# List of top-scoring protein chains for T0339.t2k-w0.5 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 1p3wA 404 1.21e-41 c.67.1.3 87752 1t3iA 420 1.37e-39 c.67.1.3 106354 1eg5A 384 8.02e-39 1ecxA c.67.1.3 34429 1kmjA 406 9.27e-38 c.67.1.3 68695 1jf9A 408 9.27e-38 1c0nA c.67.1.3 62931 1kmkA 406 2.08e-37 c.67.1.3 68696 1c0nA 406 4.10e-37 1c0nA c.67.1.3 34433 1eluA 390 1.53e-27 1elqA c.67.1.3 34434 1n2tA 386 5.16e-27 c.67.1.3 79858 1v2dA 381 3.90e-19 c.67.1.1 108281 1qz9A 416 1.04e-17 c.67.1.3 96621 1j32A 388 1.19e-17 c.67.1.1 77067 1vjoA 393 2.37e-17 c.67.1.3 100827 1kl1A 419 2.99e-17 c.67.1.4 72663 1xi9A 406 5.60e-17 1yjsA 419 1.07e-16 1yjzA 419 1.61e-16 1m32A 366 1.90e-16 c.67.1.3 78508 1o4sA 389 2.09e-16 c.67.1.1 86620 1b5pA 385 3.84e-16 c.67.1.1 90403 5bj3A 385 3.85e-16 c.67.1.1 100871 5bj4A 385 3.85e-16 c.67.1.1 100875 1b5oA 385 4.95e-16 c.67.1.1 90401 1bkgA 385 8.34e-16 1bjwA c.67.1.1 34351 1bjwA 382 9.72e-16 1bjwA c.67.1.1 34349 1dfoA 417 1.71e-15 1bj4A c.67.1.4 34480 1eqbA 417 1.76e-15 1bj4A c.67.1.4 34484 1gdeA 389 2.24e-15 c.67.1.1 60456 1djuA 388 2.39e-15 1bjwA c.67.1.1 59116 2ch1A 396 5.55e-14 1u08A 386 6.22e-14 c.67.1.1 107543 1h0cA 392 6.38e-14 c.67.1.3 83424 1j04A 392 7.58e-14 c.67.1.3 90734 1fg7A 356 1.42e-13 1gewA c.67.1.1 59819 1pffA 331 7.48e-13 c.67.1.3 104143 1x0mA 403 9.72e-13 1y4iA 398 1.33e-12 1bw0A 416 1.42e-12 1bw0A c.67.1.1 34385 1uu1A 335 2.12e-12 c.67.1.1 99993 2f8jA 347 2.14e-12 2gb3A 409 2.14e-12 1gc0A 398 2.20e-12 c.67.1.3 70168 1ibjA 464 2.93e-12 1ibjA c.67.1.3 62162 2fm1A 355 4.53e-12 1m6sA 347 4.63e-12 c.67.1.1 78701 1lc5A 364 5.19e-12 c.67.1.1 73827 1n8pA 393 1.23e-11 c.67.1.3 80304 1m7yA 435 1.38e-11 c.67.1.4 78761 1ynuA 473 1.39e-11 1b8gA 429 1.43e-11 1b8gA c.67.1.4 34499 1iugA 352 1.51e-11 c.67.1.3 90699 1e5eA 404 1.75e-11 1ibjA c.67.1.3 59265 2bkwA 385 1.91e-11 1yizA 429 2.43e-11 1wstA 417 2.77e-11 1w7lA 422 3.98e-11 c.67.1.1 109226 1vefA 395 6.24e-11 1mdoA 393 7.50e-11 c.67.1.4 79013 1cs1A 386 8.07e-11 1ibjA c.67.1.3 34399 2ctzA 421 1.05e-10 1wyuB 474 2.30e-10 1qgnA 445 3.55e-10 1ibjA c.67.1.3 34403 1iayA 428 6.50e-10 1b8gA c.67.1.4 62130 1xeyA 466 7.66e-10 1pmmA 466 7.72e-10 c.67.1.6 94901 1rvuA 483 8.35e-10 c.67.1.4 105106 1cj0A 470 8.70e-10 1bj4A c.67.1.4 34473 1ls3A 483 8.77e-10 c.67.1.4 78172 1rv3A 483 9.16e-10 c.67.1.4 105101 2a7vA 490 1.63e-09 1fc4A 401 1.83e-09 1bs0A c.67.1.4 59760 1bj4A 470 2.16e-09 1bj4A c.67.1.4 34479 1ejiA 478 2.51e-09 1bj4A c.67.1.4 34475 1svvA 359 4.84e-09 c.67.1.1 106054 1vp4A 425 6.75e-09 2bwnA 401 8.69e-09 1b9hA 388 1.90e-08 1b9hA c.67.1.4 34488 1b9iA 388 1.90e-08 1b9hA c.67.1.4 34489 1cl1A 395 3.89e-08 1cl2A c.67.1.3 34395 1wyuA 438 6.01e-08 1z7dA 433 1.00e-07 1bs0A 384 1.18e-07 1bs0A c.67.1.4 34490 1d2fA 390 1.49e-07 1d2fA c.67.1.3 34411 1djeA 384 2.23e-07 1bs0A c.67.1.4 34491 1o69A 394 6.08e-07 c.67.1.4 92560 2gsaA 432 8.79e-07 2gsaA c.67.1.4 34446 1gbnA 402 2.55e-06 2dkb c.67.1.4 34455 2oatA 439 2.56e-06 2dkb c.67.1.4 34452 2byjA 439 2.62e-06 1js3A 486 3.35e-06 c.67.1.6 67215 2bylA 439 3.52e-06 1ariA 396 3.80e-06 1ajsA c.67.1.1 34331 1qitA 396 4.49e-06 1ajsA c.67.1.1 34286 1v72A 356 4.71e-06 1c7nA 399 4.72e-06 1d2fA c.67.1.3 34413 2bigA 361 4.87e-06 1w23A 360 4.87e-06 3aat 396 5.08e-06 1ajsA c.67.1.1 34346 5eaaA 396 6.65e-06 1ajsA c.67.1.1 34328 1qisA 396 7.48e-06 1ajsA c.67.1.1 34284 1aam 396 7.69e-06 1ajsA c.67.1.1 34347 2fnuA 375 7.83e-06 2cfbA 411 7.89e-06 1ars 396 7.94e-06 1ajsA c.67.1.1 34287 1qirA 396 8.43e-06 1ajsA c.67.1.1 34290 1ix7A 396 9.21e-06 c.67.1.1 71494 1arhA 396 1.17e-05 1ajsA c.67.1.1 34321 1asg 396 1.53e-05 1ajsA c.67.1.1 34335 1togA 396 1.60e-05 1bqaA 396 1.78e-05 1ajsA c.67.1.1 34298 2ay1A 394 1.79e-05 1ajsA c.67.1.1 34357 1tokA 396 1.85e-05 1toiA 396 2.47e-05 1ahxA 396 2.79e-05 1ajsA c.67.1.1 34293 2aeuA 374 2.81e-05 1aiaA 396 3.19e-05 1ajsA c.67.1.1 34306 1bqdA 396 3.38e-05 1ajsA c.67.1.1 34296 1g7wA 396 3.87e-05 1ajsA c.67.1.1 34308 2aat 396 3.92e-05 1ajsA c.67.1.1 34348 1g7xA 396 4.44e-05 1ajsA c.67.1.1 34304 1yoo 396 4.58e-05 1ajsA c.67.1.1 34295 1sffA 426 4.99e-05 c.67.1.4 105482 1czeA 396 5.02e-05 1ajsA c.67.1.1 34301 1g4xA 396 5.03e-05 1ajsA c.67.1.1 34313 1ix8A 396 5.13e-05 c.67.1.1 71495 1szsA 426 5.23e-05 1szuA 426 5.63e-05 1z3zA 431 6.30e-05 1m0qA 433 6.43e-05 c.67.1.4 78350 3tatA 397 6.58e-05 1ajsA c.67.1.1 34379 1dgd 432 7.90e-05 2dkb c.67.1.4 34443 1d7uA 433 7.90e-05 2dkb c.67.1.4 34439 1g4vA 396 8.64e-05 1ajsA c.67.1.1 34289 1szkA 426 8.80e-05 1spa 396 1.33e-04 1ajsA c.67.1.1 34291 2c0rA 362 1.87e-04 1ax4A 467 2.55e-04 1ax4A c.67.1.2 34391 1bjnA 360 3.86e-04 1bjnA c.67.1.4 34469 1lk9A 448 5.89e-04 c.67.1.1 78057 1yaaA 412 1.13e-03 1ajsA c.67.1.1 34280 1c7gA 456 9.29e-03 c.67.1.2 90415 1tplA 456 1.46e-02 1ax4A c.67.1.2 34387 1c4kA 730 2.14e-02 1ordA c.23.1.4,c.67.1.5,d.125.1.1 31273,34502,41123 1ordA 730 2.32e-02 1ordA c.23.1.4,c.67.1.5,d.125.1.1 31274,34503,41124 2cstA 411 6.00e-02 1ajsA c.67.1.1 34273 1ajsA 412 6.94e-02 1ajsA c.67.1.1 34276 1dtyA 429 8.52e-02 1dtyA c.67.1.4 34495 1s08A 429 9.48e-02 c.67.1.4 98259 1aatA 411 1.59e-01 1s0aA 429 1.66e-01 c.67.1.4 98263 1qj5A 429 1.66e-01 1dtyA c.67.1.4 34493 1s09A 429 1.86e-01 c.67.1.4 98261 1s06A 429 2.21e-01 c.67.1.4 98255 1s07A 429 2.77e-01 c.67.1.4 98257 1mgvA 429 3.79e-01 c.67.1.4 79107 1ohvA 472 3.93e-01 c.67.1.4 93031 7aatA 401 6.56e-01 1ajsA c.67.1.1 34250 1akaA 401 2.02e+00 1ajsA c.67.1.1 34258 1nzdA 351 2.16e+00 c.87.1.1 92373 1jixA 351 2.61e+00 1c3jA c.87.1.1 63081 1y6jA 318 2.88e+00 2almA 431 2.89e+00 1ox0A 430 2.99e+00 c.95.1.1,c.95.1.1 87495,87496 2b9mY 365 3.24e+00 1pgl2 370 3.45e+00 1bmv2 374 3.47e+00 1bmv2 7taa 478 3.49e+00 7taa b.71.1.1,c.1.8.1 27778,28765 2taaA 478 3.71e+00 7taa b.71.1.1,c.1.8.1 27780,28767 2aaa 484 3.84e+00 7taa b.71.1.1,c.1.8.1 27777,28764 1pgw2 351 4.46e+00 2ffhA 425 4.89e+00 1ng1 a.24.13.1,a.36.1.1,c.37.1.10 16965,17122,32276 1ua7A 422 6.78e+00 b.71.1.1,c.1.8.1 107759,107760 1bag 425 7.06e+00 1bag b.71.1.1,c.1.8.1 27720,28707 1dhkB 223 7.13e+00 1led b.29.1.1 24157 1viwB 205 7.32e+00 1led b.29.1.1 24170 1ez4A 318 7.91e+00 c.2.1.5,d.162.1.1 64917,64918 1l3iA 192 1.04e+01 c.66.1.22 77676 1bt3A 345 1.17e+01 1bt3A a.86.1.2 18507 1xjjA 644 1.32e+01 1v25A 541 1.52e+01 e.23.1.1 108275 1kwsA 261 1.55e+01 c.68.1.7 73083 1ndaA 491 1.56e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30525,30526,40194 1f0xA 571 1.87e+01 1f0xA d.58.32.2,d.145.1.1 39483,41746 1v73A 342 1.94e+01 1euzA 419 1.94e+01 1k89 c.2.1.7,c.58.1.1 59513,59514 1wuiS 267 1.98e+01 2a1nA 415 2.09e+01 1iwkA 415 2.13e+01 a.104.1.1 71490 6cp4 414 2.14e+01 1phd a.104.1.1 18924 2a1oA 415 2.17e+01 1dz4A 414 2.17e+01 1phd a.104.1.1 18903 2cp4 414 2.21e+01 1phd a.104.1.1 18933 1t85A 414 2.22e+01 a.104.1.1 106650 2a1mA 415 2.22e+01 1qmqA 414 2.22e+01 1phd a.104.1.1 18907 1gekA 415 2.26e+01 1phd a.104.1.1 18915 1yrcA 414 2.26e+01 1lwlA 417 2.26e+01 a.104.1.1 78273 2fe6A 421 2.27e+01 1p2yA 420 2.27e+01 a.104.1.1 93961 1gebA 415 2.33e+01 1phd a.104.1.1 18932 2ferA 411 2.36e+01 1j51A 414 2.39e+01 a.104.1.1 66393 1h2aS 317 2.42e+01 2frvA e.19.1.1 43311 1iwjA 415 2.43e+01 a.104.1.1 71489 1c8jA 414 2.48e+01 1phd a.104.1.1 59085 1wblA 241 2.50e+01 1led b.29.1.1 24052 1wbfA 242 2.50e+01 1led b.29.1.1 24050 1bvuA 418 2.53e+01 1hwyA c.2.1.7,c.58.1.1 30226,33874 1iloA 77 2.70e+01 c.47.1.1 66205 1im8A 244 2.85e+01 c.66.1.14 66212 1ako 268 2.87e+01 1ako d.151.1.1 41779 1ji0A 240 3.02e+01 c.37.1.12 71665 1sa3A 262 3.13e+01 c.52.1.23 105400 1kas 412 3.24e+01 1dd8A c.95.1.1,c.95.1.1 35964,35965 1tqjA 230 3.46e+01 c.1.2.2 107228 1nkvA 256 3.54e+01 c.66.1.21 80577 1zovA 386 3.74e+01 1jqbA 351 3.76e+01 b.35.1.2,c.2.1.1 77151,77152 1dboA 506 3.90e+01 1dbgA b.80.1.4 28034 1fp0A 88 3.94e+01 1fp0A g.50.1.2 45361 2gfwA 427 4.11e+01 2gfyA 427 4.12e+01 1jeyB 565 4.18e+01 1jeqB b.131.1.2,c.62.1.4 90372,90373 1sbxA 106 4.22e+01 a.6.1.4 105414 1vgaA 248 4.26e+01 1fecA 490 4.38e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30489,30490,40176 1tytA 487 4.46e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30513,30514,40188 1tytB 486 4.47e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30515,30516,40189 2tprA 490 4.60e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30505,30506,40184 1omwA 689 4.82e+01 a.91.1.1,b.55.1.1,d.144.1.7 87086,87087,87088 1aogA 485 4.88e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30517,30518,40190 1bzlA 486 4.88e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30521,30522,40192 1v00A 242 4.88e+01 b.29.1.1 108190 1gxfA 492 4.91e+01 c.3.1.5,c.3.1.5,d.87.1.1 90527,90528,90529 1typA 487 5.06e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30509,30510,40186 1eu8A 409 5.28e+01 1eu8A c.94.1.1 59502 1o5xA 248 5.37e+01 c.1.1.1 92528 1zj8A 566 5.43e+01 1na7A 329 5.66e+01 d.144.1.7 91752 1ylxA 103 5.74e+01 1xvaA 292 5.94e+01 1xvaA c.66.1.5 34183 1pjkA 334 5.97e+01 d.144.1.7 88122 1jwhA 337 5.98e+01 d.144.1.7 71913 1ymiA 334 6.00e+01 1bi9A 499 6.02e+01 1bpwA c.82.1.1 35337 1d2gA 292 6.06e+01 1xvaA c.66.1.5 34187 1w4iA 62 6.12e+01 1j6rA 214 6.16e+01 d.173.1.2 71598 2cxxA 190 6.45e+01 2anuA 255 6.50e+01 1korA 400 6.51e+01 c.26.2.1,d.210.1.1 72824,72825 1lc0A 294 6.56e+01 c.2.1.3,d.81.1.4 73823,73824 1gtmA 419 6.63e+01 1hwyA c.2.1.7,c.58.1.1 30223,33871 3sqcA 631 6.73e+01 2sqcA a.102.4.2,a.102.4.2 18860,18861 1gcuA 295 6.73e+01 1gcuA c.2.1.3,d.81.1.4 30063,39978 1ulzA 451 6.74e+01 b.84.2.1,c.30.1.1,d.142.1.2 99575,99576,99577 1nshA 101 6.81e+01 a.39.1.2 86135 1h2hA 241 6.84e+01 d.81.1.3,c.2.1.3 70861,83058 1tluA 130 6.92e+01 d.156.1.2 107139 1vr7A 142 6.95e+01 1s5jA 847 7.00e+01 1f9kA 238 7.01e+01 1led b.29.1.1 59741 1nat 124 7.09e+01 1dz3A c.23.1.1 31113 1umpA 631 7.18e+01 a.102.4.2,a.102.4.2 99619,99620 1kevA 351 7.21e+01 1pedA b.35.1.2,c.2.1.1 24749,29765 2sqcA 631 7.24e+01 2sqcA a.102.4.2,a.102.4.2 18854,18855 1d7fA 686 7.28e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21848,22517,27755,28742 1p3jA 217 7.32e+01 c.37.1.1,g.41.2.1 94022,94023 1j5pA 253 7.34e+01 d.81.1.3,c.2.1.3 71577,83092 1x13A 401 7.45e+01 1rq2A 382 7.55e+01 c.32.1.1,d.79.2.1 105048,105049 3proC 166 7.56e+01 3proC d.52.1.1,d.52.1.1 38812,38813 1r74A 294 7.63e+01 c.66.1.5 104828 1wkvA 389 7.64e+01 1srrA 124 7.66e+01 1dz3A c.23.1.1 31110 1vl8A 267 7.72e+01 c.2.1.2 108733 1f2tB 148 7.88e+01 1f2tB 1pamA 686 7.94e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21846,22515,27753,28740 1uktA 686 8.08e+01 b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 99525,99526,99527,99528 1v3kA 686 8.11e+01 b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 108313,108314,108315,108316 1t3gA 159 8.13e+01 1dxlA 470 8.14e+01 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30585,30586,40214 1gzcA 239 8.17e+01 b.29.1.1 70803 1qs0B 338 8.18e+01 1qs0B c.36.1.7,c.48.1.2 31830,33103 2bp7B 339 8.24e+01 1v3jA 686 8.24e+01 b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 108305,108306,108307,108308 1jalA 363 8.29e+01 c.37.1.8,d.15.10.2 84138,84139 1xqlA 388 8.31e+01 1cvjA 190 8.32e+01 1cvjB d.58.7.1,d.58.7.1 39191,39192 1tmiA 130 8.35e+01 d.156.1.2 107151 2cu0A 486 8.50e+01 1f51E 119 8.51e+01 1dz3A c.23.1.1 31114 1oflA 481 8.60e+01 b.80.1.4 103934 1rvkA 382 8.62e+01 c.1.11.2,d.54.1.1 97928,97929 1d4bA 122 8.71e+01 1d4bA d.15.2.1 37638 1z6jL 142 8.85e+01 1gwiA 411 8.87e+01 a.104.1.1 76364 1ea9C 583 8.96e+01 b.1.18.2,b.71.1.1,c.1.8.1 70087,70088,70089