# List of top-scoring protein chains for t2k-100-30-stride-ebghtl 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 1mjc 69 2.58e-11 1mjc b.40.4.5 25319 1sro 76 8.44e-11 1sro b.40.4.5 25327 3mefA 69 1.53e-10 1mjc b.40.4.5 25320 1go3E 187 3.35e-09 b.40.4.5 65406 1c9oA 66 1.03e-08 1mjc b.40.4.5 25325 1kl9A 182 1.97e-05 1e3pA 757 6.14e-05 1e3hA a.4.9.1 16258 b.40.4.5 25328 d.14.1.4 37574 d.14.1.4 37575 d.52.3.1 38811 d.101.1.1 40697 d.101.1.1 40698 1bkf 107 2.94e-02 1fkj d.26.1.1 38382 1a62 130 3.10e-02 1a62 a.140.3.1 64708 b.40.4.5 64709 1fkd 107 3.21e-02 1fkj d.26.1.1 38383 1fkf 107 3.21e-02 1fkj d.26.1.1 38386 1fkj 107 3.21e-02 1fkj d.26.1.1 38384 1b8aA 438 3.71e-02 1b8aA b.40.4.1 25244 d.104.1.1 40765 2cgpA 210 5.03e-02 2cgpA a.4.5.4 16102 b.82.3.2 28141 1bfeA 119 1.34e-01 1pdr b.36.1.1 24775 1hw5A 210 1.84e-01 2cgpA a.4.5.4 16098 b.82.3.2 28137 1jvwA 167 1.89e-01 1be9A 119 2.05e-01 1pdr b.36.1.1 24774 1f3z 161 2.27e-01 1gpr b.84.3.1 28273 1a8vA 121 2.51e-01 1a62 a.140.3.1 64712 b.40.4.5 64713 4cms 323 2.52e-01 1smrA b.50.1.2 26866 1glaF 168 3.35e-01 1gpr b.84.3.1 28274 1jj2A 239 3.77e-01 1rl2A b.34.5.3 63084 b.40.4.5 63085 1f20A 435 3.89e-01 b.43.4.1 64932 c.25.1.4 64933 1pdr 99 4.17e-01 1pdr b.36.1.1 24771 1k3rA 268 4.76e-01 1bpv 112 5.47e-01 1bpv b.1.2.1 22071 1euoA 180 6.16e-01 1np1A b.60.1.1 27163 3cms 323 6.50e-01 1smrA b.50.1.2 26865 1k6wA 426 6.57e-01 b.92.1.2 68236 c.1.9.5 68237 1nif 340 6.59e-01 1nif b.6.1.3 23048 b.6.1.3 23049 3pmgA 561 7.06e-01 3pmgA c.84.1.1 35408 c.84.1.1 35409 c.84.1.1 35410 d.129.2.1 41301 1j9qA 341 9.42e-01 1nif b.6.1.3 62765 b.6.1.3 62766 1i7dA 659 9.46e-01 1d6mA e.10.1.1 61886 1np1A 184 9.61e-01 1np1A b.60.1.1 27155 1ihjA 98 1.00e+00 1pdr b.36.1.1 62382 1fd9A 213 1.04e+00 1fd9A d.26.1.1 59771 1lxtA 561 1.16e+00 3pmgA c.84.1.1 35432 c.84.1.1 35433 c.84.1.1 35434 d.129.2.1 41309 3mddA 385 1.23e+00 3mdeA a.29.3.1 16592 e.6.1.1 42853 3mdeA 385 1.24e+00 3mdeA a.29.3.1 16594 e.6.1.1 42855 1fwxA 595 1.32e+00 b.6.1.4 60069 b.69.3.1 60070 1whi 122 1.51e+00 1whi b.39.1.1 24810 1paz 123 1.53e+00 1bqk b.6.1.1 22878 1i7pA 274 1.54e+00 b.43.4.2 66048 c.25.1.1 66049 1lcyA 325 1.62e+00 1ndh 272 1.69e+00 1ndh b.43.4.2 25662 c.25.1.1 31552 1obpA 159 1.85e+00 1obpA b.60.1.1 27092 1d7qA 143 1.98e+00 1d7qA b.40.4.5 25331 2ltnA 181 1.99e+00 1led b.29.1.1 24024 1et7A 341 2.02e+00 1nif b.6.1.3 23070 b.6.1.3 23071 1ju3A 583 2.03e+00 b.18.1.13 67300 c.69.1.21 67301 1ospO 257 2.07e+00 1ospO b.76.1.1 27971 1as8A 343 2.10e+00 1nif b.6.1.3 23074 b.6.1.3 23075 1qniA 581 2.13e+00 1qniA b.6.1.4 23042 b.69.3.1 27642 1fr3A 67 2.26e+00 1fr3A b.40.6.1 25436 1gpr 162 2.45e+00 1gpr b.84.3.1 28267 1l0wA 580 2.50e+00 1bp3B 211 2.60e+00 1axiB b.1.2.1 22031 b.1.2.1 22032 1dykA 394 2.79e+00 1dykA b.29.1.4 24223 b.29.1.4 24224 1i18A 97 2.85e+00 b.43.4.3 61520 1np4A 184 2.93e+00 1np1A b.60.1.1 27166 1ebpA 211 3.11e+00 1eerB b.1.2.1 22023 b.1.2.1 22024 1kwaA 88 3.83e+00 1kwaA b.36.1.1 24772 1koiA 184 3.93e+00 b.60.1.1 68725 1jjgA 102 3.93e+00 1erxA 184 3.97e+00 1np1A b.60.1.1 27164 1tul 108 4.16e+00 1tul b.85.5.1 28373 1k0rA 366 4.39e+00 b.40.4.5 67961 d.52.3.1 67962 d.52.3.1 67963 d.202.1.1 67964 1at0 145 4.44e+00 1at0 b.86.1.1 28374 1ipwA 175 5.22e+00 2prd b.40.5.1 25427 1d4xG 126 5.22e+00 1d0nA d.109.1.1 59109 1kkhA 317 5.23e+00 1yagG 125 5.30e+00 1d0nA d.109.1.1 40846 4sli 679 5.61e+00 2sli b.29.1.9 24275 b.68.1.1 27612 1bquA 215 5.66e+00 1bquA b.1.2.1 22066 b.1.2.1 22067 2sli 679 5.72e+00 2sli b.29.1.9 24274 b.68.1.1 27611 1d6mA 653 5.73e+00 1d6mA e.10.1.1 43248 1egdA 396 5.91e+00 3mdeA a.29.3.1 16596 e.6.1.1 42857 1cbs 137 5.93e+00 1hmt b.60.1.2 27201 1lnrI 134 6.14e+00 1k8wA 327 6.41e+00 d.58.35.2 68317 d.58.35.2 68318 1fmtB 314 6.48e+00 1fmtA b.46.1.1 25759 c.65.1.1 34175 1sfp 114 6.67e+00 1sfp b.23.1.1 23895 1ah9 71 6.69e+00 1ah9 b.40.4.5 25330 1ebuA 358 6.72e+00 1ebuA c.2.1.3 30035 d.81.1.2 39950 1c0aA 585 6.85e+00 1c0aA b.40.4.1 25246 d.74.4.1 39731 d.104.1.1 40767 1qg3A 195 7.42e+00 1qg3A b.1.2.1 21993 b.1.2.1 21994 1d2sA 170 7.54e+00 1d2sA b.29.1.4 24221 3rabA 169 7.57e+00 1ctqA c.37.1.8 32018 1garA 212 7.79e+00 2gar c.65.1.1 34162 1fxjA 331 8.53e+00 1fwyA b.81.1.4 28062 c.68.1.5 34520 1fmtA 314 8.53e+00 1fmtA b.46.1.1 25758 c.65.1.1 34174 1grj 158 8.57e+00 1grj a.2.1.1 15691 d.26.1.2 38433 1ebaA 215 8.91e+00 1eerB b.1.2.1 22015 b.1.2.1 22016 1bueA 265 9.18e+00 1btl e.3.1.1 42727 1k8kB 394 9.38e+00 c.55.1.1 68307 1pinA 163 9.57e+00 1pinA b.72.1.1 