# List of top-scoring protein chains for t2k-100-30-stride-ebghtl-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 1.39e-51 1larA 575 3.65e-51 1larA c.45.1.2,c.45.1.2 32693,32694 1yfoA 302 3.03e-50 2shpA c.45.1.2 32681 1rpmA 278 1.11e-49 2shpA c.45.1.2 32679 2hnp 321 1.68e-46 1pty c.45.1.2 32678 2f71A 298 1.73e-46 2shpA 525 1.88e-46 2shpA c.45.1.2,d.93.1.1,d.93.1.1 32683,40533,40534 1g7fA 298 2.30e-46 1pty c.45.1.2 60330 1a5y 330 3.47e-46 1pty c.45.1.2 32673 1ptvA 321 4.09e-46 1pty c.45.1.2 32665 1aax 321 5.39e-46 1pty c.45.1.2 32657 1eeoA 321 6.04e-46 1pty c.45.1.2 32655 2b49A 287 6.36e-46 1pa1A 310 6.44e-46 c.45.1.2 94404 2b3oA 532 7.09e-46 1pty 321 7.20e-46 1pty c.45.1.2 32656 1p15A 253 5.00e-45 c.45.1.2 93894 2bzlA 325 1.76e-44 1wchA 315 6.36e-44 2bijA 305 1.19e-42 2bv5A 282 1.55e-42 1jlnA 297 4.62e-42 1pty c.45.1.2 63172 1ytw 306 2.19e-21 1ytw c.45.1.2 32689 1yptA 305 2.68e-21 1ytw c.45.1.2 32686 1yts 278 5.30e-21 1ytw c.45.1.2 32690 1ytn 306 6.11e-21 1ytw c.45.1.2 32688 1lyvA 306 1.33e-20 c.45.1.2 74348 1g4wR 383 3.86e-16 1g4uS a.24.11.1,c.45.1.2 16644,32692 1g4uS 383 3.93e-16 1g4uS a.24.11.1,c.45.1.2 16643,32691 1zckA 154 1.36e-09 1rxdA 159 1.45e-09 1oheA 348 1.84e-09 c.45.1.1,c.45.1.1 87013,87014 1fpzA 212 3.89e-06 1fpzA c.45.1.1 59976 1d5rA 324 3.83e-05 1d5rA b.7.1.1,c.45.1.1 23181,32697 1wrmA 165 4.69e-05 1i9sA 210 1.18e-04 1i9sA c.45.1.1 62099 2c46A 241 1.82e-04 1vhrA 184 2.05e-04 1vhrA c.45.1.1 32651 1yz4A 160 5.65e-04 1yn9A 169 3.25e-03 1lw3A 657 5.04e-03 b.55.1.8,c.45.1.3 91152,91153 1zsqA 528 6.98e-03 1u24A 337 8.70e-03 1mkp 144 1.84e-02 1vhrA c.45.1.1 32654 1xriA 151 5.76e-02 1x24A 180 1.04e-01 1ywfA 296 1.37e-01 1zclA 180 1.89e-01 1qfmA 710 3.91e-01 1qfmA b.69.7.1,c.69.1.4 27673,34641 1h2xA 710 4.12e-01 b.69.7.1,c.69.1.4 76598,76599 1e8nA 710 5.05e-01 1qfmA b.69.7.1,c.69.1.4 27675,34643 1h2wA 710 5.43e-01 b.69.7.1,c.69.1.4 76596,76597 2d5cA 263 1.08e+00 2cy0A 263 1.14e+00 1wxdA 263 1.19e+00 1xgsA 295 1.82e+00 1bn5 a.4.5.25,d.127.1.1 16216,41153 1yfsA 465 2.03e+00 1ig8A 486 2.16e+00 2yhx c.55.1.3,c.55.1.3 64746,64747 1w2xA 758 2.24e+00 c.14.1.4,c.14.1.4 109134,109135 1htyA 1015 2.24e+00 a.8.3.1,b.30.5.6,c.6.2.1 83064,83065,83066 1jgtA 513 2.40e+00 c.26.2.1,d.153.1.1 66684,66685 1d0nA 729 2.42e+00 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 1riqA 465 2.43e+00 a.203.1.1,d.104.1.1 97516,97517 1p9rA 418 2.84e+00 c.37.1.11 94399 1m1zA 513 2.93e+00 c.26.2.1,d.153.1.1 78457,78458 1qwnA 1045 3.02e+00 a.8.3.1,b.30.5.6,c.6.2.1 96487,96488,96489 1od2A 805 3.09e+00 c.14.1.4,c.14.1.4 86821,86822 2akaA 776 3.15e+00 1lvk 762 3.28e+00 1lvk b.34.3.1,c.37.1.9 24576,32173 1kbpA 432 3.32e+00 4kbpA b.1.12.1,d.159.1.1 22349,42068 4kbpA 432 3.35e+00 4kbpA b.1.12.1,d.159.1.1 22345,42064 1xg4A 295 3.35e+00 1hwwA 1015 3.37e+00 a.8.3.1,b.30.5.6,c.6.2.1 83067,83068,83069 1hxkA 1015 3.37e+00 a.8.3.1,b.30.5.6,c.6.2.1 83070,83071,83072 1xzwA 426 3.54e+00 1mumA 295 3.71e+00 c.1.12.7 85108 1jdfA 447 3.77e+00 c.1.11.2,d.54.1.1 62897,62898 1umkA 275 4.02e+00 1d0yA 761 4.06e+00 1lvk b.34.3.1,c.37.1.9 24581,32178 1zz1A 369 4.17e+00 1mnd 762 4.18e+00 1lvk b.34.3.1,c.37.1.9 24591,32188 1gvhA 396 4.18e+00 a.1.1.2,b.43.4.2,c.25.1.5 70601,70602,70603 1f48A 589 4.18e+00 1f48A c.37.1.10,c.37.1.10 32280,32281 1gt7A 274 4.29e+00 c.74.1.1 70398 1dgkN 917 4.65e+00 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33487,33488,33489,33490 1czaN 917 4.66e+00 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33463,33464,33465,33466 2pna 104 4.66e+00 1qadA d.93.1.1 40501 1hkcA 917 4.81e+00 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33475,33476,33477,33478 2bklA 695 4.94e+00 1w9iA 770 5.02e+00 1hkbA 917 5.10e+00 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33479,33480,33481,33482 1g60A 260 5.76e+00 c.66.1.11 70151 1k47A 337 6.75e+00 d.14.1.5,d.58.26.4 72040,72041 1ojrA 274 7.17e+00 c.74.1.1 93147 1uyrA 737 7.25e+00 c.14.1.4,c.14.1.4 100188,100189 2essA 248 7.51e+00 1jkmA 358 7.93e+00 1jkmA c.69.1.2 34633 1ihuA 589 8.25e+00 c.37.1.10,c.37.1.10 62394,62395 1gtmA 419 8.33e+00 1hwyA c.2.1.7,c.58.1.1 30223,33871 1jffB 445 8.47e+00 c.32.1.1,d.79.2.1 62934,62935 1yveJ 524 9.12e+00 1qmgA a.100.1.2,c.2.1.6 18790,30187 1npyA 271 9.19e+00 c.2.1.7,c.58.1.5 85995,85996 1ec7A 446 9.29e+00 1bqg c.1.11.2,d.54.1.1 29218,38862 1x6oA 174 9.62e+00 b.34.5.2,b.40.4.5 109493,109494 1rj9A 304 9.71e+00 a.24.13.1,c.37.1.10 97553,97554 1bqg 451 9.76e+00 1bqg c.1.11.2,d.54.1.1 29217,38861 1yveI 524 9.78e+00 1qmgA a.100.1.2,c.2.1.6 18789,30186 1qmgA 524 9.90e+00 1qmgA a.100.1.2,c.2.1.6 18785,30182 1w6sA 599 1.07e+01 1qg0A 308 1.07e+01 1fnc b.43.4.2,c.25.1.1 25639,31529 1vkrA 125 1.20e+01 c.44.2.1 108689 1zboA 210 1.30e+01 1b59A 370 1.33e+01 1bn5 a.4.5.25,d.127.1.1 16225,41162 1isiA 265 1.35e+01 e.4.1.1 71394 1nm8A 616 1.36e+01 c.43.1.3,c.43.1.3 85872,85873 1quqB 121 1.39e+01 1quqB b.40.4.3 25305 2az4A 429 1.40e+01 1rbp 182 1.42e+01 1aqb b.60.1.1 27085 1zkpA 268 1.55e+01 1l8qA 324 1.57e+01 a.4.12.2,c.37.1.20 77809,77810 1cpy 421 1.66e+01 1ivyA c.69.1.5 34651 1usyA 275 1.66e+01 2fsxA 148 1.69e+01 1h65A 270 1.79e+01 c.37.1.8 65640 1mucA 373 1.81e+01 1mucA c.1.11.2,d.54.1.1 29236,38880 1jkmB 361 1.88e+01 1jkmA c.69.1.2 34634 4enl 436 1.90e+01 4enl c.1.11.1,d.54.1.1 29202,38846 2a6hA 315 1.97e+01 1lf6A 684 1.99e+01 a.102.1.5,b.30.5.5 77918,77919 1vom 762 2.00e+01 1lvk b.34.3.1,c.37.1.9 24577,32174 1oneA 436 2.01e+01 4enl c.1.11.1,d.54.1.1 29200,38844 1ysc 421 2.05e+01 1ivyA c.69.1.5 34652 1zq4A 693 2.07e+01 1skyB 502 2.08e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18313,26478,32358 1cof 143 2.10e+01 1cof d.109.1.2 40860 1cfyA 143 2.17e+01 1cof d.109.1.2 40858 1fmaE 150 2.21e+01 1fmaE d.41.5.1 38630 1zoiA 276 2.24e+01 1ujqA 305 2.36e+01 c.1.12.7 99463 1qh0A 295 2.42e+01 b.43.4.2,c.25.1.1 68891,68892 1vimA 200 2.48e+01 c.80.1.3 100758 1y13A 181 2.64e+01 1vjhA 122 2.70e+01 d.129.3.1 100811 1igwA 434 2.71e+01 c.1.12.7 62370 1z3xA 238 2.71e+01 1qx4A 274 2.72e+01 b.43.4.2,c.25.1.1 104624,104625 1erjA 393 2.80e+01 1erjA b.69.4.1 27660 1sjdA 368 2.80e+01 c.1.11.2,d.54.1.1 105632,105633 1dciA 275 2.84e+01 1dciA c.14.1.3 30918 1cb0A 283 2.85e+01 1cb0A c.56.2.1 33790 1pyfA 312 2.92e+01 c.1.7.1 95334 2al1A 436 2.93e+01 1a88A 275 2.95e+01 1brt c.69.1.12 34707 1va6A 518 2.97e+01 1que 303 2.98e+01 1fnc b.43.4.2,c.25.1.1 25647,31537 1ndbA 596 2.99e+01 c.43.1.3,c.43.1.3 80411,80412 1ako 268 3.04e+01 1ako d.151.1.1 41779 2oneA 436 3.08e+01 4enl c.1.11.1,d.54.1.1 29203,38847 2b5eA 504 3.10e+01 1lnzA 342 3.13e+01 b.117.1.1,c.37.1.8 78112,78113 1b26A 416 3.14e+01 1hwyA c.2.1.7,c.58.1.1 30232,33880 1ve6A 582 3.16e+01 1ogiA 303 3.18e+01 b.43.4.2,c.25.1.1 92914,92915 1e0cA 271 3.35e+01 1e0cA c.46.1.2,c.46.1.2 32717,32718 2fl7A 232 3.40e+01 1tzjA 338 3.40e+01 1wz9A 375 3.43e+01 2bsaA 303 3.52e+01 2al2A 436 3.56e+01 1fm0E 150 3.66e+01 1fmaE d.41.5.1 38629 1pg4A 652 3.67e+01 e.23.1.1 88067 1gmxA 108 3.69e+01 c.46.1.3 65355 2f46A 156 3.76e+01 1i7pA 274 3.92e+01 b.43.4.2,c.25.1.1 66048,66049 1w34A 304 4.01e+01 1b3bA 415 4.02e+01 1hwyA c.2.1.7,c.58.1.1 30244,33892 1bh3 289 4.12e+01 3prn f.4.3.1 43766 1iw7C 1119 4.12e+01 