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
Q8BGW6 UniProt NPD GO	ST32A_MOUSE	Serine/threonine-protein kinase 32A (EC 2.7.11.1)	0.72	-	nuc	0					398
Q6BS08 UniProt NPD GO	ATG1_DEBHA	Serine/threonine-protein kinase ATG1 (EC 2.7.11.1) (Autophagy-related protein 1)	0.72	-	nuc	0	Cytoplasm (By similarity)				875
Q8TGI1 UniProt NPD GO	ATG1_PICPA	Serine/threonine-protein kinase ATG1 (EC 2.7.11.1) (Autophagy-related protein 1) (Glucose-induced se ...	0.72	-	nuc	0	Cytoplasm (By similarity)				796
Q8TFN2 UniProt NPD GO	ATG1_PICAN	Serine/threonine-protein kinase ATG1 (EC 2.7.11.1) (Autophagy-related protein 1) (Peroxisome degrada ...	0.72	-	nuc	0	Cytoplasm (By similarity)				804
Q6FQ83 UniProt NPD GO	BUR1_CANGA	Serine/threonine-protein kinase BUR1 (EC 2.7.11.22) (EC 2.7.11.23)	0.72	-	nuc	0	Nucleus (By similarity)				667
Q6BLJ9 UniProt NPD GO	CBK1_DEBHA	Serine/threonine-protein kinase CBK1 (EC 2.7.11.1)	0.72	-	nuc	0					716
P32801 UniProt NPD GO	ELM1_YEAST	Serine/threonine-protein kinase ELM1 (EC 2.7.11.1)	0.72	-	exc	0		contractile ring (sensu Saccharomyces) [IDA]			640
P25333 UniProt NPD GO	HAL4_YEAST	Serine/threonine-protein kinase HAL4/SAT4 (EC 2.7.11.1) (Halotolerence protein 4)	0.72	-	mit	0					603
Q9P0L2 UniProt NPD GO	MARK1_HUMAN	Serine/threonine-protein kinase MARK1 (EC 2.7.11.1) (MAP/microtubule affinity-regulating kinase 1)	0.72	-	nuc	0	Cytoplasm (By similarity). Appears to localize to an intracellular network (By similarity)	cytoplasm [ISS] cytoskeleton [ISS]	606511		795
Q8WNU8 UniProt NPD GO	NEK11_MACFA	Serine/threonine-protein kinase Nek11 (EC 2.7.11.1) (NimA-related protein kinase 11) (Never in mitos ...	0.72	-	nuc	0	Nucleus (By similarity). Nucleus; nucleolus (By similarity). Nuclear during interphase but moves to ...	nucleolus [ISS]			637
Q753D9 UniProt NPD GO	PKH3_ASHGO	Serine/threonine-protein kinase PKH3 (EC 2.7.11.1)	0.72	-	nuc	0					726
P53350 UniProt NPD GO	PLK1_HUMAN	Serine/threonine-protein kinase PLK1 (EC 2.7.11.21) (Polo-like kinase 1) (PLK-1) (Serine/threonine-p ...	0.72	-	cyt	0	Nucleus		602098	1UMW	603
Q12469 UniProt NPD GO	SKM1_YEAST	Serine/threonine-protein kinase SKM1 (EC 2.7.11.1) (Protein kinase 75490 D)	0.72	-	nuc	0					655
Q61IS6 UniProt NPD GO	SPK1_CAEBR	Serine/threonine-protein kinase spk-1 (EC 2.7.11.1)	0.72	+	nuc	0					771
Q2U639 UniProt NPD GO	ATM_ASPOR	Serine/threonine-protein kinase tel1 (EC 2.7.11.1) (DNA-damage checkpoint kinase tel1) (Telomere len ...	0.72	-	end	0	Nucleus. Localizes to nuclear DNA repair foci with other DNA repair proteins in response to DNA doub ...				2925
P63151 UniProt NPD GO	2ABA_HUMAN	Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform (PP2A, subunit B, ...	0.72	-	nuc	0		protein phosphatase type 2A complex [IDA]	604941		447
Q4R7Z4 UniProt NPD GO	2ABA_MACFA	Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform (PP2A, subunit B, ...	0.72	-	nuc	0					447
Q6P1F6 UniProt NPD GO	2ABA_MOUSE	Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform (PP2A, subunit B, ...	0.72	-	nuc	0					447
P63150 UniProt NPD GO	2ABA_RABIT	Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform (PP2A, subunit B, ...	0.72	-	nuc	0		protein phosphatase type 2A complex [ISS]			447
P54614 UniProt NPD GO	2ABB_PIG	Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B beta isoform (PP2A, subunit B, B ...	0.72	-	nuc	0					443
P36877 UniProt NPD GO	2ABB_RAT	Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B beta isoform (PP2A, subunit B, B ...	0.72	-	nuc	0					443
P40164 UniProt NPD GO	PP4R3_YEAST	Serine/threonine-protein phosphatase 4 regulatory subunit 3 (PP4R3)	0.72	-	nuc	0	Nucleus	nucleus [IDA]			858
P78968 UniProt NPD GO	PPZ_SCHPO	Serine/threonine-protein phosphatase PP-Z (EC 3.1.3.16)	0.72	-	nuc	0	Cytoplasm. Nucleus; nucleoplasm; nuclear rim	cytoplasm [IDA] nucleus [IDA]			515
Q17307 UniProt NPD GO	TRA2_CAEBR	Sex-determining transformer protein 2 precursor (Cb-Tra-2A)	0.72	-	end	9 *	Membrane; multi-pass membrane protein	integral to membrane [IDA]			1497
P49963 UniProt NPD GO	SRP19_DROME	Signal recognition particle 19 kDa protein (SRP19)	0.72	-	nuc	0	Cytoplasm				160
P33731 UniProt NPD GO	SRP72_CANFA	Signal recognition particle 72 kDa protein (SRP72)	0.72	+	nuc	0	Cytoplasm				670
Q68FP3 UniProt NPD GO	CCL6_RAT	Small inducible cytokine A6 precursor (CCL6)	0.72	-	exc	1 *	Secreted protein (By similarity)				115
Q91ZR2 UniProt NPD GO	SNX18_MOUSE	Sorting nexin-18 (Sorting nexin-associated Golgi protein 1)	0.72	-	cyt	0					614
Q5R9A9 UniProt NPD GO	SNX2_PONPY	Sorting nexin-2	0.72	-	nuc	0					523
P83213 UniProt NPD GO	HSP3_MURBR	Sperm protamine P3	0.72	+	nuc	0	Nucleus				54
Q17388 UniProt NPD GO	FER1_CAEEL	Sperm vesicle fusion protein fer-1	0.72	+	nuc	1	Membrane; single-pass type II membrane protein (By similarity)				2034
Q80UK7 UniProt NPD GO	SAS6_MOUSE	Spindle assembly abnormal protein 6 homolog	0.72	-	nuc	0	Centrosome. Component of the centrosome (By similarity)				654
Q6BVA0 UniProt NPD GO	IPL1_DEBHA	Spindle assembly checkpoint kinase (EC 2.7.11.1) (Aurora kinase)	0.72	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and on elongated and disassembling spin ...				412
Q01081 UniProt NPD GO	U2AF1_HUMAN	Splicing factor U2AF 35 kDa subunit (U2 auxiliary factor 35 kDa subunit) (U2 snRNP auxiliary factor ...	0.72	+	nuc	0	Nucleus	Cajal body [TAS] spliceosome complex [IDA]	191317	1JMT	239
Q9D883 UniProt NPD GO	U2AF1_MOUSE	Splicing factor U2AF 35 kDa subunit (U2 auxiliary factor 35 kDa subunit) (U2 snRNP auxiliary factor ...	0.72	+	nuc	0	Nucleus (By similarity)				238
P41901 UniProt NPD GO	SPR3_YEAST	Sporulation-regulated protein 3	0.72	-	nuc	0	Membrane; peripheral membrane protein (By similarity). Bud neck (By similarity). Present at the bud ...	prospore membrane [TAS] septin ring (sensu Saccharomyces) [TAS] spore wall (sensu Fungi) [TAS]			512
P13668 UniProt NPD GO	STMN1_RAT	Stathmin (Phosphoprotein p19) (pp19) (Oncoprotein 18) (Op18) (Leukemia-associated phosphoprotein p18 ...	0.72	-	nuc	0	Cytoplasm				148
O54981 UniProt NPD GO	STIP1_CRIGR	Stress-induced-phosphoprotein 1 (STI1) (Hsc70/Hsp90-organizing protein) (Hop)	0.72	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				543
Q9P6L8 UniProt NPD GO	SRB8_SCHPO	Suppressor of RNA polymerase B srb8	0.72	-	mit	0	Nucleus (Probable)				1233
Q5SQE2 UniProt NPD GO	STB5L_BRARE	Syntaxin-binding protein 5-like	0.72	+	end	0	Cytoplasm (Potential). Cell membrane; peripheral membrane protein (Potential). Membrane; peripheral ...				1159
P79742 UniProt NPD GO	TBX6_BRARE	T-box transcription factor TBX6 (T-box protein 6)	0.72	-	nuc	0	Nucleus (Potential)				473
Q6PIZ9 UniProt NPD GO	TRAT1_HUMAN	T-cell receptor-associated transmembrane adapter 1 (T-cell receptor-interacting molecule) (TRIM) (pp ...	0.72	-	nuc	1 *	Cell membrane; single-pass type III membrane protein	plasma membrane [IDA] T cell receptor complex [IDA]	604962		186
Q94818 UniProt NPD GO	TE80_TETTH	Telomerase component p80 (EC 2.7.7.49)	0.72	-	nuc	0	Nucleus (Potential)				719
P79005 UniProt NPD GO	TAZ1_SCHPO	Telomere length regulator taz1	0.72	-	nuc	0	Nucleus (Probable)	nuclear telomeric heterochromatin [IDA] telomere cap complex [TAS]			663
Q91242 UniProt NPD GO	THAB_PAROL	Thyroid hormone receptor alpha B (THR-alpha-B)	0.72	+	nuc	0	Nucleus				391
Q689D1 UniProt NPD GO	TLR2_CANFA	Toll-like receptor 2 precursor (CD282 antigen)	0.72	-	nuc	0	Membrane; single-pass type I membrane protein (By similarity)				785
Q921T2 UniProt NPD GO	TOIP1_MOUSE	Torsin-1A-interacting protein 1 (Lamina-associated polypeptide 1B)	0.72	-	nuc	1	Nucleus; nuclear inner membrane; single-pass membrane protein (By similarity)				520
O43493 UniProt NPD GO	TGON2_HUMAN	Trans-Golgi network integral membrane protein 2 precursor (Trans-Golgi network protein TGN51) (TGN46 ...	0.72	-	exc	1	Cell membrane; single-pass type I membrane protein. Golgi apparatus; trans-Golgi network; trans-Golg ...	Golgi trans face [TAS] transport vesicle [TAS]	603062		480
Q6IPX3 UniProt NPD GO	TCAL6_HUMAN	Transcription elongation factor A protein-like 6 (TCEA-like protein 6) (Transcription elongation fac ...	0.72	-	nuc	0	Nucleus (Probable)				200
Q91428 UniProt NPD GO	GATA3_BRARE	Transcription factor GATA-3 (GATA-binding factor 3)	0.72	-	nuc	0	Nucleus				438

You are viewing entries 13001 to 13050 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.