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
P42830 UniProt NPD GO	SCYB5_HUMAN	Small inducible cytokine B5 precursor (CXCL5) (Epithelial-derived neutrophil-activating protein 78) ...	0.04	-	exc	0	Secreted protein		600324		114
P48057 UniProt NPD GO	SC6A1_MUSCO	Sodium- and chloride-dependent GABA transporter 1	0.04	-	end	12	Cell membrane; multi-pass membrane protein. Membrane; multi-pass membrane protein. Localized at the ...				598
P27799 UniProt NPD GO	S6A12_CANFA	Sodium- and chloride-dependent betaine transporter (Na+/Cl-betaine/GABA transporter)	0.04	-	end	12 *	Membrane; multi-pass membrane protein				614
P31651 UniProt NPD GO	S6A12_MOUSE	Sodium- and chloride-dependent betaine transporter (Na+/Cl-betaine/GABA transporter) (Sodium- and ch ...	0.04	-	end	12 *	Membrane; multi-pass membrane protein				614
Q7Z1K7 UniProt NPD GO	SCX5B_CENLL	Sodium-channel modifier toxin Cll5b precursor	0.04	-	nuc	0	Secreted protein (By similarity)				87
O76689 UniProt NPD GO	SNF6_CAEEL	Sodium-dependent acetylcholine transporter	0.04	-	end	12	Cell membrane; multi-pass membrane protein. The DGC is not necessary to establish snf-6 at the posts ...	postsynaptic membrane [NAS]			713
P23975 UniProt NPD GO	SC6A2_HUMAN	Sodium-dependent noradrenaline transporter (Norepinephrine transporter) (NET)	0.04	-	end	12	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	604715		617
O55192 UniProt NPD GO	SC6A2_MOUSE	Sodium-dependent noradrenaline transporter (Norepinephrine transporter) (NET)	0.04	-	end	12	Membrane; multi-pass membrane protein				617
O97704 UniProt NPD GO	NPT2A_SHEEP	Sodium-dependent phosphate transport protein 2A (Sodium/phosphate cotransporter 2A) (Na(+)/Pi cotran ...	0.04	-	end	9	Membrane; multi-pass membrane protein (By similarity)				639
Q27960 UniProt NPD GO	NPT2B_BOVIN	Sodium-dependent phosphate transport protein 2B (Sodium/phosphate cotransporter 2B) (Na(+)/Pi cotran ...	0.04	-	end	11	Membrane; multi-pass membrane protein				693
Q5REV9 UniProt NPD GO	NPT2B_PONPY	Sodium-dependent phosphate transport protein 2B (Sodium/phosphate cotransporter 2B) (Na(+)/Pi cotran ...	0.04	-	end	11	Membrane; multi-pass membrane protein				689
Q14973 UniProt NPD GO	NTCP_HUMAN	Sodium/bile acid cotransporter (Na(+)/bile acid cotransporter) (Na(+)/taurocholate transport protein ...	0.04	-	end	8 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	182396		349
O62667 UniProt NPD GO	S28A1_PIG	Sodium/nucleoside cotransporter 1 (Na(+)/nucleoside cotransporter 1) (Sodium-coupled nucleoside tran ...	0.04	-	end	11	Membrane; multi-pass membrane protein (By similarity)				647
Q04645 UniProt NPD GO	ATNG_BOVIN	Sodium/potassium-transporting ATPase gamma chain (Sodium pump gamma chain) (Na+/K+ ATPase subunit ga ...	0.04	-	nuc	1 *	Membrane; single-pass type III membrane protein (Potential)				58
Q28030 UniProt NPD GO	AT1B2_BOVIN	Sodium/potassium-transporting ATPase subunit beta-2 (Sodium/potassium-dependent ATPase beta-2 subuni ...	0.04	-	cyt	1 *	Membrane; single-pass type II membrane protein				290
Q9VEU5 UniProt NPD GO	GCYDB_DROME	Soluble guanylate cyclase 89Db (EC 4.6.1.2)	0.04	-	cyt	0	Cytoplasm (By similarity)	guanylate cyclase complex, soluble [IC]			669
Q8TDB8 UniProt NPD GO	GTR14_HUMAN	Solute carrier family 2, facilitated glucose transporter member 14 (Glucose transporter type 14)	0.04	-	end	10 *	Membrane; multi-pass membrane protein				520
P11168 UniProt NPD GO	GTR2_HUMAN	Solute carrier family 2, facilitated glucose transporter member 2 (Glucose transporter type 2, liver ...	0.04	-	end	12 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	227810		524
P47842 UniProt NPD GO	GTR3_CANFA	Solute carrier family 2, facilitated glucose transporter member 3 (Glucose transporter type 3, brain ...	0.04	-	end	10 *	Membrane; multi-pass membrane protein				495
P11169 UniProt NPD GO	GTR3_HUMAN	Solute carrier family 2, facilitated glucose transporter member 3 (Glucose transporter type 3, brain ...	0.04	-	end	10 *	Membrane; multi-pass membrane protein		138170		496
Q5R608 UniProt NPD GO	GTR3_PONPY	Solute carrier family 2, facilitated glucose transporter member 3 (Glucose transporter type 3, brain ...	0.04	-	end	10 *	Membrane; multi-pass membrane protein				496
O62787 UniProt NPD GO	GTR3_PIG	Solute carrier family 2, facilitated glucose transporter member 3 (Glucose transporter type 3, brain ...	0.04	-	end	3 *	Membrane; multi-pass membrane protein				104
Q9XT10 UniProt NPD GO	GTR4_PIG	Solute carrier family 2, facilitated glucose transporter member 4 (Glucose transporter type 4, insul ...	0.04	-	end	4 *	Intracytoplasmic membrane; perinuclear region; multi-pass membrane protein (By similarity). Localize ...				174
Q9UGQ3 UniProt NPD GO	GTR6_HUMAN	Solute carrier family 2, facilitated glucose transporter member 6 (Glucose transporter type 6) (Gluc ...	0.04	-	end	12 *	Cell membrane; multi-pass membrane protein (By similarity). The dileucine internalization motif is c ...	membrane [NAS]	606813		507
Q9NY64 UniProt NPD GO	GTR8_HUMAN	Solute carrier family 2, facilitated glucose transporter member 8 (Glucose transporter type 8) (Gluc ...	0.04	-	end	12 *	Membrane; multi-pass membrane protein. Principally intracellular. May move between intracellular ves ...	integral to plasma membrane [TAS]	605245		477
Q9UGH3 UniProt NPD GO	S23A2_HUMAN	Solute carrier family 23 member 2 (Sodium-dependent vitamin C transporter 2) (hSVCT2) (Na(+)/L-ascor ...	0.04	-	end	10	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	603791		650
Q20787 UniProt NPD GO	S35B3_CAEEL	Solute carrier family 35 member B3 homolog	0.04	-	end	10 *	Membrane; multi-pass membrane protein (Potential)				364
Q923U9 UniProt NPD GO	S40A1_RAT	Solute carrier family 40 member 1 (Ferroportin-1) (Cell adhesion regulator) (CAR1)	0.04	-	end	10 *	Cell membrane; multi-pass membrane protein (By similarity). Localized to the basolateral membrane of ...				570
Q9JHI9 UniProt NPD GO	S40A1_MOUSE	Solute carrier family 40 member 1 (Ferroportin-1) (Iron-regulated transporter 1) (Metal transporter ...	0.04	-	end	10 *	Cell membrane; multi-pass membrane protein. Localized to the basolateral membrane of polarized epith ...	synaptic vesicle [IDA]			570
Q9QXZ6 UniProt NPD GO	SO1A1_MOUSE	Solute carrier organic anion transporter family member 1A1 (Solute carrier family 21 member 1) (Sodi ...	0.04	-	end	11 *	Membrane; multi-pass membrane protein	basolateral plasma membrane [IDA] integral to plasma membrane [IDA]			670
Q9Y512 UniProt NPD GO	SAM50_HUMAN	Sorting and assembly machinery component 50 homolog	0.04	-	cyt	0	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)				469
P11761 UniProt NPD GO	SAPR_STRPU	Sperm-activating peptides precursor [Contains: Speract-like; Speract]	0.04	-	cyt	0					296
P82292 UniProt NPD GO	Z13_BOVIN	Spermadhesin Z13	0.04	-	cyt	0	Secreted protein				116
P29392 UniProt NPD GO	SPAD1_BOVIN	Spermadhesin-1 precursor (Acidic seminal fluid protein) (ASFP)	0.04	-	exc	0	Secreted protein			1SFP	134
Q9I8K8 UniProt NPD GO	EDG5_BRARE	Sphingosine 1-phosphate receptor Edg-5 (S1P receptor Edg-5) (Sphingosine 1-phosphate receptor 2) (S1 ...	0.04	-	end	7	Membrane; multi-pass membrane protein				370
Q9NYA1 UniProt NPD GO	SPHK1_HUMAN	Sphingosine kinase 1 (EC 2.7.1.-) (SK 1) (SPK 1)	0.04	-	mit	0		cytoplasm [IDA] cytosol [TAS] membrane fraction [TAS] soluble fraction [IDA]	603730		384
P82357 UniProt NPD GO	SPING_PSEUS	Spingerin [Contains: Spingerin N-3; Spingerin C-4]	0.04	-	cyt	0	Secreted protein			1ZRW	25
Q75BD8 UniProt NPD GO	DIB1_ASHGO	Spliceosomal protein DIB1	0.04	-	cyt	0	Nucleus (By similarity)				143
P15519 UniProt NPD GO	SPG1_DICDI	Spore germination protein 1 precursor (SPG1)	0.04	-	cyt	1 *	Secreted protein (Probable)				127
P53799 UniProt NPD GO	FDFT_ARATH	Squalene synthetase (EC 2.5.1.21) (SQS) (SS) (Farnesyl-diphosphate farnesyltransferase) (FPP:FPP far ...	0.04	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				410
O74198 UniProt NPD GO	ERG6_CANAL	Sterol 24-C-methyltransferase (EC 2.1.1.41) (Delta(24)-sterol C-methyltransferase)	0.04	-	cyt	0					376
Q5R8D9 UniProt NPD GO	STCH_PONPY	Stress 70 protein chaperone microsome-associated 60 kDa protein precursor (Microsomal stress 70 prot ...	0.04	-	mit	1 *	Microsome (By similarity)				471
O62657 UniProt NPD GO	SDF1_FELCA	Stromal cell-derived factor 1 precursor (SDF-1) (CXCL12)	0.04	-	end	0	Secreted protein				93
P40224 UniProt NPD GO	SDF1_MOUSE	Stromal cell-derived factor 1 precursor (SDF-1) (CXCL12) (Pre-B cell growth-stimulating factor) (PBS ...	0.04	-	exc	0	Secreted protein				89
P48061 UniProt NPD GO	SDF1_HUMAN	Stromal cell-derived factor 1 precursor (SDF-1) (CXCL12) (Pre-B cell growth-stimulating factor) (PBS ...	0.04	-	end	0	Secreted protein		600835	2SDF	93
Q9DCT5 UniProt NPD GO	SDF2_MOUSE	Stromal cell-derived factor 2 precursor (SDF-2)	0.04	-	exc	0	Secreted protein				211
P07647 UniProt NPD GO	KLK9_RAT	Submandibular glandular kallikrein-9 precursor (EC 3.4.21.35) (Tissue kallikrein) (S3 kallikrein) (S ...	0.04	-	end	0					259
Q9Y778 UniProt NPD GO	SMP1_MAGPO	Subtilisin-like proteinase Mp1 precursor (EC 3.4.21.-)	0.04	-	exc	0	Secreted protein				404
P48934 UniProt NPD GO	C560_CHOCR	Succinate dehydrogenase cytochrome b560 subunit (Succinate dehydrogenase, subunit III)	0.04	-	end	3 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				127
P48935 UniProt NPD GO	C560_CYACA	Succinate dehydrogenase cytochrome b560 subunit (Succinate dehydrogenase, subunit III)	0.04	-	mit	3 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				132

You are viewing entries 78451 to 78500 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.