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
P36160 UniProt NPD GO	RPF2_YEAST	Ribosome biogenesis protein RPF2	0.67	-	mit	0	Nucleus; nucleolus	nucleolus [IDA]			344
Q755G5 UniProt NPD GO	RUVB2_ASHGO	RuvB-like helicase 2 (EC 3.6.1.-)	0.67	-	cyt	0	Nucleus (By similarity)				469
Q9UHR5 UniProt NPD GO	S30BP_HUMAN	SAP30-binding protein (Transcriptional regulator protein HCNGP)	0.67	-	exc	0	Nucleus				308
Q02614 UniProt NPD GO	S30BP_MOUSE	SAP30-binding protein (Transcriptional regulator protein HCNGP)	0.67	-	exc	0	Nucleus				308
Q9SD96 UniProt NPD GO	SNP29_ARATH	SNAP25 homologous protein SNAP29 (AtSNAP29) (Synaptosomal-associated protein SNAP25-like 2)	0.67	-	nuc	0					251
Q8K2M3 UniProt NPD GO	SRR1L_MOUSE	SRR1-like protein (Fragment)	0.67	+	nuc	0					243
Q8MJJ7 UniProt NPD GO	DCPS_BOVIN	Scavenger mRNA decapping enzyme DcpS (EC 3.-.-.-) (DCS-1) (Hint-related 7meGMP-directed hydrolase) ( ...	0.67	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				337
Q8WVM8 UniProt NPD GO	SCFD1_HUMAN	Sec1 family domain-containing protein 1 (Syntaxin-binding protein 1-like 2) (Sly1p)	0.67	-	nuc	0	Cytoplasm (By similarity). Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membran ...				641
O42237 UniProt NPD GO	SEM3E_CHICK	Semaphorin-3E precursor (Collapsin-5) (COLL-5)	0.67	+	mit	0	Secreted protein				785
O77733 UniProt NPD GO	SEMG1_SAGOE	Semenogelin-1 precursor (Semenogelin I) (SGI)	0.67	-	nuc	0	Secreted protein (By similarity)				615
Q4R4X5 UniProt NPD GO	SEPT4_MACFA	Septin-4	0.67	-	nuc	0					478
P26686 UniProt NPD GO	SRR55_DROME	Serine-arginine protein 55 (SRP55) (Protein enhancer of deformed) (52 kDa bracketing protein) (B52 p ...	0.67	+	nuc	0	Nucleus. Associated with boundaries of transcriptionally active chromatin	nuclear speck [IDA] nucleus [IDA]			375
O70126 UniProt NPD GO	AURKB_MOUSE	Serine/threonine-protein kinase 12 (EC 2.7.11.1) (Aurora-related kinase 2) (Serine/threonine-protein ...	0.67	-	nuc	0	Nucleus. Localizes on chromosome arms and inner centromeres from prophase through metaphase and then ...				345
O15075 UniProt NPD GO	DCAK1_HUMAN	Serine/threonine-protein kinase DCAMKL1 (EC 2.7.11.1) (Doublecortin-like and CAM kinase-like 1)	0.67	-	nuc	0		integral to plasma membrane [TAS]	604742	1UF0	740
O08678 UniProt NPD GO	MARK1_RAT	Serine/threonine-protein kinase MARK1 (EC 2.7.11.1) (MAP/microtubule affinity-regulating kinase 1)	0.67	-	nuc	0	Cytoplasm. Appears to localize to an intracellular network	cytoplasm [IDA] microtubule cytoskeleton [NAS]			793
Q8VHJ5 UniProt NPD GO	MARK1_MOUSE	Serine/threonine-protein kinase MARK1 (EC 2.7.11.1) (MAP/microtubule affinity-regulating kinase 1) ( ...	0.67	-	nuc	0	Cytoplasm (By similarity). Appears to localize to an intracellular network (By similarity)				795
Q12196 UniProt NPD GO	RIO1_YEAST	Serine/threonine-protein kinase RIO1 (EC 2.7.11.1) (Ribosomal RNA-processing protein 10)	0.67	+	nuc	0	Cytoplasm	cytoplasm [IDA] nucleus [IDA]			484
Q7ZUS1 UniProt NPD GO	VRK1_BRARE	Serine/threonine-protein kinase VRK1 (EC 2.7.11.1) (Vaccinia-related kinase 1)	0.67	+	nuc	0	Nucleus (By similarity)				425
Q5BCU8 UniProt NPD GO	ATG1_EMENI	Serine/threonine-protein kinase atg1 (EC 2.7.11.1) (Autophagy-related protein 1)	0.67	-	nuc	0	Cytoplasm (By similarity)				935
P50526 UniProt NPD GO	SSP1_SCHPO	Serine/threonine-protein kinase ssp1 (EC 2.7.11.1)	0.67	-	nuc	0	Cytoplasm (Probable)	cell cortex of cell tip [IDA] cell septum [IDA] cytoplasm [IDA]			652
Q10428 UniProt NPD GO	2AD1_SCHPO	Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta 1 isoform (PP2A, B subunit, ...	0.67	+	nuc	0	Cytoplasm. Nucleus				548
P40421 UniProt NPD GO	RDGC_DROME	Serine/threonine-protein phosphatase rdgC (EC 3.1.3.16) (Retinal degeneration C protein)	0.67	-	nuc	0					661
Q60ZS1 UniProt NPD GO	SGO1_CAEBR	Shugoshin	0.67	-	nuc	0	Nucleus (By similarity). Localizes to the centromere (By similarity)				306
Q96RL6 UniProt NPD GO	SIG11_HUMAN	Sialic acid-binding Ig-like lectin 11 precursor (Siglec-11) (Sialic acid-binding lectin 11)	0.67	-	exc	1	Membrane; single-pass type I membrane protein		607157		686
O42816 UniProt NPD GO	SRP54_CANAL	Signal recognition particle 54 kDa protein homolog	0.67	+	nuc	0	Cytoplasm (By similarity)				556
P52632 UniProt NPD GO	STA5B_RAT	Signal transducer and activator of transcription 5B	0.67	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Translocated into the nucleus in response to pho ...				786
Q9R1N3 UniProt NPD GO	S4A7_RAT	Sodium bicarbonate cotransporter 3 (Electroneutral sodium bicarbonate cotransporter 1) (NBC-like pro ...	0.67	+	end	11	Cell membrane; basolateral cell membrane; multi-pass membrane protein. Also described at the apical ...				1218
Q32LP4 UniProt NPD GO	S4A10_BOVIN	Sodium-driven chloride bicarbonate exchanger (Solute carrier family 4 member 10)	0.67	-	end	11	Cell membrane; Membrane; multi-pass membrane protein. Localizes to the basolateral membrane (By simi ...				1117
Q80ZA5 UniProt NPD GO	S4A10_RAT	Sodium-driven chloride bicarbonate exchanger (Solute carrier family 4 member 10)	0.67	-	end	11	Cell membrane; Membrane; multi-pass membrane protein. Localizes to the basolateral membrane				1117
Q6CUC4 UniProt NPD GO	MVP1_KLULA	Sorting nexin MVP1	0.67	-	cyt	0	Cytoplasm (By similarity)				512
Q4V896 UniProt NPD GO	SNX15_RAT	Sorting nexin-15	0.67	-	nuc	0					338
Q9Y5X2 UniProt NPD GO	SNX8_HUMAN	Sorting nexin-8	0.67	-	nuc	0					465
Q99NB9 UniProt NPD GO	SF3B1_MOUSE	Splicing factor 3B subunit 1 (Spliceosome-associated protein 155) (SAP 155) (SF3b155) (Pre-mRNA-spli ...	0.67	-	end	0	Nucleus (By similarity)				1304
P31395 UniProt NPD GO	STMN1_CHICK	Stathmin	0.67	-	nuc	0	Cytoplasm				148
Q8BZ60 UniProt NPD GO	STON2_MOUSE	Stonin-2 (Stoned B)	0.67	-	nuc	0					895
Q8VHQ2 UniProt NPD GO	SOCS7_MOUSE	Suppressor of cytokine signaling 7 (SOCS-7)	0.67	-	nuc	0					579
Q16637 UniProt NPD GO	SMN_HUMAN	Survival motor neuron protein (Component of gems 1) (Gemin-1)	0.67	-	nuc	0	Cytoplasm. Nucleus. Localized in subnuclear structures next to coiled bodies, called Gemini of Cajal ...	Cajal body [NAS] cytoplasm [NAS]	253300	1MHN	294
Q29IC2 UniProt NPD GO	RIC8_DROPS	Synembryn (Protein Ric-8)	0.67	-	nuc	0	Cytoplasm; cell cortex. Localizes to the cell cortex	cytoplasm [ISS]			566
Q9SUJ1 UniProt NPD GO	SYP43_ARATH	Syntaxin-43 (AtSYP43)	0.67	-	nuc	1	Membrane; single-pass type IV membrane protein (By similarity)				331
O08599 UniProt NPD GO	STXB1_MOUSE	Syntaxin-binding protein 1 (Unc-18 homolog) (Unc-18A) (Unc-18-1)	0.67	-	nuc	0		mitochondrion [IDA]			594
P61763 UniProt NPD GO	STXB1_BOVIN	Syntaxin-binding protein 1 (Unc-18 homolog) (Unc-18A) (Unc-18-1) (N-Sec1) (p67)	0.67	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein				594
P61764 UniProt NPD GO	STXB1_HUMAN	Syntaxin-binding protein 1 (Unc-18 homolog) (Unc-18A) (Unc-18-1) (N-Sec1) (p67)	0.67	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein		602926		594
P61765 UniProt NPD GO	STXB1_RAT	Syntaxin-binding protein 1 (Unc-18 homolog) (Unc-18A) (Unc-18-1) (N-Sec1) (rbSec1) (p67)	0.67	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein			1DN1	594
Q8R3T5 UniProt NPD GO	STXB6_MOUSE	Syntaxin-binding protein 6	0.67	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				210
P70324 UniProt NPD GO	TBX3_MOUSE	T-box transcription factor TBX3 (T-box protein 3)	0.67	-	exc	0	Nucleus (Potential)	nucleus [IC]			741
Q7TST9 UniProt NPD GO	TBX3_RAT	T-box transcription factor TBX3 (T-box protein 3)	0.67	-	exc	0	Nucleus (Potential)				743
P13379 UniProt NPD GO	CD5_MOUSE	T-cell surface glycoprotein CD5 precursor (Lymphocyte antigen Ly-1) (Lyt-1)	0.67	-	end	1 *	Membrane; single-pass type I membrane protein	external side of plasma membrane [IDA]			494
Q9HA65 UniProt NPD GO	TBC17_HUMAN	TBC1 domain family member 17	0.67	-	cyt	0					648
Q9NVV9 UniProt NPD GO	THAP1_HUMAN	THAP domain-containing protein 1	0.67	+	nuc	0	Nucleus; nucleoplasm. And PML nuclear bodies		609520		213
Q4R3Q6 UniProt NPD GO	THAP1_MACFA	THAP domain-containing protein 1	0.67	+	nuc	0	Nucleus; nucleoplasm (By similarity). And PML nuclear bodies (By similarity)				212

You are viewing entries 15501 to 15550 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.