# List of top-scoring protein chains for t2k-100-30-bys 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 7.66e-03 2dpmA c.66.1.28 34246 1e0tA 470 7.78e-02 1a49A b.58.1.1 27064 c.1.12.1 29292 c.49.1.1 33146 1uheA 97 1.30e-01 1o9yA 84 1.66e-01 unknown_sccs -4105 1aonO 97 2.09e-01 b.35.1.1 24642 1jnyA 435 2.57e-01 b.43.3.1 66982 b.44.1.1 66983 c.37.1.8 66984 1d2eA 397 2.70e-01 1efcA b.43.3.1 25701 b.44.1.1 25741 c.37.1.8 32136 1liuA 528 2.97e-01 b.58.1.1 77970 c.1.12.1 77971 c.49.1.1 77972 1q16A 1247 3.77e-01 b.52.2.2 -4337 c.81.1.1 -8547 1a49A 530 3.81e-01 1a49A b.58.1.1 27026 c.1.12.1 29255 c.49.1.1 33109 1uxxX 133 4.40e-01 b.18.1.10 -3107 1q1gA 276 7.14e-01 c.56.2.1 -7846 1p1cA 199 7.23e-01 c.66.1.16 87669 1ksfX 758 7.29e-01 a.174.1.1 77522 c.37.1.20 77523 c.37.1.20 77524 1r6xA 395 7.65e-01 b.122.1.3 -5125 c.26.1.5 -6620 1ndh 272 8.44e-01 1ndh b.43.4.2 25662 c.25.1.1 31552 1gmmA 133 9.28e-01 b.18.1.10 65314 1oruA 195 9.36e-01 unknown_sccs -4390 1khhA 198 9.71e-01 c.66.1.16 68615 1qf9A 194 1.06e+00 1zin c.37.1.1 31848 1o5uA 101 1.06e+00 b.82.1.8 -4845 5ukdA 194 1.12e+00 1zin c.37.1.1 31851 2plc 274 1.33e+00 2plc c.1.18.2 29614 1mxiA 160 1.34e+00 c.116.1.1 79646 4uagA 437 1.39e+00 4uagA c.5.1.1 30651 c.59.1.1 33952 c.72.2.1 34955 1i7pA 274 1.48e+00 b.43.4.2 66048 c.25.1.1 66049 1iz6A 138 1.58e+00 b.34.5.2 76976 b.40.4.5 76977 1dmr 823 1.60e+00 1dmr b.52.2.2 26904 c.81.1.1 35312 1uag 437 1.82e+00 4uagA c.5.1.1 30653 c.59.1.1 33954 c.72.2.1 34957 1g8fA 511 1.91e+00 1g8fA b.122.1.3 60348 c.26.1.5 60349 c.37.1.15 60350 1unkA 87 1.91e+00 1cei a.28.2.1 16935 1bg6 359 1.91e+00 1bg6 a.100.1.5 18810 c.2.1.6 30214 1eu1A 780 2.04e+00 1dmr b.52.2.2 26903 c.81.1.1 35311 1pkn 530 2.14e+00 1a49A b.58.1.1 27042 c.1.12.1 29271 c.49.1.1 33125 1qzzA 374 2.15e+00 a.4.5.29 -277 c.66.1.12 -8045 1cei 94 2.24e+00 1cei a.28.2.1 16939 2napA 723 2.25e+00 2napA b.52.2.2 26926 c.81.1.1 35334 1cb0A 283 2.52e+00 1cb0A c.56.2.1 33790 1kypA 237 2.56e+00 d.22.1.1 73280 1fjgD 209 2.58e+00 1c05A d.66.1.2 39553 1aqjA 421 2.65e+00 2admA c.66.1.27 34242 1ky9B 448 2.76e+00 b.36.1.4 73200 b.36.1.4 73201 b.47.1.1 73202 1odkA 235 2.92e+00 c.56.2.1 86863 1h40A 71 2.98e+00 1i18A 97 2.99e+00 b.43.4.3 61520 1f60A 458 3.01e+00 1efcA b.43.3.1 25705 b.44.1.1 25745 c.37.1.8 32140 1uzcA 71 3.02e+00 a.159.2.1 -339 3uagA 437 3.08e+00 4uagA c.5.1.1 30652 c.59.1.1 33953 c.72.2.1 34956 1khiA 176 3.32e+00 b.34.5.2 77408 b.40.4.5 77409 1ema 236 3.36e+00 1ema d.22.1.1 38339 1qcsA 211 3.38e+00 1qcsA b.52.2.3 26927 d.31.1.1 38461 1ir3A 306 3.43e+00 1fmk d.144.1.7 41702 1cl2A 395 3.60e+00 1cl2A c.67.1.3 34397 1cl1A 395 3.61e+00 1cl2A c.67.1.3 34395 1h0hA 977 3.67e+00 b.52.2.2 76435 c.81.1.1 76436 4ubpC 570 3.69e+00 1ubpC b.92.1.1 28431 c.1.9.2 29053 2cbp 96 3.74e+00 2cbp b.6.1.1 22895 1gkpA 458 3.82e+00 b.92.1.3 70231 c.1.9.6 70232 1ie7C 570 3.83e+00 1ubpC b.92.1.1 62315 c.1.9.2 62316 1r61A 207 3.89e+00 unknown_sccs -6086 1ltlA 279 4.13e+00 b.40.4.11 84701 1tmy 120 4.26e+00 1dbwA c.23.1.1 31083 1rlkA 117 4.32e+00 unknown_sccs -7526 1g38A 393 4.33e+00 2admA c.66.1.27 60235 1o7iA 119 4.45e+00 b.40.4.3 86642 1g8jA 825 4.56e+00 1g8jA b.52.2.2 26924 c.81.1.1 35332 1czfA 362 4.67e+00 1czfA b.80.1.3 28031 1kzlA 208 4.72e+00 b.43.4.3 77635 b.43.4.3 77636 1lcyA 325 4.73e+00 b.36.1.4 73834 b.47.1.1 73835 1fa4A 105 4.75e+00 1plc b.6.1.1 22867 1ubpC 570 4.80e+00 1ubpC b.92.1.1 28432 c.1.9.2 29054 1bqk 124 4.88e+00 1bqk b.6.1.1 22889 1a8vA 121 5.31e+00 1a62 a.140.3.1 64712 b.40.4.5 64713 1kqfA 1015 5.64e+00 b.52.2.2 72871 c.81.1.1 72872 1oxdA 227 5.73e+00 d.22.1.1 -9438 1epwA 1290 5.92e+00 b.29.1.6 24269 b.42.4.2 25614 d.92.1.7 40305 h.4.2.1 45785 1izcA 339 6.00e+00 c.1.12.5 83838 1l5wA 796 6.03e+00 c.87.1.4 73605 1paz 123 6.03e+00 1bqk b.6.1.1 22878 1oc2A 348 6.09e+00 c.2.1.2 -5753 1v74A 107 6.30e+00 unknown_sccs -9319 3ullA 132 6.56e+00 3ullA b.40.4.3 25282 1gl4B 98 6.73e+00 b.1.1.4 65288 1p9kA 79 6.76e+00 unknown_sccs -10238 1aac 105 7.14e+00 1aac b.6.1.1 22838 1i8dA 213 7.28e+00 b.43.4.3 61953 b.43.4.3 61954 1bxsA 501 7.41e+00 1bpwA c.82.1.1 35357 1r13A 148 7.56e+00 d.169.1.1 -11646 h.1.1.1 -12895 1oniA 137 7.57e+00 d.79.1.1 87144 1qwlA 505 7.70e+00 e.5.1.1 -11823 1enfA 212 7.76e+00 3seb b.40.2.2 25198 d.15.6.1 37787 1uok 558 7.80e+00 1uok b.71.1.1 27801 c.1.8.1 28788 1uhnA 189 7.87e+00 a.39.1.5 -853 1irk 306 8.01e+00 1fmk d.144.1.7 41703 1ky9A 448 8.55e+00 b.36.1.4 73198 b.47.1.1 73199 1g8kA 825 8.55e+00 1g8jA b.52.2.2 26920 c.81.1.1 35328 1m5yA 408 8.60e+00 a.167.1.1 78664 d.26.1.1 78665 d.26.1.1 78666 2eifA 136 8.69e+00 1bkb b.34.5.2 24607 b.40.4.5 25339 1kepA 348 8.71e+00 c.2.1.2 68536 1nhcA 336 8.82e+00 b.80.1.3 -4768 1as4B 37 8.84e+00 1as4B 1ixkA 315 9.07e+00 unknown_sccs -8099 1jg1A 235 9.20e+00 c.66.1.7 66661 1b8qA 127 9.37e+00 1qauA b.36.1.1 24781 1mg4A 113 9.42e+00 d.15.11.1 84953 1jqbA 351 9.43e+00 b.35.1.2 77151 c.2.1.1 77152 1gz8A 299 9.60e+00 d.144.1.7 83405 2admA 421 9.65e+00 2admA c.66.1.27 34238 1kevA 351 9.68e+00 1pedA b.35.1.2 24749 c.2.1.1 29765 1gc0A 398 9.70e+00 c.67.1.3 70168 1c0aA 585 9.72e+00 1c0aA b.40.4.1 25246 d.74.4.1 39731 d.104.1.1 40767 1aw8E 91 9.96e+00 1aw8B 1aw8B 91 9.97e+00 1aw8B 1bxaA 105 9.98e+00 1aac b.6.1.1 22839 1lylA 504 1.01e+01 1lylA b.40.4.1 25261 d.104.1.1 40717 1ct5A 256 1.02e+01 1ct5A c.1.6.2 28663 1hcl 298 1.02e+01 1hcl d.144.1.7 41593 1k0hA 117 1.02e+01 b.106.1.2 71975 1te5A 257 1.09e+01 1aaj 105 1.11e+01 1aac b.6.1.1 22841 1ghtA 105 1.11e+01 2rslA c.53.1.1 60526 1e1xA 299 1.21e+01 1hcl d.144.1.7 59157 1i1nA 226 1.26e+01 c.66.1.7 71102 1qexA 288 1.30e+01 1qexA b.32.1.1 24425 1sb8A 352 1.32e+01 1jraA 117 1.34e+01 a.24.15.1 67117 2arcB 164 1.34e+01 2arcA b.82.4.1 28149 1htrP 43 1.34e+01 1htrP b.50.1.2 26852 1jr8A 117 1.36e+01 a.24.15.1 67115 1ejxC 567 1.37e+01 b.92.1.1 83184 c.1.9.2 83185 1ha3A 405 1.37e+01 1efcA b.43.3.1 60869 b.44.1.1 60870 c.37.1.8 60871 1v5lA 103 1.38e+01 1fwcC 567 1.38e+01 1ubpC b.92.1.1 28410 c.1.9.2 29032 1ejrC 567 1.39e+01 1ubpC b.92.1.1 28420 c.1.9.2 29042 1g8iA 190 1.46e+01 1rec a.39.1.5 60363 1vj0A 380 1.46e+01 b.35.1.2 -3697 c.2.1.1 -5721 1e1oA 504 1.49e+01 1lylA b.40.4.1 25258 d.104.1.1 40714 1agjA 242 1.50e+01 1agjA b.47.1.1 25827 1g4fA 86 1.51e+01 1qubA g.18.1.1 44873 1jvpP 298 1.52e+01 d.144.1.7 67371 1pt1A 143 1.53e+01 b.52.2.1 -4322 2rslA 140 1.53e+01 2rslA c.53.1.1 33345 1qisA 396 1.53e+01 1ajsA c.67.1.1 34284 1hh2P 344 1.56e+01 b.40.4.5 65835 d.52.3.1 65836 d.52.3.1 65837 d.202.1.1 65838 1ars 396 1.59e+01 1ajsA c.67.1.1 34287 1ahxA 396 1.60e+01 1ajsA c.67.1.1 34293 1pedA 351 1.60e+01 1pedA b.35.1.2 24753 c.2.1.1 29769 1kr5A 226 1.63e+01 c.66.1.7 68847 1em8B 112 1.65e+01 unknown_sccs -6364 1f8aB 167 1.66e+01 1pinA b.72.1.1 27803 d.26.1.1 38432 1sjwA 144 1.68e+01 unknown_sccs -9296 1b54 257 1.68e+01 1ct5A c.1.6.2 28664 1exmA 405 1.71e+01 1efcA b.43.3.1 25696 b.44.1.1 25736 c.37.1.8 32131 1e79A 510 1.72e+01 1skyB a.69.1.1 18269 b.49.1.1 26434 c.37.1.11 32314 1jh2A 99 1.75e+01 2aacA 177 1.79e+01 2arcA b.82.4.1 28150 1t9kA 347 1.80e+01 1lzjA 292 1.82e+01 c.68.1.9 74352 1qu9A 128 1.83e+01 1qu9A d.79.1.1 39755 1qu9C 128 1.83e+01 1qu9A d.79.1.1 39757 1gdtA 183 1.83e+01 2rslA a.4.1.2 16021 c.53.1.1 33348 1se8A 301 1.85e+01 1pmy 123 1.86e+01 1bqk b.6.1.1 22888 1oohA 126 1.88e+01 a.39.2.1 -884 1pinA 163 1.89e+01 1pinA b.72.1.1 27802 d.26.1.1 38431 1h9sA 140 1.89e+01 1b9mA b.40.6.2 60843 b.40.6.2 60844 1spa 396 1.89e+01 1ajsA c.67.1.1 34291 1h8eA 510 1.92e+01 1skyB a.69.1.1 60738 b.49.1.1 60739 c.37.1.11 60740 1eljA 381 1.93e+01 4mbp c.94.1.1 35791 1cc3A 130 1.94e+01 1nwpA b.6.1.1 23008 1cbf 285 1.96e+01 1cbf c.90.1.1 35587 1a63 130 2.07e+01 1a62 a.140.3.1 64710 b.40.4.5 64711 1q3oA 109 2.14e+01 b.36.1.1 -3776 1jbaA 204 2.14e+01 1rec a.39.1.5 17330 1s6cA 183 2.20e+01 a.39.1.5 -858 1h6rA 236 2.22e+01 d.22.1.1 65683 1cz4A 185 2.23e+01 1cz4A b.52.2.3 26934 d.31.1.1 38468 1eo1A 124 2.24e+01 1eo1A c.55.5.1 33739 1k3bB 164 2.30e+01 d.3.1.1 72015 1kamA 194 2.36e+01 c.26.1.3 72254 1nffA 260 2.37e+01 c.2.1.2 80457 1eg3A 261 2.37e+01 1eg3A a.39.1.7 17376 a.39.1.7 17377 b.72.1.1 27805 1a62 130 2.38e+01 1a62 a.140.3.1 64708 b.40.4.5 64709 1o1fC 147 2.39e+01 i.15.1.1 80997 1oh0A 131 2.43e+01 d.17.4.3 87004 1rxyA 253 2.46e+01 c.56.2.1 -7834 1e32A 458 2.49e+01 1e32A b.52.2.3 59183 c.37.1.20 59184 d.31.1.1 59185 1o1zA 234 2.56e+01 c.1.18.3 86555 1jer 138 2.56e+01 2cbp b.6.1.1 23022 1o54A 277 2.60e+01 c.66.1.13 -8095 1bax 94 2.61e+01 1bax a.61.1.3 18133 1bfd 528 2.62e+01 1bfd c.31.1.3 31745 c.36.1.5 31801 c.36.1.9 31802 1k66A 149 2.64e+01 c.23.1.1 -6406 1csgA 127 2.65e+01 2gmfA a.26.1.2 16851 1ctj 89 2.66e+01 1ctj a.3.1.1 15798 1zin 217 2.67e+01 1zin c.37.1.1 31915 g.41.2.1 45178 2arcA 164 2.68e+01 2arcA b.82.4.1 28148 1mw7A 240 2.69e+01 e.39.1.1 79557 1ahpA 797 2.70e+01 1a8i c.87.1.4 35544 1art 396 2.71e+01 1ajsA c.67.1.1 34285 1mjc 69 2.73e+01 1mjc b.40.4.5 25319 1krhA 338 2.75e+01 b.43.4.2 72891 c.25.1.2 72892 d.15.4.2 72893 1a9xA 1058 2.76e+01 a.92.1.1 18550 c.24.1.1 31479 c.30.1.1 31657 c.30.1.1 31658 d.142.1.2 41502 d.142.1.2 41503 1qauA 112 2.76e+01 1qauA b.36.1.1 24779 1ewcA 214 2.79e+01 3seb b.40.2.2 25199 d.15.6.1 37788 2gmfA 127 2.79e+01 2gmfA a.26.1.2 16849 1ezjA 115 2.83e+01 1ezjA h.1.14.1 45638 1dyr 206 2.85e+01 1aoeA c.71.1.1 34916 1led 243 2.88e+01 1led b.29.1.1 24039 1cof 143 2.91e+01 1cof d.109.1.2 40860 1qavB 115 2.92e+01 1qauA b.36.1.1 24780 1p4uA 153 2.93e+01 b.1.10.2 87780 1ja9A 274 2.96e+01 c.2.1.2 62817 1hkhA 279 2.98e+01 c.69.1.12 -8342 1semA 58 3.01e+01 1ckaA b.34.2.1 24544 2cbf 234 3.02e+01 1cbf c.90.1.1 35588 1aipE 405 3.02e+01 1efcA b.43.3.1 25699 b.44.1.1 25739 c.37.1.8 32134 1ly2A 130 3.04e+01 g.18.1.1 74335 g.18.1.1 74336 1bxvA 91 3.07e+01 1aac b.6.1.1 22875 1o0yA 260 3.08e+01 c.1.10.1 80756 1br2A 791 3.13e+01 1lvk b.34.3.1 24558 c.37.1.9 32155 1iz0A 302 3.13e+01 b.35.1.2 83821 c.2.1.1 83822 1bkb 136 3.14e+01 1bkb b.34.5.2 24609 b.40.4.5 25341 1t95A 240 3.15e+01 1kte 105 3.16e+01 1kte c.47.1.1 32771 1a8q 274 3.24e+01 1brt c.69.1.12 34702 1nykA 165 3.25e+01 b.33.1.1 86408 1lkoA 191 3.25e+01 a.25.1.1 78063 g.41.5.1 78064 1ux5A 411 3.26e+01 unknown_sccs -1768 1s6bA 119 3.26e+01 a.133.1.2 -1953 1lx7A 253 3.30e+01 c.56.2.1 74329 1k8rB 110 3.32e+01 d.15.1.5 72180 1c0dA 358 3.34e+01 1eceA c.1.8.3 28815 1pqhA 143 3.36e+01 b.52.2.1 -4318 1ek9A 428 3.39e+01 1ek9A f.5.1.1 43809 1rl6A 177 3.41e+01 1rl6A d.141.1.1 41473 d.141.1.1 41474 1q0sA 259 3.44e+01 c.66.1.28 -8110 1ffkJ 164 3.44e+01 1ffkJ c.12.1.1 30880 1ckaA 57 3.45e+01 1ckaA b.34.2.1 24459 1jqhA 308 3.47e+01 d.144.1.7 71793 1aps 98 3.53e+01 2acy d.58.10.1 39299 1e4fT 419 3.56e+01 1e4fT c.55.1.1 33453 c.55.1.1 33454 1o13A 136 3.58e+01 c.55.5.1 80762 1svb 395 3.61e+01 1svb b.1.18.4 21814 f.10.1.1 43827 1cq3A 233 3.61e+01 1cq3A b.27.1.1 23923 1bb9 115 3.61e+01 1bb9 b.34.2.1 24554 1a81A 254 3.61e+01 1a81A d.93.1.1 40507 d.93.1.1 40508 1fcdA 401 3.62e+01 1fcdA c.3.1.5 30593 c.3.1.5 30594 d.87.1.1 40218 1o5zA 442 3.64e+01 c.59.1.2 -7939 c.72.2.2 -8418 1i9gA 280 3.64e+01 c.66.1.13 62090 1ujxA 119 3.64e+01 b.26.1.2 -3325 2vik 126 3.68e+01 2vil d.109.1.1 40829 1ixlA 131 3.72e+01 d.38.1.5 -9705 1bxrA 1073 3.75e+01 a.92.1.1 18570 c.24.1.1 31499 c.30.1.1 31697 c.30.1.1 31698 d.142.1.2 41542 d.142.1.2 41543 1lcjA 109 3.76e+01 1qadA d.93.1.1 40414 1aj8A 371 3.77e+01 1aj8A a.103.1.1 18900 1q7lB 88 3.78e+01 1jsmA 325 3.81e+01 b.19.1.2 63264 1r9hA 135 3.82e+01 d.26.1.1 -9482 1o6aA 96 3.88e+01 unknown_sccs -4101 1f6fB 210 3.88e+01 1axiB b.1.2.1 22033 b.1.2.1 22034 1ybvA 283 3.89e+01 1ybvA c.2.1.2 29948 1dk8A 147 3.92e+01 1agrE a.91.1.1 18548 1c3oA 1073 3.94e+01 1c3oA a.92.1.1 18562 c.24.1.1 31491 c.30.1.1 31681 c.30.1.1 31682 d.142.1.2 41526 d.142.1.2 41527 1bjt 793 3.96e+01 1bjt e.11.1.1 43249