% 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.YGL228W.t2k-w0.5.mod Host: cc73 Sat Oct 11 19:32:18 2003 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGL2/YGL228W % --------------------------------------------------------------------- % Inserted Files: YGL228W.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: YGL228W.t2k-w0.5.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 14442 sequences, 3304407 residues, 578 nodes, 709.03 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(=2.1372) * Reverse)^tau(=0.7464))) % 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 1gw5M 435 -32.14 -9.11 8.48e-01 :435 XRAY 2.59 0.268 0.335 CLATHRIN COAT ASSEMBLY PROTEIN AP50 1obbA 480 -33.02 -8.95 9.54e-01 :480 XRAY 1.90 0.199 0.235 ALPHA-GLUCOSIDASE || 1OBBB 1g63A 181 -29.82 -7.34 3.33e+00 :181 XRAY 2.50 0.230 0.263 EPIDERMIN MODIFYING ENZYME EPID || 1G63B 1G63C 1G63D 1G63E 1G63F 1G63G 1G63H 1G63I 1G63J 1G63K 1G63L 1iucA 312 -29.39 -7.14 3.89e+00 :312 XRAY 2.24 0.164 0.196 Fucose-specific lectin || 1IUBA 1nexA 169 -29.36 -7.11 3.98e+00 :169 XRAY 2.70 0.239 0.273 Centromere DNA-binding protein complex CBF3 subunit D || 1NEXC 1flcB 175 -29.86 -6.94 4.56e+00 :175 XRAY 3.20 0.223 0.267 HAEMAGGLUTININ-ESTERASE-FUSION GLYCOPROTEIN || 1FLCD 1FLCF 1lo0L 219 -28.36 -6.92 4.65e+00 :219 XRAY 2.00 0.206 0.255 If kappa light chain || 1LO0X 1LO2L 1LO2X 1LO3L 1LO3X 1fmcA 255 -28.05 -6.66 5.73e+00 :255 XRAY 1.80 0.207 0.252 7 ALPHA-HYDROXYSTEROID DEHYDROGENASE || 1AHHA 1AHHB 1AHIA 1AHIB 1FMCB 1qcrC 378 -30.42 -6.62 5.91e+00 :378 XRAY 2.70 0.300 0.375 UBIQUINOL CYTOCHROME C OXIDOREDUCTASE 1l0lC 379 -30.42 -6.62 5.92e+00 :379 XRAY 2.35 0.260 0.306 Cytochrome B || 1BE3C 1BGYC 1BGYO 1L0NC 1o0vA 327 -28.59 -6.35 7.37e+00 :327 XRAY 2.60 0.218 0.297 Immunoglobulin heavy chain epsilon-1 || 1O0VB 1g0vA 329 -30.53 -6.31 7.62e+00 :329 XRAY 2.00 0.198 0.231 PROTEINASE A 1ofzA 312 -28.37 -6.23 8.14e+00 :312 XRAY 1.50 0.144 0.179 FUCOSE-SPECIFIC LECTIN || 1OFZB 2jxrA 329 -30.36 -6.10 9.13e+00 :329 XRAY 2.40 0.193 0.270 PROTEINASE A || 1FQ4A 1FQ5A 1FQ6A 1FQ7A 1FQ8A 1dpjA 329 -30.35 -6.09 9.16e+00 :329 XRAY 1.80 0.192 0.213 PROTEINASE A || 1DP5A 1FMUA 1FMXA 1FMXB 1kb9C 385 -31.58 -6.03 9.66e+00 :385 XRAY 2.30 0.218 0.249 CYTOCHROME B || 1EZVC 1KYOC 1KYON 1P84C 1qoxA 449 -31.54 -6.02 9.72e+00 :449 XRAY 2.70 0.255 NA BETA-GLUCOSIDASE || 1QOXB 1QOXC 1QOXD 1QOXE 1QOXF 1QOXG 1QOXH 1QOXI 1QOXJ 1QOXK 1QOXL 1QOXM 1QOXN 1QOXO 1QOXP 1fqvB 149 -26.88 -6.00 9.91e+00 :149 XRAY 2.80 0.275 0.314 SKP1 || 1FQVD 1FQVF 1FQVH 1FQVJ 1FQVL 1FQVN 1FQVP 1nh3A 562 -30.40 -5.94 1.04e+01 :562 XRAY 3.10 0.235 0.311 DNA topoisomerase I 1ej9A 563 -30.41 -5.94 1.04e+01 :563 XRAY 2.60 0.214 0.281 DNA TOPOISOMERASE I 1lpqA 564 -30.41 -5.93 1.05e+01 :564 XRAY 3.14 0.256 0.298 DNA topoisomerase I 1l1yA 678 -30.40 -5.77 1.20e+01 :678 XRAY 2.40 0.191 0.224 cellobiohydrolase || 1L1YB 1L1YC 1L1YD 1L1YE 1L1YF 1L2AA 1L2AB 1L2AC 1L2AD 1L2AE 1L2AF 1bouB 302 -27.91 -5.74 1.23e+01 :302 XRAY 2.20 0.149 0.206 4,5-DIOXYGENASE BETA CHAIN || 1B4UB 1B4UD 1BOUD 1dxrL 273 -29.33 -5.71 1.26e+01 :273 XRAY 2.00 0.194 0.218 PHOTOSYNTHETIC REACTION CENTER L SUBUNIT 1a31A 590 -30.48 -5.67 1.31e+01 :590 XRAY 2.10 0.247 0.310 PROTEIN (TOPOISOMERASE I) 1a35A 591 -30.48 -5.66 1.31e+01 :591 XRAY 2.50 0.209 0.308 PROTEIN (DNA TOPOISOMERASE I) || 1A36A 1k4tA 591 -30.48 -5.66 1.32e+01 :591 XRAY 2.10 0.229 0.269 DNA topoisomerase I || 1K4SA 1h4vB 421 -28.23 -5.59 1.39e+01 :421 XRAY 2.40 0.208 0.256 HISTIDYL-TRNA SYNTHETASE || 1ADJA 1ADJB 1ADJC 1ADJD 1ADYA 1ADYB 1ADYC 1ADYD 1q0sA 259 -29.54 -5.59 1.40e+01 :259 XRAY 2.30 0.222 0.266 DNA adenine methylase || 1Q0TA 1Q0TB 6prcL 273 -28.91 -5.57 1.43e+01 :273 XRAY 2.30 0.184 0.225 PHOTOSYNTHETIC REACTION CENTER || 1PRCL 2PRCL 3PRCL 4PRCL 5PRCL 7PRCL 1n4xL 113 -25.70 -5.53 1.46e+01 :113 XRAY 1.70 0.227 0.256 immunoglobulin kappa chain variable region || 1N4XM 1iioA 84 -24.30 -5.53 1.47e+01 :84 NMR NA NA NA conserved hypothetical protein MTH865 1g5qA 181 -27.90 -5.51 1.49e+01 :181 XRAY 2.57 0.209 0.226 EPIDERMIN MODIFYING ENZYME EPID || 1G5QD 1G5QG 1G5QL 1yaaA 412 -27.81 -5.31 1.78e+01 :412 XRAY 2.05 0.231 0.299 ASPARTATE AMINOTRANSFERASE || 1YAAB 1YAAC 1YAAD 1nox 205 -26.37 -5.28 1.82e+01 :205 XRAY 1.59 0.190 0.204 NADH OXIDASE 1giqA 413 -29.04 -5.27 1.83e+01 :413 XRAY 1.80 0.224 0.250 IOTA TOXIN COMPONENT IA || 1GIQB 1GIRA 1f1uA 323 -27.44 -5.26 1.85e+01 :323 XRAY 1.50 0.162 0.185 HOMOPROTOCATECHUATE 2,3-DIOXYGENASE || 1F1RA 1F1RB 1F1UB 1F1VA 1F1VB 1lo4L 217 -26.49 -5.23 1.90e+01 :217 XRAY 2.40 0.239 0.308 If kappa light chain 1a0fA 201 -26.44 -5.18 1.99e+01 :201 XRAY 2.10 0.183 0.245 GLUTATHIONE S-TRANSFERASE || 1A0FB 1cl7L 216 -26.53 -5.09 2.14e+01 :216 XRAY 3.00 0.183 0.280 PROTEIN (IGG1 ANTIBODY 1696 (light chain)) 1fzqA 181 -26.69 -5.08 2.16e+01 :181 XRAY 1.70 0.215 0.235 ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 3 1bh9B 89 -24.45 -5.08 2.16e+01 :89 XRAY 2.60 0.205 0.257 TAFII28 || 1BH8B 1blnA 214 -26.16 -4.94 2.45e+01 :214 XRAY 2.80 0.209 0.287 PROTEIN (MONOCLONAL ANTIBODY MRK-16 (LIGHT CHAIN)) || 1BLNC 1acc 735 -29.38 -4.93 2.47e+01 :735 XRAY 2.10 0.223 0.296 ANTHRAX PROTECTIVE ANTIGEN 1jqdA 292 -28.73 -4.85 2.66e+01 :292 XRAY 2.28 0.211 0.257 Histamine N-Methyltransferase || 1JQDB 1hmcA 148 -25.79 -4.81 2.73e+01 :148 XRAY 2.50 0.197 NA HUMAN MACROPHAGE COLONY STIMULATING FACTOR || 1HMCB 1bbg 40 -23.10 -4.79 2.80e+01 :40 NMR NA NA NA POLLEN ALLERGEN 5 || 2BBG0 3BBG0 1div 149 -25.89 -4.77 2.83e+01 :149 XRAY 2.60 0.217 0.276 RIBOSOMAL PROTEIN L9 || 1GIYK 487DK 3cln 148 -25.48 -4.77 2.83e+01 :148 XRAY 2.20 0.175 NA CALMODULIN || 1DMO0 1hgxA 183 -26.31 -4.75 2.89e+01 :183 XRAY 1.90 0.175 0.234 HYPOXANTHINE-GUANINE-XANTHINE PHOSPHORIBOSYLTRANSFERASE || 1HGXB 1fl5A 217 -26.03 -4.72 2.95e+01 :217 XRAY 2.10 0.238 0.268 ANTIBODY GERMLINE PRECURSOR TO ANTIBODY 28B4 || 1FL5L 1FL6A 1FL6L 1jqeA 292 -28.61 -4.72 2.96e+01 :292 XRAY 1.91 0.210 0.235 Histamine N-Methyltransferase || 1JQEB 1gh9A 71 -23.57 -4.70 3.03e+01 :71 NMR NA NA NA 8.3 KDA PROTEIN (GENE MTH1184) 1m4jA 142 -25.14 -4.63 3.21e+01 :142 XRAY 1.60 0.235 0.251 A6 gene product || 1M4JB 1k1dA 460 -28.46 -4.61 3.26e+01 :460 XRAY 3.01 0.263 0.280 D-hydantoinase || 1K1DB 1K1DC 1K1DD 1K1DE 1K1DF 1K1DG 1K1DH 1tetL 216 -26.09 -4.60 3.31e+01 :216 XRAY 2.30 0.148 NA IGG1 TE33 FAB (LIGHT CHAIN) 1pv4A 419 -29.04 -4.57 3.40e+01 :419 XRAY 3.00 0.271 0.296 Transcription termination factor rho || 1PV4B 1PV4C 1PV4D 1PV4E 1PV4F 1PVOA 1PVOB 1PVOC 1PVOD 1PVOE 1PVOF 1jjoC 261 -26.48 -4.55 3.46e+01 :261 XRAY 3.06 0.232 0.308 NEUROSERPIN || 1JJOD 1e5wA 346 -28.69 -4.50 3.59e+01 :346 XRAY 2.70 0.254 0.297 MOESIN 1e4eA 343 -26.73 -4.50 3.61e+01 :343 XRAY 2.50 0.183 0.257 VANCOMYCIN/TEICOPLANIN A-TYPE RESISTANCE PROTEIN V 1ev8A 264 -26.63 -4.46 3.72e+01 :264 XRAY 2.60 0.223 0.264 THYMIDYLATE SYNTHASE 1o1lA 283 -27.35 -4.44 3.81e+01 :283 XRAY 1.80 0.206 0.254 Hemoglobin Alpha chain 1fkw 349 -28.60 -4.42 3.87e+01 :349 XRAY 2.40 0.176 NA ADENOSINE DEAMINASE