YRC Public Data Repository - Protein Structure Prediction

Protein:	RIB4
Organism:	Saccharomyces cerevisiae
Length:	169 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 RIB4.

Description	E-value	Query Range	Subject Range
gi\|642225 - gi\|642225\|emb\|CAA79744.1\| DMRL synthase [Saccharomyces cerevisiae]	2.0E-56	[1..169]	[1..169]
gi\|11280455 - gi\|11280455\|pir\|\|C82098 riboflavin synthase, beta chain VC2268 [similarity] - Vibrio cholerae (strai... gi\|227082392, gi... - gi\|227082392\|ref\|YP_002810943.1\| 6,7-dimethyl-8-ribityllumazine synthase [Vibrio cholerae M66-2], gi... gi\|229512146, gi... - gi\|229512146\|ref\|ZP_04401625.1\| 6,7-dimethyl-8-ribityllumazine synthase [Vibrio cholerae B33], gi\|22... gi\|229507659, gi... - gi\|229507659\|ref\|ZP_04397164.1\| 6,7-dimethyl-8-ribityllumazine synthase [Vibrio cholerae BX 330286],... gi\|148876330, gi... - gi\|153828241\|ref\|ZP_01980908.1\| 6,7-dimethyl-8-ribityllumazine synthase [Vibrio cholerae 623-39], gi... gi\|229519281, gi... - gi\|229519281\|ref\|ZP_04408724.1\| 6,7-dimethyl-8-ribityllumazine synthase [Vibrio cholerae RC9], gi\|22... gi\|227014164, gi... - gi\|227118714\|ref\|YP_002820610.1\| 6,7-dimethyl-8-ribityllumazine synthase [Vibrio cholerae O395], gi\|... gi\|229513909, gi... - gi\|229513909\|ref\|ZP_04403371.1\| 6,7-dimethyl-8-ribityllumazine synthase [Vibrio cholerae TMA 21], gi... gi\|229337851, gi... - gi\|229524270\|ref\|ZP_04413675.1\| 6,7-dimethyl-8-ribityllumazine synthase [Vibrio cholerae bv. albensi... gi\|9656830, gi\|1... - gi\|9656830\|gb\|AAF95412.1\| riboflavin synthase, beta subunit [Vibrio cholerae O1 biovar El Tor str. N... gi\|229522213, gi... - gi\|229522213\|ref\|ZP_04411630.1\| 6,7-dimethyl-8-ribityllumazine synthase [Vibrio cholerae TM 11079-80... gi\|229369818, gi... - gi\|229607163\|ref\|YP_002877811.1\| 6,7-dimethyl-8-ribityllumazine synthase [Vibrio cholerae MJ-1236], ... gi\|229332505, gi... - gi\|229528731\|ref\|ZP_04418121.1\| 6,7-dimethyl-8-ribityllumazine synthase [Vibrio cholerae 12129(1)], ... gi\|254849397, gi... - gi\|254849397\|ref\|ZP_05238747.1\| 6,7-dimethyl-8-ribityllumazine synthase [Vibrio cholerae MO10], gi\|2... gi\|121628513, gi... - gi\|121729762\|ref\|ZP_01682201.1\| 6,7-dimethyl-8-ribityllumazine synthase [Vibrio cholerae V52], gi\|12... gi\|121549601, gi... - gi\|121586189\|ref\|ZP_01675980.1\| 6,7-dimethyl-8-ribityllumazine synthase [Vibrio cholerae 2740-80], g... gi\|153803020, gi... - gi\|153803020\|ref\|ZP_01957606.1\| 6,7-dimethyl-8-ribityllumazine synthase [Vibrio cholerae MZO-3], gi\|... gi\|124119721, gi... - gi\|153221374\|ref\|ZP_01952352.1\| 6,7-dimethyl-8-ribityllumazine synthase [Vibrio cholerae MAK 757], g... gi\|150423971, gi... - gi\|254286061\|ref\|ZP_04961022.1\| 6,7-dimethyl-8-ribityllumazine synthase [Vibrio cholerae AM-19226], ... gi\|126509070, gi... - gi\|153820385\|ref\|ZP_01973052.1\| 6,7-dimethyl-8-ribityllumazine synthase [Vibrio cholerae NCTC 8457],...	4.0E-53	[6..164]	[14..168]
RISB_CLOAB - 6,7-dimethyl-8-ribityllumazine synthase OS=Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / J... RISB_CLOAB - 6,7-dimethyl-8-ribityllumazine synthase OS=Clostridium acetobutylicum GN=ribH PE=3 SV=1	5.0E-53	[10..165]	[1..151]
gi\|148992756, gi... - gi\|148992756\|ref\|ZP_01822399.1\| 6,7-dimethyl-8-ribityllumazine synthase [Streptococcus pneumoniae SP... gi\|147926377, gi... - gi\|148987913\|ref\|ZP_01819376.1\| 6,7-dimethyl-8-ribityllumazine synthase [Streptococcus pneumoniae SP... gi\|148983577, gi... - gi\|148983577\|ref\|ZP_01816896.1\| 6,7-dimethyl-8-ribityllumazine synthase [Streptococcus pneumoniae SP... RISB_STRPN - 6,7-dimethyl-8-ribityllumazine synthase OS=Streptococcus pneumoniae GN=ribH PE=3 SV=1 RISB_STRPN - 6,7-dimethyl-8-ribityllumazine synthase OS=Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 ... RISB_STRR6 - 6,7-dimethyl-8-ribityllumazine synthase OS=Streptococcus pneumoniae (strain ATCC BAA-255 / R6) GN=ri... gi\|183570838, gi... - gi\|183570838\|gb\|EDT91366.1\| 6,7-dimethyl-8-ribityllumazine synthase [Streptococcus pneumoniae CDC108... gi\|172042822, gi... - gi\|172042822\|gb\|EDT50868.1\| 6,7-dimethyl-8-ribityllumazine synthase [Streptococcus pneumoniae CDC187... gi\|183573595, gi... - gi\|183573595\|gb\|EDT94123.1\| 6,7-dimethyl-8-ribityllumazine synthase [Streptococcus pneumoniae CDC028... gi\|168490359, gi... - gi\|183571316\|gb\|EDT91844.1\| 6,7-dimethyl-8-ribityllumazine synthase [Streptococcus pneumoniae SP195]... gi\|168576393, gi... - gi\|183577842\|gb\|EDT98370.1\| 6,7-dimethyl-8-ribityllumazine synthase [Streptococcus pneumoniae MLV-01... gi\|168493873, gi... - gi\|183576061\|gb\|EDT96589.1\| 6,7-dimethyl-8-ribityllumazine synthase [Streptococcus pneumoniae CDC305... RISB_STRPS - 6,7-dimethyl-8-ribityllumazine synthase OS=Streptococcus pneumoniae (strain CGSP14) GN=ribH PE=3 SV=... RISB_STRPI - 6,7-dimethyl-8-ribityllumazine synthase OS=Streptococcus pneumoniae (strain Hungary19A-6) GN=ribH PE... RISB_STRPJ - 6,7-dimethyl-8-ribityllumazine synthase OS=Streptococcus pneumoniae (strain ATCC 700669 / Spain 23F-... RISB_STRP2 - 6,7-dimethyl-8-ribityllumazine synthase OS=Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 74... RISB_STRP4 - 6,7-dimethyl-8-ribityllumazine synthase OS=Streptococcus pneumoniae serotype 19F (strain G54) GN=rib... gi\|147764683, gi... - gi\|149011047\|ref\|ZP_01832352.1\| 6,7-dimethyl-8-ribityllumazine synthase [Streptococcus pneumoniae SP... gi\|147762284, gi... - gi\|149005928\|ref\|ZP_01829657.1\| 6,7-dimethyl-8-ribityllumazine synthase [Streptococcus pneumoniae SP... gi\|149001720, gi... - gi\|149001720\|ref\|ZP_01826693.1\| 6,7-dimethyl-8-ribityllumazine synthase [Streptococcus pneumoniae SP... gi\|148996601, gi... - gi\|148996601\|ref\|ZP_01824319.1\| 6,7-dimethyl-8-ribityllumazine synthase [Streptococcus pneumoniae SP... RISB_STRZJ - 6,7-dimethyl-8-ribityllumazine synthase OS=Streptococcus pneumoniae (strain JJA) GN=ribH PE=3 SV=1 RISB_STRZP - 6,7-dimethyl-8-ribityllumazine synthase OS=Streptococcus pneumoniae (strain P1031) GN=ribH PE=3 SV=1 RISB_STRP7 - 6,7-dimethyl-8-ribityllumazine synthase OS=Streptococcus pneumoniae (strain 70585) GN=ribH PE=3 SV=1 RISB_STRZT - 6,7-dimethyl-8-ribityllumazine synthase OS=Streptococcus pneumoniae (strain Taiwan19F-14) GN=ribH PE... gi\|237649751 - gi\|237649751\|ref\|ZP_04524003.1\| riboflavin synthase subunit beta [Streptococcus pneumoniae CCRI 1974... gi\|237821449 - gi\|237821449\|ref\|ZP_04597294.1\| riboflavin synthase subunit beta [Streptococcus pneumoniae CCRI 1974... gi\|242246256, gi... - gi\|242246256\|ref\|ZP_04800693.1\| riboflavin synthase, beta subunit [Streptococcus pneumoniae TCH8431/...	4.0E-52	[10..165]	[1..151]
