%  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.YGR218W.t2k-w0.5.mod   Host: farm16    Sun Jan 30 23:52:42 2005
%  karplus                          Dir:  /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR218W
% ---------------------------------------------------------------------
% Inserted Files:  YGR218W.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:  YGR218W.t2k-w0.5.mod
% Score DP Method: forward all-paths (dpstyle = 0)
% Align DP Method: viterbi (adpstyle = 1)
% 18859 sequences, 4341445 residues, 1085 nodes, 1620.64 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 (=11000) sequences:
%    N / (1 + exp(-(lambda(=2.0014) * Reverse)^tau(=0.8037)))
%    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
1qbkB             890      -509.10     -468.23    6.47e-103	:890 XRAY 3.00 0.267 0.315 KARYOPHERIN BETA2 <GB AA
1wa5C             960      -294.40     -270.83     4.22e-65	:960 XRAY 2.00 0.234 0.268 IMPORTIN ALPHA RE-EXPORT
1w9cA             321      -239.78     -222.72     3.78e-55	:321 XRAY 2.30 0.229 0.277 CRM1 PROTEIN <UNP O14980
1m5nS             485      -108.58      -88.87     1.27e-24	:485 XRAY 2.90 0.250 0.297 Importin beta-1 subunit 
1qgrA             876      -115.71      -87.76     2.41e-24	:876 XRAY 2.30 0.235 0.285 IMPORTIN BETA SUBUNIT <S
1uklA             876      -113.74      -87.09     3.57e-24	:876 XRAY 3.00 0.239 0.297 Importin beta-1 subunit 
1ibrB             462      -102.61      -83.21     3.49e-23	:462 XRAY 2.30 0.245 0.272 Importin beta-1 subunit 
1f59A             442       -98.88      -79.83     2.58e-22	:442 XRAY 2.80 0.225 0.262 IMPORTIN BETA-1 <SWS IMB
1gcjA             460       -97.82      -79.11     3.96e-22	:460 XRAY 2.60 0.215 0.270 IMPORTIN BETA <GB BAA082
1u6gC            1230       -55.22      -23.11     3.79e-06	:1230 XRAY 3.10 0.247 0.317 TIP120 protein <GB NP_0
1ee5A             424       -33.85      -19.20     7.71e-05	:424 XRAY 2.40 0.241 0.265 KARYOPHERIN ALPHA <SWS I
1ee4A             423       -33.65      -19.04     8.73e-05	:423 XRAY 2.10 0.246 0.277 KARYOPHERIN ALPHA <SWS M
1un0A             443       -34.94      -18.91     9.68e-05	:443 XRAY 2.60 0.218 0.257 IMPORTIN ALPHA SUBUNIT <
1pjmB             460       -36.19      -18.72     1.12e-04	:460 XRAY 2.50 0.204 0.239 Importin alpha-2 subunit
1bk6A             422       -32.75      -18.67     1.17e-04	:422 XRAY 2.80 0.256 0.307 KARYOPHERIN ALPHA <SWS I
1q1sC             466       -36.20      -18.65     1.19e-04	:466 XRAY 2.30 0.198 0.221 Importin alpha-2 subunit
1bk5A             422       -32.34      -18.37     1.49e-04	:422 XRAY 2.20 0.237 0.276 KARYOPHERIN ALPHA <SWS I
1ialA             453       -34.33      -17.92     2.13e-04	:453 XRAY 2.50 0.189 0.240 IMPORTIN ALPHA <SWS IMA2
1wa5B             530       -33.35      -17.18     3.85e-04	:530 XRAY 2.00 0.234 0.268 IMPORTIN ALPHA SUBUNIT <
1gw5B             591       -46.81      -17.13     4.00e-04	:591 XRAY 2.59 0.268 0.335 ADAPTER-RELATED PROTEIN 
1b3uA             588       -33.61      -13.25     9.74e-03	:588 XRAY 2.30 0.209 0.268 PROTEIN PHOSPHATASE PP2A
1w63A             618       -26.06       -9.60     2.35e-01	:618 XRAY 4.00 0.297 0.310 ADAPTER-RELATED PROTEIN 
1te4A             131       -21.12       -9.06     3.84e-01	:131 NMR NA NA NA conserved protein MTH187 <GB NP_2
1j6oA             268       -23.04       -8.14     8.92e-01	:268 XRAY 1.80 0.190 0.224 TatD-related deoxyribonu
1nfiA             301       -25.51       -8.06     9.60e-01	:301 XRAY 2.70 0.223 0.265 NF-KAPPA-B P65 <SWS MAD3
1gw5A             621       -29.78       -6.99     2.64e+00	:621 XRAY 2.59 0.268 0.335 ADAPTOR-RELATED PROTEIN 
1by1A             209       -18.87       -6.55     4.03e+00	:209 NMR NA NA NA PIX <SWS Y142_HUMAN> [HOMO SAPIEN
1rhzA             436       -25.34       -6.53     4.12e+00	:436 XRAY 3.50 0.254 0.330 Preprotein translocase s
1m4zA             238       -19.05       -6.37     4.82e+00	:238 XRAY 2.20 0.225 0.225 ORIGIN RECOGNITION COMPL
1ghsA             306       -18.57       -6.18     5.81e+00	:306 XRAY 2.30 0.179 NA 1,3-BETA-GLUCANASE <SWS E13
1rh5A             436       -24.85       -6.14     6.02e+00	:436 XRAY 3.20 0.242 0.288 Preprotein translocase s
1drbA             159       -19.42       -6.02     6.79e+00	:159 XRAY 1.96 0.149 NA DIHYDROFOLATE REDUCTASE <SW
1m33A             258       -18.48       -6.01     6.84e+00	:258 XRAY 1.70 0.147 0.188 BioH protein <SWS BIOH_E
1t72A             227       -19.84       -5.99     6.96e+00	:227 XRAY 2.90 0.216 0.293 Phosphate transport syst
2sqcA             631       -47.97       -5.94     7.36e+00	:631 XRAY 2.00 0.153 0.187 SQUALENE-HOPENE CYCLASE 
1umpA             631       -48.40       -5.94     7.36e+00	:631 XRAY 2.13 0.187 0.228 SQUALENE--HOPENE CYCLASE
3sqcA             631       -48.24       -5.94     7.36e+00	:631 XRAY 2.80 0.209 0.236 SQUALENE--HOPENE CYCLASE
1dhiA             159       -19.18       -5.93     7.44e+00	:159 XRAY 1.90 0.155 NA DIHYDROFOLATE REDUCTASE <SW
1ddsA             159       -19.13       -5.91     7.56e+00	:159 XRAY 2.20 0.177 0.200 DIHYDROFOLATE REDUCTASE 
153l              185       -19.40       -5.90     7.60e+00	:185 XRAY 1.60 0.150 NA GOOSE LYSOZYME <SWS LYG_ANS
1tygA             253       -17.48       -5.90     7.64e+00	:253 XRAY 3.15 0.242 0.305 Thiazole biosynthesis pr
1mqsA             671       -25.77       -5.85     8.01e+00	:671 XRAY 3.00 0.257 0.290 Sly1 Protein <SWS SLY1_Y
2drcA             159       -19.13       -5.85     8.04e+00	:159 XRAY 1.90 0.161 NA DIHYDROFOLATE REDUCTASE <SW
1q0pA             223       -19.67       -5.84     8.10e+00	:223 XRAY 1.80 0.210 0.259 Complement factor B <SWS
1dhjA             159       -19.04       -5.84     8.13e+00	:159 XRAY 1.80 0.167 NA DIHYDROFOLATE REDUCTASE <SW
1draA             159       -19.14       -5.81     8.31e+00	:159 XRAY 1.90 0.153 NA DIHYDROFOLATE REDUCTASE <SW
1ra9              159       -19.18       -5.80     8.40e+00	:159 XRAY 1.55 0.169 NA DIHYDROFOLATE REDUCTASE <SW
1aqjA             421       -26.03       -5.77     8.69e+00	:421 XRAY 2.60 0.200 0.286 ADENINE-N6-DNA-METHYLTRA
1sy7A             715       -40.34       -5.75     8.89e+00	:715 XRAY 1.75 0.183 0.206 Catalase 1 <SWS CAT1_NEU
1tuaA             191       -17.89       -5.74     8.95e+00	:191 XRAY 1.50 0.210 0.229 Hypothetical protein APE
1xm3A             264       -17.45       -5.74     8.96e+00	:264 XRAY 1.80 0.212 0.237 Thiazole biosynthesis pr
4dfrA             159       -19.07       -5.70     9.28e+00	:159 XRAY 1.70 0.155 NA DIHYDROFOLATE REDUCTASE <SW
1jqnA             883       -30.73       -5.67     9.62e+00	:883 XRAY 2.35 0.195 0.231 phosphoenolpyruvate carb
2hpaA             342       -19.31       -5.60     1.02e+01	:342 XRAY 2.90 0.211 0.308 ACID PHOSPHATASE <SWS PP
1hdmB             193       -17.44       -5.58     1.05e+01	:193 XRAY 2.50 0.197 0.257 CLASS II HISTOCOMPATIBIL
1oyzA             280       -20.53       -5.54     1.09e+01	:280 XRAY 2.10 0.219 0.269 Hypothetical protein yib
2admA             421       -25.83       -5.51     1.12e+01	:421 XRAY 2.60 0.214 0.273 ADENINE-N6-DNA-METHYLTRA
1nd6A             354       -19.27       -5.51     1.13e+01	:354 XRAY 2.40 0.198 0.256 prostatic acid phosphata
1g38A             393       -24.84       -5.43     1.22e+01	:393 XRAY 2.00 0.208 0.234 MODIFICATION METHYLASE T
1nxcA             478       -27.55       -5.39     1.27e+01	:478 XRAY 1.51 0.172 0.190 Mannosyl-oligosaccharide
1xjdA             345       -19.87       -5.37     1.29e+01	:345 XRAY 2.00 0.201 0.216 Protein kinase C, theta 
1oedA             227       -18.35       -5.36     1.31e+01	:227 EM 4.00 NA NA ACETYLCHOLINE RECEPTOR PROTEIN, 
1io0A             185       -17.46       -5.33     1.35e+01	:185 XRAY 1.45 0.203 0.220 TROPOMODULIN <GB BAB1891
1pmzA              86       -19.36       -5.32     1.36e+01	:86 XRAY 1.90 0.218 0.239 pollen allergen Che a 3 <
1ua2A             346       -19.82       -5.31     1.37e+01	:346 XRAY 3.02 0.217 0.288 Cell division protein ki
1d2nA             272       -17.70       -5.30     1.40e+01	:272 XRAY 1.75 0.199 0.223 N-ETHYLMALEIMIDE-SENSITI
1kk9A             221       -17.70       -5.27     1.43e+01	:221 XRAY 2.10 0.213 0.233 probable translation fac
1gu2A             124       -17.39       -5.24     1.48e+01	:124 XRAY 1.19 0.148 0.186 CYTOCHROME C' <SWS Q9RQB
1nsf              273       -17.82       -5.19     1.56e+01	:273 XRAY 1.90 0.224 0.244 N-ETHYLMALEIMIDE SENSITI
1rkyA             747       -43.16       -5.15     1.61e+01	:747 XRAY 1.68 0.151 0.182 lysyl oxidase <GB AAK499
2phkA             277       -21.68       -5.15     1.62e+01	:277 XRAY 2.60 0.253 0.300 PHOSPHORYLASE KINASE <SW
1jk0B             345       -20.26       -5.14     1.64e+01	:345 XRAY 2.80 0.243 0.296 ribonucleoside-diphospha
1a7w               69       -16.26       -5.12     1.66e+01	:69 XRAY 1.55 0.200 0.248 HISTONE HMFB <SWS HMFB_ME
1e3gA             263       -19.22       -5.11     1.68e+01	:263 XRAY 2.40 0.210 0.297 ANDROGEN RECEPTOR <SWS A
5hmgB             175       -19.20       -5.09     1.71e+01	:175 XRAY 3.20 0.220 NA HEMAGGLUTININ, HA1 CHAIN <S
1c4zD             154       -17.65       -5.09     1.72e+01	:154 XRAY 2.60 0.262 0.290 UBIQUITIN CONJUGATING EN
1w63B             584       -37.52       -5.05     1.79e+01	:584 XRAY 4.00 0.297 0.310 ADAPTER-RELATED PROTEIN 
1fi5A              81       -17.65       -5.05     1.79e+01	:81 NMR NA NA NA TROPONIN C <SWS TPCC_CHICK> [GALLU
1f5mA             180       -18.54       -5.02     1.84e+01	:180 XRAY 1.90 0.246 0.246 GAF <SWS YKG9_YEAST> [SA
3ctn               76       -17.49       -4.97     1.93e+01	:76 NMR NA NA NA TROPONIN C <SWS TPCC_CHICK> [GALLU
1s72G             348       -26.90       -4.97     1.95e+01	:348 XRAY 2.40 0.188 0.222 Acidic ribosomal protein
1ih0A              71       -17.47       -4.97     1.95e+01	:71 NMR NA NA NA TROPONIN C, SLOW SKELETAL AND CARD
1ozsA              73       -17.47       -4.94     2.00e+01	:73 NMR NA NA NA Troponin C, slow skeletal and card
1gweA             503       -31.66       -4.94     2.01e+01	:503 XRAY 0.88 0.089 0.096 CATALASE <SWS CAD27348> 
1mzrA             296       -19.25       -4.91     2.06e+01	:296 XRAY 2.13 0.175 0.220 2,5-diketo-D-gluconate r
1ejdA             419       -23.86       -4.87     2.15e+01	:419 XRAY 1.55 0.185 0.207 UDP-N-ACETYLGLUCOSAMINE 
1dlgA             419       -23.59       -4.87     2.16e+01	:419 XRAY 1.90 0.173 0.197 UDP-N-ACETYLGLUCOSAMINE 
1pqvD             221       -17.18       -4.86     2.18e+01	:221 XRAY 3.80 NA NA DNA-directed RNA polymerase II
1ral              308       -18.65       -4.86     2.18e+01	:308 XRAY 3.00 0.220 NA 3-ALPHA-HYDROXYSTEROID DEHY
1p14A             306       -20.87       -4.85     2.20e+01	:306 XRAY 1.90 0.225 0.240 insulin receptor <GB CAA
1dvpA             220       -18.00       -4.85     2.20e+01	:220 XRAY 2.00 0.227 0.254 HEPATOCYTE GROWTH FACTOR
1hbzA             498       -31.52       -4.84     2.21e+01	:498 XRAY 1.50 0.092 0.120 CATALASE <PDB 1HBZ> [MIC
1sojI             420       -23.79       -4.84     2.21e+01	:420 XRAY 2.90 0.235 0.249 CATALYTIC DOMAIN OF HUMA
1a8y              367       -31.46       -4.80     2.30e+01	:367 XRAY 2.40 0.188 0.242 CALSEQUESTRIN <SWS CAQS_
1t7rA             269       -18.88       -4.78     2.37e+01	:269 XRAY 1.40 0.196 0.205 Androgen receptor <SWS A
1gqiA             708       -33.67       -4.77     2.38e+01	:708 XRAY 1.48 0.133 0.168 ALPHA-GLUCURONIDASE <PDB
1h41A             708       -33.54       -4.77     2.38e+01	:708 XRAY 1.50 0.118 0.153 ALPHA-GLUCURONIDASE <SWS
1ql6A             298       -21.59       -4.76     2.41e+01	:298 XRAY 2.40 0.240 0.330 PHOSPHORYLASE KINASE <SW
1kb9E             185       -17.92       -4.75     2.44e+01	:185 XRAY 2.30 0.218 0.249 UBIQUINOL-CYTOCHROME C R
1h3fA             432       -19.28       -4.73     2.47e+01	:432 XRAY 2.00 0.234 0.261 TYROSYL-TRNA SYNTHETASE 
1phk              298       -21.72       -4.72     2.51e+01	:298 XRAY 2.20 0.210 0.288 PHOSPHORYLASE KINASE <SW
1rqqA             306       -20.87       -4.70     2.55e+01	:306 XRAY 2.60 0.229 0.277 Insulin receptor <GB NP_
1w0fA             485       -20.86       -4.70     2.57e+01	:485 XRAY 2.65 0.239 0.303 CYTOCHROME P450 3A4 <UNP
1tqnA             486       -20.91       -4.70     2.58e+01	:486 XRAY 2.05 0.241 0.293 cytochrome P450 3A4 <GB 
1m12A              84       -20.16       -4.69     2.58e+01	:84 NMR NA NA NA SAPOSIN C <SWS SAP_HUMAN> [HOMO SA
1gbs              185       -18.59       -4.68     2.61e+01	:185 XRAY 1.50 0.184 NA AUSTRALIAN BLACK SWAN EGG W
1a7m              180       -17.38       -4.67     2.65e+01	:180 NMR NA NA NA LEUKEMIA INHIBITORY FACTOR <SWS L
1mqmB             221       -19.05       -4.65     2.69e+01	:221 XRAY 2.60 0.265 0.290 Hemagglutinin HA2 chain 
1r42A             615       -31.23       -4.65     2.70e+01	:615 XRAY 2.20 0.235 0.287 angiotensin I converting
1q3gA             419       -23.46       -4.65     2.71e+01	:419 XRAY 2.65 0.217 0.253 UDP-N-acetylglucosamine 
1vpqA             273       -18.18       -4.64     2.73e+01	:273 XRAY 2.20 0.209 0.263 hypothetical protein TM1
1qd9A             124       -15.98       -4.64     2.74e+01	:124 XRAY 1.70 0.166 0.197 PURINE REGULATORY PROTEI
1lwiA             322       -18.64       -4.62     2.78e+01	:322 XRAY 2.70 0.234 0.294 3-ALPHA-HYDROXYSTEROID/D
1afsA             323       -18.63       -4.58     2.90e+01	:323 XRAY 2.50 0.188 0.242 3-ALPHA-HYDROXYSTEROID D
1gp0A             143       -16.36       -4.58     2.91e+01	:143 XRAY 1.40 0.209 0.237 CATION-INDEPENDENT MANNO
1gg1A             350       -23.96       -4.57     2.94e+01	:350 XRAY 2.00 0.211 0.237 3-DEOXY-D-ARABINO-HEPTUL
1jffA             451       -26.10       -4.56     2.96e+01	:451 ELEC 3.50 0.232 0.297 tubulin alpha chain <SWS
1n6uA             212       -17.81       -4.54     3.03e+01	:212 NMR NA NA NA Interferon-alpha/beta receptor be
1guxA             218       -18.20       -4.54     3.04e+01	:218 XRAY 1.85 0.218 0.289 RETINOBLASTOMA PROTEIN <
1iknA             286       -20.86       -4.47     3.27e+01	:286 XRAY 2.30 0.223 0.277 NF-KAPPA-B P65 SUBUNIT <
1b67A              68       -15.42       -4.46     3.27e+01	:68 XRAY 1.48 0.193 0.266 HISTONE HMFA <PIR A47036>
2eiaA             206       -19.26       -4.45     3.33e+01	:206 XRAY 2.70 0.236 0.294 EIAV CAPSID PROTEIN P26 
1eia              207       -19.25       -4.45     3.33e+01	:207 XRAY 2.70 0.227 0.275 EIAV CAPSID PROTEIN P26 
1hta               69       -15.43       -4.45     3.34e+01	:69 XRAY 1.55 0.200 0.248 HISTONE HMFA <SWS HMFA_ME
1ib2A             349       -19.66       -4.44     3.38e+01	:349 XRAY 1.90 0.198 0.242 PUMILIO 1 <GB AAG31807> 
1ffxA             451       -25.57       -4.44     3.38e+01	:451 XRAY 3.95 0.267 0.367 TUBULIN <SWS TBB_PIG> [B
1xewX             182       -16.90       -4.42     3.42e+01	:182 XRAY 2.00 0.207 0.261 SMC protein <GB CAD66602
1r4xA             275       -18.74       -4.42     3.43e+01	:275 XRAY 1.90 0.175 0.208 Coatomer gamma subunit <
1sa0A             451       -25.61       -4.40     3.50e+01	:451 XRAY 3.58 0.233 0.249 Tubulin alpha chain <SWS
1qr6A             584       -30.19       -4.39     3.55e+01	:584 XRAY 2.10 0.228 0.287 MALIC ENZYME 2 <SWS MAOM
1n8fA             350       -23.79       -4.38     3.56e+01	:350 XRAY 1.75 0.209 0.237 DAHP Synthetase <GB AAA2
1odmA             331       -18.52       -4.38     3.59e+01	:331 XRAY 1.15 0.143 0.152 ISOPENICILLIN N SYNTHASE
1fmiA             458       -22.40       -4.37     3.61e+01	:458 XRAY 1.90 0.222 0.250 ENDOPLASMIC RETICULUM AL
1ii8A             195       -17.96       -4.35     3.68e+01	:195 XRAY 3.02 0.255 0.294 Rad50 ABC-ATPase <SWS RA
1u02A             239       -20.84       -4.35     3.71e+01	:239 XRAY 1.92 0.197 0.216 trehalose-6-phosphate ph
1fo3A             460       -22.39       -4.33     3.77e+01	:460 XRAY 1.75 0.218 0.241 ALPHA1,2-MANNOSIDASE <GB
1ovlA             271       -20.12       -4.33     3.77e+01	:271 XRAY 2.20 0.231 0.259 Orphan nuclear receptor 
1pj3A             564       -30.06       -4.32     3.82e+01	:564 XRAY 2.10 0.200 0.236 NAD-dependent malic enzy
1na6A             404       -20.15       -4.31     3.86e+01	:404 XRAY 2.10 0.246 0.284 Restriction endonuclease
1i38A             260       -18.41       -4.29     3.92e+01	:260 XRAY 2.00 0.280 0.345 ANDROGEN RECEPTOR <SWS A
2av8A             340       -17.24       -4.28     3.97e+01	:340 XRAY 2.46 0.181 0.237 RIBONUCLEOTIDE REDUCTASE
1uhlA             236       -17.78       -4.28     3.98e+01	:236 XRAY 2.90 0.224 0.326 Retinoic acid receptor R