YRC Public Data Repository - Protein Structure Prediction

Protein:	YEF3
Organism:	Saccharomyces cerevisiae
Length:	1044 amino acids
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

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Top Sequence Alignment Hits

Listed below are up to the top 10 sequence alignment matches, by species, for the PSI-BLAST search against the protein sequence for YEF3.

Description	E-value	Query Range	Subject Range
gi\|173216, gi\|17... - gi\|227236\|prf\|\|1617104A elongation factor 3, gi\|173216\|gb\|AAA35233.1\| elongation factor 3, gi\|173214...	0.0	[1..1044]	[1..1044]
gi\|3786314 - gi\|3786314\|dbj\|BAA33959.1\| translation elongation factor3 [Candida glabrata]	0.0	[1..1043]	[1..1043]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	0.0	[2..1044]	[5..1050]
EF3_CANAL - Elongation factor 3 OS=Candida albicans GN=TEF3 PE=1 SV=1	0.0	[2..1044]	[5..1049]
EF3_SCHPO - Elongation factor 3 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=tef3 PE=1 SV=1 tef3 - translation elongation factor eEF3	0.0	[2..1036]	[5..1042]
EF3_PNECA - Elongation factor 3 OS=Pneumocystis carinii GN=TEF3 PE=3 SV=1	0.0	[7..1042]	[7..1042]
gi\|13442976 - gi\|13442976\|gb\|AAK26245.1\| elongation factor 3 [Cryptococcus neoformans var. neoformans] gi\|58266210, gi\|... - gi\|58266210\|ref\|XP_570261.1\| elongation factor 3 [Cryptococcus neoformans var. neoformans JEC21], gi... gi\|134111046, gi... - gi\|50258329\|gb\|EAL21018.1\| hypothetical protein CNBD3940 [Cryptococcus neoformans var. neoformans B-...	0.0	[15..1039]	[18..1052]

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Predicted Domain #1

Region A:
Residues: [1-71]

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    1 MSDSQQSIKV LEELFQKLSV ATADNRHEIA SEVASFLNGN IIEHDVPEHF FGELAKGIKD  60
   61 KKTAANAMQA V

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	13.93
Match:	1lshA
Description:	Lipovitellin-phosvitin complex, superhelical domain; Lipovitellin-phosvitin complex; beta-sheet shell regions
Matching Structure (courtesy of the PDB):

Predicted Domain #2

Region A:
Residues: [72-179]

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    1 AHIANQSNLS PSVEPYIVQL VPAICTNAGN KDKEIQSVAS ETLISIVNAV NPVAIKALLP  60
   61 HLTNAIVETN KWQEKIAILA AISAMVDAAK DQVALRMPEL IPVLSETM

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	13.93
Match:	1lshA
Description:	Lipovitellin-phosvitin complex, superhelical domain; Lipovitellin-phosvitin complex; beta-sheet shell regions
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [180-324]

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    1 WDTKKEVKAA ATAAMTKATE TVDNKDIERF IPSLIQCIAD PTEVPETVHL LGATTFVAEV  60
   61 TPATLSIMVP LLSRGLNERE TGIKRKSAVI IDNMCKLVED PQVIAPFLGK LLPGLKSNFA 120
  121 TIADPEAREV TLRALKTLRR VGNVG

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	13.93
Match:	1lshA
Description:	Lipovitellin-phosvitin complex, superhelical domain; Lipovitellin-phosvitin complex; beta-sheet shell regions
Matching Structure (courtesy of the PDB):

Predicted Domain #4

Region A:
Residues: [325-424]

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    1 EDDAIPEVSH AGDVSTTLQV VNELLKDETV APRFKIVVEY IAAIGADLID ERIIDQQAWF  60
   61 THITPYMTIF LHEKKAKDIL DEFRKRAVDN IPVGPNFDDE

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below are all of our de novo (Rosetta) predictions for this domain.
Click here to view only most confident match.

		MCM Score	SCOP Match	SCOP Description
View	Download	0.697	a.118.1	ARM repeat
View	Download	0.674	a.85.1	Hemocyanin, N-terminal domain
View	Download	0.654	d.8.1	Urease, gamma-subunit
View	Download	0.742	a.118.11	Cytochrome c oxidase subunit E
View	Download	0.674	d.58.43	Mechanosensitive channel protein MscS (YggB), C-terminal domain
View	Download	0.635	a.45.1	Glutathione S-transferase (GST), C-terminal domain
View	Download	0.620	a.118.1	ARM repeat
View	Download	0.618	a.80.1	DNA polymerase III clamp loader subunits, C-terminal domain
View	Download	0.596	a.4.6	C-terminal effector domain of the bipartite response regulators
View	Download	0.591	a.118.1	ARM repeat
View	Download	0.584	a.80.1	DNA polymerase III clamp loader subunits, C-terminal domain
View	Download	0.573	a.60.9	lambda integrase-like, N-terminal domain
View	Download	0.566	a.69.3	1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain
View	Download	0.523	a.74.1	Cyclin-like
View	Download	0.517	a.56.1	CO dehydrogenase ISP C-domain like
View	Download	0.496	a.1.1	Globin-like
View	Download	0.493	a.7.6	Ribosomal protein S20
View	Download	0.486	a.85.1	Hemocyanin, N-terminal domain
View	Download	0.478	d.14.1	Ribosomal protein S5 domain 2-like
View	Download	0.471	a.24.13	Domain of the SRP/SRP receptor G-proteins
View	Download	0.462	a.118.8	TPR-like
View	Download	0.457	a.29.2	Bromodomain
View	Download	0.440	a.181.1	Antibiotic binding domain of TipA-like multidrug resistance regulators
View	Download	0.417	a.159.1	Protein serine/threonine phosphatase 2C, C-terminal domain
View	Download	0.413	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.412	a.74.1	Cyclin-like
View	Download	0.405	d.58.44	Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
View	Download	0.403	b.55.1	PH domain-like
View	Download	0.400	c.37.1	P-loop containing nucleoside triphosphate hydrolases
View	Download	0.397	d.13.1	HIT-like
View	Download	0.393	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.390	d.129.1	TATA-box binding protein-like
View	Download	0.388	a.74.1	Cyclin-like
View	Download	0.383	a.65.1	Annexin
View	Download	0.382	d.224.1	SufE-like
View	Download	0.382	a.39.1	EF-hand
View	Download	0.379	a.60.2	RuvA domain 2-like
View	Download	0.377	a.4.9	Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3
View	Download	0.374	a.46.1	Methionine synthase domain
View	Download	0.372	a.24.17	Group V grass pollen allergen
View	Download	0.371	a.118.9	ENTH/VHS domain
View	Download	0.367	a.51.1	Cytochrome c oxidase subunit h
View	Download	0.366	a.1.1	Globin-like
View	Download	0.365	a.60.6	DNA polymerase beta, N-terminal domain-like
View	Download	0.363	d.54.1	Enolase N-terminal domain-like
View	Download	0.361	a.5.3	N-terminal domain of phosphatidylinositol transfer protein sec14p
View	Download	0.361	a.45.1	Glutathione S-transferase (GST), C-terminal domain
View	Download	0.358	a.22.1	Histone-fold
View	Download	0.357	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.356	a.76.1	Iron-dependent represor protein, dimerization domain
View	Download	0.344	a.118.13	Arp2/3 complex 16 kDa subunit ARPC5
View	Download	0.339	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.333	a.4.1	Homeodomain-like
View	Download	0.328	a.1.1	Globin-like
View	Download	0.324	a.60.8	HRDC-like
View	Download	0.322	d.188.1	Prokaryotic ribosomal protein L17
View	Download	0.319	a.1.1	Globin-like
View	Download	0.319	a.1.1	Globin-like
View	Download	0.316	a.27.1	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
View	Download	0.314	a.45.1	Glutathione S-transferase (GST), C-terminal domain
View	Download	0.310	a.61.1	Retroviral matrix proteins
View	Download	0.309	a.44.1	Disulphide-bond formation facilitator (DSBA), insertion domain
View	Download	0.305	a.118.8	TPR-like
View	Download	0.303	a.36.1	Signal peptide-binding domain
View	Download	0.299	a.74.1	Cyclin-like
View	Download	0.294	a.133.1	Phospholipase A2, PLA2
View	Download	0.292	a.66.1	Transducin (alpha subunit), insertion domain
View	Download	0.288	a.23.5	Hemolysin expression modulating protein HHA
View	Download	0.287	a.16.1	S15/NS1 RNA-binding domain
View	Download	0.286	a.64.1	Saposin
View	Download	0.285	c.58.1	Aminoacid dehydrogenase-like, N-terminal domain
View	Download	0.285	a.45.1	Glutathione S-transferase (GST), C-terminal domain
View	Download	0.281	a.52.1	Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin
View	Download	0.280	a.60.6	DNA polymerase beta, N-terminal domain-like
View	Download	0.280	a.4.6	C-terminal effector domain of the bipartite response regulators
View	Download	0.277	a.24.4	Hemerythrin
View	Download	0.276	d.129.2	Phosphoglucomutase, C-terminal domain
View	Download	0.274	a.23.3	Methane monooxygenase hydrolase, gamma subunit
View	Download	0.274	a.96.1	DNA-glycosylase
View	Download	0.272	d.79.1	YjgF-like
View	Download	0.266	a.2.3	Chaperone J-domain
View	Download	0.265	a.24.16	Nucleotidyltransferase substrate binding subunit/domain
View	Download	0.265	a.60.9	lambda integrase-like, N-terminal domain
View	Download	0.265	a.4.1	Homeodomain-like
View	Download	0.255	a.24.15	FAD-dependent thiol oxidase
View	Download	0.253	a.1.1	Globin-like
View	Download	0.253	a.24.7	FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP)
View	Download	0.246	a.74.1	Cyclin-like
View	Download	0.245	a.70.1	N-terminal domain of the delta subunit of the F1F0-ATP synthase
View	Download	0.245	i.11.1	Computational models partly based on NMR data
View	Download	0.244	a.52.1	Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin
View	Download	0.243	a.26.1	4-helical cytokines
View	Download	0.241	a.60.5	Barrier-to-autointegration factor, BAF
View	Download	0.235	a.48.3	Conserved domain common to transcription factors TFIIS, elongin A, CRSP70
View	Download	0.232	a.146.1	Telomeric repeat binding factor (TRF) dimerisation domain
View	Download	0.232	d.55.1	Ribosomal protein L22
View	Download	0.232	a.8.3	Families 57/38 glycoside transferase middle domain
View	Download	0.230	a.24.9	alpha-catenin/vinculin
View	Download	0.228	c.95.1	Thiolase-like
View	Download	0.227	a.23.2	Diol dehydratase, gamma subunit
View	Download	0.225	f.1.4	Bcl-2 inhibitors of programmed cell death
View	Download	0.223	d.211.1	Ankyrin repeat
View	Download	0.222	d.192.1	YlxR-like
View	Download	0.222	d.39.1	Dynein light chain 8 (DLC8)
View	Download	0.221	b.82.2	Clavaminate synthase-like
View	Download	0.221	a.44.1	Disulphide-bond formation facilitator (DSBA), insertion domain
View	Download	0.220	a.77.1	DEATH domain
View	Download	0.219	a.1.1	Globin-like
View	Download	0.218	a.4.12	TrpR-like
View	Download	0.215	a.24.13	Domain of the SRP/SRP receptor G-proteins
View	Download	0.212	d.54.1	Enolase N-terminal domain-like
View	Download	0.210	a.12.1	Kix domain of CBP (creb binding protein)
View	Download	0.208	c.3.1	FAD/NAD(P)-binding domain
View	Download	0.207	a.1.1	Globin-like
View	Download	0.204	d.68.6	DNA-binding protein Sso10b (AlbA)
View	Download	0.203	a.1.1	Globin-like
View	Download	0.202	a.58.1	Chemotaxis receptor methyltransferase CheR, N-terminal domain
View	Download	0.201	b.55.1	PH domain-like