e.29.1.1 71474 1gn0A 108 4.12e+01 c.46.1.3 65358 1r6lA 239 4.28e+01 d.14.1.4,d.101.1.1 97153,97154 1mtzA 293 4.28e+01 c.69.1.7 79467 1prn 289 4.31e+01 3prn f.4.3.1 43762 1fnc 314 4.42e+01 1fnc b.43.4.2,c.25.1.1 25627,31517 1l2tA 235 4.53e+01 c.37.1.12 73514 1aqb 183 4.59e+01 1aqb b.60.1.1 27084 1x3sA 195 4.64e+01 1b04A 318 4.68e+01 1b04A d.142.2.2 41579 1vj1A 363 4.72e+01 b.35.1.2,c.2.1.1 100794,100795 1hr6B 443 4.76e+01 1be3A d.185.1.1,d.185.1.1 61166,61167 1vk3A 615 4.80e+01 d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 100846,100847,100848,100849 2bmaA 470 4.82e+01 1pieA 419 4.87e+01 d.14.1.5,d.58.26.7 94706,94707 1f8mA 429 4.87e+01 1dquA c.1.12.7 29315 2cx9A 387 4.89e+01 1aokB 122 4.93e+01 1poa a.133.1.2 19561 1jltB 122 4.98e+01 a.133.1.2 66868 1rzuA 485 5.00e+01 c.87.1.8 105140 1vmeA 410 5.05e+01 c.23.5.1,d.157.1.3 108893,108894 2fbmA 291 5.06e+01 1te6A 439 5.29e+01 c.1.11.1,d.54.1.1 106797,106798 1e69B 322 5.34e+01 1e69B c.37.1.12 32377 1udsA 255 5.35e+01 d.14.1.4,d.101.1.1 99219,99220 1jjfA 268 5.37e+01 c.69.1.2 66765 2f1wA 158 5.37e+01 1gzqA 300 5.44e+01 b.1.1.2,d.19.1.1 70818,70819 2cqsA 842 5.55e+01 1z2nX 324 5.62e+01 1tvkA 440 5.63e+01 c.32.1.1,d.79.2.1 107362,107363 1xb3A 128 5.70e+01 1mz5A 638 5.77e+01 b.29.1.15,b.68.1.1 79679,79680 1u46A 291 5.78e+01 d.144.1.7 107656 2fymA 431 5.85e+01 3prn 289 5.97e+01 3prn f.4.3.1 43761 2b2nA 344 6.01e+01 2bjvA 265 6.02e+01 1bksB 397 6.06e+01 2tysB c.79.1.1 35285 1hbq 183 6.09e+01 1aqb b.60.1.1 27078 1n1tA 641 6.12e+01 b.29.1.15,b.68.1.1 79821,79822 1bwsA 321 6.12e+01 1bsvA c.2.1.2 29812 1d1rA 116 6.12e+01 1d1rA d.64.1.1 39548 1xqwA 293 6.19e+01 1b2rA 304 6.25e+01 1fnc b.43.4.2,c.25.1.1 25648,31538 1f61A 429 6.26e+01 1dquA c.1.12.7 29319 1m2xA 223 6.29e+01 d.157.1.1 84764 1rzhH 260 6.38e+01 b.41.1.1,f.23.10.1 98162,98163 1oeyJ 107 6.40e+01 d.15.2.2 92804 1k32A 1045 6.44e+01 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 68068,68069,68070,68071 1t6cA 315 6.50e+01 c.55.1.8,c.55.1.8 106558,106559 1ukfA 188 6.51e+01 d.3.1.10 99488 1ndh 272 6.58e+01 1ndh b.43.4.2,c.25.1.1 25662,31552 1ywmA 200 6.61e+01 2bwbA 46 6.62e+01 2g0qA 173 6.66e+01 1zbfA 142 6.70e+01 1q0rA 298 6.72e+01 c.69.1.28 95508 1go2A 304 6.75e+01 b.43.4.2,c.25.1.1 76243,76244 1qfjA 232 6.77e+01 1qfjA b.43.4.2,c.25.1.1 25655,31545 1tubA 440 6.87e+01 1tubA c.32.1.1,d.79.2.1 31751,39803 1lbeA 258 6.87e+01 