% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (July 15, 2005) compiled 07/18/05_14:54:13 % (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.YEL012W.t2k-w0.5.mod Host: farm09 Fri Nov 18 18:39:22 2005 % karplus Dir: /projects/compbiousr/compbio0404/experiments/protein-predict/yeast/YEL0/YEL012W % --------------------------------------------------------------------- % Inserted Files: YEL012W.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: YEL012W.t2k-w0.5.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 21677 sequences, 5008096 residues, 219 nodes, 464.48 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(=2.9030) * Reverse)^tau(=0.7192))) % 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 1ur6A 147 -168.34 -156.89 3.85e-32 :147 NMR NA NA NA UBIQUITIN-CONJUGATING ENZYME E2-1 1x23A 155 -166.61 -155.22 7.21e-32 :155 XRAY 1.85 0.204 0.282 Ubiquitin-conjugating en 1z2uA 150 -169.07 -153.56 1.35e-31 :150 XRAY 1.10 0.132 0.149 Ubiquitin-conjugating en 1qcqA 148 -164.08 -151.59 2.83e-31 :148 XRAY 2.70 0.240 0.296 UBIQUITIN CONJUGATING EN 1ayzA 169 -164.90 -150.93 3.63e-31 :169 XRAY 2.60 0.213 0.246 UBIQUITIN-CONJUGATING EN 2ayvA 166 -162.72 -149.91 5.34e-31 :166 XRAY 2.00 0.228 0.258 ubiquitin-conjugating en 2aak 152 -157.20 -146.55 1.92e-30 :152 XRAY 2.40 0.221 0.287 UBIQUITIN CONJUGATING EN 1jasA 152 -155.69 -145.57 2.79e-30 :152 NMR NA NA NA UBIQUITIN-CONJUGATING ENZYME E2-1 1y6lA 149 -154.03 -143.95 5.18e-30 :149 XRAY 1.85 0.194 0.246 Ubiquitin-conjugating en 1q34A 163 -152.97 -141.50 1.33e-29 :163 XRAY 2.90 0.239 0.266 Ubiquitin-conjugating en 1z3dA 157 -152.16 -140.67 1.83e-29 :157 XRAY 2.50 0.242 0.273 Ubiquitin-conjugating en 1j7dB 152 -146.28 -136.31 9.91e-29 :152 XRAY 1.85 0.215 0.244 UBIQUITIN-CONJUGATING EN 1jbbA 153 -147.33 -134.89 1.72e-28 :153 XRAY 2.00 0.183 0.255 ubiquitin conjugating en 1jatA 155 -147.13 -134.70 1.85e-28 :155 XRAY 1.60 0.203 0.239 Ubiquitin-Conjugating En 1ylaA 202 -144.79 -131.82 5.75e-28 :202 XRAY 2.40 0.225 0.269 Ubiquitin-conjugating en 1tteA 215 -140.90 -130.02 1.17e-27 :215 NMR NA NA NA Ubiquitin-conjugating enzyme E2-2 1pzvA 164 -141.65 -129.54 1.41e-27 :164 XRAY 2.52 0.252 0.289 Probable ubiquitin-conju 2bepA 159 -142.23 -129.03 1.73e-27 :159 XRAY 1.80 0.169 0.220 UBIQUITIN-CONJUGATING EN 1yh2A 175 -139.34 -128.78 1.91e-27 :175 XRAY 2.00 0.204 0.238 HSPC150 protein similar 1z5sA 158 -140.68 -128.55 2.08e-27 :158 XRAY 3.01 0.247 0.290 Ubiquitin-conjugating en 1kpsA 159 -140.67 -128.55 2.08e-27 :159 XRAY 2.50 0.223 0.300 Ubiquitin-like protein S 1a3s 160 -140.67 -128.55 2.08e-27 :160 XRAY 2.80 0.210 0.260 UBC9 [H 1u9aA 160 -140.67 -128.55 2.08e-27 :160 XRAY 2.00 0.160 0.250 UBIQUITIN-CONJUGATING EN 2e2c 156 -140.10 -127.93 2.67e-27 :156 XRAY 2.00 0.216 0.271 UBIQUITIN CONJUGATING EN 2ucz 165 -143.85 -127.85 2.75e-27 :165 XRAY 2.93 0.227 0.259 UBIQUITIN CONJUGATING EN 1fzyA 149 -137.72 -126.65 4.42e-27 :149 XRAY 1.90 0.209 0.241 UBIQUITIN-CONJUGATING EN 2awfA 172 -138.55 -125.95 5.85e-27 :172 XRAY 2.10 0.257 0.263 Ubiquitin-conjugating en 1i7kA 179 -131.86 -121.70 3.20e-26 :179 XRAY 1.95 0.176 0.226 UBIQUITIN-CONJUGATING EN 1zdnA 158 -128.52 -117.74 1.58e-25 :158 XRAY 1.93 0.195 0.234 Ubiquitin-conjugating en 1c4zD 154 -129.96 -117.70 1.61e-25 :154 XRAY 2.60 0.262 0.290 UBIQUITIN CONJUGATING EN 1yh6A 179 -126.42 -114.07 7.08e-25 :179 XRAY 2.10 0.184 0.216 Ubiquitin-conjugating en 1y8xA 160 -120.74 -110.89 2.61e-24 :160 XRAY 2.40 0.242 0.259 Ubiquitin-conjugating en 1yf9A 171 -119.44 -109.74 4.20e-24 :171 XRAY 2.00 0.186 0.210 Ubiquitin carrier protei 1wzvA 155 -119.51 -105.77 2.19e-23 :155 XRAY 2.10 0.210 0.267 Ubiquitin-conjugating en 1yrvA 169 -114.68 -104.89 3.16e-23 :169 XRAY 2.18 0.244 0.294 ubiquitin-conjugating li 2a4dA 160 -103.46 -93.01 4.98e-21 :160 XRAY 1.69 0.185 0.240 Ubiquitin-conjugating en 1j7dA 145 -99.91 -88.51 3.55e-20 :145 XRAY 1.85 0.215 0.244 MMS2 [HOMO 1jatB 138 -99.02 -85.78 1.19e-19 :138 XRAY 1.60 0.203 0.239 Ubiquitin-Conjugating En 2a7lA 136 -93.95 -84.38 2.21e-19 :136 XRAY 1.82 0.264 0.300 Hypothetical ubiquitin-c 1zuoA 186 -65.04 -53.98 3.81e-13 :186 XRAY 1.80 0.201 0.232 Hypothetical protein LOC 1s1qA 145 -29.41 -18.19 3.25e-04 :145 XRAY 2.00 0.191 0.240 Tumor susceptibility gen 1uzxA 169 -23.83 -10.15 1.24e-01 :169 XRAY 1.85 0.241 0.274 VACUOLAR PROTEIN SORTING 2biiA 424 -17.78 -7.76 9.16e-01 :424 XRAY 1.70 0.186 0.212 NITRATE REDUCTASE [NADPH 1ohqA 120 -16.96 -7.71 9.58e-01 :120 XRAY 2.00 0.182 0.260 IMMUNOGLOBULIN 1tcoA 375 -17.96 -7.55 1.10e+00 :375 XRAY 2.50 0.195 0.282 SERINE/THREONINE PHOSPHA 1t4kB 217 -16.13 -6.90 1.96e+00 :217 XRAY 2.50 0.233 0.281 IMMUNOGLOBULIN IGG1, HEA 1u5jA 539 -17.04 -6.78 2.19e+00 :539 XRAY 2.80 0.214 0.268 transcarboxylase 5S subu 1a7qH 116 -15.42 -6.51 2.79e+00 :116 XRAY 2.00 0.178 NA IGG1-KAPPA D1.3 FV (HEAVY C 1s3hA 539 -16.57 -6.32 3.33e+00 :539 XRAY 2.50 0.207 0.250 transcarboxylase 5S subu 1rqbA 539 -16.57 -6.32 3.33e+00 :539 XRAY 1.90 0.164 0.191 transcarboxylase 5S subu 2es9A 115 -15.66 -6.06 4.24e+00 :115 XRAY 2.00 0.242 0.260 putative cytoplasmic pro 1bvkB 117 -15.81 -6.01 4.42e+00 :117 XRAY 2.70 0.208 0.297 HULYS11 [HO 1eqfA 280 -16.87 -5.81 5.33e+00 :280 XRAY 2.10 0.246 0.246 RNA POLYMERASE II TRANSC 1a8y 367 -18.23 -5.65 6.24e+00 :367 XRAY 2.40 0.188 0.242 CALSEQUESTRIN 1dl7H 112 -14.20 -5.06 1.10e+01 :112 XRAY 2.35 0.189 0.265 ANTIBODY M3C65 (HEAVY CH 1knoB 220 -14.30 -5.03 1.13e+01 :220 XRAY 3.20 0.200 0.272 IGG2A FAB FRAGMENT CNJ20 1c5dB 215 -13.98 -5.02 1.14e+01 :215 XRAY 2.40 0.196 0.304 MONOCLONAL ANTIBODY AGAI 1v0jA 399 -15.46 -5.01 1.15e+01 :399 XRAY 2.25 0.227 0.266 UDP-GALACTOPYRANOSE MUTA 1vcjA 389 -14.97 -4.99 1.18e+01 :389 XRAY 2.40 0.214 0.255 NEURAMINIDASE 1inf 390 -14.97 -4.98 1.19e+01 :390 XRAY 2.40 0.159 NA INFLUENZA VIRUS B/LEE/40 NE 1l0qA 391 -13.90 -4.97 1.20e+01 :391 XRAY 2.40 0.217 0.263 Surface layer protein 2gfbB 219 -14.30 -4.90 1.29e+01 :219 XRAY 3.00 0.213 NA IGG2A CNJ206 FAB (HEAVY CHA 1i8kB 124 -13.70 -4.87 1.33e+01 :124 XRAY 1.80 0.179 0.224 EPIDERMAL GROWTH FACTOR 3sqcA 631 -15.39 -4.81 1.40e+01 :631 XRAY 2.80 0.209 0.236 SQUALENE--HOPENE CYCLASE 1umpA 631 -15.39 -4.81 1.41e+01 :631 XRAY 2.13 0.187 0.228 SQUALENE--HOPENE CYCLASE 1yw5A 177 -14.04 -4.71 1.56e+01 :177 XRAY 1.60 0.200 0.242 peptidyl prolyl cis/tran 2sqcA 631 -15.39 -4.68 1.60e+01 :631 XRAY 2.00 0.153 0.187 SQUALENE-HOPENE CYCLASE 1ehkA 562 -14.68 -4.66 1.64e+01 :562 XRAY 2.40 0.222 0.264 BA3-TYPE CYTOCHROME-C OX 1xmeA 568 -14.67 -4.65 1.65e+01 :568 XRAY 2.30 0.217 0.236 Cytochrome c oxidase pol 1cicD 218 -13.81 -4.62 1.71e+01 :218 XRAY 2.50 0.179 NA IG HEAVY CHAIN V REGIONS [SCIL 1y0kA 209 -14.94 -4.53 1.86e+01 :209 XRAY 1.75 0.188 0.222 hypothetical protein PA4 1ul1X 379 -14.90 -4.51 1.90e+01 :379 XRAY 2.90 0.220 0.284 Flap endonuclease-1 [SIMIAN 1uedA 406 -14.29 -4.37 2.19e+01 :406 XRAY 1.90 0.196 0.235 P450 monooxygenase [NA] 1jr6A 142 -13.26 -4.28 2.40e+01 :142 NMR NA NA NA Helicase NS3 [HEP 1nu0A 138 -14.01 -4.28 2.41e+01 :138 XRAY 1.60 0.189 0.228 Hypothetical protein yqg 1ywqA 200 -13.54 -4.27 2.43e+01 :200 XRAY 2.30 0.210 0.242 Nitroreductase family pr 1oakH 223 -13.39 -4.27 2.44e+01 :223 XRAY 2.20 0.201 0.274 NMC-4 IGG1 1fnsH 225 -13.39 -4.26 2.45e+01 :225 XRAY 2.00 0.172 0.207 IMMUNOGLOBULIN NMC-4 IGG 1eyvA 156 -13.88 -4.26 2.46e+01 :156 XRAY 1.60 0.190 0.234 N-UTILIZING SUBSTANCE PR 1sj2A 743 -14.86 -4.26 2.46e+01 :743 XRAY 2.41 0.211 0.268 Peroxidase/catalase T [NA] 1r71A 178 -14.81 -4.16 2.72e+01 :178 XRAY 2.20 0.198 0.250 Transcriptional represso 1yejH 222 -13.25 -4.16 2.73e+01 :222 XRAY 1.85 0.212 0.246 IG ANTIBODY D2.3 (HEAVY 1yedB 226 -13.14 -4.16 2.73e+01 :226 XRAY 3.10 0.215 0.260 IGG1 FAB FRAGMENT (D.2.4 1m8jA 181 -14.22 -4.14 2.77e+01 :181 XRAY 2.40 0.225 0.265 Nicotinamide-nucleotide 1uxvA 501 -14.44 -4.12 2.84e+01 :501 XRAY 2.35 0.226 0.243 GLYCERALDEHYDE-3-PHOSPHA 1ky8A 501 -14.44 -4.11 2.86e+01 :501 XRAY 2.40 0.208 0.242 glyceraldehyde-3-phospha 1p2cB 218 -13.17 -4.08 2.94e+01 :218 XRAY 2.00 0.204 0.242 heavy chain VH+CH1 anti- 1ukxA 137 -13.66 -4.06 3.00e+01 :137 NMR NA NA NA GCN2 eIF2alpha kinase [RATT 1inzA 148 -13.62 -3.89 3.60e+01 :148 NMR NA NA NA EPS15-INTERACTING PORTEIN(EPSIN) 1kf6D 119 -13.73 -3.89 3.60e+01 :119 XRAY 2.70 0.231 0.280 FUMARATE REDUCTASE 13 KD 1w2wB 191 -13.93 -3.89 3.62e+01 :191 XRAY 1.75 0.174 0.198 5-METHYLTHIORIBOSE-1-PHO 1i8tA 367 -14.06 -3.88 3.65e+01 :367 XRAY 2.40 0.185 0.245 UDP-GALACTOPYRANOSE MUTA 1l7tH 221 -12.91 -3.87 3.68e+01 :221 XRAY 2.10 0.213 0.275 anti-testosterone (heavy 1c1kA 217 -14.62 -3.86 3.72e+01 :217 XRAY 1.45 0.205 0.253 BPT4 GENE 59 HELICASE AS 1vhzA 198 -13.70 -3.86 3.72e+01 :198 XRAY 2.32 0.182 0.248 ADP compounds hydrolase 1frgH 220 -13.02 -3.85 3.75e+01 :220 XRAY 2.80 0.190 NA IGG2A 26/9 FAB (HEAVY CHAIN 2as0A 396 -14.19 -3.85 3.76e+01 :396 XRAY 1.80 0.207 0.239 hypothetical protein PH1 1wn7A 774 -14.64 -3.82 3.90e+01 :774 XRAY 2.75 0.230 0.306 Family B DNA Polymerase 2c43A 323 -13.98 -3.82 3.90e+01 :323 XRAY 1.93 0.162 0.219 AMINOADIPATE-SEMIALDEHYD 1nstA 325 -13.63 -3.81 3.91e+01 :325 XRAY 2.30 0.210 0.257 HEPARAN SULFATE N-DEACET 2c1lA 358 -13.14 -3.79 3.99e+01 :358 XRAY 1.90 0.188 0.217 RESTRICTION ENDONUCLEASE