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
P13186 UniProt NPD GO	KIN2_YEAST	Serine/threonine-protein kinase KIN2 (EC 2.7.11.1)	0.78	-	nuc	0		membrane fraction [IDA] plasma membrane [IPI]			1147
P38623 UniProt NPD GO	RCK2_YEAST	Serine/threonine-protein kinase RCK2 (EC 2.7.11.1) (CAM kinase-like protein kinase CLK1)	0.78	-	nuc	0	Cytoplasm	cytoplasm [IDA]			610
Q9BRS2 UniProt NPD GO	RIOK1_HUMAN	Serine/threonine-protein kinase RIO1 (EC 2.7.11.1) (RIO kinase 1)	0.78	+	nuc	0					568
P11792 UniProt NPD GO	SCH9_YEAST	Serine/threonine-protein kinase SCH9 (EC 2.7.11.1)	0.78	-	nuc	0		cytoplasm [IDA] nucleus [IDA] vacuolar membrane (sensu Fungi) [IDA]			823
Q03656 UniProt NPD GO	SKY1_YEAST	Serine/threonine-protein kinase SKY1 (EC 2.7.11.1) (SRPK)	0.78	-	nuc	0		cytoplasm [IDA]		1Q99	742
Q8BKX6 UniProt NPD GO	SMG1_MOUSE	Serine/threonine-protein kinase SMG1 (EC 2.7.11.1) (SMG-1)	0.78	-	cyt	0	Nucleus (By similarity). Cytoplasm (By similarity)				3658
Q96Q15 UniProt NPD GO	SMG1_HUMAN	Serine/threonine-protein kinase SMG1 (EC 2.7.11.1) (SMG-1) (hSMG-1) (Lambda/iota protein kinase C-in ...	0.78	-	nuc	0	Nucleus. Cytoplasm	cytoplasm [IDA] nucleus [IDA]	607032		3657
O54781 UniProt NPD GO	SRPK2_MOUSE	Serine/threonine-protein kinase SRPK2 (EC 2.7.11.1) (Serine/arginine-rich protein-specific kinase 2) ...	0.78	+	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			681
P22219 UniProt NPD GO	VPS15_YEAST	Serine/threonine-protein kinase VPS15 (EC 2.7.11.1) (Vacuolar protein sorting protein 15) (Golgi-ret ...	0.78	-	cyt	0	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; lipid-anchor. Endosome; endosoma ...	Golgi membrane [TAS] mitochondrion [IDA]			1453
Q9DE14 UniProt NPD GO	ATR_XENLA	Serine/threonine-protein kinase atr (EC 2.7.11.1) (Ataxia telangiectasia and Rad3-related protein) ( ...	0.78	-	end	0	Nucleus				2654
O94547 UniProt NPD GO	SRK1_SCHPO	Serine/threonine-protein kinase srk1 (EC 2.7.11.1) (Sty1-regulated kinase 1)	0.78	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			580
Q80W00 UniProt NPD GO	PP1RA_MOUSE	Serine/threonine-protein phosphatase 1 regulatory subunit 10 (MHC class I region proline-rich protei ...	0.78	+	nuc	0	Nucleus. Found in discrete nucleoplasmic bodies and within nucleoli (By similarity)				888
Q7YR38 UniProt NPD GO	PP1RA_PANTR	Serine/threonine-protein phosphatase 1 regulatory subunit 10 (MHC class I region proline-rich protei ...	0.78	+	nuc	0	Nucleus. Found in discrete nucleoplasmic bodies and within nucleoli (By similarity)				940
Q96QC0 UniProt NPD GO	PP1RA_HUMAN	Serine/threonine-protein phosphatase 1 regulatory subunit 10 (Phosphatase 1 nuclear targeting subuni ...	0.78	+	nuc	0	Nucleus. Found in discrete nucleoplasmic bodies and within nucleoli		603771		940
Q28653 UniProt NPD GO	2A5D_RABIT	Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform (PP2A, B subunit, B' ...	0.78	-	nuc	0	Nucleus (By similarity)				586
Q864P3 UniProt NPD GO	SRY_ORCBR	Sex-determining region Y protein (Testis-determining factor)	0.78	+	nuc	0	Nucleus				201
Q6PHS6 UniProt NPD GO	SNX13_MOUSE	Sorting nexin-13	0.78	-	end	2 *					957
Q5AD77 UniProt NPD GO	SNX4_CANAL	Sorting nexin-4 (Autophagy-related protein 24)	0.78	+	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Endosome; endosoma ...				630
Q8WNY9 UniProt NPD GO	HSP1_CHABE	Sperm protamine P1	0.78	+	nuc	0	Nucleus (By similarity)				45
Q8WP00 UniProt NPD GO	HSP1_CYNVA	Sperm protamine P1	0.78	+	nuc	0	Nucleus (By similarity)				46
Q8WME4 UniProt NPD GO	HSP1_DESRO	Sperm protamine P1	0.78	+	nuc	0	Nucleus (By similarity)				47
P42132 UniProt NPD GO	HSP1_DROAU	Sperm protamine P1	0.78	+	nuc	0	Nucleus				63
Q7JH06 UniProt NPD GO	HSP1_MONRE	Sperm protamine P1	0.78	+	nuc	0	Nucleus (By similarity)				47
Q8WNY7 UniProt NPD GO	HSP1_MURCY	Sperm protamine P1	0.78	+	nuc	0	Nucleus (By similarity)				47
P42145 UniProt NPD GO	HSP1_PSECU	Sperm protamine P1	0.78	+	nuc	0	Nucleus				68
Q7JH07 UniProt NPD GO	HSP1_PTEPA	Sperm protamine P1	0.78	+	nuc	0	Nucleus (By similarity)				47
Q9TUC4 UniProt NPD GO	HSP1_SMIBI	Sperm protamine P1	0.78	+	nuc	0	Nucleus (By similarity)				62
P02319 UniProt NPD GO	HSP1_MOUSE	Sperm protamine P1 (Cysteine-rich protamine)	0.78	+	nuc	0	Nucleus	nucleus [IDA]			50
P35310 UniProt NPD GO	HSP1_PONPY	Sperm protamine P1 (Cysteine-rich protamine)	0.78	-	mit	0	Nucleus	nucleoplasm [ISS]			50
P24714 UniProt NPD GO	HSP1_SAGIM	Sperm protamine P1 (Cysteine-rich protamine)	0.78	+	nuc	0	Nucleus				49
P38991 UniProt NPD GO	IPL1_YEAST	Spindle assembly checkpoint kinase (EC 2.7.11.1) (Aurora kinase) (Increase-in-ploidy protein 1)	0.78	-	mit	0	Nucleus. Associates with the mitotic spindle and on elongated and disassembling spindles. Also assoc ...	condensed nuclear chromosome kinetochore [IDA] kinetochore microtubule [IDA] spindle midzone [IDA]			367
Q92351 UniProt NPD GO	PCP1_SCHPO	Spindle pole body protein pcp1	0.78	-	nuc	0	Spindle pole body	spindle pole body [IDA]			1208
Q01649 UniProt NPD GO	CIK1_YEAST	Spindle pole body-associated protein	0.78	-	nuc	0		cytoplasmic microtubule [TAS] kinesin complex [IDA] spindle [IDA] spindle pole body [IDA]			594
P35447 UniProt NPD GO	SPON1_XENLA	Spondin-1 precursor (F-spondin)	0.78	+	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				803
Q8K031 UniProt NPD GO	STAR8_MOUSE	StAR-related lipid transfer protein 8 (StARD8) (START domain-containing protein 8)	0.78	-	nuc	0					1019
O95718 UniProt NPD GO	ERR2_HUMAN	Steroid hormone receptor ERR2 (Estrogen-related receptor, beta) (ERR-beta) (Estrogen receptor-like 2 ...	0.78	-	nuc	0	Nucleus (Potential)		602167	1LO1	500
Q70M86 UniProt NPD GO	STRN_SORMA	Striatin Pro11	0.78	+	nuc	0	Membrane; peripheral membrane protein	membrane fraction [IDA]			845
Q8CG48 UniProt NPD GO	SMC2_MOUSE	Structural maintenance of chromosome 2-like 1 protein (Chromosome-associated protein E) (XCAP-E homo ...	0.78	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). In interphase cells, the majority of the condens ...				1191
Q8ND82 UniProt NPD GO	SUHW3_HUMAN	Suppressor of hairy wing homolog 3	0.78	+	nuc	0	Nucleus (Potential)				737
Q80X82 UniProt NPD GO	SYMPK_MOUSE	Symplekin	0.78	+	cyt	0	Cytoskeleton (By similarity). Cell membrane; cell-cell junction; adherens junction; cytoplasmic side ...				1284
Q63520 UniProt NPD GO	SYCP3_RAT	Synaptonemal complex protein 3 (SCP-3)	0.78	-	nuc	0	Nucleus. In tripartite segments of synaptonemal complexes, irrespective of whether these are synapse ...				257
Q86SS6 UniProt NPD GO	SYT9_HUMAN	Synaptotagmin-9 (Synaptotagmin IX) (SytIX)	0.78	+	mit	1 *	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein (By similarity)				491
Q9R0N9 UniProt NPD GO	SYT9_MOUSE	Synaptotagmin-9 (Synaptotagmin IX) (SytIX) (Synaptotagmin V)	0.78	+	mit	1 *	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein				491
Q925C0 UniProt NPD GO	SYT9_RAT	Synaptotagmin-9 (Synaptotagmin IX) (SytIX) (Synaptotagmin V) (Synaptotagmin 5)	0.78	+	mit	1 *	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein				491
Q80XQ2 UniProt NPD GO	TBCD5_MOUSE	TBC1 domain family member 5	0.78	-	nuc	0					815
Q9Y490 UniProt NPD GO	TLN1_HUMAN	Talin-1	0.78	-	nuc	0		cytosol [ISS] focal adhesion [NAS] intercellular junction [IC] ruffle [ISS]	186745	1SYQ	2541
Q6P132 UniProt NPD GO	TAXB1_BRARE	Tax1-binding protein 1 homolog	0.78	-	nuc	0					810
P01267 UniProt NPD GO	THYG_BOVIN	Thyroglobulin precursor	0.78	-	nuc	0	Secreted protein				2769
O14248 UniProt NPD GO	TEA3_SCHPO	Tip elongation aberrant protein 3 (Cell polarity protein tea3)	0.78	-	nuc	0	Present at both poles of the cell throughout the cell cycle whether they are growing or not. Located ...	cell cortex of cell tip [IDA]			1125
P58681 UniProt NPD GO	TLR7_MOUSE	Toll-like receptor 7 precursor	0.78	-	end	2 *	Membrane; single-pass type I membrane protein (By similarity)				1050

You are viewing entries 10101 to 10150 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.