# List of top-scoring protein chains for t2k-100-30-bys-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 2fh7A 595 6.28e-41 1larA 575 9.79e-41 1larA c.45.1.2,c.45.1.2 32693,32694 1yfoA 302 6.65e-40 2shpA c.45.1.2 32681 1rpmA 278 1.16e-39 2shpA c.45.1.2 32679 2shpA 525 3.54e-37 2shpA c.45.1.2,d.93.1.1,d.93.1.1 32683,40533,40534 2b49A 287 1.43e-36 2b3oA 532 1.54e-36 2f71A 298 1.62e-36 1g7fA 298 1.69e-36 1pty c.45.1.2 60330 1pa1A 310 2.28e-36 c.45.1.2 94404 1pty 321 2.29e-36 1pty c.45.1.2 32656 1p15A 253 2.51e-36 c.45.1.2 93894 1aax 321 2.58e-36 1pty c.45.1.2 32657 1eeoA 321 3.02e-36 1pty c.45.1.2 32655 2hnp 321 3.28e-36 1pty c.45.1.2 32678 1ptvA 321 4.79e-36 1pty c.45.1.2 32665 1a5y 330 1.05e-35 1pty c.45.1.2 32673 2bzlA 325 4.32e-35 1wchA 315 1.69e-34 1jlnA 297 7.89e-34 1pty c.45.1.2 63172 2bijA 305 4.95e-33 2bv5A 282 7.00e-33 1yptA 305 6.50e-17 1ytw c.45.1.2 32686 1ytn 306 1.79e-16 1ytw c.45.1.2 32688 1lyvA 306 2.74e-16 c.45.1.2 74348 1ytw 306 3.86e-16 1ytw c.45.1.2 32689 1yts 278 4.73e-16 1ytw c.45.1.2 32690 1g4wR 383 2.98e-12 1g4uS a.24.11.1,c.45.1.2 16644,32692 1g4uS 383 3.97e-12 1g4uS a.24.11.1,c.45.1.2 16643,32691 1x24A 180 2.50e-09 1zckA 154 3.23e-09 1rxdA 159 5.76e-09 1oheA 348 1.30e-08 c.45.1.1,c.45.1.1 87013,87014 1zclA 180 2.79e-08 1fpzA 212 1.04e-05 1fpzA c.45.1.1 59976 1i9sA 210 1.43e-04 1i9sA c.45.1.1 62099 1vhrA 184 2.41e-04 1vhrA c.45.1.1 32651 2c46A 241 2.74e-04 1d5rA 324 2.76e-04 1d5rA b.7.1.1,c.45.1.1 23181,32697 1wrmA 165 2.82e-04 1yz4A 160 5.88e-04 1u24A 337 3.72e-03 1zsqA 528 7.10e-03 1lw3A 657 7.78e-03 b.55.1.8,c.45.1.3 91152,91153 1mkp 144 9.26e-03 1vhrA c.45.1.1 32654 1yn9A 169 1.00e-02 1xriA 151 1.08e-02 1ywfA 296 1.36e-02 1wxdA 263 1.39e-01 2cy0A 263 1.65e-01 2d5cA 263 1.96e-01 1npyA 271 3.68e-01 c.2.1.7,c.58.1.5 85995,85996 1f48A 589 5.21e-01 1f48A c.37.1.10,c.37.1.10 32280,32281 1ihuA 589 8.98e-01 c.37.1.10,c.37.1.10 62394,62395 1mumA 295 9.07e-01 c.1.12.7 85108 1qhhA 167 1.05e+00 1pjr c.37.1.19 32393 1xg4A 295 1.89e+00 1h2xA 710 2.88e+00 b.69.7.1,c.69.1.4 76598,76599 1ujqA 305 2.99e+00 c.1.12.7 99463 1lvwA 295 3.01e+00 c.68.1.6 84723 1tj9A 121 3.07e+00 a.133.1.2 107015 1h2wA 710 3.13e+00 b.69.7.1,c.69.1.4 76596,76597 1tk4A 121 3.49e+00 a.133.1.2 107073 1e8nA 710 3.60e+00 1qfmA b.69.7.1,c.69.1.4 27675,34643 1qfmA 710 3.63e+00 1qfmA b.69.7.1,c.69.1.4 27673,34641 1gvhA 396 3.63e+00 a.1.1.2,b.43.4.2,c.25.1.5 70601,70602,70603 2f46A 156 3.98e+00 1h65A 270 4.13e+00 c.37.1.8 65640 1a88A 275 4.96e+00 1brt c.69.1.12 34707 1mnd 762 5.19e+00 1lvk b.34.3.1,c.37.1.9 24591,32188 1gn0A 108 5.29e+00 c.46.1.3 65358 1g60A 260 5.33e+00 c.66.1.11 70151 1k3fA 253 5.42e+00 c.56.2.1 68105 2essA 248 5.42e+00 1us8A 147 6.01e+00 c.37.1.12 99859 1vl4A 447 6.22e+00 d.283.1.1 108718 1p9rA 418 6.33e+00 c.37.1.11 94399 1zwpA 121 6.52e+00 1gmxA 108 6.99e+00 c.46.1.3 65355 1rj9A 304 7.01e+00 a.24.13.1,c.37.1.10 97553,97554 1fv0A 121 7.26e+00 a.133.1.2 70147 1umkA 275 7.39e+00 1pjr 724 7.87e+00 1pjr c.37.1.19,c.37.1.19 32391,32392 1l8qA 324 7.88e+00 a.4.12.2,c.37.1.20 77809,77810 1vimA 200 8.15e+00 c.80.1.3 100758 1jltB 122 8.54e+00 a.133.1.2 66868 1zlqA 502 8.55e+00 1kpmA 121 9.45e+00 a.133.1.2 72844 2g58A 121 9.52e+00 1xhlA 297 9.59e+00 c.2.1.2 109591 1lx7A 253 9.61e+00 c.56.2.1 74329 1hkbA 917 9.91e+00 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33479,33480,33481,33482 1f2tA 149 1.00e+01 1f2tA c.37.1.12 32373 1vkrA 125 1.05e+01 c.44.2.1 108689 2bm8A 236 1.05e+01 1sqzA 121 1.10e+01 a.133.1.2 98975 1zsyA 357 1.12e+01 1m1zA 513 1.13e+01 c.26.2.1,d.153.1.1 78457,78458 1jgtA 513 1.14e+01 c.26.2.1,d.153.1.1 66684,66685 1rz3A 201 1.17e+01 c.37.1.6 98132 1vloA 381 1.26e+01 b.44.2.1,d.250.1.1 108838,108839 1igwA 434 1.31e+01 c.1.12.7 62370 2cxxA 190 1.34e+01 1zkpA 268 1.36e+01 2az4A 429 1.37e+01 1qdeA 224 1.38e+01 1qvaA c.37.1.19 32410 1cfyA 143 1.45e+01 1cof d.109.1.2 40858 1qhaA 917 1.49e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33467,33468,33469,33470 1yveJ 524 1.52e+01 1qmgA a.100.1.2,c.2.1.6 18790,30187 1zq4A 693 1.56e+01 2bwbA 46 1.59e+01 1qmgA 524 1.60e+01 1qmgA a.100.1.2,c.2.1.6 18785,30182 1aokB 122 1.60e+01 1poa a.133.1.2 19561 1rxyA 253 1.65e+01 c.56.2.1 98065 2bjvA 265 1.66e+01 3prn 289 1.67e+01 3prn f.4.3.1 43761 1yveI 524 1.72e+01 1qmgA a.100.1.2,c.2.1.6 18789,30186 1pg4A 652 1.77e+01 e.23.1.1 88067 1bh3 289 1.78e+01 3prn f.4.3.1 43766 1jroB 777 1.78e+01 d.41.1.1,d.133.1.1 67141,67142 1po5A 476 1.83e+01 a.104.1.1 94963 1czaN 917 1.84e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33463,33464,33465,33466 1jkmB 361 1.86e+01 1jkmA c.69.1.2 34634 1agi 125 1.88e+01 7rsa d.5.1.1 37303 1uaaA 673 1.89e+01 1pjr c.37.1.19,c.37.1.19 32401,32402 1usyA 275 1.91e+01 1ci3M 249 1.98e+01 1hcz b.2.6.1,b.84.2.2 22480,28266 1cof 143 2.01e+01 1cof d.109.1.2 40860 1f8mA 429 2.14e+01 1dquA c.1.12.7 29315 1jkmA 358 2.22e+01 1jkmA c.69.1.2 34633 1cei 94 2.25e+01 1cei a.28.2.1 16939 1dgkN 917 2.28e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33487,33488,33489,33490 1ukfA 188 2.30e+01 d.3.1.10 99488 1qvbA 481 2.31e+01 1qvbA c.1.8.4 28983 1w36B 1180 2.31e+01 1k47A 337 2.33e+01 d.14.1.5,d.58.26.4 72040,72041 1zoiA 276 2.38e+01 1qopB 396 2.39e+01 2tysB c.79.1.1 35270 1f61A 429 2.42e+01 1dquA c.1.12.7 29319 1hg3A 225 2.44e+01 1hg3A c.1.1.1 61025 1qgoA 264 2.52e+01 1qgoA c.92.1.2 35596 1vrvA 101 2.53e+01 1xfcA 384 2.56e+01 1ysrA 150 2.57e+01 1h7sA 365 2.69e+01 d.14.1.3,d.122.1.2 65705,65706 4kbpA 432 2.69e+01 4kbpA b.1.12.1,d.159.1.1 22345,42064 1unkA 87 2.71e+01 1cei a.28.2.1 16935 1jdfA 447 2.71e+01 c.1.11.2,d.54.1.1 62897,62898 1jbkA 195 2.73e+01 c.37.1.20 71631 1ih7A 903 2.79e+01 1clqA c.55.3.5,e.8.1.1 62375,62376 1a8s 273 2.80e+01 1brt c.69.1.12 34710 1fadA 99 2.80e+01 1fadA a.77.1.2 18428 1guaA 167 2.87e+01 1ctqA c.37.1.8 32013 1pbp 321 2.91e+01 1ixh c.94.1.1 35768 1z5vA 474 2.93e+01 1top 162 2.94e+01 1ncx a.39.1.5 17223 1wr1B 58 3.01e+01 1v04A 355 3.09e+01 b.68.6.2 100240 2fcjA 119 3.11e+01 1bksB 397 3.13e+01 2tysB c.79.1.1 35285 1fts 295 3.17e+01 1ng1 a.24.13.1,c.37.1.10 16968,32279 1hdmA 201 3.22e+01 1iakA b.1.1.2,d.19.1.1 21583,38157 1vapA 123 3.23e+01 1poa a.133.1.2 19548 1v4sA 455 3.25e+01 c.55.1.3,c.55.1.3 100309,100310 1uiuA 502 3.26e+01 c.94.1.1 99434 1t0iA 191 3.29e+01 c.23.5.4 106209 1jeoA 180 3.35e+01 c.80.1.3 66611 1u4nA 310 3.37e+01 1x1rA 178 3.43e+01 1kbpA 432 3.46e+01 4kbpA b.1.12.1,d.159.1.1 22349,42068 1a50B 396 3.53e+01 2tysB c.79.1.1 35280 1agp 166 3.53e+01 1ctqA c.37.1.8 31985 4ubpB 126 3.55e+01 1ubpB b.85.3.1 28345 2erl 40 3.56e+01 2erl a.10.1.1 16360 1i7pA 274 3.58e+01 b.43.4.2,c.25.1.1 66048,66049 1c0nA 406 3.60e+01 1c0nA c.67.1.3 34433 1a97A 148 3.60e+01 1nulA c.61.1.1 34023 1ncx 162 3.61e+01 1ncx a.39.1.5 17222 1qxmA 300 3.61e+01 b.42.2.1,b.42.2.1 96533,96534 1q2zA 120 3.63e+01 a.118.19.1 95656 2tysB 397 3.66e+01 2tysB c.79.1.1 35272 1ixh 321 3.69e+01 1ixh c.94.1.1 35761 1t3uA 104 3.72e+01 d.244.1.1 99120 1t6nA 220 3.77e+01 c.37.1.19 106576 1kao 167 3.81e+01 1ctqA c.37.1.8 32014 1o4yA 288 3.88e+01 b.29.1.2 92473 1a54A 321 3.89e+01 1ixh c.94.1.1 35763 1e0cA 271 3.91e+01 1e0cA c.46.1.2,c.46.1.2 32717,32718 1eljA 381 3.91e+01 4mbp c.94.1.1 35791 2akaA 776 3.94e+01 2f4pA 147 3.97e+01 1a40 321 3.97e+01 1ixh c.94.1.1 35767 1in6A 334 4.04e+01 1hqcA a.4.5.11,c.37.1.20 62601,62602 1iw7C 1119 4.05e+01 e.29.1.1 71474 2cqsA 842 4.12e+01 1kqfB 294 4.16e+01 d.58.1.5,f.23.22.1 75900,75901 1ail 73 4.26e+01 1ail a.16.1.1 16381 1hxkA 1015 4.26e+01 a.8.3.1,b.30.5.6,c.6.2.1 83070,83071,83072 1pyfA 312 4.37e+01 c.1.7.1 95334 1ubpB 122 4.40e+01 1ubpB b.85.3.1 28346 1xzwA 426 4.42e+01 2bsxA 253 4.42e+01 1clqA 903 4.45e+01 1clqA c.55.3.5,e.8.1.1 33717,43006 1f1oA 431 4.52e+01 1f1oA a.127.1.1 19433 1kp9B 287 4.55e+01 c.66.1.18 68734 1qvaA 223 4.58e+01 1qvaA c.37.1.19 32411 1hkcA 917 4.63e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33475,33476,33477,33478 1kpgA 287 4.72e+01 c.66.1.18 68735 1m3sA 186 4.73e+01 c.80.1.3 78573 1ei6A 406 4.73e+01 c.76.1.4 90443 2btoA 473 4.78e+01 5p21 166 4.81e+01 1ctqA c.37.1.8 31966 1d0nA 729 4.88e+01 1d0nA d.109.1.1,d.109.1.1,d.109.1.1,d.109.1.1,d.109.1.1,d.109.1.1 40834,40835,40836,40837,40838,40839 1p0iA 529 4.88e+01 c.69.1.1 93867 1g59A 468 4.91e+01 a.97.1.1,c.26.1.1 60257,60258 1tr1A 447 4.92e+01 1e70M c.1.8.4 28957 1nf3C 128 4.96e+01 b.36.1.1 85596 1j09A 468 4.97e+01 a.97.1.1,c.26.1.1 77025,77026 1oflA 481 4.98e+01 b.80.1.4 103934 1ogiA 303 4.99e+01 b.43.4.2,c.25.1.1 92914,92915 1bia 321 4.99e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1foeA 377 5.07e+01 1foeA a.87.1.1,b.55.1.1 18517,26969 1c3d 294 5.09e+01 1c3d a.102.4.4 18874 1kkoA 413 5.10e+01 c.1.11.2,d.54.1.1 68675,68676 1htyA 1015 5.14e+01 a.8.3.1,b.30.5.6,c.6.2.1 83064,83065,83066 1ctqA 166 5.19e+01 1ctqA c.37.1.8 31965 1e4iA 447 5.22e+01 1e70M c.1.8.4 59225 2pgd 482 5.25e+01 2pgd a.100.1.1,c.2.1.6 18778,30190 1qwnA 1045 5.27e+01 a.8.3.1,b.30.5.6,c.6.2.1 96487,96488,96489 1zz1A 369 5.28e+01 1u46A 291 5.40e+01 d.144.1.7 107656 1rbp 182 5.40e+01 1aqb b.60.1.1 27085 1kcfA 258 5.43e+01 a.140.2.1,c.55.3.7 68434,68435 1hwwA 1015 5.49e+01 a.8.3.1,b.30.5.6,c.6.2.1 83067,83068,83069 1lf6A 684 5.58e+01 a.102.1.5,b.30.5.5 77918,77919 1u04A 771 5.66e+01 b.34.14.1,c.55.3.10 107539,107540 1qahA 136 5.74e+01 d.79.1.1 96338 1go2A 304 5.83e+01 b.43.4.2,c.25.1.1 76243,76244 1k8yB 396 5.87e+01 c.79.1.1 72184 1b35A 260 5.91e+01 1b35A b.121.4.1 23333 1ec7A 446 5.92e+01 1bqg c.1.11.2,d.54.1.1 29218,38862 1sacA 204 5.93e+01 1sacA b.29.1.5 24237 1btmA 252 5.93e+01 1amk c.1.1.1 28513 1gveA 327 5.98e+01 c.1.7.1 70597 1krhA 338 6.07e+01 b.43.4.2,c.25.1.2,d.15.4.2 72891,72892,72893 2f02A 323 6.11e+01 1hv8A 367 6.19e+01 1hv8A c.37.1.19,c.37.1.19 32405,32406 1jf9A 408 6.24e+01 1c0nA c.67.1.3 62931 1rw2A 152 6.25e+01 a.118.19.1 97961 1umwA 237 6.25e+01 d.223.1.2,d.223.1.2 99631,99632 