% 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.YGR029W.t2k-w0.5.mod Host: cc57 Sat Oct 11 21:16:02 2003 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR029W % --------------------------------------------------------------------- % Inserted Files: YGR029W.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: YGR029W.t2k-w0.5.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 14442 sequences, 3304407 residues, 190 nodes, 226.85 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(=3.1203) * Reverse)^tau(=0.7374))) % 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 1oqcA 125 -135.51 -114.33 6.49e-30 :125 XRAY 1.80 0.202 0.240 augmenter of liver regeneration || 1OQCB 1OQCC 1OQCD 1jr8A 117 -114.15 -93.50 2.37e-25 :117 XRAY 1.50 0.208 0.233 Erv2 PROTEIN, mitochondrial || 1JR8B 1JRAA 1JRAB 1JRAC 1JRAD 1ct9A 553 -31.20 -9.21 5.58e-02 :553 XRAY 2.00 0.197 0.297 ASPARAGINE SYNTHETASE B || 1CT9B 1CT9C 1CT9D 1eyvA 156 -26.82 -7.45 3.11e-01 :156 XRAY 1.60 0.190 0.234 N-UTILIZING SUBSTANCE PROTEIN B HOMOLOG || 1EYVB 1ldjB 90 -25.44 -6.89 5.50e-01 :90 XRAY 3.00 0.247 0.288 ring-box protein 1 || 1LDKC 1dgjA 907 -29.98 -6.60 7.39e-01 :907 XRAY 2.80 0.170 0.224 ALDEHYDE OXIDOREDUCTASE 1ag9A 175 -25.94 -6.57 7.63e-01 :175 XRAY 1.80 0.196 0.250 FLAVODOXIN || 1AG9B 1AHN0 1jnuA 104 -24.51 -6.13 1.22e+00 :104 XRAY 2.60 0.238 0.259 PHY3 PROTEIN || 1G28A 1G28B 1G28C 1G28D 1JNUB 1JNUC 1JNUD 2drpA 66 -24.18 -6.09 1.27e+00 :66 XRAY 2.80 0.193 NA PROTEIN (TRAMTRACK DNA-BINDING DOMAIN) || 2DRPD 1h4rA 314 -26.09 -5.72 1.88e+00 :314 XRAY 1.80 0.193 0.227 MERLIN || 1H4RB 1isnA 323 -26.12 -5.69 1.94e+00 :323 XRAY 2.90 0.237 0.284 merlin 1dmhA 311 -26.51 -5.64 2.06e+00 :311 XRAY 1.70 0.185 0.218 CATECHOL 1,2-DIOXYGENASE || 1DLMA 1DLMB 1DLQA 1DLQB 1DLTA 1DLTB 1DMHB 2adr 60 -22.50 -5.58 2.20e+00 :60 NMR NA NA NA ADR1 1pstH 237 -25.61 -5.36 2.78e+00 :237 XRAY 3.00 0.218 NA PHOTOSYNTHETIC REACTION CENTER || 1PSSH 1ogvH 250 -25.67 -5.33 2.87e+00 :250 XRAY 2.35 0.214 0.244 REACTION CENTER PROTEIN H CHAIN 1aijH 260 -25.71 -5.31 2.96e+00 :260 XRAY 2.20 0.216 0.270 PHOTOSYNTHETIC REACTION CENTER (H SUBUNIT) || 1AIGH 1AIGP 1AIJT 1DS8H 1DS8T 1DV3H 1DV3T 1DV6H 1DV6T 1qovH 260 -25.71 -5.30 2.97e+00 :260 XRAY 2.10 0.169 0.186 PHOTOSYNTHETIC REACTION CENTER || 1E14H 1E6DH 1F6NH 1FNPH 1FNQH 1JGWH 1JGXH 1JGYH 1JGZH 1JH0H 1K6LH 1K6NH 1KBYH 1L9BH 1L9JH 1L9JT 1M3XH 1MPSH 1PCRH 1YSTH 2RCRH 4RCRH 1i1oA 147 -25.30 -5.29 3.01e+00 :147 XRAY 2.00 0.220 NA FLAVODOXIN 1j9eA 147 -25.51 -5.29 3.02e+00 :147 XRAY 1.44 0.139 0.156 FLAVODOXIN 1azl 147 -25.51 -5.24 3.17e+00 :147 XRAY 1.80 0.175 NA FLAVODOXIN 1znf 26 -20.38 -5.07 3.83e+00 :26 NMR NA NA NA 31ST ZINC FINGER FROM XFIN 1njqA 38 -20.79 -5.05 3.93e+00 :38 NMR NA NA NA superman protein 1knb 196 -24.32 -4.97 4.29e+00 :196 XRAY 1.70 0.158 NA ADENOVIRUS TYPE 5 FIBER PROTEIN 1akw 147 -25.24 -4.92 4.52e+00 :147 XRAY 1.75 0.182 0.194 FLAVODOXIN 1hgxA 183 -24.88 -4.92 4.52e+00 :183 XRAY 1.90 0.175 0.234 HYPOXANTHINE-GUANINE-XANTHINE PHOSPHORIBOSYLTRANSFERASE || 1HGXB 1fb5A 320 -25.65 -4.91 4.60e+00 :320 XRAY 3.50 0.219 0.252 ORNITHINE TRANSCARBAMOYLASE 1jt2A 268 -25.46 -4.87 4.83e+00 :268 XRAY 1.80 0.187 0.211 PROTEIN (ENDO-1,4-BETA-XYLANASE Z) 1jjfA 268 -25.46 -4.85 4.91e+00 :268 XRAY 1.75 0.191 0.206 ENDO-1,4-BETA-XYLANASE Z 1fx1 148 -25.07 -4.85 4.93e+00 :148 XRAY 2.00 NA NA FLAVODOXIN 1f4pA 147 -24.90 -4.84 4.97e+00 :147 XRAY 1.30 0.126 0.169 FLAVODOXIN 1c7fA 147 -25.12 -4.84 4.99e+00 :147 XRAY 2.00 0.190 0.240 FLAVODOXIN || 1C7EA 1C7EB 1C7FB 1j9gA 147 -25.00 -4.78 5.31e+00 :147 XRAY 2.40 0.204 0.247 Flavodoxin 1j8qA 147 -25.00 -4.78 5.33e+00 :147 XRAY 1.35 0.162 0.181 FLAVODOXIN || 2FX20 3FX20 4FX20 5FX20 1bu5A 147 -25.00 -4.78 5.33e+00 :147 XRAY 1.83 0.169 0.202 PROTEIN (FLAVODOXIN) || 1BU5B 1akr 147 -24.92 -4.72 5.71e+00 :147 XRAY 1.58 0.184 NA FLAVODOXIN 1akt 147 -24.82 -4.62 6.39e+00 :147 XRAY 1.80 0.183 NA FLAVODOXIN 1ku1A 230 -24.89 -4.55 6.89e+00 :230 XRAY 1.93 0.220 0.228 ARF guanine-nucleotide exchange factor 2 || 1KU1B 1g2fC 90 -22.46 -4.53 7.11e+00 :90 XRAY 2.00 0.233 0.263 TATA BOX ZINC FINGER PROTEIN || 1G2FF 1kqhA 38 -20.71 -4.41 8.12e+00 :38 NMR NA NA NA ACTX-Hi:OB4219 || 1KQIA 1eyeA 280 -24.48 -4.34 8.86e+00 :280 XRAY 1.70 0.185 0.243 DIHYDROPTEROATE SYNTHASE I 1k5dB 201 -24.27 -4.30 9.20e+00 :201 XRAY 2.70 0.240 0.267 Ran-specific GTPase-activating protein || 1K5DE 1K5DH 1K5DK 1K5GB 1K5GE 1K5GH 1K5GK 1mhqA 148 -23.29 -4.26 9.61e+00 :148 XRAY 2.20 0.224 0.267 ADP-ribosylation factor binding protein GGA2 || 1MHQB 1akq 147 -24.73 -4.26 9.71e+00 :147 XRAY 1.90 0.196 0.240 FLAVODOXIN || 1AKU0 1AKV0 1cc8A 73 -21.82 -4.25 9.81e+00 :73 XRAY 1.02 0.141 0.172 PROTEIN (METALLOCHAPERONE ATX1) || 1CC7A 1FD8A 1FESA 1zbdB 134 -23.69 -4.20 1.03e+01 :134 XRAY 2.60 0.226 0.263 RABPHILIN-3A 1kt2A 182 -24.11 -4.18 1.06e+01 :182 XRAY 2.80 0.220 0.294 H-2 class II histocompatibility antigen, E-D alpha chain || 1KT2C 1ktdA 182 -24.13 -4.15 1.10e+01 :182 XRAY 2.40 0.220 0.279 H-2 class II histocompatibility antigen, E-D alpha chain || 1KTDC 1h6xA 170 -23.01 -4.12 1.14e+01 :170 XRAY 2.25 0.214 0.260 ENDO-1,4-BETA-XYLANASE Y 1jj2P 95 -22.88 -4.01 1.30e+01 :95 XRAY 2.40 0.189 0.222 RIBOSOMAL PROTEIN L21E || 1FFKN 1K73R 1K8AR 1K9MR 1KC8R 1KD1R 1KQSP 1M1KR 1M90R 1N8RR 1NJIR 1cn2 66 -20.96 -3.96 1.37e+01 :66 NMR NA NA NA TOXIN 2 1fngA 192 -24.20 -3.93 1.42e+01 :192 XRAY 1.90 0.221 0.254 PROTEIN (MHC CLASS II I-EK, ALPHA CHAIN) || 1FNEA 1FNEC 1FNGC 1i3rA 192 -24.20 -3.92 1.44e+01 :192 XRAY 2.40 0.229 0.270 H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, E-K ALPHA CHAIN || 1I3RC 1I3RE 1I3RG 1izlF 44 -19.45 -3.92 1.44e+01 :44 XRAY 3.70 0.530 NA Photosystem II: Subunit PsbF || 1IZLQ 1h6wA 312 -24.52 -3.91 1.46e+01 :312 XRAY 1.90 0.228 0.255 BACTERIOPHAGE T4 SHORT TAIL FIBRE 1mjyA 175 -23.34 -3.86 1.55e+01 :175 XRAY 2.10 0.164 0.231 INORGANIC PYROPHOSPHATASE || 1MJYB 1d03A 169 -23.30 -3.85 1.57e+01 :169 XRAY 1.85 0.149 0.172 FLAVODOXIN || 1CZHA 1CZOA 1faj 175 -23.31 -3.85 1.57e+01 :175 XRAY 2.15 0.187 NA SOLUBLE INORGANIC PYROPHOSPHATASE || 1INO0 1IPWA 1IPWB 1JFDA 1JFDB 2EIPA 2EIPB 1mjz 175 -23.31 -3.84 1.59e+01 :175 XRAY 2.20 0.194 0.287 INORGANIC PYROPHOSPHATASE 1l0cA 207 -23.45 -3.84 1.59e+01 :207 XRAY 2.30 0.188 0.246 Serotonin N-acetyltransferase 1avgI 142 -22.72 -3.83 1.60e+01 :142 XRAY 2.60 0.184 0.275 TRIABIN 1ieaA 192 -24.22 -3.82 1.62e+01 :192 XRAY 2.30 0.202 0.274 MHC CLASS II I-EK || 1IEAC 1IEBA 1IEBC 1i40A 175 -23.30 -3.82 1.62e+01 :175 XRAY 1.10 0.117 0.153 INORGANIC PYROPHOSPHATASE || 1I6TA 1IGP0 1OBWA 1OBWB 1OBWC 1ktmA 139 -22.79 -3.81 1.63e+01 :139 NMR NA NA NA FOCAL ADHESION KINASE 1 1nxuA 333 -25.39 -3.80 1.65e+01 :333 XRAY 1.80 0.200 0.235 Hypothetical oxidoreductase yiaK || 1NXUB 1jdqA 98 -22.51 -3.80 1.67e+01 :98 NMR NA NA NA HYPOTHETICAL PROTEIN TM0983 1pznA 349 -24.51 -3.76 1.76e+01 :349 XRAY 2.85 0.257 0.307 DNA repair and recombination protein rad51 || 1PZNB 1PZNC 1PZND 1PZNE 1PZNF 1PZNG 1dyoA 160 -22.94 -3.75 1.77e+01 :160 XRAY 2.10 0.190 0.250 ENDO-1,4-BETA-XYLANASE Y || 1DYOB 1k40A 126 -22.66 -3.75 1.78e+01 :126 XRAY 2.25 0.236 0.294 adhesion kinase 1kpiA 302 -25.57 -3.74 1.78e+01 :302 XRAY 2.65 0.208 0.242 CYCLOPROPANE-FATTY-ACYL-PHOSPHOLIPID SYNTHASE 2 2fb4H 229 -23.52 -3.73 1.80e+01 :229 XRAY 1.90 0.189 NA IGG1-LAMBDA KOL FAB (HEAVY CHAIN) 1g2dC 90 -21.79 -3.73 1.81e+01 :90 XRAY 2.20 0.225 0.262 TATA BOX ZINC FINGER PROTEIN || 1G2DF 1meyC 87 -23.07 -3.71 1.86e+01 :87 XRAY 2.20 0.224 0.319 CONSENSUS ZINC FINGER || 1MEYF 1MEYG 1mjwA 175 -23.17 -3.70 1.87e+01 :175 XRAY 1.95 0.191 0.266 INORGANIC PYROPHOSPHATASE || 1MJWB 1ewiA 114 -21.99 -3.69 1.89e+01 :114 NMR NA NA NA REPLICATION PROTEIN A 1h6yA 170 -22.90 -3.64 2.02e+01 :170 XRAY 2.20 0.194 0.228 ENDO-1,4-BETA-XYLANASE Y || 1H6YB 1mjxA 175 -23.09 -3.63 2.04e+01 :175 XRAY 2.15 0.190 0.263 INORGANIC PYROPHOSPHATASE || 1MJXB 7znf 30 -18.75 -3.63 2.05e+01 :30 NMR NA NA NA ZINC FINGER 1kwdA 16 -16.81 -3.59 2.14e+01 :16 NMR NA NA NA MAJOR SURFACE GLYCOPROTEIN G || 1KWEA 1pkgA 327 -24.22 -3.59 2.16e+01 :327 XRAY 2.90 0.229 0.311 c-kit protein || 1PKGB 1cznA 169 -23.02 -3.58 2.16e+01 :169 XRAY 1.70 0.181 0.210 FLAVODOXIN || 1CZLA 1CZUA 1D04A 1OFV0 1czrA 169 -23.00 -3.58 2.17e+01 :169 XRAY 1.90 0.154 0.193 FLAVODOXIN 1czkA 169 -23.00 -3.57 2.21e+01 :169 XRAY 1.90 0.157 0.200 FLAVODOXIN 1m2mA 82 -20.96 -3.55 2.26e+01 :82 XRAY 1.80 0.194 0.238 cytochrome b5 || 1F03A 1F04A 1pdiA 278 -24.43 -3.54 2.27e+01 :278 EM NA NA NA Short tail fiber protein || 1PDIB 1PDIC 1PDID 1PDIE 1PDIF 1PDIG 1PDIH 1PDII 1PDIJ 1PDIK 1PDIL 1PDIM 1PDIN 1PDIO 1PDIP 1PDIQ 1PDIR 1cjwA 166 -22.64 -3.54 2.29e+01 :166 XRAY 1.80 0.180 0.230 PROTEIN (SEROTONIN N-ACETYLTRANSFERASE) 1b6bA 174 -22.71 -3.52 2.33e+01 :174 XRAY 2.50 0.217 0.282 PROTEIN (ARYLALKYLAMINE N-ACETYLTRANSFERASE) || 1B6BB 1i5uA 82 -21.00 -3.47 2.48e+01 :82 NMR NA NA NA CYTOCHROME B5 1othA 321 -24.21 -3.45 2.55e+01 :321 XRAY 1.85 0.179 0.201 PROTEIN (ORNITHINE TRANSCARBAMOYLASE) || 1C9YA 1EP9A 1FVOA 1FVOB 1m2iA 82 -20.95 -3.44 2.57e+01 :82 XRAY 1.80 0.193 0.232 cytochrome b5 1dueA 242 -23.79 -3.41 2.66e+01 :242 XRAY 2.00 0.214 0.238 EXFOLIATIVE TOXIN A 1ngkA 128 -21.53 -3.38 2.78e+01 :128 XRAY 2.11 0.188 0.226 Hemoglobin-like protein HbO || 1NGKB 1NGKC 1NGKD 1NGKE 1NGKF 1NGKG 1NGKH 1NGKI 1NGKJ 1NGKK 1NGKL 2abk 211 -23.22 -3.37 2.81e+01 :211 XRAY 1.85 0.185 0.216 ENDONUCLEASE III 1agjA 242 -23.79 -3.37 2.82e+01 :242 XRAY 1.70 0.184 0.235 EPIDERMOLYTIC TOXIN A || 1AGJB 1DUAA 1EXFA 1mqrA 679 -25.91 -3.36 2.84e+01 :679 XRAY 2.00 0.179 0.203 ALPHA-D-GLUCURONIDASE 1k9fA 679 -25.91 -3.35 2.87e+01 :679 XRAY 1.75 0.189 0.211 alpha-D-glucuronidase || 1K9EA 1mqpA 679 -25.91 -3.35 2.87e+01 :679 XRAY 1.90 0.192 0.222 alpha-D-glucuronidase 1l8nA 679 -25.92 -3.35 2.89e+01 :679 XRAY 1.50 0.140 0.172 ALPHA-D-GLUCURONIDASE || 1K9DA 1MQQA 1ib1E 200 -22.87 -3.35 2.89e+01 :200 XRAY 2.70 0.210 0.228 SEROTONIN N-ACETYLTRANSFERASE || 1IB1F 1IB1G 1IB1H 1kuxA 207 -22.91 -3.33 2.94e+01 :207 XRAY 1.80 0.200 0.225 Serotonin N-acetyltransferase || 1KUVA 1KUYA 1es1A 82 -20.97 -3.33 2.95e+01 :82 XRAY 2.10 0.192 0.244 CYTOCHROME B5 || 1J0QA 1e5tA 710 -25.95 -3.33 2.96e+01 :710 XRAY 1.70 0.184 0.206 PROLYL ENDOPEPTIDASE 1dgsA 667 -26.06 -3.32 2.99e+01 :667 XRAY 2.90 0.228 0.298 DNA LIGASE || 1DGSB 1DGTA 1DGTB 1o6gA 710 -25.99 -3.30 3.06e+01 :710 XRAY 1.40 0.200 0.216 PROLYL ENDOPEPTIDASE 1ehbA 82 -20.97 -3.30 3.08e+01 :82 XRAY 1.90 0.198 0.248 PROTEIN (CYTOCHROME B5) 1jrfA 47 -21.07 -3.26 3.20e+01 :47 NMR NA NA NA SUBGROUP A ROUS SARCOMA VIRUS RECEPTORS PG800 AND PG950 1h2wA 710 -25.95 -3.26 3.22e+01 :710 XRAY 1.39 0.212 0.230 PROLYL ENDOPEPTIDASE || 1QFMA 1QFSA 1o6fA 710 -25.95 -3.26 3.23e+01 :710 XRAY 1.60 0.202 0.221 PROLYL ENDOPEPTIDASE 1m20A 82 -20.93 -3.25 3.24e+01 :82 XRAY 1.80 0.193 0.227 Cytochrome b5 1e8nA 710 -25.92 -3.25 3.24e+01 :710 XRAY 1.50 0.192 0.212 PROLYL ENDOPEPTIDASE || 1E8MA 1H2ZA 1lr6A 82 -20.93 -3.24 3.30e+01 :82 XRAY 1.90 0.196 0.236 cytochrome b5 1m59A 82 -20.74 -3.24 3.30e+01 :82 XRAY 1.90 0.193 0.227 Cytochrome b5 1h2xA 710 -25.95 -3.20 3.48e+01 :710 XRAY 1.49 0.175 0.196 PROLYL ENDOPEPTIDASE || 1H2YA 1eexA 554 -25.37 -3.18 3.55e+01 :554 XRAY 1.70 0.164 0.226 PROPANEDIOL DEHYDRATASE || 1DIOA 1DIOL 1EEXL 1EGMA 1EGML 1EGVA 1EGVL 1IWBA 1IWBL 1UC4A 1UC4L 1UC5A 1UC5L 1fw9A 164 -22.11 -3.16 3.65e+01 :164 XRAY 1.40 0.200 0.182 CHORISMATE LYASE 1cokA 68 -20.57 -3.15 3.68e+01 :68 NMR NA NA NA PROTEIN (SECOND SPLICE VARIANT P73) 1c6vA 164 -22.24 -3.13 3.79e+01 :164 XRAY 3.00 0.203 0.362 PROTEIN (SIV INTEGRASE) || 1C6VB 1C6VC 1C6VD