# List of top-scoring protein chains for T0339.t04-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 2.34e-50 c.67.1.3 87752 1t3iA 420 1.48e-45 c.67.1.3 106354 1kmjA 406 8.75e-44 c.67.1.3 68695 1jf9A 408 8.76e-44 1c0nA c.67.1.3 62931 1eg5A 384 1.40e-43 1ecxA c.67.1.3 34429 1kmkA 406 2.54e-43 c.67.1.3 68696 1c0nA 406 8.41e-43 1c0nA c.67.1.3 34433 1y4iA 398 3.26e-41 1gc0A 398 7.00e-38 c.67.1.3 70168 1e5eA 404 1.08e-37 1ibjA c.67.1.3 59265 1pffA 331 5.81e-36 c.67.1.3 104143 1ibjA 464 8.89e-36 1ibjA c.67.1.3 62162 1n8pA 393 5.25e-35 c.67.1.3 80304 2ctzA 421 7.55e-35 1cs1A 386 1.21e-34 1ibjA c.67.1.3 34399 1qgnA 445 1.40e-34 1ibjA c.67.1.3 34403 1eluA 390 4.56e-30 1elqA c.67.1.3 34434 1n2tA 386 2.78e-29 c.67.1.3 79858 1qz9A 416 2.25e-26 c.67.1.3 96621 1cl1A 395 2.15e-23 1cl2A c.67.1.3 34395 1vjoA 393 1.40e-21 c.67.1.3 100827 1h0cA 392 3.93e-18 c.67.1.3 83424 1j04A 392 5.38e-18 c.67.1.3 90734 2ch1A 396 5.36e-17 1v2dA 381 1.51e-16 c.67.1.1 108281 1xi9A 406 5.67e-15 1j32A 388 2.97e-14 c.67.1.1 77067 1m32A 366 1.32e-13 c.67.1.3 78508 2fm1A 355 2.53e-13 1o4sA 389 2.77e-13 c.67.1.1 86620 1m6sA 347 2.89e-13 c.67.1.1 78701 2bkwA 385 2.40e-12 1mdoA 393 3.19e-12 c.67.1.4 79013 1iugA 352 5.29e-12 c.67.1.3 90699 2gb3A 409 1.28e-11 1gdeA 389 2.02e-11 c.67.1.1 60456 1djuA 388 2.04e-11 1bjwA c.67.1.1 59116 1b5pA 385 4.92e-11 c.67.1.1 90403 5bj3A 385 5.01e-11 c.67.1.1 100871 5bj4A 385 5.05e-11 c.67.1.1 100875 1b5oA 385 5.71e-11 c.67.1.1 90401 1kl1A 419 8.75e-11 c.67.1.4 72663 1bkgA 385 1.30e-10 1bjwA c.67.1.1 34351 1bjwA 382 1.90e-10 1bjwA c.67.1.1 34349 1yjsA 419 4.02e-10 1yjzA 419 6.27e-10 1w7lA 422 1.02e-09 c.67.1.1 109226 1bw0A 416 3.56e-09 1bw0A c.67.1.1 34385 1eqbA 417 6.84e-09 1bj4A c.67.1.4 34484 1svvA 359 7.32e-09 c.67.1.1 106054 1dfoA 417 7.48e-09 1bj4A c.67.1.4 34480 1b9iA 388 7.60e-09 1b9hA c.67.1.4 34489 1b9hA 388 7.60e-09 1b9hA c.67.1.4 34488 1lc5A 364 8.33e-09 c.67.1.1 73827 1yizA 429 8.39e-09 1wyuB 474 1.53e-08 1x0mA 403 2.72e-08 1vefA 395 2.80e-08 1pmmA 466 6.41e-08 c.67.1.6 94901 1xeyA 466 6.68e-08 1z7dA 433 1.06e-07 1fc4A 401 1.11e-07 1bs0A c.67.1.4 59760 1wyuA 438 1.23e-07 1djeA 384 1.35e-07 1bs0A c.67.1.4 34491 1m7yA 435 1.81e-07 c.67.1.4 78761 1ynuA 473 1.82e-07 1u08A 386 1.86e-07 c.67.1.1 107543 1b8gA 429 1.94e-07 1b8gA c.67.1.4 34499 1bs0A 384 1.95e-07 1bs0A c.67.1.4 34490 2fnuA 375 3.76e-07 1o69A 394 4.63e-07 c.67.1.4 92560 1iayA 428 5.00e-07 1b8gA c.67.1.4 62130 2bwnA 401 5.09e-07 1fg7A 356 7.32e-07 1gewA c.67.1.1 59819 2aeuA 374 1.91e-06 2a7vA 490 5.03e-06 1lk9A 448 5.05e-06 c.67.1.1 78057 1wstA 417 5.29e-06 2bigA 361 5.64e-06 1w23A 360 5.66e-06 1vp4A 425 1.27e-05 1gbnA 402 1.70e-05 2dkb c.67.1.4 34455 2oatA 439 1.96e-05 2dkb c.67.1.4 34452 2byjA 439 2.12e-05 2bylA 439 2.57e-05 2gsaA 432 2.57e-05 2gsaA c.67.1.4 34446 1v72A 356 3.00e-05 1rvuA 483 3.29e-05 c.67.1.4 105106 1rv3A 483 3.45e-05 c.67.1.4 105101 1ax4A 467 3.62e-05 1ax4A c.67.1.2 34391 1cj0A 470 3.72e-05 1bj4A c.67.1.4 34473 1ls3A 483 3.74e-05 c.67.1.4 78172 1ejiA 478 9.17e-05 1bj4A c.67.1.4 34475 1bj4A 470 2.02e-04 1bj4A c.67.1.4 34479 1szuA 426 2.31e-04 1sffA 426 2.49e-04 c.67.1.4 105482 1szsA 426 2.51e-04 1c7nA 399 2.60e-04 1d2fA c.67.1.3 34413 1uu1A 335 2.80e-04 c.67.1.1 99993 2f8jA 347 2.82e-04 1szkA 426 4.40e-04 1c7gA 456 5.82e-04 c.67.1.2 90415 2cfbA 411 6.15e-04 1bjnA 360 1.27e-03 1bjnA c.67.1.4 34469 1js3A 486 1.29e-03 c.67.1.6 67215 1tplA 456 1.31e-03 1ax4A c.67.1.2 34387 2c0rA 362 1.54e-03 1ariA 396 1.66e-03 1ajsA c.67.1.1 34331 1qitA 396 2.40e-03 1ajsA c.67.1.1 34286 1asg 396 2.56e-03 1ajsA c.67.1.1 34335 1d2fA 390 3.40e-03 1d2fA c.67.1.3 34411 5eaaA 396 3.51e-03 1ajsA c.67.1.1 34328 1qisA 396 4.09e-03 1ajsA c.67.1.1 34284 1aam 396 4.18e-03 1ajsA c.67.1.1 34347 3aat 396 4.25e-03 1ajsA c.67.1.1 34346 1qirA 396 4.36e-03 1ajsA c.67.1.1 34290 1ars 396 4.98e-03 1ajsA c.67.1.1 34287 1czeA 396 5.40e-03 1ajsA c.67.1.1 34301 1arhA 396 5.89e-03 1ajsA c.67.1.1 34321 1yoo 396 6.07e-03 1ajsA c.67.1.1 34295 1ix7A 396 6.26e-03 c.67.1.1 71494 1aiaA 396 9.07e-03 1ajsA c.67.1.1 34306 1togA 396 1.09e-02 2aat 396 1.29e-02 1ajsA c.67.1.1 34348 1tokA 396 1.38e-02 1bqaA 396 1.60e-02 1ajsA c.67.1.1 34298 1bqdA 396 1.95e-02 1ajsA c.67.1.1 34296 1g4vA 396 1.98e-02 1ajsA c.67.1.1 34289 1toiA 396 2.12e-02 1ahxA 396 2.69e-02 1ajsA c.67.1.1 34293 1g7wA 396 3.33e-02 1ajsA c.67.1.1 34308 1g7xA 396 3.35e-02 1ajsA c.67.1.1 34304 1g4xA 396 3.96e-02 1ajsA c.67.1.1 34313 1spa 396 4.17e-02 1ajsA c.67.1.1 34291 1z3zA 431 4.76e-02 1ix8A 396 4.99e-02 c.67.1.1 71495 1dgd 432 5.03e-02 2dkb c.67.1.4 34443 1d7uA 433 5.03e-02 2dkb c.67.1.4 34439 1c4kA 730 5.13e-02 1ordA c.23.1.4,c.67.1.5,d.125.1.1 31273,34502,41123 1ordA 730 5.94e-02 1ordA c.23.1.4,c.67.1.5,d.125.1.1 31274,34503,41124 1m0qA 433 5.97e-02 c.67.1.4 78350 2ffhA 425 8.65e-02 1ng1 a.24.13.1,a.36.1.1,c.37.1.10 16965,17122,32276 2ay1A 394 2.80e-01 1ajsA c.67.1.1 34357 3tatA 397 5.75e-01 1ajsA c.67.1.1 34379 1xjjA 644 1.03e+00 1vljA 407 1.53e+00 e.22.1.2 108832 1ohvA 472 1.89e+00 c.67.1.4 93031 2gjlA 328 1.89e+00 1s08A 429 2.73e+00 c.67.1.4 98259 1s07A 429 2.90e+00 c.67.1.4 98257 1dtyA 429 3.24e+00 1dtyA c.67.1.4 34495 1pjkA 334 3.30e+00 d.144.1.7 88122 1jwhA 337 3.41e+00 d.144.1.7 71913 1mgvA 429 4.27e+00 c.67.1.4 79107 1na7A 329 4.34e+00 d.144.1.7 91752 1ez4A 318 4.52e+00 c.2.1.5,d.162.1.1 64917,64918 2pgd 482 4.68e+00 2pgd a.100.1.1,c.2.1.6 18778,30190 1x9dA 538 4.71e+00 1qj5A 429 5.13e+00 1dtyA c.67.1.4 34493 1s0aA 429 5.15e+00 c.67.1.4 98263 1ymiA 334 5.18e+00 2pjrA 548 5.31e+00 1pjr c.37.1.19,c.37.1.19 32395,32396 1vbnA 318 5.48e+00 1os1A 540 5.73e+00 c.91.1.1,c.109.1.1 93467,93468 1ayl 541 5.73e+00 1ayl c.91.1.1,c.109.1.1 64718,64719 1wq4A 321 5.88e+00 1wq3A 322 5.91e+00 1vbmA 318 5.97e+00 1jeyB 565 6.22e+00 1jeqB b.131.1.2,c.62.1.4 90372,90373 1x8xA 322 6.43e+00 1fmiA 458 7.13e+00 1dl2A a.102.2.1 18846 1k30A 368 7.14e+00 c.112.1.1 68067 1iuqA 367 7.19e+00 c.112.1.1 90703 1fo3A 460 7.23e+00 1dl2A a.102.2.1 18845 1yaaA 412 7.28e+00 1ajsA c.67.1.1 34280 1pjr 724 7.36e+00 1pjr c.37.1.19,c.37.1.19 32391,32392 7aatA 401 7.52e+00 1ajsA c.67.1.1 34250 1rvkA 382 7.87e+00 c.1.11.2,d.54.1.1 97928,97929 1h8fB 350 7.96e+00 d.144.1.7 65734 1h8fA 352 7.98e+00 d.144.1.7 65733 1viwB 205 8.65e+00 1led b.29.1.1 24170 1dhkB 223 8.77e+00 1led b.29.1.1 24157 1s09A 429 8.78e+00 c.67.1.4 98261 1o9uA 350 9.46e+00 d.144.1.7 92691 1oen 540 9.63e+00 1ayl c.91.1.1,c.109.1.1 64750,64751 7taa 478 9.92e+00 7taa b.71.1.1,c.1.8.1 27778,28765 1uv5A 350 1.03e+01 d.144.1.7 100029 1akaA 401 1.10e+01 1ajsA c.67.1.1 34258 1nwyC 204 1.12e+01 i.1.1.2 86347 1pnuC 197 1.12e+01 i.1.1.1 88200 1vorF 198 1.12e+01 1nkwC 205 1.12e+01 i.1.1.2 80588 1g5aA 628 1.15e+01 b.71.1.1,c.1.8.1 65152,65153 1s06A 429 1.16e+01 c.67.1.4 98255 2cstA 411 1.16e+01 1ajsA c.67.1.1 34273 1q5kA 414 1.22e+01 d.144.1.7 104537 1q41A 424 1.23e+01 d.144.1.7 95774 1j1bA 420 1.23e+01 d.144.1.7 90758 1mvyA 628 1.23e+01 b.71.1.1,c.1.8.1 79547,79548 1jgiA 628 1.24e+01 b.71.1.1,c.1.8.1 66676,66677 1pyxA 422 1.24e+01 d.144.1.7 95383 1zj8A 566 1.29e+01 1gngA 378 1.32e+01 d.144.1.7 76239 2au3A 407 1.35e+01 1r0eA 391 1.39e+01 1v3jA 686 1.46e+01 b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 108305,108306,108307,108308 1jqvA 311 1.51e+01 c.1.4.1 90900 1d7fA 686 1.59e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21848,22517,27755,28742 2b9mY 365 1.59e+01 1v3kA 686 1.61e+01 b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 108313,108314,108315,108316 1t5hX 504 1.62e+01 e.23.1.1 106449 1uktA 686 1.63e+01 b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 99525,99526,99527,99528 2taaA 478 1.65e+01 7taa b.71.1.1,c.1.8.1 27780,28767 1pamA 686 1.68e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21846,22515,27753,28740 1rsgA 516 1.75e+01 1yy5A 513 1.75e+01 1kijA 390 1.80e+01 d.14.1.3,d.122.1.2 72514,72515 1t2dA 322 1.86e+01 c.2.1.5,d.162.1.1 99084,99085 2a94A 321 1.88e+01 1xivA 323 1.89e+01 1uksA 686 1.90e+01 b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 99517,99518,99519,99520 1t2eA 322 1.96e+01 c.2.1.5,d.162.1.1 99086,99087 1jubA 311 1.98e+01 c.1.4.1 90908 1jrbA 311 2.14e+01 c.1.4.1 90904 1jqxA 311 2.17e+01 c.1.4.1 90902 1oc4A 322 2.24e+01 c.2.1.5,d.162.1.1 92770,92771 1jueA 311 2.34e+01 c.1.4.1 90910 1r66A 337 2.35e+01 c.2.1.2 97146 1ceqA 316 2.55e+01 1ceqA c.2.1.5,d.162.1.1 30163,42130 1cyg 680 2.56e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21843,22512,27750,28737 1jrcA 311 2.86e+01 c.1.4.1 90906 1r6dA 337 2.94e+01 c.2.1.2 97148 1bvnP 496 3.01e+01 1smd b.71.1.1,c.1.8.1 27767,28754 1ldg 316 3.08e+01 1ceqA c.2.1.5,d.162.1.1 30165,42132 1tmiA 130 3.33e+01 d.156.1.2 107151 1g38A 393 3.46e+01 2admA c.66.1.27 60235 1gkrA 458 3.49e+01 b.92.1.3,c.1.9.6 70251,70252 2fj0A 551 3.50e+01 1aatA 411 3.55e+01 1tluA 130 3.58e+01 d.156.1.2 107139 2b8eA 273 3.59e+01 3pcgA 200 3.69e+01 3pchA b.3.6.1 22647 1w77A 228 3.74e+01 1hl2A 297 3.83e+01 c.1.10.1 83581 1yadA 221 3.87e+01 1mvoA 136 3.94e+01 c.23.1.1 79513 2admA 421 4.07e+01 2admA c.66.1.27 34238 1ajsA 412 4.09e+01 1ajsA c.67.1.1 34276 1h6wA 312 4.09e+01 d.231.1.1,b.108.1.1 83059,83060 1aqjA 421 4.12e+01 2admA c.66.1.27 34242 1zo1I 501 4.18e+01 1vr7A 142 4.19e+01 1vahA 496 4.20e+01 1a2oA 349 4.25e+01 1chd c.23.1.1,c.40.1.1 31120,32479 1ose 496 4.33e+01 1smd b.71.1.1,c.1.8.1 27766,28753 1wwkA 307 4.34e+01 1ltqA 301 4.39e+01 c.108.1.9,c.37.1.1 78208,78209 1jmkC 230 4.63e+01 c.69.1.22 71747 1omwA 689 4.66e+01 a.91.1.1,b.55.1.1,d.144.1.7 87086,87087,87088 1hx0A 496 4.73e+01 b.71.1.1,c.1.8.1 61346,61347 1kxqA 496 4.89e+01 b.71.1.1,c.1.8.1 73163,73164 1zorA 399 4.91e+01 2a92A 321 5.06e+01 1chd 203 5.08e+01 1chd c.40.1.1 32478 1ex5A 363 5.19e+01 1fbaA c.1.10.1 29140 1jfh 496 5.30e+01 1smd b.71.1.1,c.1.8.1 27762,28749 1ylhA 560 5.30e+01 1llc 325 5.33e+01 1hyhA c.2.1.5,d.162.1.1 30176,42143 1yzfA 195 5.37e+01 1uf9A 203 5.38e+01 c.37.1.1 99326 2ccaA 740 5.45e+01 1wz8A 264 5.47e+01 1sj2A 743 5.47e+01 a.93.1.3,a.93.1.3 105597,105598 1ua7A 422 5.49e+01 b.71.1.1,c.1.8.1 107759,107760 1ppi 496 5.50e+01 1smd b.71.1.1,c.1.8.1 27763,28750 1j6rA 214 5.52e+01 d.173.1.2 71598 2ccdA 740 5.63e+01 1dhkA 496 5.71e+01 1smd b.71.1.1,c.1.8.1 27761,28748 1up7A 417 5.71e+01 1iktA 120 5.74e+01 d.106.1.1 66188 1us8B 144 5.77e+01 1usuB 170 5.81e+01 d.83.2.1 99886 1up6A 416 5.94e+01 c.2.1.5,d.162.1.2 107976,107977 1bag 425 5.95e+01 1bag b.71.1.1,c.1.8.1 27720,28707 1fjhA 257 6.14e+01 1fjhB c.2.1.2 29870 1up4A 415 6.21e+01 1h2dA 182 6.27e+01 b.31.1.1 83463 1j3gA 187 6.42e+01 d.118.1.1 77075 1yx1A 264 6.47e+01 1ewgA 363 6.48e+01 1fbaA c.1.10.1 29128 1zovA 386 6.50e+01 1tqjA 230 6.59e+01 c.1.2.2 107228 1hskA 326 6.61e+01 2mbr d.145.1.2,d.146.1.1 61241,61242 1usvB 170 6.75e+01 d.83.2.1 99888 1iloA 77 6.79e+01 c.47.1.1 66205 1p22A 435 6.87e+01 a.158.1.1,b.69.4.1 87715,87716 1pig 496 6.87e+01 1smd b.71.1.1,c.1.8.1 27764,28751 1eweA 363 6.90e+01 1fbaA c.1.10.1 29136 1prhA 554 6.92e+01 1cqeA a.93.1.2,g.3.11.1 18710,44253 2agyA 361 7.03e+01 1iq8A 582 7.04e+01 c.1.20.1,b.122.1.1,d.17.6.1 71270,83074,83075 1adoA 363 7.09e+01 1fbaA c.1.10.1 29124 1zaiA 363 7.09e+01 1ko7A 314 7.10e+01 c.98.2.1,c.91.1.2 72797,72798 1f2tB 148 7.11e+01 1f2tB 1h8lA 380 7.20e+01 b.3.2.1,c.56.5.1 65737,65738 1ii8B 174 7.33e+01 1f2tB 1zliA 309 7.35e+01 1fdyA 297 7.37e+01 1nal3 c.1.10.1 29071 1fehA 574 7.39e+01 1fehA c.96.1.1,d.15.4.2,d.58.1.5 36015,37690,38998 1wg5A 104 7.40e+01 2aaa 484 7.44e+01 7taa b.71.1.1,c.1.8.1 27777,28764 1ht8A 551 7.56e+01 1cqeA a.93.1.2,g.3.11.1 61248,61249 1q4gA 553 7.64e+01 a.93.1.2,g.3.11.1 95789,95790 1ald 363 7.69e+01 1fbaA c.1.10.1 29100 1ebvA 551 7.75e+01 1cqeA a.93.1.2,g.3.11.1 18709,44252 2cx4A 164 7.85e+01 1qs0B 338 7.89e+01 1qs0B c.36.1.7,c.48.1.2 31830,33103 2bp7B 339 7.94e+01 1j4wA 174 7.95e+01 d.51.1.1,d.51.1.1 71529,71530 1kv7A 488 8.21e+01 b.6.1.3,b.6.1.3,b.6.1.3 68873,68874,68875 6aldA 363 8.25e+01 1fbaA c.1.10.1 29144 1hciA 476 8.41e+01 1quuA a.7.1.1,a.7.1.1,a.7.1.1,a.7.1.1 60950,60951,60952,60953 1ytmA 532 8.42e+01 1kwmA 402 8.46e+01 c.56.5.1,d.58.3.1 73079,73080 1ewdA 363 8.58e+01 1fbaA c.1.10.1 29132 1pf3A 498 8.62e+01 b.6.1.3,b.6.1.3,b.6.1.3 88049,88050,88051 1ygyA 529 8.64e+01 1nal1 297 8.82e+01 1nal3 1a0cA 438 8.94e+01 1a0cA c.1.15.3 29529 1ulyA 192 8.97e+01