b.47.1.1 25827 1jqiA 388 1.21e+01 a.29.3.1,e.6.1.1 67087,67088 1r5jA 337 1.23e+01 c.77.1.5 97097 2minA 491 1.26e+01 1qguA c.92.2.3 35609 1yndA 165 1.28e+01 1f1xA 322 1.29e+01 d.32.1.3,d.32.1.3 83208,83209 1wveC 80 1.29e+01 1llwA 1520 1.30e+01 b.80.4.1,c.1.4.1,d.153.1.1 74017,74018,74019 1pvmA 184 1.32e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 2gw2A 198 1.34e+01 1zzmA 259 1.34e+01 1cwoA 165 1.36e+01 2cpl b.62.1.1 27445 1rxyA 253 1.38e+01 c.56.2.1 98065 1zejA 293 1.41e+01 1lx7A 253 1.46e+01 c.56.2.1 74329 1awqA 164 1.46e+01 2cpl b.62.1.1 27461 1o6aA 96 1.48e+01 b.139.1.1 92562 1nxuA 333 1.49e+01 c.122.1.1 86389 1awsA 164 1.51e+01 2cpl b.62.1.1 27431 1npk 154 1.53e+01 1npk d.58.6.1 39099 1ne6A 283 1.53e+01 b.82.3.2,b.82.3.2 91831,91832 1zy9A 564 1.53e+01 1m8jA 181 1.56e+01 c.26.1.3 84875 1k8qA 377 1.61e+01 c.69.1.6 72177 1ci0A 228 1.62e+01 1ci0A b.45.1.1 25750 1f3fA 155 1.65e+01 1npk d.58.6.1 39101 1gteD 1025 1.67e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70455,70456,70457,70458,70459 1ucnA 152 1.69e+01 d.58.6.1 99183 1kllA 130 1.69e+01 d.32.1.2 72720 2gfaA 119 1.78e+01 1h0pA 182 1.78e+01 b.62.1.1 76450 1gthA 1025 1.79e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70483,70484,70485,70486,70487 1gthC 1025 1.79e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70493,70494,70495,70496,70497 1f2fA 104 1.82e+01 1fmk d.93.1.1 40455 1wzvA 155 1.82e+01 1h7xB 1025 1.82e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15688,28633,30329,30614,39012 1h7xA 1025 1.83e+01 1h7wA a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15687,28632,30328,30613,39011 1h7xC 1025 1.83e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15689,28634,30330,30615,39013 1xqiA 195 1.83e+01 1h7xD 1025 1.85e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15690,28635,30331,30616,39014 1stfI 98 1.85e+01 1stfI d.17.1.2 38006 1gt8C 1025 1.85e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70428,70429,70430,70431,70432 1j5eK 129 1.87e+01 c.55.4.1 71554 1h7wA 1025 1.90e+01 1h7wA a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15683,28628,30324,30609,39007 1gteA 1025 1.90e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70440,70441,70442,70443,70444 1e79D 482 1.90e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 18272,26437,32317 1fp4A 492 1.90e+01 c.92.2.3 76187 1h7wB 1025 1.90e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15684,28629,30325,30610,39008 1gt8D 1025 1.91e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70433,70434,70435,70436,70437 1lqpA 135 1.91e+01 d.32.1.2 78151 1nkiA 135 1.92e+01 d.32.1.2 91941 2ck3D 482 1.92e+01 1prcH 259 1.92e+01 6prcH b.41.1.1,f.23.10.1 25460,43445 1h7wD 1025 1.93e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15686,28631,30327,30612,39010 2bjrA 368 1.96e+01 1h8eD 482 1.96e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 60747,60748,60749 2cxaA 256 