% 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.YGR229C.t2k-w0.5.mod Host: cc48 Wed Nov 19 14:37:52 2003 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR229C % --------------------------------------------------------------------- % Inserted Files: YGR229C.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: YGR229C.t2k-w0.5.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 14684 sequences, 3366451 residues, 506 nodes, 607.80 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(=2.2341) * Reverse)^tau(=0.7581))) % 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 1k32A 1045 -36.33 -9.58 3.03e-01 :1045 XRAY 2.00 0.245 0.264 tricorn protease || 1K32B 1K32C 1K32D 1K32E 1K32F 1n6eA 1071 -36.36 -9.58 3.03e-01 :1071 XRAY 2.60 0.254 0.288 tricorn protease || 1N6DA 1N6DB 1N6DC 1N6DD 1N6DE 1N6DF 1N6EC 1N6EE 1N6EG 1N6EI 1N6EK 1N6FA 1N6FB 1N6FC 1N6FD 1N6FE 1N6FF 1mb4A 370 -32.10 -8.74 5.99e-01 :370 XRAY 1.84 0.192 0.229 Aspartate-Semialdehyde Dehydrogenase || 1MB4B 1MC4A 1bplA 189 -29.53 -8.00 1.12e+00 :189 XRAY 2.20 0.167 NA ALPHA-1,4-GLUCAN-4-GLUCANOHYDROLASE 1gzqA 300 -29.97 -7.65 1.50e+00 :300 XRAY 2.26 0.203 0.237 T-CELL SURFACE GLYCOPROTEIN CD1B || 1GZPA 1UQSA 1ob0A 483 -31.32 -7.56 1.62e+00 :483 XRAY 1.83 0.147 0.154 ALPHA-AMYLASE 1vjs 483 -30.64 -7.12 2.36e+00 :483 XRAY 1.70 0.199 0.226 ALPHA-AMYLASE 1e43A 483 -30.33 -7.05 2.52e+00 :483 XRAY 1.70 0.133 0.185 ALPHA-AMYLASE || 1E3XA 1E3ZA 1E40A 1bli 483 -30.59 -7.01 2.59e+00 :483 XRAY 1.90 0.154 0.185 ALPHA-AMYLASE 1gz7A 534 -31.69 -6.88 2.93e+00 :534 XRAY 1.97 0.200 0.236 LIPASE 2 || 1GZ7B 1GZ7C 1GZ7D 1fmmS 132 -27.47 -6.83 3.05e+00 :132 NMR NA NA NA ACIDIC FIBROBLAST GROWTH FACTOR 1cvuA 552 -30.91 -6.41 4.40e+00 :552 XRAY 2.40 0.204 0.235 PROSTAGLANDIN H2 SYNTHASE-2 || 1CVUB 3pghA 587 -30.94 -6.40 4.46e+00 :587 XRAY 2.50 0.236 0.316 CYCLOOXYGENASE-2 || 1CX2A 1CX2B 1CX2C 1CX2D 3PGHB 3PGHC 3PGHD 4COXA 4COXB 4COXC 4COXD 5COXA 5COXB 5COXC 5COXD 6COXA 6COXB 1j58A 385 -30.88 -6.25 5.07e+00 :385 XRAY 1.75 0.192 0.197 YVRK PROTEIN || 1L3JA 1j6rA 214 -28.11 -6.24 5.15e+00 :214 XRAY 2.30 0.251 0.290 HYPOTHETICAL PROTEIN TM0269 || 1J6RB 1jsmA 325 -29.84 -6.19 5.35e+00 :325 XRAY 1.90 0.234 0.264 HAEMAGGLUTININ (HA1 CHAIN) || 1JSNA 1JSOA 1h2bA 359 -30.41 -6.15 5.55e+00 :359 XRAY 1.62 0.168 0.203 ALCOHOL DEHYDROGENASE || 1H2BB 1ddxA 552 -30.52 -6.09 5.87e+00 :552 XRAY 3.00 0.267 0.324 PROTEIN (PROSTAGLANDIN H2 SYNTHASE-2) || 1DDXB 1DDXC 1DDXD 1pxxA 604 -30.61 -6.04 6.15e+00 :604 XRAY 2.90 0.254 0.302 Prostaglandin G/H synthase 2 || 1PXXB 1PXXC 1PXXD 1e6vA 553 -30.93 -5.95 6.67e+00 :553 XRAY 2.70 0.239 0.278 METHYL-COENZYME M REDUCTASE I ALPHA SUBUNIT || 1E6VD 1gn6A 207 -26.94 -5.93 6.79e+00 :207 XRAY 2.90 0.169 NA SUPEROXIDE DISMUTASE || 1GN6B 1GN6C 1GN6D 1ciu 683 -32.17 -5.83 7.43e+00 :683 XRAY 2.30 0.179 0.200 CYCLODEXTRIN GLYCOSYLTRANSFERASE || 1A470 1g9zA 152 -26.53 -5.79 7.74e+00 :152 XRAY 1.80 0.204 0.249 DNA ENDONUCLEASE I-CREI || 1BP7A 1BP7B 1BP7C 1BP7D 1G9YA 1G9YB 1G9ZB 1af5 135 -26.18 -5.77 7.84e+00 :135 XRAY 3.00 0.248 0.373 I-CREI 1cydA 244 -28.19 -5.70 8.39e+00 :244 XRAY 1.80 0.154 0.202 CARBONYL REDUCTASE || 1CYDB 1CYDC 1CYDD 1n3fA 163 -26.61 -5.68 8.48e+00 :163 XRAY 2.00 0.195 0.228 DNA endonuclease I-CreI || 1N3EA 1N3EB 1N3EG 1N3EH 1N3FB 1N3FG 1N3FH 1gn3A 207 -26.84 -5.65 8.72e+00 :207 XRAY 4.00 0.168 0.184 SUPEROXIDE DISMUTASE || 1GN3B 1idsA 207 -26.68 -5.64 8.85e+00 :207 XRAY 2.00 0.167 NA IRON SUPEROXIDE DISMUTASE || 1IDSB 1IDSC 1IDSD 1gn4A 207 -26.72 -5.59 9.28e+00 :207 XRAY 2.50 0.172 0.225 SUPEROXIDE DISMUTASE || 1GN4B 1GN4C 1GN4D 1tc1A 220 -27.36 -5.52 9.88e+00 :220 XRAY 1.41 0.193 0.228 PROTEIN (HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE) || 1TC1B 1tc2A 221 -27.37 -5.51 1.00e+01 :221 XRAY 1.81 0.191 0.232 PROTEIN (HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE) || 1TC2B 1n2sA 299 -27.68 -5.49 1.02e+01 :299 XRAY 2.00 0.202 0.253 dTDP-glucose oxidoreductase || 1KBZA 1KC1A 1KC3A 1dkiA 371 -28.54 -5.33 1.18e+01 :371 XRAY 1.60 0.219 0.245 PYROGENIC EXOTOXIN B ZYMOGEN || 1DKIB 1DKIC 1DKID 1ktmA 139 -26.19 -5.30 1.20e+01 :139 NMR NA NA NA FOCAL ADHESION KINASE 1 1nsa 395 -28.89 -5.27 1.25e+01 :395 XRAY 2.30 0.169 NA PROCARBOXYPEPTIDASE B 1fx0B 498 -31.70 -5.27 1.25e+01 :498 XRAY 3.20 0.319 0.350 ATP SYNTHASE BETA CHAIN || 1KMHB 1q8yA 373 -28.73 -5.27 1.25e+01 :373 XRAY 2.05 0.209 0.244 SR protein kinase || 1Q8YB 1Q8ZA 1Q8ZB 1Q97A 1Q97B 1Q99A 1Q99B 1howA 373 -28.73 -5.27 1.25e+01 :373 XRAY 2.10 0.204 0.255 SERINE/THREONINE-PROTEIN KINASE YMR216C 1gn2A 207 -26.29 -5.23 1.29e+01 :207 XRAY 3.40 0.249 0.270 SUPEROXIDE DISMUTASE || 1GN2B 1GN2C 1GN2D 1GN2E 1GN2F 1GN2G 1GN2H 1ex1A 605 -29.55 -5.21 1.31e+01 :605 XRAY 2.20 0.170 0.202 PROTEIN (BETA-D-GLUCAN EXOHYDROLASE ISOENZYME EXO1) || 1IEQA 1IEVA 1IEWA 1IEXA 1J8VA 1i13A 221 -27.02 -5.21 1.31e+01 :221 XRAY 1.84 0.250 0.252 HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE || 1I13B 1jbaA 204 -26.63 -5.19 1.33e+01 :204 NMR NA NA NA PROTEIN (GUANYLATE CYCLASE ACTIVATING PROTEIN 2) 1b4kA 337 -27.56 -5.07 1.50e+01 :337 XRAY 1.67 0.178 0.208 PROTEIN (5-AMINOLEVULINIC ACID DEHYDRATASE) || 1B4KB 1gzgA 337 -27.60 -5.06 1.51e+01 :337 XRAY 1.66 0.175 0.198 DELTA-AMINOLEVULINIC ACID DEHYDRATASE || 1GZGB 1ow6A 161 -26.88 -5.00 1.60e+01 :161 XRAY 2.35 0.243 0.274 Focal adhesion kinase 1 || 1OW6B 1OW6C 1OW7A 1OW7B 1OW7C 1OW8A 1OW8B 1OW8C 1k04A 162 -26.90 -5.00 1.61e+01 :162 XRAY 1.95 0.243 0.270 FOCAL ADHESION KINASE 1 || 1K05A 1K05B 1K05C 1evyA 366 -27.40 -4.98 1.63e+01 :366 XRAY 1.75 0.195 0.257 GLYCEROL-3-PHOSPHATE DEHYDROGENASE || 1EVZA 1JDJA 1M66A 1M67A 1N1EA 1N1EB 1N1GA 1h99A 224 -26.44 -4.97 1.64e+01 :224 XRAY 1.55 0.224 0.238 TRANSCRIPTION ANTITERMINATOR LICT 1dbrA 231 -27.44 -4.92 1.73e+01 :231 XRAY 2.40 0.168 NA HYPOXANTHINE GUANINE XANTHINE PHOSPHORIBOSYLTRANSFERASE || 1DBRB 1DBRC 1DBRD 1iqaA 160 -25.74 -4.87 1.82e+01 :160 XRAY 2.20 0.226 0.274 RECEPTOR ACTIVATOR OF NUCLEAR FACTOR KAPPA B LIGAND || 1IQAB 1IQAC 1i14A 221 -26.69 -4.85 1.85e+01 :221 XRAY 1.92 0.250 0.241 HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE || 1I14B 1rdr 461 -28.69 -4.84 1.86e+01 :461 XRAY 2.40 0.244 0.274 POLIOVIRUS 3D POLYMERASE 1fsgA 233 -27.44 -4.84 1.87e+01 :233 XRAY 1.05 0.122 0.154 HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE || 1FSGC 1QK3A 1QK3B 1QK3C 1QK3D 1QK4A 1QK4B 1QK4C 1QK4D 1lizA 136 -25.82 -4.83 1.89e+01 :136 NMR NA NA NA apo-CcmE 1jtzX 171 -25.81 -4.79 1.96e+01 :171 XRAY 2.60 0.235 0.286 TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 11 || 1JTZY 1JTZZ 1i0iA 221 -26.71 -4.78 1.98e+01 :221 XRAY 2.06 0.250 0.259 HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE || 1I0IB 1ekqA 272 -26.77 -4.78 1.98e+01 :272 XRAY 1.50 0.216 0.251 HYDROXYETHYLTHIAZOLE KINASE || 1C3QA 1C3QB 1C3QC 1EKKA 1EKKB 1EKQB 1omwA 689 -29.96 -4.77 2.00e+01 :689 XRAY 2.50 0.216 0.252 G-protein coupled receptor kinase 2 1cz7A 406 -28.46 -4.76 2.02e+01 :406 XRAY 2.90 0.258 0.294 MICROTUBULE MOTOR PROTEIN NCD || 1CZ7B 1CZ7C 1CZ7D 1rhd 293 -27.64 -4.75 2.03e+01 :293 XRAY 2.50 NA NA RHODANESE 1esjA 284 -26.82 -4.74 2.06e+01 :284 XRAY 1.80 0.231 0.253 HYDROXYETHYLTHIAZOLE KINASE || 1ESJB 1ESJC 1ESQA 1ESQB 1ESQC 1is1A 185 -26.49 -4.73 2.07e+01 :185 XRAY 2.20 0.203 0.273 RIBOSOME RECYCLING FACTOR 1i4k1 77 -23.94 -4.70 2.13e+01 :77 XRAY 2.50 0.209 0.264 PUTATIVE SNRNP SM-LIKE PROTEIN || 1I4K2 1I4KA 1I4KB 1I4KC 1I4KD 1I4KE 1I4KF 1I4KG 1I4KH 1I4KI 1I4KJ 1I4KK 1I4KL 1I4KM 1I4KN 1I4KO 1I4KP 1I4KQ 1I4KR 1I4KS 1I4KT 1I4KU 1I4KV 1I4KW 1I4KX 1I4KY 1I4KZ 1I5LA 1I5LB 1I5LC 1I5LD 1I5LE 1I5LF 1I5LG 1I5LH 1I5LI 1I5LJ 1I5LK 1I5LL 1I5LM 1I5LN 1i0lA 221 -26.62 -4.70 2.13e+01 :221 XRAY 1.72 0.250 0.267 HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE || 1I0LB 1n6mA 409 -28.46 -4.70 2.14e+01 :409 XRAY 2.50 0.260 0.302 Claret segregational protein || 1N6MB 1dq3A 454 -29.53 -4.69 2.16e+01 :454 XRAY 2.10 0.192 0.232 ENDONUCLEASE 1gt6A 269 -28.01 -4.66 2.20e+01 :269 XRAY 2.20 0.216 0.239 LIPASE || 1GT6B 2ncdA 420 -28.50 -4.66 2.22e+01 :420 XRAY 2.50 0.226 0.270 PROTEIN (Kinesin motor NCD) 1afcA 140 -25.64 -4.65 2.24e+01 :140 XRAY 2.70 0.204 NA ACIDIC FIBROBLAST GROWTH FACTOR || 1AFCB 1AFCC 1AFCD 1AFCE 1AFCF 1AFCG 1AFCH 2bce 579 -29.05 -4.60 2.34e+01 :579 XRAY 1.60 0.211 0.250 CHOLESTEROL ESTERASE 1tubB 427 -28.02 -4.60 2.35e+01 :427 ELEC 3.70 NA NA TUBULIN 1axcA 261 -27.31 -4.59 2.36e+01 :261 XRAY 2.60 0.192 0.289 PCNA || 1AXCC 1AXCE 1ycsB 239 -26.61 -4.58 2.38e+01 :239 XRAY 2.20 0.205 0.286 53BP2 1jffB 445 -28.07 -4.57 2.42e+01 :445 ELEC 3.50 0.232 0.297 tubulin beta chain || 1FFXB 1FFXD 1IA0B 1hqz1 141 -25.11 -4.55 2.47e+01 :141 XRAY 2.10 0.215 0.259 ACTIN-BINDING PROTEIN || 1HQZ2 1HQZ3 1HQZ4 1HQZ5 1HQZ6 1HQZ7 1HQZ8 1HQZ9 1qq2A 199 -27.05 -4.53 2.51e+01 :199 XRAY 2.60 0.216 0.268 THIOREDOXIN PEROXIDASE 2 || 1QQ2B 1qk5A 233 -27.10 -4.53 2.51e+01 :233 XRAY 1.60 0.234 0.260 HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE || 1QK5B 1j0mA 752 -29.37 -4.50 2.59e+01 :752 XRAY 2.30 0.175 0.240 XANTHAN LYASE || 1J0NA 1f3lA 321 -27.32 -4.49 2.62e+01 :321 XRAY 2.03 0.209 0.262 PROTEIN ARGININE METHYLTRANSFERASE PRMT3 1fobA 334 -26.96 -4.46 2.69e+01 :334 XRAY 1.80 0.211 0.251 BETA-1,4-GALACTANASE || 1FHLA 1e91A 85 -23.73 -4.44 2.73e+01 :85 NMR NA NA NA PAIRED AMPHIPATHIC HELIX PROTEIN SIN3B 1hq8A 123 -24.42 -4.28 3.19e+01 :123 XRAY 1.95 0.215 0.227 NKG2-D || 1JSKA 1JSKB 1ab4 493 -29.50 -4.27 3.24e+01 :493 XRAY 2.80 0.226 0.310 GYRASE A 1gpc 218 -26.05 -4.22 3.40e+01 :218 XRAY 2.20 0.236 NA PROTEIN (CORE GP32) 1ioiA 208 -26.14 -4.21 3.41e+01 :208 XRAY 2.70 0.210 0.243 PYRROLIDONE CARBOXYL PEPTIDASE || 1IOIB 1IOIC 1IOID 1iofA 208 -26.14 -4.20 3.44e+01 :208 XRAY 2.20 0.195 0.232 PYRROLIDONE CARBOXYL PEPTIDASE || 1IOFB 1IOFC 1IOFD 1dzdA 127 -24.21 -4.17 3.57e+01 :127 NMR NA NA NA ACIDIC FIBROBLAST GROWTH FACTOR 1rhs 296 -27.01 -4.14 3.68e+01 :296 XRAY 1.36 0.169 0.229 SULFUR-SUBSTITUTED RHODANESE || 1BOH0 1BOI0 1ORB0 2ORA0 1augA 215 -26.48 -4.13 3.71e+01 :215 XRAY 2.00 0.197 0.259 PYROGLUTAMYL PEPTIDASE-1 || 1AUGB 1AUGC 1AUGD 1dp2A 293 -26.94 -4.11 3.76e+01 :293 XRAY 2.01 0.185 0.230 RHODANESE 1n9wA 422 -27.63 -4.11 3.78e+01 :422 XRAY 2.30 0.227 0.262 aspartyl-tRNA synthetase 2 || 1N9WB 1m7yA 435 -27.39 -4.10 3.83e+01 :435 XRAY 1.60 0.205 0.219 1-aminocyclopropane-1-carboxylate synthase || 1M4NA 1fht 116 -23.98 -4.09 3.87e+01 :116 NMR NA NA NA U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A 1b8gA 429 -27.35 -4.08 3.90e+01 :429 XRAY 2.37 0.179 0.242 PROTEIN (1-AMINOCYCLOPROPANE-1-CARBOXYLATE SYNTHASE) || 1B8GB 1k40A 126 -24.85 -4.07 3.94e+01 :126 XRAY 2.25 0.236 0.294 adhesion kinase 1dgkN 917 -29.29 -4.05 4.00e+01 :917 XRAY 2.80 0.260 0.308 HEXOKINASE TYPE I