Protein Overview: YLR227W-A, YML04...

General Information:
Name(s) found:	YML040W [SGD] YLR227W-A [SGD] YJR026W [SGD]
Description(s) found: SHOW ONLY BEST	gi\|7839186\|ref\|NP_058172.1\| Retrotransposon TYA Gag gene co-transcribed with TYB Pol; translated as TYA or TYA-TYB polyprotein; Gag is a nucleocapsid protein that is the structural constituent of virus-like particles (VLPs); similar to retroviral Gag; Ylr [NCBI NR] gi\|683667\|emb\|CAA88329.1\| unnamed protein product [Saccharomyces cerevisiae] [NCBI NR] gi\|6323602\|ref\|NP_013673.1\| Retrotransposon TYA Gag gene co-transcribed with TYB Pol; translated as TYA or TYA-TYB polyprotein; Gag is a nucleocapsid protein that is the structural constituent of virus-like particles (VLPs); similar to retroviral Gag; Yml [NCBI NR] gi\|6322486\|ref\|NP_012561.1\| Retrotransposon TYA Gag gene co-transcribed with TYB Pol; translated as TYA or TYA-TYB polyprotein; Gag is a nucleocapsid protein that is the structural constituent of virus-like particles (VLPs); similar to retroviral Gag; Yjr [NCBI NR] gi\|1353061\|sp\|P47097.1\|YJ11A_YEAST RecName: Full=Transposon Ty1-JR1/Ty1-LR3/Ty1-ML2 Gag polyprotein; AltName: Full=Gag-p49; AltName: Full=Transposon Ty1 protein A; Short=TY1A; Short=TYA; AltName: Full=p58; Contains: RecName: Full=Capsid protein; Short=CA; [NCBI NR] gi\|1129162\|emb\|CAA60721.1\| Ty1A [Saccharomyces cerevisiae] [NCBI NR] pir\|\|S57044 TyA protein - yeast (Saccharomyces cerevisiae) retrotransposon Ty1.JR and others [NCBI NR] gi\|1015667\|emb\|CAA89552.1\| TY1A [Saccharomyces cerevisiae] [NCBI NR] (P47097) Transposon Ty1 protein A [Swiss-Prot] Transposon Ty1-JR1/Ty1-LR3/Ty1-ML2 Gag polyprotein OS=Saccharomyces cerevisiae GN=TY1A-JR1 PE=1 SV=1 [Swiss-Prot] TY1A TY1A protein [mips] - TY1A - TY1A protein [mips] Retrotransposon TYA Gag gene co-transcribed with TYB Pol; translated as TYA or TYA-TYB polyprotein; Gag is a nucleocapsid protein that is the structural constituent of virus-like particles (VLPs); similar to retroviral Gag [SGD] YML040W, Chr XIII from 196628-197950 [yeast_orfs2] YLR227W-A, Chr XII from 593438-594760 [yeast_orfs2] YJR026W, Chr X from 472452-473774 [yeast_orfs2] Chr XIII from 196628-197950 [yeastorf3.fasta] Chr XII from 593438-594760 [yeastorf3.fasta] Chr X from 472452-473774 [yeastorf3.fasta] Chr X from 472453-473775 [yeastorf4.fasta] Chr X from 472454-473776 [yeastorf5.fasta] YML040W SGDID:S0004504, Chr XIII from 196628-197950, Ty ORF [yeastflysequest.fasta] YLR227W-A SGDID:S0007375, Chr XII from 593440-594762, Ty ORF [yeastflysequest.fasta] YJR026W SGDID:S0003787, Chr X from 472674-473996, Ty ORF [yeastflysequest.fasta] TyA Gag protein; the main structural constituent of virus-like particles (VLPs) [Saccharomyces cerevisiae]gi\|7839186\|ref\|NP_058172.1\| TyA Gag protein; the main structural constituent of virus-like particles (VLPs) [Saccharomyces cerevisiae]gi\|6322486\|re [nrdb_11152004_Chlamydomonas] YJR026W SGDID:S000003787, Chr X from 472674-473996, transposable_element_gene, "TyA Gag protein; the main structural constituent of virus-like particles (VLPs)" [SGD_S-cerevisiae_na_12-16-2005_con_reversed.fasta] YLR227W-A SGDID:S000007375, Chr XII from 593440-594762, transposable_element_gene, "TyA Gag protein; the main structural constituent of virus-like particles (VLPs)" [SGD_S-cerevisiae_na_12-16-2005_con_reversed.fasta] YML040W SGDID:S000004504, Chr XIII from 196628-197950, transposable_element_gene, "TyA Gag protein; the main structural constituent of virus-like particles (VLPs)" [SGD_S-cerevisiae_na_12-16-2005_con_reversed.fasta] YJR026W SGDID:S000003787, Chr X from 472753-474075, transposable_element_gene, "Retrotransposon TYA Gag gene co-transcribed with TYB Pol; translated as TYA or TYA-TYB polyprotein; Gag is a nucleocapsid protein that is the structural constituent of virus-l [yeast-contam.fasta] YLR227W-A SGDID:S000007375, Chr XII from 593440-594762, transposable_element_gene, "Retrotransposon TYA Gag gene co-transcribed with TYB Pol; translated as TYA or TYA-TYB polyprotein; Gag is a nucleocapsid protein that is the structural constituent of vir [yeast-contam.fasta] YML040W SGDID:S000004504, Chr XIII from 196628-197950, transposable_element_gene, "Retrotransposon TYA Gag gene co-transcribed with TYB Pol; translated as TYA or TYA-TYB polyprotein; Gag is a nucleocapsid protein that is the structural constituent of viru [yeast-contam.fasta] YJR026W SGDID:S000003787, Chr X from 472752-474074, transposable_element_gene, "Retrotransposon TYA Gag gene co-transcribed with TYB Pol; translated as TYA or TYA-TYB polyprotein; Gag is a nucleocapsid protein that is the structural constituent of virus-l [yeast-200209-contam.fasta] Ty1A [Saccharomyces cerevisiae] [nr-271106-contam.fasta] Transposon Ty1 protein A [nr-271106-contam.fasta] Retrotransposon TYA Gag gene co-transcribed with TYB Pol; translated as TYA or TYA-TYB polyprotein; Gag is a nucleocapsid protein that is the structural constituent of virus-like particles (VLPs); similar to retroviral Gag; Ylr227w-ap [Saccharomyces cerev [nr-271106-contam.fasta] TY1A [Saccharomyces cerevisiae] [nr-271106-contam.fasta] unnamed protein product [Saccharomyces cerevisiae] [nr-271106-contam.fasta] Retrotransposon TYA Gag gene co-transcribed with TYB Pol; translated as TYA or TYA-TYB polyprotein; Gag is a nucleocapsid protein that is the structural constituent of virus-like particles (VLPs); similar to retroviral Gag; Yml040wp [Saccharomyces cerevis [nr-271106-contam.fasta] Retrotransposon TYA Gag gene co-transcribed with TYB Pol; translated as TYA or TYA-TYB polyprotein; Gag is a nucleocapsid protein that is the structural constituent of virus-like particles (VLPs); similar to retroviral Gag; Yjr026wp [Saccharomyces cerevis [nr-271106-contam.fasta] YJR026W SGDID:S000003787, Chr X from 472752-474074, transposable_element_gene, "Retrotransposon TYA Gag gene co-transcribed with TYB Pol; translated as TYA or TYA-TYB polyprotein; Gag is a nucleocapsid protein that is the structural constituent of virus-like particles (VLPs); similar to retroviral Gag" [yeast-bovrabprots.fasta] YLR227W-A SGDID:S000007375, Chr XII from 593440-594762, transposable_element_gene, "Retrotransposon TYA Gag gene co-transcribed with TYB Pol; translated as TYA or TYA-TYB polyprotein; Gag is a nucleocapsid protein that is the structural constituent of virus-like particles (VLPs); similar to retroviral Gag" [yeast-bovrabprots.fasta] YML040W SGDID:S000004504, Chr XIII from 196628-197950, transposable_element_gene, "Retrotransposon