1lbeA e.4.1.1 42773 1wrvA 308 6.90e+01 1liuA 528 6.92e+01 b.58.1.1,c.1.12.1,c.49.1.1 77970,77971,77972 2a6hC 1119 6.93e+01 2tysB 397 6.96e+01 2tysB c.79.1.1 35272 1tllA 688 7.00e+01 b.43.4.1,c.23.5.2,c.25.1.4 107128,107129,107130 1uekA 275 7.02e+01 d.14.1.5,d.58.26.5 88483,88484 1m4zA 238 7.05e+01 b.34.12.1 78630 1qhhA 167 7.05e+01 1pjr c.37.1.19 32393 1skyE 473 7.14e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 18314,26479,32359 1huxA 270 7.19e+01 1huxA c.55.1.5 61278 1zr5A 214 7.20e+01 1fnd 314 7.31e+01 1fnc b.43.4.2,c.25.1.1 25626,31516 1cqxA 403 7.33e+01 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 1e6uA 321 7.34e+01 1bsvA c.2.1.2 29805 1p3dA 475 7.36e+01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1hbp 183 7.36e+01 1aqb b.60.1.1 27079 1nx8A 273 7.45e+01 b.82.2.8 86374 1ncx 162 7.46e+01 1ncx a.39.1.5 17222 1f75A 249 7.49e+01 1f75A c.101.1.1 59662 1top 162 7.51e+01 1ncx a.39.1.5 17223 1eljA 381 7.58e+01 4mbp c.94.1.1 35791 1c93A 265 7.60e+01 2ebn c.1.8.5 28998 1uuqA 440 7.65e+01 c.1.8.3 100015 2ex4A 241 7.71e+01 1z15A 344 7.73e+01 1ws9A 387 7.74e+01 1m40A 263 7.75e+01 e.3.1.1 74437 1ehkB 168 7.77e+01 2cuaA b.6.1.2,f.17.2.1 23041,43625 1csbB 205 7.90e+01 1theB 1kyqA 274 7.98e+01 c.2.1.11,e.37.1.1 73281,73282 1a50B 396 8.02e+01 2tysB c.79.1.1 35280 1k8kD 300 8.04e+01 d.198.2.1,d.198.2.1 68309,68310 1jbkA 195 8.05e+01 c.37.1.20 71631 1nnvA 110 8.07e+01 d.17.7.1 92012 1n6eA 1071 8.21e+01 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 80149,80150,80151,80152 1lx7A 253 8.27e+01 c.56.2.1 74329 1noyA 388 8.35e+01 1clqA c.55.3.5 33713 1wouA 123 8.46e+01 c.47.1.16 109471 1ryiA 382 8.48e+01 1a8s 273 8.49e+01 1brt c.69.1.12 34710 1aorA 605 8.50e+01 1b25A a.110.1.1,d.152.1.1 19042,41794 1btl 263 8.51e+01 1btl e.3.1.1 42691 1qhaA 917 8.52e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33467,33468,33469,33470 1tyjA 170 8.57e+01 1gnxA 479 8.59e+01 c.1.8.4 76241 1pbp 321 8.65e+01 1ixh c.94.1.1 35768 1ms9A 648 8.74e+01 b.29.1.15,b.68.1.1 85088,85089 1qgoA 264 8.74e+01 1qgoA c.92.1.2 35596 2ck3A 510 8.80e+01 1rvkA 382 8.83e+01 c.1.11.2,d.54.1.1 97928,97929 1k3fA 253 8.84e+01 c.56.2.1 68105 1o9gA 250 8.87e+01 c.66.1.29 86692 2fgeA 995 8.91e+01 1yovA 537 8.92e+01 1n8kA 374 8.93e+01 b.35.1.2,c.2.1.1 80298,80299 1i1dA 161 8.93e+01 1i21A d.108.1.1 61526 2fw2A 260 8.94e+01 1rxyA 253 8.97e+01 c.56.2.1 98065