YRC Public Data Repository - Protein Structure Prediction

Protein:	ATG11
Organism:	Saccharomyces cerevisiae
Length:	1178 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 ATG11.

Description	E-value	Query Range	Subject Range
MYH4_PIG - Myosin-4 OS=Sus scrofa GN=MYH4 PE=2 SV=1	0.0	[29..1120]	[808..1928]
MYH2_HORSE - Myosin-2 OS=Equus caballus GN=MYH2 PE=2 SV=1	0.0	[29..1120]	[808..1928]
gi\|42476190, gi\|... - gi\|42476190\|ref\|NP_060004.2\| myosin, heavy polypeptide 2, skeletal muscle, adult [Homo sapiens], gi\|...	0.0	[29..1120]	[812..1932]
MYH2_BOVIN - Myosin-2 OS=Bos taurus GN=MYH2 PE=2 SV=1	0.0	[29..1120]	[811..1931]

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Predicted Domain #1

Region A:
Residues: [1-376]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MADADEYSTA PTQQEITPLQ TTATIINAIS GECITTNVDF FVSLDKFKQF IARKWKIPPD  60
   61 QLLILLPYGN KLKPSMFKEL LINRSFTLND FYVYDRRLFS LVSKPTPTNL LTSKDSNPMN 120
  121 SPNSNDLTET LEYLIKNSHI SQYQGSDTIM IKPMPSPLED ADVDLSRLNY HSVTSLLTTN 180
  181 LGWLSALEID VHYFKSLIPD IIAHIKRIFD GLTVCSQYLK LYCFDVESLY NSNVQFLNQL 240
  241 VDNGMTSKWE KCFNDTLSKL TALEGDSLQK FINIESLLEN EKSVKILNHS INGKLNKIKR 300
  301 EIDENASFRD IITVNIDRLR QMFTPNESKF ELEDQMAESF EVLVSEMRTR SRNVLDKEEE 360
  361 EFNSQEFLKS MNVMLE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	24.0
Match:	1i84S_
Description:	Heavy meromyosin subfragment
Matching Structure (courtesy of the PDB):

Predicted Domain #2

Region A:
Residues: [377-482]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KDKKESVKTL FTISQALYSQ IGELIDLKKS LQKHAVAILG NIAFTQMEIL GIKRLLLNEC  60
   61 NKDLELYKKY EVEFAQVEDL PLIYGLYLIE KYRRLSWFQQ ILSFIS

[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	GO Score	GO Term	SCOP Match	SCOP Description
View	Download	0.945	0.030	protein targeting to vacuole	a.7.1	Spectrin repeat
View	Download	0.961	0.030	protein targeting to vacuole	a.47.2	t-snare proteins
View	Download	0.958	0.030	protein targeting to vacuole	a.2.7	tRNA-binding arm
View	Download	0.941	0.030	protein targeting to vacuole	f.36.1	Neurotransmitter-gated ion-channel pransmembrane pore
View	Download	0.886	0.030	protein targeting to vacuole	a.24.3	Cytochromes
View	Download	0.851	0.030	protein targeting to vacuole	a.7.4	Smac/diablo
View	Download	0.836	0.030	protein targeting to vacuole	a.24.1	Apolipoprotein
View	Download	0.825	0.030	protein targeting to vacuole	a.24.9	alpha-catenin/vinculin
View	Download	0.823	0.030	protein targeting to vacuole	a.29.3	Acyl-CoA dehydrogenase C-terminal domain-like
View	Download	0.805	0.030	protein targeting to vacuole	a.2.6	Effector domain of the protein kinase pkn/prk1
View	Download	0.777	0.030	protein targeting to vacuole	a.69.1	C-terminal domain of alpha and beta subunits of F1 ATP synthase
View	Download	0.770	0.030	protein targeting to vacuole	a.47.2	t-snare proteins
View	Download	0.765	0.030	protein targeting to vacuole	a.29.3	Acyl-CoA dehydrogenase C-terminal domain-like
View	Download	0.750	0.030	protein targeting to vacuole	a.7.2	Enzyme IIa from lactose specific PTS, IIa-lac
View	Download	0.746	0.030	protein targeting to vacuole	a.24.9	alpha-catenin/vinculin
View	Download	0.697	0.030	protein targeting to vacuole	a.2.8	Eukaryotic DNA topoisomerase I, dispensable insert domain
View	Download	0.674	0.030	protein targeting to vacuole	a.24.3	Cytochromes
View	Download	0.652	0.030	protein targeting to vacuole	a.7.3	Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain
View	Download	0.652	0.030	protein targeting to vacuole	f.15.1	Small-conductance potassium channel
View	Download	0.633	0.030	protein targeting to vacuole	a.2.11	Fe,Mn superoxide dismutase (SOD), N-terminal domain
View	Download	0.607	0.030	protein targeting to vacuole	a.24.14	FAT domain of focal adhesion kinase
View	Download	0.604	0.030	protein targeting to vacuole	a.24.3	Cytochromes
View	Download	0.594	0.030	protein targeting to vacuole	a.19.1	Fertilization protein
View	Download	0.584	0.030	protein targeting to vacuole	a.23.1	HSC20 (HSCB), C-terminal oligomerisation domain
View	Download	0.575	0.030	protein targeting to vacuole	a.29.3	Acyl-CoA dehydrogenase C-terminal domain-like
View	Download	0.571	0.030	protein targeting to vacuole	f.31.1	Photosystem I reaction center subunit XI, PsaL
View	Download	0.565	0.030	protein targeting to vacuole	a.62.1	Hepatitis B viral capsid (hbcag)
View	Download	0.551	0.030	protein targeting to vacuole	a.54.1	Domain of early E2A DNA-binding protein, ADDBP
View	Download	0.525	0.030	protein targeting to vacuole	a.68.1	Wiscott-Aldrich syndrome protein, WASP, C-terminal domain
View	Download	0.521	0.030	protein targeting to vacuole	a.85.1	Hemocyanin, N-terminal domain
View	Download	0.499	0.030	protein targeting to vacuole	a.25.1	Ferritin-like
View	Download	0.496	0.030	protein targeting to vacuole	a.61.1	Retroviral matrix proteins
View	Download	0.492	0.030	protein targeting to vacuole	f.14.1	Voltage-gated potassium channels
View	Download	0.477	0.030	protein targeting to vacuole	a.74.1	Cyclin-like
View	Download	0.470	0.030	protein targeting to vacuole	a.60.10	Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain
View	Download	0.465	0.030	protein targeting to vacuole	d.87.1	FAD/NAD-linked reductases, dimerisation (C-terminal) domain
View	Download	0.456	0.030	protein targeting to vacuole	a.30.2	Homodimeric domain of signal transducing histidine kinase
View	Download	0.456	0.030	protein targeting to vacuole	a.24.3	Cytochromes
View	Download	0.443	0.030	protein targeting to vacuole	a.7.7	BAG domain
View	Download	0.432	0.030	protein targeting to vacuole	f.34.1	Mechanosensitive channel protein MscS (YggB), transmembrane region
View	Download	0.421	0.030	protein targeting to vacuole	a.46.1	Methionine synthase domain
View	Download	0.404	0.030	protein targeting to vacuole	a.22.1	Histone-fold
View	Download	0.399	0.030	protein targeting to vacuole	i.11.1	Computational models partly based on NMR data
View	Download	0.393	0.030	protein targeting to vacuole	a.24.13	Domain of the SRP/SRP receptor G-proteins
View	Download	0.384	0.030	protein targeting to vacuole	a.7.8	GAT domain
View	Download	0.384	0.030	protein targeting to vacuole	a.85.1	Hemocyanin, N-terminal domain
View	Download	0.382	0.030	protein targeting to vacuole	f.17.1	F1F0 ATP synthase subunit C
View	Download	0.375	0.030	protein targeting to vacuole	a.24.16	Nucleotidyltransferase substrate binding subunit/domain
View	Download	0.371	0.030	protein targeting to vacuole	a.22.1	Histone-fold
View	Download	0.369	0.030	protein targeting to vacuole	a.74.1	Cyclin-like
View	Download	0.366	0.030	protein targeting to vacuole	a.25.1	Ferritin-like
View	Download	0.362	0.030	protein targeting to vacuole	a.2.3	Chaperone J-domain
View	Download	0.351	0.030	protein targeting to vacuole	a.61.1	Retroviral matrix proteins
View	Download	0.351	0.030	protein targeting to vacuole	a.22.1	Histone-fold
View	Download	0.340	0.030	protein targeting to vacuole	f.25.1	Cytochrome c oxidase subunit III-like
View	Download	0.339	0.030	protein targeting to vacuole	a.2.5	Prefoldin
View	Download	0.331	0.030	protein targeting to vacuole	a.24.4	Hemerythrin
View	Download	0.322	0.030	protein targeting to vacuole	a.24.17	Group V grass pollen allergen
View	Download	0.320	0.030	protein targeting to vacuole	a.26.1	4-helical cytokines
View	Download	0.318	0.030	protein targeting to vacuole	a.13.1	alpha-2-Macroglobulin receptor associated protein (RAP) domain 1
View	Download	0.315	0.030	protein targeting to vacuole	a.24.16	Nucleotidyltransferase substrate binding subunit/domain
View	Download	0.306	0.030	protein targeting to vacuole	a.45.1	Glutathione S-transferase (GST), C-terminal domain
View	Download	0.306	0.030	protein targeting to vacuole	a.30.2	Homodimeric domain of signal transducing histidine kinase
View	Download	0.305	0.030	protein targeting to vacuole	a.45.1	Glutathione S-transferase (GST), C-terminal domain
View	Download	0.305	0.030	protein targeting to vacuole	f.21.2	Fumarate reductase respiratory complex transmembrane subunits
View	Download	0.300	0.030	protein targeting to vacuole	a.2.7	tRNA-binding arm
View	Download	0.299	0.030	protein targeting to vacuole	a.22.1	Histone-fold
View	Download	0.297	0.030	protein targeting to vacuole	a.24.9	alpha-catenin/vinculin
View	Download	0.297	0.030	protein targeting to vacuole	a.24.7	FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP)
View	Download	0.295	0.030	protein targeting to vacuole	a.2.11	Fe,Mn superoxide dismutase (SOD), N-terminal domain
View	Download	0.292	0.030	protein targeting to vacuole	d.67.3	Ribosome recycling factor, RRF
View	Download	0.291	0.030	protein targeting to vacuole	a.22.1	Histone-fold
View	Download	0.290	0.030	protein targeting to vacuole	a.158.1	F-box domain
View	Download	0.288	0.030	protein targeting to vacuole	d.8.1	Urease, gamma-subunit
View	Download	0.285	0.030	protein targeting to vacuole	a.2.1	GreA transcript cleavage protein, N-terminal domain
View	Download	0.284	0.030	protein targeting to vacuole	f.14.1	Voltage-gated potassium channels
View	Download	0.281	0.030	protein targeting to vacuole	f.18.1	F1F0 ATP synthase subunit A
View	Download	0.278	0.030	protein targeting to vacuole	a.21.1	HMG-box
View	Download	0.278	0.030	protein targeting to vacuole	a.142.1	PTS-regulatory domain, PRD
View	Download	0.273	0.030	protein targeting to vacuole	a.47.2	t-snare proteins
View	Download	0.273	0.030	protein targeting to vacuole	a.24.10	Histidine-containing phosphotransfer domain, HPT domain
View	Download	0.271	0.030	protein targeting to vacuole	a.4.1	Homeodomain-like
View	Download	0.270	0.030	protein targeting to vacuole	a.63.1	Apolipophorin-III
View	Download	0.264	0.030	protein targeting to vacuole	a.7.6	Ribosomal protein S20
View	Download	0.264	0.030	protein targeting to vacuole	a.118.1	ARM repeat
View	Download	0.262	0.030	protein targeting to vacuole	a.26.1	4-helical cytokines
View	Download	0.261	0.030	protein targeting to vacuole	d.122.1	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
View	Download	0.261	0.030	protein targeting to vacuole	a.30.1	ROP protein
View	Download	0.260	0.030	protein targeting to vacuole	a.4.12	TrpR-like
View	Download	0.257	0.030	protein targeting to vacuole	a.2.7	tRNA-binding arm
View	Download	0.257	0.030	protein targeting to vacuole	a.24.16	Nucleotidyltransferase substrate binding subunit/domain
View	Download	0.257	0.030	protein targeting to vacuole	a.60.6	DNA polymerase beta, N-terminal domain-like
View	Download	0.256	0.030	protein targeting to vacuole	a.71.1	Endoplasmic reticulum protein ERP29, C-domain
View	Download	0.253	0.030	protein targeting to vacuole	f.25.1	Cytochrome c oxidase subunit III-like
View	Download	0.253	0.030	protein targeting to vacuole	a.177.1	Sigma2 domain of RNA polymerase sigma factors
View	Download	0.253	0.030	protein targeting to vacuole	d.222.1	YbaB-like
View	Download	0.251	0.030	protein targeting to vacuole	a.26.1	4-helical cytokines
View	Download	0.250	0.030	protein targeting to vacuole	a.45.1	Glutathione S-transferase (GST), C-terminal domain
View	Download	0.250	0.030	protein targeting to vacuole	a.27.1	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
View	Download	0.249	0.030	protein targeting to vacuole	g.36.1	Ferredoxin thioredoxin reductase (FTR), catalytic beta chain
View	Download	0.245	0.030	protein targeting to vacuole	a.24.17	Group V grass pollen allergen
View	Download	0.243	0.030	protein targeting to vacuole	d.228.1	Replication modulator SeqA, C-terminal DNA-binding domain
View	Download	0.242	0.030	protein targeting to vacuole	a.29.2	Bromodomain
View	Download	0.242	0.030	protein targeting to vacuole	a.74.1	Cyclin-like
View	Download	0.242	0.030	protein targeting to vacuole	a.133.1	Phospholipase A2, PLA2
View	Download	0.240	0.030	protein targeting to vacuole	a.90.1	Transcription factor STAT-4 N-domain
View	Download	0.239	0.030	protein targeting to vacuole	a.118.7	14-3-3 protein
View	Download	0.238	0.030	protein targeting to vacuole	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.237	0.030	protein targeting to vacuole	f.13.1	Family A G protein-coupled receptor-like
View	Download	0.237	0.030	protein targeting to vacuole	f.32.1	a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
View	Download	0.234	0.030	protein targeting to vacuole	a.121.1	Tetracyclin repressor-like, C-terminal domain
View	Download	0.230	0.030	protein targeting to vacuole	a.118.8	TPR-like
View	Download	0.229	0.030	protein targeting to vacuole	a.59.1	PAH2 domain
View	Download	0.227	0.030	protein targeting to vacuole	a.24.11	Bacterial GAP domain
View	Download	0.227	0.030	protein targeting to vacuole	a.52.1	Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin
View	Download	0.227	0.030	protein targeting to vacuole	a.37.1	A DNA-binding domain in eukaryotic transcription factors
View	Download	0.225	0.030	protein targeting to vacuole	a.48.2	Transferrin receptor ectodomain, C-terminal domain
View	Download	0.223	0.030	protein targeting to vacuole	a.26.1	4-helical cytokines
View	Download	0.223	0.030	protein targeting to vacuole	a.151.1	Glutamyl tRNA-reductase dimerization domain
View	Download	0.220	0.030	protein targeting to vacuole	a.21.1	HMG-box
View	Download	0.219	0.030	protein targeting to vacuole	a.29.4	RecG, N-terminal domain
View	Download	0.219	0.030	protein targeting to vacuole	a.47.2	t-snare proteins
View	Download	0.218	0.030	protein targeting to vacuole	d.26.1	FKBP-like
View	Download	0.213	0.030	protein targeting to vacuole	a.39.1	EF-hand
View	Download	0.213	0.030	protein targeting to vacuole	a.142.1	PTS-regulatory domain, PRD
View	Download	0.211	0.030	protein targeting to vacuole	f.13.1	Family A G protein-coupled receptor-like
View	Download	0.207	0.030	protein targeting to vacuole	a.48.3	Conserved domain common to transcription factors TFIIS, elongin A, CRSP70
View	Download	0.206	0.030	protein targeting to vacuole	a.26.1	4-helical cytokines
View	Download	0.205	0.030	protein targeting to vacuole	f.1.3	delta-Endotoxin (insectocide), N-terminal domain
View	Download	0.202	0.030	protein targeting to vacuole	a.39.1	EF-hand
View	Download	0.201	0.030	protein targeting to vacuole	d.54.1	Enolase N-terminal domain-like
View	Download	0.201	0.030	protein targeting to vacuole	a.11.2	Second domain of FERM

Predicted functions:

Term	Confidence	Notes
binding	2.24002842608348	bayes_pls_golite062009
nucleic acid binding	1.29023721388505	bayes_pls_golite062009
transcription regulator activity	1.23558162468883	bayes_pls_golite062009
DNA binding	1.22770101477594	bayes_pls_golite062009
protein binding	1.03780839342631	bayes_pls_golite062009
transcription factor activity	0.65548647141585	bayes_pls_golite062009
RNA polymerase II transcription factor activity	0.16394692014973	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [483-553]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NFNQDLELFK QNELRTRNKW VKNFGSIATV FCEDLLSSSD FKRLNEYHSH TSPPNEDEED  60
   61 ENENSIANYR Q

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	8.30103
Match:	2tmaA_
Description:	Tropomyosin
Matching Structure (courtesy of the PDB):

Predicted Domain #4

Region A:
Residues: [554-636]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DLVKVSQAID NYMTQIKETD VSEPIIDLLS KTLFETKRFH IIYSNFKNNN NNSSNGNSIS  60
   61 PEGSIALKSD DVVKGYKTRI KKL

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	8.30103
Match:	2tmaA_
Description:	Tropomyosin
Matching Structure (courtesy of the PDB):

Predicted Domain #5

Region A:
Residues: [637-698]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ESLLHEFQYS DIGHWPQGVL NTHLKPFRGS ATSINKKKFL GASVLLEPAN ISEVNIDSVS  60
   61 QA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	8.30103
Match:	2tmaA_
Description:	Tropomyosin
Matching Structure (courtesy of the PDB):

Predicted Domain #6

Region A:
Residues: [699-768]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NNHQIQELES NVDDLLHQLQ LLKEENNRKS MQISEMGKKI SDLEVEKTAY RETLTNLNQE  60
   61 LARLTNEEQS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	8.30103
Match:	2tmaA_
Description:	Tropomyosin
Matching Structure (courtesy of the PDB):

Predicted Domain #7

Region A:
Residues: [769-925]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 HRTEIFTLNA SFKKQLNDII SQDNEKIEKL TGDYDDVSKS RERLQMDLDE SNKKHEQEVN  60
   61 LLKADIERLG KQIVTSEKSY AETNSSSMEK GEKFETIPLA EDPGRENQIS AYTQTLQDRI 120
  121 FDIISTNIFI LENIGLLLTF DNNNNIQIRR VKGLKKG

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	4.0
Match:	1jchA_
Description:	Ribonuclease domain of colicin E3; Colicin E3 translocation domain; Colicin E3 receptor domain
Matching Structure (courtesy of the PDB):

Predicted Domain #8

Region A:
Residues: [926-1178]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TAQSNILDES TQMLDAHDNS LIKSPVFQKL KDEYELIKSV ANGSEKDTQQ SIFLGNITQL  60
   61 YDNKLYEVAV IRRFKDIETL AKKLTKENKI KRTLLERFQR EKVTLRNFQI GDLALFLPTR 120
  121 ENVNSVGSMS SSTSSLSSSF SSVDLSTPPP LDAMSIQSSP SVIHSNVINQ ASISGRDKNK 180
  181 LMRPWAAFTA FEESTRYFLK DEKGLTKGKE WFVGRIVTLE HFVADSPSNN PFRLPKGSVW 240
  241 FQVTAVVVSY QGV

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below are all of our structure predictions for this domain.
Click here to view only most confident match.

Found no structure predictions for this domain.

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

Predicted functions: