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
P21840 UniProt NPD GO	VSM5_TRYBR	Variant surface glycoprotein MVAT5 precursor (VSG)	0.19	-	cyt	0	Cell membrane; lipid-anchor; GPI-anchor. A soluble form is released from ruptured cells by the actio ...				517
O95498 UniProt NPD GO	VNN2_HUMAN	Vascular non-inflammatory molecule 2 precursor (Vanin-2) (Glycosylphosphatidyl inositol-anchored pro ...	0.19	-	end	1	Cell membrane; lipid-anchor; GPI-anchor (Potential)		603571		520
P30083 UniProt NPD GO	VIPR1_RAT	Vasoactive intestinal polypeptide receptor 1 precursor (VIP-R-1) (Pituitary adenylate cyclase-activa ...	0.19	-	end	7	Membrane; multi-pass membrane protein				459
P01185 UniProt NPD GO	NEU2_HUMAN	Vasopressin-neurophysin 2-copeptin precursor (AVP-NPII) [Contains: Arg-vasopressin; Neurophysin 2 (N ...	0.19	-	nuc	0	Secreted protein	soluble fraction [TAS]	192340		164
Q96VG3 UniProt NPD GO	YL93_SCHPO	Very hypothetical protein C683.03 in chromosome I	0.19	-	nuc	0					105
P38183 UniProt NPD GO	YBH7_YEAST	Very hypothetical protein YBL077W	0.19	-	nuc	0					143
P36072 UniProt NPD GO	YKL8_YEAST	Very hypothetical protein YKL118W	0.19	-	mit	1 *					103
Q63666 UniProt NPD GO	VAMP1_RAT	Vesicle-associated membrane protein 1 (VAMP-1) (Synaptobrevin-1)	0.19	-	nuc	1	Synaptic vesicle; synaptic vesicle membrane; single-pass type IV membrane protein. Neuronal synaptic ...				118
Q6TAC4 UniProt NPD GO	V2R1B_MOUSE	Vomeronasal type-2 receptor 1b precursor (Putative pheromone receptor V2R1b)	0.19	-	end	7	Membrane; multi-pass membrane protein (Potential)				855
Q8BUB4 UniProt NPD GO	WDFY2_MOUSE	WD repeat and FYVE domain-containing protein 2 (WD40- and FYVE domain-containing protein 2)	0.19	-	cyt	0					400
Q6AY57 UniProt NPD GO	WIPI2_RAT	WD repeat domain phosphoinositide-interacting protein 2 (WIPI-2)	0.19	-	cyt	0					445
Q96EX3 UniProt NPD GO	WDR34_HUMAN	WD repeat protein 34	0.19	-	cyt	0					536
Q9NNW5 UniProt NPD GO	WDR6_HUMAN	WD repeat protein 6	0.19	-	cyt	0			606031		1121
Q5FWQ6 UniProt NPD GO	WDR69_XENLA	WD repeat protein 69	0.19	-	mit	0					415
P24335 UniProt NPD GO	WAG1_TRIWA	Waglerin-1 (Waglerin I) (Lethal peptide I)	0.19	-	nuc	0	Secreted protein				22
P01174 UniProt NPD GO	WAP_RAT	Whey acidic protein precursor (Whey phosphoprotein) (WAP)	0.19	-	exc	0	Secreted protein				137
Q9WUA1 UniProt NPD GO	WIF1_MOUSE	Wnt inhibitory factor 1 precursor (WIF-1)	0.19	-	mit	0	Secreted protein				379
P09761 UniProt NPD GO	WIN1_SOLTU	Wound-induced protein WIN1 precursor	0.19	-	nuc	0					200
P42578 UniProt NPD GO	FRIY_LYMST	Yolk ferritin precursor (EC 1.16.3.1)	0.19	-	exc	0	Secreted protein				239
O02350 UniProt NPD GO	CBPA1_ANOGA	Zinc carboxypeptidase A 1 precursor (EC 3.4.17.-) (AgCP)	0.19	-	cyt	0	Secreted protein	extracellular space [ISS]			433
P17037 UniProt NPD GO	ZNF29_HUMAN	Zinc finger protein 29 (Zinc finger protein KOX26) (Fragment)	0.19	-	nuc	0	Nucleus (Potential)		194535		56
Q90YA6 UniProt NPD GO	DIS2_TRIEL	Zinc metalloproteinase elegantin-2 precursor (EC 3.4.24.-) [Contains: Disintegrin elegantin-2a; Disi ...	0.19	-	mit	0	Secreted protein (By similarity)				481
Q6EAS5 UniProt NPD GO	GLGB_HORSE	1,4-alpha-glucan branching enzyme (EC 2.4.1.18) (Glycogen branching enzyme) (Brancher enzyme)	0.18	-	cyt	0					699
P46515 UniProt NPD GO	LEA11_HELAN	11 kDa late embryogenesis abundant protein (DS11)	0.18	-	nuc	0					104
P93211 UniProt NPD GO	14336_LYCES	14-3-3 protein 6	0.18	-	nuc	0					258
