# List of top-scoring protein chains for t2k-100-30-alpha 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 1ihoA 283 3.33e-40 1ihoA c.26.1.4 62390 1cozA 129 4.03e-03 1cozA c.26.1.2 31598 1fwkA 296 2.24e-02 1fwkA d.14.1.5 37576 d.58.26.1 39398 1h72C 296 2.49e-02 d.14.1.5 60712 d.58.26.1 60713 1jhdA 396 1.34e-01 b.58.1.2 66712 c.26.1.5 66713 1b6tA 159 1.66e-01 1b6tA c.26.1.3 31600 1dkrA 317 1.91e-01 1dkuA c.61.1.2 34114 c.61.1.2 34115 1vjs 483 2.08e-01 1bli b.71.1.1 27714 c.1.8.1 28701 1bli 483 2.36e-01 1bli b.71.1.1 27715 c.1.8.1 28702 2cbf 234 2.68e-01 1cbf c.90.1.1 35588 6acn 754 2.74e-01 1amj c.8.2.1 30721 c.83.1.1 35397 1qjcA 158 2.87e-01 1b6tA c.26.1.3 63328 1c96A 753 3.11e-01 1amj c.8.2.1 30727 c.83.1.1 35403 1cbf 285 3.40e-01 1cbf c.90.1.1 35587 1f9aA 168 3.66e-01 1f9aA c.26.1.3 31602 1kshB 152 3.71e-01 1b0jA 754 4.43e-01 1amj c.8.2.1 30719 c.83.1.1 35395 1amj 754 4.56e-01 1amj c.8.2.1 30725 c.83.1.1 35401 1ff9A 450 5.10e-01 1ff9A c.2.1.3 30039 d.81.1.2 39954 1e43A 483 5.23e-01 1bli b.71.1.1 59217 c.1.8.1 59218 1mal 421 5.83e-01 2mprA f.4.3.2 43784 1ej2A 181 6.25e-01 1f9aA c.26.1.3 59414 1dar 691 7.26e-01 1dar b.43.3.1 25707 c.37.1.8 32142 d.14.1.1 37547 d.58.11.1 39300 8acn 754 7.36e-01 1amj c.8.2.1 30724 c.83.1.1 35400 1g8fA 511 8.58e-01 1g8fA b.58.1.2 60348 c.26.1.5 60349 c.37.1.15 60350 1af6A 421 8.92e-01 2mprA f.4.3.2 43772 4ts1A 319 9.40e-01 2ts1 c.26.1.1 31565 1dkuA 317 9.90e-01 1dkuA c.61.1.2 34118 c.61.1.2 34119 1rlr 761 1.69e+00 1rlr a.98.1.1 18753 c.7.1.2 30679 1fpzA 212 1.76e+00 1fpzA c.45.1.1 59976 1e4iA 447 2.04e+00 1e70M c.1.8.4 59225 1bi0 226 2.18e+00 1bi0 a.4.5.24 16202 a.76.1.1 18408 b.34.1.2 24453 1jflA 228 2.27e+00 2ezl 99 2.33e+00 2ezk a.4.1.2 16026 1dpe 507 2.45e+00 1dpe c.94.1.1 35799 1esmA 316 2.48e+00 1esmA c.37.1.6 31953 1mjhA 162 2.60e+00 1mjhA c.29.1.2 31639 2dtr 226 2.64e+00 1bi0 a.4.5.24 16193 a.76.1.1 18399 b.34.1.2 24450 1dppA 507 2.65e+00 1dpe c.94.1.1 35800 1eceA 358 2.99e+00 1eceA c.1.8.3 28813 2kauA 100 3.31e+00 1ubpA d.8.1.1 37335 1fwcA 100 3.32e+00 1ubpA d.8.1.1 37331 1b5fA 239 3.46e+00 1smrA b.50.1.2 26836 1mjhB 162 3.57e+00 1mjhA c.29.1.2 31640 2ezk 99 3.75e+00 2ezk a.4.1.2 16027 1c0dA 358 3.90e+00 1eceA c.1.8.3 28815 1c3oB 382 4.33e+00 1c3oB c.8.3.1 30744 c.23.16.1 31421 1hv9A 456 4.73e+00 1fwyA b.81.1.4 28060 c.68.1.5 34518 1geqA 248 4.97e+00 2tysA c.1.2.4 28589 1iqvA 218 5.30e+00 1rss a.75.1.1 62661 1i58A 189 5.41e+00 1b3qA d.122.1.3 61773 1tr1A 447 