27802 d.26.1.1 38431 1bdyA 123 9.57e+00 1bdyA b.7.1.1 23190 1a8p 258 9.70e+00 1fdr b.43.4.2 25654 c.25.1.1 31544 1art 396 9.92e+00 1ajsA c.67.1.1 34285 1blxA 326 9.94e+00 1hcl d.144.1.1 41596 1gtqA 140 1.01e+01 1b66A d.96.1.2 40661 1hn2A 159 1.02e+01 b.60.1.1 65890 1b66A 140 1.03e+01 1b66A d.96.1.2 40657 1krhA 338 1.03e+01 1lkzA 219 1.04e+01 2dorA 311 1.05e+01 2dorA c.1.4.1 28593 1larA 575 1.06e+01 1larA c.45.1.2 32693 c.45.1.2 32694 1fjgQ 105 1.07e+01 1fjfQ b.40.4.5 25352 1ebfA 358 1.09e+01 1ebuA c.2.1.3 30033 d.81.1.2 39948 1eut 605 1.13e+01 1eut b.1.1.5 21891 b.18.1.1 23712 b.68.1.1 27609 2hgsA 474 1.13e+01 2hgsA c.30.1.4 31722 d.142.1.6 41575 d.142.1.6 41576 1a49A 530 1.14e+01 1a49A b.58.1.1 27026 c.1.12.1 29255 c.49.1.1 33109 1pkn 530 1.18e+01 1a49A b.58.1.1 27042 c.1.12.1 29271 c.49.1.1 33125 1cby 259 1.22e+01 1cby d.103.1.1 40705 1hlcA 129 1.25e+01 1c1lA b.29.1.3 24208 1i40A 175 1.26e+01 b.40.5.1 66024 1g2rA 100 1.29e+01 1g2rA d.192.1.1 60231 1bqk 124 1.29e+01 1bqk b.6.1.1 22889 1fdr 248 1.31e+01 1fdr b.43.4.2 25653 c.25.1.1 31543 1kb0A 677 1.41e+01 a.3.1.6 68378 b.70.1.1 68379 1h9mA 145 1.42e+01 1h9jA b.40.6.2 60833 b.40.6.2 60834 1dorA 311 1.42e+01 2dorA c.1.4.1 28595 1obwA 175 1.46e+01 2prd b.40.5.1 25416 1mat 264 1.49e+01 1c24A d.127.1.1 41152 1c24A 263 1.49e+01 1c24A d.127.1.1 41148 2matA 264 1.49e+01 1c24A d.127.1.1 41146 1jmcA 246 1.51e+01 1jmcA b.40.4.3 25300 b.40.4.3 25301 1ten 90 1.54e+01 1ten b.1.2.1 21990 1dar 691 1.55e+01 1dar b.43.3.1 25707 c.37.1.8 32142 d.14.1.1 37547 d.58.11.1 39300 1poiB 260 1.55e+01 1poiB c.63.1.1 34155 1i8dA 213 1.56e+01 b.43.4.3 61953 b.43.4.3 61954 1jt7A 146 1.57e+01 b.42.1.1 67255 1f3vA 179 1.57e+01 1f3vA d.58.22.1 39382 1whtA 256 1.63e+01 1ivyA c.69.1.5 34646 1whsA 255 1.63e+01 1ivyA c.69.1.5 34649 1i6cA 39 1.63e+01 1i6cA b.72.1.1 61828 1lvoA 302 1.65e+01 1a6jA 163 1.68e+01 1a6jA d.112.1.1 40915 1fwyA 331 1.74e+01 1fwyA b.81.1.4 28064 c.68.1.5 34522 1e25A 282 1.74e+01 1e25A e.3.1.1 42731 1kxqE 120 1.80e+01 1cb8A 678 1.81e+01 1cb8A a.102.3.2 18849 b.24.1.1 23898 b.30.3.1 24422 1f5fA 205 1.82e+01 1d2sA b.29.1.4 24222 1eu3A 210 1.89e+01 1an8 b.40.2.2 25206 d.15.6.1 37795 1h9jA 145 1.93e+01 1h9jA b.40.6.2 60829 b.40.6.2 60830 1ahjB 212 1.98e+01 2ahjB b.34.4.4 24601 1enfA 212 2.01e+01 3seb b.40.2.2 25198 d.15.6.1 37787 1yaiA 151 2.05e+01 1yaiA b.1.8.1 22289 1jdiA 231 2.08e+01 c.74.1.1 66551 1d8iA 311 2.13e+01 1d8iA d.63.1.1 39541 1kv7A 488 2.20e+01 b.6.1.3 68873 b.6.1.3 68874 b.6.1.3 68875 1jmxB 349 2.21e+01 b.69.2.2 66906 1d5tA 433 2.34e+01 1gnd c.3.1.3 30422 d.16.1.6 37986 1iakB 185 2.36e+01 1iakB b.1.1.2 21626 d.19.1.1 38200 3cox 507 2.37e+01 1b8sA c.3.1.2 30332 d.16.1.1 37863 1a73A 163 2.38e+01 1a73A d.4.1.3 37145 2cae 484 2.40e+01 1cf9A e.5.1.1 42810 1k2yX 463 2.46e+01 c.84.1.1 68063 c.84.1.1 68064 c.84.1.1 68065 c.84.1.1 68066 1h8eH 146 2.46e+01 1e79H b.93.1.1 60757 1vie 62 2.46e+01 1vie b.34.4.1 24592 1vif 62 2.46e+01 1vie b.34.4.1 24593 1g5vA 88 2.47e+01 1g5vA b.34.9.1 60292 1qhtA 775 2.51e+01 1tgoA c.55.3.5 33722 e.8.1.1 43011 1mkaA 171 2.51e+01 1mkaA d.38.1.2 38543 1hpgA 187 2.52e+01 1qq4A b.47.1.1 25813 1jjtA 228 2.54e+01 1a7tA d.157.1.1 63139 1lj5A 379 2.55e+01 1ha3A 405 2.61e+01 1efcA b.43.3.1 60869 b.44.1.1 60870 c.37.1.8 60871 1e42A 258 2.63e+01 1e42A b.1.10.1 22316 d.105.1.1 40792 2fgf 146 2.67e+01 1bfg b.42.1.1 25487 1h80A 464 2.67e+01 b.80.1.8 65714 1jtaA 361 2.71e+01 1hyxH 224 2.73e+01 1igtB b.1.1.1 20167 b.1.1.2 21191 1d8hA 311 2.75e+01 1d8iA d.63.1.1 39544 4kbpA 432 2.75e+01 4kbpA b.1.12.1 22345 d.159.1.1 42064 1ixmA 192 2.75e+01 1ixmA d.123.1.1 41114 1cqwA 295 2.77e+01 1b6g c.69.1.8 34679 1dlfH 124 2.80e+01 1igtB b.1.1.1 20383 1lab 80 2.80e+01 1ghj b.84.1.1 28226 1f3mC 297 2.80e+01 1hcl d.144.1.1 41677 1nar 290 2.84e+01 1nar c.1.8.5 28988 1hdmB 193 2.85e+01 1hdmB b.1.1.2 21584 d.19.1.1 38158 3hmgA 328 2.87e+01 1hgeA b.19.1.2 23825 1cq3A 233 2.88e+01 1cq3A b.27.1.1 23923 1kopA 223 2.89e+01 2cba b.74.1.1 27966 1evxA 162 2.89e+01 1a73A d.4.1.3 37149 1thw 207 2.92e+01 1thv b.25.1.1 23903 2sga 181 2.92e+01 1qq4A b.47.1.1 25808 1sgc 181 2.92e+01 1qq4A b.47.1.1 25810 1clc 639 2.95e+01 1clc a.102.1.2 18835 b.1.1.5 21872 1e1oA 504 2.97e+01 1lylA b.40.4.1 25258 d.104.1.1 40714 1f3uB 171 2.99e+01 1f3uB b.65.1.1 27525 1fxoA 293 3.00e+01 1g0rA c.68.1.6 34524 1ky9A 448 3.00e+01 1jnyA 435 3.03e+01 b.43.3.1 66982 b.44.1.1 66983 c.37.1.8 66984 1ahxA 396 3.03e+01 1ajsA c.67.1.1 34293 1qisA 396 3.03e+01 1ajsA c.67.1.1 34284 1lkkA 105 3.08e+01 1lckA d.93.1.1 40412 1shaA 104 3.08e+01 1fmk d.93.1.1 40424 1bmdA 327 3.12e+01 1bmdA c.2.1.5 30139 d.162.1.1 42106 1bdmA 327 3.12e+01 1bmdA c.2.1.5 30137 d.162.1.1 42104 1bdmB 327 3.13e+01 1bmdA c.2.1.5 30138 d.162.1.1 42105 1cv8 174 3.16e+01 1cv8 d.3.1.1 37089 1ckmA 330 3.19e+01 1ckmA b.40.4.6 25358 d.142.2.3 41585 1ky9B 448 3.19e+01 1hv9A 456 3.23e+01 1fwyA b.81.1.4 28060 c.68.1.5 34518 1fjgJ 105 3.23e+01 1fjfJ d.58.15.1 39330 1jr7A 311 3.24e+01 b.82.2.3 63255 1lylA 504 3.25e+01 1lylA b.40.4.1 25261 d.104.1.1 40717 4tsvA 150 3.26e+01 2tnfA b.22.1.1 23860 1ibyA 112 3.32e+01 1ibzA b.6.1.4 62233 1spa 396 3.33e+01 1ajsA c.67.1.1 34291 1kq1A 77 3.34e+01 1aipE 405 3.35e+01 1efcA b.43.3.1 25699 b.44.1.1 25739 c.37.1.8 32134 1lckA 175 3.39e+01 1lckA b.34.2.1 24552 d.93.1.1 40421 1ars 396 3.40e+01 1ajsA c.67.1.1 34287 2plt 98 3.41e+01 1plc b.6.1.1 22862 1jjuB 337 3.41e+01 b.69.2.2 66779 1k0iA 394 3.43e+01 c.3.1.2 67942 d.16.1.2 67943 1grwA 126 3.45e+01 1hfh 120 3.50e+01 1hfh g.18.1.1 44821 g.18.1.1 44822 1lfpA 249 3.54e+01 1sltB 134 3.56e+01 1c1lA b.29.1.3 24187 2pgd 482 3.57e+01 2pgd a.100.1.1 18778 c.2.1.6 30190 1h8eD 482 3.58e+01 1skyE a.69.1.1 60747 b.49.1.1 60748 c.37.1.11 60749 1jer 138 3.60e+01 2cbp b.6.1.1 23022 1bpoA 494 3.62e+01 1bpoA a.118.1.4 19143 b.69.6.1 27670 2afgA 140 3.62e+01 1bfg b.42.1.1 25514 1slaA 134 3.62e+01 1c1lA b.29.1.3 24196 1sltA 134 3.63e+01 1c1lA b.29.1.3 24186 1iraX 152 3.66e+01 1irp b.42.1.2 25556 1kqfB 294 3.66e+01 1e8cA 498 3.69e+01 c.98.1.1 59377 c.59.1.1 59378 c.72.2.1 59379 1vcaA 202 3.71e+01 1vcaA b.1.1.3 21649 b.1.1.4 21685 1ibzA 112 3.72e+01 1ibzA b.6.1.4 62237 1iqaA 160 3.73e+01 1qh4A 380 3.74e+01 1qh4A a.83.1.1 18462 d.128.1.2 41197 1cs8A 316 3.77e+01 1cs8A d.3.1.1 37065 1c96A 753 3.82e+01 1amj c.8.2.1 30727 c.83.1.1 35403 1cknA 330 3.84e+01 1ckmA b.40.4.6 25360 d.142.2.3 41587 2eifA 136 3.86e+01 1bkb b.34.5.2 24607 b.40.4.5 25339 1qftA 175 3.88e+01 1qftA b.60.1.1 27151 1quqB 121 3.88e+01 1quqB b.40.4.3 25305 3pte 349 3.88e+01 3pte e.3.1.1 42687 1ksgB 152 3.92e+01 1rypI 222 3.93e+01 d.153.1.4 41877 1ris 101 3.94e+01 1ris d.58.14.1 39314 1griA 217 3.97e+01 1griA b.34.2.1 24531 b.34.2.1 24532 d.93.1.1 40473