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
Q96DH6 UniProt NPD GO	MSI2H_HUMAN	RNA-binding protein Musashi homolog 2 (Musashi-2)	0.08	-	cyt	0	Cytoplasm. Associated with polysomes (By similarity)		607897		328
Q00363 UniProt NPD GO	AVR4_CLAFU	Race-specific elicitor A4 precursor	0.08	-	nuc	0					135
Q05144 UniProt NPD GO	RAC2_MOUSE	Ras-related C3 botulinum toxin substrate 2 precursor (p21-Rac2) (EN-7 protein)	0.08	-	cyt	0	Cytoplasm (By similarity). Membrane-associated when activated (By similarity)	cytoplasm [IDA] membrane fraction [IDA] nuclear envelope [IDA]			192
Q9HB90 UniProt NPD GO	RRAGC_HUMAN	Ras-related GTP-binding protein C (Rag C) (GTPase-interacting protein 2) (TIB929)	0.08	-	cyt	0	Cytoplasm. Nucleus. Predominantly cytoplasmic. May shuttle between the cytoplasm and nucleus, depend ...	cytoplasm [IDA] nucleus [IDA]	608267		399
P35281 UniProt NPD GO	RAB10_RAT	Ras-related protein Rab-10	0.08	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	Golgi apparatus [IPI]			200
Q3MHP2 UniProt NPD GO	RB11B_BOVIN	Ras-related protein Rab-11B	0.08	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				217
O35509 UniProt NPD GO	RB11B_RAT	Ras-related protein Rab-11B	0.08	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	cytoplasmic membrane-bound vesicle [IDA]			217
Q15907 UniProt NPD GO	RB11B_HUMAN	Ras-related protein Rab-11B (GTP-binding protein YPT3)	0.08	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)		604198	2F9M	217
P22129 UniProt NPD GO	RB11B_DISOM	Ras-related protein Rab-11B (ORA3)	0.08	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				218
P35285 UniProt NPD GO	RB22A_MOUSE	Ras-related protein Rab-22A (Rab-22) (Rab-14)	0.08	-	cyt	0	Endosome; endosomal membrane; lipid-anchor (By similarity). Cell membrane; lipid-anchor (By similari ...			1Z0J	194
P61017 UniProt NPD GO	RAB4B_CANFA	Ras-related protein Rab-4B	0.08	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				213
P61018 UniProt NPD GO	RAB4B_HUMAN	Ras-related protein Rab-4B	0.08	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	intracellular [NAS]			213
Q8VEA8 UniProt NPD GO	RAB7B_MOUSE	Ras-related protein Rab-7b	0.08	-	cyt	0	Lysosome (By similarity). Associated with lysosomal organelles (By similarity)				199
Q40191 UniProt NPD GO	RB11A_LOTJA	Ras-related protein Rab11A	0.08	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				226
P34142 UniProt NPD GO	RABB_DICDI	Ras-related protein RabB	0.08	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				213
Q6IP71 UniProt NPD GO	RALBB_XENLA	Ras-related protein ralB-B (XRalB-B)	0.08	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	membrane [ISS]			206
P34057 UniProt NPD GO	RECO_MOUSE	Recoverin (Cancer-associated retinopathy protein) (Protein CAR) (23 kDa photoreceptor cell-specific ...	0.08	-	mit	0					201
Q40375 UniProt NPD GO	PRP2_MEDTR	Repetitive proline-rich cell wall protein 2 precursor	0.08	-	exc	0					371
P00635 UniProt NPD GO	PPA5_YEAST	Repressible acid phosphatase precursor (EC 3.1.3.2) (P60)	0.08	-	vac	0	Secreted protein	cell wall (sensu Fungi) [IDA] periplasmic space (sensu Fungi) [NAS]			467
P55006 UniProt NPD GO	RDH7_RAT	Retinol dehydrogenase 7 (EC 1.1.1.105) (Retinol dehydrogenase type III) (RODH III)	0.08	-	mit	0	Microsome				317
Q03270 UniProt NPD GO	PO12_NASVI	Retrovirus-related Pol polyprotein from type-1 retrotransposable element R1 2 (Retrovirus-related Po ...	0.08	-	cyt	0					410
Q9PVW8 UniProt NPD GO	SAL_SILAS	Rhamnose-binding lectin precursor (SAL) (RBL) (Roe lectin)	0.08	-	exc	0	Secreted protein				308
Q03700 UniProt NPD GO	CARP4_RHINI	Rhizopuspepsin-4 precursor (EC 3.4.23.21) (Aspartate protease)	0.08	-	nuc	0					398
P58872 UniProt NPD GO	RHBD4_HUMAN	Rhomboid-related protein 4 (EC 3.4.21.105) (Ventrhoid transmembrane protein)	0.08	-	end	6	Membrane; multi-pass membrane protein (Probable)				404
P38145 UniProt NPD GO	RISA_YEAST	Riboflavin synthase alpha chain (EC 2.5.1.9)	0.08	-	cyt	0		soluble fraction [IDA]			238
Q8SPZ6 UniProt NPD GO	RNAS8_CERAE	Ribonuclease 8 precursor (EC 3.1.27.-) (RNase 8)	0.08	-	nuc	0	Secreted protein (Probable)				154
Q8SPZ8 UniProt NPD GO	RNAS8_PANTR	Ribonuclease 8 precursor (EC 3.1.27.-) (RNase 8)	0.08	-	exc	1 *	Secreted protein (Probable)				157
P81296 UniProt NPD GO	RNL2_LENED	Ribonuclease Le2 (EC 3.1.27.1) (RNase Le2)	0.08	-	nuc	0					239
O88796 UniProt NPD GO	RPP30_MOUSE	Ribonuclease P protein subunit p30 (EC 3.1.26.5) (RNaseP protein p30) (RNase P subunit 2)	0.08	-	cyt	0	Nucleus; nucleolus (Potential)				268
Q6CAV7 UniProt NPD GO	RNY1_YARLI	Ribonuclease T2-like precursor (EC 3.1.27.1) (RNase T2-like)	0.08	-	mit	0	Secreted protein (By similarity)				406
Q4R7Q7 UniProt NPD GO	RIR2_MACFA	Ribonucleoside-diphosphate reductase M2 subunit (EC 1.17.4.1) (Ribonucleotide reductase small subuni ...	0.08	-	cyt	0	Cytoplasm (By similarity)				389
P50649 UniProt NPD GO	RIR2_PLAFG	Ribonucleoside-diphosphate reductase small chain (EC 1.17.4.1) (Ribonucleotide reductase small subun ...	0.08	-	mit	0					322
Q680A5 UniProt NPD GO	KPRS4_ARATH	Ribose-phosphate pyrophosphokinase 4 (EC 2.7.6.1) (Phosphoribosyl pyrophosphate synthetase 4)	0.08	-	mit	0					337
P83324 UniProt NPD GO	RIP_FLAVE	Ribosome-inactivating protein velutin (EC 3.2.2.22) (rRNA N-glycosidase) (Fragment)	0.08	-	nuc	0					25
P24683 UniProt NPD GO	RBS_CYLSN	Ribulose bisphosphate carboxylase small chain (EC 4.1.1.39) (RuBisCO small subunit)	0.08	-	cyt	0	Plastid; chloroplast				139
P14961 UniProt NPD GO	RBS_OLILU	Ribulose bisphosphate carboxylase small chain (EC 4.1.1.39) (RuBisCO small subunit)	0.08	-	cyt	0	Plastid; chloroplast				139
P00873 UniProt NPD GO	RBS1_CHLRE	Ribulose bisphosphate carboxylase small chain 1, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.08	-	mit	0	Plastid; chloroplast			1UZH	185
Q39745 UniProt NPD GO	RBS3_FLAPR	Ribulose bisphosphate carboxylase small chain 3, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.08	-	cyt	0	Plastid; chloroplast				173
P12468 UniProt NPD GO	RBS4_SOYBN	Ribulose bisphosphate carboxylase small chain 4, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.08	-	cyt	0	Plastid; chloroplast				178
Q40565 UniProt NPD GO	RCA2_TOBAC	Ribulose bisphosphate carboxylase/oxygenase activase 2, chloroplast precursor (RuBisCO activase 2) ( ...	0.08	-	cyt	0	Plastid; chloroplast; chloroplast stroma				439
Q42450 UniProt NPD GO	RCAB_HORVU	Ribulose bisphosphate carboxylase/oxygenase activase B, chloroplast precursor (RuBisCO activase B) ( ...	0.08	-	mit	0	Plastid; chloroplast; chloroplast stroma				425
O49074 UniProt NPD GO	RCA_LYCPN	Ribulose bisphosphate carboxylase/oxygenase activase, chloroplast precursor (RuBisCO activase) (RA)	0.08	-	cyt	0	Plastid; chloroplast; chloroplast stroma				459
Q9DE26 UniProt NPD GO	RUVB1_XENLA	RuvB-like 1 (EC 3.6.1.-) (Pontin)	0.08	-	cyt	0	Nucleus (By similarity)				456
Q6FU78 UniProt NPD GO	RUVB1_CANGA	RuvB-like helicase 1 (EC 3.6.1.-)	0.08	-	cyt	0	Nucleus (By similarity)				457
Q6CQA9 UniProt NPD GO	RUVB1_KLULA	RuvB-like helicase 1 (EC 3.6.1.-)	0.08	-	cyt	0	Nucleus (By similarity)				457
P46255 UniProt NPD GO	DCAM_SPIOL	S-adenosylmethionine decarboxylase proenzyme (EC 4.1.1.50) (AdoMetDC) (SamDC) [Contains: S-adenosylm ...	0.08	-	cyt	0					363
Q9V784 UniProt NPD GO	SAM50_DROME	SAM50-like protein CG7639	0.08	-	cyt	0	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)				443
P55822 UniProt NPD GO	SH3BG_HUMAN	SH3 domain-binding glutamic acid-rich protein (SH3BGR protein) (21-glutamic acid-rich protein) (21-G ...	0.08	-	mit	0			602230		239
P38262 UniProt NPD GO	SIF2_YEAST	SIR4-interacting protein SIF2	0.08	-	cyt	0	Nucleus	histone deacetylase complex [IPI] nucleus [IPI]		1R5M	535
Q41495 UniProt NPD GO	ST14_SOLTU	STS14 protein precursor	0.08	-	mit	0					214

You are viewing entries 68951 to 69000 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.