# List of top-scoring protein chains for t2k-100-30-n_sep-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 2.34e-17 1tp5A 119 3.59e-16 1pdr 99 5.86e-16 1pdr b.36.1.1 24771 2fe5A 94 6.34e-16 2fcfA 103 7.04e-16 1be9A 119 7.67e-16 1pdr b.36.1.1 24774 1bfeA 119 1.54e-15 1pdr b.36.1.1 24775 1g9oA 91 2.21e-15 1pdr b.36.1.1 60400 1i92A 91 2.21e-15 1pdr b.36.1.1 61990 1qavA 90 2.29e-15 1qauA b.36.1.1 24777 1q3oA 109 8.34e-15 b.36.1.1 95700 1n7eA 97 2.51e-14 b.36.1.1 91691 1ihjA 98 3.58e-14 1pdr b.36.1.1 62382 1l6oA 95 3.65e-14 b.36.1.1 84534 2h2bA 107 4.11e-14 1n7fA 97 4.86e-14 b.36.1.1 91692 1qavB 115 1.36e-13 1qauA b.36.1.1 24780 2f0aA 98 1.52e-13 1qauA 112 1.79e-13 1qauA b.36.1.1 24779 1kwaA 88 2.85e-13 1kwaA b.36.1.1 24772 1nf3C 128 3.13e-13 b.36.1.1 85596 1wf7A 103 6.27e-13 2h3lA 103 7.18e-13 1n99A 166 9.28e-13 b.36.1.1,b.36.1.1 85459,85460 1mfgA 95 1.66e-12 b.36.1.1 79043 1v5lA 103 2.27e-12 b.36.1.1 108378 1kwaB 88 2.80e-12 1kwaA b.36.1.1 24773 1b8qA 127 8.79e-12 1qauA b.36.1.1 24781 2f5yA 91 2.02e-11 1i16 130 2.77e-11 1i16 b.36.1.2 24787 1fc6A 388 2.20e-10 1fc6A b.36.1.3,c.14.1.2 64738,64739 1nteA 82 8.39e-10 b.36.1.1 86163 1r6jA 82 9.79e-10 b.36.1.1 97151 1m5zA 91 1.29e-09 b.36.1.1 78676 1lcyA 325 5.91e-08 b.36.1.4,b.47.1.1 73834,73835 1te0A 318 2.15e-07 1ky9B 448 5.17e-06 b.36.1.4,b.36.1.4,b.47.1.1 73200,73201,73202 1y8tA 324 2.26e-05 1ky9A 448 7.00e-05 b.36.1.4,b.47.1.1 73198,73199 1sotA 320 2.41e-04 b.36.1.4,b.47.1.1 105852,105853 1zn8A 180 1.78e-03 1gph1 465 6.64e-03 1ecfB 1ao0A 459 1.03e-02 1ecfB c.61.1.1,d.153.1.1 34049,41816 2bh8A 101 1.28e-02 2d4pA 141 5.11e-02 1mwrA 646 7.63e-02 d.17.4.5,d.175.1.1,e.3.1.1 79586,79587,79588 1mwsA 646 9.91e-02 d.17.4.5,d.175.1.1,e.3.1.1 79592,79593,79594 1vqqA 646 1.05e-01 1db3A 372 1.52e-01 1db3A c.2.1.2 29813 1q52A 314 1.87e-01 c.14.1.3 95846 1qb7A 236 2.13e-01 1qb7A c.61.1.1 34087 1ecfB 504 2.41e-01 1ecfB c.61.1.1,d.153.1.1 34054,41821 1ecfA 504 2.70e-01 1ecfB c.61.1.1,d.153.1.1 34053,41820 1nkqA 259 3.30e-01 d.177.1.1 103862 1ad3A 452 4.12e-01 1ad3A c.82.1.1 35335 1fmaE 150 4.65e-01 1fmaE d.41.5.1 38630 1h3iA 293 4.66e-01 b.76.2.1,b.85.7.1 76635,76636 1earA 147 4.89e-01 b.107.1.1,d.58.38.1 64875,64876 1fm0E 150 5.13e-01 1fmaE d.41.5.1 38629 1vpqA 273 5.96e-01 1y0bA 197 6.38e-01 3mefA 69 6.78e-01 1mjc b.40.4.5 25320 1rutX 188 7.06e-01 1vkmA 297 7.20e-01 c.138.1.1 108670 1ex2A 189 7.34e-01 1ex2A c.51.4.2 33225 1zsyA 357 7.47e-01 2gm5A 139 7.62e-01 1lw6I 64 7.64e-01 d.40.1.1 74294 2ampA 304 7.80e-01 1kw4A 89 7.87e-01 a.60.1.2 73077 1lvoA 302 8.45e-01 b.47.1.4 74284 1coaI 64 8.86e-01 2sniI d.40.1.1 38574 1eb0A 147 9.15e-01 b.107.1.1,d.58.38.1 64890,64891 1p9uA 302 9.20e-01 b.47.1.4 88001 1r13A 148 9.24e-01 d.169.1.1,h.1.1.1 96782,96783 1fxlA 167 9.64e-01 1b7fA d.58.7.1,d.58.7.1 39183,39184 1uh5A 329 9.83e-01 c.2.1.2 107840 2brfA 110 1.03e+00 1n6aA 259 1.03e+00 b.76.2.1,b.85.7.1 80121,80122 1o12A 376 1.04e+00 b.92.1.5,c.1.9.10 80758,80759 1yqfA 203 1.05e+00 1yg9A 330 1.08e+00 1mjc 69 1.14e+00 1mjc b.40.4.5 25319 1lnzA 342 1.15e+00 b.117.1.1,c.37.1.8 78112,78113 1mt6A 280 1.17e+00 b.76.2.1,b.85.7.1 79446,79447 1bx4A 345 1.27e+00 1bx4A c.72.1.1 34935 1h30A 422 1.30e+00 b.29.1.4,b.29.1.4 76604,76605 1fxrA 64 1.30e+00 1fxd d.58.1.4 38993 2cc0A 195 1.31e+00 1ga0A 364 1.32e+00 1gceA e.3.1.1 60410 2fe7A 166 1.33e+00 1rgzA 363 1.33e+00 e.3.1.1 97457 1onhA 364 1.33e+00 e.3.1.1 93357 1lh0A 213 1.33e+00 c.61.1.1 73896 1g7sA 594 1.34e+00 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 1g7rA 594 1.39e+00 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25716,25717,31034,32149 1b6cB 342 1.40e+00 1b6cB d.144.1.7 41673 1u9yA 284 1.40e+00 2f69A 261 1.42e+00 1t3qB 788 1.50e+00 d.41.1.1,d.133.1.1 106369,106370 1g7tA 594 1.51e+00 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25714,25715,31033,32148 2bltA 361 1.54e+00 1gceA e.3.1.1 42739 1rgyA 360 1.57e+00 e.3.1.1 97456 1fr1A 361 1.58e+00 1gceA e.3.1.1 42734 2f51A 118 1.59e+00 1to2I 64 1.60e+00 2c9wA 169 1.70e+00 1kk1A 410 1.80e+00 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1ojhA 65 1.90e+00 a.214.1.1 103976 1a8l 226 1.99e+00 1a8l c.47.1.2,c.47.1.2 32777,32778 1csp 67 2.00e+00 1mjc b.40.4.5 25321 1py5A 326 2.05e+00 d.144.1.7 104389 1cv8 174 2.07e+00 1cv8 d.3.1.1 37089 1vmeA 410 2.09e+00 c.23.5.1,d.157.1.3 108893,108894 1l1qA 186 2.14e+00 c.61.1.1 77653 1ciqA 40 2.22e+00 2sniI d.40.1.1 38576 2sniI 83 2.24e+00 2sniI d.40.1.1 38573 1w3iA 293 2.24e+00 c.1.10.1 109152 1fsyA 358 2.27e+00 1gceA e.3.1.1 60016 1b3qA 379 2.29e+00 1b3qA a.30.2.1,b.40.7.1,d.122.1.3 16993,25454,41112 1pi4A 358 2.40e+00 e.3.1.1 94700 1vjyA 303 2.43e+00 d.144.1.7 108633 7reqB 637 2.49e+00 1reqB c.1.19.1,c.23.6.1 29617,31244 1vzoA 355 2.51e+00 d.144.1.7 108971 1sqhA 312 2.53e+00 d.108.1.5 98966 1kvlA 358 2.54e+00 e.3.1.1 73062 1ys7A 233 2.54e+00 1xtlA 175 2.56e+00 2rslA 140 2.59e+00 2rslA c.53.1.1 33345 1c9oA 66 2.61e+00 1mjc b.40.4.5 25325 1r62A 160 2.67e+00 d.122.1.3 104816 2bhoA 130 2.69e+00 1vraB 215 2.71e+00 1gceA 364 2.71e+00 1gceA e.3.1.1 42738 2c5qA 240 2.74e+00 1zkjA 359 2.74e+00 2ffyA 358 2.78e+00 1jnyA 435 2.78e+00 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1z3eA 132 2.81e+00 1yioA 208 2.83e+00 1xx6A 191 2.87e+00 1l0gA 358 2.87e+00 e.3.1.1 73400 1w0pA 781 2.90e+00 b.29.1.8,b.29.1.8,b.68.1.1 109038,109039,109040 1qhlA 227 2.92e+00 1qhlA c.37.1.12 32382 1t6t1 118 2.92e+00 1semA 58 2.96e+00 1ckaA b.34.2.1 24544 1xtmA 175 2.97e+00 1d7oA 297 2.99e+00 1enp c.2.1.2 29907 1uc2A 481 3.00e+00 d.261.1.1 99161 2blsA 358 3.03e+00 1gceA e.3.1.1 42747 1l1dA 152 3.03e+00 b.88.1.3 73452 1eno 312 3.03e+00 1enp c.2.1.2 29905 1jepA 222 3.15e+00 d.36.1.1 66612 1w6nA 134 3.20e+00 1y7rA 133 3.33e+00 1gzwA 134 3.36e+00 b.29.1.3 90535 1nwbA 124 3.42e+00 b.124.1.1 86296 1o57A 291 3.65e+00 a.4.5.40,c.61.1.1 92483,92484 1xnzA 264 3.68e+00 1reqB 637 3.73e+00 1reqB c.1.19.1,c.23.6.1 29621,31248 2b18A 164 3.73e+00 1oqvA 192 3.80e+00 d.24.1.2 87320 1fdr 248 3.83e+00 1fdr b.43.4.2,c.25.1.1 25653,31543 1pz7A 204 3.84e+00 b.29.1.4 95405 1uisA 231 3.98e+00 d.22.1.1 99431 1avaC 181 4.00e+00 1avaC b.42.4.1 25604 1x92A 199 4.05e+00 1o54A 277 4.06e+00 c.66.1.13 92482 1glaF 168 4.07e+00 1gpr b.84.3.1 28274 2bshA 125 4.17e+00 1w30A 201 4.19e+00 1vhzA 198 4.20e+00 d.113.1.1 100718 2ckiA 262 4.25e+00 1fvrA 327 4.33e+00 d.144.1.7 60047 1jxmA 301 4.35e+00 b.34.2.1,c.37.1.1 67420,67421 1cis 66 4.36e+00 2sniI k.1.1.1 46375 1f3z 161 4.43e+00 1gpr b.84.3.1 28273 1slaA 134 4.49e+00 1c1lA b.29.1.3 24196 1wbiA 129 4.58e+00 1um0A 365 4.73e+00 d.258.1.1 107942 1dfd 64 4.73e+00 1fxd d.58.1.4 38995 1wubA 178 4.79e+00 1fwkA 296 4.79e+00 1fwkA d.14.1.5,d.58.26.1 37576,39398 1unkA 87 4.84e+00 1cei a.28.2.1 16935 1cliA 345 4.84e+00 1cliA d.79.4.1,d.139.1.1 39816,41459 1sltB 134 4.86e+00 1c1lA b.29.1.3 24187 2gmqA 118 4.87e+00 1fxkC 133 5.02e+00 1fxkC a.2.5.1 15702 1iyhA 198 5.02e+00 a.45.1.1,c.47.1.5 83790,83791 2cvdA 198 5.04e+00 1enp 312 5.10e+00 1enp c.2.1.2 29906 2fsxA 148 5.14e+00 1pzxA 289 5.23e+00 c.119.1.1 95484 1uc7A 125 5.25e+00 c.47.1.1 99163 1ako 268 5.25e+00 1ako d.151.1.1 41779 1fr9A 194 5.25e+00 1fr9A c.68.1.8 34579 1mkmA 249 5.27e+00 a.4.5.33,d.110.2.2 79242,79243 1eyqA 222 5.34e+00 1eypA d.36.1.1 38534 1z4eA 153 5.38e+00 1j08A 226 5.40e+00 c.47.1.2,c.47.1.2 83855,83856 1epwA 1290 5.45e+00 b.29.1.6,b.42.4.2,d.92.1.7,h.4.2.1 24269,25614,40305,45785 1sflA 238 5.48e+00 2aop 497 5.49e+00 2aop d.58.36.1,d.58.36.1,d.134.1.1,d.134.1.1 39503,39504,41427,41428 1cei 94 5.59e+00 1cei a.28.2.1 16939 1eypA 222 5.59e+00 1eypA d.36.1.1 38536 2bsyA 278 5.61e+00 1zuoA 186 5.62e+00 2matA 264 5.64e+00 1c24A d.127.1.1 41146 1reqD 637 5.66e+00 1reqB c.1.19.1,c.23.6.1 29623,31250 2ch4A 320 5.74e+00 1dax 64 5.75e+00 1fxd d.58.1.4 38996 1xewY 172 5.76e+00 1dg6A 191 6.03e+00 1d4vB b.22.1.1 23883 1k32A 1045 6.06e+00 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 68068,68069,68070,68071 2ggcA 263 6.07e+00 1c24A 263 6.07e+00 1c24A d.127.1.1 41148 1tygB 87 6.09e+00 d.15.3.2 107455 1cskA 71 6.17e+00 1ckaA b.34.2.1 24513 1o50A 157 6.23e+00 d.37.1.1,d.37.1.1 92478,92479 2aefA 234 6.23e+00 1sltA 134 6.24e+00 1c1lA b.29.1.3 24186 1zckA 154 6.30e+00 1aop 497 6.33e+00 2aop d.58.36.1,d.58.36.1,d.134.1.1,d.134.1.1 39501,39502,41425,41426 1ti6A 875 6.41e+00 b.52.2.2,c.81.1.1 106974,106975 2hc1A 291 6.42e+00 1j0sA 157 6.49e+00 b.42.1.2 90747 1fjrA 195 6.49e+00 1fjrA b.102.1.1 59855 2b4aA 138 6.49e+00 1c0dA 358 6.57e+00 1eceA c.1.8.3 28815 1qzzA 374 6.82e+00 a.4.5.29,c.66.1.12 96719,96720 1lkkA 105 6.83e+00 1lckA d.93.1.1 40412 1rl2A 137 6.95e+00 1rl2A b.34.5.3,b.40.4.5 24610,25342 2amhA 207 6.99e+00 1lcjA 109 7.02e+00 1qadA d.93.1.1 40414 1s4iA 175 7.04e+00 1yy6A 155 7.04e+00 2fojA 155 7.04e+00 1pk1B 89 7.04e+00 1h72C 296 7.15e+00 d.14.1.5,d.58.26.1 60712,60713 1jndA 420 7.17e+00 c.1.8.5,d.26.3.1 71757,71758 1uzcA 71 7.31e+00 a.159.2.1 100222 1yu1A 381 7.33e+00 1kb5A 115 7.35e+00 1tvdA b.1.1.1 20611 1lf2A 331 7.36e+00 b.50.1.2 77914 1o5oA 221 7.39e+00 c.61.1.1 92509 1i82A 189 7.56e+00 1i82A b.1.9.2 61937 1i8aA 189 7.76e+00 1i82A b.1.9.2 61951 1e5kA 201 7.82e+00 1fr9A c.68.1.8 34578 2h03A 291 7.93e+00 1dpuA 99 8.10e+00 1dpuA a.4.5.16 16150 1l2tA 235 8.15e+00 c.37.1.12 73514 1uteA 313 8.17e+00 1uteA d.159.1.1 42078 1q0sA 259 8.17e+00 c.66.1.28 95509 1gm6A 175 8.19e+00 b.60.1.1 70272 1azeA 56 8.24e+00 b.34.2.1 24536 1jysA 242 8.27e+00 c.56.2.1 77216 1t6eX 381 8.29e+00 b.50.1.2 106564 1yu4A 381 8.42e+00 1ih8A 271 8.43e+00 2nsyA c.26.2.1 62377 1shaA 104 8.46e+00 1fmk d.93.1.1 40424 1yu2A 381 8.47e+00 1ypcI 64 8.49e+00 2sniI d.40.1.1 38570 1z5nA 242 8.60e+00 1d4vB 163 8.62e+00 1d4vB b.22.1.1 23884 1vdmA 153 8.68e+00 1mjhB 162 8.71e+00 1mjhA c.26.2.4 31640 1mjhA 162 8.71e+00 1mjhA c.26.2.4 31639 1rd5A 262 8.78e+00 1se8A 301 8.88e+00 b.40.4.3 105448 1xebA 150 8.93e+00 2nsyA 271 8.96e+00 2nsyA c.26.2.1 31612 1ay9A 108 9.05e+00 1umuA b.87.1.1 28384 1w4tA 299 9.08e+00 1lghB 45 9.12e+00 1lghB f.3.1.1 43734 1aohA 147 9.13e+00 1aohA b.2.2.2 22401 1yjmA 110 9.17e+00 1bxvA 91 9.17e+00 1aac b.6.1.1 22875 1eucA 311 9.21e+00 2scuA c.2.1.8,c.23.4.1 30311,31139 2fa1A 160 9.26e+00 1rxdA 159 9.27e+00 1xznA 179 9.28e+00 1ggrA 168 9.30e+00 1gpr b.84.3.1 28279 1rz1A 161 9.38e+00 b.45.1.2 98124 1yu0A 381 9.46e+00 1js8A 394 9.48e+00 a.86.1.1,b.112.1.1 67219,67220 2gr8A 99 9.51e+00 1z5oA 242 9.53e+00 1nsyA 271 9.53e+00 2nsyA c.26.2.1 31614 1f2fA 104 9.54e+00 1fmk d.93.1.1 40455 1yu3A 381 9.60e+00 1kqpA 271 9.61e+00 c.26.2.1 72883 1u2cA 246 9.69e+00 b.1.6.2,d.272.1.1 107610,107611 1ifyA 49 9.73e+00 a.5.2.1 71207 1koe 172 9.74e+00 1koe d.169.1.5 42448 1v0aA 178 9.77e+00 1gcqA 61 9.79e+00 1ckaA b.34.2.1 60434 2f6uA 234 9.82e+00 1yloA 348 9.93e+00 1bebA 162 9.97e+00 1bebA b.60.1.1 27115 1umuB 116 9.97e+00 1umuA b.87.1.1 28383 2bw3A 534 9.98e+00 1mpp 361 1.00e+01 2rmpA b.50.1.2 26856 1ju5A 109 1.00e+01 d.93.1.1 77173 1umuA 116 1.01e+01 1umuA b.87.1.1 28382 1skyB 502 1.01e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18313,26478,32358 1g2qA 187 1.01e+01 c.61.1.1 65117 1shbA 104 1.02e+01 1fmk d.93.1.1 40425 1xe1A 116 1.02e+01 b.43.3.1 109571 1r94A 118 1.03e+01 b.124.1.1 97251 1g38A 393 1.04e+01 2admA c.66.1.27 60235 2gs8A 317 1.04e+01 1b8aA 438 1.05e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 2gu3A 136 1.06e+01 1id2A 106 1.06e+01 1aac b.6.1.1 62288 1w99A 558 1.07e+01 1mk4A 157 1.07e+01 d.108.1.1 84979 2bjuA 453 1.07e+01 1vchA 175 1.08e+01 1g7pB 99 1.09e+01 b.1.1.2 70155 1eceA 358 1.09e+01 1eceA c.1.8.3 28813 1p7tA 731 1.10e+01 c.1.13.1 94319 1fr3A 67 1.10e+01 1fr3A b.40.6.1 25436 1oroA 213 1.10e+01 1opr c.61.1.1 34093 1tw9A 206 1.12e+01 a.45.1.1,c.47.1.5 107381,107382 2f23A 156 1.12e+01 1q1lA 401 1.14e+01 d.258.1.1 95591 1g57A 217 1.14e+01 1g57A d.115.1.2 60253 2anuA 255 1.15e+01 1m6yA 301 1.15e+01 a.60.13.1,c.66.1.23 78716,78717 1c1lA 136 1.15e+01 1c1lA b.29.1.3 24219 1vlbA 907 1.15e+01 a.56.1.1,d.15.4.2,d.41.1.1,d.133.1.1 108739,108740,108741,108742 1hlrA 907 1.15e+01 2bsjA 133 1.16e+01 1a81A 254 1.16e+01 1a81A d.93.1.1,d.93.1.1 40507,40508 1bxaA 105 1.16e+01 1aac b.6.1.1 22839 1aac 105 1.16e+01 1aac b.6.1.1 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