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anford Burnham Prebys Medical Discovery Institute
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# Query Length Result vs. Range Score %id Covered by template(s)
1 gi|6319249|ref|NP_009332.1|(removed signalp:1-20) hypothetical protein; Pau8p (YAL068C) [Saccharomyces cerevisiae] 100 PDB0516 1-91 -10.700 16  2jk1_A mol:protein length:139 HYDROGENASE TRANSCRIPTIONAL REGULATORY PROTEI
2 gi|33438754|ref|NP_878038.1| Putative protein of unknown function; identified by gene-trapping, microarray-based expression analysis, and genome-wide homology searching; Yal067w-ap (YAL067W-A) [Saccharomyces cerevisiae] 75 PDB0516 3-75 -6.070 1yr6_A mol:protein length:262 ATP(GTP)binding protein
3 gi|6319250|ref|NP_009333.1| Putative permease, member of the allantoate transporter subfamily of the major facilitator superfamily; mutation confers resistance to ethionine sulfoxide; Seo1p (YAL067C) [Saccharomyces cerevisiae] 593 PDB0516 125-568 -32.600 12  1pw4_A mol:protein length:451 Glycerol-3-phosphate transporter
4 gi|6319252|ref|NP_009335.1| Putative protein of unknown function; has homology to FLO1; possible pseudogene; (YAL065C) [Saccharomyces cerevisiae] 128 PDB0516 18-113 -7.890 25  4wse_A mol:protein length:584 Putative poly(A) polymerase catalytic subunit
5 gi|6319253|ref|NP_009336.1| Fungal-specific protein of unknown function; Yal064w-bp (YAL064W-B) [Saccharomyces cerevisiae] 126 PDB0516 13-52 -5.740 22  3tsi_A mol:protein length:65 Hemagglutinin-neuraminidase
6 gi|7839146|ref|NP_058136.1| Putative protein of unknown function; YAL064C-A is not an essential gene; Yal064c-ap (YAL064C-A) [Saccharomyces cerevisiae] 126 PDB0516 1-124 -54.800 71  4gq7_A mol:protein length:224 Flocculin
7 gi|6319254|ref|NP_009337.1| Protein of unknown function; may interact with ribosomes, based on co-purification experiments; (YAL064W) [Saccharomyces cerevisiae] 108 PDB0516 4-102 -7.700 2e1m_B mol:protein length:130 L-glutamate oxidase
8 gi|33438755|ref|NP_878039.1| Putative protein of unknown function; identified by expression profiling and mass spectrometry; Yal063c-ap (YAL063C-A) [Saccharomyces cerevisiae] 96 PDB0516 3-86 -7.290 16  2cq1_A mol:protein length:101 PTB-like protein L
9 gi|6319255|ref|NP_009338.1|(removed signalp:1-24) Lectin-like protein with similarity to Flo1p, thought to be expressed and involved in flocculation; Flo9p (YAL063C) [Saccharomyces cerevisiae] (Range: 1-500) 500 PDB0516 1-249 -56.700 87  4lhl_A mol:protein length:263 Flocculation protein FLO1
6-500 -16.500 4ee2_A mol:protein length:736 Protective antigen
10 gi|6319255|ref|NP_009338.1|(removed signalp:1-24) Lectin-like protein with similarity to Flo1p, thought to be expressed and involved in flocculation; Flo9p (YAL063C) [Saccharomyces cerevisiae] (Range: 251-750) 500 PDB0516 17-498 -13.300 3hqv_A mol:protein length:1056 Collagen alpha-1(I) chain
11 gi|6319255|ref|NP_009338.1|(removed signalp:1-24) Lectin-like protein with similarity to Flo1p, thought to be expressed and involved in flocculation; Flo9p (YAL063C) [Saccharomyces cerevisiae] (Range: 501-1000) 500 PDB0516 1-144 -11.600 13  5i4d_A mol:protein length:343 Superantigen-like protein
14-251 -9.920 10  4cwu_T mol:protein length:368 CORE-CAPSID BRIDGING PROTEIN
12 gi|6319255|ref|NP_009338.1|(removed signalp:1-24) Lectin-like protein with similarity to Flo1p, thought to be expressed and involved in flocculation; Flo9p (YAL063C) [Saccharomyces cerevisiae] (Range: 751-1250) 500 PDB0516 1-147 -11.800 5i4d_A mol:protein length:343 Superantigen-like protein
1-212 -9.670 11  5fur_J mol:protein length:677 TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT
13 gi|6319255|ref|NP_009338.1|(removed signalp:1-24) Lectin-like protein with similarity to Flo1p, thought to be expressed and involved in flocculation; Flo9p (YAL063C) [Saccharomyces cerevisiae] (Range: 1001-1298) 298 PDB0516 1-147 -14.400 5i4d_A mol:protein length:343 Superantigen-like protein
2-236 -12.100 10  5fur_J mol:protein length:677 TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT
58-298 -10.900 4cwu_T mol:protein length:368 CORE-CAPSID BRIDGING PROTEIN
14 gi|6319256|ref|NP_009339.1| NADP(+)-dependent glutamate dehydrogenase, synthesizes glutamate from ammonia and alpha-ketoglutarate; rate of alpha-ketoglutarate utilization differs from Gdh1p; expression regulated by nitrogen and carbon sources; Gdh3p (YAL062W) [Saccharomyces cerevisiae] 457 PDB0516 2-457 -131.000 48  1aup_A mol:protein length:449 NAD-SPECIFIC GLUTAMATE DEHYDROGENASE
15 gi|6319257|ref|NP_009340.1| Putative medium-chain alcohol dehydrogenase with similarity to BDH1; transcription induced by constitutively active PDR1 and PDR3; BDH2 is an essential gene; Bdh2p (YAL061W) [Saccharomyces cerevisiae] 417 PDB0516 1-376 -84.600 24  4a2c_A mol:protein length:346 GALACTITOL-1-PHOSPHATE 5-DEHYDROGENASE
1-415 -36.500 17  4a0s_A mol:protein length:447 OCTENOYL-COA REDUCTASE/CARBOXYLASE
16 gi|6319258|ref|NP_009341.1| NAD-dependent (R,R)-butanediol dehydrogenase, catalyzes oxidation of (R,R)-2,3-butanediol to (3R)-acetoin, oxidation of meso-butanediol to (3S)-acetoin, and reduction of acetoin; enhances use of 2,3-butanediol as an aerobic carbon source; Bdh1p (YAL060W) [Saccharomyces cerevisiae] 382 PDB0516 1-375 -85.000 22  4a2c_A mol:protein length:346 GALACTITOL-1-PHOSPHATE 5-DEHYDROGENASE
17 gi|6319259|ref|NP_009342.1| Protein of unknown function, localized in the nucleoplasm and the nucleolus, genetically interacts with MTR2 in 60S ribosomal protein subunit export; Ecm1p (YAL059W) [Saccharomyces cerevisiae] 212 PDB0516 18-145 -6.960 10  4h63_Q mol:protein length:469 Mediator of RNA polymerase II transcription s
18 gi|6319260|ref|NP_009343.1|(removed signalp:1-19) Calnexin; integral membrane ER chaperone involved in folding and quality control of glycoproteins; chaperone activity is inhibited by Mpd1p, with which Cne1p interacts; 24% identical to mammalian calnexin; Ca+ binding not yet shown in yeast; Cne1p (YAL058W) [Saccharomyces cerevisiae] 483 PDB0516 1-420 -115.000 31  1jhn_A mol:protein length:424 calnexin
19 gi|41629666|ref|NP_009345.2| Multistep regulator of cAMP-PKA signaling; inhibits PKA downstream of Gpa2p and Cyr1p, thereby increasing cAMP dependency; inhibits Ras activity through direct interactions with Ira1p/2p; regulated by G-alpha protein Gpa2p; homolog of Gpb1p; Gpb2p (YAL056W) [Saccharomyces cerevisiae] 880 PDB0516 1-760 -25.300 11  2zw9_A mol:protein length:695 Leucine carboxyl methyltransferase 2
258-778 -52.600 13  5a10_A mol:protein length:356 THIOCYANATE FORMING PROTEIN
356-865 -30.800 13  2uvk_A mol:protein length:357 YJHT
20 gi|6319263|ref|NP_009346.1| Putative peroxisomal membrane protein required for import of peroxisomal proteins, functionally complements a Pichia pastoris pex22 mutation; Pex22p (YAL055W) [Saccharomyces cerevisiae] 180 PDB0516 51-180 -74.500 97  2y9m_B mol:protein length:130 PEROXISOME ASSEMBLY PROTEIN 22


FFAS is supported by the NIH grant R01-GM087218-01
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Selected papers from Godzik Lab
Ying Zhang, Ines Thiele, Dana Weekes, Zhanwen Li, Lukasz Jaroszewski, Krzysztof Ginalski, Ashley Deacon, John Wooley, Scott Lesley, Ian Wilson, Bernhard Palsson, Andrei Osterman, Adam Godzik. Three-Dimensional Structural View of the Central Metabolic Network of Thermotoga maritima. Science. 2009 Sep 18;325(5947):1544-9.

Alexey M. Eroshkin, Andrew LeBlanc, Dana Weekes, Kai Post, Zhanwen Li, Akhil Rajput, Sal T. Butera, Dennis R. Burton, Adam Godzik. bNAber: database of broadly neutralizing HIV antibodies. Nucl. Acids Res. 2013; published on November 7, 2013.

Li W, Pio F, Pawlowski K, Godzik A. Saturated BLAST: an automated multiple intermediate sequence search used to detect distant homology. Bioinformatics. 2000 Dec;16(12):1105-10.