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
Q13442 UniProt NPD GO	HAP28_HUMAN	28 kDa heat- and acid-stable phosphoprotein (PDGF-associated protein) (PAP) (PDGFA-associated protei ...	0.76	-	nuc	0			607075		181
Q8WTC1 UniProt NPD GO	RT15_DROME	28S ribosomal protein S15, mitochondrial precursor (MRS-S15) (Bonsai protein) (DmMRPS15)	0.76	+	nuc	0	Mitochondrion	mitochondrial small ribosomal subunit [ISS] mitochondrion [IDA]			280
P82933 UniProt NPD GO	RT09_HUMAN	28S ribosomal protein S9, mitochondrial precursor (S9mt) (MRP-S9)	0.76	-	mit	0	Mitochondrion	mitochondrial small ribosomal subunit [NAS]			396
Q9NZE8 UniProt NPD GO	RM35_HUMAN	39S ribosomal protein L35, mitochondrial precursor (L35mt) (MRP-L35)	0.76	+	mit	0	Mitochondrion	mitochondrial ribosome [NAS]			170
P05752 UniProt NPD GO	RS6A_SCHPO	40S ribosomal protein S6-A	0.76	-	nuc	0					239
P48156 UniProt NPD GO	RS8_CAEEL	40S ribosomal protein S8	0.76	+	nuc	0					208
P28285 UniProt NPD GO	5HT2A_DROME	5-hydroxytryptamine receptor 2A (5-HT receptor) (Serotonin receptor 2A)	0.76	-	end	7	Membrane; multi-pass membrane protein				834
P41105 UniProt NPD GO	RL28_MOUSE	60S ribosomal protein L28	0.76	+	nuc	0		cytosolic large ribosomal subunit (sensu Eu... [ISS]			136
P84324 UniProt NPD GO	RL32_DROAI	60S ribosomal protein L32 (Ribosomal protein 49)	0.76	-	nuc	0					134
P84325 UniProt NPD GO	RL32_DROAZ	60S ribosomal protein L32 (Ribosomal protein 49)	0.76	-	nuc	0					134
P84326 UniProt NPD GO	RL32_DROMI	60S ribosomal protein L32 (Ribosomal protein 49)	0.76	-	nuc	0					134
P84327 UniProt NPD GO	RL32_DROPE	60S ribosomal protein L32 (Ribosomal protein 49)	0.76	-	nuc	0					134
P84323 UniProt NPD GO	RL32_DROPS	60S ribosomal protein L32 (Ribosomal protein 49)	0.76	-	nuc	0					134
Q962S7 UniProt NPD GO	RL37_SPOFR	60S ribosomal protein L37	0.76	-	mit	0					91
Q8LFH7 UniProt NPD GO	RL371_ARATH	60S ribosomal protein L37-1	0.76	-	mit	0					95
P19379 UniProt NPD GO	RL40_TOBAC	60S ribosomal protein L40 (CEP52)	0.76	+	nuc	0					72
P22225 UniProt NPD GO	PFR1_TRYBB	69 kDa paraflagellar rod protein (69 kDa PFR protein) (PFR-A/PFR-B)	0.76	-	nuc	0					600
Q8BRC6 UniProt NPD GO	AAT1_MOUSE	AMY-1-associating protein expressed in testis 1 homolog (AAT-1)	0.76	-	nuc	0	Cytoplasm (By similarity). Mitochondrion (By similarity)				345
Q9UU81 UniProt NPD GO	AP1G1_SCHPO	AP-1 complex subunit gamma-1 (Gamma(1)-adaptin) (Clathrin assembly protein large gamma-1 chain) (Cla ...	0.76	+	nuc	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...				865
Q4WMS3 UniProt NPD GO	MAK5_ASPFU	ATP-dependent RNA helicase mak5 (EC 3.6.1.-)	0.76	+	nuc	0	Nucleus; nucleolus (By similarity)				777
Q8WXE1 UniProt NPD GO	ATRIP_HUMAN	ATR-interacting protein (ATM and Rad3-related-interacting protein)	0.76	-	nuc	0	Nucleus. Redistributes to discrete nuclear foci upon DNA damage		606605		791
P11031 UniProt NPD GO	TCP4_MOUSE	Activated RNA polymerase II transcriptional coactivator p15 precursor (SUB1 homolog) (Positive cofac ...	0.76	+	nuc	0	Nucleus				126
P38700 UniProt NPD GO	APM2_YEAST	Adaptin medium chain homolog APM2	0.76	+	nuc	0		AP-1 adaptor complex [IPI]			605
Q25434 UniProt NPD GO	FP1_MYTCO	Adhesive plaque matrix protein precursor (Foot protein 1) (MCFP1)	0.76	-	nuc	0	Secreted protein				872
Q6P6C2 UniProt NPD GO	ALKB5_HUMAN	Alkylated repair protein alkB homolog 5	0.76	-	nuc	1					458
P55270 UniProt NPD GO	SCNNA_BOVIN	Amiloride-sensitive sodium channel subunit alpha (Epithelial Na+ channel subunit alpha) (Alpha ENaC) ...	0.76	-	nuc	1	Cell membrane; apical cell membrane; multi-pass membrane protein (By similarity). Apical membrane of ...				650
P15514 UniProt NPD GO	AREG_HUMAN	Amphiregulin precursor (AR) (Colorectum cell-derived growth factor) (CRDGF)	0.76	+	mit	1		extracellular space [TAS]	104640		252
P40577 UniProt NPD GO	MND2_YEAST	Anaphase-promoting complex subunit MND2 (Meiotic nuclear division protein 2)	0.76	-	nuc	0		anaphase-promoting complex [IDA] nucleus [IDA]			368
Q8VHG2 UniProt NPD GO	AMOT_MOUSE	Angiomotin (Fragment)	0.76	-	nuc	0	Cell membrane; cell-cell junction (By similarity). Localized on the cell surface. May act as a trans ...	actin filament [ISS] cytoplasmic vesicle [ISS] lamellipodium [ISS]			926
Q6ZW76 UniProt NPD GO	ANKS3_HUMAN	Ankyrin repeat and SAM domain-containing protein 3	0.76	-	nuc	0					656
O15945 UniProt NPD GO	ARNT_DROME	Aryl hydrocarbon receptor nuclear translocator homolog (dARNT) (Protein tango) (Hypoxia-inducible fa ...	0.76	+	nuc	0		nucleus [IDA]			644
Q676U5 UniProt NPD GO	A16L1_HUMAN	Autophagy-related protein 16-1 (APG16-like 1)	0.76	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Localized to preau ...				607
Q5KMS0 UniProt NPD GO	ATG2_CRYNE	Autophagy-related protein 2	0.76	-	nuc	0	Perivacuolar compartment (By similarity)				1935
Q96S65 UniProt NPD GO	AXUD1_HUMAN	Axin-1 up-regulated gene 1 protein (TGF-beta-induced apoptosis protein 3) (TAIP-3) (URAX1 protein)	0.76	-	nuc	0	Nucleus (Probable)		606458		589
P34908 UniProt NPD GO	BRAF1_COTJA	B-Raf proto-oncogene serine/threonine-protein kinase (EC 2.7.11.1) (RMIL serine/threonine-protein ki ...	0.76	-	nuc	0	Nucleus				807
Q04982 UniProt NPD GO	BRAF1_CHICK	B-Raf proto-oncogene serine/threonine-protein kinase (EC 2.7.11.1) (Rmil serine/threonine-protein ki ...	0.76	-	nuc	0	Nucleus				806
O00512 UniProt NPD GO	BCL9_HUMAN	B-cell lymphoma 9 protein (Bcl-9) (Legless homolog)	0.76	-	nuc	0	Nucleus (By similarity)		602597		1426
Q4V8K2 UniProt NPD GO	CTBL1_RAT	Beta-catenin-like protein 1 (Nuclear-associated protein) (NAP)	0.76	-	cyt	0	Nucleus (By similarity)				563
Q8VBT1 UniProt NPD GO	TXLNB_MOUSE	Beta-taxilin (Muscle-derived protein 77)	0.76	-	nuc	0					685
P30885 UniProt NPD GO	BMP4_XENLA	Bone morphogenetic protein 4 precursor (BMP-4)	0.76	-	exc	0	Secreted protein; extracellular space; extracellular matrix				401
Q02638 UniProt NPD GO	CEBP_DROVI	CCAAT/enhancer-binding protein (C/EBP) (Slow border cell protein)	0.76	+	nuc	0	Nucleus				451
P16070 UniProt NPD GO	CD44_HUMAN	CD44 antigen precursor (Phagocytic glycoprotein I) (PGP-1) (HUTCH-I) (Extracellular matrix receptor- ...	0.76	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [NAS]	107269	1UUH	742
Q9YHZ6 UniProt NPD GO	CC45L_XENLA	CDC45-related protein	0.76	-	cyt	0	Nucleus				567
Q6UUV9 UniProt NPD GO	CRTC1_HUMAN	CREB-regulated transcription coactivator 1 (Transducer of regulated cAMP response element-binding pr ...	0.76	-	nuc	0	Nucleus	nucleus [IDA]	607536		634
Q8R3V6 UniProt NPD GO	CUED1_MOUSE	CUE domain-containing protein 1	0.76	-	nuc	0					388
Q96RR4 UniProt NPD GO	KKCC2_HUMAN	Calcium/calmodulin-dependent protein kinase kinase 2 (EC 2.7.11.17) (Calcium/calmodulin-dependent pr ...	0.76	-	nuc	0	Cytoplasm (By similarity)	intracellular [ISS]			588
P40233 UniProt NPD GO	CKI1_SCHPO	Casein kinase I homolog 1 (EC 2.7.11.1)	0.76	-	nuc	0	Cytoplasm			2CSN	446
Q8BHB0 UniProt NPD GO	CARD4_MOUSE	Caspase recruitment domain-containing protein 4	0.76	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [ISS]			953
Q8BWD8 UniProt NPD GO	CD2L6_MOUSE	Cell division cycle 2-like protein kinase 6 (EC 2.7.11.22) (CDC2-related protein kinase 6)	0.76	-	nuc	0					501
Q8VXV4 UniProt NPD GO	DNJ16_ARATH	Chaperone protein dnaJ 16 (Protein ARG1-LIKE1) (AtARL1) (AtJ16) (AtDjB16)	0.76	-	nuc	0	Membrane; peripheral membrane protein (Potential)				436

You are viewing entries 10701 to 10750 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.