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
Q9QUG2 UniProt NPD GO	POLK_MOUSE	DNA polymerase kappa (EC 2.7.7.7) (DINB protein) (DINP)	0.89	-	nuc	0	Nucleus (By similarity). Detected throughout the nucleus and at replication foci (By similarity)	nucleus [IDA]			852
Q91684 UniProt NPD GO	DPOG1_XENLA	DNA polymerase subunit gamma 1 (EC 2.7.7.7) (Mitochondrial DNA polymerase catalytic subunit)	0.89	-	mit	0	Mitochondrion				1200
P40352 UniProt NPD GO	RAD26_YEAST	DNA repair and recombination protein RAD26 (EC 3.6.1.-) (ATP-dependent helicase RAD26)	0.89	-	nuc	0	Nucleus (Probable)	nucleus [NAS]			1085
P06839 UniProt NPD GO	RAD3_YEAST	DNA repair helicase RAD3 (EC 3.6.1.-) (General transcription and DNA repair factor IIH subunit RAD3) ...	0.89	-	cyt	0	Nucleus	nucleotide-excision repair factor 3 complex [TAS] transcription factor TFIIH complex [IDA]			778
Q9UBZ9 UniProt NPD GO	REV1_HUMAN	DNA repair protein REV1 (EC 2.7.7.-) (Rev1-like terminal deoxycytidyl transferase) (Alpha integrin-b ...	0.89	-	nuc	0	Nucleus (Probable)		606134		1251
P29469 UniProt NPD GO	MCM2_YEAST	DNA replication licensing factor MCM2 (Minichromosome maintenance protein 2)	0.89	+	nuc	0	Nucleus	cytoplasm [IDA] MCM complex [IDA] nucleus [IDA] pre-replicative complex [IDA]			868
Q7YR26 UniProt NPD GO	TOP1_CERAE	DNA topoisomerase 1 (EC 5.99.1.2) (DNA topoisomerase I)	0.89	+	nuc	0					767
Q92547 UniProt NPD GO	TOPB1_HUMAN	DNA topoisomerase 2-binding protein 1 (DNA topoisomerase II-binding protein 1) (DNA topoisomerase II ...	0.89	-	nuc	0	Nucleus. Detected on unpaired autosomes in meiotic prophase cells. Detected on X and Y chromosomes d ...	nucleus [TAS]	607760	1WF6	1522
Q8WXF8 UniProt NPD GO	DEDD2_HUMAN	DNA-binding death effector domain-containing protein 2 (FADD-like anti-apoptotic molecule 3) (DED-co ...	0.89	+	nuc	0	Nucleus. Nuclear, accumulated in subnuclear structures resembling nucleoli	nucleolus [IDA]			326
P48382 UniProt NPD GO	RFX5_HUMAN	DNA-binding protein RFX5 (Regulatory factor X subunit 5)	0.89	-	nuc	0	Nucleus	nucleus [TAS]	601863		616
Q60560 UniProt NPD GO	SMBP2_MESAU	DNA-binding protein SMUBP-2 (EC 3.6.1.-) (ATP-dependent helicase IGHMBP2) (Immunoglobulin mu-binding ...	0.89	-	nuc	0	Nucleus (Potential)				989
P04052 UniProt NPD GO	RPB1_DROME	DNA-directed RNA polymerase II largest subunit (EC 2.7.7.6)	0.89	-	nuc	0	Nucleus				1887
Q3BAQ2 UniProt NPD GO	RPOC2_PHAAO	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.89	+	nuc	0	Plastid; chloroplast				1388
Q8WI26 UniProt NPD GO	RPOC2_PSINU	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.89	-	nuc	0	Plastid; chloroplast				1408
Q8HVY3 UniProt NPD GO	RPOC2_SOYBN	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.89	+	nuc	0	Plastid; chloroplast				1386
Q8JJ48 UniProt NPD GO	DCT1A_XENLA	Dapper 1-A (Frodo)	0.89	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				818
Q8QG92 UniProt NPD GO	DCT1B_XENLA	Dapper 1-B (xDpr)	0.89	-	nuc	0	Cytoplasm. Nucleus				824
Q6QZN6 UniProt NPD GO	DACT1_BRARE	Dapper homolog 1 (Frodo 1)	0.89	+	nuc	0	Cytoplasm				821
P34205 UniProt NPD GO	PHR_CARAU	Deoxyribodipyrimidine photo-lyase (EC 4.1.99.3) (DNA photolyase) (Photoreactivating enzyme)	0.89	+	mit	0					556
Q5KSL6 UniProt NPD GO	DGKK_HUMAN	Diacylglycerol kinase kappa (EC 2.7.1.107) (Diglyceride kinase kappa) (DGK-kappa) (DAG kinase kappa) ...	0.89	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein	plasma membrane [IDA]			1271
Q8BJ42 UniProt NPD GO	DLGP2_MOUSE	Disks large-associated protein 2 (DAP-2) (SAP90/PSD-95-associated protein 2) (SAPAP2) (PSD-95/SAP90- ...	0.89	-	nuc	0	Cell membrane; peripheral membrane protein (By similarity). Postsynaptic density of neuronal cells ( ...				1059
P97837 UniProt NPD GO	DLGP2_RAT	Disks large-associated protein 2 (DAP-2) (SAP90/PSD-95-associated protein 2) (SAPAP2) (PSD-95/SAP90- ...	0.89	-	nuc	0	Cell membrane; peripheral membrane protein. Postsynaptic density of neuronal cells	dendrite [IDA] neurofilament [NAS] postsynaptic membrane [NAS]			1059
P59021 UniProt NPD GO	DSCR9_PANTR	Down syndrome critical region protein 9	0.89	-	nuc	0					149
O35492 UniProt NPD GO	CLK3_MOUSE	Dual specificity protein kinase CLK3 (EC 2.7.12.1) (CDC-like kinase 3)	0.89	+	nuc	0	Nucleus (By similarity)	nucleus [IDA]			490
Q10156 UniProt NPD GO	LKH1_SCHPO	Dual specificity protein kinase lkh1 (EC 2.7.12.1)	0.89	-	nuc	0					690
Q13627 UniProt NPD GO	DYR1A_HUMAN	Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) (Protein kinase minibrai ...	0.89	+	nuc	0	Nucleus	nucleus [IDA]	600855		763
Q61214 UniProt NPD GO	DYR1A_MOUSE	Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) (Protein kinase minibrai ...	0.89	+	nuc	0	Nucleus	nucleus [IDA]			763
Q63470 UniProt NPD GO	DYR1A_RAT	Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.2) (Protein kinase minibrai ...	0.89	+	nuc	0	Nucleus				763
Q56P03 UniProt NPD GO	EAPP_HUMAN	E2F-associated phosphoprotein (EAPP)	0.89	-	nuc	0	Cytoplasm. Nucleus		609486		285
Q6NRE7 UniProt NPD GO	CBLBB_XENLA	E3 ubiquitin-protein ligase CBL-B-B (EC 6.3.2.-) (Signal transduction protein CBL-B-B) (SH3-binding ...	0.89	-	mit	0	Cytoplasm (By similarity)				764
Q9ULT8 UniProt NPD GO	HECD1_HUMAN	E3 ubiquitin-protein ligase HECTD1 (HECT domain-containing protein 1) (E3 ligase for inhibin recepto ...	0.89	-	nuc	0					2612
Q9SLH0 UniProt NPD GO	EIL1_ARATH	ETHYLENE-INSENSITIVE3-like 1 protein	0.89	+	nuc	0	Nucleus (By similarity)				584
P17672 UniProt NPD GO	E75BA_DROME	Ecdysone-induced protein 75B isoform A (E75-B)	0.89	-	nuc	0	Nucleus (Potential)				1355
Q96FI4 UniProt NPD GO	NEIL1_HUMAN	Endonuclease VIII-like 1 (EC 3.2.2.-) (EC 4.2.99.18) (Nei-like 1) (DNA glycosylase/AP lyase Neil1) ( ...	0.89	-	nuc	0	Nucleus		608844	1TDH	389
Q4WDF1 UniProt NPD GO	EPL1_ASPFU	Enhancer of polycomb-like protein 1	0.89	-	nuc	0	Nucleus (By similarity)				582
Q9XHM1 UniProt NPD GO	IF38_MEDTR	Eukaryotic translation initiation factor 3 subunit 8 (eIF3 p110) (eIF3c)	0.89	-	nuc	0					935
O75006 UniProt NPD GO	SEC15_SCHPO	Exocyst complex component sec15	0.89	-	cyt	0					785
P32558 UniProt NPD GO	SPT16_YEAST	FACT complex subunit SPT16 (Facilitates chromatin transcription complex subunit SPT16) (Suppressor o ...	0.89	-	nuc	0	Nucleus. Colocalizes with RNA polymerase II on chromatin. Recruited to actively transcribed loci	alpha DNA polymerase:primase complex [IDA] FACT complex [IGI] nuclear chromatin [TAS]			1035
Q9Y613 UniProt NPD GO	FHOD1_HUMAN	FH1/FH2 domain-containing protein (Formin homolog overexpressed in spleen) (FHOS) (Formin homology 2 ...	0.89	-	nuc	0	Cytoplasm. Predominantly	cytoplasm [TAS] nucleus [TAS]	606881		1163
O88842 UniProt NPD GO	FGD3_MOUSE	FYVE, RhoGEF and PH domain-containing protein 3	0.89	-	nuc	0	Cytoplasm (Probable)				733
P97577 UniProt NPD GO	FEZ1_RAT	Fasciculation and elongation protein zeta 1 (Zygin-1) (Zygin I)	0.89	+	nuc	0	Cytoplasm. Cell membrane. Translocated from the plasma membrane to the cytoplasm by activation of th ...	plasma membrane [IDA]			393
O60129 UniProt NPD GO	FKH2_SCHPO	Fork head protein homolog 2	0.89	-	nuc	0	Nucleus				642
Q8WXT5 UniProt NPD GO	FX4L4_HUMAN	Forkhead box protein D4-like 4 (Forkhead box protein D4B) (Myeloid factor-gamma)	0.89	-	nuc	0	Nucleus (By similarity)				416
O88621 UniProt NPD GO	FOXH1_MOUSE	Forkhead box protein H1 (Forkhead activin signal transducer 1) (Fast-1) (Forkhead activin signal tra ...	0.89	+	nuc	0	Nucleus	nucleus [IDA] transcription factor complex [IDA]			401
P25364 UniProt NPD GO	HCM1_YEAST	Forkhead transcription factor HCM1 (High-copy suppressor of calmodulin protein 1)	0.89	+	nuc	0	Cytoplasm. Nucleus	nucleus [IPI]			564
Q9JL26 UniProt NPD GO	FMNL_MOUSE	Formin-like 1 protein (Formin-related protein)	0.89	-	nuc	0	Cytoplasm	cytosol [IDA]			1094
Q12361 UniProt NPD GO	GPR1_YEAST	G protein-coupled receptor GPR1	0.89	-	nuc	6	Membrane; multi-pass membrane protein (Probable)	plasma membrane [IDA]			961
Q5HZ36 UniProt NPD GO	GAT24_ARATH	GATA transcription factor 24	0.89	+	nuc	0	Nucleus (Probable)				398
Q4WPG0 UniProt NPD GO	GPI10_ASPFU	GPI mannosyltransferase 3 (EC 2.4.1.-) (GPI mannosyltransferase III) (GPI-MT-III) (Glycosylphosphati ...	0.89	+	end	6	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				771
Q3ZU82 UniProt NPD GO	GOGA5_RAT	Golgin subfamily A member 5 (Golgin-84)	0.89	+	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein. Found throughout the Golgi	Golgi apparatus [ISS]			728

You are viewing entries 4601 to 4650 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.