# List of top-scoring protein chains for t2k-100-30-str2 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 2trxA 108 2.98e-06 1thx c.47.1.1 32719 1egr 85 3.10e-06 1kte c.47.1.1 32765 1ego 85 5.63e-06 1kte c.47.1.1 32767 1thx 115 6.28e-06 1thx c.47.1.1 32732 1hyuA 521 8.94e-06 1hyuA c.3.1.5 30547 c.3.1.5 30548 c.47.1.2 32779 c.47.1.2 32780 1nw2A 105 1.00e-05 1fo5A 85 1.18e-05 1fo5A c.47.1.1 59922 1j08A 226 1.23e-05 c.47.1.2 83855 c.47.1.2 83856 1kte 105 1.45e-05 1kte c.47.1.1 32771 1h75A 81 2.15e-05 1h75A c.47.1.1 60716 1a8l 226 2.53e-05 1a8l c.47.1.2 32777 c.47.1.2 32778 1jhb 106 2.67e-05 1kte c.47.1.1 32772 1kebA 108 5.32e-05 c.47.1.1 77341 1fb6A 105 9.25e-05 1thx c.47.1.1 32739 1iloA 77 1.24e-04 c.47.1.1 66205 1g7oA 215 1.31e-04 1g7oA a.45.1.1 60332 c.47.1.5 60333 1r26A 125 3.36e-04 1grx 85 6.55e-04 1kte c.47.1.1 32766 3grx 82 7.07e-04 1aba c.47.1.1 32769 1o6jA 150 7.72e-04 c.47.1.10 81089 1qfnA 85 7.94e-04 1qfnA c.47.1.1 32768 1eemA 241 1.11e-03 1eemA a.45.1.1 17717 c.47.1.5 33011 1erv 105 1.96e-03 1erv c.47.1.1 32743 1ewxA 146 1.96e-03 1ewxA c.47.1.10 33062 1st9A 143 2.61e-03 1aba 87 3.44e-03 1aba c.47.1.1 32760 1qk8A 146 6.41e-03 1ewxA c.47.1.10 33061 1pmt 203 8.60e-03 1a0fA a.45.1.1 17740 c.47.1.5 33034 1k0mA 241 1.03e-02 a.45.1.1 67949 c.47.1.5 67950 1k0nA 241 1.39e-02 a.45.1.1 67953 c.47.1.5 67954 1tof 112 1.40e-02 1erv c.47.1.1 32733 1aiu 105 1.57e-02 1erv c.47.1.1 32746 1oyjA 231 1.85e-02 a.45.1.1 87597 c.47.1.5 87598 1i5gA 144 1.89e-02 1ewxA c.47.1.10 61784 1gwcA 230 2.95e-02 a.45.1.1 70660 c.47.1.5 70661 1lu4A 136 3.00e-02 1kngA 156 3.35e-02 c.47.1.10 72777 1o8xA 146 5.19e-02 c.47.1.10 86681 1n2aA 201 5.19e-02 1eejA 216 6.37e-02 1eejA c.47.1.9 33057 d.17.3.1 38071 1f2eA 201 8.57e-02 1a0fA a.45.1.1 17745 c.47.1.5 33039 1a0fA 201 8.69e-02 1a0fA a.45.1.1 17737 c.47.1.5 33031 1qgvA 142 9.95e-02 1qgvA c.47.1.8 33056 1faaA 124 1.04e-01 1erv c.47.1.1 32738 1jlvA 209 1.04e-01 a.45.1.1 71729 c.47.1.5 71730 1f9mA 112 1.05e-01 1erv c.47.1.1 32736 1e6bA 221 1.07e-01 1e6bA a.45.1.1 59294 c.47.1.5 59295 1pqnA 127 1.21e-01 1jfuA 186 1.40e-01 c.47.1.10 62940 2gsq 202 1.47e-01 1pd21 a.45.1.1 17715 c.47.1.5 33009 1gh2A 107 1.66e-01 1erv c.47.1.1 60515 1f3aA 222 2.86e-01 1pgtA a.45.1.1 17701 c.47.1.5 32995 1uc7A 125 3.15e-01 1aw9 216 3.25e-01 1gnwA a.45.1.1 17736 c.47.1.5 33030 1fw1A 216 3.84e-01 a.45.1.1 60051 c.47.1.5 60052 1bjx 110 3.97e-01 1bjx c.47.1.2 32774 2bjxA 110 3.97e-01 