YRC Public Data Repository - Protein Structure Prediction

Protein:	TRM5
Organism:	Saccharomyces cerevisiae
Length:	499 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 TRM5.

Description	E-value	Query Range	Subject Range
gi\|190405852 - gi\|190405852\|gb\|EDV09119.1\| hypothetical protein SCRG_04781 [Saccharomyces cerevisiae RM11-1a] gi\|151944014 - gi\|151944014\|gb\|EDN62307.1\| tRNA methyltransferase [Saccharomyces cerevisiae YJM789] TRM5 - tRNA(m(1)G37)methyltransferase, methylates a tRNA base adjacent to the anticodon that has a role in ... TRM5_YEAST - tRNA (guanine(37)-N1)-methyltransferase OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=...	0.0	[1..499]	[1..499]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	6.0E-81	[9..499]	[5..469]
Y687_BACHD - Uncharacterized RNA methyltransferase BH0687 OS=Bacillus halodurans GN=BH0687 PE=3 SV=1 Y687_BACHD - Uncharacterized RNA methyltransferase BH0687 OS=Bacillus halodurans (strain ATCC BAA-125 / DSM 18197...	3.0E-77	[10..440]	[53..455]
Y1863_LISIN - Uncharacterized RNA methyltransferase lin1863 OS=Listeria innocua serovar 6a (strain CLIP 11262) GN=... Y1863_LISIN, YI6... - (Q92AQ7) Hypothetical RNA methyltransferase lin1863 (EC 2.1.1.-), Uncharacterized RNA methyltransfer...	1.0E-75	[10..440]	[51..451]
gi\|47095677, gi\|... - gi\|47095677\|ref\|ZP_00233284.1\| RNA methyltransferase, TrmA family [Listeria monocytogenes str. 1/2a ... gi\|255028262 - gi\|255028262\|ref\|ZP_05300213.1\| hypothetical protein LmonL_01654 [Listeria monocytogenes LO28] YH51_LISMO, Y175... - (Q8Y6D6) Hypothetical RNA methyltransferase lmo1751 (EC 2.1.1.-), Uncharacterized RNA methyltransfer... gi\|126941860, gi... - gi\|254900744\|ref\|ZP_05260668.1\| hypothetical protein LmonJ_13049 [Listeria monocytogenes J0161], gi\|... gi\|224503324 - gi\|224503324\|ref\|ZP_03671631.1\| hypothetical protein LmonFR_12550 [Listeria monocytogenes FSL R2-561... Y1751_LISMO - Uncharacterized RNA methyltransferase lmo1751 OS=Listeria monocytogenes serovar 1/2a (strain ATCC BA... gi\|127765381, gi... - gi\|254913771\|ref\|ZP_05263783.1\| hypothetical protein LmonJ2_13279 [Listeria monocytogenes J2818], gi... gi\|133732615, gi... - gi\|254938158\|ref\|ZP_05269855.1\| hypothetical protein LmonF6_13559 [Listeria monocytogenes F6900], gi...	2.0E-75	[10..439]	[51..450]
YEFA_BACSU, RLMC... - Uncharacterized RNA methyltransferase yefA OS=Bacillus subtilis GN=yefA PE=3 SV=1, 23S rRNA (uracil-... gi\|221312833 - gi\|221312833\|ref\|ZP_03594638.1\| hypothetical protein BsubsN3_03754 [Bacillus subtilis subsp. subtili... RLMCD_BACSU - 23S rRNA (uracil-C(5))-methyltransferase RlmCD OS=Bacillus subtilis (strain 168) GN=rlmCD PE=1 SV=1 gi\|221317757 - gi\|221317757\|ref\|ZP_03599051.1\| hypothetical protein BsubsJ_03708 [Bacillus subtilis subsp. subtilis... gi\|221322036 - gi\|221322036\|ref\|ZP_03603330.1\| hypothetical protein BsubsS_03794 [Bacillus subtilis subsp. subtilis...	8.0E-70	[8..440]	[50..456]
TRM5_MOUSE - tRNA (guanine(37)-N1)-methyltransferase OS=Mus musculus GN=Trmt5 PE=1 SV=1	1.0E-68	[17..496]	[57..462]
TRM5_MACFA - tRNA (guanine(37)-N1)-methyltransferase OS=Macaca fascicularis GN=TRMT5 PE=2 SV=1	2.0E-68	[20..499]	[67..472]
gi\|147931000, gi... - gi\|149019625\|ref\|ZP_01834944.1\| 23S rRNA (uracil-5-)-methyltransferase RumA [Streptococcus pneumonia... gi\|25508684 - gi\|25508684\|pir\|\|D97988 conserved hypothetical protein spr0932 [imported] - Streptococcus pneumoniae... Y932_STRR6 - Uncharacterized RNA methyltransferase spr0932 OS=Streptococcus pneumoniae (strain ATCC BAA-255 / R6)... gi\|116515807, gi... - gi\|116515807\|ref\|YP_816392.1\| 23S rRNA (uracil-5-)-methyltransferase RumA [Streptococcus pneumoniae ... gi\|168483100, gi... - gi\|172043444\|gb\|EDT51490.1\| 23S rRNA (uracil-5-)-methyltransferase RumA [Streptococcus pneumoniae CD...	9.0E-68	[2..481]	[40..486]
Y1029_STRPN - Uncharacterized RNA methyltransferase SP_1029 OS=Streptococcus pneumoniae serotype 4 (strain ATCC BA... YA29_STRPN, Y102... - (Q97R12) Hypothetical RNA methyltransferase SP1029 (EC 2.1.1.-), Uncharacterized RNA methyltransfera...	3.0E-67	[2..481]	[40..486]

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Predicted Domain #1

Region A:
Residues: [1-106]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MKIALPVFQK FNRLISSCKM SGVFPYNPPV NRQMRELDRS FFITKIPMCA VKFPEPKNIS  60
   61 VFSKNFKNCI LRVPRIPHVV KLNSSKPKDE LTSVQNKKLK TADGNN

[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	0.204	a.77.1	DEATH domain
View	Download	0.228	a.4.6	C-terminal effector domain of the bipartite response regulators
View	Download	0.305	d.58.49	YajQ-like
View	Download	0.221	d.58.43	Mechanosensitive channel protein MscS (YggB), C-terminal domain

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
tRNA methyltransferase activity	2.5931020126592	bayes_pls_golite062009
rRNA methyltransferase activity	2.5924681776558	bayes_pls_golite062009
DNA-methyltransferase activity	2.43145108778901	bayes_pls_golite062009
arginine N-methyltransferase activity	2.41876112831625	bayes_pls_golite062009
protein-arginine N-methyltransferase activity	2.41876112831625	bayes_pls_golite062009
transferase activity	2.22303238506686	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
rRNA (guanine) methyltransferase activity	0.979380410238071	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
rRNA (uridine) methyltransferase activity	0.511874381049553	bayes_pls_golite062009
RNA binding	0.417524996559564	bayes_pls_golite062009
binding	0.383237930789959	bayes_pls_golite062009
tRNA (guanine) methyltransferase activity	0.203168546434167	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [107-327]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TPVTKGVLLH ESIHSVEDAY GKLPEDALAF LKENSAEIVP HEYVLDYDFW KAEEILRAVL  60
   61 PEQFLEEVPT GFTITGHIAH LNLRTEFKPF DSLIGQVILD KNNKIECVVD KVSSIATQFR 120
  121 TFPMKVIAGK SDSLVVEQKE SNCTFKFDFS KVYWNSRLHT EHERLVKQYF QPGQVVCDVF 180
  181 AGVGPFAVPA GKKDVIVLAN DLNPESYKYL KENIALNKVA K

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	6.69897
Match:	1g60A_
Description:	Methyltransferase mboII
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [328-379]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TVKSFNMDGA DFIRQSPQLL QQWIQDEEGG KITIPLPLKK RHRSQQHNDQ QP

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	14.221849
Match:	1dusA_
Description:	Hypothetical protein MJ0882
Matching Structure (courtesy of the PDB):

Predicted Domain #4

Region A:
Residues: [380-499]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PQPRTKELII PSHISHYVMN LPDSAISFLG NFRGIFAAHT KGATDTIQMP WVHVHCFEKY  60
   61 PPGDQVTEDE LHARVHARII AALKVTADDL PLNAVSLHLV RKVAPTKPMY CASFQLPANV 120
  121

[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	0.689	c.95.1	Thiolase-like
View	Download	0.585	d.13.1	HIT-like
View	Download	0.904	c.58.1	Aminoacid dehydrogenase-like, N-terminal domain
View	Download	0.709	c.49.1	Pyruvate kinase, C-terminal domain
View	Download	0.604	c.49.1	Pyruvate kinase, C-terminal domain
View	Download	0.517	d.58.21	Molybdenum cofactor biosynthesis protein C, MoaC
View	Download	0.509	c.78.2	Aspartate/glutamate racemase
View	Download	0.475	a.71.1	Endoplasmic reticulum protein ERP29, C-domain
View	Download	0.435	d.14.1	Ribosomal protein S5 domain 2-like
View	Download	0.434	d.8.1	Urease, gamma-subunit
View	Download	0.429	d.16.1	FAD-linked reductases, C-terminal domain
View	Download	0.426	d.60.1	Probable bacterial effector-binding domain
View	Download	0.420	d.96.1	Tetrahydrobiopterin biosynthesis enzymes-like
View	Download	0.416	d.208.1	MTH1598-like
View	Download	0.404	a.24.15	FAD-dependent thiol oxidase
View	Download	0.403	d.81.1	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
View	Download	0.374	a.56.1	CO dehydrogenase ISP C-domain like
View	Download	0.372	d.80.1	Tautomerase/MIF
View	Download	0.344	c.78.2	Aspartate/glutamate racemase
View	Download	0.340	c.25.1	Ferredoxin reductase-like, C-terminal NADP-linked domain
View	Download	0.339	a.74.1	Cyclin-like
View	Download	0.336	d.38.1	Thioesterase/thiol ester dehydrase-isomerase
View	Download	0.330	d.16.1	FAD-linked reductases, C-terminal domain
View	Download	0.311	d.1.1	Microbial ribonucleases
View	Download	0.309	a.26.1	4-helical cytokines
View	Download	0.309	c.2.1	NAD(P)-binding Rossmann-fold domains
View	Download	0.308	a.100.1	6-phosphogluconate dehydrogenase C-terminal domain-like
View	Download	0.302	c.30.1	PreATP-grasp domain
View	Download	0.302	a.1.1	Globin-like
View	Download	0.296	b.1.5	Transglutaminase, two C-terminal domains
View	Download	0.293	d.17.1	Cystatin/monellin
View	Download	0.289	d.79.2	Tubulin/Dihydroxyacetone kinase C-terminal domain
View	Download	0.282	d.68.1	Translation initiation factor IF3, C-terminal domain
View	Download	0.281	d.6.1	Prion-like
View	Download	0.270	c.26.1	Nucleotidylyl transferase
View	Download	0.269	a.1.1	Globin-like
View	Download	0.268	a.61.1	Retroviral matrix proteins
View	Download	0.262	d.26.1	FKBP-like
View	Download	0.256	d.104.1	Class II aaRS and biotin synthetases
View	Download	0.249	c.23.5	Flavoproteins
View	Download	0.248	c.49.2	ATP synthase (F1-ATPase), gamma subunit
View	Download	0.247	a.24.13	Domain of the SRP/SRP receptor G-proteins
View	Download	0.245	d.134.1	Sulfite reductase hemoprotein (SiRHP), domains 2 and 4
View	Download	0.240	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.226	c.58.1	Aminoacid dehydrogenase-like, N-terminal domain
View	Download	0.225	d.96.1	Tetrahydrobiopterin biosynthesis enzymes-like
View	Download	0.225	c.55.6	DNA repair protein MutS, domain II
View	Download	0.223	a.24.17	Group V grass pollen allergen
View	Download	0.222	c.2.1	NAD(P)-binding Rossmann-fold domains
View	Download	0.220	d.122.1	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
View	Download	0.220	a.118.8	TPR-like
View	Download	0.217	c.48.1	TK C-terminal domain-like
View	Download	0.214	a.24.13	Domain of the SRP/SRP receptor G-proteins
View	Download	0.214	d.58.44	Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
View	Download	0.213	c.2.1	NAD(P)-binding Rossmann-fold domains
View	Download	0.205	c.2.1	NAD(P)-binding Rossmann-fold domains

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: