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
P11710 UniProt NPD GO	FUS1_YEAST	Nuclear fusion protein FUS1	0.96	+	nuc	1		mating projection tip [IDA] plasma membrane [IDA]			512
Q14686 UniProt NPD GO	NCOA6_HUMAN	Nuclear receptor coactivator 6 (Amplified in breast cancer protein 3) (Cancer-amplified transcriptio ...	0.96	-	nuc	0	Nucleus	nucleus [IDA] transcription factor complex [TAS]	605299		2063
P48552 UniProt NPD GO	NRIP1_HUMAN	Nuclear receptor-interacting protein 1 (Nuclear factor RIP140) (Receptor-interacting protein 140)	0.96	+	nuc	0	Nucleus. Localized to discrete foci and redistributes to larger nuclear domains upon binding to liga ...	nucleus [IDA]	602490		1158
Q8CBD1 UniProt NPD GO	NRIP1_MOUSE	Nuclear receptor-interacting protein 1 (Nuclear factor RIP140) (Receptor-interacting protein 140)	0.96	+	nuc	0	Nucleus	histone deacetylase complex [IPI] nucleus [IDA]			1161
P11378 UniProt NPD GO	STP2_MOUSE	Nuclear transition protein 2 (TP-2) (TP2)	0.96	+	nuc	0	Nucleus	male germ cell nucleus [TAS]			117
P11101 UniProt NPD GO	STP2_RAT	Nuclear transition protein 2 (TP-2) (TP2)	0.96	+	nuc	0	Nucleus. Nucleus; nucleolus. Nuclear import is ATP-dependent and nucleolar localization requires the ...				114
Q9Y3T9 UniProt NPD GO	NOC2L_HUMAN	Nucleolar complex protein 2 homolog (Protein NOC2 homolog) (NOC2-like)	0.96	-	nuc	0	Nucleus; nucleolus				749
Q5R952 UniProt NPD GO	NOC3L_PONPY	Nucleolar complex protein 3 homolog (NOC3 protein homolog) (NOC3-like protein) (Nucleolar complex-as ...	0.96	+	nuc	0	Nucleus; nucleolus (By similarity). Localizes to nuclear speckles (By similarity)				800
Q5XGZ8 UniProt NPD GO	NOC3L_XENLA	Nucleolar complex protein 3 homolog (NOC3 protein homolog) (NOC3-like protein) (Nucleolar complex-as ...	0.96	+	nuc	0	Nucleus; nucleolus (By similarity)				795
Q58DC8 UniProt NPD GO	ORC1_BOVIN	Origin recognition complex subunit 1	0.96	-	nuc	0	Nucleus (By similarity)				871
O74270 UniProt NPD GO	ORC1_CANAL	Origin recognition complex subunit 1	0.96	-	nuc	0	Nucleus (By similarity)				805
Q6BSE2 UniProt NPD GO	ORC1_DEBHA	Origin recognition complex subunit 1	0.96	+	nuc	0	Nucleus (By similarity)				810
Q24168 UniProt NPD GO	ORC2_DROME	Origin recognition complex subunit 2 (DmORC2)	0.96	+	nuc	0	Nucleus. Centromeres of metaphase and anaphase chromosomes of early syncytial embryos. Later in deve ...	nuclear origin of replication recognition c... [IDA]			618
P55055 UniProt NPD GO	NR1H2_HUMAN	Oxysterols receptor LXR-beta (Liver X receptor beta) (Nuclear orphan receptor LXR-beta) (Ubiquitousl ...	0.96	+	nuc	0	Nucleus (Potential)	nucleus [TAS]	600380	1UPW	461
Q60644 UniProt NPD GO	NR1H2_MOUSE	Oxysterols receptor LXR-beta (Liver X receptor beta) (Nuclear orphan receptor LXR-beta) (Ubiquitousl ...	0.96	+	nuc	0	Nucleus (Potential)	nucleus [IDA]			446