1bjx c.47.1.2 32776 1g7eA 122 4.30e-01 1g7eA c.47.1.7 33055 1cc8A 73 4.34e-01 1cc8A d.58.17.1 39343 1m0uA 249 4.78e-01 a.45.1.1 78359 c.47.1.5 78360 1pd21 199 6.39e-01 1pd21 1iyhA 198 6.44e-01 a.45.1.1 83790 c.47.1.5 83791 1bed 181 7.88e-01 1fvkA a.44.1.1 17514 c.47.1.4 32808 1j9bA 141 8.47e-01 c.47.1.12 66459 1gseA 221 8.48e-01 1pgtA a.45.1.1 17667 c.47.1.5 32961 1oe8A 211 8.49e-01 a.45.1.1 86905 c.47.1.5 86906 1oktA 211 9.35e-01 1k3yA 221 9.75e-01 a.45.1.1 77245 c.47.1.5 77246 1k3lA 221 1.01e+00 a.45.1.1 77229 c.47.1.5 77230 1a8y 367 1.07e+00 1a8y c.47.1.3 32781 c.47.1.3 32782 c.47.1.3 32783 1alq 266 1.09e+00 1btl e.3.1.1 42707 1mek 120 1.15e+00 1erv c.47.1.2 32775 1fe0A 68 1.25e+00 1cc8A d.58.17.1 39345 1qvbA 481 1.34e+00 1qvbA c.1.8.4 28983 1j0fA 100 1.35e+00 1g6wA 261 1.53e+00 1hqoA a.45.1.1 17751 c.47.1.5 33045 1gnuA 117 1.67e+00 d.15.1.3 65403 1ur5A 309 1.81e+00 1k0dA 260 1.99e+00 a.45.1.1 67930 c.47.1.5 67931 1mdiA 105 2.08e+00 1erv c.47.1.1 32755 1o5iA 249 2.09e+00 1k0rA 366 2.09e+00 b.40.4.5 67961 d.52.3.1 67962 d.52.3.1 67963 d.202.1.1 67964 1ex2A 189 2.13e+00 1ex2A c.51.4.2 33225 1eo6A 117 2.28e+00 1eo6A d.15.1.3 37609 1r5pA 108 2.33e+00 1kotA 119 2.67e+00 d.15.1.3 68732 1jjoC 261 2.69e+00 1j4aA 333 2.97e+00 c.2.1.4 71502 c.23.12.1 71503 1grj 158 3.14e+00 1grj a.2.1.1 15691 d.26.1.2 38433 9apiA 347 3.16e+00 1ovaA e.1.1.1 42630 1hqoA 258 3.26e+00 1hqoA a.45.1.1 17749 c.47.1.5 33043 1s3iA 310 3.52e+00 1pvuA 154 3.58e+00 3pviA c.52.1.6 33306 1qlpA 394 3.59e+00 1ovaA e.1.1.1 42628 1cs1C 386 3.64e+00 1ibjA c.67.1.3 34401 1gulA 222 3.70e+00 1pgtA a.45.1.1 17675 c.47.1.5 32969 1f37A 110 4.08e+00 1f37A c.47.1.11 33088 1jr3A 373 4.10e+00 a.80.1.1 63245 c.37.1.20 63246 1gnwA 211 4.26e+00 1gnwA a.45.1.1 17727 c.47.1.5 33021 1gumA 222 4.48e+00 1pgtA a.45.1.1 17683 c.47.1.5 32977 1o1yA 239 4.93e+00 c.23.16.1 86554 1fd8A 73 5.30e+00 1cc8A d.58.17.1 59770 1pioA 257 5.59e+00 1btl e.3.1.1 42719 1ghpA 258 6.11e+00 1btl e.3.1.1 60520 1p8xA 344 6.20e+00 1fvkA 189 6.74e+00 1fvkA a.44.1.1 17490 c.47.1.4 32784 3blm 257 7.06e+00 1btl e.3.1.1 42709 1q7lB 88 7.36e+00 1awe 130 8.70e+00 1awe b.55.1.1 26968 1svb 395 9.77e+00 1svb b.1.18.4 21814 f.10.1.1 43827 2nmbA 160 1.04e+01 2nmbA b.55.1.2 26994 1d9tA 289 1.08e+01 1deaA 1ja9A 274 1.08e+01 c.2.1.2 62817 1ne7A 289 1.12e+01 1b4pA 217 1.13e+01 a.45.1.1 83158 c.47.1.5 83159 1dsbA 189 1.18e+01 1fvkA a.44.1.1 17497 c.47.1.4 32791 1cs1A 386 1.26e+01 1ibjA c.67.1.3 34399 1qzmA 94 1.30e+01 1of9A 77 1.31e+01 1e19A 314 1.35e+01 1b7bA c.73.1.1 34967 3pviA 157 1.36e+01 3pviA c.52.1.6 33300 1g8aA 227 1.40e+01 1fts 295 1.40e+01 1ng1 a.24.13.1 16968 c.37.1.10 32279 1akr 147 1.43e+01 1rcf c.23.5.1 31152 1pb7A 292 1.45e+01 c.94.1.1 88025 1nx8A 273 1.46e+01 b.82.2.8 86374 1e7lA 157 1.46e+01 1en7A a.140.4.1 64728 d.4.1.5 64729 1heiA 451 1.51e+01 1heiA c.37.1.14 32463 c.37.1.14 32464 1j9eA 147 1.51e+01 c.23.5.1 62756 6cts 433 1.52e+01 1csh a.103.1.1 18891 1bu5A 147 1.54e+01 5nul c.23.5.1 31155 1gr2A 279 1.56e+01 1gr2A c.94.1.1 35825 1r5tA 142 1.58e+01 1f4pA 147 1.60e+01 5nul c.23.5.1 59651 1zfjA 491 1.62e+01 1ak5 c.1.5.1 28638 d.37.1.1 38540 d.37.1.1 38541 1dfwA 25 1.67e+01 j.35.1.1 46255 1dfuP 94 1.71e+01 1dfuP b.53.1.1 26936 1ljrA 244 1.72e+01 1ljrA a.45.1.1 17707 c.47.1.5 33001 1daaA 282 1.74e+01 1daaA e.17.1.1 43270 1ag9A 175 1.76e+01 1rcf c.23.5.1 31178 1ddmA 135 1.77e+01 2nmbA b.55.1.2 26993 1upiA 225 1.80e+01 1h5yA 253 1.81e+01 c.1.2.1 65638 1gutA 68 1.84e+01 b.40.6.1 65576 1qtoA 122 1.85e+01 1bylA d.32.1.2 38494 1stfI 98 1.93e+01 1stfI d.17.1.2 38006 1nsj 205 1.96e+01 1nsj c.1.2.4 28560 3daaA 277 2.00e+01 1daaA e.17.1.1 43272 1hh2P 344 2.04e+01 b.40.4.5 65835 d.52.3.1 65836 d.52.3.1 65837 d.202.1.1 65838 1fjhA 257 2.05e+01 1fjhB c.2.1.2 29870 3csuA 310 2.06e+01 3csuA c.78.1.1 35094 c.78.1.1 35095 1g4uS 383 2.06e+01 1g4uS a.24.11.1 16643 c.45.1.2 32691 1ftkA 279 2.07e+01 1gr2A c.94.1.1 35819 1d4xG 126 2.10e+01 1d0nA d.109.1.1 59109 1nm1G 125 2.11e+01 d.109.1.1 80653 1ukuA 102 2.11e+01 1yagG 125 2.12e+01 1d0nA d.109.1.1 40846 2fx2 147 2.12e+01 1rcf c.23.5.1 31158 1dugA 234 2.15e+01 1b8xA a.45.1.1 17718 c.47.1.5 33012 1s48A 609 2.16e+01 1g4wR 383 2.27e+01 1g4uS a.24.11.1 16644 c.45.1.2 32692 1nffA 260 2.28e+01 c.2.1.2 80457 1mqiA 263 2.29e+01 1mqdA 261 2.29e+01 c.94.1.1 85049 1m5dA 263 2.29e+01 c.94.1.1 78641 1v5xA 203 2.30e+01 1iu4A 331 2.31e+01 d.3.1.8 71430 1erw 105 2.31e+01 1erv c.47.1.1 32745 2dabA 282 2.31e+01 1daaA e.17.1.1 43274 1dqpA 230 2.32e+01 1dqnA c.61.1.1 34069 1bxkA 355 2.34e+01 1bxkA c.2.1.2 29803 1jqeA 292 2.35e+01 c.66.1.19 71789 1gajA 257 2.36e+01 1gajA c.37.1.12 60416 1axdA 209 2.39e+01 1gnwA a.45.1.1 17730 c.47.1.5 33024 1ne6A 283 2.40e+01 1iba 101 2.41e+01 1iba d.95.1.1 40567 3vtk 343 2.47e+01 1qhiA c.37.1.1 31884 1m2bA 110 2.51e+01 c.47.1.11 78474 1epuA 591 2.52e+01 1dn1A e.25.1.1 43358 1jqjC 343 2.53e+01 a.80.1.1 67097 c.37.1.20 67098 1mwyA 73 2.55e+01 d.58.17.1 79616 1xat 212 2.57e+01 2xat b.81.1.3 28059 1m2aA 110 2.58e+01 c.47.1.11 78472 1orrA 347 2.68e+01 1p6oA 161 2.81e+01 1uaqA 158 2.82e+01 c.97.1.2 88386 1o0uA 429 2.84e+01 c.118.1.1 80743 1c1dA 355 2.90e+01 1bw9A c.2.1.7 30270 c.58.1.1 33918 1m5eA 263 2.92e+01 c.94.1.1 78642 1b9mA 265 2.93e+01 1b9mA a.4.5.8 16118 b.40.6.2 58938 b.40.6.2 58939 1f2tB 148 2.95e+01 1f2tB 1uqrA 154 2.96e+01 1amz 435 2.98e+01 1csh a.103.1.1 18884 1nxqA 251 3.00e+01 c.2.1.2 86388 1csc 433 3.00e+01 1csh a.103.1.1 18886 1dqnA 230 3.01e+01 1dqnA c.61.1.1 34067 1nkl 78 3.04e+01 1nkl a.64.1.1 18140 1v74A 107 3.04e+01 1aw0 72 3.05e+01 1aw0 d.58.17.1 39342 1c3oB 382 3.07e+01 1c3oB c.8.3.1 30744 c.23.16.1 31421 1ekxA 311 3.07e+01 3csuA c.78.1.1 35088 c.78.1.1 35089 1guzA 310 3.08e+01 c.2.1.5 65586 d.162.1.1 65587 1m2dA 110 3.10e+01 c.47.1.11 78476 1at1A 310 3.10e+01 3csuA c.78.1.1 35168 c.78.1.1 35169 1qklA 127 3.12e+01 1qklA d.78.1.2 39754 1sdoA 203 3.12e+01 1ek1A 554 3.13e+01 1cr6B c.108.1.2 43335 c.69.1.11 34685 1qdlB 195 3.14e+01 1qdlB c.23.16.1 31437 1b75A 94 3.16e+01 1dfuP b.53.1.1 26937 1pgtA 210 3.17e+01 1pgtA a.45.1.1 17515 c.47.1.5 32809 1rgs 288 3.19e+01 1rgs b.82.3.2 28146 b.82.3.2 28147 1sayA 361 3.20e+01 1sayA c.2.1.4 30102 c.23.12.2 31362 1rpuA 172 3.23e+01 1fjhB 257 3.38e+01 1fjhB c.2.1.2 29871 1a9xB 379 3.38e+01 1c3oB c.8.3.1 30732 c.23.16.1 31409 1lv7A 257 3.41e+01 c.37.1.20 78232 1pjcA 361 3.46e+01 1sayA c.2.1.4 30101 c.23.12.2 31361 1g3uA 214 3.46e+01 c.37.1.1 65132 1pea 385 3.47e+01 1pea c.93.1.1 35662 1e6cA 173 3.51e+01 1shkA c.37.1.2 59296 1p6xA 334 3.53e+01 1di6A 195 3.54e+01 1di6A c.57.1.1 33863 1m9xC 146 3.60e+01 a.73.1.1 84907 1ak4C 145 3.61e+01 1ak4C a.73.1.1 18321 1e2kA 331 3.62e+01 1qhiA c.37.1.1 31854 1cznA 169 3.64e+01 1rcf c.23.5.1 31181 1dl2A 511 3.66e+01 1dl2A a.102.2.1 18844 1nkxA 348 3.67e+01 1r9lA 309 3.74e+01 1n2sA 299 3.76e+01 c.2.1.2 79857 1ffkC 246 3.78e+01 1ffkC c.22.1.1 31037 1kc0A 299 3.81e+01 1h0hB 214 3.82e+01 d.58.1.5 76437 1r4wA 226 3.82e+01 1uhwA 109 3.83e+01 6gsvA 217 3.83e+01 1b8xA a.45.1.1 17633 c.47.1.5 32925 1ojxA 263 3.85e+01 1ofv 169 3.88e+01 1rcf c.23.5.1 31184 1dtx 59 3.90e+01 1bpi g.8.1.1 44551 1a0rP 245 3.91e+01 1b9yC c.47.1.6 33054 1bdg 451 3.95e+01 1qhaA c.55.1.3 33461 c.55.1.3 33462 2vik 126 3.96e+01 2vil d.109.1.1 40829 1kewA 361 3.98e+01 c.2.1.2 68544 1dn1A 594 3.99e+01 1dn1A e.25.1.1 43357