# List of top-scoring protein chains for t2k-100-30-o_notor2-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 2fneA 117 2.95e-11 2fe5A 94 1.02e-10 1tp5A 119 2.05e-10 1be9A 119 2.08e-10 1pdr b.36.1.1 24774 2fcfA 103 2.98e-10 1bfeA 119 3.53e-10 1pdr b.36.1.1 24775 1g9oA 91 5.59e-10 1pdr b.36.1.1 60400 1pdr 99 6.68e-10 1pdr b.36.1.1 24771 1i92A 91 6.94e-10 1pdr b.36.1.1 61990 1qavA 90 1.13e-09 1qauA b.36.1.1 24777 1q3oA 109 1.66e-09 b.36.1.1 95700 1n7eA 97 1.82e-09 b.36.1.1 91691 1n7fA 97 2.40e-09 b.36.1.1 91692 1ihjA 98 4.91e-09 1pdr b.36.1.1 62382 2h2bA 107 6.67e-09 1l6oA 95 1.41e-08 b.36.1.1 84534 1qavB 115 1.68e-08 1qauA b.36.1.1 24780 1qauA 112 1.74e-08 1qauA b.36.1.1 24779 2f0aA 98 2.01e-08 1wf7A 103 2.47e-08 1nf3C 128 2.53e-08 b.36.1.1 85596 2h3lA 103 2.57e-08 1kwaA 88 2.63e-08 1kwaA b.36.1.1 24772 1mfgA 95 3.09e-08 b.36.1.1 79043 1n99A 166 5.19e-08 b.36.1.1,b.36.1.1 85459,85460 1v5lA 103 7.51e-08 b.36.1.1 108378 1kwaB 88 9.98e-08 1kwaA b.36.1.1 24773 1b8qA 127 1.17e-07 1qauA b.36.1.1 24781 2f5yA 91 1.79e-07 1i16 130 2.95e-07 1i16 b.36.1.2 24787 1m5zA 91 7.22e-07 b.36.1.1 78676 1r6jA 82 3.90e-06 b.36.1.1 97151 1nteA 82 4.66e-06 b.36.1.1 86163 1fc6A 388 1.01e-05 1fc6A b.36.1.3,c.14.1.2 64738,64739 1lcyA 325 2.69e-04 b.36.1.4,b.47.1.1 73834,73835 1te0A 318 1.13e-03 1ky9B 448 1.43e-02 b.36.1.4,b.36.1.4,b.47.1.1 73200,73201,73202 1y8tA 324 1.55e-02 1sotA 320 1.63e-02 b.36.1.4,b.47.1.1 105852,105853 1ky9A 448 3.17e-02 b.36.1.4,b.47.1.1 73198,73199 1gph1 465 2.13e-01 1ecfB 1ao0A 459 2.87e-01 1ecfB c.61.1.1,d.153.1.1 34049,41816 1zn8A 180 4.02e-01 1vqqA 646 1.26e+00 1t3qB 788 3.20e+00 d.41.1.1,d.133.1.1 106369,106370 2bh8A 101 3.38e+00 1mwsA 646 3.76e+00 d.17.4.5,d.175.1.1,e.3.1.1 79592,79593,79594 1g7tA 594 3.79e+00 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25714,25715,31033,32148 1ecfA 504 3.82e+00 1ecfB c.61.1.1,d.153.1.1 34053,41820 1g7sA 594 3.86e+00 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 1db3A 372 4.16e+00 1db3A c.2.1.2 29813 1w78A 422 4.74e+00 1g7rA 594 4.84e+00 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25716,25717,31034,32149 1fm0E 150 5.13e+00 1fmaE d.41.5.1 38629 1fmaE 150 5.18e+00 1fmaE d.41.5.1 38630 1mwrA 646 5.45e+00 d.17.4.5,d.175.1.1,e.3.1.1 79586,79587,79588 1ecfB 504 5.55e+00 1ecfB c.61.1.1,d.153.1.1 34054,41821 1qb7A 236 5.64e+00 1qb7A c.61.1.1 34087 1a8l 226 5.75e+00 1a8l c.47.1.2,c.47.1.2 32777,32778 1yg9A 330 5.79e+00 1bx4A 345 5.99e+00 1bx4A c.72.1.1 34935 1y0bA 197 6.04e+00 1aiqA 264 7.33e+00 1bkpA d.117.1.1 40967 1tys 265 7.98e+00 1bkpA d.117.1.1 40937 2g8oA 264 8.06e+00 1xx6A 191 8.07e+00 1axwA 265 8.35e+00 1bkpA d.117.1.1 40938 2g8mA 264 8.64e+00 1r13A 148 8.69e+00 d.169.1.1,h.1.1.1 96782,96783 1l1qA 186 9.58e+00 c.61.1.1 77653 1jnyA 435 1.06e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1n0qA 93 1.09e+01 k.37.1.1 79754 1kw4A 89 1.13e+01 a.60.1.2 73077 1z3eA 132 1.15e+01 1reqD 637 1.17e+01 1reqB c.1.19.1,c.23.6.1 29623,31250 1xtmA 175 1.23e+01 1uc2A 481 1.25e+01 d.261.1.1 99161 1bu6O 501 1.31e+01 1glcG c.55.1.4,c.55.1.4 33499,33500 2tscA 264 1.32e+01 1bkpA d.117.1.1 40952 1p99A 295 1.33e+01 c.94.1.1 94384 1qqqA 264 1.33e+01 1bkpA d.117.1.1 40931 1wrvA 308 1.35e+01 1t6t1 118 1.35e+01 1evfA 264 1.36e+01 1bkpA d.117.1.1 40932 2f51A 118 1.38e+01 1ojhA 65 1.39e+01 a.214.1.1 103976 2d4pA 141 1.43e+01 1reqB 637 1.45e+01 1reqB c.1.19.1,c.23.6.1 29621,31248 2f23A 156 1.46e+01 1j08A 226 1.50e+01 c.47.1.2,c.47.1.2 83855,83856 7reqB 637 1.53e+01 1reqB c.1.19.1,c.23.6.1 29617,31244 1x3mA 415 1.53e+01 1eb0A 147 1.53e+01 b.107.1.1,d.58.38.1 64890,64891 1mjc 69 1.54e+01 1mjc b.40.4.5 25319 1earA 147 1.55e+01 b.107.1.1,d.58.38.1 64875,64876 2gwnA 452 1.56e+01 1vlbA 907 1.59e+01 a.56.1.1,d.15.4.2,d.41.1.1,d.133.1.1 108739,108740,108741,108742 1hlrA 907 1.59e+01 1tsm 316 1.60e+01 1bkpA d.117.1.1 41024 1b6cB 342 1.61e+01 1b6cB d.144.1.7 41673 1r62A 160 1.63e+01 d.122.1.3 104816 1gky 187 1.67e+01 1gky c.37.1.1 31839 1uh5A 329 1.70e+01 c.2.1.2 107840 1mkmA 249 1.73e+01 a.4.5.33,d.110.2.2 79242,79243 2cc0A 195 1.73e+01 2h03A 291 1.79e+01 1xtlA 175 1.84e+01 1n6aA 259 1.85e+01 b.76.2.1,b.85.7.1 80121,80122 1ex7A 186 1.85e+01 1gky c.37.1.1 59537 1q0sA 259 1.93e+01 c.66.1.28 95509 1rl2A 137 2.00e+01 1rl2A b.34.5.3,b.40.4.5 24610,25342 1o5oA 221 2.03e+01 c.61.1.1 92509 1sw5A 275 2.03e+01 c.94.1.1 106069 2hc1A 291 2.05e+01 1dpuA 99 2.07e+01 1dpuA a.4.5.16 16150 1avaC 181 2.08e+01 1avaC b.42.4.1 25604 1mjhB 162 2.09e+01 1mjhA c.26.2.4 31640 1koe 172 2.10e+01 1koe d.169.1.5 42448 1cliA 345 2.12e+01 1cliA d.79.4.1,d.139.1.1 39816,41459 2fojA 155 2.14e+01 1s50A 259 2.14e+01 1mjhA 162 2.15e+01 1mjhA c.26.2.4 31639 1coaI 64 2.15e+01 2sniI d.40.1.1 38574 1s4iA 175 2.16e+01 1a62 130 2.16e+01 1a62 a.140.3.1,b.40.4.5 64708,64709 1fxrA 64 2.17e+01 1fxd d.58.1.4 38993 1fdr 248 2.24e+01 1fdr b.43.4.2,c.25.1.1 25653,31543 1zsyA 357 2.24e+01 1ti6A 875 2.26e+01 b.52.2.2,c.81.1.1 106974,106975 1iz0A 302 2.33e+01 b.35.1.2,c.2.1.1 83821,83822 1yf3A 259 2.40e+01 1eno 312 2.42e+01 1enp c.2.1.2 29905 1ad3A 452 2.42e+01 1ad3A c.82.1.1 35335 1a63 130 2.46e+01 1a62 a.140.3.1,b.40.4.5 