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
Q42954 UniProt NPD GO	KPYC_TOBAC	Pyruvate kinase, cytosolic isozyme (EC 2.7.1.40) (PK)	0.05	-	cyt	0	Cytoplasm				508
Q921W4 UniProt NPD GO	QORL_MOUSE	Quinone oxidoreductase-like 1 (EC 1.-.-.-) (QOH-1) (Zeta-crystallin homolog)	0.05	-	cyt	0					348
Q01921 UniProt NPD GO	PHEA_POLBO	R-phycoerythrin alpha chain	0.05	-	cyt	0	Periphery of the rods of the phycobilisome				164
Q03206 UniProt NPD GO	RAC1_CAEEL	RAS-related protein ced-10 (Cell-corpse engulfment protein ced-10) (Cell death protein 10) (RAS-rela ...	0.05	-	cyt	0	Cell surface. Preferentially localized at the cell surface and especially condensed at cell boundari ...	integral to membrane [IDA] plasma membrane [IDA]			191
Q24815 UniProt NPD GO	RACB_ENTHI	RAS-related protein racB (Fragment)	0.05	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				163
Q24816 UniProt NPD GO	RACC_ENTHI	RAS-related protein racC	0.05	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				194
Q5RCZ7 UniProt NPD GO	RCBT2_PONPY	RCC1 and BTB domain-containing protein 2 (Regulator of chromosome condensation and BTB domain-contai ...	0.05	-	mit	0					551
Q6P798 UniProt NPD GO	RCBT2_RAT	RCC1 and BTB domain-containing protein 2 (Regulator of chromosome condensation and BTB domain-contai ...	0.05	-	cyt	0					551
O95199 UniProt NPD GO	RCBT2_HUMAN	RCC1 and BTB domain-containing protein 2 (Regulator of chromosome condensation and BTB domain-contai ...	0.05	-	mit	0			603524		551
Q9MA63 UniProt NPD GO	Y3550_ARATH	REF/SRPP-like protein At3g05500	0.05	-	nuc	0					246
O48671 UniProt NPD GO	RER1B_ARATH	RER1B protein (AtRER1B)	0.05	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				195
Q8WVZ7 UniProt NPD GO	RN133_HUMAN	RING finger protein 133	0.05	-	nuc	1	Membrane; single-pass membrane protein (Potential)				376
Q95K04 UniProt NPD GO	RN133_MACFA	RING finger protein 133	0.05	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				376
Q9SUS4 UniProt NPD GO	RHA1A_ARATH	RING-H2 zinc finger protein RHA1a	0.05	-	cyt	0					159
Q9UBF6 UniProt NPD GO	RBX2_HUMAN	RING-box protein 2 (Rbx2) (RING finger protein 7) (Regulator of cullins 2) (CKII beta-binding protei ...	0.05	-	mit	0	Cytoplasm. Nucleus	cytoplasm [NAS] nucleus [NAS]	603863		113
O00442 UniProt NPD GO	RTC1_HUMAN	RNA 3'-terminal phosphate cyclase (EC 6.5.1.4) (RNA-3'-phosphate cyclase) (RNA cyclase)	0.05	-	mit	0	Nucleus; nucleoplasm	nucleoplasm [TAS]			366
Q9D7H3 UniProt NPD GO	RTC1_MOUSE	RNA 3'-terminal phosphate cyclase (EC 6.5.1.4) (RNA-3'-phosphate cyclase) (RNA cyclase)	0.05	-	mit	0	Nucleus; nucleoplasm (By similarity)				366
P81928 UniProt NPD GO	140U_DROME	RPII140-upstream gene protein	0.05	-	mit	3	Membrane; multi-pass membrane protein (Potential)				261
P08950 UniProt NPD GO	RANA_RANPI	Ranatensin precursor	0.05	-	nuc	1 *	Secreted protein				82
Q9TU25 UniProt NPD GO	RAC2_BOVIN	Ras-related C3 botulinum toxin substrate 2 precursor (p21-Rac2)	0.05	-	cyt	0	Cytoplasm (By similarity). Membrane-associated when activated (By similarity)				192
P28185 UniProt NPD GO	ARA2_ARATH	Ras-related protein ARA-2	0.05	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				216
P40392 UniProt NPD GO	RIC1_ORYSA	Ras-related protein RIC1	0.05	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				202
Q3ZC27 UniProt NPD GO	RAB19_BOVIN	Ras-related protein Rab-19	0.05	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				217
P35295 UniProt NPD GO	RAB20_MOUSE	Ras-related protein Rab-20	0.05	-	cyt	0	Highly enriched on apical endocytic structures in polarized epithelial cells of kidney proximal tubu ...				233
Q9UL26 UniProt NPD GO	RB22A_HUMAN	Ras-related protein Rab-22A (Rab-22)	0.05	-	cyt	0	Endosome; endosomal membrane; lipid-anchor (By similarity). Cell membrane; lipid-anchor (By similari ...	early endosome [IDA] plasma membrane [IDA]			194
Q13637 UniProt NPD GO	RAB32_HUMAN	Ras-related protein Rab-32	0.05	-	cyt	0	Mitochondrion				224
Q14088 UniProt NPD GO	RB33A_HUMAN	Ras-related protein Rab-33A (Small GTP-binding protein S10)	0.05	-	mit	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)		300333		237
P35276 UniProt NPD GO	RAB3D_MOUSE	Ras-related protein Rab-3D	0.05	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	zymogen granule [IDA]			219
P36410 UniProt NPD GO	RAB14_DICDI	Ras-related protein Rab14 (Rab4-like GTPase)	0.05	-	cyt	0	Endosome. Vacuole. Endosomal pathway and the contractile vacuole membrane system				206
P34141 UniProt NPD GO	RABA_DICDI	Ras-related protein RabA (Fragment)	0.05	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				199
Q94694 UniProt NPD GO	RAP1_PHYPO	Ras-related protein Rap-1 (Pprap1)	0.05	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				188
P61233 UniProt NPD GO	TXR1_MACRV	Raventoxin-1 (Raventoxin I)	0.05	-	nuc	0	Secreted protein (By similarity)				43
P22332 UniProt NPD GO	OPSR_ASTFA	Red-sensitive opsin (Red cone photoreceptor pigment)	0.05	-	end	7	Membrane; multi-pass membrane protein				357
Q9W6A7 UniProt NPD GO	OPSR1_BRARE	Red-sensitive opsin-1 (Red cone photoreceptor pigment 1) (Opsin-1, long-wave-sensitive 1) (Opsin LWS ...	0.05	-	end	7	Membrane; multi-pass membrane protein	integral to membrane [NAS]			357
Q9M8R9 UniProt NPD GO	RRAA1_ARATH	Regulator of ribonuclease-like protein 1	0.05	-	cyt	0					166
Q8CHK2 UniProt NPD GO	REL3_MOUSE	Relaxin-3 precursor (Prorelaxin M3) (Insulin-like peptide INSL7) (Insulin-like peptide 7) [Contains: ...	0.05	-	exc	0	Secreted protein	extracellular region [TAS]			141
Q7TQP4 UniProt NPD GO	RL3R2_MOUSE	Relaxin-3 receptor 2 (Relaxin family peptide receptor 4) (G-protein coupled receptor 100)	0.05	-	end	7 *	Membrane; multi-pass membrane protein				414
P52115 UniProt NPD GO	RENI_SHEEP	Renin precursor (EC 3.4.23.15) (Angiotensinogenase)	0.05	-	exc	0	Secreted protein (By similarity). Membrane (By similarity). Associated to membranes via binding to A ...				400
Q43564 UniProt NPD GO	PRP1_MEDTR	Repetitive proline-rich cell wall protein 1 precursor	0.05	-	exc	0					206
P15642 UniProt NPD GO	PRP3_SOYBN	Repetitive proline-rich cell wall protein 3 precursor	0.05	-	nuc	1 *					90
Q40358 UniProt NPD GO	PRP_MEDSA	Repetitive proline-rich cell wall protein precursor (MSPRP)	0.05	-	exc	0					236
Q92373 UniProt NPD GO	RFA2_SCHPO	Replication factor-A protein 2 (Single-stranded DNA-binding protein P30 subunit)	0.05	-	cyt	0	Nucleus	DNA replication factor A complex [IDA]			279
Q7T3C7 UniProt NPD GO	RT4I1_BRARE	Reticulon-4-interacting protein 1 homolog, mitochondrial precursor	0.05	-	mit	0	Mitochondrion (By similarity)				387
P27463 UniProt NPD GO	AL1A1_CHICK	Retinal dehydrogenase 1 (EC 1.2.1.36) (RalDH1) (RALDH 1) (Aldehyde dehydrogenase family 1 member A1) ...	0.05	-	cyt	0	Cytoplasm				509
O88451 UniProt NPD GO	RDH7_MOUSE	Retinol dehydrogenase 7 (EC 1.1.1.105) (Cis-retinol/androgen dehydrogenase type 2) (CRAD-2) (cis-ret ...	0.05	-	cyt	0	Microsome (By similarity)				316
P52566 UniProt NPD GO	GDIS_HUMAN	Rho GDP-dissociation inhibitor 2 (Rho GDI 2) (Rho-GDI beta) (Ly-GDI)	0.05	-	cyt	0	Cytoplasm	cytoplasm [TAS] cytoplasmic membrane-bound vesicle [TAS] cytoskeleton [TAS]	602843	1DS6	200
Q9Y3P4 UniProt NPD GO	RHBD3_HUMAN	Rhomboid domain-containing protein 3	0.05	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				386
P34356 UniProt NPD GO	ROM2_CAEEL	Rhomboid-related protein 2 (EC 3.4.21.105)	0.05	-	end	8	Membrane; multi-pass membrane protein (Potential)				435
O75792 UniProt NPD GO	RNHL_HUMAN	Ribonuclease HI large subunit (EC 3.1.26.4) (RNase HI large subunit) (Ribonuclease H2) (RNase H2) (R ...	0.05	-	cyt	0			606034		299
Q3SZ21 UniProt NPD GO	RPP30_BOVIN	Ribonuclease P protein subunit p30 (EC 3.1.26.5) (RNaseP protein p30) (RNase P subunit 2)	0.05	-	cyt	0	Nucleus; nucleolus (By similarity)				268

You are viewing entries 75551 to 75600 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.