# List of top-scoring protein chains for t2k-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 3.39e-03 unknown_sccs -4566 1f2tA 149 1.87e-01 1f2tA c.37.1.12 32373 1us8A 147 3.37e-01 c.37.1.12 -7194 2aacA 177 5.99e-01 2arcA b.82.4.1 28150 1msaA 109 6.15e-01 1b2pA b.78.1.1 27987 1b4aA 149 6.44e-01 1b4aA a.4.5.3 16088 d.74.2.1 39721 1jpc 109 6.53e-01 1b2pA b.78.1.1 27986 1amuA 563 7.32e-01 1amuA e.23.1.1 43351 2arcB 164 8.19e-01 2arcA b.82.4.1 28149 1d5tA 433 1.12e+00 1gnd c.3.1.3 30422 d.16.1.6 37986 2arcA 164 1.25e+00 2arcA b.82.4.1 28148 1jhgA 101 1.42e+00 1jhgA a.4.12.1 19009 1smlA 269 1.57e+00 1smlA d.157.1.1 42053 2wrpR 107 1.76e+00 1jhgA a.4.12.1 19010 1dv2A 452 1.76e+00 1bncA b.84.2.1 28238 c.30.1.1 31645 d.142.1.2 41490 1ghj 79 1.93e+00 1ghj b.84.1.1 28232 1trrA 107 2.12e+00 1jhgA a.4.12.1 19017 1ugmA 125 2.12e+00 1oeyA 83 2.45e+00 d.15.2.2 -9162 1bveA 99 2.56e+00 1hvc b.50.1.1 26713 1r0vA 305 2.65e+00 c.52.2.1 -7572 c.52.2.1 -7573 d.75.1.1 -10344 1o5nA 126 2.72e+00 1vj2A 126 2.72e+00 unknown_sccs -4850 1jj2R 84 2.78e+00 1ffkP d.12.1.1 63103 1s72S 85 2.78e+00 1ffkP 84 2.78e+00 1ffkP d.12.1.1 37493 1kk6A 209 2.93e+00 b.81.1.3 68657 1bncA 449 2.93e+00 1bncA b.84.2.1 28236 c.30.1.1 31643 d.142.1.2 41488 1kb0A 677 2.96e+00 a.3.1.6 68378 b.70.1.1 68379 1dl5A 317 3.06e+00 1dl5A c.66.1.7 64720 d.197.1.1 64721 1garA 212 3.42e+00 2gar c.65.1.1 34162 1q4rA 112 3.42e+00 d.58.4.4 -9943 1cr5A 189 3.59e+00 1cr5A b.52.2.3 26931 d.31.1.1 38465 1h09A 338 3.62e+00 b.109.1.1 83420 c.1.8.8 83421 1h4rA 314 3.81e+00 a.11.2.1 65616 b.55.1.5 65617 d.15.1.4 65618 1b4bA 71 3.88e+00 1b4aA d.74.2.1 39718 1n9eA 787 4.00e+00 b.30.2.1 -3529 d.17.2.1 -9278 d.17.2.1 -9279 1kzkA 99 4.02e+00 b.50.1.1 73371 1cklB 126 4.13e+00 1cklB g.18.1.1 44853 g.18.1.1 44854 1vkxA 273 4.14e+00 1a3qA b.1.18.1 21941 b.2.5.3 22454 1bmlC 362 4.30e+00 1bmlC d.15.5.1 37729 d.15.5.1 37730 d.15.5.1 37731 1eljA 381 4.44e+00 4mbp c.94.1.1 35791 1js8A 394 4.62e+00 a.86.1.1 67219 b.112.1.1 67220 1gt1A 159 4.76e+00 b.60.1.1 -4436 1a0rP 245 4.80e+00 1b9yC c.47.1.6 33054 1ii7A 333 4.85e+00 1ii7A d.159.1.4 62415 1uxxX 133 5.03e+00 b.18.1.10 -3107 1mejA 223 5.16e+00 c.65.1.1 79029 1hvc 203 5.31e+00 1hvc b.50.1.1 26614 1dv1A 449 5.35e+00 1bncA b.84.2.1 28234 c.30.1.1 31641 d.142.1.2 41486 1ed7A 45 5.36e+00 1ed7A b.72.2.1 27809 1ip9A 85 5.40e+00 1ip9A d.15.2.2 62638 1mr7A 209 5.40e+00 b.81.1.3 -4798 1meoA 209 5.50e+00 c.65.1.1 79035 1nfiA 301 5.57e+00 1a3qA b.1.18.1 21942 b.2.5.3 22455 1nfiC 301 5.63e+00 b.1.18.1 21943 b.2.5.3 22456 1kv9A 668 5.94e+00 a.3.1.6 73056 b.70.1.1 73057 1hn2A 159 6.01e+00 b.60.1.1 65890 1jkxA 212 6.10e+00 c.65.1.1 66813 1r4wA 226 6.10e+00 unknown_sccs -7447 1k6dA 220 6.10e+00 unknown_sccs 72082 1bncB 449 6.14e+00 1bncA b.84.2.1 28237 c.30.1.1 31644 d.142.1.2 41489 1mngA 203 6.30e+00 1avmA a.2.11.1 15776 d.44.1.1 38701 1viaA 175 6.37e+00 c.37.1.2 -7021 1rypG 244 6.57e+00 d.153.1.4 41938 1tiqA 180 6.60e+00 2gar 212 6.72e+00 2gar c.65.1.1 34161 1imoA 88 6.77e+00 1imoA c.15.1.2 62590 1jenA 267 6.89e+00 1jenA 1fnnA 389 7.13e+00 1fnnA a.4.5.11 16129 c.37.1.20 32426 1o6aA 96 7.18e+00 unknown_sccs -4101 1difA 99 7.23e+00 1fmb b.50.1.1 26503 1qwyA 291 7.28e+00 unknown_sccs -5023 1sefA 274 7.29e+00 1d2qA 173 7.45e+00 1d4vB b.22.1.1 23894 1gvmA 136 7.46e+00 b.109.1.1 70612 2trcP 217 7.59e+00 1b9yC c.47.1.6 33051 4pep 326 7.71e+00 1smrA b.50.1.2 26843 1obpA 159 7.83e+00 1obpA b.60.1.1 27092 1o12A 376 7.85e+00 b.92.1.5 80758 c.1.9.10 80759 1o5uA 101 8.20e+00 b.82.1.8 -4845 1qmyA 167 8.22e+00 1qmyA d.3.1.2 37094 1ukmB 128 8.25e+00 d.169.1.1 -11625 1hizA 379 8.58e+00 c.1.8.3 65841 1jl0A 334 8.60e+00 1jenA d.156.1.1 63155 1nh0A 99 8.85e+00 b.50.1.1 -4299 1e6wA 260 9.01e+00 1e6wA c.2.1.2 59326 1o5zA 442 9.16e+00 c.59.1.2 -7939 c.72.2.2 -8418 1l1jA 239 9.30e+00 b.47.1.1 84516 1okiA 210 9.33e+00 b.11.1.1 -3030 b.11.1.1 -3031 1qy6A 274 9.36e+00 b.47.1.1 -4126 1cauA 181 9.40e+00 1dgwA b.82.1.2 28102 1k5cA 335 9.65e+00 b.80.1.3 72076 1f06A 320 9.66e+00 1dapA c.2.1.3 59556 d.81.1.3 59557 1cklA 126 9.93e+00 1cklB g.18.1.1 44851 g.18.1.1 44852 1fvrA 327 1.01e+01 d.144.1.7 60047 3psg 370 1.02e+01 1smrA b.50.1.2 26841 1gmmA 133 1.03e+01 b.18.1.10 65314 5hvpA 99 1.04e+01 1fmb b.50.1.1 26605 1c0eA 157 1.04e+01 1dg9A c.44.1.1 32638 1hcd 118 1.05e+01 1hce b.42.5.2 25624 1hnuA 280 1.07e+01 1hnoA c.14.1.3 61096 1e3sA 261 1.14e+01 1e6wA c.2.1.2 59201 1hcxA 127 1.17e+01 b.109.1.1 65800 1p5dX 463 1.18e+01 c.84.1.1 -8554 c.84.1.1 -8555 c.84.1.1 -8556 d.129.2.1 -11029 1dapA 320 1.19e+01 1dapA c.2.1.3 30053 d.81.1.3 39968 1l4zB 136 1.19e+01 d.15.5.1 77704 1k1tA 99 1.23e+01 b.50.1.1 71995 1nofA 383 1.24e+01 b.71.1.2 -4668 c.1.8.3 -5339 1hnoA 280 1.25e+01 1hnoA c.14.1.3 61095 1b7yB 785 1.28e+01 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 1ae9A 179 1.34e+01 1ae9A d.163.1.1 42153 1pjhA 280 1.34e+01 c.14.1.3 -6229 1itwA 741 1.35e+01 c.77.1.2 76793 1l1nA 183 1.35e+01 b.47.1.4 73476 1jacA 133 1.36e+01 1jotA 1s8fA 177 1.38e+01 1nh2D 121 1.40e+01 a.32.1.1 -780 b.56.1.1 -4384 1l4dB 122 1.40e+01 d.15.5.1 77684 1viuA 203 1.42e+01 d.113.1.1 -10889 1rifA 282 1.43e+01 unknown_sccs -7265 1jacC 133 1.50e+01 1jotA 1qw2A 102 1.51e+01 unknown_sccs -9601 2gmfA 127 1.53e+01 2gmfA a.26.1.2 16849 1q53A 112 1.54e+01 d.58.4.4 -9944 1qhtA 775 1.54e+01 1tgoA c.55.3.5 33722 e.8.1.1 43011 1q15A 503 1.56e+01 c.26.2.1 -6625 d.153.1.1 -11400 1dgrC 178 1.56e+01 1dgwA b.82.1.2 28100 1pgvA 197 1.57e+01 c.10.1.1 88073 1o50A 157 1.57e+01 d.37.1.1 -9604 d.37.1.1 -9605 1ytfD 121 1.62e+01 1ytfD a.32.1.1 16998 b.56.1.1 27011 1i9sA 210 1.62e+01 1i9sA c.45.1.1 62099 1m26A 133 1.63e+01 1uayA 242 1.64e+01 c.2.1.2 88390 1d2gA 292 1.64e+01 1xvaA c.66.1.5 34187 1skoA 143 1.67e+01 1pbuA 162 1.67e+01 d.58.46.1 88030 1orc 71 1.70e+01 1orc a.35.1.2 17054 1fqvA 336 1.74e+01 1fqvA a.158.1.1 19254 c.10.1.3 30856 1pcl 355 1.75e+01 1pcl b.80.1.1 28021 1uch 230 1.81e+01 1uch d.3.1.6 37129 1lkdA 297 1.82e+01 d.32.1.3 78059 d.32.1.3 78060 1eiyB 785 1.83e+01 1pysB a.6.1.1 16305 a.6.1.1 16306 b.40.4.4 25314 d.58.13.1 39313 d.104.1.1 40782 d.138.1.1 41458 1plq 258 1.86e+01 1plq d.131.1.2 41388 d.131.1.2 41389 1nrjB 218 1.88e+01 c.37.1.8 86125 1b8aA 438 1.90e+01 1b8aA b.40.4.1 25244 d.104.1.1 40765 1cghA 224 1.91e+01 1a7s b.47.1.2 26290 1oejA 193 1.96e+01 unknown_sccs -4461 8prkB 287 1.96e+01 1wgjA b.40.5.1 25396 1g72A 573 1.96e+01 4aahA b.70.1.1 27680 1b0uA 262 1.97e+01 1b0uA c.37.1.12 32370 3dapA 320 1.99e+01 1dapA c.2.1.3 30051 d.81.1.3 39966 1fx3B 169 1.99e+01 1fx3B d.33.1.1 38525 1vfbA 107 2.04e+01 8fabA b.1.1.1 19930 4aahA 571 2.04e+01 4aahA b.70.1.1 27678 1lm8V 160 2.05e+01 b.3.3.1 74035 1vie 62 2.06e+01 1vie b.34.4.1 24592 1vif 62 2.07e+01 1vie b.34.4.1 24593 1k2yX 463 2.07e+01 c.84.1.1 68063 c.84.1.1 68064 c.84.1.1 68065 d.129.2.1 68066 1lgtA 297 2.08e+01 d.32.1.3 77956 d.32.1.3 77957 1m6eX 359 2.09e+01 unknown_sccs -8071 1r62A 160 2.09e+01 1csgA 127 2.11e+01 2gmfA a.26.1.2 16851 1xvaA 292 2.11e+01 1xvaA c.66.1.5 34183 1plr 258 2.13e+01 1plq d.131.1.2 41390 d.131.1.2 41391 1n1tA 641 2.13e+01 b.29.1.15 79821 b.68.1.1 79822 1lldA 319 2.14e+01 3ldh c.2.1.5 30177 d.162.1.1 42144 1nwbA 124 2.16e+01 b.124.1.1 86296 1devC 196 2.19e+01 1ygs b.26.1.1 23915 1mmsA 140 2.20e+01 1mmsA a.4.7.1 16247 d.47.1.1 38766 3adk 195 2.21e+01 1zin c.37.1.1 31885 1jtaA 361 2.21e+01 b.80.1.1 71859 1tsm 316 2.25e+01 1bkpA d.117.1.1 41024 1dypA 271 2.27e+01 1dypA b.29.1.2 24185 1hce 118 2.27e+01 1hce b.42.5.2 25625 1a7qL 106 2.29e+01 8fabA b.1.1.1 19954 1phr 157 2.30e+01 1dg9A c.44.1.1 32635 1dy9A 187 2.33e+01 1jxpA b.47.1.3 26400 1nzhA 282 2.34e+01 d.151.1.2 -11398 1thx 115 2.37e+01 1thx c.47.1.1 32732 1k3sA 113 2.38e+01 d.198.1.1 68120 1ezvB 352 2.39e+01 1ezvB d.185.1.1 59543 d.185.1.1 59544 1aiw 62 2.40e+01 1aiw b.72.2.1 27808 1uv7A 110 2.42e+01 unknown_sccs -10256 1cxyA 90 2.43e+01 1cyo d.120.1.1 41085 1d4vB 163 2.44e+01 1d4vB b.22.1.1 23884 1lpuA 332 2.47e+01 d.144.1.7 74177 1dg9A 157 2.52e+01 1dg9A c.44.1.1 32637 1vokA 200 2.53e+01 1ytbA d.129.1.1 41242 d.129.1.1 41243 1m2rA 327 2.56e+01 d.144.1.7 84760 487dL 133 2.56e+01 1mmsA i.1.1.2 45839 1mz5A 638 2.59e+01 b.29.1.15 79679 b.68.1.1 79680 1bihA 395 2.60e+01 1bihA b.1.1.4 21752 b.1.1.4 21753 b.1.1.4 21754 b.1.1.4 21755 1ooyA 481 2.61e+01 unknown_sccs -6867 unknown_sccs -6873 1ugxA 133 2.65e+01 1xxcA 78 2.66e+01 1xxaA d.74.2.1 39712 1ffkV 143 2.67e+01 1ffkV c.9.2.1 30849 1ffkQ 119 2.71e+01 1ffkQ b.34.5.1 24605 1r26A 125 2.72e+01 c.47.1.1 -7389 1kb9B 352 2.74e+01 d.185.1.1 77313 d.185.1.1 77314 1hh2P 344 2.77e+01 b.40.4.5 65835 d.52.3.1 65836 d.52.3.1 65837 d.202.1.1 65838 1e2tA 284 2.80e+01 1e2tA d.3.1.5 37121 1dazC 99 2.80e+01 1hvc b.50.1.1 26501 1m5oC 100 2.83e+01 d.58.7.1 78654 1ufkA 254 2.91e+01 unknown_sccs -8103 1inlA 296 2.92e+01 c.66.1.17 66220 1nmtA 392 2.95e+01 1nmtA d.108.1.2 40823 d.108.1.2 40824 2glsA 470 2.96e+01 1lgr d.15.9.1 37851 d.128.1.1 41181 1ctj 89 2.96e+01 1ctj a.3.1.1 15798 1iknA 286 2.96e+01 1a3qA b.1.18.1 21936 b.2.5.3 22449 1ef1A 294 2.96e+01 1ef1A a.11.2.1 16368 b.55.1.5 27003 d.15.1.4 37611 1qg3A 195 2.98e+01 1qg3A b.1.2.1 21993 b.1.2.1 21994 1k07A 263 2.98e+01 d.157.1.1 77218 1f8yA 157 2.98e+01 1f8xA c.23.14.1 31395 1gvfA 286 2.99e+01 c.1.10.2 70599 1mb4A 370 3.00e+01 c.2.1.3 78908 d.81.1.1 78909 1dgwA 178 3.01e+01 1dgwA b.82.1.2 28090 1oiaA 95 3.02e+01 d.58.7.1 87051 1lqbC 162 3.02e+01 b.3.3.1 74186 1xxaA 78 3.06e+01 1xxaA d.74.2.1 39700 1ku8A 133 3.10e+01 1juhA 350 3.10e+01 b.82.1.5 71884 1e9gA 286 3.12e+01 1wgjA b.40.5.1 59393 1b9yC 246 3.13e+01 1b9yC c.47.1.6 33052 1qu0A 191 3.13e+01 1dykA b.29.1.4 24225 1s0yA 76 3.16e+01 d.80.1.1 -10434 2sak 121 3.18e+01 2sak d.15.5.1 37711 1a62 130 3.19e+01 1a62 a.140.3.1 64708 b.40.4.5 64709 1k8hA 133 3.20e+01 b.111.1.1 72176 1ew4A 106 3.20e+01 1ew4A d.82.2.1 40023 1suuA 312 3.21e+01 unknown_sccs -4610 1aw0 72 3.21e+01 1aw0 d.58.17.1 39342 1wgjA 286 3.21e+01 1wgjA b.40.5.1 25397 1v3vA 333 3.25e+01 1qp8A 303 3.26e+01 1qp8A c.2.1.4 30092 c.23.12.1 31352 1us5A 314 3.26e+01 c.94.1.1 -8686 1e9gB 286 3.27e+01 1wgjA b.40.5.1 59394 1vjw 60 3.29e+01 1fxd d.58.1.4 38991 1f8xA 157 3.33e+01 1f8xA c.23.14.1 31397 1han 297 3.35e+01 1han d.32.1.3 38506 d.32.1.3 38507 1dfcA 493 3.37e+01 1dfcA b.42.5.1 25616 b.42.5.1 25617 b.42.5.1 25618 b.42.5.1 25619 1egdA 396 3.37e+01 3mdeA a.29.3.1 16596 e.6.1.1 42857 1a2yA 107 3.38e+01 8fabA b.1.1.1 19926 1a8y 367 3.38e+01 1a8y c.47.1.3 32781 c.47.1.3 32782 c.47.1.3 32783 1umuA 116 3.39e+01 1umuA b.87.1.1 28382 1umuB 116 3.39e+01 1umuA b.87.1.1 28383 1korA 400 3.39e+01 c.26.2.1 72824 d.210.1.1 72825 1ag9A 175 3.41e+01 1rcf c.23.5.1 31178 1rypC 244 3.41e+01 1rypC d.153.1.4 41934 1c76A 136 3.42e+01 2sak d.15.5.1 37718 2orc 71 3.42e+01 1orc a.35.1.2 17060 8prkA 287 3.42e+01 1wgjA b.40.5.1 25395 1o9lA 481 3.44e+01 unknown_sccs 81242 unknown_sccs 81241 1om1A 332 3.45e+01 d.144.1.7 -11318 1lufA 343 3.47e+01 d.144.1.7 78223 1pcfA 66 3.50e+01 1pcfA d.18.1.1 38142 1alq 266 3.50e+01 1btl e.3.1.1 42707 1in4A 334 3.53e+01 1hqcA a.4.5.11 62597 c.37.1.20 62598 1dg6A 191 3.53e+01 1d4vB b.22.1.1 23883 1kebA 108 3.57e+01 c.47.1.1 77341 1g7jA 107 3.58e+01 32c2A b.1.1.1 19932 1yna 194 3.59e+01 1axkA b.29.1.11 24335 1in6A 334 3.61e+01 1hqcA a.4.5.11 62601 c.37.1.20 62602 1pfo 500 3.63e+01 1pfo f.9.1.1 43826 1ytbB 180 3.65e+01 1ytbA d.129.1.1 41278 d.129.1.1 41279 1qgjA 300 3.66e+01 1bgp a.93.1.1 18691 1dfmA 223 3.66e+01 1d2iA c.52.1.5 33295 1htjF 210 3.67e+01 1htjF a.91.1.1 61254 1s14A 194 3.68e+01 d.122.1.2 -10973 1jztA 246 3.69e+01 c.104.1.1 63319 1d2iA 223 3.71e+01 1d2iA c.52.1.5 33297 1ltsA 185 3.71e+01 1lt3A d.166.1.1 42229 1k4nA 192 3.71e+01 d.32.1.5 72059 1tgoA 773 3.72e+01 1tgoA c.55.3.5 33721 e.8.1.1 43010 1tbaB 180 3.73e+01 1ytbA d.129.1.1 41286 d.129.1.1 41287 1f1sA 814 3.73e+01 a.102.3.2 64928 b.1.18.2 64929 b.24.1.1 64930 b.30.5.2 64931 1ntfA 282 3.75e+01 d.151.1.2 -11397 1qtnA 164 3.76e+01 1pauA c.17.1.1 30999 1lp4A 332 3.76e+01 d.144.1.7 74170 1d3bA 75 3.80e+01 1d3bA b.38.1.1 24798 1wkqA 164 3.80e+01 1b04A 318 3.89e+01 1b04A d.142.2.2 41579 1f00I 282 3.91e+01 1f00I b.1.14.1 22368 b.1.14.1 22369 d.169.1.3 42439 1o0pA 104 3.93e+01 d.58.7.1 86535 1odkA 235 3.95e+01 c.56.2.1 86863 1m3uA 264 3.95e+01 c.1.12.8 84784 1f7uA 607 3.99e+01 1bs2A a.27.1.1 59673 c.26.1.1 59674 d.67.2.1 59675 1fxzA 476 4.00e+01 b.82.1.2 65059 b.82.1.2 65060