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
P21924 UniProt NPD GO	SIA2_SORBI	Small protein inhibitor of insect alpha-amylases 2 (SI alpha-2)	0.06	-	nuc	0					48
Q5E9D1 UniProt NPD GO	SUMO1_BOVIN	Small ubiquitin-related modifier 1 precursor (SUMO-1)	0.06	-	nuc	0	Nucleus; nuclear membrane (By similarity). Nucleus; nucleoplasm; nuclear speckle (By similarity). Cy ...				101
Q5R6J4 UniProt NPD GO	SUMO1_PONPY	Small ubiquitin-related modifier 1 precursor (SUMO-1)	0.06	-	nuc	0	Nucleus; nuclear membrane (By similarity). Nucleus; nucleoplasm; nuclear speckle (By similarity). Cy ...				101
Q9MZD5 UniProt NPD GO	SUMO1_CERNI	Small ubiquitin-related modifier 1 precursor (SUMO-1) (Sentrin)	0.06	-	nuc	0	Nucleus; nuclear membrane (By similarity). Nucleus; nucleoplasm; nuclear speckle (By similarity). Cy ...				101
P63166 UniProt NPD GO	SUMO1_MOUSE	Small ubiquitin-related modifier 1 precursor (SUMO-1) (Ubiquitin-like protein SMT3C) (SMT3 homolog 3 ...	0.06	-	nuc	0	Nucleus; nuclear membrane. Nucleus; nucleoplasm; nuclear speckle. Cytoplasm	nucleus [IDA] PML body [TAS]			101
P63165 UniProt NPD GO	SUMO1_HUMAN	Small ubiquitin-related modifier 1 precursor (SUMO-1) (Ubiquitin-like protein SMT3C) (SMT3 homolog 3 ...	0.06	-	nuc	0	Nucleus; nuclear membrane. Nucleus; nucleoplasm; nuclear speckle. Cytoplasm		601912	2BF8	101
Q9NRT5 UniProt NPD GO	SMG64_HUMAN	Smooth muscle cell-expressed and macrophage conditioned medium-induced protein 64 (Smag-64)	0.06	-	nuc	0					66
Q8IWT1 UniProt NPD GO	SCN4B_HUMAN	Sodium channel beta-4 subunit precursor	0.06	-	end	1 *	Membrane; single-pass type I membrane protein (Probable)	voltage-gated sodium channel complex [IDA]	608256		228
Q7M729 UniProt NPD GO	SCN4B_MOUSE	Sodium channel beta-4 subunit precursor	0.06	-	mit	2 *	Membrane; single-pass type I membrane protein (Probable)				228
Q7M730 UniProt NPD GO	SCN4B_RAT	Sodium channel beta-4 subunit precursor	0.06	-	end	2 *	Membrane; single-pass type I membrane protein (Probable)				228
P48067 UniProt NPD GO	SC6A9_HUMAN	Sodium- and chloride-dependent glycine transporter 1 (GlyT1) (GlyT-1) (Solute carrier family 6 membe ...	0.06	-	end	12	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	601019		692
Q03614 UniProt NPD GO	NTDO_CAEEL	Sodium-dependent dopamine transporter (DA transporter) (DAT)	0.06	-	end	11	Membrane; multi-pass membrane protein (Probable)				615
Q93655 UniProt NPD GO	NAD1_CAEEL	Sodium-dependent low-affinity dicarboxylate transporter 1 (Na(+)/dicarboxylate cotransporter 1) (NaD ...	0.06	-	end	11 *	Membrane; multi-pass membrane protein (Potential)				582
O95436 UniProt NPD GO	NPT2B_HUMAN	Sodium-dependent phosphate transport protein 2B (Sodium/phosphate cotransporter 2B) (Na(+)/Pi cotran ...	0.06	-	end	11	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	604217		690
Q9JJ09 UniProt NPD GO	NPT2B_RAT	Sodium-dependent phosphate transport protein 2B (Sodium/phosphate cotransporter 2B) (Na(+)/Pi cotran ...	0.06	-	end	9	Membrane; multi-pass membrane protein				695
Q60857 UniProt NPD GO	SC6A4_MOUSE	Sodium-dependent serotonin transporter (5HT transporter) (5HTT)	0.06	-	end	12	Membrane; multi-pass membrane protein				630
P31652 UniProt NPD GO	SC6A4_RAT	Sodium-dependent serotonin transporter (5HT transporter) (5HTT)	0.06	-	end	12	Membrane; multi-pass membrane protein				630
O08705 UniProt NPD GO	NTCP_MOUSE	Sodium/bile acid cotransporter (Na(+)/bile acid cotransporter) (Na(+)/taurocholate transport protein ...	0.06	-	end	7 *	Membrane; multi-pass membrane protein				362
Q8S396 UniProt NPD GO	NHX5_ARATH	Sodium/hydrogen exchanger 5 (Na(+)/H(+) exchanger 5) (NHE-5)	0.06	-	end	10 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity). Tonoplast				517
O88627 UniProt NPD GO	S28A2_MOUSE	Sodium/nucleoside cotransporter 2 (Na(+)/nucleoside cotransporter 2) (Sodium-coupled nucleoside tran ...	0.06	-	end	11	Membrane; multi-pass membrane protein				660
Q04646 UniProt NPD GO	ATNG_MOUSE	Sodium/potassium-transporting ATPase gamma chain (Sodium pump gamma chain) (Na+/K+ ATPase subunit ga ...	0.06	-	nuc	1 *	Membrane; single-pass type III membrane protein (Potential)				70
Q04679 UniProt NPD GO	ATNG_RAT	Sodium/potassium-transporting ATPase gamma chain (Sodium pump gamma chain) (Na+/K+ ATPase subunit ga ...	0.06	-	nuc	1 *	Membrane; single-pass type III membrane protein (Potential)				66
P21188 UniProt NPD GO	AT1B3_XENLA	Sodium/potassium-transporting ATPase subunit beta-3 (Sodium/potassium-dependent ATPase beta-3 subuni ...	0.06	-	cyt	1 *	Membrane; single-pass type II membrane protein				277
Q9ES88 UniProt NPD GO	S13A2_MOUSE	Solute carrier family 13 member 2 (Renal sodium/dicarboxylate cotransporter) (Na(+)/dicarboxylate co ...	0.06	-	end	13 *	Membrane; multi-pass membrane protein (Potential)				586
P14246 UniProt NPD GO	GTR2_MOUSE	Solute carrier family 2, facilitated glucose transporter member 2 (Glucose transporter type 2, liver ...	0.06	-	end	11 *	Membrane; multi-pass membrane protein	brush border [IDA] plasma membrane [IDA]			523
P12336 UniProt NPD GO	GTR2_RAT	Solute carrier family 2, facilitated glucose transporter member 2 (Glucose transporter type 2, liver ...	0.06	-	end	11 *	Membrane; multi-pass membrane protein	brush border [IDA]			522
Q9NSA0 UniProt NPD GO	OAT4_HUMAN	Solute carrier family 22 member 11 (Organic anion transporter 4)	0.06	-	end	10 *	Cell membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	607097		550
Q9EPR4 UniProt NPD GO	S23A2_MOUSE	Solute carrier family 23 member 2 (Sodium-dependent vitamin C transporter 2) (mSVCT2) (Na(+)/L-ascor ...	0.06	-	end	10	Membrane; multi-pass membrane protein	integral to membrane [ISS]			647
Q66HX0 UniProt NPD GO	S35B1_BRARE	Solute carrier family 35 member B1	0.06	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)				329
Q95KI5 UniProt NPD GO	S45A3_MACFA	Solute carrier family 45 member 3 (Prostate cancer-associated protein 6) (Prostein)	0.06	-	end	11 *	Membrane; multi-pass membrane protein (Potential)				553
Q8K0H7 UniProt NPD GO	S45A3_MOUSE	Solute carrier family 45 member 3 (Prostate cancer-associated protein 6) (Prostein)	0.06	-	end	11 *	Membrane; multi-pass membrane protein (Potential)				553
O88397 UniProt NPD GO	SO1A5_RAT	Solute carrier organic anion transporter family member 1A5 (Solute carrier family 21 member 7) (Sodi ...	0.06	-	end	11 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]			670
Q99J94 UniProt NPD GO	SO1A6_MOUSE	Solute carrier organic anion transporter family member 1A6 (Solute carrier family 21 member 13) (Kid ...	0.06	-	end	11 *	Membrane; multi-pass membrane protein				670
P79869 UniProt NPD GO	SHH_RASPA	Sonic hedgehog protein (SHH) (Fragments)	0.06	-	mit	0	Sonic hedgehog protein C-product: Secreted protein; extracellular space (By similarity). Sonic hedge ...				121
Q8K4N2 UniProt NPD GO	SPG11_MOUSE	Sperm-associated antigen 11 precursor	0.06	-	exc	0	Secreted protein (By similarity)				69
Q9ZTR0 UniProt NPD GO	SPD2_PEA	Spermidine synthase 2 (EC 2.5.1.16) (Putrescine aminopropyltransferase 2) (SPDSY 2)	0.06	-	cyt	0					342
P11113 UniProt NPD GO	SR4_PHYPO	Spherulin-4 precursor	0.06	-	end	1 *					332
Q6YNI2 UniProt NPD GO	GPR6_MOUSE	Sphingosine 1-phosphate receptor GPR6 (G-protein coupled receptor 6)	0.06	-	end	7	Membrane; multi-pass membrane protein				363
Q9V7Y2 UniProt NPD GO	SGPL_DROME	Sphingosine-1-phosphate lyase (EC 4.1.2.27) (SP-lyase) (SPL) (Sphingosine-1-phosphate aldolase)	0.06	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type III membrane protein (By sim ...	integral to endoplasmic reticulum membrane [NAS]			545
Q06819 UniProt NPD GO	DIB1_YEAST	Spliceosomal protein DIB1	0.06	-	cyt	0	Nucleus	snRNP U5 [IPI] U4/U6 x U5 tri-snRNP complex [IDA]			143
P58864 UniProt NPD GO	STAR_SALAL	Steroidogenic acute regulatory protein (StAR) (StARD1) (Fragment)	0.06	-	nuc	0	Mitochondrion (By similarity)				73
P20178 UniProt NPD GO	THS1_ARAHY	Stilbene synthase 1 (EC 2.3.1.95) (Resveratrol synthase 1) (RS1) (Trihydroxystilbene synthase 1)	0.06	-	nuc	0	Cytoplasm				389
Q9UBI4 UniProt NPD GO	STML1_HUMAN	Stomatin-like protein 1 (SLP-1) (Stomatin-related protein) (STORP) (EPB72-like 1) (UNC24 homolog)	0.06	-	nuc	1	Membrane; single-pass type III membrane protein (Potential)		608326		398
O35162 UniProt NPD GO	STCH_RAT	Stress 70 protein chaperone microsome-associated 60 kDa protein precursor (Microsomal stress 70 prot ...	0.06	-	cyt	1 *	Microsome (By similarity)				471
P60991 UniProt NPD GO	TX1_STRCF	Stromatoxin-1 (ScTx1)	0.06	-	nuc	0	Secreted protein				34
P98162 UniProt NPD GO	RSVR_COTJA	Subgroup A Rous sarcoma virus receptor PG900 precursor (Low density lipoprotein receptor-related pro ...	0.06	-	exc	1	Membrane; single-pass type I membrane protein (Probable)			1K7B	157
P30549 UniProt NPD GO	NK2R_MOUSE	Substance-K receptor (SKR) (Neurokinin A receptor) (NK-2 receptor) (NK-2R) (Tachykinin receptor 2)	0.06	-	end	7 *	Membrane; multi-pass membrane protein				384
Q5DUB1 UniProt NPD GO	NK1R_MERUN	Substance-P receptor (SPR) (NK-1 receptor) (NK-1R) (Tachykinin receptor 1)	0.06	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)				407
Q7SGY6 UniProt NPD GO	DHSD_NEUCR	Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (CybS) (Suc ...	0.06	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				166
P33421 UniProt NPD GO	SDH3_YEAST	Succinate dehydrogenase cytochrome B subunit, mitochondrial precursor	0.06	-	nuc	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	respiratory chain complex II (sensu Eukaryota) [TAS]		1PB4	198

You are viewing entries 73201 to 73250 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.