# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7-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 1gbg 214 3.84e-01 1axkA b.29.1.2 24171 1vcaA 202 4.62e-01 1vcaA b.1.1.3 21649 b.1.1.4 21685 1s14A 194 5.07e-01 d.122.1.2 -10973 1my7A 114 1.20e+00 b.1.18.1 79675 1my5A 114 1.22e+00 b.1.18.1 79673 1gmiA 136 1.39e+00 b.7.1.1 65309 1g4mA 393 1.40e+00 b.1.18.11 65143 b.1.18.11 65144 1n9pA 207 1.52e+00 b.1.18.16 80343 1d3bA 75 1.73e+00 1d3bA b.38.1.1 24798 1nngA 153 1.94e+00 d.38.1.1 -9636 1ttbA 127 1.95e+00 1etb1 b.3.4.1 22543 1f41A 127 1.98e+00 1etb1 b.3.4.1 22539 2ayh 214 2.11e+00 1axkA b.29.1.2 24172 1tfpA 130 2.19e+00 1etb1 b.3.4.1 22623 1l1zA 274 2.43e+00 a.156.1.2 75911 b.113.1.1 75912 g.39.1.8 75913 1c4rA 182 2.44e+00 1c4rA b.29.1.4 24229 1eta1 127 2.60e+00 1etb1 2pabA 127 2.84e+00 1etb1 b.3.4.1 22597 1jb0D 138 3.10e+00 1jb0D d.187.1.1 62823 1j1tA 233 3.14e+00 unknown_sccs -3462 1ic7H 114 3.61e+00 1f3rB b.1.1.1 62258 1cknA 330 3.66e+00 1ckmA b.40.4.6 25360 d.142.2.3 41587 1f86A 115 3.78e+00 1etb1 b.3.4.1 59689 1etb1 127 3.83e+00 1etb1 1qunB 279 4.18e+00 b.2.3.2 22411 b.2.3.2 22412 1kypA 237 4.32e+00 d.22.1.1 73280 1ebpA 211 4.44e+00 1eerB b.1.2.1 22023 b.1.2.1 22024 1gppA 237 4.53e+00 b.86.1.2 76262 1jhjA 171 4.73e+00 b.18.1.9 66714 1oxdA 227 4.74e+00 d.22.1.1 -9438 1h4rA 314 4.87e+00 a.11.2.1 65616 b.55.1.5 65617 d.15.1.4 65618 1fo0A 116 4.96e+00 1tvdA b.1.1.1 20610 1qs8A 329 5.06e+00 1smrA b.50.1.2 26887 7ahlA 293 5.09e+00 7ahlA f.6.1.1 43812 1rhoA 145 5.13e+00 1rhoA b.1.18.8 21899 1jx4A 352 5.32e+00 unknown_sccs -10188 unknown_sccs -11898 1vzoA 355 5.37e+00 2rspB 124 5.38e+00 2rspB b.50.1.1 26772 1i31A 314 5.46e+00 1bw8A b.2.7.1 22481 1c0pA 363 5.94e+00 1an9A c.4.1.2 30647 d.16.1.3 37934 1ckmA 330 6.03e+00 1ckmA b.40.4.6 25358 d.142.2.3 41585 1mvpA 124 6.04e+00 2rspB b.50.1.1 26775 1kn9A 249 6.06e+00 b.87.1.2 68699 1cpn 208 6.10e+00 1axkA b.29.1.2 24175 1jhfA 202 6.38e+00 a.4.5.2 63057 b.87.1.1 63058 1klfB 279 6.65e+00 b.2.3.2 72684 b.2.3.2 72685 1r2zA 274 6.68e+00 a.156.1.2 -370 b.113.1.1 -5094 g.39.1.8 -12748 1ollA 188 7.01e+00 b.1.1.4 -2690 b.1.1.4 -2691 2dpg 485 7.24e+00 1dpgA c.2.1.3 30076 d.81.1.5 39991 1dpgA 485 7.35e+00 1dpgA c.2.1.3 30074 d.81.1.5 39989 1dgmA 363 7.50e+00 1bx4A c.72.1.1 34936 1j1xH 114 7.94e+00 b.1.1.1 77063 1kmtA 141 8.04e+00 b.1.18.8 77442 1gw5M 435 8.84e+00 b.2.7.1 70631 d.110.4.2 70632 1qg3A 195 8.96e+00 1qg3A b.1.2.1 21993 b.1.2.1 21994 1eerB 227 9.51e+00 1eerB b.1.2.1 22011 b.1.2.1 22012 1kiuB 279 9.73e+00 b.2.3.2 72525 b.2.3.2 72526 1gqpA 221 9.79e+00 b.18.1.9 70372 1vdeA 454 9.83e+00 1vdeA b.86.1.2 28378 d.95.2.2 40581 d.95.2.2 40582 2rspA 124 9.85e+00 2rspB b.50.1.1 26771 1bywA 110 1.03e+01 1bywA d.110.3.6 40912 1q4uA 151 1.04e+01 d.38.1.5 -9701 1vcbC 160 1.04e+01 1vcbC b.3.3.1 22535 1lmeA 176 1.06e+01 d.167.1.1 84629 1kijA 390 1.07e+01 d.14.1.3 72514 d.122.1.2 72515 1rlw 126 1.07e+01 1rlw b.7.1.1 23177 1bxxA 285 1.10e+01 1bw8A b.2.7.1 22483 1lqbC 162 1.10e+01 b.3.3.1 74186 1viwB 198 1.11e+01 1led b.29.1.1 24170 1bw8A 321 1.13e+01 1bw8A b.2.7.1 22482 1iqaA 160 1.14e+01 b.22.1.1 71274 1pvl 301 1.16e+01 1pvl f.6.1.1 43819 1d2oA 187 1.18e+01 1d2oA b.3.5.1 22625 b.3.5.1 22626 1pe0A 197 1.19e+01 c.23.16.2 88045 1ge8A 249 1.20e+01 1plq d.131.1.2 41398 d.131.1.2 41399 1p5fA 189 1.20e+01 c.23.16.2 -6508 1jeyA 609 1.22e+01 1jeqA unknown_sccs -4426 unknown_sccs -7990 1cfyA 143 1.22e+01 1cof d.109.1.2 40858 3kvt 115 1.23e+01 1t1dA d.42.1.2 38642 2emo 237 1.23e+01 1ema d.22.1.1 38366 1lqwA 183 1.24e+01 d.167.1.1 74210 1oo2A 119 1.26e+01 b.3.4.1 -2925 1mm4A 170 1.26e+01 f.4.1.2 79294 1f39A 101 1.29e+01 1umuA b.87.1.1 28386 1miqA 375 1.31e+01 b.50.1.2 79151 1b12A 248 1.38e+01 1b12A b.87.1.2 28388 1ospO 257 1.42e+01 1ospO b.76.1.1 27971 1q8fA 313 1.43e+01 c.70.1.1 -8358 1lm8V 160 1.43e+01 b.3.3.1 74035 1r64A 481 1.46e+01 b.18.1.20 -3151 c.41.1.1 -7297 1dhkB 223 1.52e+01 1led b.29.1.1 24157 1lmhA 184 1.56e+01 d.167.1.1 74036 1uacH 114 1.58e+01 b.1.1.1 -2285 1eg2A 319 1.58e+01 1eg2A c.66.1.11 34249 1rhoC 145 1.60e+01 1rhoA b.1.18.8 21901 1eudB 396 1.60e+01 2scuB c.23.4.1 31150 d.142.1.4 41571 1j2gA 319 1.63e+01 1jeqA 609 1.64e+01 1jeqA a.140.2.1 64748 unknown_sccs -4427 unknown_sccs -7991 1n57A 291 1.65e+01 c.23.16.2 85328 1eucB 396 1.65e+01 2scuB c.23.4.1 31149 d.142.1.4 41570 1ac5 483 1.67e+01 1ac5 c.69.1.5 34653 1o5oA 221 1.67e+01 c.61.1.1 -7954 1cof 143 1.67e+01 1cof d.109.1.2 40860 1dbhA 354 1.73e+01 1awe a.87.1.1 18514 b.55.1.1 26967 1ema 236 1.75e+01 1ema d.22.1.1 38339 1havA 217 1.76e+01 1havA b.47.1.4 26423 1nnjA 271 1.76e+01 a.156.1.2 80669 b.113.1.1 80670 g.39.1.8 80671 1bw4 125 1.83e+01 1bw4 b.52.1.2 26900 1adeA 431 1.85e+01 1adeA c.37.1.10 32213 1ot5A 477 1.87e+01 b.18.1.20 87409 c.41.1.1 87410 1qa7A 217 1.90e+01 1havA b.47.1.4 26425 1h6rA 236 1.92e+01 d.22.1.1 65683 1at0 145 1.93e+01 1at0 b.86.1.1 28374 1fsoA 139 1.98e+01 1rhoA b.1.18.8 60007 1lf2A 331 2.00e+01 b.50.1.2 77914 1axkA 394 2.02e+01 1axkA b.29.1.2 24181 b.29.1.11 24315 1ystH 260 2.05e+01 6prcH b.41.1.1 25482 f.23.10.1 43511 1ha1 184 2.09e+01 1ha1 d.58.7.1 39147 d.58.7.1 39148 1cf1A 404 2.09e+01 1cf1A b.1.18.11 21907 b.1.18.11 21908 1mmiA 366 2.12e+01 d.131.1.1 -11093 d.131.1.1 -11094 d.131.1.1 -11095 1a3qA 285 2.16e+01 1a3qA b.1.18.1 21932 b.2.5.3 22447 1pfsA 78 2.18e+01 1pfsA b.40.4.7 25391 1gwmA 153 2.19e+01 b.18.1.19 83348 2polA 366 2.21e+01 2polA d.131.1.1 41356 d.131.1.1 41357 d.131.1.1 41358 1ouwA 152 2.23e+01 b.77.3.1 -4759 1i3uA 127 2.25e+01 1gc1H b.1.1.1 61636 1fjrA 195 2.26e+01 1fjrA b.102.1.1 59855 1ksiB 642 2.30e+01 1ksiB b.30.2.1 24409 d.17.2.1 38045 d.17.2.1 38046 1nw8A 319 2.35e+01 c.66.1.11 86292 1pysA 350 2.39e+01 1pysA d.104.1.1 40775 1ivwA 638 2.48e+01 b.30.2.1 71456 d.17.2.1 71457 d.17.2.1 71458 1bhjA 292 2.49e+01 1xvaA c.66.1.5 34189 3hhrB 203 2.57e+01 1axiB b.1.2.1 22005 b.1.2.1 22006 1ui7A 638 2.58e+01 b.30.2.1 -3523 d.17.2.1 -9268 d.17.2.1 -9269 1roaA 122 2.63e+01 1is3A 135 2.65e+01 b.29.1.3 76773 1n99A 166 2.72e+01 b.36.1.1 85459 b.36.1.1 85460 1ui8A 638 2.72e+01 b.30.2.1 -3525 d.17.2.1 -9272 d.17.2.1 -9273 1fmtA 314 2.78e+01 1fmtA b.46.1.1 25758 c.65.1.1 34174 1gv3A 248 2.78e+01 a.2.11.1 70585 d.44.1.1 70586 1m7vA 363 2.79e+01 d.174.1.1 78748 1iznB 277 2.86e+01 e.43.1.2 83848 1pfzA 380 2.87e+01 1smrA b.50.1.2 26881 1qa7B 217 2.91e+01 1havA b.47.1.4 26426 1g0xA 197 2.95e+01 1nkr b.1.1.4 21805 b.1.1.4 21806 2phlA 397 2.98e+01 1dgwA b.82.1.2 28082 b.82.1.2 28083 1lnrI 134 2.99e+01 1k0rA 366 3.05e+01 b.40.4.5 67961 d.52.3.1 67962 d.52.3.1 67963 d.202.1.1 67964 1d1gA 168 3.15e+01 1d1gA c.71.1.1 34889 1b7yA 350 3.21e+01 1pysA d.104.1.1 40776 1ntyA 311 3.21e+01 1f3lA 321 3.25e+01 1g6q2 c.66.1.6 59630 1b9kA 238 3.27e+01 1qtsA b.1.10.1 22315 d.105.1.1 40791 1bw3 125 3.28e+01 1bw4 b.52.1.2 26899 1ajw 145 3.32e+01 1rhoA b.1.18.8 21905 1ksiA 642 3.33e+01 1ksiB b.30.2.1 24408 d.17.2.1 38043 d.17.2.1 38044 1ej6A 1289 3.39e+01 i.7.1.1 45967 1iqyA 638 3.44e+01 b.30.2.1 76763 d.17.2.1 76764 d.17.2.1 76765 1sy6A 204 3.45e+01 1ef1A 294 3.48e+01 1ef1A a.11.2.1 16368 b.55.1.5 27003 d.15.1.4 37611 1fmtB 314 3.51e+01 1fmtA b.46.1.1 25759 c.65.1.1 34175 1v04A 355 3.55e+01 unknown_sccs -4592 1iz5A 249 3.59e+01 d.131.1.2 83834 d.131.1.2 83835 1pk6A 133 3.59e+01 b.22.1.1 -3287 1cztA 160 3.61e+01 1cztA b.18.1.2 23715 1qz8A 113 3.72e+01 unknown_sccs -4264 1hxs1 302 3.73e+01 1ey4A 149 3.73e+01 1snc b.40.1.1 24815 2mcm 112 3.76e+01 2mcm b.1.7.1 22207 1iktA 120 3.79e+01 d.106.1.1 66188 1p27B 106 3.80e+01 d.58.7.1 -10020 1fjgP 88 3.82e+01 1emwA d.27.1.1 38444 1pkoA 139 3.85e+01 b.1.1.1 88147 1g9mC 185 3.86e+01 1cdy b.1.1.1 19721 b.1.1.3 21660 1mrzA 293 3.88e+01 b.43.5.1 -4048 c.26.1.3 -6616 1tyu 543 3.91e+01 1tyv b.80.1.6 28037 1kopA 223 3.92e+01 2cba b.74.1.1 27966 1cvjA 190 3.94e+01 1cvjB d.58.7.1 39191 d.58.7.1 39192 1grj 158 3.96e+01 1grj a.2.1.1 15691 d.26.1.2 38433 1ca1 370 3.96e+01 1ca1 a.124.1.1 19340 b.12.1.3 23648 1a8d 452 3.98e+01 1a8d b.29.1.6 24262 b.42.4.2 25607