# List of top-scoring protein chains for t2k-100-30-n_notor2-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 1yndA 165 2.49e-19 2bitX 165 3.19e-19 1cwoA 165 3.33e-19 2cpl b.62.1.1 27445 1dywA 173 9.30e-19 2cpl b.62.1.1 27505 2cpl 165 1.19e-18 2cpl b.62.1.1 27420 1a58 177 1.49e-18 2cpl b.62.1.1 27495 1qoiA 177 1.89e-18 2cpl b.62.1.1 27490 2cfeA 162 2.01e-18 1awqA 164 2.11e-18 2cpl b.62.1.1 27461 1awsA 164 3.71e-18 2cpl b.62.1.1 27431 2rmcA 182 4.54e-18 2cpl b.62.1.1 27491 1xo7A 166 5.27e-18 1ihgA 370 6.46e-18 2cpl a.118.8.1,b.62.1.1 62380,62381 1h0pA 182 1.08e-17 b.62.1.1 76450 1zcxA 178 1.27e-17 1vdnA 162 2.03e-17 1zkcA 197 1.53e-16 2a2nA 176 1.65e-16 2fu0A 160 2.15e-16 2b71A 196 1.49e-15 1xwnA 174 2.32e-15 1j2aA 166 1.27e-14 b.62.1.1 90779 1v9tA 166 1.72e-14 b.62.1.1 108451 1lopA 164 2.44e-14 2cpl b.62.1.1 27510 1clh 166 7.35e-13 2cpl b.62.1.1 27512 1ush 550 3.03e-01 1ush d.114.1.1,d.159.1.2 40923,42079 1j0mA 752 9.76e-01 a.102.3.2,b.24.1.1,b.30.5.2 83910,83911,83912 1mxiA 160 1.24e+00 c.116.1.1 79646 1vj0A 380 1.53e+00 b.35.1.2,c.2.1.1 100786,100787 1l7jB 347 1.78e+00 b.30.5.4 73661 2b30A 301 3.16e+00 1ta8A 332 3.68e+00 1w18A 493 4.10e+00 1zx8A 136 4.57e+00 1erjA 393 5.15e+00 1erjA b.69.4.1 27660 1b0lA 691 5.99e+00 1cb6A c.94.1.2,c.94.1.2 35847,35848 1mdbA 539 6.67e+00 e.23.1.1 79008 1ih7A 903 6.94e+00 1clqA c.55.3.5,e.8.1.1 62375,62376 1qjdA 571 6.95e+00 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19695,30432,42315 1vr0A 247 7.11e+00 1l5aA 436 7.12e+00 c.43.1.2,c.43.1.2 75923,75924 1p1xA 260 7.26e+00 c.1.10.1 104060 1nd4A 264 7.94e+00 d.144.1.6 91815 1f48A 589 8.21e+00 1f48A c.37.1.10,c.37.1.10 32280,32281 1e7uA 961 8.32e+00 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 1qx4A 274 9.22e+00 b.43.4.2,c.25.1.1 104624,104625 1ndh 272 9.29e+00 1ndh b.43.4.2,c.25.1.1 25662,31552 1ir3A 306 9.83e+00 1fmk d.144.1.7 41702 1b77A 228 1.09e+01 1b77A d.131.1.2,d.131.1.2 41362,41363 2d0oA 610 1.12e+01 2gk3A 256 1.16e+01 1tf5A 844 1.20e+01 a.162.1.1,a.172.1.1,c.37.1.19,c.37.1.19 106834,106835,106836,106837 2gsaA 432 1.20e+01 2gsaA c.67.1.4 34446 1ntfA 282 1.21e+01 d.151.1.2 92104 1xipA 388 1.25e+01 1e5kA 201 1.30e+01 1fr9A c.68.1.8 34578 1nrwA 288 1.38e+01 c.108.1.10 86128 1gycA 499 1.40e+01 b.6.1.3,b.6.1.3,b.6.1.3 70748,70749,70750 1cll 148 1.49e+01 1cll a.39.1.5 17263 1qjwA 365 1.61e+01 1bvwA c.6.1.1 30657 1vyrA 364 1.62e+01 c.1.4.1 108906 1j58A 385 1.63e+01 b.82.1.2 71531 1jb7A 495 1.71e+01 1otcA b.40.4.3,b.40.4.3,b.40.4.3 62836,62837,62838 1gylA 369 1.73e+01 1gox c.1.4.1 28610 1e39A 571 1.79e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19694,30431,42314 1m8uA 173 1.83e+01 b.11.1.1,b.11.1.1 91233,91234 1h7xC 1025 2.02e+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 1pguA 615 2.02e+01 b.69.4.1,b.69.4.1 88069,88070 1h7xD 1025 2.03e+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 2abbA 364 2.09e+01 1w6sA 599 2.18e+01 1q9rB 222 2.19e+01 b.1.1.1,b.1.1.2 96307,96308 1q1lA 401 2.26e+01 d.258.1.1 95591 2jdxA 385 2.26e+01 1jdw d.126.1.2 41139 1b3bA 415 2.27e+01 1hwyA c.2.1.7,c.58.1.1 30244,33892 2essA 248 2.32e+01 1agx 331 2.43e+01 4pgaA c.88.1.1 35564 1mt6A 280 2.44e+01 b.76.2.1,b.85.7.1 79446,79447 2scpA 174 2.52e+01 2scpA a.39.1.5 17256 1lf7A 182 2.54e+01 b.60.1.1 73878 1cs0C 1073 2.59e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18559,31488,31675,31676,41520,41521 2bjfA 329 2.59e+01 1mc0A 368 2.65e+01 d.110.2.1,d.110.2.1 78937,78938 2fflA 756 2.67e+01 1evlA 401 2.69e+01 1qf6A c.51.1.1,d.104.1.1 33202,40751 1fm2B 520 2.71e+01 1fm2B 2bsxA 253 2.74e+01 1juvA 193 2.74e+01 c.71.1.1 90912 1j5eE 161 2.76e+01 d.14.1.1,d.50.1.2 71547,71548 1bglA 1023 2.80e+01 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 2b43A 526 2.81e+01 1e8yA 966 2.84e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 1hxmD 242 2.86e+01 b.1.1.1,b.1.1.2 61373,61374 1hl9A 449 2.88e+01 b.71.1.3,c.1.8.11 90650,90651 1gz6A 319 2.91e+01 c.2.1.2 76410 1qorA 327 2.99e+01 1qorA b.35.1.2,c.2.1.1 24766,29782 1n9eA 787 3.01e+01 b.30.2.1,d.17.2.1,d.17.2.1 91708,91709,91710 1a5dA 173 3.06e+01 1amm b.11.1.1,b.11.1.1 23614,23615 1g4yR 148 3.07e+01 1cll a.39.1.5 60252 1rvkA 382 3.09e+01 c.1.11.2,d.54.1.1 97928,97929 1v2xA 194 3.16e+01 c.116.1.1 100274 1k7iA 479 3.24e+01 b.80.7.1,d.92.1.6 77281,77282 1mnaA 298 3.25e+01 c.69.1.22 79322 1askA 127 3.30e+01 1ounA d.17.4.2 38094 1h7wD 1025 3.32e+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 1udxA 416 3.33e+01 b.117.1.1,c.37.1.8,d.242.1.1 99228,99229,99230 1h7xA 1025 3.40e+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 2bdvA 231 3.43e+01 1h7xB 1025 3.46e+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 1d0hA 469 3.47e+01 1a8d b.29.1.6,b.42.4.2 24265,25610 1jmmA 377 3.52e+01 b.30.6.1 71749 1fy7A 278 3.56e+01 1fy7A d.108.1.1 40817 1u0fA 564 3.57e+01 1nekA 588 3.58e+01 a.7.3.1,c.3.1.4,d.168.1.1 80426,80427,80428 1riqA 465 3.67e+01 a.203.1.1,d.104.1.1 97516,97517 1hp1A 516 3.68e+01 d.114.1.1,d.159.1.2 70976,70977 1jmcA 246 3.69e+01 1jmcA b.40.4.3,b.40.4.3 25300,25301 1y08A 323 3.69e+01 1zoxA 113 3.69e+01 1qs8A 329 3.74e+01 1smrA b.50.1.2 26887 1jdw 423 3.76e+01 1jdw d.126.1.2 41129 1epwA 1290 3.79e+01 b.29.1.6,b.42.4.2,d.92.1.7,h.4.2.1 24269,25614,40305,45785 1zj8A 566 3.86e+01 1ordA 730 3.89e+01 1ordA c.23.1.4,c.67.1.5,d.125.1.1 31274,34503,41124 1ezoA 370 3.92e+01 4mbp c.94.1.1 59539 1xknA 355 3.94e+01 1txvA 452 3.94e+01 1l1nA 183 4.00e+01 b.47.1.4 73476 1ehaA 558 4.06e+01 1ehaA b.1.18.2,b.71.1.1,c.1.8.1 21859,27786,28773 1d8vA 263 4.16e+01 1mrj d.165.1.1 42193 1oya 400 4.17e+01 1oyc c.1.4.1 28604 1crkA 380 4.17e+01 1qh4A a.83.1.1,d.128.1.2 18458,41193 1wp5A 323 4.18e+01 1gt7A 274 4.27e+01 c.74.1.1 70398 1ux5A 411 4.29e+01 a.207.1.1 100144 2as9A 210 4.32e+01 1wdkC 390 4.35e+01 c.95.1.1,c.95.1.1 109258,109259 2fiqA 420 4.37e+01 1h7wA 1025 4.38e+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 1barA 140 4.42e+01 1bfg b.42.1.1 25504 1a71A 374 4.50e+01 2ohxA b.35.1.2,c.2.1.1 24673,29689 1a9xB 379 4.52e+01 1c3oB c.8.3.1,c.23.16.1 30732,31409 1oyjA 231 4.63e+01 a.45.1.1,c.47.1.5 87597,87598 1c7iA 489 4.64e+01 1thg c.69.1.1 34632 3cln 148 4.93e+01 1cll a.39.1.5 17286 1nf2A 268 5.02e+01 c.108.1.10 91849 1mu5A 471 5.10e+01 a.156.1.3,d.14.1.3,d.122.1.2 79472,79473,79474 1nowA 507 5.14e+01 c.1.8.6,d.92.2.1 85936,85937 1rwhA 757 5.17e+01 a.102.3.2,b.24.1.1,b.30.5.2 97984,97985,97986 1r64A 481 5.17e+01 b.18.1.20,c.41.1.1 97140,97141 1zrzA 364 5.20e+01 1hizA 379 5.44e+01 c.1.8.3 65841 1de4C 640 5.48e+01 1cx8B a.48.2.1,c.8.4.1,c.56.5.5 17779,30760,33848 1hg8A 349 5.57e+01 b.80.1.3 65830 1oc2A 348 5.60e+01 c.2.1.2 92765 1fvzA 271 5.68e+01 1fvzA 1xsjA 778 5.80e+01 1nr6A 473 5.83e+01 a.104.1.1 92085 1b9hA 388 5.91e+01 1b9hA c.67.1.4 34488 1ospO 257 5.99e+01 1ospO b.76.1.1 27971 1b1yA 500 6.03e+01 1byb c.1.8.1 28796 1e6yA 569 6.03e+01 1mroA a.89.1.1,d.58.31.2 18529,39447 1gteA 1025 6.06e+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 