# List of top-scoring protein chains for t2k-100-30-bys-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.soe.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 1pvdA 537 3.33e-01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31737,31777,31778 1pydA 556 3.70e-01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31735,31773,31774 2ko6A 89 3.71e-01 1dfoA 417 4.07e-01 1bj4A c.67.1.4 34480 2vk8A 563 4.98e-01 3fc7A 125 5.47e-01 1qpbA 563 5.86e-01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31739,31781,31782 3gbxA 420 7.10e-01 3fncA 163 1.28e+00 2dtxA 264 1.55e+00 2z7eA 157 1.58e+00 2boyA 254 1.61e+00 1m70A 190 1.66e+00 a.3.1.4,a.3.1.4 91200,91201 3huiA 126 1.79e+00 3bhwA 209 1.86e+00 3dm8A 143 1.89e+00 d.17.4.20 157804 2o4cA 380 1.98e+00 3f8mA 248 2.09e+00 1qwtA 255 2.85e+00 b.26.1.3 96501 3lfkA 129 3.22e+00 2wnpF 217 3.48e+00 1l8rA 101 3.76e+00 a.6.1.4 73700 1fzdA 201 4.48e+00 3fib d.171.1.1 42484 3c1qA 123 4.59e+00 2jhmF 218 4.83e+00 1fc4A 401 4.93e+00 1bs0A c.67.1.4 59760 2v9dA 343 5.63e+00 3e4rA 324 5.73e+00 1gxmA 332 5.93e+00 a.102.5.1 76371 1gdtA 183 6.20e+00 2rslA a.4.1.2,c.53.1.1 16021,33348 3kraB 274 6.32e+00 3e0jB 144 6.74e+00 1ru3A 732 6.76e+00 e.26.1.3 97835 3ch3X 265 6.87e+00 3cqcB 227 7.05e+00 2d39A 237 7.20e+00 1a81A 254 7.37e+00 1a81A d.93.1.1,d.93.1.1 40507,40508 3hinA 275 8.52e+00 1rhs 296 8.60e+00 1rhs 1rhsA 296 8.60e+00 c.46.1.2,c.46.1.2 32703,32704 1v9sA 208 9.35e+00 c.61.1.1 119894 1pjaA 302 1.03e+01 c.69.1.13 94758 1itwA 741 1.05e+01 c.77.1.2 76793 2peqA 134 1.05e+01 a.280.1.1 149443 1uddA 226 1.08e+01 a.132.1.3 107776 1zghA 260 1.12e+01 b.46.1.1,c.65.1.1 125028,125029 3cg1A 296 1.14e+01 2cvkA 110 1.15e+01 3c7mA 195 1.15e+01 2j41A 207 1.16e+01 2j5zA 221 1.17e+01 2i4lA 458 1.17e+01 1csyA 112 1.18e+01 1lckA d.93.1.1 40519 1p3dA 475 1.26e+01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 3kzqA 208 1.30e+01 1rv3A 483 1.34e+01 c.67.1.4 105101 2qzqA 152 1.36e+01 3d5lA 221 1.42e+01 2fjuB 799 1.44e+01 a.39.1.7,b.7.1.1,b.55.1.1,c.1.18.1 145170,145171,145172,145173 3l6dA 306 1.46e+01 3e38A 343 1.47e+01 2wbfX 265 1.49e+01 3gv5B 420 1.52e+01 1zetA 388 1.52e+01 d.240.1.1,e.8.1.7 124997,124998 1b4fA 82 1.53e+01 1b4fA a.60.1.2 17934 3h40A 389 1.55e+01 2yzuA 109 1.56e+01 1rm6C 161 1.65e+01 a.56.1.1,d.15.4.2 111876,111877 3fseA 365 1.65e+01 2c5rA 67 1.66e+01 a.251.1.1 129944 1tfe 145 1.67e+01 1tfe 1tfeA 145 1.67e+01 d.43.1.1 38680 3ctdA 213 1.70e+01 a.80.1.2 156981 1sq9A 397 1.70e+01 b.69.4.1 105889 2ot4A 525 1.70e+01 3fo3A 525 1.71e+01 3g6xA 420 1.73e+01 3l9uA 201 1.81e+01 1wyjA 125 1.87e+01 3dxqA 301 1.91e+01 1b0jA 754 2.04e+01 1amj c.8.2.1,c.83.1.1 30719,35395 1j7nA 776 2.07e+01 d.92.1.14,d.92.1.14,d.166.1.1 66409,66410,66411 2zkmX 799 2.10e+01 a.39.1.7,b.7.1.1,b.55.1.1,c.1.18.1 154587,154588,154589,154590 3loyA 633 2.19e+01 2ga8A 359 2.20e+01 1bcsB 160 2.23e+01 1whtB 3h4dA 390 2.25e+01 1ugjA 141 2.28e+01 b.41.1.3 107826 3h35A 185 2.30e+01 2dpiA 420 2.33e+01 d.240.1.1,e.8.1.7 131612,131613 1pjcA 361 2.36e+01 1sayA c.2.1.4,c.23.12.2 30101,31361 1zin 217 2.40e+01 1zin 1zinA 217 2.40e+01 c.37.1.1,g.41.2.1 31915,45178 2gf4A 100 2.41e+01 a.8.10.1 135074 1f8yA 157 2.42e+01 1f8xA c.23.14.1 31395 2ogrA 229 2.52e+01 2qsfX 171 2.54e+01 3ctlA 231 2.56e+01 1sayA 361 2.57e+01 1sayA c.2.1.4,c.23.12.2 30102,31362 1bj4A 470 2.61e+01 1bj4A c.67.1.4 34479 3cg3A 320 2.64e+01 1yqyA 523 2.65e+01 d.92.1.14,d.166.1.1 123903,123904 1txdA 385 2.67e+01 a.87.1.1,b.55.1.1 107422,107423 3lnoA 108 2.68e+01 3jv1A 182 2.69e+01 2nn6B 249 2.72e+01 d.14.1.4,d.101.1.1 148297,148298 2zeqA 78 2.75e+01 d.15.1.1 154405 2nnwA 376 2.77e+01 3k8pD 709 2.79e+01 3ct7A 231 2.87e+01 1f0yA 302 2.95e+01 2hdhA a.100.1.3,c.2.1.6 18793,30197 1fr2B 134 3.02e+01 d.4.1.1 83257 1kcqA 104 3.06e+01 d.109.1.1 68449 2glwA 92 3.07e+01 1whtB 153 3.09e+01 1whtB 3f9sA 146 3.11e+01 3kdqA 154 3.13e+01 1r5mA 425 3.17e+01 2alzA 390 3.20e+01 d.240.1.1,e.8.1.7 126994,126995 3k2yA 109 3.21e+01 2wkbA 125 3.25e+01 2bjoA 136 3.30e+01 1whsB 153 3.32e+01 1whtB 1ehwA 162 3.32e+01 1npk d.58.6.1 39088 2gykB 134 3.44e+01 d.4.1.1 135857 2vyoA 254 3.47e+01 2g5xA 234 3.48e+01 3emvA 253 3.52e+01 1zcjA 463 3.53e+01 3kusA 88 3.64e+01 3hhtB 229 3.67e+01 2x04A 80 3.67e+01 1s4uX 407 3.69e+01 b.69.4.1 112027 1awcB 153 3.74e+01 1bd8 d.211.1.1 19156 2jexA 209 3.81e+01 2d74B 148 3.86e+01 1akyA 220 3.87e+01 c.37.1.1,g.41.2.1 31896,45197 1db3A 372 3.88e+01 1db3A c.2.1.2 29813 1gtfA 74 3.88e+01 b.82.5.1 70460 1yaiA 151 3.96e+01 1yaiA b.1.8.1 22289 1rqjA 299 3.99e+01 a.128.1.1 97744 1bgf 124 4.00e+01 1bgf 1bgfA 124 4.00e+01 a.90.1.1 18537 2o37A 92 4.04e+01 1v5dA 386 4.12e+01 a.102.1.2 113537 2d4gA 171 4.16e+01 3i4fA 264 4.19e+01 1c0aA 585 4.19e+01 1c0aA b.40.4.1,d.74.4.1,d.104.1.1 25246,39731,40767 2hurA 142 4.22e+01 2duyA 75 4.24e+01 a.60.2.7 146589 2extA 77 4.27e+01 b.82.5.1 132563 3dcmX 192 4.28e+01 2depA 356 4.28e+01 2gm2A 132 4.33e+01 1vyxA 60 4.38e+01 g.44.1.3 114033 1mjgM 729 4.42e+01 e.26.1.3 79204 1u6mA 199 4.47e+01 d.108.1.1 113069 3hadA 308 4.48e+01 2hdhA a.100.1.3,c.2.1.6 18799,30203 1irzA 64 4.49e+01 a.4.1.11 76772 3c6fA 153 4.49e+01 3fmsA 209 4.58e+01 2v7kA 361 4.59e+01 1hy3A 294 4.61e+01 c.37.1.5 71090 3i3qA 211 4.61e+01 3gl5A 239 4.68e+01 2ekpA 239 4.69e+01 1w0mA 226 4.78e+01 c.1.1.1 109027 2bjqA 345 4.78e+01 b.169.1.1,b.169.1.1 128626,128627 1oaoC 729 4.86e+01 e.26.1.3 86746 1rhxA 87 4.87e+01 c.114.1.2 111805 3k26A 366 4.91e+01 1qwlA 505 4.92e+01 e.5.1.1 96483 1iynA 295 4.97e+01 a.93.1.1 90722 2dkjA 407 5.00e+01 3dc8A 490 5.18e+01 3k28A 429 5.20e+01 2gv5C 73 5.23e+01 2vhfA 374 5.29e+01 1jcfA 344 5.37e+01 c.55.1.1,c.55.1.1 62878,62879 2x75A 431 5.40e+01 1vliA 385 5.41e+01 b.85.1.1,c.1.10.6 108830,108831 3bkzA 201 5.41e+01 1uehA 253 5.42e+01 c.101.1.1 99259 1ta8A 332 5.45e+01 d.142.2.2 112375 1hgeB 175 5.51e+01 1hgeB h.3.1.1 45680 1to4A 156 5.57e+01 b.1.8.1 107162 1jroA 462 5.64e+01 a.56.1.1,d.15.4.2,d.87.2.1,d.145.1.3 67137,67138,67139,67140 3c25A 383 5.65e+01 3e0dA 1220 5.66e+01 1zm8A 259 5.66e+01 2hdhA 293 5.68e+01 2hdhA a.100.1.3,c.2.1.6 18795,30199 3i04M 728 5.69e+01 2qruA 274 5.71e+01 2g5dA 422 5.73e+01 b.52.1.4 147083 1ed7A 45 5.73e+01 1ed7A b.72.2.1 27809 2vlqB 134 5.84e+01 3bblA 287 5.89e+01 2ghaA 382 5.94e+01 2zfoC 147 6.03e+01 2pvpA 367 6.05e+01 1o26A 232 6.06e+01 d.207.1.1 86566 1f00I 282 6.12e+01 1f00I b.1.14.1,b.1.14.1,d.169.1.3 22368,22369,42439 1kpeA 126 6.13e+01 1kpf d.13.1.1 37508 1emvB 134 6.14e+01 1bxiB d.4.1.1 37135 1esc 306 6.23e+01 1esc 1escA 306 6.23e+01 c.23.10.1 31334 1f6yA 262 6.24e+01 1f6yA c.1.21.2 29673 2r44A 331 6.24e+01 1x1eA 239 6.30e+01 2pnfA 248 6.33e+01 2e0cA 409 6.34e+01 1dx4A 586 6.36e+01 2bce c.69.1.1 34622 1b97A 244 6.43e+01 1rvaA c.52.1.2 33252 1t3qA 168 6.44e+01 a.56.1.1,d.15.4.2 106367,106368 2bjrA 368 6.45e+01 b.169.1.1,b.169.1.1 128628,128629 2viuB 175 6.51e+01 1hgeB h.3.1.1 45676 1vjeA 166 6.55e+01 d.185.1.2 100807 2regA 298 6.60e+01 2o9pA 454 6.61e+01 3icvA 316 6.63e+01 1t64A 377 6.69e+01 c.42.1.2 106543 1vrbA 342 6.70e+01 b.82.2.11 120450 2bolA 314 6.70e+01 3g2mA 299 6.70e+01 3fm5A 150 6.75e+01 2hi2A 158 6.76e+01 2nsaA 170 6.76e+01 2uubD 209 6.79e+01 d.66.1.2 139935 1keaA 221 7.08e+01 a.96.1.2 68491 1ha0A 494 7.09e+01 1hgeA b.19.1.2,h.3.1.1 23824,45697 2nt2A 145 7.10e+01 3a0yA 152 7.13e+01 1f8xA 157 7.14e+01 1f8xA c.23.14.1 31397 3kxeA 110 7.17e+01 1rzsA 61 7.17e+01 a.35.1.2 105139 1peqA 714 7.20e+01 a.98.1.1,c.7.1.2 104131,104132 1n62A 166 7.26e+01 a.56.1.1,d.15.4.2 80090,80091 3dzzA 391 7.26e+01 1zx2A 147 7.28e+01 d.17.4.2 146033 2vqeD 209 7.32e+01 d.66.1.2 153428 3g3lA 327 7.33e+01 3md3A 166 7.33e+01 3iiwA 365 7.39e+01 3gnhA 403 7.49e+01 2hd1A 326 7.53e+01 a.211.1.2 136338 2ipcA 997 7.56e+01 2jovA 85 7.60e+01 d.349.1.1 148162 3dynA 329 7.75e+01 a.211.1.2 157942 3ch0A 272 7.82e+01 2e7fA 262 7.86e+01 2gz4A 207 7.90e+01 a.211.1.1 147196 3e9hA 493 7.92e+01 2d2mC 147 7.92e+01 2gmnA 274 7.95e+01 d.157.1.1 147132 3hhyA 280 7.98e+01