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
P97300 UniProt NPD GO	NPTN_MOUSE	Neuroplastin precursor (Stromal cell-derived receptor 1) (SDR-1)	0.57	+	exc	1	Cell membrane; single-pass type I membrane protein (Potential)	integral to membrane of membrane fraction [ISS] postsynaptic membrane [ISS] presynaptic membrane [ISS]			281
P29475 UniProt NPD GO	NOS1_HUMAN	Nitric-oxide synthase, brain (EC 1.14.13.39) (NOS type I) (Neuronal NOS) (N-NOS) (nNOS) (Constitutiv ...	0.57	-	nuc	0	Sarcolemma; sarcolemmal membrane; peripheral membrane protein. In skeletal muscle, it is localized b ...	membrane fraction [TAS]	163731		1434
P12274 UniProt NPD GO	HMGN1_CHICK	Nonhistone chromosomal protein HMG-14B	0.57	-	nuc	0	Nucleus				102
P58797 UniProt NPD GO	NXF1_COTJA	Nuclear RNA export factor 1 (Tip-associating protein) (Tip-associated protein) (mRNA export factor T ...	0.57	-	nuc	0	Nucleus				616
Q5ZKH4 UniProt NPD GO	NDEL1_CHICK	Nuclear distribution protein nudE-like 1	0.57	-	nuc	0	Cytoplasm (By similarity). Centrosome (By similarity). Spindle (By similarity). Localizes to the int ...				343
Q66IZ7 UniProt NPD GO	NDL1B_XENLA	Nuclear distribution protein nudE-like 1-B	0.57	-	nuc	0	Cytoplasm (By similarity). Centrosome (By similarity). Spindle (By similarity). Localizes to the int ...				344
Q8R1B8 UniProt NPD GO	RORB_MOUSE	Nuclear receptor ROR-beta (Nuclear receptor RZR-beta)	0.57	-	nuc	0	Nucleus (Probable)				459
Q5R4C9 UniProt NPD GO	NRBF2_PONPY	Nuclear receptor-binding factor 2 (NRBF-2)	0.57	-	nuc	0	Nucleus. Cytoplasm (By similarity)				287
Q9M9X4 UniProt NPD GO	NFYA2_ARATH	Nuclear transcription factor Y subunit A-2 (AtNF-YA-2) (Transcriptional activator HAP2B)	0.57	-	nuc	0	Nucleus (Probable)				295
P70353 UniProt NPD GO	NFYC_MOUSE	Nuclear transcription factor Y subunit gamma (Nuclear transcription factor Y subunit C) (NF-YC) (CAA ...	0.57	+	nuc	0	Nucleus	transcription factor complex [IC]			335
Q62725 UniProt NPD GO	NFYC_RAT	Nuclear transcription factor Y subunit gamma (Nuclear transcription factor Y subunit C) (NF-YC) (CAA ...	0.57	+	nuc	0	Nucleus				335
Q924R9 UniProt NPD GO	NP1L3_RAT	Nucleosome assembly protein 1-like 3	0.57	+	nuc	0	Nucleus (By similarity)				536
Q7RTU3 UniProt NPD GO	OLIG3_HUMAN	Oligodendrocyte transcription factor 3 (Oligo3) (Basic helix-loop-helix domain-containing class B pr ...	0.57	-	nuc	0	Nucleus (By similarity)		609323		272
P13725 UniProt NPD GO	ONCM_HUMAN	Oncostatin M precursor (OSM)	0.57	-	exc	0	Secreted protein	extracellular space [TAS]	165095	1EVS	252
P61365 UniProt NPD GO	OSTN_RAT	Osteocrin precursor (Musclin)	0.57	-	exc	0	Secreted protein				132
Q9ESF1 UniProt NPD GO	OTOF_MOUSE	Otoferlin (Fer-1-like protein 2)	0.57	+	nuc	1	Membrane; single-pass type II membrane protein (By similarity)				1997
Q5VWM4 UniProt NPD GO	PRAM8_HUMAN	PRAME family member 8	0.57	-	mit	0					474
Q4I2M7 UniProt NPD GO	ERFB_GIBZE	Palmitoyltransferase ERF2 (EC 2.3.1.-) (DHHC cysteine-rich domain-containing protein ERF2) (Ras prot ...	0.57	-	nuc	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				679
Q5B3W7 UniProt NPD GO	ERFB_EMENI	Palmitoyltransferase erf2 (EC 2.3.1.-) (DHHC cysteine-rich domain-containing protein erf2) (Ras prot ...	0.57	-	nuc	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				601
Q4WUK1 UniProt NPD GO	PFA5_ASPFU	Palmitoyltransferase pfa5 (EC 2.3.1.-) (Protein fatty acyltransferase 5)	0.57	+	end	4 *	Membrane; multi-pass membrane protein (Potential)				446
Q9MUV9 UniProt NPD GO	FTSI_MESVI	Peptidoglycan synthetase ftsI homolog (EC 2.4.1.129) (Peptidoglycan glycosyltransferase)	0.57	-	mit	1 *	Membrane; single-pass membrane protein (Potential)				598
O60240 UniProt NPD GO	PLIN_HUMAN	Perilipin (PERI) (Lipid droplet-associated protein)	0.57	-	nuc	0	Lipid droplet surface-associated (By similarity)	lipid particle [NAS]	170290		522
Q03353 UniProt NPD GO	PER_DROMA	Period circadian protein (Fragments)	0.57	-	nuc	0	Nucleus (By similarity). Cytoplasm; perinuclear region (By similarity). Nuclear at specific periods ...				676
Q03354 UniProt NPD GO	PER_DROSE	Period circadian protein (Fragments)	0.57	-	nuc	0	Nucleus (By similarity). Cytoplasm; perinuclear region (By similarity). Nuclear at specific periods ...				661
Q03355 UniProt NPD GO	PER_DROSI	Period circadian protein (Fragments)	0.57	-	nuc	0	Nucleus (By similarity). Cytoplasm; perinuclear region (By similarity). Nuclear at specific periods ...				656
Q96520 UniProt NPD GO	PER12_ARATH	Peroxidase 12 precursor (EC 1.11.1.7) (Atperox P12) (PRXR6) (ATP4a)	0.57	-	mit	1 *	Or: Secreted protein (Probable). Or: Vacuole (Probable). Carboxy-terminal extension appears to targe ...				358
Q9Y5Y5 UniProt NPD GO	PEX16_HUMAN	Peroxisomal membrane protein PEX16 (Peroxin-16) (Peroxisomal biogenesis factor 16)	0.57	-	nuc	0	Peroxisome; peroxisomal membrane; multi-pass membrane protein	peroxisome [TAS]	603360		336
Q6FP25 UniProt NPD GO	PEX22_CANGA	Peroxisome assembly protein 22 (Peroxin-22)	0.57	-	mit	1 *	Peroxisome; peroxisomal membrane; single-pass membrane protein (By similarity)				174
O35904 UniProt NPD GO	PK3CD_MOUSE	Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit delta isoform (EC 2.7.1.153) (PI3-k ...	0.57	-	nuc	0					1043
P40345 UniProt NPD GO	PDAT_YEAST	Phospholipid:diacylglycerol acyltransferase (EC 2.3.1.158) (PDAT)	0.57	+	mit	1		endoplasmic reticulum [TAS]			661
P12798 UniProt NPD GO	KPBB_RABIT	Phosphorylase b kinase regulatory subunit beta (Phosphorylase kinase subunit beta)	0.57	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				1092
P18917 UniProt NPD GO	PRP4_BOVIN	Placental prolactin-related protein 4 precursor (PLP-III)	0.57	-	cyt	0	Secreted protein				239
