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
P35132 UniProt NPD GO	UBC9_ARATH	SUMO-conjugating enzyme UBC9 (EC 6.3.2.19) (Ubiquitin-conjugating enzyme E2-17 kDa) (Ubiquitin-prote ...	0.08	-	nuc	0					148
Q9UL12 UniProt NPD GO	SARDH_HUMAN	Sarcosine dehydrogenase, mitochondrial precursor (EC 1.5.99.1) (SarDH) (BPR-2)	0.08	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)	mitochondrion [ISS]	604455		918
P15369 UniProt NPD GO	PRTB_SCYLI	Scytalidopepsin B precursor (EC 3.4.23.32) (Acid protease B) (SLB)	0.08	-	cyt	0				1S2K	260
Q7YWA8 UniProt NPD GO	SECP_VESVN	Secapin precursor	0.08	-	exc	1 *	Secreted protein (By similarity)				77
Q3UN54 UniProt NPD GO	SSLP1_MOUSE	Secreted seminal-vesicle Ly-6 protein 1 precursor (SSLP-1)	0.08	-	nuc	0	Secreted protein				99
Q5FWI2 UniProt NPD GO	SCTR_MOUSE	Secretin receptor precursor (SCT-R)	0.08	-	end	7 *	Membrane; multi-pass membrane protein				447
Q9UGK8 UniProt NPD GO	SRGEF_HUMAN	Secretion-regulating guanine nucleotide exchange factor (Guanine nucleotide exchange factor-related ...	0.08	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]	606051		458
Q6XE38 UniProt NPD GO	SG1D4_HUMAN	Secretoglobin family 1D member 4 precursor (IFN-gamma-inducible secretoglobin) (IIS)	0.08	-	end	0	Secreted protein				83
P14856 UniProt NPD GO	LOX2_PEA	Seed lipoxygenase-2 (EC 1.13.11.12)	0.08	-	nuc	0	Cytoplasm				864
Q9EPB5 UniProt NPD GO	SERHL_MOUSE	Serine hydrolase-like protein (EC 3.1.-.-) (SHL)	0.08	-	mit	0	Cytoplasm; perinuclear region. Concentrated in perinuclear vesicles. Peroxisome. May be located in p ...	cytoplasmic membrane-bound vesicle [IDA]			311
Q9NQF3 UniProt NPD GO	SEHL2_HUMAN	Serine hydrolase-like protein 2 (EC 3.1.-.-)	0.08	-	mit	0					203
Q09925 UniProt NPD GO	LCB2_SCHPO	Serine palmitoyltransferase 2 (EC 2.3.1.50) (Long chain base biosynthesis protein 2) (SPT 2)	0.08	-	nuc	1	Membrane; single-pass membrane protein				603
Q8BYY9 UniProt NPD GO	SPA3B_MOUSE	Serine protease inhibitor A3B precursor (Serpin A3B)	0.08	-	cyt	0	Secreted protein (By similarity)				420
P20155 UniProt NPD GO	IPK2_HUMAN	Serine protease inhibitor Kazal-type 2 precursor (Acrosin-trypsin inhibitor) (HUSI-II)	0.08	-	nuc	1 *	Secreted protein		605753		84
Q9P1W9 UniProt NPD GO	PIM2_HUMAN	Serine/threonine-protein kinase Pim-2 (EC 2.7.11.1) (Pim-2h)	0.08	-	cyt	0			300295		311
Q7TNP2 UniProt NPD GO	2AAB_MOUSE	Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform (PP2A, subunit A, P ...	0.08	-	cyt	0					601
Q753L9 UniProt NPD GO	PTPA1_ASHGO	Serine/threonine-protein phosphatase 2A activator 1 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomeras ...	0.08	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				365
P58389 UniProt NPD GO	PTPA_MOUSE	Serine/threonine-protein phosphatase 2A regulatory subunit B' (PP2A, subunit B', PR53 isoform) (Phos ...	0.08	-	nuc	0		protein phosphatase type 2A complex [ISS] soluble fraction [ISS]			323
Q28717 UniProt NPD GO	PTPA_RABIT	Serine/threonine-protein phosphatase 2A regulatory subunit B' (PP2A, subunit B', PR53 isoform) (Phos ...	0.08	-	nuc	0					323
P32838 UniProt NPD GO	PP2A4_YEAST	Serine/threonine-protein phosphatase PP2A-like PPG1 (EC 3.1.3.16)	0.08	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			368
P19134 UniProt NPD GO	TRFE_RABIT	Serotransferrin precursor (Transferrin) (Siderophilin) (Beta-1 metal-binding globulin)	0.08	-	end	0	Secreted protein			1TFD	695
P02787 UniProt NPD GO	TRFE_HUMAN	Serotransferrin precursor (Transferrin) (Siderophilin) (Beta-1-metal-binding globulin)	0.08	-	nuc	0	Secreted protein	endocytic vesicle [IDA] extracellular region [NAS]	190000	2HAV	698
O16975 UniProt NPD GO	SRJ38_CAEEL	Serpentine receptor class J-38 (Protein srj-38)	0.08	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				330
Q21767 UniProt NPD GO	SRD2_CAEEL	Serpentine receptor class delta-2 (Protein srd-2)	0.08	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				347
Q19975 UniProt NPD GO	SRD34_CAEEL	Serpentine receptor class delta-34 (Protein srd-34)	0.08	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				339
O17818 UniProt NPD GO	SRE37_CAEEL	Serpentine receptor class epsilon-37 (Protein sre-37)	0.08	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				362
P46565 UniProt NPD GO	SRG8_CAEEL	Serpentine receptor class gamma-8 (Protein srg-8)	0.08	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				316
P49065 UniProt NPD GO	ALBU_RABIT	Serum albumin precursor	0.08	-	exc	0	Secreted protein	extracellular region [ISS] protein complex [ISS]			608
P02735 UniProt NPD GO	SAA_HUMAN	Serum amyloid A protein precursor (SAA) [Contains: Amyloid protein A (Amyloid fibril protein AA); Se ...	0.08	-	exc	0		extracellular region [NAS]	104751		122
Q40518 UniProt NPD GO	MSK1_TOBAC	Shaggy-related protein kinase NtK-1 (EC 2.7.11.1)	0.08	-	cyt	0					409
Q16836 UniProt NPD GO	HCDH_HUMAN	Short chain 3-hydroxyacyl-CoA dehydrogenase, mitochondrial precursor (EC 1.1.1.35) (HCDH) (Medium an ...	0.08	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [TAS]	231530	3HAD	314
P19960 UniProt NPD GO	NXS4_AIPLA	Short neurotoxin D precursor	0.08	-	nuc	1 *	Secreted protein				81
P45954 UniProt NPD GO	ACDSB_HUMAN	Short/branched chain specific acyl-CoA dehydrogenase, mitochondrial precursor (EC 1.3.99.-) (SBCAD) ...	0.08	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [TAS]	610006		432
P18270 UniProt NPD GO	8512_TRYCR	Sialidase 85-1.2 (EC 3.2.1.18) (Neuraminidase) (NA) (Major 85 kDa surface antigen) (SA85-1.2 protein ...	0.08	-	nuc	0					240
Q99JR1 UniProt NPD GO	SFXN1_MOUSE	Sideroflexin-1	0.08	-	nuc	4	Mitochondrion; mitochondrial membrane; multi-pass membrane protein	mitochondrial inner membrane [IDA] mitochondrion [IDA]			321
P38731 UniProt NPD GO	ARN1_YEAST	Siderophore iron transporter ARN1 (Ferrichrome permease)	0.08	-	end	13	Cell membrane; multi-pass membrane protein. Endosome; endosomal membrane; multi-pass membrane protei ...	cytoplasmic membrane-bound vesicle [IDA] endosome [TAS]			627
Q870L3 UniProt NPD GO	MIRC_EMENI	Siderophore iron transporter mirC (Major facilitator iron-regulated transporter C)	0.08	-	end	12	Membrane; multi-pass membrane protein (Potential)				607
P34642 UniProt NPD GO	SRP09_CAEEL	Signal recognition particle 9 kDa protein homolog (SRP9)	0.08	-	cyt	0	Cytoplasm (By similarity)				76
P09892 UniProt NPD GO	SCPB_APLSP	Small cardioactive peptide B precursor (SCP-B)	0.08	-	mit	1 *	Secreted protein				136
Q95661 UniProt NPD GO	HS21C_LYCES	Small heat shock protein, chloroplast precursor	0.08	-	mit	0	Plastid; chloroplast				235
O70460 UniProt NPD GO	CCL19_MOUSE	Small inducible cytokine A19 precursor (CCL19) (Epstein-Barr virus-induced molecule 1 ligand chemoki ...	0.08	-	exc	0	Secreted protein				108
O00175 UniProt NPD GO	CCL24_HUMAN	Small inducible cytokine A24 precursor (CCL24) (Myeloid progenitor inhibitory factor 2) (MPIF-2) (CK ...	0.08	-	mit	1 *	Secreted protein			1EIH	119
P13501 UniProt NPD GO	CCL5_HUMAN	Small inducible cytokine A5 precursor (CCL5) (T-cell-specific RANTES protein) (SIS-delta) (T cell-sp ...	0.08	-	exc	1 *	Secreted protein		187011	1U4R	91
P21923 UniProt NPD GO	SIA1_SORBI	Small protein inhibitor of insect alpha-amylases 1 (SI alpha-1)	0.08	-	nuc	0					47
P48056 UniProt NPD GO	S6A12_RAT	Sodium- and chloride-dependent betaine transporter (Na+/Cl-betaine/GABA transporter)	0.08	-	end	12 *	Membrane; multi-pass membrane protein	integral to membrane [IDA]			614
P32739 UniProt NPD GO	NAD2_CAEEL	Sodium-dependent high-affinity dicarboxylate transporter 2 (Na(+)/dicarboxylate cotransporter 2) (Na ...	0.08	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				551
P31645 UniProt NPD GO	SC6A4_HUMAN	Sodium-dependent serotonin transporter (5HT transporter) (5HTT)	0.08	-	end	12	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	182138		630
Q8S397 UniProt NPD GO	NHX4_ARATH	Sodium/hydrogen exchanger 4 (Na(+)/H(+) exchanger 4) (NHE-4)	0.08	-	end	11 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity). Tonoplast				529
Q8RWU6 UniProt NPD GO	NHX6_ARATH	Sodium/hydrogen exchanger 6 (Na(+)/H(+) exchanger 6) (NHE-6)	0.08	-	end	9 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity). Tonoplast				535
Q9Y2E8 UniProt NPD GO	SL9A8_HUMAN	Sodium/hydrogen exchanger 8 (Na(+)/H(+) exchanger 8) (NHE-8) (Solute carrier family 9 member 8)	0.08	-	end	11	Golgi apparatus; Golgi membrane; multi-pass membrane protein				577

You are viewing entries 69001 to 69050 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.