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
Q535K8 UniProt NPD GO	GON4L_RAT	GON-4-like protein (Protein GON4) (GON-4 homolog)	0.97	+	nuc	0	Nucleus (Potential)				2256
Q6BU76 UniProt NPD GO	GYP7_DEBHA	GTPase-activating protein GYP7 (GAP for YPT7)	0.97	-	nuc	0					757
Q12789 UniProt NPD GO	TF3C1_HUMAN	General transcription factor 3C polypeptide 1 (Transcription factor IIIC-subunit alpha) (TF3C-alpha) ...	0.97	+	nuc	0	Nucleus		603246		2109
Q91YM2 UniProt NPD GO	GRLF1_MOUSE	Glucocorticoid receptor DNA-binding factor 1 (Fragment)	0.97	-	nuc	0	Nucleus (Potential)	actin cytoskeleton [IDA] cytoplasm [IDA]			1337
P81128 UniProt NPD GO	GRLF1_RAT	Glucocorticoid receptor DNA-binding factor 1 (GAP-associated protein p190)	0.97	-	nuc	0	Cytoplasm. When bound to GAP. Nucleus. Also partially found to be associated with nuclei				1513
P14771 UniProt NPD GO	SDC25_YEAST	Guanine nucleotide exchange factor SDC25	0.97	+	nuc	0		membrane [IDA]			1252
Q00416 UniProt NPD GO	SEN1_YEAST	Helicase SEN1 (EC 3.6.1.-) (tRNA-splicing endonuclease positive effector)	0.97	+	nuc	0	Nucleus	nucleus [IDA]			2231
P28569 UniProt NPD GO	TRK1_SACBA	High-affinity potassium transport protein	0.97	+	nuc	9 *	Membrane; multi-pass membrane protein				1241
Q4IEV4 UniProt NPD GO	ESA1_GIBZE	Histone acetyltransferase ESA1 (EC 2.3.1.48)	0.97	-	nuc	0	Nucleus (By similarity)				502
O95251 UniProt NPD GO	MYST2_HUMAN	Histone acetyltransferase MYST2 (EC 2.3.1.48) (MYST protein 2) (MOZ, YBF2/SAS3, SAS2 and TIP60 prote ...	0.97	+	nuc	0	Nucleus	nucleus [TAS]	609880		611
Q5TKR9 UniProt NPD GO	MYST3_RAT	Histone acetyltransferase MYST3 (EC 2.3.1.48) (EC 2.3.1.-) (MYST protein 3) (MOZ, YBF2/SAS3, SAS2 an ...	0.97	+	nuc	0	Nucleus (By similarity)	nucleus [ISS]			1998
P34218 UniProt NPD GO	SAS3_YEAST	Histone acetyltransferase SAS3 (EC 2.3.1.48) (Something about silencing protein 3)	0.97	+	nuc	0	Nucleus	histone acetyltransferase complex [IPI] nuclear nucleosome [TAS]			831
P38827 UniProt NPD GO	SET1_YEAST	Histone-lysine N-methyltransferase, H3 lysine-4 specific (EC 2.1.1.43) (COMPASS component SET1) (SET ...	0.97	-	nuc	0	Nucleus (Probable)	COMPASS complex [IPI]			1080
Q91018 UniProt NPD GO	PROX1_CHICK	Homeobox prospero-like protein PROX1 (PROX 1)	0.97	+	nuc	0	Nucleus (Probable)				736
Q26604 UniProt NPD GO	SMOX5_SCHMA	Homeobox protein SMOX-5	0.97	+	nuc	0	Nucleus (Probable)				284
P22809 UniProt NPD GO	BAGP_DROME	Homeobox protein bagpipe (NK-3)	0.97	+	nuc	0	Nucleus (Probable)				382
Q22811 UniProt NPD GO	HM21_CAEEL	Homeobox protein ceh-21	0.97	-	nuc	0	Nucleus (Potential)				495
P53564 UniProt NPD GO	CUTL1_MOUSE	Homeobox protein cut-like 1 (CCAAT displacement protein) (CDP) (Homeobox protein Cux)	0.97	-	nuc	0	Nucleus	nucleus [IDA]			1515
P25439 UniProt NPD GO	BRM_DROME	Homeotic gene regulator (EC 3.6.1.-) (ATP-dependent helicase brm) (Protein brahma)	0.97	+	nuc	0	Nucleus	brahma complex [IDA]			1638
P39806 UniProt NPD GO	SALM_DROVI	Homeotic protein spalt-major	0.97	+	nuc	0	Nucleus (Probable)				1402
P31629 UniProt NPD GO	ZEP2_HUMAN	Human immunodeficiency virus type I enhancer-binding protein 2 (HIV-EP2) (MHC-binding protein 2) (MB ...	0.97	+	nuc	0	Nucleus	nucleus [NAS]	143054		2446
P34250 UniProt NPD GO	YKK5_YEAST	Hypothetical 125.6 kDa protein in AAT1-GFA1 intergenic region	0.97	-	nuc	0					1132
P12221 UniProt NPD GO	YCF1A_MARPO	Hypothetical 127 kDa protein ycf1 (ORF 1068)	0.97	+	end	4 *	Plastid; chloroplast				1068
Q85FG7 UniProt NPD GO	YCF1_ADICA	Hypothetical 199.0 kDa protein ycf1	0.97	+	end	6 *	Plastid; chloroplast				1691
Q09477 UniProt NPD GO	YP99_CAEEL	Hypothetical C28H8.9 in chromosome III	0.97	-	nuc	0	Nucleus (Potential)				372
Q9Y7N0 UniProt NPD GO	YCK2_SCHPO	Hypothetical bromodomain protein C1450.02	0.97	+	nuc	0					578
Q11100 UniProt NPD GO	YL14_CAEEL	Hypothetical protein C02F12.4	0.97	+	nuc	0					665
P34278 UniProt NPD GO	YKK1_CAEEL	Hypothetical protein C02F5.1	0.97	-	nuc	0					1010
Q09441 UniProt NPD GO	YP83_CAEEL	Hypothetical protein C08B11.3 in chromosome II	0.97	+	nuc	0					1244
Q10148 UniProt NPD GO	YAT1_SCHPO	Hypothetical protein C1D4.01 in chromosome I	0.97	+	nuc	0		nucleus [IDA]			285
Q09255 UniProt NPD GO	YQB1_CAEEL	Hypothetical protein C30G12.1	0.97	-	nuc	0					469
P46582 UniProt NPD GO	YLB8_CAEEL	Hypothetical protein C34E10.8	0.97	-	nuc	0					1024
P46504 UniProt NPD GO	YLX8_CAEEL	Hypothetical protein F23F12.8 precursor	0.97	+	exc	1 *					980
Q09314 UniProt NPD GO	YQT2_CAEEL	Hypothetical protein F25B5.2	0.97	+	nuc	0					757
P30640 UniProt NPD GO	YNE1_CAEEL	Hypothetical protein R08D7.1	0.97	-	nuc	0					458
P31563 UniProt NPD GO	YCF1_OENBE	Hypothetical protein ycf1 (ORF 1005) (Fragment)	0.97	+	end	6 *	Plastid; chloroplast				1005
O14066 UniProt NPD GO	YFF9_SCHPO	Hypothetical serine-rich protein C1687.09 in chromosome I	0.97	+	nuc	0					1379
Q9I8A9 UniProt NPD GO	HIF1A_XENLA	Hypoxia-inducible factor 1 alpha (HIF-1 alpha) (HIF1 alpha)	0.97	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Cytoplasmic in normoxia, nuclear translocation i ...				805
Q505H7 UniProt NPD GO	IWS1_XENTR	IWS1 homolog (IWS1-like protein)	0.97	+	nuc	0	Nucleus (By similarity)				909
Q61MR2 UniProt NPD GO	IWS1_CAEBR	IWS1-like protein	0.97	+	nuc	0	Nucleus (By similarity)				507
P43579 UniProt NPD GO	IES1_YEAST	Ino eighty subunit 1	0.97	+	nuc	0	Nucleus	INO80 complex [IPI] nucleus [IDA]			692
Q9Z0R4 UniProt NPD GO	ITSN1_MOUSE	Intersectin-1 (EH and SH3 domains protein 1)	0.97	+	nuc	0	Intracytoplasmic membrane (By similarity). Synaptosome (By similarity). Enriched in synaptosomes (By ...	lamellipodium [IDA]			1714
Q9Z0R6 UniProt NPD GO	ITSN2_MOUSE	Intersectin-2 (SH3 domain-containing protein 1B) (EH and SH3 domains protein 2) (EH domain and SH3 d ...	0.97	+	nuc	0	Cytoplasm (By similarity)				1658
O89019 UniProt NPD GO	INVS_MOUSE	Inversin (Inversion of embryo turning protein) (Nephrocystin-2)	0.97	+	nuc	0	Cytoplasm. Cytoskeleton. Associates with several components of the cytoskeleton including ciliary, r ...				1062
Q4WHB7 UniProt NPD GO	JHD1_ASPFU	JmjC domain-containing histone demethylation protein 1 (EC 1.14.11.-)	0.97	+	nuc	0	Nucleus (By similarity)				1418
Q95Q98 UniProt NPD GO	JHD1_CAEEL	JmjC domain-containing histone demethylation protein 1 (EC 1.14.11.-)	0.97	+	nuc	0	Nucleus (By similarity)				1076
Q5AW75 UniProt NPD GO	JHD1_EMENI	JmjC domain-containing histone demethylation protein 1 (EC 1.14.11.-)	0.97	-	nuc	0	Nucleus (By similarity)				1407
Q9Y2K7 UniProt NPD GO	JHD1A_HUMAN	JmjC domain-containing histone demethylation protein 1A (EC 1.14.11.-) (F-box/LRR-repeat protein 11) ...	0.97	-	nuc	0	Nucleus (Probable)		605657		1162
Q62315 UniProt NPD GO	JARD2_MOUSE	Jumonji protein (Jumonji/ARID domain-containing protein 2)	0.97	-	nuc	0	Nucleus	nucleus [IDA]			1234
O95235 UniProt NPD GO	KI20A_HUMAN	Kinesin family member 20A (Rabkinesin-6) (Rab6-interacting kinesin-like protein) (GG10_2)	0.97	-	nuc	0	Golgi apparatus (By similarity)	Golgi apparatus [TAS]	605664		890

You are viewing entries 1001 to 1050 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.