YRC Public Data Repository - Protein Structure Prediction

Protein:	YNL040W
Organism:	Saccharomyces cerevisiae
Length:	456 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

[What does the above image mean?]

[Show Ginzu Version Information]

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 YNL040W.

Description	E-value	Query Range	Subject Range
gi\|75512393, gi\|... - gi\|75512393\|ref\|ZP_00734945.1\| COG0013: Alanyl-tRNA synthetase [Escherichia coli 53638], gi\|18849203... gi\|238901834, gi... - gi\|238901834\|ref\|YP_002927630.1\| alanyl-tRNA synthetase [Escherichia coli BW2952], gi\|238859951\|gb\|A... SYA_ECODH - Alanine--tRNA ligase OS=Escherichia coli (strain K12 / DH10B) GN=alaS PE=3 SV=1 SYA_ECOLI - Alanyl-tRNA synthetase (EC 6.1.1.7) (Alanine--tRNA ligase) (AlaRS) - Escherichia coli gi\|1800083, gi\|8... - gi\|89109484\|ref\|AP_003264.1\| alanyl-tRNA synthetase [Escherichia coli str. K-12 substr. W3110], gi\|1... EG10034 - alanyl-tRNA synthetase / Alanine--tRNA ligase, autorepressor gi\|194422121, gi... - gi\|83585644\|ref\|ZP_00924287.1\| COG0013: Alanyl-tRNA synthetase [Escherichia coli 101-1], gi\|19443900... gi\|226839360, gi... - gi\|254037736\|ref\|ZP_04871794.1\| alanyl t-RNA synthetase [Escherichia sp. 1_1_43], gi\|226839360\|gb\|EE... EG10034 - alanyl-tRNA synthetase / Alanine--tRNA ligase, autorepressor	0.0	[5..453]	[450..875]
gi\|145220 - gi\|145220\|gb\|AAA03208.1\| alanyl-tRNA synthetase [Escherichia coli]	0.0	[5..453]	[450..875]
gi\|15832808, gi\|... - gi\|15832808\|ref\|NP_311581.1\| alanyl-tRNA synthetase [Escherichia coli O157:H7 str. Sakai], gi\|133630... gi\|168774775, gi... - gi\|187769613\|gb\|EDU33457.1\| alanyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4196], gi\|168774... gi\|189003197, gi... - gi\|189003197\|gb\|EDU72183.1\| alanyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4076], gi\|168778... gi\|189377449, gi... - gi\|189377449\|gb\|EDU95865.1\| alanyl-tRNA synthetase [Escherichia coli O157:H7 str. EC508], gi\|1688002... gi\|25293071 - pir\|\|B91073 alanyl-tRNA synthetase [imported] - Escherichia coli (strain O157:H7, substrain RIMD 050... gi\|195938445 - gi\|195938445\|ref\|ZP_03083827.1\| alanyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4024] gi\|208805868, gi... - gi\|208805868\|ref\|ZP_03248205.1\| alanyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4206], gi\|20... gi\|208735038, gi... - gi\|208813761\|ref\|ZP_03255090.1\| alanyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4045], gi\|20... gi\|208738409, gi... - gi\|208818286\|ref\|ZP_03258606.1\| alanyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4042], gi\|20... gi\|209160191, gi... - gi\|209398791\|ref\|YP_002272160.1\| alanyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4115], gi\|2... gi\|168749982, gi... - gi\|188015823\|gb\|EDU53945.1\| alanyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4113], gi\|168749... gi\|189357241, gi... - gi\|189357241\|gb\|EDU75660.1\| alanyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4401], gi\|168755... gi\|189366853, gi... - gi\|189366853\|gb\|EDU85269.1\| alanyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4501], gi\|168762... SYA_ECO57 - Alanine--tRNA ligase OS=Escherichia coli O157:H7 GN=alaS PE=3 SV=2 gi\|189362083, gi... - gi\|189362083\|gb\|EDU80502.1\| alanyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4486], gi\|168768... gi\|83569947, gi\|... - gi\|83569947\|ref\|ZP_00921395.1\| COG0013: Alanyl-tRNA synthetase [Shigella dysenteriae 1012], gi\|19443... gi\|217327497, gi... - gi\|217327497\|ref\|ZP_03443580.1\| alanyl-tRNA synthetase [Escherichia coli O157:H7 str. TW14588], gi\|2... gi\|254594038, gi... - gi\|254794638\|ref\|YP_003079475.1\| alanyl-tRNA synthetase [Escherichia coli O157:H7 str. TW14359], gi\|...	0.0	[5..453]	[450..875]
gi\|12517136, gi\|... - gi\|15803211\|ref\|NP_289243.1\| alanyl-tRNA synthetase [Escherichia coli O157:H7 EDL933], gi\|12517136\|g... gi\|25293079 - pir\|\|E85917 alanyl-tRNA synthetase [imported] - Escherichia coli (strain O157:H7, substrain EDL933)	0.0	[5..435]	[450..855]
SYA_SALTI - Alanyl-tRNA synthetase OS=Salmonella typhi GN=alaS PE=3 SV=1 gi\|213852307 - gi\|213852307\|ref\|ZP_03381839.1\| alanyl-tRNA synthetase [Salmonella enterica subsp. enterica serovar ... gi\|214000006 - gi\|214000006\|ref\|ZP_03410741.1\| alanyl-tRNA synthetase [Salmonella enterica subsp. enterica serovar ... gi\|213052376 - gi\|213052376\|ref\|ZP_03345254.1\| alanyl-tRNA synthetase [Salmonella enterica subsp. enterica serovar ... gi\|213426121 - gi\|213426121\|ref\|ZP_03358871.1\| alanyl-tRNA synthetase [Salmonella enterica subsp. enterica serovar ... gi\|213579902 - gi\|213579902\|ref\|ZP_03361728.1\| alanyl-tRNA synthetase [Salmonella enterica subsp. enterica serovar ... gi\|213622611 - gi\|213622611\|ref\|ZP_03375394.1\| alanyl-tRNA synthetase [Salmonella enterica subsp. enterica serovar ... gi\|16761603 - gi\|16761603\|ref\|NP_457220.1\| alanyl-tRNA synthetase [Salmonella enterica subsp. enterica serovar Typ... SYA_SALTI - Alanine--tRNA ligase OS=Salmonella typhi GN=alaS PE=3 SV=1 gi\|29143087, gi\|... - gi\|29143087\|ref\|NP_806429.1\| alanyl-tRNA synthetase [Salmonella enterica subsp. enterica serovar Typ...	0.0	[5..453]	[450..875]
SYA_SALTY - Alanyl-tRNA synthetase OS=Salmonella typhimurium GN=alaS PE=3 SV=1 gi\|197243057, gi... - gi\|197264802\|ref\|ZP_03164876.1\| alanyl-tRNA synthetase [Salmonella enterica subsp. enterica serovar ... gi\|195633250, gi... - gi\|195633250\|gb\|EDX51664.1\| alanyl-tRNA synthetase [Salmonella enterica subsp. enterica serovar Newp... gi\|168245264, gi... - gi\|205335995\|gb\|EDZ22759.1\| alanyl-tRNA synthetase [Salmonella enterica subsp. enterica serovar Heid... gi\|194408310, gi... - gi\|194450006\|ref\|YP_002046787.1\| alanyl-tRNA synthetase [Salmonella enterica subsp. enterica serovar... SYA_SALTY - Alanine--tRNA ligase OS=Salmonella typhimurium GN=alaS PE=3 SV=1 SYA_SALTY - Alanine--tRNA ligase OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=alaS PE=3 SV... gi\|194402019, gi... - gi\|194443356\|ref\|YP_002042068.1\| alanyl-tRNA synthetase [Salmonella enterica subsp. enterica serovar... lcl\|NC_016856.1_... - [gene=alaS] [protein=alanyl-tRNA synthetase] [protein_id=YP_005238923.1] [location=complement(299160...	0.0	[5..453]	[450..875]
SYA_PASMU - Alanyl-tRNA synthetase OS=Pasteurella multocida GN=alaS PE=3 SV=1 SYA_PASMU - Alanine--tRNA ligase OS=Pasteurella multocida (strain Pm70) GN=alaS PE=3 SV=1	0.0	[5..444]	[449..863]
gi\|167467648 - gi\|167467648\|ref\|ZP_02332352.1\| alanyl-tRNA synthetase [Yersinia pestis FV-1] gi\|167057445, gi... - gi\|167423275\|ref\|ZP_02315028.1\| alanyl-tRNA synthetase [Yersinia pestis biovar Mediaevalis str. K197... SYA_YERPG - Alanine--tRNA ligase OS=Yersinia pestis bv. Antiqua (strain Angola) GN=alaS PE=3 SV=1 gi\|229695291, gi... - gi\|229838925\|ref\|ZP_04459084.1\| alanyl-tRNA synthetase [Yersinia pestis biovar Orientalis str. PEXU2... gi\|229896406, gi... - gi\|229896406\|ref\|ZP_04511574.1\| alanyl-tRNA synthetase [Yersinia pestis Pestoides A], gi\|229700480\|g... SYA_YERPE - Alanine--tRNA ligase OS=Yersinia pestis GN=alaS PE=3 SV=1 gi\|229899492, gi... - gi\|229899492\|ref\|ZP_04514633.1\| alanyl-tRNA synthetase [Yersinia pestis biovar Orientalis str. India... gi\|45435094, gi\|... - gi\|45440238\|ref\|NP_991777.1\| alanyl-tRNA synthetase [Yersinia pestis biovar Microtus str. 91001], gi... gi\|21957617, gi\|... - gi\|22124793\|ref\|NP_668216.1\| alanyl-tRNA synthetase [Yersinia pestis KIM], gi\|21957617\|gb\|AAM84467.1... gi\|165925794, gi... - gi\|165925794\|ref\|ZP_02221626.1\| alanyl-tRNA synthetase [Yersinia pestis biovar Orientalis str. F1991... gi\|115348937, gi... - gi\|218930326\|ref\|YP_002348201.1\| alanyl-tRNA synthetase [Yersinia pestis CO92], gi\|16123458\|ref\|NP_4... gi\|165915408, gi... - gi\|89105927\|ref\|ZP_01178439.1\| COG0013: Alanyl-tRNA synthetase [Yersinia pestis biovar Orientalis st... gi\|166213026, gi... - gi\|166213026\|ref\|ZP_02239061.1\| alanyl-tRNA synthetase [Yersinia pestis biovar Antiqua str. B4200300... SYA_YERPN - Alanine--tRNA ligase OS=Yersinia pestis bv. Antiqua (strain Nepal516) GN=alaS PE=3 SV=1 gi\|165991074, gi... - gi\|166010167\|ref\|ZP_02231065.1\| alanyl-tRNA synthetase [Yersinia pestis biovar Antiqua str. E1979001... gi\|166960551, gi... - gi\|167421632\|ref\|ZP_02313385.1\| alanyl-tRNA synthetase [Yersinia pestis biovar Orientalis str. MG05-... gi\|167050846, gi... - gi\|167398342\|ref\|ZP_02303866.1\| alanyl-tRNA synthetase [Yersinia pestis biovar Antiqua str. UG05-045... gi\|153997648, gi... - gi\|153997648\|ref\|ZP_02022748.1\| alanyl-tRNA synthetase [Yersinia pestis CA88-4125], gi\|149289285\|gb\|... SYA_YERPP - Alanine--tRNA ligase OS=Yersinia pestis (strain Pestoides F) GN=alaS PE=3 SV=1	0.0	[13..452]	[458..874]
gi\|10803041 - gi\|10803041\|gb\|AAG23689.1\|AF297520_1 alanyl-tRNA synthase [Haemophilus ducreyi]	0.0	[11..453]	[364..783]
SYA_HAEIN - Alanine--tRNA ligase OS=Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) GN=alaS P... SYA_HAEIN - Alanyl-tRNA synthetase OS=Haemophilus influenzae GN=alaS PE=3 SV=1	0.0	[11..449]	[455..870]

Back

Predicted Domain #1

Region A:
Residues: [1-59]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MPTPMTPVKV GALACQRNSF LFDGFKTLVV SCEPTKNKKG EIEGYEIELQ DTILFPEGG

[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	0.629	b.34.2	SH3-domain
View	Download	0.455	g.18.1	Complement control module/SCR domain
View	Download	0.677	g.41.7	Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain
View	Download	0.442	g.27.1	Fibronectin type I module
View	Download	0.438	g.18.1	Complement control module/SCR domain
View	Download	0.396	d.93.1	SH2 domain
View	Download	0.388	g.18.1	Complement control module/SCR domain
View	Download	0.373	b.122.1	PUA domain-like
View	Download	0.368	b.34.2	SH3-domain
View	Download	0.364	d.47.1	Ribosomal protein L11, N-terminal domain
View	Download	0.352	b.34.2	SH3-domain
View	Download	0.351	b.34.5	Translation proteins SH3-like domain
View	Download	0.339	g.18.1	Complement control module/SCR domain
View	Download	0.335	b.34.3	Myosin S1 fragment, N-terminal domain
View	Download	0.310	d.50.1	dsRNA-binding domain-like
View	Download	0.240	b.34.5	Translation proteins SH3-like domain
View	Download	0.222	b.5.1	alpha-Amylase inhibitor tendamistat
View	Download	0.211	b.114.1	N-utilization substance G protein NusG, insert domain
View	Download	0.206	d.93.1	SH2 domain
View	Download	0.203	b.61.3	D-aminopeptidase, middle and C-terminal domains