TYA Gag gene co-transcribed with TYB Pol; translated as TYA or TYA-TYB polyprotein; Gag is a nucleocapsid protein that is the structural constituent of virus-like particles (VLPs); similar to retroviral Gag" [yeast-bovrabprots.fasta] YJR026W SGDID:S000003787, Chr X from 472753-474075, transposable_element_gene, "Retrotransposon TYA Gag gene co-transcribed with TYB Pol; translated as TYA or TYA-TYB polyprotein; Gag is a nucleocapsid protein that is the structural constituent of virus-like particles (VLPs); similar to retroviral Gag" [yeast-contam_custom.fasta] [chemostatdb.fasta] Transposon Ty1-JR1 Gag polyprotein OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=TY1A-JR1 PE=1 SV=1 [UniProt_S_cerevisiae_20120516_05-16-2012_reversed.fasta] YJR026W SGDID:S000003787, Chr X from 472760-474082, Genome Release 64-1-1, transposable_element_gene, "Retrotransposon TYA Gag gene co-transcribed with TYB Pol; translated as TYA or TYA-TYB polyprotein; Gag is a nucleocapsid protein that is the structural constituent of virus-like particles (VLPs); similar to retroviral Gag" [yeast-030211-contam.fasta] YLR227W-A SGDID:S000007375, Chr XII from 593438-594760, Genome Release 64-1-1, transposable_element_gene, "Retrotransposon TYA Gag gene co-transcribed with TYB Pol; translated as TYA or TYA-TYB polyprotein; Gag is a nucleocapsid protein that is the structural constituent of virus-like particles (VLPs); similar to retroviral Gag" [yeast-030211-contam.fasta] YML040W SGDID:S000004504, Chr XIII from 196628-197950, Genome Release 64-1-1, transposable_element_gene, "Retrotransposon TYA Gag gene co-transcribed with TYB Pol; translated as TYA or TYA-TYB polyprotein; Gag is a nucleocapsid protein that is the structural constituent of virus-like particles (VLPs); similar to retroviral Gag" [yeast-030211-contam.fasta] Transposon Ty1-JR1 Gag polyprotein OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=TY1A-JR1 PE=2 SV=1 [YEAST.fasta.20131015] YJR026W SGDID:S000003787, Chr X from 472760-474082, Genome Release 64-2-1, transposable_element_gene, "Retrotransposon TYA Gag gene co-transcribed with TYB Pol; translated as TYA or TYA-TYB polyprotein; Gag is a nucleocapsid protein that is the structural constituent of virus-like particles (VLPs); similar to retroviral Gag" [20141208_orf_trans.fasta] YLR227W-A SGDID:S000007375, Chr XII from 593438-594760, Genome Release 64-2-1, transposable_element_gene, "Retrotransposon TYA Gag gene co-transcribed with TYB Pol; translated as TYA or TYA-TYB polyprotein; Gag is a nucleocapsid protein that is the structural constituent of virus-like particles (VLPs); similar to retroviral Gag" [20141208_orf_trans.fasta] YML040W SGDID:S000004504, Chr XIII from 196628-197950, Genome Release 64-2-1, transposable_element_gene, "Retrotransposon TYA Gag gene co-transcribed with TYB Pol; translated as TYA or TYA-TYB polyprotein; Gag is a nucleocapsid protein that is the structural constituent of virus-like particles (VLPs); similar to retroviral Gag" [20141208_orf_trans.fasta]
Organism:	Saccharomyces cerevisiae
Length:	440 amino acids
Gene Ontology:
Cellular Component:	retrotransposon nucleocapsid [ISS]
Biological Process:	transposition, RNA-mediated [ISS]
Molecular Function:	RNA binding [ISS] protein binding [ISS]

