# 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 1tp5A 119 1.82e-16 2fe5A 94 2.19e-16 1be9A 119 3.00e-16 1pdr b.36.1.1 24774 1bfeA 119 5.12e-16 1pdr b.36.1.1 24775 2fneA 117 9.66e-16 1g9oA 91 1.13e-15 1pdr b.36.1.1 60400 1pdr 99 2.19e-15 1pdr b.36.1.1 24771 2fcfA 103 3.24e-15 1n7eA 97 4.02e-15 b.36.1.1 91691 1qavA 90 4.58e-15 1qauA b.36.1.1 24777 1i92A 91 4.67e-15 1pdr b.36.1.1 61990 1q3oA 109 1.48e-14 b.36.1.1 95700 1n7fA 97 1.54e-14 b.36.1.1 91692 2h2bA 107 1.06e-13 1ihjA 98 1.48e-13 1pdr b.36.1.1 62382 1kwaA 88 3.91e-13 1kwaA b.36.1.1 24772 1l6oA 95 3.99e-13 b.36.1.1 84534 2h3lA 103 7.32e-13 1mfgA 95 8.74e-13 b.36.1.1 79043 1n99A 166 8.96e-13 b.36.1.1,b.36.1.1 85459,85460 1wf7A 103 1.06e-12 1i16 130 1.19e-12 1i16 b.36.1.2 24787 1qavB 115 1.32e-12 1qauA b.36.1.1 24780 1kwaB 88 1.48e-12 1kwaA b.36.1.1 24773 2f0aA 98 1.68e-12 1nf3C 128 2.11e-12 b.36.1.1 85596 1qauA 112 2.21e-12 1qauA b.36.1.1 24779 1b8qA 127 6.09e-12 1qauA b.36.1.1 24781 2f5yA 91 1.33e-11 1v5lA 103 1.67e-11 b.36.1.1 108378 1m5zA 91 2.82e-11 b.36.1.1 78676 1nteA 82 3.41e-10 b.36.1.1 86163 1r6jA 82 5.38e-10 b.36.1.1 97151 1fc6A 388 8.01e-10 1fc6A b.36.1.3,c.14.1.2 64738,64739 1lcyA 325 4.10e-07 b.36.1.4,b.47.1.1 73834,73835 1te0A 318 1.26e-05 1ky9B 448 1.12e-04 b.36.1.4,b.36.1.4,b.47.1.1 73200,73201,73202 1y8tA 324 1.58e-04 1sotA 320 1.15e-02 b.36.1.4,b.47.1.1 105852,105853 1ky9A 448 1.87e-02 b.36.1.4,b.47.1.1 73198,73199 2d4pA 141 9.12e-01 1vqqA 646 1.61e+00 1bx4A 345 2.22e+00 1bx4A c.72.1.1 34935 1mwsA 646 2.55e+00 d.17.4.5,d.175.1.1,e.3.1.1 79592,79593,79594 1mwrA 646 2.69e+00 d.17.4.5,d.175.1.1,e.3.1.1 79586,79587,79588 1db3A 372 2.70e+00 1db3A c.2.1.2 29813 1gph1 465 2.97e+00 1ecfB 1ao0A 459 3.03e+00 1ecfB c.61.1.1,d.153.1.1 34049,41816 2fe7A 166 3.45e+00 1uc2A 481 3.52e+00 d.261.1.1 99161 1fr3A 67 3.76e+00 1fr3A b.40.6.1 25436 1t6t1 118 4.09e+00 2bh8A 101 4.67e+00 1ciqA 40 4.75e+00 2sniI d.40.1.1 38576 1o6uA 403 4.90e+00 a.5.3.1,b.132.1.1,c.13.1.1 92589,92590,92591 1coaI 64 5.12e+00 2sniI d.40.1.1 38574 1olmA 403 5.25e+00 a.5.3.1,b.132.1.1,c.13.1.1 104008,104009,104010 1g2qA 187 5.44e+00 c.61.1.1 65117 1x3mA 415 6.12e+00 1g57A 217 6.77e+00 1g57A d.115.1.2 60253 1vheA 373 7.40e+00 b.49.3.1,c.56.5.4 100669,100670 1ti6A 875 7.44e+00 b.52.2.2,c.81.1.1 106974,106975 2b18A 164 7.72e+00 1fxlA 167 8.01e+00 1b7fA d.58.7.1,d.58.7.1 39183,39184 1dfd 64 8.31e+00 1fxd d.58.1.4 38995 1jjiA 311 8.94e+00 c.69.1.2 66766 2bs3A 656 9.17e+00 1cis 66 9.34e+00 2sniI k.1.1.1 46375 1qlaA 656 9.56e+00 1qlaA a.7.3.1,c.3.1.4,d.168.1.1 16328,30427,42310 1jnyA 435 9.68e+00 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1rutX 188 9.80e+00 1dax 64 9.80e+00 1fxd d.58.1.4 38996 1g7rA 594 1.00e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25716,25717,31034,32149 1r13A 148 1.05e+01 d.169.1.1,h.1.1.1 96782,96783 1to2I 64 1.07e+01 1rgzA 363 1.08e+01 e.3.1.1 97457 1ga0A 364 1.08e+01 1gceA e.3.1.1 60410 1onhA 364 1.08e+01 e.3.1.1 93357 2bltA 361 1.10e+01 1gceA e.3.1.1 42739 2sniI 83 1.11e+01 2sniI d.40.1.1 38573 1gceA 364 1.11e+01 1gceA e.3.1.1 42738 1lw6I 64 1.11e+01 d.40.1.1 74294 1x47A 98 1.26e+01 1rgyA 360 1.28e+01 e.3.1.1 97456 1s4iA 175 1.31e+01 1fxrA 64 1.35e+01 1fxd d.58.1.4 38993 1zkjA 359 1.41e+01 1kw4A 89 1.44e+01 a.60.1.2 73077 1a62 130 1.47e+01 1a62 a.140.3.1,b.40.4.5 64708,64709 1fr1A 361 1.51e+01 1gceA e.3.1.1 42734 1g7sA 594 1.60e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 1xtlA 175 1.67e+01 1earA 147 1.68e+01 b.107.1.1,d.58.38.1 64875,64876 1xtmA 175 1.71e+01 1zsyA 357 1.74e+01 1y0bA 197 1.75e+01 1vkmA 297 1.78e+01 c.138.1.1 108670 1skyB 502 1.82e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18313,26478,32358 1ugmA 125 1.85e+01 d.15.1.3 107827 1g8aA 227 1.93e+01 c.66.1.3 90506 1q52A 314 1.95e+01 c.14.1.3 95846 2aexA 346 1.97e+01 1pi4A 358 2.02e+01 e.3.1.1 94700 1fsyA 358 2.03e+01 1gceA e.3.1.1 60016 2c5qA 240 2.03e+01 1viuA 203 2.27e+01 d.113.1.1 100771 2blsA 358 2.29e+01 1gceA e.3.1.1 42747 1t3qB 788 2.30e+01 d.41.1.1,d.133.1.1 106369,106370 2bsyA 278 2.31e+01 1kzlA 208 2.36e+01 b.43.4.3,b.43.4.3 77635,77636 2ffyA 358 2.39e+01 1l0gA 358 2.42e+01 e.3.1.1 73400 1ypcI 64 2.45e+01 2sniI d.40.1.1 38570 1kvlA 358 2.49e+01 e.3.1.1 73062 1g7tA 594 2.57e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25714,25715,31033,32148 1vraB 215 2.62e+01 1eb0A 147 2.66e+01 b.107.1.1,d.58.38.1 64890,64891 3mefA 69 2.69e+01 1mjc b.40.4.5 25320 1koe 172 2.71e+01 1koe d.169.1.5 42448 1a63 130 2.72e+01 1a62 a.140.3.1,b.40.4.5 64710,64711 1eypA 222 2.77e+01 1eypA d.36.1.1 38536 1ojhA 65 2.77e+01 a.214.1.1 103976 1eyqA 222 2.78e+01 1eypA d.36.1.1 38534 1jepA 222 2.78e+01 d.36.1.1 66612 1zn8A 180 2.99e+01 1xfoA 357 3.05e+01 2fvgA 340 3.12e+01 1vybA 238 3.15e+01 d.151.1.1 108897 3sxlA 184 3.18e+01 1b7fA d.58.7.1,d.58.7.1 39173,39174 1h3iA 293 3.18e+01 b.76.2.1,b.85.7.1 76635,76636 1y9kA 157 3.22e+01 1se8A 301 3.27e+01 b.40.4.3 105448 1y9wA 140 3.29e+01 2sxl 88 3.29e+01 1b7fA d.58.7.1 39179 1kk1A 410 3.31e+01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1iyu 79 3.34e+01 1iyu b.84.1.1 28227 2gwnA 452 3.38e+01 2cc0A 195 3.44e+01 1y0yA 353 3.52e+01 1ifyA 49 3.53e+01 a.5.2.1 71207 1rd5A 262 3.55e+01 1trb 320 3.64e+01 1trb c.3.1.5,c.3.1.5 30529,30530 1mt6A 280 3.67e+01 b.76.2.1,b.85.7.1 79446,79447 1xdnA 277 3.74e+01 1kssA 571 3.75e+01 a.138.1.3,c.3.1.4,d.168.1.1 72928,72929,72930 1uh5A 329 3.76e+01 c.2.1.2 107840 1qjdA 571 3.77e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19695,30432,42315 1e39A 571 3.78e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19694,30431,42314 1m64A 571 3.78e+01 a.138.1.3,c.3.1.4,d.168.1.1 78683,78684,78685 1uc7A 125 3.85e+01 c.47.1.1 99163 2a6zA 222 3.85e+01 1zn6A 227 3.88e+01 1csp 67 3.91e+01 1mjc b.40.4.5 25321 1cq3A 233 3.98e+01 1cq3A b.27.1.1 23923 1l1dA 152 4.02e+01 b.88.1.3 73452 1sw5A 275 4.08e+01 c.94.1.1 106069 1vj0A 380 4.10e+01 b.35.1.2,c.2.1.1 100786,100787 2ck3A 510 4.12e+01 1vc3B 97 4.15e+01 1e79A 510 4.27e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18269,26434,32314 1ih8A 271 4.30e+01 2nsyA c.26.2.1 62377 2nsyA 271 4.30e+01 2nsyA c.26.2.1 31612 1s50A 259 4.30e+01 1nsyA 271 4.31e+01 2nsyA c.26.2.1 31614 1n0qA 93 4.32e+01 k.37.1.1 79754 1kqpA 271 4.32e+01 c.26.2.1 72883 1mkmA 249 4.39e+01 a.4.5.33,d.110.2.2 79242,79243 1on0A 158 4.47e+01 d.108.1.1 87095 1bzyA 217 4.49e+01 1qk3A c.61.1.1 34071 1ufhA 180 4.49e+01 d.108.1.1 88485 1rxdA 159 4.54e+01 1whi 122 4.55e+01 1whi b.39.1.1 24810 1b4uB 302 4.62e+01 1bouB c.56.6.1 33861 1iezA 217 4.65e+01 d.115.1.2 66129 2f4iA 197 4.67e+01 1wvhA 134 4.68e+01 1p7tA 731 4.68e+01 c.1.13.1 94319 1mjc 69 4.72e+01 1mjc b.40.4.5 25319 1bmfA 510 4.83e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18281,26446,32326 1y1uA 585 4.85e+01 1ggrA 168 4.87e+01 1gpr b.84.3.1 28279 1kf6A 602 4.93e+01 a.7.3.1,c.3.1.4,d.168.1.1 72394,72395,72396 1reqD 637 4.96e+01 1reqB c.1.19.1,c.23.6.1 29623,31250 1pzxA 289 4.98e+01 c.119.1.1 95484 1h8eA 510 4.98e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 60738,60739,60740 7reqB 637 5.04e+01 1reqB c.1.19.1,c.23.6.1 29617,31244 1c9oA 66 5.08e+01 1mjc b.40.4.5 25325 1jndA 420 5.08e+01 c.1.8.5,d.26.3.1 71757,71758 1mqdA 261 5.19e+01 c.94.1.1 85049 1m5dA 263 5.19e+01 c.94.1.1 78641 1tde 316 5.22e+01 1trb c.3.1.5,c.3.1.5 30531,30532 1axwA 265 5.22e+01 1bkpA d.117.1.1 40938 2aop 497 5.25e+01 2aop d.58.36.1,d.58.36.1,d.134.1.1,d.134.1.1 39503,39504,41427,41428 1tys 265 5.26e+01 1bkpA d.117.1.1 40937 1mqiA 263 5.27e+01 c.94.1.1 91398 1fl2A 310 5.30e+01 1hyuA c.3.1.5,c.3.1.5 59869,59870 1shsA 147 5.33e+01 1shsA b.15.1.1 23675 1lcjA 109 5.43e+01 1qadA d.93.1.1 40414 1m5eA 263 5.43e+01 c.94.1.1 78642 1bdfA 235 5.49e+01 1bdfA d.74.3.1,d.181.1.1 39727,42602 2g8oA 264 5.53e+01 1aiqA 264 5.58e+01 1bkpA d.117.1.1 40967 1egpA 45 5.60e+01 1egpA d.40.1.1 38561 1yy6A 155 5.61e+01 1lkkA 105 5.64e+01 1lckA d.93.1.1 40412 1vjuA 309 5.68e+01 d.248.1.1 100835 1qhlA 227 5.74e+01 1qhlA c.37.1.12 32382 1lj1A 571 5.78e+01 a.138.1.3,c.3.1.4,d.168.1.1 78023,78024,78025 2fwhA 134 5.78e+01 2g8mA 264 5.80e+01 1y0pA 571 5.81e+01 1p2hA 571 5.83e+01 a.138.1.3,c.3.1.4,d.168.1.1 93930,93931,93932 1q9iA 571 5.85e+01 a.138.1.3,c.3.1.4,d.168.1.1 96273,96274,96275 1aop 497 5.85e+01 2aop d.58.36.1,d.58.36.1,d.134.1.1,d.134.1.1 39501,39502,41425,41426 1f3z 161 5.87e+01 1gpr b.84.3.1 28273 1rl2A 137 5.89e+01 1rl2A b.34.5.3,b.40.4.5 24610,25342 1z3eA 132 5.94e+01 1uzcA 71 5.97e+01 a.159.2.1 100222 2go8A 122 5.98e+01 2asi 360 6.06e+01 2rmpA b.50.1.2 26824 1oi7A 288 6.07e+01 c.2.1.8,c.23.4.1 87049,87050 1pfzA 380 6.10e+01 1smrA b.50.1.2 26881 1qqqA 264 6.16e+01 1bkpA d.117.1.1 40931 1evfA 264 6.16e+01 1bkpA d.117.1.1 40932 1kiuB 279 6.19e+01 b.2.3.2,b.2.3.2 72525,72526 1xtoA 311 6.23e+01 1g6hA 257 6.33e+01 1gajA c.37.1.12 60318 1wywA 230 6.47e+01 2fa1A 160 6.51e+01 1reqB 637 6.52e+01 1reqB c.1.19.1,c.23.6.1 29621,31248 1zkpA 268 6.54e+01 1o50A 157 6.72e+01 d.37.1.1,d.37.1.1 92478,92479 2fojA 155 6.77e+01 1xe1A 116 6.85e+01 b.43.3.1 109571 1gutA 68 6.86e+01 b.40.6.1 65576 1ex2A 189 6.88e+01 1ex2A c.51.4.2 33225 1fm0E 150 6.94e+01 1fmaE d.41.5.1 38629 1uwdA 103 7.04e+01 1qb5D 99 7.09e+01 b.40.2.1 88357 1glaF 168 7.12e+01 1gpr b.84.3.1 28274 1xebA 150 7.20e+01 2cyjA 118 7.21e+01 1zclA 180 7.21e+01 1cjaA 342 7.28e+01 1cjaA d.144.1.3 41708 1a8vA 121 7.34e+01 1a62 a.140.3.1,b.40.4.5 64712,64713 1fmaE 150 7.36e+01 1fmaE d.41.5.1 38630 1zoyA 622 7.36e+01 2f6uA 234 7.37e+01 1ako 268 7.41e+01 1ako d.151.1.1 41779 1tiiD 99 7.42e+01 1tiiD b.40.2.1 24965 1sflA 238 7.44e+01 1v77A 212 7.52e+01 c.6.3.2 108402 1bouB 302 7.57e+01 1bouB c.56.6.1 33859 1uwfA 158 7.60e+01 1lf2A 331 7.60e+01 b.50.1.2 77914 1dioA 554 7.77e+01 1dioA c.1.19.3 29656 2rmpA 361 7.90e+01 2rmpA b.50.1.2 26825 1m1hA 248 7.90e+01 b.114.1.1,d.58.42.1 78415,78416 1eexA 554 7.95e+01 1dioA c.1.19.3 29650 1vhzA 198 8.04e+01 d.113.1.1 100718 1tsm 316 8.05e+01 1bkpA d.117.1.1 41024 1hcz 252 8.08e+01 1hcz b.2.6.1,b.84.2.2 22464,28250 2pcfB 250 8.12e+01 1hcz i.4.1.1 45911 1aipC 196 8.13e+01 1tfe a.5.2.2,d.43.1.1 58930,58931 1qadA 111 8.21e+01 1qadA d.93.1.1 40498 1nziA 159 8.24e+01 b.23.1.1,g.3.11.1 86449,86450 1g2hA 61 8.24e+01 1g2hA a.4.1.12 60224 1ad3A 452 8.33e+01 1ad3A c.82.1.1 35335 1ei1A 391 8.51e+01 1aj6 d.14.1.3,d.122.1.2 37570,41104 2cu3A 64 8.58e+01 1vkcA 158 8.65e+01 2ampA 304 8.66e+01 1uheA 97 8.75e+01 1ybhA 590 8.80e+01 1mvwB 145 8.91e+01 i.15.1.1 79524 1hvyA 288 8.96e+01 1bkpA d.117.1.1 41049