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
Q863K0 UniProt NPD GO	RNAS9_GORGO	Ribonuclease-like protein 9 precursor	0.28	-	exc	0	Secreted protein (Probable)				205
P60153 UniProt NPD GO	RNAS9_HUMAN	Ribonuclease-like protein 9 precursor	0.28	-	exc	0	Secreted protein (Probable)				205
Q9C167 UniProt NPD GO	RIR2_NEUCR	Ribonucleoside-diphosphate reductase small chain (EC 1.17.4.1) (Ribonucleotide reductase small subun ...	0.28	-	nuc	1					410
Q69XQ6 UniProt NPD GO	KPRS2_ORYSA	Ribose-phosphate pyrophosphokinase 2 (EC 2.7.6.1) (Phosphoribosyl pyrophosphate synthetase 2)	0.28	-	mit	0					399
Q15418 UniProt NPD GO	KS6A1_HUMAN	Ribosomal protein S6 kinase alpha-1 (EC 2.7.11.1) (S6K-alpha 1) (90 kDa ribosomal protein S6 kinase ...	0.28	-	cyt	0			601684		735
Q96E11 UniProt NPD GO	RRFM_HUMAN	Ribosome recycling factor, mitochondrial precursor	0.28	-	nuc	0	Mitochondrion (By similarity)		604602		262
P18426 UniProt NPD GO	SCR11_OMMSL	S-crystallin SL11 (Major lens polypeptide)	0.28	-	cyt	0					205
Q9NXL6 UniProt NPD GO	SIDT1_HUMAN	SID1 transmembrane family member 1 precursor	0.28	-	end	11	Membrane; multi-pass membrane protein (Potential)		606816		827
Q2VLG6 UniProt NPD GO	C163A_CANFA	Scavenger receptor cysteine-rich type 1 protein M130 precursor (CD163 antigen) [Contains: Soluble CD ...	0.28	-	end	2 *	Cell membrane; single-pass type I membrane protein (By similarity). Soluble CD163: Secreted protein ...				1133
Q9R168 UniProt NPD GO	SFRP1_RAT	Secreted frizzled-related protein 1 (sFRP-1) (Fragment)	0.28	-	nuc	0	Secreted protein. Cell membrane or extracellular matrix-associated. Released by heparin-binding (By ...				158
P84877 UniProt NPD GO	SPF2_PYTHP	Secreted protein F2 (Fragments)	0.28	-	nuc	0	Secreted protein				32
O54951 UniProt NPD GO	SEM6B_MOUSE	Semaphorin-6B precursor (Semaphorin VIB) (Sema VIB) (Semaphorin N) (Sema N)	0.28	+	end	2 *	Membrane; single-pass type I membrane protein				886
Q5QSK2 UniProt NPD GO	DESC4_RAT	Serine protease DESC4 precursor (EC 3.4.21.-) [Contains: Serine protease DESC4 non-catalytic chain; ...	0.28	-	mit	1 *	Membrane; single-pass type II membrane protein	plasma membrane [IDA]			417
Q9HC98 UniProt NPD GO	NEK6_HUMAN	Serine/threonine-protein kinase Nek6 (EC 2.7.11.1) (NimA-related protein kinase 6) (Protein kinase S ...	0.28	-	cyt	0	Cytoplasm. Nucleus		604884		313
Q6ZI44 UniProt NPD GO	SAPK6_ORYSA	Serine/threonine-protein kinase SAPK6 (EC 2.7.11.1) (Osmotic stress/abscisic acid-activated protein ...	0.28	-	nuc	0					365
Q01577 UniProt NPD GO	PKPA_PHYBL	Serine/threonine-protein kinase pkpA (EC 2.7.11.1)	0.28	-	cyt	0					613
Q5RAN0 UniProt NPD GO	ACVL1_PONPY	Serine/threonine-protein kinase receptor R3 precursor (EC 2.7.11.30) (SKR3) (Activin receptor-like k ...	0.28	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				503
P40454 UniProt NPD GO	PTPA1_YEAST	Serine/threonine-protein phosphatase 2A activator 1 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomeras ...	0.28	-	cyt	0	Cytoplasm. Nucleus	cell fraction [IDA] cytoplasm [IDA] nucleus [IDA]			393
Q12461 UniProt NPD GO	PTPA2_YEAST	Serine/threonine-protein phosphatase 2A activator 2 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomeras ...	0.28	-	nuc	0	Cytoplasm	cell fraction [IDA] cytosol [TAS]			358
P48487 UniProt NPD GO	PP1_BRAOL	Serine/threonine-protein phosphatase PP1 (EC 3.1.3.16)	0.28	-	cyt	0					316
P48484 UniProt NPD GO	PP14_ARATH	Serine/threonine-protein phosphatase PP1 isozyme 4 (EC 3.1.3.16)	0.28	-	cyt	0					321
P62137 UniProt NPD GO	PP1A_MOUSE	Serine/threonine-protein phosphatase PP1-alpha catalytic subunit (EC 3.1.3.16) (PP-1A)	0.28	-	mit	0	Cytoplasm (By similarity)	cytoplasm [IDA] nucleoplasm [IDA]			330
P46570 UniProt NPD GO	SRG1_CAEEL	Serpentine receptor class gamma-1 (Protein srg-1)	0.28	-	end	6 *	Membrane; multi-pass membrane protein (Probable)				288
Q7TMF5 UniProt NPD GO	SPA12_MOUSE	Serpin A12 precursor (Visceral adipose-specific serpin) (Visceral adipose tissue-derived serine prot ...	0.28	-	end	0	Secreted protein (Potential)				413
O74861 UniProt NPD GO	SDC1_SCHPO	Set1 complex component sdc1 (Set1C component sdc1) (COMPASS component sdc1) (Complex proteins associ ...	0.28	-	nuc	0	Nucleus (Probable)	COMPASS complex [IDA] Lid2 complex [IDA]			109
O60137 UniProt NPD GO	SWD2_SCHPO	Set1 complex component swd2 (Set1C component swd2) (COMPASS component swd2) (Complex proteins associ ...	0.28	-	nuc	0	Nucleus (Probable)	COMPASS complex [IDA]			357
P15196 UniProt NPD GO	SHBG_RABIT	Sex hormone-binding globulin precursor (SHBG) (Sex steroid-binding protein) (SBP) (Testis-specific a ...	0.28	-	mit	0	Secreted protein (By similarity). In testis, it is synthesized by the Sertoli cells, secreted into t ...				398
O62826 UniProt NPD GO	TRPC2_BOVIN	Short transient receptor potential channel 2 homolog (TrpC2) (btrp2)	0.28	-	end	2 *	Membrane; multi-pass membrane protein (Probable)				432
Q9WVC5 UniProt NPD GO	TRPC7_MOUSE	Short transient receptor potential channel 7 (TrpC7) (mTRP7)	0.28	-	end	5	Membrane; multi-pass membrane protein (Probable)				862
O16927 UniProt NPD GO	SRP14_CAEEL	Signal recognition particle 14 kDa protein homolog (SRP14)	0.28	-	nuc	0	Cytoplasm				116
P49972 UniProt NPD GO	SR542_LYCES	Signal recognition particle 54 kDa protein 2 (SRP54)	0.28	-	cyt	0	Cytoplasm				499
Q9QUM4 UniProt NPD GO	SLAF1_MOUSE	Signaling lymphocytic activation molecule precursor	0.28	-	exc	2 *	Cell membrane; single-pass type I membrane protein. Present on the surface of B-cells and T-cells				343
Q10426 UniProt NPD GO	RIK1_SCHPO	Silencing protein rik1	0.28	-	cyt	0		nuclear chromatin [TAS] Rik1-E3 ubiquitin ligase complex [IDA]			1040
Q98948 UniProt NPD GO	SSBP3_CHICK	Single-stranded DNA-binding protein 3 (Sequence-specific single-stranded-DNA-binding protein)	0.28	-	nuc	0	Nucleus	nucleus [ISS]			368
Q9R050 UniProt NPD GO	SSBP3_RAT	Single-stranded DNA-binding protein 3 (Sequence-specific single-stranded-DNA-binding protein)	0.28	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			361
P80098 UniProt NPD GO	CCL7_HUMAN	Small inducible cytokine A7 precursor (CCL7) (Monocyte chemotactic protein 3) (MCP-3) (Monocyte chem ...	0.28	-	exc	0	Secreted protein	extracellular space [TAS]	158106	1NCV	99
Q3ZC10 UniProt NPD GO	SMD1_BOVIN	Small nuclear ribonucleoprotein Sm D1 (snRNP core protein D1) (Sm-D1)	0.28	+	cyt	0	Nucleus (By similarity)				119
P62314 UniProt NPD GO	SMD1_HUMAN	Small nuclear ribonucleoprotein Sm D1 (snRNP core protein D1) (Sm-D1) (Sm-D autoantigen)	0.28	+	cyt	0	Nucleus		601063	1B34	119
P62315 UniProt NPD GO	SMD1_MOUSE	Small nuclear ribonucleoprotein Sm D1 (snRNP core protein D1) (Sm-D1) (Sm-D autoantigen)	0.28	+	cyt	0	Nucleus	cytoplasm [IDA] nucleus [IDA]			119
Q9CQK8 UniProt NPD GO	SPR2A_MOUSE	Small proline-rich protein 2A	0.28	-	nuc	0	Cytoplasm (By similarity)	cornified envelope [NAS]			83
Q05973 UniProt NPD GO	SCN1_LOLBL	Sodium channel protein I, brain	0.28	-	end	18 *	Membrane; multi-pass membrane protein				1522
P35499 UniProt NPD GO	SCN4A_HUMAN	Sodium channel protein type 4 subunit alpha (Sodium channel protein type IV subunit alpha) (Voltage- ...	0.28	-	end	21	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	608390		1836
Q13733 UniProt NPD GO	AT1A4_HUMAN	Sodium/potassium-transporting ATPase alpha-4 chain (EC 3.6.3.9) (Sodium pump 4) (Na+/K+ ATPase 4)	0.28	-	end	8	Membrane; multi-pass membrane protein	sodium:potassium-exchanging ATPase complex [TAS]	607321		1029
Q99PD7 UniProt NPD GO	NCKX3_MOUSE	Sodium/potassium/calcium exchanger 3 precursor (Na(+)/K(+)/Ca(2+)-exchange protein 3)	0.28	+	end	11 *	Membrane; multi-pass membrane protein	plasma membrane [TAS]			645
Q9HC58 UniProt NPD GO	NCKX3_HUMAN	Sodium/potassium/calcium exchanger 3 precursor (Na(+)/K(+)/Ca(2+)-exchange protein 3) (Solute carrie ...	0.28	+	end	11 *	Membrane; multi-pass membrane protein		609839		644
Q9Y6L6 UniProt NPD GO	SO1B1_HUMAN	Solute carrier organic anion transporter family member 1B1 (Solute carrier family 21 member 6) (Sodi ...	0.28	-	end	11 *	Cell membrane; basolateral cell membrane; multi-pass membrane protein. Detected in basolateral membr ...	integral to plasma membrane [TAS] membrane fraction [TAS]	604843		691
Q99N02 UniProt NPD GO	SO3A1_RAT	Solute carrier organic anion transporter family member 3A1 (Solute carrier family 21 member 11) (Sod ...	0.28	-	end	12 *	Membrane; multi-pass membrane protein				710
P30875 UniProt NPD GO	SSR2_MOUSE	Somatostatin receptor type 2 (SS2R) (SRIF-1)	0.28	-	vac	7 *	Membrane; multi-pass membrane protein	membrane fraction [IDA] plasma membrane [IDA]			369
P34994 UniProt NPD GO	SSR2_PIG	Somatostatin receptor type 2 (SS2R) (SRIF-1)	0.28	-	vac	7 *	Membrane; multi-pass membrane protein				369
P30680 UniProt NPD GO	SSR2_RAT	Somatostatin receptor type 2 (SS2R) (SRIF-1)	0.28	-	vac	7 *	Membrane; multi-pass membrane protein				369

You are viewing entries 42701 to 42750 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.