%  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.YGR009C.t2k-w0.5.mod   Host: farm20    Wed Nov 17 16:17:49 2004
%  karplus                          Dir:  /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR009C
% ---------------------------------------------------------------------
% Inserted Files:  YGR009C.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:  YGR009C.t2k-w0.5.mod
% Score DP Method: forward all-paths (dpstyle = 0)
% Align DP Method: viterbi (adpstyle = 1)
% 17959 sequences, 4153001 residues, 652 nodes, 891.05 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(=1.4008) * Reverse)^tau(=0.8426)))
%    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
1l4aC              83       -97.33      -84.35     6.53e-21	:83 XRAY 2.95 0.300 0.344 S-SNAP25 fusion protein <
1sfcD              87       -95.28      -81.42     3.35e-20	:87 XRAY 2.40 0.265 0.303 SNAP-25B <SWS SN25_HUMAN>
1jthA              82       -93.32      -81.18     3.84e-20	:82 XRAY 2.00 0.266 0.289 SNAP25 <SWS ST1A_RAT> [RA
1l4aD              87       -92.59      -81.13     3.95e-20	:87 XRAY 2.95 0.300 0.344 S-SNAP25 fusion protein <
1sfcC              83       -88.05      -76.08     6.77e-19	:83 XRAY 2.40 0.265 0.303 SNAP-25B <SWS SN25_HUMAN>
1urqC              80       -87.82      -75.84     7.75e-19	:80 XRAY 2.00 0.166 0.225 SYNAPTOSOMAL-ASSOCIATED P
1n7sC              79       -87.79      -75.83     7.81e-19	:79 XRAY 1.45 0.201 0.224 SNAP-25A <gb BAA20151> [R
1kilC              74       -86.17      -74.51     1.65e-18	:74 XRAY 2.30 0.287 0.305 SNAP-25 N-terminal SNARE 
1kilD              66       -81.06      -67.04     1.19e-16	:66 XRAY 2.30 0.287 0.305 SNAP-25 C-terminal SNARE 
1n7sD              66       -81.06      -67.03     1.19e-16	:66 XRAY 1.45 0.201 0.224 SNAP-25A <gb BAA20151> [R
1urqD              69       -80.10      -66.09     2.06e-16	:69 XRAY 2.00 0.166 0.225 SYNAPTOSOMAL-ASSOCIATED P
1nhlA              54       -67.98      -56.31     6.35e-14	:54 XRAY 2.30 0.281 0.316 Synaptosomal-associated p
1gl2D              65       -55.51      -43.04     1.97e-10	:65 XRAY 1.90 0.176 0.224 SYNTAXIN 8 <NA NA> [RATTU
1gl2C              65       -50.34      -40.13     1.20e-09	:65 XRAY 1.90 0.176 0.224 VESICLE TRANSPORT V-SNARE
1lvfA             110       -30.99      -17.99     2.77e-03	:110 XRAY 2.10 0.269 0.269 syntaxin 6 <SWS STX6_RAT
1jthB              77       -26.56      -15.23     2.03e-02	:77 XRAY 2.00 0.266 0.289 syntaxin 1a <SWS SN25_RAT
1hvvA              75       -26.60      -15.22     2.04e-02	:75 XRAY 2.40 0.238 0.273 SYNTAXIN 1A <SWS ST1A_RAT
1n7sB              68       -26.69      -15.22     2.04e-02	:68 XRAY 1.45 0.201 0.224 Syntaxin 1A <sws ST1A_RAT
1kilB              62       -26.53      -15.07     2.28e-02	:62 XRAY 2.30 0.287 0.305 Syntaxin SNARE motif shor
1urqB              75       -26.64      -14.85     2.66e-02	:75 XRAY 2.00 0.166 0.225 SYNTAXIN 1A <SWS SN25_HUM
1l4aB              88       -27.64      -13.68     6.32e-02	:88 XRAY 2.95 0.300 0.344 S-SYNTAXIN <GB CAA74913> 
1sfcB              83       -26.61      -13.67     6.39e-02	:83 XRAY 2.40 0.265 0.303 SYNTAXIN 1A <SWS SYNA_RAT
1s4nA             348       -27.95      -12.80     1.21e-01	:348 XRAY 2.01 0.180 0.232 Glycolipid 2-alpha-manno
1dn1B             267       -26.15      -12.06     2.12e-01	:267 XRAY 2.60 0.239 0.294 SYNTAXIN 1A <SWS STXA_RA
1gl2B              65       -23.45      -11.76     2.67e-01	:65 XRAY 1.90 0.176 0.224 SYNTAXIN 7 <SWS VTL1_MOUS
5csmA             256       -23.83       -9.33     1.75e+00	:256 XRAY 2.00 0.186 0.236 CHORISMATE MUTASE <SWS C
3csmA             256       -23.63       -9.27     1.83e+00	:256 XRAY 3.00 0.204 0.247 CHORISMATE MUTASE <SWS C
1sbzA             197       -20.76       -8.92     2.40e+00	:197 XRAY 2.00 0.180 0.216 Probable aromatic acid d
1rurL             217       -20.10       -8.69     2.89e+00	:217 XRAY 1.50 0.191 0.238 immunoglobulin 13G5, lig
2csmA             256       -23.07       -8.66     2.97e+00	:256 XRAY 2.80 0.213 0.321 CHORISMATE MUTASE <SWS C
1j3vA             289       -20.66       -8.35     3.81e+00	:289 XRAY 1.80 0.182 0.200 Dehydrogenase <NA NA> [T
1uypA             432       -22.00       -8.02     4.94e+00	:432 XRAY 1.90 0.179 0.220 BETA-FRUCTOSIDASE <UNP B
1m6yA             301       -21.52       -8.02     4.97e+00	:301 XRAY 1.90 0.197 0.212 S-adenosyl-methyltransfe
1s58A             554       -21.16       -8.02     4.97e+00	:554 XRAY 3.50 0.313 0.316 B19 parvovirus capsid <N
1csmA             256       -23.09       -8.02     4.97e+00	:256 XRAY 2.20 0.196 0.310 CHORISMATE MUTASE <SWS C
1qe0A             420       -22.08       -7.98     5.10e+00	:420 XRAY 2.70 0.192 0.270 HISTIDYL-TRNA SYNTHETASE
1o5kA             306       -21.87       -7.87     5.60e+00	:306 XRAY 1.80 0.142 0.186 Dihydrodipicolinate synt
1jeyB             565       -24.64       -7.79     5.98e+00	:565 XRAY 2.50 0.220 0.280 Ku80 <SWS KU86_HUMAN> [H
1qyrA             252       -20.73       -7.70     6.40e+00	:252 XRAY 2.10 0.194 0.238 High level Kasugamycin r
1izlB             472       -25.36       -7.53     7.38e+00	:472 XRAY 3.70 0.530 NA Photosystem II: Subunit Psb
1fcqA             350       -20.89       -7.43     7.97e+00	:350 XRAY 1.60 0.192 0.227 HYALURONOGLUCOSAMINIDASE
1q47A             495       -21.70       -7.40     8.18e+00	:495 XRAY 2.80 0.249 0.294 Semaphorin 3A <SWS SM3A_
1n6aA             259       -20.13       -7.40     8.20e+00	:259 XRAY 1.70 0.221 0.217 SET domain-containing pr
1cjxA             357       -21.67       -7.39     8.29e+00	:357 XRAY 2.40 0.219 0.276 4-HYDROXYPHENYLPYRUVATE 
1k92A             455       -21.02       -7.25     9.22e+00	:455 XRAY 1.60 0.163 0.188 ARGININOSUCCINATE SYNTHA
1ls5A             328       -22.43       -7.20     9.62e+00	:328 XRAY 2.80 0.220 0.290 plasmepsin IV <NA NA> [P
1hxs2             272       -20.13       -7.17     9.85e+00	:272 XRAY 2.20 0.268 NA GENOME POLYPROTEIN, COAT PR
1dgi2             268       -20.10       -7.16     9.95e+00	:268 EM 22.00 NA NA VP2 <NA NA> [NA]               
1h4lA             292       -20.90       -7.10     1.05e+01	:292 XRAY 2.65 0.236 0.287 CELL DIVISION PROTEIN KI
1ar72             272       -20.12       -7.04     1.10e+01	:272 XRAY 2.90 0.234 NA P1/MAHONEY POLIOVIRUS <SWS 
1k47A             337       -19.45       -6.94     1.19e+01	:337 XRAY 2.42 0.217 0.257 phosphomevalonate kinase
1a7cA             379       -19.10       -6.88     1.25e+01	:379 XRAY 1.95 0.181 0.210 PLASMINOGEN ACTIVATOR IN
1pov              341       -19.95       -6.87     1.27e+01	:341 XRAY 2.80 0.281 NA POLIOVIRUS NATIVE EMPTY CAP
1olxB             342       -21.29       -6.83     1.30e+01	:342 XRAY 2.25 0.161 0.214 2-OXOISOVALERATE DEHYDRO
9paiA             379       -18.95       -6.73     1.43e+01	:379 XRAY 2.70 0.181 0.295 PLASMINOGEN ACTIVATOR IN
1lj5A             379       -18.97       -6.68     1.48e+01	:379 XRAY 1.80 0.198 0.241 PLASMINOGEN ACTIVATOR IN
1oc0A             379       -18.94       -6.64     1.53e+01	:379 XRAY 2.28 0.198 0.252 PLASMINOGEN ACTIVATOR IN
1pvc2             271       -21.61       -6.63     1.54e+01	:271 XRAY 2.40 0.205 NA POLIOVIRUS TYPE 3, SABIN ST
1db2A             377       -18.96       -6.61     1.56e+01	:377 XRAY 2.70 0.255 0.299 PLASMINOGEN ACTIVATOR IN
1c5gA             402       -18.91       -6.57     1.62e+01	:402 XRAY 2.60 NA NA PLASMINOGEN ACTIVATOR INHIBITO
1hciA             476       -19.29       -6.56     1.63e+01	:476 XRAY 2.80 0.270 0.295 ALPHA-ACTININ 2 <SWS AAC
1ic2A              81       -17.34       -6.56     1.64e+01	:81 XRAY 2.00 0.249 0.283 TROPOMYOSIN ALPHA CHAIN, 
1vl6A             388       -21.52       -6.53     1.68e+01	:388 XRAY 2.61 0.194 0.239 malate oxidoreductase <G
1mxgA             435       -23.12       -6.50     1.71e+01	:435 XRAY 1.60 0.159 0.172 alpha amylase <gb AAD543
1n6cA             297       -20.01       -6.48     1.75e+01	:297 XRAY 2.30 0.240 0.243 SET domain-containing pr
1nmoA             247       -19.49       -6.43     1.82e+01	:247 XRAY 2.20 0.211 0.259 Hypothetical protein ybg
1ukhA             363       -21.16       -6.42     1.84e+01	:363 XRAY 2.35 0.229 0.245 Mitogen-activated protei
1sziA             247       -18.36       -6.39     1.88e+01	:247 XRAY 2.80 0.238 0.272 mannose-6-phosphate rece
1q44A             326       -19.26       -6.39     1.89e+01	:326 XRAY 1.90 0.191 0.222 Steroid Sulphotransferas
1dvmA             379       -18.56       -6.30     2.03e+01	:379 XRAY 2.40 0.214 0.292 PLASMINOGEN ACTIVATOR IN
1izjA             637       -20.40       -6.21     2.18e+01	:637 XRAY 2.20 0.180 0.220 amylase <GB BAA02471> [T
1ei5A             520       -20.39       -6.20     2.22e+01	:520 XRAY 1.90 0.163 0.192 D-AMINOPEPTIDASE <GB AAA
1m3kA             392       -18.45       -6.18     2.26e+01	:392 XRAY 1.70 0.201 0.243 Acetyl-CoA acetyltransfe
1m1tA             392       -18.46       -6.17     2.26e+01	:392 XRAY 1.94 0.201 0.245 Acetyl-CoA acetyltransfe
1dluA             389       -18.46       -6.17     2.26e+01	:389 XRAY 2.25 0.212 0.263 BIOSYNTHETIC THIOLASE <S
1ou6A             392       -18.46       -6.17     2.27e+01	:392 XRAY 2.07 0.163 0.212 Acetyl-CoA acetyltransfe
1qflA             389       -18.46       -6.16     2.29e+01	:389 XRAY 1.92 0.209 0.256 ACETOACETYL-COA THIOLASE
1m4tA             392       -18.46       -6.15     2.30e+01	:392 XRAY 1.77 0.207 0.242 Acetyl-CoA acetyltransfe
1d00A             168       -19.13       -6.15     2.31e+01	:168 XRAY 2.00 0.219 0.254 TUMOR NECROSIS FACTOR RE
1vk4A             298       -18.58       -6.13     2.34e+01	:298 XRAY 1.91 0.170 0.219 PfkB Carbohydrate kinase
1m33A             258       -18.46       -6.12     2.35e+01	:258 XRAY 1.70 0.147 0.188 BioH protein <SWS BIOH_E
1czyA             168       -19.16       -6.11     2.37e+01	:168 XRAY 2.00 0.206 0.245 TUMOR NECROSIS FACTOR RE
1f3vB             171       -19.18       -6.07     2.46e+01	:171 XRAY 2.00 0.229 0.261 TUMOR NECROSIS FACTOR RE
1h21A             247       -19.88       -5.98     2.67e+01	:247 XRAY 2.50 0.199 0.264 SPLIT-SORET CYTOCHROME C
1v1rB             342       -20.34       -5.95     2.73e+01	:342 XRAY 1.80 0.158 0.183 2-OXOISOVALERATE DEHYDRO
1vi6A             208       -18.46       -5.93     2.77e+01	:208 XRAY 1.95 0.208 0.243 30S ribosomal protein S2
1mufA             257       -19.11       -5.93     2.78e+01	:257 XRAY 2.26 0.229 0.249 SET9 <GB AAL69901> [HOMO
2gsrA             207       -17.74       -5.89     2.88e+01	:207 XRAY 2.11 0.165 NA CLASS PI GST GLUTATHIONE S-
1s9aA             257       -21.90       -5.88     2.89e+01	:257 XRAY 2.47 0.216 0.290 Chlorocatechol 1,2-dioxy
1czzA             187       -19.29       -5.83     3.02e+01	:187 XRAY 2.70 0.221 0.267 TUMOR NECROSIS FACTOR RE
1pdkB             157       -18.35       -5.82     3.05e+01	:157 XRAY 2.40 0.235 0.273 PROTEIN PAPK <SWS PAPK_E
1ry6A             360       -19.81       -5.75     3.22e+01	:360 XRAY 1.60 0.207 0.231 INTERNAL KINESIN <GB NP_
1qppA             218       -19.18       -5.75     3.24e+01	:218 XRAY 2.60 0.203 0.286 PAPD CHAPERONE <SWS PAPD
1vkyA             347       -19.16       -5.74     3.26e+01	:347 XRAY 2.00 0.181 0.210 S-adenosylmethionine:tRN
1qpxA             218       -19.25       -5.73     3.29e+01	:218 XRAY 2.40 0.189 0.265 PAPD CHAPERONE <SWS PAPD
1ehyA             294       -21.23       -5.71     3.33e+01	:294 XRAY 2.10 0.190 0.227 SOLUBLE EPOXIDE HYDROLAS
1pdkA             218       -19.09       -5.70     3.37e+01	:218 XRAY 2.40 0.235 0.273 CHAPERONE PROTEIN PAPD <
1qscA             191       -19.30       -5.67     3.46e+01	:191 XRAY 2.40 0.215 0.257 TNF RECEPTOR ASSOCIATED 
3dpa              218       -19.10       -5.66     3.47e+01	:218 XRAY 2.50 0.184 NA CHAPERONE PROTEIN PAPD <SWS
1n0lA             224       -19.09       -5.66     3.48e+01	:224 XRAY 2.30 0.230 0.279 Chaperone protein PapD <
1ca9A             192       -19.31       -5.66     3.48e+01	:192 XRAY 2.30 0.234 0.289 TNF RECEPTOR ASSOCIATED 
1r31A             428       -17.99       -5.65     3.50e+01	:428 XRAY 2.10 0.222 0.241 3-hydroxy-3-methylglutar
1woqA             267       -18.78       -5.62     3.59e+01	:267 XRAY 1.80 0.193 0.223 Inorganic polyphosphate/
1izkA             637       -20.02       -5.60     3.66e+01	:637 XRAY 2.20 0.196 0.238 amylase <GB BAA02471> [T
1v58A             241       -18.85       -5.58     3.73e+01	:241 XRAY 1.70 0.186 0.207 Thiol:disulfide intercha
1av6A             295       -19.15       -5.50     4.00e+01	:295 XRAY 2.80 0.215 0.285 VP39 PROTEIN (E.C.2.7.7.