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
P35274 UniProt NPD GO	ZN125_HUMAN	Zinc finger protein 125 (HZF-3) (Fragment)	0.52	-	nuc	0	Nucleus (Potential)	nucleus [NAS]	194632		116
Q13106 UniProt NPD GO	ZN154_HUMAN	Zinc finger protein 154	0.52	-	nuc	0	Nucleus (Potential)	nucleus [NAS]	604085		437
O43829 UniProt NPD GO	ZF161_HUMAN	Zinc finger protein 161 homolog (Zfp-161) (Zinc finger protein 5) (hZF5) (Zinc finger and BTB domain ...	0.52	-	nuc	0	Nucleus	nucleus [TAS]	602126		449
Q9JKY3 UniProt NPD GO	ZN238_RAT	Zinc finger protein 238 (Transcriptional repressor RP58) (58 kDa repressor protein) (rRP58)	0.52	-	nuc	0	Nucleus. Associates with condensed chromatin				522
Q14587 UniProt NPD GO	ZN268_HUMAN	Zinc finger protein 268 (Zinc finger protein HZF3)	0.52	-	nuc	0	Nucleus (Probable)	nucleus [NAS]	604753		947
Q8TF32 UniProt NPD GO	ZN431_HUMAN	Zinc finger protein 431	0.52	-	nuc	0	Nucleus (Potential)				576
Q5JVG8 UniProt NPD GO	ZN506_HUMAN	Zinc finger protein 506	0.52	-	nuc	0	Nucleus (Potential)				444
Q96MR9 UniProt NPD GO	ZN560_HUMAN	Zinc finger protein 560	0.52	-	nuc	0	Nucleus (Probable)				790
Q8IYB9 UniProt NPD GO	ZN595_HUMAN	Zinc finger protein 595	0.52	-	nuc	0	Nucleus (Probable)				648
Q9Y462 UniProt NPD GO	ZN711_HUMAN	Zinc finger protein 711 (Zinc finger protein 6)	0.52	+	nuc	0	Nucleus (Probable)		314990		771
Q99684 UniProt NPD GO	GFI1_HUMAN	Zinc finger protein Gfi-1 (Growth factor independence 1)	0.52	-	nuc	0	Nucleus		607847		422
P70338 UniProt NPD GO	GFI1_MOUSE	Zinc finger protein Gfi-1 (Growth factor independence 1)	0.52	-	nuc	0	Nucleus				423
O95863 UniProt NPD GO	SNAI_HUMAN	Zinc finger protein SNAI1 (Protein snail homolog) (Protein sna)	0.52	-	nuc	0	Nucleus (Potential)		604238		264
O95409 UniProt NPD GO	ZIC2_HUMAN	Zinc finger protein ZIC 2 (Zinc finger protein of the cerebellum 2)	0.52	-	nuc	0	Nucleus		609637		532
Q62520 UniProt NPD GO	ZIC2_MOUSE	Zinc finger protein ZIC 2 (Zinc finger protein of the cerebellum 2)	0.52	-	nuc	0	Nucleus	nucleus [IDA]			530
Q62521 UniProt NPD GO	ZIC3_MOUSE	Zinc finger protein ZIC 3 (Zinc finger protein of the cerebellum 3)	0.52	-	nuc	0	Nucleus				466
Q7T3U0 UniProt NPD GO	ZAR1_XENLA	Zygote arrest 1 (Oocyte-specific maternal effect factor)	0.52	-	nuc	0	Cytoplasm				295
P07802 UniProt NPD GO	KAP0_PIG	cAMP-dependent protein kinase type I-alpha regulatory subunit	0.52	-	mit	0					379
Q01062 UniProt NPD GO	PDE2A_RAT	cGMP-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) (Cyclic GMP-stimulated phosphodiesterase ...	0.52	-	cyt	0	Membrane; peripheral membrane protein (Potential)				928
Q6FTL0 UniProt NPD GO	YTH1_CANGA	mRNA 3'-end-processing protein YTH1	0.52	-	nuc	0	Nucleus (By similarity)				209
Q9NWT1 UniProt NPD GO	PK1IP_HUMAN	p21-activated protein kinase-interacting protein 1 (PAK1-interacting protein 1) (PAK/PLC-interacting ...	0.52	+	cyt	0	Nucleus; nucleolus		607811		392
Q04338 UniProt NPD GO	VTI1_YEAST	t-SNARE VTI1 (Qb-SNARE VTI1) (Vesicle transport v-SNARE protein VTI1) (VPS10-interacting protein 1)	0.52	-	nuc	1	Prevacuolar compartment; prevacuolar compartment membrane; single-pass type IV membrane protein. Gol ...	integral to Golgi membrane [IDA]			216
Q03774 UniProt NPD GO	TRM82_YEAST	tRNA (guanine-N(7)-)-methyltransferase-associated WD repeat protein TRM82	0.52	-	nuc	0		nucleus [IDA]			444
Q9JI38 UniProt NPD GO	PUS3_MOUSE	tRNA pseudouridine synthase 3 (EC 5.4.99.-) (tRNA-uridine isomerase 3) (tRNA pseudouridylate synthas ...	0.52	+	cyt	0	Nucleus (Potential)				481
P48567 UniProt NPD GO	PUS4_YEAST	tRNA pseudouridine synthase 4 (EC 5.4.99.-) (tRNA pseudouridine 55 synthase) (Psi55 synthase) (tRNA- ...	0.52	+	nuc	0	Nucleus. Mitochondrion	mitochondrion [IMP] nucleus [IMP]			403
P04275 UniProt NPD GO	VWF_HUMAN	von Willebrand factor precursor (vWF) [Contains: von Willebrand antigen 2 (von Willebrand antigen II ...	0.52	-	nuc	0	Secreted protein. Localized to storage granules	extracellular region [NAS]	193400	2ADF	2813
Q3TFD2 UniProt NPD GO	PCAT1_MOUSE	1-acylglycerophosphocholine O-acyltransferase 1 (EC 2.3.1.23) (Lung-type acyl-coa:lysophosphatidylch ...	0.51	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein. Golgi a ...				534
Q06429 UniProt NPD GO	1A11_ARATH	1-aminocyclopropane-1-carboxylate synthase-like protein 1	0.51	-	cyt	0					488
P10688 UniProt NPD GO	PLCD1_RAT	1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase delta 1 (EC 3.1.4.11) (Phosphoinositide ph ...	0.51	-	nuc	0				2ISD	756
P20967 UniProt NPD GO	ODO1_YEAST	2-oxoglutarate dehydrogenase E1 component, mitochondrial precursor (EC 1.2.4.2) (Alpha-ketoglutarate ...	0.51	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial nucleoid [IDA] oxoglutarate dehydrogenase complex (sensu E... [IDA]			1014
P34123 UniProt NPD GO	PRS6B_DICDI	26S protease regulatory subunit 6B homolog (TAT-binding protein homolog 2)	0.51	-	cyt	0	Cytoplasm (Potential). Nucleus (Potential)				403
P40016 UniProt NPD GO	RPN3_YEAST	26S proteasome regulatory subunit RPN3	0.51	-	nuc	0		proteasome regulatory particle, lid subcomp... [IPI]			522
Q9UTM3 UniProt NPD GO	RPN5_SCHPO	26S proteasome regulatory subunit rpn5	0.51	-	cyt	0	Nucleus	nuclear membrane [IDA]			443
P15461 UniProt NPD GO	2SS5_HELAN	2S seed storage protein precursor (2S albumin storage protein)	0.51	-	exc	1 *					295
Q4IJK2 UniProt NPD GO	RT10_GIBZE	30S ribosomal protein S10, mitochondrial precursor (Mitochondrial ribosomal small subunit protein 10 ...	0.51	-	mit	0	Mitochondrion (By similarity)				236
P46301 UniProt NPD GO	RS25_LYCES	40S ribosomal protein S25	0.51	-	nuc	0					108
P13008 UniProt NPD GO	RS26_DROME	40S ribosomal protein S26 (DS31)	0.51	-	nuc	0					114
P39938 UniProt NPD GO	RS26A_YEAST	40S ribosomal protein S26-A	0.51	-	nuc	0	Cytoplasm	cytosolic small ribosomal subunit (sensu Eu... [TAS]			119
P62983 UniProt NPD GO	RS27A_MOUSE	40S ribosomal protein S27a	0.51	+	nuc	0					80
P62982 UniProt NPD GO	RS27A_RAT	40S ribosomal protein S27a	0.51	+	nuc	0					80
P13195 UniProt NPD GO	HEM1_RAT	5-aminolevulinate synthase, nonspecific, mitochondrial precursor (EC 2.3.1.37) (5-aminolevulinic aci ...	0.51	-	mit	0	Mitochondrion; mitochondrial matrix				642
Q25190 UniProt NPD GO	5HTR_HELVI	5-hydroxytryptamine receptor (5-HT receptor) (Serotonin receptor)	0.51	+	end	7	Membrane; multi-pass membrane protein				466
P91953 UniProt NPD GO	HE_HEMPU	50 kDa hatching enzyme precursor (EC 3.4.24.12) (HE) (HEZ) (Envelysin) (Sea-urchin-hatching proteina ...	0.51	-	mit	0					591
Q9FLN4 UniProt NPD GO	RK27_ARATH	50S ribosomal protein L27, chloroplast precursor	0.51	-	nuc	0	Plastid; chloroplast				198
Q12471 UniProt NPD GO	6P22_YEAST	6-phosphofructo-2-kinase 2 (EC 2.7.1.105) (Phosphofructokinase 2 II) (6PF-2-K 2)	0.51	-	nuc	0					397
P41126 UniProt NPD GO	RL13_DROME	60S ribosomal protein L13 (BBC1 protein homolog)	0.51	-	mit	0					218
Q9LRX8 UniProt NPD GO	R13A2_ARATH	60S ribosomal protein L13a-2	0.51	+	cyt	0					206
Q9FKC0 UniProt NPD GO	R13A4_ARATH	60S ribosomal protein L13a-4	0.51	+	cyt	0					206
P55841 UniProt NPD GO	RL14_DROME	60S ribosomal protein L14	0.51	-	nuc	0		ribosome [NAS]			166
P05740 UniProt NPD GO	RL17A_YEAST	60S ribosomal protein L17-A (YL17-A)	0.51	-	mit	0		cytoplasm [IDA] cytosolic large ribosomal subunit (sensu Eu... [TAS]		1K5Y	183

You are viewing entries 24101 to 24150 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.