# List of top-scoring protein chains for t04-100-30-str2 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 1c7qA 445 8.63e-34 2pgi c.80.1.2 35307 1iatA 557 1.64e-07 1dqrA c.80.1.2 62123 1moq 368 5.68e-02 1moq c.80.1.1 35302 1j5xA 342 1.40e-01 c.80.1.1 71591 1gpmA 525 1.72e-01 1gpmA c.23.16.1 31405 c.26.2.1 31608 d.52.2.1 38826 1o58A 303 1.72e-01 c.79.1.1 -8503 1sxjE 354 1.88e-01 1iv8A 720 2.01e-01 b.71.1.1 76842 c.1.8.1 76843 1kay 381 2.04e-01 1ba1 c.55.1.1 33385 c.55.1.1 33386 1bupA 386 2.35e-01 1ba1 c.55.1.1 33377 c.55.1.1 33378 1vimA 200 2.55e-01 c.80.1.3 -8532 1kaeA 434 2.90e-01 c.82.1.2 72247 1m6jA 261 3.84e-01 c.1.1.1 78693 1eziA 228 4.00e-01 1eyrA c.68.1.13 34512 1ad2 228 4.78e-01 1ad2 e.24.1.1 43353 1f0kA 364 8.12e-01 1f0kA c.87.1.2 35465 1jz8A 1023 9.34e-01 b.1.4.1 67830 b.1.4.1 67831 b.18.1.5 67832 b.30.5.1 67833 c.1.8.3 67834 1knqA 175 9.35e-01 c.37.1.17 72786 1q1gA 276 9.42e-01 c.56.2.1 -7846 1jx2B 315 1.06e+00 c.37.1.8 67404 1mldA 314 1.24e+00 2cmd c.2.1.5 30122 d.162.1.1 42089 1n2zA 245 1.24e+00 c.92.2.2 79865 1dp0A 1023 1.31e+00 b.1.4.1 22073 b.1.4.1 22074 b.18.1.5 23722 b.30.5.1 24346 c.1.8.3 28845 1ptvA 321 1.55e+00 1pty c.45.1.2 32665 1k8tA 510 1.59e+00 e.41.1.1 68316 1t35A 191 1.59e+00 unknown_sccs -7285 1ur5A 309 1.63e+00 c.2.1.5 -5910 d.162.1.1 -11477 1kyqA 274 1.67e+00 c.2.1.11 73281 e.37.1.1 73282 1q15A 503 1.70e+00 c.26.2.1 -6625 d.153.1.1 -11400 1mv8A 436 1.95e+00 a.100.1.4 85128 c.2.1.6 85129 c.26.3.1 85130 1meoA 209 2.23e+00 c.65.1.1 79035 1jeoA 180 2.95e+00 c.80.1.3 66611 1r3eA 309 3.05e+00 b.122.1.1 -5118 unknown_sccs -10146 1qv9A 283 3.08e+00 unknown_sccs -6888 1dp4A 435 3.09e+00 1dp4A c.93.1.1 35710 1i6lA 328 3.11e+00 c.26.1.1 66041 1e8cA 498 3.28e+00 c.98.1.1 59377 c.59.1.1 59378 c.72.2.1 59379 1mtzA 293 3.51e+00 c.69.1.7 79467 1qopA 268 3.69e+00 2tysA c.1.2.4 28570 1rqpA 299 3.75e+00 unknown_sccs -4411 unknown_sccs -7908 1e3jA 352 4.19e+00 1e3jA b.35.1.2 24765 c.2.1.1 29781 1e5xA 486 4.31e+00 c.79.1.1 59283 1q7hA 153 4.33e+00 b.122.1.1 -5124 unknown_sccs -9313 1lj8A 493 4.43e+00 a.100.1.9 78033 c.2.1.6 78034 1q8iA 783 4.70e+00 c.55.3.5 -7635 e.8.1.1 -11885 1a12A 413 4.97e+00 1a12A b.69.5.1 27663 1pa1A 310 5.04e+00 c.45.1.2 -7332 2liv 344 5.18e+00 2liv c.93.1.1 35708 1bpoA 494 5.20e+00 1bpoA a.118.1.4 19143 b.69.6.1 27670 1us5A 314 5.31e+00 c.94.1.1 -8686 1iq6A 134 5.54e+00 d.38.1.4 76755 1je0A 236 5.67e+00 c.56.2.1 66581 6ldh 330 5.71e+00 3ldh c.2.1.5 30161 d.162.1.1 42128 1j6rA 214 5.79e+00 d.173.1.2 71598 1dxeA 256 6.19e+00 1dxeA c.1.12.5 29310 1qs1A 462 6.29e+00 1qs1A d.166.1.1 42260 d.166.1.1 42261 1cs1A 386 6.65e+00 1ibjA c.67.1.3 34399 1jjvA 206 6.70e+00 c.37.1.1 71698 1oeqA 418 7.33e+00 1d2rA 326 7.78e+00 1d2rB c.26.1.1 31572 1ecfA 504 8.08e+00 1ecfB c.61.1.1 34053 d.153.1.1 41820 1f0xA 571 8.09e+00 1f0xA d.58.32.2 39483 d.145.1.1 41746 1i24A 404 8.16e+00 c.2.1.2 83663 1iw7C 1119 8.52e+00 e.29.1.1 71474 2cmd 312 8.91e+00 2cmd c.2.1.5 30135 d.162.1.1 42102 1qo0D 196 9.29e+00 1qo0D c.23.1.3 31125 2tysA 268 9.50e+00 2tysA c.1.2.4 28572 1b8aA 438 1.01e+01 1b8aA b.40.4.1 25244 d.104.1.1 40765 1g0hA 252 1.02e+01 1dk4A e.7.1.1 60171 1q4gA 553 1.08e+01 a.93.1.2 -1248 g.3.11.1 -12492 1sf8A 126 1.10e+01 2masA 314 1.11e+01 2masA c.70.1.1 34810 1uouA 474 1.13e+01 a.46.2.1 -951 c.27.1.1 -6642 d.41.3.1 -9715 1o66A 275 1.14e+01 c.1.12.8 -5590 1mnaA 298 1.17e+01 c.69.1.22 79322 1imjA 210 1.20e+01 c.69.1.23 71246 1usgA 346 1.20e+01 c.93.1.1 -8635 1oe8A 211 1.22e+01 a.45.1.1 86905 c.47.1.5 86906 1i2aA 219 1.23e+01 e.24.1.1 -12012 1su4A 994 1.23e+01 b.82.7.1 -4927 c.108.1.7 -6854 d.220.1.1 -11668 f.33.1.1 -12333 1rtu 114 1.26e+01 9rnt d.1.1.4 36139 1p99A 295 1.29e+01 c.94.1.1 -8697 1ek4A 418 1.30e+01 1dd8A c.95.1.1 59436 c.95.1.1 59437 1io7A 368 1.41e+01 1f4tA a.104.1.1 18971 1j08A 226 1.41e+01 c.47.1.2 83855 c.47.1.2 83856 1n25A 368 1.43e+01 c.37.1.20 85264 1kevA 351 1.44e+01 1pedA b.35.1.2 24749 c.2.1.1 29765 1a8l 226 1.51e+01 1a8l c.47.1.2 32777 c.47.1.2 32778 1p0hA 318 1.52e+01 d.108.1.1 -10802 1k8kA 418 1.60e+01 c.55.1.1 68305 c.55.1.1 68306 1rqlA 267 1.61e+01 c.108.1.3 -6814 1h6dA 433 1.68e+01 c.2.1.3 65656 d.81.1.5 65657 1uq5A 263 1.68e+01 d.165.1.1 -11555 1axn 323 1.69e+01 1avc a.65.1.1 18149 1i39A 225 1.69e+01 1ekeA c.55.3.1 61585 1i2oA 316 1.70e+01 1onrA c.1.10.1 61574 1nytA 271 1.72e+01 c.2.1.7 86417 c.58.1.5 86418 1ky3A 182 1.73e+01 c.37.1.8 73193 1v9dA 340 1.75e+01 unknown_sccs -1762 1jqbA 351 1.76e+01 b.35.1.2 77151 c.2.1.1 77152 1umdB 324 1.76e+01 c.36.1.7 -6929 c.48.1.2 -7539 1noyA 388 1.81e+01 1clqA c.55.3.5 33713 1nogA 177 1.84e+01 a.25.2.2 85923 4pfk 319 1.85e+01 3pfk c.89.1.1 35582 1sixA 174 1.90e+01 b.85.4.1 -5030 1p5sA 203 1.91e+01 a.40.1.1 -900 1im8A 244 1.91e+01 c.66.1.14 66212 1xel 338 1.92e+01 1xel c.2.1.2 29786 1jbiA 100 2.01e+01 d.209.1.1 66481 1vjrA 271 2.01e+01 unknown_sccs -6853 1b0uA 262 2.07e+01 1b0uA c.37.1.12 32370 1o54A 277 2.07e+01 c.66.1.13 -8095 1udc 338 2.08e+01 1xel c.2.1.2 29785 1jb9A 316 2.08e+01 1fnc b.43.4.2 62840 c.25.1.1 62841 1inlA 296 2.30e+01 c.66.1.17 66220 7aatA 401 2.38e+01 1ajsA c.67.1.1 34250 4uagA 437 2.38e+01 4uagA c.5.1.1 30651 c.59.1.1 33952 c.72.2.1 34955 1ofgA 381 2.42e+01 1ofgA c.2.1.3 30064 d.81.1.5 39979 1o13A 136 2.46e+01 c.55.5.1 80762 1azwA 313 2.46e+01 1qtrA c.69.1.7 34658 1m2tA 254 2.48e+01 d.165.1.1 84761 1mk0A 97 2.53e+01 d.226.1.1 79216 1atg 231 2.54e+01 1atg c.94.1.1 35834 1dbqA 289 2.54e+01 1qpzA c.93.1.1 35666 4ubpC 570 2.56e+01 1ubpC b.92.1.1 28431 c.1.9.2 29053 1onrA 316 2.58e+01 1onrA c.1.10.1 29169 1spgA 144 2.61e+01 1abwA a.1.1.2 15409 1pswA 348 2.62e+01 c.87.1.7 88287 1pq4A 291 2.67e+01 c.92.2.2 -8633 1pea 385 2.71e+01 1pea c.93.1.1 35662 1gntA 553 2.75e+01 e.26.1.1 70290 1e2uA 553 2.77e+01 1e1dA e.26.1.1 43362 1fg7A 356 2.79e+01 1gewA c.67.1.1 59819 1nlfA 279 2.82e+01 c.37.1.11 85850 1a9nA 176 2.84e+01 1a9nA c.10.2.4 30875 1g8yA 279 2.90e+01 1g8yA c.37.1.11 32302 1hrkA 359 2.92e+01 1hrkA c.92.1.1 61228 1vhqA 232 2.93e+01 c.23.16.2 -6514 1grj 158 2.96e+01 1grj a.2.1.1 15691 d.26.1.2 38433 1ois 223 3.03e+01 1a36A e.15.1.1 43267 1mkaA 171 3.05e+01 1mkaA d.38.1.2 38543 1ei7A 158 3.06e+01 1rmvA a.24.5.1 16584 1ursA 402 3.10e+01 c.94.1.1 -8651 1yacA 208 3.15e+01 1yacA unknown_sccs 31757 1gewA 356 3.19e+01 1gewA c.67.1.1 60470 1fjgB 256 3.21e+01 1fjfB c.23.15.1 31400 1i88A 389 3.21e+01 c.95.1.2 66070 c.95.1.2 66071 1fcjA 322 3.25e+01 1oasA c.79.1.1 35289 1kq3A 376 3.25e+01 e.22.1.2 68790 1fezA 256 3.25e+01 1fezA c.108.1.3 43343 1p5fA 189 3.27e+01 c.23.16.2 -6508 1bi5A 389 3.29e+01 1bi5A c.95.1.2 35985 c.95.1.2 35986 2pfkA 320 3.30e+01 3pfk c.89.1.1 35577 1qrrA 394 3.33e+01 1qrrA c.2.1.2 29824 1qorA 327 3.33e+01 1qorA b.35.1.2 24766 c.2.1.1 29782 1nksA 194 3.34e+01 1nksA c.37.1.1 31886 1gpjA 404 3.41e+01 a.151.1.1 65451 c.2.1.7 65452 d.58.39.1 65453 1ufoA 238 3.42e+01 unknown_sccs -8303 1qhlA 227 3.46e+01 1qhlA c.37.1.12 32382 1p4xA 250 3.47e+01 a.4.5.28 87784 a.4.5.28 87785 1ni3A 392 3.48e+01 c.37.1.8 80531 d.15.10.2 80532 1m2kA 249 3.48e+01 c.31.1.5 84754 1jjiA 311 3.49e+01 c.69.1.2 66766 1uyrA 737 3.52e+01 c.14.1.4 -6258 c.14.1.4 -6259 1ni9A 338 3.55e+01 e.7.1.2 85739 1vdkA 466 3.57e+01 a.127.1.1 -1752 1lh0A 213 3.58e+01 c.61.1.1 73896 1gz6A 319 3.68e+01 c.2.1.2 76410 1ytw 306 3.69e+01 1ytw c.45.1.2 32689 1opr 213 3.72e+01 1opr c.61.1.1 34091 1mb4A 370 3.78e+01 c.2.1.3 78908 d.81.1.1 78909 1paqA 189 3.79e+01 unknown_sccs -1557 1lo6A 223 3.83e+01 b.47.1.2 74143 1gnwA 211 3.84e+01 1gnwA a.45.1.1 17727 c.47.1.5 33021 1tltA 319 3.85e+01 1d2mA 665 3.87e+01 1d2mA c.37.1.19 32417 c.37.1.19 32418 1ei5A 520 3.87e+01 1ei5A b.61.3.1 27418 b.61.3.1 27419 e.3.1.1 42772 1dfoA 417 3.87e+01 1bj4A c.67.1.4 34480 1e79A 510 3.89e+01 1skyB a.69.1.1 18269 b.49.1.1 26434 c.37.1.11 32314 1vi6A 208 3.91e+01 c.23.15.1 -6489 1k82A 268 3.99e+01 a.156.1.2 75866 b.113.1.1 75867 g.39.1.8 75868