%  SAM: /projects/compbio/bin/i686/hmmscore v3.5 (May 1, 2004) compiled 08/09/04_15:52:12
%  (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.YGR034W.t2k-w0.5.mod   Host: farm20    Wed Nov 17 18:44:01 2004
%  karplus                          Dir:  /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR034W
% ---------------------------------------------------------------------
% Inserted Files:  YGR034W.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:  YGR034W.t2k-w0.5.mod
% Score DP Method: forward all-paths (dpstyle = 0)
% Align DP Method: viterbi (adpstyle = 1)
% 17959 sequences, 4153001 residues, 130 nodes, 177.49 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 (=10700) sequences:
%    N / (1 + exp(-(lambda(=3.1115) * Reverse)^tau(=0.6952)))
%    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
1s1iU             126      -106.05      -96.83     1.14e-19	:126 EM NA NA NA 60S ribosomal protein L26-A <SWS R
1s72T             120       -89.90      -79.91     8.49e-17	:120 XRAY 2.40 0.188 0.222 50S ribosomal protein L2
1jj2S             119       -89.38      -79.38     1.05e-16	:119 XRAY 2.40 0.189 0.222 RIBOSOMAL PROTEIN L24 <S
1p85S             103       -67.03      -54.73     3.79e-12	:103 EM NA NA NA 50S ribosomal protein L24 <SWS RL2
1nkwS             115       -63.45      -52.88     8.78e-12	:115 XRAY 3.10 0.240 0.274 50S ribosomal protein L2
1pnuS             113       -63.39      -52.83     8.99e-12	:113 XRAY 8.70 0.394 0.415 50S ribosomal protein L2
1nz9A              58       -26.37      -17.12     1.39e-03	:58 NMR NA NA NA TRANSCRIPTION ANTITERMINATION PROT
1m1hA             248       -20.41       -9.85     2.19e-01	:248 XRAY 1.95 0.234 0.259 Transcription antitermin
1uezA             101       -16.77       -7.99     9.44e-01	:101 NMR NA NA NA KIAA1526 Protein <GB BAA96050> [H
1sxjA             511       -16.70       -7.74     1.16e+00	:511 XRAY 2.85 0.251 0.306 Activator 1 95 kDa subun
1jj2R              84       -15.29       -7.41     1.52e+00	:84 XRAY 2.40 0.189 0.222 RIBOSOMAL PROTEIN L23 <SW
1s72S              85       -15.28       -7.39     1.54e+00	:85 XRAY 2.40 0.188 0.222 50S ribosomal protein L23
1s4vA             229       -15.76       -7.38     1.56e+00	:229 XRAY 2.00 0.181 0.226 cysteine endopeptidase <
1fl2A             310       -16.12       -6.93     2.27e+00	:310 XRAY 1.90 0.197 0.217 ALKYL HYDROPEROXIDE REDU
1a4yA             460       -15.33       -6.89     2.35e+00	:460 XRAY 2.00 0.193 0.286 RIBONUCLEASE INHIBITOR <
1hyuA             521       -15.57       -6.36     3.72e+00	:521 XRAY 2.00 0.199 0.235 ALKYL HYDROPEROXIDE REDU
1nykA             165       -15.29       -6.20     4.25e+00	:165 XRAY 1.31 0.159 0.212 Rieske iron-sulfur prote
1n8nA             212       -14.40       -5.96     5.26e+00	:212 XRAY 1.69 0.179 0.207 Class B acid phosphatase
1trjA             314       -14.19       -5.47     8.19e+00	:314 EM 11.70 NA NA Guanine nucleotide-binding prot
1eysH             259       -14.51       -5.38     8.93e+00	:259 XRAY 2.20 0.234 0.287 PHOTOSYNTHETIC REACTION 
1vib               55       -13.29       -5.16     1.09e+01	:55 NMR NA NA NA NEUROTOXIN B-IV <SWS NXB4_CERLA> [
1e32A             458       -14.52       -5.11     1.14e+01	:458 XRAY 2.90 0.224 0.283 P97 <SWS TERA_MOUSE> [MU
1uoeA             366       -13.63       -4.99     1.27e+01	:366 XRAY 2.00 0.179 0.231 DIHYDROXYACETONE KINASE 
1gowA             489       -13.83       -4.94     1.34e+01	:489 XRAY 2.60 0.219 0.259 BETA-GLYCOSIDASE <SWS BG
1mjfA             281       -14.48       -4.91     1.37e+01	:281 XRAY 1.80 0.207 0.242 spermidine synthase <GB 
1ilr1             152       -13.41       -4.86     1.44e+01	:152 XRAY 2.10 0.197 NA INTERLEUKIN-1 RECEPTOR ANTA
1irp              153       -13.41       -4.86     1.44e+01	:153 NMR NA NA NA INTERLEUKIN-1 RECEPTOR ANTAGONIST
1oi2A             366       -13.63       -4.84     1.47e+01	:366 XRAY 1.75 0.172 0.201 HYPOTHETICAL PROTEIN YCG
1uwsA             489       -13.62       -4.73     1.63e+01	:489 XRAY 1.95 0.193 0.229 BETA-GALACTOSIDASE <UNP 
1g1pA              33       -12.30       -4.65     1.77e+01	:33 NMR NA NA NA CONOTOXIN EVIA <SWS CXDA_CONER> [N
2dynA             122       -13.05       -4.60     1.84e+01	:122 XRAY 2.30 0.214 0.296 DYNAMIN <SWS DYN1_HUMAN>
1dynA             125       -13.01       -4.57     1.89e+01	:125 XRAY 2.20 0.200 0.320 DYNAMIN <SWS DYN1_HUMAN>
1m2tA             254       -12.99       -4.50     2.04e+01	:254 XRAY 1.89 0.210 0.240 mistletoe lectin I A cha
1on2A             142       -13.62       -4.42     2.19e+01	:142 XRAY 1.61 0.220 0.258 Transcriptional regulato
1eg0J             171       -14.24       -4.41     2.22e+01	:171 EM 11.50 NA NA RIBOSOMAL PROTEIN L6 <SWS RL6_B
1oz4A             806       -13.98       -4.40     2.23e+01	:806 XRAY 4.70 0.289 0.307 Transitional endoplasmic
1r7rA             816       -13.97       -4.40     2.24e+01	:816 XRAY 3.60 0.327 0.358 Transitional endoplasmic
1qs0B             338       -14.13       -4.39     2.27e+01	:338 XRAY 2.40 0.218 0.265 2-OXOISOVALERATE DEHYDRO
1u5vA             273       -12.40       -4.36     2.32e+01	:273 XRAY 1.85 0.212 0.234 citE <GB NP_217014> [MYC
1u5hA             273       -12.40       -4.36     2.32e+01	:273 XRAY 1.65 0.268 0.272 citE <GB NP_217014> [MYC
1q5vA             133       -13.40       -4.32     2.43e+01	:133 XRAY 2.30 0.253 0.305 Nickel responsive regula
1vecA             206       -13.20       -4.24     2.61e+01	:206 XRAY 2.01 0.198 0.251 ATP-dependent RNA helica
1nhp              447       -13.66       -4.23     2.64e+01	:447 XRAY 2.00 0.176 NA NADH PEROXIDASE <SWS NAPE_E
1nhq              447       -13.66       -4.23     2.64e+01	:447 XRAY 2.00 0.183 NA NADH PEROXIDASE <SWS NAPE_E
1npx              447       -13.66       -4.22     2.66e+01	:447 XRAY 2.16 0.177 NA NADH PEROXIDASE <SWS NAPE_E
1gs5A             258       -13.12       -4.22     2.67e+01	:258 XRAY 1.50 0.209 0.213 ACETYLGLUTAMATE KINASE <
1f8wA             447       -13.66       -4.22     2.68e+01	:447 XRAY 2.45 0.281 0.234 NADH PEROXIDASE <SWS NAP
1nhr              447       -13.66       -4.21     2.69e+01	:447 XRAY 2.10 0.170 NA NADH PEROXIDASE <SWS NAPE_E
1nhs              447       -13.66       -4.21     2.69e+01	:447 XRAY 2.00 0.174 NA NADH PEROXIDASE <SWS NAPE_E
1mmq              170       -13.02       -4.21     2.70e+01	:170 XRAY 1.90 0.179 NA MATRILYSIN <SWS MM07_HUMAN>
1stzA             338       -13.14       -4.19     2.75e+01	:338 XRAY 2.20 0.217 0.258 Heat-inducible transcrip
1frvA             264       -13.21       -4.15     2.87e+01	:264 XRAY 2.85 0.178 NA HYDROGENASE <SWS PHNS_DESGI
487dJ             164       -13.86       -4.14     2.90e+01	:164 EM 7.50 NA NA 50S L6 RIBOSOMAL PROTEIN <SWS RL
1sgzA             389       -13.00       -4.11     2.97e+01	:389 XRAY 2.00 0.196 0.228 Beta-secretase <SWS BACE
1s1iQ             100       -12.60       -4.07     3.10e+01	:100 EM NA NA NA 60S ribosomal protein L21-A <SWS R
1oz7A             131       -12.93       -4.06     3.12e+01	:131 XRAY 2.40 0.188 0.244 echicetin A-chain <GB AA
1fknA             391       -12.99       -4.06     3.13e+01	:391 XRAY 1.90 0.180 0.224 MEMAPSIN 2 <GB AAF13715>
1dzfA             215       -12.49       -4.06     3.14e+01	:215 XRAY 1.90 0.217 0.271 DNA-DIRECTED RNA POLYMER
1ge9A             184       -12.48       -4.05     3.17e+01	:184 NMR NA NA NA RIBOSOME RECYCLING FACTOR <SWS RR
1jehA             478       -13.42       -4.03     3.22e+01	:478 XRAY 2.40 0.202 0.260 DIHYDROLIPOAMIDE DEHYDRO
1vmeA             410       -13.61       -4.02     3.24e+01	:410 XRAY 1.80 0.149 0.181 Flavoprotein <GB NP_2285
1ksiA             642       -14.29       -4.00     3.33e+01	:642 XRAY 2.20 0.181 NA COPPER AMINE OXIDASE <SWS A
1iweA             457       -14.86       -3.99     3.37e+01	:457 XRAY 2.10 0.202 0.253 Adenylosuccinate Synthet
1f5qB             252       -12.52       -3.97     3.42e+01	:252 XRAY 2.50 0.234 0.278 GAMMA HERPESVIRUS CYCLIN
1vlbA             907       -13.53       -3.97     3.44e+01	:907 XRAY 1.28 0.148 0.193 ALDEHYDE OXIDOREDUCTASE 
1cs8A             316       -12.71       -3.96     3.48e+01	:316 XRAY 1.80 0.207 0.229 HUMAN PROCATHEPSIN L <SW
1bwzA             274       -13.14       -3.90     3.68e+01	:274 XRAY 2.72 0.190 0.242 DIAMINOPIMELATE EPIMERAS
1vl6A             388       -12.62       -3.90     3.69e+01	:388 XRAY 2.61 0.194 0.239 malate oxidoreductase <G
1hdkA             141       -12.99       -3.88     3.74e+01	:141 XRAY 1.80 0.199 0.221 EOSINOPHIL LYSOPHOSPHOLI
1um8A             376       -12.69       -3.88     3.76e+01	:376 XRAY 2.60 0.219 0.258 ATP-dependent Clp protea
1lcl              142       -12.98       -3.88     3.76e+01	:142 XRAY 1.80 0.200 0.258 LYSOPHOSPHOLIPASE <SWS L
1k23A             309       -12.61       -3.87     3.77e+01	:309 XRAY 3.00 0.260 0.293 Manganese-dependent inor
1w50A             411       -12.94       -3.85     3.88e+01	:411 XRAY 1.75 0.245 0.283 BETA-SECRETASE 1 <UNP BA