# List of top-scoring protein chains for t2k-100-30-str2 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 1rz1A 161 6.04e-28 b.45.1.2 -4088 1i0rA 169 5.56e-23 1i0rA b.45.1.2 61489 1i0sA 169 5.56e-23 1i0rA b.45.1.2 61491 1uscA 178 2.48e-22 b.45.1.2 -4074 1ejeA 192 1.95e-21 1ejeA b.45.1.2 25757 1cz3A 168 2.65e-01 1d1gA c.71.1.1 34891 1krhA 338 3.26e-01 b.43.4.2 72891 c.25.1.2 72892 d.15.4.2 72893 1d1gA 168 3.36e-01 1d1gA c.71.1.1 34889 1ne2A 200 3.68e-01 c.66.1.32 85586 1rxxA 421 8.25e-01 unknown_sccs -10982 1axj 122 9.31e-01 1axj b.45.1.1 25749 1fhgA 154 1.01e+00 1tlk b.1.1.4 21706 1flmA 122 1.05e+00 1axj b.45.1.1 25747 1uaqA 158 1.15e+00 c.97.1.2 88386 1p6oA 161 1.16e+00 c.97.1.2 -8774 1tlk 154 1.21e+00 1tlk b.1.1.4 21707 1bv1 159 1.41e+00 1bv1 d.129.3.1 41313 1pda 315 1.42e+00 1pda c.94.1.1 35751 d.50.2.1 38794 1r9hA 135 1.60e+00 d.26.1.1 -9482 1mal 421 1.72e+00 2mprA f.4.3.2 43784 1af6A 421 1.73e+00 2mprA f.4.3.2 43772 1vcaA 202 1.75e+00 1vcaA b.1.1.3 21649 b.1.1.4 21685 1i58A 189 1.84e+00 1b3qA d.122.1.3 61773 1iq6A 134 2.31e+00 d.38.1.4 76755 1qmrA 159 2.85e+00 1bv1 d.129.3.1 41314 1h6hA 143 2.87e+00 d.189.1.1 65681 1ytw 306 3.18e+00 1ytw c.45.1.2 32689 1yptA 305 3.27e+00 1ytw c.45.1.2 32686 1zxq 192 3.35e+00 1zxq b.1.1.3 21657 b.1.1.4 21693 1fthA 122 3.44e+00 d.150.1.2 60028 1ig8A 486 3.59e+00 2yhx c.55.1.3 64746 c.55.1.3 64747 1f7lA 121 3.59e+00 1f7lA d.150.1.2 59666 1sefA 274 3.74e+00 1hywA 68 4.07e+00 1hywA d.186.1.1 61425 1pzdA 322 4.26e+00 unknown_sccs -2848 unknown_sccs -10778 1ytn 306 4.74e+00 1ytw c.45.1.2 32688 1lyvA 306 4.99e+00 c.45.1.2 74348 1kwmA 402 5.29e+00 c.56.5.1 73079 d.58.3.1 73080 1fm4A 159 5.93e+00 1bv1 d.129.3.1 76186 1fzkB 99 5.98e+00 1agdB b.1.1.2 60151 1kpuB 99 5.98e+00 b.1.1.2 84458 1lk2B 99 5.98e+00 b.1.1.2 -2576 1g7pB 99 6.06e+00 b.1.1.2 70155 3dapA 320 6.15e+00 1dapA c.2.1.3 30051 d.81.1.3 39966 1f06A 320 6.49e+00 1dapA c.2.1.3 59556 d.81.1.3 59557 1dnlA 199 6.56e+00 1ci0A b.45.1.1 25753 1yts 278 6.58e+00 1ytw c.45.1.2 32690 1k9sA 237 6.78e+00 c.56.2.1 68359 1jb3A 131 6.94e+00 1jc7A b.40.3.2 62833 1mkyA 439 7.16e+00 c.37.1.8 79250 c.37.1.8 79251 d.52.5.1 79252 1fzoB 99 7.16e+00 1agdB b.1.1.2 60157 1t62A 166 7.16e+00 1ecpA 238 7.46e+00 1ecpA c.56.2.1 33775 1pk9A 237 7.49e+00 c.56.2.1 -7734 1fbnA 230 7.88e+00 1fbnA c.66.1.3 34181 1h2aL 567 7.88e+00 1h2rL e.18.1.1 43299 1d3bB 91 7.96e+00 1d3bB b.38.1.1 24804 1nktA 922 7.97e+00 a.162.1.1 85830 a.172.1.1 85831 c.37.1.19 85832 c.37.1.19 85833 1g8sA 230 8.02e+00 c.66.1.3 -8047 1kyfA 247 8.10e+00 b.1.10.1 73220 d.105.1.1 73221 1jc7A 131 8.46e+00 1jc7A b.40.3.2 62873 1dapA 320 8.48e+00 1dapA c.2.1.3 30053 d.81.1.3 39968 1br9 194 8.53e+00 1br9 b.40.3.1 25235 1qtsA 247 8.60e+00 1qtsA b.1.10.1 22313 d.105.1.1 40789 2shpA 525 9.00e+00 2shpA c.45.1.2 32683 d.93.1.1 40533 d.93.1.1 40534 1ivg 388 9.09e+00 2qwc b.68.1.1 27578 1ejjA 511 9.10e+00 1ejjA c.105.1.1 59422 c.76.1.3 59423 2mprA 421 9.28e+00 2mprA f.4.3.2 43788 1eqjA 511 9.29e+00 1ejjA c.105.1.1 59495 c.76.1.3 59496 1gtkA 313 9.32e+00 c.94.1.1 76346 d.50.2.1 76347 1l4sA 112 9.60e+00 d.204.1.1 77693 1asx 159 9.69e+00 1a6dA c.8.5.2 30821 1qhfA 240 1.00e+01 1qhfA c.60.1.1 33960 1o98A 511 1.02e+01 c.105.1.1 86684 c.76.1.3 86685 1b8aA 438 1.04e+01 1b8aA b.40.4.1 25244 d.104.1.1 40765 1bq3B 246 1.14e+01 1qhfA c.60.1.1 33979 1s9rA 410 1.14e+01 unknown_sccs -10989 1lxyA 409 1.14e+01 unknown_sccs -10987 1g7rA 594 1.16e+01 1g7rA b.43.3.1 25716 b.43.3.1 25717 c.20.1.1 31034 c.37.1.8 32149 1zpdA 568 1.18e+01 1zpdA c.31.1.3 31741 c.36.1.5 31785 c.36.1.9 31786 1yer 228 1.18e+01 1yer d.122.1.1 41101 1ltoA 245 1.19e+01 b.47.1.2 84707 1fxxA 482 1.19e+01 1fxxA c.55.3.5 33726 2phh 394 1.26e+01 1pbe c.3.1.2 30353 d.16.1.2 37884 1sr4B 261 1.29e+01 1ew0A 130 1.29e+01 1drmA d.110.3.2 40905 1ubkL 534 1.33e+01 e.18.1.1 88422 1e58A 249 1.33e+01 1qhfA c.60.1.1 59262 1h2rL 534 1.33e+01 1h2rL e.18.1.1 43298 1kvdB 77 1.35e+01 1kveB 1kveB 77 1.35e+01 1kveB 1hruA 188 1.37e+01 1hruA d.115.1.1 40926 1i3cA 149 1.43e+01 c.23.1.1 71112 1d06A 130 1.44e+01 1drmA d.110.3.2 40906 1p0kA 349 1.48e+01 c.1.4.1 87648 1f7tA 122 1.48e+01 1f7lA d.150.1.2 59667 1larA 575 1.49e+01 1larA c.45.1.2 32693 c.45.1.2 32694 1juk 248 1.50e+01 1a53 c.1.2.4 28567 1bqhG 129 1.64e+01 1cd8 b.1.1.1 19715 1asyA 490 1.68e+01 1b8aA b.40.4.1 25242 d.104.1.1 40763 1igs 248 1.70e+01 1a53 c.1.2.4 28565 1s7jA 262 1.70e+01 d.21.1.2 -9424 1g7sA 594 1.70e+01 1g7rA b.43.3.1 25712 b.43.3.1 25713 c.20.1.1 31032 c.37.1.8 32147 1drmA 131 1.77e+01 1drmA d.110.3.2 40908 1tvfA 369 1.82e+01 1smvA 260 1.82e+01 1smvA b.121.4.7 23288 1pxvA 183 1.82e+01 d.3.1.1 -8881 1v5xA 203 1.85e+01 c.1.2.4 -5169 1nscA 390 1.85e+01 2qwc b.68.1.1 27591 1g79A 218 1.86e+01 1ci0A b.45.1.1 25752 1uylA 236 1.87e+01 1a12A 413 1.90e+01 1a12A b.69.5.1 27663 1a53 247 1.90e+01 1a53 c.1.2.4 28564 1byqA 228 1.92e+01 1yer d.122.1.1 41100 2dnjA 260 1.94e+01 3dni d.151.1.1 41790 1qw2A 102 1.95e+01 unknown_sccs -9601 1lswA 131 1.95e+01 d.110.3.2 78181 1n6eA 1071 1.98e+01 b.36.1.3 80149 b.68.7.1 80150 b.69.9.1 80151 c.14.1.2 80152 1b3qA 379 2.01e+01 1b3qA a.30.2.1 16993 b.40.7.1 25454 d.122.1.3 41112 1ha3A 405 2.04e+01 1efcA b.43.3.1 60869 b.44.1.1 60870 c.37.1.8 60871 1go3E 187 2.05e+01 b.40.4.5 83054 d.230.1.1 83055 1l0wA 580 2.08e+01 b.40.4.1 73426 d.74.4.1 73427 d.104.1.1 73428 1o5kA 306 2.14e+01 c.1.10.1 -5482 1vkdA 338 2.20e+01 1mhcB 99 2.24e+01 1agdB b.1.1.2 20832 1eqkA 102 2.25e+01 1eqkA d.17.1.2 37998 1bovA 69 2.26e+01 2bosA b.40.2.1 25070 1tm0A 350 2.26e+01 1mkp 144 2.34e+01 1vhrA c.45.1.1 32654 1ughI 82 2.34e+01 1ugiA d.17.5.1 38133 1g7tA 594 2.35e+01 1g7rA b.43.3.1 25714 b.43.3.1 25715 c.20.1.1 31033 c.37.1.8 32148 1v2bA 177 2.36e+01 1j1yA 136 2.38e+01 d.38.1.5 -9671 1fztA 211 2.44e+01 1qhfA c.60.1.1 60158 1i8kA 107 2.46e+01 b.1.1.1 71130 1uj6A 227 2.48e+01 1dypA 271 2.49e+01 1dypA b.29.1.2 24185 1fxlA 167 2.49e+01 1b7fA d.58.7.1 39183 d.58.7.1 39184 2reb 352 2.52e+01 2reb c.37.1.11 32282 d.48.1.1 38767 1pcfA 66 2.55e+01 1pcfA d.18.1.1 38142 1dxy 333 2.56e+01 1dxy c.2.1.4 30094 c.23.12.1 31354 1q8iA 783 2.59e+01 c.55.3.5 -7635 e.8.1.1 -11885 1ubeA 349 2.69e+01 c.37.1.11 88412 d.48.1.1 88413 1isaA 192 2.69e+01 1avmA a.2.11.1 15731 d.44.1.1 38724 1e69B 322 2.69e+01 1e69B c.37.1.12 32377 1n0uA 842 2.70e+01 b.43.3.1 79757 c.37.1.8 79758 d.14.1.1 79759 d.58.11.1 79760 d.58.11.1 79761 1vavA 222 2.70e+01 1i2aA 219 2.71e+01 e.24.1.1 -12012 1u9aA 160 2.74e+01 1u9aA d.20.1.1 38333 1efcA 393 2.79e+01 1efcA b.43.3.1 25680 b.44.1.1 25720 c.37.1.8 32113 1c4qA 69 2.80e+01 2bosA b.40.2.1 25010 1nezG 128 2.80e+01 b.1.1.1 85592 1vpsB 289 2.81e+01 1vpsA b.121.6.1 23337 1gd7A 109 2.82e+01 b.40.4.4 60441 1iscA 192 2.83e+01 1avmA a.2.11.1 15733 d.44.1.1 38726 1pxfA 111 2.85e+01 b.40.4.4 88341 1b1cA 181 2.88e+01 1amoA c.23.5.2 31212 1j0sA 157 2.91e+01 b.42.1.2 -4016 1dcfA 136 2.91e+01 1dcfA c.23.1.2 31124 1kebA 108 2.96e+01 c.47.1.1 77341 1pytA 94 3.00e+01 1pytA d.58.3.1 39064 1k2fA 190 3.01e+01 b.8.1.2 68054 2bosA 68 3.06e+01 2bosA b.40.2.1 25025 1qhtA 775 3.07e+01 1tgoA c.55.3.5 33722 e.8.1.1 43011 1aipE 405 3.12e+01 1efcA b.43.3.1 25699 b.44.1.1 25739 c.37.1.8 32134 1d2sA 170 3.14e+01 1d2sA b.29.1.4 24221 1ixlA 131 3.15e+01 d.38.1.5 -9705 1nh9A 87 3.20e+01 d.68.6.1 -10287 1kkcA 221 3.20e+01 a.2.11.1 68660 d.44.1.1 68661 1fx3B 169 3.21e+01 1fx3B d.33.1.1 38525 1ass 159 3.23e+01 1a6dA c.8.5.2 30818 1vpsA 289 3.25e+01 1vpsA b.121.6.1 23336 1ift 263 3.27e+01 1mrj d.165.1.1 42211 1jksA 294 3.27e+01 d.144.1.7 71710 1mbyA 88 3.30e+01 d.223.1.1 78931 1louA 101 3.32e+01 1ris d.58.14.1 39323 1uhvA 500 3.37e+01 b.71.1.2 -4683 c.1.8.3 -5354 1cjsA 219 3.39e+01 1cjsA e.24.1.1 43354 1aye 401 3.41e+01 1aye c.56.5.1 33824 d.58.3.1 39065 1tk9A 188 3.42e+01 1cr5A 189 3.49e+01 1cr5A b.52.2.3 26931 d.31.1.1 38465 1ucdA 190 3.55e+01 1quqB 121 3.56e+01 1quqB b.40.4.3 25305 1exmA 405 3.56e+01 1efcA b.43.3.1 25696 b.44.1.1 25736 c.37.1.8 32131 1drqA 131 3.56e+01 1drmA 1ucaA 190 3.58e+01 d.124.1.1 88462 1qynA 153 3.60e+01 d.33.1.1 -9585 1ap8 213 3.64e+01 1ap8 d.86.1.1 40151 1bk7A 190 3.67e+01 1bk7A d.124.1.1 41121 1nnxA 109 3.68e+01 unknown_sccs -3899 1aqzA 149 3.69e+01 1aqzA d.1.1.3 36238 1hyuA 521 3.74e+01 1hyuA c.3.1.5 30547 c.3.1.5 30548 c.47.1.2 32779 c.47.1.2 32780 1tgoA 773 3.77e+01 1tgoA c.55.3.5 33721 e.8.1.1 43010 1at3A 247 3.78e+01 1at3A b.57.1.1 27021 1aisA 182 3.89e+01 1ytbA d.129.1.1 41288 d.129.1.1 41289 1kdkA 177 3.93e+01 b.29.1.4 72351 1hjp 203 3.96e+01 1hjp a.5.1.1 16274 a.60.2.1 17947 b.40.4.2 25266