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
Q8N7E2 UniProt NPD GO	ZN645_HUMAN	Zinc finger protein 645	0.95	-	nuc	0					425
Q8BMD2 UniProt NPD GO	DZIP1_MOUSE	Zinc finger protein DZIP1 (DAZ-interacting protein 1 homolog)	0.95	-	nuc	0	Nucleus. Cytoplasm. In primary and secondary spermatocytes, it is predominantly cytoplasmic. Colocal ...	cytoplasm [ISS] nucleus [ISS]			852
Q61602 UniProt NPD GO	GLI3_MOUSE	Zinc finger protein GLI3	0.95	-	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA] transcriptional repressor complex [IDA]			1596
Q04311 UniProt NPD GO	YD049_YEAST	Zinc finger protein YDR049W	0.95	-	nuc	0	Cytoplasm	cytoplasm [IDA] mitochondrion [IDA]			632
Q9W636 UniProt NPD GO	REQUB_XENLA	Zinc-finger protein ubi-d4 B (Requiem B) (xReq B) (Apoptosis response zinc finger protein B) (Fragme ...	0.95	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				366
Q02930 UniProt NPD GO	CREB5_HUMAN	cAMP response element-binding protein 5 (CRE-BPa)	0.95	+	nuc	0	Nucleus (Probable)	nucleus [IC]			508
Q9Y8G3 UniProt NPD GO	MEX67_SCHPO	mRNA export factor mex67	0.95	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Localizes at both the nuclear and cytoplasmic si ...	nuclear membrane [IDA] nucleolus [IDA] nucleus [IDA]			596
Q7S532 UniProt NPD GO	PALA_NEUCR	pH-response regulator protein palA/rim-20	0.95	+	nuc	0					886
Q8J1U9 UniProt NPD GO	PACC_GIBFU	pH-response transcription factor pacC/RIM101	0.95	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				618
Q873X0 UniProt NPD GO	PACC_GIBMO	pH-response transcription factor pacC/RIM101	0.95	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				613
O13433 UniProt NPD GO	PLC1_CANAL	1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase 1 (EC 3.1.4.11) (Phosphoinositide phosphol ...	0.94	-	nuc	0					1099
Q9NQ66 UniProt NPD GO	PLCB1_HUMAN	1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta 1 (EC 3.1.4.11) (Phosphoinositide pho ...	0.94	+	nuc	0		cytoplasm [IDA] nucleus [NAS]	607120		1216
P10687 UniProt NPD GO	PLCB1_RAT	1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta 1 (EC 3.1.4.11) (Phosphoinositide pho ...	0.94	+	nuc	0	Cytoplasm. Membrane. And particulate fractions				1216
Q00722 UniProt NPD GO	PLCB2_HUMAN	1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta 2 (EC 3.1.4.11) (Phosphoinositide pho ...	0.94	-	nuc	0			604114		1181
Q03465 UniProt NPD GO	RPN4_YEAST	26S proteasome regulatory subunit RPN4 (Nuclear protein SON1) (Ubiquitin fusion degradation protein ...	0.94	+	nuc	0	Nucleus	proteasome core complex (sensu Eukaryota) [IDA] proteasome regulatory particle (sensu Eukar... [IPI]			531
Q92665 UniProt NPD GO	RT31_HUMAN	28S ribosomal protein S31, mitochondrial precursor (S31mt) (MRP-S31) (Imogen 38)	0.94	-	nuc	0	Mitochondrion	mitochondrion [TAS]			395
P40433 UniProt NPD GO	6P21_YEAST	6-phosphofructo-2-kinase 1 (EC 2.7.1.105) (Phosphofructokinase 2 I) (6PF-2-K 1)	0.94	-	nuc	0					827
Q08951 UniProt NPD GO	AP3D_YEAST	AP-3 complex subunit delta (Adapter-related protein complex 3 subunit delta) (Delta-adaptin 3) (AP-3 ...	0.94	+	nuc	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...				932
P12956 UniProt NPD GO	KU70_HUMAN	ATP-dependent DNA helicase 2 subunit 1 (EC 3.6.1.-) (ATP-dependent DNA helicase II 70 kDa subunit) ( ...	0.94	+	cyt	0	Nucleus	membrane fraction [TAS] nucleus [TAS] transcription factor complex [IDA]	152690	1JJR	608
Q9Y7C4 UniProt NPD GO	ROK1_CANAL	ATP-dependent RNA helicase CHR1 (EC 3.6.1.-)	0.94	+	nuc	0	Nucleus; nucleolus (By similarity)				578
Q6CJV1 UniProt NPD GO	DRS1_KLULA	ATP-dependent RNA helicase DRS1 (EC 3.6.1.-)	0.94	+	nuc	0	Nucleus; nucleolus (By similarity)				748
Q6CSW1 UniProt NPD GO	ROK1_KLULA	ATP-dependent RNA helicase ROK1 (EC 3.6.1.-)	0.94	+	nuc	0	Nucleus; nucleolus (By similarity)				579
P62290 UniProt NPD GO	ASPM_HYLLA	Abnormal spindle-like microcephaly-associated protein homolog	0.94	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). The nuclear-cytoplasmic distribution could be re ...				3477
P62294 UniProt NPD GO	ASPM_PONPY	Abnormal spindle-like microcephaly-associated protein homolog	0.94	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). The nuclear-cytoplasmic distribution could be re ...				3471
P62286 UniProt NPD GO	ASPM_CANFA	Abnormal spindle-like microcephaly-associated protein homolog (Fragment)	0.94	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). The nuclear-cytoplasmic distribution could be re ...				3452
Q8K298 UniProt NPD GO	ANLN_MOUSE	Actin-binding protein anillin	0.94	-	nuc	0	Nucleus (By similarity). Mainly found in the nucleus during interphase. Colocalizes with cortical F- ...				1121
P40494 UniProt NPD GO	PRK1_YEAST	Actin-regulating kinase PRK1 (EC 2.7.11.1) (p53-regulating kinase 1)	0.94	-	nuc	0	Actin patch. Cortical actin patches	actin cortical patch [IDA]			810
Q9H2P0 UniProt NPD GO	ADNP_HUMAN	Activity-dependent neuroprotector (Activity-dependent neuroprotective protein)	0.94	+	nuc	0	Nucleus (Potential)				1102
Q9QZ39 UniProt NPD GO	SIA7A_MOUSE	Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 1 (EC 2.4.99.3) (GalNAc alpha-2,6-sialyltr ...	0.94	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				526
Q95LD9 UniProt NPD GO	AHR_DELLE	Aryl hydrocarbon receptor precursor (Ah receptor) (AhR)	0.94	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). First cytoplasmic, upon binding with ligand and ...				845
P30561 UniProt NPD GO	AHR_MOUSE	Aryl hydrocarbon receptor precursor (Ah receptor) (AhR)	0.94	-	nuc	0	Cytoplasm. Nucleus. First cytoplasmic, upon binding with ligand and interaction with a HSP90, it tra ...	cytoplasm [IDA] nucleus [IDA] transcription factor complex [TAS]			848
Q8R4S6 UniProt NPD GO	AHR_MUSMC	Aryl hydrocarbon receptor precursor (Ah receptor) (AhR)	0.94	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). First cytoplasmic, upon binding with ligand and ...	cytoplasm [IDA] nucleus [ISS] transcription factor complex [TAS]			848
Q8R4S5 UniProt NPD GO	AHR_MUSMM	Aryl hydrocarbon receptor precursor (Ah receptor) (AhR)	0.94	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). First cytoplasmic, upon binding with ligand and ...	cytoplasm [IDA] nucleus [ISS] transcription factor complex [TAS]			883
Q8R4S4 UniProt NPD GO	AHR_MUSSI	Aryl hydrocarbon receptor precursor (Ah receptor) (AhR)	0.94	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). First cytoplasmic, upon binding with ligand and ...	nucleus [ISS]			854
P41738 UniProt NPD GO	AHR_RAT	Aryl hydrocarbon receptor precursor (Ah receptor) (AhR)	0.94	-	nuc	0	Cytoplasm. Nucleus. First cytoplasmic, upon binding with ligand and interaction with a HSP90, it tra ...	cytosol [TAS] nucleus [IDA]			853
Q6W2J9 UniProt NPD GO	BCOR_HUMAN	BCoR protein (BCL-6 corepressor)	0.94	+	nuc	0	Nucleus	nucleus [IDA]	300485		1755
Q99728 UniProt NPD GO	BARD1_HUMAN	BRCA1-associated RING domain protein 1 (BARD-1)	0.94	-	nuc	0	Nucleus. During S phase of the cell cycle, colocalizes with BRCA1 into discrete subnuclear foci. Can ...	BRCA1-BARD1 complex [IDA] cytoplasm [IDA] nucleus [IDA] ubiquitin ligase complex [NAS]	601593	1JM7	777
P97929 UniProt NPD GO	BRCA2_MOUSE	Breast cancer type 2 susceptibility protein homolog (Fanconi anemia group D1 protein homolog)	0.94	-	nuc	0		cytoplasm [IDA] nucleus [IDA]		1MIU	3329
Q15059 UniProt NPD GO	BRD3_HUMAN	Bromodomain-containing protein 3 (RING3-like protein)	0.94	+	nuc	0	Nucleus (Potential)	nucleus [NAS]	601541		726
Q9URT4 UniProt NPD GO	AMS2_SCHPO	CENP-A multicopy suppressor protein 2	0.94	-	nuc	0	Nucleus. Centromeric	chromosome, pericentric region [IDA]			697
P27398 UniProt NPD GO	CAND_DROME	Calpain D (EC 3.4.22.-) (Calcium-activated neutral proteinase D) (CANP D) (Small optic lobes protein ...	0.94	-	nuc	0		intracellular [ISS]			1594
Q15642 UniProt NPD GO	CIP4_HUMAN	Cdc42-interacting protein 4 (Thyroid receptor-interacting protein 10) (TRIP-10)	0.94	+	nuc	0		cytoplasm [NAS]	604504	2CT4	545
P11433 UniProt NPD GO	CDC24_YEAST	Cell division control protein 24 (Calcium regulatory protein)	0.94	-	nuc	0		bud neck [IDA] incipient bud site [IDA] mating projection tip [IDA] nucleus [IDA]		1Q1O	854
Q9NGC3 UniProt NPD GO	CEG1A_DROME	Centaurin-gamma 1A	0.94	-	nuc	0		nucleus [NAS]			995
Q8VHH5 UniProt NPD GO	CENG3_MOUSE	Centaurin-gamma 3 (ARF-GAP with GTP-binding protein-like, ankyrin repeat and pleckstrin homology dom ...	0.94	-	nuc	0	Cytoplasm. Upon oxidative stress, translocates to PML nuclear bodies (By similarity)				910
Q06675 UniProt NPD GO	MCM21_YEAST	Central kinetochore subunit MCM21 (Minichromosome maintenance protein 21) (Chromosome transmission f ...	0.94	-	cyt	0	Nucleus. Associated with kinetochores	COMA complex [IDA]			368
Q7L2Z9 UniProt NPD GO	CENPQ_HUMAN	Centromere protein Q (CENP-Q)	0.94	-	nuc	0					268
Q66GS9 UniProt NPD GO	CP135_HUMAN	Centrosomal protein of 135 kDa (Cep135 protein) (Centrosomal protein 4)	0.94	+	nuc	0	Centrosome				1140
Q5A119 UniProt NPD GO	VID21_CANAL	Chromatin modification-related protein VID21	0.94	-	nuc	0	Nucleus (Probable)				686
P48996 UniProt NPD GO	DPY27_CAEEL	Chromosome condensation protein dpy-27 (Protein dumpy-27)	0.94	+	nuc	0	Nucleus. Associates with chromatin after 30-cell stage. It specifically localizes to the X chromosom ...	nuclear chromosome [IDA] nucleus [IDA]			1469

You are viewing entries 2201 to 2250 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.