1gotB 340 6.08e+01 1tbgA b.69.4.1 27648 1m64A 571 6.34e+01 a.138.1.3,c.3.1.4,d.168.1.1 78683,78684,78685 2biqA 219 6.34e+01 1fjgE 162 6.35e+01 1pkp d.14.1.1,d.50.1.2 37553,38789 1viwB 198 6.37e+01 1led b.29.1.1 24170 1ffk1 177 6.38e+01 1ffk1 1w36C 1122 6.40e+01 1ynmA 247 6.48e+01 1diwA 441 6.60e+01 1a8d b.29.1.6,b.42.4.2 24264,25609 1uby 367 6.60e+01 1uby a.128.1.1 19435 2nlrA 234 6.70e+01 2nlrA b.29.1.11 24344 1k4gA 386 6.73e+01 c.1.20.1 72054 1qatB 622 6.82e+01 1djxB a.39.1.7,b.7.1.1,c.1.18.1 17355,23172,29600 2bg9A 370 6.83e+01 1n82A 331 6.84e+01 c.1.8.3 91703 1hkcA 917 6.86e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33475,33476,33477,33478 1xksA 450 6.93e+01 1ezwA 349 6.93e+01 1ezwA c.1.16.3 29558 2a5kA 307 7.01e+01 1gifA 115 7.02e+01 1dptA d.80.1.3 39837 1d8yA 605 7.04e+01 1xwl c.55.3.5,e.8.1.1 33684,42977 1jlyA 304 7.06e+01 1jlyA b.42.3.1,b.42.3.1 25587,25588 1dciA 275 7.07e+01 1dciA c.14.1.3 30918 2a1dD 329 7.09e+01 1vq2A 193 7.09e+01 1p1jA 533 7.11e+01 c.2.1.3,d.81.1.3 87687,87688 1ecpA 238 7.14e+01 1ecpA c.56.2.1 33775 2f3yA 148 7.18e+01 1whsA 255 7.20e+01 1ivyA c.69.1.5 34649 1uiuA 502 7.21e+01 c.94.1.1 99434 1m3iA 471 7.21e+01 f.9.1.1 91178 2ohxA 374 7.24e+01 2ohxA b.35.1.2,c.2.1.1 24669,29685 1hzgA 295 7.31e+01 1hzgA d.194.1.1 61436 1qr6A 584 7.32e+01 1qr6A c.2.1.7,c.58.1.3 30293,33941 1qupA 222 7.33e+01 1qupA b.1.8.1,d.58.17.1 22301,39352 1nw1A 429 7.39e+01 d.144.1.8 86286 3csuA 310 7.41e+01 3csuA c.78.1.1,c.78.1.1 35094,35095 2ffcA 353 7.44e+01 1qv9A 283 7.59e+01 c.127.1.1 96356 1gggA 226 7.69e+01 1lst c.94.1.1 35817 1z0nA 96 7.71e+01 1pswA 348 7.75e+01 c.87.1.7 88287 1ztuA 341 7.78e+01 1mfa 247 7.79e+01 1mfa b.1.1.1,b.1.1.1 19888,19889 1rsgA 516 7.87e+01 2cn3A 737 7.98e+01 2cunA 410 8.01e+01 1z2lA 423 8.03e+01 1pfo 500 8.04e+01 1pfo f.9.1.1 43826 1ajqB 557 8.07e+01 1ajqB 1dqiA 124 8.14e+01 1do6A b.1.13.1 22357 1amy 403 8.35e+01 1jdc b.71.1.1,c.1.8.1 27799,28786 1su4A 994 8.43e+01 b.82.7.1,c.108.1.7,d.220.1.1,f.33.1.1 98993,98994,98995,98996 1gthA 1025 8.45e+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 1lf6A 684 8.48e+01 a.102.1.5,b.30.5.5 77918,77919 2amdA 311 8.50e+01 1xkyA 301 8.67e+01 1g72A 573 8.75e+01 4aahA b.70.1.1 27680 1hbnB 442 8.93e+01 1mroB a.89.1.1,d.58.31.2 60900,60901 2sil 381 8.98e+01 3sil b.68.1.1 27543