%  SAM: /projects/compbio/bin/i686/hmmscore v3.5 (July 15, 2005) compiled 07/18/05_14:54:13
%  (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.YGR023W.t2k-w0.5.mod   Host: farm19.cse.ucsc.edu    Sun Mar 19 10:20:28 2006
%  karplus                          Dir:  /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR023W
% ---------------------------------------------------------------------
% Inserted Files:  YGR023W.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:  YGR023W.t2k-w0.5.mod
% Score DP Method: forward all-paths (dpstyle = 0)
% Align DP Method: viterbi (adpstyle = 1)
% 23081 sequences, 5302281 residues, 552 nodes, 1209.72 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 (10000.00)
% E-value on N (=11000) sequences:
%    N / (1 + exp(-(lambda(=3.0325) * Reverse)^tau(=0.6775)))
%    Calculated when Simple < simple_threshold (10000.00)
%    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
1nphA             329       -18.89       -7.89     2.04e+00	:329 XRAY 3.00 0.247 0.299 Gelsolin <SWS GELS_MOUSE
1p8xA             344       -17.92       -7.05     3.82e+00	:344 XRAY 2.00 0.205 0.245 Gelsolin precursor, plas
1h1vG             331       -17.82       -6.94     4.15e+00	:331 XRAY 2.99 0.219 0.268 GELSOLIN <SWS GELS_HUMAN
1zckA             154       -18.32       -6.82     4.57e+00	:154 XRAY 1.90 0.245 0.257 protein tyrosine phospha
1rxdA             159       -18.29       -6.77     4.75e+00	:159 XRAY 1.90 0.226 0.242 protein tyrosine phospha
1x24A             180       -18.17       -6.61     5.36e+00	:180 XRAY 3.20 0.241 0.285 protein tyrosine phospha
1q55A             880       -19.62       -6.51     5.82e+00	:880 EM NA NA NA EP-cadherin <SWS CADHF_XENLA> [MUS
1vrnL             273       -20.28       -6.50     5.88e+00	:273 XRAY 2.20 0.191 0.212 Reaction center protein 
1dxrL             273       -20.27       -6.49     5.90e+00	:273 XRAY 2.00 0.194 0.218 PHOTOSYNTHETIC REACTION 
2bzlA             325       -17.27       -6.45     6.10e+00	:325 XRAY 1.65 0.186 0.217 TYROSINE-PROTEIN PHOSPHA
1jfjA             134       -17.73       -6.40     6.33e+00	:134 NMR NA NA NA CALCIUM-BINDING PROTEIN <SWS CABP
1xm7A             195       -17.25       -6.39     6.40e+00	:195 XRAY 2.40 0.220 0.267 hypothetical protein aq_
1thm              279       -19.72       -6.31     6.79e+00	:279 XRAY 1.37 0.166 NA THERMITASE <SWS THET_THEVU>
1v3aA             173       -17.19       -6.31     6.81e+00	:173 NMR NA NA NA protein tyrosine phosphatase type
1r6hA             172       -17.15       -6.25     7.12e+00	:172 NMR NA NA NA protein tyrosine phosphatase type
1pujA             282       -17.93       -5.99     8.80e+00	:282 XRAY 2.00 0.216 0.250 conserved hypothetical p
1d03A             169       -18.04       -5.90     9.47e+00	:169 XRAY 1.85 0.149 0.172 FLAVODOXIN <SWS FLAV_SYN
1x1iA             752       -17.23       -5.89     9.56e+00	:752 XRAY 1.80 0.176 0.204 xanthan lyase <GB BAB210
1emn               82       -15.71       -5.79     1.03e+01	:82 NMR NA NA NA FIBRILLIN <SWS FBN1_HUMAN> [HOMO S
2tecE             279       -18.31       -5.66     1.15e+01	:279 XRAY 1.98 0.165 NA THERMITASE <SWS THET_THEVU>
1dqpA             230       -16.85       -5.66     1.15e+01	:230 XRAY 1.75 0.210 0.232 GUANINE PHOSPHORIBOSYLTR
1snyA             267       -16.89       -5.64     1.17e+01	:267 XRAY 1.75 0.247 0.284 sniffer CG10964-PA <GB N
1odfA             290       -17.56       -5.54     1.26e+01	:290 XRAY 2.25 0.206 0.260 HYPOTHETICAL 33.3 KDA PR
2as8A             222       -16.16       -5.50     1.31e+01	:222 XRAY 1.95 0.191 0.252 Major mite fecal allerge
1oboA             169       -17.07       -5.49     1.33e+01	:169 XRAY 1.20 0.186 0.202 FLAVODOXIN <SWS FLAV_ANA
2a2jA             246       -16.52       -5.49     1.33e+01	:246 XRAY 2.50 0.209 0.260 Pyridoxamine 5'-phosphat
1jjvA             206       -16.82       -5.45     1.37e+01	:206 XRAY 2.00 0.168 0.218 DEPHOSPHO-COA KINASE <SW
1dx9A             169       -16.86       -5.45     1.37e+01	:169 XRAY 2.05 0.169 0.225 FLAVODOXIN <SWS FLAV_ANA
1d0nA             729       -16.97       -5.44     1.38e+01	:729 XRAY 2.50 0.212 0.238 HORSE PLASMA GELSOLIN <S
1xuqA             212       -15.64       -5.41     1.42e+01	:212 XRAY 1.80 0.172 0.228 Superoxide dismutase <SW
1czkA             169       -17.46       -5.38     1.45e+01	:169 XRAY 1.90 0.157 0.200 FLAVODOXIN <SWS FLAV_SYN
1t5hX             504       -17.22       -5.37     1.47e+01	:504 XRAY 2.00 0.184 0.206 4-chlorobenzoyl CoA liga
1u32A             293       -16.84       -5.27     1.59e+01	:293 XRAY 2.00 0.220 0.254 Serine/threonine protein
1xkgA             312       -15.90       -5.26     1.60e+01	:312 XRAY 1.61 0.154 0.186 Major mite fecal allerge
1qheA             168       -16.85       -5.25     1.61e+01	:168 XRAY 2.00 0.181 0.257 FLAVODOXIN <SWS FLAV_ANA
1rcf              169       -16.84       -5.24     1.64e+01	:169 XRAY 1.40 0.139 NA FLAVODOXIN <SWS FLAV_ANASP>
1cznA             169       -17.45       -5.22     1.65e+01	:169 XRAY 1.70 0.181 0.210 FLAVODOXIN <SWS FLAV_SYN
1t0qB             330       -16.41       -5.19     1.70e+01	:330 XRAY 2.15 0.199 0.225 toluene, o-xylene monoox
1obvA             169       -16.69       -5.16     1.75e+01	:169 XRAY 2.10 0.180 0.242 FLAVODOXIN <SWS FLAV_ANA
1jk7A             323       -16.64       -5.10     1.83e+01	:323 XRAY 1.90 0.199 0.225 SERINE/THREONINE PROTEIN
1f28A             297       -16.00       -5.05     1.91e+01	:297 XRAY 1.90 0.217 0.247 THYMIDYLATE SYNTHASE <SW
1s4eA             352       -16.32       -4.83     2.31e+01	:352 XRAY 2.90 0.232 0.270 Galactokinase <SWS GAL1_
1v59A             478       -16.55       -4.81     2.35e+01	:478 XRAY 2.20 0.203 0.246 Dihydrolipoamide dehydro
1czrA             169       -17.37       -4.77     2.44e+01	:169 XRAY 1.90 0.154 0.193 FLAVODOXIN <SWS FLAV_SYN
1lrzA             426       -17.47       -4.68     2.63e+01	:426 XRAY 2.10 0.183 0.212 factor essential for exp
2corA              79       -14.82       -4.66     2.68e+01	:79 NMR NA NA NA PINCH protein <SWS PINC_HUMAN> [HO
2a5gA             175       -15.61       -4.62     2.77e+01	:175 XRAY 2.66 0.202 0.265 ADP-ribosylation factor 
1vlcA             366       -15.49       -4.58     2.88e+01	:366 XRAY 1.90 0.189 0.218 3-isopropylmalate dehydr
1e0sA             174       -15.34       -4.56     2.92e+01	:174 XRAY 2.28 0.172 0.234 ADP-RIBOSYLATION FACTOR 
2a5dA             175       -15.34       -4.56     2.93e+01	:175 XRAY 1.80 0.169 0.199 ADP-ribosylation factor 
1c9mA             269       -16.12       -4.55     2.95e+01	:269 XRAY 1.67 0.168 NA SERINE PROTEASE <SWS SUBS_B
1hfvA             174       -15.37       -4.54     2.97e+01	:174 XRAY 2.80 0.234 0.276 ADP-RIBOSYLATION FACTOR 
1m14A             333       -16.81       -4.53     2.99e+01	:333 XRAY 2.60 0.240 0.286 Epidermal growth factor 
1xkkA             352       -16.76       -4.47     3.16e+01	:352 XRAY 2.40 0.209 0.255 Epidermal growth factor 
1fjmA             330       -15.94       -4.47     3.17e+01	:330 XRAY 2.10 0.178 NA PROTEIN SERINE/THREONINE PH
1tolA             222       -14.86       -4.43     3.29e+01	:222 XRAY 1.85 0.230 0.293 FUSION PROTEIN CONSISTIN
2fcr              173       -17.14       -4.39     3.40e+01	:173 XRAY 1.80 0.188 NA FLAVODOXIN <SWS FLAV_CHOCR>
1gmiA             136       -14.47       -4.32     3.63e+01	:136 XRAY 1.70 0.234 0.262 PROTEIN KINASE C, EPSILO
1qkzH             219       -16.72       -4.32     3.63e+01	:219 XRAY 1.95 0.209 0.262 ANTIBODY <NA NA> [MUS MU
1q40B             219       -15.29       -4.29     3.72e+01	:219 XRAY 1.95 0.178 0.219 mRNA export factor MEX67
1s70A             330       -16.17       -4.27     3.79e+01	:330 XRAY 2.70 0.223 0.293 Serine/threonine protein
1xn6A             143       -14.70       -4.25     3.84e+01	:143 NMR NA NA NA hypothetical protein BC4709 <GB N
1r8oB              71       -14.25       -4.23     3.92e+01	:71 XRAY 1.83 0.170 0.212 Kunitz trypsin inhibitor