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
Q9UKA4 UniProt NPD GO	AKA11_HUMAN	A-kinase anchor protein 11 (Protein kinase A-anchoring protein 11) (PRKA11) (A kinase anchor protein ...	0.72	-	nuc	0	Cytoplasm. Centrosome. Cytoplasmic in premeiotic pachytene spermatocytes and in the centrosome of de ...		604696		1901
O88839 UniProt NPD GO	ADA15_MOUSE	ADAM 15 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase domain 15) (Metalloproteinase-l ...	0.72	-	exc	1	Intracytoplasmic membrane; single-pass type I membrane protein. The majority of the protein is local ...				864
O77559 UniProt NPD GO	ADML_CANFA	ADM precursor [Contains: Adrenomedullin (AM); Proadrenomedullin N-20 terminal peptide (ProAM-N20) (P ...	0.72	-	nuc	0	Secreted protein				188
P51827 UniProt NPD GO	AFF3_MOUSE	AF4/FMR2 family member 3 (Protein LAF-4) (Lymphoid nuclear protein related to AF4) (Fragment)	0.72	-	nuc	0	Nucleus				204
P23109 UniProt NPD GO	AMPD1_HUMAN	AMP deaminase 1 (EC 3.5.4.6) (Myoadenylate deaminase) (AMP deaminase isoform M)	0.72	-	cyt	0			102770		747
Q02486 UniProt NPD GO	ABF2_YEAST	ARS-binding factor 2, mitochondrial precursor	0.72	-	mit	0	Mitochondrion. Nucleus (Probable)	mitochondrial chromosome [IDA]			183
Q4I662 UniProt NPD GO	DBP8_GIBZE	ATP-dependent RNA helicase DBP8 (EC 3.6.1.-)	0.72	+	cyt	0	Nucleus; nucleolus (By similarity)				547
P53166 UniProt NPD GO	MRH4_YEAST	ATP-dependent RNA helicase MRH4, mitochondrial precursor (EC 3.6.1.-) (Mitochondrial RNA helicase 4) ...	0.72	+	nuc	0	Mitochondrion	mitochondrion [IDA]			561
Q7RYZ7 UniProt NPD GO	DBP8_NEUCR	ATP-dependent RNA helicase dbp-8 (EC 3.6.1.-)	0.72	+	cyt	0	Nucleus; nucleolus (By similarity)				626
Q38876 UniProt NPD GO	AGL8_ARATH	Agamous-like MADS-box protein AGL8 (Floral homeotic protein AGL8) (Transcription factor FRUITFULL)	0.72	-	nuc	0	Nucleus (By similarity)				242
Q40170 UniProt NPD GO	AGL8_LYCES	Agamous-like MADS-box protein AGL8 homolog (TM4)	0.72	-	nuc	0	Nucleus (By similarity)				227
Q90WY5 UniProt NPD GO	ADA2B_BRARE	Alpha-2B adrenergic receptor (Alpha-2B adrenoceptor) (Alpha-2B adrenoreceptor) (Alpha(2B)AR)	0.72	+	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [IC]			510
O88990 UniProt NPD GO	ACTN3_MOUSE	Alpha-actinin-3 (Alpha actinin skeletal muscle isoform 3) (F-actin cross linking protein)	0.72	-	cyt	0		striated muscle thin filament [TAS]			900
Q63028 UniProt NPD GO	ADDA_RAT	Alpha-adducin (Erythrocyte adducin subunit alpha)	0.72	+	nuc	0					735
Q5RD33 UniProt NPD GO	APBA2_PONPY	Amyloid beta A4 precursor protein-binding family A member 2	0.72	-	nuc	0					749
Q92870 UniProt NPD GO	APBB2_HUMAN	Amyloid beta A4 precursor protein-binding family B member 2 (Fe65-like protein)	0.72	-	nuc	0		growth cone [ISS] lamellipodium [ISS] membrane [NAS] nucleus [ISS] synapse [ISS]	602710		758
Q9UJX6 UniProt NPD GO	ANC2_HUMAN	Anaphase-promoting complex subunit 2 (APC2) (Cyclosome subunit 2)	0.72	-	cyt	0			606946		822
Q9GKL7 UniProt NPD GO	ANDR_PIG	Androgen receptor (Dihydrotestosterone receptor)	0.72	+	nuc	0	Nucleus (By similarity)				896
Q8IY63 UniProt NPD GO	AMOL1_HUMAN	Angiomotin-like protein 1	0.72	-	nuc	0		tight junction [IDA]			956
P0C0T2 UniProt NPD GO	ANKS6_RAT	Ankyrin repeat and SAM domain-containing protein 6 (Sterile alpha motif domain-containing protein 6) ...	0.72	-	nuc	0					871
P17785 UniProt NPD GO	ANXA2_CHICK	Annexin A2 (Annexin II) (Lipocortin II) (Calpactin I heavy chain) (Chromobindin-8) (p36) (Protein I) ...	0.72	-	nuc	0	Secreted protein; extracellular space; extracellular matrix; basement membrane. In the lamina beneat ...				338
Q6BRA6 UniProt NPD GO	ATG11_DEBHA	Autophagy-related protein 11	0.72	-	end	0	Vacuole; vacuolar membrane; peripheral membrane protein (By similarity). Vacuolar and perivacuolar p ...				1282
Q8C0J2 UniProt NPD GO	A16L1_MOUSE	Autophagy-related protein 16-1 (APG16-like 1)	0.72	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Localized to preautophagosomal structure (PAS) whe ...	autophagic vacuole [IDA]			607
O74312 UniProt NPD GO	ATG9_SCHPO	Autophagy-related protein 9	0.72	-	end	6	Membrane; multi-pass membrane protein. Pre-autophagosomal and other perivacuolar punctate structures ...				702
P15391 UniProt NPD GO	CD19_HUMAN	B-lymphocyte antigen CD19 precursor (Differentiation antigen CD19) (B-lymphocyte surface antigen B4) ...	0.72	+	exc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	107265		556
O49404 UniProt NPD GO	BEH3_ARATH	BES1/BZR1 homolog protein 3	0.72	-	nuc	0					284
Q80X66 UniProt NPD GO	BTBDA_MOUSE	BTB/POZ domain-containing protein 10	0.72	-	nuc	0	Nucleus (By similarity)				475
Q8VIB5 UniProt NPD GO	BARH2_MOUSE	BarH-like 2 homeobox protein (Bar-class homeodomain protein MBH1) (Homeobox protein B-H1)	0.72	+	nuc	0	Nucleus (By similarity)				384
O88181 UniProt NPD GO	BARH2_RAT	BarH-like 2 homeobox protein (Bar-class homeodomain protein MBH1) (Homeobox protein B-H1)	0.72	+	nuc	0	Nucleus				384
O13911 UniProt NPD GO	PNK1_SCHPO	Bifunctional polynucleotide phosphatase/kinase (Polynucleotide kinase-3'-phosphatase) (DNA 5'-kinase ...	0.72	-	nuc	0	Nucleus	nucleus [IDA]			421
Q9BUH8 UniProt NPD GO	BEGIN_HUMAN	Brain-enriched guanylate kinase-associated protein	0.72	+	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				593
Q8CGM1 UniProt NPD GO	BAI2_MOUSE	Brain-specific angiogenesis inhibitor 2 precursor	0.72	-	end	8	Membrane; multi-pass membrane protein				1561
P47136 UniProt NPD GO	BUD4_YEAST	Bud site selection protein BUD4	0.72	-	nuc	0		contractile ring (sensu Saccharomyces) [TAS]			1447
Q9ESN9 UniProt NPD GO	JIP3_MOUSE	C-jun-amino-terminal kinase-interacting protein 3 (JNK-interacting protein 3) (JIP-3) (JNK MAP kinas ...	0.72	-	nuc	0	Cytoplasm. Golgi apparatus. Cytoplasmic vesicle. Localized in the soma and growth cones of different ...	cytoplasm [IEP]			1337
P79001 UniProt NPD GO	PGS1_SACPS	CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase (EC 2.7.8.5) (Phosphatidylglycero ...	0.72	-	mit	0	Mitochondrion (By similarity)				521
Q6FVG5 UniProt NPD GO	CSN10_CANGA	COP9 signalosome complex subunit 10	0.72	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				643
Q9NVC6 UniProt NPD GO	CRSP6_HUMAN	CRSP complex subunit 6 (Cofactor required for Sp1 transcriptional activation subunit 6) (Transcripti ...	0.72	-	nuc	0	Nucleus	mediator complex [IDA] nucleus [IDA] transcription factor complex [IDA]	603810		651
Q9H5V8 UniProt NPD GO	CDCP1_HUMAN	CUB domain-containing protein 1 precursor (Transmembrane and associated with src kinases) (Membrane ...	0.72	-	exc	1 *	Cell membrane; single-pass membrane protein (Potential). Its shedding may lead to a soluble peptide				836
P33450 UniProt NPD GO	FAT_DROME	Cadherin-related tumor suppressor precursor (Protein fat)	0.72	-	exc	1		integral to plasma membrane [NAS]			5147
P28582 UniProt NPD GO	CDPK_DAUCA	Calcium-dependent protein kinase (EC 2.7.11.1) (CDPK)	0.72	-	cyt	0					532
Q8GSA7 UniProt NPD GO	CMTA3_ARATH	Calmodulin-binding transcription activator 3 (Signal-responsive protein 1) (Ethylene-induced calmodu ...	0.72	-	nuc	0	Nucleus				1032
P20811 UniProt NPD GO	ICAL_BOVIN	Calpastatin (Calpain inhibitor)	0.72	-	nuc	0					705
Q9JME2 UniProt NPD GO	CHSTB_MOUSE	Carbohydrate sulfotransferase 11 (EC 2.8.2.5) (Chondroitin 4-O-sulfotransferase 1) (Chondroitin 4-su ...	0.72	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				352
P69478 UniProt NPD GO	CHSTB_RAT	Carbohydrate sulfotransferase 11 (EC 2.8.2.5) (Chondroitin 4-O-sulfotransferase 1) (Chondroitin 4-su ...	0.72	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				352
Q92851 UniProt NPD GO	CASPA_HUMAN	Caspase-10 precursor (EC 3.4.22.-) (CASP-10) (ICE-like apoptotic protease 4) (Apoptotic protease Mch ...	0.72	-	nuc	0			603909		521
P56198 UniProt NPD GO	CIDEC_MOUSE	Cell death activator CIDE-3 (Cell death-inducing DFFA-like effector protein C) (Fat-specific protein ...	0.72	-	mit	0	Cytoplasm (By similarity). Cytoplasmic in a punctate manner (By similarity)	cytosol [ISS]			239
P41892 UniProt NPD GO	CDC7_SCHPO	Cell division control protein 7 (EC 2.7.11.1)	0.72	-	nuc	0		spindle pole body [IDA]			1062
Q9Y812 UniProt NPD GO	CNP1_SCHPO	Centromere protein 1 (CENP-A homolog) (Centromere autoantigen A homolog) (Silencing in the middle of ...	0.72	-	nuc	0	Nucleus. Centromeric	inner kinetochore of condensed chromosome [IDA]			120
P49450 UniProt NPD GO	CENPA_HUMAN	Centromere protein A (CENP-A) (Centromere autoantigen A)	0.72	-	nuc	0	Nucleus	chromosome, pericentric region [IDA] nucleus [TAS]	117139		140
Q01850 UniProt NPD GO	CDR2_HUMAN	Cerebellar degeneration-related protein 2 (Paraneoplastic cerebellar degeneration-associated antigen ...	0.72	-	nuc	0		nucleus [NAS]	117340		454

You are viewing entries 12651 to 12700 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.