# List of top-scoring protein chains for t2k-100-30-str2-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 2fe5A 94 6.80e-20 1g9oA 91 3.29e-19 1pdr b.36.1.1 60400 1tp5A 119 5.06e-19 2fneA 117 1.19e-18 1be9A 119 1.60e-18 1pdr b.36.1.1 24774 1bfeA 119 2.05e-18 1pdr b.36.1.1 24775 1i92A 91 3.05e-18 1pdr b.36.1.1 61990 1n7eA 97 3.23e-18 b.36.1.1 91691 1pdr 99 7.68e-18 1pdr b.36.1.1 24771 2fcfA 103 8.13e-18 1qavA 90 1.26e-17 1qauA b.36.1.1 24777 1n7fA 97 1.66e-17 b.36.1.1 91692 1q3oA 109 1.23e-16 b.36.1.1 95700 1ihjA 98 5.14e-16 1pdr b.36.1.1 62382 1kwaA 88 2.31e-15 1kwaA b.36.1.1 24772 2h2bA 107 2.74e-15 2h3lA 103 2.92e-15 1mfgA 95 3.39e-15 b.36.1.1 79043 1l6oA 95 3.45e-15 b.36.1.1 84534 1n99A 166 3.90e-15 b.36.1.1,b.36.1.1 85459,85460 2f0aA 98 9.30e-15 1nf3C 128 1.17e-14 b.36.1.1 85596 1qavB 115 1.21e-14 1qauA b.36.1.1 24780 1i16 130 1.56e-14 1i16 b.36.1.2 24787 2f5yA 91 2.03e-14 1qauA 112 2.16e-14 1qauA b.36.1.1 24779 1wf7A 103 3.02e-14 1kwaB 88 4.13e-14 1kwaA b.36.1.1 24773 1b8qA 127 5.20e-14 1qauA b.36.1.1 24781 1m5zA 91 3.44e-13 b.36.1.1 78676 1v5lA 103 5.28e-13 b.36.1.1 108378 1nteA 82 3.26e-12 b.36.1.1 86163 1r6jA 82 5.01e-12 b.36.1.1 97151 1fc6A 388 1.34e-11 1fc6A b.36.1.3,c.14.1.2 64738,64739 1lcyA 325 2.82e-08 b.36.1.4,b.47.1.1 73834,73835 1te0A 318 2.28e-07 1y8tA 324 5.68e-06 1ky9B 448 7.09e-06 b.36.1.4,b.36.1.4,b.47.1.1 73200,73201,73202 1sotA 320 1.17e-03 b.36.1.4,b.47.1.1 105852,105853 1ky9A 448 1.62e-03 b.36.1.4,b.47.1.1 73198,73199 2fe7A 166 7.47e-02 2d4pA 141 1.08e-01 1db3A 372 2.86e-01 1db3A c.2.1.2 29813 1bx4A 345 8.38e-01 1bx4A c.72.1.1 34935 1uc2A 481 1.25e+00 d.261.1.1 99161 1t6t1 118 1.48e+00 1ugmA 125 2.13e+00 d.15.1.3 107827 1q52A 314 2.16e+00 c.14.1.3 95846 1ggrA 168 2.17e+00 1gpr b.84.3.1 28279 2bh8A 101 2.20e+00 1g2qA 187 2.23e+00 c.61.1.1 65117 1ti6A 875 2.26e+00 b.52.2.2,c.81.1.1 106974,106975 1f3z 161 2.61e+00 1gpr b.84.3.1 28273 1glaF 168 2.68e+00 1gpr b.84.3.1 28274 1g57A 217 3.05e+00 1g57A d.115.1.2 60253 1rutX 188 3.25e+00 1x47A 98 3.29e+00 1fxlA 167 3.33e+00 1b7fA d.58.7.1,d.58.7.1 39183,39184 1vqqA 646 3.48e+00 1bo4B 168 3.52e+00 1bo4A d.108.1.1 40799 1ao0A 459 3.64e+00 1ecfB c.61.1.1,d.153.1.1 34049,41816 1gph1 465 3.69e+00 1ecfB 1zsyA 357 3.78e+00 1y0bA 197 4.07e+00 1r13A 148 4.09e+00 d.169.1.1,h.1.1.1 96782,96783 1mwsA 646 4.70e+00 d.17.4.5,d.175.1.1,e.3.1.1 79592,79593,79594 1kw4A 89 4.79e+00 a.60.1.2 73077 3mefA 69 4.89e+00 1mjc b.40.4.5 25320 1dfd 64 5.35e+00 1fxd d.58.1.4 38995 1ciqA 40 5.95e+00 2sniI d.40.1.1 38576 1mwrA 646 6.05e+00 d.17.4.5,d.175.1.1,e.3.1.1 79586,79587,79588 1dax 64 6.68e+00 1fxd d.58.1.4 38996 2c5qA 240 6.92e+00 1s4iA 175 7.07e+00 1s3zA 165 7.53e+00 d.108.1.1 105250 1a62 130 7.68e+00 1a62 a.140.3.1,b.40.4.5 64708,64709 1y9kA 157 8.00e+00 1vkmA 297 8.60e+00 c.138.1.1 108670 1y9wA 140 8.71e+00 1vraB 215 8.75e+00 1csp 67 8.75e+00 1mjc b.40.4.5 25321 1rgzA 363 9.41e+00 e.3.1.1 97457 1onhA 364 9.41e+00 e.3.1.1 93357 1ga0A 364 9.41e+00 1gceA e.3.1.1 60410 1vheA 373 9.59e+00 b.49.3.1,c.56.5.4 100669,100670 2bltA 361 9.70e+00 1gceA e.3.1.1 42739 2aexA 346 9.99e+00 1g7rA 594 1.01e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25716,25717,31034,32149 1zm8A 259 1.03e+01 2sniI 83 1.04e+01 2sniI d.40.1.1 38573 1fxrA 64 1.04e+01 1fxd d.58.1.4 38993 1cis 66 1.04e+01 2sniI k.1.1.1 46375 3sxlA 184 1.08e+01 1b7fA d.58.7.1,d.58.7.1 39173,39174 1jjiA 311 1.12e+01 c.69.1.2 66766 1xtlA 175 1.12e+01 1vkcA 158 1.16e+01 1coaI 64 1.17e+01 2sniI d.40.1.1 38574 2cc0A 195 1.17e+01 1fr3A 67 1.17e+01 1fr3A b.40.6.1 25436 1gceA 364 1.18e+01 1gceA e.3.1.1 42738 3proD 166 1.19e+01 3proC d.52.1.1,d.52.1.1 38814,38815 1c9oA 66 1.22e+01 1mjc b.40.4.5 25325 1lw6I 64 1.26e+01 d.40.1.1 74294 1bo4A 168 1.26e+01 1bo4A d.108.1.1 40798 1rgyA 360 1.30e+01 e.3.1.1 97456 1bw9A 356 1.30e+01 1bw9A c.2.1.7,c.58.1.1 30274,33922 1to2I 64 1.32e+01 2bsyA 278 1.35e+01 1viuA 203 1.40e+01 d.113.1.1 100771 1a63 130 1.41e+01 1a62 a.140.3.1,b.40.4.5 64710,64711 2b18A 164 1.42e+01 2atrA 138 1.43e+01 1koe 172 1.44e+01 1koe d.169.1.5 42448 2bs3A 656 1.45e+01 1yjmA 110 1.45e+01 1cq3A 233 1.46e+01 1cq3A b.27.1.1 23923 1qlaA 656 1.50e+01 1qlaA a.7.3.1,c.3.1.4,d.168.1.1 16328,30427,42310 1fr1A 361 1.51e+01 1gceA e.3.1.1 42734 1pi4A 358 1.56e+01 e.3.1.1 94700 1fsyA 358 1.59e+01 1gceA e.3.1.1 60016 1jnyA 435 1.63e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 2gwnA 452 1.65e+01 1g7sA 594 1.65e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 1earA 147 1.65e+01 b.107.1.1,d.58.38.1 64875,64876 1xtmA 175 1.68e+01 2blsA 358 1.68e+01 1gceA e.3.1.1 42747 2fvgA 340 1.69e+01 1xfoA 357 1.70e+01 1vc3B 97 1.73e+01 1kvlA 358 1.75e+01 e.3.1.1 73062 1y0yA 353 1.79e+01 1l0gA 358 1.82e+01 e.3.1.1 73400 1tys 265 1.83e+01 1bkpA d.117.1.1 40937 1axwA 265 1.84e+01 1bkpA d.117.1.1 40938 1dioA 554 1.84e+01 1dioA c.1.19.3 29656 3proC 166 1.85e+01 3proC d.52.1.1,d.52.1.1 38812,38813 1wpgA 994 1.86e+01 1eexA 554 1.86e+01 1dioA c.1.19.3 29650 1sw5A 275 1.88e+01 c.94.1.1 106069 1mjc 69 1.88e+01 1mjc b.40.4.5 25319 2g8oA 264 1.92e+01 1ad3A 452 1.92e+01 1ad3A c.82.1.1 35335 1aiqA 264 1.93e+01 1bkpA d.117.1.1 40967 2brfA 110 1.93e+01 1skyB 502 1.97e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18313,26478,32358 2ffyA 358 1.98e+01 2g8mA 264 2.04e+01 1oi7A 288 2.05e+01 c.2.1.8,c.23.4.1 87049,87050 1zkjA 359 2.07e+01 1ifyA 49 2.12e+01 a.5.2.1 71207 1qqqA 264 2.16e+01 1bkpA d.117.1.1 40931 1evfA 264 2.17e+01 1bkpA d.117.1.1 40932 1vj0A 380 2.18e+01 b.35.1.2,c.2.1.1 100786,100787 1g8aA 227 2.19e+01 c.66.1.3 90506 7reqB 637 2.27e+01 1reqB c.1.19.1,c.23.6.1 29617,31244 1reqD 637 2.27e+01 1reqB c.1.19.1,c.23.6.1 29623,31250 1t3qB 788 2.27e+01 d.41.1.1,d.133.1.1 106369,106370 2sxl 88 2.28e+01 1b7fA d.58.7.1 39179 1c1dA 355 2.38e+01 1bw9A c.2.1.7,c.58.1.1 30270,33918 1zkpA 268 2.41e+01 1eb0A 147 2.42e+01 b.107.1.1,d.58.38.1 64890,64891 2fa1A 160 2.48e+01 1r88A 280 2.51e+01 c.69.1.3 97219 1x3mA 415 2.61e+01 1zhhB 242 2.62e+01 1uc7A 125 2.63e+01 c.47.1.1 99163 1b4uB 302 2.66e+01 1bouB c.56.6.1 33861 2cyjA 118 2.68e+01 2fokA 579 2.69e+01 2fokA a.4.5.12,a.4.5.12,a.4.5.12,c.52.1.12 16131,16132,16133,33323 1uh5A 329 2.75e+01 c.2.1.2 107840 1pzxA 289 2.81e+01 c.119.1.1 95484 1kzlA 208 2.83e+01 b.43.4.3,b.43.4.3 77635,77636 1qsmA 152 2.85e+01 1qsmA d.108.1.1 40808 1zoxA 113 2.85e+01 1vybA 238 2.88e+01 d.151.1.1 108897 1ih8A 271 2.89e+01 2nsyA c.26.2.1 62377 2nsyA 271 2.90e+01 2nsyA c.26.2.1 31612 1nsyA 271 2.90e+01 2nsyA c.26.2.1 31614 1kqpA 271 2.91e+01 c.26.2.1 72883 1whi 122 2.91e+01 1whi b.39.1.1 24810 1mkmA 249 2.92e+01 a.4.5.33,d.110.2.2 79242,79243 1o6uA 403 3.07e+01 a.5.3.1,b.132.1.1,c.13.1.1 92589,92590,92591 1reqB 637 3.10e+01 1reqB c.1.19.1,c.23.6.1 29621,31248 1fl2A 310 3.14e+01 1hyuA c.3.1.5,c.3.1.5 59869,59870 1iezA 217 3.14e+01 d.115.1.2 66129 1g7tA 594 3.17e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25714,25715,31033,32148 1wvhA 134 3.21e+01 1ojhA 65 3.22e+01 a.214.1.1 103976 1wmiA 90 3.22e+01 1bzyA 217 3.26e+01 1qk3A c.61.1.1 34071 1lckA 175 3.45e+01 1lckA b.34.2.1,d.93.1.1 24552,40421 1xbsA 149 3.55e+01 2ck3A 510 3.72e+01 1opr 213 3.73e+01 1opr c.61.1.1 34091 1egpA 45 3.75e+01 1egpA d.40.1.1 38561 1y1uA 585 3.78e+01 1qb7A 236 3.81e+01 1qb7A c.61.1.1 34087 1b7fA 168 3.86e+01 1b7fA d.58.7.1,d.58.7.1 39169,39170 2b8wA 328 3.87e+01 1jv1A 505 3.91e+01 c.68.1.5 71892 1hzdA 272 3.92e+01 c.14.1.3 65969 1olmA 403 3.99e+01 a.5.3.1,b.132.1.1,c.13.1.1 104008,104009,104010 1bfi 112 4.02e+01 1qadA d.93.1.1 40499 1p7tA 731 4.04e+01 c.1.13.1 94319 1mo1A 87 4.07e+01 d.94.1.1 91363 2g3aA 152 4.14e+01 1iyu 79 4.15e+01 1iyu b.84.1.1 28227 1tfe 145 4.19e+01 1tfe d.43.1.1 38680 1vjuA 309 4.22e+01 d.248.1.1 100835 1hgxA 183 4.25e+01 1tc1A c.61.1.1 34027 1gpr 162 4.35e+01 1gpr b.84.3.1 28267 2fwhA 134 4.37e+01 1xtoA 311 4.38e+01 1a8vA 121 4.40e+01 1a62 a.140.3.1,b.40.4.5 64712,64713 1jqpA 438 4.41e+01 b.61.5.1,d.3.1.1 77162,77163 1fdr 248 4.42e+01 1fdr b.43.4.2,c.25.1.1 25653,31543 1aipC 196 4.53e+01 1tfe a.5.2.2,d.43.1.1 58930,58931 1lh0A 213 4.55e+01 c.61.1.1 73896 1f5nA 592 4.55e+01 1dg3A a.114.1.1,c.37.1.8 19077,32152 1e79A 510 4.63e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18269,26434,32314 1ogsA 497 4.66e+01 b.71.1.2,c.1.8.3 86997,86998 1t9fA 187 4.71e+01 b.42.6.1 106710 1xdnA 277 4.74e+01 1yvkA 163 4.75e+01 1kf6A 602 4.76e+01 a.7.3.1,c.3.1.4,d.168.1.1 72394,72395,72396 2ampA 304 4.77e+01 1g6hA 257 4.82e+01 1gajA c.37.1.12 60318 1bouB 302 4.86e+01 1bouB c.56.6.1 33859 1uwdA 103 4.87e+01 1eulA 994 4.91e+01 1eulA 1qadA 111 4.96e+01 1qadA d.93.1.1 40498 1ybhA 590 4.98e+01 1nkqA 259 4.99e+01 d.177.1.1 103862 1zn6A 227 5.02e+01 1bb9 115 5.18e+01 1bb9 b.34.2.1 24554 1fokA 568 5.23e+01 2fokA a.4.5.12,a.4.5.12,a.4.5.12,c.52.1.12 16137,16138,16139,33325 1bmfA 510 5.23e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18281,26446,32326 1vmeA 410 5.25e+01 c.23.5.1,d.157.1.3 108893,108894 1rxdA 159 5.27e+01 1ex2A 189 5.29e+01 1ex2A c.51.4.2 33225 1l1dA 152 5.30e+01 b.88.1.3 73452 1rd5A 262 5.35e+01 1yy6A 155 5.42e+01 1b8mA 119 5.44e+01 1bndA g.17.1.3 44797 1h8eA 510 5.44e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 60738,60739,60740 1shsA 147 5.50e+01 1shsA b.15.1.1 23675 1y7rA 133 5.51e+01 2tscA 264 5.60e+01 1bkpA d.117.1.1 40952 1o9yA 84 5.66e+01 b.139.1.1 92692 1bndA 119 5.71e+01 1bndA g.17.1.3 44793 1kiuB 279 5.71e+01 b.2.3.2,b.2.3.2 72525,72526 1ei1A 391 5.79e+01 1aj6 d.14.1.3,d.122.1.2 37570,41104 1y7mA 164 5.81e+01 1s3iA 310 5.82e+01 b.46.1.1,c.65.1.1 98435,98436 1lkkA 105 5.85e+01 1lckA d.93.1.1 40412 1uzcA 71 5.86e+01 a.159.2.1 100222 1fm0E 150 5.87e+01 1fmaE d.41.5.1 38629 1n0qA 93 5.88e+01 k.37.1.1 79754 1vm8A 534 5.90e+01 1l2tA 235 5.91e+01 c.37.1.12 73514 1v77A 212 5.92e+01 c.6.3.2 108402 1fjeB 175 5.93e+01 1fj7A d.58.7.1,d.58.7.1 39210,39211 1fmaE 150 5.98e+01 1fmaE d.41.5.1 38630 2f6uA 234 5.99e+01 1xebA 150 6.05e+01 2rmpA 361 6.09e+01 2rmpA b.50.1.2 26825 1se8A 301 6.12e+01 b.40.4.3 105448 1ci8A 392 6.14e+01 e.3.1.1 64765 1txyA 104 6.14e+01 1kssA 571 6.15e+01 a.138.1.3,c.3.1.4,d.168.1.1 72928,72929,72930 1wosA 364 6.15e+01 b.44.2.1,d.250.1.1 109468,109469 2cu3A 64 6.18e+01 1qjdA 571 6.19e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19695,30432,42315 1e39A 571 6.20e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19694,30431,42314 1m64A 571 6.20e+01 a.138.1.3,c.3.1.4,d.168.1.1 78683,78684,78685 2go8A 122 6.21e+01 1gutA 68 6.27e+01 b.40.6.1 65576 1cof 143 6.28e+01 1cof d.109.1.2 40860 1xssA 225 6.30e+01 1zn8A 180 6.32e+01 1xtqA 177 6.33e+01 1mzhA 225 6.39e+01 c.1.10.1 79698 1mn4A 282 6.39e+01 b.2.5.7 79313 2fnaA 357 6.40e+01 1n3jA 119 6.42e+01 b.85.7.2 79963 1q2yA 140 6.43e+01 d.108.1.1 95655 1h3iA 293 6.45e+01 b.76.2.1,b.85.7.1 76635,76636 1qsoA 149 6.48e+01 1qsmA d.108.1.1 40812 1o4tA 133 6.49e+01 b.82.1.9 86622 2bkdN 134 6.54e+01 2asi 360 6.58e+01 2rmpA b.50.1.2 26824 1bywA 110 6.63e+01 1bywA d.110.3.6 40912 1m56B 264 6.63e+01 b.6.1.2,f.17.2.1 74472,74473 2c0cA 362 6.65e+01 1ynmA 247 6.68e+01 1cjaA 342 6.85e+01 1cjaA d.144.1.3 41708 1w79A 489 6.86e+01 2f4iA 197 6.88e+01 2c71A 216 6.95e+01 1lvoA 302 6.97e+01 b.47.1.4 74284 2gpr 154 6.99e+01 1gpr b.84.3.1 28269 1hvyA 288 6.99e+01 1bkpA d.117.1.1 41049 1eguA 731 7.06e+01 1eguA a.102.3.2,b.24.1.1,b.30.5.2 18850,23899,24423 1ge8A 249 7.06e+01 1plq d.131.1.2,d.131.1.2 41398,41399 2ahqA 76 7.16e+01 1mvwB 145 7.16e+01 i.15.1.1 79524 1ypcI 64 7.21e+01 2sniI d.40.1.1 38570 1sflA 238 7.23e+01 1pqzA 238 7.23e+01 b.1.1.2,d.19.1.1 104297,104298 2abwA 227 7.33e+01 1eu1A 780 7.36e+01 1dmr b.52.2.2,c.81.1.1 26903,35311 1dg6A 191 7.45e+01 1d4vB b.22.1.1 23883 1iyxA 432 7.56e+01 c.1.11.1,d.54.1.1 83815,83816 2a4nA 182 7.56e+01 1l0bA 229 7.57e+01 c.15.1.3,c.15.1.3 73391,73392 2ffjA 300 7.66e+01 1mt6A 280 7.66e+01 b.76.2.1,b.85.7.1 79446,79447 1tib 269 7.68e+01 3tgl c.69.1.17 34738 1scmB 145 7.69e+01 1wdcB a.39.1.5 17304 1q3iA 214 7.72e+01 d.220.1.1 104524 1uwfA 158 7.73e+01 1hkfA 122 7.76e+01 b.1.1.1 83553 1e8uA 454 7.76e+01 1e8tA b.68.1.1 59389 1g2hA 61 7.83e+01 1g2hA a.4.1.12 60224 1su4A 994 7.87e+01 b.82.7.1,c.108.1.7,d.220.1.1,f.33.1.1 98993,98994,98995,98996 1iq8A 582 7.87e+01 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8.91e+01 1lxkA 721 8.94e+01 a.102.3.2,b.24.1.1,b.30.5.2 74331,74332,74333 1o50A 157 8.96e+01 d.37.1.1,d.37.1.1 92478,92479 1sfjA 238 8.97e+01 1vif 62 8.97e+01 1vie b.34.4.1 24593 1s5lO 246 8.99e+01