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
Q9I962 UniProt NPD GO	SMAD1_COTJA	Mothers against decapentaplegic homolog 1 (SMAD 1) (Mothers against DPP homolog 1) (Mad-related prot ...	0.54	-	nuc	0	Cytoplasm (By similarity). In the cytoplasm in the absence of ligand. Nucleus (By similarity). Migra ...	integral to membrane [ISS] intracellular [ISS] nucleus [ISS]			465
Q15797 UniProt NPD GO	SMAD1_HUMAN	Mothers against decapentaplegic homolog 1 (SMAD 1) (Mothers against DPP homolog 1) (Mad-related prot ...	0.54	-	nuc	0	Cytoplasm. In the cytoplasm in the absence of ligand. Nucleus. Migration to the nucleus when complex ...	integral to membrane [NAS] intracellular [NAS] nucleus [NAS]	601595	1KHU	465
Q9I8V2 UniProt NPD GO	SMAD1_BRARE	Mothers against decapentaplegic homolog 1 (SMAD 1) (Mothers against DPP homolog 1) (Smad1)	0.54	-	nuc	0	Cytoplasm (By similarity). In the cytoplasm in the absence of ligand. Nucleus (By similarity). Migra ...	nucleus [ISS]			472
Q15773 UniProt NPD GO	MLF2_HUMAN	Myeloid leukemia factor 2 (Myelodysplasia-myeloid leukemia factor 2)	0.54	-	nuc	1	Cytoplasm (By similarity). Nucleus (By similarity)		601401		248
Q866N2 UniProt NPD GO	MYOC_RABIT	Myocilin precursor (Trabecular meshwork-induced glucocorticoid response protein)	0.54	-	mit	0	Located preferentially in the ciliary rootlet and basal body of the connecting cilium of photorecept ...	cilium [NAS] extracellular space [ISS]			490
Q23978 UniProt NPD GO	MY31D_DROME	Myosin IA (MIA) (Brush border myosin IA) (BBMIA)	0.54	-	cyt	0	Cytoplasm. Protein shifts from the basolateral to apical domain in enterocytes and follicle cells				1011
Q62774 UniProt NPD GO	MYO1A_RAT	Myosin Ia (Brush border myosin I) (BBM-I) (BBMI) (Myosin I heavy chain) (MIHC) (Fragment)	0.54	-	cyt	0					842
Q5SYD0 UniProt NPD GO	MYO1D_MOUSE	Myosin Id	0.54	-	nuc	0					1006
Q63357 UniProt NPD GO	MYO1D_RAT	Myosin Id (Myosin heavy chain myr 4)	0.54	-	nuc	0		myosin [IDA]			1006
Q9NPC6 UniProt NPD GO	MYOZ2_HUMAN	Myozenin-2 (Calsarcin-1) (FATZ-related protein 2)	0.54	-	nuc	0	Colocalizes with ACTN1 and PPP3CA at the Z-line of heart and skeletal muscle (By similarity)	sarcomere [TAS]	605602		264
P16527 UniProt NPD GO	MARCS_CHICK	Myristoylated alanine-rich C-kinase substrate (MARCKS)	0.54	+	nuc	0					280
P26046 UniProt NPD GO	ACVS2_PENCH	N-(5-amino-5-carboxypentanoyl)-L-cysteinyl-D-valine synthase (EC 6.3.2.26) (Delta-(L-alpha-aminoadip ...	0.54	-	end	0					3791
Q86W24 UniProt NPD GO	NAL14_HUMAN	NACHT, LRR and PYD-containing protein 14 (Nucleotide-binding oligomerization domain protein 5)	0.54	-	nuc	0			609665		1093
P58058 UniProt NPD GO	NADK_MOUSE	NAD kinase (EC 2.7.1.23) (Poly(P)/ATP NAD kinase)	0.54	-	cyt	0		cytosol [ISS]			439
P21617 UniProt NPD GO	NGF_XENLA	Nerve growth factor precursor (NGF)	0.54	-	nuc	0	Secreted protein				231
O94856 UniProt NPD GO	NFASC_HUMAN	Neurofascin precursor	0.54	-	exc	1	Membrane; single-pass type I membrane protein		609145		1347
P16884 UniProt NPD GO	NFH_RAT	Neurofilament triplet H protein (200 kDa neurofilament protein) (Neurofilament heavy polypeptide) (N ...	0.54	-	nuc	0					1072
Q8NFZ3 UniProt NPD GO	NLGNY_HUMAN	Neuroligin-4, Y linked precursor (Neuroligin Y)	0.54	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)		400028		816
Q9QXK8 UniProt NPD GO	NEUU_MOUSE	Neuromedin U-23 precursor (NmU-23)	0.54	-	exc	0	Secreted protein				174
Q63634 UniProt NPD GO	NPY5R_RAT	Neuropeptide Y receptor type 5 (NPY5-R) (NPY-Y5 receptor) (Y5 receptor)	0.54	-	end	7	Membrane; multi-pass membrane protein				456
Q15761 UniProt NPD GO	NPY5R_HUMAN	Neuropeptide Y receptor type 5 (NPY5-R) (NPY-Y5 receptor) (Y5 receptor) (NPYY5)	0.54	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	602001		455
O73797 UniProt NPD GO	NT7_BRARE	Neurotrophin-7 precursor (NT-7) (zNT-7)	0.54	-	exc	0	Secreted protein				233
O42783 UniProt NPD GO	TREB_NEUCR	Neutral trehalase (EC 3.2.1.28) (Alpha,alpha-trehalase) (Alpha,alpha-trehalose glucohydrolase)	0.54	+	nuc	0	Cytoplasm (By similarity)				744
O76464 UniProt NPD GO	NFT1_DROME	Nitrilase and fragile histidine triad fusion protein NitFhit (NFT-1 protein) [Includes: Bis(5'-adeno ...	0.54	-	mit	0					460
O35710 UniProt NPD GO	NOCT_MOUSE	Nocturnin (CCR4 protein homolog)	0.54	-	mit	0					429
Q9UVL1 UniProt NPD GO	NHP6_CANAL	Nonhistone chromosomal protein 6	0.54	-	nuc	0	Nucleus (By similarity)				92
Q6BRB4 UniProt NPD GO	NHP6_DEBHA	Nonhistone chromosomal protein 6	0.54	-	nuc	0	Nucleus (By similarity)				92
Q803Q2 UniProt NPD GO	NDL1B_BRARE	Nuclear distribution protein nudE-like 1-B	0.54	-	nuc	0	Cytoplasm (By similarity). Centrosome (By similarity). Spindle (By similarity). Localizes to the int ...				344
Q9TXJ1 UniProt NPD GO	NHR59_CAEEL	Nuclear hormone receptor family member nhr-59	0.54	-	nuc	0	Nucleus (Potential)				416
P45446 UniProt NPD GO	RORB_RAT	Nuclear receptor ROR-beta (Nuclear receptor RZR-beta)	0.54	-	nuc	0	Nucleus (Probable)			1NQ7	459
Q9Y2X3 UniProt NPD GO	NOP5_HUMAN	Nucleolar protein NOP5 (Nucleolar protein 5) (NOP58)	0.54	+	nuc	0	Nucleus; nucleolus	nucleolus [TAS]			529
Q02629 UniProt NPD GO	NU100_YEAST	Nucleoporin NUP100/NSP100 (Nuclear pore protein NUP100/NSP100)	0.54	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side; nucleoplasmic side. Biased toward ...	nuclear pore [IDA]			959
P40477 UniProt NPD GO	NU159_YEAST	Nucleoporin NUP159 (Nuclear pore protein NUP159)	0.54	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side	nuclear pore [TAS]		1XIP	1460
Q32KV6 UniProt NPD GO	SIL1_BOVIN	Nucleotide exchange factor SIL1 precursor	0.54	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				462
Q4LBB9 UniProt NPD GO	OCTB2_DROME	Octopamine receptor beta-2R (DmOct-beta-2R) (DmOct-beta-12)	0.54	-	end	7	Membrane; multi-pass membrane protein (Potential)	integral to membrane [ISS]			536
Q9Y3B8 UniProt NPD GO	ORN_HUMAN	Oligoribonuclease, mitochondrial precursor (EC 3.1.-.-) (Small fragment nuclease) (RNA exonuclease 2 ...	0.54	-	cyt	0	Isoform 1: Mitochondrion. Isoform 2: Nucleus		607149		237
O88708 UniProt NPD GO	ORC4_MOUSE	Origin recognition complex subunit 4	0.54	-	mit	0	Nucleus				433
P31097 UniProt NPD GO	OSTP_RABIT	Osteopontin precursor (Bone sialoprotein-1) (Secreted phosphoprotein 1) (SPP-1) (OC-1)	0.54	-	exc	0	Secreted protein				311
P78380 UniProt NPD GO	OLR1_HUMAN	Oxidized low-density lipoprotein receptor 1 (Ox-LDL receptor 1) (Lectin-type oxidized LDL receptor 1 ...	0.54	-	nuc	1 *	Cell membrane; single-pass type II membrane protein. Secreted protein. A secreted form also exists	integral to plasma membrane [TAS] membrane fraction [TAS]	104300	1YXK	273
Q9BXB4 UniProt NPD GO	OSB11_HUMAN	Oxysterol-binding protein-related protein 11 (OSBP-related protein 11) (ORP-11)	0.54	-	nuc	0			606739		747
Q3T0C8 UniProt NPD GO	PDLI2_BOVIN	PDZ and LIM domain protein 2	0.54	-	nuc	0	Cytoplasm. Cytoskeleton. Localizes at the cytoskeleton. Colocalizes with beta-1 integrin (ITGB1) and ...				348
Q5KAW8 UniProt NPD GO	PPIL2_CRYNE	Peptidyl-prolyl cis-trans isomerase-like 2 (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin-60) (Cyclop ...	0.54	-	cyt	0	Nucleus (By similarity)				573
Q9JJK4 UniProt NPD GO	PEX3_RAT	Peroxisomal biogenesis factor 3 (Peroxin-3) (Peroxisomal assembly protein PEX3)	0.54	-	nuc	0	Peroxisome; peroxisomal membrane; multi-pass membrane protein	integral to membrane [TAS]			372
P41909 UniProt NPD GO	PXA1_YEAST	Peroxisomal long-chain fatty acid import protein 2 (Peroxisomal ABC transporter 1)	0.54	-	nuc	2	Peroxisome; peroxisomal membrane; multi-pass membrane protein	integral to peroxisomal membrane [IDA]			758
Q03181 UniProt NPD GO	PPARB_HUMAN	Peroxisome proliferator-activated receptor delta (PPAR-delta) (PPAR-beta) (Nuclear hormone receptor ...	0.54	+	cyt	0	Nucleus	nucleus [NAS]	600409	3GWX	441
Q25519 UniProt NPD GO	PRP2_MANSE	Phenoloxidase subunit 2 (EC 1.14.18.1) (proPO-p2)	0.54	-	cyt	0	Secreted protein	extracellular region [IDA]			694
Q9Y285 UniProt NPD GO	SYFA_HUMAN	Phenylalanyl-tRNA synthetase alpha chain (EC 6.1.1.20) (Phenylalanine--tRNA ligase alpha chain) (Phe ...	0.54	+	cyt	0	Cytoplasm (By similarity)	cytoplasm [TAS] soluble fraction [TAS]	602918		507
P40025 UniProt NPD GO	PHM8_YEAST	Phosphate metabolism protein 8	0.54	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			321
P42339 UniProt NPD GO	PI3K_ARATH	Phosphatidylinositol 3-kinase VPS34 (EC 2.7.1.137) (PtdIns-3-kinase VSP34) (PI3-kinase VPS34) (PI3K ...	0.54	-	cyt	0					814
P42347 UniProt NPD GO	PI3K1_SOYBN	Phosphatidylinositol 3-kinase, root isoform (EC 2.7.1.137) (PI3-kinase) (PtdIns-3-kinase) (PI3K) (SP ...	0.54	-	cyt	0					814

You are viewing entries 22651 to 22700 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.