% 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.YGR207C.t2k-w0.5.mod Host: cc63 Sat Oct 11 23:56:33 2003 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR207C % --------------------------------------------------------------------- % Inserted Files: YGR207C.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: YGR207C.t2k-w0.5.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 14442 sequences, 3304407 residues, 262 nodes, 309.57 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(=2.3310) * Reverse)^tau(=0.7207))) % 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 1efvB 255 -223.87 -199.31 4.07e-33 :255 XRAY 2.10 0.172 0.222 ELECTRON TRANSFER FLAVOPROTEIN 1efpB 252 -220.98 -198.09 5.88e-33 :252 XRAY 2.60 0.193 0.286 PROTEIN (ELECTRON TRANSFER FLAVOPROTEIN) || 1EFPD 1o97C 264 -188.20 -165.81 1.31e-28 :264 XRAY 1.60 0.203 0.229 ELECTRON TRANSFERRING FLAVOPROTEIN BETA-SUBUNIT || 1O94C 1O94E 1O95C 1O95E 1O96A 1O96C 1O96E 1O96Q 1o97D 320 -57.90 -34.20 5.25e-07 :320 XRAY 1.60 0.203 0.229 ELECTRON TRANSFERRING FLAVOPROTEIN ALPHA-SUBUNIT || 1O94D 1O94F 1O95D 1O95F 1O96B 1O96D 1O96F 1O96Z 1efvA 315 -41.15 -19.27 1.49e-03 :315 XRAY 2.10 0.172 0.222 ELECTRON TRANSFER FLAVOPROTEIN 1efpA 307 -33.81 -11.82 1.49e-01 :307 XRAY 2.60 0.193 0.286 PROTEIN (ELECTRON TRANSFER FLAVOPROTEIN) || 1EFPC 1qo8A 566 -32.70 -9.43 7.68e-01 :566 XRAY 2.15 0.225 0.281 FLAVOCYTOCHROME C3 FUMARATE REDUCTASE || 1QO8D 1augA 215 -29.27 -7.93 2.27e+00 :215 XRAY 2.00 0.197 0.259 PYROGLUTAMYL PEPTIDASE-1 || 1AUGB 1AUGC 1AUGD 1avu 181 -28.67 -7.76 2.59e+00 :181 XRAY 2.30 0.198 0.269 TRYPSIN INHIBITOR || 1BA7A 1BA7B 1avwB 177 -28.60 -7.73 2.65e+00 :177 XRAY 1.75 0.189 0.214 TRYPSIN INHIBITOR || 1AVXB 1qhbA 596 -31.05 -7.71 2.68e+00 :596 XRAY 2.30 0.172 0.227 HALOPEROXIDASE || 1QHBB 1QHBC 1QHBD 1QHBE 1QHBF 1ad1A 266 -29.64 -7.64 2.83e+00 :266 XRAY 2.20 0.159 0.218 DIHYDROPTEROATE SYNTHETASE || 1AD1B 1AD4A 1AD4B 1b09A 206 -28.95 -7.62 2.86e+00 :206 XRAY 2.50 0.196 0.242 PROTEIN (C-REACTIVE PROTEIN) || 1B09B 1B09C 1B09D 1B09E 1GNHA 1GNHB 1GNHC 1GNHD 1GNHE 1GNHF 1GNHG 1GNHH 1GNHI 1GNHJ 1LJ7A 1LJ7B 1LJ7C 1LJ7D 1LJ7E 1LJ7F 1LJ7G 1LJ7H 1LJ7I 1LJ7J 1l2lA 457 -30.70 -7.22 3.90e+00 :457 XRAY 2.00 0.213 0.277 ADP-dependent Glucokinase 1i69A 219 -27.92 -7.12 4.20e+00 :219 XRAY 2.70 0.247 0.278 HYDROGEN PEROXIDE-INDUCIBLE GENES ACTIVATOR || 1I69B 1odxA 99 -25.99 -6.78 5.46e+00 :99 XRAY 2.00 0.166 NA HIV-1 PROTEASE || 1ODXB 1hvsA 99 -25.94 -6.72 5.70e+00 :99 XRAY 2.25 0.150 NA HIV-1 PROTEASE || 1HVSB 1dgiR 302 -28.53 -6.72 5.73e+00 :302 EM 22.00 NA NA POLIOVIRUS RECEPTOR 1nvmA 345 -28.76 -6.67 5.96e+00 :345 XRAY 1.70 0.189 0.230 4-hydroxy-2-oxovalerate aldolase || 1NVMC 1NVME 1NVMG 1fvqA 72 -24.70 -6.62 6.18e+00 :72 NMR NA NA NA COPPER-TRANSPORTING ATPASE || 1FVSA 1dljA 402 -28.81 -6.58 6.38e+00 :402 XRAY 1.80 0.179 0.213 UDP-GLUCOSE DEHYDROGENASE 1mt7A 99 -25.59 -6.30 7.93e+00 :99 XRAY 1.90 0.201 0.227 PROTEASE RETROPEPSIN || 1MT7B 1MT8A 1MT8B 1MT9A 1MT9B 1N49A 1N49B 1N49C 1N49D 1jmvA 141 -26.07 -6.30 7.94e+00 :141 XRAY 1.85 0.220 0.242 Universal Stress Protein A || 1JMVB 1JMVC 1JMVD 1o7dE 126 -25.38 -6.20 8.58e+00 :126 XRAY 2.70 0.257 0.289 LYSOSOMAL ALPHA-MANNOSIDASE 1i6aA 219 -26.80 -5.95 1.05e+01 :219 XRAY 2.30 0.169 0.216 HYDROGEN PEROXIDE-INDUCIBLE GENES ACTIVATOR 1cl1A 395 -28.39 -5.95 1.05e+01 :395 XRAY 1.83 0.151 0.221 CYSTATHIONINE BETA-LYASE || 1CL1B 1CL2A 1CL2B 1g0dA 695 -30.18 -5.94 1.06e+01 :695 XRAY 2.50 0.200 0.249 PROTEIN-GLUTAMINE GAMMA-GLUTAMYLTRANSFERASE 1a8s 273 -29.88 -5.92 1.08e+01 :273 XRAY 1.80 0.173 0.205 CHLOROPEROXIDASE F 1dcfA 136 -25.48 -5.89 1.11e+01 :136 XRAY 2.50 0.227 0.271 ETR1 PROTEIN 1ql0A 241 -27.79 -5.88 1.11e+01 :241 XRAY 1.10 0.128 0.147 NUCLEASE || 1QL0B 1dliA 402 -28.08 -5.86 1.13e+01 :402 XRAY 2.31 0.186 0.259 UDP-GLUCOSE DEHYDROGENASE 1g8tA 245 -27.81 -5.85 1.14e+01 :245 XRAY 1.10 0.129 0.156 NUCLEASE SM2 ISOFORM || 1G8TB 1QAEA 1QAEB 1SMNA 1SMNB 1necA 216 -26.19 -5.84 1.15e+01 :216 XRAY 1.95 0.170 0.240 PROTEIN (NITROREDUCTASE) || 1NECB 1NECC 1NECD 1kqbA 217 -26.20 -5.83 1.15e+01 :217 XRAY 1.80 0.190 0.217 OXYGEN-INSENSITIVE NAD(P)H NITROREDUCTASE || 1KQBB 1KQBC 1KQBD 1KQCA 1KQCB 1KQCC 1KQCD 1KQDA 1KQDB 1KQDC 1KQDD 1j0aA 325 -29.36 -5.83 1.15e+01 :325 XRAY 2.50 0.201 0.270 1-aminocyclopropane-1-carboxylate deaminase || 1J0AB 1J0AC 1J0BA 1J0BB 1J0BC 1J0BD 1J0BE 1J0BF 1J0BG 1J0BH 1J0BI 1J0BJ 1J0BK 1J0BL 1J0BM 1J0BN 1J0BO 1J0BP 1J0BQ 1J0BR 1J0BS 1J0BT 1J0BU 1J0BV 1J0BW 1J0BX 1qgnA 445 -28.70 -5.63 1.36e+01 :445 XRAY 2.90 0.201 0.250 PROTEIN (CYSTATHIONINE GAMMA-SYNTHASE) || 1I41A 1I41B 1I41C 1I41D 1I41E 1I41F 1I41G 1I41H 1I41I 1I41J 1I41K 1I41L 1I43A 1I43B 1I43C 1I43D 1I43E 1I43F 1I43G 1I43H 1I43I 1I43J 1I43K 1I43L 1I48A 1I48B 1I48C 1I48D 1I48E 1I48F 1I48G 1I48H 1I48I 1I48J 1I48K 1I48L 1QGNB 1QGNC 1QGND 1QGNE 1QGNF 1QGNG 1QGNH 1ujpA 271 -27.32 -5.51 1.50e+01 :271 XRAY 1.34 0.204 0.221 Tryptophan synthase alpha chain 1g16A 170 -25.75 -5.46 1.57e+01 :170 XRAY 1.80 0.276 0.296 RAS-RELATED PROTEIN SEC4 || 1G16B 1G16C 1G16D 1G17A 1G17B 1cs1A 386 -27.64 -5.36 1.70e+01 :386 XRAY 1.50 0.200 0.255 PROTEIN (CYSTATHIONINE GAMMA-SYNTHASE) || 1CS1B 1CS1C 1CS1D 1jk7A 323 -27.16 -5.32 1.76e+01 :323 XRAY 1.90 0.199 0.225 SERINE/THREONINE PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT || 1IT6A 1IT6B 1eudB 396 -27.32 -5.31 1.77e+01 :396 XRAY 2.10 0.162 0.215 SUCCINYL-COA SYNTHETASE, BETA CHAIN || 1EUCB 1gzdA 557 -29.66 -5.29 1.81e+01 :557 XRAY 2.50 0.175 0.241 GLUCOSE-6-PHOSPHATE ISOMERASE || 1GZVA 1lnsA 763 -29.05 -5.26 1.85e+01 :763 XRAY 2.20 0.184 0.223 X-PROLYL DIPEPTIDYL AMINOPETIDASE 2a0b 125 -25.02 -5.25 1.87e+01 :125 XRAY 1.57 0.190 0.245 HPT DOMAIN || 1A0B0 1BDJB 1FR0A 1i2mB 402 -27.03 -5.22 1.91e+01 :402 XRAY 1.76 0.192 0.223 REGULATOR OF CHROMOSOME CONDENSATION 1 || 1I2MD 1a12A 413 -27.07 -5.20 1.94e+01 :413 XRAY 1.70 0.189 0.219 REGULATOR OF CHROMOSOME CONDENSATION 1 || 1A12B 1A12C 1b1yA 500 -28.00 -5.20 1.94e+01 :500 XRAY 2.50 0.187 0.256 PROTEIN (BETA-AMYLASE) 1icrA 217 -25.55 -5.14 2.05e+01 :217 XRAY 1.70 0.182 0.204 OXYGEN-INSENSITIVE NAD(P)H NITROREDUCTASE || 1DS7A 1DS7B 1ICRB 1ICUA 1ICUB 1ICUC 1ICUD 1ICVA 1ICVB 1ICVC 1ICVD 1IDTA 1IDTB 1OO5A 1OO5B 1OO6A 1OO6B 1OONA 1OONB 1OOQA 1OOQB 1yfpA 224 -25.58 -5.01 2.29e+01 :224 XRAY 2.50 0.196 NA YELLOW FLUORESCENT PROTEIN || 1YFPB 1f0bA 235 -25.67 -4.99 2.31e+01 :235 XRAY 2.10 0.188 NA GREEN FLUORESCENT PROTEIN || 1F09A 1h4vB 421 -26.72 -4.97 2.35e+01 :421 XRAY 2.40 0.208 0.256 HISTIDYL-TRNA SYNTHETASE || 1ADJA 1ADJB 1ADJC 1ADJD 1ADYA 1ADYB 1ADYC 1ADYD 1cot 129 -24.85 -4.97 2.36e+01 :129 XRAY 1.70 0.175 NA CYTOCHROME C2 2yfpA 235 -25.67 -4.95 2.40e+01 :235 XRAY 2.60 0.161 NA PROTEIN (GREEN FLUORESCENT PROTEIN) 1h6rA 235 -25.64 -4.93 2.44e+01 :235 XRAY 1.50 0.183 0.212 GREEN FLUORESCENT PROTEIN || 1H6RB 1H6RC 1a04A 215 -26.85 -4.93 2.44e+01 :215 XRAY 2.20 0.211 0.267 NITRATE/NITRITE RESPONSE REGULATOR PROTEIN NARL || 1A04B 1RNL0 1bykA 255 -25.48 -4.91 2.48e+01 :255 XRAY 2.50 0.173 0.216 PROTEIN (TREHALOSE OPERON REPRESSOR) || 1BYKB 1gbnA 402 -28.24 -4.91 2.48e+01 :402 XRAY 2.30 0.209 0.235 ORNITHINE AMINOTRANSFERASE || 1GBNB 1GBNC 2CANA 2CANB 2CANC 2oatA 439 -28.33 -4.91 2.48e+01 :439 XRAY 1.95 0.206 0.232 ORNITHINE AMINOTRANSFERASE || 1OATA 1OATB 1OATC 2OATB 2OATC 1hefE 99 -24.34 -4.90 2.50e+01 :99 XRAY 2.20 0.159 NA HIV-1 PROTEASE || 1HEGE 1mc3A 296 -27.45 -4.87 2.56e+01 :296 XRAY 2.60 0.223 0.280 GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE || 1MC3B 1i36A 264 -26.07 -4.85 2.60e+01 :264 XRAY 2.00 0.203 0.230 CONSERVED HYPOTHETICAL PROTEIN MTH1747 || 1I36B 1mywA 238 -25.80 -4.85 2.62e+01 :238 XRAY 2.20 0.218 0.248 Green fluorescent protein 1iwpA 555 -27.69 -4.84 2.62e+01 :555 XRAY 2.10 0.209 0.247 Glycerol Dehydratase Alpha subunit || 1IWPL 1MMFA 1MMFL 1n8tA 557 -30.03 -4.82 2.67e+01 :557 XRAY 2.50 0.181 0.234 Glucose-6-phosphate isomerase || 1N8TB 1kojA 557 -30.03 -4.81 2.70e+01 :557 XRAY 1.90 0.223 0.254 Glucose-6-phosphate isomerase || 1DQRA 1DQRB 1KOJB 1hm5A 558 -30.03 -4.81 2.70e+01 :558 XRAY 1.80 0.186 0.212 PHOSPHOGLUCOSE ISOMERASE || 1G98A 1G98B 1HM5B 1HOXA 1HOXB 1ddbA 195 -24.92 -4.80 2.72e+01 :195 NMR NA NA NA PROTEIN (BID) 1ag9A 175 -25.28 -4.72 2.90e+01 :175 XRAY 1.80 0.196 0.250 FLAVODOXIN || 1AG9B 1AHN0 1kq3A 376 -26.84 -4.67 3.04e+01 :376 XRAY 1.50 0.173 0.189 glycerol dehydrogenase 1gt6A 269 -26.69 -4.67 3.04e+01 :269 XRAY 2.20 0.216 0.239 LIPASE || 1GT6B 1jiqA 558 -29.57 -4.67 3.05e+01 :558 XRAY 1.90 0.169 0.198 autocrine motility factor || 1IRIA 1IRIB 1IRIC 1IRID 1JIQB 1JIQC 1JIQD 1NUHA 1jlhA 558 -29.57 -4.67 3.05e+01 :558 XRAY 2.10 0.197 0.237 phosphoglucose isomerase || 1JLHB 1JLHC 1JLHD 1aop 497 -28.19 -4.67 3.05e+01 :497 XRAY 1.60 0.182 0.218 SULFITE REDUCTASE HEMOPROTEIN || 2AOP0 2GEP0 3AOP0 3GEO0 4AOP0 4GEP0 5AOP0 5GEP0 6GEP0 7GEP0 8GEP0 1iatA 557 -29.57 -4.67 3.05e+01 :557 XRAY 1.62 0.147 0.170 PHOSPHOGLUCOSE ISOMERASE 1korA 400 -27.03 -4.65 3.11e+01 :400 XRAY 1.95 0.230 0.250 Argininosuccinate Synthetase || 1J1ZA 1J1ZB 1J1ZC 1J1ZD 1J20A 1J20B 1J20C 1J20D 1J21A 1J21B 1J21C 1J21D 1KH1A 1KH1B 1KH1C 1KH1D 1KH2A 1KH2B 1KH2C 1KH2D 1KH3A 1KH3B 1KH3C 1KH3D 1KORB 1KORC 1KORD 1o0lA 188 -25.24 -4.58 3.28e+01 :188 NMR NA NA NA Apoptosis regulator Bcl-W 1mjfA 281 -27.45 -4.55 3.38e+01 :281 XRAY 1.80 0.207 0.242 spermidine synthase || 1MJFB 1tib 269 -26.87 -4.53 3.42e+01 :269 XRAY 1.84 0.188 NA LIPASE || 1DT3A 1DT3B 1DT5A 1DT5B 1DT5C 1DT5D 1DT5E 1DT5F 1DT5G 1DT5H 1DTEA 1DTEB 1DU4A 1DU4B 1DU4C 1DU4D 1EINA 1EINB 1EINC 1lg7A 182 -25.85 -4.52 3.47e+01 :182 XRAY 1.96 0.218 0.241 VSV matrix protein 1l1qA 186 -25.42 -4.50 3.51e+01 :186 XRAY 1.85 0.222 0.251 Adenine phosphoribosyltransferase || 1L1RA 1mra 359 -26.10 -4.48 3.58e+01 :359 XRAY 2.10 0.190 NA MANDELATE RACEMASE 1kp5A 245 -25.28 -4.48 3.59e+01 :245 XRAY 2.60 0.208 0.256 Green Fluorescent Protein || 1KP5B 1dmuA 299 -26.77 -4.47 3.61e+01 :299 XRAY 2.20 0.185 0.239 BGLI RESTRICTION ENDONUCLEASE 1mslA 109 -23.35 -4.47 3.62e+01 :109 XRAY 3.50 0.260 0.350 PROTEIN (MECHANOSENSITIVE ION CHANNEL) || 1MSLB 1MSLC 1MSLD 1MSLE 1i52A 236 -26.15 -4.46 3.65e+01 :236 XRAY 1.50 0.227 0.247 4-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL SYNTHASE || 1INIA 1INJA 1m1fA 110 -23.01 -4.43 3.75e+01 :110 XRAY 1.40 0.161 0.182 Kid toxin protein || 1M1FB 1proA 99 -23.97 -4.41 3.81e+01 :99 XRAY 1.80 0.185 0.310 HIV-1 PROTEASE || 1A8GA 1A8GB 1EBYA 1EBYB 1HXWA 1HXWB 1IZHA 1IZHB 1PROB 1SBGA 1SBGB 1VIJA 1VIJB 1VIKA 1VIKB 2HVP0 4PHVA 4PHVB 5HVPA 5HVPB 9HVPA 9HVPB 1h3mA 235 -26.11 -4.40 3.84e+01 :235 XRAY 2.40 0.241 0.333 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE || 1H3MB 1mkaA 171 -24.70 -4.40 3.85e+01 :171 XRAY 2.00 0.163 0.214 BETA-HYDROXYDECANOYL THIOL ESTER DEHYDRASE || 1MKAB 1MKBA 1MKBB 1ktnA 250 -26.77 -4.36 4.00e+01 :250 XRAY 1.40 0.186 0.205 2-deoxyribose-5-phosphate aldolase || 1KTNB