5.44e+00 1e70M c.1.8.4 28957 1han 297 5.70e+00 1han d.32.1.3 38506 d.32.1.3 38507 1f74A 293 5.76e+00 1nal3 c.1.10.1 29079 1ehyA 294 5.82e+00 1ehyA c.69.1.11 34693 1jbwA 428 5.89e+00 c.59.1.2 62860 c.72.2.2 62861 1krrA 203 6.09e+00 1cs0B 382 6.10e+00 1c3oB c.8.3.1 30740 c.23.16.1 31417 1qvbA 481 6.54e+00 1qvbA c.1.8.4 28983 1httA 423 6.61e+00 1adjA c.51.1.1 33178 d.104.1.1 40727 1ee8A 266 6.63e+00 1ee8A e.14.1.1 43261 1a9xB 379 6.94e+00 1c3oB c.8.3.1 30732 c.23.16.1 31409 1i60A 278 7.03e+00 1bh5A 183 7.57e+00 1qipA d.32.1.1 38476 1yaiA 151 7.67e+00 1yaiA b.1.8.1 22289 1ktbA 405 7.71e+00 1ceo 343 7.85e+00 1ceo c.1.8.3 28808 1lci 550 8.01e+00 1lci e.23.1.1 43349 1k77A 260 8.11e+00 1cec 343 8.16e+00 1ceo c.1.8.3 28809 1cvrA 435 8.22e+00 1cvrA b.1.1.5 21949 c.17.1.2 31006 1io2A 213 8.24e+00 1ekeA c.55.3.1 62612 2dhqA 146 8.29e+00 2dhqA c.23.13.1 31382 1reqA 727 8.59e+00 1reqA c.1.19.1 29620 c.23.6.1 31247 1gs5A 258 8.69e+00 12asA 330 8.93e+00 12asA d.104.1.1 40783 1adjA 421 8.96e+00 1adjA c.51.1.1 33188 d.104.1.1 40737 1uok 558 9.04e+00 1uok b.71.1.1 27801 c.1.8.1 28788 1eziA 228 9.34e+00 1eyrA c.68.1.3 34512 1bg1A 722 9.38e+00 1bg1A a.47.1.1 17767 b.2.5.1 22461 d.93.1.1 40527 1qipA 183 9.68e+00 1qipA d.32.1.1 38470 1kq3A 376 9.73e+00 e.22.1.2 68790 2pfkA 320 9.81e+00 3pfk c.89.1.1 35577 1e55A 512 9.84e+00 1e70M c.1.8.4 28934 1g61A 228 9.88e+00 1g61A d.126.1.1 41126 1hg3A 225 9.96e+00 1hg3A c.1.1.1 61025 1fxjA 331 1.01e+01 1fwyA b.81.1.4 28062 c.68.1.5 34520 1c4oA 664 1.03e+01 1d2mA c.37.1.13 32415 c.37.1.13 32416 1e6uA 321 1.04e+01 1bsvA c.2.1.2 29805 1gtrA 553 1.07e+01 1gtrA b.53.1.2 26939 c.26.1.1 31578 1pinA 163 1.11e+01 1pinA b.72.1.1 27802 d.26.1.1 38431 1sur 215 1.12e+01 1sur c.26.2.2 31620 1ffkP 84 1.12e+01 1ffkP d.12.1.1 37493 3rubS 123 1.14e+01 1rboC d.73.1.1 39616 1f0yA 302 1.14e+01 2hdhA a.100.1.3 18793 c.2.1.6 30197 1xjo 284 1.17e+01 1xjo c.56.5.4 33843 1qtqA 553 1.17e+01 1gtrA b.53.1.2 26940 c.26.1.1 31579 1fukA 165 1.19e+01 1fukA c.37.1.13 32409 1fwyA 331 1.19e+01 1fwyA b.81.1.4 28064 c.68.1.5 34522 1qguB 519 1.22e+01 1qguB c.92.2.3 35626 1bia 321 1.23e+01 1bia a.4.5.1 16083 b.34.1.1 24447 d.104.1.2 40787 1fgs 428 1.23e+01 1fgs c.59.1.2 33959 c.72.2.2 34962 1kafA 108 1.23e+01 d.199.1.1 68372 1fe0A 68 1.25e+01 1cc8A d.58.17.1 39345 4ubpA 101 1.26e+01 1ubpA d.8.1.1 37352 1ubpA 101 1.26e+01 1ubpA d.8.1.1 37353 1f5sA 211 1.27e+01 1f5sA c.108.1.4 59656 1jj2R 84 1.28e+01 1ffkP d.12.1.1 63103 1qh8B 519 1.28e+01 1qguB c.92.2.3 35634 1emsA 440 1.30e+01 1emsA d.13.1.1 37520 d.160.1.1 42086 1gfsA 321 1.32e+01 c.2.1.2 29811 1bwsA 321 1.32e+01 1bsvA c.2.1.2 29812 1h7sA 365 1.33e+01 d.14.1.3 65705 d.122.1.2 65706 1cqmA 101 1.33e+01 1ris d.58.14.1 39321 2ts1 419 1.35e+01 2ts1 c.26.1.1 31564 2hdhA 293 1.39e+01 2hdhA a.100.1.3 18795 c.2.1.6 30199 1kwhA 492 1.43e+01 c.94.1.1 68876 1j97A 211 1.44e+01 1f5sA c.108.1.4 62753 1tnfA 158 1.45e+01 2tnfA b.22.1.1 23871 1dyqA 234 1.46e+01 3seb b.40.2.2 59140 d.15.6.1 59141 1bib 321 1.48e+01 1bia a.4.5.1 16084 b.34.1.1 24448 d.104.1.2 40788 1kcvL 214 1.49e+01 1fds 327 1.50e+01 1fds c.2.1.2 29838 1hdhA 536 1.52e+01 c.76.1.2 65805 1a26 361 1.56e+01 1a26 a.41.1.1 17412 d.166.1.2 42274 1h4vB 421 1.56e+01 1adjA c.51.1.1 60624 d.104.1.1 60625 1pfkA 320 1.57e+01 3pfk c.89.1.1 35575 1fo3A 460 1.59e+01 1dl2A a.102.2.1 18845 2minB 522 1.64e+01 1qguB c.92.2.3 35610 2lefA 86 1.65e+01 2lefA a.21.1.1 16433 3minB 522 1.65e+01 1qguB c.92.2.3 35606 1ysc 421 1.65e+01 1ivyA c.69.1.5 34652 1az9 457 1.69e+01 1az9 c.55.2.1 33547 d.127.1.1 41164 1l7mA 211 1.70e+01 1fdt 327 1.70e+01 1fds c.2.1.2 29841 1bsvA 321 1.70e+01 1bsvA c.2.1.2 29809 1qcwA 410 1.71e+01 1gox c.1.4.1 28622 1iirA 415 1.71e+01 1iirA c.87.1.5 62453 1ihnA 113 1.73e+01 1ihnA c.103.1.1 62388 1fwsA 267 1.74e+01 1d9eA c.1.10.4 60063 1zfjA 491 1.74e+01 1ak5 c.1.5.1 28638 d.37.1.1 38540 d.37.1.1 38541 1fhdA 312 1.74e+01 1taxA c.1.8.3 28915 1fh9A 312 1.75e+01 1taxA c.1.8.3 28913 1fwrA 213 1.75e+01 1fwrA c.1.10.1 29164 1gajA 257 1.75e+01 1gajA c.37.1.12 60416 1f2tB 148 1.81e+01 1f2tB 3pbgA 468 1.81e+01 1e70M c.1.8.4 28951 1jhgA 101 1.81e+01 1jhgA a.107.1.1 19009 1b0uA 262 1.83e+01 1b0uA c.37.1.12 32370 1oya 400 1.83e+01 1oyc c.1.4.1 28604 1fsd 28 1.85e+01 k.14.1.1 46439 1d3hA 367 1.89e+01 1d3gA c.1.4.1 28601 1fq0A 213 1.92e+01 1fwrA c.1.10.1 29161 1kmmA 424 1.93e+01 1adjA c.51.1.1 33174 d.104.1.1 40723 1i82A 189 1.94e+01 1i82A b.1.9.2 61937 1knvA 293 1.98e+01 c.52.1.7 68707 1i8aA 189 2.03e+01 1i82A b.1.9.2 61951 1ccwA 137 2.04e+01 1be1 c.23.6.1 31238 1a27 289 2.08e+01 1fds c.2.1.2 29839 1auvA 311 2.08e+01 1auvA c.30.1.5 31723 d.142.1.3 41558 1oyc 400 2.09e+01 1oyc c.1.4.1 28603 1tig 94 2.09e+01 1tig d.68.1.1 39566 1fjgL 135 2.10e+01 1fjfL b.40.4.5 25346 1pbgA 468 2.11e+01 1e70M c.1.8.4 28946 1eyrA 228 2.13e+01 1eyrA c.68.1.3 34514 1bdb 277 2.14e+01 1bdb c.2.1.2 29874 1smlA 269 2.17e+01 1smlA d.157.1.1 42053 1augA 215 2.24e+01 1a2zA c.56.4.1 33798 1g24A 211 2.24e+01 1g24A d.166.1.1 42270 1f1zA 273 2.26e+01 1f1zA a.4.5.27 16081 c.52.1.16 33334 1pgtA 210 2.28e+01 1pgtA a.45.1.1 17515 c.47.1.5 32809 1esfA 233 2.29e+01 3seb b.40.2.2 25146 d.15.6.1 37735 1eu8A 409 2.29e+01 1eu8A c.94.1.1 59502 1kwaB 88 2.32e+01 1kwaA b.36.1.1 24773 1qoxN 449 2.33e+01 1qoxN c.1.8.4 28978 1brsD 89 2.35e+01 1ay7B c.9.1.1 30825 1fbnA 230 2.40e+01 1fbnA c.66.1.3 34181 1iq8A 582 2.41e+01 1ayl 541 2.41e+01 1ayl c.91.1.1 64718 c.109.1.1 64719 1im8A 244 2.42e+01 c.66.1.14 66212 2dkb 433 2.42e+01 2dkb c.67.1.4 34438 2fbjL 213 2.42e+01 8fabA b.1.1.1 19850 b.1.1.2 20954 1kyoA 430 2.43e+01 4tsvA 150 2.44e+01 2tnfA b.22.1.1 23860 2wrpR 107 2.45e+01 1jhgA a.107.1.1 19010 2madH 373 2.46e+01 2bbkH b.69.2.1 27639 1d3gA 367 2.47e+01 1d3gA c.1.4.1 28600 1rpxA 230 2.48e+01 1rpxA c.1.2.2 28536 1thjA 214 2.57e+01 1qreA b.81.1.5 28072 1qo7A 394 2.58e+01 1qo7A c.69.1.11 34697 1g0oA 283 2.59e+01 1ybvA c.2.1.2 60181 3aig 202 2.60e+01 1atlA d.92.1.9 40321 1jj2U 70 2.60e+01 1ffkS a.2.2.1 63106 1cbg 490 2.61e+01 1e70M c.1.8.4 28933 1ka1A 357 2.63e+01 e.7.1.1 68369 1kepA 348 2.69e+01 c.2.1.2 68536 1g6hA 257 2.71e+01 1gajA c.37.1.12 60318 1g2qA 187 2.71e+01 c.61.1.1 65117 1nsj 205 2.76e+01 1nsj c.1.2.4 28560 1f45B 197 2.77e+01 1f45B a.26.1.1 59642 1hjrA 158 2.79e+01 1hjrA c.55.3.6 33727 2lbp 346 2.80e+01 2liv c.93.1.1 35709 1uxy 340 2.81e+01 2mbr d.145.1.2 41748 d.146.1.1 41761 1gq6A 313 2.81e+01 1ll1 590 2.82e+01 1lla a.85.1.1 18488 a.86.1.1 18499 b.1.1.5 21864 1icpA 376 2.83e+01 1oyc c.1.4.1 62270 1e0wA 313 2.83e+01 1taxA c.1.8.3 59150 1f20A 435 2.84e+01 b.43.4.1 64932 c.25.1.4 64933 1bf8 205 2.85e+01 1qpxA b.1.11.1 22332 b.7.2.1 23214 1cs1A 386 2.86e+01 1ibjA c.67.1.3 34399 1trrA 107 2.86e+01 1jhgA a.107.1.1 19017 1il8A 72 2.89e+01 1tvxA d.9.1.1 37365 1jjiA 311 2.90e+01 c.69.1.2 66766 1hv8A 367 2.91e+01 1hv8A c.37.1.13 32405 c.37.1.13 32406 1cs1C 386 2.95e+01 1ibjA c.67.1.3 34401 1hxmD 242 3.00e+01 b.1.1.1 61373 b.1.1.2 61374 1om2A 95 3.06e+01 1om2A a.23.4.1 16520 1pamA 686 3.06e+01 1cxlA b.1.1.5 21846 b.3.1.1 22515 b.71.1.1 27753 c.1.8.1 28740 1enh 54 3.07e+01 2hddA a.4.1.1 15973 1g63A 181 3.10e+01 1g5qA c.34.1.1 60299 1j4aA 333 3.10e+01 1lla 628 3.12e+01 1lla a.85.1.1 18485 a.86.1.1 18496 b.1.1.5 21861 1fcbA 511 3.13e+01 1gox c.1.4.1 28620 d.120.1.1 41087 1oen 540 3.14e+01 1ayl c.91.1.1 64750 c.109.1.1 64751 2mbr 340 3.14e+01 2mbr d.145.1.2 41749 d.146.1.1 41762 1vaoA 560 3.15e+01 1qltA d.58.32.1 39461 d.145.1.1 41724 1fd9A 213 3.15e+01 1fd9A d.26.1.1 59771 1efyA 350 3.15e+01 1a26 a.41.1.1 17413 d.166.1.2 42275 1ki1B 352 3.15e+01 12e8L 214 3.16e+01 8fabA b.1.1.1 20268 b.1.1.2 21268 1l1oC 181 3.17e+01 1b24A 188 3.19e+01 1b24A d.95.2.1 40573 d.95.2.1 40574 2hvm 273 3.22e+01 1cnv c.1.8.5 28985 1qltA 560 3.23e+01 1qltA d.58.32.1 39457 d.145.1.1 41720 2ae2A 260 3.24e+01 1bdb c.2.1.2 29945 1hu4A 288 3.25e+01 1hu4A c.2.1.2 61268 1eqjA 511 3.26e+01 1ejjA c.105.1.1 59495 c.76.1.3 59496 1eudA 311 3.26e+01 2scuA c.2.1.8 30312 c.23.4.1 31140 1g97A 459 3.27e+01 1fwyA b.81.1.4 60394 c.68.1.5 60395 1heuA 374 3.27e+01 2ohxA b.35.1.2 60979 c.2.1.1 60980 1ho1A 242 3.28e+01 1ho1A c.1.24.1 61097 2liv 344 3.28e+01 2liv c.93.1.1 35708 1ris 101 3.31e+01 1ris d.58.14.1 39314 1e8gA 560 3.32e+01 1qltA d.58.32.1 39455 d.145.1.1 41718 4ubpC 570 3.33e+01 1ubpC b.92.1.1 28431 c.1.9.2 29053 1h70A 255 3.33e+01 1h70A d.126.1.3 60711 1pkn 530 3.36e+01 1a49A b.58.1.1 27042 c.1.12.1 29271 c.49.1.1 33125 1cf2O 337 3.38e+01 1b7gO c.2.1.3 29994 d.81.1.1 39909 1f5nA 592 3.39e+01 1dg3A a.114.1.1 19077 c.37.1.8 32152 1ek9A 428 3.40e+01 1ek9A f.5.1.1 43809 1r2fA 319 3.40e+01 1r2fA a.25.1.2 16800 1b43A 340 3.41e+01 1a76 a.60.7.1 18092 c.53.1.2 33362 1eiyB 785 3.43e+01 1pysB a.6.1.1 16305 a.6.1.1 16306 b.40.4.4 25314 d.58.13.1 39313 d.104.1.1 40782 d.138.1.1 41458 1ffkM 148 3.43e+01 1ffkM a.94.1.1 18740 1au1A 166 3.44e+01 1ifa a.26.1.3 16889 1jmtA 104 3.44e+01 d.58.7.3 63180 1hetA 374 3.48e+01 2ohxA b.35.1.2 60975 c.2.1.1 60976 1dl5A 317 3.49e+01 1dl5A c.66.1.7 64720 d.197.1.1 64721 1bjmA 216 3.56e+01 8fabA b.1.1.1 20524 b.1.1.2 21460 1louA 101 3.65e+01 1ris d.58.14.1 39323 1ejdA 419 3.68e+01 1uae d.68.2.2 39576 1kk1A 410 3.68e+01 1ybvA 283 3.70e+01 1ybvA c.2.1.2 29948 1cgt 684 3.76e+01 1cxlA b.1.1.5 21815 b.3.1.1 22484 b.71.1.1 27722 c.1.8.1 28709 2matA 264 3.78e+01 1c24A d.127.1.1 41146 1ezvA 430 3.78e+01 1be3A d.185.1.1 59541 d.185.1.1 59542 1eg2A 319 3.80e+01 1eg2A c.66.1.11 34249 1iu8A 206 3.86e+01 2hddA 61 3.86e+01 2hddA a.4.1.1 15971 1a3lL 217 3.89e+01 8fabA b.1.1.1 20240 b.1.1.2 21252 1np1A 184 3.89e+01 1np1A b.60.1.1 27155 1gw9A 388 3.90e+01 1cv8 174 3.90e+01 1cv8 d.3.1.1 37089 1din 236 3.94e+01 1din c.69.1.9 34682 1d7uA 433 3.95e+01 2dkb c.67.1.4 34439 2rslA 140 3.97e+01 2rslA c.53.1.1 33345 1kwaA 88 3.98e+01 1kwaA b.36.1.1 24772 1eaxA 241 3.98e+01 b.47.1.2 64889 32c2A 217 3.99e+01 32c2A b.1.1.1 20438 b.1.1.2 21404