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
Q6PEV3 UniProt NPD GO	WIRE_MOUSE	WIP-related protein (WASP-interacting protein-related protein)	0.50	-	nuc	0	Localized to stress fibers and bundles of actin filaments (By similarity)				440
Q8TF74 UniProt NPD GO	WIRE_HUMAN	WIP-related protein (WASP-interacting protein-related protein) (WIP-and CR16-homologous protein)	0.50	-	nuc	0	Localized to stress fibers and bundles of actin filaments		609692		440
Q70UV1 UniProt NPD GO	WOX3A_MAIZE	WUSCHEL-related homeobox 3A (Narrow sheath protein 1)	0.50	-	nuc	0	Nucleus (By similarity)				262
Q6S3I3 UniProt NPD GO	WOX3B_MAIZE	WUSCHEL-related homeobox 3B (Narrow sheath protein 2)	0.50	-	nuc	0	Nucleus (By similarity)				265
Q9NUD5 UniProt NPD GO	ZCHC3_HUMAN	Zinc finger CCHC domain-containing protein 3	0.50	+	cyt	0					404
Q7Z7L9 UniProt NPD GO	ZSCA2_HUMAN	Zinc finger and SCAN domain-containing protein 2 (Zinc finger protein 29 homolog) (Zfp-29)	0.50	-	nuc	0	Nucleus (By similarity)				613
P52738 UniProt NPD GO	ZN140_HUMAN	Zinc finger protein 140	0.50	-	nuc	0	Nucleus (Potential)		604082		457
Q810A1 UniProt NPD GO	ZNF18_MOUSE	Zinc finger protein 18 (Zinc finger protein 535)	0.50	-	nuc	0	Nucleus (Potential)				556
Q9Y5A6 UniProt NPD GO	ZFP38_HUMAN	Zinc finger protein 38 homolog (Zfp-38) (Zinc finger and SCAN domain-containing protein 21) (NY-REN- ...	0.50	-	nuc	0	Nucleus (By similarity)	nucleus [NAS]			473
Q9ULM2 UniProt NPD GO	ZN490_HUMAN	Zinc finger protein 490	0.50	-	nuc	0	Nucleus (Probable)				529
Q8N141 UniProt NPD GO	ZN545_HUMAN	Zinc finger protein 545	0.50	-	nuc	0	Nucleus (Probable)				532
Q96N58 UniProt NPD GO	ZN578_HUMAN	Zinc finger protein 578	0.50	-	nuc	0	Nucleus (Probable)				365
Q5RDX1 UniProt NPD GO	Z585A_PONPY	Zinc finger protein 585A	0.50	-	nuc	0	Nucleus (Potential)				737
Q9P2J8 UniProt NPD GO	ZN624_HUMAN	Zinc finger protein 624	0.50	-	nuc	0	Nucleus (Probable)				739
Q15937 UniProt NPD GO	ZNF79_HUMAN	Zinc finger protein 79 (ZNFpT7)	0.50	-	nuc	0	Nucleus (Potential)	nucleus [NAS]	194552		498
Q8LG76 UniProt NPD GO	COL6_ARATH	Zinc finger protein CONSTANS-LIKE 6	0.50	+	cyt	0	Nucleus (Potential)				406
O73689 UniProt NPD GO	ZIC1_XENLA	Zinc finger protein ZIC 1 (Zinc finger protein of the cerebellum 1) (ZIC-related protein 1) (ZIC-R1) ...	0.50	-	nuc	0	Nucleus				443
Q91689 UniProt NPD GO	ZIC2_XENLA	Zinc finger protein ZIC 2 (Zinc finger protein of the cerebellum 2) (Zinc finger DNA-binding protein ...	0.50	-	nuc	0	Nucleus (By similarity)				501
O60481 UniProt NPD GO	ZIC3_HUMAN	Zinc finger protein ZIC 3 (Zinc finger protein of the cerebellum 3)	0.50	-	nuc	0	Nucleus		306955		467
Q6FQL6 UniProt NPD GO	KAPR_CANGA	cAMP-dependent protein kinase regulatory subunit (PKA regulatory subunit)	0.50	-	nuc	0					404
P81377 UniProt NPD GO	KAP1_RAT	cAMP-dependent protein kinase type I-beta regulatory subunit	0.50	-	cyt	0					380
P14644 UniProt NPD GO	PDE4C_RAT	cAMP-specific 3',5'-cyclic phosphodiesterase 4C (EC 3.1.4.17) (DPDE1) (Fragment)	0.50	-	nuc	0					536
Q4P384 UniProt NPD GO	YTH1_USTMA	mRNA 3'-end-processing protein YTH1	0.50	-	nuc	0	Nucleus (By similarity)				366
Q99257 UniProt NPD GO	MEX67_YEAST	mRNA export factor MEX67	0.50	-	nuc	0	Nucleus. Cytoplasm. Localizes at both the nuclear and cytoplasmic site of the pores. Shuttles betwee ...	cytoplasm [IDA] nuclear pore [IDA]		1OF5	599
Q8M9Y1 UniProt NPD GO	TILS_CHAGL	tRNA(Ile)-lysidine synthase (EC 6.3.4.-) (tRNA(Ile)-lysidine synthetase) (tRNA(Ile)-2-lysyl-cytidine ...	0.50	-	nuc	0	Plastid; chloroplast				341
O81193 UniProt NPD GO	SSS_SALOF	(+)-sabinene synthase, chloroplast precursor (EC 4.2.3.11) (SSS)	0.49	-	cyt	0	Plastid; chloroplast				590
Q37001 UniProt NPD GO	1A15_ARATH	1-aminocyclopropane-1-carboxylate synthase 5 (EC 4.4.1.14) (ACC synthase 5) (S-adenosyl-L-methionine ...	0.49	-	cyt	0					470
P14812 UniProt NPD GO	SSG2_AVESA	12S seed storage globulin 2 precursor [Contains: 12S seed storage globulin 2 acidic chain; 12S seed ...	0.49	-	mit	0					518
P26202 UniProt NPD GO	P15A_RABIT	15 kDa protein A precursor (Protein P15A) (P15R)	0.49	-	exc	1 *	Secreted protein				137
O17453 UniProt NPD GO	PSD4_SCHMA	26S proteasome non-ATPase regulatory subunit 4 (26S proteasome regulatory subunit S5A)	0.49	-	nuc	0					420
P04403 UniProt NPD GO	2SS_BEREX	2S sulfur-rich seed storage protein precursor (Allergen Ber e 1) [Contains: 2S sulfur-rich seed stor ...	0.49	-	exc	1 *				1GYS	146
P06916 UniProt NPD GO	FIRA_PLAFF	300 kDa antigen AG231 (Fragment)	0.49	-	nuc	0					310
Q5REY8 UniProt NPD GO	RM44_PONPY	39S ribosomal protein L44, mitochondrial precursor (EC 3.1.26.-)	0.49	-	mit	0	Mitochondrion (By similarity)				332
P80404 UniProt NPD GO	GABT_HUMAN	4-aminobutyrate aminotransferase, mitochondrial precursor (EC 2.6.1.19) ((S)-3-amino-2-methylpropion ...	0.49	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [NAS]	137150		500
Q9UTG4 UniProt NPD GO	RS26B_SCHPO	40S ribosomal protein S26-B	0.49	-	nuc	0					119
P62866 UniProt NPD GO	RS30_BOVIN	40S ribosomal protein S30	0.49	+	nuc	0					59
P62860 UniProt NPD GO	RS30_CRIGR	40S ribosomal protein S30	0.49	+	nuc	0					59
P62861 UniProt NPD GO	RS30_HUMAN	40S ribosomal protein S30	0.49	+	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [IDA]	134690		59
P62862 UniProt NPD GO	RS30_MOUSE	40S ribosomal protein S30	0.49	+	nuc	0					59
P62867 UniProt NPD GO	RS30_MUSSI	40S ribosomal protein S30	0.49	+	nuc	0					59
P62863 UniProt NPD GO	RS30_PIG	40S ribosomal protein S30	0.49	+	nuc	0					59
P62864 UniProt NPD GO	RS30_RAT	40S ribosomal protein S30	0.49	+	nuc	0					59
P49198 UniProt NPD GO	RS3A_HELAN	40S ribosomal protein S3a	0.49	-	nuc	0					259
P30939 UniProt NPD GO	5HT1F_HUMAN	5-hydroxytryptamine 1F receptor (5-HT-1F) (Serotonin receptor 1F)	0.49	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	182134		366
P30940 UniProt NPD GO	5HT1F_RAT	5-hydroxytryptamine 1F receptor (5-HT-1F) (Serotonin receptor 1F)	0.49	-	end	7 *	Membrane; multi-pass membrane protein				366
Q9N2D9 UniProt NPD GO	5HT1F_PANTR	5-hydroxytryptamine 1F receptor (5-HT-1F) (Serotonin receptor 1F) (Fragment)	0.49	-	end	7 *	Membrane; multi-pass membrane protein				365
Q09127 UniProt NPD GO	RL10A_SCHPO	60S ribosomal protein L10-A (QM protein homolog) (SpQM)	0.49	-	mit	0	Cytoplasm				221
Q90YV7 UniProt NPD GO	RL11_ICTPU	60S ribosomal protein L11	0.49	+	cyt	0					177
P93099 UniProt NPD GO	RL13A_CYAPA	60S ribosomal protein L13a	0.49	+	cyt	0					200
Q5RA38 UniProt NPD GO	RL13A_PONPY	60S ribosomal protein L13a	0.49	+	cyt	0					202

You are viewing entries 25351 to 25400 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.