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
Q9ER71 UniProt NPD GO	RHOJ_MOUSE	Rho-related GTP-binding protein RhoJ (Tc10-like GTP-binding protein TCL)	0.16	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				214
P42814 UniProt NPD GO	RNS2_ARATH	Ribonuclease 2 precursor (EC 3.1.27.1)	0.16	-	exc	0					259
P00662 UniProt NPD GO	RNAS1_GIRCA	Ribonuclease pancreatic (EC 3.1.27.5) (RNase 1) (RNase A)	0.16	-	nuc	0	Secreted protein				124
P42170 UniProt NPD GO	RIR2_CAEEL	Ribonucleoside-diphosphate reductase small chain (EC 1.17.4.1) (Ribonucleotide reductase small subun ...	0.16	-	cyt	1					381
P50650 UniProt NPD GO	RIR2_PLAF4	Ribonucleoside-diphosphate reductase small chain (EC 1.17.4.1) (Ribonucleotide reductase small subun ...	0.16	-	cyt	0					349
O64888 UniProt NPD GO	KPRS5_ARATH	Ribose-phosphate pyrophosphokinase 5 (EC 2.7.6.1) (Phosphoribosyl pyrophosphate synthetase 5)	0.16	-	mit	0					394
Q4R4R7 UniProt NPD GO	PRPS2_MACFA	Ribose-phosphate pyrophosphokinase II (EC 2.7.6.1) (Phosphoribosyl pyrophosphate synthetase II) (PRS ...	0.16	-	cyt	0					317
P11908 UniProt NPD GO	PRPS2_HUMAN	Ribose-phosphate pyrophosphokinase II (EC 2.7.6.1) (Phosphoribosyl pyrophosphate synthetase II) (PRS ...	0.16	-	cyt	0			311860		317
P21108 UniProt NPD GO	PRPS3_HUMAN	Ribose-phosphate pyrophosphokinase III (EC 2.7.6.1) (Phosphoribosyl pyrophosphate synthetase III) (P ...	0.16	-	cyt	0					317
P93543 UniProt NPD GO	RIP1_SAMNI	Ribosome-inactivating protein SNAI' precursor [Contains: SNAI' A chain (EC 3.2.2.22) (rRNA N-glycosi ...	0.16	-	mit	1 *					569
Q6Y9H0 UniProt NPD GO	RBL2_PROMN	Ribulose bisphosphate carboxylase precursor (EC 4.1.1.39) (RuBisCO) [Contains: Ribulose bisphosphate ...	0.16	-	cyt	0	Plastid; chloroplast (Probable). In this organism the plastid is the result of a secondary endosymbi ...				1563
P49521 UniProt NPD GO	RBS_ODOSI	Ribulose bisphosphate carboxylase small chain (EC 4.1.1.39) (RuBisCO small subunit)	0.16	-	cyt	0	Plastid; chloroplast				139
P16135 UniProt NPD GO	RBS2_ACEME	Ribulose bisphosphate carboxylase small chain 2, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.16	-	cyt	0	Plastid; chloroplast				173
Q42823 UniProt NPD GO	RBS_GLYTA	Ribulose bisphosphate carboxylase small chain, chloroplast precursor (EC 4.1.1.39) (RuBisCO small su ...	0.16	-	cyt	0	Plastid; chloroplast				178
P23489 UniProt NPD GO	RCA_CHLRE	Ribulose bisphosphate carboxylase/oxygenase activase, chloroplast precursor (RuBisCO activase) (RA)	0.16	-	mit	0	Plastid; chloroplast; chloroplast stroma				408
Q26005 UniProt NPD GO	RESA_PLAFP	Ring-infected erythrocyte surface antigen (Fragment)	0.16	+	cyt	0	Cell membrane; cytoplasmic side. Probably located on the cytoplasmic face of the membrane where it a ...				304
O49972 UniProt NPD GO	DCAM2_BRAJU	S-adenosylmethionine decarboxylase proenzyme 2 (EC 4.1.1.50) (AdoMetDC 2) (SamDC 2) [Contains: S-ade ...	0.16	-	nuc	0					369
Q9SDM8 UniProt NPD GO	DCAM3_BRAJU	S-adenosylmethionine decarboxylase proenzyme 3 (EC 4.1.1.50) (AdoMetDC 3) (SamDC 3) [Contains: S-ade ...	0.16	-	nuc	0					367
Q9NFP5 UniProt NPD GO	SH3BG_DROME	SH3 domain-binding glutamic acid-rich protein homolog (SH3BGR protein)	0.16	-	nuc	0					158
Q9P0V8 UniProt NPD GO	SLAF8_HUMAN	SLAM family member 8 precursor (B-lymphocyte activator macrophage expressed) (BCM-like membrane prot ...	0.16	-	end	1	Membrane; single-pass type I membrane protein		606620		285
Q84VQ1 UniProt NPD GO	KINB1_ARATH	SNF1-related protein kinase regulatory subunit beta-1 (AKIN beta1) (AKINB1)	0.16	-	nuc	0					283
Q06177 UniProt NPD GO	STF2L_YEAST	STF2-like protein YLR327C	0.16	-	nuc	0	Mitochondrion (Potential)	cytoplasm [IDA] nucleus [IDA]			85
Q9C0C4 UniProt NPD GO	SEM4C_HUMAN	Semaphorin-4C precursor	0.16	-	end	1	Membrane; single-pass type I membrane protein (By similarity)		604462		833
Q29535 UniProt NPD GO	RNS_GIRCA	Seminal ribonuclease (EC 3.1.27.5) (Seminal RNase) (Fragment)	0.16	-	nuc	0	Secreted protein (By similarity)				84
P97321 UniProt NPD GO	SEPR_MOUSE	Seprase (EC 3.4.21.-) (Fibroblast activation protein alpha) (Integral membrane serine protease)	0.16	-	exc	1 *	Membrane; single-pass type II membrane protein (By similarity)				761
P42207 UniProt NPD GO	SEPT1_DROME	Septin-1 (DIFF6 protein homolog) (Protein innocent bystander)	0.16	-	cyt	0		ring canal (sensu Insecta) [NAS]			361
P07519 UniProt NPD GO	CBP1_HORVU	Serine carboxypeptidase 1 precursor (EC 3.4.16.5) (Serine carboxypeptidase I) (Carboxypeptidase C) ( ...	0.16	-	pox	1 *	Secreted protein. Secreted into the endosperm				499
P97363 UniProt NPD GO	LCB2_MOUSE	Serine palmitoyltransferase 2 (EC 2.3.1.50) (Long chain base biosynthesis protein 2) (LCB 2) (Serine ...	0.16	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein				560
Q3E790 UniProt NPD GO	TSC3_YEAST	Serine palmitoyltransferase-regulating protein TSC3 (Temperature-sensitive CSG2-mutant suppressor pr ...	0.16	-	mit	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein	membrane fraction [IDA] microsome [IDA]			80
O46162 UniProt NPD GO	SGP1_SCHGR	Serine protease inhibitor I/II precursor [Contains: Protease inhibitor SGPI-1 (Schistocerca gregaria ...	0.16	-	exc	0	Secreted protein			2F91	92
Q9N0X0 UniProt NPD GO	AURKB_PIG	Serine/threonine-protein kinase 12 (EC 2.7.11.1) (Aurora-B) (Fragment)	0.16	-	nuc	0	Nucleus. Localizes on chromosome arms and inner centromeres from prophase through metaphase and then ...				156
Q09170 UniProt NPD GO	CDS1_SCHPO	Serine/threonine-protein kinase cds1 (EC 2.7.11.1) (Checkpoint kinase cds1)	0.16	-	cyt	0					460
Q38845 UniProt NPD GO	2AAA_ARATH	Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform (PP2A, subunit A, ...	0.16	-	cyt	0					588
Q9ZSE4 UniProt NPD GO	PP2A_HEVBR	Serine/threonine-protein phosphatase PP2A catalytic subunit (EC 3.1.3.16)	0.16	-	cyt	0	Cytoplasm (By similarity)				306
Q9ZSS3 UniProt NPD GO	PP2A1_ORYSA	Serine/threonine-protein phosphatase PP2A-1 catalytic subunit (EC 3.1.3.16)	0.16	-	cyt	0	Cytoplasm (By similarity)				306
P79774 UniProt NPD GO	SNAT_CHICK	Serotonin N-acetyltransferase (EC 2.3.1.87) (Aralkylamine N-acetyltransferase) (AA-NAT) (Serotonin a ...	0.16	-	mit	0					205
O97756 UniProt NPD GO	SNAT_MACMU	Serotonin N-acetyltransferase (EC 2.3.1.87) (Aralkylamine N-acetyltransferase) (AA-NAT) (Serotonin a ...	0.16	-	mit	0					204
Q9R0A9 UniProt NPD GO	SNAT_MESAU	Serotonin N-acetyltransferase (EC 2.3.1.87) (Aralkylamine N-acetyltransferase) (AA-NAT) (Serotonin a ...	0.16	-	cyt	0					207
Q8IW75 UniProt NPD GO	SPA12_HUMAN	Serpin A12 precursor (Visceral adipose-specific serpin) (Visceral adipose tissue-derived serine prot ...	0.16	-	nuc	0	Secreted protein (Potential)				414
P20727 UniProt NPD GO	SAA2_MESAU	Serum amyloid A-2 protein precursor	0.16	-	exc	0					122
P19453 UniProt NPD GO	SAA3_MESAU	Serum amyloid A-3 protein precursor	0.16	-	exc	0					122
P04918 UniProt NPD GO	SAA3_MOUSE	Serum amyloid A-3 protein precursor	0.16	-	exc	0					122
P01417 UniProt NPD GO	NXS1_DENJA	Short neurotoxin 1	0.16	-	nuc	0	Secreted protein				60
P60773 UniProt NPD GO	NXS1_NAJPH	Short neurotoxin 1 (NTX I)	0.16	-	nuc	0	Secreted protein				61
Q9DBL1 UniProt NPD GO	ACDSB_MOUSE	Short/branched chain specific acyl-CoA dehydrogenase, mitochondrial precursor (EC 1.3.99.-) (SBCAD) ...	0.16	-	mit	0	Mitochondrion; mitochondrial matrix (Probable)	mitochondrion [IDA]			432
Q9Y3A5 UniProt NPD GO	SBDS_HUMAN	Shwachman-Bodian-Diamond syndrome protein	0.16	-	mit	0			607444		249
Q925N0 UniProt NPD GO	SFXN5_MOUSE	Sideroflexin-5	0.16	-	end	5	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (By similarity)	mitochondrial inner membrane [IDA]			342
Q8CFD0 UniProt NPD GO	SFXN5_RAT	Sideroflexin-5 (Tricarboxylate carrier BBG-TCC)	0.16	-	end	5	Mitochondrion; mitochondrial membrane; multi-pass membrane protein	mitochondrion [IDA]			342
P24807 UniProt NPD GO	CD24_MOUSE	Signal transducer CD24 precursor (M1/69-J11D heat stable antigen) (HSA) (Nectadrin) (Lymphocyte anti ...	0.16	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor	external side of plasma membrane [IDA]			76
P10855 UniProt NPD GO	CCL3_MOUSE	Small inducible cytokine A3 precursor (CCL3) (Macrophage inflammatory protein 1-alpha) (MIP-1-alpha) ...	0.16	-	exc	0	Secreted protein				92

You are viewing entries 56251 to 56300 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.