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
Q96FZ2 UniProt NPD GO	DC12_HUMAN	UPF0361 protein DC12	0.54	-	nuc	0					354
Q9CQ37 UniProt NPD GO	UBE2T_MOUSE	Ubiquitin-conjugating enzyme E2 T (EC 6.3.2.19) (Ubiquitin-protein ligase T) (Ubiquitin carrier prot ...	0.54	-	nuc	0					204
Q5VVX9 UniProt NPD GO	UBE2U_HUMAN	Ubiquitin-conjugating enzyme E2 U (EC 6.3.2.19) (Ubiquitin-protein ligase U) (Ubiquitin carrier prot ...	0.54	-	nuc	0				1YRV	321
Q6ZRI6 UniProt NPD GO	CO039_HUMAN	Uncharacterized protein C15orf39	0.54	-	nuc	0					1047
Q8CB14 UniProt NPD GO	CR054_MOUSE	Uncharacterized protein C18orf54 homolog precursor	0.54	-	nuc	0	Secreted protein (Potential)				526
Q3SY05 UniProt NPD GO	CA157_HUMAN	Uncharacterized protein C1orf157	0.54	-	nuc	0					128
Q5BK24 UniProt NPD GO	CH076_RAT	Uncharacterized protein C8orf76 homolog	0.54	-	nuc	0					374
P47175 UniProt NPD GO	YJ9L_YEAST	Uncharacterized protein YJR147W	0.54	-	nuc	0	Nucleus (Potential)	cytoplasm [IDA] nucleus [IDA]			358
P27514 UniProt NPD GO	YN86_YEAST	Uncharacterized transporter YNR013C	0.54	+	end	12	Membrane; multi-pass membrane protein (Potential)				894
P35457 UniProt NPD GO	UPAS_MOUSE	Urokinase plasminogen activator surface receptor, secreted form precursor (uPAR) (U-PAR) (CD87 antig ...	0.54	-	exc	0	Secreted protein (Probable)				222
O59941 UniProt NPD GO	VATD_NEUCR	Vacuolar ATP synthase subunit D (EC 3.6.3.14) (V-ATPase D subunit) (Vacuolar proton pump D subunit)	0.54	-	cyt	0					264
O59823 UniProt NPD GO	VATD_SCHPO	Vacuolar ATP synthase subunit D (EC 3.6.3.14) (V-ATPase D subunit) (Vacuolar proton pump D subunit)	0.54	-	mit	0					285
P32610 UniProt NPD GO	VATD_YEAST	Vacuolar ATP synthase subunit D (EC 3.6.3.14) (V-ATPase D subunit) (Vacuolar proton pump D subunit)	0.54	-	cyt	0		hydrogen-transporting ATPase V1 domain [TAS] vacuolar membrane (sensu Fungi) [TAS]			256
P53076 UniProt NPD GO	VID30_YEAST	Vacuolar import and degradation protein 30 (Glucose-induced degradation protein 1)	0.54	-	nuc	0	Nucleus. Cytoplasm	cytoplasm [IDA] nucleus [IDA]			958
Q96RL7 UniProt NPD GO	VP13A_HUMAN	Vacuolar protein sorting 13A (Chorein) (Chorea-acanthocytosis protein)	0.54	+	end	0		intracellular [NAS]	605978		3174
Q96AX1 UniProt NPD GO	VP33A_HUMAN	Vacuolar protein sorting 33A (hVPS33A)	0.54	-	cyt	0	Late endosome; late endosomal membrane; peripheral membrane protein (By similarity). Lysosome; lysos ...				596
Q8IRR1 UniProt NPD GO	VNNL2_DROME	Vanin-like protein 2 precursor	0.54	-	mit	1 *		extrinsic to membrane [ISS]			517
P26326 UniProt NPD GO	VSI1_TRYBB	Variant surface glycoprotein ILTAT 1.21 precursor (VSG)	0.54	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor. A soluble form is released from ruptured cells by the actio ...				471
P49151 UniProt NPD GO	VEGFA_PIG	Vascular endothelial growth factor A precursor (VEGF-A) (Vascular permeability factor) (VPF)	0.54	-	exc	0	Secreted protein (By similarity). Secreted but remains associated to cells or to the extracellular m ...				190
P83942 UniProt NPD GO	TXVE_VIPAP	Vascular endothelial growth factor toxin (svVEGF) (Heparin-binding dimeric hypotensive factor) (HF)	0.54	+	nuc	0	Secreted protein				110
P82475 UniProt NPD GO	TXVE_VIPLE	Vascular endothelial growth factor toxin (svVEGF) (Increasing capillary permeability protein) (ICPP) ...	0.54	+	nuc	0	Secreted protein				110
Q801E0 UniProt NPD GO	VAX1_BRARE	Ventral anterior homeobox 1	0.54	+	nuc	0	Nucleus (By similarity)				317
Q2NKI2 UniProt NPD GO	VAX1_MOUSE	Ventral anterior homeobox 1	0.54	+	nuc	0	Nucleus (By similarity)				338
Q9JM00 UniProt NPD GO	VAX1_RAT	Ventral anterior homeobox 1	0.54	+	nuc	0	Nucleus (By similarity)				336
Q9USX2 UniProt NPD GO	YO74_SCHPO	Very hypothetical protein C1921.04c in chromosome II	0.54	-	nuc	0					117
Q96WU9 UniProt NPD GO	YJO6_SCHPO	Very hypothetical protein PB16A4.06c in chromosome III	0.54	-	nuc	0					126
P97764 UniProt NPD GO	WBP1_MOUSE	WW domain-binding protein 1 (WBP-1)	0.54	-	nuc	1					304
O88878 UniProt NPD GO	Z20D2_MOUSE	Zinc finger A20 domain-containing protein 2 (Zinc finger protein 216)	0.54	-	nuc	0				1WFL	213
Q9HBF4 UniProt NPD GO	ZFYV1_HUMAN	Zinc finger FYVE domain-containing protein 1 (Double FYVE-containing protein 1) (Tandem FYVE fingers ...	0.54	-	nuc	0	Golgi apparatus; Golgi stack. Resides predominantly in the cisternal stacks of the Golgi	endoplasmic reticulum [IDA] Golgi stack [IDA] perinuclear region [IDA]	605471		777
O95405 UniProt NPD GO	ZFYV9_HUMAN	Zinc finger FYVE domain-containing protein 9 (Mothers against decapentaplegic homolog-interacting pr ...	0.54	-	nuc	0	Cytoplasm	cytoplasm [NAS] early endosome [NAS]	603755	1MK2	1425
P17012 UniProt NPD GO	ZFX_MOUSE	Zinc finger X-chromosomal protein	0.54	+	nuc	0	Nucleus				799
O15060 UniProt NPD GO	ZBT39_HUMAN	Zinc finger and BTB domain-containing protein 39	0.54	-	nuc	0	Nucleus (Potential)				712
P10751 UniProt NPD GO	ZFP11_MOUSE	Zinc finger protein 11 (Zfp-11) (Krox-6.1A protein)	0.54	-	nuc	0	Nucleus (Potential)				647
Q08376 UniProt NPD GO	ZF161_MOUSE	Zinc finger protein 161 (Zfp-161) (Zinc finger protein 5) (ZF5)	0.54	-	nuc	0	Nucleus (By similarity)				449
Q9P0L1 UniProt NPD GO	ZN167_HUMAN	Zinc finger protein 167 (Zinc finger protein 64) (Zinc finger protein 448) (ZFP)	0.54	-	nuc	0	Nucleus (Potential)				754
Q9UJW8 UniProt NPD GO	ZN180_HUMAN	Zinc finger protein 180 (HHZ168)	0.54	-	nuc	0	Nucleus (Probable)		606740		692
Q86WZ6 UniProt NPD GO	ZN227_HUMAN	Zinc finger protein 227	0.54	-	nuc	0	Nucleus (Probable)				799
O75467 UniProt NPD GO	ZN324_HUMAN	Zinc finger protein 324 (Zinc finger protein ZF5128)	0.54	-	nuc	0	Nucleus (Probable)				553
Q5R4W8 UniProt NPD GO	ZN346_PONPY	Zinc finger protein 346	0.54	-	nuc	0	Nucleus; nucleolus (By similarity). Cytoplasm (By similarity). Nuclear at steady state, primarily in ...				310
Q9DB38 UniProt NPD GO	ZN580_MOUSE	Zinc finger protein 580	0.54	-	nuc	0	Nucleus (Probable)				172
Q5RB30 UniProt NPD GO	Z585B_PONPY	Zinc finger protein 585B	0.54	-	nuc	0	Nucleus (Potential)				769
Q52M93 UniProt NPD GO	Z585B_HUMAN	Zinc finger protein 585B (zinc finger protein 41-like protein)	0.54	-	nuc	0	Nucleus (Potential)				769
Q2M3X9 UniProt NPD GO	ZN674_HUMAN	Zinc finger protein 674	0.54	-	nuc	0	Nucleus (Probable)		300573		581
P16415 UniProt NPD GO	ZF36_HUMAN	Zinc finger protein ZFP-36 (Fragment)	0.54	-	nuc	0	Nucleus (Probable)				582
Q9GL73 UniProt NPD GO	RNZ2_GORGO	Zinc phosphodiesterase ELAC protein 2 (EC 3.1.26.11) (Ribonuclease Z 2) (RNase Z 2) (tRNase Z 2) (tR ...	0.54	+	cyt	0	Nucleus (Probable)				826
Q04584 UniProt NPD GO	ZYX_CHICK	Zyxin	0.54	-	nuc	0	Cytoplasm. Cytoskeleton. Associates with the actin cytoskeleton near the adhesion plaques				542
P09456 UniProt NPD GO	KAP0_RAT	cAMP-dependent protein kinase type I-alpha regulatory subunit	0.54	-	cyt	0					380
Q5ZKU8 UniProt NPD GO	PK1IP_CHICK	p21-activated protein kinase-interacting protein 1-like (PAK1-interacting protein 1-like)	0.54	+	nuc	0	Nucleus; nucleolus (By similarity)				369
Q12009 UniProt NPD GO	TRM8_YEAST	tRNA (guanine-N(7)-)-methyltransferase (EC 2.1.1.33) (tRNA(m7G46)-methyltransferase)	0.54	-	nuc	0		nucleus [IDA]			286
Q755C8 UniProt NPD GO	PUS1_ASHGO	tRNA pseudouridine synthase 1 (EC 5.4.99.-) (tRNA-uridine isomerase 1) (tRNA pseudouridylate synthas ...	0.54	-	nuc	0	Nucleus (By similarity)				528

You are viewing entries 22851 to 22900 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.