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
P19791 UniProt NPD GO	RNM_ASPSA	Ribonuclease M (EC 3.1.27.1) (RNase M)	0.15	-	nuc	0					238
Q40381 UniProt NPD GO	RNS7_NICAL	Ribonuclease S-7 precursor (EC 3.1.27.1) (Stylar glycoprotein 7) (S7-RNase)	0.15	-	exc	1 *	Secreted protein; extracellular space				218
P61824 UniProt NPD GO	RNAS1_BISBI	Ribonuclease pancreatic (EC 3.1.27.5) (RNase 1) (RNase A)	0.15	-	nuc	0	Secreted protein				124
P84072 UniProt NPD GO	CHAR_MOMCH	Ribosome-inactivating protein charantin (EC 3.2.2.22) (rRNA N-glycosidase) (Fragment)	0.15	-	mit	0					25
P18062 UniProt NPD GO	RBS_CYAPA	Ribulose bisphosphate carboxylase small chain (EC 4.1.1.39) (RuBisCO small subunit)	0.15	-	cyt	0	Plastid; cyanelle				106
P15312 UniProt NPD GO	AGI_HORVU	Root-specific lectin precursor	0.15	-	exc	1 *					212
Q9NV23 UniProt NPD GO	SAST_HUMAN	S-acyl fatty acid synthase thioesterase, medium chain (EC 3.1.2.14) (Oleoyl-ACP hydrolase) (Thioeste ...	0.15	-	cyt	0					265
Q96286 UniProt NPD GO	DCAM1_ARATH	S-adenosylmethionine decarboxylase proenzyme 1 (EC 4.1.1.50) (AdoMetDC 1) (SamDC 1) [Contains: S-ade ...	0.15	-	cyt	0					366
P31227 UniProt NPD GO	SMOD_RANCA	S-modulin (Sensitivity-modulating protein)	0.15	-	nuc	0	The binding target of the Ca(2+)/S-modulin complex is possibly ROS membrane lipid(s)				201
P24280 UniProt NPD GO	SEC14_YEAST	SEC14 cytosolic factor (Phosphatidylinositol/phosphatidylcholine transfer protein) (PI/PC TP)	0.15	-	cyt	0	Golgi apparatus; Golgi membrane; peripheral membrane protein	cytosol [IDA]		1AUA	303
Q7M6Z3 UniProt NPD GO	SMYD2_RAT	SET and MYND domain-containing protein 2	0.15	-	cyt	0					433
Q8BG73 UniProt NPD GO	SH3L2_MOUSE	SH3 domain-binding glutamic acid-rich-like protein 2	0.15	-	cyt	0	Nucleus (By similarity)				107
Q9UJC5 UniProt NPD GO	SH3L2_HUMAN	SH3 domain-binding glutamic acid-rich-like protein 2 (Fovea-associated SH3 domain-binding protein)	0.15	-	mit	0	Nucleus			2CT6	107
Q6AXF6 UniProt NPD GO	SIDT1_MOUSE	SID1 transmembrane family member 1 precursor	0.15	-	end	11	Membrane; multi-pass membrane protein (Potential)				827
P04111 UniProt NPD GO	SPE2C_STRPU	SPEC 2C protein	0.15	-	nuc	0					151
Q8R5B6 UniProt NPD GO	SSB4_MOUSE	SPRY domain-containing SOCS box protein 4 (SSB-4)	0.15	-	nuc	0	Cytoplasm (Probable)				273
Q8NCJ5 UniProt NPD GO	SPRY3_HUMAN	SPRY domain-containing protein 3	0.15	-	mit	0					442
Q5RBR6 UniProt NPD GO	SPRY3_PONPY	SPRY domain-containing protein 3	0.15	-	mit	0					442
Q92154 UniProt NPD GO	SMP_COTJA	Schwann cell myelin protein precursor (Siglec-4b)	0.15	-	end	2 *	Membrane; single-pass type I membrane protein				620
Q9BDP6 UniProt NPD GO	PTTG1_PIG	Securin (Pituitary tumor-transforming protein 1) (Fragment)	0.15	-	nuc	0	Cytoplasm. Nucleus				121
O95997 UniProt NPD GO	PTTG1_HUMAN	Securin (Pituitary tumor-transforming protein 1) (Tumor-transforming protein 1) (Esp1-associated pro ...	0.15	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [TAS] nucleus [TAS]	604147		202
P24095 UniProt NPD GO	LOXX_SOYBN	Seed lipoxygenase (EC 1.13.11.12)	0.15	-	cyt	0	Cytoplasm				864
Q26972 UniProt NPD GO	SEM1A_TRICF	Semaphorin-1A precursor (Semaphorin-I)	0.15	-	end	1	Membrane; single-pass type I membrane protein				712
Q6FQ44 UniProt NPD GO	GLYM_CANGA	Serine hydroxymethyltransferase, mitochondrial precursor (EC 2.1.2.1) (Serine methylase) (Glycine hy ...	0.15	-	mit	0	Mitochondrion				485
P41689 UniProt NPD GO	SPYA_FELCA	Serine--pyruvate aminotransferase, mitochondrial precursor (EC 2.6.1.51) (SPT) (Alanine--glyoxylate ...	0.15	-	mit	0	Mitochondrion; mitochondrial matrix. >90%. Peroxisome				414
P21138 UniProt NPD GO	SERA_ENTHI	Serine-rich 25 kDa antigen protein (SHEHP) (SREHP)	0.15	-	exc	0	Membrane				233
Q39030 UniProt NPD GO	KPK19_ARATH	Serine/threonine-protein kinase AtPK19 (EC 2.7.11.1) (Ribosomal-protein S6 kinase homolog)	0.15	-	cyt	0					471
Q8QZR7 UniProt NPD GO	PDK1L_MOUSE	Serine/threonine-protein kinase PDIK1L (EC 2.7.11.1) (PDLIM1-interacting kinase 1-like)	0.15	-	nuc	0	Nucleus (By similarity)				341
Q1RMT7 UniProt NPD GO	RIOK3_BOVIN	Serine/threonine-protein kinase RIO3 (EC 2.7.11.1) (RIO kinase 3)	0.15	-	cyt	0					519
Q75H77 UniProt NPD GO	SAPKA_ORYSA	Serine/threonine-protein kinase SAPK10 (EC 2.7.11.1) (Osmotic stress/abscisic acid-activated protein ...	0.15	-	cyt	0					362
Q32PP3 UniProt NPD GO	PDK1L_BRARE	Serine/threonine-protein kinase pdik1l (EC 2.7.11.1)	0.15	-	mit	0	Nucleus (By similarity)				341
Q2UN27 UniProt NPD GO	PTPA1_ASPOR	Serine/threonine-protein phosphatase 2A activator 1 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomeras ...	0.15	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				478
Q59ST6 UniProt NPD GO	PTPA2_CANAL	Serine/threonine-protein phosphatase 2A activator 2 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomeras ...	0.15	-	nuc	0	Cytoplasm (By similarity)				358
Q60676 UniProt NPD GO	PPP5_MOUSE	Serine/threonine-protein phosphatase 5 (EC 3.1.3.16) (PP5) (Protein phosphatase T) (PPT)	0.15	-	cyt	0	Nucleus	cytosol [IDA]			499
P53042 UniProt NPD GO	PPP5_RAT	Serine/threonine-protein phosphatase 5 (EC 3.1.3.16) (PP5) (Protein phosphatase T) (PPT)	0.15	-	cyt	0	Nucleus				499
P48579 UniProt NPD GO	PP2A_HELAN	Serine/threonine-protein phosphatase PP2A catalytic subunit (EC 3.1.3.16)	0.15	-	cyt	0					305
Q07098 UniProt NPD GO	PP2A1_ARATH	Serine/threonine-protein phosphatase PP2A-1 catalytic subunit (EC 3.1.3.16)	0.15	-	cyt	0	Cytoplasm				306
Q9XF94 UniProt NPD GO	PP2A2_ORYSA	Serine/threonine-protein phosphatase PP2A-2 catalytic subunit (EC 3.1.3.16)	0.15	-	nuc	0	Cytoplasm (By similarity)				307
Q9XGT7 UniProt NPD GO	PP2A3_ORYSA	Serine/threonine-protein phosphatase PP2A-3 catalytic subunit (EC 3.1.3.16)	0.15	-	cyt	0	Cytoplasm (By similarity)				307
P36614 UniProt NPD GO	PPE1_SCHPO	Serine/threonine-protein phosphatase ppe1 (EC 3.1.3.16) (Phosphatase esp1)	0.15	-	cyt	0	Nucleus. Associated with chromatin	nucleus [IDA]			305
O02785 UniProt NPD GO	SNAT_BOVIN	Serotonin N-acetyltransferase (EC 2.3.1.87) (Aralkylamine N-acetyltransferase) (AA-NAT) (Serotonin a ...	0.15	-	mit	0					207
O93429 UniProt NPD GO	TRFE_PAROL	Serotransferrin precursor	0.15	-	exc	0	Secreted protein				685
O62266 UniProt NPD GO	SRE31_CAEEL	Serpentine receptor class epsilon-31 (Protein sre-31)	0.15	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				357
P54129 UniProt NPD GO	SRG7_CAEEL	Serpentine receptor class gamma-7 (Protein srg-7)	0.15	-	vac	7 *	Membrane; multi-pass membrane protein (Probable)				339
O75635 UniProt NPD GO	SPB7_HUMAN	Serpin B7 (Megsin) (TP55)	0.15	-	nuc	0	Cytoplasm (By similarity)		603357		380
P02768 UniProt NPD GO	ALBU_HUMAN	Serum albumin precursor	0.15	-	exc	0	Secreted protein	extracellular region [NAS] protein complex [IDA]	103600	2ESG	609
P19857 UniProt NPD GO	SAA_HORSE	Serum amyloid A protein (SAA) [Contains: Amyloid protein A (Amyloid fibril protein AA)]	0.15	-	cyt	0					110
P12246 UniProt NPD GO	SAMP_MOUSE	Serum amyloid P-component precursor (SAP)	0.15	-	vac	0	Secreted protein				224
Q9HGT6 UniProt NPD GO	SYSC_CANAL	Seryl-tRNA synthetase, cytoplasmic (EC 6.1.1.11) (Serine--tRNA ligase) (SerRS)	0.15	-	cyt	0	Cytoplasm				462
O42858 UniProt NPD GO	SWD1_SCHPO	Set1 complex component swd1 (Set1C component swd1) (COMPASS component swd1) (Complex proteins associ ...	0.15	-	cyt	0	Nucleus (By similarity)	COMPASS complex [IDA]			398

You are viewing entries 57601 to 57650 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.