YRC Public Data Repository - Protein Structure Prediction

Protein:	TYW1
Organism:	Saccharomyces cerevisiae
Length:	810 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 TYW1.

Description	E-value	Query Range	Subject Range
TYW1_YEAST - S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase OS=Saccharomyces cerevisiae (strai... gi\|151942594 - gi\|151942594\|gb\|EDN60940.1\| tRNA-YW synthesizing protein [Saccharomyces cerevisiae YJM789] TYW1 - Protein required for the synthesis of wybutosine, a modified guanosine found at the 3'-position adja... gi\|190407756 - gi\|190407756\|gb\|EDV11021.1\| hypothetical protein SCRG_02292 [Saccharomyces cerevisiae RM11-1a]	0.0	[1..810]	[1..810]
TYW1_MOUSE - S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase OS=Mus musculus GN=Tyw1 PE=1 SV=1	0.0	[139..790]	[9..716]
TYW1_SCHPO - S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase OS=Schizosaccharomyces pombe (stra... SPCC1020.08 - wybutosine biosynthesis protein Tyw1	0.0	[126..803]	[13..680]
gi\|33991532 - gi\|33991532\|gb\|AAH15591.1\| TYW1 protein [Homo sapiens]	0.0	[138..733]	[10..662]
TYW1_ARATH - S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase OS=Arabidopsis thaliana GN=TYW1 PE...	0.0	[199..795]	[44..643]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	0.0	[199..795]	[44..650]
gi\|85104851 - gi\|85104851\|ref\|XP_961821.1\| hypothetical protein NCU06633 [Neurospora crassa OR74A] gi\|28923398, gi\|... - gi\|32412015\|ref\|XP_326488.1\| hypothetical protein [Neurospora crassa], gi\|28923398\|gb\|EAA32585.1\| hy...	0.0	[145..788]	[352..1056]
TYW1_ORYSJ - S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase OS=Oryza sativa subsp. japonica GN... gi\|125545879 - gi\|125545879\|gb\|EAY92018.1\| hypothetical protein OsI_13711 [Oryza sativa Indica Group]	0.0	[206..790]	[57..646]

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Predicted Domain #1

Region A:
Residues: [1-123]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MDGFRVAGAL VVGALTAAYL YFGGRFSIAL VIIVGYGIYC NEASGGSQDS QEKLDLNKQQ  60
   61 KKPCCSDKKI ADGGKKTGGC CSDKKNGGGK GGGCCSSKGG KKGGCCSSKG GKKGGCCSSK 120
  121 KNI

[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	0.343	d.93.1	SH2 domain
View	Download	0.250	d.122.1	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
View	Download	0.386	d.131.1	DNA clamp
View	Download	0.259	c.78.2	Aspartate/glutamate racemase
View	Download	0.217	d.58.34	Formiminotransferase domain of formiminotransferase-cyclodeaminase.
View	Download	0.386	d.131.1	DNA clamp
View	Download	0.343	d.93.1	SH2 domain
View	Download	0.259	c.78.2	Aspartate/glutamate racemase
View	Download	0.250	d.122.1	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
View	Download	0.217	d.58.34	Formiminotransferase domain of formiminotransferase-cyclodeaminase.

Predicted Domain #2

Region A:
Residues: [124-173]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GDNENTATEV EKAVNYPVTV DFTEVFRKPT KKRSSTPKVF SKNSSSNSRV

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	12.522879
Match:	4nosA_
Description:	Nitric oxide (NO) synthase oxygenase domain
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [174-388]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GKKLSVSKKI GPDGLIKSAL TISNETLLSS QIYVLYSSLQ GAASKAAKSV YDKLKELDEL  60
   61 TNEPKLLNLD DLSDFDDYFI NVPVENALYV LVLPSYDIDC PLDYFLQTLE ENANDFRVDS 120
  121 FPLRKLVGYT VLGLGDSESW PEKFCYQAKR ADHWISRLGG RRIFPLGKVC MKTGGSAKID 180
  181 EWTSLLAETL KDDEPIIYEY DENADSEEDE EEGNG

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	67.39794
Match:	1j9zA_
Description:	NADPH-cytochrome p450 reductase; NADPH-cytochrome p450 reductase, N-terminal domain
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
transcription regulator activity	0.62629924591908	bayes_pls_golite062009
binding	0.523120840489436	bayes_pls_golite062009
catalytic activity	0.275631658558537	bayes_pls_golite062009

Predicted Domain #4

Region A:
Residues: [389-445]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SDELGDVEDI GGKGSNGKFS GADEIKQMVA KDSPTYKNLT KQGYKVIGSH SGVKICR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	67.39794
Match:	1j9zA_
Description:	NADPH-cytochrome p450 reductase; NADPH-cytochrome p450 reductase, N-terminal domain
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
catalytic activity	1.48331922124015	bayes_pls_golite062009
transferase activity	0.685192555939835	bayes_pls_golite062009
binding	0.60397276396442	bayes_pls_golite062009
protein binding	0.124485878765261	bayes_pls_golite062009

Predicted Domain #5

Region A:
Residues: [446-728]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 WTKNELRGKG SCYKKSLFNI ASSRCMELTP SLACSSKCVF CWRHGTNPVS KNWRWEVDEP  60
   61 EYILENALKG HYSMIKQMRG VPGVIAERFA KAFEVRHCAL SLVGEPILYP HINKFIQLLH 120
  121 QKGITSFLVC NAQHPEALRN IVKVTQLYVS IDAPTKTELK KVDRPLYKDF WERMVECLEI 180
  181 LKTVQNHQRT VFRLTLVKGF NMGDVSAYAD LVQRGLPGFI EVKGATFSGS SDGNGNPLTM 240
  241 QNIPFYEECV KFVKAFTTEL QRRGLHYDLA AEHAHSNCLL IAD

[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.

Predicted Domain #6

Region A:
Residues: [729-810]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TKFKINGEWH THIDFDKFFV LLNSGKDFTY MDYLEKTPEW ALFGNGGFAP GNTRVYRKDK  60
   61 KKQNKENQET TTRETPLPPI PA

[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	0.291	0.086	endoplasmic reticulum	a.4.1	Homeodomain-like
View	Download	0.284	0.007	endoplasmic reticulum	a.46.2	Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain
View	Download	0.263	0.001	endoplasmic reticulum	a.4.9	Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3
View	Download	0.238	N/A	N/A	a.4.1	Homeodomain-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

Predicted functions:

Predicted functions: