# 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 1ego 85 1.97e-07 1kte c.47.1.1 32767 2trxA 108 2.71e-07 1thx c.47.1.1 32719 1kebA 108 2.88e-07 c.47.1.1 77341 1j08A 226 3.39e-07 c.47.1.2 83855 c.47.1.2 83856 1nw2A 105 8.33e-07 1thx 115 1.05e-06 1thx c.47.1.1 32732 1egr 85 1.17e-06 1kte c.47.1.1 32765 1a8l 226 2.23e-06 1a8l c.47.1.2 32777 c.47.1.2 32778 1h75A 81 3.44e-06 1h75A c.47.1.1 60716 1hyuA 521 1.00e-05 1hyuA c.3.1.5 30547 c.3.1.5 30548 c.47.1.2 32779 c.47.1.2 32780 1kte 105 1.12e-05 1kte c.47.1.1 32771 1fo5A 85 1.46e-05 1fo5A c.47.1.1 59922 1jhb 106 3.24e-05 1kte c.47.1.1 32772 1fb6A 105 4.74e-05 1thx c.47.1.1 32739 1qk8A 146 1.09e-04 1ewxA c.47.1.10 33061 1o6jA 150 1.16e-04 c.47.1.10 81089 1ewxA 146 2.16e-04 1ewxA c.47.1.10 33062 1grx 85 3.44e-04 1kte c.47.1.1 32766 1g7oA 215 4.21e-04 1g7oA a.45.1.1 60332 c.47.1.5 60333 3grx 82 5.02e-04 1aba c.47.1.1 32769 1qfnA 85 5.47e-04 1qfnA c.47.1.1 32768 1iloA 77 9.13e-04 c.47.1.1 66205 1r26A 125 1.00e-03 1st9A 143 2.10e-03 1eejA 216 6.32e-03 1eejA c.47.1.9 33057 d.17.3.1 38071 1lu4A 136 8.23e-03 1eemA 241 1.12e-02 1eemA a.45.1.1 17717 c.47.1.5 33011 1erv 105 1.28e-02 1erv c.47.1.1 32743 1aiu 105 1.41e-02 1erv c.47.1.1 32746 1qgvA 142 1.70e-02 1qgvA c.47.1.8 33056 1i5gA 144 1.79e-02 1ewxA c.47.1.10 61784 1aba 87 2.33e-02 1aba c.47.1.1 32760 1bjx 110 2.59e-02 1bjx c.47.1.2 32774 2bjxA 110 2.59e-02 1bjx c.47.1.2 32776 1f9mA 112 2.61e-02 1erv c.47.1.1 32736 1tof 112 2.72e-02 1erv c.47.1.1 32733 1mek 120 2.83e-02 1erv c.47.1.2 32775 1kngA 156 2.87e-02 c.47.1.10 72777 1o8xA 146 3.36e-02 c.47.1.10 86681 1gnuA 117 6.08e-02 d.15.1.3 65403 1kotA 119 6.47e-02 d.15.1.3 68732 1f6bA 198 7.30e-02 c.37.1.8 64986 1faaA 124 7.52e-02 1erv c.47.1.1 32738 1pmt 203 1.04e-01 1a0fA a.45.1.1 17740 c.47.1.5 33034 1k0mA 241 1.07e-01 a.45.1.1 67949 c.47.1.5 67950 1gh2A 107 1.42e-01 1erv c.47.1.1 60515 1jfuA 186 1.53e-01 c.47.1.10 62940 1eo6A 117 2.02e-01 1eo6A d.15.1.3 37609 1j0fA 100 2.26e-01 1k0nA 241 2.31e-01 a.45.1.1 67953 c.47.1.5 67954 1fe0A 68 2.45e-01 1cc8A d.58.17.1 39345 1at1A 310 3.02e-01 3csuA c.78.1.1 35168 c.78.1.1 35169 1i4nA 251 3.86e-01 c.1.2.4 71114 1h5yA 253 