YRC Public Data Repository - Protein Structure Prediction

Protein:	ALA1
Organism:	Saccharomyces cerevisiae
Length:	958 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 ALA1.

Description	E-value	Query Range	Subject Range
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	[10..957]	[4..876]
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	[10..957]	[4..876]
SYA_HAEDU - Alanine--tRNA ligase OS=Haemophilus ducreyi (strain 35000HP / ATCC 700724) GN=alaS PE=3 SV=1 SYA_HAEDU - Alanyl-tRNA synthetase OS=Haemophilus ducreyi GN=alaS PE=3 SV=1	0.0	[10..956]	[3..874]
SO3428 - alanyl-tRNA synthetase SYA_SHEON - Alanine--tRNA ligase OS=Shewanella oneidensis (strain MR-1) GN=alaS PE=3 SV=1	0.0	[10..957]	[4..874]
gi\|1097386, gi\|6... - gi\|609338\|gb\|AAC49007.1\| cytoplasmic alanyl-tRNA synthetase, gi\|1097386\|prf\|\|2113423A Ala-tRNA synth...	0.0	[1..958]	[1..958]
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	[10..956]	[3..874]
gi\|26336489 - gi\|26336489\|dbj\|BAC31927.1\| unnamed protein product [Mus musculus]	0.0	[9..956]	[5..963]
gi\|27262306 - gi\|27262306\|gb\|AAN87434.1\| Alanyl-tRNA synthetase [Heliobacillus mobilis]	0.0	[8..956]	[2..882]
gi\|11271393 - pir\|\|C81804 alanine-tRNA ligase (EC 6.1.1.7) NMA1788 [imported] - Neisseria meningitidis (strain Z24... SYA_NEIMA - Alanine--tRNA ligase OS=Neisseria meningitidis serogroup A / serotype 4A (strain Z2491) GN=alaS PE=3... SYA_NEIMA - Alanine--tRNA ligase OS=Neisseria meningitidis serogroup A GN=alaS PE=3 SV=1	0.0	[9..957]	[1..874]
gi\|15836729, gi\|... - gi\|9104908\|gb\|AAF82937.1\|AE003866_2 alanyl-tRNA synthetase [Xylella fastidiosa 9a5c], gi\|15836729\|re... gi\|11271364 - gi\|11271364\|pir\|\|C82844 alanyl-tRNA synthetase XF0124 [imported] - Xylella fastidiosa (strain 9a5c)	0.0	[2..957]	[32..916]

Back

Predicted Domain #1

Region A:
Residues: [1-570]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MTIGDKQKWT ATNVRNTFLD YFKSKEHKFV KSSPVVPFDD PTLLFANAGM NQYKPIFLGT  60
   61 VDPASDFYTL KRAYNSQKCI RAGGKHNDLE DVGKDSYHHT FFEMLGNWSF GDYFKKEAIT 120
  121 YSWTLLTEVY GIPKDRLYVT YFEGDEKLGL EPDTEARELW KNVGVPDDHI LPGNAKDNFW 180
  181 EMGDQGPCGP CSEIHYDRIG GRNAASLVNM DDPDVLEVWN LVFIQFNREQ DGSLKPLPAK 240
  241 HIDTGMGFER LVSVLQDVRS NYDTDVFTPL FERIQEITSV RPYSGNFGEN DKDGIDTAYR 300
  301 VLADHVRTLT FALADGGVPN NEGRGYVLRR ILRRGARYAR KYMNYPIGNF FSTLAPTLIS 360
  361 QVQDIFPELA KDPAFLFEIL DEEEASFAKT LDRGERLFEK YASAASKTES KTLDGKQVWR 420
  421 LYDTYGFPVD LTELMAEEQG LKIDGPGFEK AKQESYEASK RGGKKDQSDL IKLNVHELSE 480
  481 LNDAKVPKTN DEFKYGSANV EGTILKLHDG TNFVDEITEP GKKYGIILDK TCFYAEQGGQ 540
  541 EYDTGKIVID DAAEFNVENV QLYNGFVFHT

[Run NCBI BLAST on this sequence.]

