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
P24793 UniProt NPD GO	MYCN_XENLA	N-myc protein	0.71	+	nuc	0	Nucleus (Potential)				437
P03966 UniProt NPD GO	MYCN_MOUSE	N-myc proto-oncogene protein	0.71	+	nuc	0	Nucleus	nucleus [IDA]			462
Q9CR61 UniProt NPD GO	NDUB7_MOUSE	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiquin ...	0.71	-	nuc	0	Mitochondrion; mitochondrial inner membrane; matrix side (By similarity)	mitochondrial inner membrane [IDA] mitochondrion [IDA]			136
Q9VJQ5 UniProt NPD GO	NC2B_DROME	Negative cofactor 2 beta (dNC2) (Down-regulator of transcription 1)	0.71	-	nuc	0	Nucleus	nucleus [IDA]			183
P07196 UniProt NPD GO	NFL_HUMAN	Neurofilament triplet L protein (68 kDa neurofilament protein) (Neurofilament light polypeptide) (NF ...	0.71	-	nuc	0		axon [IDA] neurofilament [TAS]	607734		542
P02548 UniProt NPD GO	NFL_BOVIN	Neurofilament triplet L protein (68 kDa neurofilament protein) (Neurofilament light polypeptide) (NF ...	0.71	-	nuc	0					554
O09105 UniProt NPD GO	NDF4_MOUSE	Neurogenic differentiation factor 4 (NeuroD4) (Atonal protein homolog 3) (Helix-loop-helix protein m ...	0.71	-	nuc	0	Nucleus (Potential)				330
P70660 UniProt NPD GO	NGN1_MOUSE	Neurogenin 1 (Neurogenic differentiation factor 3) (NeuroD3) (Neurogenic basic-helix-loop-helix prot ...	0.71	+	nuc	0	Nucleus (Probable)				244
P01156 UniProt NPD GO	NEUT_BOVIN	Neurotensin/neuromedin N precursor [Contains: Large neuromedin N (NmN-125); Neuromedin N (NmN) (NN); ...	0.71	-	exc	0	Secreted protein. Packaged within secretory vesicles				169
Q4WY33 UniProt NPD GO	NHP6_ASPFU	Nonhistone chromosomal protein 6	0.71	+	nuc	0	Nucleus (By similarity)				104
Q5KBH9 UniProt NPD GO	NDE1_CRYNE	Nuclear distribution protein nudE homolog 1	0.71	-	nuc	0	Cytoplasm. Localizes to the plus ends of microtubules (By similarity)				666
Q9WTK5 UniProt NPD GO	NFKB2_MOUSE	Nuclear factor NF-kappa-B p100 subunit (DNA-binding factor KBF2) [Contains: Nuclear factor NF-kappa- ...	0.71	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Nuclear, but also found in the cytoplasm in an i ...				899
O16361 UniProt NPD GO	NH134_CAEEL	Nuclear hormone receptor family member nhr-134	0.71	-	nuc	0	Nucleus (Potential)				407
Q09587 UniProt NPD GO	NHR22_CAEEL	Nuclear hormone receptor family member nhr-22	0.71	-	nuc	0	Nucleus (Potential)				579
O45436 UniProt NPD GO	NHR4_CAEEL	Nuclear hormone receptor family member nhr-4	0.71	-	nuc	0	Nucleus (Potential)				492
Q9U2R6 UniProt NPD GO	NHR91_CAEEL	Nuclear hormone receptor family member nhr-91	0.71	-	nuc	0	Nucleus (Potential)				474
Q8N1F7 UniProt NPD GO	NUP93_HUMAN	Nuclear pore complex protein Nup93 (Nucleoporin Nup93) (93 kDa nucleoporin)	0.71	-	cyt	0	Nucleus; nuclear envelope; nuclear pore complex. Localizes at the nuclear basket and at or near the ...				819
Q9D1J3 UniProt NPD GO	HCC1_MOUSE	Nuclear protein Hcc-1	0.71	+	nuc	0	Nucleus (By similarity)				209
Q02818 UniProt NPD GO	NUCB1_HUMAN	Nucleobindin-1 precursor (CALNUC)	0.71	-	exc	0	Golgi apparatus; cis-Golgi network; cis-Golgi network membrane; peripheral membrane protein; luminal ...	ER-Golgi intermediate compartment [IDA] extracellular space [TAS]	601323	1SNL	461
Q75BJ7 UniProt NPD GO	NOP12_ASHGO	Nucleolar protein 12	0.71	-	nuc	0	Nucleus; nucleolus (By similarity)				426
O13741 UniProt NPD GO	NOP12_SCHPO	Nucleolar protein 12	0.71	+	nuc	0	Nucleus; nucleolus (By similarity)				438
Q6IE21 UniProt NPD GO	OTU6A_MOUSE	OTU domain-containing protein 6A (Hin-6 protease)	0.71	+	nuc	0					290
P83286 UniProt NPD GO	OPT_CANFA	Opticin precursor (Oculoglycan)	0.71	+	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				327
Q96CV9 UniProt NPD GO	OPTN_HUMAN	Optineurin (Optic neuropathy-inducing protein) (E3-14.7K-interacting protein) (FIP-2) (Huntingtin-in ...	0.71	-	nuc	0	Cytoplasm; perinuclear region. Golgi apparatus. Found in the perinuclear region and associates with ...		606657		577
Q09142 UniProt NPD GO	ORC2_SCHPO	Origin recognition complex subunit 2	0.71	-	cyt	0	Nucleus	nuclear origin of replication recognition c... [IDA]			535
P17208 UniProt NPD GO	PO4F1_MOUSE	POU domain, class 4, transcription factor 1 (Brain-specific homeobox/POU domain protein 3A) (Brn-3A) ...	0.71	+	nuc	0	Nucleus	nucleus [IDA]			421
Q01851 UniProt NPD GO	PO4F1_HUMAN	POU domain, class 4, transcription factor 1 (Brain-specific homeobox/POU domain protein 3A) (Brn-3A) ...	0.71	+	nuc	0	Nucleus		601632		423
Q60636 UniProt NPD GO	PRDM1_MOUSE	PR domain zinc finger protein 1 (PR domain-containing protein 1) (Beta-interferon gene positive-regu ...	0.71	-	nuc	0	Nucleus (By similarity)				856
P47240 UniProt NPD GO	PAX8_CANFA	Paired box protein Pax-8	0.71	-	nuc	0	Nucleus				459
Q96RD6 UniProt NPD GO	PANX2_HUMAN	Pannexin-2	0.71	-	nuc	4 *	Membrane; multi-pass membrane protein (Potential)		608421		633
Q12659 UniProt NPD GO	ARO1_PNECA	Pentafunctional AROM polypeptide [Includes: 3-dehydroquinate synthase (EC 4.2.3.4); 3-dehydroquinate ...	0.71	-	vac	0	Cytoplasm				1581
Q9CXG3 UniProt NPD GO	PPIL4_MOUSE	Peptidyl-prolyl cis-trans isomerase-like 4 (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin-like protei ...	0.71	+	nuc	0	Nucleus (By similarity)				492
Q9R0A0 UniProt NPD GO	PEX14_MOUSE	Peroxisomal membrane protein PEX14 (Peroxin-14) (Peroxisomal membrane anchor protein PEX14) (PTS1 re ...	0.71	-	nuc	1	Peroxisome; peroxisomal membrane; peripheral membrane protein; cytoplasmic side (By similarity)				376
Q07800 UniProt NPD GO	PSR1_YEAST	Phosphatase PSR1 (EC 3.1.3.-) (Plasma membrane sodium response protein 1)	0.71	-	mit	0	Cell membrane	plasma membrane [IDA]			427
Q92213 UniProt NPD GO	VPS34_CANAL	Phosphatidylinositol 3-kinase VPS34 (EC 2.7.1.137) (PtdIns-3-kinase VPS34) (PI3-kinase VPS34) (PI3K ...	0.71	-	nuc	0					1020
P70181 UniProt NPD GO	PI51B_MOUSE	Phosphatidylinositol-4-phosphate 5-kinase type-1 beta (EC 2.7.1.68) (Phosphatidylinositol-4-phosphat ...	0.71	-	nuc	0	Intracytoplasmic membrane (By similarity). Associated with membranes (By similarity)				539
Q5BMR2 UniProt NPD GO	PLD_PHYIN	Phospholipase D (EC 3.1.4.4) (PiPLD1)	0.71	+	end	3	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			1807
Q9M9W8 UniProt NPD GO	PLDP2_ARATH	Phospholipase D p2 (EC 3.1.4.4) (AtPLDp2) (Phospholipase D2 PHOX and PX containing domain) (Phosphol ...	0.71	-	cyt	0					1046
Q64649 UniProt NPD GO	KPB1_RAT	Phosphorylase b kinase regulatory subunit alpha, skeletal muscle isoform (Phosphorylase kinase alpha ...	0.71	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				1242
P70206 UniProt NPD GO	PLXA1_MOUSE	Plexin-A1 precursor (Plexin-1) (Plex 1)	0.71	-	end	1 *	Membrane; single-pass type I membrane protein (Potential)	plasma membrane [IC]			1894
O35730 UniProt NPD GO	RING1_MOUSE	Polycomb complex protein RING1 (RING finger protein 1) (Transcription repressor Ring1A)	0.71	-	nuc	0		nuclear body [IDA]			406
P27536 UniProt NPD GO	POST_XENLA	Posterior protein (xPO)	0.71	-	nuc	0					555
Q8QFV0 UniProt NPD GO	KCNT1_CHICK	Potassium channel subfamily T member 1 (Sequence-like a calcium-activated potassium channel subunit) ...	0.71	-	end	7	Membrane; multi-pass membrane protein (Potential)				1201
Q9UK17 UniProt NPD GO	KCND3_HUMAN	Potassium voltage-gated channel subfamily D member 3 (Voltage-gated potassium channel subunit Kv4.3) ...	0.71	-	end	6	Membrane; multi-pass membrane protein	voltage-gated potassium channel complex [TAS]	605411	1S1G	655
Q62897 UniProt NPD GO	KCND3_RAT	Potassium voltage-gated channel subfamily D member 3 (Voltage-gated potassium channel subunit Kv4.3) ...	0.71	-	end	6	Cell membrane; multi-pass membrane protein. Interaction with palmitoylated KCNIP2 and KCNIP3 enhance ...	integral to plasma membrane [IDA]			655
Q9Y3Q4 UniProt NPD GO	HCN4_HUMAN	Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4	0.71	-	nuc	2	Membrane; multi-pass membrane protein		605206		1203
Q9JKA7 UniProt NPD GO	HCN4_RAT	Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4	0.71	-	nuc	2	Membrane; multi-pass membrane protein	terminal button [IDA]			1198
P33411 UniProt NPD GO	PRP18_YEAST	Pre-mRNA-splicing factor 18	0.71	-	nuc	0	Nucleus	spliceosome complex [IDA] U4/U6 x U5 tri-snRNP complex [TAS]		1DVK	251
P34369 UniProt NPD GO	PRP8_CAEEL	Pre-mRNA-splicing factor 8 homolog	0.71	+	gol	0	Nucleus (By similarity)				2329
Q6BV91 UniProt NPD GO	PRP45_DEBHA	Pre-mRNA-splicing factor PRP45 (Pre-mRNA-processing protein 45)	0.71	-	nuc	0	Nucleus (By similarity)				341

You are viewing entries 13401 to 13450 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.