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
P62856 UniProt NPD GO	RS26_RAT	40S ribosomal protein S26	0.48	-	nuc	0					114
P68200 UniProt NPD GO	RS27A_ICTPU	40S ribosomal protein S27a	0.48	+	nuc	0					80
Q7YRV4 UniProt NPD GO	RO52_BOVIN	52 kDa Ro protein (Sjoegren syndrome type A antigen) (SS-A) (Ro(SS-A)) (52 kDa ribonucleoprotein aut ...	0.48	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				469
Q9P769 UniProt NPD GO	RL10B_SCHPO	60S ribosomal protein L10-B	0.48	-	mit	0	Cytoplasm				221
Q5E9E6 UniProt NPD GO	RL10A_BOVIN	60S ribosomal protein L10a	0.48	+	nuc	0					216
P62907 UniProt NPD GO	RL10A_RAT	60S ribosomal protein L10a	0.48	+	nuc	0					216
P62906 UniProt NPD GO	RL10A_HUMAN	60S ribosomal protein L10a (CSA-19)	0.48	+	nuc	0					216
Q9HE25 UniProt NPD GO	RL17_NEUCR	60S ribosomal protein L17	0.48	-	mit	0					186
P05735 UniProt NPD GO	RL19_YEAST	60S ribosomal protein L19 (L23) (YL14) (RP33) (RP15L)	0.48	-	nuc	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]		1K5Y	188
Q7RXY1 UniProt NPD GO	RL32_NEUCR	60S ribosomal protein L32	0.48	-	nuc	0					131
P79015 UniProt NPD GO	RL32A_SCHPO	60S ribosomal protein L32-A	0.48	-	nuc	0					127
O80626 UniProt NPD GO	RL352_ARATH	60S ribosomal protein L35-2	0.48	-	nuc	0					123
O22860 UniProt NPD GO	RL38_ARATH	60S ribosomal protein L38	0.48	-	nuc	0					69
P49213 UniProt NPD GO	RL44_CHLRE	60S ribosomal protein L44 (L41)	0.48	-	nuc	0					98
P31028 UniProt NPD GO	RL44_DEBOC	60S ribosomal protein L44 (L41)	0.48	-	nuc	0					105
Q8SS93 UniProt NPD GO	RL7_ENCCU	60S ribosomal protein L7	0.48	-	nuc	0					239
O08715 UniProt NPD GO	AKAP1_MOUSE	A kinase anchor protein 1, mitochondrial precursor (Protein kinase A-anchoring protein 1) (PRKA1) (D ...	0.48	-	nuc	1 *	Isoform 2/D-AKAP1B, isoform 4/D-AKAP1D: Endoplasmic reticulum. Isoform 1/D-AKAP1A, isoform 3/D-AKAP1 ...				857
Q76N33 UniProt NPD GO	STALP_MOUSE	AMSH-like protease (EC 3.1.2.15) (AMSH-LP) (STAM-binding protein-like 1) (AMSH family protein) (AMSH ...	0.48	-	nuc	0					436
Q9BZC7 UniProt NPD GO	ABCA2_HUMAN	ATP-binding cassette sub-family A member 2 (ATP-binding cassette transporter 2) (ATP-binding cassett ...	0.48	-	end	12 *	Membrane; multi-pass membrane protein (Potential)	ATP-binding cassette (ABC) transporter complex [NAS] integral to membrane [NAS]	600047		2436
Q9ESR9 UniProt NPD GO	ABCA2_RAT	ATP-binding cassette sub-family A member 2 (ATP-binding cassette transporter 2) (ATP-binding cassett ...	0.48	-	end	11 *	Membrane; multi-pass membrane protein (Potential)	ATP-binding cassette (ABC) transporter complex [ISS] integral to membrane [NAS]			2434
P42379 UniProt NPD GO	CLPP_CHLEU	ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) (Endopeptidase Clp) [Contains: Ceu clp ...	0.48	-	nuc	0	Plastid; chloroplast				1010
Q6BGU8 UniProt NPD GO	DBP8_DEBHA	ATP-dependent RNA helicase DBP8 (EC 3.6.1.-)	0.48	-	cyt	0	Nucleus; nucleolus (By similarity)				441
Q5AAW3 UniProt NPD GO	DHH1_CANAL	ATP-dependent RNA helicase DHH1 (EC 3.6.1.-)	0.48	-	nuc	0	Cytoplasm. Is concentrated in several cytoplasmic foci called P bodies (or cytoplasmic processing bo ...				549
Q7ZZ25 UniProt NPD GO	ATD1A_BRARE	ATPase family AAA domain-containing protein 1-A	0.48	-	mit	0					380
P62484 UniProt NPD GO	ABI2_MOUSE	Abl interactor 2 (Abelson interactor 2) (Abi-2)	0.48	-	nuc	0	Cytoplasm. Localized to protruding lamellipodia and filopodia tips	cell-cell adherens junction [IDA] dendrite [IDA]			446
Q4PCI7 UniProt NPD GO	ACN9_USTMA	Acetate non-utilizing protein 9, mitochondrial precursor	0.48	-	mit	0	Mitochondrion; mitochondrial intermembrane space (By similarity)				173
P56765 UniProt NPD GO	ACCD_ARATH	Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta (EC 6.4.1.2) (ACCase beta chain)	0.48	-	nuc	0	Plastid; chloroplast; chloroplast membrane; peripheral membrane protein. Plastid; chloroplast; chlor ...				488
Q02752 UniProt NPD GO	PHPA_PLACH	Acidic phosphoprotein precursor (50 kDa antigen)	0.48	+	nuc	0	Cell membrane; peripheral membrane protein; cytoplasmic side. Peripheral membrane protein on the cyt ...				441
Q8NC06 UniProt NPD GO	ACBD4_HUMAN	Acyl-CoA-binding domain-containing protein 4	0.48	-	nuc	0					268
Q8VHQ9 UniProt NPD GO	ACO11_MOUSE	Acyl-coenzyme A thioesterase 11 (EC 3.1.2.-) (Acyl-CoA thioesterase 11) (Acyl-CoA thioester hydrolas ...	0.48	-	mit	0	Cytoplasm (By similarity)	cytoplasm [IC]			594
O60503 UniProt NPD GO	ADCY9_HUMAN	Adenylate cyclase type 9 (EC 4.6.1.1) (Adenylate cyclase type IX) (ATP pyrophosphate-lyase 9) (Adeny ...	0.48	-	end	8	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	603302		1353
P51195 UniProt NPD GO	PHAC_PORPU	Allophycocyanin alpha-B chain (Allophycocyanin gamma chain)	0.48	-	cyt	0	Plastid; chloroplast				161
P28549 UniProt NPD GO	CAS1_MACEU	Alpha-casein precursor	0.48	-	exc	0	Secreted protein				237
P0C1D0 UniProt NPD GO	CXA1A_CONRE	Alpha-conotoxin RgIA precursor (Fragment)	0.48	-	nuc	0	Secreted protein				32
Q12358 UniProt NPD GO	JLP1_YEAST	Alpha-ketoglutarate-dependent sulfonate dioxygenase (EC 1.14.11.-)	0.48	-	cyt	0					412
Q9HB97 UniProt NPD GO	PARVA_RAT	Alpha-parvin (Actopaxin)	0.48	+	nuc	0	Cell membrane; cell-matrix junction; focal adhesion; cytoplasmic side. Constituent of focal adhesion ...	focal adhesion [NAS]			372
P39189 UniProt NPD GO	ALU2_HUMAN	Alu subfamily SB sequence contamination warning entry	0.48	-	exc	0					587
P39191 UniProt NPD GO	ALU4_HUMAN	Alu subfamily SB2 sequence contamination warning entry	0.48	-	exc	0					603
Q9UHC3 UniProt NPD GO	ACCN3_HUMAN	Amiloride-sensitive cation channel 3 (Acid-sensing ion channel 3) (ASIC3) (hASIC3) (Testis sodium ch ...	0.48	-	nuc	0	Cell membrane; multi-pass membrane protein (By similarity). Cell surface expression may be stabilize ...				531
O96018 UniProt NPD GO	APBA3_HUMAN	Amyloid beta A4 precursor protein-binding family A member 3 (Neuron-specific X11L2 protein) (Neurona ...	0.48	+	nuc	0		membrane [NAS]	604262		575
Q8WTY4 UniProt NPD GO	CPIN1_MOUSE	Anamorsin (Cytokine-induced apoptosis inhibitor 1)	0.48	-	nuc	0	Cytoplasm	cytoplasm [IDA]			309
Q9H1A4 UniProt NPD GO	ANC1_HUMAN	Anaphase-promoting complex subunit 1 (APC1) (Cyclosome subunit 1) (Protein Tsg24) (Mitotic checkpoin ...	0.48	-	end	0					1944
Q8K2H6 UniProt NPD GO	APC10_MOUSE	Anaphase-promoting complex subunit 10 (APC10) (Cyclosome subunit 10)	0.48	-	nuc	0					185
Q8N961 UniProt NPD GO	ABTB2_HUMAN	Ankyrin repeat and BTB/POZ domain-containing protein 2	0.48	-	nuc	0					839
Q7TQI7 UniProt NPD GO	ABTB2_MOUSE	Ankyrin repeat and BTB/POZ domain-containing protein 2	0.48	-	nuc	0					1024
Q8HYV8 UniProt NPD GO	ASB17_CANFA	Ankyrin repeat and SOCS box protein 17 (ASB-17)	0.48	-	mit	0					295
Q569N2 UniProt NPD GO	ANR37_MOUSE	Ankyrin repeat domain-containing protein 37	0.48	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity)				159
P40602 UniProt NPD GO	APG_ARATH	Anter-specific proline-rich protein APG precursor	0.48	-	nuc	1 *					534
Q01133 UniProt NPD GO	FMRA_CALPA	Antho-RFamide neuropeptides precursor [Contains: Antho-RFamide]	0.48	-	mit	1 *	Secreted protein				334
Q62893 UniProt NPD GO	AMHR2_RAT	Anti-Muellerian hormone type-2 receptor precursor (EC 2.7.11.30) (Anti-Muellerian hormone type II re ...	0.48	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [IDA]			557

You are viewing entries 26051 to 26100 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.