Detection Method:	Pfam
Confidence:	288.026872
Match:	PF01411
Description:	tRNA synthetases class II (A)

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.

Predicted functions:

Term	Confidence	Notes
ligase activity, forming aminoacyl-tRNA and related compounds	7.89468709683036	bayes_pls_golite062009
ligase activity, forming carbon-oxygen bonds	7.89468709683036	bayes_pls_golite062009
aminoacyl-tRNA ligase activity	7.88410036819636	bayes_pls_golite062009
ligase activity	6.92073480193262	bayes_pls_golite062009
alanine-tRNA ligase activity	6.00693881794242	bayes_pls_golite062009
phenylalanine-tRNA ligase activity	2.99105702052936	bayes_pls_golite062009
serine-tRNA ligase activity	2.46505535069103	bayes_pls_golite062009
glycine-tRNA ligase activity	2.29229136935761	bayes_pls_golite062009
threonine-tRNA ligase activity	2.18642354927	bayes_pls_golite062009
catalytic activity	1.99372273395202	bayes_pls_golite062009
lysine-tRNA ligase activity	1.72324031407565	bayes_pls_golite062009
histidine-tRNA ligase activity	1.72215103383322	bayes_pls_golite062009
transcription regulator activity	1.47976803533584	bayes_pls_golite062009
nucleic acid binding	1.30216701059664	bayes_pls_golite062009
DNA binding	1.1862497958336	bayes_pls_golite062009
binding	1.11470390774037	bayes_pls_golite062009
asparagine-tRNA ligase activity	0.921492123574877	bayes_pls_golite062009
transcription repressor activity	0.80781620905336	bayes_pls_golite062009
transcription factor activity	0.566858624145031	bayes_pls_golite062009
RNA binding	0.0221706730298825	bayes_pls_golite062009
aspartate-tRNA ligase activity	0.00572514744734753	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [571-889]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GSLEEGKLSV GDKIIASFDE LRRFPIKNNH TGTHILNFAL KETLGNDVDQ KGSLVAPEKL  60
   61 RFDFSHKKAV SNEELKKVED ICNEQIKENL QVFYKEIPLD LAKSIDGVRA VFGETYPDPV 120
  121 RVVSVGKPIE ELLANPANEE WTKYSIEFCG GTHVNKTGDI KYFVILEESG IAKGIRRIVA 180
  181 VTGTEAFEAQ RLAEQFAADL DAADKLPFSP IKEKKLKELG VKLGQLSISV ITKNELKQKF 240
  241 NKIEKAVKDE VKSRAKKENK QTLDEVKTFF ETNENAPYLV KFIDISPNAK AITEAINYMK 300
  301 SNDSVKDKSI YLLAGNDPE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	65.69897
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: [890-958]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GRVAHGCYIS NAALAKGIDG SALAKKVSSI IGGKAGGKGN VFQGMGDKPA AIKDAVDDLE  60
   61 SLFKEKLSI

[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	0.752	0.849	mitochondrion	a.3.1	Cytochrome c
View	Download	0.722	0.008	cytoplasm	a.144.1	PABC (PABP) domain
View	Download	0.515	0.006	cytoplasm	a.4.1	Homeodomain-like
View	Download	0.560	0.000	mitochondrion	a.60.5	Barrier-to-autointegration factor, BAF
View	Download	0.542	0.000	mitochondrion	a.4.9	Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3
View	Download	0.513	N/A	N/A	a.144.2	Ribosomal protein L20
View	Download	0.436	N/A	N/A	a.159.1	Protein serine/threonine phosphatase 2C, C-terminal domain
View	Download	0.413	N/A	N/A	a.144.1	PABC (PABP) domain
View	Download	0.409	N/A	N/A	a.101.1	Uteroglobin-like
View	Download	0.393	N/A	N/A	a.6.1	Putative DNA-binding domain
View	Download	0.379	N/A	N/A	a.8.3	Families 57/38 glycoside transferase middle domain
View	Download	0.378	N/A	N/A	a.35.1	lambda repressor-like DNA-binding domains
View	Download	0.375	N/A	N/A	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.374	N/A	N/A	a.60.2	RuvA domain 2-like
View	Download	0.351	N/A	N/A	a.36.1	Signal peptide-binding domain
View	Download	0.344	N/A	N/A	a.64.1	Saposin
View	Download	0.320	N/A	N/A	a.13.1	alpha-2-Macroglobulin receptor associated protein (RAP) domain 1
View	Download	0.312	N/A	N/A	d.201.1	SRP19
View	Download	0.302	N/A	N/A	d.74.2	C-terminal domain of arginine repressor
View	Download	0.299	N/A	N/A	a.58.1	Chemotaxis receptor methyltransferase CheR, N-terminal domain
View	Download	0.285	N/A	N/A	a.4.12	TrpR-like
View	Download	0.281	N/A	N/A	a.112.1	Description not found.
View	Download	0.280	N/A	N/A	a.60.11	Hypothetical protein YjbJ
View	Download	0.277	N/A	N/A	a.156.1	S13-like H2TH domain
View	Download	0.272	N/A	N/A	a.3.1	Cytochrome c
View	Download	0.258	N/A	N/A	d.58.11	EF-G/eEF-2 domains III and V
View	Download	0.245	N/A	N/A	d.45.1	ClpS-like
View	Download	0.244	N/A	N/A	a.24.13	Domain of the SRP/SRP receptor G-proteins
View	Download	0.244	N/A	N/A	d.234.1	Proguanylin
View	Download	0.237	N/A	N/A	a.28.1	ACP-like
View	Download	0.235	N/A	N/A	a.57.1	Protein HNS-dependent expression A; HdeA
View	Download	0.233	N/A	N/A	d.80.1	Tautomerase/MIF
View	Download	0.231	N/A	N/A	a.112.1	Description not found.
View	Download	0.229	N/A	N/A	a.48.3	Conserved domain common to transcription factors TFIIS, elongin A, CRSP70
View	Download	0.225	N/A	N/A	d.51.1	Eukaryotic type KH-domain (KH-domain type I)
View	Download	0.224	N/A	N/A	d.58.25	Killer toxin KP6 alpha-subunit
View	Download	0.222	N/A	N/A	d.58.13	Anticodon-binding domain of PheRS
View	Download	0.220	N/A	N/A	c.30.1	PreATP-grasp domain
View	Download	0.217	N/A	N/A	a.24.13	Domain of the SRP/SRP receptor G-proteins
View	Download	0.215	N/A	N/A	a.8.1	Bacterial immunoglobulin/albumin-binding domains
View	Download	0.214	N/A	N/A	a.77.1	DEATH domain
View	Download	0.211	N/A	N/A	a.37.1	A DNA-binding domain in eukaryotic transcription factors
View	Download	0.211	N/A	N/A	a.4.3	ARID-like
View	Download	0.209	N/A	N/A	d.29.1	Ribosomal protein L31e
View	Download	0.206	N/A	N/A	c.15.1	BRCT domain

Predicted Domain #4

Region A:
Residues: [876-958]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KDKSIYLLAG NDPEGRVAHG CYISNAALAK GIDGSALAKK VSSIIGGKAG GKGNVFQGMG  60
   61 DKPAAIKDAV DDLESLFKEK LSI

[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	0.752	N/A	N/A	a.3.1	Cytochrome c
View	Download	0.722	N/A	N/A	a.144.1	PABC (PABP) domain
View	Download	0.586	N/A	N/A	a.144.1	PABC (PABP) domain
View	Download	0.560	N/A	N/A	a.60.5	Barrier-to-autointegration factor, BAF
View	Download	0.542	N/A	N/A	a.4.9	Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3

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: