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
Q9D8T7 UniProt NPD GO	SLIRP_MOUSE	SRA stem-loop-interacting RNA-binding protein, mitochondrial precursor	0.17	-	mit	0	Mitochondrion; predominantly. Nucleus; some fraction is nuclear. In the nucleus, it is recruited to ...				112
Q05018 UniProt NPD GO	S40A_CHITE	Salivary gland SP38-40.A protein precursor	0.17	+	nuc	1 *	Secreted protein				244
Q05019 UniProt NPD GO	S40B_CHITE	Salivary gland SP38-40.B protein precursor	0.17	+	nuc	1 *	Secreted protein				253
Q9NR16 UniProt NPD GO	C163B_HUMAN	Scavenger receptor cysteine-rich type 1 protein M160 precursor (CD163 antigen-like 1) (CD163b antige ...	0.17	-	end	2 *	Isoform 1, isoform 2: Cell membrane; single-pass type I membrane protein (Probable). Isoform 3: Secr ...		606079		1453
P56707 UniProt NPD GO	SMTA_ASTBI	Selenocysteine methyltransferase (EC 2.1.1.-) (SECYS-methyltransferase) (SECYS-MT)	0.17	-	cyt	0					338
Q9XZC8 UniProt NPD GO	SEM2A_SCHGR	Semaphorin-2A precursor (Sema-2A) (Sema II)	0.17	-	vac	0	Secreted protein (Potential)				697
Q92854 UniProt NPD GO	SEM4D_HUMAN	Semaphorin-4D precursor (Leukocyte activation antigen CD100) (BB18) (A8) (GR3)	0.17	-	end	2 *	Membrane; single-pass type I membrane protein		601866	1OLZ	862
P55747 UniProt NPD GO	CBP21_HORVU	Serine carboxypeptidase II-1 precursor (EC 3.4.16.6) (CP-MII.1) [Contains: Serine carboxypeptidase I ...	0.17	-	cyt	0					324
Q9H4I8 UniProt NPD GO	SERHL_HUMAN	Serine hydrolase-like protein (EC 3.1.-.-)	0.17	-	mit	0	Cytoplasm; perinuclear region (By similarity). Concentrated in perinuclear vesicles. Peroxisome (By ...		607979		314
P31030 UniProt NPD GO	SPYA_RABIT	Serine--pyruvate aminotransferase (EC 2.6.1.51) (SPT) (Alanine--glyoxylate aminotransferase) (EC 2.6 ...	0.17	-	cyt	0	Peroxisome				392
P06242 UniProt NPD GO	KIN28_YEAST	Serine/threonine-protein kinase KIN28 (EC 2.7.11.23)	0.17	-	cyt	0		transcription factor TFIIH complex [IDA]			306
Q9DBU3 UniProt NPD GO	RIOK3_MOUSE	Serine/threonine-protein kinase RIO3 (EC 2.7.11.1) (RIO kinase 3)	0.17	-	cyt	0					519
Q9WUN2 UniProt NPD GO	TBK1_MOUSE	Serine/threonine-protein kinase TBK1 (EC 2.7.11.1) (TANK-binding kinase 1) (T2K)	0.17	-	cyt	0	Cytoplasm (By similarity)				729
P80426 UniProt NPD GO	TRF1_SALSA	Serotransferrin I precursor (Siderophilin I) (STF I)	0.17	-	exc	0	Secreted protein				690
O17822 UniProt NPD GO	SRD48_CAEEL	Serpentine receptor class delta-48 (Protein srd-48)	0.17	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				316
O62489 UniProt NPD GO	SRE26_CAEEL	Serpentine receptor class epsilon-26 (Protein sre-26)	0.17	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				359
O18175 UniProt NPD GO	SRE33_CAEEL	Serpentine receptor class epsilon-33 (Protein sre-33)	0.17	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				359
Q19897 UniProt NPD GO	SRE6_CAEEL	Serpentine receptor class epsilon-6 (Protein sre-6)	0.17	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				366
Q9DG84 UniProt NPD GO	VSP7_TRIMU	Serpentokallikrein-2 precursor (EC 3.4.21.-)	0.17	-	exc	0	Secreted protein				257
P35541 UniProt NPD GO	SAA_BOVIN	Serum amyloid A protein (SAA) [Contains: Amyloid protein A (Amyloid fibril protein AA)]	0.17	-	cyt	0					112
P53613 UniProt NPD GO	SAA_MACEU	Serum amyloid A protein precursor (SAA)	0.17	-	exc	0					127
P10733 UniProt NPD GO	SEVE_DICDI	Severin	0.17	-	cyt	0				1SVY	362
P34076 UniProt NPD GO	NXS1_BOUCH	Short neurotoxin 1	0.17	-	nuc	0	Secreted protein				62
P25497 UniProt NPD GO	NXS1_PSEAU	Short neurotoxin 1 (Neurotoxin PA A)	0.17	-	nuc	0	Secreted protein				62
P10459 UniProt NPD GO	NXSB_LATLA	Short neurotoxin B precursor	0.17	-	nuc	0	Secreted protein				83
Q3SWZ6 UniProt NPD GO	SBDS_BOVIN	Shwachman-Bodian-Diamond syndrome protein homolog	0.17	-	cyt	0					250
Q99PW3 UniProt NPD GO	NEUR1_RAT	Sialidase-1 precursor (EC 3.2.1.18) (Lysosomal sialidase) (N-acetyl-alpha-neuraminidase 1)	0.17	-	mit	0	Lysosome; lysosomal membrane; peripheral membrane; lumenal side. Lysosome; lysosomal lumen. Cell mem ...				409
Q9CYN2 UniProt NPD GO	SPCS2_MOUSE	Signal peptidase complex subunit 2 (EC 3.4.-.-) (Microsomal signal peptidase 25 kDa subunit) (SPase ...	0.17	+	end	2	Membrane; multi-pass membrane protein (Potential)				226
Q9JJF9 UniProt NPD GO	PSL2_MOUSE	Signal peptide peptidase-like 2A (EC 3.4.23.-) (SPP-like 2A protein) (SPPL2a protein) (Intramembrane ...	0.17	-	end	9	Membrane; multi-pass membrane protein (Probable)				523
P10080 UniProt NPD GO	SSB1_YEAST	Single-stranded nucleic acid-binding protein	0.17	-	cyt	0	Nucleus; nucleolus	nucleolus [IDA]			294
Q5RA36 UniProt NPD GO	CCL2_PONPY	Small inducible cytokine A2 precursor (CCL2)	0.17	-	exc	0	Secreted protein (By similarity)				99
P28292 UniProt NPD GO	CCL2_RABIT	Small inducible cytokine A2 precursor (CCL2) (Monocyte chemotactic protein 1) (MCP-1) (Monocyte chem ...	0.17	-	exc	0	Secreted protein				125
P13500 UniProt NPD GO	CCL2_HUMAN	Small inducible cytokine A2 precursor (CCL2) (Monocyte chemotactic protein 1) (MCP-1) (Monocyte chem ...	0.17	-	exc	0	Secreted protein	extracellular space [TAS]	158105	1ML0	99
Q68Y86 UniProt NPD GO	CCL24_CANFA	Small inducible cytokine A24 precursor (CCL24) (Eosinophil chemotactic protein 2) (Eotaxin-2)	0.17	-	exc	0	Secreted protein (By similarity)				119
Q9PV94 UniProt NPD GO	RSMB_CHICK	Small nuclear ribonucleoprotein-associated protein B' (snRNP-B') (Sm protein B') (Sm-B') (SmB') (snR ...	0.17	-	nuc	0	Nucleus				240
P63164 UniProt NPD GO	RSMN_RAT	Small nuclear ribonucleoprotein-associated protein N (snRNP-N) (Sm protein N) (Sm-N) (SmN) (Sm-D)	0.17	-	nuc	0	Nucleus				240
P63162 UniProt NPD GO	RSMN_HUMAN	Small nuclear ribonucleoprotein-associated protein N (snRNP-N) (Sm protein N) (Sm-N) (SmN) (Sm-D) (T ...	0.17	-	nuc	0	Nucleus		182279		240
P63163 UniProt NPD GO	RSMN_MOUSE	Small nuclear ribonucleoprotein-associated protein N (snRNP-N) (Sm protein N) (Sm-N) (SmN) (Sm-D) (T ...	0.17	-	nuc	0	Nucleus	nucleus [TAS]			240
P42579 UniProt NPD GO	SIS_LYMST	Sodium-influx-stimulating peptide precursor	0.17	-	exc	1 *					100
Q28036 UniProt NPD GO	SL9A1_BOVIN	Sodium/hydrogen exchanger 1 (Na(+)/H(+) exchanger 1) (NHE-1) (Solute carrier family 9 member 1)	0.17	-	end	13 *	Membrane; multi-pass membrane protein				817
Q96T83 UniProt NPD GO	SL9A7_HUMAN	Sodium/hydrogen exchanger 7 (Na(+)/H(+) exchanger 7) (NHE-7) (Solute carrier family 9 member 7)	0.17	-	end	12	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; multi-pass membrane protein	Golgi apparatus [IDA] Golgi trans face [IDA] integral to membrane [IDA]	300368		725
P05023 UniProt NPD GO	AT1A1_HUMAN	Sodium/potassium-transporting ATPase alpha-1 chain precursor (EC 3.6.3.9) (Sodium pump 1) (Na+/K+ AT ...	0.17	-	end	10	Membrane; multi-pass membrane protein	membrane fraction [TAS] sodium:potassium-exchanging ATPase complex [ISS]	182310		1023
P24798 UniProt NPD GO	AT1A3_CHICK	Sodium/potassium-transporting ATPase alpha-3 chain (EC 3.6.3.9) (Sodium pump 3) (Na+/K+ ATPase 3) (A ...	0.17	-	end	8	Membrane; multi-pass membrane protein	sodium:potassium-exchanging ATPase complex [ISS]			1010
P13637 UniProt NPD GO	AT1A3_HUMAN	Sodium/potassium-transporting ATPase alpha-3 chain (EC 3.6.3.9) (Sodium pump 3) (Na+/K+ ATPase 3) (A ...	0.17	-	end	8	Membrane; multi-pass membrane protein	sodium:potassium-exchanging ATPase complex [ISS]	182350		1013
P51165 UniProt NPD GO	AT1B1_ANGAN	Sodium/potassium-transporting ATPase subunit beta-1 (Sodium/potassium-dependent ATPase beta subunit) ...	0.17	-	mit	1 *	Membrane; single-pass type II membrane protein				303
Q24046 UniProt NPD GO	ATPB1_DROME	Sodium/potassium-transporting ATPase subunit beta-1 (Sodium/potassium-dependent ATPase beta-1 subuni ...	0.17	-	mit	1 *	Membrane; single-pass type II membrane protein (Probable)				309
Q6J4K2 UniProt NPD GO	NCKX6_HUMAN	Sodium/potassium/calcium exchanger 6 precursor (Na(+)/K(+)/Ca(2+)-exchange protein 6) (Solute carrie ...	0.17	-	end	13 *	Cell membrane; multi-pass membrane protein (By similarity)		609841		584
O48556 UniProt NPD GO	IPYR_MAIZE	Soluble inorganic pyrophosphatase (EC 3.6.1.1) (Pyrophosphate phospho-hydrolase) (PPase)	0.17	-	cyt	0	Cytoplasm				214
Q5R831 UniProt NPD GO	S35B3_PONPY	Solute carrier family 35 member B3	0.17	+	end	10	Membrane; multi-pass membrane protein (Potential)				401
O94956 UniProt NPD GO	SO2B1_HUMAN	Solute carrier organic anion transporter family member 2B1 (Solute carrier family 21 member 9) (Orga ...	0.17	-	end	11	Membrane; multi-pass membrane protein		604988		709

You are viewing entries 54951 to 55000 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.