# List of top-scoring protein chains for t2k-100-30-str2-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 1yr0A 175 4.61e-18 2fe7A 166 6.10e-18 1yvoA 172 3.14e-17 2bl1A 172 1.30e-16 2ge3A 170 1.93e-16 2beiA 170 3.98e-16 2cy2A 174 3.26e-15 1tiqA 180 3.64e-15 d.108.1.1 107010 1vhsA 175 7.45e-15 d.108.1.1 100698 1s3zA 165 7.57e-15 d.108.1.1 105250 1u6mA 199 1.49e-14 1z4eA 153 1.92e-14 2ae6A 166 2.97e-14 2b5gA 171 3.79e-14 1qsmA 152 8.91e-14 1qsmA d.108.1.1 40808 1qsoA 149 1.67e-13 1qsmA d.108.1.1 40812 1wwzA 159 1.75e-13 1gheA 177 2.88e-13 d.108.1.1 76222 1y9kA 157 5.24e-13 2fl4A 149 1.23e-12 1vkcA 158 6.56e-12 1ufhA 180 7.77e-12 d.108.1.1 88485 1nslA 184 9.15e-12 d.108.1.1 86137 1on0A 158 1.09e-11 d.108.1.1 87095 2c27A 315 1.33e-11 1i12A 160 1.65e-11 1i21A d.108.1.1 61515 1kuxA 207 1.90e-11 d.108.1.1 73021 1cjwA 166 2.12e-11 1cjwA d.108.1.1 40818 1mk4A 157 2.24e-11 d.108.1.1 84979 1i1dA 161 2.49e-11 1i21A d.108.1.1 61526 1p0hA 318 2.62e-11 d.108.1.1 93866 1yx0A 159 2.91e-11 1yreA 197 3.13e-11 1i21A 159 4.59e-11 1i21A d.108.1.1 61549 1yvkA 163 6.33e-11 1b87A 181 7.25e-11 1b87A d.108.1.1 40797 2a4nA 182 7.30e-11 2ganA 190 8.85e-11 1n71A 180 1.08e-10 d.108.1.1 85370 1q2yA 140 1.11e-10 d.108.1.1 95655 1y9wA 140 1.11e-10 1s7kA 182 1.67e-10 2bswA 146 1.77e-10 2g3aA 152 1.86e-10 1xebA 150 3.20e-10 2fckA 181 3.60e-10 2atrA 138 8.24e-10 1bo4B 168 8.72e-10 1bo4A d.108.1.1 40799 1z4rA 168 1.58e-09 1bo4A 168 2.04e-09 1bo4A d.108.1.1 40798 1b6bA 174 2.33e-09 1cjwA d.108.1.1 40819 1qstA 160 3.97e-09 1yghA d.108.1.1 40804 2aj6A 159 4.77e-09 5gcnA 166 1.98e-08 1yghA d.108.1.1 40807 1y7rA 133 2.22e-08 1yghA 164 3.67e-08 1yghA d.108.1.1 40802 1m4iA 181 6.03e-08 d.108.1.1 74457 1sqhA 312 1.57e-07 d.108.1.5 98966 2fsrA 195 2.83e-07 1yk3A 210 1.05e-06 1nmtA 392 6.19e-06 1nmtA d.108.1.2,d.108.1.2 40823,40824 2d4pA 141 6.05e-05 1bob 320 2.83e-04 1bob d.108.1.1 40816 1fy7A 278 3.73e-04 1fy7A d.108.1.1 40817 1iicA 422 3.74e-04 1nmtA d.108.1.2,d.108.1.2 62422,62423 1yleA 342 6.27e-04 1kzfA 230 1.07e-03 d.108.1.3 73354 1k4jA 230 2.07e-03 d.108.1.3 72057 1xmtA 103 2.23e-03 1ne9A 335 2.55e-03 d.108.1.4,d.108.1.4 91839,91840 2givA 295 3.25e-03 1ro5A 201 5.76e-03 d.108.1.3 105023 1svjA 156 2.46e-02 d.220.1.1 106049 2b8eA 273 2.22e-01 2cxaA 256 2.79e-01 1vdnA 162 4.00e-01 1vicA 262 5.50e-01 c.68.1.13 100756 2gw2A 198 6.27e-01 2cfeA 162 6.71e-01 1cwoA 165 7.34e-01 2cpl b.62.1.1 27445 1yndA 165 7.56e-01 2cpl 165 7.61e-01 2cpl b.62.1.1 27420 1lx7A 253 8.10e-01 c.56.2.1 74329 1shdA 107 8.89e-01 1fmk d.93.1.1 40440 1o50A 157 9.79e-01 d.37.1.1,d.37.1.1 92478,92479 1xtmA 175 1.00e-00 1awqA 164 1.03e+00 2cpl b.62.1.1 27461 1xtlA 175 1.04e+00 2aop 497 1.19e+00 2aop d.58.36.1,d.58.36.1,d.134.1.1,d.134.1.1 39503,39504,41427,41428 1awsA 164 1.36e+00 2cpl b.62.1.1 27431 2bitX 165 1.40e+00 2arhA 203 1.81e+00 1rxyA 253 1.83e+00 c.56.2.1 98065 1zmaA 118 1.93e+00 1h7wB 1025 1.98e+00 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 1bglA 1023 2.02e+00 1bglA b.1.4.1,b.1.4.1,b.18.1.5,b.30.5.1,c.1.8.3 22097,22098,23734,24358,28857 1aop 497 2.03e+00 2aop d.58.36.1,d.58.36.1,d.134.1.1,d.134.1.1 39501,39502,41425,41426 1h7xC 1025 2.20e+00 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 1h7wD 1025 2.20e+00 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 1h7xB 1025 2.20e+00 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 1h7xD 1025 2.23e+00 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 1gteA 1025 2.26e+00 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 1h3iA 293 2.43e+00 b.76.2.1,b.85.7.1 76635,76636 1kllA 130 2.45e+00 d.32.1.2 72720 1s4iA 175 2.46e+00 1vq2A 193 2.51e+00 1h0pA 182 2.57e+00 b.62.1.1 76450 1ni9A 338 2.57e+00 e.7.1.2 85739 2cxhA 217 2.69e+00 1zyoA 191 2.73e+00 1qflA 389 2.89e+00 1afwA c.95.1.1,c.95.1.1 35908,35909 1fp4A 492 3.01e+00 c.92.2.3 76187 1m3kA 392 3.08e+00 c.95.1.1,c.95.1.1 78565,78566 1w94A 156 3.10e+00 1xo7A 166 3.10e+00 1pvmA 184 3.12e+00 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1m4tA 392 3.18e+00 c.95.1.1,c.95.1.1 78617,78618 1pxtB 390 3.19e+00 1afwA c.95.1.1,c.95.1.1 35906,35907 1qq4A 198 3.23e+00 1qq4A b.47.1.1 25768 1p04A 198 3.23e+00 1qq4A b.47.1.1 25805 2alp 198 3.24e+00 1qq4A b.47.1.1 25772 1ssxA 198 3.25e+00 b.47.1.1 98978 1afwA 393 3.30e+00 1afwA c.95.1.1,c.95.1.1 35900,35901 1a58 177 3.34e+00 2cpl b.62.1.1 27495 1o0wA 252 3.41e+00 a.149.1.1,d.50.1.1 80751,80752 1o13A 136 3.62e+00 c.55.5.1 80762 2a5kA 307 3.63e+00 1o9yA 84 3.67e+00 b.139.1.1 92692 1to6A 371 3.70e+00 c.141.1.1 107170 1qysA 106 3.76e+00 k.41.1.1 96603 1ihgA 370 3.77e+00 2cpl a.118.8.1,b.62.1.1 62380,62381 1gthC 1025 3.83e+00 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 2amdA 311 3.83e+00 1q2wA 308 3.85e+00 b.47.1.4 88355 1dp0A 1023 3.86e+00 b.1.4.1,b.1.4.1,b.18.1.5,b.30.5.1,c.1.8.3 22073,22074,23722,24346,28845 1h7wA 1025 3.88e+00 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 1gteD 1025 3.97e+00 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 1f1uA 323 4.08e+00 d.32.1.3,d.32.1.3 83200,83201 1cvrA 435 4.13e+00 1cvrA b.1.18.12,c.17.1.2 21949,31006 1v2xA 194 4.14e+00 c.116.1.1 100274 1vl2A 421 4.24e+00 c.26.2.1,d.210.1.1 108708,108709 1gt8C 1025 4.32e+00 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 1h7xA 1025 4.32e+00 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 1ss4A 153 4.49e+00 d.32.1.6 105976 1jz8A 1023 4.53e+00 b.1.4.1,b.1.4.1,b.18.1.5,b.30.5.1,c.1.8.3 67830,67831,67832,67833,67834 1rfmA 344 5.05e+00 c.122.1.1 97385 1f1xA 322 5.07e+00 d.32.1.3,d.32.1.3 83208,83209 1rypH 205 5.07e+00 d.153.1.4 41876 1kolA 398 5.21e+00 b.35.1.2,c.2.1.1 77474,77475 1pbjA 125 5.31e+00 d.37.1.1,d.37.1.1 94414,94415 1y81A 138 5.32e+00 2minA 491 5.52e+00 1qguA c.92.2.3 35609 1dapA 320 5.79e+00 1dapA c.2.1.3,d.81.1.3 30053,39968 1qoiA 177 5.89e+00 2cpl b.62.1.1 27490 1lqpA 135 5.93e+00 d.32.1.2 78151 1nkiA 135 5.93e+00 d.32.1.2 91941 2trxA 108 6.11e+00 1thx c.47.1.1 32719 3dapA 320 6.18e+00 1dapA c.2.1.3,d.81.1.3 30051,39966 1g4uS 383 6.19e+00 1g4uS a.24.11.1,c.45.1.2 16643,32691 1ecfA 504 6.29e+00 1ecfB c.61.1.1,d.153.1.1 34053,41820 1k3fA 253 6.56e+00 c.56.2.1 68105 1ecfB 504 6.57e+00 1ecfB c.61.1.1,d.153.1.1 34054,41821 1r5jA 337 6.68e+00 c.77.1.5 97097 1dywA 173 6.69e+00 2cpl b.62.1.1 27505 1gthA 1025 6.70e+00 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 1f06A 320 6.72e+00 1dapA c.2.1.3,d.81.1.3 59556,59557 3minC 491 6.74e+00 1qguA c.92.2.3 35607 1ofdA 1520 6.81e+00 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 1s57A 153 6.82e+00 2bhmA 164 6.85e+00 1oalA 151 6.93e+00 b.1.8.1 86739 1zcxA 178 7.12e+00 2bklA 695 7.24e+00 1j5eK 129 7.55e+00 c.55.4.1 71554 2b18A 164 7.56e+00 1pea 385 8.25e+00 1pea c.93.1.1 35662 1wzlA 585 8.33e+00 1lkdA 297 8.33e+00 d.32.1.3,d.32.1.3 78059,78060 2atzA 180 8.33e+00 1xmzA 241 8.40e+00 2bj7A 138 8.48e+00 1han 297 8.71e+00 1han d.32.1.3,d.32.1.3 38506,38507 1ji2A 585 8.98e+00 b.1.18.2,b.71.1.1,c.1.8.1 71672,71673,71674 1ne6A 283 9.03e+00 b.82.3.2,b.82.3.2 91831,91832 1yaiA 151 9.32e+00 1yaiA b.1.8.1 22289 2a8nA 144 9.45e+00 1try 224 9.68e+00 5ptp b.47.1.2 26017 1gsa 316 9.83e+00 1gsa c.30.1.3,d.142.1.1 31718,41477 1u7eB 154 9.95e+00 1o6aA 96 1.02e+01 b.139.1.1 92562 1f2fA 104 1.04e+01 1fmk d.93.1.1 40455 1p5dX 463 1.05e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1oniA 137 1.06e+01 d.79.1.1 87144 1g4wR 383 1.06e+01 1g4uS a.24.11.1,c.45.1.2 16644,32692 1wkqA 164 1.06e+01 c.97.1.2 109393 1su4A 994 1.07e+01 b.82.7.1,c.108.1.7,d.220.1.1,f.33.1.1 98993,98994,98995,98996 1jp4A 308 1.07e+01 1jp4A e.7.1.1 63223 1hqsA 423 1.08e+01 1iso c.77.1.1 61154 2a50B 168 1.09e+01 1gt8A 1025 1.09e+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 1fn8A 224 1.10e+01 5ptp b.47.1.2 26012 1lgtA 297 1.12e+01 d.32.1.3,d.32.1.3 77956,77957 1tiyA 164 1.13e+01 c.97.1.2 107012 1shbA 104 1.14e+01 1fmk d.93.1.1 40425 1ydgA 211 1.18e+01 1eulA 994 1.19e+01 1eulA 1erv 105 1.20e+01 1erv c.47.1.1 32743 1wqaA 455 1.21e+01 1m8jA 181 1.23e+01 c.26.1.3 84875 2d5cA 263 1.25e+01 1k2yX 463 1.25e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 1q3iA 214 1.26e+01 d.220.1.1 104524 1mt6A 280 1.27e+01 b.76.2.1,b.85.7.1 79446,79447 1llwA 1520 1.27e+01 b.80.4.1,c.1.4.1,d.153.1.1 74017,74018,74019 1lrzA 426 1.27e+01 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 1uwfA 158 1.28e+01 1yemA 179 1.28e+01 9rnt 104 1.28e+01 9rnt d.1.1.4 36055 1mtpB 43 1.29e+01 1rg9A 383 1.29e+01 d.130.1.1,d.130.1.1,d.130.1.1 97427,97428,97429 1d5tA 433 1.30e+01 1gnd c.3.1.3,d.16.1.6 30422,37986 1sqwA 188 1.32e+01 1zo0A 126 1.33e+01 1d2pA 373 1.33e+01 1d2oA b.3.5.1,b.3.5.1,b.3.5.1,b.3.5.1 22629,22630,22631,22632 1azvA 153 1.35e+01 1mfmA b.1.8.1 22247 1mgpA 313 1.36e+01 c.119.1.1 79098 1b0tA 106 1.38e+01 1a6l d.58.1.2 38965 1wxdA 263 1.39e+01 2cy0A 263 1.40e+01 1bo1A 416 1.42e+01 1bo1A d.143.1.2 41591 1nxuA 333 1.42e+01 c.122.1.1 86389 2cvjA 180 1.43e+01 1kw3B 292 1.46e+01 d.32.1.3,d.32.1.3 77549,77550 1kebA 108 1.46e+01 c.47.1.1 77341 1skyE 473 1.48e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 18314,26479,32359 2essA 248 1.48e+01 2gwdA 449 1.49e+01 1zejA 293 1.53e+01 2agcA 162 1.55e+01 1o12A 376 1.59e+01 b.92.1.5,c.1.9.10 80758,80759 1wpgA 994 1.59e+01 1y1uA 585 1.60e+01 1zn6A 227 1.61e+01 1w4vA 119 1.63e+01 1zq7A 207 1.63e+01 1m1nA 491 1.63e+01 c.92.2.3 78417 1w0nA 131 1.64e+01 1yocA 147 1.64e+01 1stfI 98 1.65e+01 1stfI d.17.1.2 38006 1tr7A 164 1.68e+01 1gt7A 274 1.72e+01 c.74.1.1 70398 1rgs 288 1.74e+01 1rgs b.82.3.2,b.82.3.2 28146,28147 1qunB 279 1.75e+01 b.2.3.2,b.2.3.2 22411,22412 1klfB 279 1.75e+01 b.2.3.2,b.2.3.2 72684,72685 1ojrA 274 1.79e+01 c.74.1.1 93147 1uae 419 1.80e+01 1uae d.68.2.2 39574 1ti6B 274 1.81e+01 b.3.5.1,d.58.1.5 106976,106977 1ypyA 184 1.83e+01 1gpl 432 1.83e+01 1gpl b.12.1.2,c.69.1.19 23645,34793 1l0wA 580 1.84e+01 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1pu5A 164 1.85e+01 b.95.1.1 104310 1tahB 318 1.86e+01 1cvl c.69.1.18 34774 1v93A 296 1.87e+01 c.1.23.1 100532 1uvzA 119 1.88e+01 1gthB 1025 1.89e+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 1dioA 554 1.90e+01 1dioA c.1.19.3 29656 1eexA 554 1.90e+01 1dioA c.1.19.3 29650 1qgxA 357 1.91e+01 1qgxA e.7.1.1 42973 1tahA 318 1.93e+01 1cvl c.69.1.18 34775 1pmhX 185 1.93e+01 b.18.1.18 104193 1edzA 320 1.94e+01 1ee9A c.2.1.7,c.58.1.2 30287,33935 1eysH 259 1.96e+01 6prcH b.41.1.1,f.23.10.1 25484,43517 1t0aA 159 1.96e+01 1i0vA 104 1.97e+01 9rnt d.1.1.4 36054 3rnt 104 1.97e+01 9rnt d.1.1.4 36069 1uehA 253 1.98e+01 c.101.1.1 99259 1zcoA 262 1.99e+01 1o4rA 108 1.99e+01 d.93.1.1 92469 1st9A 143 2.00e+01 c.47.1.10 98987 1ebdA 455 2.00e+01 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30577,30578,40210 1l8qA 324 2.01e+01 a.4.12.2,c.37.1.20 77809,77810 1tuoA 464 2.01e+01 1r6xA 395 2.01e+01 b.122.1.3,c.26.1.5 97167,97168 1ka1A 357 2.02e+01 e.7.1.1 68369 1gt8B 1025 2.02e+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 1ei5A 520 2.03e+01 1ei5A b.61.3.1,b.61.3.1,e.3.1.1 27418,27419,42772 1iznB 277 2.03e+01 e.43.1.2 83848 1fjgK 129 2.05e+01 1fjfK c.55.4.1 33733 1s8nA 205 2.06e+01 c.23.1.1 105374 1shaA 104 2.06e+01 1fmk d.93.1.1 40424 1jp3A 253 2.08e+01 1f75A c.101.1.1 63221 1mxb 383 2.09e+01 1mxb d.130.1.1,d.130.1.1,d.130.1.1 41329,41330,41331 1rypI 222 2.09e+01 d.153.1.4 41877 2au3A 407 2.10e+01 1whtB 153 2.10e+01 1whtB 1whsB 153 2.10e+01 1whtB 1hw7A 255 2.16e+01 1i7fA d.193.1.1 61297 2f9sA 151 2.18e+01 1cx4A 305 2.18e+01 b.82.3.2,b.82.3.2 59099,59100 1a6l 106 2.20e+01 1a6l d.58.1.2 38966 1ucnA 152 2.20e+01 d.58.6.1 99183 1n7kA 234 2.22e+01 c.1.10.1 85374 1g13A 162 2.22e+01 1g13A b.95.1.1 60194 7fd1A 106 2.23e+01 1a6l d.58.1.2 38953 1bcsB 160 2.24e+01 1whtB 1ej2A 181 2.24e+01 1f9aA c.26.1.3 59414 1yagA 375 2.24e+01 1yagA c.55.1.1,c.55.1.1 33449,33450 2gfaA 119 2.25e+01 1onqA 283 2.25e+01 b.1.1.2,d.19.1.1 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