Predicted Domain #2

Region A:
Residues: [60-375]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GQPSDSGFLK IVEGNRNSSK IEKILVSHVS RFGLHAKHHV NDYIEPGTTV EVAVDEQKRM  60
   61 DYMQQHTGQH LLSAILERNY KVDTVSWSMG GIITKKKPVL EPSDYFNYIE LNRKLTLDEI 120
  121 TNVSDEINQL IINFPQEIIV EERIGEETVD EVSTSKIPDD YDLSKGVLRT IHIGDIDSNP 180
  181 CCGTHLKCTS QIGSILILSN QSAVRGSNSR LYFMCGKRVS LYAKSVNKIL LDSKNLLSCS 240
  241 ETQISEKITR QTKQIQQLNK REQYWIKRLA RTASEELMNT LKASGKKRAY FMEEEYGTLE 300
  301 LLLQIHKEVS NFLKDD

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	50.69897
Match:	1qf6A_
Description:	Threonyl-tRNA synthetase (ThrRS), C-terminal domain; Threonyl-tRNA synthetase (ThrRS), N-terminal 'additional' domain; Threonyl-tRNA synthetase (ThrRS), second 'additional' domain; Threonyl-tRNA synthetase (ThrRS)
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [376-456]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TEGYEIILCG YERQTNTGSL LILSESGEKI ANLAANLGSI LQNLKGGGGK KGGKWQGKIT  60
   61 SISNAEFAAL SDYLSHDFAS C

[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.

		MCM Score	GO Score	GO Term	SCOP Match	SCOP Description
View	Download	0.357	0.416	cytoplasm	a.118.1	ARM repeat
View	Download	0.469	0.327	cytoplasm	d.109.1	Actin depolymerizing proteins
View	Download	0.432	0.000	cytoplasm	a.60.9	lambda integrase-like, N-terminal domain
View	Download	0.474	0.000	cytoplasm	d.43.1	Elongation factor Ts (EF-Ts), dimerisation domain
View	Download	0.372	N/A	N/A	d.43.1	Elongation factor Ts (EF-Ts), dimerisation domain
View	Download	0.351	N/A	N/A	a.51.1	Cytochrome c oxidase subunit h
View	Download	0.315	N/A	N/A	a.81.1	N-terminal domain of DnaB helicase
View	Download	0.308	N/A	N/A	a.60.5	Barrier-to-autointegration factor, BAF
View	Download	0.299	N/A	N/A	d.54.1	Enolase N-terminal domain-like
View	Download	0.294	N/A	N/A	d.14.1	Ribosomal protein S5 domain 2-like
View	Download	0.282	N/A	N/A	d.15.1	Ubiquitin-like
View	Download	0.280	N/A	N/A	a.4.1	Homeodomain-like
View	Download	0.256	N/A	N/A	a.7.6	Ribosomal protein S20
View	Download	0.254	N/A	N/A	d.16.1	FAD-linked reductases, C-terminal domain
View	Download	0.240	N/A	N/A	d.42.1	POZ domain
View	Download	0.240	N/A	N/A	d.58.3	Protease propeptides/inhibitors
View	Download	0.236	N/A	N/A	a.71.1	Endoplasmic reticulum protein ERP29, C-domain
View	Download	0.233	N/A	N/A	a.28.1	ACP-like
View	Download	0.232	N/A	N/A	b.55.1	PH domain-like
View	Download	0.228	N/A	N/A	a.56.1	CO dehydrogenase ISP C-domain like
View	Download	0.227	N/A	N/A	a.81.1	N-terminal domain of DnaB helicase
View	Download	0.227	N/A	N/A	d.74.3	RBP11-like subunits of RNA polymerase
View	Download	0.224	N/A	N/A	a.60.2	RuvA domain 2-like
View	Download	0.222	N/A	N/A	b.55.1	PH domain-like
View	Download	0.220	N/A	N/A	d.14.1	Ribosomal protein S5 domain 2-like
View	Download	0.216	N/A	N/A	d.54.1	Enolase N-terminal domain-like
View	Download	0.216	N/A	N/A	c.2.1	NAD(P)-binding Rossmann-fold domains
View	Download	0.215	N/A	N/A	a.165.1	Myosin phosphatase inhibitor 17kDa protein, CPI-17
View	Download	0.214	N/A	N/A	d.13.1	HIT-like
View	Download	0.211	N/A	N/A	a.60.5	Barrier-to-autointegration factor, BAF
View	Download	0.206	N/A	N/A	a.2.11	Fe,Mn superoxide dismutase (SOD), N-terminal domain
View	Download	0.203	N/A	N/A	a.74.1	Cyclin-like
View	Download	0.201	N/A	N/A	a.4.5	"Winged helix" DNA-binding 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