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
Q9VDE5 UniProt NPD GO	PPAN_DROME	Protein Peter pan	0.88	+	nuc	0					460
Q9UPR3 UniProt NPD GO	SMG5_HUMAN	Protein SMG5 (SMG-5 homolog) (EST1-like protein B) (LPTS-interacting protein) (LPTS-RP1)	0.88	+	nuc	0	Cytoplasm. Nucleus. Predominantly cytoplasmic, and nuclear. Shuttles between nucleus and cytoplasm	cytoplasm [IDA] nucleus [IDA]			1016
Q08831 UniProt NPD GO	VTS1_YEAST	Protein VTS1 (VTI1-2 suppressor protein 1)	0.88	-	nuc	0	Cytoplasm	cytosol [IDA]		2FE9	523
Q5SV77 UniProt NPD GO	ZN403_MOUSE	Protein ZNF403 (Gametogenetin-binding protein 2) (Dioxin-inducible factor 3) (DIF-3)	0.88	+	nuc	0	Cytoplasmic vesicle. Associated with vesicular structures				696
Q10951 UniProt NPD GO	BYR4_SCHPO	Protein byr4	0.88	-	nuc	0	Cell membrane; peripheral membrane protein. Cytoplasm				665
P29303 UniProt NPD GO	HAIR_DROVI	Protein hairy	0.88	-	nuc	0	Nucleus				378
Q6C5G0 UniProt NPD GO	SEC9_YARLI	Protein transport protein SEC9	0.88	-	nuc	0					608
Q8I1G0 UniProt NPD GO	TWIST_DROER	Protein twist	0.88	+	nuc	0	Nucleus (By similarity)	nucleus [ISS]			490
Q7Z478 UniProt NPD GO	DHX29_HUMAN	Putative ATP-dependent RNA helicase DHX29 (EC 3.6.1.-) (DEAH box protein 29) (Nucleic acid helicase ...	0.88	-	nuc	0					1369
P40434 UniProt NPD GO	YIR7_YEAST	Putative ATP-dependent helicase YIL177C (EC 3.6.1.-)	0.88	+	nuc	0					1758
P40889 UniProt NPD GO	YJW5_YEAST	Putative ATP-dependent helicase YJL225C (EC 3.6.1.-)	0.88	+	nuc	0					1758
O17917 UniProt NPD GO	RN113_CAEEL	Putative RING finger protein 113 homolog	0.88	+	nuc	0					384
Q9P5N7 UniProt NPD GO	TFB1_NEUCR	Putative RNA polymerase II transcription factor B subunit 1 (RNA polymerase II transcription factor ...	0.88	+	nuc	0	Nucleus (By similarity)				663
Q8NDT2 UniProt NPD GO	RB15B_HUMAN	Putative RNA-binding protein 15B (RNA-binding motif protein 15B)	0.88	-	nuc	0	Nucleus (Probable)				563
Q04164 UniProt NPD GO	SAS_DROME	Putative epidermal cell surface receptor precursor (Stranded at second protein)	0.88	-	nuc	1	Membrane; single-pass type I membrane protein	apical plasma membrane [NAS] integral to plasma membrane [NAS]			1693
Q9DBE9 UniProt NPD GO	RRMJ3_MOUSE	Putative rRNA methyltransferase 3 (EC 2.1.1.-) (rRNA (uridine-2'-O-)-methyltransferase 3)	0.88	+	nuc	0	Nucleus; nucleolus (By similarity)				838
Q8N0V3 UniProt NPD GO	RBFAL_HUMAN	Putative ribosome-binding factor A, mitochondrial precursor	0.88	-	nuc	0	Mitochondrion (Potential)				343
Q11179 UniProt NPD GO	YPC2_CAEEL	Putative serine/threonine-protein kinase C05D10.2 in chromosome III (EC 2.7.11.24)	0.88	-	nuc	0					470
P34269 UniProt NPD GO	TYR1_CAEEL	Putative tyrosinase-like protein tyr-1 precursor	0.88	-	exc	0					601
P34337 UniProt NPD GO	YK13_CAEEL	Putative tyrosine-protein phosphatase C15H7.3 (EC 3.1.3.48)	0.88	+	nuc	0					398
Q8BJ73 UniProt NPD GO	RSPO4_MOUSE	R-spondin-4 precursor (Roof plate-specific spondin-4) (Cysteine-rich and single thrombospondin domai ...	0.88	+	exc	0	Secreted protein (By similarity)				228
O88846 UniProt NPD GO	RNF4_RAT	RING finger protein 4 (SNURF)	0.88	-	mit	0	Cytoplasm. Nucleus	nucleus [IDA]			194
Q9UST5 UniProt NPD GO	RRN7_SCHPO	RNA polymerase I-specific transcription initiation factor rrn7	0.88	-	end	0	Nucleus (Potential)	RNA polymerase I transcription factor complex [IDA]			537
Q8CGC6 UniProt NPD GO	RBM28_MOUSE	RNA-binding protein 28 (RNA-binding motif protein 28)	0.88	+	nuc	0	Nucleus; nucleolus (By similarity)			1X4H	749
Q6WKZ4 UniProt NPD GO	RFIP1_HUMAN	Rab11 family-interacting protein 1 (Rab11-FIP1) (Rab-coupling protein)	0.88	-	nuc	0	Membrane-bound (isoform 2). Rab11A rather than Rab4A mediates localization in the endocytic recyclin ...		608737		1283
Q9VQ26 UniProt NPD GO	RB3GP_DROME	Rab3 GTPase-activating protein catalytic subunit	0.88	-	nuc	0	Cytoplasm (Probable)	soluble fraction [ISS]			916
P83900 UniProt NPD GO	RPGF5_RAT	Rap guanine nucleotide exchange factor 5 (M-Ras-regulated Rap GEF) (MR-GEF) (rMR-GEF)	0.88	-	cyt	0	Nucleus (By similarity)				580
Q70E73 UniProt NPD GO	RAPH1_HUMAN	Ras-associated and pleckstrin homology domains-containing protein 1 (RAPH1) (Lamellipodin) (Proline- ...	0.88	-	nuc	0	Cell membrane; peripheral membrane protein. Recruited to the membrane, via the PH domain, by the pho ...		609035		1302
Q6FIZ7 UniProt NPD GO	MAF1_CANGA	Repressor of RNA polymerase III transcription MAF1	0.88	-	nuc	0	Nucleus (By similarity)				391
Q9Z1I6 UniProt NPD GO	ARHG1_RAT	Rho guanine nucleotide exchange factor 1 (Lbc's second cousin)	0.88	-	nuc	0	Cytoplasm (By similarity). Membrane (By similarity). Translocated to the membrane by activated GNA13 ...				919
Q5VV41 UniProt NPD GO	ARHGG_HUMAN	Rho guanine nucleotide exchange factor 16	0.88	-	nuc	0				1X6B	709
Q5XXR3 UniProt NPD GO	ARHG6_RAT	Rho guanine nucleotide exchange factor 6 (Rac/Cdc42 guanine nucleotide exchange factor 6)	0.88	-	nuc	0					772
Q14155 UniProt NPD GO	ARHG7_HUMAN	Rho guanine nucleotide exchange factor 7 (PAK-interacting exchange factor beta) (Beta-Pix) (COOL-1) ...	0.88	-	nuc	0			605477	1ZSG	803
Q9R0Z9 UniProt NPD GO	RHG07_MOUSE	Rho-GTPase-activating protein 7 (Rho-type GTPase-activating protein 7) (Deleted in liver cancer 1 pr ...	0.88	+	nuc	0	Cytoplasm (Potential)	cytoplasm [NAS]			1092
Q5TC82 UniProt NPD GO	RC3H1_HUMAN	Roquin (RING finger and C3H zinc finger protein 1)	0.88	-	nuc	0	Cytoplasm (By similarity). Localizes to cytosolic RNA granules, which are sites for regulating mRNA ...		609424		1133
Q6NUC6 UniProt NPD GO	RC3H1_XENLA	Roquin (RING finger and C3H zinc finger protein 1)	0.88	-	nuc	0	Cytoplasm (By similarity)				1114
Q9Y3L3 UniProt NPD GO	3BP1_HUMAN	SH3 domain-binding protein 1 (3BP-1)	0.88	-	mit	0					701
Q9NZC9 UniProt NPD GO	SMAL1_HUMAN	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 ...	0.88	-	nuc	0	Nucleus (By similarity)		606622		954
Q8TAQ2 UniProt NPD GO	SMRC2_HUMAN	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily C member 2 (SWI/S ...	0.88	+	nuc	0	Nucleus	nucleoplasm [TAS] SWI/SNF complex [IDA]	601734		1214
Q4PG15 UniProt NPD GO	SWC4_USTMA	SWR1-complex protein 4	0.88	-	nuc	0	Nucleus (By similarity)				615
Q9NZJ4 UniProt NPD GO	SACS_HUMAN	Sacsin	0.88	-	nuc	0			270550	1IUR	3829
Q9JMD2 UniProt NPD GO	SMBT1_RAT	Scm-like with four MBT domains protein 1	0.88	+	nuc	0					863
Q90663 UniProt NPD GO	SEM3D_CHICK	Semaphorin-3D precursor (Collapsin-2) (COLL-2)	0.88	+	exc	0	Secreted protein				761
P38080 UniProt NPD GO	AKL1_YEAST	Serine/threonine-protein kinase AKL1 (EC 2.7.11.1)	0.88	-	nuc	0		bud neck [IDA] cytoplasm [IDA]			1108
Q52EB3 UniProt NPD GO	ATG1_MAGGR	Serine/threonine-protein kinase ATG1 (EC 2.7.11.1) (Autophagy-related protein 1)	0.88	-	nuc	0	Cytoplasm (By similarity)				982
P48562 UniProt NPD GO	CLA4_YEAST	Serine/threonine-protein kinase CLA4 (EC 2.7.11.1)	0.88	-	nuc	0		actin cap [IDA]			842
P32328 UniProt NPD GO	DBF20_YEAST	Serine/threonine-protein kinase DBF20 (EC 2.7.11.1)	0.88	-	nuc	0		cytoplasm [IDA]			564
Q03407 UniProt NPD GO	PKH1_YEAST	Serine/threonine-protein kinase PKH1 (EC 2.7.11.1) (3-phosphoinositide-dependent protein kinase 1)	0.88	-	nuc	0		cytosol [IDA]			766
Q03497 UniProt NPD GO	STE20_YEAST	Serine/threonine-protein kinase STE20 (EC 2.7.11.1)	0.88	-	nuc	0	Cytoplasm. Nucleus. The translocation from the cytoplasm to the nucleus is stimulated by H(2)O(2). L ...	incipient bud site [IDA] mating projection tip [IDA]			939
Q5ABX0 UniProt NPD GO	ATM_CANAL	Serine/threonine-protein kinase TEL1 (EC 2.7.11.1) (DNA-damage checkpoint kinase TEL1) (Telomere len ...	0.88	-	end	0	Nucleus. Localizes to nuclear DNA repair foci with other DNA repair proteins in response to DNA doub ...				2873

You are viewing entries 5301 to 5350 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.