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
Q05752 UniProt NPD GO	NDUA7_BOVIN	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqui ...	0.45	-	nuc	0	Mitochondrion; mitochondrial inner membrane; matrix side	mitochondrial inner membrane [IDA] mitochondrion [TAS]			112
Q02369 UniProt NPD GO	NDUB9_BOVIN	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiquin ...	0.45	-	mit	0	Mitochondrion; mitochondrial inner membrane; matrix side				178
Q9Y6M9 UniProt NPD GO	NDUB9_HUMAN	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiquin ...	0.45	-	nuc	0	Mitochondrion; mitochondrial inner membrane; matrix side	mitochondrial inner membrane [TAS]	601445		178
Q9GME8 UniProt NPD GO	NKG2C_PANTR	NKG2-C type II integral membrane protein (NKG2-C-activating NK receptor) (NK cell receptor C) (CD159 ...	0.45	-	nuc	1	Membrane; single-pass type II membrane protein				233
O08721 UniProt NPD GO	UNC5A_RAT	Netrin receptor UNC5A precursor (Unc-5 homolog A) (Unc-5 homolog 1)	0.45	-	end	2	Cell membrane; single-pass type I membrane protein. The interaction with PRKCABP regulates its surfa ...				898
Q9Y4C0 UniProt NPD GO	NRX3A_HUMAN	Neurexin-3-alpha precursor (Neurexin III-alpha)	0.45	-	end	1 *	Membrane; single-pass type I membrane protein (Potential)	integral to plasma membrane [TAS]	600567		1541
Q99K10 UniProt NPD GO	NLGN1_MOUSE	Neuroligin-1 precursor	0.45	-	cyt	1 *	Cell membrane; single-pass type I membrane protein (By similarity). Enriched in synaptic plasma memb ...	integral to plasma membrane [IMP] synapse [ISS]			843
Q05531 UniProt NPD GO	NIA_USTMA	Nitrate reductase [NADPH] (EC 1.7.1.3) (NR)	0.45	-	cyt	0					908
Q9YHV3 UniProt NPD GO	NOGG3_BRARE	Noggin-3 precursor	0.45	-	nuc	0	Secreted protein				223
Q06568 UniProt NPD GO	NDE1_YEAST	Nuclear distribution protein nudE homolog 1 (Nuclear distribution protein nudE-like 1)	0.45	-	nuc	0	Nucleus. Also localizes to the plus ends of cytoplasmic microtubules, and this requires PAC1	cytoplasm [IDA] cytoplasmic microtubule [IDA] nucleus [IDA]			189
P14057 UniProt NPD GO	NFIL_PIG	Nuclear factor 1 (NF-I) (CCAAT-box-binding transcription factor) (CTF) (TGGCA-binding protein) (Frag ...	0.45	+	cyt	0	Nucleus				231
Q6F3J0 UniProt NPD GO	NFKB1_CANFA	Nuclear factor NF-kappa-B p105 subunit [Contains: Nuclear factor NF-kappa-B p50 subunit]	0.45	+	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Nuclear, but also found in the cytoplasm in an i ...				972
O17683 UniProt NPD GO	NH167_CAEEL	Nuclear hormone receptor family member nhr-167	0.45	-	cyt	0	Nucleus (Potential)				343
Q90X44 UniProt NPD GO	NRF1_BRARE	Nuclear respiratory factor 1 (Nrf-1) (Not really finished protein)	0.45	-	cyt	0	Nucleus				514
P25210 UniProt NPD GO	NFYB_PETMA	Nuclear transcription factor Y subunit beta (Nuclear transcription factor Y subunit B) (NF-YB) (CAAT ...	0.45	-	nuc	0	Nucleus				209
Q8J109 UniProt NPD GO	NOG2_CRYNV	Nucleolar GTP-binding protein 2	0.45	-	cyt	0	Nucleus; nucleolus (By similarity)				720
Q06512 UniProt NPD GO	NOC4_YEAST	Nucleolar complex protein 4 (U3 small nucleolar RNA-associated protein 19) (U3 snoRNA-associated pro ...	0.45	-	cyt	0	Nucleus; nucleolus	Noc4p-Nop14p complex [IPI] nucleolus [IDA] nucleus [IDA] small nucleolar ribonucleoprotein complex [IPI]			552
Q9UTK4 UniProt NPD GO	NU189_SCHPO	Nucleoporin nup189 (Nuclear pore protein nup189)	0.45	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex (By similarity)	Nup107-160 complex [IDA]			1778
Q8CIC2 UniProt NPD GO	NUPL2_MOUSE	Nucleoporin-like 2 (NLP-1)	0.45	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side (By similarity). Excluded from the ...				420
Q9VBV5 UniProt NPD GO	SIL1_DROME	Nucleotide exchange factor SIL1 precursor	0.45	-	exc	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)	endoplasmic reticulum [ISS]			429
Q08199 UniProt NPD GO	SIL1_YEAST	Nucleotide exchange factor SIL1 precursor (Protein SLS1)	0.45	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum lumen	endoplasmic reticulum [IPI]			421
Q63912 UniProt NPD GO	OMGP_MOUSE	Oligodendrocyte-myelin glycoprotein precursor	0.45	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				440
Q9H668 UniProt NPD GO	OBFC1_HUMAN	Oligonucleotide/oligosaccharide-binding fold-containing protein 1	0.45	-	mit	0					368
P14287 UniProt NPD GO	OSTP_PIG	Osteopontin precursor (Bone sialoprotein-1) (Secreted phosphoprotein 1) (SPP-1)	0.45	-	exc	0	Secreted protein	extracellular matrix (sensu Metazoa) [ISS] extracellular region [ISS]			303
P79391 UniProt NPD GO	OLR1_BOVIN	Oxidized low-density lipoprotein receptor 1 (Ox-LDL receptor 1) (Lectin-type oxidized LDL receptor 1 ...	0.45	-	nuc	1 *	Cell membrane; single-pass type II membrane protein. Secreted protein. A secreted form also exists				270
P29146 UniProt NPD GO	NECA_HYDAT	PC3-like endoprotease variant A precursor (EC 3.4.21.-) (SPC3)	0.45	-	exc	1 *					793
Q64693 UniProt NPD GO	OBF1_MOUSE	POU domain class 2-associating factor 1 (B-cell-specific coactivator OBF-1) (OCT-binding factor 1) ( ...	0.45	-	nuc	0	Nucleus				256
Q9NQW5 UniProt NPD GO	PRDM7_HUMAN	PR domain zinc finger protein 7 (PR domain-containing protein 7)	0.45	-	nuc	0	Nucleus (Potential)		609759		407
Q4IMZ7 UniProt NPD GO	PFA4_GIBZE	Palmitoyltransferase PFA4 (EC 2.3.1.-) (Protein fatty acyltransferase 4)	0.45	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				437
Q8L5Y9 UniProt NPD GO	PANK2_ARATH	Pantothenate kinase 2 (EC 2.7.1.33) (Pantothenic acid kinase 2)	0.45	-	cyt	0					870
Q9JK83 UniProt NPD GO	PAR6B_MOUSE	Partitioning defective 6 homolog beta (PAR-6 beta) (PAR-6B)	0.45	-	nuc	0	Cytoplasm. Cell membrane. Colocalizes with active form of CDC42 or RAC1 at membrane ruffles. Cell me ...	apical part of cell [IDA] cell cortex [IDA] nucleus [IDA] plasma membrane [ISS] tight junction [ISS]		1NF3	371
Q5BIN5 UniProt NPD GO	PIN1_BOVIN	Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (EC 5.2.1.8) (Rotamase Pin1) (PPIase Pin1)	0.45	-	nuc	0	Nucleus (By similarity)				163
Q13526 UniProt NPD GO	PIN1_HUMAN	Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (EC 5.2.1.8) (Rotamase Pin1) (PPIase Pin1)	0.45	-	nuc	0	Nucleus	nucleus [TAS]	601052	2F21	163
Q8CGN5 UniProt NPD GO	PLIN_MOUSE	Perilipin (PERI) (Lipid droplet-associated protein)	0.45	-	nuc	0	Lipid droplet surface-associated (By similarity)	lipid particle [IDA]			517
Q96518 UniProt NPD GO	PER16_ARATH	Peroxidase 16 precursor (EC 1.11.1.7) (Atperox P16) (ATP22a)	0.45	-	exc	1 *	Secreted protein (By similarity)				323
Q9LVL1 UniProt NPD GO	PER68_ARATH	Peroxidase 68 precursor (EC 1.11.1.7) (Atperox P68)	0.45	-	exc	1 *	Secreted protein (By similarity)				325
Q9FJZ9 UniProt NPD GO	PER72_ARATH	Peroxidase 72 precursor (EC 1.11.1.7) (Atperox P72) (PRXR8) (ATP6a)	0.45	-	exc	1 *	Secreted protein (By similarity)				336
Q759H4 UniProt NPD GO	PEX3_ASHGO	Peroxisomal biogenesis factor 3 (Peroxin-3)	0.45	-	mit	1 *	Peroxisome; peroxisomal membrane; multi-pass membrane protein (By similarity)				446
P56589 UniProt NPD GO	PEX3_HUMAN	Peroxisomal biogenesis factor 3 (Peroxin-3) (Peroxisomal assembly protein PEX3)	0.45	-	mit	0	Peroxisome; peroxisomal membrane; multi-pass membrane protein	integral to plasma membrane [TAS] peroxisome [TAS]	603164		373
O09012 UniProt NPD GO	PEX5_MOUSE	Peroxisomal targeting signal 1 receptor (Peroxisome receptor 1) (Peroxisomal C-terminal targeting si ...	0.45	-	cyt	0	Cytoplasm. Peroxisome; peroxisomal membrane; peripheral membrane protein. Its distribution appears t ...				639
Q6FM42 UniProt NPD GO	PEX5_CANGA	Peroxisomal targeting signal receptor (Peroxin-5) (PTS1 receptor)	0.45	-	nuc	0	Cytoplasm (By similarity). Peroxisome; peroxisomal membrane; peripheral membrane protein (By similar ...				590
Q9SYU4 UniProt NPD GO	PEX10_ARATH	Peroxisome assembly protein 10 (Peroxin-10) (AthPEX10) (Pex10p) (PER8)	0.45	-	mit	0	Peroxisome; peroxisomal membrane; peripheral membrane protein (Potential)				381
Q4U3Q4 UniProt NPD GO	PPARG_CANFA	Peroxisome proliferator-activated receptor gamma (PPAR-gamma)	0.45	+	cyt	0	Nucleus (By similarity)				505
Q27451 UniProt NPD GO	PRP1_BOMMO	Phenoloxidase subunit 1 precursor (EC 1.14.18.1) (Tyrosinase 1) (PO 1)	0.45	-	cyt	0	Secreted protein	extracellular region [TAS]			685
Q12498 UniProt NPD GO	PRM4_YEAST	Pheromone-regulated membrane protein 4	0.45	-	nuc	1 *	Membrane; single-pass membrane protein (Potential)				284
P41686 UniProt NPD GO	PHOS_FELCA	Phosducin (PHD) (33 kDa phototransducing protein)	0.45	-	nuc	0	Outer and inner segments of the rod cells (By similarity)				245
Q75LR2 UniProt NPD GO	AROF_ORYSA	Phospho-2-dehydro-3-deoxyheptonate aldolase 1, chloroplast precursor (EC 2.5.1.54) (Phospho-2-keto-3 ...	0.45	+	mit	0	Plastid; chloroplast (Potential)				554
P14843 UniProt NPD GO	AROF_YEAST	Phospho-2-dehydro-3-deoxyheptonate aldolase, phenylalanine-inhibited (EC 2.5.1.54) (Phospho-2-keto-3 ...	0.45	-	nuc	0		cytoplasm [IDA] mitochondrion [IDA] nucleus [IDA]			370
Q6R2V6 UniProt NPD GO	CAPP2_CHLRE	Phosphoenolpyruvate carboxylase 2 (EC 4.1.1.31) (PEP carboxylase 2) (PEPCase 2) (PEPC 2)	0.45	+	cyt	0	Cytoplasm (By similarity)				1221
Q02074 UniProt NPD GO	PYG_GALSU	Phycobilisome rod-core linker polypeptide cpcG	0.45	-	cyt	0	Plastid; chloroplast				242

You are viewing entries 28451 to 28500 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.