1sc3B 88 6.31e+01 1s57A 153 6.35e+01 1bqg 451 6.35e+01 1bqg c.1.11.2,d.54.1.1 29217,38861 2a74A 643 6.37e+01 1paqA 189 6.41e+01 a.118.1.14 94413 1ndh 272 6.46e+01 1ndh b.43.4.2,c.25.1.1 25662,31552 1gln 468 6.47e+01 1gln a.97.1.1,c.26.1.1 18752,31588 1d4vB 163 6.48e+01 1d4vB b.22.1.1 23884 1m2xA 223 6.48e+01 d.157.1.1 84764 1x6oA 174 6.55e+01 b.34.5.2,b.40.4.5 109493,109494 1t3gA 159 6.57e+01 1zac 90 6.60e+01 1ncx a.39.1.5 17236 2bp1A 360 6.61e+01 8prn 289 6.67e+01 3prn f.4.3.1 43767 1ve6A 582 6.69e+01 1k6iA 352 6.71e+01 c.2.1.2 68223 1b0tA 106 6.74e+01 1a6l d.58.1.2 38965 1x3sA 195 6.79e+01 1cpy 421 6.82e+01 1ivyA c.69.1.5 34651 2g8yA 385 6.84e+01 1xv5A 401 6.93e+01 1pl8A 356 6.97e+01 b.35.1.2,c.2.1.1 94878,94879 2awdA 323 7.00e+01 1gio 125 7.05e+01 7rsa d.5.1.1 37304 1bmqB 88 7.08e+01 1pauB 1b25A 619 7.15e+01 1b25A a.110.1.1,d.152.1.1 19044,41796 1lt3A 240 7.20e+01 1lt3A d.166.1.1 42230 1lvk 762 7.36e+01 1lvk b.34.3.1,c.37.1.9 24576,32173 1oqcA 125 7.38e+01 a.24.15.1 87264 1ibcB 88 7.40e+01 1pauB 1mnaA 298 7.46e+01 c.69.1.22 79322 1k8kA 418 7.49e+01 c.55.1.1,c.55.1.1 68305,68306 1mc3A 296 7.52e+01 c.68.1.6 78943 1ysc 421 7.61e+01 1ivyA c.69.1.5 34652 1y44A 320 7.63e+01 2bd0A 244 7.65e+01 1zhxA 438 7.69e+01 1d0yA 761 7.71e+01 1lvk b.34.3.1,c.37.1.9 24581,32178 2a6hC 1119 7.77e+01 2ftwA 521 7.81e+01 1jslA 327 7.85e+01 c.88.1.1 67233 1u3eM 174 7.85e+01 d.4.1.3,d.285.1.1 107640,107641 1prn 289 7.87e+01 3prn f.4.3.1 43762 1mt6A 280 7.90e+01 b.76.2.1,b.85.7.1 79446,79447 1xb3A 128 7.93e+01 1qh0A 295 7.93e+01 b.43.4.2,c.25.1.1 68891,68892 7fd1A 106 7.99e+01 1a6l d.58.1.2 38953 1xeuA 263 8.02e+01 1vqvA 306 8.09e+01 1vecA 206 8.12e+01 c.37.1.19 100575 1thfD 253 8.20e+01 1thfD c.1.2.1 28535 1fmaE 150 8.22e+01 1fmaE d.41.5.1 38630 1a6l 106 8.23e+01 1a6l d.58.1.2 38966 1i12A 160 8.43e+01 1i21A d.108.1.1 61515 1fm0E 150 8.43e+01 1fmaE d.41.5.1 38629 1sjwA 144 8.45e+01 d.17.4.9 98899 1a3qA 285 8.47e+01 1a3qA b.1.18.1,b.2.5.3 21932,22447 1ri6A 343 8.49e+01 b.69.11.1 97503 1iv8A 720 8.52e+01 b.71.1.1,c.1.8.1 76842,76843 2fbmA 291 8.52e+01 1xkqA 280 8.57e+01 1azwA 313 8.65e+01 1qtrA c.69.1.7 34658 1ws6A 171 8.68e+01 189l 164 8.69e+01 1l92 d.2.1.3 36960 1oniA 137 8.71e+01 d.79.1.1 87144 2pna 104 8.73e+01 1qadA d.93.1.1 40501 1pz7A 204 8.79e+01 b.29.1.4 95405 2bc4A 211 8.93e+01 1i1dA 161 8.94e+01 1i21A d.108.1.1 61526 2fgeA 995 8.95e+01 1frvA 264 8.97e+01 2frvA e.19.1.1 43308 1qqfA 277 8.99e+01 1c3d a.102.4.4 18875