gi\|251814758, gi... - gi\|251814758\|ref\|ZP_04829231.1\| 6,7-dimethyl-8-ribityllumazine synthase [Staphylococcus aureus subsp... RISB_STAA2 - 6,7-dimethyl-8-ribityllumazine synthase OS=Staphylococcus aureus (strain JH1) GN=ribH PE=3 SV=1 gi\|253315861 - gi\|253315861\|ref\|ZP_04839074.1\| 6,7-dimethyl-8-ribityllumazine synthase [Staphylococcus aureus subsp... RISB_STAAN - 6,7-dimethyl-8-ribityllumazine synthase OS=Staphylococcus aureus (strain N315) GN=ribH PE=1 SV=1 gi\|255006553 - gi\|255006553\|ref\|ZP_05145154.2\| 6,7-dimethyl-8-ribityllumazine synthase [Staphylococcus aureus subsp... RISB_STAAU - 6,7-dimethyl-8-ribityllumazine synthase OS=Staphylococcus aureus GN=ribH PE=3 SV=1 RISB_STAAW - 6,7-dimethyl-8-ribityllumazine synthase OS=Staphylococcus aureus (strain MW2) GN=ribH PE=3 SV=1 RISB_STAAS - 6,7-dimethyl-8-ribityllumazine synthase OS=Staphylococcus aureus (strain MSSA476) GN=ribH PE=3 SV=1 gi\|269203404\|ref... - 6,7-dimethyl-8-ribityllumazine synthase [Staphylococcus aureus subsp. aureus ED98] RISB_STAAM - 6,7-dimethyl-8-ribityllumazine synthase OS=Staphylococcus aureus (strain Mu50 / ATCC 700699) GN=ribH... RISB_STAA9 - 6,7-dimethyl-8-ribityllumazine synthase OS=Staphylococcus aureus (strain JH9) GN=ribH PE=3 SV=1 RISB_STAA1 - 6,7-dimethyl-8-ribityllumazine synthase OS=Staphylococcus aureus (strain Mu3 / ATCC 700698) GN=ribH ...	1.0E-51	[15..165]	[9..150]
RISB_LACLA - 6,7-dimethyl-8-ribityllumazine synthase OS=Lactococcus lactis subsp. lactis (strain IL1403) GN=ribH ... RISB_LACLA - 6,7-dimethyl-8-ribityllumazine synthase OS=Lactococcus lactis subsp. lactis GN=ribH PE=3 SV=1	3.0E-51	[10..166]	[1..152]
gi\|75814844 - gi\|75814844\|ref\|ZP_00745389.1\| COG0054: Riboflavin synthase beta-chain [Vibrio cholerae V52] gi\|75827556 - gi\|75827556\|ref\|ZP_00756991.1\| COG0054: Riboflavin synthase beta-chain [Vibrio cholerae O395] RISB_VIBCH - 6,7-dimethyl-8-ribityllumazine synthase OS=Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor I... RISB_VIBCH - 6,7-dimethyl-8-ribityllumazine synthase OS=Vibrio cholerae GN=ribH PE=3 SV=2 gi\|75828877, gi\|... - gi\|75828877\|ref\|ZP_00758209.1\| COG0054: Riboflavin synthase beta-chain [Vibrio cholerae MO10], gi\|11...	3.0E-51	[10..164]	[1..151]
RISB_CLOPE - 6,7-dimethyl-8-ribityllumazine synthase OS=Clostridium perfringens GN=ribH PE=3 SV=1 gi\|170714001, gi... - gi\|170714001\|gb\|EDT26183.1\| 6,7-dimethyl-8-ribityllumazine synthase [Clostridium perfringens CPE str... RISB_CLOPE - 6,7-dimethyl-8-ribityllumazine synthase OS=Clostridium perfringens (strain 13 / Type A) GN=ribH PE=3... RISB_CLOPS - 6,7-dimethyl-8-ribityllumazine synthase OS=Clostridium perfringens (strain SM101 / Type A) GN=ribH P...	1.0E-50	[10..164]	[1..150]

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Predicted Domain #1

Region A:
Residues: [1-169]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MAVKGLGKPD QVYDGSKIRV GIIHARWNRV IIDALVKGAI ERMASLGVEE NNIIIETVPG  60
   61 SYELPWGTKR FVDRQAKLGK PLDVVIPIGV LIKGSTMHFE YISDSTTHAL MNLQEKVDMP 120
  121 VIFGLLTCMT EEQALARAGI DEAHSMHNHG EDWGAAAVEM AVKFGKNAF

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	986.39794
Match:	1ejbA_
Description:	Lumazine synthase
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
6,7-dimethyl-8-ribityllumazine synthase activity	5.61825642183907	bayes_pls_golite062009
intramolecular transferase activity, transferring acyl groups	4.02275160603209	bayes_pls_golite062009
catalytic activity	1.78070169551865	bayes_pls_golite062009
riboflavin synthase activity	1.72639804812167	bayes_pls_golite062009
isomerase activity	0.268840799327499	bayes_pls_golite062009

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: