%  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.YGR035W-A.t2k-w0.5.mod   Host: farm09.cse.ucsc.edu    Sun Feb 12 21:46:17 2006
%  karplus                            Dir:  /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR035W-A
% ---------------------------------------------------------------------
% Inserted Files:  YGR035W-A.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:  YGR035W-A.t2k-w0.5.mod
% Score DP Method: forward all-paths (dpstyle = 0)
% Align DP Method: viterbi (adpstyle = 1)
% 22744 sequences, 5224462 residues, 74 nodes, 166.93 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(=3.5195) * Reverse)^tau(=0.7270)))
%    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
1p47A              87       -15.40       -8.28     1.01e-01	:87 XRAY 2.20 0.219 0.267 Early growth response pro
1zaaC              87       -15.39       -8.26     1.02e-01	:87 XRAY 2.10 0.182 NA ZIF268 <SWS EGR1_MOUSE> [MUS
1aayA              90       -15.38       -8.26     1.03e-01	:90 XRAY 1.60 0.203 0.242 ZIF268 ZINC FINGER PEPTID
1jk2A              90       -15.37       -8.24     1.05e-01	:90 XRAY 1.65 0.230 0.273 ZIF268 <SWS EGR1_MOUSE> [
1a1iA              90       -15.36       -8.21     1.08e-01	:90 XRAY 1.60 0.191 0.216 RADR ZIF268 ZINC FINGER P
1a1hA              90       -15.36       -8.17     1.12e-01	:90 XRAY 1.60 0.235 0.277 QGSR ZINC FINGER PEPTIDE 
1a1gA              90       -15.36       -8.16     1.13e-01	:90 XRAY 1.90 0.215 0.275 DSNR ZINC FINGER PEPTIDE 
1f2iG              73       -14.52       -7.30     2.78e-01	:73 XRAY 2.35 0.250 0.256 FUSION OF N-TERMINAL 17-M
1g2dC              90       -14.30       -6.93     4.08e-01	:90 XRAY 2.20 0.225 0.262 TATA BOX ZINC FINGER PROT
1g2fC              90       -14.20       -6.91     4.21e-01	:90 XRAY 2.00 0.233 0.263 TATA BOX ZINC FINGER PROT
1llmC              88       -13.16       -6.18     9.29e-01	:88 XRAY 1.50 0.226 0.234 chimera of Zif23-GCN4 <SW
1x63A              82       -13.77       -5.48     2.04e+00	:82 NMR NA NA NA Skeletal muscle LIM-protein 1 <SWS
1x3hA              80       -14.42       -5.43     2.15e+00	:80 NMR NA NA NA Leupaxin <SWS LPXN_HUMAN> [HOMO SA
1jnrB             150       -13.83       -5.37     2.31e+00	:150 XRAY 1.60 0.180 0.202 adenylylsulfate reductas
1jfuA             186       -12.08       -4.99     3.56e+00	:186 XRAY 1.60 0.181 0.234 THIOL:DISULFIDE INTERCHA
1xxsA             122       -13.22       -4.83     4.32e+00	:122 XRAY 1.80 0.170 0.247 Phospholipase A2 homolog
1hzdA             272       -12.49       -4.73     4.88e+00	:272 XRAY 2.20 0.212 0.253 AU-BINDING PROTEIN/ENOYL
1k8iA             191       -12.73       -4.69     5.09e+00	:191 XRAY 3.10 0.205 0.256 MHC class II H2-M alpha 
1tfi               50       -11.93       -4.64     5.42e+00	:50 NMR NA NA NA TRANSCRIPTIONAL ELONGATION FACTOR 
1xf7A              29       -11.26       -4.60     5.65e+00	:29 NMR NA NA NA Wilms' Tumor Protein <SWS WT1_HUMA
1dbnA             239       -12.69       -4.55     6.05e+00	:239 XRAY 2.75 0.224 0.253 LEUKOAGGLUTININ <PIR JC5
1zcjA             463       -12.39       -4.51     6.30e+00	:463 XRAY 1.90 0.171 0.221 Peroxisomal bifunctional
1pa0A             121       -13.37       -4.44     6.88e+00	:121 XRAY 2.20 0.208 0.266 Myotoxic phospholipase A
1pc9A             121       -13.37       -4.43     6.97e+00	:121 XRAY 2.50 0.186 0.255 BnSP-6 <SWS PA2H_BOTNE> 
1tzpA             255       -12.06       -4.37     7.53e+00	:255 XRAY 1.40 0.184 0.206 Penicillin-insensitive m
1yk3A             210       -11.75       -4.36     7.53e+00	:210 XRAY 2.20 0.229 0.258 Hypothetical protein Rv1
2bs3B             239       -12.21       -4.13     1.00e+01	:239 XRAY 2.19 0.183 0.198 QUINOL-FUMARATE REDUCTAS
1uyjA             296       -11.84       -4.10     1.05e+01	:296 XRAY 2.60 0.239 0.290 EPSILON-TOXIN <UNP Q5739
1udh              244       -12.04       -4.08     1.07e+01	:244 XRAY 1.75 0.191 0.237 URACIL-DNA GLYCOSYLASE <
2c53A             244       -12.00       -4.05     1.11e+01	:244 XRAY 1.80 0.164 0.216 URACIL DNA GLYCOSYLASE <
2ashA             381       -11.91       -3.96     1.23e+01	:381 XRAY 1.90 0.195 0.229 Queuine tRNA-ribosyltran
1sorA             235       -11.70       -3.95     1.25e+01	:235 ELEC 3.00 0.307 0.338 Aquaporin-0 <SWS MIP_SHE
1iznA             286       -11.73       -3.93     1.28e+01	:286 XRAY 2.10 0.222 0.262 CapZ alpha-1 subunit <SW
1pbyC              79       -11.84       -3.88     1.36e+01	:79 XRAY 1.70 0.191 0.224 quinohemoprotein amine de
1iru2             219       -11.25       -3.82     1.48e+01	:219 XRAY 2.75 0.252 0.294 20S proteasome <SWS PSB3
1q20A             299       -11.62       -3.78     1.54e+01	:299 XRAY 2.30 0.212 0.225 sulfotransferase family,
1wf9A             107       -11.14       -3.77     1.58e+01	:107 NMR NA NA NA NPL4 family protein <GB NP_191859
2cszA              76       -12.25       -3.76     1.60e+01	:76 NMR NA NA NA Synaptotagmin-like protein 4 <SWS 
1a0hA             159       -11.42       -3.68     1.76e+01	:159 XRAY 3.20 0.205 0.242 MEIZOTHROMBIN <SWS THRB_
1ymgA             263       -11.59       -3.68     1.77e+01	:263 XRAY 2.24 0.246 0.303 Lens fiber major intrins
1nypA              66       -11.15       -3.67     1.78e+01	:66 NMR NA NA NA PINCH protein <SWS PINC_HUMAN> [HO
2b6oA             263       -11.60       -3.60     1.94e+01	:263 ELEC 1.90 0.258 0.299 Lens fiber major intrins
1x64A              89       -11.23       -3.59     1.96e+01	:89 NMR NA NA NA Alpha-actinin-2 associated LIM pro
1y4lA             121       -11.86       -3.58     2.01e+01	:121 XRAY 1.70 0.227 0.240 Phospholipase A2 homolog
1x4lA              72       -12.91       -3.56     2.04e+01	:72 NMR NA NA NA Skeletal muscle LIM-protein 3 <SWS
1yroA             123       -11.29       -3.55     2.09e+01	:123 XRAY 1.90 0.189 0.225 ALPHA-LACTALBUMIN <SWS L
2b25A             336       -11.37       -3.54     2.10e+01	:336 XRAY 2.50 0.248 0.282 hypothetical protein <GB
1h2oA             159       -11.37       -3.49     2.25e+01	:159 NMR NA NA NA MAJOR ALLERGEN PRU AV 1 <SWS PRU1
1xy7A             166       -10.62       -3.47     2.29e+01	:166 XRAY 1.80 0.184 0.228 unknown protein <GB AAM9
1zfuA              40       -11.00       -3.47     2.29e+01	:40 NMR NA NA NA Plectasin <GB 62750870> [PSEUDOPLE
2bxwA             141       -10.81       -3.46     2.34e+01	:141 XRAY 2.40 0.180 0.222 RHO GDP-DISSOCIATION INH
1s8iA             121       -12.74       -3.42     2.45e+01	:121 XRAY 1.61 0.187 0.205 Phospholipase A2 homolog
1e09A             159       -11.37       -3.42     2.46e+01	:159 NMR NA NA NA PRU AV 1 <SWS O24248> [PRUNUS AVI
1ppa              121       -12.74       -3.41     2.48e+01	:121 XRAY 2.00 0.157 NA PHOSPHOLIPASE A2 <SWS PA2H_
1ryuA             120       -10.49       -3.41     2.49e+01	:120 NMR NA NA NA SWI/SNF-related, matrix-associate
1gl8A             104       -11.42       -3.41     2.49e+01	:104 NMR NA NA NA THIOREDOXIN <SWS THIM_SPIOL> [SPI
1fb6A             105       -11.42       -3.40     2.51e+01	:105 XRAY 2.10 0.204 0.230 THIOREDOXIN M <SWS THIM_
1fsoA             139       -10.68       -3.39     2.57e+01	:139 XRAY 2.00 0.218 0.232 RHO GDP-DISSOCIATION INH
1kmtA             141       -10.67       -3.35     2.69e+01	:141 XRAY 1.30 0.160 0.195 Rho GDP-dissociation inh
1ft3A             139       -10.66       -3.33     2.75e+01	:139 XRAY 2.80 0.216 0.260 RHO GDP-DISSOCIATION INH
1t0lA             414       -10.90       -3.32     2.80e+01	:414 XRAY 2.41 0.214 0.253 Isocitrate dehydrogenase
1ft0A             139       -10.67       -3.32     2.82e+01	:139 XRAY 2.60 0.226 0.260 RHO GDP-DISSOCIATION INH
1tc5A             194       -11.43       -3.30     2.86e+01	:194 XRAY 1.93 0.201 0.234 Probable eukaryotic D-am
1jmxG              79       -11.21       -3.29     2.91e+01	:79 XRAY 1.90 0.209 0.267 Amine Dehydrogenase <SWS 
1qvyA             139       -10.67       -3.29     2.91e+01	:139 XRAY 1.60 0.173 0.210 Rho GDP-dissociation inh
2aw4Z              70       -11.40       -3.28     2.93e+01	:70 XRAY 3.46 0.279 0.331 50S ribosomal protein L31
1hcd              118       -10.97       -3.28     2.96e+01	:118 NMR NA NA NA HISACTOPHILIN <SWS HIA1_DICDI> [D
1k1gA             131       -11.44       -3.26     3.03e+01	:131 NMR NA NA NA SF1-Bo isoform <GB CAA70019> [HOM
1cqa              133       -10.80       -3.25     3.05e+01	:133 XRAY 2.40 0.178 NA PROFILIN <SWS PROF_BETVE> [
1rhoA             145       -10.63       -3.24     3.10e+01	:145 XRAY 2.50 0.225 0.298 RHO GDP-DISSOCIATION INH
2aw2A             120       -11.23       -3.19     3.33e+01	:120 XRAY 2.80 0.236 0.278 B and T lymphocyte atten
1w0fA             485       -10.97       -3.18     3.37e+01	:485 XRAY 2.65 0.239 0.303 CYTOCHROME P450 3A4 <UNP
1tqnA             486       -10.96       -3.18     3.37e+01	:486 XRAY 2.05 0.241 0.293 cytochrome P450 3A4 <GB 
1nmlA             326       -11.00       -3.18     3.37e+01	:326 XRAY 2.20 0.179 0.199 di-haem cytochrome c per
2cxhA             217       -10.99       -3.14     3.55e+01	:217 XRAY 1.80 0.184 0.209 Probable brix-domain rib
1h1jS              51       -10.02       -3.14     3.56e+01	:51 NMR NA NA NA THO1 PROTEIN <SWS THO1_YEAST> [SAC
1rkuA             206       -10.52       -3.14     3.56e+01	:206 XRAY 1.47 0.191 0.221 homoserine kinase <GB NP
2bl5A             140       -10.52       -3.13     3.57e+01	:140 NMR NA NA NA MGC83862 PROTEIN <PDB 2BL5> [XENO
1ytvM              84       -10.75       -3.13     3.58e+01	:84 XRAY 1.80 0.196 0.225 Vasopressin V1a receptor 
1hn6A             110       -11.51       -3.13     3.61e+01	:110 NMR NA NA NA APICAL MEMBRANE ANTIGEN 1 <SWS Q9
1q1qA             350       -11.46       -3.13     3.61e+01	:350 XRAY 2.91 0.250 0.269 sulfotransferase family,
1nciA             110       -10.43       -3.12     3.64e+01	:110 XRAY 2.10 0.195 0.253 N-CADHERIN <SWS CAD2_MOU
1mm2A              61       -13.07       -3.10     3.71e+01	:61 NMR NA NA NA Mi2-beta <SWS CHD4_HUMAN> [HOMO SA
1jltA             122       -11.03       -3.10     3.74e+01	:122 XRAY 1.40 0.182 0.195 PHOSPHOLIPASE A2 INHIBIT
2bsdA             264       -11.15       -3.10     3.76e+01	:264 XRAY 2.30 0.221 0.252 RECEPTOR BINDING PROTEIN
1exsA             160       -10.27       -3.08     3.81e+01	:160 XRAY 2.39 0.219 0.282 BETA-LACTOGLOBULIN <SWS 
1taq              832       -11.24       -3.08     3.83e+01	:832 XRAY 2.40 0.202 0.323 TAQ DNA POLYMERASE <SWS 
1qllA             121       -12.01       -3.07     3.87e+01	:121 XRAY 2.04 0.176 0.268 PHOSPHOLIPASE A2 <SWS PA
5rxn               54       -11.33       -3.06     3.94e+01	:54 XRAY 1.20 0.115 NA RUBREDOXIN <SWS RUBR_CLOPA> 
1yc61             154       -10.38       -3.05     3.97e+01	:154 XRAY 2.90 0.234 0.239 Coat protein <SWS COAT_B