# List of top-scoring protein chains for t04-100-30-alpha 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 1s1dA 331 1.23e-04 unknown_sccs -4566 1r0vA 305 7.85e-02 c.52.2.1 -7572 c.52.2.1 -7573 d.75.1.1 -10344 1kzkA 99 1.81e-01 b.50.1.1 73371 1dl5A 317 2.61e-01 1dl5A c.66.1.7 64720 d.197.1.1 64721 1ugmA 125 3.03e-01 1nh0A 99 3.09e-01 b.50.1.1 -4299 1smlA 269 3.43e-01 1smlA d.157.1.1 42053 1jpc 109 3.45e-01 1b2pA b.78.1.1 27986 1o5zA 442 3.52e-01 c.59.1.2 -7939 c.72.2.2 -8418 1difA 99 3.67e-01 1fmb b.50.1.1 26503 1hn2A 159 4.07e-01 b.60.1.1 65890 1gt1A 159 4.69e-01 b.60.1.1 -4436 1cr5A 189 5.34e-01 1cr5A b.52.2.3 26931 d.31.1.1 38465 1dv1A 449 6.10e-01 1bncA b.84.2.1 28234 c.30.1.1 31641 d.142.1.2 41486 1amuA 563 6.30e-01 1amuA e.23.1.1 43351 1ii7A 333 6.93e-01 1ii7A d.159.1.4 62415 1viuA 203 7.31e-01 d.113.1.1 -10889 1jj2R 84 7.76e-01 1ffkP d.12.1.1 63103 1s72S 85 7.79e-01 1obpA 159 7.99e-01 1obpA b.60.1.1 27092 2arcA 164 8.50e-01 2arcA b.82.4.1 28148 1h09A 338 8.56e-01 b.109.1.1 83420 c.1.8.8 83421 1xvaA 292 8.95e-01 1xvaA c.66.1.5 34183 1n9eA 787 9.15e-01 b.30.2.1 -3529 d.17.2.1 -9278 d.17.2.1 -9279 1ed7A 45 1.00e+00 1ed7A b.72.2.1 27809 1vj2A 126 1.02e+00 unknown_sccs -4850 1k4zA 159 1.07e+00 b.80.5.1 72070 4pep 326 1.09e+00 1smrA b.50.1.2 26843 1oeyA 83 1.10e+00 d.15.2.2 -9162 1o5uA 101 1.13e+00 b.82.1.8 -4845 1o6aA 96 1.14e+00 unknown_sccs -4101 1dazC 99 1.15e+00 1hvc b.50.1.1 26501 1b7yB 785 1.17e+00 1pysB a.6.1.1 16301 a.6.1.1 16302 b.40.4.4 25312 d.58.13.1 39311 d.104.1.1 40780 d.138.1.1 41456 1mr7A 209 1.32e+00 b.81.1.3 -4798 1sefA 274 1.38e+00 1q4rA 112 1.40e+00 d.58.4.4 -9943 1suuA 312 1.41e+00 unknown_sccs -4610 1qy6A 274 1.41e+00 b.47.1.1 -4126 3psg 370 1.45e+00 1smrA b.50.1.2 26841 1d5tA 433 1.48e+00 1gnd c.3.1.3 30422 d.16.1.6 37986 1eljA 381 1.63e+00 4mbp c.94.1.1 35791 1juhA 350 1.66e+00 b.82.1.5 71884 1h4rA 314 1.71e+00 a.11.2.1 65616 b.55.1.5 65617 d.15.1.4 65618 1f06A 320 1.72e+00 1dapA c.2.1.3 59556 d.81.1.3 59557 1fnnA 389 1.72e+00 1fnnA a.4.5.11 16129 c.37.1.20 32426 1qwyA 291 1.84e+00 unknown_sccs -5023 1mxmA 254 2.22e+00 b.38.1.3 79647 d.58.43.1 79648 f.34.1.1 79649 1kb0A 677 2.25e+00 a.3.1.6 68378 b.70.1.1 68379 1l4dB 122 2.53e+00 d.15.5.1 77684 1m2rA 327 2.64e+00 d.144.1.7 84760 1nzhA 282 2.67e+00 d.151.1.2 -11398 1uxxX 133 2.72e+00 b.18.1.10 -3107 1js8A 394 2.74e+00 a.86.1.1 67219 b.112.1.1 67220 1r4wA 226 2.81e+00 unknown_sccs -7447 1us8A 147 2.88e+00 c.37.1.12 -7194 1k6dA 220 2.90e+00 unknown_sccs 72082 1jtaA 361 3.27e+00 b.80.1.1 71859 1kv9A 668 3.51e+00 a.3.1.6 73056 b.70.1.1 73057 1f2tA 149 3.59e+00 1f2tA c.37.1.12 32373 1gmmA 133 3.65e+00 b.18.1.10 65314 1meoA 209 3.69e+00 c.65.1.1 79035 1i58A 189 3.70e+00 1b3qA d.122.1.3 61773 1fvrA 327 4.04e+00 d.144.1.7 60047 1qg3A 195 4.12e+00 1qg3A b.1.2.1 21993 b.1.2.1 21994 1o6zA 303 4.32e+00 c.2.1.5 81107 d.162.1.1 81108 1e6wA 260 4.38e+00 1e6wA c.2.1.2 59326 1a6o 332 4.48e+00 1a6o 1garA 212 4.50e+00 2gar c.65.1.1 34162 1jqgA 433 4.66e+00 c.56.5.1 71791 d.58.3.1 71792 1ukmB 128 4.72e+00 d.169.1.1 -11625 1lkdA 297 4.92e+00 d.32.1.3 78059 d.32.1.3 78060 1k8tA 510 4.92e+00 e.41.1.1 68316 1p5dX 463 4.95e+00 c.84.1.1 -8554 c.84.1.1 -8555 c.84.1.1 -8556 d.129.2.1 -11029 1ae9A 179 5.24e+00 1ae9A d.163.1.1 42153 1uch 230 5.28e+00 1uch d.3.1.6 37129 1r62A 160 5.29e+00 1skoA 143 5.32e+00 1vheA 373 5.42e+00 unknown_sccs -4280 c.56.5.4 -7890 1dg6A 191 5.67e+00 1d4vB b.22.1.1 23883 1mb4A 370 5.69e+00 c.2.1.3 78908 d.81.1.1 78909 1ytfD 121 5.76e+00 1ytfD a.32.1.1 16998 b.56.1.1 27011 1jkxA 212 5.79e+00 c.65.1.1 66813 1hcd 118 5.94e+00 1hce b.42.5.2 25624 1rypH 205 5.98e+00 d.153.1.4 41876 1nzyA 269 6.15e+00 1nzyA c.14.1.3 30903 1s8fA 177 6.16e+00 1pe9A 361 6.24e+00 b.80.1.1 -4765 1rypG 244 6.24e+00 d.153.1.4 41938 1ghj 79 6.43e+00 1ghj b.84.1.1 28232 1b04A 318 6.66e+00 1b04A d.142.2.2 41579 1nh2D 121 6.76e+00 a.32.1.1 -780 b.56.1.1 -4384 1uzbA 516 6.77e+00 c.82.1.1 -8552 1pcfA 66 6.85e+00 1pcfA d.18.1.1 38142 1c0eA 157 6.87e+00 1dg9A c.44.1.1 32638 1qw2A 102 7.24e+00 unknown_sccs -9601 1k5cA 335 7.38e+00 b.80.1.3 72076 1aiw 62 7.58e+00 1aiw b.72.2.1 27808 1jhgA 101 7.65e+00 1jhgA a.4.12.1 19009 1f00I 282 7.87e+00 1f00I b.1.14.1 22368 b.1.14.1 22369 d.169.1.3 42439 1pbuA 162 7.98e+00 d.58.46.1 88030 1n1tA 641 8.03e+00 b.29.1.15 79821 b.68.1.1 79822 1han 297 8.30e+00 1han d.32.1.3 38506 d.32.1.3 38507 1d3bA 75 8.31e+00 1d3bA b.38.1.1 24798 1jsmA 325 8.32e+00 b.19.1.2 63264 1nrjB 218 8.38e+00 c.37.1.8 86125 1ooyA 481 8.71e+00 unknown_sccs -6867 unknown_sccs -6873 1uv7A 110 8.73e+00 unknown_sccs -10256 1g72A 573 8.82e+00 4aahA b.70.1.1 27680 1o7kA 131 8.96e+00 d.189.1.1 81144 1htjF 210 9.10e+00 1htjF a.91.1.1 61254 1ujpA 271 9.29e+00 c.1.2.4 -5177 1om1A 332 9.40e+00 d.144.1.7 -11318 1ip9A 85 9.78e+00 1ip9A d.15.2.2 62638 1v84A 253 9.78e+00 1okiA 210 9.90e+00 b.11.1.1 -3030 b.11.1.1 -3031 1hssA 124 9.90e+00 1bea a.52.1.2 17819 1korA 400 9.91e+00 c.26.2.1 72824 d.210.1.1 72825 1ogaD 215 1.01e+01 b.1.1.1 86990 b.1.1.2 86991 1q1oA 98 1.01e+01 d.15.2.2 -9172 1mngA 203 1.02e+01 1avmA a.2.11.1 15776 d.44.1.1 38701 2gar 212 1.07e+01 2gar c.65.1.1 34161 1b4bA 71 1.07e+01 1b4aA d.74.2.1 39718 1oiaA 95 1.12e+01 d.58.7.1 87051 1m4iA 181 1.13e+01 d.108.1.1 74457 1l1jA 239 1.14e+01 b.47.1.1 84516 1jenA 267 1.15e+01 1jenA 1uayA 242 1.16e+01 c.2.1.2 88390 1b6rA 355 1.18e+01 1b6rA b.84.2.1 28241 c.30.1.1 31648 d.142.1.2 41493 1dmlA 319 1.19e+01 1dmlA d.131.1.2 41380 d.131.1.2 41381 1plq 258 1.20e+01 1plq d.131.1.2 41388 d.131.1.2 41389 1vie 62 1.20e+01 1vie b.34.4.1 24592 1idpA 172 1.22e+01 d.17.4.1 83685 1vj1A 363 1.24e+01 b.35.1.2 -3728 c.2.1.1 -5752 1k2yX 463 1.24e+01 c.84.1.1 68063 c.84.1.1 68064 c.84.1.1 68065 d.129.2.1 68066 1dgwA 178 1.25e+01 1dgwA b.82.1.2 28090 1a7qL 106 1.27e+01 8fabA b.1.1.1 19954 1of4A 179 1.27e+01 b.18.1.18 86932 1orc 71 1.28e+01 1orc a.35.1.2 17054 1dfcA 493 1.29e+01 1dfcA b.42.5.1 25616 b.42.5.1 25617 b.42.5.1 25618 b.42.5.1 25619 1oh4A 179 1.32e+01 b.18.1.18 -3123 1mbmA 198 1.33e+01 b.47.1.3 78916 1i9sA 210 1.37e+01 1i9sA c.45.1.1 62099 1e1aA 314 1.38e+01 1e1aA b.68.6.1 59155 1jdpA 441 1.39e+01 c.93.1.1 62906 1hnuA 280 1.39e+01 1hnoA c.14.1.3 61096 1qjcA 158 1.43e+01 1b6tA c.26.1.3 63328 1mjnA 179 1.45e+01 c.62.1.1 79210 1enfA 212 1.46e+01 3seb b.40.2.2 25198 d.15.6.1 37787 1b2pA 119 1.47e+01 1b2pA b.78.1.1 27998 1hh1A 143 1.50e+01 1gefA c.52.1.18 61036 1pkhA 204 1.51e+01 b.85.4.1 -5053 1ukfA 188 1.52e+01 unknown_sccs -8886 2hft 218 1.53e+01 1boy b.1.2.1 21951 b.1.2.1 21952 1cxyA 90 1.53e+01 1cyo d.120.1.1 41085 1qx2A 76 1.55e+01 1lfaA 187 1.56e+01 1ido c.62.1.1 34122 1djnA 729 1.57e+01 2tmdA c.1.4.1 28612 c.3.1.1 30313 c.4.1.1 30598 1mmsA 140 1.57e+01 1mmsA a.4.7.1 16247 d.47.1.1 38766 1dusA 194 1.57e+01 1dusA c.66.1.4 34182 1h8uA 117 1.60e+01 1h8uA d.169.1.1 60793 1qgjA 300 1.64e+01 1bgp a.93.1.1 18691 1s0yA 76 1.68e+01 d.80.1.1 -10434 1m26A 133 1.69e+01 1g97A 459 1.69e+01 1fwyA b.81.1.4 60394 c.68.1.5 60395 1l9vA 317 1.70e+01 d.13.2.1 73760 d.216.1.1 73761 1hm9A 468 1.70e+01 b.81.1.4 65866 c.68.1.5 65867 1ag9A 175 1.70e+01 1rcf c.23.5.1 31178 1o50A 157 1.72e+01 d.37.1.1 -9604 d.37.1.1 -9605 1rifA 282 1.76e+01 unknown_sccs -7265 1nu4A 97 1.76e+01 d.58.7.1 80731 1vjw 60 1.77e+01 1fxd d.58.1.4 38991 1jjtA 228 1.77e+01 1a7tA d.157.1.1 63139 1iow 306 1.77e+01 1iow c.30.1.2 31713 d.142.1.1 41481 3stdA 165 1.78e+01 3stdA d.17.4.1 38073 1cjbA 231 1.79e+01 1qk3A c.61.1.1 34079 1brmA 367 1.80e+01 1brmA c.2.1.3 30030 d.81.1.1 39945 1gvfA 286 1.81e+01 c.1.10.2 70599 1pjhA 280 1.82e+01 c.14.1.3 -6229 1t0yA 122 1.82e+01 d.15.1.1 -9151 1lldA 319 1.82e+01 3ldh c.2.1.5 30177 d.162.1.1 42144 5croA 66 1.86e+01 1orc a.35.1.2 17044 1h80A 464 1.87e+01 b.80.1.8 65714 1gadO 330 1.87e+01 1dssG c.2.1.3 29950 d.81.1.1 39865 2tmdA 729 1.90e+01 2tmdA c.1.4.1 28616 c.3.1.1 30317 c.4.1.1 30602 1lcyA 325 1.91e+01 b.36.1.4 73834 b.47.1.1 73835 1f20A 435 1.92e+01 b.43.4.1 64932 c.25.1.4 64933 1dkzA 219 1.93e+01 1dkzA unknown_sccs -445 unknown_sccs -3060 1bolA 222 1.94e+01 1bolA d.124.1.1 41120 1j9bA 141 1.95e+01 c.47.1.12 66459 1jl0A 334 2.01e+01 1jenA d.156.1.1 63155 1p9kA 79 2.01e+01 unknown_sccs -10238 1oxxK 353 2.02e+01 b.40.6.3 -3969 c.37.1.12 -7187 1ksiA 642 2.02e+01 1ksiB b.30.2.1 24408 d.17.2.1 38043 d.17.2.1 38044 1o6dA 163 2.06e+01 c.116.1.3 -6689 1d1gA 168 2.06e+01 1d1gA c.71.1.1 34889 1urnA 97 2.11e+01 1urnA d.58.7.1 39153 1ko3A 230 2.13e+01 d.157.1.1 -11454 1nsf 273 2.14e+01 1d2nA c.37.1.20 32429 1cl8A 276 2.16e+01 1ckqA c.52.1.1 33230 1gefA 123 2.17e+01 1gefA c.52.1.18 60465 1gsmA 210 2.19e+01 b.1.1.4 65535 b.1.1.4 65536 1fmtA 314 2.21e+01 1fmtA b.46.1.1 25758 c.65.1.1 34174 1ush 550 2.23e+01 1ush d.114.1.1 40923 d.159.1.2 42079 1io0A 185 2.24e+01 c.10.1.1 76753 1gd1O 334 2.24e+01 1dssG c.2.1.3 29962 d.81.1.1 39877 1d2nA 272 2.30e+01 1d2nA c.37.1.20 32428 1dypA 271 2.32e+01 1dypA b.29.1.2 24185 1a2yA 107 2.33e+01 8fabA b.1.1.1 19926 1nf2A 268 2.35e+01 c.108.1.10 -6842 1g7jA 107 2.37e+01 32c2A b.1.1.1 19932 2dkb 433 2.38e+01 2dkb c.67.1.4 34438 1a0rP 245 2.38e+01 1b9yC c.47.1.6 33054 1ef1A 294 2.42e+01 1ef1A a.11.2.1 16368 b.55.1.5 27003 d.15.1.4 37611 1oivA 191 2.42e+01 c.37.1.8 -7074 1pjxA 314 2.43e+01 1yna 194 2.43e+01 1axkA b.29.1.11 24335 1a8y 367 2.48e+01 1a8y c.47.1.3 32781 c.47.1.3 32782 c.47.1.3 32783 1ad2 228 2.51e+01 1ad2 e.24.1.1 43353 1v2bA 177 2.51e+01 1r53A 382 2.51e+01 unknown_sccs -11177 1h9oA 112 2.53e+01 1qadA d.93.1.1 60837 1nofA 383 2.54e+01 b.71.1.2 -4668 c.1.8.3 -5339 1ex2A 189 2.56e+01 1ex2A c.51.4.2 33225 1vhsA 175 2.57e+01 d.108.1.1 -10794 1qnaA 200 2.57e+01 1ytbA d.129.1.1 41226 d.129.1.1 41227 1ufkA 254 2.58e+01 unknown_sccs -8103 1ms9A 648 2.63e+01 b.29.1.15 85088 b.68.1.1 85089 1m5q1 130 2.65e+01 4gcr 174 2.65e+01 1amm b.11.1.1 23589 b.11.1.1 23590 2bb2 181 2.68e+01 2bb2 b.11.1.1 23604 b.11.1.1 23605 1f3aA 222 2.72e+01 1pgtA a.45.1.1 17701 c.47.1.5 32995 1amm 174 2.72e+01 1amm b.11.1.1 23587 b.11.1.1 23588 1xxaA 78 2.72e+01 1xxaA d.74.2.1 39700 1oxsC 353 2.76e+01 b.40.6.3 87519 c.37.1.12 87520 1g0cA 364 2.76e+01 7a3hA c.1.8.3 60165 1crzA 403 2.77e+01 1crzA b.68.4.1 27629 c.51.2.1 33211 3pcgA 200 2.78e+01 3pchA b.3.6.1 22647 1std 172 2.79e+01 3stdA d.17.4.1 38089 1dl2A 511 2.82e+01 1dl2A a.102.2.1 18844 1a62 130 2.82e+01 1a62 a.140.3.1 64708 b.40.4.5 64709 1fvuA 133 2.82e+01 1ixxB d.169.1.1 42345 1thx 115 2.84e+01 1thx c.47.1.1 32732 1nijA 318 2.84e+01 c.37.1.10 85741 d.237.1.1 85742 1oqkA 97 2.87e+01 unknown_sccs -3814 1kpgA 287 2.89e+01 c.66.1.18 68735 1qv1A 195 2.95e+01 a.39.1.5 -830 1dg9A 157 2.95e+01 1dg9A c.44.1.1 32637 1bn7A 294 2.97e+01 1bn6A c.69.1.8 34677 1g26A 31 3.00e+01 1g26A g.3.16.1 44381 1bj7 156 3.01e+01 1bj7 b.60.1.1 27113 1k07A 263 3.03e+01 d.157.1.1 77218 1gk9B 557 3.05e+01 1itwA 741 3.06e+01 c.77.1.2 76793 1nrwA 288 3.06e+01 c.108.1.10 86128 1r2rA 248 3.11e+01 c.1.1.1 -5147 1f8yA 157 3.12e+01 1f8xA c.23.14.1 31395 1ua4A 455 3.12e+01 c.72.1.3 -8416 1k3yA 221 3.18e+01 a.45.1.1 77245 c.47.1.5 77246 1jjeA 222 3.20e+01 1a7tA d.157.1.1 63117 1hp1A 516 3.23e+01 d.114.1.1 70976 d.159.1.2 70977 1iznA 286 3.24e+01 e.43.1.1 83847 1cy9A 264 3.26e+01 1ecl e.10.1.1 43236 1vi6A 208 3.27e+01 c.23.15.1 -6489 1d3bB 91 3.28e+01 1d3bB b.38.1.1 24804 1iqaA 160 3.29e+01 b.22.1.1 71274 1mgqA 83 3.33e+01 b.38.1.1 79099 1kmqA 184 3.38e+01 c.37.1.8 84412 1rwzA 245 3.39e+01 d.131.1.2 -11106 d.131.1.2 -11107 1kq6A 141 3.40e+01 d.189.1.1 -9926 1r89A 437 3.41e+01 unknown_sccs -1147 unknown_sccs -9801 unknown_sccs -10061 1q38A 89 3.46e+01 b.1.2.1 -2765 1k2fA 190 3.53e+01 b.8.1.2 68054 1pfo 500 3.53e+01 1pfo f.9.1.1 43826 1gvzA 237 3.57e+01 b.47.1.2 76360 1mkyA 439 3.58e+01 c.37.1.8 79250 c.37.1.8 79251 d.52.5.1 79252 2dorA 311 3.59e+01 2dorA c.1.4.1 28593 1o94A 729 3.60e+01 c.1.4.1 81200 c.3.1.1 81201 c.4.1.1 81202 1b24A 188 3.63e+01 1b24A d.95.2.1 40573 d.95.2.1 40574 1d7uA 433 3.65e+01 2dkb c.67.1.4 34439 1fc4A 401 3.70e+01 1bs0A c.67.1.4 59760 1nxzA 246 3.74e+01 b.122.1.2 86391 c.116.1.5 86392 1upiA 225 3.76e+01 b.82.1.1 -4823 1n9dA 199 3.78e+01 a.26.1.1 85464 1pvxA 194 3.80e+01 1axkA b.29.1.11 24341 1ud9A 245 3.80e+01 1f39A 101 3.83e+01 1umuA b.87.1.1 28386 4icb 76 3.83e+01 4icb a.39.1.1 17145 1obfO 335 3.89e+01 c.2.1.3 86768 d.81.1.1 86769 1onwA 390 3.92e+01 b.92.1.7 87172 c.1.9.13 87173 1m1hA 248 3.96e+01 b.114.1.1 78415 d.58.42.1 78416 1r0tB 62 3.96e+01 unknown_sccs -12573 1eueA 86 3.97e+01 1cyo d.120.1.1 59504 1s14A 194 3.98e+01 d.122.1.2 -10973 1umuA 116 3.98e+01 1umuA b.87.1.1 28382 1ugxA 133 3.98e+01 1qtnA 164 3.99e+01 1pauA c.17.1.1 30999