% SAM: /projects/compbio/bin/i686/hmmscore v3.4 (July 31, 2003) compiled 09/03/03_16:30:36 % (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.YGR212W.t2k-w0.5.mod Host: cc50 Sun Oct 12 00:18:42 2003 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR212W % --------------------------------------------------------------------- % Inserted Files: YGR212W.t2k-w0.5.mod % Database Files: /projects/compbio/data/pdb/dunbrack-pdbaa % % Subsequence-submodel (local) (SW = 2) % Simple scores adjusted by ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Single Track Model: YGR212W.t2k-w0.5.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 14442 sequences, 3304407 residues, 469 nodes, 538.71 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 (0.00) % E-value on N (=8162) sequences: % N / (1 + exp(-(lambda(=2.6549) * Reverse)^tau(=0.6693))) % Calculated when Simple < simple_threshold (0.00) % 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 1bmlC 362 -32.38 -9.69 1.24e+00 :362 XRAY 2.90 0.201 0.291 STREPTOKINASE || 1BMLD 1fvrA 327 -30.13 -7.73 4.26e+00 :327 XRAY 2.20 0.195 0.225 TYROSINE-PROTEIN KINASE TIE-2 || 1FVRB 1fgyA 127 -26.99 -6.84 7.72e+00 :127 XRAY 1.50 0.213 0.247 GRP1 || 1FGZA 1m54A 363 -28.89 -6.43 1.03e+01 :363 XRAY 2.90 0.271 0.365 CYSTATHIONINE BETA-SYNTHASE || 1M54B 1M54C 1M54D 1M54E 1M54F 1lshB 319 -28.37 -6.25 1.16e+01 :319 XRAY 1.90 0.193 0.255 LIPOVITELLIN (LV-2) 1j3iA 280 -28.01 -6.01 1.37e+01 :280 XRAY 2.33 0.187 0.236 Bifunctional dihydrofolate reductase-thymidylate synthase || 1J3IB 8pchA 220 -27.00 -5.97 1.42e+01 :220 XRAY 2.10 0.198 0.245 CATHEPSIN H || 1NB3A 1NB3B 1NB3C 1NB3D 1NB5A 1NB5B 1NB5C 1NB5D 1j3jA 280 -28.01 -5.97 1.42e+01 :280 XRAY 2.30 0.200 0.231 Bifunctional dihydrofolate reductase-thymidylate synthase || 1J3JB 1jbqA 435 -29.07 -5.96 1.42e+01 :435 XRAY 2.60 0.257 0.296 CYSTATHIONINE BETA-SYNTHASE || 1JBQB 1JBQC 1JBQD 1JBQE 1JBQF 1jk0B 345 -28.44 -5.94 1.45e+01 :345 XRAY 2.80 0.243 0.296 ribonucleoside-diphosphate reductase small chain 2 1mr7A 209 -29.32 -5.85 1.54e+01 :209 XRAY 1.80 0.178 0.207 Streptogramin A Acetyltransferase || 1KHRA 1KHRB 1KHRC 1KHRD 1KHRE 1KHRF 1KK4A 1KK4B 1KK4C 1KK4D 1KK4E 1KK4F 1KK5A 1KK5B 1KK5C 1KK5D 1KK5E 1KK5F 1KK6A 1KK6B 1KK6C 1MR7B 1MR7C 1MR7X 1MR7Y 1MR7Z 1MR9A 1MR9B 1MR9C 1MR9X 1MR9Y 1MR9Z 1MRLA 1MRLB 1MRLC 1iznA 286 -27.60 -5.80 1.60e+01 :286 XRAY 2.10 0.222 0.262 CapZ alpha-1 subunit || 1IZNC 1j3kA 280 -27.55 -5.59 1.86e+01 :280 XRAY 2.10 0.184 0.222 Bifunctional dihydrofolate reductase-thymidylate synthase || 1J3KB 1fiqA 219 -26.72 -5.48 2.01e+01 :219 XRAY 2.50 0.212 0.275 XANTHINE OXIDASE 1fhwA 129 -25.35 -5.32 2.26e+01 :129 XRAY 1.90 0.229 0.270 GUANINE NUCLEOTIDE EXCHANGE FACTOR AND INTEGRIN BINDING PROTEIN HOMOLOG GRP1 || 1FHWB 1FHXA 1FHXB 1ntx 60 -22.42 -5.03 2.80e+01 :60 NMR NA NA NA ALPHA-NEUROTOXIN 1ldjB 90 -23.69 -4.94 3.00e+01 :90 XRAY 3.00 0.247 0.288 ring-box protein 1 || 1LDKC 1azzA 226 -26.27 -4.89 3.13e+01 :226 XRAY 2.30 0.189 0.238 COLLAGENASE || 1AZZB 1eaxA 241 -26.05 -4.79 3.37e+01 :241 XRAY 1.30 0.184 0.193 SUPPRESSOR OF TUMORIGENICITY 14 || 1EAWA 1EAWC 1d6vL 211 -26.32 -4.66 3.73e+01 :211 XRAY 2.00 0.224 0.264 CHIMERIC GERMLINE PRECURSOR OF OXY-COPE CATALYTIC ANTIBODY AZ-28 (LIGHT CHAIN) || 1D5IL 1jb4A 127 -24.27 -4.62 3.83e+01 :127 XRAY 2.23 0.204 0.241 NUCLEAR TRANSPORT FACTOR 2 || 1JB4B 1jb2A 127 -24.32 -4.61 3.87e+01 :127 XRAY 2.00 0.207 0.251 NUCLEAR TRANSPORT FACTOR 2 || 1JB2B 1kvzA 107 -24.93 -4.60 3.91e+01 :107 NMR NA NA NA RC-RNase4 1ipaA 274 -25.73 -4.58 3.95e+01 :274 XRAY 2.40 0.226 0.286 RNA 2-O-RIBOSE METHYLTRANSFERASE 1pme 380 -28.87 -4.57 3.98e+01 :380 XRAY 2.00 0.212 0.273 ERK2 1jb5A 127 -24.24 -4.57 3.98e+01 :127 XRAY 2.30 0.203 0.289 NUCLEAR TRANSPORT FACTOR 2 || 1JB5B