2.00e+01 1skyE 473 2.08e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 18314,26479,32359 1ofdA 1520 2.12e+01 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 1zo0A 126 2.12e+01 1ssxA 198 2.12e+01 b.47.1.1 98978 2alp 198 2.12e+01 1qq4A b.47.1.1 25772 1p04A 198 2.12e+01 1qq4A b.47.1.1 25805 1qq4A 198 2.13e+01 1qq4A b.47.1.1 25768 1zmaA 118 2.14e+01 1dioA 554 2.14e+01 1dioA c.1.19.3 29656 1eexA 554 2.16e+01 1dioA c.1.19.3 29650 4pfk 319 2.20e+01 3pfk c.89.1.1 35582 1m1nA 491 2.23e+01 c.92.2.3 78417 1df9A 191 2.25e+01 1befA b.47.1.3 26420 1dgaA 375 2.26e+01 1yagA 1hqsA 423 2.29e+01 1iso c.77.1.1 61154 1shbA 104 2.32e+01 1fmk d.93.1.1 40425 1zcoA 262 2.35e+01 1wqaA 455 2.39e+01 1f1uA 323 2.41e+01 d.32.1.3,d.32.1.3 83200,83201 1hrdA 449 2.42e+01 1k89 c.2.1.7,c.58.1.1 30219,33867 3pfk 319 2.42e+01 3pfk c.89.1.1 35581 1pea 385 2.43e+01 1pea c.93.1.1 35662 1ej2A 181 2.43e+01 1f9aA c.26.1.3 59414 1aop 497 2.44e+01 2aop d.58.36.1,d.58.36.1,d.134.1.1,d.134.1.1 39501,39502,41425,41426 1zn6A 227 2.45e+01 1g4uS 383 2.45e+01 1g4uS a.24.11.1,c.45.1.2 16643,32691 2aop 497 2.47e+01 2aop d.58.36.1,d.58.36.1,d.134.1.1,d.134.1.1 39503,39504,41427,41428 6pfkA 319 2.51e+01 3pfk c.89.1.1 35583 1gthB 1025 2.54e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70488,70489,70490,70491,70492 1gt8B 1025 2.54e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70423,70424,70425,70426,70427 1g2qA 187 2.56e+01 c.61.1.1 65117 1gt8A 1025 2.59e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70418,70419,70420,70421,70422 1wn5A 130 2.60e+01 2cfeA 162 2.61e+01 1t0aA 159 2.77e+01 2cwkA 160 2.78e+01 1ss4A 153 2.82e+01 d.32.1.6 105976 2bklA 695 2.84e+01 2d5cA 263 2.87e+01 1u7eB 154 2.87e+01 1rgs 288 2.89e+01 1rgs b.82.3.2,b.82.3.2 28146,28147 2gwdA 449 2.92e+01 1q3iA 214 2.95e+01 d.220.1.1 104524 2cy0A 263 2.99e+01 1gt7A 274 3.01e+01 c.74.1.1 70398 2ew2A 316 3.04e+01 1tr7A 164 3.13e+01 2a50B 168 3.15e+01 1y0hA 105 3.19e+01 1dceA 567 3.20e+01 1dceA a.118.6.1,b.7.4.1,c.10.2.2 19191,23218,30867 1ojrA 274 3.22e+01 c.74.1.1 93147 2btoA 473 3.22e+01 1b0vA 106 3.24e+01 1a6l d.58.1.2 38982 1n6zA 105 3.24e+01 d.263.1.1 85369 1shaA 104 3.30e+01 1fmk d.93.1.1 40424 1wxdA 263 3.30e+01 1ni9A 338 3.32e+01 e.7.1.2 85739 1o13A 136 3.32e+01 c.55.5.1 80762 1ut1A 148 3.33e+01 b.2.3.6 108014 1nhkL 144 3.36e+01 1npk d.58.6.1 39142 2g5dA 422 3.36e+01 1y81A 138 3.38e+01 1vhmA 195 3.39e+01 d.110.2.1 100691 2bitX 165 3.40e+01 6prcH 258 3.41e+01 6prcH b.41.1.1,f.23.10.1 25457,43436 1o4rA 108 3.41e+01 d.93.1.1 92469 1o9yA 84 3.41e+01 b.139.1.1 92692 1uwfA 158 3.42e+01 1yagA 375 3.43e+01 1yagA c.55.1.1,c.55.1.1 33449,33450 1a1aA 107 3.44e+01 1fmk d.93.1.1 40449 1gpwB 201 3.48e+01 c.23.16.1 65461 2f7fA 494 3.56e+01 1p5dX 463 3.57e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1dxrH 258 3.77e+01 6prcH b.41.1.1,f.23.10.1 25456,43433 1o0wA 252 3.79e+01 a.149.1.1,d.50.1.1 80751,80752 1k2yX 463 3.82e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 1g4wR 383 3.84e+01 1g4uS a.24.11.1,c.45.1.2 16644,32692 1tkjA 284 3.86e+01 1tf9A 284 3.88e+01 1ufoA 238 3.89e+01 c.69.1.27 99344 1oo4A 111 3.92e+01 d.93.1.1 87185 1fsgA 233 3.96e+01 1qk3A c.61.1.1 34029 2cxhA 217 3.96e+01 1w94A 156 3.96e+01 1fjgK 129 4.00e+01 1fjfK c.55.4.1 33733 1gsa 316 4.01e+01 1gsa c.30.1.3,d.142.1.1 31718,41477 1jkmB 361 4.04e+01 1jkmA c.69.1.2 34634 1uxaA 194 4.08e+01 b.21.1.1 108091 1qq9A 284 4.09e+01 1xjo c.56.5.4 33841 1w44A 331 4.11e+01 1xjo 284 4.14e+01 1xjo c.56.5.4 33843 1oalA 151 4.23e+01 b.1.8.1 86739 2fyxA 143 4.23e+01 1f9aA 168 4.25e+01 1f9aA c.26.1.3 31602 1lrzA 426 4.28e+01 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 1fjcA 96 4.28e+01 1fjcA d.58.7.1 39212 1oniA 137 4.28e+01 d.79.1.1 87144 1flcA 432 4.37e+01 1flcA b.19.1.3,c.23.10.2 23837,31337 1q2wA 308 4.38e+01 b.47.1.4 88355 1wl4A 397 4.40e+01 2as9A 210 4.40e+01 1apyA 162 4.47e+01 1apyA d.153.1.5 42004 1fjeB 175 4.47e+01 1fj7A d.58.7.1,d.58.7.1 39210,39211 1d4xA 375 4.51e+01 1yagA c.55.1.1,c.55.1.1 59107,59108 2ae2A 260 4.61e+01 1bdb c.2.1.2 29945 2a5kA 307 4.61e+01 1rqpA 299 4.63e+01 b.141.1.1,c.132.1.1 97754,97755 1gtmA 419 4.64e+01 1hwyA c.2.1.7,c.58.1.1 30223,33871 1h7zA 194 4.69e+01 1qhvA b.21.1.1 60733 2db1A 118 4.79e+01 1t5yA 190 4.79e+01 b.122.1.1,d.17.6.3 106495,106496 1bgvA 449 4.80e+01 1k89 c.2.1.7,c.58.1.1 30217,33865 1ipiA 123 4.80e+01 c.52.1.18 66255 1vl2A 421 4.81e+01 c.26.2.1,d.210.1.1 108708,108709 1nrgA 261 4.85e+01 b.45.1.1 80694 1klfB 279 4.88e+01 b.2.3.2,b.2.3.2 72684,72685 1j6zA 376 4.88e+01 1yagA c.55.1.1,c.55.1.1 62667,62668 1wuaA 375 4.95e+01 1u60A 310 4.96e+01 e.3.1.2 107692 1bo1A 416 4.96e+01 1bo1A d.143.1.2 41591 1yaiA 151 4.97e+01 1yaiA b.1.8.1 22289 1ykdA 398 4.97e+01 1l8qA 324 4.98e+01 a.4.12.2,c.37.1.20 77809,77810 2bj7A 138 4.98e+01 1hybA 181 4.99e+01 1f9aA c.26.1.3 61399 1qz5A 375 5.05e+01 c.55.1.1,c.55.1.1 96614,96615 1bvoA 175 5.05e+01 1a3qA b.2.5.3 22457 1bia 321 5.10e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1scfA 273 5.12e+01 1exzA a.26.1.2 16873 1gefA 123 5.12e+01 1gefA c.52.1.18 60465 2fxuA 375 5.15e+01 1bawA 105 5.15e+01 1plc b.6.1.1 22868 2fpnA 216 5.22e+01 1ockA 412 5.23e+01 c.117.1.1 86802 1uebA 184 5.23e+01 b.34.5.2,b.40.4.5,b.40.4.5 107782,107783,107784 1tahA 318 5.26e+01 1cvl c.69.1.18 34775 1qunB 279 5.27e+01 b.2.3.2,b.2.3.2 22411,22412 1h3nA 878 5.28e+01 a.27.1.1,b.51.1.1,c.26.1.1 76641,76642,76643 2fsjA 346 5.30e+01 1f32A 149 5.30e+01 1f32A d.62.1.1 39539 2btfA 375 5.31e+01 1yagA c.55.1.1,c.55.1.1 33429,33430 1sqwA 188 5.32e+01 1ecfA 504 5.34e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 1l3kA 196 5.38e+01 d.58.7.1,d.58.7.1 73539,73540 1cvl 319 5.41e+01 1cvl c.69.1.18 34786 1cvrA 435 5.43e+01 1cvrA b.1.18.12,c.17.1.2 21949,31006 1xo7A 166 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