# 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 1lvwA 295 9.78e-02 c.68.1.6 84723 1top 162 4.04e-01 1ncx a.39.1.5 17223 1ub4C 85 4.06e-01 b.129.1.1 88401 1v54J 59 4.06e-01 f.23.4.1 -12112 2occJ 59 4.70e-01 2occJ f.23.4.1 43524 1ncx 162 5.82e-01 1ncx a.39.1.5 17222 1m12A 84 8.33e-01 a.64.1.1 84745 1s9aA 257 9.58e-01 1g1eB 89 1.27e+00 1g1eB a.59.1.1 17931 1g8iA 190 1.32e+00 1rec a.39.1.5 60363 2occC 261 2.01e+00 1ocrC f.25.1.1 43520 1v54C 261 2.25e+00 f.25.1.1 -12239 1us7B 265 2.33e+00 unknown_sccs -1518 1ocrC 261 3.46e+00 1ocrC f.25.1.1 43540 1jggA 60 3.67e+00 2hddA a.4.1.1 62950 1nz6A 101 3.71e+00 a.2.3.1 86441 1jr8A 117 4.10e+00 a.24.15.1 67115 1pmnA 364 4.52e+00 d.144.1.7 -11297 1rprA 63 4.61e+00 1nkd a.30.1.1 16989 1ezjA 115 5.13e+00 1ezjA h.1.14.1 45638 1avoA 60 5.30e+00 1avoA a.24.8.1 16619 1mc3A 296 5.44e+00 c.68.1.6 78943 1en7A 157 5.49e+00 1en7A a.140.4.1 64733 d.4.1.5 64734 1rylA 167 5.63e+00 1jdqA 98 5.95e+00 d.68.3.3 66559 1ctdA 36 6.12e+00 1ctdA a.39.1.5 17230 1jk0B 345 6.55e+00 a.25.1.2 63143 1oivA 191 6.94e+00 c.37.1.8 -7074 1jraA 117 7.01e+00 a.24.15.1 67117 2hts 88 7.17e+00 2hts a.4.5.22 16174 1aba 87 7.18e+00 1aba c.47.1.1 32760 1us6A 102 7.36e+00 1ftt 68 7.41e+00 2hddA a.4.1.1 15997 1gmxA 108 7.43e+00 c.46.1.3 65355 1j03A 102 7.55e+00 unknown_sccs -10954 1g4yR 148 8.04e+00 1cll a.39.1.5 60252 1mr8A 93 8.28e+00 1b4cA a.39.1.2 17186 1byuA 216 8.29e+00 1byuA c.37.1.8 32032 1sedA 117 8.39e+00 1o6uA 403 8.60e+00 a.5.3.1 -366 unknown_sccs -3048 c.13.1.1 -6221 1e7lA 157 8.62e+00 1en7A a.140.4.1 64728 d.4.1.5 64729 1hkhA 279 8.66e+00 c.69.1.12 -8342 1dd9A 338 8.76e+00 1dd9A e.13.1.1 43254 1f45B 197 9.04e+00 1f45B a.26.1.1 59642 1broA 277 9.15e+00 1brt c.69.1.12 34700 1huw 166 9.42e+00 1huw a.26.1.1 16831 1ehkC 33 9.46e+00 1ehkC f.23.9.1 43626 1mp4A 292 9.74e+00 c.68.1.6 79376 1gcvB 136 9.90e+00 1cg5B a.1.1.2 15589 1kq6A 141 1.00e+01 d.189.1.1 -9926 1h3lA 87 1.07e+01 a.177.1.1 76639 1k5nA 276 1.10e+01 b.1.1.2 77266 d.19.1.1 77267 1od2A 805 1.16e+01 c.14.1.4 86821 c.14.1.4 86822 1htrP 43 1.16e+01 1htrP b.50.1.2 26852 1ktpB 172 1.19e+01 a.1.1.3 72991 1d66A 66 1.20e+01 1d66A g.38.1.1 45076 h.1.3.1 45510 1ggzA 148 1.21e+01 a.39.1.5 70176 1ddzA 496 1.22e+01 1ddzA c.53.2.1 33372 c.53.2.1 33373 1a88A 275 1.22e+01 1brt c.69.1.12 34707 1l8yA 91 1.25e+01 a.21.1.1 73708 1k8kG 151 1.26e+01 a.118.13.1 68313 1pyaB 228 1.28e+01 1pyaB 1uelB 48 1.29e+01 j.105.1.1 -13406 1jjhA 86 1.30e+01 2bopA d.58.8.1 63119 1e01A 48 1.31e+01 1e01A 1tvs 75 1.34e+01 1tvs j.40.1.1 46303 1cll 148 1.35e+01 1cll a.39.1.5 17263 1gotG 73 1.47e+01 1tbgE a.137.3.1 19629 1kn1A 160 1.48e+01 a.1.1.3 77455 1a5j 110 1.50e+01 1a5j a.4.1.3 16043 a.4.1.3 16044 1iieA 75 1.58e+01 1iieA a.109.1.1 19039 1m46A 148 1.58e+01 a.39.1.5 78599 1maz 221 1.61e+01 1maz f.1.4.1 43393 1eqnA 321 1.66e+01 1dd9A e.13.1.1 43256 1giqA 413 1.67e+01 d.166.1.1 76224 d.166.1.1 76225 1b79A 119 1.69e+01 1b79A a.81.1.1 18451 1w0bA 102 1.69e+01 1j8iA 93 1.69e+01 d.9.1.1 66438 1aje 194 1.72e+01 1ctqA c.37.1.8 32071 1neq 74 1.77e+01 1neq a.35.1.2 17063 1il6 185 1.77e+01 1alu a.26.1.1 16827 1pufA 77 1.77e+01 a.4.1.1 -191 1ddeA 338 1.80e+01 1dd9A e.13.1.1 43255 1t0gA 109 1.83e+01 unknown_sccs -10955 1sv7A 109 1.86e+01 1brt 277 1.89e+01 1brt c.69.1.12 34699 1lj2A 110 1.94e+01 h.1.13.2 73926 1jjrA 151 2.00e+01 a.140.2.1 66772 2hdhA 293 2.01e+01 2hdhA a.100.1.3 18795 c.2.1.6 30199 1s1hM 132 2.01e+01 1fgyA 127 2.06e+01 1faoA b.55.1.1 26976 2nef 136 2.06e+01 1efnB d.102.1.1 40704 1rec 201 2.08e+01 1rec a.39.1.5 17326 1fcdA 401 2.09e+01 1fcdA c.3.1.5 30593 c.3.1.5 30594 d.87.1.1 40218 2hddA 61 2.13e+01 2hddA a.4.1.1 15971 1fzkA 274 2.14e+01 1agdA b.1.1.2 60149 d.19.1.1 60150 1j99A 293 2.16e+01 c.37.1.5 71618 1ebdC 41 2.17e+01 1ebdC a.9.1.1 16355 1zac 90 2.18e+01 1ncx a.39.1.5 17236 1ibvB 229 2.18e+01 1ln4A 104 2.19e+01 d.68.4.1 74043 1gn0A 108 2.21e+01 c.46.1.3 65358 1efdN 266 2.22e+01 1efdN c.92.2.1 35597 1hllA 32 2.23e+01 j.94.1.1 70966 1cpcB 172 2.25e+01 1qgwC a.1.1.3 15644 1g8mA 593 2.28e+01 1g8mA c.24.1.3 60371 c.97.2.1 60372 1etxA 98 2.34e+01 1fipA unknown_sccs 18978 1o08A 221 2.36e+01 c.108.1.6 86525 3proD 166 2.36e+01 3proC d.52.1.1 38814 d.52.1.1 38815 1vsgA 364 2.39e+01 1vsgA h.4.1.1 45782 1dmhA 311 2.40e+01 1dmhA b.3.6.1 22633 1tk4A 121 2.42e+01 1b72A 97 2.44e+01 2hddA a.4.1.1 16000 1exrA 148 2.46e+01 1cll a.39.1.5 17299 1pyiA 96 2.46e+01 1pyiA g.38.1.1 45079 h.1.3.1 45512 1af3 196 2.47e+01 1maz f.1.4.1 43397 1b9xB 68 2.51e+01 1tbgE a.137.3.1 19638 1s6cA 183 2.53e+01 a.39.1.5 -858 1o7kA 131 2.55e+01 d.189.1.1 81144 1s4xA 67 2.56e+01 j.60.1.1 -13383 1jnrB 150 2.59e+01 d.58.1.5 66969 1hdj 77 2.63e+01 1bqz a.2.3.1 15696 1omrA 201 2.69e+01 a.39.1.5 -854 2dubE 261 2.71e+01 1nzyA c.14.1.3 30916 1be3H 78 2.72e+01 1be3H f.28.1.1 43670 1qn2A 100 2.72e+01 1ycc a.3.1.1 15882 1beg 98 2.82e+01 1bxm a.134.1.1 19620 1ds6B 180 2.85e+01 1rhoA b.1.18.8 21898 1cfzA 162 2.94e+01 1cfzA c.56.1.1 33754 1f0yA 302 2.94e+01 2hdhA a.100.1.3 18793 c.2.1.6 30197 1sqgA 429 2.95e+01 1qgtA 149 2.95e+01 1qgtA a.62.1.1 18135 1fv0A 121 2.97e+01 a.133.1.2 70147 1ash 150 2.98e+01 1ash a.1.1.2 15622 1crxA 322 3.01e+01 4crxA a.60.9.1 18097 d.163.1.1 42157 1k3yA 221 3.03e+01 a.45.1.1 77245 c.47.1.5 77246 3crxA 343 3.07e+01 4crxA a.60.9.1 18101 d.163.1.1 42161 1gpc 218 3.08e+01 1gpc b.40.4.7 25393 1m1eB 81 3.09e+01 a.161.1.1 78400 1dj0A 264 3.09e+01 1dj0A unknown_sccs -10141 1nvpB 57 3.14e+01 a.32.1.1 -779 1n1cA 217 3.21e+01 a.184.1.1 85254 1q8iA 783 3.21e+01 c.55.3.5 -7635 e.8.1.1 -11885 1jboB 172 3.23e+01 a.1.1.3 84151 1k3lA 221 3.32e+01 a.45.1.1 77229 c.47.1.5 77230 1hnuA 280 3.33e+01 1hnoA c.14.1.3 61096 1cpcL 172 3.34e+01 1qgwC a.1.1.3 15646 4crxA 322 3.35e+01 4crxA a.60.9.1 18095 d.163.1.1 42155 1kpmA 121 3.35e+01 a.133.1.2 72844 1idsA 207 3.40e+01 1avmA a.2.11.1 15722 d.44.1.1 38730 1hb6A 86 3.41e+01 a.11.1.1 70959 1h3fA 432 3.44e+01 c.26.1.1 76631 d.66.1.4 76632 1gnwA 211 3.47e+01 1gnwA a.45.1.1 17727 c.47.1.5 33021 1m9nA 613 3.49e+01 c.24.1.3 78870 c.97.2.1 78871 4ubpA 101 3.56e+01 1ubpA d.8.1.1 37352 1enh 54 3.58e+01 2hddA a.4.1.1 15973 1b72B 87 3.59e+01 1akhA a.4.1.1 16001 1gseA 221 3.60e+01 1pgtA a.45.1.1 17667 c.47.1.5 32961 1hnoA 280 3.65e+01 1hnoA c.14.1.3 61095 1lvhA 221 3.65e+01 c.108.1.6 74282 1tbgE 68 3.65e+01 1tbgE a.137.3.1 19630 1m45A 148 3.69e+01 a.39.1.5 78598 1fpzA 212 3.70e+01 1fpzA c.45.1.1 59976 1ubpA 101 3.72e+01 1ubpA d.8.1.1 37353 1nubA 229 3.76e+01 1sra a.39.1.3 17191 g.3.11.3 44330 unknown_sccs 44715 1lkxA 697 3.76e+01 c.37.1.9 73981 1vk9A 151 3.79e+01 1gr8A 412 3.79e+01 1ockA 412 3.79e+01 c.117.1.1 86802 1gln 468 3.84e+01 1gln a.97.1.1 18752 c.26.1.1 31588 1csgA 127 3.88e+01 2gmfA a.26.1.2 16851 1irqA 71 3.89e+01 unknown_sccs 66297 2gmfA 127 3.91e+01 2gmfA a.26.1.2 16849 2occM 46 3.94e+01 2occM f.23.7.1 43527 1a5t 334 3.97e+01 1a5t a.80.1.1 18450 c.37.1.20 32423