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
Q99207 UniProt NPD GO	NOP14_YEAST	Nucleolar complex protein 14 (U3 small nucleolar RNA-associated protein 2) (U3 snoRNA-associated pro ...	0.97	+	nuc	0	Nucleus; nucleolus	mitochondrion [IDA] Noc4p-Nop14p complex [IPI] nucleolus [IDA] small nucleolar ribonucleoprotein complex [IPI]			810
P47035 UniProt NPD GO	NET1_YEAST	Nucleolar protein NET1	0.97	-	nuc	0	Nucleus; nucleolus	nucleolus [TAS] RENT complex [IDA]			1189
Q9JI69 UniProt NPD GO	ORC1_CRIGR	Origin recognition complex subunit 1	0.97	+	nuc	0	Nucleus				850
Q13415 UniProt NPD GO	ORC1_HUMAN	Origin recognition complex subunit 1 (Replication control protein 1)	0.97	-	nuc	0	Nucleus	nucleus [TAS]	601902		861
Q9UBD5 UniProt NPD GO	ORC3_HUMAN	Origin recognition complex subunit 3 (Origin recognition complex subunit Latheo)	0.97	-	nuc	0	Nucleus		604972		711
Q9Y794 UniProt NPD GO	ORC4_SCHPO	Origin recognition complex subunit 4	0.97	+	nuc	0	Nucleus	nuclear origin of replication recognition c... [IDA]			972
P38826 UniProt NPD GO	ORC6_YEAST	Origin recognition complex subunit 6 (Origin recognition complex 50 kDa subunit) (ACS-associated pro ...	0.97	-	nuc	0	Nucleus	nuclear origin of replication recognition c... [TAS] pre-replicative complex [TAS]			435
Q8MJ03 UniProt NPD GO	RP1_SAIBB	Oxygen-regulated protein 1 (Retinitis pigmentosa RP1 protein homolog)	0.97	-	nuc	0					2149
P56715 UniProt NPD GO	RP1_HUMAN	Oxygen-regulated protein 1 (Retinitis pigmentosa RP1 protein) (Retinitis pigmentosa 1 protein)	0.97	-	nuc	0			603937		2156
P38713 UniProt NPD GO	OSH3_YEAST	Oxysterol-binding protein homolog 3	0.97	+	nuc	0	Cytoplasm. Enriched at the cell periphery in a SCS2-dependent manner	cytoplasm [IDA]			996
Q9BZF2 UniProt NPD GO	OSBL7_HUMAN	Oxysterol-binding protein-related protein 7 (OSBP-related protein 7) (ORP-7)	0.97	-	nuc	0			606735		842
Q5BIS6 UniProt NPD GO	NR1H2_BOVIN	Oxysterols receptor LXR-beta	0.97	+	nuc	0	Nucleus (Potential)				455
Q66T72 UniProt NPD GO	PSIP1_FELCA	PC4 and SFRS1-interacting protein (Lens epithelium-derived growth factor) (Transcription coactivator ...	0.97	+	nuc	0	Nucleus (By similarity)				530
Q76G19 UniProt NPD GO	PDZK4_HUMAN	PDZ domain-containing protein 4 (PDZ domain-containing RING finger protein 4-like protein)	0.97	+	nuc	0	Cytoplasm; cell cortex. Mainly localized under the plasma membrane				769
Q7Z7A4 UniProt NPD GO	PXK_HUMAN	PX domain-containing protein kinase-like protein (Modulator of Na,K-ATPase) (MONaKA)	0.97	-	nuc	0	Cytoplasm. Cell membrane; peripheral membrane protein. Also associates with the plasma membrane. Iso ...	cytoplasm [IDA]			578
O13919 UniProt NPD GO	PST2_SCHPO	Paired amphipathic helix protein pst2 (SIN3 homolog 2)	0.97	-	nuc	0	Nucleus	histone deacetylase complex [IDA] nucleus [IDA]			1075
Q9Z340 UniProt NPD GO	PARD3_RAT	Partitioning-defective 3 homolog (PARD-3) (PAR-3) (Atypical PKC isotype-specific-interacting protein ...	0.97	-	nuc	0	Intracytoplasmic membrane. Cell membrane; cell-cell junction. Cell membrane; cell-cell junction; tig ...	tight junction [ISS]			1337
Q99NH2 UniProt NPD GO	PARD3_MOUSE	Partitioning-defective 3 homolog (PARD-3) (PAR-3) (Atypical PKC isotype-specific-interacting protein ...	0.97	-	nuc	0	Intracytoplasmic membrane. Cell membrane; cell-cell junction. Cell membrane; cell-cell junction; tig ...	cell cortex [IDA] cell-cell adherens junction [IDA] cytoplasm [IDA] spindle [IDA] tight junction [IDA]			1333
O95613 UniProt NPD GO	PCNT_HUMAN	Pericentrin (Pericentrin B) (Kendrin)	0.97	-	nuc	0	Centrosome. Centrosomal at all stages of the cell cycle. Remains associated with centrosomes followi ...		605925		3336
O95153 UniProt NPD GO	RIMB1_HUMAN	Peripheral-type benzodiazepine receptor-associated protein 1 (PRAX-1) (Peripheral benzodiazepine rec ...	0.97	+	nuc	0	Cytoplasm. Mitochondrion. Preferentially expressed in the mitochondria in the presence of BZRP	cytoplasm [IDA] mitochondrion [IDA]			1857
Q7TNF8 UniProt NPD GO	RIMB1_MOUSE	Peripheral-type benzodiazepine receptor-associated protein 1 (PRAX-1) (Peripheral benzodiazepine rec ...	0.97	+	nuc	0	Cytoplasm (By similarity). Mitochondrion (By similarity). Preferentially expressed in the mitochondr ...				1846
Q6VY07 UniProt NPD GO	PACS1_HUMAN	Phosphofurin acidic cluster sorting protein 1 (PACS-1)	0.97	+	nuc	0	Golgi apparatus; trans-Golgi network (By similarity). Localizes in the paranuclear region, probably ...		607492		963
Q8K212 UniProt NPD GO	PACS1_MOUSE	Phosphofurin acidic cluster sorting protein 1 (PACS-1)	0.97	+	nuc	0	Golgi apparatus; trans-Golgi network (By similarity). Localizes in the paranuclear region, probably ...	COPI-coated vesicle [IDA]			961
O88588 UniProt NPD GO	PACS1_RAT	Phosphofurin acidic cluster sorting protein 1 (PACS-1)	0.97	+	nuc	0	Golgi apparatus; trans-Golgi network. Localizes in the paranuclear region, probably the TGN				961
P79149 UniProt NPD GO	PININ_CANFA	Pinin	0.97	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle. Cell membrane; cell-cell junction (By similarity). Cell-cell ...				772
O35691 UniProt NPD GO	PININ_MOUSE	Pinin	0.97	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Cell membrane; cell-cell junction (By similar ...				724
Q7ZU92 UniProt NPD GO	PARN_BRARE	Poly(A)-specific ribonuclease PARN (EC 3.1.13.4) (Polyadenylate-specific ribonuclease)	0.97	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				660
P15938 UniProt NPD GO	PRP16_YEAST	Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 (EC 3.6.1.-)	0.97	-	nuc	0	Nucleus. Binds to the spliceosome	spliceosome complex [TAS]			1071
Q92620 UniProt NPD GO	PRP16_HUMAN	Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 (EC 3.6.1.-) (ATP-dependent RNA helicase D ...	0.97	-	nuc	0	Nucleus (By similarity)	nucleus [NAS]	605584		1227
Q6C8C5 UniProt NPD GO	CWC22_YARLI	Pre-mRNA-splicing factor CWC22	0.97	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				954
Q759B6 UniProt NPD GO	PRP45_ASHGO	Pre-mRNA-splicing factor PRP45 (Pre-mRNA-processing protein 45)	0.97	+	nuc	0	Nucleus (By similarity)				443
Q9P7C6 UniProt NPD GO	CWC23_SCHPO	Pre-mRNA-splicing factor cwc23 (Complexed with cdc5 protein 23) (Cell cycle control protein cwf23)	0.97	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				289
Q9Y805 UniProt NPD GO	CWC25_SCHPO	Pre-mRNA-splicing factor cwc25 (Complexed with cdc5 protein 25) (Cell cycle control protein cwf25)	0.97	-	nuc	0	Nucleus (By similarity)				376
Q5T848 UniProt NPD GO	GP158_HUMAN	Probable G-protein coupled receptor 158 precursor	0.97	-	end	6	Membrane; multi-pass membrane protein				1215
Q69ZK6 UniProt NPD GO	JHD2C_MOUSE	Probable JmjC domain-containing histone demethylation protein 2C (EC 1.14.11.-) (Jumonji domain-cont ...	0.97	-	nuc	0	Nucleus (By similarity)				2350
Q15652 UniProt NPD GO	JHD2C_HUMAN	Probable JmjC domain-containing histone demethylation protein 2C (EC 1.14.11.-) (Jumonji domain-cont ...	0.97	-	nuc	0	Nucleus (By similarity)	intracellular [NAS]	604503		2540
Q5A216 UniProt NPD GO	NDC80_CANAL	Probable kinetochore protein NDC80	0.97	-	nuc	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				788
P78316 UniProt NPD GO	NOP14_HUMAN	Probable nucleolar complex protein 14	0.97	+	end	0	Nucleus; nucleolus (By similarity)				857
Q8R3N1 UniProt NPD GO	NOP14_MOUSE	Probable nucleolar complex protein 14	0.97	+	end	0	Nucleus; nucleolus (By similarity)				860
P34244 UniProt NPD GO	KKK1_YEAST	Probable serine/threonine-protein kinase YKL101W (EC 2.7.11.1)	0.97	-	nuc	0		bud neck [IDA] septin ring [IDA]			1518
Q12236 UniProt NPD GO	KOK0_YEAST	Probable serine/threonine-protein kinase YOL100W (EC 2.7.11.1)	0.97	-	nuc	0		nucleus [IDA]			1081
P36023 UniProt NPD GO	YK44_YEAST	Probable transcriptional regulatory protein YKR064W	0.97	+	end	0	Nucleus (Probable)	cytoplasm [IDA] mitochondrion [IDA] nucleus [IDA]			863
P33304 UniProt NPD GO	AFR1_YEAST	Protein AFR1	0.97	+	nuc	0		mating projection base [IDA]			620
Q6FU75 UniProt NPD GO	LIC4_CANGA	Protein ATC1/LIC4	0.97	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				348
Q4P5V5 UniProt NPD GO	BFR2_USTMA	Protein BFR2	0.97	-	exc	0	Nucleus; nucleolus (By similarity)				581
P47134 UniProt NPD GO	BIR1_YEAST	Protein BIR1	0.97	-	nuc	0		condensed nuclear chromosome kinetochore [IGI] mitochondrion [IDA] spindle midzone [IDA]			954
Q6P0N0 UniProt NPD GO	CV106_HUMAN	Protein C14orf106 (P243)	0.97	-	nuc	0	Nucleus (Probable)			1WGX	1132
P78312 UniProt NPD GO	CD008_HUMAN	Protein C4orf8 (Protein IT14)	0.97	-	nuc	0					1265
Q8NG31 UniProt NPD GO	CASC5_HUMAN	Protein CASC5 (Cancer susceptibility candidate gene 5 protein) (ALL1-fused gene from chromosome 15q1 ...	0.97	-	nuc	0	Nucleus	acrosome [IDA] nucleus [IDA]	609173		2342
P42695 UniProt NPD GO	K0056_HUMAN	Protein KIAA0056	0.97	+	nuc	0					1498

You are viewing entries 1101 to 1150 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.