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
P49206 UniProt NPD GO	RS26_ARATH	40S ribosomal protein S26	0.58	-	nuc	0					131
P47839 UniProt NPD GO	RS7_SALSA	40S ribosomal protein S7 (Fragment)	0.58	-	mit	0					44
O49885 UniProt NPD GO	RL13A_LUPLU	60S ribosomal protein L13a	0.58	+	cyt	0					205
Q5EAD6 UniProt NPD GO	RL15_BOVIN	60S ribosomal protein L15	0.58	-	nuc	0					203
Q7T3N8 UniProt NPD GO	RL15_CTEID	60S ribosomal protein L15	0.58	-	nuc	0					203
P61313 UniProt NPD GO	RL15_HUMAN	60S ribosomal protein L15	0.58	-	nuc	0			604174		203
Q7T3N2 UniProt NPD GO	RL15_MONAL	60S ribosomal protein L15	0.58	-	nuc	0					203
Q9CZM2 UniProt NPD GO	RL15_MOUSE	60S ribosomal protein L15	0.58	-	nuc	0					203
Q7T3N1 UniProt NPD GO	RL15_MYLPI	60S ribosomal protein L15	0.58	-	nuc	0					203
Q5NVE0 UniProt NPD GO	RL15_PONPY	60S ribosomal protein L15	0.58	-	nuc	0					203
P61314 UniProt NPD GO	RL15_RAT	60S ribosomal protein L15	0.58	-	nuc	0					203
Q7T2N4 UniProt NPD GO	RL15_SILME	60S ribosomal protein L15	0.58	-	nuc	0					203
Q7T3M9 UniProt NPD GO	RL15_SINKN	60S ribosomal protein L15	0.58	-	nuc	0					203
O65050 UniProt NPD GO	RL15A_PICMA	60S ribosomal protein L15-1	0.58	-	nuc	0					204
P35267 UniProt NPD GO	RL172_HORVU	60S ribosomal protein L17-2	0.58	-	nuc	0					172
P78946 UniProt NPD GO	RL26_SCHPO	60S ribosomal protein L26	0.58	-	nuc	0					126
P17078 UniProt NPD GO	RL35_RAT	60S ribosomal protein L35	0.58	-	nuc	0					122
Q9M3D2 UniProt NPD GO	RL353_ARATH	60S ribosomal protein L35-3	0.58	-	nuc	0					123
Q9P836 UniProt NPD GO	RL37_CANAL	60S ribosomal protein L37 (Fragment)	0.58	-	mit	0					88
P49166 UniProt NPD GO	RL37A_YEAST	60S ribosomal protein L37-A (L35) (YP55)	0.58	-	mit	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]		1K5Y	87
P04650 UniProt NPD GO	RL39_YEAST	60S ribosomal protein L39 (L46) (YL40)	0.58	-	mit	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]			50
Q96EH5 UniProt NPD GO	RL39L_HUMAN	60S ribosomal protein L39-like (L39-2)	0.58	-	mit	0		cytosolic large ribosomal subunit (sensu Eu... [NAS]	607547		50
P19232 UniProt NPD GO	RL40_ARATH	60S ribosomal protein L40 (CEP52)	0.58	-	nuc	0					52
P49632 UniProt NPD GO	RL40_CAEEL	60S ribosomal protein L40 (CEP52)	0.58	-	nuc	0					52
P46937 UniProt NPD GO	YAP1_HUMAN	65 kDa Yes-associated protein (YAP65)	0.58	-	nuc	0			606608	1K9R	454
Q60662 UniProt NPD GO	AKAP4_MOUSE	A-kinase anchor protein 4 precursor (Major fibrous sheath protein) (FSC1) (AKAP82) (p82)	0.58	-	nuc	0		flagellum (sensu Eukaryota) [IDA]			849
Q9UKQ2 UniProt NPD GO	ADA28_HUMAN	ADAM 28 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase domain 28) (Metalloproteinase-l ...	0.58	-	exc	1	Isoform 1: Cell membrane; single-pass type I membrane protein. Isoform 2: Secreted protein		606188		775
P79331 UniProt NPD GO	ATS2_BOVIN	ADAMTS-2 precursor (EC 3.4.24.14) (A disintegrin and metalloproteinase with thrombospondin motifs 2) ...	0.58	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				1205
Q8R0H9 UniProt NPD GO	GGA1_MOUSE	ADP-ribosylation factor-binding protein GGA1 (Golgi-localized, gamma ear-containing, ARF-binding pro ...	0.58	-	nuc	0	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; peripheral membrane protein (By ...				635
P17426 UniProt NPD GO	AP2A1_MOUSE	AP-2 complex subunit alpha-1 (Adapter-related protein complex 2 alpha-1 subunit) (Alpha-adaptin A) ( ...	0.58	-	cyt	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...	AP-2 adaptor complex [ISS] clathrin coat of trans-Golgi network vesicle [ISS] membrane coat [IDA] secretory granule [TAS]			977
Q04412 UniProt NPD GO	AGE1_YEAST	ARF GAP effector protein 1 (ADP-ribosylation factor GTPase-activating protein effector protein 1) (S ...	0.58	-	nuc	0	Cytoplasm	cytoplasm [IDA]			482
Q9JJR7 UniProt NPD GO	ASCL3_MOUSE	Achaete-scute homolog 3 (bHLH transcriptional regulator Sgn-1) (Mash-3)	0.58	-	nuc	0	Nucleus	nucleus [IDA] transcription factor complex [IPI]			174
Q5ZJA4 UniProt NPD GO	ARP5_CHICK	Actin-related protein 5	0.58	-	cyt	0					611
Q9H981 UniProt NPD GO	ARP8_HUMAN	Actin-related protein 8	0.58	-	nuc	0					624
Q9JKV1 UniProt NPD GO	ADRM1_MOUSE	Adhesion-regulating molecule 1 precursor (110 kDa cell membrane glycoprotein) (Gp110) (ARM-1)	0.58	-	nuc	0					407
Q90734 UniProt NPD GO	ACTN4_CHICK	Alpha-actinin-4 (Non-muscle alpha-actinin 4) (F-actin cross linking protein)	0.58	-	cyt	0					904
P49066 UniProt NPD GO	FETA_HORSE	Alpha-fetoprotein precursor (Alpha-fetoglobulin) (Alpha-1-fetoprotein)	0.58	-	exc	0	Secreted protein				609
P39192 UniProt NPD GO	ALU5_HUMAN	Alu subfamily SC sequence contamination warning entry	0.58	-	exc	0					585
Q6PFT9 UniProt NPD GO	AB1IP_BRARE	Amyloid beta A4 precursor protein-binding family B member 1-interacting protein (APBB1-interacting p ...	0.58	-	nuc	0	Cell membrane; peripheral membrane protein (By similarity)				646
Q12440 UniProt NPD GO	APC2_YEAST	Anaphase-promoting complex subunit 2	0.58	-	cyt	0	Cytoplasm. Nucleus	anaphase-promoting complex [TAS]		1LDD	853
Q9UKU9 UniProt NPD GO	ANGL2_HUMAN	Angiopoietin-related protein 2 precursor (Angiopoietin-like 2)	0.58	-	exc	0	Secreted protein	extracellular space [TAS]	605001		493
O43827 UniProt NPD GO	ANGL7_HUMAN	Angiopoietin-related protein 7 precursor (Angiopoietin-like 7) (Angiopoietin-like factor) (Cornea-de ...	0.58	-	nuc	1 *	Secreted protein (Probable)				346
Q8R0I0 UniProt NPD GO	ACE2_MOUSE	Angiotensin-converting enzyme 2 precursor (EC 3.4.17.-) (ACE-related carboxypeptidase)	0.58	-	end	1	Cell membrane; single-pass type I membrane protein (By similarity). Processed form: Secreted protein ...				805
Q8NAG6 UniProt NPD GO	ANR41_HUMAN	Ankyrin repeat domain-containing protein 41	0.58	-	nuc	0					575
P28794 UniProt NPD GO	MBP1_MAIZE	Antimicrobial peptide MBP-1	0.58	-	nuc	0	Secreted protein				33
Q9BGQ0 UniProt NPD GO	APTX_MACFA	Aprataxin homolog (Forkhead-associated domain histidine triad-like protein) (FHA-HIT)	0.58	+	cyt	0	Nucleus (By similarity). Upon genotoxic stress, it colocalizes with XRCC1 at sites of DNA damage (By ...				356
O96539 UniProt NPD GO	ATE1_DROME	Arginyl-tRNA--protein transferase 1 (EC 2.3.2.8) (R-transferase 1) (Arginyltransferase 1) (Arginine- ...	0.58	-	nuc	0					484
Q9NVT9 UniProt NPD GO	ARMC1_HUMAN	Armadillo repeat-containing protein 1	0.58	-	nuc	0					282
P55789 UniProt NPD GO	ALR_HUMAN	Augmenter of liver regeneration (hERV1 protein)	0.58	-	nuc	0			600924		125
Q5BH90 UniProt NPD GO	ATG16_EMENI	Autophagy protein 16	0.58	-	nuc	0	Vacuole (By similarity). Cytoplasmic vesicle (By similarity). Vesicular and vacuolar. Found in punct ...				202

You are viewing entries 20001 to 20050 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.