# 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 1ggiH 222 1.22e-01 1igtB b.1.1.1 19877 b.1.1.2 20973 1ggbH 215 1.22e-01 1igtB b.1.1.1 19875 b.1.1.2 20971 2occC 261 2.38e-01 1ocrC f.2.1.3 43520 1ocrC 261 2.38e-01 1ocrC f.2.1.3 43540 1fhxB 129 1.76e+00 1faoA b.55.1.1 26981 1fhwB 129 1.85e+00 1faoA b.55.1.1 26978 1fgyA 127 2.03e+00 1faoA b.55.1.1 26976 1l6jA 425 2.53e+00 1f28A 297 3.39e+00 1bkpA d.117.1.1 59608 1iruL 204 3.72e+00 1eb4A 509 4.00e+00 a.127.1.2 64894 1gk2A 509 4.01e+00 a.127.1.2 65229 1gkjA 509 4.03e+00 1gkmA 509 4.03e+00 1b8fA 509 4.03e+00 1b8fA a.127.1.2 19434 1j5oH 220 4.07e+00 1gk3A 509 5.09e+00 a.127.1.2 65233 1bwvS 138 5.77e+00 1rboC d.73.1.1 39662 1iu4A 331 6.68e+00 3pbgA 468 7.51e+00 1e70M c.1.8.4 28951 1pbgA 468 7.51e+00 1e70M c.1.8.4 28946 2pbg 468 7.53e+00 1e70M c.1.8.4 28948 4pbgA 468 7.56e+00 1e70M c.1.8.4 28949 1j6yA 139 7.71e+00 1d6vH 221 7.78e+00 1igtB b.1.1.1 20197 b.1.1.2 21213 1etzB 228 7.80e+00 1igtB b.1.1.1 20481 b.1.1.2 21445 1lucB 324 8.04e+00 1lucA c.1.16.1 29548 1brlB 324 8.04e+00 1lucA c.1.16.1 29554 1jrhH 219 8.55e+00 1igtB b.1.1.1 20223 b.1.1.2 21235 1emtH 213 8.97e+00 1igtB b.1.1.1 20483 b.1.1.2 21447 1cy9A 264 9.01e+00 1ecl e.10.1.1 43236 1i3gH 121 1.00e+01 b.1.1.1 66018 1en2A 91 1.08e+01 1hev g.3.1.1 44048 g.3.1.1 44049 1jhlH 116 1.17e+01 1mfa b.1.1.1 19967 1hxmA 229 1.20e+01 1hxmA b.1.1.1 61367 b.1.1.2 61368 1mi2A 73 1.28e+01 1tvxA d.9.1.1 37455 1b4jH 220 1.29e+01 1igtB b.1.1.1 20309 b.1.1.2 21301 1cxwA 60 1.33e+01 g.14.1.2 44677 1b2wH 220 1.36e+01 1igtB b.1.1.1 20307 b.1.1.2 21299 1fj7A 101 1.52e+01 1fj7A d.58.7.1 39209 1d5bB 221 1.63e+01 8fabA b.1.1.1 20205 b.1.1.2 21221 3hflH 215 1.70e+01 1igtB b.1.1.1 19969 b.1.1.2 21027 1a88A 275 1.71e+01 1brt c.69.1.12 34707 1axsB 221 1.71e+01 1mfa b.1.1.1 20201 b.1.1.2 21217 1rvfH 119 1.77e+01 1mfa b.1.1.1 19991 1fskC 220 1.80e+01 1igtB b.1.1.1 20467 b.1.1.2 21431 1cy7A 599 1.87e+01 1ecl e.10.1.1 43244 1afvH 220 1.91e+01 1mfa b.1.1.1 20131 b.1.1.2 21161 1fjeB 175 1.97e+01 1fj7A d.58.7.1 39210 d.58.7.1 39211 1ecl 597 1.98e+01 1ecl e.10.1.1 43238 1cf7B 95 1.98e+01 1cf7B a.4.5.17 16152 1lnrE 185 2.03e+01 1iawA 317 2.08e+01 c.52.1.9 62126 1ev7A 317 2.08e+01 1ev7B c.52.1.9 33315 1ev7B 317 2.08e+01 1ev7B c.52.1.9 33316 1a7qH 116 2.16e+01 1gc1H b.1.1.1 19955 5csmA 256 2.16e+01 5csmA a.130.1.2 19494 3csmA 256 2.26e+01 5csmA a.130.1.2 19500 1qfwH 117 2.30e+01 1gc1H b.1.1.1 20435 1csmA 256 2.32e+01 5csmA a.130.1.2 19495 1dqdH 222 2.32e+01 1igtB b.1.1.1 20441 b.1.1.2 21407 1eb7A 323 2.34e+01 1eb7A a.3.1.5 59404 a.3.1.5 59405 1eg9A 449 2.39e+01 1ndoA b.33.1.2 24443 d.129.3.3 41322 1ndoA 449 2.39e+01 1ndoA b.33.1.2 24444 d.129.3.3 41323 1gnxA 479 2.43e+01 1mlcB 218 2.44e+01 1igtB b.1.1.1 20053 b.1.1.2 21095 4csmA 256 2.59e+01 5csmA a.130.1.2 19498 1cicB 217 3.00e+01 1igtB b.1.1.1 19965 b.1.1.2 21025 1vng 609 3.08e+01 1vns a.111.1.3 19066 1gff2 177 3.13e+01 2bpa2 1e9eA 215 3.14e+01 c.37.1.1 64810 1e9cA 215 3.14e+01 c.37.1.1 64808 1lmkA 238 3.22e+01 1mfa b.1.1.1 20034 b.1.1.1 20035 1bgaA 447 3.31e+01 1e70M c.1.8.4 28961 1bggA 448 3.32e+01 1e70M c.1.8.4 28953 1gyxA 76 3.39e+01 1qnmA 198 3.41e+01 1avmA a.2.11.1 15754 d.44.1.1 38713 2occB 227 3.42e+01 2occB b.6.1.2 23027 f.2.1.3 43519 1tr1A 447 3.42e+01 1e70M c.1.8.4 28957 1e4iA 447 3.42e+01 1e70M c.1.8.4 59225 1k4cA 219 3.43e+01 b.1.1.1 68126 b.1.1.2 68127 1qnkA 69 3.47e+01 1tvxA d.9.1.1 37458 1qcnA 421 3.49e+01 1qcnA b.34.8.1 59017 d.177.1.1 59018 1h3fA 432 3.52e+01 1vne 609 3.56e+01 1vns a.111.1.3 19063 1vns 609 3.57e+01 1vns a.111.1.3 19061 1vnc 609 3.57e+01 1vns a.111.1.3 19065 1iduA 609 3.57e+01 1vns a.111.1.3 62303 1vnh 609 3.59e+01 1vns a.111.1.3 19062 1em1A 198 3.61e+01 1avmA a.2.11.1 15752 d.44.1.1 38711 1hxvA 113 3.67e+01 1jjiA 311 3.71e+01 c.69.1.2 66766 1i49A 224 3.94e+01 1i49A h.4.7.1 61679 1i4dA 224 3.94e+01 h.4.7.1 61682 1i4lA 224 3.94e+01 1i49A h.4.7.1 61718 1i4tB 224 3.94e+01 h.4.7.1 61730