Predicted Domain #5

Region A:
Residues: [425-662]

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    1 EDEGEDLCNC EFSLAYGAKI LLNKTQLRLK RARRYGICGP NGCGKSTLMR AIANGQVDGF  60
   61 PTQEECRTVY VEHDIDGTHS DTSVLDFVFE SGVGTKEAIK DKLIEFGFTD EMIAMPISAL 120
  121 SGGWKMKLAL ARAVLRNADI LLLDEPTNHL DTVNVAWLVN YLNTCGITSI TISHDSVFLD 180
  181 NVCEYIINYE GLKLRKYKGN FTEFVKKCPA AKAYEELSNT DLEFKFPEPG YLEGVKTK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	105.0
Match:	1g291_
Description:	Maltose transport protein MalK, C-terminal domain; Maltose transport protein MalK, N-terminal domain
Matching Structure (courtesy of the PDB):

Predicted Domain #6

Region A:
Residues: [663-686]

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    1 QKAIVKVTNM EFQYPGTSKP QITD

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [707-806]

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    1 KSTLINVLTG ELLPTSGEVY THENCRIAYI KQHAFAHIES HLDKTPSEYI QWRFQTGEDR  60
   61 ETMDRANRQI NENDAEAMNK IFKIEGTPRR IAGIHSRRKF

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	4.69897
Match:	1e69A_
Description:	Smc head domain
Matching Structure (courtesy of the PDB):

Predicted Domain #7

Region A:
Residues: [687-706]

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    1 INFQCSLSSR IAVIGPNGAG

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [807-975]

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    1 KNTYEYECSF LLGENIGMKS ERWVPMMSVD NAWIPRGELV ESHSKMVAEV DMKEALASGQ  60
   61 FRPLTRKEIE EHCSMLGLDP EIVSHSRIRG LSGGQKVKLV LAAGTWQRPH LIVLDEPTNY 120
  121 LDRDSLGALS KALKEFEGGV IIITHSAEFT KNLTEEVWAV KDGRMTPSG

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	4.69897
Match:	1e69A_
Description:	Smc head domain
Matching Structure (courtesy of the PDB):

Predicted Domain #8

Region A:
Residues: [976-1044]

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    1 HNWVSGQGAG PRIEKKEDEE DKFDAMGNKI AGGKKKKKLS SAELRKKKKE RMKKKKELGD  60
   61 AYVSSDEEF

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below are all of our de novo (Rosetta) predictions for this domain.
Click here to view only most confident match.

		MCM Score	SCOP Match	SCOP Description
View	Download	0.321	a.4.1	Homeodomain-like
View	Download	0.373	a.24.13	Domain of the SRP/SRP receptor G-proteins
View	Download	0.393	a.37.1	A DNA-binding domain in eukaryotic transcription factors
View	Download	0.490	a.76.1	Iron-dependent represor protein, dimerization domain
View	Download	0.349	a.76.1	Iron-dependent represor protein, dimerization domain
View	Download	0.248	d.58.44	Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
View	Download	0.243	d.109.1	Actin depolymerizing proteins
View	Download	0.211	a.1.1	Globin-like

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

View Structure Prediction Details

Top Sequence Alignment Hits