YRC Public Data Repository - Protein Structure Prediction

Protein:	RIB1
Organism:	Saccharomyces cerevisiae
Length:	345 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 RIB1.

Description	E-value	Query Range	Subject Range
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	0.0	[1..345]	[1..345]
RIB1_YEAST - GTP cyclohydrolase-2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RIB1 PE=1 SV=2 RIB1 - GTP cyclohydrolase II; catalyzes the first step of the riboflavin biosynthesis pathway gi\|207347849 - gi\|207347849\|gb\|EDZ73895.1\| YBL033Cp-like protein [Saccharomyces cerevisiae AWRI1631] gi\|190408859 - gi\|190408859\|gb\|EDV12124.1\| GTP cyclohydrolase II [Saccharomyces cerevisiae RM11-1a]	0.0	[1..345]	[1..345]
GCH2_PICGU - GTP cyclohydrolase-2 (EC 3.5.4.25) (GTP cyclohydrolase II) - Pichia guilliermondii (Yeast) (Candida ...	1.0E-88	[31..309]	[61..326]
RIBAB_AQUAE, RIB... - Riboflavin biosynthesis protein ribBA OS=Aquifex aeolicus GN=ribBA PE=3 SV=1, Riboflavin biosynthesi... RIBBA_AQUAE - Riboflavin biosynthesis protein RibBA OS=Aquifex aeolicus (strain VF5) GN=ribBA PE=3 SV=1	2.0E-88	[58..309]	[157..406]
gi\|18309550, gi\|... - gi\|18309550\|ref\|NP_561484.1\| riboflavin biosynthesis protein RibA [Clostridium perfringens str. 13],...	8.0E-88	[58..309]	[131..379]
gi\|17132669, gi\|... - gi\|17231028\|ref\|NP_487576.1\| bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohyd... gi\|25290330 - pir\|\|AI2247 GTP cyclohydrolase II / 3,4-dihydroxy-2-butanone 4-phosphate synthase [imported] - Nosto...	6.0E-87	[58..322]	[186..453]
gi\|34873547 - gi\|34873547\|gb\|AAQ83287.1\| RibA [Cloning vector pRFN4] RIBBA_BACSU - Riboflavin biosynthesis protein RibBA OS=Bacillus subtilis (strain 168) GN=ribBA PE=3 SV=1 RIBBA_BACSU, RIB... - Riboflavin biosynthesis protein ribBA OS=Bacillus subtilis GN=ribBA PE=3 SV=1, Riboflavin biosynthes... gi\|221323765 - gi\|221323765\|ref\|ZP_03605059.1\| bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclo... gi\|221319489 - gi\|221319489\|ref\|ZP_03600783.1\| bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclo... gi\|221314567 - gi\|221314567\|ref\|ZP_03596372.1\| bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclo...	7.0E-87	[68..311]	[159..398]
gi\|25290325 - pir\|\|D83844 GTP cyclohydrolase II / 3, 4-dihydroxy-2-butanone 4-phosphate synthase ribA [imported] -... gi\|10174173, gi\|... - gi\|15614119\|ref\|NP_242422.1\| bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohyd...	3.0E-86	[58..311]	[151..401]
RIB1_SCHPO - Probable GTP cyclohydrolase-2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rib1 PE=3 SV... SPAP27G11.09c - GTP cyclohydrolase	7.0E-86	[31..312]	[63..324]

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Predicted Domain #1

Region A:
Residues: [1-134]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MTIDNYDNSK QDSSKYEVSG TGDGRNGDGG LPLVQCVARA RIPTTQGPDI FLHLYSNNRD  60
   61 NKEHLAIVFG EDIRSRSLFR RRQCETQQDR MIRGAYIGKL YPGRTVADED DRLGLALEFD 120
  121 DSTGELLASK ATTW

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	5.69897
Match:	1g57A_
Description:	3,4-dihydroxy-2-butanone 4-phosphate synthase, DHBP synthase, RibB
Matching Structure (courtesy of the PDB):

Predicted Domain #2

Region A:
Residues: [135-186]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DAHNDTLVRI HSECYTGENA WSARCDCGEQ FDRAGRLIAC DHEPTSNIKG GN

[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	0.311	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.379	a.4.6	C-terminal effector domain of the bipartite response regulators
View	Download	0.281	a.16.1	S15/NS1 RNA-binding domain
View	Download	0.282	a.4.5	"Winged helix" DNA-binding domain

Predicted functions:

Term	Confidence	Notes
GTP cyclohydrolase activity	4.36867535385235	bayes_pls_golite062009
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines	3.7708397651039	bayes_pls_golite062009
cyclohydrolase activity	3.33696578638249	bayes_pls_golite062009
catalytic activity	1.40764037338379	bayes_pls_golite062009
binding	1.36587778604607	bayes_pls_golite062009
protein binding	0.182596805520355	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [187-345]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GHGVIVYLRQ EGRGIGLGEK LKAYNLQDLG ADTVQANLML KHPVDARDFS LGKAILLDLG  60
   61 IGNVRLLTNN PEKIKQVDHA PYLKCVERVP MVPIHWTNSS EGIDSKEIEG YLRTKIERMG 120
  121 HLLTEPLKLH TNPQPTETSE AQNQNRMNSA LSSTSTLAI

[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: