# List of top-scoring protein chains for t2k-100-30-dssp-ebghstl-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 1tffA 234 3.23e-01 d.3.1.11 106854 1b8zA 90 5.12e-01 1huuA a.55.1.1 17902 1qs1A 462 5.67e-01 1qs1A d.166.1.1,d.166.1.1 42260,42261 1wgzA 510 7.22e-01 1a16 440 7.34e-01 1az9 c.55.2.1,d.127.1.1 33548,41165 1wl9A 440 7.51e-01 2bwvA 440 7.62e-01 1az9 457 7.83e-01 1az9 c.55.2.1,d.127.1.1 33547,41164 1q3eA 207 8.87e-01 b.82.3.2 95669 2fbwC 141 9.22e-01 1qs2A 401 1.22e+00 1qs1A d.166.1.1,d.166.1.1 42268,42269 1sheA 103 1.26e+00 d.274.1.1 105551 1g291 372 1.48e+00 1g291 2bh9A 489 1.73e+00 1mojA 182 2.36e+00 a.25.1.1 91367 1tjoA 182 2.36e+00 1kz7A 353 2.60e+00 a.87.1.1,b.55.1.1 73333,73334 1qhbA 596 4.14e+00 1qhbA a.111.1.2 19055 1lj2A 110 4.32e+00 h.1.13.2 73926 1spgB 147 4.42e+00 1cg5B a.1.1.2 15588 1xl7A 612 5.19e+00 1csn 298 5.73e+00 1csn d.144.1.7 41664 1ev7B 317 5.92e+00 1ev7B c.52.1.9 33316 1iawA 317 6.00e+00 c.52.1.9 62126 1qc7A 101 6.18e+00 1qc7A a.118.14.1 18456 2fvhA 120 6.32e+00 1vgmA 378 6.43e+00 1hhsA 664 6.96e+00 1hi0P e.8.1.6 61045 2anuA 255 7.09e+00 1hi0P 664 7.13e+00 1hi0P e.8.1.6 61051 1nd6A 354 7.14e+00 c.60.1.2 80407 1u8vA 490 7.88e+00 1nw2A 105 7.91e+00 c.47.1.1 92215 1uvjA 664 7.95e+00 e.8.1.6 100045 2ahrA 259 8.88e+00 1av1A 201 9.13e+00 1av1A h.5.1.1 45796 2hpaA 342 9.24e+00 1cviA c.60.1.2 33985 1r2zA 274 9.59e+00 a.156.1.2,b.113.1.1,g.39.1.8 96892,96893,96894 1urvA 190 9.69e+00 1ut0A 190 9.69e+00 a.1.1.2 108012 1cviA 342 1.01e+01 1cviA c.60.1.2 33989 2fflA 756 1.04e+01 1l1zA 274 1.08e+01 a.156.1.2,b.113.1.1,g.39.1.8 75911,75912,75913 2aelA 374 1.08e+01 1v1rA 400 1.08e+01 c.36.1.11 108272 1am4A 199 1.13e+01 1tx4A a.116.1.1 19100 1dbhA 354 1.13e+01 1awe a.87.1.1,b.55.1.1 18514,26967 1b27D 90 1.18e+01 1ay7B c.9.1.1 30840 1ev7A 317 1.22e+01 1ev7B c.52.1.9 33315 1rcwA 231 1.23e+01 a.132.1.4 97299 1z47A 355 1.23e+01 1jk0B 345 1.24e+01 a.25.1.2 63143 1nswA 105 1.25e+01 c.47.1.1 92097 1tk9A 188 1.29e+01 c.80.1.3 107082 1uor 585 1.34e+01 1bj5 a.126.1.1,a.126.1.1,a.126.1.1 19396,19397,19398 1dh3A 55 1.36e+01 1a02J h.1.3.1 45546 1yz7A 188 1.36e+01 2f94F 350 1.40e+01 1rwtA 232 1.40e+01 f.43.1.1 97992 1rtwA 220 1.42e+01 a.132.1.3 97823 1khoA 370 1.56e+01 a.124.1.1,b.12.1.3 72489,72490 1bg1A 722 1.62e+01 1bg1A a.47.1.1,b.2.5.5,d.93.1.1 17767,22461,40527 1w9cA 321 1.63e+01 1bxnA 485 1.65e+01 1burA c.1.14.1,d.58.9.1 29376,39282 1chkA 238 1.66e+01 1chkA d.2.1.7 36999 1jqaA 370 1.69e+01 e.22.1.2 67085 1tc6A 236 1.72e+01 d.122.1.1 106756 1fmhB 33 1.72e+01 1fmhB k.6.1.1 46410 1v9nA 360 1.75e+01 1jq5A 370 1.75e+01 e.22.1.2 67084 1al6 437 1.77e+01 1csh a.103.1.1 18885 1gm7A 209 1.77e+01 d.153.1.2 65302 1zq9A 285 1.77e+01 2sas 185 1.77e+01 2sas a.39.1.5 17258 1myf 153 1.78e+01 1a6m a.1.1.2 15147 1pnkA 209 1.86e+01 1ajqA d.153.1.2 41839 1up8A 598 1.87e+01 a.111.1.2 99710 1wy0A 342 1.90e+01 1e3aA 260 1.95e+01 1ajqA d.153.1.2 41838 1j34A 129 1.95e+01 d.169.1.1 84048 1yv5A 374 1.98e+01 1ajqA 209 1.99e+01 1ajqA d.153.1.2 41840 1gk9A 260 1.99e+01 d.153.1.2 65246 1u61A 138 2.00e+01 a.149.1.1 107696 1jfgA 374 2.10e+01 a.128.1.5 66636 1s1fA 406 2.11e+01 1x7yA 400 2.20e+01 1fx8A 281 2.38e+01 f.19.1.1 43651 1tx4A 198 2.39e+01 1tx4A a.116.1.1 19098 1amz 435 2.40e+01 1csh a.103.1.1 18884 2aaoA 166 2.43e+01 1ai7A 209 2.43e+01 1ajqA d.153.1.2 41845 1yq7A 374 2.45e+01 103m 154 2.46e+01 1a6m a.1.1.2 15124 2c2aA 258 2.47e+01 1mod 154 2.51e+01 1a6m a.1.1.2 15107 1nox 205 2.51e+01 1nox d.90.1.1 40242 1ywfA 296 2.56e+01 1mll 154 2.57e+01 1a6m a.1.1.2 15057 1rprA 63 2.59e+01 1nkd a.30.1.1 16989 1csh 435 2.59e+01 1csh a.103.1.1 18880 1ab7 89 2.60e+01 1ay7B c.9.1.1 30835 1vasA 137 2.61e+01 2end a.18.1.1 16404 1g5aA 628 2.62e+01 b.71.1.1,c.1.8.1 65152,65153 1enj 138 2.66e+01 2end a.18.1.1 16401 1brsD 89 2.71e+01 1ay7B c.9.1.1 30825 2g7lA 243 2.71e+01 1iq8A 582 2.73e+01 c.1.20.1,b.122.1.1,d.17.6.1 71270,83074,83075 1zoyC 140 2.80e+01 1b2uD 90 2.80e+01 1ay7B c.9.1.1 30843 1mlg 154 2.81e+01 1a6m a.1.1.2 15104 1l2lA 457 2.82e+01 c.72.1.3 77656 1b2sD 90 2.84e+01 1ay7B c.9.1.1 30837 1enk 138 2.84e+01 2end a.18.1.1 16402 1mlo 154 2.84e+01 1a6m a.1.1.2 15085 2mgg 154 2.87e+01 1a6m a.1.1.2 15069 1xqwA 293 2.89e+01 1a6g 151 2.89e+01 1a6m a.1.1.2 15021 1gvnA 90 2.89e+01 a.8.2.1 76353 2mgb 154 2.91e+01 1a6m a.1.1.2 15102 2spo 154 2.91e+01 1a6m a.1.1.2 15053 1va6A 518 2.92e+01 1iwgA 1053 2.94e+01 d.58.44.1,d.58.44.1,d.58.44.1,d.58.44.1,d.225.1.1,d.225.1.1,f.35.1.1,f.35.1.1 76874,76875,76876,76877,76878,76879,76880,76881 6cts 433 2.96e+01 1csh a.103.1.1 18891 1mym 154 2.96e+01 1a6m a.1.1.2 15054 1mgn 154 2.97e+01 1a6m a.1.1.2 15097 2end 138 2.98e+01 2end a.18.1.1 16400 1eni 138 3.00e+01 2end a.18.1.1 16403 1gpmA 525 3.02e+01 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 2spl 154 3.02e+01 1a6m a.1.1.2 15047 1wu9A 80 3.05e+01 1mbd 153 3.05e+01 1a6m a.1.1.2 15033 1lq7A 67 3.07e+01 k.9.1.1 74183 1w5rA 278 3.09e+01 1a6m 151 3.10e+01 1a6m a.1.1.2 15018 1yyqA 374 3.10e+01 1ec7A 446 3.11e+01 1bqg c.1.11.2,d.54.1.1 29218,38862 1xewX 182 3.12e+01 1qsdA 106 3.14e+01 1qsdA a.7.5.1 16335 1huuA 90 3.17e+01 1huuA a.55.1.1 17897 2fh5A 185 3.17e+01 1bzpA 153 3.18e+01 1a6m a.1.1.2 15020 1jq0A 84 3.18e+01 h.3.2.1 71786 2abqA 306 3.20e+01 102m 154 3.22e+01 1a6m a.1.1.2 15073 1qy5A 269 3.22e+01 d.122.1.1 96573 1en7A 157 3.24e+01 1en7A a.140.4.1,d.4.1.5 64733,64734 1kiyA 374 3.28e+01 a.128.1.5 72555 1fxxA 482 3.32e+01 1fxxA c.55.3.5 33726 1h1wA 289 3.32e+01 d.144.1.7 83460 1pah 308 3.33e+01 4pah d.178.1.1 42578 1k8kA 418 3.34e+01 c.55.1.1,c.55.1.1 68305,68306 2ae0X 345 3.35e+01 1u19A 349 3.38e+01 1wtyA 119 3.39e+01 2sniI 83 3.41e+01 2sniI d.40.1.1 38573 2scpA 174 3.41e+01 2scpA a.39.1.5 17256 1af7 274 3.41e+01 1af7 a.58.1.1,c.66.1.8 17928,34203 1rw6A 210 3.42e+01 a.47.4.1 105113 1bc5A 269 3.43e+01 1af7 a.58.1.1,c.66.1.8 17929,34204 1chuA 540 3.43e+01 1chuA a.7.3.1,c.3.1.4,d.168.1.1 16325,30424,42307 1j8uA 325 3.44e+01 d.178.1.1 71611 1chrA 370 3.45e+01 1mucA c.1.11.2,d.54.1.1 29252,38896 1dmwA 307 3.49e+01 4pah d.178.1.1 42580 1f16A 192 3.50e+01 1f16A f.1.4.1 43400 4pah 308 3.51e+01 4pah d.178.1.1 42576 1ciqA 40 3.51e+01 2sniI d.40.1.1 38576 1olsA 400 3.53e+01 c.36.1.11 93331 1f88A 348 3.56e+01 1f88A f.13.1.2 43429 1mtzA 293 3.61e+01 c.69.1.7 79467 1v4xA 144 3.61e+01 a.1.1.2 108363 1qddA 144 3.62e+01 1qddA d.169.1.1 42324 1e7lA 157 3.68e+01 1en7A a.140.4.1,d.4.1.5 64728,64729 1vpqA 273 3.68e+01 1na3A 91 3.69e+01 k.38.1.1 85481 1b3sD 90 3.76e+01 1ay7B c.9.1.1 30846 1y14A 187 3.76e+01 2bfdA 400 3.77e+01 1c9bA 207 3.88e+01 1tfb a.74.1.2,a.74.1.2 18372,18373 1wnfA 328 3.90e+01 1r0rI 51 3.97e+01 g.68.1.1 96736 1sgpI 51 3.97e+01 2ovo g.68.1.1 44678 1hzxA 349 3.98e+01 1f88A f.13.1.2 61466 1tufA 434 3.98e+01 b.49.2.3,c.1.6.1 107335,107336 1ab4 477 4.00e+01 1ab4 e.11.1.1 43251 1ofgA 381 4.00e+01 1ofgA c.2.1.3,d.81.1.5 30064,39979 1ovoA 56 4.03e+01 2ovo g.68.1.1 44697 2ovo 56 4.11e+01 2ovo g.68.1.1 44701 1aorA 605 4.12e+01 1b25A a.110.1.1,d.152.1.1 19042,41794 1l7vC 249 4.12e+01 c.37.1.12 73674 1uu3A 310 4.14e+01 d.144.1.7 99999 1h6dA 433 4.15e+01 c.2.1.3,d.81.1.5 65656,65657 1to2I 64 4.17e+01 1ay7B 89 4.19e+01 1ay7B c.9.1.1 30836 1coaI 64 4.21e+01 2sniI d.40.1.1 38574 1l9hA 349 4.22e+01 f.13.1.2 73720 1b3uA 588 4.22e+01 1b3uA a.118.1.2 19135 1vpmA 169 4.24e+01 3sgbI 56 4.27e+01 2ovo g.68.1.1 44679 1d3uB 201 4.36e+01 1aisB a.74.1.2,a.74.1.2 18386,18387 1csc 433 4.38e+01 1csh a.103.1.1 18886 1uz3A 102 4.42e+01 1ldfA 281 4.47e+01 f.19.1.1 73845 1q8dA 108 4.49e+01 a.228.1.1 104554 1rcsA 105 4.51e+01 1jhgA a.4.12.1 19025 2ex3B 264 4.52e+01 1or0A 160 4.68e+01 d.153.1.2 93445 1fm2A 169 4.71e+01 1fm2A d.153.1.2 59877 1q1aA 289 4.71e+01 c.31.1.5 95561 1mhyG 169 4.71e+01 1mtyG a.23.3.1 16518 1lit 144 4.72e+01 1qddA d.169.1.1 42325 1g6hA 257 4.75e+01 1gajA c.37.1.12 60318 1txgA 335 4.76e+01 1wkbA 810 4.80e+01 1f2eA 201 4.81e+01 1a0fA a.45.1.1,c.47.1.5 17745,33039 1itkA 731 4.83e+01 a.93.1.3,a.93.1.3 71417,71418 1vprA 374 4.85e+01 1isaA 192 4.87e+01 1avmA a.2.11.1,d.44.1.1 15731,38724 1wlsA 328 4.88e+01 1kshA 186 4.89e+01 c.37.1.8 72914 2c9lY 63 4.91e+01 1ft1A 377 4.92e+01 1ft1A a.118.6.1 19186 1cjbA 231 4.93e+01 1qk3A c.61.1.1 34079 1t98A 287 4.94e+01 1iscA 192 4.95e+01 1avmA a.2.11.1,d.44.1.1 15733,38726 1ihfB 94 4.97e+01 1huuA a.55.1.1 17894 1dwtA 153 4.99e+01 1a6m a.1.1.2 15190 1ypcI 64 5.01e+01 2sniI d.40.1.1 38570 1utuA 108 5.05e+01 1s5jA 847 5.06e+01 1qgrA 876 5.06e+01 1qgrA a.118.1.1 19119 1a19A 90 5.10e+01 1ay7B c.9.1.1 30831 1lkvX 232 5.17e+01 a.118.14.1 73980 1e8xA 961 5.18e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19148,23183,37631,41711 1gjnA 153 5.20e+01 a.1.1.2 70191 1yagA 375 5.26e+01 1yagA c.55.1.1,c.55.1.1 33449,33450 1x46A 150 5.30e+01 1wr8A 231 5.41e+01 1ca1 370 5.47e+01 1ca1 a.124.1.1,b.12.1.3 19340,23648 1gajA 257 5.57e+01 1gajA c.37.1.12 60416 1owfB 94 5.58e+01 a.55.1.1 87488 1ixxA 129 5.59e+01 1ixxB d.169.1.1 42335 1ajsA 412 5.61e+01 1ajsA c.67.1.1 34276 1hueA 90 5.62e+01 1huuA a.55.1.1 17900 1srvA 145 5.74e+01 1derA c.8.5.1 30817 1tvzA 388 5.75e+01 c.95.1.2,c.95.1.2 107367,107368 1v8cA 168 5.77e+01 d.15.3.1,d.129.5.1 100495,100496 1jdfA 447 5.78e+01 c.1.11.2,d.54.1.1 62897,62898 1d8dA 377 5.82e+01 1ft1A a.118.6.1 19185 1jfaA 374 5.88e+01 a.128.1.5 66622 1ew6A 137 5.89e+01 1ewaA a.1.1.2 15637 1ewaA 137 5.89e+01 1ewaA a.1.1.2 15639 1ew6B 137 5.91e+01 1ewaA a.1.1.2 15638 1twiA 434 5.97e+01 b.49.2.3,c.1.6.1 107399,107400 1rpa 342 5.98e+01 1cviA c.60.1.2 33983 1zowA 313 6.04e+01 1ki1B 352 6.10e+01 a.87.1.1,b.55.1.1 72497,72498 1gx3A 284 6.12e+01 d.3.1.5 70678 1v9dA 340 6.14e+01 a.207.1.1 100535 1q5yA 85 6.29e+01 d.58.18.4 95950 1gnwA 211 6.32e+01 1gnwA a.45.1.1,c.47.1.5 17727,33021 1xsm 390 6.35e+01 1xsm a.25.1.2 16804 1a2f 291 6.35e+01 1ryc a.93.1.1 18619 1ccg 291 6.36e+01 1ryc a.93.1.1 18627 1a2g 291 6.38e+01 1ryc a.93.1.1 18620 2fbmA 291 6.40e+01 1nuuA 252 6.50e+01 c.26.1.3 86209 1pzgA 331 6.50e+01 c.2.1.5,d.162.1.1 95425,95426 1w68A 390 6.53e+01 a.25.1.2 109216 2b8wA 328 6.55e+01 1d4xA 375 6.60e+01 1yagA c.55.1.1,c.55.1.1 59107,59108 1lw6I 64 6.61e+01 d.40.1.1 74294 2a2dA 478 6.65e+01 1jdrA 294 6.72e+01 1ryc a.93.1.1 62908 2eboA 74 6.73e+01 2eboA h.3.2.1 45754 1tdzA 272 6.74e+01 a.156.1.2,b.113.1.1,g.39.1.8 106787,106788,106789 1vz6A 393 6.77e+01 d.154.1.2 108949 1buoA 121 6.83e+01 1buoA d.42.1.1 38631 1ds4A 292 6.84e+01 1ryc a.93.1.1 59129 1ryc 294 6.84e+01 1ryc a.93.1.1 18601 1xk4A 93 6.85e+01 1qh8B 519 6.85e+01 1qguB c.92.2.3 35634 1nnjA 271 6.85e+01 a.156.1.2,b.113.1.1,g.39.1.8 80669,80670,80671 1dgaA 375 6.87e+01 1yagA 1qguB 519 6.88e+01 1qguB c.92.2.3 35626 1nwzA 125 6.88e+01 d.110.3.1 86370 3pyp 125 6.88e+01 3pyp d.110.3.1 40897 1pii 452 6.91e+01 1pii c.1.2.4,c.1.2.4 28559,28563 1qz5A 375 6.93e+01 c.55.1.1,c.55.1.1 96614,96615 1j6zA 376 6.94e+01 1yagA c.55.1.1,c.55.1.1 62667,62668 1ac4 294 6.97e+01 1ryc a.93.1.1 18657 1zs9A 261 7.03e+01 2a2cA 478 7.11e+01 1rsoB 56 7.12e+01 a.194.1.1 97812 1dseA 292 7.13e+01 1ryc a.93.1.1 59130 1xo1A 291 7.14e+01 1exnA a.60.7.1,c.120.1.2 18086,33356 1tia 279 7.17e+01 3tgl c.69.1.17 34737 1iseA 185 7.19e+01 d.67.3.1 90691 1jcrA 377 7.25e+01 a.118.6.1 66506 2cyp 294 7.25e+01 1ryc a.93.1.1 18600 2ifo 46 7.27e+01 2ifo h.1.4.1 45567 2d09A 407 7.29e+01 1atnA 373 7.33e+01 1yagA c.55.1.1,c.55.1.1 33437,33438 1jcqA 382 7.45e+01 a.118.6.1 66504 1wwpA 119 7.54e+01 1wuaA 375 7.54e+01 1kktA 511 7.54e+01 a.102.2.1 68687 1asyA 490 7.56e+01 1b8aA b.40.4.1,d.104.1.1 25242,40763 1ua4A 455 7.57e+01 c.72.1.3 99128 1f15B 218 7.61e+01 1f15B b.121.4.5 23321 1ld8A 382 7.63e+01 a.118.6.1 73838 1pjjA 271 7.71e+01 a.156.1.2,b.113.1.1,g.39.1.8 104164,104165,104166 1guxB 152 7.72e+01 1guxB a.74.1.3 18389 1aszB 490 7.73e+01 1b8aA b.40.4.1,d.104.1.1 25241,40762 1twfB 1224 7.80e+01 1fumC 130 7.84e+01 1fumC 1y9aA 360 7.86e+01 2es9A 115 7.89e+01 1vin 268 7.93e+01 1vin a.74.1.1,a.74.1.1 18354,18355 1o89A 345 7.98e+01 b.35.1.2,c.2.1.1 92644,92645 1uv0A 149 8.00e+01 d.169.1.1 100028 1lk9A 448 8.06e+01 c.67.1.1 78057 1fchA 368 8.07e+01 1fchA a.118.8.1 19212 1nm2A 317 8.11e+01 c.19.1.1,d.58.23.1 80654,80655 1b6q 63 8.14e+01 1nkd a.30.1.1 16977 2eutA 294 8.17e+01 1aisB 200 8.33e+01 1aisB a.74.1.2,a.74.1.2 18384,18385 5abp 306 8.39e+01 8abp c.93.1.1 35651 1idsA 207 8.39e+01 1avmA a.2.11.1,d.44.1.1 15722,38730 1jfiA 98 8.42e+01 1jfiA a.22.1.3 62936 1av8A 340 8.44e+01 1xikA a.25.1.2 16796 1z53A 294 8.47e+01 1zbyA 294 8.48e+01 2fxuA 375 8.50e+01 1bh9A 45 8.57e+01 1bh9A a.22.1.3 16483 1as0 353 8.62e+01 1cipA a.66.1.1,c.37.1.8 18212,32095 1e7uA 961 8.62e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 8abp 306 8.69e+01 8abp c.93.1.1 35647 1colA 204 8.73e+01 1a87 f.1.1.1 43378 1jy5A 212 8.77e+01 d.124.1.1 71940 1zavA 180 8.80e+01 1abe 306 8.82e+01 8abp c.93.1.1 35648 1tn6A 382 8.97e+01 1bap 306 8.99e+01 8abp c.93.1.1 35654 1cseI 71 8.99e+01 1egpA d.40.1.1 38559