64710,64711 1dfd 64 2.47e+01 1fxd d.58.1.4 38995 1zhvA 134 2.49e+01 1mqdA 261 2.54e+01 c.94.1.1 85049 1mqiA 263 2.60e+01 c.94.1.1 91398 1sqhA 312 2.60e+01 d.108.1.5 98966 1un8A 552 2.60e+01 c.119.1.2,a.208.1.1 103806,99661 1m5dA 263 2.62e+01 c.94.1.1 78641 1yy6A 155 2.63e+01 1m5eA 263 2.66e+01 c.94.1.1 78642 1jhfA 202 2.67e+01 a.4.5.2,b.87.1.1 63057,63058 1rd5A 262 2.69e+01 1dax 64 2.71e+01 1fxd d.58.1.4 38996 1xdnA 277 2.73e+01 1z7gA 217 2.74e+01 1hvyA 288 2.78e+01 1bkpA d.117.1.1 41049 1epwA 1290 2.79e+01 b.29.1.6,b.42.4.2,d.92.1.7,h.4.2.1 24269,25614,40305,45785 1d1nA 99 2.86e+01 1d1nA b.43.3.1 25718 2f69A 261 2.93e+01 1to2I 64 2.93e+01 1u9yA 284 3.01e+01 1enp 312 3.07e+01 1enp c.2.1.2 29906 1xmrA 243 3.10e+01 1ciqA 40 3.16e+01 2sniI d.40.1.1 38576 1z5nA 242 3.16e+01 1rutX 188 3.22e+01 1d7oA 297 3.22e+01 1enp c.2.1.2 29907 1h3gA 601 3.25e+01 b.1.18.2,b.71.1.1,c.1.8.1 90594,90595,90596 1yjmA 110 3.34e+01 2b4aA 138 3.37e+01 1gjjA 168 3.40e+01 a.140.1.1,a.140.1.1 83291,83292 1wywA 230 3.46e+01 1rxdA 159 3.47e+01 1lw6I 64 3.54e+01 d.40.1.1 74294 1vpqA 273 3.54e+01 1sknP 92 3.55e+01 1sknP a.37.1.1 17127 1o6uA 403 3.55e+01 a.5.3.1,b.132.1.1,c.13.1.1 92589,92590,92591 1x6vA 630 3.61e+01 1olmA 403 3.62e+01 a.5.3.1,b.132.1.1,c.13.1.1 104008,104009,104010 1ex2A 189 3.62e+01 1ex2A c.51.4.2 33225 1z8gA 372 3.63e+01 1cis 66 3.64e+01 2sniI k.1.1.1 46375 1x24A 180 3.65e+01 1awcB 153 3.68e+01 1bd8 d.211.1.1 19156 1h3iA 293 3.70e+01 b.76.2.1,b.85.7.1 76635,76636 2brfA 110 3.73e+01 2bb3A 221 3.74e+01 1zckA 154 3.75e+01 1zq1C 633 3.80e+01 2anuA 255 3.82e+01 2csbA 519 3.86e+01 2a7mA 250 3.86e+01 1nsyA 271 3.88e+01 2nsyA c.26.2.1 31614 1poiA 317 3.89e+01 1poiA c.124.1.2 34153 1ih8A 271 3.93e+01 2nsyA c.26.2.1 62377 1ypvA 313 3.93e+01 2b8tA 223 3.96e+01 1zclA 180 4.00e+01 2nsyA 271 4.01e+01 2nsyA c.26.2.1 31612 1kqpA 271 4.01e+01 c.26.2.1 72883 1rfmA 344 4.07e+01 c.122.1.1 97385 1lnzA 342 4.09e+01 b.117.1.1,c.37.1.8 78112,78113 1a04A 215 4.10e+01 1a04A a.4.6.2,c.23.1.1 16234,31089 1uheA 97 4.11e+01 1glaF 168 4.12e+01 1gpr b.84.3.1 28274 1pg4A 652 4.13e+01 e.23.1.1 88067 1z5oA 242 4.17e+01 1ci9A 392 4.29e+01 e.3.1.1 64767 1yz7A 188 4.36e+01 1pzxA 289 4.39e+01 c.119.1.1 95484 1w30A 201 4.40e+01 1g6sA 427 4.44e+01 1eps d.68.2.2 39584 1bouA 139 4.48e+01 1bouA a.88.1.1 18521 1b4uA 139 4.48e+01 1bouA a.88.1.1 18523 1oktA 211 4.56e+01 a.45.1.1,c.47.1.5 93272,93273 1ys7A 233 4.58e+01 6paxA 133 4.58e+01 6paxA a.4.1.5,a.4.1.5 64758,64759 1z1dA 103 4.60e+01 2cyjA 118 4.62e+01 1skyB 502 4.62e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18313,26478,32358 1mt6A 280 4.62e+01 b.76.2.1,b.85.7.1 79446,79447 2sniI 83 4.62e+01 2sniI d.40.1.1 38573 1fwkA 296 4.63e+01 1fwkA d.14.1.5,d.58.26.1 37576,39398 2az4A 429 4.64e+01 1nkqA 259 4.68e+01 d.177.1.1 103862 1onhA 364 4.68e+01 e.3.1.1 93357 1csp 67 4.72e+01 1mjc b.40.4.5 25321 1ccwA 137 4.73e+01 1be1 c.23.6.1 31238 2fvgA 340 4.75e+01 1h5zA 455 4.81e+01 a.104.1.1 90622 1rgzA 363 4.83e+01 e.3.1.1 97457 1py5A 326 4.86e+01 d.144.1.7 104389 2fe7A 166 4.89e+01 1xv2A 237 4.92e+01 2b18A 164 4.95e+01 1vj0A 380 4.96e+01 b.35.1.2,c.2.1.1 100786,100787 1yloA 348 5.03e+01 1vbkA 307 5.08e+01 1xewY 172 5.10e+01 1vkmA 297 5.17e+01 c.138.1.1 108670 1viuA 203 5.18e+01 d.113.1.1 100771 1ga0A 364 5.20e+01 1gceA e.3.1.1 60410 1ftkA 279 5.26e+01 1gr2A c.94.1.1 35819 2affA 120 5.27e+01 1hcz 252 5.28e+01 1hcz b.2.6.1,b.84.2.2 22464,28250 1gr2A 279 5.33e+01 1gr2A c.94.1.1 35825 1qlaB 239 5.35e+01 1qlaB a.1.2.1,d.15.4.2 15679,37707 1rrmA 386 5.36e+01 e.22.1.2 105081 2ahqA 76 5.47e+01 6prcH 258 5.51e+01 6prcH b.41.1.1,f.23.10.1 25457,43436 2bhoA 130 5.58e+01 1pk1B 89 5.72e+01 1ho1A 242 5.77e+01 1ho1A c.1.24.1 61097 1zoxA 113 5.82e+01 1bh9B 89 5.82e+01 1bh9B a.22.1.3 16485 1vdmA 153 5.85e+01 1ttzA 87 5.86e+01 c.47.1.1 107309 2aawA 222 5.92e+01 2matA 264 5.92e+01 1c24A d.127.1.1 41146 1x8vA 455 5.96e+01 1mzbA 136 5.96e+01 a.4.5.42 91497 1lh0A 213 6.01e+01 c.61.1.1 73896 1jysA 242 6.11e+01 c.56.2.1 77216 1x47A 98 6.14e+01 2gm5A 139 6.16e+01 1c24A 263 6.16e+01 1c24A d.127.1.1 41148 2ggcA 263 6.16e+01 1jxmA 301 6.19e+01 b.34.2.1,c.37.1.1 67420,67421 1bvwA 360 6.21e+01 1bvwA c.6.1.1 30668 1vpjA 192 6.23e+01 1dxrH 258 6.26e+01 6prcH b.41.1.1,f.23.10.1 25456,43433 2amhA 207 6.30e+01 1sflA 238 6.34e+01 1lghB 45 6.38e+01 1lghB f.3.1.1 43734 1yruB 74 6.40e+01 2bzsA 236 6.44e+01 1joa 447 6.49e+01 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30563,30564,40203 1a97A 148 6.56e+01 1nulA c.61.1.1 34023 1c3oE 1073 6.57e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18564,31493,31685,31686,41530,41531 1xnzA 264 6.59e+01 2abwA 227 6.73e+01 1jalA 363 6.75e+01 c.37.1.8,d.15.10.2 84138,84139 2a9iA 113 6.75e+01 2bshA 125 6.75e+01 2f1wA 158 6.82e+01 1vjyA 303 6.88e+01 d.144.1.7 108633 1ybhA 590 6.91e+01 1u13A 455 6.91e+01 a.104.1.1 107578 1fxlA 167 7.08e+01 1b7fA d.58.7.1,d.58.7.1 39183,39184 1at0 145 7.09e+01 1at0 b.86.1.1 28374 1w99A 558 7.09e+01 1vid 221 7.16e+01 1vid c.66.1.1 34178 1js8A 394 7.19e+01 a.86.1.1,b.112.1.1 67219,67220 2bltA 361 7.24e+01 1gceA e.3.1.1 42739 1ci8A 392 7.25e+01 e.3.1.1 64765 1ctf 74 7.28e+01 1ctf d.45.1.1 38759 1o50A 157 7.30e+01 d.37.1.1,d.37.1.1 92478,92479 1uylA 236 7.34e+01 d.122.1.1 108147 1e9xA 455 7.34e+01 1ea1A a.104.1.1 18969 1av6A 289 7.35e+01 3mag c.66.1.25 34218 1lx7A 253 7.37e+01 c.56.2.1 74329 1ujkA 147 7.38e+01 a.118.9.2 99457 1sg0A 230 7.42e+01 1xv5A 401 7.42e+01 1h9oA 112 7.53e+01 1qadA d.93.1.1 60837 1jwgA 147 7.54e+01 a.118.9.2 71911 1w94A 156 7.55e+01 2bsjA 133 7.58e+01 1zq9A 285 7.61e+01 1ueoA 63 7.61e+01 j.107.1.1 99269 1f3z 161 7.69e+01 1gpr b.84.3.1 28273 1uzcA 71 7.69e+01 a.159.2.1 100222 2rslA 140 7.74e+01 2rslA c.53.1.1 33345 1kk1A 410 7.76e+01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1keeC 1073 7.76e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 68500,68501,68502,68503,68504,68505 2go8A 122 7.76e+01 1ea1A 455 7.81e+01 1ea1A a.104.1.1 18970 1nhs 447 7.88e+01 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30555,30556,40199 1htrB 329 7.93e+01 1smrA 1zx1A 231 7.96e+01 1g57A 217 7.99e+01 1g57A d.115.1.2 60253 2h0uA 217 8.00e+01 3aprE 325 8.06e+01 2er7E b.50.1.2 26820 1qadA 111 8.06e+01 1qadA d.93.1.1 40498 1mhqA 148 8.06e+01 a.118.9.2 84973 1l1dA 152 8.13e+01 b.88.1.3 73452 1h6pA 203 8.13e+01 a.146.1.1 60690 1n3jA 119 8.14e+01 b.85.7.2 79963 1g8fA 511 8.14e+01 1g8fA b.122.1.3,c.26.1.5,c.37.1.15 60348,60349,60350 1zkpA 268 8.16e+01 1keeA 1073 8.17e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 68492,68493,68494,68495,68496,68497 1rypL 212 8.19e+01 d.153.1.4 41880 1sw5B 275 8.23e+01 c.94.1.1 106070 2bs3A 656 8.35e+01 1ggrA 168 8.40e+01 1gpr b.84.3.1 28279 2f7fA 494 8.42e+01 1kzhA 555 8.43e+01 c.89.1.1 73361 1c3jA 351 8.45e+01 1c3jA c.87.1.1 35459 1x6mA 196 8.45e+01 1tr8A 102 8.49e+01 1o54A 277 8.50e+01 c.66.1.13 92482 1efvA 315 8.50e+01 1efvA c.26.2.3,c.31.1.2 31633,31728 1nwbA 124 8.52e+01 b.124.1.1 86296 1c3oG 1073 8.53e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18565,31494,31687,31688,41532,41533 1o65A 246 8.55e+01 b.58.1.2 92544 1nhp 447 8.56e+01 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30549,30550,40196 1xocA 520 8.56e+01 1ocnA 362 8.57e+01 c.6.1.1 86808 1bxeA 113 8.57e+01 1bxeA d.55.1.1 38898 1p2fA 220 8.57e+01 a.4.6.1,c.23.1.1 87720,87721 1kvlA 358 8.60e+01 e.3.1.1 73062 1prcH 259 8.63e+01 6prcH b.41.1.1,f.23.10.1 25460,43445 1ah1 129 8.69e+01 1ah1 b.1.1.1 20652 2d1pC 95 8.71e+01 1yllA 200 8.77e+01 1xznA 179 8.81e+01 1iyu 79 8.84e+01 1iyu b.84.1.1 28227 1eswA 500 8.86e+01 1cwyA c.1.8.1 59500 1yqgA 263 8.87e+01 1rgyA 360 8.92e+01 e.3.1.1 97456 1bh5A 183 8.97e+01 1qipA d.32.1.1 38476 1zavU 30 8.98e+01