YRC Public Data Repository - Protein Structure Prediction

Protein:	TRM9
Organism:	Saccharomyces cerevisiae
Length:	279 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 TRM9.

Description	E-value	Query Range	Subject Range
ALKB8_MACFA - Alkylated DNA repair protein alkB homolog 8 OS=Macaca fascicularis GN=ALKBH8 PE=2 SV=1	1.0E-55	[2..278]	[363..663]
TRM9 - tRNA methyltransferase, catalyzes esterification of modified uridine nucleotides in tRNA(Arg3) and t... TRM9_YEAST - tRNA (carboxymethyluridine(34)-5-O)-methyltransferase OS=Saccharomyces cerevisiae (strain ATCC 20450...	1.0E-52	[1..279]	[1..279]
CG17807-PA - This gene is referred to in FlyBase by the symbol Dmel\CG17807 (CG17807, FBgn0034748). It is a prote...	3.0E-46	[5..278]	[355..609]
UBIE_PSEPU - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Pseudomonas putida GN=ubiE PE=3 SV=1	6.0E-46	[2..208]	[25..242]
UBIE_PASMU - Ubiquinone/menaquinone biosynthesis methyltransferase ubiE OS=Pasteurella multocida GN=ubiE PE=3 SV=... UBIE_PASMU - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Pasteurella multocida (strain Pm70) ...	7.0E-46	[2..209]	[37..255]
UBIE_PSEAE - Ubiquinone/menaquinone biosynthesis methyltransferase ubiE OS=Pseudomonas aeruginosa GN=ubiE PE=3 SV... UBIE_PSEA8 - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Pseudomonas aeruginosa (strain LESB5... gi\|254244055, gi... - gi\|84323851\|ref\|ZP_00971918.1\| COG2226: Methylase involved in ubiquinone/menaquinone biosynthesis [P... gi\|126170161, gi... - gi\|84317690\|ref\|ZP_00966128.1\| COG2226: Methylase involved in ubiquinone/menaquinone biosynthesis [P... UBIE_PSEAB - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Pseudomonas aeruginosa (strain UCBPP... UBIE_PSEAE - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Pseudomonas aeruginosa (strain ATCC ...	8.0E-46	[2..208]	[25..242]
MENG_STAA1 - Demethylmenaquinone methyltransferase OS=Staphylococcus aureus (strain Mu3 / ATCC 700698) GN=menG PE... MENG_STAAW - Demethylmenaquinone methyltransferase OS=Staphylococcus aureus (strain MW2) GN=menG PE=3 SV=1 MENG_STAAE - Demethylmenaquinone methyltransferase OS=Staphylococcus aureus (strain Newman) GN=menG PE=3 SV=1 MENG_STAA9 - Demethylmenaquinone methyltransferase OS=Staphylococcus aureus (strain JH9) GN=menG PE=3 SV=1 gi\|269203096\|ref... - ubiquinone/menaquinone biosynthesis methyltransferase [Staphylococcus aureus subsp. aureus ED98] gi\|25304996 - pir\|\|G89925 menaquinone biosynthesis methyltransferase [imported] - Staphylococcus aureus (strain N3... MENG_STAAT - Demethylmenaquinone methyltransferase OS=Staphylococcus aureus (strain USA300 / TCH1516) GN=menG PE=... gi\|221140962 - gi\|221140962\|ref\|ZP_03565455.1\| ubiquinone/menaquinone biosynthesis methyltransferase [Staphylococcu... MENG_STAAS - Demethylmenaquinone methyltransferase OS=Staphylococcus aureus (strain MSSA476) GN=menG PE=3 SV=1 gi\|221138325 - gi\|221138325\|ref\|ZP_03563127.1\| ubiquinone/menaquinone biosynthesis methyltransferase [Staphylococcu... MENG_STAAM - Demethylmenaquinone methyltransferase OS=Staphylococcus aureus (strain Mu50 / ATCC 700699) GN=menG P... MENG_STAAN - Demethylmenaquinone methyltransferase OS=Staphylococcus aureus (strain N315) GN=menG PE=1 SV=1 gi\|251802063, gi... - gi\|251814398\|ref\|ZP_04828871.1\| ubiquinone/menaquinone biosynthesis methyltransferase [Staphylococcu... gi\|253315978 - gi\|253315978\|ref\|ZP_04839191.1\| ubiquinone/menaquinone biosynthesis methyltransferase [Staphylococcu... gi\|253732113, gi... - gi\|253732113\|ref\|ZP_04866278.1\| ubiquinone/menaquinone biosynthesis methyltransferase [Staphylococcu... gi\|253728822, gi... - gi\|253733282\|ref\|ZP_04867447.1\| ubiquinone/menaquinone biosynthesis methyltransferase [Staphylococcu... gi\|255006257 - gi\|255006257\|ref\|ZP_05144858.2\| ubiquinone/menaquinone biosynthesis methyltransferase [Staphylococcu... MENG_STAA2 - Demethylmenaquinone methyltransferase OS=Staphylococcus aureus (strain JH1) GN=menG PE=3 SV=1 MENG_STAAC - Demethylmenaquinone methyltransferase OS=Staphylococcus aureus (strain COL) GN=menG PE=3 SV=1	4.0E-45	[3..210]	[7..222]
UBIE_VIBCH - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Vibrio cholerae serotype O1 (strain ... UBIE_VIBCM - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Vibrio cholerae serotype O1 (strain ... gi\|229508366, gi... - gi\|229508366\|ref\|ZP_04397870.1\| ubiquinone/menaquinone biosynthesis methyltransferase UbiE/COQ5 [Vib... gi\|229346129, gi... - gi\|229517066\|ref\|ZP_04406512.1\| ubiquinone/menaquinone biosynthesis methyltransferase UbiE/COQ5 [Vib... gi\|229520118, gi... - gi\|229520118\|ref\|ZP_04409546.1\| ubiquinone/menaquinone biosynthesis methyltransferase UbiE/COQ5 [Vib... gi\|229527169, gi... - gi\|229527169\|ref\|ZP_04416563.1\| ubiquinone/menaquinone biosynthesis methyltransferase UbiE/COQ5 [Vib... gi\|229369296, gi... - gi\|229606641\|ref\|YP_002877289.1\| ubiquinone/menaquinone biosynthesis methyltransferase UbiE/COQ5 [Vi... gi\|121587669, gi... - gi\|121587669\|ref\|ZP_01677432.1\| ubiquinone/menaquinone biosynthesis methlytransferase UbiE [Vibrio c... gi\|124115249, gi... - gi\|153214643\|ref\|ZP_01949519.1\| ubiquinone/menaquinone biosynthesis methlytransferase UbiE [Vibrio c... gi\|254851469, gi... - gi\|75829374\|ref\|ZP_00758679.1\| COG2226: Methylase involved in ubiquinone/menaquinone biosynthesis [V... gi\|153222877, gi... - gi\|153222877\|ref\|ZP_01953501.1\| ubiquinone/menaquinone biosynthesis methlytransferase UbiE [Vibrio c... gi\|153801700, gi... - gi\|153801700\|ref\|ZP_01956286.1\| ubiquinone/menaquinone biosynthesis methlytransferase UbiE [Vibrio c... gi\|116216422, gi... - gi\|75823221\|ref\|ZP_00752740.1\| COG2226: Methylase involved in ubiquinone/menaquinone biosynthesis [V... gi\|153818222, gi... - gi\|153818222\|ref\|ZP_01970889.1\| ubiquinone/menaquinone biosynthesis methlytransferase UbiE [Vibrio c... UBIE_VIBC3 - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Vibrio cholerae serotype O1 (strain ... gi\|126520347, gi... - gi\|229508952\|ref\|ZP_04398442.1\| ubiquinone/menaquinone biosynthesis methyltransferase UbiE/COQ5 [Vib... gi\|121727801, gi... - gi\|75816414\|ref\|ZP_00746885.1\| COG2226: Methylase involved in ubiquinone/menaquinone biosynthesis [V... gi\|254291829, gi... - gi\|254291829\|ref\|ZP_04962613.1\| ubiquinone/menaquinone biosynthesis methlytransferase UbiE [Vibrio c... gi\|153829106, gi... - gi\|153829106\|ref\|ZP_01981773.1\| ubiquinone/menaquinone biosynthesis methlytransferase UbiE [Vibrio c... UBIE_VIBCH - Ubiquinone/menaquinone biosynthesis methyltransferase ubiE OS=Vibrio cholerae GN=ubiE PE=3 SV=1 gi\|149739586, gi... - gi\|153826648\|ref\|ZP_01979315.1\| ubiquinone/menaquinone biosynthesis methlytransferase UbiE [Vibrio c...	4.0E-45	[6..210]	[33..248]
UBIE_SALTI - Ubiquinone/menaquinone biosynthesis methyltransferase ubiE OS=Salmonella typhi GN=ubiE PE=3 SV=1 UBIE_SALTI - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Salmonella typhi GN=ubiE PE=3 SV=1 UBIE_SALCH - Ubiquinone/menaquinone biosynthesis methyltransferase ubiE OS=Salmonella choleraesuis GN=ubiE PE=3 S... gi\|16762164 - gi\|16762164\|ref\|NP_457781.1\| ubiquinone/menaquinone biosynthesis methyltransferase [Salmonella enter... UBIE_SALTY - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Salmonella typhimurium (strain LT2 /... gi\|29139288, gi\|... - gi\|29143653\|ref\|NP_806995.1\| ubiquinone/menaquinone biosynthesis methyltransferase [Salmonella enter... gi\|238912974 - gi\|238912974\|ref\|ZP_04656811.1\| ubiquinone/menaquinone biosynthesis methyltransferase [Salmonella en... UBIE_SALCH - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Salmonella choleraesuis (strain SC-B... UBIE_SALPA - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Salmonella paratyphi A (strain ATCC ... lcl\|NC_016856.1_... - [gene=ubiE] [protein=ubiquinone/menaquinone biosynthesis methyltransferase] [protein_id=YP_005240235... gi\|168822658, gi... - gi\|205340946\|gb\|EDZ27710.1\| ubiquinone/menaquinone biosynthesis methyltransferase UbiE [Salmonella e... UBIE_SALNS - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Salmonella newport (strain SL254) GN... UBIE_SALHS - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Salmonella heidelberg (strain SL476)... gi\|194470348, gi... - gi\|194470348\|ref\|ZP_03076332.1\| ubiquinone/menaquinone biosynthesis methyltransferase UbiE [Salmonel... gi\|197288775, gi... - gi\|197288775\|gb\|EDY28150.1\| ubiquinone/menaquinone biosynthesis methyltransferase UbiE [Salmonella e... gi\|205336500, gi... - gi\|205336500\|gb\|EDZ23264.1\| ubiquinone/menaquinone biosynthesis methyltransferase UbiE [Salmonella e... gi\|168263138, gi... - gi\|205348076\|gb\|EDZ34707.1\| ubiquinone/menaquinone biosynthesis methyltransferase UbiE [Salmonella e... gi\|168467613, gi... - gi\|195629964\|gb\|EDX48624.1\| ubiquinone/menaquinone biosynthesis methyltransferase UbiE [Salmonella e... UBIE_SALTY - Ubiquinone/menaquinone biosynthesis methyltransferase ubiE OS=Salmonella typhimurium GN=ubiE PE=3 SV... gi\|205322164, gi... - gi\|205322164\|gb\|EDZ10003.1\| ubiquinone/menaquinone biosynthesis methyltransferase UbiE [Salmonella e... UBIE_SALPB - Ubiquinone/menaquinone biosynthesis methyltransferase ubiE OS=Salmonella paratyphi B (strain ATCC BA... gi\|205328148, gi... - gi\|205328148\|gb\|EDZ14912.1\| ubiquinone/menaquinone biosynthesis methyltransferase UbiE [Salmonella e... UBIE_SALPA - Ubiquinone/menaquinone biosynthesis methyltransferase ubiE OS=Salmonella paratyphi A GN=ubiE PE=3 SV... gi\|205332091, gi... - gi\|205332091\|gb\|EDZ18855.1\| ubiquinone/menaquinone biosynthesis methyltransferase UbiE [Salmonella e... UBIE_SALCH - Ubiquinone/menaquinone biosynthesis methyltransferase ubiE OS=Salmonella choleraesuis GN=ubiE PE=3 S... UBIE_SALTY - Ubiquinone/menaquinone biosynthesis methyltransferase ubiE OS=Salmonella typhimurium GN=ubiE PE=3 SV... gi\|213613265 - gi\|213613265\|ref\|ZP_03371091.1\| ubiquinone/menaquinone biosynthesis methyltransferase [Salmonella en... gi\|213646460 - gi\|213646460\|ref\|ZP_03376513.1\| ubiquinone/menaquinone biosynthesis methyltransferase [Salmonella en... UBIE_SALPB - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Salmonella paratyphi B (strain ATCC ... gi\|213980489 - gi\|213980489\|ref\|ZP_03407748.1\| ubiquinone/menaquinone biosynthesis methyltransferase [Salmonella en... UBIE_SALPC - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Salmonella paratyphi C (strain RKS45... UBIE_SALEP - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Salmonella enteritidis PT4 (strain P... gi\|213023279 - gi\|213023279\|ref\|ZP_03337726.1\| ubiquinone/menaquinone biosynthesis methyltransferase [Salmonella en... gi\|213052868 - gi\|213052868\|ref\|ZP_03345746.1\| ubiquinone/menaquinone biosynthesis methyltransferase [Salmonella en... gi\|213427342 - gi\|213427342\|ref\|ZP_03360092.1\| ubiquinone/menaquinone biosynthesis methyltransferase [Salmonella en... UBIE_SALDC - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Salmonella dublin (strain CT_0202185... gi\|200389228, gi... - gi\|200389228\|ref\|ZP_03215840.1\| ubiquinone/menaquinone biosynthesis methyltransferase UbiE [Salmonel... gi\|204320666, gi... - gi\|204930262\|ref\|ZP_03221239.1\| ubiquinone/menaquinone biosynthesis methyltransferase UbiE [Salmonel... UBIE_SALG2 - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Salmonella gallinarum (strain 287/91... UBIE_SALSV - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Salmonella schwarzengrund (strain CV... UBIE_SALA4 - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Salmonella agona (strain SL483) GN=u... gi\|197242042, gi... - gi\|197263787\|ref\|ZP_03163861.1\| ubiquinone/menaquinone biosynthesis methyltransferase UbiE [Salmonel... UBIE_SALPK - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Salmonella paratyphi A (strain AKU_1...	3.0E-44	[2..210]	[20..239]

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Predicted Domain #1

Region A:
Residues: [1-26]

      1          11         21         31         41         51         
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    1 MEINQAAEKE QEYVHKVYNE IAPHFS

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [147-173]

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    1 LEQGSSRRGY HEGMEQDVFV PWVLPKS

[Run NCBI BLAST on this sequence.]

Region C:
Residues: [220-279]

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    1 LDDNDEKQQQ DQEQEREEVK YRYYHLYREG ELAEDCRQAG AAVHSEGFER DNWWVVAQKR  60
   61

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	15.69897
Match:	1kp9A_
Description:	CmaA1
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
methyltransferase activity	4.15445027778357	bayes_pls_golite062009
N-methyltransferase activity	4.07806017452628	bayes_pls_golite062009
transferase activity, transferring one-carbon groups	4.07153733729662	bayes_pls_golite062009
protein methyltransferase activity	3.92746815303714	bayes_pls_golite062009
S-adenosylmethionine-dependent methyltransferase activity	3.39429041855776	bayes_pls_golite062009
RNA methyltransferase activity	3.07428840534971	bayes_pls_golite062009
histone methyltransferase activity	2.99461585647365	bayes_pls_golite062009
transferase activity	2.926540904444	bayes_pls_golite062009
tRNA methyltransferase activity	2.5931020126592	bayes_pls_golite062009
rRNA methyltransferase activity	2.5924681776558	bayes_pls_golite062009
arginine N-methyltransferase activity	2.41876112831625	bayes_pls_golite062009
protein-arginine N-methyltransferase activity	2.41876112831625	bayes_pls_golite062009
DNA-methyltransferase activity	2.18991764495147	bayes_pls_golite062009
histone-arginine N-methyltransferase activity	2.04296107639729	bayes_pls_golite062009
tRNA (cytosine-5-)-methyltransferase activity	1.88889414729709	bayes_pls_golite062009
tRNA (cytosine)-methyltransferase activity	1.88889414729709	bayes_pls_golite062009
protein-arginine omega-N monomethyltransferase activity	1.66871163498737	bayes_pls_golite062009
tRNA (adenine-N1-)-methyltransferase activity	1.29759910099835	bayes_pls_golite062009
tRNA (adenine)-methyltransferase activity	1.29759910099835	bayes_pls_golite062009
catalytic activity	1.25333584501255	bayes_pls_golite062009
histone methyltransferase activity (H4-R3 specific)	1.1103522853299	bayes_pls_golite062009
transcription regulator activity	0.914549843668268	bayes_pls_golite062009
protein-arginine omega-N asymmetric methyltransferase activity	0.89325812193225	bayes_pls_golite062009
DNA binding	0.86027591375666	bayes_pls_golite062009
rRNA (adenine) methyltransferase activity	0.794703281700029	bayes_pls_golite062009
rRNA (adenine-N6,N6-)-dimethyltransferase activity	0.716476158062361	bayes_pls_golite062009
site-specific DNA-methyltransferase (adenine-specific) activity	0.703178429468566	bayes_pls_golite062009
nucleic acid binding	0.616949327277483	bayes_pls_golite062009
RNA binding	0.417524996559564	bayes_pls_golite062009
binding	0.383237930789959	bayes_pls_golite062009
protein-arginine omega-N symmetric methyltransferase activity	0.364369105571521	bayes_pls_golite062009
tRNA (guanine) methyltransferase activity	0.203168546434167	bayes_pls_golite062009
rRNA (guanine) methyltransferase activity	0.0854264678700428	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [27-146]

      1          11         21         31         41         51         
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    1 QTRYKPWPIV TQFLKTRPMG SIGIDVGCGN GKYLGVNPDI YIIGSDRSDG LIECARGINP  60
   61 SYNLLVADGL NLPHKNETFD FAISIAVVHH WSTRERRVEV IRHVLSKLRQ GGQALIYCWA 120
  121

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [174-219]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KSKPKTKSTP PAKVKTRPKP NLMNIPPKER SEYLQRWKEE QQRSKS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	15.69897
Match:	1kp9A_
Description:	CmaA1
Matching Structure (courtesy of the PDB):

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: