YRC Public Data Repository - Protein Structure Prediction

Protein:	YNL022C
Organism:	Saccharomyces cerevisiae
Length:	490 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 YNL022C.

Description	E-value	Query Range	Subject Range
YNL022C - Putative cytosine 5-methyltransferase, contains seven beta-strand methyltransferase motif similar to... RCM1_YEAST - 25S rRNA (cytosine(2278)-C(5))-methyltransferase OS=Saccharomyces cerevisiae (strain ATCC 204508 / S... gi\|151944502 - gi\|151944502\|gb\|EDN62780.1\| conserved protein [Saccharomyces cerevisiae YJM789]	6.0E-91	[1..490]	[1..490]
gi\|15833408, gi\|... - gi\|15833408\|ref\|NP_312181.1\| 16S rRNA methyltransferase B [Escherichia coli O157:H7 str. Sakai], gi\|... gi\|25303751 - pir\|\|B91148 RNA methyltransferase [imported] - Escherichia coli (strain O157:H7, substrain RIMD 0509... gi\|15833408, gi\|... - gi\|15833408\|ref\|NP_312181.1\| RNA methyltransferase [Escherichia coli O157:H7], gi\|13363627\|dbj\|BAB37...	1.0E-78	[2..451]	[6..425]
RSMB_SALTY - Ribosomal RNA small subunit methyltransferase B OS=Salmonella typhimurium (strain LT2 / SGSC1412 / A... lcl\|NC_016856.1_... - [gene=sun] [protein=16S rRNA methyltransferase B] [protein_id=YP_005239598.1] [location=3592318..359... gi\|167995183, gi... - gi\|205327090\|gb\|EDZ13854.1\| ribosomal RNA small subunit methyltransferase B [Salmonella enterica sub... RSMB_SALTY - Ribosomal RNA small subunit methyltransferase B OS=Salmonella typhimurium GN=rsmB PE=3 SV=1 RSMB_SALTY - Ribosomal RNA small subunit methyltransferase B OS=Salmonella typhimurium GN=rsmB PE=3 SV=1	1.0E-78	[2..451]	[6..425]
gi\|12517918, gi\|... - gi\|15803816\|ref\|NP_289850.1\| 16S rRNA methyltransferase B [Escherichia coli O157:H7 EDL933], gi\|1251... gi\|208812777, gi... - gi\|208812777\|ref\|ZP_03254106.1\| ribosomal RNA small subunit methyltransferase B [Escherichia coli O1... gi\|209757340, gi... - pir\|\|F85993 hypothetical protein sun [imported] - Escherichia coli (strain O157:H7, substrain EDL93... gi\|208808123, gi... - gi\|208808123\|ref\|ZP_03250460.1\| ribosomal RNA small subunit methyltransferase B [Escherichia coli O1... gi\|195939836 - gi\|195939836\|ref\|ZP_03085218.1\| 16S rRNA methyltransferase B [Escherichia coli O157:H7 str. EC4024] gi\|189375353, gi... - gi\|189375353\|gb\|EDU93769.1\| ribosomal RNA small subunit methyltransferase B [Escherichia coli O157:H... gi\|217326360, gi... - gi\|217326360\|ref\|ZP_03442444.1\| ribosomal RNA small subunit methyltransferase B [Escherichia coli O1... RSMB_ECO5E - Ribosomal RNA small subunit methyltransferase B OS=Escherichia coli O157:H7 (strain EC4115 / EHEC) G... gi\|208820338, gi... - gi\|208820338\|ref\|ZP_03260658.1\| ribosomal RNA small subunit methyltransferase B [Escherichia coli O1... RSMB_ECO57 - Ribosomal RNA small subunit methyltransferase B OS=Escherichia coli O157:H7 GN=rsmB PE=3 SV=1 gi\|189365121, gi... - gi\|189365121\|gb\|EDU83537.1\| ribosomal RNA small subunit methyltransferase B [Escherichia coli O157:H... gi\|189354681, gi... - gi\|189354681\|gb\|EDU73100.1\| ribosomal RNA small subunit methyltransferase B [Escherichia coli O157:H... gi\|168752263, gi... - gi\|188013841\|gb\|EDU51963.1\| ribosomal RNA small subunit methyltransferase B [Escherichia coli O157:H... gi\|189373894, gi... - gi\|189373894\|gb\|EDU92310.1\| ribosomal RNA small subunit methyltransferase B [Escherichia coli O157:H... gi\|188998877, gi... - gi\|188998877\|gb\|EDU67863.1\| ribosomal RNA small subunit methyltransferase B [Escherichia coli O157:H... gi\|168777854, gi... - gi\|187767005\|gb\|EDU30849.1\| ribosomal RNA small subunit methyltransferase B [Escherichia coli O157:H... gi\|189361764, gi... - gi\|189361764\|gb\|EDU80183.1\| ribosomal RNA small subunit methyltransferase B [Escherichia coli O157:H... gi\|254594625, gi... - gi\|254795225\|ref\|YP_003080062.1\| 16S rRNA m5C967 methyltransferase [Escherichia coli O157:H7 str. TW...	2.0E-78	[2..451]	[6..425]
gi\|150260712, gi... - gi\|150260712\|ref\|ZP_01917440.1\| 16S rRNA m5C967 methyltransferase [Yersinia pestis CA88-4125], gi\|14... RSMB_YERPP - Ribosomal RNA small subunit methyltransferase B OS=Yersinia pestis (strain Pestoides F) GN=rsmB PE=3... RSMB_YERP3 - Ribosomal RNA small subunit methyltransferase B OS=Yersinia pseudotuberculosis serotype O:1b (strain... RSMB_YERPS - Ribosomal RNA small subunit methyltransferase B OS=Yersinia pseudotuberculosis GN=rsmB PE=3 SV=1 RSMB_YERPB - Ribosomal RNA small subunit methyltransferase B OS=Yersinia pseudotuberculosis serotype IB (strain P... RSMB_YERPE - Ribosomal RNA small subunit methyltransferase B OS=Yersinia pestis GN=rsmB PE=3 SV=1 gi\|21961028, gi\|... - gi\|22127891\|ref\|NP_671314.1\| 16S rRNA methyltransferase B [Yersinia pestis KIM], gi\|21961028\|gb\|AAM8... gi\|16120578, gi\|... - gi\|218927446\|ref\|YP_002345321.1\| 16S rRNA methyltransferase B [Yersinia pestis CO92], gi\|16120578\|re... gi\|229706346, gi... - gi\|229836278\|ref\|ZP_04456445.1\| 16S rRNA m5C967 methyltransferase [Yersinia pestis Pestoides A], gi\|... RSMB_YERPS - Ribosomal RNA small subunit methyltransferase B OS=Yersinia pseudotuberculosis serotype I (strain IP... gi\|229696464, gi... - gi\|229840098\|ref\|ZP_04460257.1\| 16S rRNA m5C967 methyltransferase [Yersinia pestis biovar Orientalis... gi\|229690490, gi... - gi\|229842180\|ref\|ZP_04462335.1\| 16S rRNA m5C967 methyltransferase [Yersinia pestis biovar Orientalis... gi\|161511468 - gi\|161511468\|ref\|NP_991637.2\| 16S rRNA methyltransferase B [Yersinia pestis biovar Microtus str. 910... gi\|89104537 - gi\|89104537\|ref\|ZP_01177077.1\| COG0144: tRNA and rRNA cytosine-C5-methylases [Yersinia pestis biovar... gi\|165990624, gi... - gi\|166010534\|ref\|ZP_02231432.1\| ribosomal RNA small subunit methyltransferase B [Yersinia pestis bio... RSMB_YERPA - Ribosomal RNA small subunit methyltransferase B OS=Yersinia pestis bv. Antiqua (strain Antiqua) GN=r... gi\|165920172, gi... - gi\|165927896\|ref\|ZP_02223728.1\| ribosomal RNA small subunit methyltransferase B [Yersinia pestis bio... RSMB_YERPN - Ribosomal RNA small subunit methyltransferase B OS=Yersinia pestis bv. Antiqua (strain Nepal516) GN=... RSMB_YERPY - Ribosomal RNA small subunit methyltransferase B OS=Yersinia pseudotuberculosis serotype O:3 (strain ... gi\|167468244 - gi\|167468244\|ref\|ZP_02332948.1\| 16S rRNA methyltransferase B [Yersinia pestis FV-1]	2.0E-78	[2..489]	[6..428]
gi\|253979273, gi... - gi\|254289966\|ref\|YP_003055714.1\| 16S rRNA m5C967 methyltransferase, S-adenosyl-L-methionine-dependen... gi\|124532220, gi... - gi\|124532220\|ref\|ZP_01702158.1\| sun protein [Escherichia coli B], gi\|124498110\|gb\|EAY45637.1\| sun pr... gi\|254038449, gi... - gi\|254038449\|ref\|ZP_04872505.1\| ribosomal RNA small subunit methyltransferase B [Escherichia sp. 1_1... gi\|253975117, gi... - gi\|254163216\|ref\|YP_003046324.1\| 16S rRNA m5C967 methyltransferase, S-adenosyl-L-methionine-dependen... RSMB_ECOLI - Ribosomal RNA small subunit methyltransferase B (EC 2.1.1.-) (rRNA (cytosine-C(5)-)-methyltransferas... EG12163 - 16S rRNA m(5)C967 methyltransferase, SAM-dependent / 16S rRNA m(5)C967 methyltransferase, SAM-depend... RSMB_ECODH - Ribosomal RNA small subunit methyltransferase B OS=Escherichia coli (strain K12 / DH10B) GN=rsmB PE=... RSMB_ECOLC - Ribosomal RNA small subunit methyltransferase B OS=Escherichia coli (strain ATCC 8739 / DSM 1576 / C... gi\|194439994, gi... - gi\|83584647\|ref\|ZP_00923314.1\| COG0144: tRNA and rRNA cytosine-C5-methylases [Escherichia coli 101-1... RSMB_ECOHS - Ribosomal RNA small subunit methyltransferase B OS=Escherichia coli O9:H4 (strain HS) GN=rsmB PE=3 S... gi\|188488402, gi... - gi\|75511168\|ref\|ZP_00733880.1\| COG0144: tRNA and rRNA cytosine-C5-methylases [Escherichia coli 53638... gi\|89110722, gi\|... - gi\|89110722\|ref\|AP_004502.1\| 16S rRNA m5C967 methyltransferase, S-adenosyl-L-methionine-dependent [E... RSMB_ECOBW - Ribosomal RNA small subunit methyltransferase B OS=Escherichia coli (strain K12 / MC4100 / BW2952) G... EG12163 - 16S rRNA m(5)C967 methyltransferase, SAM-dependent / 16S rRNA m(5)C967 methyltransferase, SAM-depend... gi\|242378815, gi... - gi\|251786542\|ref\|YP_003000846.1\| hypothetical protein B21_03090 [Escherichia coli BL21], gi\|24237881...	2.0E-78	[2..451]	[6..425]
gi\|213425783 - gi\|213425783\|ref\|ZP_03358533.1\| 16S rRNA methyltransferase B [Salmonella enterica subsp. enterica se... gi\|29144361, gi\|... - gi\|29144361\|ref\|NP_807703.1\| 16S rRNA methyltransferase B [Salmonella enterica subsp. enterica serov... gi\|16762874 - gi\|16762874\|ref\|NP_458491.1\| 16S rRNA methyltransferase B [Salmonella enterica subsp. enterica serov... RSMB_SALTI - Ribosomal RNA small subunit methyltransferase B OS=Salmonella typhi GN=rsmB PE=3 SV=1 gi\|213859535 - gi\|213859535\|ref\|ZP_03385239.1\| 16S rRNA methyltransferase B [Salmonella enterica subsp. enterica se... RSMB_SALTI - Ribosomal RNA small subunit methyltransferase B OS=Salmonella typhi GN=rsmB PE=3 SV=1 gi\|213976152 - gi\|213976152\|ref\|ZP_03403411.1\| 16S rRNA methyltransferase B [Salmonella enterica subsp. enterica se...	1.0E-77	[2..451]	[6..425]
gi\|227008169, gi... - gi\|227080281\|ref\|YP_002808832.1\| sun protein [Vibrio cholerae M66-2], gi\|227008169\|gb\|ACP04381.1\| su... gi\|146317167, gi... - gi\|227116503\|ref\|YP_002818399.1\| sun protein [Vibrio cholerae O395], gi\|227011953\|gb\|ACP08163.1\| sun... gi\|121548521, gi... - gi\|121587275\|ref\|ZP_01677048.1\| sun protein [Vibrio cholerae 2740-80], gi\|121548521\|gb\|EAX58577.1\| s... gi\|153224327, gi... - gi\|153224327\|ref\|ZP_01954384.1\| sun protein [Vibrio cholerae MAK 757], gi\|124117693\|gb\|EAY36436.1\| s... gi\|121629806, gi... - gi\|121727862\|ref\|ZP_01680921.1\| sun protein [Vibrio cholerae V52], gi\|121629806\|gb\|EAX62221.1\| sun p... RSMB_VIBCH - Ribosomal RNA small subunit methyltransferase B OS=Vibrio cholerae serotype O1 (strain ATCC 39315 / ... gi\|126511874, gi... - gi\|153817606\|ref\|ZP_01970273.1\| sun protein [Vibrio cholerae NCTC 8457], gi\|126511874\|gb\|EAZ74468.1\|... RSMB_VIBCH - Ribosomal RNA small subunit methyltransferase B OS=Vibrio cholerae GN=rsmB PE=3 SV=1	3.0E-77	[1..453]	[9..431]
gi\|124493661, gi... - gi\|125624853\|ref\|YP_001033336.1\| ribosomal RNA small subunit methyltransferase B [Lactococcus lactis... gi\|4210751 - gi\|4210751\|emb\|CAA10711.1\| sunL protein [Lactococcus lactis]	5.0E-74	[2..489]	[4..421]
gi\|606223 - gi\|606223\|gb\|AAA58086.1\| we have one ORF, ECFMT has fmu and fmv [Escherichia coli] gi\|606223\|gb\|AAA... - we have one ORF, ECFMT has fmu and fmv [Escherichia coli]	8.0E-73	[2..411]	[6..382]

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Predicted Domain #1

Region A:
Residues: [1-96]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MNFYRDATWV LEDIEKEAAK ERISGSMQTL VLKSCKRYKL KSNPKHIYAV LDSCWKYKPY  60
   61 LEKVMKKAHI LEDIPKKKGK PLFSRLTLLL LCHDLL

[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	0.970	0.000	nucleus	a.80.1	DNA polymerase III clamp loader subunits, C-terminal domain

Predicted functions:

Term	Confidence	Notes
transcription regulator activity	1.25899985044692	bayes_pls_golite062009
binding	1.16354923842292	bayes_pls_golite062009
nucleic acid binding	1.07556382810506	bayes_pls_golite062009
DNA binding	1.00086161863786	bayes_pls_golite062009
transcription factor activity	0.459074630080185	bayes_pls_golite062009
ligase activity	0.168590365006694	bayes_pls_golite062009
catalytic activity	0.147263815852997	bayes_pls_golite062009
protein binding	0.127144933340806	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [97-152]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LSKQKRIQMG KHPIKDYVLK FKSPLHSEMV KLKLKLKVRE LSELVLSEDI SNDLPP

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below is our most confident de novo (Rosetta) prediction for this domain.
Click here to view all matches.

		MCM Score	GO Score	GO Term	SCOP Match	SCOP Description
View	Download	0.416	0.912	nucleus	a.4.5	"Winged helix" DNA-binding domain

Predicted functions:

Term	Confidence	Notes
methyltransferase activity	4.15445027778357	bayes_pls_golite062009
rRNA methyltransferase activity	4.09362182773099	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
DNA-methyltransferase activity	2.43145108778901	bayes_pls_golite062009
protein-arginine N-methyltransferase activity	2.41876112831625	bayes_pls_golite062009
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
rRNA (guanine) methyltransferase activity	2.00108769169811	bayes_pls_golite062009
rRNA (adenine) methyltransferase activity	1.83964463328968	bayes_pls_golite062009
tRNA methyltransferase activity	1.76571145896453	bayes_pls_golite062009
rRNA (adenine-N6,N6-)-dimethyltransferase activity	1.75675289134467	bayes_pls_golite062009
protein-arginine omega-N monomethyltransferase activity	1.66871163498737	bayes_pls_golite062009
catalytic activity	1.25333584501255	bayes_pls_golite062009
histone methyltransferase activity (H4-R3 specific)	1.1103522853299	bayes_pls_golite062009
transcription regulator activity	0.914549843668268	bayes_pls_golite062009
rRNA (uridine-2'-O-)-methyltransferase activity	0.90544396691236	bayes_pls_golite062009
protein-arginine omega-N asymmetric methyltransferase activity	0.89325812193225	bayes_pls_golite062009
DNA binding	0.86027591375666	bayes_pls_golite062009
rRNA (uridine) methyltransferase activity	0.742142092552002	bayes_pls_golite062009
site-specific DNA-methyltransferase (adenine-specific) activity	0.703178429468566	bayes_pls_golite062009
tRNA (cytosine)-methyltransferase activity	0.672282175551951	bayes_pls_golite062009
tRNA (cytosine-5-)-methyltransferase activity	0.672282175551951	bayes_pls_golite062009
nucleic acid binding	0.616949327277483	bayes_pls_golite062009
RNA binding	0.417524996559564	bayes_pls_golite062009
binding	0.383237930789959	bayes_pls_golite062009
O-methyltransferase activity	0.250946859465502	bayes_pls_golite062009
tRNA (adenine)-methyltransferase activity	0.0803947886180681	bayes_pls_golite062009
tRNA (adenine-N1-)-methyltransferase activity	0.0803947886180681	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [153-223]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 VRWIRINPLK CHPNGETEPV LAELRKKFTL KVDKWSELVP GSIYYDEFIP NLFGIHPSDK  60
   61 ITAHELYKHG K

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	13.30103
Match:	1jg1A_
Description:	Protein-L-isoaspartyl O-methyltransferase
Matching Structure (courtesy of the PDB):

Predicted Domain #4

Region A:
Residues: [224-490]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 IIIQDRASCF PAHILNPGPS DIVIDSCSAP GNKTTHTASY IYPEPPKDNN TRIYAFEKDP  60
   61 ERAKVLQKMI KIAGCSPNIS VNVGDFTKLA TPEKYKDVTC FIVDPSCSGS GIFGRKFFDS 120
  121 FNRRKIDDKD DDGGIVPDEQ EEFIAKEELQ TRLAKLSSFQ FQMVKHAMSF PAAKKIVYST 180
  181 CSIHAEENER VVIDLLLDKS VREWGWKVAP KREVIPSWPR RGKVEEFEEV FRDGVTYDPQ 240
  241 QLAEGCIRAL PKSDGGIGFF AVCFERD

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	40.221849
Match:	1j4fA_
Description:	No description for 1j4fA_ was found.

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: