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
Q4WPW8 UniProt NPD GO	RUVB1_ASPFU	RuvB-like helicase 1 (EC 3.6.1.-)	0.07	-	cyt	0	Nucleus (By similarity)				458
Q8WZS3 UniProt NPD GO	RUVB1_NEUCR	RuvB-like helicase 1 (EC 3.6.1.-)	0.07	-	nuc	0	Nucleus (By similarity)				458
Q4P112 UniProt NPD GO	RUVB1_USTMA	RuvB-like helicase 1 (EC 3.6.1.-)	0.07	-	cyt	0	Nucleus (By similarity)				488
O04009 UniProt NPD GO	DCAM_TOBAC	S-adenosylmethionine decarboxylase proenzyme (EC 4.1.1.50) (AdoMetDC) (SamDC) [Contains: S-adenosylm ...	0.07	-	mit	0					361
P19358 UniProt NPD GO	METL_YEAST	S-adenosylmethionine synthetase 2 (EC 2.5.1.6) (Methionine adenosyltransferase 2) (AdoMet synthetase ...	0.07	-	cyt	0					383
P15887 UniProt NPD GO	ARRS_RAT	S-arrestin (Retinal S-antigen) (48 kDa protein) (S-AG) (Rod photoreceptor arrestin)	0.07	-	cyt	0					403
P53989 UniProt NPD GO	SEC14_CANGA	SEC14 cytosolic factor (Phosphatidylinositol/phosphatidylcholine transfer protein) (PI/PC TP)	0.07	-	cyt	0	Golgi apparatus; Golgi membrane; peripheral membrane protein (By similarity)				302
O60880 UniProt NPD GO	SH21A_HUMAN	SH2 domain protein 1A (Signaling lymphocyte activation molecule-associated protein) (SLAM-associated ...	0.07	-	nuc	0	Cytoplasm (Potential)	cytoplasm [IDA]	300490	1M27	128
Q8WW59 UniProt NPD GO	SPRY4_HUMAN	SPRY domain-containing protein 4	0.07	-	mit	0					207
Q91WK1 UniProt NPD GO	SPRY4_MOUSE	SPRY domain-containing protein 4	0.07	-	mit	0					207
Q32P59 UniProt NPD GO	SLIRP_BOVIN	SRA stem-loop-interacting RNA-binding protein, mitochondrial precursor	0.07	-	mit	0	Mitochondrion; predominantly. Nucleus; some fraction is nuclear. In the nucleus, it is recruited to ...				111
P70083 UniProt NPD GO	AT2A1_MAKNI	Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 (EC 3.6.3.8) (Calcium pump 1) (SERCA1) (SR Ca(2+ ...	0.07	-	end	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Sarcoplasmic ret ...				996
Q92105 UniProt NPD GO	AT2A1_RANES	Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 (EC 3.6.3.8) (Calcium pump 1) (SERCA1) (SR Ca(2+ ...	0.07	-	end	7	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Sarcoplasmic ret ...				994
Q03669 UniProt NPD GO	AT2A2_CHICK	Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 (EC 3.6.3.8) (Calcium pump 2) (SERCA2) (SR Ca(2+ ...	0.07	-	end	9	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Sarcoplasmic ret ...	microsome [ISS] sarcoplasmic reticulum [ISS]			1041
P24490 UniProt NPD GO	SRX23_SARPE	Sarcotoxin II-3 precursor	0.07	-	exc	0	Secreted protein				294
P08377 UniProt NPD GO	SRX1C_SARPE	Sarcotoxin-1C (Sarcotoxin IC)	0.07	-	nuc	0	Secreted protein				39
Q7YWA7 UniProt NPD GO	SECP_VESMG	Secapin precursor	0.07	-	exc	1 *	Secreted protein (By similarity)				77
Q12765 UniProt NPD GO	SCRN1_HUMAN	Secernin-1	0.07	-	cyt	0	Cytoplasm (By similarity)	nuclear membrane [IDA] nucleus [IDA]			414
Q9CZC8 UniProt NPD GO	SCRN1_MOUSE	Secernin-1	0.07	-	cyt	0	Cytoplasm (By similarity)				414
Q8WVN6 UniProt NPD GO	SCTM1_HUMAN	Secreted and transmembrane protein 1 precursor (Protein K12)	0.07	-	end	1	Cell membrane; single-pass type I membrane protein (Probable). Secreted protein. Also found as secre ...	extracellular space [TAS] Golgi apparatus [TAS] integral to membrane [TAS]	602602		248
Q9IA95 UniProt NPD GO	SFRP3_CHICK	Secreted frizzled-related protein 3 precursor (sFRP-3) (Frizzled-related protein 1) (FrzB-1)	0.07	-	exc	0	Secreted protein (By similarity)	extracellular region [ISS] membrane [ISS]			315
P13609 UniProt NPD GO	PGSG_MOUSE	Secretory granule proteoglycan core protein precursor (Mastocytoma proteoglycan core protein) (Sergl ...	0.07	-	mit	1 *					152
Q41162 UniProt NPD GO	LCS1_ROBPS	Seed agglutinin I precursor (RPSAI) (LECRPAS1)	0.07	-	exc	1 *					285
Q94497 UniProt NPD GO	SELD_DICDI	Selenide, water dikinase (EC 2.7.9.3) (Selenophosphate synthetase) (Selenium donor protein) (Fragmen ...	0.07	-	cyt	1					370
Q8TDD7 UniProt NPD GO	SNSR5_HUMAN	Sensory neuron-specific G-protein coupled receptor 5	0.07	-	end	7 *	Membrane; multi-pass membrane protein				322
P54797 UniProt NPD GO	T10_MOUSE	Ser/Thr-rich protein T10 in DGCR region	0.07	-	nuc	0					276
Q42588 UniProt NPD GO	SAT1_ARATH	Serine acetyltransferase 1 (EC 2.3.1.30) (AtSAT-1) (SAT-p) (AtSERAT2;1)	0.07	-	nuc	0	Plastid; chloroplast. Cytoplasm. First chloroplastic and progressively cytoplasmic during aging				314
Q42538 UniProt NPD GO	SAT5_ARATH	Serine acetyltransferase 5 (EC 2.3.1.30) (AtSAT-5) (SAT-c) (AtSERAT1;1)	0.07	-	nuc	0	Cytoplasm				312
P07511 UniProt NPD GO	GLYC_RABIT	Serine hydroxymethyltransferase, cytosolic (EC 2.1.2.1) (Serine methylase) (Glycine hydroxymethyltra ...	0.07	-	cyt	0	Cytoplasm			1RVY	483
Q60HD1 UniProt NPD GO	LCB1_MACFA	Serine palmitoyltransferase 1 (EC 2.3.1.50) (Long chain base biosynthesis protein 1) (LCB 1) (Serine ...	0.07	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				473
Q63ZK0 UniProt NPD GO	AMI_XENLA	Serine protease ami precursor (EC 3.4.21.-)	0.07	-	cyt	0	Secreted protein (By similarity)				263
Q6P326 UniProt NPD GO	AMI_XENTR	Serine protease ami precursor (EC 3.4.21.-)	0.07	-	nuc	0	Secreted protein (By similarity)				265
P58515 UniProt NPD GO	SPI2_SOLTU	Serine protease inhibitor 2 (PSPI-21) (PSPI-21-5.2) [Contains: Serine protease inhibitor 2 chain A; ...	0.07	-	cyt	0	Vacuole (By similarity)				186
P30941 UniProt NPD GO	SPI7_SOLTU	Serine protease inhibitor 7 precursor (PIG) (PIGEN1) (Allergen Sola t 4) (STPIB) (STPIA) (pKEN14-28) ...	0.07	-	exc	0	Vacuole	vacuole [IDA]			221
Q8BT20 UniProt NPD GO	ISK6_MOUSE	Serine protease inhibitor Kazal-type 6 precursor	0.07	-	end	1 *	Secreted protein (Potential)				105
Q6IE47 UniProt NPD GO	ISK6_RAT	Serine protease inhibitor Kazal-type 6 precursor	0.07	-	vac	0	Secreted protein (Potential)				105
P43291 UniProt NPD GO	ASK1_ARATH	Serine/threonine-protein kinase ASK1 (EC 2.7.11.1)	0.07	-	cyt	0					363
Q8TAS1 UniProt NPD GO	UHMK1_HUMAN	Serine/threonine-protein kinase Kist (EC 2.7.11.1) (Kinase interacting with stathmin) (U2AF homology ...	0.07	-	cyt	0	Nucleus. Mostly nuclear (By similarity)	cytoplasm [ISS] nucleus [ISS]	608849		419
Q63285 UniProt NPD GO	UHMK1_RAT	Serine/threonine-protein kinase Kist (EC 2.7.11.1) (Kinase interacting with stathmin) (U2AF homology ...	0.07	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			419
Q5KCM5 UniProt NPD GO	PTPA2_CRYNE	Serine/threonine-protein phosphatase 2A activator 2 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomeras ...	0.07	-	cyt	0	Cytoplasm (By similarity)				382
P55739 UniProt NPD GO	PPP5_RABIT	Serine/threonine-protein phosphatase 5 (EC 3.1.3.16) (PP5) (Protein phosphatase T) (PPT) (Fragment)	0.07	-	cyt	0	Nucleus				42
O62367 UniProt NPD GO	SRA23_CAEEL	Serpentine receptor class alpha-23 (Protein sra-23)	0.07	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				340
P05366 UniProt NPD GO	SAA1_MOUSE	Serum amyloid A-1 protein precursor	0.07	-	exc	1 *					122
P53614 UniProt NPD GO	SAA1_RABIT	Serum amyloid A-1 protein precursor	0.07	-	exc	0					122
P05367 UniProt NPD GO	SAA2_MOUSE	Serum amyloid A-2 protein precursor [Contains: Amyloid protein A (Amyloid fibril protein AA)]	0.07	-	exc	1 *					122
P54364 UniProt NPD GO	JANA_DROPS	Sex-regulated protein janus-A	0.07	-	mit	0					149
P40903 UniProt NPD GO	ISP6_SCHPO	Sexual differentiation process putative subtilase-type proteinase isp6 (EC 3.4.21.-)	0.07	-	exc	0					467
P43288 UniProt NPD GO	KSG1_ARATH	Shaggy-related protein kinase alpha (EC 2.7.11.1) (ASK-alpha)	0.07	-	cyt	0					405
Q9W7J6 UniProt NPD GO	NXS7_PSETE	Short neurotoxin 7 precursor (Alpha neurotoxin 7)	0.07	-	mit	0	Secreted protein (By similarity)				79
P18503 UniProt NPD GO	CAS4_EPHMU	Short-chain collagen C4 (Fragment)	0.07	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				366

You are viewing entries 71001 to 71050 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.