NucPred on Proteomes

Authors: Andrea Krings, Amine Heddad, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred - predictions for eukaryotic proteomes

Species:

Note: All filters/tests are combined with AND unless otherwise stated

Show only the proteins with links to database(s):
OMIM - human disease genes
PDB - protein 3D structure
( AND OR combination )

Annotation filters (can be slow! - Perl regexps allowed: e.g. nucleus|nucleolus)

UniProt ID (e.g. "PK3B_")
UniProt description (e.g. "kinase")
UniProt subcellular location
AND
UniProt GO component
AND
AND the
AND the

Only show proteins where the PredictNLS prediction is:

positive
negative

Only show proteins where the PSORT II predicted location

is is not

Click here: to filter by NucPred score

exclude all transmembrane proteins predicted by TMHMM
don't exclude lone N-terminal predicted transmembrane helices
(these could be signal peptides)

export all ACs and IDs as text file

Show proteins (ordered by NucPred score ) from to (currently 98716 matches)

You can bookmark/save your search criteria with this link. You can also start again with default settings.

UniProt accession	UniProt ID	UniProt description	NucPred score	Predict- NLS	PSORT II	TMHMM #helices	UniProt annotation for subcellular location	Uniprot GO cellular component	OMIM	PDB	sequence length
Q6CSP9 UniProt NPD GO	NOG2_KLULA	Nucleolar GTP-binding protein 2	0.87	-	nuc	0	Nucleus; nucleolus (By similarity)				513
Q4WCH5 UniProt NPD GO	NOP12_ASPFU	Nucleolar protein 12	0.87	+	nuc	0	Nucleus; nucleolus (By similarity)				538
Q9Z1N2 UniProt NPD GO	ORC1_MOUSE	Origin recognition complex subunit 1	0.87	-	mit	0	Nucleus (By similarity)	nucleus [TAS]			840
P43354 UniProt NPD GO	NR4A2_HUMAN	Orphan nuclear receptor NR4A2 (Orphan nuclear receptor NURR1) (Immediate-early response protein NOT) ...	0.87	-	nuc	0	Nucleus (Probable)	nucleus [TAS]	601828	1OVL	598
Q07917 UniProt NPD GO	NR4A2_RAT	Orphan nuclear receptor NR4A2 (Orphan nuclear receptor NURR1) (NUR-related factor 1) (Regenerating l ...	0.87	-	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA]			598
O54915 UniProt NPD GO	PXR_MOUSE	Orphan nuclear receptor PXR (Pregnane X receptor)	0.87	+	cyt	0	Nucleus (By similarity)	nucleus [IC]			431
Q8NDF8 UniProt NPD GO	PAPD5_HUMAN	PAP-associated domain-containing protein 5 (EC 2.7.7.-) (Topoisomerase-related function protein 4-2) ...	0.87	+	nuc	0	Nucleus (Probable)		605540		572
Q9QZR8 UniProt NPD GO	PDZD2_RAT	PDZ domain-containing protein 2 (PDZ domain-containing protein 3) (Plakophilin-related armadillo rep ...	0.87	+	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Endoplasmic reticulum. Cell membrane; cell-cell ...	cytoplasm [ISS] endoplasmic reticulum [IDA] extracellular region [IDA] intercellular junction [IDA] nucleus [IDA]			2766
Q6NUJ5 UniProt NPD GO	PWWP2_HUMAN	PWWP domain-containing protein 2	0.87	-	nuc	0					513
Q4P555 UniProt NPD GO	PPIL2_USTMA	Peptidyl-prolyl cis-trans isomerase-like 2 (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin-60) (Cyclop ...	0.87	+	nuc	0	Nucleus (By similarity)				582
O70361 UniProt NPD GO	PER3_MOUSE	Period circadian protein 3 (mPER3)	0.87	-	nuc	0	Nucleus (Potential)				1113
Q9R269 UniProt NPD GO	PEPL_MOUSE	Periplakin	0.87	-	nuc	0	Cell membrane. Nucleus. Mitochondrion. Cell membrane; cell-cell junction; desmosome. Associated with ...	extrinsic to plasma membrane [TAS]			1755
P78926 UniProt NPD GO	MAP1_SCHPO	Pheromone receptor transcription activator (Protein map1)	0.87	-	nuc	0	Nucleus				398
O70167 UniProt NPD GO	P3C2G_MOUSE	Phosphatidylinositol-4-phosphate 3-kinase C2 domain-containing gamma polypeptide (EC 2.7.1.154) (Pho ...	0.87	-	nuc	0	Membrane; peripheral membrane protein				1506
P51263 UniProt NPD GO	APCE_PORPU	Phycobilisome linker polypeptide (Anchor polypeptide) (PBS-anchor protein)	0.87	+	nuc	0	Plastid; chloroplast				886
Q68FH0 UniProt NPD GO	PKP4_MOUSE	Plakophilin-4 (Armadillo-related protein)	0.87	+	nuc	0	Cell membrane; cell-cell junction; desmosome (By similarity). Colocalized with desmoplakin at desmos ...				1190
Q7TQG1 UniProt NPD GO	PKHA6_MOUSE	Pleckstrin homology domain-containing family A member 6 (Phosphoinositol 3-phosphate-binding protein ...	0.87	-	nuc	0					1173
Q9JI55 UniProt NPD GO	PLEC1_CRIGR	Plectin-1 (PLTN) (PCN) (300 kDa intermediate filament-associated protein) (IFAP300) (Fragment)	0.87	+	nuc	0					4473
P35875 UniProt NPD GO	PARP_DROME	Poly [ADP-ribose] polymerase (EC 2.4.2.30) (PARP) (ADPRT) (NAD(+) ADP-ribosyltransferase) (Poly[ADP- ...	0.87	+	nuc	0	Nucleus. Nucleus; nucleolus. Highly enriched in nucleoli, heterochromatic chromosomal regions, and d ...	nuclear euchromatin [IDA] nucleolus [TAS] polytene chromosome puff [IDA]			994
Q9QYM2 UniProt NPD GO	PARG_RAT	Poly(ADP-ribose) glycohydrolase (EC 3.2.1.143)	0.87	-	nuc	0	Nucleus (By similarity)				972
P42124 UniProt NPD GO	EZ_DROME	Polycomb protein E(z) (Protein enhancer of zeste)	0.87	+	nuc	0	Nucleus	ESC/E(Z) complex [IDA] nuclear chromatin [NAS] nucleus [IDA]			760
Q5JUK3 UniProt NPD GO	KCNT1_HUMAN	Potassium channel subfamily T member 1 (KCa4.1)	0.87	-	end	5	Membrane; multi-pass membrane protein (Potential)		608167		1230
O18868 UniProt NPD GO	KCNB1_PIG	Potassium voltage-gated channel subfamily B member 1 (Voltage-gated potassium channel subunit Kv2.1) ...	0.87	-	nuc	5	Membrane; multi-pass membrane protein				858
P15387 UniProt NPD GO	KCNB1_RAT	Potassium voltage-gated channel subfamily B member 1 (Voltage-gated potassium channel subunit Kv2.1) ...	0.87	-	nuc	5	Membrane; multi-pass membrane protein				857
Q03717 UniProt NPD GO	KCNB1_MOUSE	Potassium voltage-gated channel subfamily B member 1 (Voltage-gated potassium channel subunit Kv2.1) ...	0.87	-	nuc	5	Membrane; multi-pass membrane protein				857
Q5KME7 UniProt NPD GO	PRP5_CRYNE	Pre-mRNA-processing ATP-dependent RNA helicase PRP5 (EC 3.6.1.-)	0.87	+	nuc	0	Nucleus (By similarity)				1072
Q7SH33 UniProt NPD GO	PRP5_NEUCR	Pre-mRNA-processing ATP-dependent RNA helicase prp-5 (EC 3.6.1.-)	0.87	+	nuc	0	Nucleus (By similarity)				1194
Q2U2J6 UniProt NPD GO	PRP5_ASPOR	Pre-mRNA-processing ATP-dependent RNA helicase prp5 (EC 3.6.1.-)	0.87	+	nuc	0	Nucleus (By similarity)				1186
Q6FW76 UniProt NPD GO	CLF1_CANGA	Pre-mRNA-splicing factor CLF1	0.87	-	cyt	0	Nucleus (By similarity)				695
Q6CB23 UniProt NPD GO	CWC24_YARLI	Pre-mRNA-splicing factor CWC24	0.87	+	nuc	0	Nucleus (By similarity)				256
P53769 UniProt NPD GO	CWC24_YEAST	Pre-mRNA-splicing factor CWC24 (Complexed with CEF1 protein 24)	0.87	-	nuc	0	Nucleus	spliceosome complex [IPI]			259
Q52F10 UniProt NPD GO	CWC26_MAGGR	Pre-mRNA-splicing factor CWC26	0.87	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				352
Q6CAX1 UniProt NPD GO	CWC26_YARLI	Pre-mRNA-splicing factor CWC26	0.87	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				221
P40968 UniProt NPD GO	PRP17_YEAST	Pre-mRNA-splicing factor PRP17 (Cell division control protein 40)	0.87	+	nuc	0	Nucleus	nuclear envelope [IDA] nuclear pore [IDA] spliceosome complex [IGI]			455
Q5KCF5 UniProt NPD GO	PRP45_CRYNE	Pre-mRNA-splicing factor PRP45 (Pre-mRNA-processing protein 45)	0.87	-	nuc	0	Nucleus (By similarity)				594
Q6CK06 UniProt NPD GO	SLU7_KLULA	Pre-mRNA-splicing factor SLU7	0.87	-	nuc	0	Nucleus (By similarity)				341
Q4P7S1 UniProt NPD GO	SYF1_USTMA	Pre-mRNA-splicing factor SYF1	0.87	-	cyt	0	Nucleus (By similarity)				1081
Q6CFW4 UniProt NPD GO	SYF2_YARLI	Pre-mRNA-splicing factor SYF2	0.87	-	nuc	0	Nucleus (By similarity)				195
Q7SDY3 UniProt NPD GO	CWC24_NEUCR	Pre-mRNA-splicing factor cwc-24	0.87	-	nuc	0	Nucleus (By similarity)				405
Q05199 UniProt NPD GO	NRG1_CHICK	Pro-neuregulin-1, membrane-bound isoform precursor (Pro-NRG1) [Contains: Neuregulin-1 (Acetylcholine ...	0.87	+	nuc	1	Pro-neuregulin-1, membrane-bound isoform: Cell membrane; single-pass type I membrane protein (By sim ...				602
Q6AXC6 UniProt NPD GO	DDX11_MOUSE	Probable ATP-dependent RNA helicase DDX11 (EC 3.6.1.-) (DEAD/H box protein 11)	0.87	-	nuc	0	Nucleus; nucleolus (By similarity)				880
Q96FC9 UniProt NPD GO	DDX11_HUMAN	Probable ATP-dependent RNA helicase DDX11 (EC 3.6.1.-) (DEAD/H box protein 11) (CHL1 homolog) (Kerat ...	0.87	+	mit	0	Nucleus; nucleolus		601150		970
Q96GQ7 UniProt NPD GO	DDX27_HUMAN	Probable ATP-dependent RNA helicase DDX27 (EC 3.6.1.-) (DEAD box protein 27)	0.87	+	nuc	0	Nucleus (Potential)				796
Q9W3C0 UniProt NPD GO	UTP11_DROME	Probable U3 small nucleolar RNA-associated protein 11 (U3 snoRNA-associated protein 11)	0.87	-	nuc	0	Nucleus; nucleolus (By similarity)	small nucleolar ribonucleoprotein complex [ISS]			237
Q9ZQ70 UniProt NPD GO	WRKY3_ARATH	Probable WRKY transcription factor 3 (WRKY DNA-binding protein 3)	0.87	-	nuc	0	Nucleus (Probable)				513
Q03603 UniProt NPD GO	DGK3_CAEEL	Probable diacylglycerol kinase 3 (EC 2.7.1.107) (Diglyceride kinase 3) (DGK-3) (DAG kinase 3)	0.87	-	nuc	0					812
O02328 UniProt NPD GO	IF38_CAEEL	Probable eukaryotic translation initiation factor 3 subunit 8 (eIF3 p110) (eIF3c)	0.87	+	nuc	0					898
Q6BPZ9 UniProt NPD GO	NDC80_DEBHA	Probable kinetochore protein NDC80	0.87	-	nuc	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				650
Q10021 UniProt NPD GO	RSP5_CAEEL	Probable splicing factor, arginine/serine-rich 5 (RNA-binding protein srp-3) (CeSC35-2)	0.87	+	nuc	0	Nucleus	nucleus [IDA]			208
P24641 UniProt NPD GO	PRT1_BUFJA	Protamine-1 (P1)	0.87	+	nuc	0	Nucleus				39

You are viewing entries 5701 to 5750 of 98716. You can see more proteins by changing the limits in the form at the top of this page, or click here for the next page of proteins .

If you find NucPred useful, please cite this paper:

NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022

The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold	Specificity	Sensitivity
see above	fraction of proteins predicted to be nuclear that actually are nuclear	fraction of true nuclear proteins that are predicted (coverage)
0.10	0.45	0.88
0.20	0.52	0.83
0.30	0.57	0.77
0.40	0.63	0.69
0.50	0.70	0.62
0.60	0.71	0.53
0.70	0.81	0.44
0.80	0.84	0.32
0.90	0.88	0.21
1.00	1.00	0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

Go back to the NucPred Home Page.