YRC Public Data Repository - Protein Structure Prediction

Protein:	SLM3
Organism:	Saccharomyces cerevisiae
Length:	417 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 SLM3.

Description	E-value	Query Range	Subject Range
SLM3 - tRNA-specific 2-thiouridylase, responsible for 2-thiolation of the wobble base of mitochondrial tRNA... MTU1_YEAST - Mitochondrial tRNA-specific 2-thiouridylase 1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288... gi\|190405047 - gi\|190405047\|gb\|EDV08314.1\| hypothetical protein SCRG_00535 [Saccharomyces cerevisiae RM11-1a] gi\|207346911 - gi\|207346911\|gb\|EDZ73261.1\| YDL033Cp-like protein [Saccharomyces cerevisiae AWRI1631]	0.0	[1..417]	[1..417]
gi\|254898322, gi... - gi\|254898322\|ref\|ZP_05258246.1\| tRNA-specific 2-thiouridylase MnmA [Listeria monocytogenes J0161], g... gi\|127765519, gi... - gi\|254912186\|ref\|ZP_05262198.1\| tRNA-specific 2-thiouridylase MnmA [Listeria monocytogenes J2818], g... MNMA_LISMO, TRMU... - Probable tRNA - Listeria monocytogenes, tRNA-specific 2-thiouridylase mnmA OS=Listeria monocytogenes... gi\|133729902, gi... - gi\|254828254\|ref\|ZP_05232941.1\| tRNA-specific 2-thiouridylase MnmA [Listeria monocytogenes FSL N3-16... gi\|224500677 - gi\|224500677\|ref\|ZP_03669026.1\| tRNA-specific 2-thiouridylase MnmA [Listeria monocytogenes Finland 1... MNMA_LISMO - tRNA-specific 2-thiouridylase MnmA OS=Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD... gi\|224501548 - gi\|224501548\|ref\|ZP_03669855.1\| tRNA-specific 2-thiouridylase MnmA [Listeria monocytogenes FSL R2-56... gi\|47097209, gi\|... - gi\|47097209\|ref\|ZP_00234773.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Listeri... gi\|254936514 - gi\|254936514\|ref\|ZP_05268211.1\| tRNA-specific 2-thiouridylase MnmA [Listeria monocytogenes F6900]	0.0	[28..414]	[9..364]
gi\|45436440, gi\|... - gi\|45441579\|ref\|NP_993118.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Yersinia ... gi\|22125693, gi\|... - gi\|22125693\|ref\|NP_669116.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Yersinia ... gi\|115347385, gi... - gi\|218928774\|ref\|YP_002346649.1\| tRNA-specific 2-thiouridylase MnmA [Yersinia pestis CO92], gi\|16121... gi\|149366398, gi... - gi\|149366398\|ref\|ZP_01888432.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Yersin... gi\|167470788 - gi\|167470788\|ref\|ZP_02335492.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Yersin... MNMA_YERPS - tRNA-specific 2-thiouridylase MnmA OS=Yersinia pseudotuberculosis serotype I (strain IP32953) GN=mnm... MNMA_YERPP - tRNA-specific 2-thiouridylase MnmA OS=Yersinia pestis (strain Pestoides F) GN=mnmA PE=3 SV=1 gi\|166211105, gi... - gi\|166211105\|ref\|ZP_02237140.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Yersin... gi\|229694088, gi... - gi\|229841625\|ref\|ZP_04461783.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Yersin... gi\|167048808, gi... - gi\|167401703\|ref\|ZP_02307194.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Yersin... gi\|229843742, gi... - gi\|229843742\|ref\|ZP_04463885.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Yersin... gi\|167421866, gi... - gi\|167421866\|ref\|ZP_02313619.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Yersin... gi\|167054667, gi... - gi\|167426312\|ref\|ZP_02318065.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Yersin... MNMA_YERPA - tRNA-specific 2-thiouridylase MnmA OS=Yersinia pestis bv. Antiqua (strain Antiqua) GN=mnmA PE=3 SV=1 MNMA_YERPN - tRNA-specific 2-thiouridylase MnmA OS=Yersinia pestis bv. Antiqua (strain Nepal516) GN=mnmA PE=3 SV=... gi\|165925423, gi... - gi\|165925423\|ref\|ZP_02221255.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Yersin... MNMA_YERPE - tRNA-specific 2-thiouridylase MnmA OS=Yersinia pestis GN=mnmA PE=3 SV=1 gi\|165938528, gi... - gi\|165938528\|ref\|ZP_02227085.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Yersin... gi\|229703505, gi... - gi\|229894486\|ref\|ZP_04509668.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Yersin... MNMA_YERPY - tRNA-specific 2-thiouridylase MnmA OS=Yersinia pseudotuberculosis serotype O:3 (strain YPIII) GN=mnm... gi\|166008070, gi... - gi\|166008070\|ref\|ZP_02228968.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Yersin... MNMA_YERPG - tRNA-specific 2-thiouridylase MnmA OS=Yersinia pestis bv. Antiqua (strain Angola) GN=mnmA PE=3 SV=1 MNMA_YERPB - tRNA-specific 2-thiouridylase MnmA OS=Yersinia pseudotuberculosis serotype IB (strain PB1/+) GN=mnmA... TRMU_YERPS, MNMA... - tRNA - Yersinia pseudotuberculosis, tRNA-specific 2-thiouridylase mnmA OS=Yersinia pseudotuberculosi...	0.0	[24..408]	[4..362]
TRMU_LISIN, MNMA... - Probable tRNA - Listeria innocua, tRNA-specific 2-thiouridylase mnmA OS=Listeria innocua GN=mnmA PE=... MNMA_LISIN - tRNA-specific 2-thiouridylase MnmA OS=Listeria innocua serovar 6a (strain CLIP 11262) GN=mnmA PE=3 S...	0.0	[28..414]	[9..364]
MNMA_BACHD - tRNA-specific 2-thiouridylase MnmA OS=Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 73... TRMU_BACHD, MNMA... - Probable tRNA - Bacillus halodurans, tRNA-specific 2-thiouridylase mnmA OS=Bacillus halodurans GN=mn...	0.0	[28..412]	[10..363]
gi\|121587442, gi... - gi\|121587442\|ref\|ZP_01677211.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Vibrio... gi\|227081301, gi... - gi\|227081301\|ref\|YP_002809852.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Vibri... gi\|153222294, gi... - gi\|153222294\|ref\|ZP_01953054.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Vibrio... gi\|121631189, gi... - gi\|121726243\|ref\|ZP_01679533.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Vibrio... gi\|126512511, gi... - gi\|153816924\|ref\|ZP_01969591.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Vibrio... gi\|125618841 - gi\|125618841\|gb\|EAZ47374.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Vibrio cho... gi\|153822021, gi... - gi\|153822021\|ref\|ZP_01974688.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Vibrio... MNMA_VIBC3 - tRNA-specific 2-thiouridylase MnmA OS=Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Oga... TRMU_VIBCH, MNMA... - Probable tRNA - Vibrio cholerae, tRNA-specific 2-thiouridylase mnmA OS=Vibrio cholerae GN=mnmA PE=3 ... MNMA_VIBCH - tRNA-specific 2-thiouridylase MnmA OS=Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba ...	0.0	[24..409]	[9..370]
gi\|209772838, gi... - gi\|25298374\|pir\|\|C85687 hypothetical protein ycfB [imported] - Escherichia coli (strain O157:H7, su... gi\|15801330, gi\|... - gi\|15801330\|ref\|NP_287347.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Escherich... gi\|13361069 - gi\|13361069\|dbj\|BAB35028.1\| hypothetical protein [Escherichia coli O157:H7] gi\|13361069 - gi\|13361069\|dbj\|BAB35028.1\| hypothetical protein [Escherichia coli O157:H7 str. Sakai]	0.0	[22..408]	[16..376]
EG11344 - tRNA(Gln,Lys,Glu) U34 2-thiouridylase / tRNA(Gln,Lys,Glu) U34 2-thiouridylase; first step in mnm(5)-... gi\|83587305, gi\|... - gi\|83587305\|ref\|ZP_00925933.1\| COG0482: Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltr... MNMA_ECO24 - tRNA-specific 2-thiouridylase MnmA OS=Escherichia coli O139:H28 (strain E24377A / ETEC) GN=mnmA PE=3... MNMA_ECOHS - tRNA-specific 2-thiouridylase MnmA OS=Escherichia coli O9:H4 (strain HS) GN=mnmA PE=3 SV=1 TRMU_ECOLI - tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase (EC 2.1.1.61) - Escherichia coli gi\|238863704, gi... - gi\|238900387\|ref\|YP_002926183.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Esche... gi\|251784662, gi... - gi\|251784662\|ref\|YP_002998966.1\| hypothetical protein B21_01139 [Escherichia coli BL21], gi\|24237693... gi\|254288048, gi... - gi\|254288048\|ref\|YP_003053796.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Esche... gi\|89107979, gi\|... - gi\|89107979\|ref\|AP_001759.1\| tRNA (5-methylaminomethyl-2-thiouridylate)- methyltransferase [Escheric... gi\|253973141, gi... - gi\|254161240\|ref\|YP_003044348.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Esche... gi\|209911649, gi... - gi\|209918390\|ref\|YP_002292474.1\| tRNA-specific 2-thiouridylase MnmA [Escherichia coli SE11], gi\|2099... gi\|124499586, gi... - gi\|124529878\|ref\|ZP_01700722.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Escher... gi\|218351399, gi... - gi\|218694667\|ref\|YP_002402334.1\| tRNA-specific 2-thiouridylase MnmA [Escherichia coli 55989], gi\|218... gi\|218553711, gi... - gi\|218553711\|ref\|YP_002386624.1\| tRNA-specific 2-thiouridylase MnmA [Escherichia coli IAI1], gi\|2183... gi\|75214686, gi\|... - gi\|75214686\|ref\|ZP_00713197.1\| COG0482: Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltr... gi\|191168327, gi... - gi\|75228455\|ref\|ZP_00715095.1\| COG0482: Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltr... gi\|75255663, gi\|... - gi\|75255663\|ref\|ZP_00727435.1\| COG0482: Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltr... MNMA_ECOLC - tRNA-specific 2-thiouridylase MnmA OS=Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks) GN=mnm... MNMA_ECODH - tRNA-specific 2-thiouridylase MnmA OS=Escherichia coli (strain K12 / DH10B) GN=mnmA PE=3 SV=1 EG11344 - tRNA(Gln,Lys,Glu) U34 2-thiouridylase / tRNA(Gln,Lys,Glu) U34 2-thiouridylase; first step in mnm(5)-...	0.0	[22..408]	[1..361]
gi\|213428090 - gi\|213428090\|ref\|ZP_03360840.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Salmon... gi\|207857259, gi... - gi\|207857259\|ref\|YP_002243910.1\| tRNA-specific 2-thiouridylase MnmA [Salmonella enterica subsp. ente... gi\|213612639 - gi\|213612639\|ref\|ZP_03370465.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Salmon... gi\|213580464 - gi\|213580464\|ref\|ZP_03362290.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Salmon... gi\|197940188, gi... - gi\|198245672\|ref\|YP_002215901.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Salmo... gi\|197094180, gi... - gi\|197362703\|ref\|YP_002142340.1\| tRNA-specific 2-thiouridylase MnmA [Salmonella enterica subsp. ente... gi\|205272813, gi... - gi\|205353032\|ref\|YP_002226833.1\| tRNA-specific 2-thiouridylase MnmA [Salmonella enterica subsp. ente... gi\|204930753, gi... - gi\|204930753\|ref\|ZP_03221626.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Salmon... gi\|194408232, gi... - gi\|194449928\|ref\|YP_002045236.1\| tRNA-specific 2-thiouridylase MnmA [Salmonella enterica subsp. ente... gi\|194444280, gi... - gi\|194444280\|ref\|YP_002040490.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Salmo... gi\|197249278, gi... - gi\|197249278\|ref\|YP_002146807.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Salmo... gi\|194458461, gi... - gi\|194472097\|ref\|ZP_03078081.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Salmon... gi\|168244308, gi... - gi\|205336786\|gb\|EDZ23550.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Salmonella... gi\|168233116, gi... - gi\|205332653\|gb\|EDZ19417.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Salmonella... gi\|205341217, gi... - gi\|205341217\|gb\|EDZ27981.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Salmonella... gi\|195630429, gi... - gi\|195630429\|gb\|EDX49055.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Salmonella... MNMA_SALTI - tRNA-specific 2-thiouridylase MnmA OS=Salmonella typhi GN=mnmA PE=3 SV=1 gi\|29137749, gi\|... - gi\|29142120\|ref\|NP_805462.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Salmonell... MNMA_SALPA, TRMU... - tRNA - Salmonella paratyphi-a, tRNA-specific 2-thiouridylase mnmA OS=Salmonella paratyphi A GN=mnmA ... gi\|16760109 - gi\|16760109\|ref\|NP_455726.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Salmonell... gi\|224584258, gi... - gi\|224584258\|ref\|YP_002638056.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Salmo... gi\|213648222 - gi\|213648222\|ref\|ZP_03378275.1\| tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Salmon... MNMA_SALPB - tRNA-specific 2-thiouridylase MnmA OS=Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7) GN=mnmA P... MNMA_SALPB - tRNA-specific 2-thiouridylase mnmA OS=Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7) GN=mnmA P... MNMA_SALPA - tRNA-specific 2-thiouridylase MnmA OS=Salmonella paratyphi A (strain ATCC 9150 / SARB42) GN=mnmA PE=... MNMA_SALTI, TRMU... - tRNA - Salmonella typhi, tRNA-specific 2-thiouridylase mnmA OS=Salmonella typhi GN=mnmA PE=3 SV=1	0.0	[22..408]	[1..361]
gi\|255006407 - gi\|255006407\|ref\|ZP_05145008.2\| tRNA-specific 2-thiouridylase MnmA [Staphylococcus aureus subsp. aur... MNMA_STAAM - tRNA-specific 2-thiouridylase MnmA OS=Staphylococcus aureus (strain Mu50 / ATCC 700699) GN=mnmA PE=3... MNMA_STAA1 - tRNA-specific 2-thiouridylase MnmA OS=Staphylococcus aureus (strain Mu3 / ATCC 700698) GN=mnmA PE=3 ...	0.0	[22..414]	[1..365]

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Predicted Domain #1

Region A:
Residues: [1-283]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MLARYLNLIG RRSASPYRPQ RLPAKFDNVI VAMSSGVDSS VAAALFAGEF PNTRGVYMQN  60
   61 WSESQSLDDP GKEPCYERDW RDVNRVAKHL NIRVDKVNFE QDYWIDVFEP MLRGYSEGST 120
  121 PNPDIGCNKF VKFGKLREWL DEKYGTGNYW LVTGHYARVM QEMNGKGLFH LLRSIYRPKD 180
  181 QSYYLSQINS TVLSSLLLPI GHLTKPEVRD LAKYAGLPTA EKPDSQGICF VNNSQHGKFK 240
  241 NFLKHYLPSS PGDIITVDPQ SGAKTTWGRH DGLWSYTIGQ KVG

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	40.0
Match:	1gpmA_
Description:	GMP synthetase; GMP synthetase, central domain; GMP synthetase C-terminal dimerisation domain
Matching Structure (courtesy of the PDB):

Predicted Domain #2

Region A:
Residues: [284-417]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ISMPQADPNY QGTWFVSEKL RDTNEILIVR GRDNPALYSD TMRIENFSSL GPREDTINAF  60
   61 QNTGALTLQF RSLQVPVQIK SCKLNRSADN LDITIHLASK QRAITPGQSC CLYIDDRVLG 120
  121 SGPISHVNNN DTHA

[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.

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