YRC Public Data Repository - Protein Structure Prediction

Protein:	NRD1
Organism:	Saccharomyces cerevisiae
Length:	575 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 NRD1.

Description	E-value	Query Range	Subject Range
NRD1 - RNA-binding protein that interacts with the C-terminal domain of the RNA polymerase II large subunit... NRD1_YEAST - Protein NRD1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=NRD1 PE=1 SV=1 gi\|190409225 - gi\|190409225\|gb\|EDV12490.1\| protein NRD1 [Saccharomyces cerevisiae RM11-1a]	0.0	[1..566]	[1..566]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	7.0E-70	[179..573]	[76..480]
gi\|13560783 - gi\|13560783\|gb\|AAK30205.1\|AF349964_1 poly(A)-binding protein [Daucus carota]	2.0E-68	[184..565]	[87..482]
PABPC4 - poly(A) binding protein, cytoplasmic 4 (inducible form)	6.0E-68	[179..574]	[55..459]
PAB5_ARATH, PABP... - Polyadenylate-binding protein 5 OS=Arabidopsis thaliana GN=PAB5 PE=1 SV=2, (Q05196) Polyadenylate-bi...	7.0E-68	[180..574]	[81..499]
gi\|126540996, gi... - gi\|22507391\|ref\|NP_683717.1\| poly(A) binding protein, cytoplasmic 4 isoform 2 [Mus musculus], gi\|163...	2.0E-67	[179..574]	[55..459]

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Predicted Domain #1

Region A:
Residues: [1-200]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MQQDDDFQNF VATLESFKDL KSGISGSRIK KLTTYALDHI DIESKIISLI IDYSRLCPDS  60
   61 HKLGSLYIID SIGRAYLDET RSNSNSSSNK PGTCAHAINT LGEVIQELLS DAIAKSNQDH 120
  121 KEKIRMLLDI WDRSGLFQKS YLNAIRSKCF AMDISNNTAN TASQQLSLDP KQRSKQILSN 180
  181 LKKSPPLNLN ISLPTDLTST

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below are all of our structure predictions for this domain.
Click here to view only most confident match.

Found no structure predictions for this domain.

Predicted Domain #2

Region A:
Residues: [201-301]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DPAKQQAALF QVIAALQKHF KTLPSHTSVG TVAPPQAHTI TEYGSRRERE RERERYNSRR  60
   61 NRSRSPPAPF SQPSTGRKDR YPSVAQDQYS IGAPNTTFGT N

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	52.69897
Match:	2up1A_
Description:	Nuclear ribonucleoprotein A1 (RNP A1, UP1)
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
nucleic acid binding	4.50398990564944	bayes_pls_golite062009
binding	4.16717332578111	bayes_pls_golite062009
RNA binding	2.92438188845619	bayes_pls_golite062009
transcription regulator activity	2.18211199677674	bayes_pls_golite062009
mRNA binding	1.94495589345842	bayes_pls_golite062009
DNA binding	1.73925834998328	bayes_pls_golite062009
hydrolase activity, acting on ester bonds	1.59667241219553	bayes_pls_golite062009
protein binding	1.32954276279597	bayes_pls_golite062009
transcription factor activity	0.873765500321315	bayes_pls_golite062009
	0.84116054461637	bayes_pls_golite062009
RNA polymerase II transcription factor activity	0.632534695085793	bayes_pls_golite062009
hydrolase activity	0.520121701073354	bayes_pls_golite062009
sequence-specific DNA binding	0.294937517750882	bayes_pls_golite062009
general RNA polymerase II transcription factor activity	0.100880394187931	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [302-413]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NHHLYPDELN VSNNPHYRPK PVSYDSTLPP DHIKVYSRTL FIGGVPLNMK EWDLANVLKP  60
   61 FAEVQSVILN NSRKHAFVKV YSRHEAENVL QNFNKDGALP LRTRWGVGFG PR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	52.69897
Match:	2up1A_
Description:	Nuclear ribonucleoprotein A1 (RNP A1, UP1)
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
nucleic acid binding	4.50398990564944	bayes_pls_golite062009
binding	4.16717332578111	bayes_pls_golite062009
RNA binding	2.92438188845619	bayes_pls_golite062009
transcription regulator activity	2.18211199677674	bayes_pls_golite062009
mRNA binding	1.94495589345842	bayes_pls_golite062009
DNA binding	1.73925834998328	bayes_pls_golite062009
hydrolase activity, acting on ester bonds	1.59667241219553	bayes_pls_golite062009
protein binding	1.32954276279597	bayes_pls_golite062009
transcription factor activity	0.873765500321315	bayes_pls_golite062009
	0.84116054461637	bayes_pls_golite062009
RNA polymerase II transcription factor activity	0.632534695085793	bayes_pls_golite062009
hydrolase activity	0.520121701073354	bayes_pls_golite062009
sequence-specific DNA binding	0.294937517750882	bayes_pls_golite062009
general RNA polymerase II transcription factor activity	0.100880394187931	bayes_pls_golite062009

Predicted Domain #4

Region A:
Residues: [414-508]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DCCDYQHGYS IIPMHRLTDA DKKWSVSAQW GGTSGQPLVT GIVFEEPDII VGEGVSSKAI  60
   61 SQKMPTDSGR NGPRSGKPNK SGSISSISPV PYGNA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	36.69897
Match:	1fxlA_
Description:	Hu antigen D (Hud)
Matching Structure (courtesy of the PDB):

Predicted Domain #5

Region A:
Residues: [509-575]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PLASPPPQQY VQPMMQQPYG YAPNQPLPSQ GPAAAAPPVP QQQFDPTAQL NSLMNMLNQQ  60
   61 QQQQQQS

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below are all of our de novo (Rosetta) predictions for this domain.
Click here to view only most confident match.

		MCM Score	SCOP Match	SCOP Description
View	Download	0.441	a.4.1	Homeodomain-like
View	Download	0.434	a.60.4	DNA repair protein Rad51, N-terminal domain
View	Download	0.361	a.4.13	Sigma3 and sigma4 domains of RNA polymerase sigma factors
View	Download	0.410	f.14.1	Voltage-gated potassium channels
View	Download	0.364	d.234.1	Proguanylin
View	Download	0.347	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.335	a.4.1	Homeodomain-like
View	Download	0.323	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.323	a.159.1	Protein serine/threonine phosphatase 2C, C-terminal domain
View	Download	0.321	d.52.4	YhbC-like, N-terminal domain
View	Download	0.309	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.298	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.290	a.35.1	lambda repressor-like DNA-binding domains
View	Download	0.290	d.58.13	Anticodon-binding domain of PheRS
View	Download	0.255	a.36.1	Signal peptide-binding domain
View	Download	0.253	g.57.1	Serine proteinase inhibitor lekti
View	Download	0.251	a.4.1	Homeodomain-like
View	Download	0.232	a.60.1	SAM/Pointed domain
View	Download	0.226	a.108.1	Ribosomal protein L7/12, oligomerisation (N-terminal) domain
View	Download	0.218	a.112.1	Description not found.
View	Download	0.215	a.4.1	Homeodomain-like
View	Download	0.211	a.5.1	DNA helicase RuvA subunit, C-terminal domain
View	Download	0.205	a.5.2	UBA-like

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: