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
P17246 UniProt NPD GO	TGFB1_RAT	Transforming growth factor beta-1 precursor (TGF-beta-1) [Contains: Latency-associated peptide (LAP) ...	0.70	-	exc	0	Secreted protein				390
Q99598 UniProt NPD GO	TSNAX_HUMAN	Translin-associated protein X (Translin-associated factor X)	0.70	-	nuc	0	Nucleus		602964		290
Q5RC21 UniProt NPD GO	TSNAX_PONPY	Translin-associated protein X (Translin-associated factor X)	0.70	-	nuc	0	Nucleus (By similarity)				290
Q20334 UniProt NPD GO	TNNI1_CAEEL	Troponin I 1 (TnI 1)	0.70	+	nuc	0					250
Q863B6 UniProt NPD GO	TNNI3_FELCA	Troponin I, cardiac muscle (Cardiac troponin I)	0.70	-	nuc	0					209
P02646 UniProt NPD GO	TNNI3_RABIT	Troponin I, cardiac muscle (Cardiac troponin I)	0.70	-	nuc	0					211
P17290 UniProt NPD GO	TPH1_RABIT	Tryptophan 5-hydroxylase 1 (EC 1.14.16.4) (Tryptophan 5-monooxygenase 1)	0.70	-	cyt	0					444
P26842 UniProt NPD GO	TNR7_HUMAN	Tumor necrosis factor receptor superfamily member 7 precursor (CD27L receptor) (T-cell activation an ...	0.70	-	exc	1	Membrane; single-pass type I membrane protein	extracellular region [NAS] integral to plasma membrane [NAS]	186711		260
Q4R8W3 UniProt NPD GO	TNAP3_MACFA	Tumor necrosis factor, alpha-induced protein 3 (EC 3.-.-.-)	0.70	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				790
P21580 UniProt NPD GO	TNAP3_HUMAN	Tumor necrosis factor, alpha-induced protein 3 (EC 3.-.-.-) (Putative DNA-binding protein A20) (Zinc ...	0.70	-	nuc	0	Cytoplasm. Nucleus	nucleus [IDA]	191163		790
P55024 UniProt NPD GO	TYRO_CHICK	Tyrosinase precursor (EC 1.14.18.1) (Monophenol monooxygenase)	0.70	-	end	1	Melanosome; melanosomal membrane; single-pass type I membrane protein				529
P29349 UniProt NPD GO	CSW_DROME	Tyrosine-protein phosphatase corkscrew (EC 3.1.3.48)	0.70	-	nuc	0	Cytoplasm	cytoplasm [IEP]			845
O00124 UniProt NPD GO	UBXD6_HUMAN	UBX domain-containing protein 6 (Rep-8 protein) (Reproduction 8 protein)	0.70	-	exc	2 *			602155		270
Q9FPT5 UniProt NPD GO	UBP1_ARATH	Ubiquitin carboxyl-terminal hydrolase 1 (EC 3.1.2.15) (Ubiquitin thioesterase 1) (Ubiquitin-specific ...	0.70	-	nuc	0					1083
O75317 UniProt NPD GO	UBP12_HUMAN	Ubiquitin carboxyl-terminal hydrolase 12 (EC 3.1.2.15) (Ubiquitin thioesterase 12) (Ubiquitin-specif ...	0.70	+	nuc	0			603091		355
Q9Y4E8 UniProt NPD GO	UBP15_HUMAN	Ubiquitin carboxyl-terminal hydrolase 15 (EC 3.1.2.15) (Ubiquitin thioesterase 15) (Ubiquitin-specif ...	0.70	-	nuc	0			604731	1W6V	981
P35123 UniProt NPD GO	UBP4_MOUSE	Ubiquitin carboxyl-terminal hydrolase 4 (EC 3.1.2.15) (Ubiquitin thioesterase 4) (Ubiquitin-specific ...	0.70	-	nuc	0	Nucleus				962
Q6B4Z3 UniProt NPD GO	UTY_PANTR	Ubiquitously transcribed Y chromosome tetratricopeptide repeat protein (Ubiquitously transcribed TPR ...	0.70	-	nuc	1	Nucleus (Potential)				1079
Q70J99 UniProt NPD GO	UN13D_HUMAN	Unc-13 homolog D (Munc13-4)	0.70	+	mit	0	Cytoplasm. Membrane; peripheral membrane protein. Colocalizes with cytotoxic granules at the plasma ...		608898		1090
Q68D86 UniProt NPD GO	CR014_HUMAN	Uncharacterized protein C18orf14	0.70	-	nuc	0					513
Q5R4B7 UniProt NPD GO	CR025_PONPY	Uncharacterized protein C18orf25 homolog	0.70	-	nuc	0					275
Q9D279 UniProt NPD GO	CS021_MOUSE	Uncharacterized protein C19orf21 homolog	0.70	-	mit	0					648
Q68FS7 UniProt NPD GO	CA037_RAT	Uncharacterized protein C1orf37 homolog	0.70	-	nuc	1					376
P38175 UniProt NPD GO	YBJ0_YEAST	Uncharacterized protein YBL090W	0.70	-	mit	0		mitochondrial small ribosomal subunit [IDA]			177
P38824 UniProt NPD GO	YHR6_YEAST	Uncharacterized protein YHR116W	0.70	-	nuc	0		cytoplasm [IDA] mitochondrion [IDA]			151
P38867 UniProt NPD GO	YHX7_YEAST	Uncharacterized protein YHR177W	0.70	-	nuc	0					452
Q91193 UniProt NPD GO	RAG2_ONCMY	V(D)J recombination-activating protein 2 (RAG-2)	0.70	-	nuc	0	Nucleus				533
Q24314 UniProt NPD GO	VPS18_DROME	Vacuolar protein sorting 18 (Protein deep orange)	0.70	-	end	0	Late endosome; late endosomal membrane; peripheral membrane protein. Lysosome; lysosomal membrane; p ...	lysosome [IDA] synapse [IMP]			1002
Q5ZLD7 UniProt NPD GO	VPS53_CHICK	Vacuolar protein sorting protein 53 homolog	0.70	-	mit	0	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; peripheral membrane protein (By ...				831
Q03390 UniProt NPD GO	VPS60_YEAST	Vacuolar protein sorting-associated protein VPS60	0.70	-	nuc	0	Endosome; endosomal membrane; peripheral membrane protein	cytoplasm [IDA] vacuolar membrane (sensu Fungi) [IDA]			262
Q4IBS9 UniProt NPD GO	BRO1_GIBZE	Vacuolar protein-sorting protein BRO1 (BRO domain-containing protein 1)	0.70	-	nuc	0	Cytoplasm (By similarity). Endosome (By similarity)				995
Q8R5L3 UniProt NPD GO	VPS39_MOUSE	Vam6/Vps39-like protein (Vps39 protein)	0.70	-	cyt	0	Cytoplasm (By similarity). Lysosome; lysosomal membrane; peripheral membrane protein (By similarity) ...				886
Q91ZT1 UniProt NPD GO	VGFR3_RAT	Vascular endothelial growth factor receptor 3 precursor (EC 2.7.10.1) (VEGFR-3) (Tyrosine-protein ki ...	0.70	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				1363
Q8C5G2 UniProt NPD GO	VASHL_MOUSE	Vasohibin-like protein	0.70	-	nuc	0					355
Q9ERB4 UniProt NPD GO	CSPG2_RAT	Versican core protein precursor (Large fibroblast proteoglycan) (Chondroitin sulfate proteoglycan co ...	0.70	-	nuc	0	Secreted protein; extracellular space; extracellular matrix	extracellular matrix [TAS]			2738
Q9USI0 UniProt NPD GO	YCTF_SCHPO	Very hypothetical protein C794.15 in chromosome III	0.70	-	mit	0					86
Q9GL59 UniProt NPD GO	VKGC_SHEEP	Vitamin K-dependent gamma-carboxylase (EC 6.4.-.-) (Gamma-glutamyl carboxylase) (Vitamin K gamma glu ...	0.70	-	end	5	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				758
P02844 UniProt NPD GO	VIT2_DROME	Vitellogenin-2 precursor (Vitellogenin II) (Yolk protein 2)	0.70	-	exc	0	Secreted protein	extracellular region [TAS]			442
Q13936 UniProt NPD GO	CAC1C_HUMAN	Voltage-dependent L-type calcium channel subunit alpha-1C (Voltage-gated calcium channel subunit alp ...	0.70	+	end	21	Membrane; multi-pass membrane protein	voltage-gated calcium channel complex [TAS]	114205	2BE6	2221
Q8CBE3 UniProt NPD GO	WDR37_MOUSE	WD repeat protein 37	0.70	+	nuc	0					496
Q9C519 UniProt NPD GO	WRKY6_ARATH	WRKY transcription factor 6 (WRKY DNA-binding protein 6) (AtWRKY6)	0.70	-	nuc	0	Nucleus				553
Q9ULM3 UniProt NPD GO	YETS2_HUMAN	YEATS domain-containing protein 2	0.70	-	nuc	0	Nucleus (Probable)				1422
Q8IY57 UniProt NPD GO	YAF2_HUMAN	YY1-associated factor 2	0.70	-	nuc	0	Nucleus	nucleus [IDA]	607534		180
O95229 UniProt NPD GO	ZWINT_HUMAN	ZW10 interactor (ZW10-interacting protein 1) (Zwint-1)	0.70	-	cyt	0	Nucleus. Associated with the kinetochore		609177		277
Q5BIM5 UniProt NPD GO	ZFY27_BOVIN	Zinc finger FYVE domain-containing protein 27	0.70	-	mit	3	Membrane; multi-pass membrane protein (Potential)				404
Q9Y2P7 UniProt NPD GO	ZN256_HUMAN	Zinc finger protein 256 (Bone marrow zinc finger 3) (BMZF-3)	0.70	-	nuc	0	Nucleus (Probable)		606956		474
Q8CE64 UniProt NPD GO	ZF276_MOUSE	Zinc finger protein 276 (Zfp-276)	0.70	-	nuc	0	Nucleus (Potential)				538
Q9H4T2 UniProt NPD GO	ZN435_HUMAN	Zinc finger protein 435 (Zinc finger and SCAN domain-containing protein 16)	0.70	-	nuc	0	Nucleus (Probable)			2COT	348
Q8NDP4 UniProt NPD GO	ZN439_HUMAN	Zinc finger protein 439	0.70	-	nuc	0	Nucleus (Potential)				499
Q8BXX2 UniProt NPD GO	ZN509_MOUSE	Zinc finger protein 509	0.70	-	nuc	0	Nucleus (Potential)				756

You are viewing entries 14051 to 14100 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.