# List of top-scoring protein chains for t2k-100-30-dssp-ehl2-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 4.90e-45 1larA 575 1.47e-44 1larA c.45.1.2,c.45.1.2 32693,32694 1yfoA 302 5.35e-44 2shpA c.45.1.2 32681 1rpmA 278 1.65e-43 2shpA c.45.1.2 32679 2shpA 525 1.11e-40 2shpA c.45.1.2,d.93.1.1,d.93.1.1 32683,40533,40534 1p15A 253 1.63e-40 c.45.1.2 93894 2hnp 321 2.00e-40 1pty c.45.1.2 32678 2f71A 298 2.34e-40 1eeoA 321 2.98e-40 1pty c.45.1.2 32655 1g7fA 298 2.99e-40 1pty c.45.1.2 60330 1aax 321 3.60e-40 1pty c.45.1.2 32657 1ptvA 321 3.97e-40 1pty c.45.1.2 32665 1pa1A 310 4.26e-40 c.45.1.2 94404 2b49A 287 5.74e-40 1a5y 330 6.32e-40 1pty c.45.1.2 32673 2b3oA 532 6.75e-40 1pty 321 7.81e-40 1pty c.45.1.2 32656 2bzlA 325 2.71e-38 1wchA 315 2.75e-38 2bv5A 282 1.54e-36 2bijA 305 2.10e-36 1jlnA 297 3.73e-36 1pty c.45.1.2 63172 1yptA 305 5.75e-19 1ytw c.45.1.2 32686 1ytw 306 8.35e-19 1ytw c.45.1.2 32689 1ytn 306 1.16e-18 1ytw c.45.1.2 32688 1lyvA 306 2.21e-18 c.45.1.2 74348 1yts 278 2.78e-18 1ytw c.45.1.2 32690 1g4wR 383 5.95e-14 1g4uS a.24.11.1,c.45.1.2 16644,32692 1g4uS 383 5.96e-14 1g4uS a.24.11.1,c.45.1.2 16643,32691 1x24A 180 4.03e-09 1zclA 180 8.62e-09 1zckA 154 1.55e-08 1rxdA 159 2.16e-08 1oheA 348 2.89e-08 c.45.1.1,c.45.1.1 87013,87014 1fpzA 212 1.06e-05 1fpzA c.45.1.1 59976 1d5rA 324 1.42e-04 1d5rA b.7.1.1,c.45.1.1 23181,32697 1vhrA 184 4.47e-04 1vhrA c.45.1.1 32651 1wrmA 165 4.50e-04 1i9sA 210 1.24e-03 1i9sA c.45.1.1 62099 1yz4A 160 1.25e-03 2c46A 241 1.73e-03 1yn9A 169 6.13e-03 1lw3A 657 7.04e-03 b.55.1.8,c.45.1.3 91152,91153 1u24A 337 8.01e-03 1zsqA 528 9.35e-03 1mkp 144 2.38e-02 1vhrA c.45.1.1 32654 1ywfA 296 8.35e-02 1xriA 151 1.27e-01 1w6sA 599 1.47e+00 2akaA 776 1.71e+00 2d5cA 263 1.84e+00 1wxdA 263 1.88e+00 2cy0A 263 1.91e+00 1e8nA 710 2.02e+00 1qfmA b.69.7.1,c.69.1.4 27675,34643 1h2xA 710 3.01e+00 b.69.7.1,c.69.1.4 76598,76599 1h2wA 710 3.05e+00 b.69.7.1,c.69.1.4 76596,76597 1qfmA 710 3.05e+00 1qfmA b.69.7.1,c.69.1.4 27673,34641 2pna 104 3.81e+00 1qadA d.93.1.1 40501 1kbpA 432 4.98e+00 4kbpA b.1.12.1,d.159.1.1 22349,42068 1jgtA 513 5.28e+00 c.26.2.1,d.153.1.1 66684,66685 1mnd 762 5.33e+00 1lvk b.34.3.1,c.37.1.9 24591,32188 1czaN 917 5.40e+00 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33463,33464,33465,33466 4kbpA 432 5.58e+00 4kbpA b.1.12.1,d.159.1.1 22345,42064 1m1zA 513 5.66e+00 c.26.2.1,d.153.1.1 78457,78458 1ysc 421 5.68e+00 1ivyA c.69.1.5 34652 1g60A 260 5.69e+00 c.66.1.11 70151 1jkmA 358 5.94e+00 1jkmA c.69.1.2 34633 1dgkN 917 6.03e+00 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33487,33488,33489,33490 1npyA 271 6.92e+00 c.2.1.7,c.58.1.5 85995,85996 2essA 248 6.95e+00 1erjA 393 7.76e+00 1erjA b.69.4.1 27660 1ig8A 486 7.92e+00 2yhx c.55.1.3,c.55.1.3 64746,64747 1hwwA 1015 7.95e+00 a.8.3.1,b.30.5.6,c.6.2.1 83067,83068,83069 1w9iA 770 8.56e+00 1cpy 421 8.63e+00 1ivyA c.69.1.5 34651 1qhhA 167 9.27e+00 1pjr c.37.1.19 32393 1ihuA 589 9.29e+00 c.37.1.10,c.37.1.10 62394,62395 1hkbA 917 9.61e+00 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33479,33480,33481,33482 1mumA 295 9.63e+00 c.1.12.7 85108 1hxkA 1015 1.00e+01 a.8.3.1,b.30.5.6,c.6.2.1 83070,83071,83072 1htyA 1015 1.00e+01 a.8.3.1,b.30.5.6,c.6.2.1 83064,83065,83066 1hkcA 917 1.03e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33475,33476,33477,33478 1xg4A 295 1.03e+01 1xzwA 426 1.04e+01 1k47A 337 1.05e+01 d.14.1.5,d.58.26.4 72040,72041 1d0nA 729 1.09e+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 1qwnA 1045 1.16e+01 a.8.3.1,b.30.5.6,c.6.2.1 96487,96488,96489 1xgsA 295 1.17e+01 1bn5 a.4.5.25,d.127.1.1 16216,41153 1gvhA 396 1.21e+01 a.1.1.2,b.43.4.2,c.25.1.5 70601,70602,70603 1usyA 275 1.22e+01 1lvk 762 1.25e+01 1lvk b.34.3.1,c.37.1.9 24576,32173 1nm8A 616 1.26e+01 c.43.1.3,c.43.1.3 85872,85873 1jkmB 361 1.26e+01 1jkmA c.69.1.2 34634 1zoiA 276 1.37e+01 1a88A 275 1.42e+01 1brt c.69.1.12 34707 1d0yA 761 1.42e+01 1lvk b.34.3.1,c.37.1.9 24581,32178 1f48A 589 1.46e+01 1f48A c.37.1.10,c.37.1.10 32280,32281 1rj9A 304 1.61e+01 a.24.13.1,c.37.1.10 97553,97554 1ojrA 274 1.63e+01 c.74.1.1 93147 1umkA 275 1.67e+01 1jdfA 447 1.67e+01 c.1.11.2,d.54.1.1 62897,62898 1p9rA 418 1.70e+01 c.37.1.11 94399 1yfsA 465 1.74e+01 1a8s 273 1.74e+01 1brt c.69.1.12 34710 2az4A 429 1.80e+01 1gt7A 274 1.96e+01 c.74.1.1 70398 1vimA 200 1.98e+01 c.80.1.3 100758 1f2tA 149 2.00e+01 1f2tA c.37.1.12 32373 1mtzA 293 2.10e+01 c.69.1.7 79467 2fl7A 232 2.11e+01 1zboA 210 2.18e+01 1rbp 182 2.19e+01 1aqb b.60.1.1 27085 1ndbA 596 2.19e+01 c.43.1.3,c.43.1.3 80411,80412 1us8A 147 2.21e+01 c.37.1.12 99859 1l8qA 324 2.30e+01 a.4.12.2,c.37.1.20 77809,77810 1jltB 122 2.37e+01 a.133.1.2 66868 1x6oA 174 2.39e+01 b.34.5.2,b.40.4.5 109493,109494 1xqwA 293 2.44e+01 1vkrA 125 2.47e+01 c.44.2.1 108689 1oo4A 111 2.52e+01 d.93.1.1 87185 1od2A 805 2.62e+01 c.14.1.4,c.14.1.4 86821,86822 1yveJ 524 2.64e+01 1qmgA a.100.1.2,c.2.1.6 18790,30187 1h65A 270 2.65e+01 c.37.1.8 65640 1aokB 122 2.67e+01 1poa a.133.1.2 19561 1qg0A 308 2.76e+01 1fnc b.43.4.2,c.25.1.1 25639,31529 1ujqA 305 2.84e+01 c.1.12.7 99463 1zz1A 369 2.92e+01 1yveI 524 2.98e+01 1qmgA a.100.1.2,c.2.1.6 18789,30186 2a6hA 315 3.05e+01 1lrwA 600 3.06e+01 b.70.1.1 91111 1bqg 451 3.06e+01 1bqg c.1.11.2,d.54.1.1 29217,38861 1zq4A 693 3.08e+01 1zkpA 268 3.19e+01 1btmA 252 3.23e+01 1amk c.1.1.1 28513 1gmxA 108 3.25e+01 c.46.1.3 65355 1c3d 294 3.29e+01 1c3d a.102.4.4 18874 1ec7A 446 3.31e+01 1bqg c.1.11.2,d.54.1.1 29218,38862 1kvkA 395 3.46e+01 d.14.1.5,d.58.26.3 73060,73061 1riqA 465 3.48e+01 a.203.1.1,d.104.1.1 97516,97517 1huxA 270 3.58e+01 1huxA c.55.1.5 61278 1gtmA 419 3.62e+01 1hwyA c.2.1.7,c.58.1.1 30223,33871 1bksB 397 3.74e+01 2tysB c.79.1.1 35285 3kar 346 3.76e+01 1bg2 c.37.1.9 32198 2f46A 156 3.87e+01 1cfyA 143 3.89e+01 1cof d.109.1.2 40858 1quqB 121 3.91e+01 1quqB b.40.4.3 25305 1cof 143 4.00e+01 1cof d.109.1.2 40860 1ako 268 4.41e+01 1ako d.151.1.1 41779 1jjfA 268 4.42e+01 c.69.1.2 66765 1f1oA 431 4.43e+01 1f1oA a.127.1.1 19433 1vmeA 410 4.53e+01 c.23.5.1,d.157.1.3 108893,108894 1jffB 445 4.54e+01 c.32.1.1,d.79.2.1 62934,62935 1fmaE 150 4.58e+01 1fmaE d.41.5.1 38630 1y13A 181 4.60e+01 1z6aA 500 4.61e+01 2exrA 524 4.62e+01 1lf6A 684 4.63e+01 a.102.1.5,b.30.5.5 77918,77919 1gn0A 108 4.65e+01 c.46.1.3 65358 1mucA 373 4.65e+01 1mucA c.1.11.2,d.54.1.1 29236,38880 1qmgA 524 4.69e+01 1qmgA a.100.1.2,c.2.1.6 18785,30182 1mqeA 207 4.72e+01 d.113.1.1 91394 2g0qA 173 4.89e+01 2minB 522 4.93e+01 1qguB c.92.2.3 35610 2b5eA 504 5.06e+01 1mvoA 136 5.08e+01 c.23.1.1 79513 1k8yB 396 5.10e+01 c.79.1.1 72184 1ukfA 188 5.11e+01 d.3.1.10 99488 1zlqA 502 5.12e+01 1a50B 396 5.26e+01 2tysB c.79.1.1 35280 1a6q 382 5.27e+01 1a6q a.159.1.1,d.219.1.1 75801,75802 1aorA 605 5.27e+01 1b25A a.110.1.1,d.152.1.1 19042,41794 1bsvA 321 5.27e+01 1bsvA c.2.1.2 29809 1skyB 502 5.29e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18313,26478,32358 1e69B 322 5.30e+01 1e69B c.37.1.12 32377 1gfsA 321 5.30e+01 c.2.1.2 29811 1bwsA 321 5.32e+01 1bsvA c.2.1.2 29812 2tysB 397 5.32e+01 2tysB c.79.1.1 35272 1hr6B 443 5.36e+01 1be3A d.185.1.1,d.185.1.1 61166,61167 1pyfA 312 5.41e+01 c.1.7.1 95334 2d29A 387 5.45e+01 1qhaA 917 5.58e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33467,33468,33469,33470 1jhdA 396 5.64e+01 b.122.1.3,c.26.1.5 66712,66713 1kyqA 274 5.65e+01 c.2.1.11,e.37.1.1 73281,73282 2btoA 473 5.67e+01 1jffA 451 5.67e+01 c.32.1.1,d.79.2.1 62932,62933 1j5eK 129 5.81e+01 c.55.4.1 71554 1pg4A 652 5.81e+01 e.23.1.1 88067 1vk3A 615 5.86e+01 d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 100846,100847,100848,100849 1gqyA 475 5.87e+01 c.5.1.1,c.59.1.1,c.72.2.1 83305,83306,83307 1uuqA 440 5.88e+01 c.1.8.3 100015 1skyE 473 5.91e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 18314,26479,32359 1zmbA 290 5.91e+01 1k3fA 253 5.94e+01 c.56.2.1 68105 2fsxA 148 5.94e+01 1cqxA 403 5.97e+01 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 2bjvA 265 5.98e+01 1tj9A 121 6.10e+01 a.133.1.2 107015 1qgoA 264 6.14e+01 1qgoA c.92.1.2 35596 1isiA 265 6.19e+01 e.4.1.1 71394 1z3xA 238 6.21e+01 1fv0A 121 6.21e+01 a.133.1.2 70147 1kpmA 121 6.21e+01 a.133.1.2 72844 1l2tA 235 6.21e+01 c.37.1.12 73514 1ws9A 387 6.27e+01 1qdeA 224 6.31e+01 1qvaA c.37.1.19 32410 1wkbA 810 6.33e+01 1qx4A 274 6.34e+01 b.43.4.2,c.25.1.1 104624,104625 1lnzA 342 6.34e+01 b.117.1.1,c.37.1.8 78112,78113 1nx8A 273 6.43e+01 b.82.2.8 86374 1dbqA 289 6.43e+01 1qpzA c.93.1.1 35666 1aqb 183 6.47e+01 1aqb b.60.1.1 27084 1e7rA 321 6.48e+01 1bsvA c.2.1.2 29808 1euvA 221 6.50e+01 1euvA d.3.1.7 37133 1hyqA 263 6.53e+01 1hyqA c.37.1.10 61412 1fm0E 150 6.58e+01 1fmaE d.41.5.1 38629 1vpwA 340 6.60e+01 1qpzA a.35.1.5,c.93.1.1 17087,35680 1sqzA 121 6.63e+01 a.133.1.2 98975 1tk4A 121 6.63e+01 a.133.1.2 107073 1igwA 434 6.66e+01 c.1.12.7 62370 1x3sA 195 6.66e+01 1gh9A 71 6.86e+01 1gh9A g.41.6.1 45266 1jroB 777 6.87e+01 d.41.1.1,d.133.1.1 67141,67142 1sjdA 368 6.89e+01 c.1.11.2,d.54.1.1 105632,105633 1wx1A 335 6.90e+01 1zwpA 121 6.94e+01 2g58A 121 6.94e+01 1x54A 434 6.95e+01 1r6lA 239 6.98e+01 d.14.1.4,d.101.1.1 97153,97154 1sazA 381 7.03e+01 1fjgK 129 7.05e+01 1fjfK c.55.4.1 33733 1eljA 381 7.16e+01 4mbp c.94.1.1 35791 2b2nA 344 7.18e+01 1zsyA 357 7.22e+01 1hg3A 225 7.22e+01 1hg3A c.1.1.1 61025 1dciA 275 7.30e+01 1dciA c.14.1.3 30918 2fgeA 995 7.36e+01 1e0cA 271 7.36e+01 1e0cA c.46.1.2,c.46.1.2 32717,32718 1rzuA 485 7.37e+01 c.87.1.8 105140 1vjhA 122 7.38e+01 d.129.3.1 100811 2bklA 695 7.54e+01 1e6uA 321 7.55e+01 1bsvA c.2.1.2 29805 1ndh 272 7.59e+01 1ndh b.43.4.2,c.25.1.1 25662,31552 1m2xA 223 7.60e+01 d.157.1.1 84764 1qpzA 340 7.71e+01 1qpzA a.35.1.5,c.93.1.1 17097,35673 1lvwA 295 7.77e+01 c.68.1.6 84723 1lfwA 470 7.84e+01 c.56.5.4,d.58.19.1 77942,77943 1u59A 287 7.84e+01 d.144.1.7 107681 2fbmA 291 7.85e+01 1w2xA 758 7.86e+01 c.14.1.4,c.14.1.4 109134,109135 1jbkA 195 7.98e+01 c.37.1.20 71631 1vapA 123 8.21e+01 1poa a.133.1.2 19548 1qopB 396 8.27e+01 2tysB c.79.1.1 35270 1azwA 313 8.31e+01 1qtrA c.69.1.7 34658 1c1dA 355 8.41e+01 1bw9A c.2.1.7,c.58.1.1 30270,33918 1o6yA 299 8.51e+01 d.144.1.7 81106 1v4sA 455 8.52e+01 c.55.1.3,c.55.1.3 100309,100310 168lA 164 8.52e+01 1l92 d.2.1.3 36975 1rxyA 253 8.53e+01 c.56.2.1 98065 1z5vA 474 8.53e+01 4enl 436 8.73e+01 4enl c.1.11.1,d.54.1.1 29202,38846 2f02A 323 8.76e+01 1yixA 265 8.76e+01 1kqfB 294 8.78e+01 d.58.1.5,f.23.22.1 75900,75901 3minB 522 8.81e+01 1qguB c.92.2.3 35606 1wetA 340 8.86e+01 1qpzA a.35.1.5,c.93.1.1 17093,35670 1hp5A 512 8.90e+01 1hp4A c.1.8.6,d.92.2.1 61113,61114 1hp4A 512 8.90e+01 1hp4A c.1.8.6,d.92.2.1 61111,61112