# List of top-scoring protein chains for t2k-w0.5 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 1j7nA 776 7.05e-01 d.92.1.14 66409 d.92.1.14 66410 d.166.1.1 66411 1jhdA 396 1.42e+00 b.58.1.2 66712 c.26.1.5 66713 1bkhB 361 2.01e+00 1mucA c.1.11.2 29239 d.54.1.1 38883 1esmA 316 2.28e+00 1esmA c.37.1.6 31953 1qadA 111 4.69e+00 1qadA d.93.1.1 40498 1h9oA 112 4.69e+00 1qadA d.93.1.1 60837 1bfi 112 4.71e+00 1qadA d.93.1.1 40499 1euzE 419 5.98e+00 1k89 c.2.1.7 59521 c.58.1.1 59522 1ucyE 109 7.87e+00 1ucyE 1jr7A 311 8.42e+00 b.82.2.3 63255 1bhxF 105 8.89e+00 1ucyE 3sqcA 631 9.05e+00 2sqcA a.102.4.2 18860 a.102.4.2 18861 1fatB 252 9.16e+00 1led b.29.1.1 24165 2sqcA 631 9.34e+00 2sqcA a.102.4.2 18854 a.102.4.2 18855 1sqc 631 9.42e+00 2sqcA a.102.4.2 18858 a.102.4.2 18859 1dehA 374 1.04e+01 2ohxA b.35.1.2 24713 c.2.1.1 29729 1g8wB 233 1.08e+01 1led b.29.1.1 24161 1htbA 374 1.09e+01 2ohxA b.35.1.2 24715 c.2.1.1 29731 1jvnA 555 1.12e+01 c.1.2.1 67355 c.23.16.1 67356 1hdzA 374 1.13e+01 2ohxA b.35.1.2 24725 c.2.1.1 29741 1gesA 450 1.19e+01 3grs c.3.1.5 30473 c.3.1.5 30474 d.87.1.1 40168 1hdyA 374 1.20e+01 2ohxA b.35.1.2 24723 c.2.1.1 29739 1gerB 450 1.22e+01 3grs c.3.1.5 30479 c.3.1.5 30480 d.87.1.1 40171 1hu8A 186 1.57e+01 1tupA b.2.5.1 61269 1d4gA 430 1.64e+01 1b3rA c.2.1.4 30114 c.23.12.3 31374 1pysB 785 1.66e+01 1pysB a.6.1.1 16299 a.6.1.1 16300 b.40.4.4 25311 d.58.13.1 39310 d.104.1.1 40779 d.138.1.1 41455 1eiyB 785 1.66e+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 1b7yB 785 1.66e+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 1jraA 117 1.66e+01 a.24.15.1 67117 1jr8A 117 1.66e+01 a.24.15.1 67115 1hna 217 1.67e+01 1b8xA a.45.1.1 17604 c.47.1.5 32898 1axiB 236 1.68e+01 1axiB b.1.2.1 21997 b.1.2.1 21998 2gtuA 217 1.69e+01 1b8xA a.45.1.1 17605 c.47.1.5 32899 2asr 142 1.70e+01 1vls a.24.2.1 16529 1d4fA 431 1.72e+01 1b3rA c.2.1.4 30110 c.23.12.3 31370 1b3rA 431 1.74e+01 1b3rA c.2.1.4 30106 c.23.12.3 31366 1mabB 479 1.79e+01 1skyE a.69.1.1 18312 b.49.1.1 26477 c.37.1.11 32357 3gtuB 224 1.81e+01 1b8xA a.45.1.1 17612 c.47.1.5 32906 1gegA 256 1.95e+01 1ybvA c.2.1.2 29888 1bpyA 335 2.04e+01 1bpyA a.60.6.1 17980 e.9.1.1 43122 1fgkA 310 2.09e+01 1fgkA d.144.1.2 41693 1rpl 251 2.13e+01 1bpyA e.9.1.1 43212 1nom 248 2.17e+01 1bpyA e.9.1.1 43220 1bpb 248 2.17e+01 1bpyA e.9.1.1 43215 2pcbB 104 2.17e+01 1ycc a.3.1.1 15869 1giw 104 2.18e+01 1ycc a.3.1.1 15874 1wejF 105 2.21e+01 1ycc a.3.1.1 15865 1fl2A 310 2.22e+01 1hyuA c.3.1.5 59869 c.3.1.5 59870 1d5wC 126 2.22e+01 1dbwA c.23.1.1 31101 1huoA 335 2.24e+01 1bpyA a.60.6.1 61273 e.9.1.1 61274 1hzjA 348 2.26e+01 1xel c.2.1.2 61450 1i3kA 348 2.28e+01 1xel c.2.1.2 61595 1bpe 335 2.30e+01 1bpyA a.60.6.1 18076 e.9.1.1 43228 1dbwA 126 2.31e+01 1dbwA c.23.1.1 31095 1dckA 126 2.31e+01 1dbwA c.23.1.1 31097 1jn3A 251 2.31e+01 1bpyA e.9.1.1 63183 1bkhA 358 2.32e+01 1mucA c.1.11.2 29238 d.54.1.1 38882 2up1A 183 2.37e+01 1ha1 d.58.7.1 39151 d.58.7.1 39152 1ek6A 348 2.37e+01 1xel c.2.1.2 29800 1up1 182 2.49e+01 1ha1 d.58.7.1 39149 d.58.7.1 39150 1ha1 184 2.62e+01 1ha1 d.58.7.1 39147 d.58.7.1 39148 1qk5B 233 2.62e+01 1qk3A c.61.1.1 34036 1l3kA 196 2.65e+01 3tatA 397 2.66e+01 1ajsA c.67.1.1 34379 1ht0A 374 2.72e+01 2ohxA b.35.1.2 24709 c.2.1.1 29725 1bqqT 184 2.82e+01 1br9 b.40.3.1 25237 1dqpA 230 2.84e+01 1dqnA c.61.1.1 34069 1dqnA 230 2.84e+01 1dqnA c.61.1.1 34067 1wit 93 2.85e+01 1wit b.1.1.4 21714 1g97A 459 2.91e+01 1fwyA b.81.1.4 60394 c.68.1.5 60395 1g79A 218 2.93e+01 1ci0A b.45.1.1 25752 1ibfA 151 3.04e+01 1yaiA b.1.8.1 62158 1cnsA 243 3.05e+01 1cnsA d.2.1.1 36241 1jksA 294 3.08e+01 1eexA 554 3.13e+01 1dioA c.1.19.3 29650 1dioA 554 3.13e+01 1dioA c.1.19.3 29656 1lml 478 3.14e+01 1lml d.92.1.3 40295 1e4eB 343 3.17e+01 c.30.1.2 59223 d.142.1.1 59224 1thpB 259 3.18e+01 5ptp 1e4eA 343 3.18e+01 1iow c.30.1.2 59221 d.142.1.1 59222 1ayzA 169 3.18e+01 1u9aA d.20.1.1 38326 1iruN 219 3.19e+01 1qgiA 259 3.20e+01 1qgiA d.2.1.7 37001 1fsgA 233 3.27e+01 1qk3A c.61.1.1 34029 1qk3A 233 3.27e+01 1qk3A c.61.1.1 34031 1qk4A 233 3.27e+01 1qk3A c.61.1.1 34037 1fqiA 147 3.36e+01 1agrE a.91.1.1 18542 1avoA 60 3.40e+01 1avoA a.24.8.1 16619 1hm9A 468 3.44e+01 b.81.1.4 65866 c.68.1.5 65867 1ee2A 373 3.48e+01 2ohxA b.35.1.2 24663 c.2.1.1 29679 1ee2B 373 3.48e+01 2ohxA b.35.1.2 24664 c.2.1.1 29680 1br9 194 3.49e+01 1br9 b.40.3.1 25235 1nbmD 480 3.50e+01 1skyE a.69.1.1 18290 b.49.1.1 26455 c.37.1.11 32335 1nbmE 480 3.50e+01 1skyE a.69.1.1 18291 b.49.1.1 26456 c.37.1.11 32336 1k2yX 463 3.63e+01 c.84.1.1 68063 c.84.1.1 68064 c.84.1.1 68065 c.84.1.1 68066 1ibdA 151 3.65e+01 1yaiA b.1.8.1 62157 1gmoC 183 3.66e+01 g.10.1.1 65323 g.14.1.1 65324 1hwgB 237 3.67e+01 1axiB b.1.2.1 21999 b.1.2.1 22000 1ef7A 242 3.69e+01 1theB d.3.1.1 37087 1h8eD 482 3.71e+01 1skyE a.69.1.1 60747 b.49.1.1 60748 c.37.1.11 60749 1e79D 482 3.71e+01 1skyE a.69.1.1 18272 b.49.1.1 26437 c.37.1.11 32317 1jkkA 277 3.72e+01 1a22B 238 3.72e+01 1axiB b.1.2.1 22003 b.1.2.1 22004 1dbrA 231 3.75e+01 1qk3A c.61.1.1 34041 1be3K 56 3.76e+01 f.2.1.8 43672 1nk1A 183 3.82e+01 1bhtA g.10.1.1 44605 g.14.1.1 44665 1qhkA 47 3.84e+01 1qhkA d.100.1.2 40694 1osmA 342 3.85e+01 2omf f.4.3.1 43769 1k35A 463 3.92e+01 c.84.1.1 68094 c.84.1.1 68095 c.84.1.1 68096 c.84.1.1 68097 1dbhA 354 3.97e+01 1awe a.87.1.1 18514 b.55.1.1 26967 1d09A 310 3.97e+01 3csuA c.78.1.1 35100 c.78.1.1 35101 1deqB 408 3.98e+01 i.9.1.1 45991