YRC Public Data Repository - Protein Structure Prediction

Protein:	YCBY_ECOLI
Organism:	Escherichia coli
Length:	702 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 YCBY_ECOLI.

Description	E-value	Query Range	Subject Range
RLMKL_SHEDO - Ribosomal RNA large subunit methyltransferase K/L OS=Shewanella denitrificans (strain OS217 / ATCC B...	655.0	[0..1]	[702..1]
gi\|167993433, gi... - gi\|205328551\|gb\|EDZ15315.1\| putative RNA methylase family UPF0020 [Salmonella enterica subsp. enteri... gi\|205337189, gi... - gi\|205337189\|gb\|EDZ23953.1\| putative RNA methylase family UPF0020 [Salmonella enterica subsp. enteri... lcl\|NC_016856.1_... - [gene=ycbY] [protein=23S rRNA m(2)G2445 methyltransferase] [protein_id=YP_005236793.1] [location=110... RLML_SALPA - Ribosomal RNA large subunit methyltransferase L OS=Salmonella paratyphi A GN=rlmL PE=3 SV=1 RLML_SALTY - Ribosomal RNA large subunit methyltransferase L OS=Salmonella typhimurium GN=rlmL PE=3 SV=1 RLMKL_SALTY - Ribosomal RNA large subunit methyltransferase K/L OS=Salmonella typhimurium (strain LT2 / SGSC1412 /... RLMKL_SALDC - Ribosomal RNA large subunit methyltransferase K/L OS=Salmonella dublin (strain CT_02021853) GN=rlmL ... RLMKL_SALPA - Ribosomal RNA large subunit methyltransferase K/L OS=Salmonella paratyphi A (strain ATCC 9150 / SARB... RLMKL_SALEP - Ribosomal RNA large subunit methyltransferase K/L OS=Salmonella enteritidis PT4 (strain P125109) GN=... gi\|197264036, gi... - gi\|197264036\|ref\|ZP_03164110.1\| putative RNA methylase family UPF0020 [Salmonella enterica subsp. en... RLMKL_SALPK - Ribosomal RNA large subunit methyltransferase K/L OS=Salmonella paratyphi A (strain AKU_12601) GN=rl... RLMKL_SALHS - Ribosomal RNA large subunit methyltransferase K/L OS=Salmonella heidelberg (strain SL476) GN=rlmL PE... RLMKL_SALA4 - Ribosomal RNA large subunit methyltransferase K/L OS=Salmonella agona (strain SL483) GN=rlmL PE=3 SV... gi\|205341529, gi... - gi\|205341529\|gb\|EDZ28293.1\| putative RNA methylase family UPF0020 [Salmonella enterica subsp. enteri... RLMKL_SALNS - Ribosomal RNA large subunit methyltransferase K/L OS=Salmonella newport (strain SL254) GN=rlmL PE=3 ... gi\|205346845, gi... - gi\|205346845\|gb\|EDZ33476.1\| putative RNA methylase family UPF0020 [Salmonella enterica subsp. enteri... gi\|195630073, gi... - gi\|195630073\|gb\|EDX48725.1\| putative RNA methylase family UPF0020 [Salmonella enterica subsp. enteri...	652.0	[0..1]	[702..1]
gi\|191166960, gi... - gi\|75229846\|ref\|ZP_00716369.1\| COG0116: Predicted N6-adenine-specific DNA methylase [Escherichia col... gi\|193071757, gi... - gi\|75214605\|ref\|ZP_00713143.1\| COG0116: Predicted N6-adenine-specific DNA methylase [Escherichia col... gi\|209918200, gi... - gi\|209918200\|ref\|YP_002292284.1\| 23S rRNA m(2)G2445 methyltransferase [Escherichia coli SE11], gi\|20...	651.0	[0..1]	[702..1]
RLMKL_SHISS - Ribosomal RNA large subunit methyltransferase K/L OS=Shigella sonnei (strain Ss046) GN=rlmL PE=3 SV=...	651.0	[0..1]	[702..1]
RLMKL_ECO24 - Ribosomal RNA large subunit methyltransferase K/L OS=Escherichia coli O139:H28 (strain E24377A / ETE... gi\|218351155, gi... - gi\|218694423\|ref\|YP_002402090.1\| 23S rRNA m(2)G2445 methyltransferase [Escherichia coli 55989], gi\|2...	651.0	[0..1]	[702..1]
RLMKL_SHIBS - Ribosomal RNA large subunit methyltransferase K/L OS=Shigella boydii serotype 4 (strain Sb227) GN=rl...	651.0	[0..1]	[702..1]
gi\|189375248, gi... - gi\|189375248\|gb\|EDU93664.1\| putative RNA methylase family UPF0020 [Escherichia coli O157:H7 str. EC5... gi\|168787379, gi... - gi\|189372718\|gb\|EDU91134.1\| putative RNA methylase family UPF0020 [Escherichia coli O157:H7 str. EC8... gi\|25499331, gi\|... - pir\|\|F85621 probable oxidoreductase ycbY [imported] - Escherichia coli (strain O157:H7, substrain E... gi\|188998771, gi... - gi\|188998771\|gb\|EDU67757.1\| putative RNA methylase family UPF0020 [Escherichia coli O157:H7 str. EC4... gi\|187768361, gi... - gi\|187768361\|gb\|EDU32205.1\| putative RNA methylase family UPF0020 [Escherichia coli O157:H7 str. EC4... gi\|15800807, gi\|... - gi\|15800807\|ref\|NP_286823.1\| 23S rRNA m(2)G2445 methyltransferase [Escherichia coli O157:H7 EDL933],... RLMKL_ECO5E - Ribosomal RNA large subunit methyltransferase K/L OS=Escherichia coli O157:H7 (strain EC4115 / EHEC)... RLMKL_ECO57 - Ribosomal RNA large subunit methyltransferase K/L OS=Escherichia coli O157:H7 GN=rlmL PE=3 SV=1 gi\|208816186, gi... - gi\|208816186\|ref\|ZP_03257365.1\| putative RNA methylase family UPF0020 [Escherichia coli O157:H7 str.... gi\|208809391, gi... - gi\|208809391\|ref\|ZP_03251728.1\| putative RNA methylase family UPF0020 [Escherichia coli O157:H7 str.... gi\|195939638 - gi\|195939638\|ref\|ZP_03085020.1\| 23S rRNA m(2)G2445 methyltransferase [Escherichia coli O157:H7 str. ... gi\|189366794, gi... - gi\|189366794\|gb\|EDU85210.1\| putative RNA methylase family UPF0020 [Escherichia coli O157:H7 str. EC4... gi\|254792148, gi... - gi\|254792148\|ref\|YP_003076985.1\| 23S rRNA m2G2445 methyltransferase [Escherichia coli O157:H7 str. T... gi\|217324956, gi... - gi\|217324956\|ref\|ZP_03441040.1\| UPF0020, RNA methylase family [Escherichia coli O157:H7 str. TW14588... gi\|15830286, gi\|... - gi\|15830286\|ref\|NP_309059.1\| 23S rRNA m(2)G2445 methyltransferase [Escherichia coli O157:H7 str. Sak...	650.0	[0..1]	[702..1]
RLMKL_SHIDS - Ribosomal RNA large subunit methyltransferase K/L OS=Shigella dysenteriae serotype 1 (strain Sd197) ...	650.0	[0..1]	[702..1]
gi\|224468959, gi... - gi\|224584432\|ref\|YP_002638230.1\| hypothetical protein SPC_2688 [Salmonella enterica subsp. enterica ... RLML_SALCH - Ribosomal RNA large subunit methyltransferase L OS=Salmonella choleraesuis GN=rlmL PE=3 SV=1 RLMKL_SALCH - Ribosomal RNA large subunit methyltransferase K/L OS=Salmonella choleraesuis (strain SC-B67) GN=rlmL...	650.0	[0..1]	[702..1]
RLMKL_ECOL5 - Ribosomal RNA large subunit methyltransferase K/L OS=Escherichia coli O6:K15:H31 (strain 536 / UPEC)... gi\|191172055, gi... - gi\|75241016\|ref\|ZP_00724905.1\| COG0116: Predicted N6-adenine-specific DNA methylase [Escherichia col...	650.0	[0..1]	[702..1]

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Predicted Domain #1

Region A:
Residues: [1-359]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MNSLFASTAR GLEELLKTEL ENLGAVECQV VQGGVHFKGD TRLVYQSLMW SRLASRIMLP  60
   61 LGECKVYSDL DLYLGVQAIN WTEMFNPGAT FAVHFSGLND TIRNSQYGAM KVKDAIVDAF 120
  121 TRKNLPRPNV DRDAPDIRVN VWLHKETASI ALDLSGDGLH LRGYRDRAGI APIKETLAAA 180
  181 IVMRSGWQPG TPLLDPMCGS GTLLIEAAML ATDRAPGLHR GRWGFSGWAQ HDEAIWQEVK 240
  241 AEAQTRARKG LAEYSSHFYG SDSDARVIQR ARTNARLAGI GELITFEVKD VAQLTNPLPK 300
  301 GPYGTVLSNP PYGERLDSEP ALIALHSLLG RIMKNQFGGW NLSLFSASPD LLSCLQLRA

[Run NCBI BLAST on this sequence.]

Detection Method:	FFAS03
Confidence:	2.65
Match:	2okcA
Description:	No description for 2okcA was found.

Predicted functions:

Term	Confidence	Notes
methyltransferase activity	3.68431317301075	bayes_pls_golite062009
rRNA methyltransferase activity	3.65102636703195	bayes_pls_golite062009
transferase activity, transferring one-carbon groups	3.60853685152199	bayes_pls_golite062009
S-adenosylmethionine-dependent methyltransferase activity	2.91374296950366	bayes_pls_golite062009
RNA methyltransferase activity	2.63941856307703	bayes_pls_golite062009
N-methyltransferase activity	2.62081022854657	bayes_pls_golite062009
protein methyltransferase activity	2.60624413031692	bayes_pls_golite062009
transferase activity	1.97261773840408	bayes_pls_golite062009
histone methyltransferase activity	1.5770892133978	bayes_pls_golite062009
rRNA (adenine) methyltransferase activity	1.41988260132739	bayes_pls_golite062009
rRNA (adenine-N6,N6-)-dimethyltransferase activity	1.34038096673696	bayes_pls_golite062009
DNA-methyltransferase activity	1.22300870226526	bayes_pls_golite062009
arginine N-methyltransferase activity	1.17774160785818	bayes_pls_golite062009
protein-arginine N-methyltransferase activity	1.17774160785818	bayes_pls_golite062009
catalytic activity	1.16970557486814	bayes_pls_golite062009
tRNA methyltransferase activity	0.752031224323003	bayes_pls_golite062009
rRNA (guanine) methyltransferase activity	0.724178554958878	bayes_pls_golite062009
histone-arginine N-methyltransferase activity	0.663671542316122	bayes_pls_golite062009
site-specific DNA-methyltransferase (adenine-specific) activity	0.286806504860858	bayes_pls_golite062009
protein-arginine omega-N monomethyltransferase activity	0.24819970199694	bayes_pls_golite062009
rRNA (guanine-N2-)-methyltransferase activity	0.0808109576693168	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [360-702]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DKQYKAKNGP LDCVQKNYHV AESTPDSKPA MVAEDYTNRL RKNLKKFEKW ARQEGIECYR  60
   61 LYDADLPEYN VAVDRYADWV VVQEYAPPKT IDAHKARQRL FDIIAATISV LGIAPNKLVL 120
  121 KTRERQKGKN QYQKLGEKGE FLEVTEYNAH LWVNLTDYLD TGLFLDHRIA RRMLGQMSKG 180
  181 KDFLNLFSYT GSATVHAGLG GARSTTTVDM SRTYLEWAER NLRLNGLTGR AHRLIQADCL 240
  241 AWLREANEQF DLIFIDPPTF SNSKRMEDAF DVQRDHLALM KDLKRLLRAG GTIMFSNNKR 300
  301 GFRMDLDGLA KLGLKAQEIT QKTLSQDFAR NRQIHNCWLI TAA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	44.69897
Match:	2as0A
Description:	Crystal Structure of PH1915 (APC 5817): A Hypothetical RNA Methyltransferase
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
S-adenosylmethionine-dependent methyltransferase activity	3.39429041855776	bayes_pls_golite062009
RNA methyltransferase activity	3.07428840534971	bayes_pls_golite062009
N-methyltransferase activity	3.0539218951403	bayes_pls_golite062009
protein methyltransferase activity	3.01384869242051	bayes_pls_golite062009
transferase activity	2.22303238506686	bayes_pls_golite062009
histone methyltransferase activity	1.90505369820945	bayes_pls_golite062009
rRNA (adenine) methyltransferase activity	1.83964463328968	bayes_pls_golite062009
rRNA (adenine-N6,N6-)-dimethyltransferase activity	1.75675289134467	bayes_pls_golite062009
DNA-methyltransferase activity	1.63765148226572	bayes_pls_golite062009
protein-arginine N-methyltransferase activity	1.6030970825293	bayes_pls_golite062009
arginine N-methyltransferase activity	1.6030970825293	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
histone-arginine N-methyltransferase activity	1.05897361334523	bayes_pls_golite062009
site-specific DNA-methyltransferase (adenine-specific) activity	0.703178429468566	bayes_pls_golite062009
protein-arginine omega-N monomethyltransferase activity	0.639377525568296	bayes_pls_golite062009
rRNA (guanine-N2-)-methyltransferase activity	0.427131446117391	bayes_pls_golite062009
rRNA (cytosine) methyltransferase activity	0.346042596102079	bayes_pls_golite062009
O-methyltransferase activity	0.250946859465502	bayes_pls_golite062009
protein-arginine omega-N asymmetric methyltransferase activity	0.130104080746388	bayes_pls_golite062009
histone methyltransferase activity (H4-R3 specific)	0.130042730841119	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:

Predicted functions: