# List of top-scoring protein chains for t2k-100-30-n_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 1nxmA 197 1.91e-01 b.82.1.1 86385 1ih7A 903 6.48e-01 1clqA c.55.3.5,e.8.1.1 62375,62376 1mwrA 646 1.15e+00 d.17.4.5,d.175.1.1,e.3.1.1 79586,79587,79588 2al3A 90 1.25e+00 1ld4A 264 1.43e+00 i.6.1.1 77886 1a0cA 438 1.48e+00 1a0cA c.1.15.3 29529 1svpA 161 1.52e+00 1svpA b.47.1.3 26384 1i1qA 520 1.90e+00 1qdlA d.161.1.1 61543 1wxxA 382 2.36e+00 1goh 639 2.83e+00 1gof b.1.18.2,b.18.1.1,b.69.1.1 21809,23711,27633 1fkoA 543 3.18e+00 1rthA c.55.3.1,e.8.1.2 33612,43094 1gzwA 134 3.74e+00 b.29.1.3 90535 1jlxA 304 4.10e+00 1jlyA b.42.3.1,b.42.3.1 25583,25584 1bio 228 4.13e+00 5ptp b.47.1.2 26314 1bkcE 256 4.54e+00 1bkcA d.92.1.10 40333 1uwwA 191 4.74e+00 b.18.1.23 108079 1bkcI 256 4.82e+00 1bkcA d.92.1.10 40334 1dst 228 5.07e+00 1a7s b.47.1.2 26318 1y7bA 542 5.10e+00 2gupA 292 5.13e+00 6prcH 258 5.33e+00 6prcH b.41.1.1,f.23.10.1 25457,43436 1atg 231 5.41e+00 1atg c.94.1.1 35834 1igwA 434 5.46e+00 c.1.12.7 62370 2bepA 159 5.52e+00 1h9hE 223 5.54e+00 b.47.1.2 103810 1jatA 155 5.73e+00 1u9aA d.20.1.1 62818 1b9kA 238 6.89e+00 1qtsA b.1.10.1,d.105.1.1 22315,40791 1qipA 183 7.55e+00 1qipA d.32.1.1 38470 1l0qA 391 7.67e+00 b.1.3.1,b.69.2.3 77644,77645 1ecpA 238 7.89e+00 1ecpA c.56.2.1 33775 1gyfA 62 8.06e+00 1gyfA d.76.1.1 39749 1rthA 560 8.08e+00 1rthA c.55.3.1,e.8.1.2 33576,43028 1fniA 223 8.10e+00 5ptp b.47.1.2 25962 1fjsA 234 8.36e+00 1ucyE b.47.1.2 26336 1gxrA 337 9.31e+00 b.69.4.1 70722 1ppjA 446 9.96e+00 d.185.1.1,d.185.1.1 104252,104253 1csyA 112 1.00e+01 1lckA d.93.1.1 40519 1aorA 605 1.01e+01 1b25A a.110.1.1,d.152.1.1 19042,41794 1hnjA 317 1.01e+01 1hn9A c.95.1.2,c.95.1.2 35969,35970 1kqfA 1015 1.02e+01 b.52.2.2,c.81.1.1 72871,72872 2mprA 421 1.03e+01 2mprA f.4.3.2 43788 2awaA 390 1.05e+01 1d2kA 392 1.11e+01 1d2kA c.1.8.5,d.26.3.1 29008,38442 1wkbA 810 1.12e+01 1tqzA 133 1.15e+01 1umwA 237 1.16e+01 d.223.1.2,d.223.1.2 99631,99632 1a22B 238 1.16e+01 1axiB b.1.2.1,b.1.2.1 22003,22004 2pia 321 1.22e+01 2pia b.43.4.2,c.25.1.2,d.15.4.2 25663,31553,37704 1uwcA 261 1.23e+01 c.69.1.17 100101 1d7pM 159 1.26e+01 1cztA b.18.1.2 23718 1h4wA 224 1.27e+01 b.47.1.2 65622 1xbfA 140 1.28e+01 d.273.1.1 109538 1qtsA 247 1.35e+01 1qtsA b.1.10.1,d.105.1.1 22313,40789 1kyfA 247 1.35e+01 b.1.10.1,d.105.1.1 73220,73221 1s31A 273 1.36e+01 1ll7A 392 1.40e+01 c.1.8.5,d.26.3.1 78085,78086 1um5H 217 1.41e+01 1rz2A 254 1.41e+01 b.100.1.1 105130 1nziA 159 1.47e+01 b.23.1.1,g.3.11.1 86449,86450 3pga1 337 1.52e+01 4pgaA 1ayzA 169 1.53e+01 1u9aA d.20.1.1 38326 1at1A 310 1.56e+01 3csuA c.78.1.1,c.78.1.1 35168,35169 1euu 605 1.58e+01 1eut b.1.18.2,b.18.1.1,b.68.1.1 21892,23713,27610 1axiB 236 1.58e+01 1axiB b.1.2.1,b.1.2.1 21997,21998 1hcxA 127 1.61e+01 b.109.1.1 65800 1q8bA 105 1.64e+01 d.58.4.6 96201 1khiA 176 1.68e+01 b.34.5.2,b.40.4.5 77408,77409 2gd9A 189 1.68e+01 1iyeA 309 1.74e+01 e.17.1.1 83786 1kum 108 1.78e+01 1kum b.3.1.1 22525 1kw3B 292 1.80e+01 d.32.1.3,d.32.1.3 77549,77550 1f3yA 165 1.84e+01 d.113.1.1 59635 1fl2A 310 1.84e+01 1hyuA c.3.1.5,c.3.1.5 59869,59870 2a31A 223 1.97e+01 1ed5A 444 2.00e+01 1nseA d.174.1.1 42530 1cjaA 342 2.04e+01 1cjaA d.144.1.3 41708 2aiqA 231 2.08e+01 1j58A 385 2.10e+01 b.82.1.2 71531 1wcqA 601 2.10e+01 1eps 427 2.12e+01 1eps d.68.2.2 39586 1mctA 223 2.14e+01 5ptp b.47.1.2 25961 2ghsA 326 2.15e+01 1h8gA 95 2.18e+01 b.109.1.1 65735 1ppjD 241 2.27e+01 a.3.1.3,f.23.11.1 104258,104259 1s83A 223 2.27e+01 b.47.1.2 98718 1rypI 222 2.28e+01 d.153.1.4 41877 1musA 477 2.28e+01 c.55.3.4 79494 2gu3A 136 2.28e+01 1avwA 223 2.37e+01 5ptp b.47.1.2 25965 1eut 605 2.40e+01 1eut b.1.18.2,b.18.1.1,b.68.1.1 21891,23712,27609 1khdA 345 2.51e+01 a.46.2.1,c.27.1.1 77400,77401 1ywsA 82 2.51e+01 2fafA 608 2.54e+01 4bcl 366 2.54e+01 4bcl b.75.1.1 27968 1gr0A 367 2.58e+01 c.2.1.3,d.81.1.3 70379,70380 1p8xA 344 2.59e+01 d.109.1.1,d.109.1.1,d.109.1.1 94365,94366,94367 2fh1A 344 2.62e+01 1gjjA 168 2.65e+01 a.140.1.1,a.140.1.1 83291,83292 1lcyA 325 2.66e+01 b.36.1.4,b.47.1.1 73834,73835 1z2uA 150 2.71e+01 1p63A 144 2.75e+01 b.42.1.1 94153 1prq 125 2.77e+01 3nul d.110.1.1 40883 1lopA 164 2.79e+01 2cpl b.62.1.1 27510 1j4aA 333 2.82e+01 c.2.1.4,c.23.12.1 71502,71503 1w2wB 191 2.85e+01 1xsjA 778 2.86e+01 1lp3A 519 2.86e+01 b.121.5.2 74169 1m2tB 263 2.89e+01 b.42.2.1,b.42.2.1 84762,84763 1xdwA 331 2.89e+01 1dxrH 258 2.96e+01 6prcH b.41.1.1,f.23.10.1 25456,43433 1a3qA 285 3.00e+01 1a3qA b.1.18.1,b.2.5.3 21932,22447 2fimA 276 3.05e+01 1dzfA 215 3.05e+01 1dzfA c.52.3.1,d.78.1.1 33344,39753 1x8qA 184 3.09e+01 1ido 192 3.09e+01 1ido c.62.1.1 34139 1um0A 365 3.16e+01 d.258.1.1 107942 1lam 484 3.19e+01 1lam c.50.1.1,c.56.5.3 33166,33829 1qmuA 380 3.22e+01 1qmuA b.3.2.1,c.56.5.1 22534,33827 1olzA 663 3.23e+01 b.1.1.4,b.69.12.1,g.16.2.1 93341,93342,93343 1dpo 223 3.26e+01 5ptp b.47.1.2 25975 1jq4A 98 3.29e+01 d.15.4.2 67083 1delA 241 3.36e+01 1dekA c.37.1.1 31844 1l5oA 356 3.38e+01 c.39.1.1 77711 1k2fA 190 3.44e+01 b.8.1.2 68054 2al1A 436 3.53e+01 1d1vA 444 3.55e+01 1nseA d.174.1.1 59101 2d09A 407 3.57e+01 1q1uA 144 3.59e+01 b.42.1.1 95608 1kl7A 514 3.67e+01 c.79.1.1 72678 1eq9A 222 3.68e+01 5ptp b.47.1.2 26068 1h1iB 350 3.70e+01 b.82.1.5 76470 1vzwA 244 3.71e+01 1af6A 421 3.76e+01 2mprA f.4.3.2 43772 1jbaA 204 3.76e+01 1rec a.39.1.5 17330 1qq2A 199 3.78e+01 1qq2A c.47.1.10 33064 1plq 258 3.82e+01 1plq d.131.1.2,d.131.1.2 41388,41389 1abrB 267 3.84e+01 1abrB b.42.2.1,b.42.2.1 25563,25564 1dx5I 118 3.88e+01 1dx5I g.3.11.1,g.3.11.1,g.3.11.1 44302,44303,44304 1qhtA 775 3.92e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1cojA 212 3.95e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1b63A 333 3.96e+01 1b63A d.14.1.3,d.122.1.2 37566,41107 1gw9A 388 3.97e+01 c.1.15.3 70658 1oq1A 223 3.97e+01 b.29.1.17 93408 1szqA 483 3.98e+01 e.44.1.1 99045 1ebuA 358 3.98e+01 1ebuA c.2.1.3,d.81.1.2 30035,39950 1t3bA 211 4.01e+01 c.47.1.9,d.17.3.1 106341,106342 1dioB 224 4.05e+01 1dioB c.51.3.1 33219 1deuA 277 4.09e+01 1theB d.3.1.1 37085 1a67 108 4.12e+01 1cewI d.17.1.2 38000 1mnzA 388 4.13e+01 c.1.15.3 79328 2d2jA 329 4.13e+01 1sqsA 242 4.15e+01 c.23.5.5 98968 2gnpA 266 4.17e+01 2be1A 339 4.19e+01 1s5aA 150 4.20e+01 d.17.4.10 98525 1anc 223 4.20e+01 5ptp b.47.1.2 25982 1iraX 152 4.27e+01 1irp b.42.1.2 25556 1aky 221 4.29e+01 1zin c.37.1.1,g.41.2.1 31896,45197 1k1eA 180 4.31e+01 c.108.1.5 67995 2cnqA 306 4.31e+01 1nnxA 109 4.32e+01 b.40.10.1 92013 1ry9A 145 4.35e+01 d.198.1.1 98094 1gy7A 125 4.36e+01 d.17.4.2 70738 1aohB 147 4.43e+01 1aohA b.2.2.2 22402 1syxB 86 4.44e+01 1ycsA 199 4.48e+01 1tupA b.2.5.2 22433 1yuwA 554 4.49e+01 1jqgA 433 4.54e+01 c.56.5.1,d.58.3.1 71791,71792 1yprA 125 4.56e+01 3nul d.110.1.1 40888 1hmvA 560 4.59e+01 1rthA c.55.3.1,e.8.1.2 33587,43046 1vl2A 421 4.63e+01 c.26.2.1,d.210.1.1 108708,108709 1qfoC 119 4.73e+01 1qfoA b.1.1.1 19710 2olbA 517 4.76e+01 1jevA c.94.1.1 35721 1oneA 436 4.79e+01 4enl c.1.11.1,d.54.1.1 29200,38844 1ps2 60 4.79e+01 2pspA g.16.1.1 44746 1fa8A 135 4.81e+01 1qipA d.32.1.1 38486 1qx4A 274 4.81e+01 b.43.4.2,c.25.1.1 104624,104625 1gbg 214 4.82e+01 1axkA b.29.1.2 24171 5reqA 727 4.82e+01 1reqA c.1.19.1,c.23.6.1 29632,31259 1lxdA 100 4.87e+01 1lfdA d.15.1.5 37624 1dxrL 273 4.91e+01 6prcL f.26.1.1 43431 2b18A 164 4.92e+01 1an1E 223 4.94e+01 5ptp b.47.1.2 25970 1who 96 4.98e+01 1who b.7.3.1 23215 2cw6A 298 5.00e+01 1vr3A 191 5.04e+01 1m98A 317 5.06e+01 a.175.1.1,d.17.4.6 78866,78867 1lybB 241 5.06e+01 1smrA 1h7sA 365 5.06e+01 d.14.1.3,d.122.1.2 65705,65706 1zq1C 633 5.06e+01 1ve4A 206 5.10e+01 1eu8A 409 5.11e+01 1eu8A c.94.1.1 59502 1cqyA 99 5.15e+01 1b9zA b.3.1.1 22527 1ao5A 237 5.16e+01 5ptp b.47.1.2 26334 1acf 125 5.22e+01 3nul d.110.1.1 40882 2ab5A 269 5.26e+01 1wljA 189 5.28e+01 1urrA 102 5.31e+01 d.58.10.1 107998 1ffkI 194 5.31e+01 1ffkI d.12.1.2 37494 3nul 130 5.32e+01 3nul d.110.1.1 40891 1gifA 115 5.34e+01 1dptA d.80.1.3 39837 1cewI 108 5.36e+01 1cewI d.17.1.2 37999 2apjA 260 5.38e+01 1ijqA 316 5.40e+01 1ijqA b.68.5.1,g.3.11.1 62506,62507 1pjbA 361 5.40e+01 1sayA c.2.1.4,c.23.12.2 30103,31363 1a63 130 5.40e+01 1a62 a.140.3.1,b.40.4.5 64710,64711 1f9zA 135 5.42e+01 1qipA d.32.1.1 38484 1r62A 160 5.44e+01 d.122.1.3 104816 1inp 400 5.46e+01 1inp e.7.1.1 42972 1apa 266 5.46e+01 1qi7A d.165.1.1 42205 1qrkA 731 5.46e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21889,22187,22188,37119 1ri6A 343 5.46e+01 b.69.11.1 97503 1sy3A 184 5.60e+01 b.60.1.1 106110 1nseA 444 5.61e+01 1nseA d.174.1.1 42534 1y4hA 188 5.66e+01 1q2bA 434 5.67e+01 b.29.1.10 95624 1q8fA 313 5.67e+01 c.70.1.1 96203 1yspA 181 5.74e+01 1vcdA 126 5.74e+01 1kvkA 395 5.75e+01 d.14.1.5,d.58.26.3 73060,73061 2al2A 436 5.81e+01 1ntyA 311 5.85e+01 a.87.1.1,b.55.1.1 103873,103874 1yr4A 237 5.87e+01 2ayh 214 5.89e+01 1axkA b.29.1.2 24172 1jqzA 146 5.89e+01 b.42.1.1 67109 1kn0A 212 5.92e+01 d.50.1.3 77444 1wwrA 171 5.95e+01 2f91A 237 6.03e+01 1cnzA 363 6.03e+01 1cnzA c.77.1.1 35061 1c1bB 440 6.03e+01 1rthA e.8.1.2 43077 1qttA 117 6.04e+01 1a1x b.63.1.1 27516 2bsaA 303 6.08e+01 3fruA 269 6.12e+01 1agdA b.1.1.2,d.19.1.1 20657,38150 1mf7A 194 6.19e+01 c.62.1.1 84937 1aliA 449 6.22e+01 1b8jA c.76.1.1 34996 1r8nA 185 6.23e+01 b.42.4.1 104851 1e4mM 501 6.23e+01 1e70M c.1.8.4 59226 1z90A 469 6.26e+01 1w5cB 510 6.27e+01 2cw9A 194 6.30e+01 1hxmA 229 6.30e+01 1hxmA b.1.1.1,b.1.1.2 61367,61368 1ge8A 249 6.30e+01 1plq d.131.1.2,d.131.1.2 41398,41399 1z47A 355 6.34e+01 1w34A 304 6.35e+01 1erxA 184 6.35e+01 1np1A b.60.1.1 27164 1a0k 131 6.35e+01 3nul d.110.1.1 40892 1b37B 472 6.35e+01 1b37B c.3.1.2,d.16.1.5 30390,37954 1q59A 172 6.39e+01 f.1.4.1 95881 1b37A 472 6.43e+01 1b37B c.3.1.2,d.16.1.5 30389,37953 1anjA 446 6.47e+01 1b8jA c.76.1.1 35008 1gmmA 133 6.51e+01 b.18.1.10 65314 1lrzA 426 6.56e+01 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 1i50H 146 6.56e+01 b.40.4.8 61761 1n1tA 641 6.57e+01 b.29.1.15,b.68.1.1 79821,79822 3ladA 476 6.61e+01 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30573,30574,40208 1aohA 147 6.63e+01 1aohA b.2.2.2 22401 1ojqA 212 6.68e+01 d.166.1.1 93146 1r77A 103 6.72e+01 1npuA 117 6.79e+01 b.1.1.1 92038 1zbtA 371 6.82e+01 1n62B 809 6.89e+01 d.41.1.1,d.133.1.1 80092,80093 1rdr 461 6.90e+01 1rdr e.8.1.4 43116 1b7gO 340 7.04e+01 1b7gO c.2.1.3,d.81.1.1 29992,39907 1by3A 714 7.07e+01 1by5A f.4.3.3 43801 3pchM 238 7.07e+01 3pchM b.3.6.1 22748 1xaa 345 7.09e+01 1cnzA c.77.1.1 35033 1dekA 241 7.13e+01 1dekA c.37.1.1 31842 1fkoB 440 7.14e+01 1rthA e.8.1.2 43095 1nlr 234 7.16e+01 2nlrA b.29.1.11 24345 1hzoA 271 7.19e+01 e.3.1.1 71092 1gosA 520 7.22e+01 c.3.1.2,d.16.1.5 65425,65426 1is2A 661 7.25e+01 a.29.3.2,a.29.3.2,e.6.1.2 71382,71383,71384 1dgfA 497 7.25e+01 1cf9A e.5.1.1 42782 1zsoA 164 7.36e+01 1pbyB 337 7.39e+01 b.69.2.2 94422 1a1nA 276 7.44e+01 1agdA b.1.1.2,d.19.1.1 20755,38267 1ts9A 102 7.46e+01 1wfyA 104 7.48e+01 1kyaA 499 7.49e+01 b.6.1.3,b.6.1.3,b.6.1.3 73203,73204,73205 7ahlA 293 7.49e+01 7ahlA f.6.1.1 43812 1qniA 581 7.51e+01 1qniA b.6.1.4,b.69.3.1 23042,27642 1xh3A 276 7.66e+01 1d6aB 262 7.71e+01 1qi7A d.165.1.1 42198 1vm7A 311 7.76e+01 c.72.1.1 108884 1i3zA 103 7.83e+01 d.93.1.1 83667 2bg9A 370 7.84e+01 1wvqA 167 7.84e+01 1r5tA 142 7.89e+01 c.97.1.1 104812 1h8eD 482 7.96e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 60747,60748,60749 1el5A 389 7.97e+01 1b3mA c.3.1.2,d.16.1.3 30369,37937 1u5uA 374 8.01e+01 1ybiA 288 8.08e+01 2c4xA 260 8.10e+01 1a3aA 148 8.15e+01 1a3aA d.112.1.1 40917 1q0qA 406 8.17e+01 a.69.3.1,c.2.1.3,d.81.1.3 104464,104465,104466 1bf2 750 8.18e+01 1bf2 b.1.18.2,b.71.1.1,c.1.8.1 21860,27787,28774 1mt6A 280 8.18e+01 b.76.2.1,b.85.7.1 79446,79447 1erjA 393 8.22e+01 1erjA b.69.4.1 27660 1vmhA 144 8.29e+01 3eipA 84 8.29e+01 3eipA d.26.2.1 38434 1c93A 265 8.31e+01 2ebn c.1.8.5 28998 1g5hA 454 8.31e+01 1g5hA c.51.1.1,d.104.1.1 60270,60271 1hs6A 611 8.32e+01 1hs6A a.118.1.7,b.98.1.1,d.92.1.13 61233,61234,61235 1jsg 114 8.33e+01 1a1x b.63.1.1 27513 1wzoA 246 8.33e+01 1tm0A 350 8.35e+01 d.21.1.3 107147 4ptp 223 8.37e+01 1vc3B 97 8.41e+01 2culA 232 8.48e+01 1b7fA 168 8.48e+01 1b7fA d.58.7.1,d.58.7.1 39169,39170 1han 297 8.50e+01 1han d.32.1.3,d.32.1.3 38506,38507 2pcdM 238 8.51e+01 3pchM b.3.6.1 22760 2gm6A 208 8.52e+01 1skoA 143 8.52e+01 d.110.7.1 105676 2gfaA 119 8.54e+01 1rdzA 337 8.56e+01 1frpA e.7.1.1 42882 1co6A 107 8.62e+01 1ycc a.3.1.1 15894 1eulA 994 8.63e+01 1eulA 1cv8 174 8.67e+01 1cv8 d.3.1.1 37089 1wakA 397 8.68e+01 1uv6A 210 8.83e+01 b.96.1.1 100030 2ddrA 306 8.86e+01 1upqA 123 8.88e+01 1eh9A 558 8.93e+01 1ehaA b.1.18.2,b.71.1.1,c.1.8.1 21858,27785,28772 1cvmA 353 8.93e+01 1qlgA b.68.3.1 27628 2aujD 309 8.95e+01 2az4A 429 8.97e+01 1yw5A 177 8.97e+01 1j99A 293 9.00e+01 c.37.1.5 71618