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
P46063 UniProt NPD GO	RECQ1_HUMAN	ATP-dependent DNA helicase Q1 (EC 3.6.1.-) (DNA-dependent ATPase Q1)	0.68	+	nuc	0	Nucleus	nucleus [TAS]	600537		649
Q68FK8 UniProt NPD GO	DHX9_XENLA	ATP-dependent RNA helicase A-like protein (EC 3.6.1.-) (Nuclear DNA helicase II) (NDH II) (DEAH box ...	0.68	+	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				1262
P38719 UniProt NPD GO	DBP8_YEAST	ATP-dependent RNA helicase DBP8 (EC 3.6.1.-) (DEAD box protein 8)	0.68	-	cyt	0	Nucleus; nucleolus	nucleolus [IDA]			431
Q9HGM5 UniProt NPD GO	DBP8_SCHPO	ATP-dependent RNA helicase dbp8 (EC 3.6.1.-)	0.68	-	cyt	0	Nucleus; nucleolus (By similarity)				453
Q9NVI7 UniProt NPD GO	ATD3A_HUMAN	ATPase family AAA domain-containing protein 3A	0.68	-	nuc	0					634
O35885 UniProt NPD GO	ASCL2_MOUSE	Achaete-scute homolog 2 (Mash-2)	0.68	+	nuc	0	Nucleus				263
Q7ZY40 UniProt NPD GO	AN32E_XENLA	Acidic leucine-rich nuclear phosphoprotein 32 family member E	0.68	-	nuc	0	Cytoplasm. Nucleus (By similarity)				263
P53974 UniProt NPD GO	ARK1_YEAST	Actin-regulating kinase 1 (EC 2.7.11.1)	0.68	-	nuc	0	Actin patch. Cortical actin patches	actin cortical patch [IDA]			638
Q5EE38 UniProt NPD GO	ACD_MOUSE	Adrenocortical dysplasia protein	0.68	-	nuc	0	Nucleus (Potential)				416
P31696 UniProt NPD GO	AGRN_CHICK	Agrin (Fragment)	0.68	-	nuc	0	Synaptic basal lamina at the neuromuscular junction			1Q56	1955
P18091 UniProt NPD GO	ACTN_DROME	Alpha-actinin, sarcomeric (F-actin cross linking protein)	0.68	-	nuc	0					924
Q08043 UniProt NPD GO	ACTN3_HUMAN	Alpha-actinin-3 (Alpha actinin skeletal muscle isoform 3) (F-actin cross linking protein)	0.68	-	cyt	0		actin filament [TAS]	102574	1WKU	901
O43707 UniProt NPD GO	ACTN4_HUMAN	Alpha-actinin-4 (Non-muscle alpha-actinin 4) (F-actin cross linking protein)	0.68	-	cyt	0	Nucleus. Cytoplasm. Colocalizes with actin stress fibers. Nuclear translocation can be induced by th ...	actin cytoskeleton [TAS] cytoplasm [TAS] nucleus [TAS]	603278	1YDI	911
Q8R5A3 UniProt NPD GO	AB1IP_MOUSE	Amyloid beta A4 precursor protein-binding family B member 1-interacting protein (APBB1-interacting p ...	0.68	-	nuc	0	Cell membrane; peripheral membrane protein. Colocalizes with ENA/VASP proteins at lamellipodia tips ...				670
Q8BZQ7 UniProt NPD GO	ANC2_MOUSE	Anaphase-promoting complex subunit 2 (APC2) (Cyclosome subunit 2)	0.68	-	cyt	0					837
Q6GQX6 UniProt NPD GO	ANKS6_MOUSE	Ankyrin repeat and SAM domain-containing protein 6 (Sterile alpha motif domain-containing protein 6) ...	0.68	-	nuc	0					883
P32448 UniProt NPD GO	ASF2_YEAST	Anti-silencing protein 2	0.68	-	nuc	0		nuclear chromosome, telomeric region [IDA] nucleus [IDA]			525
P61797 UniProt NPD GO	APTX_CANFA	Aprataxin homolog (Forkhead-associated domain histidine triad-like protein) (FHA-HIT)	0.68	-	nuc	0	Nucleus (By similarity). Upon genotoxic stress, it colocalizes with XRCC1 at sites of DNA damage (By ...				342
Q8BM89 UniProt NPD GO	ARSJ_MOUSE	Arylsulfatase J precursor (EC 3.1.6.-) (ASJ)	0.68	-	mit	0	Secreted protein (Potential)				598
Q9Z0E3 UniProt NPD GO	AIRE_MOUSE	Autoimmune regulator (Autoimmune polyendocrinopathy candidiasis ectodermal dystrophy protein homolog ...	0.68	-	nuc	0	Nucleus. Cytoplasm. Predominantly nuclear but also cytoplasmic. Found in nuclear body-like structure ...	nucleus [IDA]			552
Q6FRH2 UniProt NPD GO	ATG11_CANGA	Autophagy-related protein 11	0.68	-	nuc	0	Vacuole; vacuolar membrane; peripheral membrane protein (By similarity). Vacuolar and perivacuolar p ...				1110
Q5BH53 UniProt NPD GO	ATG18_EMENI	Autophagy-related protein 18	0.68	-	nuc	0	Membrane-associated. Peripheral membrane protein of pre-autophagosomal structure (PAS) and vacuole ( ...				444
Q4WLK5 UniProt NPD GO	ATG2_ASPFU	Autophagy-related protein 2	0.68	-	nuc	0	Perivacuolar compartment (By similarity)				2160
Q4WLT9 UniProt NPD GO	ATG9_ASPFU	Autophagy-related protein 9	0.68	-	vac	6	Membrane; multi-pass membrane protein. Pre-autophagosomal and other perivacuolar punctate structures ...				951
Q5B6U6 UniProt NPD GO	ATG9_EMENI	Autophagy-related protein 9	0.68	-	vac	5	Membrane; multi-pass membrane protein. Pre-autophagosomal and other perivacuolar punctate structures ...				820
Q875A7 UniProt NPD GO	ATG9_PODAN	Autophagy-related protein 9	0.68	-	end	6	Membrane; multi-pass membrane protein. Pre-autophagosomal and other perivacuolar punctate structures ...				900
Q9UL15 UniProt NPD GO	BAG5_HUMAN	BAG family molecular chaperone regulator 5 (BCL2-associated athanogene 5) (BAG-5)	0.68	-	nuc	0			603885		447
Q62735 UniProt NPD GO	NR1H4_RAT	Bile acid receptor (Farnesoid X-activated receptor) (Farnesol receptor HRR-1) (Retinoid X receptor-i ...	0.68	-	nuc	0	Nucleus (Probable)			1OT7	469
P98070 UniProt NPD GO	BMP1_XENLA	Bone morphogenetic protein 1 precursor (EC 3.4.24.-) (BMP-1)	0.68	-	nuc	0					707
O19006 UniProt NPD GO	BMP2_DAMDA	Bone morphogenetic protein 2 precursor (BMP-2)	0.68	+	exc	1 *	Secreted protein (By similarity)				396
P21275 UniProt NPD GO	BMP4_MOUSE	Bone morphogenetic protein 4 precursor (BMP-4) (BMP-2B)	0.68	-	exc	0	Secreted protein; extracellular space; extracellular matrix				408
Q06826 UniProt NPD GO	BMP4_RAT	Bone morphogenetic protein 4 precursor (BMP-4) (BMP-2B)	0.68	-	exc	0	Secreted protein; extracellular space; extracellular matrix				408
Q60437 UniProt NPD GO	BAIP2_CRIGR	Brain-specific angiogenesis inhibitor 1-associated protein 2 (BAI1-associated protein 2) (BAI-associ ...	0.68	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Detected throughou ...				521
Q9UQB8 UniProt NPD GO	BAIP2_HUMAN	Brain-specific angiogenesis inhibitor 1-associated protein 2 (BAI1-associated protein 2) (BAI-associ ...	0.68	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Detected throughout the cytoplasm in the absence o ...		605475	1Y2O	552
P15036 UniProt NPD GO	ETS2_HUMAN	C-ets-2 protein	0.68	+	nuc	0	Nucleus		164740		469
Q8BVP5 UniProt NPD GO	KC1G2_MOUSE	Casein kinase I isoform gamma-2 (EC 2.7.11.1) (CKI-gamma 2)	0.68	-	nuc	0	Cytoplasm (By similarity)				415
Q8BHE3 UniProt NPD GO	ATCAY_MOUSE	Caytaxin	0.68	-	cyt	2					372
Q9JM96 UniProt NPD GO	BORG4_MOUSE	Cdc42 effector protein 4 (Binder of Rho GTPases 4)	0.68	-	nuc	0	Intracytoplasmic membrane; peripheral membrane protein (By similarity)	cytoplasm [IDA]			349
P30260 UniProt NPD GO	CDC27_HUMAN	Cell division cycle protein 27 homolog (CDC27Hs) (H-NUC)	0.68	-	nuc	0	Nucleus	centrosome [IDA] spindle microtubule [IDA]	116946		824
P32566 UniProt NPD GO	SMI1_YEAST	Cell wall assembly regulator SMI1 (Killer toxin-resistance protein 4)	0.68	-	nuc	0	Nucleus	bud tip [TAS] nucleus [IDA]			505
O35216 UniProt NPD GO	CENPA_MOUSE	Centromere protein A (CENP-A) (Centromere autoantigen A)	0.68	-	mit	0	Nucleus	inner kinetochore of condensed chromosome [IDA]			134
Q92674 UniProt NPD GO	CENPI_HUMAN	Centromere protein I (CENP-I) (Follicle-stimulating hormone primary response protein) (FSH primary r ...	0.68	-	nuc	0			300065		756
P53865 UniProt NPD GO	CNM67_YEAST	Chaotic nuclear migration protein 67	0.68	-	nuc	0	Localizes to the meiotic outer plaque of the SPB, at the end of the meiotic spindles	outer plaque of spindle pole body [IDA]			581
P42825 UniProt NPD GO	DNAJ2_ARATH	Chaperone protein dnaJ 2 (AtDjA2)	0.68	-	nuc	0	Membrane; lipid-anchor (Probable)				419
Q6IQ73 UniProt NPD GO	CHM4C_BRARE	Charged multivesicular body protein 4c (Chromatin-modifying protein 4c) (CHMP4c)	0.68	-	nuc	0	Cytoplasm (By similarity)				224
O20032 UniProt NPD GO	RR18_CHLRE	Chloroplast 30S ribosomal protein S18	0.68	-	mit	0	Plastid; chloroplast				137
Q6ENF1 UniProt NPD GO	RR18_ORYNI	Chloroplast 30S ribosomal protein S18	0.68	+	nuc	0	Plastid; chloroplast				163
P12152 UniProt NPD GO	RR18_ORYSA	Chloroplast 30S ribosomal protein S18	0.68	+	nuc	0	Plastid; chloroplast				163
P16037 UniProt NPD GO	RR2_MAIZE	Chloroplast 30S ribosomal protein S2	0.68	-	mit	0	Plastid; chloroplast				236
Q8M9W2 UniProt NPD GO	RR4_CHAGL	Chloroplast 30S ribosomal protein S4	0.68	-	mit	0	Plastid; chloroplast				205

You are viewing entries 14601 to 14650 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.