YRC Public Data Repository - Protein Structure Prediction

Protein:	MSS1
Organism:	Saccharomyces cerevisiae
Length:	526 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 MSS1.

Description	E-value	Query Range	Subject Range
MSS1_YEAST - tRNA modification GTPase MSS1, mitochondrial OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c... MSS1 - Mitochondrial protein, forms a heterodimer complex with Mto1p that performs the 5-carboxymethylamino... gi\|190408262 - gi\|190408262\|gb\|EDV11527.1\| GTPase MSS1, mitochondrial precursor [Saccharomyces cerevisiae RM11-1a]	0.0	[1..526]	[1..526]
gi\|12721514, gi\|... - gi\|15603031\|ref\|NP_246103.1\| tRNA modification GTPase TrmE [Pasteurella multocida subsp. multocida s...	0.0	[31..526]	[10..465]
gi\|254795709, gi... - gi\|254795709\|ref\|YP_003080546.1\| 5-methylaminomethyl-2-thiouridine-synthesizing GTPase [Escherichia ... gi\|25319352, gi\|... - pir\|\|A98209 hypothetical protein ECs4641 [imported] - Escherichia coli (strain O157:H7, substrain R... MNME_ECO57 - tRNA modification GTPase MnmE OS=Escherichia coli O157:H7 GN=mnmE PE=3 SV=1 gi\|208814185, gi... - gi\|208814185\|ref\|ZP_03255514.1\| tRNA modification GTPase TrmE [Escherichia coli O157:H7 str. EC4045]... gi\|208740195, gi... - gi\|208820072\|ref\|ZP_03260392.1\| tRNA modification GTPase TrmE [Escherichia coli O157:H7 str. EC4042]... MNME_ECO5E - tRNA modification GTPase MnmE OS=Escherichia coli O157:H7 (strain EC4115 / EHEC) GN=mnmE PE=3 SV=1 gi\|217324903, gi... - gi\|217324903\|ref\|ZP_03440987.1\| tRNA modification GTPase TrmE [Escherichia coli O157:H7 str. TW14588... gi\|189373460, gi... - gi\|189373460\|gb\|EDU91876.1\| tRNA modification GTPase TrmE [Escherichia coli O157:H7 str. EC869], gi\|... gi\|168798745, gi... - gi\|189378836\|gb\|EDU97252.1\| tRNA modification GTPase TrmE [Escherichia coli O157:H7 str. EC508], gi\|... gi\|195936329 - gi\|195936329\|ref\|ZP_03081711.1\| tRNA modification GTPase TrmE [Escherichia coli O157:H7 str. EC4024] gi\|208808040, gi... - gi\|208808040\|ref\|ZP_03250377.1\| tRNA modification GTPase TrmE [Escherichia coli O157:H7 str. EC4206]... gi\|189369584, gi... - gi\|189369584\|gb\|EDU88000.1\| tRNA modification GTPase TrmE [Escherichia coli O157:H7 str. EC4501], gi... gi\|189364418, gi... - gi\|189364418\|gb\|EDU82837.1\| tRNA modification GTPase TrmE [Escherichia coli O157:H7 str. EC4486], gi... gi\|168772255, gi... - gi\|187771576\|gb\|EDU35420.1\| tRNA modification GTPase TrmE [Escherichia coli O157:H7 str. EC4196], gi... gi\|168779932, gi... - gi\|189002302\|gb\|EDU71288.1\| tRNA modification GTPase TrmE [Escherichia coli O157:H7 str. EC4076], gi... gi\|15833895, gi\|... - gi\|15833895\|ref\|NP_312668.1\| tRNA modification GTPase TrmE [Escherichia coli O157:H7 str. Sakai], gi... gi\|168748574, gi... - gi\|188016998\|gb\|EDU55120.1\| tRNA modification GTPase TrmE [Escherichia coli O157:H7 str. EC4113], gi... gi\|189359120, gi... - gi\|189359120\|gb\|EDU77539.1\| tRNA modification GTPase TrmE [Escherichia coli O157:H7 str. EC4401], gi...	0.0	[36..526]	[4..454]
MNME_ECOLC - tRNA modification GTPase MnmE OS=Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks) GN=mnmE PE=... MNME_ECO8A - tRNA modification GTPase MnmE OS=Escherichia coli O8 (strain IAI1) GN=mnmE PE=3 SV=1 MNME_ECODH - tRNA modification GTPase MnmE OS=Escherichia coli (strain K12 / DH10B) GN=mnmE PE=3 SV=1 MNME_ECOSE - tRNA modification GTPase MnmE OS=Escherichia coli (strain SE11) GN=mnmE PE=3 SV=1 MNME_ECOBW - tRNA modification GTPase MnmE OS=Escherichia coli (strain K12 / MC4100 / BW2952) GN=mnmE PE=3 SV=1 gi\|124530079, gi... - gi\|124530079\|ref\|ZP_01700862.1\| tRNA modification GTPase TrmE [Escherichia coli B], gi\|124499484\|gb\|... gi\|226838890, gi... - gi\|254038925\|ref\|ZP_04872977.1\| tRNA modification GTPase TrmE [Escherichia sp. 1_1_43], gi\|226838890... TRME_ECOLI - Probable tRNA modification GTPase trmE - Escherichia coli MNME_SHIBS - tRNA modification GTPase MnmE OS=Shigella boydii serotype 4 (strain Sb227) GN=mnmE PE=3 SV=1 gi\|89110306, gi\|... - gi\|89110306\|ref\|AP_004086.1\| GTPase [Escherichia coli str. K-12 substr. W3110], gi\|85676337\|dbj\|BAE7... EG10997 - tRNA U34 5-methylaminomethyl-2-thiouridine modification GTPase / GTPase required for 5-methylaminome... MNME_SHIB3 - tRNA modification GTPase MnmE OS=Shigella boydii serotype 18 (strain CDC 3083-94 / BS512) GN=mnmE PE... gi\|188493740, gi... - gi\|75514232\|ref\|ZP_00736540.1\| COG0486: Predicted GTPase [Escherichia coli 53638], gi\|188493740\|ref\|... EG10997 - tRNA U34 5-methylaminomethyl-2-thiouridine modification GTPase / GTPase required for 5-methylaminome...	0.0	[36..526]	[4..454]
TRME_PASMU, MNME... - Probable tRNA modification GTPase trmE - Pasteurella multocida, tRNA modification GTPase mnmE OS=Pas... MNME_PASMU - tRNA modification GTPase MnmE OS=Pasteurella multocida (strain Pm70) GN=mnmE PE=3 SV=1	0.0	[35..526]	[1..452]
gi\|290554 - gi\|290554\|gb\|AAA62057.1\| 50 kD protein	0.0	[36..526]	[4..454]
MNME_SALTY - tRNA modification GTPase MnmE OS=Salmonella typhimurium GN=mnmE PE=3 SV=1 TRME_SALTY, MNME... - tRNA modification GTPase trmE - Salmonella typhimurium, tRNA modification GTPase mnmE OS=Salmonella ... MNME_SALTY - tRNA modification GTPase MnmE OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=mnm... lcl\|NC_016856.1_... - [gene=trmE] [protein=tRNA modification GTPase TrmE] [protein_id=YP_005240111.1] [location=4061906..4...	0.0	[36..526]	[4..454]
GTPBP3 - GTP binding protein 3 (mitochondrial)	0.0	[19..526]	[18..492]
gi\|213052691 - gi\|213052691\|ref\|ZP_03345569.1\| tRNA modification GTPase TrmE [Salmonella enterica subsp. enterica s... gi\|213424947 - gi\|213424947\|ref\|ZP_03357697.1\| tRNA modification GTPase TrmE [Salmonella enterica subsp. enterica s... gi\|213580794 - gi\|213580794\|ref\|ZP_03362620.1\| tRNA modification GTPase TrmE [Salmonella enterica subsp. enterica s... TRME_SALTI, MNME... - tRNA modification GTPase trmE - Salmonella typhi, tRNA modification GTPase mnmE OS=Salmonella typhi ... MNME_SALTI - tRNA modification GTPase MnmE OS=Salmonella typhi GN=mnmE PE=3 SV=1 gi\|29139607, gi\|... - gi\|29143971\|ref\|NP_807313.1\| tRNA modification GTPase TrmE [Salmonella enterica subsp. enterica sero... gi\|16762483 - gi\|16762483\|ref\|NP_458100.1\| tRNA modification GTPase TrmE [Salmonella enterica subsp. enterica sero... gi\|213865392 - gi\|213865392\|ref\|ZP_03387511.1\| tRNA modification GTPase TrmE [Salmonella enterica subsp. enterica s...	0.0	[36..526]	[4..454]

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Predicted Domain #1

Region A:
Residues: [1-87]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MNSASFLQSR LISRSFLVRR SLKRYSGLAK PYTFQQPTIY ALSTPANQTS AIAIIRISGT  60
   61 HAKYIYNRLV DSSTVPPIRK AILRNIY

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below is our most confident prediction for this domain.
Click here to view all matches.

		MCM Score	GO Score	GO Term	SCOP Match	SCOP Description
View	Download	0.917	0.004	mitochondrial inner membrane	d.58.5	GlnB-like

Predicted functions:

Term	Confidence	Notes
methyltransferase activity	3.28983380541263	bayes_pls_golite062009
transferase activity, transferring one-carbon groups	3.20782575104451	bayes_pls_golite062009
catalytic activity	1.65079399897053	bayes_pls_golite062009
transferase activity	1.3676947912529	bayes_pls_golite062009
coenzyme binding	1.08379167900905	bayes_pls_golite062009
nucleic acid binding	0.913322399315129	bayes_pls_golite062009
structural constituent of ribosome	0.738234102557832	bayes_pls_golite062009
RNA helicase activity	0.73539642422624	bayes_pls_golite062009
RNA-dependent ATPase activity	0.70759024918936	bayes_pls_golite062009
ATP-dependent RNA helicase activity	0.68122080550778	bayes_pls_golite062009
ATP binding	0.60527666756293	bayes_pls_golite062009
binding	0.604868700215668	bayes_pls_golite062009
aminomethyltransferase activity	0.573831999310668	bayes_pls_golite062009
adenyl ribonucleotide binding	0.573214556107072	bayes_pls_golite062009
ligase activity	0.417681194526243	bayes_pls_golite062009
transcription regulator activity	0.390949264169589	bayes_pls_golite062009
DNA binding	0.376487324624615	bayes_pls_golite062009
translation regulator activity	0.29096092258568	bayes_pls_golite062009
translation factor activity, nucleic acid binding	0.274994961137851	bayes_pls_golite062009
structural molecule activity	0.0558641287316701	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [88-264]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SPSSCSVKPH DQKESKILLD TSLLLYFQAP YSFTGEDVLE LHVHGGKAVV NSILKAIGSL  60
   61 HDRSSGKDIR FALPGDFSRR AFQNGKFDLT QLEGIKDLID SETESQRRSA LSSFNGDNKI 120
  121 LFENWRETII ENMAQLTAII DFADDNSQEI QNTDEIFHNV EKNIICLRDQ IVTFMQK

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below is our most confident prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #3

Region A:
Residues: [265-526]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 VEKSTILQNG IKLVLLGAPN VGKSSLVNSL TNDDISIVSD IPGTTRDSID AMINVNGYKV  60
   61 IICDTAGIRE KSSDKIEMLG IDRAKKKSVQ SDLCLFIVDP TDLSKLLPED ILAHLSSKTF 120
  121 GNKRIIIVVN KSDLVSDDEM TKVLNKLQTR LGSKYPILSV SCKTKEGIES LISTLTSNFE 180
  181 SLSQSSADAS PVIVSKRVSE ILKNDVLYGL EEFFKSKDFH NDIVLATENL RYASDGIAKI 240
  241 TGQAIGIEEI LDSVFSKFCI GK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	125.9794
Match:	1egaA_
Description:	GTPase Era, N-terminal domain; GTPase Era C-terminal domain
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: