% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (July 15, 2005) compiled 06/01/06_09:03:53 % (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-T2K, 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, et al., What is the value added by human intervention in protein % structure prediction, Proteins: Stucture, Function, Genetics 45(S5):86--91, 2001. % A. Krogh et al., Hidden Markov models in computational biology: % Applications to protein modeling, JMB 235:1501-1531, Feb 1994. % --------------------------------------------------------------------- % w0.5foo.1.YGR017W.t2k-w0.5.mod Host: farm03-10.kilokluster.ucsc.edu Fri Oct 6 03:21:45 2006 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR017W % --------------------------------------------------------------------- % Inserted Files: YGR017W.t2k-w0.5.mod % Database Files: /projects/compbio/data/pdb/dunbrack-pdbaa % % Subsequence-submodel (local) (SW = 2) % Simple scores adjusted by +1.5*ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Single Track Model: YGR017W.t2k-w0.5.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 25505 sequences, 5873420 residues, 298 nodes, 635.16 seconds % % Sequence scores selected if better than: % E-value (Emax 4.0e+01) (select_score=4) % % Simple: NLL-NULL using FIM probabilities % Reverse: NLL-NULL for the reverse sequence NULL model % Calculated when Simple < simple_threshold (10000.00) % E-value on N (=11000) sequences: % N / (1 + exp(-(lambda(=2.2450) * Reverse)^tau(=0.7525))) % Calculated when Simple < simple_threshold (10000.00) % Rescale E-values or use -dbsize for multiple scoring runs. % Scores sorted by E-value, best first % % Sequence ID Length Simple Reverse E-value X count 2i51A 195 -204.55 -193.37 1.29e-38 :195 XRAY 1.40 0.166 0.188 Uncharacterized conserve 1t9mA 214 -52.32 -41.16 8.96e-10 :214 XRAY 1.90 0.186 0.231 probable pyridoxamine 5' 1ty9A 222 -44.41 -33.76 5.83e-08 :222 XRAY 1.80 0.195 0.246 Phenazine biosynthesis p 1nrgA 261 -44.22 -33.07 8.69e-08 :261 XRAY 1.95 0.201 0.253 pyridoxine 5'-phosphate 1dnlA 199 -32.88 -22.29 6.17e-05 :199 XRAY 1.80 0.212 0.233 PYRIDOXINE 5'-PHOSPHATE 1g79A 218 -32.79 -22.22 6.46e-05 :218 XRAY 2.00 0.211 0.224 PYRIDOXINE 5'-PHOSPHATE 2a2jA 246 -28.75 -18.03 1.02e-03 :246 XRAY 2.50 0.209 0.260 Pyridoxamine 5'-phosphat 1ci0A 228 -23.74 -11.34 1.20e-01 :228 XRAY 2.70 0.230 0.274 PNP OXIDASE [H 1itcA 516 -19.47 -6.91 4.19e+00 :516 XRAY 2.10 0.178 0.212 Beta-Amylase [HO 1i5kA 84 -15.90 -6.11 8.44e+00 :84 XRAY 2.70 0.195 0.262 PLASMINOGEN 1ki0A 253 -17.03 -6.10 8.53e+00 :253 XRAY 1.75 0.196 0.263 ANGIOSTATIN [C 1qc6A 130 -14.97 -5.43 1.54e+01 :130 XRAY 2.60 0.237 0.298 EVH1 DOMAIN FROM ENA/VAS 2droA 396 -16.11 -5.42 1.56e+01 :396 XRAY 1.70 0.162 0.187 Xylanase Y [HOMO SAPI 1d8hA 311 -16.10 -5.37 1.64e+01 :311 XRAY 2.00 0.229 0.310 mRNA TRIPHOSPHATASE CET1 1efxA 278 -15.63 -5.37 1.64e+01 :278 XRAY 3.00 0.212 0.294 HLA-CW3 (HEAVY CHAIN) [H 1avaA 403 -18.08 -5.15 2.00e+01 :403 XRAY 1.90 0.208 0.269 BARLEY ALPHA-AMYLASE 2(C 1y7bA 542 -16.12 -5.11 2.08e+01 :542 XRAY 1.60 0.158 0.206 Beta-xylosidase, family 2f2fC 186 -15.18 -5.08 2.13e+01 :186 XRAY 2.40 0.224 0.251 cytolethal distending to 1dgsA 667 -15.29 -5.07 2.15e+01 :667 XRAY 2.90 0.228 0.298 DNA LIGASE 1a45 173 -15.92 -5.07 2.16e+01 :173 XRAY 2.30 0.186 NA GAMMAF CRYSTALLIN 1o7dC 159 -14.99 -4.92 2.47e+01 :159 XRAY 2.70 0.257 0.289 LYSOSOMAL ALPHA-MANNOSID 8cho 125 -14.37 -4.91 2.50e+01 :125 XRAY 2.30 0.205 0.271 STEROID DELTA-ISOMERASE 2a4aA 281 -16.44 -4.91 2.51e+01 :281 XRAY 1.84 0.205 0.248 deoxyribose-phosphate al 1ydpA 275 -14.88 -4.90 2.51e+01 :275 XRAY 1.90 0.235 0.264 MHC class I antigen [E 2d31A 276 -14.81 -4.87 2.59e+01 :276 XRAY 3.20 0.239 0.298 HLA class I histocompati 1ocvA 125 -14.30 -4.84 2.66e+01 :125 XRAY 2.00 0.229 0.282 STEROID DELTA-ISOMERASE 2dpmA 284 -14.90 -4.75 2.89e+01 :284 XRAY 1.80 0.238 0.284 ADENINE-SPECIFIC METHYLT 2a87A 335 -14.45 -4.75 2.89e+01 :335 XRAY 3.00 0.215 0.291 Thioredoxin reductase 1u07A 90 -14.12 -4.56 3.46e+01 :90 XRAY 1.13 0.139 0.183 TonB protein