3.94e-01 c.1.2.1 65638 1fd8A 73 4.42e-01 1cc8A d.58.17.1 59770 1kmqA 184 4.43e-01 c.37.1.8 84412 1ekxA 311 5.30e-01 3csuA c.78.1.1 35088 c.78.1.1 35089 3csuA 310 5.48e-01 3csuA c.78.1.1 35094 c.78.1.1 35095 1qvbA 481 5.67e-01 1qvbA c.1.8.4 28983 1alq 266 6.45e-01 1btl e.3.1.1 42707 1s3iA 310 6.90e-01 1oyjA 231 7.08e-01 a.45.1.1 87597 c.47.1.5 87598 1cc8A 73 7.21e-01 1cc8A d.58.17.1 39343 1nsj 205 7.86e-01 1nsj c.1.2.4 28560 1g7eA 122 8.40e-01 1g7eA c.47.1.7 33055 1tx4B 178 8.59e-01 1ctqA c.37.1.8 32045 1pg5A 299 8.61e-01 1im8A 244 9.78e-01 c.66.1.14 66212 1taq 832 1.01e+00 1taq a.60.7.1 18082 c.120.1.2 33352 c.55.3.5 33698 e.8.1.1 42991 1grj 158 1.10e+00 1grj a.2.1.1 15691 d.26.1.2 38433 1j4aA 333 1.44e+00 c.2.1.4 71502 c.23.12.1 71503 1gwcA 230 1.47e+00 a.45.1.1 70660 c.47.1.5 70661 2gsq 202 1.47e+00 1pd21 a.45.1.1 17715 c.47.1.5 33009 1n2aA 201 1.53e+00 1a0fA 201 1.61e+00 1a0fA a.45.1.1 17737 c.47.1.5 33031 1nx8A 273 1.68e+00 b.82.2.8 86374 1pqnA 127 1.75e+00 1v5xA 203 1.92e+00 1uc7A 125 1.92e+00 1jqeA 292 2.04e+00 c.66.1.19 71789 1e7lA 157 2.11e+00 1en7A a.140.4.1 64728 d.4.1.5 64729 1m0uA 249 2.21e+00 a.45.1.1 78359 c.47.1.5 78360 1oxxK 353 2.21e+00 1oxsC 353 2.24e+00 b.40.6.3 87519 c.37.1.12 87520 1pii 452 2.25e+00 1pii c.1.2.4 28559 c.1.2.4 28563 1m2oB 190 2.72e+00 c.37.1.8 78485 1j9bA 141 2.88e+00 c.47.1.12 66459 1ex2A 189 3.07e+00 1ex2A c.51.4.2 33225 1m2aA 110 3.12e+00 c.47.1.11 78472 1m2bA 110 3.23e+00 c.47.1.11 78474 1m2dA 110 3.35e+00 c.47.1.11 78476 1k0rA 366 3.44e+00 b.40.4.5 67961 d.52.3.1 67962 d.52.3.1 67963 d.202.1.1 67964 1ml4A 308 3.63e+00 c.78.1.1 79255 c.78.1.1 79256 1of9A 77 3.66e+00 1f0kA 364 3.68e+00 1f0kA c.87.1.2 35465 1o5iA 249 3.79e+00 1nkl 78 3.80e+00 1nkl a.64.1.1 18140 2dri 271 4.08e+00 2dri c.93.1.1 35637 1dfwA 25 4.09e+00 j.35.1.1 46255 1gajA 257 4.17e+00 1gajA c.37.1.12 60416 1sviA 195 4.28e+00 1hskA 326 4.43e+00 2mbr d.145.1.2 61241 d.146.1.1 61242 1f3aA 222 4.43e+00 1pgtA a.45.1.1 17701 c.47.1.5 32995 1q77A 138 4.44e+00 1pioA 257 4.53e+00 1btl e.3.1.1 42719 1r88A 280 4.59e+00 1bxkA 355 4.75e+00 1bxkA c.2.1.2 29803 1cs0B 382 5.21e+00 1c3oB c.8.3.1 30740 c.23.16.1 31417 1mgtA 174 5.23e+00 1mgtA a.4.2.1 16078 c.55.7.1 33753 1g291 372 5.26e+00 1g291 1f37A 110 5.36e+00 1f37A c.47.1.11 33088 1cs1C 386 5.53e+00 1ibjA c.67.1.3 34401 1jlvA 209 5.63e+00 a.45.1.1 71729 c.47.1.5 71730 1f2tB 148 5.65e+00 1f2tB 1ojxA 263 5.71e+00 1e19A 314 5.83e+00 1b7bA c.73.1.1 34967 3blm 257 5.88e+00 1btl e.3.1.1 42709 1us5A 314 5.94e+00 1aw0 72 6.23e+00 1aw0 d.58.17.1 39342 1fzqA 181 6.32e+00 1hurA c.37.1.8 32060 1bed 181 6.33e+00 1fvkA a.44.1.1 17514 c.47.1.4 32808 1gca 309 6.63e+00 1gca c.93.1.1 35659 1okgA 373 6.72e+00 1jtkA 136 6.77e+00 c.97.1.1 71862 1uwzA 136 6.94e+00 1cs1A 386 7.03e+00 1ibjA c.67.1.3 34399 1pms 136 7.07e+00 1awe b.55.1.1 26966 1ghpA 258 7.50e+00 1btl e.3.1.1 60520 1m12A 84 7.70e+00 a.64.1.1 84745 1jmkC 230 7.96e+00 c.69.1.22 71747 1c3oB 382 8.08e+00 1c3oB c.8.3.1 30744 c.23.16.1 31421 1juk 248 8.28e+00 1a53 c.1.2.4 28567 1inlA 296 8.42e+00 c.66.1.17 66220 2gbp 309 8.55e+00 1gca c.93.1.1 35657 1j24A 143 8.57e+00 c.52.1.20 84008 1gnwA 211 8.62e+00 1gnwA a.45.1.1 17727 c.47.1.5 33021 3daaA 277 8.81e+00 1daaA e.17.1.1 43272 1qamA 244 8.91e+00 2ercA c.66.1.24 34220 1gox 370 9.08e+00 1gox c.1.4.1 28607 1e6bA 221 9.74e+00 1e6bA a.45.1.1 59294 c.47.1.5 59295 1gqyA 475 9.82e+00 c.5.1.1 83305 c.59.1.1 83306 c.72.2.1 83307 1tlfA 301 9.86e+00 1tlfA c.93.1.1 35687 1f6dA 376 9.91e+00 1f6dA c.87.1.3 35467 1zfjA 491 9.95e+00 1ak5 c.1.5.1 28638 d.37.1.1 38540 d.37.1.1 38541 1lv7A 257 1.02e+01 c.37.1.20 78232 1qzmA 94 1.02e+01 1a53 247 1.03e+01 1a53 c.1.2.4 28564 1ffkC 246 1.04e+01 1ffkC c.22.1.1 31037 1igs 248 1.04e+01 1a53 c.1.2.4 28565 1pd21 199 1.04e+01 1pd21 1k3yA 221 1.07e+01 a.45.1.1 77245 c.47.1.5 77246 1ib8A 164 1.07e+01 b.38.2.1 71168 d.52.4.1 71169 1jq3A 296 1.08e+01 c.66.1.17 67079 1ak5 503 1.10e+01 1ak5 c.1.5.1 28639 1ni4A 365 1.10e+01 c.36.1.7 85728 1daaA 282 1.10e+01 1daaA e.17.1.1 43270 2dabA 282 1.13e+01 1daaA e.17.1.1 43274 1g6hA 257 1.15e+01 1gajA c.37.1.12 60318 1b75A 94 1.16e+01 1dfuP b.53.1.1 26937 1vjoA 393 1.20e+01 1gr0A 367 1.25e+01 c.2.1.3 70379 d.81.1.3 70380 1jyeA 349 1.25e+01 c.93.1.1 67455 1a8y 367 1.26e+01 1a8y c.47.1.3 32781 c.47.1.3 32782 c.47.1.3 32783 1gylA 369 1.27e+01 1gox c.1.4.1 28610 1fp6A 289 1.27e+01 1cp2A c.37.1.10 32243 1a0rP 245 1.28e+01 1b9yC c.47.1.6 33054 1ofv 169 1.28e+01 1rcf c.23.5.1 31184 1ne7A 289 1.34e+01 1mla 309 1.36e+01 1mla c.19.1.1 31031 d.58.23.1 39383 1ur5A 309 1.36e+01 1r5tA 142 1.37e+01 9apiA 347 1.37e+01 1ovaA e.1.1.1 42630 1mb3A 124 1.39e+01 c.23.1.1 78907 1akr 147 1.40e+01 1rcf c.23.5.1 31152 1pb7A 292 1.40e+01 c.94.1.1 88025 1gyfA 62 1.40e+01 1gyfA d.76.1.1 39749 1oivA 191 1.42e+01 1s4zC 30 1.44e+01 1jr3A 373 1.45e+01 a.80.1.1 63245 c.37.1.20 63246 1pjqA 457 1.45e+01 1f2eA 201 1.46e+01 1a0fA a.45.1.1 17745 c.47.1.5 33039 1d9tA 289 1.48e+01 1deaA 1k3lA 221 1.48e+01 a.45.1.1 77229 c.47.1.5 77230 1vgvA 384 1.49e+01 1kimA 366 1.51e+01 1qhiA c.37.1.1 31864 1r5pA 108 1.51e+01 1l2tA 235 1.51e+01 c.37.1.12 73514 1g8pA 350 1.53e+01 1g8pA c.37.1.20 60376 1cznA 169 1.53e+01 1rcf c.23.5.1 31181 1a9xB 379 1.56e+01 1c3oB c.8.3.1 30732 c.23.16.1 31409 1lsuA 147 1.57e+01 c.2.1.9 74250 1en7A 157 1.57e+01 1en7A a.140.4.1 64733 d.4.1.5 64734 1jjoC 261 1.57e+01 2shkA 173 1.59e+01 1shkA c.37.1.2 31934 1f4pA 147 1.61e+01 5nul c.23.5.1 59651 1iyhA 198 1.64e+01 a.45.1.1 83790 c.47.1.5 83791 1kgsA 225 1.68e+01 a.4.6.1 68596 c.23.1.1 68597 1mdiA 105 1.68e+01 1erv c.47.1.1 32755 1ihuA 589 1.69e+01 c.37.1.10 62394 c.37.1.10 62395 1b4cA 92 1.73e+01 1b4cA a.39.1.2 17169 1kwkA 645 1.74e+01 b.71.1.1 77565 c.1.8.1 77566 c.23.16.5 77567 1gseA 221 1.74e+01 1pgtA a.45.1.1 17667 c.47.1.5 32961 1s48A 609 1.75e+01 1sayA 361 1.76e+01 1sayA c.2.1.4 30102 c.23.12.2 31362 1fc1A 224 1.77e+01 1igtB b.1.1.2 21520 b.1.1.2 21521 1jj2C 246 1.78e+01 1ffkC c.22.1.1 63087 1gtmA 419 1.78e+01 1hwyA c.2.1.7 30223 c.58.1.1 33871 1nh9A 87 1.81e+01 1f81A 88 1.83e+01 1f81A g.53.1.1 45383 2scuB 388 1.89e+01 2scuB c.23.4.1 31141 d.142.1.4 41562 2fx2 147 1.89e+01 1rcf c.23.5.1 31158 1qydA 313 1.91e+01 1e2kA 331 1.92e+01 1qhiA c.37.1.1 31854 1j8yF 297 1.94e+01 1ng1 a.24.13.1 62747 c.37.1.10 62748 1vhxA 150 1.94e+01 1rthA 560 1.95e+01 1rthA c.55.3.1 33576 e.8.1.2 43028 1fmjA 351 1.97e+01 c.37.1.5 59879 1div 149 1.98e+01 1div d.99.1.1 40692 d.100.1.1 40693 1dfuP 94 2.00e+01 1dfuP b.53.1.1 26936 1j9eA 147 2.01e+01 c.23.5.1 62756 1pjcA 361 2.02e+01 1sayA c.2.1.4 30101 c.23.12.2 31361 1ukuA 102 2.03e+01 1tul 108 2.04e+01 1tul b.85.5.1 28373 1fc2D 224 2.05e+01 1igtB b.1.1.2 21516 b.1.1.2 21517 1uaqA 158 2.06e+01 c.97.1.2 88386 1shkA 173 2.10e+01 1shkA c.37.1.2 31932 1uhwA 109 2.11e+01 1skoA 143 2.13e+01 1qhlA 227 2.13e+01 1qhlA c.37.1.12 32382 1f3mC 297 2.14e+01 1hcl d.144.1.7 41677 1l6xA 207 2.16e+01 b.1.1.2 73642 b.1.1.2 73643 1jw9B 249 2.16e+01 c.111.1.1 67377 1bvb 211 2.17e+01 1bvb a.138.1.3 19683 1osdA 72 2.18e+01 1i3cA 149 2.21e+01 c.23.1.1 71112 1ru8A 232 2.21e+01 1k68A 140 2.22e+01 1p6oA 161 2.23e+01 1xxbA 78 2.24e+01 1xxaA d.74.2.1 39706 1jsuC 84 2.24e+01 1jsuC j.55.1.1 46339 1h7sA 365 2.24e+01 d.14.1.3 65705 d.122.1.2 65706 1b57A 358 2.26e+01 1dosA c.1.10.2 29177 1me8A 503 2.27e+01 c.1.5.1 79028 1mwyA 73 2.29e+01 d.58.17.1 79616 2trcP 217 2.35e+01 1b9yC c.47.1.6 33051 1dttA 560 2.36e+01 1rthA c.55.3.1 33611 e.8.1.2 43088 1mumA 295 2.40e+01 c.1.12.7 85108 1h9sA 140 2.40e+01 1b9mA b.40.6.2 60843 b.40.6.2 60844 1v74A 107 2.40e+01 1fts 295 2.44e+01 1ng1 a.24.13.1 16968 c.37.1.10 32279 1g4uS 383 2.44e+01 1g4uS a.24.11.1 16643 c.45.1.2 32691 1sedA 117 2.48e+01 1kwgA 645 2.49e+01 b.71.1.1 77561 c.1.8.1 77562 c.23.16.5 77563 1qs0B 338 2.50e+01 1qs0B c.36.1.7 31830 c.48.1.2 33103 1k47A 337 2.53e+01 d.14.1.5 72040 d.58.26.4 72041 2ki5A 366 2.56e+01 1qhiA c.37.1.1 31862 1k66A 149 2.57e+01 1iu4A 331 2.59e+01 d.3.1.8 71430 1awe 130 2.60e+01 1awe b.55.1.1 26968 1pne 140 2.61e+01 1pne d.110.1.1 40866 1g4wR 383 2.66e+01 1g4uS a.24.11.1 16644 c.45.1.2 32692 5nul 138 2.70e+01 5nul c.23.5.1 31191 1g71A 347 2.76e+01 1g71A e.16.1.1 43268 1b00A 127 2.77e+01 3chy c.23.1.1 31122 1n99A 166 2.79e+01 b.36.1.1 85459 b.36.1.1 85460 1omzA 293 2.81e+01 c.68.1.15 87093 1pjbA 361 2.82e+01 1sayA c.2.1.4 30103 c.23.12.2 31363 1p3dA 475 2.85e+01 c.5.1.1 87728 c.59.1.1 87729 c.72.2.1 87730 1uv7A 110 2.85e+01 1rpuA 172 2.86e+01 1b9yC 246 2.89e+01 1b9yC c.47.1.6 33052 1apyB 141 2.91e+01 1apyB 1kao 167 2.95e+01 1ctqA c.37.1.8 32014 1bu5A 147 2.95e+01 5nul c.23.5.1 31155 1mo2A 294 2.97e+01 c.69.1.22 79331 1kqfB 294 2.98e+01 d.58.1.5 75900 f.23.22.1 75901 1ovxA 67 2.98e+01 1g8aA 227 3.02e+01 1r9fA 136 3.02e+01 1jscA 630 3.03e+01 c.31.1.3 67224 c.36.1.5 67225 c.36.1.9 67226 1iwdA 215 3.04e+01 d.3.1.1 83756 1ujnA 348 3.05e+01 1qhiA 366 3.06e+01 1qhiA c.37.1.1 31860 1sur 215 3.06e+01 1sur c.26.2.2 31620 1hm9A 468 3.08e+01 b.81.1.4 65866 c.68.1.5 65867 1k0dA 260 3.09e+01 a.45.1.1 67930 c.47.1.5 67931 2fox 138 3.10e+01 5nul c.23.5.1 31197 1sdoA 203 3.12e+01 1stfI 98 3.13e+01 1stfI d.17.1.2 38006 1nqzA 194 3.15e+01 d.113.1.1 86077 1vrtA 560 3.16e+01 1rthA c.55.3.1 33574 e.8.1.2 43023 1vi1A 345 3.16e+01 1sluA 142 3.16e+01 1sluA b.16.1.1 23685 1kolA 398 3.18e+01 b.35.1.2 77474 c.2.1.1 77475 1svb 395 3.19e+01 1svb b.1.18.4 21814 f.10.1.1 43827 1hucA 47 3.19e+01 1hucA d.3.1.1 37049 1jagA 241 3.20e+01 c.37.1.1 66463 1g5pA 289 3.20e+01 1cp2A c.37.1.10 32253 1fil 139 3.26e+01 1pne d.110.1.1 40869 1qgwA 76 3.29e+01 1qgwA d.184.1.1 42616 2at2A 300 3.33e+01 3csuA c.78.1.1 35196 c.78.1.1 35197 1huxA 270 3.34e+01 1huxA c.55.1.5 61278 1o1zA 234 3.34e+01 c.1.18.3 86555 1lssA 140 3.37e+01 c.2.1.9 74246 1jtvA 327 3.37e+01 c.2.1.2 84230 1kq3A 376 3.40e+01 e.22.1.2 68790 1qgwB 67 3.42e+01 1qgwA d.184.1.1 42617 1csn 298 3.42e+01 1csn d.144.1.7 41664 1d6zA 727 3.44e+01 1oacA b.30.2.1 24394 d.17.2.1 38015 d.17.2.1 38016 d.82.1.1 40007 1vi4A 174 3.49e+01 2hmiA 558 3.52e+01 1rthA c.55.3.1 33604 e.8.1.2 43106 1rypC 244 3.54e+01 1rypC d.153.1.4 41934 1qqtA 551 3.56e+01 1qqtA a.27.1.1 16923 c.26.1.1 31590 g.41.1.1 45175 1ako 268 3.61e+01 1ako d.151.1.1 41779 2nmbA 160 3.63e+01 2nmbA b.55.1.2 26994 1nmtA 392 3.68e+01 1nmtA d.108.1.2 40823 d.108.1.2 40824 1kshA 186 3.68e+01 c.37.1.8 72914 1tfr 305 3.71e+01 1tfr a.60.7.1 18081 c.120.1.2 33351 1ne6A 283 3.77e+01 1hqoA 258 3.80e+01 1hqoA a.45.1.1 17749 c.47.1.5 33043 1h3fA 432 3.81e+01 c.26.1.1 76631 d.66.1.4 76632 1lgr 468 3.85e+01 1lgr d.15.9.1 37837 d.128.1.1 41167 1psdA 409 3.89e+01 1psdA c.2.1.4 30097 c.23.12.1 31357 d.58.18.1 39354 2lgsA 468 3.90e+01 1lgr d.15.9.1 37838 d.128.1.1 41168 1dmlA 319 3.96e+01 1dmlA d.131.1.2 41380 d.131.1.2 41381 1v4vA 376 3.96e+01 1xxaA 78 3.98e+01 1xxaA d.74.2.1 39700