# 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 1kq3A 376 1.21e-01 e.22.1.2 68790 1ipwA 175 7.56e-01 2prd b.40.5.1 25427 1b16A 254 1.15e+00 1b16A c.2.1.2 29875 1a4uA 254 1.36e+00 1b16A c.2.1.2 29878 1i40A 175 1.38e+00 b.40.5.1 66024 1f6dA 376 1.46e+00 1f6dA c.87.1.3 35467 1dkrA 317 1.56e+00 1dkuA c.61.1.2 34114 c.61.1.2 34115 1dkuA 317 1.97e+00 1dkuA c.61.1.2 34118 c.61.1.2 34119 1qjdA 571 2.02e+00 1qjdA a.138.1.3 19695 c.3.1.4 30432 d.168.1.1 42315 1pot 325 2.15e+00 1pot c.94.1.1 35807 1obwA 175 2.54e+00 2prd b.40.5.1 25416 1fehA 574 2.76e+00 1fehA c.96.1.1 36015 d.15.4.2 37690 d.58.1.5 38998 1e32A 458 3.12e+00 1e32A b.52.2.3 59183 c.37.1.13 59184 d.31.1.1 59185 3gcb 470 3.19e+00 3gcb d.3.1.1 37032 1f2vA 219 3.29e+00 1f2vA c.23.17.1 59627 1gcb 454 3.31e+00 3gcb d.3.1.1 37034 1e39A 571 3.51e+00 1qjdA a.138.1.3 19694 c.3.1.4 30431 d.168.1.1 42314 1i50F 155 3.70e+00 d.78.1.2 61760 1i1hA 219 3.89e+00 1f2vA c.23.17.1 61530 1akeA 214 4.29e+00 1zin c.37.1.1 31905 g.41.2.1 45185 1bfd 528 4.32e+00 1bfd c.31.1.3 31745 c.36.1.1 31801 c.36.1.1 31802 1aogA 485 4.34e+00 3grs c.3.1.5 30517 c.3.1.5 30518 d.87.1.1 40190 2dhqA 146 4.74e+00 2dhqA c.23.13.1 31382 1myt 146 5.22e+00 1a6m a.1.1.2 15207 1s01 283 5.36e+00 1gci c.41.1.1 32511 1l6wA 220 5.38e+00 1qo7A 394 5.46e+00 1qo7A c.69.1.11 34697 1rdzA 337 6.32e+00 1frpA e.7.1.1 42882 1l1eA 287 6.52e+00 1cqxA 403 6.77e+00 1cqxA a.1.1.2 15635 b.43.4.2 25667 c.25.1.5 31562 1ik6A 369 6.96e+00 c.36.1.3 66174 c.48.1.2 66175 1gc5A 467 7.85e+00 1gc5A c.72.1.3 60429 1gq6A 313 8.06e+00 5fbpA 335 8.08e+00 1frpA e.7.1.1 42873 1sup 275 8.09e+00 1gci c.41.1.1 32510 2ercA 244 8.58e+00 2ercA c.66.1.9 34224 1ukz 203 8.61e+00 1zin c.37.1.1 31840 2dpg 485 8.70e+00 1dpgA c.2.1.3 30076 d.81.1.5 39991 1gnuA 117 9.56e+00 d.15.1.3 65403 1nulA 152 9.83e+00 1nulA c.61.1.1 34011 1cl1A 395 9.86e+00 1cl2A c.67.1.3 34395 1qklA 127 1.03e+01 1qklA d.78.1.2 39754 1xvaA 292 1.06e+01 1xvaA c.66.1.5 34183 1d0bA 213 1.06e+01 1d0bA c.10.2.1 30866 3adk 195 1.06e+01 1zin c.37.1.1 31885 1es6A 296 1.07e+01 1es6A b.31.1.1 24424 1frpA 335 1.07e+01 1frpA e.7.1.1 42875 1bjnA 360 1.09e+01 1bjnA c.67.1.4 34469 1mldA 314 1.10e+01 2cmd c.2.1.5 30122 d.162.1.1 42089 1qtrA 317 1.18e+01 1qtrA c.69.1.7 34660 1bjoA 360 1.22e+01 1bjnA c.67.1.4 34471 1ii5A 233 1.22e+01 c.94.1.1 62412 1ykfA 352 1.25e+01 1pedA b.35.1.2 24757 c.2.1.1 29773 1iiwA 232 1.26e+01 c.94.1.1 62461 1jm6A 407 1.28e+01 a.29.5.1 66876 d.122.1.4 66877 1nhs 447 1.30e+01 1nhp c.3.1.5 30555 c.3.1.5 30556 d.87.1.1 40199 1bhjA 292 1.30e+01 1xvaA c.66.1.5 34189 1hqkA 154 1.30e+01 c.16.1.1 65902 1kp9B 287 1.32e+01 c.66.1.18 68734 1ezvB 352 1.37e+01 1ezvB d.185.1.1 59543 d.185.1.1 59544 1kpgA 287 1.39e+01 c.66.1.18 68735 1js1X 324 1.39e+01 1gtzA 156 1.44e+01 1cl2A 395 1.44e+01 1cl2A c.67.1.3 34397 1hruA 188 1.46e+01 1hruA d.115.1.1 40926 2cpgA 45 1.48e+01 2cpgA a.43.1.2 17455 1qr7A 350 1.48e+01 1qr7A c.1.10.4 29191 1trb 320 1.49e+01 1trb c.3.1.5 30529 c.3.1.5 30530 1vaoA 560 1.52e+01 1qltA d.58.32.1 39461 d.145.1.1 41724 1ak7 174 1.53e+01 1cof d.109.1.2 40864 1nhp 447 1.54e+01 1nhp c.3.1.5 30549 c.3.1.5 30550 d.87.1.1 40196 1qf9A 194 1.56e+01 1zin c.37.1.1 31848 5ukdA 194 1.57e+01 1zin c.37.1.1 31851 1dctA 324 1.57e+01 6mhtA c.66.1.10 34244 1a62 130 1.57e+01 1a62 a.140.3.1 64708 b.40.4.5 64709 1el5A 389 1.58e+01 1b3mA c.3.1.2 30369 d.16.1.3 37937 1qltA 560 1.59e+01 1qltA d.58.32.1 39457 d.145.1.1 41720 1je5A 206 1.59e+01 1je5A b.40.4.7 62909 1i1gA 141 1.60e+01 a.4.5.32 65982 d.58.37.1 65983 1joa 447 1.63e+01 1nhp c.3.1.5 30563 c.3.1.5 30564 d.87.1.1 40203 1isiA 265 1.66e+01 1c4xA 285 1.71e+01 1c4xA c.69.1.10 34684 1a8vA 121 1.73e+01 1a62 a.140.3.1 64712 b.40.4.5 64713 2pviA 157 1.78e+01 3pviA c.52.1.6 33302 1qamA 244 1.82e+01 2ercA c.66.1.9 34220 1h6tA 291 1.87e+01 b.1.1.6 65686 c.10.2.1 65687 1fm0E 150 1.91e+01 1fmaE d.41.5.1 38629 1noyA 388 1.91e+01 1clqA c.55.3.5 33713 1gjuA 637 1.92e+01 b.71.1.1 60580 c.1.8.1 60581 1eqnA 321 1.94e+01 1dd9A e.13.1.1 43256 1ebbA 202 2.01e+01 c.60.1.1 64900 1e8gA 560 2.03e+01 1qltA d.58.32.1 39455 d.145.1.1 41718 1l9fA 389 2.04e+01 1fpkA 335 2.05e+01 1frpA e.7.1.1 42930 2phlA 397 2.08e+01 1dgwA b.82.1.2 28082 b.82.1.2 28083 1srrA 124 2.09e+01 1dz3A c.23.1.1 31110 1im5A 180 2.11e+01 c.33.1.2 66211 2mbr 340 2.11e+01 2mbr d.145.1.2 41749 d.146.1.1 41762 1uxy 340 2.12e+01 2mbr d.145.1.2 41748 d.146.1.1 41761 1e3jA 352 2.15e+01 1e3jA b.35.1.2 24765 c.2.1.1 29781 1fmaE 150 2.15e+01 1fmaE d.41.5.1 38630 1eokA 290 2.17e+01 1eokA c.1.8.5 28991 1phnB 172 2.33e+01 1qgwC a.1.1.3 15642 1dpgA 485 2.36e+01 1dpgA c.2.1.3 30074 d.81.1.5 39989 1dcqA 278 2.36e+01 1dcqA a.118.2.1 19178 g.45.1.1 45326 1yacA 208 2.37e+01 1yacA c.33.1.2 31757 1hd2A 161 2.44e+01 c.47.1.10 60962 1gg1A 350 2.44e+01 1qr7A c.1.10.4 29187 1hgxA 183 2.45e+01 1tc1A c.61.1.1 34027 1hdr 244 2.47e+01 1dhr c.2.1.2 29837 1jkw 323 2.48e+01 1jkw a.74.1.1 18356 a.74.1.1 18357 1gjwA 637 2.49e+01 b.71.1.1 60582 c.1.8.1 60583 1qfmA 710 2.52e+01 1qfmA b.69.7.1 27673 c.69.1.4 34641 1puc 105 2.52e+01 1puc d.97.1.1 40675 1i50K 120 2.52e+01 d.74.3.2 61765 1jg1A 235 2.60e+01 c.66.1.7 66661 1dhr 241 2.60e+01 1dhr c.2.1.2 29832 1jx6A 342 2.60e+01 c.93.1.1 67406 1im8A 244 2.61e+01 c.66.1.14 66212 1adoA 363 2.71e+01 1fbaA c.1.10.1 29124 1lst 239 2.76e+01 1lst c.94.1.1 35755 1sceA 112 2.77e+01 1puc d.97.1.1 40676 2dln 306 2.83e+01 1iow c.30.1.2 31715 d.142.1.1 41483 1fnnA 389 2.84e+01 1fnnA a.4.5.11 16129 c.37.1.13 32426 1lvl 458 2.89e+01 1lvl c.3.1.5 30567 c.3.1.5 30568 d.87.1.1 40205 1h8eA 510 2.90e+01 1skyB a.69.1.1 60738 b.49.1.1 60739 c.37.1.11 60740 1oaa 259 2.90e+01 1oaa c.2.1.2 29829 1dcs 311 2.93e+01 1dcs b.82.2.1 28124 1in4A 334 2.96e+01 1hqcA a.4.5.11 62597 c.37.1.13 62598 1lk5A 229 2.98e+01 1jeiA 53 3.05e+01 1jeiA a.140.1.1 62918 1qbkB 890 3.16e+01 1qbkB a.118.1.1 19127 2fsp 124 3.17e+01 1dz3A c.23.1.1 31119 1jj2X 240 3.18e+01 1ffkV c.9.2.1 63109 1a2zA 220 3.22e+01 1a2zA c.56.4.1 33794 1clqA 903 3.22e+01 1clqA c.55.3.5 33717 e.8.1.1 43006 1azwA 313 3.23e+01 1qtrA c.69.1.7 34658 1ahsA 126 3.26e+01 1ahsA b.19.1.1 23794 1thx 115 3.27e+01 1thx c.47.1.1 32732 1kzhA 555 3.27e+01 1dosA 358 3.29e+01 1dosA c.1.10.2 29175 1rvv1 154 3.31e+01 1rvv1 1rvvA 154 3.31e+01 1rvv1 c.16.1.1 30927 1qorA 327 3.32e+01 1qorA b.35.1.2 24766 c.2.1.1 29782 1ecfB 504 3.37e+01 1ecfB c.61.1.1 34054 d.153.1.1 41821 1di0A 158 3.39e+01 1di0A c.16.1.1 30957 1f0kA 364 3.45e+01 1f0kA c.87.1.2 35465 1cs1C 386 3.45e+01 1ibjA c.67.1.3 34401 1fe0A 68 3.48e+01 1cc8A d.58.17.1 39345 1fcjA 322 3.50e+01 1oasA c.79.1.1 35289 1oasA 322 3.51e+01 1oasA c.79.1.1 35293 1brt 277 3.53e+01 1brt c.69.1.12 34699 3pviA 157 3.58e+01 3pviA c.52.1.6 33300 1cv2A 296 3.59e+01 1bn6A c.69.1.8 34680 1b57A 358 3.61e+01 1dosA c.1.10.2 29177 1de5A 426 3.64e+01 1de5A c.1.15.2 29402 1pvuA 154 3.69e+01 3pviA c.52.1.6 33306 1qgjA 300 3.75e+01 1bgp a.93.1.1 18691 1kngA 156 3.77e+01 9ldtA 332 3.84e+01 3ldh c.2.1.5 30154 d.162.1.1 42121 1jwiB 125 3.85e+01 d.169.1.1 67384 1cvrA 435 3.90e+01 1cvrA b.1.1.5 21949 c.17.1.2 31006 1a8s 273 3.91e+01 1brt c.69.1.12 34710 1sur 215 3.92e+01 1sur c.26.2.2 31620 1iow 306 3.94e+01 1iow c.30.1.2 31713 d.142.1.1 41481 1qk4A 233 3.97e+01 1qk3A c.61.1.1 34037 1qf8A 182 3.99e+01 1qf8A g.41.4.1 45212