P68253 UniProt NPD GO	1433G_SHEEP	14-3-3 protein gamma (Protein kinase C inhibitor protein 1) (KCIP-1) (Fragments)	0.18	-	nuc	0	Cytoplasm	cytoplasm [ISS]			158
Q9U408 UniProt NPD GO	14331_ECHGR	14-3-3 protein homolog 1	0.18	-	nuc	0					244
O49997 UniProt NPD GO	1433E_TOBAC	14-3-3-like protein E	0.18	-	nuc	0					272
Q96300 UniProt NPD GO	14337_ARATH	14-3-3-like protein GF14 nu (General regulatory factor 7)	0.18	-	nuc	0					265
Q5M875 UniProt NPD GO	DHB13_RAT	17-beta hydroxysteroid dehydrogenase 13 precursor (EC 1.1.-.-) (Short-chain dehydrogenase/reductase ...	0.18	-	nuc	0	Secreted protein (Potential)				300
O24364 UniProt NPD GO	BAS1_SPIOL	2-cys peroxiredoxin BAS1, chloroplast precursor (EC 1.11.1.15) (Thiol-specific antioxidant protein)	0.18	-	mit	0	Plastid; chloroplast (By similarity)				265
O94742 UniProt NPD GO	SEM1_YEAST	26 proteasome complex subunit SEM1	0.18	-	nuc	0		cytosol [IDA] microsome [IDA] nucleus [IPI] proteasome regulatory particle, lid subcomp... [IDA]			89
Q99460 UniProt NPD GO	PSD1_HUMAN	26S proteasome non-ATPase regulatory subunit 1 (26S proteasome regulatory subunit RPN2) (26S proteas ...	0.18	-	cyt	0		proteasome regulatory particle (sensu Eukar... [TAS]			953
Q58DA0 UniProt NPD GO	PSD4_BOVIN	26S proteasome non-ATPase regulatory subunit 4	0.18	-	nuc	0					382
P55035 UniProt NPD GO	PSD4_DROME	26S proteasome non-ATPase regulatory subunit 4 (26S proteasome regulatory subunit S5A) (Multiubiquit ...	0.18	-	nuc	0		proteasome regulatory particle (sensu Eukar... [IDA]			396
Q6FIP2 UniProt NPD GO	RPN2_CANGA	26S proteasome regulatory subunit RPN2	0.18	-	cyt	0					941
Q61767 UniProt NPD GO	3BHS4_MOUSE	3 beta-hydroxysteroid dehydrogenase type 4 (3 beta-hydroxysteroid dehydrogenase type IV) (3Beta-HSD ...	0.18	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein. Mitochondrion; ...	mitochondrial inner membrane [IDA] mitochondrion [IDA]			372
O74164 UniProt NPD GO	HMDH_PICJA	3-hydroxy-3-methylglutaryl-coenzyme A reductase (EC 1.1.1.34) (HMG-CoA reductase)	0.18	-	end	6	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				934
P16393 UniProt NPD GO	HMDH_STRPU	3-hydroxy-3-methylglutaryl-coenzyme A reductase (EC 1.1.1.34) (HMG-CoA reductase)	0.18	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				932
P46952 UniProt NPD GO	3HAO_HUMAN	3-hydroxyanthranilate 3,4-dioxygenase (EC 1.13.11.6) (3-HAO) (3-hydroxyanthranilic acid dioxygenase) ...	0.18	-	mit	0	Cytoplasm		604521		286
Q9Y7B6 UniProt NPD GO	PANB_EMENI	3-methyl-2-oxobutanoate hydroxymethyltransferase (EC 2.1.2.11) (Ketopantoate hydroxymethyltransferas ...	0.18	-	mit	0					349
P49314 UniProt NPD GO	ROC2_NICPL	31 kDa ribonucleoprotein, chloroplast precursor (CP-RBP31)	0.18	-	mit	0	Plastid; chloroplast				292
P80831 UniProt NPD GO	CWP07_ARATH	34 kDa cell wall protein (Fragment)	0.18	-		0	Cell wall				5
Q00451 UniProt NPD GO	PRF1_LYCES	36.4 kDa proline-rich protein	0.18	-	nuc	0					346
Q9FFS8 UniProt NPD GO	RS10B_ARATH	40S ribosomal protein S10-2	0.18	-	cyt	0	Cytoplasm (By similarity)				180
Q98TR7 UniProt NPD GO	RS16_HETFO	40S ribosomal protein S16	0.18	-	cyt	0					146
P40978 UniProt NPD GO	RS19_ORYSA	40S ribosomal protein S19	0.18	-	mit	0					146
Q9N9V4 UniProt NPD GO	RS25_LEIIN	40S ribosomal protein S25	0.18	-	nuc	0					120
Q03409 UniProt NPD GO	RS25_DICDI	40S ribosomal protein S25 (S31)	0.18	-	nuc	0					110
P38654 UniProt NPD GO	RS27_ENTHI	40S ribosomal protein S27 (EHZC3 protein)	0.18	-	nuc	0					84

You are viewing entries 52601 to 52650 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.