YRC Public Data Repository - Protein Structure Prediction

Protein:	NCL1
Organism:	Saccharomyces cerevisiae
Length:	684 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 NCL1.

Description	E-value	Query Range	Subject Range
NCL1_YEAST - Multisite-specific tRNA:(cytosine-C(5))-methyltransferase OS=Saccharomyces cerevisiae (strain ATCC 2... NCL1 - S-adenosyl-L-methionine-dependent tRNA: m5C-methyltransferase, methylates cytosine to m5C at several...	0.0	[1..684]	[1..684]
SPAC23C4.17 - tRNA (cytosine-5-)-methyltransferase YF6H_SCHPO - Putative tRNA (cytosine-5-)-methyltransferase C23C4.17 OS=Schizosaccharomyces pombe (strain 972 / AT...	0.0	[12..636]	[3..674]
CG6133-PA - This gene is referred to in FlyBase by the symbol Dmel\CG6133 (CG6133, FBgn0026079). It is a protein...	0.0	[3..646]	[5..674]
gi\|15489014 - gi\|15489014\|gb\|AAH13625.1\| Nsun2 protein [Mus musculus]	0.0	[225..682]	[2..517]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	4.0E-91	[3..490]	[187..620]
gi\|19170955, gi\|... - gi\|19173366\|ref\|NP_597169.1\| PUTATIVE METHYLTRANSFERASE [Encephalitozoon cuniculi GB-M1], gi\|1917095... gi\|19173366 - gi\|19173366\|ref\|NP_597169.1\| PUTATIVE METHYLTRANSFERASE [Encephalitozoon cuniculi GB-M1]	7.0E-85	[35..575]	[4..465]
gi\|189422 - gi\|189422\|gb\|AAA36398.1\| proliferating cell nuclear protein P120	1.0E-81	[3..442]	[255..635]

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Predicted Domain #1

Region A:
Residues: [1-74]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MARRKNFKKG NKKTFGARDD SRAQKNWSEL VKENEKWEKY YKTLALFPED QWEEFKKTCQ  60
   61 APLPLTFRIT GSRK

[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.

Found no confident structure predictions for this domain.

Predicted functions:

Term	Confidence	Notes
methyltransferase activity	4.15445027778357	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
transferase activity	2.926540904444	bayes_pls_golite062009
tRNA methyltransferase activity	2.5931020126592	bayes_pls_golite062009
DNA-methyltransferase activity	2.43145108778901	bayes_pls_golite062009
arginine N-methyltransferase activity	2.41876112831625	bayes_pls_golite062009
protein-arginine N-methyltransferase activity	2.41876112831625	bayes_pls_golite062009
rRNA methyltransferase activity	2.29640050660273	bayes_pls_golite062009
histone-arginine N-methyltransferase activity	2.04296107639729	bayes_pls_golite062009
tRNA (cytosine-5-)-methyltransferase activity	1.88889414729709	bayes_pls_golite062009
tRNA (cytosine)-methyltransferase activity	1.88889414729709	bayes_pls_golite062009
protein-arginine omega-N monomethyltransferase activity	1.66871163498737	bayes_pls_golite062009
tRNA (adenine-N1-)-methyltransferase activity	1.29759910099835	bayes_pls_golite062009
tRNA (adenine)-methyltransferase activity	1.29759910099835	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
protein-arginine omega-N asymmetric methyltransferase activity	0.89325812193225	bayes_pls_golite062009
DNA binding	0.86027591375666	bayes_pls_golite062009
rRNA (guanine) methyltransferase activity	0.720972789045101	bayes_pls_golite062009
site-specific DNA-methyltransferase (adenine-specific) activity	0.703178429468566	bayes_pls_golite062009
nucleic acid binding	0.616949327277483	bayes_pls_golite062009
rRNA (adenine) methyltransferase activity	0.533090627724779	bayes_pls_golite062009
rRNA (adenine-N6,N6-)-dimethyltransferase activity	0.455449410561251	bayes_pls_golite062009
RNA binding	0.417524996559564	bayes_pls_golite062009
binding	0.383237930789959	bayes_pls_golite062009
protein-arginine omega-N symmetric methyltransferase activity	0.364369105571521	bayes_pls_golite062009
tRNA (guanine) methyltransferase activity	0.203168546434167	bayes_pls_golite062009
rRNA (uridine) methyltransferase activity	0.0858581024725429	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [75-146]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 HAGEVLNLFK ERHLPNLTNV EFEGEKIKAP VELPWYPDHL AWQLDVPKTV IRKNEQFAKT  60
   61 QRFLVVENAV GN

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	5.69897
Match:	1fbnA_
Description:	Fibrillarin homologue
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [147-364]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ISRQEAVSMI PPIVLEVKPH HTVLDMCAAP GSKTAQLIEA LHKDTDEPSG FVVANDADAR  60
   61 RSHMLVHQLK RLNSANLMVV NHDAQFFPRI RLHGNSNNKN DVLKFDRILC DVPCSGDGTM 120
  121 RKNVNVWKDW NTQAGLGLHA VQLNILNRGL HLLKNNGRLV YSTCSLNPIE NEAVVAEALR 180
  181 KWGDKIRLVN CDDKLPGLIR SKGVSKWPVY DRNLTEKT

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	164.10721
Match:	1j4fA_
Description:	No description for 1j4fA_ was found.

Predicted Domain #4

Region A:
Residues: [365-494]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KGDEGTLDSF FSPSEEEASK FNLQNCMRVY PHQQNTGGFF ITVFEKVEDS TEAATEKLSS  60
   61 ETPALESEGP QTKKIKVEEV QKKERLPRDA NEEPFVFVDP QHEALKVCWD FYGIDNIFDR 120
  121 NTCLVRNATG

[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 #5

Region A:
Residues: [495-684]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EPTRVVYTVC PALKDVIQAN DDRLKIIYSG VKLFVSQRSD IECSWRIQSE SLPIMKHHMK  60
   61 SNRIVEANLE MLKHLLIESF PNFDDIRSKN IDNDFVEKMT KLSSGCAFID VSRNDPAKEN 120
  121 LFLPVWKGNK CINLMVCKED THELLYRIFG IDANAKATPS AEEKEKEKET TESPAETTTG 180
  181 TSTEAPSAAN

[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

Predicted functions: