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
Q5SXJ3 UniProt NPD GO	FANCJ_MOUSE	Fanconi anemia group J protein homolog (EC 3.6.1.-) (ATP-dependent RNA helicase BRIP1) (Protein FACJ ...	0.96	-	nuc	0	Nucleus (By similarity)				1174
P42775 UniProt NPD GO	GBF2_ARATH	G-box-binding factor 2 (AtbZIP54)	0.96	+	nuc	0	Nucleus				360
P11837 UniProt NPD GO	NIMA_EMENI	G2-specific protein kinase nimA (EC 2.7.11.1) (Never in mitosis)	0.96	+	nuc	0	Nucleus (Probable)				699
P41002 UniProt NPD GO	CCNF_HUMAN	G2/mitotic-specific cyclin-F	0.96	+	nuc	0	Nucleus		600227		786
Q6PGG2 UniProt NPD GO	GMIP_MOUSE	GEM-interacting protein (GMIP)	0.96	-	nuc	0					971
Q9HF75 UniProt NPD GO	BEM2_ASHGO	GTPase-activating protein BEM2	0.96	-	nuc	0					2071
P06102 UniProt NPD GO	NOT3_YEAST	General negative regulator of transcription subunit 3	0.96	-	nuc	0	Cytoplasm (Probable). Nucleus	CCR4-NOT core complex [IPI] cytoplasm [IDA]			836
P34909 UniProt NPD GO	NOT4_YEAST	General negative regulator of transcription subunit 4	0.96	-	nuc	0	Cytoplasm (Probable). Nucleus	CCR4-NOT core complex [IPI] cytoplasm [IDA]			587
Q9NRY4 UniProt NPD GO	GRLF1_HUMAN	Glucocorticoid receptor DNA-binding factor 1 (Glucocorticoid receptor repression factor 1) (GRF-1) ( ...	0.96	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	nucleus [IC]	605277		1513
P83509 UniProt NPD GO	GRLF1_CANFA	Glucocorticoid receptor DNA-binding factor 1 (Rho GAP p190A) (p190-A)	0.96	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	nucleus [ISS]			1500
Q8WY36 UniProt NPD GO	BBX_HUMAN	HMG box transcription factor BBX (Bobby sox homolog) (HMG box-containing protein 2)	0.96	+	nuc	0	Nucleus (Probable)				941
Q8VBW5 UniProt NPD GO	BBX_MOUSE	HMG box transcription factor BBX (Bobby sox homolog) (HMG box-containing protein 2)	0.96	+	nuc	0	Nucleus (Probable)			1WZ6	907
Q6FK48 UniProt NPD GO	SWR1_CANGA	Helicase SWR1 (EC 3.6.1.-)	0.96	+	nuc	0	Nucleus (By similarity)				1450
Q7S133 UniProt NPD GO	SWR1_NEUCR	Helicase swr-1 (EC 3.6.1.-)	0.96	+	nuc	0	Nucleus (By similarity)				1845
Q8BZ21 UniProt NPD GO	MYST3_MOUSE	Histone acetyltransferase MYST3 (EC 2.3.1.48) (EC 2.3.1.-) (MYST protein 3) (MOZ, YBF2/SAS3, SAS2 an ...	0.96	+	nuc	0	Nucleus (By similarity)	nucleus [ISS]			2003
Q9Y7R4 UniProt NPD GO	SET1_SCHPO	Histone-lysine N-methyltransferase, H3 lysine-4 specific (EC 2.1.1.43) (Set1 complex component set1) ...	0.96	+	nuc	0	Nucleus (Probable)	COMPASS complex [IDA]			920
P28468 UniProt NPD GO	HOX1_HALRO	Homeobox protein AHox1	0.96	+	nuc	0	Nucleus (Probable)				741
P20268 UniProt NPD GO	HM06_CAEEL	Homeobox protein ceh-6	0.96	+	nuc	0	Nucleus (Probable)	cytoplasm [IDA] nucleus [IDA]			380
P56672 UniProt NPD GO	OTP_DROME	Homeobox protein orthopedia	0.96	+	nuc	0	Nucleus (By similarity)				264
P38800 UniProt NPD GO	YHO0_YEAST	Hypothetical 149.7 kDa protein in IRE1-KSP1 intergenic region	0.96	+	nuc	0		mitochondrion [IDA]			1345
P36080 UniProt NPD GO	YKI2_YEAST	Hypothetical 50.5 kDa protein in MDH1-VMA5 intergenic region	0.96	+	nuc	0		nucleolus [IDA]			434
P38299 UniProt NPD GO	YB34_YEAST	Hypothetical 60.6 kDa protein in SMP1-MBA1 intergenic region	0.96	-	nuc	0					523
Q03281 UniProt NPD GO	YD458_YEAST	Hypothetical 76.4 kDa protein in GUK1-MFA1 intergenic region	0.96	+	nuc	1					663
Q09842 UniProt NPD GO	YAE1_SCHPO	Hypothetical PWWP domain protein C23D3.01	0.96	-	nuc	0					407
Q09602 UniProt NPD GO	YRM6_CAEEL	Hypothetical homeobox protein R06F6.6 in chromosome II	0.96	+	nuc	0	Nucleus (Probable)				416
Q09221 UniProt NPD GO	YP74_CAEEL	Hypothetical protein B0228.4	0.96	+	nuc	0					1633
Q11069 UniProt NPD GO	YT41_CAEEL	Hypothetical protein B0416.1 in chromosome X	0.96	+	end	8	Membrane; multi-pass membrane protein (Potential)				1203
O13855 UniProt NPD GO	YEX1_SCHPO	Hypothetical protein C1A6.01c in chromosome I	0.96	-	nuc	0					455
Q09779 UniProt NPD GO	YATE_SCHPO	Hypothetical protein C1D4.14 in chromosome I	0.96	-	nuc	0					1628
Q09908 UniProt NPD GO	YAJ8_SCHPO	Hypothetical protein C30D11.08c in chromosome I	0.96	-	nuc	0					538
Q92349 UniProt NPD GO	YDH4_SCHPO	Hypothetical protein C6G9.04 in chromosome I	0.96	-	nuc	0					1318
P41954 UniProt NPD GO	YLK6_CAEEL	Hypothetical protein D1044.6	0.96	+	nuc	0					1009
Q9XTA5 UniProt NPD GO	HIF1A_BOVIN	Hypoxia-inducible factor 1 alpha (HIF-1 alpha) (HIF1 alpha)	0.96	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Cytoplasmic in normoxia, nuclear translocation i ...				823
Q61221 UniProt NPD GO	HIF1A_MOUSE	Hypoxia-inducible factor 1 alpha (HIF-1 alpha) (HIF1 alpha) (ARNT-interacting protein)	0.96	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Cytoplasmic in normoxia, nuclear translocation i ...	flagellum (sensu Eukaryota) [IDA] nucleus [ISS]			836
P38144 UniProt NPD GO	ISW1_YEAST	ISWI chromatin remodeling complex ATPase ISW1 (EC 3.6.1.-)	0.96	-	nuc	0	Nucleus	ISW1 complex [IPI]			1129
Q08773 UniProt NPD GO	ISW2_YEAST	ISWI chromatin remodeling complex ATPase ISW2 (EC 3.6.1.-) (Imitation switch protein 2)	0.96	-	nuc	0	Nucleus	chromatin accessibility complex [IPI] nucleus [IPI]			1120
Q96ST2 UniProt NPD GO	IWS1_HUMAN	IWS1 homolog (IWS1-like protein)	0.96	-	nuc	0	Nucleus (By similarity)				819
O61643 UniProt NPD GO	INHB_DROME	Inhibin beta chain precursor (Activin beta chain)	0.96	+	end	0	Secreted protein (Potential)	extracellular region [NAS]			946
Q8WYA0 UniProt NPD GO	IFT81_HUMAN	Intraflagellar transport 81 (Carnitine deficiency-associated protein expressed in ventricle 1) (CDV- ...	0.96	-	nuc	0			605489		676
Q10134 UniProt NPD GO	FEP1_SCHPO	Iron-sensing transcription factor 1 (Transcription factor gaf2) (Gaf-2)	0.96	-	nuc	0	Nucleus (Probable)	nucleus [IDA]			564
Q8N157 UniProt NPD GO	AHI1_HUMAN	Jouberin (Abelson helper integration site 1 protein homolog) (AHI-1)	0.96	+	nuc	0			608894		1196
Q96L93 UniProt NPD GO	SNX23_HUMAN	Kinesin-like motor protein C20orf23 (Sorting nexin-23)	0.96	-	nuc	0					1317
Q15058 UniProt NPD GO	KIF14_HUMAN	Kinesin-like protein KIF14	0.96	-	nuc	0					1648
Q99PW8 UniProt NPD GO	KIF17_MOUSE	Kinesin-like protein KIF17 (MmKIF17)	0.96	+	nuc	0		kinesin complex [IDA]			1038
O35071 UniProt NPD GO	KIF1C_MOUSE	Kinesin-like protein KIF1C	0.96	-	nuc	0		Golgi apparatus [IDA]			1100
O35787 UniProt NPD GO	KIF1C_RAT	Kinesin-like protein KIF1C (Kinesin-like protein KIF1D)	0.96	-	nuc	0		kinesin complex [TAS]			1097
P40568 UniProt NPD GO	DSN1_YEAST	Kinetochore-associated protein DSN1	0.96	-	nuc	0	Nucleus. Associated with the kinetochore	kinetochore [IDA] MIND complex [IDA] spindle pole [IDA]			576
P08657 UniProt NPD GO	LAC9_KLULA	Lactose regulatory protein LAC9	0.96	-	nuc	0	Nucleus			1CLD	865
P48634 UniProt NPD GO	BAT2_HUMAN	Large proline-rich protein BAT2 (HLA-B-associated transcript 2)	0.96	+	nuc	0	Cytoplasm. Nucleus		142580		2157
Q5TM26 UniProt NPD GO	BAT2_MACMU	Large proline-rich protein BAT2 (HLA-B-associated transcript 2)	0.96	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				2160

You are viewing entries 1401 to 1450 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.