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
Q29466 UniProt NPD GO	VPP1_BOVIN	Vacuolar proton translocating ATPase 116 kDa subunit a isoform 1 (V-ATPase 116 kDa isoform a1) (Clat ...	0.20	-	end	6	Integral membrane protein. Coated vesicle				838
Q9HBG4 UniProt NPD GO	VPP4_HUMAN	Vacuolar proton translocating ATPase 116 kDa subunit a isoform 4 (V-ATPase 116 kDa isoform a4) (Vacu ...	0.20	-	end	6	Cell membrane; apical cell membrane; multi-pass membrane protein. Present at high density almost exc ...	hydrogen-translocating V-type ATPase complex [NAS]	605239		840
O64758 UniProt NPD GO	VSR5_ARATH	Vacuolar sorting receptor 5 precursor (AtVSR5) (Epidermal growth factor receptor-like protein 5) (At ...	0.20	-	end	3 *					618
P49044 UniProt NPD GO	VPE_VICSA	Vacuolar-processing enzyme precursor (EC 3.4.22.-) (VPE) (Proteinase B)	0.20	-	exc	1 *					493
O15886 UniProt NPD GO	PHLC_TRYCR	Variant-surface-glycoprotein phospholipase C (EC 4.6.1.14) (VSG lipase) (Glycosylphosphatidylinosito ...	0.20	-	cyt	0	Membrane; peripheral membrane protein				380
Q28260 UniProt NPD GO	VCAM1_CANFA	Vascular cell adhesion protein 1 precursor (V-CAM 1)	0.20	-	end	2 *	Membrane; single-pass type I membrane protein (By similarity)				739
P35000 UniProt NPD GO	VIPR2_RAT	Vasoactive intestinal polypeptide receptor 2 precursor (VIP-R-2) (Pituitary adenylate cyclase-activa ...	0.20	-	end	7	Membrane; multi-pass membrane protein				437
O88721 UniProt NPD GO	V2R_MOUSE	Vasopressin V2 receptor (Renal-type arginine vasopressin receptor) (Antidiuretic hormone receptor) ( ...	0.20	-	end	7 *	Membrane; multi-pass membrane protein				371
P01180 UniProt NPD GO	NEU2_BOVIN	Vasopressin-neurophysin 2-copeptin precursor (AVP-NPII) [Contains: Arg-vasopressin; Neurophysin 2 (N ...	0.20	-	nuc	0	Secreted protein			2BN2	166
P01183 UniProt NPD GO	NEU2_PIG	Vasopressin-neurophysin 2-copeptin precursor (AVP-NPII) [Contains: Lys-vasopressin; Neurophysin 2 (N ...	0.20	-	nuc	0	Secreted protein				166
P22642 UniProt NPD GO	ANFV_ANGJA	Ventricular natriuretic peptide precursor (VNP)	0.20	-	nuc	1 *	Secreted protein				150
Q9Y7R0 UniProt NPD GO	YCX3_SCHPO	Very hypothetical protein C2H8.03 in chromosome III	0.20	-	nuc	0					75
Q9C109 UniProt NPD GO	YIOG_SCHPO	Very hypothetical protein P27G11.16 in chromosome I	0.20	-	nuc	0					104
P39550 UniProt NPD GO	YAK0_YEAST	Very hypothetical protein YAR030C	0.20	-	mit	0					113
P53092 UniProt NPD GO	YGU9_YEAST	Very hypothetical protein YGL199C	0.20	-	nuc	0					156
Q03879 UniProt NPD GO	YM09_YEAST	Very hypothetical protein YMR122C	0.20	-	nuc	0					124
Q9SIQ9 UniProt NPD GO	VA712_ARATH	Vesicle-associated membrane protein 712 (AtVAMP712)	0.20	-	nuc	1	Membrane; single-pass type IV membrane protein (By similarity)				219
Q9M376 UniProt NPD GO	VA727_ARATH	Vesicle-associated membrane protein 727 (AtVAMP727)	0.20	-	nuc	1	Membrane; single-pass type IV membrane protein (By similarity)				240
Q9Z270 UniProt NPD GO	VAPA_RAT	Vesicle-associated membrane protein-associated protein A (VAMP-associated protein A) (VAMP-A) (VAP-A ...	0.20	-	nuc	1	Cell membrane; single-pass type IV membrane protein (By similarity). Intracellular membrane; single- ...			1Z9O	242
Q9M0Y8 UniProt NPD GO	NSF_ARATH	Vesicle-fusing ATPase (EC 3.6.4.6) (Vesicular-fusion protein NSF) (N-ethylmaleimide sensitive fusion ...	0.20	-	cyt	0	Cytoplasm (By similarity)				742
Q91514 UniProt NPD GO	VACHT_TOROC	Vesicular acetylcholine transporter (VAChT) (Vesamicol-binding protein)	0.20	-	end	10 *	Membrane; multi-pass membrane protein				511
P53099 UniProt NPD GO	TPN1_YEAST	Vitamin B6 transporter TPN1 (Transport of pyridoxine protein 1)	0.20	-	end	10	Membrane; multi-pass membrane protein	plasma membrane [IDA]			579
Q2TBP4 UniProt NPD GO	WD51A_BOVIN	WD repeat protein 51A	0.20	-	cyt	0					407
P01399 UniProt NPD GO	TXW3B_NAJHA	Weak toxin CM-13b	0.20	-	nuc	0	Secreted protein				65
O49146 UniProt NPD GO	IP22_CAPAN	Wound-induced proteinase inhibitor 2 precursor (Wound-induced proteinase inhibitor II)	0.20	-	nuc	0					204
P56725 UniProt NPD GO	ZOX_PHAVU	Zeatin O-xylosyltransferase (EC 2.4.2.40) (Zeatin O-beta-D-xylosyltransferase)	0.20	-	mit	0					454
P42788 UniProt NPD GO	CBPZ_SIMVI	Zinc carboxypeptidase (EC 3.4.17.-) (Fragment)	0.20	-	cyt	0	Secreted protein				304
O15209 UniProt NPD GO	ZN297_HUMAN	Zinc finger protein 297 (BING1 protein) (Zinc finger and BTB domain-containing protein 22A)	0.20	-	nuc	0	Nucleus (Probable)	nucleus [TAS]			634
Q940T9 UniProt NPD GO	COL4_ARATH	Zinc finger protein CONSTANS-LIKE 4	0.20	-	nuc	0	Nucleus (Potential)				362
Q15072 UniProt NPD GO	OZF_HUMAN	Zinc finger protein OZF (Only zinc finger protein) (Zinc finger protein 146)	0.20	-	nuc	0	Nucleus	nucleus [TAS]	601505		292
Q7ZZS9 UniProt NPD GO	DISN_TRIJE	Zinc metalloproteinase jerdonin precursor (EC 3.4.24.-) [Contains: Disintegrin jerdonin]	0.20	-	nuc	0	Secreted protein				481
O54766 UniProt NPD GO	ZP1_RAT	Zona pellucida sperm-binding protein 1 precursor (Zona pellucida glycoprotein 1) (Zp-1)	0.20	-	exc	1	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein; extracellular ...				617
P48829 UniProt NPD GO	ZP2_RABIT	Zona pellucida sperm-binding protein 2 precursor (Zona pellucida glycoprotein ZP2) (Zona pellucida p ...	0.20	-	nuc	1	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein; extracellular ...				666
P53785 UniProt NPD GO	ZP3_MACRA	Zona pellucida sperm-binding protein 3 precursor (Zona pellucida glycoprotein ZP3) (Zona pellucida p ...	0.20	-	end	1	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein; extracellular ...				424
Q6PVW7 UniProt NPD GO	ZPBP2_CHICK	Zona pellucida-binding protein 2 precursor	0.20	-	mit	0	Secreted protein (By similarity)				352
Q6X784 UniProt NPD GO	ZPBP2_HUMAN	Zona pellucida-binding protein 2 precursor (ZPBP-like protein)	0.20	-	exc	0	Secreted protein (Potential)		608499		338
P21850 UniProt NPD GO	DA2D_PHYBI	[D-Ala2]-deltorphins precursor [Contains: [D-Ala2]-dermorphin-like; [D-Ala2]-deltorphin-2 ([D-Ala2]- ...	0.20	+	exc	0	Secreted protein				227
P47751 UniProt NPD GO	BRS4_BOMOR	[Phe13]-bombesin receptor (Bombesin receptor subtype-4) (BRS-4)	0.20	-	end	7 *	Membrane; multi-pass membrane protein				392
Q9C010 UniProt NPD GO	IPKB_HUMAN	cAMP-dependent protein kinase inhibitor beta (PKI-beta)	0.20	-	nuc	0			606914		78
P11872 UniProt NPD GO	M3R_DICDI	cAMP-regulated M3R protein (Fragment)	0.20	-	nuc	0					256
Q74Z05 UniProt NPD GO	DCP1_ASHGO	mRNA decapping enzyme 1	0.20	-	cyt	0	Cytoplasm. Is concentrated in several cytoplasmic foci called P bodies (or cytoplasmic processing bo ...				193
Q6BPR6 UniProt NPD GO	PALH_DEBHA	pH-response regulator protein palH/RIM21	0.20	-	end	6	Cell membrane; multi-pass membrane protein (By similarity)				537
Q4R6Y6 UniProt NPD GO	SNPC3_MACFA	snRNA-activating protein complex subunit 3 (SNAPc subunit 3) (snRNA-activating protein complex 50 kD ...	0.20	-	cyt	0	Nucleus (By similarity)				412
P09880 UniProt NPD GO	TRNL_YEAST	tRNA ligase (EC 6.5.1.3)	0.20	-	cyt	0		nuclear inner membrane [IDA] nucleoplasm [IDA]			827
Q562C9 UniProt NPD GO	MTND_RAT	1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase (EC 1.13.-.-) (Aci-reductone dioxygenase) (ARD) ...	0.19	-	cyt	0	Cell membrane; peripheral membrane protein; cytoplasmic side. Nucleus	cytoplasm [ISS] nucleus [ISS] plasma membrane [ISS]			179
P30924 UniProt NPD GO	GLGB_SOLTU	1,4-alpha-glucan branching enzyme (EC 2.4.1.18) (Starch branching enzyme) (Q-enzyme)	0.19	-	cyt	0	Plastid; chloroplast. Plastid; amyloplast				861
P23599 UniProt NPD GO	1A11_CUCMA	1-aminocyclopropane-1-carboxylate synthase CMW33 (EC 4.4.1.14) (ACC synthase) (S-adenosyl-L-methioni ...	0.19	-	cyt	0					493
P93784 UniProt NPD GO	14335_SOLTU	14-3-3-like protein 16R	0.19	-	nuc	0					258
Q96452 UniProt NPD GO	1433C_SOYBN	14-3-3-like protein C (SGF14C)	0.19	-	cyt	0					258
Q9S9Z8 UniProt NPD GO	14311_ARATH	14-3-3-like protein GF14 omicron (General regulatory factor 11)	0.19	-	cyt	0					241

You are viewing entries 51401 to 51450 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.