# List of top-scoring protein chains for t2k-100-30-dssp-ebghstl 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 2dpmA 284 4.08e-02 2dpmA c.66.1.28 34246 1i18A 97 4.80e-02 b.43.4.3 61520 1i8dA 213 9.27e-02 b.43.4.3 61953 b.43.4.3 61954 1jnyA 435 1.44e-01 b.43.3.1 66982 b.44.1.1 66983 c.37.1.8 66984 1f60A 458 2.04e-01 1efcA b.43.3.1 25705 b.44.1.1 25745 c.37.1.8 32140 1oruA 195 2.87e-01 unknown_sccs -4390 1db3A 372 5.29e-01 1db3A c.2.1.2 29813 1uheA 97 6.73e-01 1ltlA 279 7.63e-01 b.40.4.11 84701 2napA 723 8.52e-01 2napA b.52.2.2 26926 c.81.1.1 35334 1eu1A 780 9.39e-01 1dmr b.52.2.2 26903 c.81.1.1 35311 1e0tA 470 9.58e-01 1a49A b.58.1.1 27064 c.1.12.1 29292 c.49.1.1 33146 2plc 274 9.84e-01 2plc c.1.18.2 29614 1q16A 1247 1.06e+00 b.52.2.2 -4337 c.81.1.1 -8547 1t82A 155 1.09e+00 1r6xA 395 1.26e+00 b.122.1.3 -5125 c.26.1.5 -6620 1khiA 176 1.33e+00 b.34.5.2 77408 b.40.4.5 77409 1earA 147 1.47e+00 b.107.1.1 64875 d.58.38.1 64876 1eb0A 147 1.48e+00 b.107.1.1 64890 d.58.38.1 64891 1g8fA 511 1.50e+00 1g8fA b.122.1.3 60348 c.26.1.5 60349 c.37.1.15 60350 1odkA 235 1.57e+00 c.56.2.1 86863 1ky9B 448 1.64e+00 b.36.1.4 73200 b.36.1.4 73201 b.47.1.1 73202 1lcyA 325 1.74e+00 b.36.1.4 73834 b.47.1.1 73835 1o5uA 101 1.78e+00 b.82.1.8 -4845 1v5lA 103 1.94e+00 1aw8B 91 1.95e+00 1aw8B 1unkA 87 2.04e+00 1cei a.28.2.1 16935 1fjgD 209 2.05e+00 1c05A d.66.1.2 39553 1aw8E 91 2.07e+00 1aw8B 1o9yA 84 2.08e+00 unknown_sccs -4105 1ijaA 148 2.18e+00 1ijaA b.100.1.1 62484 1v74A 107 2.22e+00 unknown_sccs -9319 1h0hA 977 2.22e+00 b.52.2.2 76435 c.81.1.1 76436 1mxiA 160 2.37e+00 c.116.1.1 79646 1nngA 153 2.50e+00 d.38.1.1 -9636 1liuA 528 2.57e+00 b.58.1.1 77970 c.1.12.1 77971 c.49.1.1 77972 1qtqA 553 2.66e+00 1gtrA b.53.1.2 26940 c.26.1.1 31579 1pqhA 143 2.73e+00 b.52.2.1 -4318 1pkn 530 3.18e+00 1a49A b.58.1.1 27042 c.1.12.1 29271 c.49.1.1 33125 1pt1A 143 3.23e+00 b.52.2.1 -4322 1l7yA 94 3.28e+00 d.15.1.6 73676 1j2rA 199 3.43e+00 unknown_sccs -6799 1iz6A 138 3.48e+00 b.34.5.2 76976 b.40.4.5 76977 1kqfA 1015 3.49e+00 b.52.2.2 72871 c.81.1.1 72872 1dmr 823 3.55e+00 1dmr b.52.2.2 26904 c.81.1.1 35312 1ksfX 758 3.73e+00 a.174.1.1 77522 c.37.1.20 77523 c.37.1.20 77524 1a49A 530 3.98e+00 1a49A b.58.1.1 27026 c.1.12.1 29255 c.49.1.1 33109 1rie 129 4.03e+00 1rie b.33.1.1 24427 1aj8A 371 4.26e+00 1aj8A a.103.1.1 18900 1pwt 61 4.52e+00 1tud b.34.2.1 24490 1cof 143 5.01e+00 1cof d.109.1.2 40860 1l6oA 95 5.04e+00 b.36.1.1 84534 1gtrA 553 5.15e+00 1gtrA b.53.1.2 26939 c.26.1.1 31578 1jvpP 298 5.29e+00 d.144.1.7 67371 1gz8A 299 5.31e+00 d.144.1.7 83405 1e1xA 299 5.43e+00 1hcl d.144.1.7 59157 1kzlA 208 5.61e+00 b.43.4.3 77635 b.43.4.3 77636 1shg 62 5.61e+00 1ckaA b.34.2.1 24493 1q1gA 276 5.79e+00 c.56.2.1 -7846 1hcl 298 5.94e+00 1hcl d.144.1.7 41593 1p9kA 79 6.03e+00 unknown_sccs -10238 1mg4A 113 6.39e+00 d.15.11.1 84953 1k0hA 117 6.40e+00 b.106.1.2 71975 1e79A 510 6.44e+00 1skyB a.69.1.1 18269 b.49.1.1 26434 c.37.1.11 32314 1l5wA 796 6.46e+00 c.87.1.4 73605 1cei 94 6.68e+00 1cei a.28.2.1 16939 1n3lA 372 6.89e+00 c.26.1.1 79966 1qauA 112 7.22e+00 1qauA b.36.1.1 24779 1i7dA 659 7.27e+00 1d6mA e.10.1.1 61886 1q3oA 109 7.28e+00 b.36.1.1 -3776 1irk 306 7.49e+00 1fmk d.144.1.7 41703 1qu9A 128 7.71e+00 1qu9A d.79.1.1 39755 1qu9C 128 7.71e+00 1qu9A d.79.1.1 39757 1d2eA 397 7.71e+00 1efcA b.43.3.1 25701 b.44.1.1 25741 c.37.1.8 32136 1cz4A 185 7.81e+00 1cz4A b.52.2.3 26934 d.31.1.1 38468 1fqtA 112 7.90e+00 1fqtA b.33.1.1 24441 1n9eA 787 8.05e+00 b.30.2.1 -3529 d.17.2.1 -9278 d.17.2.1 -9279 2cbp 96 8.27e+00 2cbp b.6.1.1 22895 1ahxA 396 8.40e+00 1ajsA c.67.1.1 34293 1g8kA 825 8.41e+00 1g8jA b.52.2.2 26920 c.81.1.1 35328 1art 396 8.51e+00 1ajsA c.67.1.1 34285 1h40A 71 8.69e+00 1uzcA 71 8.71e+00 a.159.2.1 -339 1qwlA 505 8.83e+00 e.5.1.1 -11823 1ars 396 8.90e+00 1ajsA c.67.1.1 34287 1epwA 1290 8.91e+00 b.29.1.6 24269 b.42.4.2 25614 d.92.1.7 40305 h.4.2.1 45785 1vdeA 454 9.16e+00 1vdeA b.86.1.2 28378 d.95.2.2 40581 d.95.2.2 40582 1h5rA 293 9.18e+00 c.68.1.6 65623 1fa4A 105 9.28e+00 1plc b.6.1.1 22867 1djxA 624 9.30e+00 1djxB a.39.1.7 17342 b.7.1.1 23159 c.1.18.1 29587 1qcsA 211 9.30e+00 1qcsA b.52.2.3 26927 d.31.1.1 38461 1nykA 165 9.65e+00 b.33.1.1 86408 1semA 58 9.89e+00 1ckaA b.34.2.1 24544 1uwwA 191 9.97e+00 1djxB 624 1.01e+01 1djxB a.39.1.7 17343 b.7.1.1 23160 c.1.18.1 29588 1hyoA 421 1.02e+01 1qcnA b.34.8.1 59001 d.177.1.1 59002 1mp4A 292 1.02e+01 c.68.1.6 79376 1qqjA 419 1.04e+01 1qcnA b.34.8.1 59034 d.177.1.1 59035 1bmfA 510 1.04e+01 1skyB a.69.1.1 18281 b.49.1.1 26446 c.37.1.11 32326 1rqpA 299 1.05e+01 unknown_sccs -4411 unknown_sccs -7908 1hh2P 344 1.05e+01 b.40.4.5 65835 d.52.3.1 65836 d.52.3.1 65837 d.202.1.1 65838 1v8cA 168 1.06e+01 d.15.3.1 -9175 unknown_sccs -11012 1vj0A 380 1.06e+01 b.35.1.2 -3697 c.2.1.1 -5721 1l5jA 865 1.09e+01 a.118.15.1 73592 c.8.2.1 73593 c.83.1.1 73594 1ir3A 306 1.11e+01 1fmk d.144.1.7 41702 1tuc 63 1.12e+01 1tuc b.34.2.1 24492 1g8jA 825 1.14e+01 1g8jA b.52.2.2 26924 c.81.1.1 35332 1g2bA 62 1.14e+01 1tud b.34.2.1 24488 1aonO 97 1.14e+01 b.35.1.1 24642 1gmuA 143 1.18e+01 b.107.1.1 65335 d.58.38.1 65336 2eifA 136 1.21e+01 1bkb b.34.5.2 24607 b.40.4.5 25339 1qcnA 421 1.21e+01 1qcnA b.34.8.1 59017 d.177.1.1 59018 1tud 62 1.22e+01 1tud b.34.2.1 24489 1oc2A 348 1.24e+01 c.2.1.2 -5753 1dmmA 131 1.28e+01 1opy d.17.4.3 38114 1spa 396 1.28e+01 1ajsA c.67.1.1 34291 1udzA 182 1.34e+01 b.51.1.1 -4307 1pzwA 80 1.36e+01 unknown_sccs -12740 1cb0A 283 1.36e+01 1cb0A c.56.2.1 33790 1k47A 337 1.37e+01 d.14.1.5 72040 d.58.26.4 72041 1s3iA 310 1.39e+01 b.46.1.1 -4111 c.65.1.1 -8042 1qasA 622 1.40e+01 1djxB a.39.1.7 17340 b.7.1.1 23157 c.1.18.1 29585 1qatB 622 1.42e+01 1djxB a.39.1.7 17355 b.7.1.1 23172 c.1.18.1 29600 1jc7A 131 1.44e+01 1jc7A b.40.3.2 62873 1ha3A 405 1.45e+01 1efcA b.43.3.1 60869 b.44.1.1 60870 c.37.1.8 60871 1dgjA 907 1.46e+01 1alo a.56.1.1 17909 d.15.4.2 37694 d.41.1.1 38585 d.133.1.1 41415 1np7A 489 1.49e+01 a.99.1.1 80677 c.28.1.1 80678 1gmmA 133 1.49e+01 b.18.1.10 65314 1m5yA 408 1.51e+01 a.167.1.1 78664 d.26.1.1 78665 d.26.1.1 78666 1a81A 254 1.53e+01 1a81A d.93.1.1 40507 d.93.1.1 40508 1qavB 115 1.54e+01 1qauA b.36.1.1 24780 1cl2A 395 1.56e+01 1cl2A c.67.1.3 34397 1mfgA 95 1.58e+01 b.36.1.1 79043 1gppA 237 1.58e+01 b.86.1.2 76262 1o0iA 138 1.59e+01 d.38.1.5 86532 1rlkA 117 1.63e+01 unknown_sccs -7526 1qcoA 423 1.65e+01 1qcnA b.34.8.1 59021 d.177.1.1 59022 1b54 257 1.65e+01 1ct5A c.1.6.2 28664 1opy 131 1.66e+01 1opy d.17.4.3 38113 1a9xB 379 1.68e+01 1c3oB c.8.3.1 30732 c.23.16.1 31409 1o1fC 147 1.68e+01 i.15.1.1 80997 1l1nA 183 1.68e+01 b.47.1.4 73476 1uxxX 133 1.70e+01 b.18.1.10 -3107 1o54A 277 1.71e+01 c.66.1.13 -8095 1jb3A 131 1.72e+01 1jc7A b.40.3.2 62833 1o13A 136 1.73e+01 c.55.5.1 80762 1iw7C 1119 1.74e+01 e.29.1.1 71474 1gmwA 143 1.74e+01 b.107.1.1 65347 d.58.38.1 65348 1c3oB 382 1.76e+01 1c3oB c.8.3.1 30744 c.23.16.1 31421 1lepA 99 1.76e+01 1lepA b.35.1.1 24649 1aipE 405 1.78e+01 1efcA b.43.3.1 25699 b.44.1.1 25739 c.37.1.8 32134 1s6bA 119 1.81e+01 a.133.1.2 -1953 1qisA 396 1.81e+01 1ajsA c.67.1.1 34284 1eqoA 158 1.82e+01 1hka 1dvh 79 1.83e+01 1c53 a.3.1.1 15802 1bxsA 501 1.84e+01 1bpwA c.82.1.1 35357 1iieA 75 1.84e+01 1iieA a.109.1.1 19039 1ea2A 131 1.89e+01 d.17.4.3 64860 1eq0A 158 1.90e+01 d.58.30.1 64909 1keoA 154 1.90e+01 b.64.1.1 68534 2plt 98 1.91e+01 1plc b.6.1.1 22862 1aaj 105 1.92e+01 1aac b.6.1.1 22841 1bxaA 105 1.92e+01 1aac b.6.1.1 22839 1qorA 327 1.95e+01 1qorA b.35.1.2 24766 c.2.1.1 29782 1bkb 136 2.02e+01 1bkb b.34.5.2 24609 b.40.4.5 25341 1r53A 382 2.04e+01 unknown_sccs -11177 1ct5A 256 2.04e+01 1ct5A c.1.6.2 28663 1f9yA 158 2.06e+01 d.58.30.1 83249 1eg7A 557 2.08e+01 1eg7A c.37.1.10 32241 1ht6A 405 2.10e+01 b.71.1.1 83629 c.1.8.1 83630 1eljA 381 2.13e+01 4mbp c.94.1.1 35791 1q41A 424 2.13e+01 d.144.1.7 -11308 1aac 105 2.16e+01 1aac b.6.1.1 22838 1cfyA 143 2.17e+01 1cof d.109.1.2 40858 1ewnA 219 2.17e+01 1bnkA b.46.1.2 25762 1bg6 359 2.20e+01 1bg6 a.100.1.5 18810 c.2.1.6 30214 1kepA 348 2.20e+01 c.2.1.2 68536 1exmA 405 2.20e+01 1efcA b.43.3.1 25696 b.44.1.1 25736 c.37.1.8 32131 1s6bB 119 2.21e+01 a.133.1.2 -1954 1hka 158 2.21e+01 1hka d.58.30.1 39433 1poa 118 2.23e+01 1poa a.133.1.2 19514 1s9rA 410 2.24e+01 unknown_sccs -10989 1ky9A 448 2.29e+01 b.36.1.4 73198 b.47.1.1 73199 1tmy 120 2.29e+01 1dbwA c.23.1.1 31083 1dcfA 136 2.31e+01 1dcfA c.23.1.2 31124 1e4fT 419 2.31e+01 1e4fT c.55.1.1 33453 c.55.1.1 33454 1bb9 115 2.31e+01 1bb9 b.34.2.1 24554 1lylA 504 2.34e+01 1lylA b.40.4.1 25261 d.104.1.1 40717 1f20A 435 2.37e+01 b.43.4.1 64932 c.25.1.4 64933 1lxyA 409 2.37e+01 unknown_sccs -10987 1gp7A 151 2.44e+01 a.133.1.2 76251 1puc 105 2.44e+01 1puc d.97.1.1 40675 1fjgQ 105 2.45e+01 1fjfQ b.40.4.5 25352 1je0A 236 2.45e+01 c.56.2.1 66581 1ek9A 428 2.49e+01 1ek9A f.5.1.1 43809 1o7iA 119 2.59e+01 b.40.4.3 86642 1mjc 69 2.62e+01 1mjc b.40.4.5 25319 1e0gA 48 2.62e+01 1e01A d.7.1.1 37325 1qgvA 142 2.63e+01 1qgvA c.47.1.8 33056 1j5pA 253 2.65e+01 c.2.1.3 83092 d.81.1.3 71577 1oh0A 131 2.65e+01 d.17.4.3 87004 1qciA 262 2.66e+01 1qi7A d.165.1.1 42201 1v2bA 177 2.70e+01 1q7hA 153 2.71e+01 b.122.1.1 -5124 unknown_sccs -9313 1n7eA 97 2.72e+01 b.36.1.1 -3745 1dk8A 147 2.75e+01 1agrE a.91.1.1 18548 1cl1A 395 2.75e+01 1cl2A c.67.1.3 34395 1rnbA 110 2.75e+01 1b20A d.1.1.2 36196 1svy 114 2.79e+01 1svy d.109.1.1 40831 1eceA 358 2.84e+01 1eceA c.1.8.3 28813 1ugpB 226 2.84e+01 1bngA 110 2.85e+01 1b20A d.1.1.2 36184 1lfjB 119 2.86e+01 2vil 126 2.86e+01 2vil d.109.1.1 40830 1brnL 110 2.87e+01 1b20A d.1.1.2 36143 1h8eA 510 2.88e+01 1skyB a.69.1.1 60738 b.49.1.1 60739 c.37.1.11 60740 1l0oA 150 2.90e+01 d.122.1.3 73403 1ireB 228 2.90e+01 b.34.4.4 76770 1rxyA 253 2.91e+01 c.56.2.1 -7834 1izcA 339 2.92e+01 c.1.12.5 83838 1bnr 110 2.95e+01 1b20A d.1.1.2 36206 1kcqA 104 2.97e+01 d.109.1.1 68449 1lfjA 119 3.00e+01 1lx7A 253 3.01e+01 c.56.2.1 74329 1c0dA 358 3.04e+01 1eceA c.1.8.3 28815 1fvaA 217 3.08e+01 1fvaA d.58.28.1 39409 1q15A 503 3.09e+01 c.26.2.1 -6625 d.153.1.1 -11400 1cs0C 1073 3.09e+01 a.92.1.1 18559 c.24.1.1 31488 c.30.1.1 31675 c.30.1.1 31676 d.142.1.2 41520 d.142.1.2 41521 1ee9A 320 3.10e+01 1ee9A c.2.1.7 30288 c.58.1.2 33936 2vik 126 3.10e+01 2vil d.109.1.1 40829 1tadA 324 3.12e+01 1cipA a.66.1.1 18194 c.37.1.8 32077 1fzdA 201 3.14e+01 3fib d.171.1.1 42484 2cbf 234 3.16e+01 1cbf c.90.1.1 35588 1gcqA 61 3.17e+01 1ckaA b.34.2.1 60434 1em8B 112 3.18e+01 unknown_sccs -6364 1bjt 793 3.22e+01 1bjt e.11.1.1 43249 1uu1A 335 3.27e+01 c.67.1.1 -8146 1cs0B 382 3.29e+01 1c3oB c.8.3.1 30740 c.23.16.1 31417 1ofgA 381 3.29e+01 1ofgA c.2.1.3 30064 d.81.1.5 39979 1tag 324 3.30e+01 1cipA a.66.1.1 18197 c.37.1.8 32080 1dekA 241 3.33e+01 1dekA c.37.1.1 31842 1dklA 410 3.37e+01 1dklA c.60.1.2 33996 3adk 195 3.39e+01 1zin c.37.1.1 31885 1qexA 288 3.40e+01 1qexA b.32.1.1 24425 1hryA 76 3.41e+01 1hryA a.21.1.1 16429 1a2pA 110 3.44e+01 1b20A d.1.1.2 36140 1edg 380 3.47e+01 1edg c.1.8.3 28807 1th8A 145 3.53e+01 1g4iA 123 3.53e+01 1poa a.133.1.2 60241 1gkpA 458 3.54e+01 b.92.1.3 70231 c.1.9.6 70232 1nw2A 105 3.55e+01 c.47.1.1 -7380 1bqk 124 3.56e+01 1bqk b.6.1.1 22889 1h6dA 433 3.58e+01 c.2.1.3 65656 d.81.1.5 65657 1dkqA 410 3.58e+01 1dklA c.60.1.2 33998 1nt4A 391 3.59e+01 c.60.1.2 -7942 1j1bA 420 3.60e+01 d.144.1.7 -11312 1skyB 502 3.62e+01 1skyB a.69.1.1 18313 b.49.1.1 26478 c.37.1.11 32358 1lffA 119 3.64e+01 1ckaA 57 3.64e+01 1ckaA b.34.2.1 24459 1ixlA 131 3.66e+01 d.38.1.5 -9705 1n25A 368 3.68e+01 c.37.1.20 85264 1te5A 257 3.69e+01 1t4hA 290 3.71e+01 4ubpB 126 3.73e+01 1ubpB b.85.3.1 28345 1iqsA 88 3.73e+01 d.214.1.1 71278 1jh2A 99 3.74e+01 1ng5A 215 3.74e+01 b.100.1.1 -4541 1ihjA 98 3.75e+01 1pdr b.36.1.1 62382 1ubpB 122 3.75e+01 1ubpB b.85.3.1 28346 1bnkA 216 3.75e+01 1bnkA b.46.1.2 25765 1delA 241 3.75e+01 1dekA c.37.1.1 31844 1qkfA 92 3.76e+01 1qkfA d.28.1.1 38456 1kwaB 88 3.76e+01 1kwaA b.36.1.1 24773 1b00A 127 3.77e+01 3chy c.23.1.1 31122 1fcdA 401 3.78e+01 1fcdA c.3.1.5 30593 c.3.1.5 30594 d.87.1.1 40218 1htrP 43 3.83e+01 1htrP b.50.1.2 26852 7odcA 424 3.84e+01 7odcA b.49.2.3 26488 c.1.6.1 28650 1pk6C 129 3.85e+01 b.22.1.1 -3293 1q8bA 105 3.87e+01 unknown_sccs -9958 1at0 145 3.88e+01 1at0 b.86.1.1 28374 1fvgA 199 3.89e+01 1fvaA d.58.28.1 39408 1k1zA 78 3.93e+01 b.34.2.1 68026 1rypG 244 3.97e+01 d.153.1.4 41938 1h9sA 140 3.98e+01 1b9mA b.40.6.2 60843 b.40.6.2 60844