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
P54831 UniProt NPD GO	TGFB1_CANFA	Transforming growth factor beta-1 precursor (TGF-beta-1) [Contains: Latency-associated peptide (LAP) ...	0.66	-	mit	0	Secreted protein				390
P01137 UniProt NPD GO	TGFB1_HUMAN	Transforming growth factor beta-1 precursor (TGF-beta-1) [Contains: Latency-associated peptide (LAP) ...	0.66	-	exc	0	Secreted protein	extracellular matrix (sensu Metazoa) [ISS] extracellular space [ISS]	131300	1KLD	390
Q38HS2 UniProt NPD GO	TGFB1_MUSPF	Transforming growth factor beta-1 precursor (TGF-beta-1) [Contains: Latency-associated peptide (LAP) ...	0.66	-	exc	0	Secreted protein				390
Q75V66 UniProt NPD GO	TM16E_HUMAN	Transmembrane protein 16E (Gnathodiaphyseal dysplasia 1 protein)	0.66	-	end	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Co-localized wit ...		608662		913
P48788 UniProt NPD GO	TNNI2_HUMAN	Troponin I, fast skeletal muscle (Troponin I, fast-twitch isoform)	0.66	-	nuc	0			601680		181
P13412 UniProt NPD GO	TNNI2_MOUSE	Troponin I, fast skeletal muscle (Troponin I, fast-twitch isoform)	0.66	-	nuc	0					181
P09810 UniProt NPD GO	TPH1_RAT	Tryptophan 5-hydroxylase 1 (EC 1.14.16.4) (Tryptophan 5-monooxygenase 1)	0.66	-	cyt	0					444
P36941 UniProt NPD GO	TNR3_HUMAN	Tumor necrosis factor receptor superfamily member 3 precursor (Lymphotoxin-beta receptor) (Tumor nec ...	0.66	-	exc	1	Membrane; single-pass type I membrane protein		600979	1RF3	435
Q03169 UniProt NPD GO	TNAP2_HUMAN	Tumor necrosis factor, alpha-induced protein 2 (Primary response gene B94 protein)	0.66	+	cyt	0		extracellular space [TAS]	603300		654
P18459 UniProt NPD GO	TY3H_DROME	Tyrosine 3-monooxygenase (EC 1.14.16.2) (Tyrosine 3-hydroxylase) (TH) (Protein Pale)	0.66	-	nuc	0					579
Q9NUW8 UniProt NPD GO	TYDP1_HUMAN	Tyrosyl-DNA phosphodiesterase 1 (EC 3.1.4.-) (Tyr-DNA phosphodiesterase 1)	0.66	-	nuc	0	Nucleus (Probable)	nucleus [NAS]	607198	1RH0	608
Q8BJ37 UniProt NPD GO	TYDP1_MOUSE	Tyrosyl-DNA phosphodiesterase 1 (EC 3.1.4.-) (Tyr-DNA phosphodiesterase 1)	0.66	-	nuc	0	Nucleus (Probable)				609
Q6IND6 UniProt NPD GO	DC12_XENLA	UPF0361 protein DC12 homolog	0.66	-	nuc	0					336
Q96PU4 UniProt NPD GO	UHRF2_HUMAN	Ubiquitin-like PHD and RING finger domain-containing protein 2 (EC 6.3.2.-) (Ubiquitin-like-containi ...	0.66	-	nuc	0	Nucleus	nucleus [IDA]		1Z6U	802
P42843 UniProt NPD GO	YN51_YEAST	Uncharacterized F-box protein YNL311C	0.66	-	nuc	0					763
Q8IV36 UniProt NPD GO	CQ028_HUMAN	Uncharacterized protein C17orf28 (Down-regulated in multiple cancers-1)	0.66	-	nuc	0	Membrane; multi-pass membrane protein (Potential)		605752		788
Q8R1F6 UniProt NPD GO	CQ028_MOUSE	Uncharacterized protein C17orf28 homolog	0.66	-	nuc	0	Membrane; multi-pass membrane protein (Potential)				788
Q8IVT2 UniProt NPD GO	CS021_HUMAN	Uncharacterized protein C19orf21	0.66	-	nuc	0					679
Q8N1D5 UniProt NPD GO	CA158_HUMAN	Uncharacterized protein C1orf158	0.66	-	nuc	0					194
Q9NR00 UniProt NPD GO	CH004_HUMAN	Uncharacterized protein C8orf4 (Thyroid cancer protein 1) (TC-1)	0.66	-	nuc	0			607702		106
Q12069 UniProt NPD GO	YD36C_YEAST	Uncharacterized protein YDL036C	0.66	+	mit	0		cytoplasm [IDA] mitochondrion [IMP] nucleus [IDA]			462
P40077 UniProt NPD GO	YEV4_YEAST	Uncharacterized protein YER124C	0.66	-	nuc	0		bud neck [IDA]			573
P38803 UniProt NPD GO	YHO5_YEAST	Uncharacterized protein YHR085W	0.66	+	nuc	0		nucleoplasm [IDA] nucleus [IDA]			334
P35732 UniProt NPD GO	YKF4_YEAST	Uncharacterized protein YKL054C	0.66	-	nuc	0		nucleus [IMP]			738
Q03525 UniProt NPD GO	YM8H_YEAST	Uncharacterized protein YMR269W	0.66	+	nuc	0	Nucleus; nucleolus	nucleolus [IDA]			211
P53897 UniProt NPD GO	YNP7_YEAST	Uncharacterized protein YNL157W	0.66	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			168
Q12383 UniProt NPD GO	YO125_YEAST	Uncharacterized protein YOL125W	0.66	+	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			476
P36025 UniProt NPD GO	YO062_YEAST	Uncharacterized protein YOR062C	0.66	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			268
Q6XBT4 UniProt NPD GO	USF1_BOVIN	Upstream stimulatory factor 1	0.66	+	nuc	0	Nucleus (By similarity)				310
P38784 UniProt NPD GO	VMA22_YEAST	Vacuolar ATPase assembly protein VMA22	0.66	-	nuc	0		endoplasmic reticulum membrane [TAS]			181
Q9P1Q0 UniProt NPD GO	VPS54_HUMAN	Vacuolar protein sorting protein 54 (Tumor antigen SLP-8p) (Hepatocellular carcinoma protein 8)	0.66	-	nuc	0					977
P54787 UniProt NPD GO	VPS9_YEAST	Vacuolar protein sorting-associated protein VPS9	0.66	-	nuc	0	Cytoplasm	cytosol [IDA]		1P3Q	451
Q9ULK5 UniProt NPD GO	VANG2_HUMAN	Vang-like protein 2 (Van Gogh-like protein 2) (Strabismus 1) (Loop-tail protein 1 homolog)	0.66	+	end	4	Membrane; multi-pass membrane protein (Potential)		600533		521
P26617 UniProt NPD GO	VEGFA_CAVPO	Vascular endothelial growth factor A (VEGF-A) (Vascular permeability factor) (VPF)	0.66	-	nuc	0	Secreted protein (By similarity). Secreted but remains associated to cells or to the extracellular m ...				164
Q3HXY6 UniProt NPD GO	NGFV2_NOTSC	Venom nerve growth factor 2 precursor (vNGF-2)	0.66	-	exc	0	Secreted protein				244
O93528 UniProt NPD GO	VAX1A_XENLA	Ventral anterior homeobox 1a	0.66	+	nuc	0	Nucleus (By similarity)				295
P13611 UniProt NPD GO	CSPG2_HUMAN	Versican core protein precursor (Large fibroblast proteoglycan) (Chondroitin sulfate proteoglycan co ...	0.66	-	nuc	0	Secreted protein; extracellular space; extracellular matrix	extracellular matrix (sensu Metazoa) [TAS]	118661		3396
P87498 UniProt NPD GO	VIT1_CHICK	Vitellogenin-1 precursor (Vitellogenin I) (Minor vitellogenin) [Contains: Lipovitellin-1 (Lipovitell ...	0.66	-	exc	0					1912
Q8CGF6 UniProt NPD GO	WDR47_MOUSE	WD repeat protein 47	0.66	-	nuc	0					920
Q06078 UniProt NPD GO	YL409_YEAST	WD repeat protein YLR409C	0.66	-	end	0		nucleolus [IDA] nucleus [IDA] small nucleolar ribonucleoprotein complex [IPI]			939
P87060 UniProt NPD GO	POP1_SCHPO	WD repeat protein pop1	0.66	-	nuc	0	Nucleus	SCF ubiquitin ligase complex [IDA]			775
P19544 UniProt NPD GO	WT1_HUMAN	Wilms' tumor protein (WT33)	0.66	+	nuc	0	Nucleus	nucleus [NAS]	136680	1XF7	449
O62651 UniProt NPD GO	WT1_PIG	Wilms' tumor protein homolog	0.66	+	nuc	0	Nucleus				449
Q9Z2C8 UniProt NPD GO	YBOX2_MOUSE	Y-box-binding protein 2 (Germ cell-specific Y-box-binding protein) (FRGY2 homolog)	0.66	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA]			360
Q99LW6 UniProt NPD GO	YAF2_MOUSE	YY1-associated factor 2	0.66	-	nuc	0	Nucleus	nucleus [IDA]			179
Q8R331 UniProt NPD GO	ZNHI1_MOUSE	Zinc finger HIT domain-containing protein 1	0.66	-	nuc	0					154
Q12901 UniProt NPD GO	ZN155_HUMAN	Zinc finger protein 155	0.66	-	nuc	0	Nucleus (Potential)		604086		538
P17025 UniProt NPD GO	ZN182_HUMAN	Zinc finger protein 182 (Zinc finger protein 21) (Zinc finger protein KOX14)	0.66	-	nuc	0	Nucleus (Potential)		314993		639
Q8NDW4 UniProt NPD GO	ZN248_HUMAN	Zinc finger protein 248	0.66	-	nuc	0	Nucleus (Probable)				579
P17035 UniProt NPD GO	ZNF28_HUMAN	Zinc finger protein 28 (Zinc finger protein KOX24)	0.66	-	nuc	0	Nucleus (Potential)				665

You are viewing entries 16101 to 16150 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.