YRC Public Data Repository - Protein Structure Prediction

Protein:	YDR109C
Organism:	Saccharomyces cerevisiae
Length:	715 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 YDR109C.

Description	E-value	Query Range	Subject Range
YDR109C - Putative kinase YDR09_YEAST - Uncharacterized sugar kinase YDR109C OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=YDR... gi\|190404928 - gi\|190404928\|gb\|EDV08195.1\| conserved hypothetical protein [Saccharomyces cerevisiae RM11-1a]	0.0	[1..715]	[1..715]
GLPK2_THEMA, GLK... - Glycerol kinase 2 OS=Thermotoga maritima GN=glpK2 PE=3 SV=2, (Q9X1E4) Glycerol kinase 2 (EC 2.7.1.30... GLPK2_THEMA - Glycerol kinase 2 OS=Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) GN=glpK2 ...	0.0	[37..598]	[1..495]
gi\|7434247 - gi\|7434247\|pir\|\|C72254 glycerol kinase - Thermotoga maritima (strain MSB8) gi\|15644181, gi\|... - gi\|4981995\|gb\|AAD36500.1\|AE001795_3 glycerol kinase [Thermotoga maritima MSB8], gi\|15644181\|ref\|NP_2...	0.0	[37..585]	[1..482]
GLPK_PYRAB - Glycerol kinase OS=Pyrococcus abyssi GN=glpK PE=3 SV=1 GLPK_PYRAB - Glycerol kinase OS=Pyrococcus abyssi (strain GE5 / Orsay) GN=glpK PE=3 SV=1	0.0	[33..602]	[1..494]
GLPK_PYRFU - Glycerol kinase OS=Pyrococcus furiosus GN=glpK PE=3 SV=1 GLPK_PYRFU - Glycerol kinase OS=Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) GN=glpK PE=3 ...	0.0	[36..599]	[1..488]
GLPK_PYRKO - Glycerol kinase OS=Pyrococcus kodakaraensis GN=glpK PE=1 SV=2 GLPK_THEKO - Glycerol kinase OS=Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) GN=glpK PE=1 S...	0.0	[36..602]	[1..493]
GLPK_BACSU - Glycerol kinase OS=Bacillus subtilis GN=glpK PE=1 SV=1 gi\|2633252, gi\|1... - gi\|2633252\|emb\|CAB12757.1\| glycerol kinase [Bacillus subtilis subsp. subtilis str. 168], gi\|16077994...	0.0	[36..595]	[1..494]
GLPK_CLOPE - Glycerol kinase OS=Clostridium perfringens GN=glpK PE=3 SV=1 GLPK_CLOPE - Glycerol kinase OS=Clostridium perfringens (strain 13 / Type A) GN=glpK PE=3 SV=1 gi\|168205814, gi... - gi\|170662693\|gb\|EDT15376.1\| glycerol kinase [Clostridium perfringens E str. JGS1987], gi\|168205814\|r... gi\|182624319, gi... - gi\|182624319\|ref\|ZP_02952104.1\| glycerol kinase [Clostridium perfringens D str. JGS1721], gi\|1779105...	0.0	[36..598]	[1..498]
GLPK_CLOAB - Glycerol kinase OS=Clostridium acetobutylicum GN=glpK PE=3 SV=1 GLPK_CLOAB - Glycerol kinase OS=Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM...	0.0	[36..596]	[1..496]
GLPK_STAA2 - Glycerol kinase OS=Staphylococcus aureus (strain JH1) GN=glpK PE=3 SV=1 GLPK_STAA9 - Glycerol kinase OS=Staphylococcus aureus (strain JH9) GN=glpK PE=3 SV=1 GLPK_STAA1 - Glycerol kinase OS=Staphylococcus aureus (strain Mu3 / ATCC 700698) GN=glpK PE=3 SV=1 GLPK_STAAN - Glycerol kinase OS=Staphylococcus aureus (strain N315) GN=glpK PE=1 SV=1 gi\|269202916\|ref... - glycerol kinase [Staphylococcus aureus subsp. aureus ED98] gi\|255006086 - gi\|255006086\|ref\|ZP_05144687.2\| glycerol kinase [Staphylococcus aureus subsp. aureus Mu50-omega] GLPK_STAAM - Glycerol kinase OS=Staphylococcus aureus (strain Mu50 / ATCC 700699) GN=glpK PE=3 SV=1 gi\|25287514 - pir\|\|G89904 glycerol kinase [imported] - Staphylococcus aureus (strain N315)	0.0	[36..593]	[1..492]

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Predicted Domain #1

Region A:
Residues: [1-302]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MKSRKRQNNM QNETREPAVL SSQETSISRI SPQDPEAKFY VGVDVGTGSA RACVIDQSGN  60
   61 MLSLAEKPIK REQLISNFIT QSSREIWNAV CYCVRTVVEE SGVDPERVRG IGFDATCSLV 120
  121 VVSATNFEEI AVGPDFTNND QNIILWMDHR AMKETEEINS SGDKCLKYVG GQMSVEMEIP 180
  181 KIKWLKNNLE AGIFQDCKFF DLPDYLTFKA TGKENRSFCS AVCKQGFLPV GVEGSDIGWS 240
  241 KEFLNSIGLS ELTKNDFERL GGSLREKKNF LTAGECISPL DKKAACQLGL TEHCVVSSGI 300
  301 ID

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [533-565]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RYVDAAVVFG SALLGAAASE DFDYTREKRT LKG

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	190.9897
Match:	1bwfY_
Description:	Glycerol kinase
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
binding	1.49074335090904	bayes_pls_golite062009
protein binding	0.856838411407636	bayes_pls_golite062009
catalytic activity	0.296484721581333	bayes_pls_golite062009
unfolded protein binding	0.25172220535776	bayes_pls_golite062009
carbohydrate kinase activity	0.0904842102388556	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [303-379]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 AYAGWVGTVA AKPESAVKGL AETENYKKDF NGAIGRLAAV AGTSTCHILL SKNPIFVHGV  60
   61 WGPYRDVLAR GFWAAEG

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	190.9897
Match:	1bwfY_
Description:	Glycerol kinase
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [380-532]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GQSCTGVLLD HLITTHPAFT ELSHMANLAG VSKFEYLNKI LETLVEKRKV RSVISLAKHL  60
   61 FFYGDYHGNR SPIADPNMRA CIIGQSMDNS IEDLAVMYLS ACEFISQQTR QIIEVMLKSG 120
  121 HEINAIFMSG GQCRNSLLMR LLADCTGLPI VIP

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [566-625]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 QKSSQTKTER FNDSYSSIQK LSMEDRNSTN GFVSPHNLQL STPSAPAKIN NYSLPICTQQ  60
   61

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	190.9897
Match:	1bwfY_
Description:	Glycerol kinase
Matching Structure (courtesy of the PDB):

Predicted Domain #4

Region A:
Residues: [626-715]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PLDKTSEESS KDASLTVGQE SLGEGRYNGT SFLWKVMQEL TGNARIVNPN EKTHPDRILL  60
   61 DTKYQIFLDM IETQRKYRRM VDKVEGSFSR

[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	0.695	a.24.10	Histidine-containing phosphotransfer domain, HPT domain
View	Download	0.748	a.77.1	DEATH domain
View	Download	0.535	a.35.1	lambda repressor-like DNA-binding domains
View	Download	0.343	a.28.3	Retrovirus capsid protein C-terminal domain
View	Download	0.319	a.60.6	DNA polymerase beta, N-terminal domain-like
View	Download	0.317	a.39.1	EF-hand
View	Download	0.303	a.144.1	PABC (PABP) domain
View	Download	0.300	a.61.1	Retroviral matrix proteins
View	Download	0.296	a.1.1	Globin-like
View	Download	0.291	a.70.1	N-terminal domain of the delta subunit of the F1F0-ATP synthase
View	Download	0.283	a.81.1	N-terminal domain of DnaB helicase
View	Download	0.276	a.77.1	DEATH domain
View	Download	0.250	a.76.1	Iron-dependent represor protein, dimerization domain
View	Download	0.243	i.1.1	Ribosome and ribosomal fragments
View	Download	0.243	a.39.1	EF-hand
View	Download	0.239	a.36.1	Signal peptide-binding domain
View	Download	0.238	a.51.1	Cytochrome c oxidase subunit h
View	Download	0.237	a.177.1	Sigma2 domain of RNA polymerase sigma factors
View	Download	0.230	a.60.1	SAM/Pointed domain
View	Download	0.227	a.74.1	Cyclin-like
View	Download	0.217	a.60.4	DNA repair protein Rad51, N-terminal domain
View	Download	0.210	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.203	a.80.1	DNA polymerase III clamp loader subunits, C-terminal domain
View	Download	0.201	b.34.9	Tudor/PWWP/MBT

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: