YRC Public Data Repository - Protein Structure Prediction

Protein:	RKM1
Organism:	Saccharomyces cerevisiae
Length:	583 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 RKM1.

Description	E-value	Query Range	Subject Range
RKM1_YEAST - Ribosomal lysine N-methyltransferase 1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=R... RKM1 - SET-domain lysine-N-methyltransferase, catalyzes the formation of dimethyllysine residues on the lar...	0.0	[1..583]	[1..583]
SETD3_MOUSE - Histone-lysine N-methyltransferase setd3 OS=Mus musculus GN=Setd3 PE=1 SV=1	8.0E-90	[4..464]	[77..509]
SETD3 - SET domain containing 3	5.0E-89	[4..464]	[77..509]
SET10_SCHPO - Ribosomal lysine N-methyltransferase set10 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN... SPBC1709.13c - lysine methyltransferase	4.0E-78	[6..504]	[1..463]
SETD3_DANRE - Histone-lysine N-methyltransferase setd3 OS=Danio rerio GN=setd3 PE=1 SV=1	1.0E-77	[4..443]	[77..479]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	6.0E-76	[6..464]	[56..477]
RBCMT_ARATH - [Fructose-bisphosphate aldolase]-lysine N-methyltransferase, chloroplastic OS=Arabidopsis thaliana G...	4.0E-74	[2..464]	[45..469]

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Predicted Domain #1

Region A:
Residues: [1-113]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSSDALKALL QWGASFGVIV PEELKFLYTD LKGIICVCEK DIDNPSIKIP PEIVISRNLP  60
   61 MKFFGLSEST KNINGWLKLF FAKIKFDRDN DTIVDNVRVN DKFKPYLDAL PSR

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [142-274]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EGIFKEWFEL VSSSDMFDLE RVADDVQTFH NLDELTYEAL YEKILKITEL QRPTIWYSFP  60
   61 AFLWSHLIFI SRAFPEYVLN RNCPDNSIVL LPIVDLLNHD YRSKVKWYPE NGWFCYEKIG 120
  121 TASQSRELSN NYG

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	72.0
Match:	1mlvA_
Description:	RuBisCo LSMT C-terminal, substrate-binding domain; RuBisCo LSMT catalytic domain
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
histone methyltransferase activity	6.20878333364554	bayes_pls_golite062009
protein methyltransferase activity	6.08778683840554	bayes_pls_golite062009
lysine N-methyltransferase activity	5.45106430536252	bayes_pls_golite062009
protein-lysine N-methyltransferase activity	5.45106430536252	bayes_pls_golite062009
histone-lysine N-methyltransferase activity	5.45106430536252	bayes_pls_golite062009
N-methyltransferase activity	3.98411678860954	bayes_pls_golite062009
histone methyltransferase activity (H3-K9 specific)	3.54138873512018	bayes_pls_golite062009
S-adenosylmethionine-dependent methyltransferase activity	2.69428385009711	bayes_pls_golite062009
methyltransferase activity	2.33114816345072	bayes_pls_golite062009
binding	2.2675356705139	bayes_pls_golite062009
transferase activity, transferring one-carbon groups	2.25175257044903	bayes_pls_golite062009
nucleic acid binding	1.79964884912488	bayes_pls_golite062009
chromatin binding	1.00298380074254	bayes_pls_golite062009
protein binding	0.938282161933492	bayes_pls_golite062009
transferase activity	0.653108419761009	bayes_pls_golite062009
catalytic activity	0.414641636618101	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [114-141]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LNSPLVWNPS ELKRLSSTNI GNSIHEKF

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [275-299]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GKGNEELLSG YGFVLEDNIF DSVAL

[Run NCBI BLAST on this sequence.]

Region C:
Residues: [401-442]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LQSKLNSITG PPATDDSYAI DPYRVYCADV YTKGQKQILK EA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	72.0
Match:	1mlvA_
Description:	RuBisCo LSMT C-terminal, substrate-binding domain; RuBisCo LSMT catalytic domain
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [300-400]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KVKLPLDVVS TILETEPSLK LPLLSDYTTY AFENKDCVQQ EKKATRSATD YINGVTYFIN  60
   61 IQNEQCLEPL LDLFTYLSKA EEEDLHDLRA RLQGIQMLRN A

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [443-512]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LTRLKKLEKT MLSENKHQLL TMSKILKNDP AFAETELPSL FSNEDGEEVI FESTYDLLIL  60
   61 WILLKTKKNS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	72.0
Match:	1mlvA_
Description:	RuBisCo LSMT C-terminal, substrate-binding domain; RuBisCo LSMT catalytic domain
Matching Structure (courtesy of the PDB):

Predicted Domain #4

Region A:
Residues: [513-583]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 YPTKYEWVGQ QYTNFKQTAY ISDDAKAFHT AYFEKQDDVD LAEVDHAIQF VVDNSFTRTS  60
   61 STTEETILVR K

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below is our most confident de novo (Rosetta) prediction for this domain.
Click here to view all matches.

Found no confident 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: