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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 HGM_OVER 24-94 -4.750 PB025553 _HOMD.0078651_ pint_c_1_4510 Prevotella intermedia 17 [1755134 - 1755736] ORF
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 HGM_OVER 18-74 -3.800 PB037276 Q24TM0_DESHY/1-190 PB037276; Pfam-B_37276;
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 HGM_OVER 258-359 -4.420 12  PB006154 _JGI.0331794_ 2004021056 [Human Gut Community Subject 7]
4 gi|6319252|ref|NP_009335.1| Putative protein of unknown function; has homology to FLO1; possible pseudogene; (YAL065C) [Saccharomyces cerevisiae] 128 HGM_OVER 99-122 -4.560 12  HGC00690 gi|162868815|dbj|BABB01001192.1|3.0 TMP00870;
5 gi|6319253|ref|NP_009336.1| Fungal-specific protein of unknown function; Yal064w-bp (YAL064W-B) [Saccharomyces cerevisiae] 126 HGM_OVER 60-126 -3.870 15  PB001404 Q2S5L8_SALRD/1-256 PB001404; Pfam-B_1404;
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 HGM_OVER 8-94 -4.700 PB017610 Q11T14_CYTH3/22-188 PB017610; Pfam-B_17610;
7 gi|6319254|ref|NP_009337.1| Protein of unknown function; may interact with ribosomes, based on co-purification experiments; (YAL064W) [Saccharomyces cerevisiae] 108 HGM_OVER 14-73 -4.040 16  PB045813 Q5LF03_BACFN/1-275 PB045813; Pfam-B_45813;
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 HGM_OVER 7-83 -5.650 15  PB002776 gi|157737147|ref|YP_001489830.1| hypothetical protein Abu_0901 [Arcobacter butzleri RM4018]gi|157699001|gb|ABV67161.1| hypothetical protein Abu_0901 [Arcobacter butzleri RM4018]
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 HGM_OVER 3-144 -3.530 11  PB009233 Q7MX23_PORGI/1-175 PB009233; Pfam-B_9233;
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 HGM_OVER 10-89 -1.240 PB069407 _HOMD.0084606_ pint_c_2_12 Prevotella intermedia 17 [3585 - 4295] ORF
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 HGM_OVER 1-81 -2.430 PB069407 _HOMD.0084606_ pint_c_2_12 Prevotella intermedia 17 [3585 - 4295] ORF
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 HGM_OVER 10-86 -2.070 PB069407 _HOMD.0084606_ pint_c_2_12 Prevotella intermedia 17 [3585 - 4295] ORF
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 HGM_OVER 229-298 -3.180 PB030138 Q7MX14_PORGI/1-113 PB030138; Pfam-B_30138;
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 HGM_OVER 1-128 -2.950 PB007733 A3U921_9FLAO/1-209 PB007733; Pfam-B_7733;
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 HGM_OVER 197-288 -3.920 15  HGC00711 gi|162743779|dbj|BAAZ01020484.1|1.0 TMP00907;
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 HGM_OVER 197-292 -4.380 18  HGC00711 gi|162743779|dbj|BAAZ01020484.1|1.0 TMP00907;
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 HGM_OVER 2-130 -4.780 10  PB202086 Q8G498_BIFLO/2-200 PB202086; Pfam-B_202086;
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 HGM_OVER 153-264 -3.090 HGC00965 gi|163282470|dbj|BABD01028218.1|2.0 TMP01310;
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 HGM_OVER 1-540 -5.670 PB048631 gi|160885545|ref|ZP_02066548.1| hypothetical protein BACOVA_03545 [Bacteroides ovatus ATCC 8483]gi|156109167|gb|EDO10912.1| hypothetical protein BACOVA_03545 [Bacteroides ovatus ATCC 8483]
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 HGM_OVER 1-95 -4.820 12  HGC00672 gi|162843654|dbj|BABA01001055.1|4.0 TMP00845;


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, Godzik A. cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006 May 26;