# List of top-scoring protein chains for t2k-100-30-dssp-ehl2-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 1g9oA 91 3.88e-23 1pdr b.36.1.1 60400 1i92A 91 6.53e-23 1pdr b.36.1.1 61990 1tp5A 119 7.39e-21 1be9A 119 1.28e-20 1pdr b.36.1.1 24774 1bfeA 119 1.30e-20 1pdr b.36.1.1 24775 1pdr 99 7.10e-20 1pdr b.36.1.1 24771 2fcfA 103 1.08e-19 2fe5A 94 1.56e-19 2fneA 117 2.39e-19 1q3oA 109 2.26e-18 b.36.1.1 95700 1n99A 166 1.28e-17 b.36.1.1,b.36.1.1 85459,85460 1qavA 90 1.76e-17 1qauA b.36.1.1 24777 1qavB 115 2.86e-17 1qauA b.36.1.1 24780 1wf7A 103 3.57e-17 2f5yA 91 7.43e-17 1n7fA 97 1.06e-16 b.36.1.1 91692 1n7eA 97 1.42e-16 b.36.1.1 91691 1qauA 112 1.77e-16 1qauA b.36.1.1 24779 1b8qA 127 2.11e-16 1qauA b.36.1.1 24781 1ihjA 98 3.68e-16 1pdr b.36.1.1 62382 1v5lA 103 4.10e-16 b.36.1.1 108378 1mfgA 95 1.89e-15 b.36.1.1 79043 1l6oA 95 3.20e-15 b.36.1.1 84534 1nf3C 128 5.45e-15 b.36.1.1 85596 2f0aA 98 5.94e-15 1m5zA 91 8.71e-15 b.36.1.1 78676 1kwaB 88 2.03e-14 1kwaA b.36.1.1 24773 1fc6A 388 2.70e-14 1fc6A b.36.1.3,c.14.1.2 64738,64739 1kwaA 88 4.30e-14 1kwaA b.36.1.1 24772 1i16 130 2.28e-13 1i16 b.36.1.2 24787 1nteA 82 1.67e-12 b.36.1.1 86163 1r6jA 82 1.67e-12 b.36.1.1 97151 1lcyA 325 4.81e-11 b.36.1.4,b.47.1.1 73834,73835 1te0A 318 3.13e-10 1ky9B 448 7.85e-10 b.36.1.4,b.36.1.4,b.47.1.1 73200,73201,73202 1sotA 320 3.44e-08 b.36.1.4,b.47.1.1 105852,105853 1y8tA 324 4.33e-08 1ky9A 448 1.32e-07 b.36.1.4,b.47.1.1 73198,73199 1bx4A 345 9.79e-03 1bx4A c.72.1.1 34935 1db3A 372 1.96e-02 1db3A c.2.1.2 29813 1gph1 465 2.40e-02 1ecfB 1ao0A 459 2.87e-02 1ecfB c.61.1.1,d.153.1.1 34049,41816 1zn8A 180 4.81e-02 1fwkA 296 2.25e-01 1fwkA d.14.1.5,d.58.26.1 37576,39398 1wnfA 328 5.07e-01 1wlsA 328 5.18e-01 1lnzA 342 5.26e-01 b.117.1.1,c.37.1.8 78112,78113 1bu6O 501 7.47e-01 1glcG c.55.1.4,c.55.1.4 33499,33500 1hvyA 288 7.78e-01 1bkpA d.117.1.1 41049 1h72C 296 9.16e-01 d.14.1.5,d.58.26.1 60712,60713 1lh0A 213 9.36e-01 c.61.1.1 73896 1jzxK 205 1.11e+00 i.1.1.2 67885 1t6t1 118 1.17e+00 1opr 213 1.17e+00 1opr c.61.1.1 34091 1fr3A 67 1.22e+00 1fr3A b.40.6.1 25436 1uc2A 481 1.25e+00 d.261.1.1 99161 1eu1A 780 1.47e+00 1dmr b.52.2.2,c.81.1.1 26903,35311 2fa1A 160 1.47e+00 1l1dA 152 1.58e+00 b.88.1.3 73452 1fdr 248 1.67e+00 1fdr b.43.4.2,c.25.1.1 25653,31543 1jalA 363 1.68e+00 c.37.1.8,d.15.10.2 84138,84139 1r13A 148 1.78e+00 d.169.1.1,h.1.1.1 96782,96783 1xocA 520 1.83e+00 1ypvA 313 1.88e+00 1ugmA 125 1.91e+00 d.15.1.3 107827 1xebA 150 1.93e+00 1vpqA 273 2.24e+00 1evfA 264 2.37e+00 1bkpA d.117.1.1 40932 1qqqA 264 2.47e+00 1bkpA d.117.1.1 40931 2g8oA 264 2.48e+00 1tys 265 2.58e+00 1bkpA d.117.1.1 40937 1skyB 502 2.58e+00 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18313,26478,32358 1axwA 265 2.68e+00 1bkpA d.117.1.1 40938 1mo1A 87 2.77e+00 d.94.1.1 91363 1aiqA 264 2.83e+00 1bkpA d.117.1.1 40967 1cfyA 143 2.96e+00 1cof d.109.1.2 40858 1cof 143 2.97e+00 1cof d.109.1.2 40860 1kw4A 89 3.14e+00 a.60.1.2 73077 2g8mA 264 3.30e+00 2aynA 404 3.32e+00 1qb7A 236 3.34e+00 1qb7A c.61.1.1 34087 1zq9A 285 3.49e+00 1xv5A 401 3.94e+00 1se8A 301 4.09e+00 b.40.4.3 105448 1efvA 315 4.11e+00 1efvA c.26.2.3,c.31.1.2 31633,31728 1oroA 213 4.21e+00 1opr c.61.1.1 34093 1u5vA 273 4.70e+00 1y0yA 353 4.97e+00 1xfoA 357 5.11e+00 1u5hA 273 5.13e+00 1befA 181 5.13e+00 1befA b.47.1.3 26419 1a8uA 277 5.15e+00 1brt c.69.1.12 34703 1f28A 297 5.15e+00 1bkpA d.117.1.1 59608 1bxrA 1073 5.21e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18570,31499,31697,31698,41542,41543 1ecfA 504 5.30e+00 1ecfB c.61.1.1,d.153.1.1 34053,41820 1ecfB 504 5.36e+00 1ecfB c.61.1.1,d.153.1.1 34054,41821 1vc3B 97 5.53e+00 1vkmA 297 5.93e+00 c.138.1.1 108670 1oi7A 288 5.98e+00 c.2.1.8,c.23.4.1 87049,87050 1zsyA 357 6.04e+00 1x3mA 415 6.05e+00 1ti6A 875 6.34e+00 b.52.2.2,c.81.1.1 106974,106975 1a8p 258 7.11e+00 1fdr b.43.4.2,c.25.1.1 25654,31544 2tscA 264 7.21e+00 1bkpA d.117.1.1 40952 1koe 172 7.23e+00 1koe d.169.1.5 42448 1a4yA 460 7.36e+00 1a4yA c.10.1.1 30852 1w78A 422 7.40e+00 1zm8A 259 7.65e+00 1brt 277 8.24e+00 1brt c.69.1.12 34699 1broA 277 8.43e+00 1brt c.69.1.12 34700 1lnh 857 8.79e+00 1yge a.119.1.1,b.12.1.1 19237,23637 1p35A 299 9.31e+00 1p35A b.28.1.1 23925 1c3oA 1073 9.35e+00 1c3oA a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18562,31491,31681,31682,41526,41527 1keeA 1073 9.51e+00 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 1cs0A 1073 9.56e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18558,31487,31673,31674,41518,41519 1jdbB 1073 9.58e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18574,31503,31705,31706,41550,41551 1keeC 1073 9.63e+00 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 1cs0C 1073 9.70e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18559,31488,31675,31676,41520,41521 1rovA 857 1.00e+01 a.119.1.1,b.12.1.1 97674,97675 1dxrH 258 1.02e+01 6prcH b.41.1.1,f.23.10.1 25456,43433 6prcH 258 1.02e+01 6prcH b.41.1.1,f.23.10.1 25457,43436 1a9xA 1058 1.02e+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 18550,31479,31657,31658,41502,41503 2bh8A 101 1.04e+01 1g57A 217 1.05e+01 1g57A d.115.1.2 60253 1x92A 199 1.08e+01 1keeG 1073 1.09e+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 68516,68517,68518,68519,68520,68521 1fxrA 64 1.09e+01 1fxd d.58.1.4 38993 1c3oC 1073 1.11e+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 18563,31492,31683,31684,41528,41529 1c3oG 1073 1.12e+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 1xx6A 191 1.14e+01 1iezA 217 1.18e+01 d.115.1.2 66129 1z6kA 293 1.18e+01 1keeE 1073 1.19e+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 68508,68509,68510,68511,68512,68513 1wl4A 397 1.19e+01 1wspA 84 1.23e+01 1c3oE 1073 1.23e+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 1df9A 191 1.26e+01 1befA b.47.1.3 26420 2sxl 88 1.32e+01 1b7fA d.58.7.1 39179 1t3qB 788 1.35e+01 d.41.1.1,d.133.1.1 106369,106370 1y0bA 197 1.35e+01 1uh5A 329 1.38e+01 c.2.1.2 107840 1sw5A 275 1.39e+01 c.94.1.1 106069 1fsgA 233 1.41e+01 1qk3A c.61.1.1 34029 1g2qA 187 1.42e+01 c.61.1.1 65117 1reqD 637 1.42e+01 1reqB c.1.19.1,c.23.6.1 29623,31250 1r62A 160 1.44e+01 d.122.1.3 104816 1z1dA 103 1.49e+01 7reqB 637 1.58e+01 1reqB c.1.19.1,c.23.6.1 29617,31244 1glaG 501 1.58e+01 1glcG c.55.1.4,c.55.1.4 33507,33508 1reqB 637 1.60e+01 1reqB c.1.19.1,c.23.6.1 29621,31248 1tsm 316 1.63e+01 1bkpA d.117.1.1 41024 1vheA 373 1.70e+01 b.49.3.1,c.56.5.4 100669,100670 1dpuA 99 1.72e+01 1dpuA a.4.5.16 16150 2d00A 109 1.74e+01 2def 147 1.74e+01 1bs4A d.167.1.1 42305 1ah1 129 1.74e+01 1ah1 b.1.1.1 20652 1fm0E 150 1.86e+01 1fmaE d.41.5.1 38629 1fmaE 150 1.86e+01 1fmaE d.41.5.1 38630 1yjmA 110 1.88e+01 1j08A 226 1.90e+01 c.47.1.2,c.47.1.2 83855,83856 1mkmA 249 1.96e+01 a.4.5.33,d.110.2.2 79242,79243 1l0wA 580 2.00e+01 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1vraB 215 2.00e+01 2cw8A 537 2.01e+01 1h3gA 601 2.01e+01 b.1.18.2,b.71.1.1,c.1.8.1 90594,90595,90596 1ojhA 65 2.02e+01 a.214.1.1 103976 1hi9A 274 2.02e+01 1hi9A c.99.1.1 61063 1bvoA 175 2.06e+01 1a3qA b.2.5.3 22457 1cis 66 2.14e+01 2sniI k.1.1.1 46375 1h8eA 510 2.24e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 60738,60739,60740 2f51A 118 2.29e+01 1ad3A 452 2.35e+01 1ad3A c.82.1.1 35335 2fvgA 340 2.37e+01 1mek 120 2.40e+01 1erv c.47.1.2 32775 1wywA 230 2.44e+01 1rypL 212 2.46e+01 d.153.1.4 41880 1g65K 211 2.46e+01 d.153.1.4 41907 1fxlA 167 2.51e+01 1b7fA d.58.7.1,d.58.7.1 39183,39184 1xm7A 195 2.51e+01 2ck3A 510 2.55e+01 1e79A 510 2.56e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18269,26434,32314 1w30A 201 2.57e+01 1p99A 295 2.57e+01 c.94.1.1 94384 1nepA 130 2.59e+01 b.1.18.7 80440 1yb2A 275 2.60e+01 1fxkC 133 2.61e+01 1fxkC a.2.5.1 15702 1eb0A 147 2.67e+01 b.107.1.1,d.58.38.1 64890,64891 1i0hA 205 2.69e+01 1avmA a.2.11.1,d.44.1.1 15760,38685 1ix9A 205 2.69e+01 a.2.11.1,d.44.1.1 76899,76900 1uheA 97 2.70e+01 1vj0A 380 2.71e+01 b.35.1.2,c.2.1.1 100786,100787 1jv2B 692 2.71e+01 b.1.15.1,c.62.1.1,d.200.1.1,g.3.11.6,g.3.11.6 67338,67339,67340,67341,67342 2ckiA 262 2.75e+01 1u4nA 310 2.83e+01 1q8yA 373 2.87e+01 d.144.1.7 96234 1d5nA 205 2.88e+01 1avmA a.2.11.1,d.44.1.1 15762,38687 2c3zA 222 2.89e+01 2cc0A 195 2.90e+01 1howA 373 2.90e+01 1hcl d.144.1.7 41679 1xdyA 298 2.91e+01 1r2jA 366 3.12e+01 a.29.3.1,e.6.1.1 96869,96870 1lnqA 336 3.14e+01 c.2.1.9,f.14.1.1 74049,74050 2aefA 234 3.16e+01 1a53 247 3.17e+01 1a53 c.1.2.4 28564 1vybA 238 3.27e+01 d.151.1.1 108897 1mn4A 282 3.32e+01 b.2.5.7 79313 3sxlA 184 3.36e+01 1b7fA d.58.7.1,d.58.7.1 39173,39174 1prcH 259 3.39e+01 6prcH b.41.1.1,f.23.10.1 25460,43445 1dfd 64 3.41e+01 1fxd d.58.1.4 38995 1earA 147 3.52e+01 b.107.1.1,d.58.38.1 64875,64876 1cliA 345 3.55e+01 1cliA d.79.4.1,d.139.1.1 39816,41459 1y96A 86 3.58e+01 1gutA 68 3.64e+01 b.40.6.1 65576 1uw0A 117 3.66e+01 g.39.1.12 108063 1bmfA 510 3.70e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18281,26446,32326 1yloA 348 3.72e+01 1vhoA 346 3.76e+01 b.49.3.1,c.56.5.4 100694,100695 1rhd 293 3.80e+01 1rhs c.46.1.2,c.46.1.2 32715,32716 1def 147 3.81e+01 1bs4A d.167.1.1 42306 1xdnA 277 3.85e+01 1kuuA 202 3.88e+01 d.153.2.1 73019 1gv3A 248 4.00e+01 a.2.11.1,d.44.1.1 70585,70586 1wmiA 90 4.03e+01 2bikB 313 4.04e+01 1v5iB 76 4.07e+01 1sw5B 275 4.08e+01 c.94.1.1 106070 1dgsA 667 4.10e+01 1dgsA a.60.2.2,b.40.4.6,d.142.2.2 17963,25365,41581 1n0qA 93 4.20e+01 k.37.1.1 79754 1bouA 139 4.24e+01 1bouA a.88.1.1 18521 1s72M 194 4.29e+01 d.12.1.2 105332 1b4uA 139 4.29e+01 1bouA a.88.1.1 18523 1dax 64 4.29e+01 1fxd d.58.1.4 38996 1mdoA 393 4.30e+01 c.67.1.4 79013 1dl5A 317 4.32e+01 1dl5A c.66.1.7,d.197.1.1 64720,64721 1txvB 440 4.35e+01 1pbyB 337 4.37e+01 b.69.2.2 94422 1jndA 420 4.41e+01 c.1.8.5,d.26.3.1 71757,71758 1igs 248 4.41e+01 1a53 c.1.2.4 28565 1jjuB 337 4.42e+01 b.69.2.2 66779 2bb3A 221 4.43e+01 1qhlA 227 4.48e+01 1qhlA c.37.1.12 32382 1evhA 112 4.54e+01 1evhA b.55.1.4 26997 1juk 248 4.55e+01 1a53 c.1.2.4 28567 1z60A 59 4.57e+01 1ffkE 119 4.58e+01 1ffkE d.79.3.1 39812 1kz8A 337 4.59e+01 e.7.1.1 77633 1g8aA 227 4.78e+01 c.66.1.3 90506 1nwaA 203 4.79e+01 d.58.28.1 86295 1jem 87 4.80e+01 1ptf d.94.1.1 40548 1b62A 349 4.80e+01 1b63A d.14.1.3,d.122.1.2 37567,41108 1wvhA 134 4.82e+01 1e53A 59 4.85e+01 1e53A g.49.1.2 45356 1z85A 234 4.89e+01 1xmrA 243 4.90e+01 1t5eA 360 4.95e+01 f.46.1.1 106436 2fp7B 172 4.95e+01 1cozA 129 4.98e+01 1cozA c.26.1.2 31598 1itpA 77 4.98e+01 d.58.3.2 66371 1y5eA 169 4.99e+01 1vdmA 153 5.03e+01 1g6sA 427 5.13e+01 1eps d.68.2.2 39584 1qgdA 662 5.23e+01 c.36.1.6,c.36.1.10,c.48.1.1 88367,88368,88369 1ug8A 87 5.23e+01 d.68.7.1 107825 1b63A 333 5.25e+01 1b63A d.14.1.3,d.122.1.2 37566,41107 1wkvA 389 5.26e+01 1zesA 125 5.35e+01 1mjhA 162 5.36e+01 1mjhA c.26.2.4 31639 1ptf 88 5.37e+01 1ptf d.94.1.1 40549 1uzcA 71 5.37e+01 a.159.2.1 100222 1xwsA 313 5.44e+01 1j24A 143 5.49e+01 c.52.1.20 84008 2b8tA 223 5.51e+01 1qfrA 89 5.53e+01 1ptf d.94.1.1 40552 1dzfA 215 5.54e+01 1dzfA c.52.3.1,d.78.1.1 33344,39753 1rwzA 245 5.54e+01 d.131.1.2,d.131.1.2 98005,98006 1mjhB 162 5.57e+01 1mjhA c.26.2.4 31640 2ahqA 76 5.59e+01 1ciqA 40 5.66e+01 2sniI d.40.1.1 38576 1vqqA 646 5.70e+01 1zp4A 304 5.81e+01 2bw3A 534 5.92e+01 1amm 174 5.95e+01 1amm b.11.1.1,b.11.1.1 23587,23588 4gcr 174 5.95e+01 1amm b.11.1.1,b.11.1.1 23589,23590 1sphA 88 6.03e+01 1ptf d.94.1.1 40544 1jj2L 194 6.04e+01 1ffkI d.12.1.2 63097 1ar1B 298 6.08e+01 2occB b.6.1.2,f.17.2.1 23037,43619 1qk4A 233 6.13e+01 1qk3A c.61.1.1 34037 1hkfA 122 6.17e+01 b.1.1.1 83553 1dekA 241 6.29e+01 1dekA c.37.1.1 31842 1ybhA 590 6.35e+01 1obfO 335 6.46e+01 c.2.1.3,d.81.1.1 86768,86769 2gvaA 87 6.49e+01 1gvp b.40.4.7 25389 1eo9B 241 6.56e+01 3pchM b.3.6.1 22826 1ifyA 49 6.70e+01 a.5.2.1 71207 1eucA 311 6.75e+01 2scuA c.2.1.8,c.23.4.1 30311,31139 1eudA 311 6.78e+01 2scuA c.2.1.8,c.23.4.1 30312,31140 1glcG 501 6.78e+01 1glcG c.55.1.4,c.55.1.4 33519,33520 2sodB 152 6.80e+01 1mfmA b.1.8.1 22242 1mt6A 280 6.89e+01 b.76.2.1,b.85.7.1 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