P30061 UniProt NPD GO	RR18_EPIVI	Plastid 30S ribosomal protein S18	0.57	-	mit	0	Plastid				92
Q9TJR1 UniProt NPD GO	RK20_PROWI	Plastid 50S ribosomal protein L20	0.57	-	nuc	0	Plastid				114
Q8CIB5 UniProt NPD GO	PKHC1_MOUSE	Pleckstrin homology domain-containing family C member 1	0.57	+	cyt	0	Cytoplasm; cell cortex (By similarity). Within actin stress fibers at cell-ECM focal adhesion sites ...				680
Q62392 UniProt NPD GO	PHLA1_MOUSE	Pleckstrin homology-like domain family A member 1 (T-cell death-associated gene 51 protein) (Proline ...	0.57	-	nuc	0	Cytoplasm (By similarity). Colocalizes with intracellular vesicles. Nucleus; nucleolus (By similarit ...				261
P79281 UniProt NPD GO	PTN_PIG	Pleiotrophin precursor (PTN) (Pleiotrophic factor beta) (PTF-beta)	0.57	-	nuc	1 *	Secreted protein (By similarity)				168
Q11208 UniProt NPD GO	PARP_SARPE	Poly [ADP-ribose] polymerase (EC 2.4.2.30) (PARP) (ADPRT) (NAD(+) ADP-ribosyltransferase) (Poly[ADP- ...	0.57	-	nuc	0	Nucleus				996
Q9LG26 UniProt NPD GO	PARN_ARATH	Poly(A)-specific ribonuclease PARN (EC 3.1.13.4) (Polyadenylate-specific ribonuclease) (AtPARN)	0.57	-	gol	0	Nucleus. Cytoplasm. Only cytoplasmic (Ref.3)				689
Q5EA41 UniProt NPD GO	GALT6_BOVIN	Polypeptide N-acetylgalactosaminyltransferase 6 (EC 2.4.1.41) (Protein-UDP acetylgalactosaminyltrans ...	0.57	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				622
Q9NSA2 UniProt NPD GO	KCND1_HUMAN	Potassium voltage-gated channel subfamily D member 1 (Voltage-gated potassium channel subunit Kv4.1) ...	0.57	-	end	5	Membrane; multi-pass membrane protein		300281		647
Q9ULR0 UniProt NPD GO	ISY1_HUMAN	Pre-mRNA-splicing factor ISY1 homolog	0.57	-	nuc	0	Nucleus (Potential)				331
P51381 UniProt NPD GO	SECA_PORPU	Preprotein translocase secA subunit	0.57	-	nuc	0	Plastid; chloroplast				884
Q2NL22 UniProt NPD GO	DDX48_BOVIN	Probable ATP-dependent RNA helicase DDX48 (EC 3.6.1.-) (DEAD box protein 48)	0.57	-	cyt	0	Nucleus (By similarity)				410
Q9VRL2 UniProt NPD GO	GOSR2_DROME	Probable Golgi SNAP receptor complex member 2	0.57	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (Potential)				216
Q9VSR3 UniProt NPD GO	ORB2_DROME	Probable RNA-binding protein orb2	0.57	-	nuc	0					704
Q9V4T5 UniProt NPD GO	CP4E1_DROME	Probable cytochrome P450 4e1 (EC 1.14.-.-) (CYPIVE1)	0.57	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				531
Q9V557 UniProt NPD GO	CP4P2_DROME	Probable cytochrome P450 4p2 (EC 1.14.-.-) (CYPIVP2)	0.57	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				520
Q9FJB5 UniProt NPD GO	RP8L3_ARATH	Probable disease resistance RPP8-like protein 3	0.57	-	cyt	0					901
Q4WVA0 UniProt NPD GO	NUF2_ASPFU	Probable kinetochore protein nuf2	0.57	-	nuc	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				439

You are viewing entries 20901 to 20950 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.