O75475 UniProt NPD GO	PSIP1_HUMAN	PC4 and SFRS1-interacting protein (Lens epithelium-derived growth factor) (Transcriptional coactivat ...	0.96	+	nuc	0	Nucleus. Remains chromatin-associated throughout the cell cycle		603620	2B4J	530
Q9UPQ7 UniProt NPD GO	PZRN3_HUMAN	PDZ domain-containing RING finger protein 3 (Ligand of Numb-protein X 3) (Semaphorin cytoplasmic dom ...	0.96	+	nuc	0			609729	1WH1	1066
Q69ZS0 UniProt NPD GO	PZRN3_MOUSE	PDZ domain-containing RING finger protein 3 (Semaphorin cytoplasmic domain-associated protein 3) (SE ...	0.96	+	nuc	0					1063
Q96QT6 UniProt NPD GO	PHF12_HUMAN	PHD finger protein 12 (PHD factor 1) (Pf1)	0.96	-	nuc	0	Nucleus	nucleus [IDA] transcriptional repressor complex [IDA]			1004
Q9UPP1 UniProt NPD GO	PHF8_HUMAN	PHD finger protein 8	0.96	-	nuc	0			300560		1060
P31362 UniProt NPD GO	PO2F3_MOUSE	POU domain, class 2, transcription factor 3 (Octamer-binding transcription factor 11) (Oct-11) (Epoc ...	0.96	+	nuc	0	Nucleus				431
Q9UKI9 UniProt NPD GO	PO2F3_HUMAN	POU domain, class 2, transcription factor 3 (Octamer-binding transcription factor 11) (Oct-11) (Tran ...	0.96	+	nuc	0	Nucleus		607394		436
P78424 UniProt NPD GO	PO6F2_HUMAN	POU domain, class 6, transcription factor 2 (Retina-derived POU-domain factor 1) (RPF-1)	0.96	+	nuc	0	Nucleus (Probable)	nucleus [IC]	609062		684
Q8BX57 UniProt NPD GO	PXK_MOUSE	PX domain-containing protein kinase-like protein (Modulator of Na,K-ATPase) (MONaKA)	0.96	+	nuc	0	Cytoplasm. Cell membrane; peripheral membrane protein. Also associates with the plasma membrane	cytoplasm [IDA]			582
Q4FZZ1 UniProt NPD GO	PXK_RAT	PX domain-containing protein kinase-like protein (Modulator of Na,K-ATPase) (MONaKA)	0.96	+	nuc	0	Cytoplasm (By similarity). Cell membrane; peripheral membrane protein (By similarity). Also associat ...				580
P48786 UniProt NPD GO	PRH_PETCR	Pathogenesis-related homeodomain protein (PRHP)	0.96	+	nuc	0	Nucleus				1088
Q6GLU8 UniProt NPD GO	PHAR1_XENLA	Phosphatase and actin regulator 1	0.96	+	nuc	0	Cytoplasm (By similarity). Enriched at synapses (By similarity)				586
O75167 UniProt NPD GO	PHAR2_HUMAN	Phosphatase and actin regulator 2	0.96	+	nuc	0			608724		634
P54673 UniProt NPD GO	PI3K1_DICDI	Phosphatidylinositol 3-kinase 1 (EC 2.7.1.137) (PI3-kinase) (PtdIns-3-kinase) (PI3K)	0.96	-	nuc	0					1570
Q5R5X0 UniProt NPD GO	PININ_PONPY	Pinin	0.96	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle. Cell membrane; cell-cell junction (By similarity). Cell-cell ...				719
Q9HAU0 UniProt NPD GO	PKHA5_HUMAN	Pleckstrin homology domain-containing family A member 5 (Phosphoinositol 3-phosphate-binding protein ...	0.96	-	nuc	0			607770		1116
Q86UU1 UniProt NPD GO	PHLB1_HUMAN	Pleckstrin homology-like domain family B member 1 (Protein LL5-alpha)	0.96	+	nuc	0					1377
Q6PDH0 UniProt NPD GO	PHLB1_MOUSE	Pleckstrin homology-like domain family B member 1 (Protein LL5-alpha)	0.96	+	nuc	0					1371
Q15022 UniProt NPD GO	SUZ12_HUMAN	Polycomb protein SUZ12 (Suppressor of zeste 12 protein homolog) (Joined to JAZF1 protein) (Chromatin ...	0.96	+	nuc	0	Nucleus (Probable)		606245		739
Q10665 UniProt NPD GO	MES3_CAEEL	Polycomb protein mes-3 (Maternal-effect sterile protein 3)	0.96	-	nuc	0	Nucleus				754
Q64028 UniProt NPD GO	PHC1_MOUSE	Polyhomeotic-like protein 1 (mPH1) (Early development regulatory protein 1) (RAE-28)	0.96	-	nuc	0	Nucleus	nuclear body [IDA] nucleus [IDA]			1012
P33288 UniProt NPD GO	RAD18_NEUCR	Postreplication repair ubiquitin-protein ligase E3 rad-18 (EC 6.-.-.-) (UV radiation sensitivity pro ...	0.96	-	nuc	0	Nucleus (Probable)				501
Q5ADL0 UniProt NPD GO	PRP5_CANAL	Pre-mRNA-processing ATP-dependent RNA helicase PRP5 (EC 3.6.1.-)	0.96	+	nuc	0	Nucleus (By similarity)				884
P21372 UniProt NPD GO	PRP5_YEAST	Pre-mRNA-processing ATP-dependent RNA helicase PRP5 (EC 3.6.1.-)	0.96	+	nuc	0	Nucleus	spliceosome complex [TAS]			849
P24384 UniProt NPD GO	PRP22_YEAST	Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22 (EC 3.6.1.-)	0.96	-	nuc	0	Nucleus	spliceosome complex [TAS]			1145
Q6C0M9 UniProt NPD GO	CWC21_YARLI	Pre-mRNA-splicing factor CWC21	0.96	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				284
Q5KFX4 UniProt NPD GO	CWC22_CRYNE	Pre-mRNA-splicing factor CWC22	0.96	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				831
Q6CLJ7 UniProt NPD GO	PRP45_KLULA	Pre-mRNA-splicing factor PRP45 (Pre-mRNA-processing protein 45)	0.96	-	nuc	0	Nucleus (By similarity)				430
P39964 UniProt NPD GO	CEF1_SCHPO	Pre-mRNA-splicing factor cef1 (Cell division control protein 5)	0.96	+	nuc	0	Nucleus	spliceosome complex [IDA]			757
Q7SI59 UniProt NPD GO	CWC25_NEUCR	Pre-mRNA-splicing factor cwc-25	0.96	+	nuc	0	Nucleus (By similarity)				444
Q7RZK5 UniProt NPD GO	SYF2_NEUCR	Pre-mRNA-splicing factor syf-2	0.96	-	nuc	0	Nucleus (By similarity)				339
Q80Y24 UniProt NPD GO	PRIC2_MOUSE	Prickle-like protein 2	0.96	-	nuc	0	Nucleus; nuclear membrane (Potential)				845
P43322 UniProt NPD GO	NRG1_RAT	Pro-neuregulin-1, membrane-bound isoform precursor (Pro-NRG1) [Contains: Neuregulin-1 (Neu different ...	0.96	+	nuc	1	Pro-neuregulin-1, membrane-bound isoform: Cell membrane; single-pass type I membrane protein. Neureg ...				662
Q5RC67 UniProt NPD GO	DDX23_PONPY	Probable ATP-dependent RNA helicase DDX23 (EC 3.6.1.-) (DEAD box protein 23)	0.96	+	nuc	0	Nucleus (By similarity)				820
Q9BUQ8 UniProt NPD GO	DDX23_HUMAN	Probable ATP-dependent RNA helicase DDX23 (EC 3.6.1.-) (DEAD box protein 23) (100 kDa U5 snRNP-speci ...	0.96	+	nuc	0	Nucleus	snRNP U5 [IDA]			820

You are viewing entries 1501 to 1550 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.