YRC Public Data Repository - Protein Structure Prediction

Protein:	RSMA_SHIFL
Organism:	Shigella flexneri
Length:	273 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

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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 RSMA_SHIFL.

Description	E-value	Query Range	Subject Range
RSMA_PHOLL, KSGA... - Ribosomal RNA small subunit methyltransferase A OS=Photorhabdus luminescens subsp. laumondii GN=rsmA... RSMA_PHOLL - Ribosomal RNA small subunit methyltransferase A OS=Photorhabdus luminescens subsp. laumondii (strain...	252.0	[0..1]	[271..1]
RSMA_SALTY - Ribosomal RNA small subunit methyltransferase A OS=Salmonella typhimurium (strain LT2 / SGSC1412 / A... RSMA_SALTY - Ribosomal RNA small subunit methyltransferase A OS=Salmonella typhimurium GN=rsmA PE=3 SV=2 KSGA_SALTY - Dimethyladenosine transferase OS=Salmonella typhimurium GN=ksgA PE=3 SV=2	252.0	[0..1]	[273..1]
gi\|205331535, gi... - gi\|205331535\|gb\|EDZ18299.1\| dimethyladenosine transferase [Salmonella enterica subsp. enterica serov... gi\|205324333, gi... - gi\|205324333\|gb\|EDZ12172.1\| dimethyladenosine transferase [Salmonella enterica subsp. enterica serov... RSMA_SALEP - Ribosomal RNA small subunit methyltransferase A OS=Salmonella enteritidis PT4 (strain P125109) GN=rs... RSMA_SALG2 - Ribosomal RNA small subunit methyltransferase A OS=Salmonella gallinarum (strain 287/91 / NCTC 13346... gi\|213427533 - gi\|213427533\|ref\|ZP_03360283.1\| dimethyladenosine transferase [Salmonella enterica subsp. enterica s... gi\|213161029 - gi\|213161029\|ref\|ZP_03346739.1\| dimethyladenosine transferase [Salmonella enterica subsp. enterica s... RSMA_SALDC - Ribosomal RNA small subunit methyltransferase A OS=Salmonella dublin (strain CT_02021853) GN=rsmA PE... RSMA_SALPK - Ribosomal RNA small subunit methyltransferase A OS=Salmonella paratyphi A (strain AKU_12601) GN=rsmA... gi\|204926662, gi... - gi\|204926662\|ref\|ZP_03217864.1\| dimethyladenosine transferase [Salmonella enterica subsp. enterica s... gi\|200389272, gi... - gi\|200389272\|ref\|ZP_03215884.1\| dimethyladenosine transferase [Salmonella enterica subsp. enterica s... gi\|194470287, gi... - gi\|194470287\|ref\|ZP_03076271.1\| dimethyladenosine transferase [Salmonella enterica subsp. enterica s... RSMA_SALHS - Ribosomal RNA small subunit methyltransferase A OS=Salmonella heidelberg (strain SL476) GN=rsmA PE=3... gi\|197241265, gi... - gi\|197263010\|ref\|ZP_03163084.1\| dimethyladenosine transferase [Salmonella enterica subsp. enterica s... RSMA_SALA4 - Ribosomal RNA small subunit methyltransferase A OS=Salmonella agona (strain SL483) GN=rsmA PE=3 SV=1 RSMA_SALPB - Ribosomal RNA small subunit methyltransferase A OS=Salmonella paratyphi B (strain ATCC BAA-1250 / SP... gi\|205337400, gi... - gi\|205337400\|gb\|EDZ24164.1\| dimethyladenosine transferase [Salmonella enterica subsp. enterica serov... gi\|168230359, gi... - gi\|205335041\|gb\|EDZ21805.1\| dimethyladenosine transferase [Salmonella enterica subsp. enterica serov... gi\|205342515, gi... - gi\|205342515\|gb\|EDZ29279.1\| dimethyladenosine transferase [Salmonella enterica subsp. enterica serov... gi\|205348868, gi... - gi\|205348868\|gb\|EDZ35499.1\| dimethyladenosine transferase [Salmonella enterica subsp. enterica serov... RSMA_SALPB, KSGA... - Ribosomal RNA small subunit methyltransferase A OS=Salmonella paratyphi B (strain ATCC BAA-1250 / SP... lcl\|NC_016856.1_... - [gene=ksgA] [protein=dimethyladenosine transferase] [protein_id=YP_005235742.1] [location=complement... RSMA_SALPA, KSGA... - Ribosomal RNA small subunit methyltransferase A OS=Salmonella paratyphi A GN=rsmA PE=3 SV=1, Dimethy... gi\|214001248 - gi\|214001248\|ref\|ZP_03411983.1\| dimethyladenosine transferase [Salmonella enterica subsp. enterica s... gi\|213648900 - gi\|213648900\|ref\|ZP_03378953.1\| dimethyladenosine transferase [Salmonella enterica subsp. enterica s... RSMA_SALPC - Ribosomal RNA small subunit methyltransferase A OS=Salmonella paratyphi C (strain RKS4594) GN=rsmA P... gi\|238911148 - gi\|238911148\|ref\|ZP_04654985.1\| dimethyladenosine transferase [Salmonella enterica subsp. enterica s... RSMA_SALTI - Ribosomal RNA small subunit methyltransferase A OS=Salmonella typhi GN=rsmA PE=3 SV=1 gi\|29140635, gi\|... - gi\|29140635\|ref\|NP_803977.1\| dimethyladenosine transferase [Salmonella enterica subsp. enterica sero... RSMA_SALPA - Ribosomal RNA small subunit methyltransferase A OS=Salmonella paratyphi A (strain ATCC 9150 / SARB42... gi\|16759085 - gi\|16759085\|ref\|NP_454702.1\| dimethyladenosine transferase [Salmonella enterica subsp. enterica sero... KSGA_SALTI - Dimethyladenosine transferase OS=Salmonella typhi GN=ksgA PE=3 SV=1	252.0	[0..1]	[273..1]
RSMA_SALCH - Ribosomal RNA small subunit methyltransferase A OS=Salmonella choleraesuis GN=rsmA PE=3 SV=1 KSGA_SALCH - Dimethyladenosine transferase OS=Salmonella choleraesuis GN=ksgA PE=3 SV=1 RSMA_SALCH - Ribosomal RNA small subunit methyltransferase A OS=Salmonella choleraesuis (strain SC-B67) GN=rsmA P...	251.0	[0..1]	[273..1]
RSMA_ERWCT, KSGA... - Ribosomal RNA small subunit methyltransferase A OS=Erwinia carotovora subsp. atroseptica GN=rsmA PE=... RSMA_PECAS - Ribosomal RNA small subunit methyltransferase A OS=Pectobacterium atrosepticum (strain SCRI 1043 / A...	249.0	[0..1]	[272..1]
RSMA_YERPG - Ribosomal RNA small subunit methyltransferase A OS=Yersinia pestis bv. Antiqua (strain Angola) GN=rs... gi\|166008750, gi... - gi\|166008750\|ref\|ZP_02229648.1\| dimethyladenosine transferase [Yersinia pestis biovar Antiqua str. E... gi\|165919942, gi... - gi\|165928081\|ref\|ZP_02223913.1\| dimethyladenosine transferase [Yersinia pestis biovar Orientalis str... gi\|229705868, gi... - gi\|229836925\|ref\|ZP_04457090.1\| S-adenosylmethionine-6-N',N'-adenosyl (rRNA) dimethyltransferase [Ye... gi\|167401583, gi... - gi\|167401583\|ref\|ZP_02307077.1\| dimethyladenosine transferase [Yersinia pestis biovar Antiqua str. U... gi\|229696746, gi... - gi\|229840380\|ref\|ZP_04460539.1\| S-adenosylmethionine-6-N',N'-adenosyl (rRNA) dimethyltransferase [Ye... gi\|166212108, gi... - gi\|166212108\|ref\|ZP_02238143.1\| dimethyladenosine transferase [Yersinia pestis biovar Antiqua str. B... gi\|229690770, gi... - gi\|229842460\|ref\|ZP_04462615.1\| S-adenosylmethionine-6-N',N'-adenosyl (rRNA) dimethyltransferase [Ye... gi\|167426031, gi... - gi\|167426031\|ref\|ZP_02317784.1\| dimethyladenosine transferase [Yersinia pestis biovar Mediaevalis st... gi\|166960157, gi... - gi\|167422020\|ref\|ZP_02313773.1\| dimethyladenosine transferase [Yersinia pestis biovar Orientalis str... gi\|22127557, gi\|... - gi\|22127557\|ref\|NP_670980.1\| dimethyladenosine transferase [Yersinia pestis KIM], gi\|21960661\|gb\|AAM... gi\|218927690, gi... - gi\|218927690\|ref\|YP_002345565.1\| dimethyladenosine transferase [Yersinia pestis CO92], gi\|16120822\|r... gi\|45438288, gi\|... - gi\|45443419\|ref\|NP_994958.1\| dimethyladenosine transferase [Yersinia pestis biovar Microtus str. 910... gi\|165914189, gi... - gi\|89102169\|ref\|ZP_01174824.1\| COG0030: Dimethyladenosine transferase (rRNA methylation) [Yersinia p... RSMA_YERPA - Ribosomal RNA small subunit methyltransferase A OS=Yersinia pestis bv. Antiqua (strain Antiqua) GN=r... RSMA_YERPN - Ribosomal RNA small subunit methyltransferase A OS=Yersinia pestis bv. Antiqua (strain Nepal516) GN=... RSMA_YERPE - Ribosomal RNA small subunit methyltransferase A OS=Yersinia pestis GN=rsmA PE=3 SV=1 gi\|149289879, gi... - gi\|150260471\|ref\|ZP_01917199.1\| dimethyladenosine transferase [Yersinia pestis CA88-4125], gi\|149289... RSMA_YERPP - Ribosomal RNA small subunit methyltransferase A OS=Yersinia pestis (strain Pestoides F) GN=rsmA PE=3...	249.0	[0..1]	[272..1]
RSMA_YERP3 - Ribosomal RNA small subunit methyltransferase A OS=Yersinia pseudotuberculosis serotype O:1b (strain... RSMA_YERPB - Ribosomal RNA small subunit methyltransferase A OS=Yersinia pseudotuberculosis serotype IB (strain P... RSMA_YERPY - Ribosomal RNA small subunit methyltransferase A OS=Yersinia pseudotuberculosis serotype O:3 (strain ... KSGA_YERPS, RSMA... - Ribosomal RNA small subunit methyltransferase A OS=Yersinia pseudotuberculosis GN=rsmA PE=3 SV=1, Di... RSMA_YERPS - Ribosomal RNA small subunit methyltransferase A OS=Yersinia pseudotuberculosis serotype I (strain IP...	248.0	[0..1]	[272..1]
RSMA_SHIDS - Ribosomal RNA small subunit methyltransferase A OS=Shigella dysenteriae serotype 1 (strain Sd197) GN...	247.0	[0..1]	[273..1]
KSGA_ECOLI - Dimethyladenosine transferase (EC 2.1.1.-) (S-adenosylmethionine-6-N', N'-adenosyl(rRNA) dimethyltra... EG10523 - 16S rRNA m(6)A1518, m(6)A1519 dimethyltransferase, SAM-dependent / 16S rRNA m(6)A1518, m(6)A1519 dim... RSMA_ECOLC - Ribosomal RNA small subunit methyltransferase A OS=Escherichia coli (strain ATCC 8739 / DSM 1576 / C... RSMA_ECOBW - Ribosomal RNA small subunit methyltransferase A OS=Escherichia coli (strain K12 / MC4100 / BW2952) G... gi\|251783617, gi... - gi\|251783617\|ref\|YP_002997921.1\| hypothetical protein B21_00054 [Escherichia coli BL21], gi\|24237589... gi\|253325961, gi... - gi\|254286979\|ref\|YP_003052727.1\| dimethyladenosine transferase [Escherichia coli BL21(DE3)], gi\|2539... gi\|254037468, gi... - gi\|254037468\|ref\|ZP_04871545.1\| methyltransferase [Escherichia sp. 1_1_43], gi\|226840574\|gb\|EEH72576... gi\|253972077, gi... - gi\|254160176\|ref\|YP_003043284.1\| dimethyladenosine transferase [Escherichia coli B str. REL606], gi\|... gi\|192926150, gi... - gi\|75255706\|ref\|ZP_00727472.1\| COG0030: Dimethyladenosine transferase (rRNA methylation) [Escherichi... RSMA_ECOSM - Ribosomal RNA small subunit methyltransferase A OS=Escherichia coli (strain SMS-3-5 / SECEC) GN=rsmA... gi\|188492783, gi... - gi\|75515639\|ref\|ZP_00737796.1\| COG0030: Dimethyladenosine transferase (rRNA methylation) [Escherichi... RSMA_ECODH - Ribosomal RNA small subunit methyltransferase A OS=Escherichia coli (strain K12 / DH10B) GN=rsmA PE=... gi\|194412078, gi... - gi\|75208907\|ref\|ZP_00709184.1\| COG0030: Dimethyladenosine transferase (rRNA methylation) [Escherichi... RSMA_ECO8A - Ribosomal RNA small subunit methyltransferase A OS=Escherichia coli O8 (strain IAI1) GN=rsmA PE=3 SV... gi\|193070981, gi... - gi\|75234136\|ref\|ZP_00718540.1\| COG0030: Dimethyladenosine transferase (rRNA methylation) [Escherichi... gi\|194417209, gi... - gi\|194434556\|ref\|ZP_03066814.1\| dimethyladenosine transferase [Shigella dysenteriae 1012], gi\|194417... gi\|85674303, gi\|... - gi\|89106935\|ref\|AP_000715.1\| S-adenosylmethionine-6-N',N'-adenosyl (rRNA) dimethyltransferase [Esche... RSMA_ECO7I - Ribosomal RNA small subunit methyltransferase A OS=Escherichia coli O7:K1 (strain IAI39 / ExPEC) GN=... RSMA_SHISS - Ribosomal RNA small subunit methyltransferase A OS=Shigella sonnei (strain Ss046) GN=rsmA PE=3 SV=1 RSMA_SHIBS - Ribosomal RNA small subunit methyltransferase A OS=Shigella boydii serotype 4 (strain Sb227) GN=rsmA... RSMA_SHIF8 - Ribosomal RNA small subunit methyltransferase A OS=Shigella flexneri serotype 5b (strain 8401) GN=rs... gi\|194439700, gi... - gi\|83584904\|ref\|ZP_00923561.1\| COG0030: Dimethyladenosine transferase (rRNA methylation) [Escherichi... RSMA_ECOHS - Ribosomal RNA small subunit methyltransferase A OS=Escherichia coli O9:H4 (strain HS) GN=rsmA PE=3 S... EG10523 - 16S rRNA m(6)A1518, m(6)A1519 dimethyltransferase, SAM-dependent / 16S rRNA m(6)A1518, m(6)A1519 dim... gi\|124531315, gi... - gi\|124531315\|ref\|ZP_01701643.1\| dimethyladenosine transferase [Escherichia coli B], gi\|124498615\|gb\|...	246.0	[0..1]	[273..1]
RSMA_ECO24 - Ribosomal RNA small subunit methyltransferase A OS=Escherichia coli O139:H28 (strain E24377A / ETEC)...	246.0	[0..1]	[273..1]

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Predicted Domain #1

Region A:
Residues: [1-273]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MNNRVHQGHL ARKRFGQNFL NDQFVIDSIV SAINPQKGQA MVEIGPGLAA LTEPVGERLD  60
   61 QLTVIELDRD LAARLQTHPF LGPKLTIYQQ DAMTFNFGEL AEKMGQPLRV FGNLPYNIST 120
  121 PLMFHLFSYT DAIADMHFML QKEVVNRLVA GPNSKAYGRL SVMAQYYCNV IPVLEVPPSA 180
  181 FTPPPKVDSA VVRLVPHATM PHPVKDIRVL SRITTEAFNQ RRKTIRNSLG NLFSVEVLTG 240
  241 MGIDPAMRAE NISVAQYCQM ANYLAENAPL QES

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	56.39794
Match:	1qyrA
Description:	2.1 Angstrom Crystal structure of KsgA: A Universally Conserved Adenosine Dimethyltransferase
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
methyltransferase activity	4.15445027778357	bayes_pls_golite062009
rRNA methyltransferase activity	4.09362182773099	bayes_pls_golite062009
transferase activity, transferring one-carbon groups	4.07153733729662	bayes_pls_golite062009
N-methyltransferase activity	3.67177992319602	bayes_pls_golite062009
protein methyltransferase activity	3.5512266163483	bayes_pls_golite062009
S-adenosylmethionine-dependent methyltransferase activity	3.39429041855776	bayes_pls_golite062009
RNA methyltransferase activity	3.07428840534971	bayes_pls_golite062009
histone methyltransferase activity	2.49492581548369	bayes_pls_golite062009
transferase activity	2.22303238506686	bayes_pls_golite062009
DNA-methyltransferase activity	2.14498896320526	bayes_pls_golite062009
protein-arginine N-methyltransferase activity	2.06652984530965	bayes_pls_golite062009
arginine N-methyltransferase activity	2.06652984530965	bayes_pls_golite062009
rRNA (adenine) methyltransferase activity	1.83964463328968	bayes_pls_golite062009
rRNA (adenine-N6,N6-)-dimethyltransferase activity	1.75675289134467	bayes_pls_golite062009
histone-arginine N-methyltransferase activity	1.63076727020333	bayes_pls_golite062009
transcription regulator activity	1.42049721553167	bayes_pls_golite062009
protein-arginine omega-N monomethyltransferase activity	1.26493190370687	bayes_pls_golite062009
catalytic activity	1.25333584501255	bayes_pls_golite062009
tRNA methyltransferase activity	1.12859857407629	bayes_pls_golite062009
rRNA (guanine) methyltransferase activity	1.10713374933008	bayes_pls_golite062009
DNA binding	1.03011331296251	bayes_pls_golite062009
nucleic acid binding	0.731396842794323	bayes_pls_golite062009
histone methyltransferase activity (H4-R3 specific)	0.720411427168235	bayes_pls_golite062009
site-specific DNA-methyltransferase (adenine-specific) activity	0.703178429468566	bayes_pls_golite062009
protein-arginine omega-N asymmetric methyltransferase activity	0.606920378432989	bayes_pls_golite062009
binding	0.546744797014504	bayes_pls_golite062009
mitochondrial transcription initiation factor activity	0.481383105532041	bayes_pls_golite062009
tRNA (cytosine-5-)-methyltransferase activity	0.299393192819978	bayes_pls_golite062009
tRNA (cytosine)-methyltransferase activity	0.299393192819978	bayes_pls_golite062009
rRNA (guanine-N1-)-methyltransferase activity	0.234572322347698	bayes_pls_golite062009
rRNA (uridine-2'-O-)-methyltransferase activity	0.188049877065151	bayes_pls_golite062009
transcription factor binding	0.149382105526243	bayes_pls_golite062009
rRNA (uridine) methyltransferase activity	0.130647573658872	bayes_pls_golite062009

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: