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
Q8N554 UniProt NPD GO	ZF276_HUMAN	Zinc finger protein 276 homolog (Zfp-276)	0.65	-	nuc	0	Nucleus (Potential)		608460		539
Q9VAU9 UniProt NPD GO	ZN330_DROME	Zinc finger protein 330 homolog (Nucleolar autoantigen 36 homolog)	0.65	-	nuc	0	Nucleus (By similarity). Nucleus; nucleolus (By similarity). Predominantly expressed in the nucleolu ...	chromosome, pericentric region [ISS] midbody [ISS] nucleolus [ISS]			315
Q8TAF7 UniProt NPD GO	ZN461_HUMAN	Zinc finger protein 461 (Gonadotropin-inducible transcription repressor 1) (GIOT-1)	0.65	-	nuc	0	Nucleus (Probable)		608640		563
Q7Z7K2 UniProt NPD GO	ZN467_HUMAN	Zinc finger protein 467	0.65	-	nuc	0	Nucleus (By similarity)				595
Q9Y2H8 UniProt NPD GO	ZN510_HUMAN	Zinc finger protein 510	0.65	-	nuc	0	Nucleus (Probable)				683
Q7Z398 UniProt NPD GO	ZN550_HUMAN	Zinc finger protein 550	0.65	+	nuc	0	Nucleus (Probable)				422
Q80VM4 UniProt NPD GO	ZN759_MOUSE	Zinc finger protein 579	0.65	+	nuc	0	Nucleus (Potential)				562
Q6PF04 UniProt NPD GO	ZN613_HUMAN	Zinc finger protein 613	0.65	-	nuc	0	Nucleus (Probable)				617
Q8IWY8 UniProt NPD GO	ZN690_HUMAN	Zinc finger protein 690	0.65	-	nuc	0	Nucleus (Probable)				851
Q8NBF1 UniProt NPD GO	GLIS1_HUMAN	Zinc finger protein GLIS1 (GLI-similar 1)	0.65	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			620
Q8CH34 UniProt NPD GO	ZP4_RAT	Zona pellucida sperm-binding protein 4 precursor (Zona pellucida sperm-binding protein B)	0.65	-	exc	1	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein; extracellular ...				545
P34099 UniProt NPD GO	KAPC_DICDI	cAMP-dependent protein kinase catalytic subunit (EC 2.7.11.11)	0.65	-	nuc	0					648
O77746 UniProt NPD GO	PDE5A_CANFA	cGMP-specific 3',5'-cyclic phosphodiesterase (EC 3.1.4.35) (CGB-PDE) (cGMP-binding cGMP-specific pho ...	0.65	-	cyt	0	PDE5A1 and PDE5A2 are located mostly to soluble cellular fractions and some to particulate cellular ...				865
Q68FX5 UniProt NPD GO	SNPC2_RAT	snRNA-activating protein complex subunit 2 (SNAPc subunit 2) (snRNA-activating protein complex 45 kD ...	0.65	+	nuc	0	Nucleus (By similarity)				359
P36048 UniProt NPD GO	SN114_YEAST	114 kDa U5 small nuclear ribonucleoprotein component (GIN10 protein)	0.64	-	nuc	0	Nucleus	snRNP U5 [IPI] U4/U6 x U5 tri-snRNP complex [IDA]			1008
P29728 UniProt NPD GO	OAS2_HUMAN	2'-5'-oligoadenylate synthetase 2 (EC 2.7.7.-) ((2-5')oligo(A) synthetase 2) (2-5A synthetase 2) (p6 ...	0.64	-	cyt	0	Mitochondrion. Nucleus. Microsome. Associated with different subcellular fractions such as mitochond ...	membrane [TAS] microsome [TAS]	603350		726
P11960 UniProt NPD GO	ODBA_RAT	2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial precursor (EC 1.2.4.4) (Branched-chain a ...	0.64	-	mit	0	Mitochondrion; mitochondrial matrix	alpha-ketoglutarate dehydrogenase complex (... [ISS] mitochondrion [ISS]			441
Q28181 UniProt NPD GO	CNGB1_BOVIN	240 kDa protein of rod photoreceptor CNG-channel [Contains: Glutamic acid-rich protein (GARP); Cycli ...	0.64	-	nuc	2	Membrane; multi-pass membrane protein				1394
Q9D8W5 UniProt NPD GO	PSD12_MOUSE	26S proteasome non-ATPase regulatory subunit 12 (26S proteasome regulatory subunit p55)	0.64	-	cyt	0					455
Q2TBI6 UniProt NPD GO	RM32_BOVIN	39S ribosomal protein L32, mitochondrial precursor (L32mt) (MRP-L32)	0.64	-	nuc	0	Mitochondrion (By similarity)	mitochondrial ribosome [ISS]			188
Q9BYC8 UniProt NPD GO	RM32_HUMAN	39S ribosomal protein L32, mitochondrial precursor (L32mt) (MRP-L32)	0.64	-	nuc	0	Mitochondrion	mitochondrial inner membrane [ISS] mitochondrial ribosome [NAS]			188
P20342 UniProt NPD GO	RS15_XENLA	40S ribosomal protein S15 (RIG protein)	0.64	-	nuc	0					144
P70066 UniProt NPD GO	RS15_XIPMA	40S ribosomal protein S15 (RIG protein)	0.64	-	nuc	0					145
P33444 UniProt NPD GO	RS3A_CATRO	40S ribosomal protein S3a (CYC07 protein)	0.64	-	nuc	0	Cytoplasm				259
Q9FJP3 UniProt NPD GO	RK29_ARATH	50S ribosomal protein L29, chloroplast precursor	0.64	-	mit	0	Plastid; chloroplast				173
Q7T3N6 UniProt NPD GO	RL15_HYPMO	60S ribosomal protein L15	0.64	-	nuc	0					203
Q7SDU2 UniProt NPD GO	RL24_NEUCR	60S ribosomal protein L24	0.64	-	nuc	0					156
Q6C4U6 UniProt NPD GO	RL24_YARLI	60S ribosomal protein L24	0.64	-	nuc	0					155
P61257 UniProt NPD GO	RL26_BOVIN	60S ribosomal protein L26	0.64	-	nuc	0					145
P61254 UniProt NPD GO	RL26_HUMAN	60S ribosomal protein L26	0.64	-	nuc	0			603704		145
P61256 UniProt NPD GO	RL26_MACFA	60S ribosomal protein L26	0.64	-	nuc	0					145
P61255 UniProt NPD GO	RL26_MOUSE	60S ribosomal protein L26 (Silica-induced gene 20 protein) (SIG-20)	0.64	-	nuc	0					145
Q9FE65 UniProt NPD GO	RL342_ARATH	60S ribosomal protein L34-2	0.64	-	mit	0					119
Q5DVH6 UniProt NPD GO	RL35_PLAFE	60S ribosomal protein L35	0.64	-	nuc	0					122
Q6QMZ4 UniProt NPD GO	RL6_CHILA	60S ribosomal protein L6	0.64	+	nuc	0					287
Q8BMI3 UniProt NPD GO	GGA3_MOUSE	ADP-ribosylation factor-binding protein GGA3 (Golgi-localized, gamma ear-containing, ARF-binding pro ...	0.64	-	nuc	0	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; peripheral membrane protein (By ...				718
Q9UG63 UniProt NPD GO	ABCF2_HUMAN	ATP-binding cassette sub-family F member 2 (Iron-inhibited ABC transporter 2)	0.64	-	nuc	0		ATP-binding cassette (ABC) transporter complex [TAS] mitochondrial envelope [TAS]			623
P23475 UniProt NPD GO	KU70_MOUSE	ATP-dependent DNA helicase 2 subunit 1 (EC 3.6.1.-) (ATP-dependent DNA helicase II 70 kDa subunit) ( ...	0.64	+	cyt	0	Nucleus	cytoplasm [IDA] nucleus [IDA]			607
Q4IBS2 UniProt NPD GO	MAK5_GIBZE	ATP-dependent RNA helicase MAK5 (EC 3.6.1.-)	0.64	+	mit	0	Nucleus; nucleolus (By similarity)				783
P02829 UniProt NPD GO	HSP82_YEAST	ATP-dependent molecular chaperone HSP82 (Heat shock protein Hsp90 heat-inducible isoform) (82 kDa he ...	0.64	-	cyt	0	Cytoplasm	cytoplasm [IDA]		2CGE	709
Q750F8 UniProt NPD GO	SPB4_ASHGO	ATP-dependent rRNA helicase SPB4 (EC 3.6.1.-)	0.64	-	nuc	0	Nucleus; nucleolus (By similarity)				599
Q6C193 UniProt NPD GO	SPB4_YARLI	ATP-dependent rRNA helicase SPB4 (EC 3.6.1.-)	0.64	-	nuc	0	Nucleus; nucleolus (By similarity)				626
P09774 UniProt NPD GO	AST3_DROME	Achaete-scute complex protein T3 (Lethal of sc) (Lethal of scute protein)	0.64	-	nuc	0					257
Q2EGB9 UniProt NPD GO	ASCL2_BOVIN	Achaete-scute homolog 2 (Mash2)	0.64	+	nuc	0	Nucleus (By similarity)				193
P59679 UniProt NPD GO	ARP8_BRARE	Actin-related protein 8	0.64	-	nuc	0					623
Q1XGU5 UniProt NPD GO	ASIP_COLPO	Agouti signaling protein precursor (ASP) (Agouti switch protein)	0.64	-	nuc	1 *	Secreted protein (By similarity)				132
Q9ERA0 UniProt NPD GO	TFCP2_MOUSE	Alpha-globin transcription factor CP2	0.64	-	nuc	0	Nucleus (By similarity)	transcription factor complex [TAS]			502
P28494 UniProt NPD GO	MA2A1_RAT	Alpha-mannosidase 2 (EC 3.2.1.114) (Alpha-mannosidase II) (Mannosyl-oligosaccharide 1,3-1,6-alpha-ma ...	0.64	-	cyt	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein				489
Q7TQF7 UniProt NPD GO	AMPH_MOUSE	Amphiphysin	0.64	-	nuc	0	Synaptic vesicle; synaptic vesicle membrane; peripheral membrane protein; cytoplasmic side (By simil ...	synaptic vesicle [IDA]			686
P24338 UniProt NPD GO	AREG_RAT	Amphiregulin precursor (AR) (Schwannoma-derived growth factor) (SDGF)	0.64	+	exc	1 *					243

You are viewing entries 16701 to 16750 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.