Sequence:

Sequence:
[PDR BLAST]
[ProtParam]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MESQQLSQHS HISHGSACAS VTSKEVHTNQ DPLDVSASKT EECEKASTKA NSQQTTTPAS  60
   61 SAVPENPHHA SPQPASVPPP QNGPYPQQCM MTQNQANPSG WSFYGHPSMI PYTPYQMSPM 120
  121 YFPPGPQSQF PQYPSSVGTP LSTPSPESGN TFTDSSSADS DMTSTKKYVR PPPMLTSPND 180
  181 FPNWVKTYIK FLQNSNLGGI IPTVNGKPVR QITDDELTFL YNTFQIFAPS QFLPTWVKDI 240
  241 LSVDYTDIMK ILSKSIEKMQ SDTQEANDIV TLANLQYNGS TPADAFETKV TNIIDRLNNN 300
  301 GIHINNKVAC QLIMRGLSGE YKFLRYTRHR HLNMTVAELF LDIHAIYEEQ QGSRNSKPNY 360
  361 RRNLSDEKND SRSYTNTTKP KVIARNPQKT NNSKSKTARA HNVSTSNNSP STDNDSISKS 420
  421 TTEPIQLNNK HDLHLRPGTY

Protein Complex Data

	PUBLICATION	TOPOLOGY	COCOMPLEXED PROTEINS
View Details	Qiu et al. (2008)		YDR210C-C YDR210C-D YER159C-A, YDR31... YER160C YJR027W YJR028W YJR029W YLR227W-A, YML04... YOR343W-A YOR343W-B YPR137C-A, YAR010C

Mass Spectrometry Data

The following runs contain data for this protein:

	BAIT	COMMENTS	PUBLICATION
View Run	TOR2	No Comments	Reinke A, et al. (2004)
View Run	RPA135	his-HA tag on RPA135	Schneider, DA, et al. (2006)
View Run	RPA135	his-HA tag on RPA135	Schneider, DA, et al. (2006)
View Run	RPA135	his-HA tag on RPA135	Schneider, DA, et al. (2006)
View Run	RPA135	his-HA tag on RPA135	Schneider, DA, et al. (2006)
View Run	RPA135	his-HA tag on RPA135	Schneider, DA, et al. (2006)
View Run	RPA135	his-HA tag on RPA135	Schneider, DA, et al. (2006)
View Run	RPA135	his-HA tag on RPA135	Schneider, DA, et al. (2006)
View Run	RPA135	his-HA tag on RPA135	Schneider, DA, et al. (2006)
View Run	RPA135	his-HA tag on RPA135	Schneider, DA, et al. (2006)
View Run	CEP3	sample cbf3 from feb 2005	Sandall S, et all (2006)
View Run	ZDS1	Sample 2- cpn2 from june 2005	McCusker D, et al (2007)
View Run	ZDS1	Sample 3 - cpn + atp, from june 2005	McCusker D, et al (2007)
View Run	BOI1	Sample boi 1 with ha tag from october 2005	McCusker D, et al (2007)
View Run	BOI1	Sample boi1 with gst from october 2005	McCusker D, et al (2007)
View Run	BOI1	Sample bob1 (2nd set) from october 2005	McCusker D, et al (2007)

Yeast Two-Hybrid Data

The following interactions contain this protein:

NOT SHOWING SINGLE HITS. [ Show Single Hits ]

[View our yeast two-hybrid interpretation guidelines.]

	BAIT	PREY	HITS	PUBLICATION
View Screen	RAD1	YLR227W-A, YML04...	2	Unpublished Fields Lab Data

Microscopy / Localization Data

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No microscopy data found in the PDR for this protein.

Protein Structure Data

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[View Top Sequence Alignments] [Show Ginzu Version Information]

Domains predicted:

#		Region(s)	Method	Confidence	Match Description
1	View Details	[1..164]	PSI-BLAST	3.522879	Sec24
2	View Details	[165..212]	MSA	1.170996	View MSA. No confident structure predictions are available.
3	View Details	[213..373]	deduced	N/A	No confident structure predictions are available.
4	View Details	[374..440]	FFAS03	1.34	No description for 2ihxA was found.

Reference: Malmström L, et al. (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5(4): e76. doi:10.1371/journal.pbio.0050076

Philius Transmembrane Prediction:

Protein predicted to be:	GLOBULAR (No transmembrane regions or signal peptide)
Confidence of classification:	0.98

Source: Reynolds et al. (2008)

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2